title: run_13_seq_2_PE-02F_S302

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-12E_S285

status: Public on Apr 07 2023

type: SRA

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

description: sci-RNA-seq3 library

library_source: transcriptomic single cell

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

molecule: polyA RNA

organism: Mus musculus

source_name: sci-RNA-seq3 of mouse organogenesis and fetal development

growth_protocol: For the newly generated mouse embryo data (ranging from E8 to P0), we employed a combination of staging methodologies depending on gestational age of harvest. To maximize temporal coherence, resolution, and accuracy, we sought to stage individual embryos based on well-defined morphological criteria, rather than by gestational day alone. Embryos harvested between E8.0 - E10.0 were staged based upon the number of somites counted at the time of harvest and further characterized by morphological features. Based upon an estimated 1.5 to 2 hour periodicity for somite formation, E8.0 - E10.0 embryos were grouped into 4 somite bins. For E10.25-E14.75 embryos, developmental age was determined using the embryonic Mouse Ontogenetic Staging System (eMOSS, https://limbstaging.embl.es/), which leverages dynamic changes in hindlimb bud morphology and landmark-free based morphometry to estimate the absolute developmental stage of a sample. A modified staging tool, implemented in python, with increased performance on E14.0-E15.0 samples was used to confirm staging of samples within this window (documentation and python scripts available at: https://github.com/marcomusy/welsh_embryo_stager). To distinguish samples staged via eMOSS, these samples are designated with “mE” for morphometric embryonic day (e.g. mE13.5). Due to the increased complexity of limb morphology at later stages automated staging beyond ~E15.0 is not possible. As a consequence, harvests for all remaining embryonic samples (E15.0-E18.75) were performed precisely at 00:00, 06:00, 12:00, and 18:00 on the targeted day. From close inspection of limbs in this sample set we defined additional dynamics related to digit morphogenesis that allowed further binning of samples collected on Days 15 and 16. Therefore, amongst samples profiled in this study only the E17.0-E18.75 samples were staged solely by gestational age. Lastly, P0 samples were harvested from litters at noon of the day of birth (parturition for C57BL/6NJ occurs between E18.75 and E19.0).

extract_protocol: To generate the dataset, we used the optimized sci-RNA-seq3 protocol, adjusting the volume and type of lysis buffer to the size of the embryos. Briefly, frozen embryos were pulverized on dry ice and cells were lysed with a phosphate-based, hypotonic lysis buffer containing magnesium chloride, Igepal, diethyl pyrocarbonate (DEPC) as an RNase inhibitor, and either sucrose or bovine serum albumin (BSA). Lysate is passed over a 20um filter, and the nuclei-containing flow-through is fixed with a mixture of methanol and dithiobis (succinimidyl propionate) (DSP). Nuclei are rehydrated and washed in a sucrose/PBS/triton/magnesium chloride buffer (SPBSTM), then counted and distributed into 96-well plates for reverse transcription with indexed oligo-dT primers.

tag: developmental stage

value: mouse embryos spanning late gastrulation (E8) to birth (P0)

