title: EBs.MUA_EV_001_X367

description: Transcriptome measurement of sample EBs.MUA_EV_001_X367


title: EBs.MUA_EV_002_X012

status: Public on Mar 05 2022

type: SRA

city: Utrecht

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Transcriptome measurement of sample EBs.MUA_EV_002_X012

library_source: transcriptomic

data_processing:
Demultiplexing of raw data (previously demultiplexed on Illumina index) was done using barcodes. Read1 measurements contained only the barcode and UMI followed by unalignable sequence , usually polyT and are therefore not included. Read2 of the transcriptomic measurements contains the mRNA sequence. All reads provided are read 2. The sequencing was run in 4 lanes: L001-L004.
mRNA reads (in read2) were aligned using tophat2 (v2.1.1) using parameters ‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200’ to a transcriptome (options ‘--GTF’ and ‘--transcriptome-index’) obtained from GENCODE (v26) supplemented with ERCC mRNA spike-in sequences.
Reads and unique UMIs were counted per gene (according to the “intersection-strict” algorithm of `htseq-count` [http://htseq.readthedocs.io/en/master/count.html]). For each gene, the number of unique observed UMIs was trimmed by starting at the UMI with highest read count and setting UMIs with Hamming distance of 1 to zero, and iteratively filtering all UMI sequences (in case of equal read counts for a UMI, ties were broking by lexicographic sorting of the UMIs). The number of observed distinct UMIs after trimming was taken as the transcript count for that gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tables are provided with the number of transcripts per gene.

molecule: polyA RNA

organism: Mus musculus

source_name: embryoid bodies from mouse ESCs

growth_protocol:
Advanced N2B27 medium was used as the basic medium consisting of 2% B27 (Gibco, 17504-044) and 1% N2 (Gibco, 17502-048), a 1/1 mixture of Advanced DMEM/F12 (ThermoFisher, 12634028) with Neurobasal (ThermoFisher, 12348017), 2 mM Glutamax (Gibco), 10mM NEAA (ThermoFisher, 11140050), 0.5% Bovine Serum Albumin (Sigma-Aldrich, A7979), 10 mM HEPES (Gibco, 15630056), 1 mM Sodium Pyruvate (ThermoFisher, 11360070). supplemented right before use with 10 ng/mL leukaemia inhibitory factor (Lif, Merck Millipore ESG1106), 1 ?M PD0325901 (AxonMed, 1408), 3 ?M CHIR99021 (AxonMed, 1386) and 50 ?M 2-mercaptoethanol (Gibco, 11528926). For ESC expansion the cells were expanded for minimally 2 passages on gelatin-coated tissue-culture plastic in advanced N2B27 medium was supplemented right before use with 3 ?M CHIR99021 (AxonMed 1386), 10 ng/mL Lif (Merck Millipore ESG1106), 1 ?M PD0325901 (AxonMed 1408) and 50 µM 2-mercaptoethanol (Gibco 11528926).
PrE-induction for Rosette formation was done by seeding an average of 14 ESC per microwell in Advanced B27N2 medium supplemented with 10 mM HEPES and penicillin/streptomycin, and the PrE-induction compounds 3 ?M CHIR99021 (AxonMed 1386), 50 ng/mL Fgf4 (RnD systems, 5846-F4-025), 10 nM RA (Sigma R2625), 1 mM 8Br-cAMP (Biolog, B007-50E), 1 µg/mL heparin (Sigma) and 50 µM 2-mercaptoethanol (Gibco 11528926). When seeding the cells in the microwells 2 µM Y27632 (AxonMed 1683) was added. Microwell arrays were pre-wetted in serum-medium containing 100U/ml penicillin/streptomycin before use. After 24 h or 48 h of culture, cells were washed once with advanced N2B27 medium and then refreshed with advanced N2B27 supplemented with 50 µM 2-mercaptoethanol. After 72 h EBs were flushed out and transferred into non-TCPS 6-well plates with 2 mL advanced N2B27 medium supplemented with 50 µM 2-mercaptoethanol.

extract_protocol:
EBs were washed twice in PBS before collagenase IV (600 U/ml) was added. Plates were shaken at 350 RPM for 30 minutes before being transferred to TrypLE 10X (Thermofisher, A1217701, no dilution) and shaken again for 20 minutes. EBs were dissociated into single cell suspensions using a small capillary. The resulting suspension was quenched using PBS with 50% FBS, centrifuged and resuspended in 230 µl of PBS with 10% FBS. Cells were stained with Pdgfr? antibody (1:150 dilution) for 30 min at 4°C followed by three PBS (+10%FBS) washes, secondary antibody incubation (1:400) for 30 min. Cells were washed three times in PBS and sorted for further processing.
Rosettes were manually picked and placed in a round-bottom 96wp-well containing 100 µl PBS + 0.5% BSA. When sufficient numbers were collected, they were transferred to an Eppendorf tube with 600 µl Accumax and incubated at 37 degree C for 30 min. Every 5-10 minutes the mixture was resuspended using a 200 µl pipette. When single cells were observed under the microscope the suspension was centrifuged at 200g for 4 min and, supernatant was removed and cells were resuspended in staining solution in PBS (2 µM Di-I + 0.1% Dead-stain-647 ) and incubated for 20 min at RT in the dark. Epiblast-only rosettes were washed once with PBS before domes were disrupted using 150 µl of a 1:1 DipaseII:N2B27 mixture and incubated for 20 min at 37 degree C in a 1.5ml Eppendorf tube (4 domes per tube). Solution was resuspended every 5-10 minutes using a 200 µl pipette tip. Finally, the cell suspension was resuspended in 700 µl Accumax with 100 µl of PBS with 0.5% BSA and incubated for 25 min at 37 degree C. Single cells were stained with 2 µM Di-I + 0.1% Dead-stain-647) and incubated for 20 min at RT in the dark.