tag: strain


title: run_13_seq_2_PE-02E_S301

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-02C_S299

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-02B_S298

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-03A_S305

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-01G_S295

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-11G_S279

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-11H_S280

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-12C_S283

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-01E_S293

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-01D_S292

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-02D_S300

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-11B_S274

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-12G_S287

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-11A_S273

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-01B_S290

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-10G_S271

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-01A_S289

description: sci-RNA-seq3 library


title: run_13_seq_2_PE-02A_S297

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-12H_S288

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-12F_S286

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-12B_S282

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-12A_S281

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-11E_S277

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-09G_S263

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-09H_S264

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-11D_S276

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-11F_S278

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-11C_S275

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-10H_S272

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-10D_S268

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-10C_S267

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-07G_S247

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-07F_S246

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-08B_S250

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-10B_S266

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-07E_S245

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-09C_S259

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-09F_S262

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-09E_S261

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-09A_S257

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-07A_S241

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-10A_S265

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-08F_S254

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-08G_S255

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-09D_S260

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-06G_S239

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-08E_S253

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-10E_S269

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-08D_S252

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-06D_S236

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-08C_S251

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-06B_S234

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-06A_S233

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-07H_S248

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-05G_S231

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-09B_S258

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-07D_S244

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-08A_S249

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-07B_S242

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-07C_S243

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-06H_S240

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-04H_S224

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-05C_S227

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-04G_S223

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-06F_S238

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-06E_S237

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-06C_S235

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-04E_S221

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-05D_S228

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-05E_S229

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-05F_S230

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-04C_S219

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-05A_S225

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-05H_S232

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-04B_S218

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-03H_S216

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-04D_S220

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-03G_S215

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-05B_S226

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-03B_S210

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-03C_S211

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-03D_S212

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-03E_S213

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-03A_S209

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-02H_S208

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-02G_S207

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-04F_S222

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-02E_S205

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-02D_S204

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-02F_S206

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-02C_S203

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-02A_S201

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-04A_S217

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-02B_S202

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-01E_S197

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-01G_S199

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-01F_S198

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-01B_S194

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-12H_S192

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-01D_S196

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-12G_S191

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-12F_S190

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-01C_S195

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-03F_S214

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-12A_S185

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-12B_S186

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-12D_S188

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-01H_S200

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-12E_S189

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-01A_S193

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-10F_S270

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-12C_S187

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-11G_S183

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-11E_S181

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-11F_S182

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-11D_S180

description: sci-RNA-seq3 library


title: run_13_seq_2_PD-08H_S256

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-11C_S179

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-11B_S178

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-11A_S177

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-10F_S174

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-10G_S175

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-10D_S172

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-09H_S168

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-10A_S169

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-10E_S173

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-10H_S176

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-10B_S170

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-09G_S167

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-11H_S184

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-09F_S166

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-09E_S165

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-09D_S164

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-08C_S155

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-10C_S171

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-08F_S158

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-08D_S156

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-07H_S152

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-09B_S162

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-08G_S159

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-09C_S163

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-09A_S161

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-08E_S157

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-07G_S151

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-07F_S150

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-07D_S148

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-08B_S154

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-08H_S160

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-07E_S149

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-07B_S146

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-07A_S145

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-06F_S142

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-06C_S139

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-06G_S143

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-06B_S138

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-06D_S140

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-06A_S137

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-08A_S153

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-05H_S136

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-05G_S135

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-07C_S147

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-05F_S134

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-05E_S133

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-05D_S132

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-06H_S144

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-04H_S128

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-03H_S120

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-05A_S129

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-04G_S127

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-04E_S125

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-05C_S131

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-05B_S130

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-04D_S124

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-04B_S122

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-04F_S126

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-03F_S118

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-04A_S121

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-03C_S115

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-03A_S113

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-03G_S119

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-03B_S114

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-02H_S112

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-02D_S108

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-03D_S116

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-06E_S141

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-02C_S107

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-04C_S123

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-02E_S109

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-02F_S110

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-02B_S106

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-02A_S105

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-01G_S103

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-01F_S102

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-01H_S104

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-03E_S117

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-01D_S100

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-01E_S101

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-01A_S97

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-12H_S96

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-12E_S93

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-01B_S98

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-12G_S95

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-12D_S92

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-12F_S94

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-12C_S91

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-12A_S89

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-11H_S88

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-02G_S111

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-12B_S90

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-11F_S86

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-11E_S85

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-11G_S87

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-11B_S82

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-11C_S83

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-10H_S80

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-11A_S81

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-10G_S79

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-10F_S78

description: sci-RNA-seq3 library


title: run_13_seq_2_PC-01C_S99

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-10E_S77

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-10D_S76

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-10C_S75

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-10A_S73

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-09H_S72

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-09G_S71

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-09C_S67

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-09A_S65

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-11D_S84

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-08E_S61

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-08G_S63

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-09B_S66

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-08F_S62

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-08D_S60

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-08B_S58

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-08C_S59

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-07H_S56

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-09F_S70

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-08A_S57

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-07F_S54

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-06H_S48

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-07D_S52

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-07G_S55

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-07E_S53

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-07A_S49

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-10B_S74

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-07C_S51

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-07B_S50

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-08H_S64

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-09D_S68

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-06E_S45

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-09E_S69

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-06D_S44

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-06G_S47

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-06C_S43

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-05H_S40

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-06F_S46

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-05F_S38

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-06B_S42

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-05D_S36

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-06A_S41

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-05G_S39

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-05C_S35

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-05B_S34

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-05A_S33

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-04H_S32

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-04F_S30

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-04E_S29

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-04D_S28

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-04B_S26

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-04C_S27

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-04G_S31

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-03F_S22

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-04A_S25

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-03E_S21

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-03H_S24

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-03D_S20

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-03C_S19

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-03B_S18

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-03A_S17

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-03G_S23

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-05E_S37

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-02G_S15

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-02E_S13

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-02H_S16

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-02D_S12

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-02A_S9

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-02B_S10

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-01G_S7

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-02C_S11

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-01F_S6

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-01E_S5

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-01D_S4

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-01H_S8

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-01B_S2

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-01A_S1

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-02F_S14

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-12D_S668

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-12E_S669

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-12H_S672

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-12F_S670

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-12A_S665

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-12G_S671

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-11F_S662

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-12C_S667

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-11G_S663

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-11H_S664

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-11E_S661

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-11D_S660

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-11C_S659

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-11B_S658

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-10G_S655

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-10H_S656

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-11A_S657

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-10C_S651

description: sci-RNA-seq3 library


title: run_13_seq_2_PA-01C_S3

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-10B_S650

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-10F_S654

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-10A_S649

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-09G_S647

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-09F_S646

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-09H_S648

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-12B_S666

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-09E_S645

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-09B_S642

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-08G_S639

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-09D_S644

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-09C_S643

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-09A_S641

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-08F_S638

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-08E_S637

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-08C_S635

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-10D_S652

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-10E_S653

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-08D_S636

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-08H_S640

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-07G_S631

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-07H_S632

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-08A_S633

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-07E_S629

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-07D_S628

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-06H_S624

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-07F_S630

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-07B_S626

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-06G_S623

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-07C_S627

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-07A_S625