tag: celseq2 adapter

tag: pdgfra staining

value: positive

tag: sample type


title: EBs.MUA_EV_001_X377

description: Transcriptome measurement of sample EBs.MUA_EV_001_X377


title: EBs.MUA_EV_001_X355

description: Transcriptome measurement of sample EBs.MUA_EV_001_X355


title: EBs.MUA_EV_001_X370

description: Transcriptome measurement of sample EBs.MUA_EV_001_X370


title: EBs.MUA_EV_001_X363

description: Transcriptome measurement of sample EBs.MUA_EV_001_X363


title: EBs.MUA_EV_001_X368

description: Transcriptome measurement of sample EBs.MUA_EV_001_X368


title: EBs.MUA_EV_001_X366

description: Transcriptome measurement of sample EBs.MUA_EV_001_X366


title: EBs.MUA_EV_001_X371

description: Transcriptome measurement of sample EBs.MUA_EV_001_X371


title: EBs.MUA_EV_001_X352

description: Transcriptome measurement of sample EBs.MUA_EV_001_X352


title: EBs.MUA_EV_001_X351

description: Transcriptome measurement of sample EBs.MUA_EV_001_X351


title: EBs.MUA_EV_002_X013

description: Transcriptome measurement of sample EBs.MUA_EV_002_X013


title: EBs.MUA_EV_001_X353

description: Transcriptome measurement of sample EBs.MUA_EV_001_X353


title: EBs.MUA_EV_001_X364

description: Transcriptome measurement of sample EBs.MUA_EV_001_X364


title: EBs.MUA_EV_001_X348

description: Transcriptome measurement of sample EBs.MUA_EV_001_X348


title: EBs.MUA_EV_001_X354

description: Transcriptome measurement of sample EBs.MUA_EV_001_X354


title: EBs.MUA_EV_001_X350

description: Transcriptome measurement of sample EBs.MUA_EV_001_X350


title: EBs.MUA_EV_001_X349

description: Transcriptome measurement of sample EBs.MUA_EV_001_X349


title: EBs.MUA_EV_001_X346

description: Transcriptome measurement of sample EBs.MUA_EV_001_X346


title: EBs.MUA_EV_001_X347

description: Transcriptome measurement of sample EBs.MUA_EV_001_X347


title: EBs.MUA_EV_001_X344

description: Transcriptome measurement of sample EBs.MUA_EV_001_X344


title: EBs.MUA_EV_001_X345

description: Transcriptome measurement of sample EBs.MUA_EV_001_X345


title: EBs.MUA_EV_001_X360

description: Transcriptome measurement of sample EBs.MUA_EV_001_X360


title: EBs.MUA_EV_001_X361

description: Transcriptome measurement of sample EBs.MUA_EV_001_X361


title: EBs.MUA_EV_001_X343

description: Transcriptome measurement of sample EBs.MUA_EV_001_X343


title: EBs.MUA_EV_001_X342

description: Transcriptome measurement of sample EBs.MUA_EV_001_X342


title: EBs.MUA_EV_001_X341

description: Transcriptome measurement of sample EBs.MUA_EV_001_X341


title: EBs.MUA_EV_001_X339

description: Transcriptome measurement of sample EBs.MUA_EV_001_X339


title: EBs.MUA_EV_001_X340

description: Transcriptome measurement of sample EBs.MUA_EV_001_X340


title: EBs.MUA_EV_001_X338

description: Transcriptome measurement of sample EBs.MUA_EV_001_X338


title: EBs.MUA_EV_001_X335

description: Transcriptome measurement of sample EBs.MUA_EV_001_X335


title: EBs.MUA_EV_001_X336

description: Transcriptome measurement of sample EBs.MUA_EV_001_X336


title: EBs.MUA_EV_001_X334

description: Transcriptome measurement of sample EBs.MUA_EV_001_X334


title: EBs.MUA_EV_001_X337

description: Transcriptome measurement of sample EBs.MUA_EV_001_X337


title: EBs.MUA_EV_001_X356

description: Transcriptome measurement of sample EBs.MUA_EV_001_X356


title: EBs.MUA_EV_001_X330

description: Transcriptome measurement of sample EBs.MUA_EV_001_X330


title: EBs.MUA_EV_001_X327

description: Transcriptome measurement of sample EBs.MUA_EV_001_X327


title: EBs.MUA_EV_001_X333

description: Transcriptome measurement of sample EBs.MUA_EV_001_X333


title: EBs.MUA_EV_001_X332

description: Transcriptome measurement of sample EBs.MUA_EV_001_X332


title: EBs.MUA_EV_001_X325

description: Transcriptome measurement of sample EBs.MUA_EV_001_X325


title: EBs.MUA_EV_001_X324

description: Transcriptome measurement of sample EBs.MUA_EV_001_X324


title: EBs.MUA_EV_001_X322

description: Transcriptome measurement of sample EBs.MUA_EV_001_X322


title: EBs.MUA_EV_001_X326

description: Transcriptome measurement of sample EBs.MUA_EV_001_X326


title: EBs.MUA_EV_001_X320

description: Transcriptome measurement of sample EBs.MUA_EV_001_X320


title: EBs.MUA_EV_001_X321

description: Transcriptome measurement of sample EBs.MUA_EV_001_X321


title: EBs.MUA_EV_001_X323

description: Transcriptome measurement of sample EBs.MUA_EV_001_X323


title: EBs.MUA_EV_001_X319

description: Transcriptome measurement of sample EBs.MUA_EV_001_X319


title: EBs.MUA_EV_001_X318

description: Transcriptome measurement of sample EBs.MUA_EV_001_X318


title: EBs.MUA_EV_001_X315

description: Transcriptome measurement of sample EBs.MUA_EV_001_X315


title: EBs.MUA_EV_001_X314

description: Transcriptome measurement of sample EBs.MUA_EV_001_X314


title: EBs.MUA_EV_001_X312

description: Transcriptome measurement of sample EBs.MUA_EV_001_X312


title: EBs.MUA_EV_001_X313

description: Transcriptome measurement of sample EBs.MUA_EV_001_X313


title: EBs.MUA_EV_001_X316

description: Transcriptome measurement of sample EBs.MUA_EV_001_X316


title: EBs.MUA_EV_001_X309

description: Transcriptome measurement of sample EBs.MUA_EV_001_X309


title: EBs.MUA_EV_001_X308

description: Transcriptome measurement of sample EBs.MUA_EV_001_X308


title: EBs.MUA_EV_001_X310

description: Transcriptome measurement of sample EBs.MUA_EV_001_X310


title: EBs.MUA_EV_001_X305

description: Transcriptome measurement of sample EBs.MUA_EV_001_X305


title: EBs.MUA_EV_001_X306

description: Transcriptome measurement of sample EBs.MUA_EV_001_X306


title: EBs.MUA_EV_001_X311

description: Transcriptome measurement of sample EBs.MUA_EV_001_X311


title: EBs.MUA_EV_001_X307

description: Transcriptome measurement of sample EBs.MUA_EV_001_X307


title: EBs.MUA_EV_001_X300

description: Transcriptome measurement of sample EBs.MUA_EV_001_X300


title: EBs.MUA_EV_001_X331

description: Transcriptome measurement of sample EBs.MUA_EV_001_X331


title: EBs.MUA_EV_001_X303

description: Transcriptome measurement of sample EBs.MUA_EV_001_X303


title: EBs.MUA_EV_001_X302

description: Transcriptome measurement of sample EBs.MUA_EV_001_X302


title: EBs.MUA_EV_001_X301

description: Transcriptome measurement of sample EBs.MUA_EV_001_X301


title: EBs.MUA_EV_001_X304

description: Transcriptome measurement of sample EBs.MUA_EV_001_X304


title: EBs.MUA_EV_001_X298

description: Transcriptome measurement of sample EBs.MUA_EV_001_X298


title: EBs.MUA_EV_001_X329

description: Transcriptome measurement of sample EBs.MUA_EV_001_X329


title: EBs.MUA_EV_001_X297

description: Transcriptome measurement of sample EBs.MUA_EV_001_X297


title: EBs.MUA_EV_001_X328

description: Transcriptome measurement of sample EBs.MUA_EV_001_X328


title: EBs.MUA_EV_001_X299

description: Transcriptome measurement of sample EBs.MUA_EV_001_X299


title: EBs.MUA_EV_001_X296

description: Transcriptome measurement of sample EBs.MUA_EV_001_X296


title: EBs.MUA_EV_001_X293

description: Transcriptome measurement of sample EBs.MUA_EV_001_X293


title: EBs.MUA_EV_001_X294

description: Transcriptome measurement of sample EBs.MUA_EV_001_X294


title: EBs.MUA_EV_001_X295

description: Transcriptome measurement of sample EBs.MUA_EV_001_X295


title: EBs.MUA_EV_001_X292

description: Transcriptome measurement of sample EBs.MUA_EV_001_X292


title: EBs.MUA_EV_001_X317

description: Transcriptome measurement of sample EBs.MUA_EV_001_X317


title: EBs.MUA_EV_001_X290

description: Transcriptome measurement of sample EBs.MUA_EV_001_X290


title: EBs.MUA_EV_001_X291

description: Transcriptome measurement of sample EBs.MUA_EV_001_X291


title: EBs.MUA_EV_001_X289

description: Transcriptome measurement of sample EBs.MUA_EV_001_X289


title: EBs.MUA_EV_001_X288

description: Transcriptome measurement of sample EBs.MUA_EV_001_X288


title: EBs.MUA_EV_001_X287

description: Transcriptome measurement of sample EBs.MUA_EV_001_X287


title: EBs.MUA_EV_001_X286

description: Transcriptome measurement of sample EBs.MUA_EV_001_X286


title: EBs.MUA_EV_001_X282

description: Transcriptome measurement of sample EBs.MUA_EV_001_X282


title: EBs.MUA_EV_001_X285

description: Transcriptome measurement of sample EBs.MUA_EV_001_X285


title: EBs.MUA_EV_001_X284

description: Transcriptome measurement of sample EBs.MUA_EV_001_X284


title: EBs.MUA_EV_001_X280

description: Transcriptome measurement of sample EBs.MUA_EV_001_X280


title: EBs.MUA_EV_001_X283

description: Transcriptome measurement of sample EBs.MUA_EV_001_X283


title: EBs.MUA_EV_001_X278

description: Transcriptome measurement of sample EBs.MUA_EV_001_X278


title: EBs.MUA_EV_001_X279

description: Transcriptome measurement of sample EBs.MUA_EV_001_X279


title: EBs.MUA_EV_001_X275

description: Transcriptome measurement of sample EBs.MUA_EV_001_X275


title: EBs.MUA_EV_001_X274

description: Transcriptome measurement of sample EBs.MUA_EV_001_X274


title: EBs.MUA_EV_001_X270

description: Transcriptome measurement of sample EBs.MUA_EV_001_X270


title: EBs.MUA_EV_001_X277

description: Transcriptome measurement of sample EBs.MUA_EV_001_X277


title: EBs.MUA_EV_001_X272

description: Transcriptome measurement of sample EBs.MUA_EV_001_X272


title: EBs.MUA_EV_001_X276

description: Transcriptome measurement of sample EBs.MUA_EV_001_X276


title: EBs.MUA_EV_001_X269

description: Transcriptome measurement of sample EBs.MUA_EV_001_X269


title: EBs.MUA_EV_001_X273

description: Transcriptome measurement of sample EBs.MUA_EV_001_X273


title: EBs.MUA_EV_001_X266

description: Transcriptome measurement of sample EBs.MUA_EV_001_X266


title: EBs.MUA_EV_001_X268

description: Transcriptome measurement of sample EBs.MUA_EV_001_X268


title: EBs.MUA_EV_001_X271

description: Transcriptome measurement of sample EBs.MUA_EV_001_X271


title: EBs.MUA_EV_001_X267

description: Transcriptome measurement of sample EBs.MUA_EV_001_X267


title: EBs.MUA_EV_001_X265

description: Transcriptome measurement of sample EBs.MUA_EV_001_X265


title: EBs.MUA_EV_001_X264

description: Transcriptome measurement of sample EBs.MUA_EV_001_X264


title: EBs.MUA_EV_001_X263

description: Transcriptome measurement of sample EBs.MUA_EV_001_X263


title: EBs.MUA_EV_001_X262

description: Transcriptome measurement of sample EBs.MUA_EV_001_X262


title: EBs.MUA_EV_001_X261

description: Transcriptome measurement of sample EBs.MUA_EV_001_X261


title: EBs.MUA_EV_001_X260

description: Transcriptome measurement of sample EBs.MUA_EV_001_X260


title: EBs.MUA_EV_001_X258

description: Transcriptome measurement of sample EBs.MUA_EV_001_X258


title: EBs.MUA_EV_001_X259

description: Transcriptome measurement of sample EBs.MUA_EV_001_X259


title: EBs.MUA_EV_001_X257

description: Transcriptome measurement of sample EBs.MUA_EV_001_X257


title: EBs.MUA_EV_001_X256

description: Transcriptome measurement of sample EBs.MUA_EV_001_X256


title: EBs.MUA_EV_001_X281

description: Transcriptome measurement of sample EBs.MUA_EV_001_X281


title: EBs.MUA_EV_001_X255

description: Transcriptome measurement of sample EBs.MUA_EV_001_X255


title: EBs.MUA_EV_001_X252

description: Transcriptome measurement of sample EBs.MUA_EV_001_X252


title: EBs.MUA_EV_001_X253

description: Transcriptome measurement of sample EBs.MUA_EV_001_X253


title: EBs.MUA_EV_001_X254

description: Transcriptome measurement of sample EBs.MUA_EV_001_X254


title: EBs.MUA_EV_001_X250

description: Transcriptome measurement of sample EBs.MUA_EV_001_X250


title: EBs.MUA_EV_001_X251

description: Transcriptome measurement of sample EBs.MUA_EV_001_X251


title: EBs.MUA_EV_001_X248

description: Transcriptome measurement of sample EBs.MUA_EV_001_X248


title: EBs.MUA_EV_001_X245

description: Transcriptome measurement of sample EBs.MUA_EV_001_X245


title: EBs.MUA_EV_001_X243

description: Transcriptome measurement of sample EBs.MUA_EV_001_X243


title: EBs.MUA_EV_001_X246

description: Transcriptome measurement of sample EBs.MUA_EV_001_X246


title: EBs.MUA_EV_001_X247

description: Transcriptome measurement of sample EBs.MUA_EV_001_X247


title: EBs.MUA_EV_001_X249

description: Transcriptome measurement of sample EBs.MUA_EV_001_X249


title: EBs.MUA_EV_001_X244

description: Transcriptome measurement of sample EBs.MUA_EV_001_X244


title: EBs.MUA_EV_001_X240

description: Transcriptome measurement of sample EBs.MUA_EV_001_X240


title: EBs.MUA_EV_001_X242

description: Transcriptome measurement of sample EBs.MUA_EV_001_X242


title: EBs.MUA_EV_001_X239

description: Transcriptome measurement of sample EBs.MUA_EV_001_X239


title: EBs.MUA_EV_001_X238

description: Transcriptome measurement of sample EBs.MUA_EV_001_X238


title: EBs.MUA_EV_001_X241

description: Transcriptome measurement of sample EBs.MUA_EV_001_X241


title: EBs.MUA_EV_001_X236

description: Transcriptome measurement of sample EBs.MUA_EV_001_X236


title: EBs.MUA_EV_001_X235

description: Transcriptome measurement of sample EBs.MUA_EV_001_X235


title: EBs.MUA_EV_001_X232

description: Transcriptome measurement of sample EBs.MUA_EV_001_X232


title: EBs.MUA_EV_001_X233

description: Transcriptome measurement of sample EBs.MUA_EV_001_X233


title: EBs.MUA_EV_001_X231

description: Transcriptome measurement of sample EBs.MUA_EV_001_X231


title: EBs.MUA_EV_001_X228

description: Transcriptome measurement of sample EBs.MUA_EV_001_X228


title: EBs.MUA_EV_001_X230

description: Transcriptome measurement of sample EBs.MUA_EV_001_X230


title: EBs.MUA_EV_001_X229

description: Transcriptome measurement of sample EBs.MUA_EV_001_X229


title: EBs.MUA_EV_001_X227

description: Transcriptome measurement of sample EBs.MUA_EV_001_X227


title: EBs.MUA_EV_001_X226

description: Transcriptome measurement of sample EBs.MUA_EV_001_X226


title: EBs.MUA_EV_001_X225

description: Transcriptome measurement of sample EBs.MUA_EV_001_X225


title: EBs.MUA_EV_001_X224

description: Transcriptome measurement of sample EBs.MUA_EV_001_X224


title: EBs.MUA_EV_001_X221

description: Transcriptome measurement of sample EBs.MUA_EV_001_X221


title: EBs.MUA_EV_001_X223

description: Transcriptome measurement of sample EBs.MUA_EV_001_X223


title: EBs.MUA_EV_001_X222

description: Transcriptome measurement of sample EBs.MUA_EV_001_X222


title: EBs.MUA_EV_001_X220

description: Transcriptome measurement of sample EBs.MUA_EV_001_X220


title: EBs.MUA_EV_001_X219

description: Transcriptome measurement of sample EBs.MUA_EV_001_X219


title: EBs.MUA_EV_001_X218

description: Transcriptome measurement of sample EBs.MUA_EV_001_X218


title: EBs.MUA_EV_001_X217

description: Transcriptome measurement of sample EBs.MUA_EV_001_X217


title: EBs.MUA_EV_001_X215

description: Transcriptome measurement of sample EBs.MUA_EV_001_X215


title: EBs.MUA_EV_001_X216

description: Transcriptome measurement of sample EBs.MUA_EV_001_X216


title: EBs.MUA_EV_001_X214

description: Transcriptome measurement of sample EBs.MUA_EV_001_X214


title: EBs.MUA_EV_001_X212

description: Transcriptome measurement of sample EBs.MUA_EV_001_X212


title: EBs.MUA_EV_001_X213

description: Transcriptome measurement of sample EBs.MUA_EV_001_X213


title: EBs.MUA_EV_001_X209

description: Transcriptome measurement of sample EBs.MUA_EV_001_X209


title: EBs.MUA_EV_001_X210

description: Transcriptome measurement of sample EBs.MUA_EV_001_X210


title: EBs.MUA_EV_001_X237

description: Transcriptome measurement of sample EBs.MUA_EV_001_X237


title: EBs.MUA_EV_001_X211

description: Transcriptome measurement of sample EBs.MUA_EV_001_X211


title: EBs.MUA_EV_001_X206

description: Transcriptome measurement of sample EBs.MUA_EV_001_X206


title: EBs.MUA_EV_001_X207

description: Transcriptome measurement of sample EBs.MUA_EV_001_X207


title: EBs.MUA_EV_001_X205

description: Transcriptome measurement of sample EBs.MUA_EV_001_X205


title: EBs.MUA_EV_001_X234

description: Transcriptome measurement of sample EBs.MUA_EV_001_X234


title: EBs.MUA_EV_001_X204

description: Transcriptome measurement of sample EBs.MUA_EV_001_X204


title: EBs.MUA_EV_001_X208

description: Transcriptome measurement of sample EBs.MUA_EV_001_X208


title: EBs.MUA_EV_001_X202

description: Transcriptome measurement of sample EBs.MUA_EV_001_X202


title: EBs.MUA_EV_001_X201

description: Transcriptome measurement of sample EBs.MUA_EV_001_X201


title: EBs.MUA_EV_001_X203

description: Transcriptome measurement of sample EBs.MUA_EV_001_X203


title: EBs.MUA_EV_001_X197

description: Transcriptome measurement of sample EBs.MUA_EV_001_X197


title: EBs.MUA_EV_001_X199

description: Transcriptome measurement of sample EBs.MUA_EV_001_X199


title: EBs.MUA_EV_001_X198

description: Transcriptome measurement of sample EBs.MUA_EV_001_X198


title: EBs.MUA_EV_001_X196

description: Transcriptome measurement of sample EBs.MUA_EV_001_X196


title: EBs.MUA_EV_001_X193

description: Transcriptome measurement of sample EBs.MUA_EV_001_X193


title: EBs.MUA_EV_001_X195

description: Transcriptome measurement of sample EBs.MUA_EV_001_X195


title: EBs.MUA_EV_001_X194

description: Transcriptome measurement of sample EBs.MUA_EV_001_X194


title: EBs.MUA_EV_001_X191

description: Transcriptome measurement of sample EBs.MUA_EV_001_X191


title: EBs.MUA_EV_001_X187

description: Transcriptome measurement of sample EBs.MUA_EV_001_X187


title: EBs.MUA_EV_001_X186

description: Transcriptome measurement of sample EBs.MUA_EV_001_X186


title: EBs.MUA_EV_001_X190

description: Transcriptome measurement of sample EBs.MUA_EV_001_X190


title: EBs.MUA_EV_001_X189

description: Transcriptome measurement of sample EBs.MUA_EV_001_X189


title: EBs.MUA_EV_001_X184

description: Transcriptome measurement of sample EBs.MUA_EV_001_X184


title: EBs.MUA_EV_001_X185

description: Transcriptome measurement of sample EBs.MUA_EV_001_X185


title: EBs.MUA_EV_001_X182

description: Transcriptome measurement of sample EBs.MUA_EV_001_X182


title: EBs.MUA_EV_001_X181

description: Transcriptome measurement of sample EBs.MUA_EV_001_X181


title: EBs.MUA_EV_001_X178

description: Transcriptome measurement of sample EBs.MUA_EV_001_X178


title: EBs.MUA_EV_001_X183

description: Transcriptome measurement of sample EBs.MUA_EV_001_X183


title: EBs.MUA_EV_001_X180

description: Transcriptome measurement of sample EBs.MUA_EV_001_X180


title: EBs.MUA_EV_001_X179

description: Transcriptome measurement of sample EBs.MUA_EV_001_X179


title: EBs.MUA_EV_001_X175

description: Transcriptome measurement of sample EBs.MUA_EV_001_X175


title: EBs.MUA_EV_001_X174

description: Transcriptome measurement of sample EBs.MUA_EV_001_X174


title: EBs.MUA_EV_001_X176

description: Transcriptome measurement of sample EBs.MUA_EV_001_X176


title: EBs.MUA_EV_001_X172

description: Transcriptome measurement of sample EBs.MUA_EV_001_X172


title: EBs.MUA_EV_001_X171

description: Transcriptome measurement of sample EBs.MUA_EV_001_X171


title: EBs.MUA_EV_001_X177

description: Transcriptome measurement of sample EBs.MUA_EV_001_X177


title: EBs.MUA_EV_001_X200

description: Transcriptome measurement of sample EBs.MUA_EV_001_X200


title: EBs.MUA_EV_001_X170

description: Transcriptome measurement of sample EBs.MUA_EV_001_X170


title: EBs.MUA_EV_001_X168

description: Transcriptome measurement of sample EBs.MUA_EV_001_X168


title: EBs.MUA_EV_001_X169

description: Transcriptome measurement of sample EBs.MUA_EV_001_X169


title: EBs.MUA_EV_001_X167

description: Transcriptome measurement of sample EBs.MUA_EV_001_X167


title: EBs.MUA_EV_001_X165

description: Transcriptome measurement of sample EBs.MUA_EV_001_X165


title: EBs.MUA_EV_001_X192

description: Transcriptome measurement of sample EBs.MUA_EV_001_X192


title: EBs.MUA_EV_001_X163

description: Transcriptome measurement of sample EBs.MUA_EV_001_X163


title: EBs.MUA_EV_001_X188

description: Transcriptome measurement of sample EBs.MUA_EV_001_X188


title: EBs.MUA_EV_001_X161

description: Transcriptome measurement of sample EBs.MUA_EV_001_X161


title: EBs.MUA_EV_001_X162

description: Transcriptome measurement of sample EBs.MUA_EV_001_X162


title: EBs.MUA_EV_001_X160

description: Transcriptome measurement of sample EBs.MUA_EV_001_X160


title: EBs.MUA_EV_001_X157

description: Transcriptome measurement of sample EBs.MUA_EV_001_X157


title: EBs.MUA_EV_001_X156

description: Transcriptome measurement of sample EBs.MUA_EV_001_X156


title: EBs.MUA_EV_001_X154

description: Transcriptome measurement of sample EBs.MUA_EV_001_X154


title: EBs.MUA_EV_001_X155

description: Transcriptome measurement of sample EBs.MUA_EV_001_X155


title: EBs.MUA_EV_001_X158

description: Transcriptome measurement of sample EBs.MUA_EV_001_X158


title: EBs.MUA_EV_001_X173

description: Transcriptome measurement of sample EBs.MUA_EV_001_X173


title: EBs.MUA_EV_001_X151

description: Transcriptome measurement of sample EBs.MUA_EV_001_X151


title: EBs.MUA_EV_001_X153

description: Transcriptome measurement of sample EBs.MUA_EV_001_X153


title: EBs.MUA_EV_001_X150

description: Transcriptome measurement of sample EBs.MUA_EV_001_X150


title: EBs.MUA_EV_001_X149

description: Transcriptome measurement of sample EBs.MUA_EV_001_X149


title: EBs.MUA_EV_001_X152

description: Transcriptome measurement of sample EBs.MUA_EV_001_X152


title: EBs.MUA_EV_001_X145

description: Transcriptome measurement of sample EBs.MUA_EV_001_X145


title: EBs.MUA_EV_001_X144

description: Transcriptome measurement of sample EBs.MUA_EV_001_X144


title: EBs.MUA_EV_001_X143

description: Transcriptome measurement of sample EBs.MUA_EV_001_X143


title: EBs.MUA_EV_001_X142

description: Transcriptome measurement of sample EBs.MUA_EV_001_X142


title: EBs.MUA_EV_001_X148

description: Transcriptome measurement of sample EBs.MUA_EV_001_X148


title: EBs.MUA_EV_001_X140

description: Transcriptome measurement of sample EBs.MUA_EV_001_X140