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-06E_S621

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-06F_S622

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-08B_S634

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-06B_S618

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-06A_S617

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-05F_S614

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-05H_S616

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-05D_S612

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-05G_S615

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-05E_S613

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-05B_S610

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-05C_S611

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-04H_S608

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-05A_S609

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-04B_S602

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-04D_S604

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-04C_S603

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-04G_S607

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-03D_S596

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-03E_S597

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-03F_S598

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-03G_S599

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-04E_S605

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-04A_S601

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-06C_S619

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-03A_S593

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-03B_S594

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-03C_S595

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-02F_S590

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-02G_S591

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-02E_S589

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-02D_S588

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-04F_S606

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-02C_S587

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-03H_S600

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-06D_S620

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-02A_S585

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-02B_S586

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-01E_S581

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-01G_S583

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-01F_S582

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-01A_S577

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-12H_S576

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-01C_S579

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-01H_S584

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-01B_S578

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-02H_S592

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-12D_S572

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-12E_S573

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-12G_S575

description: sci-RNA-seq3 library


title: run_13_seq_1_PH-01D_S580

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-12A_S569

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-11G_S567

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-11F_S566

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-12C_S571

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-11E_S565

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-11D_S564

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-11C_S563

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-10H_S560

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-11B_S562

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-10E_S557

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-10F_S558

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-11A_S561

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-10G_S559

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-10B_S554

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-12F_S574

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-09H_S552

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-10D_S556

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-10C_S555

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-09G_S551

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-12B_S570

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-09F_S550

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-09A_S545

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-09E_S549

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-09B_S546

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-09D_S548

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-08G_S543

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-09C_S547

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-08E_S541

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-10A_S553

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-08F_S542

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-08C_S539

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-08D_S540

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-11H_S568

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-08B_S538

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-07H_S536

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-08A_S537

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-07F_S534

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-07E_S533

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-07G_S535

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-07C_S531

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-07B_S530

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-07A_S529

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-06H_S528

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-08H_S544

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-06E_S525

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-06D_S524

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-06C_S523

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-06A_S521

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-06G_S527

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-06B_S522

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-05H_S520

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-05E_S517

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-05D_S516

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-05F_S518

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-05B_S514

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-05A_S513

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-04H_S512

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-05C_S515

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-04G_S511

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-05G_S519

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-04F_S510

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-04D_S508

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-04E_S509

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-04B_S506

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-06F_S526

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-07D_S532

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-03E_S501

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-04A_S505

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-04C_S507

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-03H_S504

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-03D_S500

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-03B_S498

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-03G_S503

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-02H_S496

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-02F_S494

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-02E_S493

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-03A_S497

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-02C_S491

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-02A_S489

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-03C_S499

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-02B_S490

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-01F_S486

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-03F_S502

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-01C_S483

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-01E_S485

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-01D_S484

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-01B_S482

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-01G_S487

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-12H_S480

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-02G_S495

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-12G_S479

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-02D_S492

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-12F_S478

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-12E_S477

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-12C_S475

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-11H_S472

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-12A_S473

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-11G_S471

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-01H_S488

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-12B_S474

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-11E_S469

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-11F_S470

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-11B_S466

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-11C_S467

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-10H_S464

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-11D_S468

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-10G_S463

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-10F_S462

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-11A_S465

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-10D_S460

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-09H_S456

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-10B_S458

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-10A_S457

description: sci-RNA-seq3 library


title: run_13_seq_1_PG-01A_S481

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-09G_S455

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-12D_S476

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-09F_S454

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-09E_S453

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-09D_S452

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-09A_S449

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-09B_S450

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-09C_S451

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-08G_S447

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-08E_S445

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-08F_S446

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-08D_S444

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-08C_S443

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-08B_S442

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-08A_S441

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-10C_S459

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-10E_S461

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-07H_S440

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-07G_S439

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-07F_S438

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-07E_S437

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-07D_S436

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-07C_S435

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-07B_S434

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-06H_S432

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-06D_S428

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-07A_S433

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-06G_S431

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-06E_S429

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-08H_S448

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-06C_S427

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-06A_S425

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-06B_S426

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-05H_S424

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-05G_S423

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-05F_S422

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-05D_S420

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-05C_S419

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-05E_S421

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-05A_S417

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-04H_S416

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-04F_S414

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-04G_S415

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-04E_S413

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-04C_S411

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-03F_S406

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-03G_S407

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-06F_S430

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-04A_S409

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-04D_S412

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-03D_S404

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-03B_S402

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-03C_S403

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-02H_S400

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-03A_S401

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-02F_S398

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-02G_S399

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-02D_S396

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-05B_S418

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-02C_S395

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-02E_S397

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-02B_S394

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-01G_S391

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-01H_S392

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-02A_S393

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-01F_S390

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-01E_S389

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-01B_S386

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-01C_S387

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-03H_S408

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-03E_S405

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-01A_S385

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-12H_S384

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-12F_S382

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-12G_S383

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-12E_S381

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-12C_S379

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-04B_S410

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-12B_S378

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-11H_S376

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-11G_S375

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-12A_S377

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-11F_S374

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-11E_S373

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-11D_S372

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-11B_S370

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-11C_S371

description: sci-RNA-seq3 library


title: run_13_seq_1_PF-01D_S388

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-10G_S367

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-12D_S380

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-10D_S364

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-10B_S362

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-10F_S366

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-10C_S363

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-09H_S360

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-10E_S365

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-10A_S361

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-09E_S357

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-09F_S358

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-10H_S368

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-09G_S359

description: sci-RNA-seq3 library


title: SN_TRAP Tamoxifen  replicate  K

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

library_source: transcriptomic

data_processing:
Runs one and two were merged, for batch one
Illumina sequencing adaptors were removed using Trimmomatic (version 0.38), and reads aligning to the mouse rRNA were removed using bowtie2 (version 2.3.5)
Sequencing results were quality-tested using FastQC (version 0.11.7)
Merged reads were then aligned, using STAR (version 2.7.0d), to the mouse transcriptome (Ensembl Release 93)
The number of reads mapped to each feature were counted using htseq-count (version 0.9.1)
Assembly: Mouse: Ensembl 104
Supplementary files format and content: Gene counts

molecule: total RNA

source_name: Brain-Dorsal cortex and hippocampus

growth_protocol: Harvest mice at postnatal day 28-29

extract_protocol:
Dorsal cortex and hippocampus was removed, immediately immersed within ice-cold homogenization buffer, homogenized by hand within 10 minutes, and prepared for TRAP and synaptosome-TRAP as described (Sakers et al., 2017). RNA was purified using a Qiagen RNEasy MinElute kit per the manufacturer's instructions.
RNA samples were reverse transcribed into cDNA and amplified using Smartseq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) per the manufacturer's instructions. Then sequencing adaptors were added using the NEBNext Ultra II DNA Library Prep Kit for Illumina per the manufacturer's instructions.

treatment_protocol: Tamoxifen 100 mg/kg in 9:1 Sunflower seed oil:Ethanol or vehicle (control) at p15, p17, and p19

tag: fraction

tag: treatment

value: Tamoxifen

tag: cell type

value: Microglia, synaptosomes

tag: genotype

value: CX3CR1-CreERT2 (+/-) x RPL10a-GFP flox (+/-)


title: run_13_seq_1_PE-09B_S354

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-09A_S353

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-08H_S352

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-09C_S355

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-09D_S356

description: sci-RNA-seq3 library


title: SN_TRAP Tamoxifen  replicate  I


title: SN_TRAP Tamoxifen  replicate  J


title: run_13_seq_1_PE-11A_S369

description: sci-RNA-seq3 library


title: SN_TRAP Tamoxifen  replicate  H


title: run_13_seq_1_PE-08E_S349

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-08G_S351

description: sci-RNA-seq3 library


title: SN_TRAP Tamoxifen  replicate  G


title: SN_input Tamoxifen  replicate  K

value: Mixed, synaptosomes


title: run_13_seq_1_PE-08C_S347

description: sci-RNA-seq3 library


title: SN_input Tamoxifen  replicate  J


title: run_13_seq_1_PE-08B_S346

description: sci-RNA-seq3 library


title: SN_input Tamoxifen  replicate  I


title: SN_input Tamoxifen  replicate  G


title: run_13_seq_1_PE-07G_S343

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-07H_S344

description: sci-RNA-seq3 library


title: SN_input Tamoxifen  replicate  H


title: MG_TRAP Tamoxifen  replicate  J

value: Microglia


title: MG_TRAP Tamoxifen  replicate  K


title: run_13_seq_1_PE-07E_S341

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-07F_S342

description: sci-RNA-seq3 library


title: MG_TRAP Tamoxifen  replicate  I


title: run_13_seq_1_PE-07C_S339

description: sci-RNA-seq3 library


title: Input Tamoxifen  replicate  K

value: Input

value: Mixed


title: run_13_seq_1_PE-07D_S340

description: sci-RNA-seq3 library


title: MG_TRAP Tamoxifen  replicate  H


title: run_13_seq_1_PE-08F_S350

description: sci-RNA-seq3 library


title: MG_TRAP Tamoxifen  replicate  G


title: run_13_seq_1_PE-06H_S336

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-07A_S337

description: sci-RNA-seq3 library


title: Input Tamoxifen  replicate  J


title: Input Tamoxifen  replicate  H


title: run_13_seq_1_PE-06G_S335

description: sci-RNA-seq3 library


title: Input Tamoxifen  replicate  G


title: run_13_seq_1_PE-08D_S348

description: sci-RNA-seq3 library


title: PeMP_TRAP_Tamoxifen_F

description: PeMP_TRAP Tamoxifen  replicate  F

data_processing:
Sequencing results were quality-tested using FastQC (version 0.11.7)
Illumina sequencing adaptors were removed using Trimmomatic (version 0.38), and reads aligning to the mouse rRNA were removed using bowtie2 (version 2.3.5)
Same samples were sequenced twice to increased read depth (run 2834, 2798). At this step, surviving reads from two runs were merged for each sample.
Merged reads were then aligned, using STAR (version 2.7.0d), to the mouse transcriptome (Ensembl Release 93)
The number of reads mapped to each feature were counted using htseq-count (version 0.9.1)
Gene counts were then processed in R/EdgeR to summarize CPMs and conduct differential expression (DE) and this is reported in the supplemental file CPM_and_DE_Table.csv. DE was only conducted in genes above an expression threshold.
Genome_build: Mouse: Ensembl 93
Supplementary_files_format_and_content: Gene counts

tag: tissue

value: Brain-Dorsal cortex and hippocampus


title: run_13_seq_1_PE-08A_S345

description: sci-RNA-seq3 library


title: Input Tamoxifen  replicate  I


title: run_13_seq_1_PE-06D_S332

description: sci-RNA-seq3 library


title: PeMP_TRAP_Tamoxifen_E

description: PeMP_TRAP Tamoxifen  replicate  E


title: run_13_seq_1_PE-06C_S331

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-06B_S330

description: sci-RNA-seq3 library


title: PeMP_TRAP_Tamoxifen_D

description: PeMP_TRAP Tamoxifen  replicate  D


title: run_13_seq_1_PE-07B_S338

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-05H_S328

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-06A_S329

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-06F_S334

description: sci-RNA-seq3 library


title: PeMP_TRAP_Control_C

description: PeMP_TRAP Control  replicate  C

value: Control


title: PeMP_TRAP_Control_A

description: PeMP_TRAP Control  replicate  A


title: PeMP_TRAP_Control_B

description: PeMP_TRAP Control  replicate  B


title: SN_input_Tamoxifen_F

description: SN_input Tamoxifen  replicate  F


title: run_13_seq_1_PE-05G_S327

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-05E_S325

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-05D_S324

description: sci-RNA-seq3 library


title: SN_input_Tamoxifen_E

description: SN_input Tamoxifen  replicate  E


title: SN_input_Tamoxifen_D

description: SN_input Tamoxifen  replicate  D


title: SN_input_Control_A

description: SN_input Control  replicate  A


title: run_13_seq_1_PE-05B_S322

description: sci-RNA-seq3 library


title: MG_TRAP_Tamoxifen_F

description: MG_TRAP Tamoxifen  replicate  F


title: SN_input_Control_B

description: SN_input Control  replicate  B


title: run_13_seq_1_PE-05F_S326

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-05A_S321

description: sci-RNA-seq3 library


title: SN_input_Control_C

description: SN_input Control  replicate  C


title: MG_TRAP_Tamoxifen_E

description: MG_TRAP Tamoxifen  replicate  E


title: run_13_seq_1_PE-04H_S320

description: sci-RNA-seq3 library


title: MG_TRAP_Tamoxifen_D

description: MG_TRAP Tamoxifen  replicate  D


title: run_13_seq_1_PE-04G_S319

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-04F_S318

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-04E_S317

description: sci-RNA-seq3 library


title: MG_TRAP_Control_B

description: MG_TRAP Control  replicate  B


title: Input_Tamoxifen_F

description: Input Tamoxifen  replicate  F


title: run_13_seq_1_PE-04D_S316

description: sci-RNA-seq3 library


title: MG_TRAP_Control_A

description: MG_TRAP Control  replicate  A


title: run_13_seq_1_PE-04B_S314

description: sci-RNA-seq3 library


title: Input_Tamoxifen_D

description: Input Tamoxifen  replicate  D


title: MG_TRAP_Control_C

description: MG_TRAP Control  replicate  C


title: run_13_seq_1_PE-04A_S313

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-05C_S323

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-04C_S315

description: sci-RNA-seq3 library


title: Input_Control_C

description: Input Control  replicate  C


title: run_13_seq_1_PE-03H_S312

description: sci-RNA-seq3 library


title: Input_Control_A

description: Input Control  replicate  A


title: run_13_seq_1_PE-03E_S309

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-03G_S311

description: sci-RNA-seq3 library


title: T-OF-2

city: Chicago

first: Brian

middle: J

last: Lee

state: IL

address: 500 N Lake Shore Dr, Apt 601

institute: Northwestern Feinberg School of Medicine

data_processing:
Reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt, and fastQC
Reads were mapped to the reference genome/transcriptome (Ensembl GRCh38) using STAR v2.7.0e
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

growth_protocol: U2932 and TMD8 cell lines were maintained in RPMI 1640 with 2mM L-glutamine (Gibco), supplemented with 10% FBS heat inactivated at 56 C for 30 minutes (Gibo), 100 micrograms/mL penicillin and 100 micrograms/mL streptomycin 9Gibco), and 1 mM HEPES (Gibco)

extract_protocol:
Total RNA was purified using Trizol (Thermo Fisher) according to the commercial protocol with the following additions: after the first phase separation, additional chloroform extraction step of the aqueous layer in Phase-lock Gel heavy tubes (Quanta Biosciences); addition of 1ul Glyco-blue (Thermo Fisher) immediately prior to isopropanol precipitation; two washes of the RNA pellet with 75% ethanol. If the RNA integrity results indicate co-purified genomic DNA, it will be removed with the RapidOUT DNA Removal kit (Thermo Fisher).
RNA-seq libraries for RNA-seq were prepared using NEBNext ultra II RNA Library Prep Kit (New England Biolabs). Each library will be quantified with a Qubit (dsDNA HS kit; Thermo Fisher) and the size distribution determined with a Fragment Analyzer (Agilent) prior to pooling

treatment_protocol: TMD8 and U2932 were split and cultured separately for a week to create two biological replicates per cell line. They were then treated with 20 ug/mL  rituximab, ofatumumab, or a human IgG1 isotype (SouthernBiotech).

tag: cell line

value: DLBCL

value: WT

value: Ofatumumab


title: run_13_seq_1_PE-03F_S310

description: sci-RNA-seq3 library


title: T-I-2

value: IgG isotype


title: run_13_seq_1_PE-03C_S307

description: sci-RNA-seq3 library


title: T-I-1


title: T-R-2

value: Rituximab


title: run_13_seq_1_PE-03B_S306

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-02H_S304

description: sci-RNA-seq3 library


title: T-OF-1


title: Input_Tamoxifen_E

description: Input Tamoxifen  replicate  E


title: U-I-2


title: U-I-1


title: U-OF-2


title: U-OF-1


title: run_13_seq_1_PE-02E_S301

description: sci-RNA-seq3 library


title: Input_Control_B

description: Input Control  replicate  B


title: run_13_seq_1_PE-03D_S308

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-02C_S299

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-02B_S298

description: sci-RNA-seq3 library


title: U-R-2


title: run_13_seq_1_PE-02D_S300

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-06E_S333

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-01H_S296

description: sci-RNA-seq3 library


title: Prim_hep_indiv_studyteam_run 5

city: Indianapolis

first: Nick

last: Powell

state: United States

address: 950 W. Walnut St.