title: EBs.MUA_EV_001_X139

description: Transcriptome measurement of sample EBs.MUA_EV_001_X139


title: EBs.MUA_EV_001_X166

description: Transcriptome measurement of sample EBs.MUA_EV_001_X166


title: EBs.MUA_EV_001_X138

description: Transcriptome measurement of sample EBs.MUA_EV_001_X138


title: EBs.MUA_EV_001_X141

description: Transcriptome measurement of sample EBs.MUA_EV_001_X141


title: EBs.MUA_EV_001_X137

description: Transcriptome measurement of sample EBs.MUA_EV_001_X137


title: EBs.MUA_EV_001_X164

description: Transcriptome measurement of sample EBs.MUA_EV_001_X164


title: EBs.MUA_EV_001_X135

description: Transcriptome measurement of sample EBs.MUA_EV_001_X135


title: EBs.MUA_EV_001_X136

description: Transcriptome measurement of sample EBs.MUA_EV_001_X136


title: EBs.MUA_EV_001_X134

description: Transcriptome measurement of sample EBs.MUA_EV_001_X134


title: EBs.MUA_EV_001_X133

description: Transcriptome measurement of sample EBs.MUA_EV_001_X133


title: EBs.MUA_EV_001_X159

description: Transcriptome measurement of sample EBs.MUA_EV_001_X159


title: EBs.MUA_EV_001_X132

description: Transcriptome measurement of sample EBs.MUA_EV_001_X132


title: EBs.MUA_EV_001_X127

description: Transcriptome measurement of sample EBs.MUA_EV_001_X127


title: EBs.MUA_EV_001_X129

description: Transcriptome measurement of sample EBs.MUA_EV_001_X129


title: EBs.MUA_EV_001_X130

description: Transcriptome measurement of sample EBs.MUA_EV_001_X130


title: EBs.MUA_EV_001_X131

description: Transcriptome measurement of sample EBs.MUA_EV_001_X131


title: EBs.MUA_EV_001_X128

description: Transcriptome measurement of sample EBs.MUA_EV_001_X128


title: EBs.MUA_EV_001_X125

description: Transcriptome measurement of sample EBs.MUA_EV_001_X125


title: EBs.MUA_EV_001_X124

description: Transcriptome measurement of sample EBs.MUA_EV_001_X124


title: EBs.MUA_EV_001_X146

description: Transcriptome measurement of sample EBs.MUA_EV_001_X146


title: EBs.MUA_EV_001_X123

description: Transcriptome measurement of sample EBs.MUA_EV_001_X123


title: EBs.MUA_EV_001_X126

description: Transcriptome measurement of sample EBs.MUA_EV_001_X126


title: EBs.MUA_EV_001_X119

description: Transcriptome measurement of sample EBs.MUA_EV_001_X119


title: EBs.MUA_EV_001_X147

description: Transcriptome measurement of sample EBs.MUA_EV_001_X147


title: EBs.MUA_EV_001_X122

description: Transcriptome measurement of sample EBs.MUA_EV_001_X122


title: EBs.MUA_EV_001_X120

description: Transcriptome measurement of sample EBs.MUA_EV_001_X120


title: EBs.MUA_EV_001_X121

description: Transcriptome measurement of sample EBs.MUA_EV_001_X121


title: EBs.MUA_EV_001_X117

description: Transcriptome measurement of sample EBs.MUA_EV_001_X117


title: EBs.MUA_EV_001_X118

description: Transcriptome measurement of sample EBs.MUA_EV_001_X118


title: EBs.MUA_EV_001_X115

description: Transcriptome measurement of sample EBs.MUA_EV_001_X115


title: EBs.MUA_EV_001_X116

description: Transcriptome measurement of sample EBs.MUA_EV_001_X116


title: EBs.MUA_EV_001_X114

description: Transcriptome measurement of sample EBs.MUA_EV_001_X114


title: EBs.MUA_EV_001_X113

description: Transcriptome measurement of sample EBs.MUA_EV_001_X113


title: EBs.MUA_EV_001_X112

description: Transcriptome measurement of sample EBs.MUA_EV_001_X112


title: EBs.MUA_EV_001_X111

description: Transcriptome measurement of sample EBs.MUA_EV_001_X111


title: EBs.MUA_EV_001_X109

description: Transcriptome measurement of sample EBs.MUA_EV_001_X109


title: EBs.MUA_EV_001_X108

description: Transcriptome measurement of sample EBs.MUA_EV_001_X108


title: EBs.MUA_EV_001_X106

description: Transcriptome measurement of sample EBs.MUA_EV_001_X106


title: EBs.MUA_EV_001_X107

description: Transcriptome measurement of sample EBs.MUA_EV_001_X107


title: EBs.MUA_EV_001_X105

description: Transcriptome measurement of sample EBs.MUA_EV_001_X105


title: EBs.MUA_EV_001_X110

description: Transcriptome measurement of sample EBs.MUA_EV_001_X110


title: EBs.MUA_EV_001_X099

description: Transcriptome measurement of sample EBs.MUA_EV_001_X099


title: EBs.MUA_EV_001_X104

description: Transcriptome measurement of sample EBs.MUA_EV_001_X104


title: EBs.MUA_EV_001_X103

description: Transcriptome measurement of sample EBs.MUA_EV_001_X103


title: EBs.MUA_EV_001_X096

description: Transcriptome measurement of sample EBs.MUA_EV_001_X096


title: EBs.MUA_EV_001_X098

description: Transcriptome measurement of sample EBs.MUA_EV_001_X098


title: EBs.MUA_EV_001_X102

description: Transcriptome measurement of sample EBs.MUA_EV_001_X102


title: EBs.MUA_EV_001_X092

description: Transcriptome measurement of sample EBs.MUA_EV_001_X092


title: EBs.MUA_EV_001_X091

description: Transcriptome measurement of sample EBs.MUA_EV_001_X091


title: EBs.MUA_EV_001_X097

description: Transcriptome measurement of sample EBs.MUA_EV_001_X097


title: EBs.MUA_EV_001_X095

description: Transcriptome measurement of sample EBs.MUA_EV_001_X095


title: EBs.MUA_EV_001_X089

description: Transcriptome measurement of sample EBs.MUA_EV_001_X089


title: EBs.MUA_EV_001_X087

description: Transcriptome measurement of sample EBs.MUA_EV_001_X087


title: EBs.MUA_EV_001_X094

description: Transcriptome measurement of sample EBs.MUA_EV_001_X094


title: EBs.MUA_EV_001_X090

description: Transcriptome measurement of sample EBs.MUA_EV_001_X090


title: EBs.MUA_EV_001_X093

description: Transcriptome measurement of sample EBs.MUA_EV_001_X093


title: EBs.MUA_EV_001_X088

description: Transcriptome measurement of sample EBs.MUA_EV_001_X088


title: EBs.MUA_EV_001_X085

description: Transcriptome measurement of sample EBs.MUA_EV_001_X085


title: EBs.MUA_EV_001_X084

description: Transcriptome measurement of sample EBs.MUA_EV_001_X084


title: EBs.MUA_EV_001_X081

description: Transcriptome measurement of sample EBs.MUA_EV_001_X081


title: EBs.MUA_EV_001_X083

description: Transcriptome measurement of sample EBs.MUA_EV_001_X083


title: EBs.MUA_EV_001_X082

description: Transcriptome measurement of sample EBs.MUA_EV_001_X082


title: EBs.MUA_EV_001_X080

description: Transcriptome measurement of sample EBs.MUA_EV_001_X080


title: EBs.MUA_EV_001_X079

description: Transcriptome measurement of sample EBs.MUA_EV_001_X079


title: EBs.MUA_EV_001_X078

description: Transcriptome measurement of sample EBs.MUA_EV_001_X078


title: EBs.MUA_EV_001_X076

description: Transcriptome measurement of sample EBs.MUA_EV_001_X076


title: EBs.MUA_EV_001_X075

description: Transcriptome measurement of sample EBs.MUA_EV_001_X075


title: EBs.MUA_EV_001_X070

description: Transcriptome measurement of sample EBs.MUA_EV_001_X070


title: EBs.MUA_EV_001_X071

description: Transcriptome measurement of sample EBs.MUA_EV_001_X071


title: EBs.MUA_EV_001_X101

description: Transcriptome measurement of sample EBs.MUA_EV_001_X101


title: EBs.MUA_EV_001_X072

description: Transcriptome measurement of sample EBs.MUA_EV_001_X072


title: EBs.MUA_EV_001_X100

description: Transcriptome measurement of sample EBs.MUA_EV_001_X100


title: EBs.MUA_EV_001_X067

description: Transcriptome measurement of sample EBs.MUA_EV_001_X067


title: EBs.MUA_EV_001_X066

description: Transcriptome measurement of sample EBs.MUA_EV_001_X066


title: EBs.MUA_EV_001_X068

description: Transcriptome measurement of sample EBs.MUA_EV_001_X068


title: EBs.MUA_EV_001_X069

description: Transcriptome measurement of sample EBs.MUA_EV_001_X069


title: EBs.MUA_EV_001_X065

description: Transcriptome measurement of sample EBs.MUA_EV_001_X065


title: EBs.MUA_EV_001_X064

description: Transcriptome measurement of sample EBs.MUA_EV_001_X064


title: EBs.MUA_EV_001_X063

description: Transcriptome measurement of sample EBs.MUA_EV_001_X063


title: EBs.MUA_EV_001_X061

description: Transcriptome measurement of sample EBs.MUA_EV_001_X061


title: EBs.MUA_EV_001_X059

description: Transcriptome measurement of sample EBs.MUA_EV_001_X059


title: EBs.MUA_EV_001_X086

description: Transcriptome measurement of sample EBs.MUA_EV_001_X086


title: EBs.MUA_EV_001_X054

description: Transcriptome measurement of sample EBs.MUA_EV_001_X054


title: EBs.MUA_EV_001_X055

description: Transcriptome measurement of sample EBs.MUA_EV_001_X055


title: EBs.MUA_EV_001_X057

description: Transcriptome measurement of sample EBs.MUA_EV_001_X057


title: EBs.MUA_EV_001_X052

description: Transcriptome measurement of sample EBs.MUA_EV_001_X052


title: EBs.MUA_EV_001_X077

description: Transcriptome measurement of sample EBs.MUA_EV_001_X077


title: EBs.MUA_EV_001_X051

description: Transcriptome measurement of sample EBs.MUA_EV_001_X051


title: EBs.MUA_EV_001_X050

description: Transcriptome measurement of sample EBs.MUA_EV_001_X050


title: EBs.MUA_EV_001_X048

description: Transcriptome measurement of sample EBs.MUA_EV_001_X048


title: EBs.MUA_EV_001_X046

description: Transcriptome measurement of sample EBs.MUA_EV_001_X046


title: EBs.MUA_EV_001_X044

description: Transcriptome measurement of sample EBs.MUA_EV_001_X044


title: EBs.MUA_EV_001_X049

description: Transcriptome measurement of sample EBs.MUA_EV_001_X049


title: EBs.MUA_EV_001_X042

description: Transcriptome measurement of sample EBs.MUA_EV_001_X042


title: EBs.MUA_EV_001_X045

description: Transcriptome measurement of sample EBs.MUA_EV_001_X045


title: EBs.MUA_EV_001_X047

description: Transcriptome measurement of sample EBs.MUA_EV_001_X047


title: EBs.MUA_EV_001_X074

description: Transcriptome measurement of sample EBs.MUA_EV_001_X074


title: EBs.MUA_EV_001_X041

description: Transcriptome measurement of sample EBs.MUA_EV_001_X041


title: EBs.MUA_EV_001_X073

description: Transcriptome measurement of sample EBs.MUA_EV_001_X073


title: EBs.MUA_EV_001_X043

description: Transcriptome measurement of sample EBs.MUA_EV_001_X043


title: EBs.MUA_EV_001_X037

description: Transcriptome measurement of sample EBs.MUA_EV_001_X037


title: EBs.MUA_EV_001_X040

description: Transcriptome measurement of sample EBs.MUA_EV_001_X040


title: EBs.MUA_EV_001_X039

description: Transcriptome measurement of sample EBs.MUA_EV_001_X039


title: EBs.MUA_EV_001_X036

description: Transcriptome measurement of sample EBs.MUA_EV_001_X036


title: EBs.MUA_EV_001_X058

description: Transcriptome measurement of sample EBs.MUA_EV_001_X058


title: EBs.MUA_EV_001_X032

description: Transcriptome measurement of sample EBs.MUA_EV_001_X032


title: EBs.MUA_EV_001_X056

description: Transcriptome measurement of sample EBs.MUA_EV_001_X056


title: EBs.MUA_EV_001_X062

description: Transcriptome measurement of sample EBs.MUA_EV_001_X062


title: EBs.MUA_EV_001_X060

description: Transcriptome measurement of sample EBs.MUA_EV_001_X060


title: EBs.MUA_EV_001_X035

description: Transcriptome measurement of sample EBs.MUA_EV_001_X035


title: EBs.MUA_EV_001_X053

description: Transcriptome measurement of sample EBs.MUA_EV_001_X053


title: EBs.MUA_EV_001_X030

description: Transcriptome measurement of sample EBs.MUA_EV_001_X030


title: EBs.MUA_EV_001_X034

description: Transcriptome measurement of sample EBs.MUA_EV_001_X034


title: EBs.MUA_EV_001_X027

description: Transcriptome measurement of sample EBs.MUA_EV_001_X027


title: EBs.MUA_EV_001_X031

description: Transcriptome measurement of sample EBs.MUA_EV_001_X031


title: EBs.MUA_EV_001_X029

description: Transcriptome measurement of sample EBs.MUA_EV_001_X029


title: EBs.MUA_EV_001_X025

description: Transcriptome measurement of sample EBs.MUA_EV_001_X025


title: EBs.MUA_EV_001_X024

description: Transcriptome measurement of sample EBs.MUA_EV_001_X024


title: EBs.MUA_EV_001_X023

description: Transcriptome measurement of sample EBs.MUA_EV_001_X023


title: EBs.MUA_EV_001_X028

description: Transcriptome measurement of sample EBs.MUA_EV_001_X028


title: EBs.MUA_EV_001_X020

description: Transcriptome measurement of sample EBs.MUA_EV_001_X020


title: EBs.MUA_EV_001_X021

description: Transcriptome measurement of sample EBs.MUA_EV_001_X021


title: EBs.MUA_EV_001_X026

description: Transcriptome measurement of sample EBs.MUA_EV_001_X026


title: EBs.MUA_EV_001_X022

description: Transcriptome measurement of sample EBs.MUA_EV_001_X022


title: EBs.MUA_EV_001_X018

description: Transcriptome measurement of sample EBs.MUA_EV_001_X018


title: EBs.MUA_EV_001_X019

description: Transcriptome measurement of sample EBs.MUA_EV_001_X019


title: EBs.MUA_EV_001_X016

description: Transcriptome measurement of sample EBs.MUA_EV_001_X016


title: EBs.MUA_EV_001_X017

description: Transcriptome measurement of sample EBs.MUA_EV_001_X017


title: EBs.MUA_EV_001_X038

description: Transcriptome measurement of sample EBs.MUA_EV_001_X038


title: EBs.MUA_EV_001_X015

description: Transcriptome measurement of sample EBs.MUA_EV_001_X015


title: EBs.MUA_EV_001_X014

description: Transcriptome measurement of sample EBs.MUA_EV_001_X014


title: EBs.MUA_EV_001_X011

description: Transcriptome measurement of sample EBs.MUA_EV_001_X011


title: EBs.MUA_EV_001_X010

description: Transcriptome measurement of sample EBs.MUA_EV_001_X010


title: EBs.MUA_EV_001_X012

description: Transcriptome measurement of sample EBs.MUA_EV_001_X012


title: EBs.MUA_EV_001_X006

description: Transcriptome measurement of sample EBs.MUA_EV_001_X006


title: EBs.MUA_EV_001_X005

description: Transcriptome measurement of sample EBs.MUA_EV_001_X005


title: EBs.MUA_EV_001_X004

description: Transcriptome measurement of sample EBs.MUA_EV_001_X004


title: EBs.MUA_EV_001_X033

description: Transcriptome measurement of sample EBs.MUA_EV_001_X033


title: EBs.MUA_EV_001_X007

description: Transcriptome measurement of sample EBs.MUA_EV_001_X007


title: EBs.MUA_EV_001_X009

description: Transcriptome measurement of sample EBs.MUA_EV_001_X009


title: EBs.MUA_EV_001_X001

description: Transcriptome measurement of sample EBs.MUA_EV_001_X001


title: EBs.MUA_EV_001_X003

description: Transcriptome measurement of sample EBs.MUA_EV_001_X003


title: EBs.MUA_EV_001_X002

description: Transcriptome measurement of sample EBs.MUA_EV_001_X002


title: EBs.MUA_EV_001_X008

description: Transcriptome measurement of sample EBs.MUA_EV_001_X008


title: Allo_4_ST2ko

city: Pittsburgh

first: Heth

last: Turnquist

state: PA

address: 200 Lothrop Street , E1554 BST

department: Surgery

country: USA

institute: University Of Pittsburgh

data_processing:
Raw sequencing data were processed using CLC Genomics Workbench 20.0.3 and aligned to the Mus musculus genome version GRCm38.p6.
Reads assigned to each gene underwent TMM normalization and differential expression analysis was performed using edgeR within CLC Genomics to compare ST2WT versus ST2fl/fl donor T cells
The top differentially expressed genes were filtered by adjusted p-value q<0.05 and fold-change greater than 1.5 for subsequent downstream pathway analysis.
The relative expression shown in heatmaps was calculated as the fragments per kilobase exon per million mapped reads value for each sample divided by the mean expression of that gene in all samples per each experiment
GSEA from the Broad Institute was used to calculate the enrichment of genes in each set

molecule: total RNA

source_name: Spleen

extract_protocol:
into SmartSeq low-input RNA kit lysis buffer
Nextera XT DNA library prep kits

tag: cell type

value: B6 Donor  CD4+ T cells

tag: genotype

tag: population


title: Allo_4_ST2wt


title: Allo_3_ST2wt


title: Allo_3_ST2ko


title: Allo_1_ST2ko


title: Allo_2_ST2wt


title: T10H_C5KO_M4

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences III

institute: UC Irvine

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Paired-end RNA-seq reads were aligned to mm10 reference genome and annotated to Gencode v21 transcriptome using STAR v.5.1 (Dobin et al.  2013).
Gene expression was calculated using RSEM v1.2.25 (Li and Dewey  2011).
Possible noise introduced by batch effects was corrected by the R (version 3.6.2) package Combat-seq (Zhang et al.  2020).
Data was then normalized using edgeR trimmed mean of M-values (TMM) function (Robinson et al.  2010). TPM was calculated utilizing a custom script and ComBat-seq batch corrected counts as input
Genome_build: mm10
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM

source_name: hippocampus

extract_protocol:
Total RNA of each tissue was extracted using the QIAGEN RNeasy mini kit and QIAcube (Qiagen # 80204 and # 9002864)
Smart-seq2 protocol (Picelli et al.  2013); Nextera DNA Flex Library Prep Kit (20018704  Illumina);

tag: Sex

value: Male

tag: age

value: 10 months

value: WT mice with C5ar1 knocked out (constitutive KO)


title: T10H_Arc_M4

value: Arc

value: Arctic mouse model of AD


title: T10H_Arc_F4

value: Female


title: T10C_Arc_M4

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

source_name: cortex


title: T10C_Arc_F4


title: EBs.MUA_EV_001_X013

description: Transcriptome measurement of sample EBs.MUA_EV_001_X013


title: T10H_WT_F4

value: WT

value: Wild type


title: T10C_C5KO_F4


title: T10C_WT_F4


title: T10C_WT_M4


title: T10H_WT_M4


title: T10H_ArcC5GFAP_M3

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: T10C_ArcC5GFAP_M3


title: T10C_C5GFAP_M5

value: WT mice overexpressing C5a under the GFAP promoter


title: T10H_C5GFAP_M4


title: T10H_ArcC5KO_F3

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: T10H_C5GFAP_M3


title: T10C_C5GFAP_M4


title: T10H_C5GFAP_M5


title: T10C_ArcC5KO_M3


title: T10C_C5GFAP_M3


title: T10C_ArcC5KO_F3


title: T10H_ArcC5KO_M3


title: T10H_C5KO_F3


title: Allo_2_ST2ko


title: T10C_C5KO_F3


title: T10H_C5KO_M3


title: T10H_C5KO_F4


title: Allo_1_ST2wt


title: T10C_C5KO_M3


title: T10H_Arc_M3


title: T10H_WT_F3


title: T10C_Arc_F3


title: T10C_C5KO_M4


title: T10C_Arc_M3


title: T10H_WT_M3


title: T10C_WT_F3


title: T10C_WT_M3


title: T10H_ArcC5GFAP_F2


title: T10C_ArcC5GFAP_F2


title: T10H_ArcC5GFAP_M2


title: T10H_C5GFAP_F2


title: T10H_C5GFAP_M2


title: T10C_C5GFAP_F2


title: T10H_ArcC5KO_F2


title: T10C_ArcC5GFAP_M2


title: T10C_ArcC5KO_F2


title: T10H_ArcC5KO_M2


title: T10C_C5GFAP_M2


title: T10C_ArcC5KO_M2


title: T10C_C5KO_F2


title: T10H_C5KO_F2


title: T10H_C5KO_M2


title: T10C_C5KO_M2


title: T10H_Arc_F2


title: T10C_Arc_F2


title: T10H_WT_F2


title: T10H_Arc_M2


title: T10H_ArcC5GFAP_F1


title: T10C_ArcC5GFAP_F1


title: T10C_Arc_M2


title: T10H_WT_M2


title: T10C_WT_M2


title: T10C_WT_F2


title: T10H_C5GFAP_F1


title: T10C_ArcC5GFAP_M1


title: T10H_Arc_F3


title: T10H_C5GFAP_M1


title: T10H_ArcC5GFAP_M1


title: T10C_C5GFAP_F1


title: T10C_C5GFAP_M1


title: T10H_ArcC5KO_F1


title: T10H_ArcC5KO_M1


title: T10H_C5KO_F1


title: T10C_ArcC5KO_F1


title: T10C_C5KO_F1


title: T10H_C5KO_M1


title: T10C_C5KO_M1


title: T10C_ArcC5KO_M1


title: T10H_Arc_M1


title: T10C_Arc_F1


title: T10H_Arc_F1


title: T10C_Arc_M1


title: T10H_WT_F1


title: T10H_WT_M1


title: T10C_WT_F1


title: T7C_C5KO_F4

value: 7 months


title: T7C_ArcC5GFAP_F4


title: T7C_ArcC5GFAP_M4


title: T7H_ArcC5GFAP_F4


title: T10C_WT_M1


title: T7H_C5KO_F4


title: T7H_ArcC5GFAP_M4


title: T7H_C5GFAP_M4


title: T7C_C5GFAP_F4


title: T7H_ArcC5KO_F4


title: T7C_C5GFAP_M4


title: T7C_ArcC5KO_F4


title: T7C_ArcC5KO_M4


title: T7C_Arc_F4


title: T7H_Arc_F4


title: T7H_C5KO_M4


title: T7C_Arc_M4


title: T7C_WT_F4


title: T7C_C5KO_M4


title: T7H_Arc_M4


title: T7H_WT_F4


title: T7H_WT_M4


title: T7C_WT_M4


title: T7H_ArcC5GFAP_F3


title: T7C_ArcC5GFAP_F3


title: T7H_ArcC5GFAP_M3


title: T7C_ArcC5GFAP_M3


title: T7H_C5GFAP_F3


title: T7H_C5GFAP_M3


title: T7C_C5GFAP_M3


title: T7C_C5GFAP_F3


title: T7H_ArcC5KO_F3


title: T7H_ArcC5KO_M3


title: T7C_ArcC5KO_F3


title: T7C_ArcC5KO_M3


title: T7H_C5KO_F3


title: T7H_C5GFAP_F4


title: T7C_C5KO_M3


title: T7H_Arc_F3


title: T7H_Arc_M3


title: T7C_Arc_F3


title: T7H_WT_F3


title: T7C_WT_F3


title: T7H_WT_M3


title: T7C_WT_M3


title: T7H_ArcC5GFAP_F2


title: T7C_ArcC5GFAP_F2


title: T7H_ArcC5KO_M4


title: T7H_ArcC5GFAP_M2


title: T7H_C5GFAP_F2


title: T7C_ArcC5GFAP_M2


title: T7C_C5GFAP_F2


title: T7C_C5GFAP_M2


title: T7H_C5GFAP_M2


title: T7C_ArcC5KO_F2


title: T7H_ArcC5KO_M2


title: T7H_C5KO_F2


title: T7C_ArcC5KO_M2


title: T7C_C5KO_F2


title: T7C_C5KO_M2


title: T7H_C5KO_M2


title: T7H_Arc_F2


title: T7C_Arc_F2


title: T7C_Arc_M2


title: T7H_WT_F2


title: T7H_Arc_M2


title: T7C_ArcC5GFAP_F1


title: T7C_WT_F2


title: T7H_C5KO_M3


title: T7C_C5KO_F3


title: T7H_WT_M2


title: T7H_ArcC5GFAP_M1


title: T7C_ArcC5GFAP_M1


title: T7H_C5GFAP_F1


title: T7C_C5GFAP_F1


title: T7C_Arc_M3


title: T7H_ArcC5KO_F1


title: T7C_C5GFAP_M1


title: T7H_ArcC5KO_M1


title: T7C_ArcC5KO_M1


title: T7C_C5KO_F1


title: T7H_C5KO_F1


title: T7H_C5KO_M1


title: T7C_C5KO_M1


title: T7H_ArcC5KO_F2


title: T7H_Arc_M1


title: T7H_Arc_F1


title: T7C_Arc_F1


title: T7C_Arc_M1


title: T7C_WT_M1


title: T5H_C5KO_F4

value: 5 months


title: T7H_WT_M1


title: T5H_C5KO_M4


title: T7C_WT_F1


title: T5H_Arc_F5


title: T5C_C5KO_M4


title: T5C_Arc_F5


title: T5C_C5KO_F4


title: T5C_Arc_M5


title: T5H_WT_F5


title: T5C_WT_F5


title: T5H_Arc_M5


title: T5H_WT_M6


title: T7H_ArcC5GFAP_F1


title: T5C_WT_M6


title: T7C_WT_M2


title: T5H_Arc_F4


title: T7C_ArcC5KO_F1


title: T7H_C5GFAP_M1


title: T5C_WT_M5


title: Mycelia_△stk-12_5D_2

city: Tianjin

first: liangcai

last: lin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Neurospora crassa OR74A genome (version 12) using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p3).
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM) and differential gene expression was determined by NOISeq package (v2.6.0).
Genome_build: NC12 (Neurospora crassa OR74A)
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample.