institute: IUSM

data_processing:
https://pubmed.ncbi.nlm.nih.gov/34314509/
https://github.com/Nickpowe/AGT_rs699_HTN
Assembly: hg38
Supplementary files format and content: BED files formatted for UCSC genome browser upload

source_name: individual donor hepatocytes

value: individual donor hepatocytes

tag: protocol

value: CLIP-seq

value: AGO IP RNA


title: Prim_hep_indiv_studyteam_run 6


title: run_13_seq_1_PE-01G_S295

description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


title: Prim_hep_indiv_studyteam_run 4


title: run_13_seq_1_PE-02A_S297

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-01F_S294

description: sci-RNA-seq3 library


title: T-R-1


title: Prim_hep_indiv_eclipse_run 2


title: run_13_seq_1_PE-01D_S292

description: sci-RNA-seq3 library


title: Prim_hep_pooled_eclipse_run 1

source_name: pooled primary hepatocytes

value: pooled primary hepatocytes


title: run_13_seq_1_PE-01C_S291

description: sci-RNA-seq3 library


title: AMO1 cells treated with periplocin 1

city: Nagoya city

first: Muneshige

last: Tokugawa

address: 3-1 Tanabe-dori, Mizuhoku

country: Japan

institute: Nagoya City University

data_processing:
Read count estimation/normalization and analysis of differentially expressed genes were carried out by RaNA-seq (https://ranaseq.eu/).
Reference genome assembly = Human, Homo sapiens (GRCh38), Method = DESeq2, Test = Wald, Fit Type = parametric.
Supplementary files format and content: Homo sapiens (GRCh38)
Supplementary files format and content: Excel files include TPM values for each Sample

growth_protocol: AMO1 myeloma cells were maintained in RPMI1640 supplemented with 8% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using FastGene RNA Premium Kit (Nippon Genetics Co., Ltd.). Total RNA was used for the construction of sequencing libraries.
Pair-end Illumina sequencing were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).

treatment_protocol: The cells were treated with DMSO (as vehicle control) or 0.2 mM periplocin for 6 h.

value: plasmacytoma

value: Periplocin

tag: concentration

tag: time

value: 6 h


title: U-R-1


title: run_13_seq_1_PE-01B_S290

description: sci-RNA-seq3 library


title: AMO1 cells treated with periplocin 2


title: AMO1 cells treated with DMSO 1

value: DMSO


title: run_13_seq_1_PE-02G_S303

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-12F_S286

description: sci-RNA-seq3 library


title: run_13_seq_1_PE-01A_S289

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-12G_S287

description: sci-RNA-seq3 library


title: NB4 cells, D27 BCL7A, replicate 2

city: Granada

first: Pedro

middle: P

last: Medina

state: Andalucía

address: Av. de la Ilustración, 114

country: Spain

institute: Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica (GENYO)

data_processing:
Reads were aligned to the human genome GRCh38.d1.vd1 (downloaded from https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files) using STAR (version 2.7.10b) in “two-pass mode”. GENCODE v36 was used as an annotation reference.
The multi-sample BAM was split into single-sample BAMs.
Read counts per gene were obtained using htseq-count (v0.6.1p1) with the following options: “-m intersection-nonempty -f bam -t exon -i gene_id -r pos -s reverse”.
Further analyses were performed using R (version 3.6.3, Bioconductor version 3.10) and the packages ‘edgeR’, ‘DESeq2’ and ‘EnhancedVolcano’. DESeq2 was used for the differential expression analysis testing for abs(logFC) > log2(1.5) specifying a threshold of alpha = 0.01. logFC values were shrunk using the ashr method while preserving the original p and adjusted p values.
Assembly: hg38
Supplementary files format and content: Tab-delimited files containing the output from htseq-count (total read counts per gene).

growth_protocol: NB4 cell lines were cultured at 37°C with a 5% CO2 atmosphere. They were grown in RPMI 1640 medium (Cat#L0498-500, Biowest, Riverside, MO, USA) supplemented with 10% fetal bovine serum (Cat#10270-106, Gibco™ Thermo Fisher Scientific), and 100 U/mL streptomycin and penicillin (Cat#P0781-100ML, Sigma-Aldrich).

extract_protocol:
Total RNA extraction was carried out using mirVana™ miRNA Isolation Kit, with phenol (Cat#AM1560, Thermo Fisher Scientific). We extracted total RNA from 3×10^6 of NB4 cells of each condition per sample. RNA concentration and quality were measured using Qubit 4 Fluorometer (ThermoFisher Scientific) and 2100 Bioanalyzer Instrument (Agilent Technologies, Santa Clara, CA, USA) respectively.
Strand-specific RNA libraries for RNA-seq with PolyA selection were prepared by Genewiz (Azenta Life Sciences).

treatment_protocol: NB4 cells were transduced with pLVX-BCL7A-IRES-ZsGreen1 coding for wild-type BCL7A or mutant BCL7A (Δ27-BCL7A). We transduced the cells for 3 consecutive cycles of infection at MOI=2 with different lentiviral constructions stably co-expressing BCL7A variants.

value: acute promyelocytic leukemia

value: D27 BCL7A

value: lentiviral transfection of D27 BCL7A


title: NB4 cells, D27 BCL7A, replicate 1


title: run_13_seq_1_PE-03A_S305

description: sci-RNA-seq3 library


title: AMO1 cells treated with DMSO 2


title: run_13_seq_1_PE-01E_S293

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-12H_S288

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-12D_S284

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-12E_S285

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-12C_S283

description: sci-RNA-seq3 library


title: Prim_hep_indiv_eclipse_run 3


title: run_13_seq_1_PD-12B_S282

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-H10

city: New Haven

first: Niki

last: Gavrielatou

address: 310 Cedar Street

institute: Yale University School of Medicine

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx®-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered/counted as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Supplementary files format and content: CD45_10%_norm.xlsx  contains read counts from the leukocyte (CD45) compartment over the 10% LoD threshold, after Q3 normalization
Supplementary files format and content: CD68_10%_norm.xlsx  contains read counts from the macrophage (CD68) compartment over the 10% LoD threshold, after Q3 normalization
Supplementary files format and content: CK_10%_norm.xlsx  contains read counts from the tumor (CK) compartment over the 10% LoD threshold, after Q3 normalization

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx®-DSP protocol (MAN-10150-01).Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5/666 nm, excitation 645/19 nm, emission 683/30 nm), CD45 for lymphocyte compartment (Texas Red/615 nm, excitation 588/19 nm, emission 623/30 nm), S100B (Cy3/568 nm, excitation 538/19 nm, emission 564/15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx®-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx®-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

value: tumor

tag: disease state

value: HNSCC

tag: patient

value: ICI


title: DSP-1001660008747-A-H05


title: DSP-1001660008747-A-H07


title: run_13_seq_1_PD-12A_S281

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-11H_S280

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-G09


title: DSP-1001660008747-A-G06


title: run_13_seq_1_PD-11G_S279

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-11F_S278

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-11E_S277

description: sci-RNA-seq3 library


title: NB4 cells, WT BCL7A, replicate 1

value: WT BCL7A

value: lentiviral transfection of WT BCL7A


title: DSP-1001660008747-A-G03


title: run_13_seq_1_PD-11C_S275

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-11D_S276

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-11B_S274

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F09


title: DSP-1001660008747-A-F12


title: DSP-1001660008747-A-E12


title: run_13_seq_1_PD-10H_S272

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F06


title: run_13_seq_1_PD-10G_S271

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F03


title: DSP-1001660008747-A-E09


title: DSP-1001660008747-A-E07


title: DSP-1001660008747-A-E04


title: run_13_seq_1_PD-10F_S270

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-H02


title: run_13_seq_1_PD-10D_S268

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-10E_S269

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-E02


title: DSP-1001660008747-A-D11


title: run_13_seq_1_PD-11A_S273

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-10A_S265

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-D06


title: run_13_seq_1_PD-09H_S264

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-D03


title: run_13_seq_1_PD-09G_S263

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-C12


title: run_13_seq_1_PD-09F_S262

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-09E_S261

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-09C_S259

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-09B_S258

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-09D_S260

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-C06


title: DSP-1001660008747-A-B05


title: DSP-1001660008747-A-C01


title: DSP-1001660008747-A-B08


title: DSP-1001660008747-A-C03


title: run_13_seq_1_PD-09A_S257

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-08H_S256

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-B02


title: run_13_seq_1_PD-10C_S267

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-10B_S266

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A08


title: run_13_seq_1_PD-08F_S254

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-D09


title: DSP-1001660008747-A-C09


title: DSP-1001660008747-A-A03


title: run_13_seq_1_PD-08E_S253

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-08C_S251

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B11


title: run_13_seq_1_PE-02F_S302

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-08D_S252

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-C01


title: run_13_seq_1_PD-08B_S250

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B08


title: run_13_seq_1_PD-08G_S255

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A11


title: DSP-1001660008746-B-B02


title: DSP-1001660008746-B-B05


title: run_13_seq_1_PD-07H_S248

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-07F_S246

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-07E_S245

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-A06


title: DSP-1001660008746-B-A08


title: run_13_seq_1_PD-08A_S249

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-07D_S244

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-07C_S243

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H12


title: DSP-1001660008746-B-A04


title: DSP-1001660008746-B-A02


title: DSP-1001660008745-C-H10


title: run_13_seq_1_PD-07B_S242

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H07


title: run_13_seq_1_PD-06H_S240

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H02


title: run_13_seq_1_PD-06G_S239

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-07G_S247

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-A11


title: run_13_seq_1_PD-06F_S238

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-06E_S237

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-07A_S241

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-G05


title: DSP-1001660008745-C-F12


title: DSP-1001660008745-C-G03


title: run_13_seq_1_PD-06D_S236

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-G08


title: DSP-1001660008745-C-F09


title: run_13_seq_1_PD-06A_S233

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-G11


title: run_13_seq_1_PD-05H_S232

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-06B_S234

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-05F_S230

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-F06


title: run_13_seq_1_PD-05E_S229

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-F04


title: DSP-1001660008745-C-E08


title: run_13_seq_1_PD-05D_S228

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E11


title: DSP-1001660008745-C-F01


title: DSP-1001660008745-C-E06


title: run_13_seq_1_PD-05A_S225

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-06C_S235

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-05B_S226

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D12


title: DSP-1001660008745-C-E03


title: run_13_seq_1_PD-04H_S224

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D09


title: run_13_seq_1_PD-04G_S223

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D06


title: run_13_seq_1_PD-04F_S222

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-C12


title: run_13_seq_1_PD-05G_S231

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-C06


title: DSP-1001660008745-C-C03


title: DSP-1001660008745-C-D03


title: run_13_seq_1_PD-04B_S218

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-B12


title: run_13_seq_1_PD-04A_S217

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-03H_S216

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-03G_S215

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-B06


title: run_13_seq_1_PD-05C_S227

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-B03


title: DSP-1001660008745-C-B09


title: run_13_seq_1_PD-03F_S214

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A12


title: DSP-1001660008745-C-A09


title: run_13_seq_1_PD-03E_S213

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-03D_S212

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-04E_S221

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A06


title: NB4 cells, WT BCL7A, replicate 2


title: run_13_seq_1_PD-03C_S211

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A03


title: run_13_seq_1_PD-04C_S219

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-03B_S210

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-03A_S209

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-C03


title: DSP-1001660008744-D-B12


title: DSP-1001660008744-D-B09


title: run_13_seq_1_PD-02G_S207

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-B07


title: DSP-1001660008745-C-C09


title: run_13_seq_1_PD-02F_S206

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-02E_S205

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-02H_S208

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-04D_S220

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-B04


title: run_13_seq_1_PD-02D_S204

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-02C_S203

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-B01


title: DSP-1001660008744-D-A08


title: DSP-1001660008744-D-A06


title: run_13_seq_1_PD-02B_S202

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-02A_S201

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-A04


title: run_13_seq_1_PD-01H_S200

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-01G_S199

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-H11

value: macrophage


title: DSP-1001660008744-D-A10


title: DSP-1001660008747-A-H06


title: run_13_seq_1_PD-01F_S198

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-01E_S197

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-H03


title: run_13_seq_1_PD-01C_S195

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-G12


title: DSP-1001660008747-A-G10


title: run_13_seq_1_PD-01B_S194

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-01D_S196

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-12H_S192

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-12G_S191

description: sci-RNA-seq3 library


title: run_13_seq_1_PD-01A_S193

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-12E_S189

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-G04


title: DSP-1001660008747-A-H08


title: DSP-1001660008747-A-G01


title: DSP-1001660008747-A-G07


title: run_13_seq_1_PC-12F_S190

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F04


title: DSP-1001660008747-A-F10


title: DSP-1001660008747-A-F07


title: run_13_seq_1_PC-12D_S188

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F01


title: DSP-1001660008747-A-E10


title: run_13_seq_1_PC-12B_S186

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-E08


title: run_13_seq_1_PC-12A_S185

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-11H_S184

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-11G_S183

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-E05


title: DSP-1001660008747-A-E03


title: DSP-1001660008747-A-D12


title: run_13_seq_1_PC-11F_S182

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-D04


title: DSP-1001660008747-A-D10


title: DSP-1001660008747-A-D01


title: DSP-1001660008747-A-D07


title: run_13_seq_1_PC-11D_S180

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-12C_S187

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-11E_S181

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-C02


title: DSP-1001660008747-A-C07


title: DSP-1001660008747-A-B11


title: DSP-1001660008747-A-C04


title: DSP-1001660008747-A-C10


title: run_13_seq_1_PC-11C_S179

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-10H_S176

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-10F_S174

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-11B_S178

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-10E_S173

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-B09


title: run_13_seq_1_PC-10D_S172

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-B06


title: run_13_seq_1_PC-10C_S171

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-10B_S170

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-B03


title: run_13_seq_1_PC-11A_S177

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A12


title: run_13_seq_1_PC-10A_S169

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-10G_S175

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A06


title: run_13_seq_1_PC-09H_S168

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A04


title: run_13_seq_1_PC-09G_S167

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A02


title: run_13_seq_1_PC-09F_S166

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-09E_S165

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B12


title: run_13_seq_1_PC-09D_S164

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-09C_S163

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-09B_S162

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B06


title: run_13_seq_1_PC-09A_S161

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B03


title: run_13_seq_1_PC-08H_S160

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B09


title: DSP-1001660008746-B-A09


title: DSP-1001660008746-B-A12


title: DSP-1001660008747-A-A09


title: DSP-1001660008746-B-A07


title: run_13_seq_1_PC-08F_S158

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-08E_S157

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-A05


title: DSP-1001660008746-B-A03


title: run_13_seq_1_PC-08D_S156

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H11


title: run_13_seq_1_PC-08C_S155

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-08G_S159

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H05


title: DSP-1001660008745-C-H03


title: run_13_seq_1_PC-08A_S153

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-07G_S151

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H08


title: run_13_seq_1_PC-07H_S152

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-G09


title: Combination treatment arm, mouse 4

type: RNA

city: Barcelona

first: Laura

last: Torrens

state: Barcelona

address: Esther Koplowitz Center, 3rd Floor. C/ Rosselló 149-153

institute: IDIBAPS, Hospital Clínic Barcelona

hyb_protocol: Hybridization was conducted at the Albert Einstein College of Medicine genomics Facility following the recommendations of the array manufacturer (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000 at the Albert Einstein College of Medicine genomics Facility following the recommendations of the array manufacturer (Affymetrix).