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: Conidia of △stk-12 and wild-type (WT) strains were separately inoculated into Avicel medium (1×Vogel's salt, 2% w/v crystalline cellulose) and batch cultured for 5 days at 25 ℃ with constant light.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Mycelia

tag: time (culture)


title: T5C_Arc_F4


title: T5H_WT_M5


title: T5H_Arc_M4


title: Mycelia_△stk-12_5D_1


title: IonXpress_016

city: Toronto

first: YU XUAN

last: LUO

state: ON

address: 2075 Bayview Avenue

department: Biological sciences

country: Canada

institute: Sunnybrook research institute

description:
raw counts of sequencing reads_K13-16_ 20180124_1_Ion_AmpliSeq_Transcriptome_Human_s5xl-server_324.bcmatrix.txt
normalized abundance measurements_K13-16_20180124_1_Ion_AmpliSeq_Transcriptome_Human_s5xl-server_324.rpm.bcmatrix.txt

data_processing:
Ion Torrent sequencing was performed for 500 flows on an Ion S5XL Sequencer with Ion 540 Chips.
Ion Torrent platform-specific pipeline software (Torrent Suite version 5.08.0; ThermoFisher Scientific) was used to remove polyclonal, low quality and adapter dimer reads and then separate barcoded reads for each sample.
Ion Torrent platform-specific ampliSeqRNA plug-in (v5.08.0) was used to analyze the sequencing reads.
Reads were aligned to the human transcriptome reference and target regions flle (hg19_AmpliSeq_Transcriptome__21K_v1) With TMAP mapper in Torrent Suite version 5.08.0.
Genome_build: hg19 Human genome reference
Supplementary_files_format_and_content: text files.  Raw read count and normalized reads count (RPM, reads per million).

organism: Homo sapiens

source_name: JAK 13 ruxolitinib

growth_protocol: Leukemia cells were purified from the blood and RNA was made immediately and frozen until used for RNAseq.

extract_protocol:
RNA was prepared using the RNeasy mini kit (Qiagen, Valencia, CA, USA), and cDNA was synthesized from 2 μg of RNA using Superscript II reverse transcriptase (Invitrogen), according to the instructions of the manufacturer.
Complementary DNA (cDNA) libraries were constructed from the total RNA using the Ion AmpliSeq Transcriptome Human Gene Expression kit (ThermoFisher Scientific) in accordance with the manufacturer’s manuals.
Targeted RNA sequencing

treatment_protocol: CLL cells were isolated from blood by negative selection with the Rosette Sep Human B cell enrichment cocktail (StemCell Technologies, Vancouver BC, Canada) and density centrifugation. This method yields percentages of CD19+ and CD19+/CD5+ cells of >98 and >96%, respectively. Aliquots were cryopreserved until used for RNAseq.

tag: individual

value: patient  13

tag: disease state

value: chronic lymphocytic leukemia (CLL)

value: blood

value: purified blood CLL cells

tag: cell state

value: ex vivo

tag: treatment

value: ruxolitinib


title: IonXpress_015

source_name: JAK 13 baseline

value: baseline


title: IonXpress_014

source_name: JAK 10 ruxolitinib

value: patient  10


title: Mycelia_△stk-12_1D_2


title: IonXpress_011

description:
raw counts of sequencing reads_K09-12_ 20180123_2_Ion_AmpliSeq_Transcriptome_Human_s5xl-server_323.bcmatrix.txt
normalized abundance measurements_K09-12_20180123_2_Ion_AmpliSeq_Transcriptome_Human_s5xl-server_323.rpm.bcmatrix.txt

source_name: JAK 9 baseline

value: patient  9


title: Mycelia_△stk-12_3D_2


title: IonXpress_010

source_name: JAK 8 ruxolitinib

value: patient  8


title: T5C_WT_F4

value: Female

value: WT

value: Wild type


title: T7H_WT_F1


title: IonXpress_012

source_name: JAK 9 ruxolitinib


title: IonXpress_013

source_name: JAK 10 baseline


title: Mycelia_△stk-12_3D_1


title: T5C_Arc_M4

value: Male

value: Arc

value: Arctic mouse model of AD


title: T5H_WT_F4

value: 5 months


title: IonXpress_009

source_name: JAK 8 baseline


title: IonXpress_005

description:
raw counts of sequencing reads_K01_02_05_06_ 20180123_1_Ion_AmpliSeq_Transcriptome_Human_s5xl-server_322.bcmatrix.txt
normalized abundance measurements_K01_02_05_06_20180123_1_Ion_AmpliSeq_Transcriptome_Human_s5xl-server_322.rpm.bcmatrix.txt

source_name: JAK 3 baseline

value: patient  3


title: IonXpress_006

source_name: JAK 3 ruxolitinib

value: chronic lymphocytic leukemia (CLL)


title: IonXpress_002

source_name: JAK 5 ruxolitinib

value: patient  5

value: blood


title: Mycelia_△stk-12_12hrs_2

value: Mycelia


title: Mycelia_△stk-12_12hrs_1


title: IonXpress_001

source_name: JAK 5 baseline

value: purified blood CLL cells

value: ex vivo


title: T5C_WT_M4


title: T5H_ArcC5GFAP_F4

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: KI_TAC_3587

city: Guangzhou

first: Youchen

last: Yan

state: Guangdong

address: No.58 Zhongshan Road II

institute: The First Affiliated Hospital, Sun Yat-sen University

description: "KI" refered to CIP overexpression (CIP-OE) mice. CIP-KI-flox mice, which have a Rosa-CIP allele (the stop codon is present and floxed) were bred with aMHC-Mer-Cre-Mer mice to obtain CIP-OE (CIP-KI-flox;aMHC-Mer-Cre-Mer) mouse. Tamoxifen was administrated through intraperitoneal injection to activate the expression of Cre recombinase and the excision of the stop codon for the ectopic expression of CIP transgene in the heart in CIP-OE mice. “Ctrl” refered to CIP-KI-flox littermates.

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%.
The clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) using HISAT2(v2.0.4). Expression level of gene was calculated by StringTie (v2.1.4).
Differential expression analysis was performed using the DESeq2(v1.4.5) with adjusted p value≤ 0.05.
GO and KEGG enrichment analysis of annotated different expressed gene was performed by Phyper based on Hypergeometric test.The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Genome_build: Mus_musculus.GRCm38

source_name: mouse heart

extract_protocol:
Total RNAs were isolated using Trizol Reagent from tissue samples.
RNA libraries were prepared for sequencing using standard BGIseq protocols

treatment_protocol: transverse aortic constriction (TAC)

tag: strain

value: 4-month old

value: heart

value: CIP-OE


title: KI_TAC_3579


title: KI_TAC_3577


title: Mycelia_WT_5D_2


title: KI_Sham_3737


title: T5C_ArcC5GFAP_F4

value: Female


title: Mycelia_WT_5D_1

value: Wild type


title: KI_Sham_3644


title: Mycelia_WT_3D_2


title: KI_Sham_3643


title: Ctrl_TAC_3800

value: CIP-KI-flox


title: Ctrl_TAC_4231


title: Mycelia_WT_3D_1


title: Ctrl_TAC_3586


title: T5H_C5GFAP_F4

value: WT mice overexpressing C5a under the GFAP promoter


title: Ctrl_Sham_4033


title: Ctrl_Sham_4011


title: Mycelia_WT_1D_2


title: Ctrl_Sham_4010


title: T5H_C5GFAP_M4

value: Male


title: Mycelia_WT_1D_1


title: T5C_C5GFAP_M4

value: 5 months


title: Mycelia_△stk-12_1D_1


title: T5H_WT_M4

value: WT


title: T5H_ArcC5KO_F4

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: Mycelia_WT_12hrs_1


title: Control subjects gut microbiota Replicate 43

type: genomic

city: Changsha City of Hunan Province

first: xuan

last: peng

state: Hunan

address: 88 Xiangya Road

institute: Kaifu District, Changsha City, Hunan Province

description: Biological replicate 43 of control subjects, untreated, without UFs

hyb_protocol: Oligoarray control targets and hybridization buffer provided by the manufacturer were added, and 500ng labeled sample DNA were applied to microarrays enclosed in the hybrid cassette. After hybridization, slides were washed sequential.

scan_protocol: Scans were performed on a GenePix4000B scanner.Images were quantified using Bluefuse software.

data_processing:
LOWESS normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Bluefuse software was used.
The output.txt is the result from fluorescence array. All information about array was demonstrated in the head of output.txt file.
The output.xls.result.txt is the relative abundances of each identified species, which are calculated base on fluorescence value in output.txt.
The relative abundances of each identified species, which are calculated base on the program,which first calculated the mean intensities of the 3 replicated spots corresponding to each species for the Cy5 and Cy3 channels. The mean Cy5/Cy3 ratio was calculated from the mean intensity of the two channels. The species were ranked by their mean signal intensity from which the background fluorescent signal was calculated from the median of mean intensity of the lower 30% of the species. For a species to be judged as positive detection, its mean signal intensity must be 10 fold above the background fluorescent signal. To calculate the relative abundance of the positive species, we normalize the mean Cy5/Cy3 ratios of all the positive species and the percentage of each species  multiply a fix factor 100000, and round up the result ,which is presented as the relative abundance value.

molecule: genomic DNA

organism: human feces metagenome

source_name: Control subject fecal microbiota

label_protocol: 10-20ng of DNA was amplified by PCR reaction with 16S universal primers.5ul PCR product was labelled with Bst enzyme and random primers at 45°C for 3 hours.The labeled product was stained with 20 μg of Cy5 dye and dissolved at 100 ng/ul after precipitation.