data_processing: Raw CEL files were background corrected and normalized using the Robust Multiarray Averaging (RMA) procedure using the oligo R package. Intensity values were log transformed and mice genes were humanized. Briefly, mouse-human orthologues were obtained from the BioMart database through the BiomaRt R package and expression values for each human gene were calculated using the CollapseDataset module from GenePattern.

label: Biotin

source_name: Tumor sample from syngeneic mouse model

label_protocol: RNA biotin labeling was conducted at the Albert Einstein College of Medicine genomics Facility following the recommendations of the array manufacturer (Affymetrix).

growth_protocol: A syngeneic HCC model was generated by subcutaneously injecting 5x106 Hepa1-6 cells (ATCC) in 100 μl PBS in 5-6-week old female C57BL/6J mice (Charles River Laboratories). Animals were weighed and tumor volume was assessed 3 times per week.

extract_protocol: Total RNA was extracted from 30 mg of tissue using Trizol reagent (Invitrogen) and purified with RNeasy columns (Qiagen, Valencia, CA). RNA sample concentration and quality were assessed by NanoDrop ND-1000 spectrometer (NanoDrop, Wilmington, DE) and bioanalyzer (Agilent, Palo Alto, CA), respectively.

treatment_protocol: Once tumors reached 200 mm3, animals were randomly assigned to receive lenvatinib (Eisai, Ibaraki, Japan), anti-PD1 (anti-murine PD-1 mab clone J43 BioXcell), combination therapy (lenvatinib plus anti-PD1) or placebo (drug vehicle plus polyclonal IgG BE0091, BioXcell). Lenvatinib (10 mg/kg) was administered daily by oral gavage). Anti-PD1 (10 mg/kg) was intraperitoneally administered every 3 days for a total of 5 doses.

value: combination treatment (anti-PD1 monoclonal antibody plus lenvatinib)

tag: Sex

value: Female

value: Tumor sample


title: DSP-1001660008745-C-G12


title: Lenvatinib treatment arm, mouse 5

value: lenvatinib


title: Anti-PD1 treatment arm, mouse 3

value: anti-PD1 monoclonal antibody


title: Combination treatment arm, mouse 5


title: run_13_seq_1_PC-08B_S154

description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


title: Combination treatment arm, mouse 1


title: Lenvatinib treatment arm, mouse 2


title: Combination treatment arm, mouse 2


title: Anti-PD1 treatment arm, mouse 5


title: DSP-1001660008745-C-G06


title: Placebo treatment arm, mouse 1

value: placebo (drug vehicle plus polyclonal IgG)


title: Combination treatment arm, mouse 3


title: Anti-PD1 treatment arm, mouse 1


title: Placebo treatment arm, mouse 5


title: Lenvatinib treatment arm, mouse 4


title: Lenvatinib treatment arm, mouse 3


title: Placebo treatment arm, mouse 3


title: Anti-PD1 treatment arm, mouse 2


title: Placebo treatment arm, mouse 2


title: Anti-PD1 treatment arm, mouse 4


title: Placebo treatment arm, mouse 4


title: run_13_seq_1_PC-07F_S150

description: sci-RNA-seq3 library


title: Placebo treatment arm, mouse 6


title: run_29_P4-12G_S191

description: sci-RNA-seq3 library

value: somitogenesis validation (ranging from 8 to 21 somites)


title: run_29_P4-12H_S192

description: sci-RNA-seq3 library


title: run_29_P4-12F_S190

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-07E_S149

description: sci-RNA-seq3 library


title: Lenvatinib treatment arm, mouse 1


title: DSP-1001660008745-C-G04


title: run_29_P4-12D_S188

description: sci-RNA-seq3 library


title: run_29_P4-12E_S189

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-G01


title: run_13_seq_1_PC-07D_S148

description: sci-RNA-seq3 library


title: run_29_P4-12C_S187

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-07B_S146

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-F10


title: run_29_P4-12B_S186

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-F07


title: run_29_P4-12A_S185

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-07C_S147

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-07A_S145

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-F05


title: run_29_P4-11G_S183

description: sci-RNA-seq3 library


title: run_29_P4-11F_S182

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-06H_S144

description: sci-RNA-seq3 library


title: run_29_P4-11D_S180

description: sci-RNA-seq3 library


title: run_29_P4-11E_S181

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E12


title: run_13_seq_1_PC-06F_S142

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-06G_S143

description: sci-RNA-seq3 library


title: run_29_P4-11A_S177

description: sci-RNA-seq3 library


title: run_29_P4-10H_S176

description: sci-RNA-seq3 library


title: run_29_P4-11B_S178

description: sci-RNA-seq3 library


title: run_29_P4-11C_S179

description: sci-RNA-seq3 library


title: run_29_P4-11H_S184

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E09


title: run_13_seq_1_PC-06E_S141

description: sci-RNA-seq3 library


title: run_29_P4-10F_S174

description: sci-RNA-seq3 library


title: run_29_P4-10G_S175

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-06D_S140

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E04


title: run_29_P4-10C_S171

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-06C_S139

description: sci-RNA-seq3 library


title: run_29_P4-10D_S172

description: sci-RNA-seq3 library


title: run_29_P4-10B_S170

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E01


title: DSP-1001660008745-C-F02


title: run_13_seq_1_PC-06B_S138

description: sci-RNA-seq3 library


title: run_29_P4-10A_S169

description: sci-RNA-seq3 library


title: run_29_P4-09H_S168

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-06A_S137

description: sci-RNA-seq3 library


title: run_29_P4-09G_S167

description: sci-RNA-seq3 library


title: run_29_P4-09F_S166

description: sci-RNA-seq3 library


title: run_29_P4-09E_S165

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-05H_S136

description: sci-RNA-seq3 library


title: run_29_P4-10E_S173

description: sci-RNA-seq3 library


title: run_29_P4-09B_S162

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-05G_S135

description: sci-RNA-seq3 library


title: run_29_P4-09C_S163

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D10


title: run_29_P4-08H_S160

description: sci-RNA-seq3 library


title: run_29_P4-09A_S161

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D01


title: run_13_seq_1_PC-05E_S133

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-C10


title: run_13_seq_1_PC-05D_S132

description: sci-RNA-seq3 library


title: run_29_P4-08C_S155

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E07


title: run_13_seq_1_PC-05C_S131

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D07


title: run_29_P4-08D_S156

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-C04


title: DSP-1001660008745-C-C07


title: run_29_P4-08E_S157

description: sci-RNA-seq3 library


title: run_29_P4-08F_S158

description: sci-RNA-seq3 library


title: run_29_P4-08A_S153

description: sci-RNA-seq3 library


title: run_29_P4-08B_S154

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D04


title: run_13_seq_1_PC-05F_S134

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-05B_S130

description: sci-RNA-seq3 library


title: run_29_P4-07G_S151

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-05A_S129

description: sci-RNA-seq3 library


title: run_29_P4-07F_S150

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-B10


title: DSP-1001660008745-C-B07


title: run_13_seq_1_PC-04H_S128

description: sci-RNA-seq3 library


title: run_29_P4-07D_S148

description: sci-RNA-seq3 library


title: run_29_P4-07E_S149

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-B04


title: run_13_seq_1_PC-04F_S126

description: sci-RNA-seq3 library


title: run_29_P4-07B_S146

description: sci-RNA-seq3 library


title: run_29_P4-07A_S145

description: sci-RNA-seq3 library


title: run_29_P4-06H_S144

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A10


title: run_13_seq_1_PC-04E_S125

description: sci-RNA-seq3 library


title: run_29_P4-06E_S141

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-B01


title: DSP-1001660008745-C-C01


title: DSP-1001660008745-C-A07


title: run_29_P4-06G_S143

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-04D_S124

description: sci-RNA-seq3 library


title: run_29_P4-07H_S152

description: sci-RNA-seq3 library


title: run_29_P4-06F_S142

description: sci-RNA-seq3 library


title: run_29_P4-06D_S140

description: sci-RNA-seq3 library


title: run_29_P4-06C_S139

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A04


title: run_13_seq_1_PC-04C_S123

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-04B_S122

description: sci-RNA-seq3 library


title: run_29_P4-06A_S137

description: sci-RNA-seq3 library


title: run_29_P4-05H_S136

description: sci-RNA-seq3 library


title: run_29_P4-06B_S138

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A02


title: DSP-1001660008744-D-C01


title: run_29_P4-05G_S135

description: sci-RNA-seq3 library


title: run_29_P4-07C_S147

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-04G_S127

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-04A_S121

description: sci-RNA-seq3 library


title: run_29_P4-09D_S164

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-03H_S120

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-B10


title: run_29_P4-05E_S133

description: sci-RNA-seq3 library


title: run_29_P4-05D_S132

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-B08


title: run_29_P4-05C_S131

description: sci-RNA-seq3 library


title: run_29_P4-05F_S134

description: sci-RNA-seq3 library


title: run_29_P4-05B_S130

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-B05


title: run_13_seq_1_PC-03F_S118

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-B02


title: run_29_P4-04G_S127

description: sci-RNA-seq3 library


title: run_29_P4-04H_S128

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-03E_S117

description: sci-RNA-seq3 library


title: run_29_P4-04F_S126

description: sci-RNA-seq3 library


title: run_29_P4-05A_S129

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-03G_S119

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-A11


title: run_13_seq_1_PC-03D_S116

description: sci-RNA-seq3 library


title: run_29_P4-04E_S125

description: sci-RNA-seq3 library


title: run_29_P4-04D_S124

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-A09


title: run_29_P4-04C_S123

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-03C_S115

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-A07


title: run_13_seq_1_PC-03B_S114

description: sci-RNA-seq3 library


title: run_29_P4-03H_S120

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-A05


title: run_13_seq_1_PC-03A_S113

description: sci-RNA-seq3 library


title: run_29_P4-03G_S119

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-02H_S112

description: sci-RNA-seq3 library


title: run_29_P4-03E_S117

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-A02


title: run_29_P4-03D_S116

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-02G_S111

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-02E_S109

description: sci-RNA-seq3 library


title: run_29_P4-03B_S114

description: sci-RNA-seq3 library


title: run_29_P4-03C_S115

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-02D_S108

description: sci-RNA-seq3 library


title: run_29_P4-04A_S121

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-H01

value: leukocyte


title: run_29_P4-03A_S113

description: sci-RNA-seq3 library


title: run_29_P4-02F_S110

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-02F_S110

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-H09


title: run_29_P4-02E_S109

description: sci-RNA-seq3 library


title: run_29_P4-02D_S108

description: sci-RNA-seq3 library


title: run_29_P4-02H_S112

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-G11


title: run_29_P4-02G_S111

description: sci-RNA-seq3 library


title: run_29_P4-04B_S122

description: sci-RNA-seq3 library


title: run_29_P4-02C_S107

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-02C_S107

description: sci-RNA-seq3 library


title: run_29_P4-02B_S106

description: sci-RNA-seq3 library


title: run_29_P4-03F_S118

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-G08


title: run_13_seq_1_PC-02B_S106

description: sci-RNA-seq3 library


title: run_29_P4-02A_S105

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-H12


title: DSP-1001660008747-A-H04


title: run_29_P4-08G_S159

description: sci-RNA-seq3 library


title: run_29_P4-01G_S103

description: sci-RNA-seq3 library


title: run_29_P4-01F_S102

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-01H_S104

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-02A_S105

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-G02


title: run_29_P4-01E_S101

description: sci-RNA-seq3 library


title: run_29_P4-01D_S100

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F11


title: run_29_P4-01C_S99

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-01G_S103

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-01F_S102

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-G05


title: run_29_P1-12H_S96

description: sci-RNA-seq3 library


title: run_29_P4-01H_S104

description: sci-RNA-seq3 library


title: run_29_P4-01B_S98

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F08


title: run_13_seq_1_PC-01D_S100

description: sci-RNA-seq3 library


title: run_29_P1-12E_S93

description: sci-RNA-seq3 library


title: run_29_P1-12D_S92

description: sci-RNA-seq3 library


title: run_29_P4-01A_S97

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F02


title: DSP-1001660008747-A-E11


title: run_29_P1-12C_S91

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-01E_S101

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-F05


title: run_29_P1-12G_S95

description: sci-RNA-seq3 library


title: run_29_P1-12F_S94

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-01C_S99

description: sci-RNA-seq3 library


title: run_29_P1-12B_S90

description: sci-RNA-seq3 library


title: run_29_P1-12A_S89

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-01B_S98

description: sci-RNA-seq3 library


title: run_29_P1-11H_S88

description: sci-RNA-seq3 library


title: run_29_P1-11F_S86

description: sci-RNA-seq3 library


title: run_29_P1-11G_S87

description: sci-RNA-seq3 library


title: run_29_P1-11E_S85

description: sci-RNA-seq3 library


title: run_29_P1-11D_S84

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-D05


title: run_29_P1-11B_S82

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-12G_S95

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-12F_S94

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-D02


title: DSP-1001660008747-A-C08


title: run_29_P1-11C_S83

description: sci-RNA-seq3 library


title: run_29_P1-10F_S78

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-12E_S93

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-C11