extract_protocol: Total DNA extracted  following manufacturer's instructions

tag: condition

value: Control

value: fecal microbiota

organism: synthetic construct

source_name: Internal reference provided by the manufacturer

value: Internal reference (synthetic oligos)

tag: concentration


title: Control subjects gut microbiota Replicate 42

description: Biological replicate 42 of control subjects, untreated, without UFs


title: Control subjects gut microbiota Replicate 41

description: Biological replicate 41 of control subjects, untreated, without UFs


title: Control subjects gut microbiota Replicate 40

description: Biological replicate 40 of control subjects, untreated, without UFs


title: T5H_ArcC5KO_M4

source_name: hippocampus


title: Control subjects gut microbiota Replicate 38

description: Biological replicate 38 of control subjects, untreated, without UFs


title: Control subjects gut microbiota Replicate 39

description: Biological replicate 39 of control subjects, untreated, without UFs


title: RF 293T4A DOX-2 [ribo_DOX_2]

city: New York

first: Prathibha

last: Mohan

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
library strategy: ribosome footprinting
Sequence Alignment
The human genome sequence GRCh37 was downloaded from Ensembl public database: http:// www.ensembl.org. Ribosome footprint (RF) reads were aligned to reference genome GRCh37 using STAR26. STAR clips the linker sequence (5’- CTGTAGGCACCATCAAT-3’), which is technically introduced during RF library construction, and trims the remaining sequence from the 3’ end while aligning the reads to reference sequence. Briefly, we set the parameters for PALMapper as follows: maximum number of mismatches: 2; minimum aligning length: 15; maximum intron length (splice alignment): 10000. We only use the uniquely aligned reads for further analysis. To remove ribosomal RNA, the footprint reads were also aligned to a ribosome sequence database using STAR with the same parameters except not allowing splice alignment. We retrieved the human ribosome sequences from SILVA30 databases. The FASTA file was used as reference sequence to align against. The rRNA-aligned reads were filtered out from GRCh37-aligned reads.After removing the ribosomal RNA, we still observed a portion of reads that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, we searched a string of 1~8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. We removed the read if there was no such linker sequence. Finally, we filtered out reads ≤ 24-bp and ≥ 36-bp, and the remaining reads with aligned length from 25- to 35-bp were used to analyse the translational effects of CR31B.
Total mRNA sequencing reads were aligned to the GRCh37 reference using STAR31. We performed the splice alignment and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.
Footprint Profile Analysis using Ribodiff
For each gene, we only counted the number of aligned reads that were mapped within exonic regions. The genome annotation was downloaded from Ensembl database. We used our recently developed tool Ribodiff to analyze the ribosome footprinting data. Ribodiff uses a negative binomial based generalized linear model to detect the significant difference of footprint read counts in two conditions, taking the RNA-Seq transcriptional measurements as the confounding factor. Therefore it is capable of identifying the genes having translational control that is independent of the transcriptional regulation. The statistical test is a chi-squared test on the deviances of the H0 and H1 model fitting. Benjamini–Hochberg procedure was used to obtain the false discovery rate. The ribosomal distribution curves for a single gene were plotted in a similar way but without normalizing the read coverage, and the coverage was smoothed using ‘moving average’ smoothing algorithm.
Motif analysis
The transcripts of each gene were quantified based on the total mRNA-seq data using MISO26,32. The 5’UTR of most abundant transcript was collected for predicting motifs. Both the significant genes with increased or decreased TE and altered ribosomal distribution and the corresponding background gene sets were predicted by DREME26. We considered the predicted consensus sequences with P < 1×10-4 as significant motifs. Motif occurrences were called using FIMO26 with default parameters for strand specific prediction in human and other species using gene orthologs.
Genome_build: GRCh37

source_name: Human embryonic kidney 293 cells

growth_protocol: 293T4A cell lines were cultured in DMEM media supplemented with 10% fetal bovine serum and Penicillin/Streptomycin and 10mM Glutamine or as per the ATCC recommended medium.

extract_protocol: 293T4A cells were treated with DMSO or DOX (2mg/ml - 12hr) followed by cycloheximide treatment for 10 minutes. Total RNA and ribosome-protected fragments were isolated following published protocol (Ingolia et al 2012). Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2000 platform. Genome annotation was from the Ensembl database release 75 (http:// www.ensembl.org).

treatment_protocol: Cells wre treated with DMSO (CT) or DOX (2mg/ml for 12 hr).

tag: cell line

value: Human embryonic kidney cell line

tag: tag

value: Dox Treated


title: Control subjects gut microbiota Replicate 35

description: Biological replicate 35 of control subjects, untreated, without UFs

tag: sample type


title: RF 293T4A DOX-1  [ribo_DOX_1]

tag: cell type


title: T5H_ArcC5GFAP_M4

tag: genotype

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: T5H_ArcC5GFAP_F3


title: T5C_ArcC5GFAP_M4

source_name: cortex


title: RF 293T4A DMSO-3  [ribo_noDOX_3]

value: Untreated


title: Rat2 CRL-1764

city: Haifa

first: Noam

last: Kaplan

address: Efron 1

country: Israel

institute: Technion - Israel Institute of Technology

library_source: genomic

data_processing:
Iterative mapping with Bowtie2/cMapping (Dekker pipeline)
Conversion validpairs->mcool: Binning, filtering and balancing with Cooler
Genome_build: rn6
Supplementary_files_format_and_content: validpairs format is (U, side1_chromosome, side1_position, side1_orientation, side1_readID, side1_restrictionFragmentNum, U, side2_chromosome, side2_position, side2_orientation, side2_readID, side2_restrictionFragmentNum)
Supplementary_files_format_and_content: mcool is a multiresolution container format used by 4D Nucleome and described at https://cooler.readthedocs.io/en/latest/schema.html

organism: Rattus norvegicus

source_name: Fibroblasts

extract_protocol: Hi-C was performed as described previously (PMID 28435001). Briefly, ~1,000,000 cells were cross-linked with 1% formaldehyde, permeabilized and digested with DpnII. Next, sticky ends were filled with nucleotides including biotinylated dATP, followed by blunt-end ligation, cross-link reversal and DNA purification. This was followed by biotin removal from unligated ends, sonication, and pulldown of biotinylated fragments with streptavidin beads. Finally, the library was amplified, size selected and sequenced using 75bp paired-end sequencing on a NextSeq500.

treatment_protocol: No treatment


title: Control subjects gut microbiota Replicate 32

description: Biological replicate 32 of control subjects, untreated, without UFs


title: RF 293T4A DMSO-2  [ribo_noDOX_2]


title: Control subjects gut microbiota Replicate 34

description: Biological replicate 34 of control subjects, untreated, without UFs


title: PGCLC_d3ag3_rep2

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

country: Japan

institute: Nara Medical University

description: Rat_Gene-Exp_ESC-EpiLC-PGCLC_log2(TPM+1).txt

data_processing:
>Basecalls were performed using NextSeq 500/550 RTA software, v.2.4.11-2.11.6.
>FASTQ files were generated using bcl2fastq, v.2.20
>The first 3 bases were trimmed out from raw reads using FASTX-Toolkit 0.0.14
>Trimmed reads were further quality-trimmed using Cutadapt v.1.1.6 program with the following configurations: trimming of the primer sequence "Clontech SMART CDS Primer II A: AAGCAGTGGTATCAACGCAGAGTAC", minimal base quality is 20, minimal read length after trimming is 35 nt
>RNA-seq reads were aligned to the rn7 Rat genome assembly using Hisat2, v.2.1.0
>featureCounts (Subread, v1.6.5) program and Refseq gene annotation (rn7, 33294 genes) were used to calculate TPM values
>TPM values of all protein-coding gene (22228 genes) were log2-transformed (log2(TPM+1) values).
Genome_build: rn7
Supplementary_files_format_and_content: A single text file that lists coding gene log2(TPM+1) values for each sample

source_name: Primordial germ cell-like cell

growth_protocol:
Rat ESCs were maintained on mouse embryonic fibroblast feeders in rat ESC medium: N2B27 containing 2i (PD0325901, 1 µM, AXON; CHIR99021, 3 µM, AXON) and rat LIF (1,000 U/ml, Merck). They were routinely passaged every 2-3 days.
For rat EpiLC induction, rat ESCs were dissociated into single cell using 0.25% Trypsin-EDTA. Then, the cells were harvested in a well of 96-well Nunclon Sphera-Treated U-shaped microplate (Thermo Fisher Scientific) filled with freshly made EpiLC medium containing KSR(1%), Activin A (20 ng/ml) and bFGF(12 ng/ml), at 4 x 103 cells per well, and cultured for 60 hours.
For rat PGCLC induction, rat EpiLC-aggregates were transferred into new well of 96-well Nunclon Sphera-Treated U-shaped microplate filled with freshly made PGCLC medium composed of N2B27 containing BMP4 (500 ng/ml; PEPRO TECH), rat LIF (1000 U/ml; Merck), SCF (100 ng/ml; R&D systems), EGF (50 ng/ml; R&D systems). At day 3, Nanos3-T2A-tdTomato positive PGCLCs were FACS-sorted for RNA extraction.
For rat PGCLC aggregation, N3T(+) d3 rPGCLCs sorted by FACS were mixed with E15.5 female rat gonadal somatic cells depleted c-KIT positive rPGCs, at 5,000 rPGCLCs to 50,000 somatic cells. Mixed suspensions were plated into a 96-well Nunclon Sphera-Treated U-shaped microplate (Thermo Fisher Scientific) in N2B27 medium containing 5% KSR. At day 3 after aggregation (d3ag3), Nanos3-T2A-tdTomato positive PGCLCs were FACS-sorted for RNA extraction.

extract_protocol:
Total RNA was extracted using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to manufacturer’s protocols.
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) and KAPA Hyper Prep Kit (Kapa Biosystems).

value: Primordial germ cell-like cell


title: Control subjects gut microbiota Replicate 31

description: Biological replicate 31 of control subjects, untreated, without UFs


title: Mycelia_WT_12hrs_2

source_name: Mycelia

value: Mycelia


title: PGCLC_d3ag3_rep1


title: T5C_ArcC5GFAP_M3

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: RF 293T4A DMSO-1  [ribo_noDOX_1]


title: Control subjects gut microbiota Replicate 30

description: Biological replicate 30 of control subjects, untreated, without UFs


title: Total 293T4A DOX-3 [total_DOX_3]

data_processing:
Sequence Alignment
The human genome sequence GRCh37 was downloaded from Ensembl public database: http:// www.ensembl.org. Ribosome footprint (RF) reads were aligned to reference genome GRCh37 using STAR26. STAR clips the linker sequence (5’- CTGTAGGCACCATCAAT-3’), which is technically introduced during RF library construction, and trims the remaining sequence from the 3’ end while aligning the reads to reference sequence. Briefly, we set the parameters for PALMapper as follows: maximum number of mismatches: 2; minimum aligning length: 15; maximum intron length (splice alignment): 10000. We only use the uniquely aligned reads for further analysis. To remove ribosomal RNA, the footprint reads were also aligned to a ribosome sequence database using STAR with the same parameters except not allowing splice alignment. We retrieved the human ribosome sequences from SILVA30 databases. The FASTA file was used as reference sequence to align against. The rRNA-aligned reads were filtered out from GRCh37-aligned reads.After removing the ribosomal RNA, we still observed a portion of reads that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, we searched a string of 1~8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. We removed the read if there was no such linker sequence. Finally, we filtered out reads ≤ 24-bp and ≥ 36-bp, and the remaining reads with aligned length from 25- to 35-bp were used to analyse the translational effects of CR31B.
Total mRNA sequencing reads were aligned to the GRCh37 reference using STAR31. We performed the splice alignment and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.
Footprint Profile Analysis using Ribodiff
For each gene, we only counted the number of aligned reads that were mapped within exonic regions. The genome annotation was downloaded from Ensembl database. We used our recently developed tool Ribodiff to analyze the ribosome footprinting data. Ribodiff uses a negative binomial based generalized linear model to detect the significant difference of footprint read counts in two conditions, taking the RNA-Seq transcriptional measurements as the confounding factor. Therefore it is capable of identifying the genes having translational control that is independent of the transcriptional regulation. The statistical test is a chi-squared test on the deviances of the H0 and H1 model fitting. Benjamini–Hochberg procedure was used to obtain the false discovery rate. The ribosomal distribution curves for a single gene were plotted in a similar way but without normalizing the read coverage, and the coverage was smoothed using ‘moving average’ smoothing algorithm.
Motif analysis
The transcripts of each gene were quantified based on the total mRNA-seq data using MISO26,32. The 5’UTR of most abundant transcript was collected for predicting motifs. Both the significant genes with increased or decreased TE and altered ribosomal distribution and the corresponding background gene sets were predicted by DREME26. We considered the predicted consensus sequences with P < 1×10-4 as significant motifs. Motif occurrences were called using FIMO26 with default parameters for strand specific prediction in human and other species using gene orthologs.
Genome_build: GRCh37


title: Control subjects gut microbiota Replicate 29

description: Biological replicate 29 of control subjects, untreated, without UFs


title: PGCLC_d3_rep2

data_processing:
>Basecalls were performed using NextSeq 500/550 RTA software, v.2.4.11-2.11.6.
>FASTQ files were generated using bcl2fastq, v.2.20
>The first 3 bases were trimmed out from raw reads using FASTX-Toolkit 0.0.14
>Trimmed reads were further quality-trimmed using Cutadapt v.1.1.6 program with the following configurations: trimming of the primer sequence "Clontech SMART CDS Primer II A: AAGCAGTGGTATCAACGCAGAGTAC", minimal base quality is 20, minimal read length after trimming is 35 nt
>RNA-seq reads were aligned to the rn7 Rat genome assembly using Hisat2, v.2.1.0
>featureCounts (Subread, v1.6.5) program and Refseq gene annotation (rn7, 33294 genes) were used to calculate TPM values
>TPM values of all protein-coding gene (22228 genes) were log2-transformed (log2(TPM+1) values).
genome build: rn7
processed data files format and content: A single text file that lists coding gene log2(TPM+1) values for each sample


title: T5C_ArcC5KO_F4

value: Female


title: T5H_C5GFAP_F3

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: RF 293T4A DOX-3  [ribo_DOX_3]


title: Control subjects gut microbiota Replicate 28

description: Biological replicate 28 of control subjects, untreated, without UFs


title: PGCLC_d3_rep1

value: Wild type


title: Total 293T4A DOX-2 [total_DOX_2]


title: Control subjects gut microbiota Replicate 37

description: Biological replicate 37 of control subjects, untreated, without UFs


title: T5C_C5GFAP_F3


title: Total 293T4A DOX-1  [total_DOX_1]


title: EpiLC_rep2

source_name: Epiblast-like cell

value: Epiblast-like cell


title: Control subjects gut microbiota Replicate 27

description: Biological replicate 27 of control subjects, untreated, without UFs


title: Control subjects gut microbiota Replicate 36

description: Biological replicate 36 of control subjects, untreated, without UFs


title: EpiLC_rep1


title: T5C_ArcC5GFAP_F3


title: T5C_ArcC5KO_M4


title: Total 293T4A DMSO-3 [total_noDOX_3]


title: T5H_C5GFAP_M3

value: WT mice overexpressing C5a under the GFAP promoter


title: Control subjects gut microbiota Replicate 33

description: Biological replicate 33 of control subjects, untreated, without UFs


title: T5C_C5GFAP_M3

value: Male


title: Total 293T4A DMSO-2 [total_noDOX_2]


title: ESC_rep2

source_name: Embryonic stem cell

value: Embryonic stem cell


title: Control subjects gut microbiota Replicate 25

description: Biological replicate 25 of control subjects, untreated, without UFs


title: T5H_ArcC5KO_F3

value: 5 months


title: T5H_ArcC5GFAP_M3


title: Control subjects gut microbiota Replicate 24

description: Biological replicate 24 of control subjects, untreated, without UFs


title: ESC_rep1


title: T5C_ArcC5KO_F3

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: T5H_ArcC5KO_M3


title: In-vitro Day-4 Cultured human myoblasts with young serum  - Rep. 3.2

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

description:
In-vitro Day-4 Cultured human myoblasts with young serum
htseq_invitro.csv

data_processing:
Genome build: Homo sapiens GRCh38
Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2
Supplementary_files_format_and_content: comma separated value file including counts per gene (row)  for each sample (column)

source_name: Cultured human skeletal myoblasts

growth_protocol: Human skeletal myoblasts (hskMPs, Lonza, CC-2580) isolated from donated human tissue of 20 year old healthy Caucasians were used at passages 3-5 after obtaining permission for their use in research applications by the Cantonal Ethical Commission of canton de Vaud (CER-VD). For in vitro expansion, the cells were maintained in human skeletal muscle myoblast growth medium (Zenbio, SKM-M) in human fibronectin coated dishes fibronectin (Corning, 356008) in a 37°C, 5% CO2 incubator, and were passaged once confluency reached 50%.

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified with the Quant-iT Picogreen (Invitrogen, 10545213) on a FilterMax F3 (Molecular Devices, F3). Size pattern was assessed with Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, DNF-474-0500).
Libraries (Average size: 295 bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pM on a single read sequencing flow cell.

value: Young

value: Primary myoblasts isolated from skeletal muscle


title: Control subjects gut microbiota Replicate 23

description: Biological replicate 23 of control subjects, untreated, without UFs

value: Control

value: fecal microbiota

value: Internal reference (synthetic oligos)


title: In-vitro Day-4 Cultured human myoblasts with young serum  - Rep. 3.1


title: AOM+DSS

city: Shanghai

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
MapSplice mapping to reference genome
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain RPKM  for each sample

source_name: colon adenoma

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DPP-0 (control): normal colon tissue from C57BL/6 Wild-type mice without AOM/DSS treatment. DPP-4 (AOM+DSS): adenoma in colon tissue from C57BL/6 WT mice after AOM/DSS treatment.

value: colon

value: colon adenoma


title: Control

source_name: colon tissue

value: normal colon tissue


title: T5C_ArcC5KO_M3


title: Control subjects gut microbiota Replicate 22

description: Biological replicate 22 of control subjects, untreated, without UFs


title: In-vitro Day-4 Cultured human myoblasts with young serum  - Rep. 2.1


title: T5H_C5KO_F3

value: WT mice with C5ar1 knocked out (constitutive KO)


title: In-vitro Day-4 Cultured human myoblasts with young serum  - Rep. 2.2


title: Control subjects gut microbiota Replicate 21

description: Biological replicate 21 of control subjects, untreated, without UFs


title: In-vitro Day-4 Cultured human myoblasts with young serum  - Rep. 1.2


title: T5H_C5KO_M3


title: T5C_C5KO_F3

value: Female


title: In-vitro Day-4 Cultured human myoblasts with young serum  - Rep. 1.1


title: Control subjects gut microbiota Replicate 20

description: Biological replicate 20 of control subjects, untreated, without UFs


title: T5C_C5KO_M3


title: Control subjects gut microbiota Replicate 19

description: Biological replicate 19 of control subjects, untreated, without UFs


title: In-vitro Day-4 Cultured human myoblasts with control - Rep. 4

description:
In-vitro Day-4 Cultured human myoblasts with control
htseq_invitro.csv

value: Standard


title: T5H_Arc_MX

value: Arc

value: Arctic mouse model of AD


title: Control subjects gut microbiota Replicate 18

description: Biological replicate 18 of control subjects, untreated, without UFs


title: Control subjects gut microbiota Replicate 17

description: Biological replicate 17 of control subjects, untreated, without UFs


title: In-vitro Day-4 Cultured human myoblasts with control - Rep. 3


title: Control subjects gut microbiota Replicate 26

description: Biological replicate 26 of control subjects, untreated, without UFs


title: Total 293T4A DMSO-1  [total_noDOX_1]

value: Human embryonic kidney cell line

value: Untreated


title: Control subjects gut microbiota Replicate 15

description: Biological replicate 15 of control subjects, untreated, without UFs


title: In-vitro Day-4 Cultured human myoblasts with control - Rep. 1


title: T5C_Arc_M3

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

value: Male

value: 5 months


title: T5H_Arc_M3

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: In-vitro Day-4 Cultured human myoblast with aged serum  - Rep. 3.2

description:
In-vitro Day-4 Cultured human myoblast with aged serum
htseq_invitro.csv

value: Old


title: Control subjects gut microbiota Replicate 14

description: Biological replicate 14 of control subjects, untreated, without UFs


title: T5H_WT_F3

value: WT

value: Wild type


title: In-vitro Day-4 Cultured human myoblast with aged serum  - Rep. 3.1

value: Primary myoblasts isolated from skeletal muscle


title: Control subjects gut microbiota Replicate 12

description: Biological replicate 12 of control subjects, untreated, without UFs

value: Control

value: fecal microbiota

value: Internal reference (synthetic oligos)


title: In-vitro Day-4 Cultured human myoblast with aged serum  - Rep. 2.2


title: T5C_WT_F3


title: Control subjects gut microbiota Replicate 11

description: Biological replicate 11 of control subjects, untreated, without UFs


title: T5H_ArcC5GFAP_F2

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: In-vitro Day-4 Cultured human myoblast with aged serum  - Rep. 2.1


title: T5C_ArcC5GFAP_F2


title: In-vitro Day-4 Cultured human myoblast with aged serum  - Rep. 1.2


title: Control subjects gut microbiota Replicate 10

description: Biological replicate 10 of control subjects, untreated, without UFs


title: Control subjects gut microbiota Replicate 9

description: Biological replicate 9 of control subjects, untreated, without UFs


title: In-vitro Day-4 Cultured human myoblast with aged serum  - Rep. 1.1


title: T5H_ArcC5GFAP_M2


title: Control subjects gut microbiota Replicate 8

description: Biological replicate 8 of control subjects, untreated, without UFs


title: T5C_ArcC5GFAP_M2


title: blank control - rep3

type: RNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol  Standard Illumina scanning protocol

data_processing:
Data have been extracted using GenomeStudio software V2011.1 (Illumina). GenomeStudio identified missing bead types. We decided not to impute missing data, resulting in the exclusion of missing bead types for all the microarrays of the experiment. Number of retained probes is 31942.
Log2 quantile normalised signal intensity, encapsulted myoblasts were quantile normalised separetely from the connective tissues and blanks. Only the normalised myoblasts were considered in the differential expression analysis.

label: biotin

organism: unidentified

source_name: blank control

label_protocol: Two rounds cRNA synthesis starting with 5 ng of total RNA using MessageAmp™ II aRNA amplification kit (AM1751) and MessageAmp™ II-biotin enhanced aRNA amplification kit (AM1791,  Life Technologies, Carlsbad, California, USA) following provider recommandations.

extract_protocol: RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical)

value: blank control


title: Control subjects gut microbiota Replicate 16

description: Biological replicate 16 of control subjects, untreated, without UFs


title: Control subjects gut microbiota Replicate 7

description: Biological replicate 7 of control subjects, untreated, without UFs


title: blank control - rep1


title: In-vitro Day-10 Cultured human myoblasts with young serum  - Rep. 3.2

description:
In-vitro Day-10 Cultured human myoblasts with young serum
htseq_invitro.csv

value: Young


title: T5C_Arc_MX


title: In-vitro Day-4 Cultured human myoblasts with control - Rep. 2

description:
In-vitro Day-4 Cultured human myoblasts with control
htseq_invitro.csv

value: Standard


title: T5H_C5GFAP_F2

value: Female

value: WT mice overexpressing C5a under the GFAP promoter


title: blank control - rep2


title: In-vitro Day-10 Cultured human myoblasts with young serum  - Rep. 3.1


title: T5C_C5GFAP_F2


title: Control subjects gut microbiota Replicate 6

description: Biological replicate 6 of control subjects, untreated, without UFs


title: In-vitro Day-10 Cultured human myoblasts with young serum  - Rep. 2.2


title: In-vitro Day-10 Cultured human myoblasts with young serum  - Rep. 2.1


title: T5H_C5GFAP_M2


title: Connective tissue surrounding a capsule implanted in a young mouse - rep6

source_name: Mouse connective tissue

tag: tissue/cell type

value: connective tissue surrounding a capsule implanted in a young mouse

tag: mouse strain

tag: mouse age

value: 1.5 months


title: Control subjects gut microbiota Replicate 5

description: Biological replicate 5 of control subjects, untreated, without UFs

tag: age


title: Control subjects gut microbiota Replicate 4

description: Biological replicate 4 of control subjects, untreated, without UFs


title: Connective tissue surrounding a capsule implanted in a young mouse - rep5


title: Control subjects gut microbiota Replicate 13

description: Biological replicate 13 of control subjects, untreated, without UFs


title: T5C_C5GFAP_M2

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

tag: Sex

value: Male


title: Connective tissue surrounding a capsule implanted in a young mouse - rep4


title: In-vitro Day-10 Cultured human myoblasts with young serum  - Rep. 1.2


title: Connective tissue surrounding a capsule implanted in a young mouse - rep3


title: T5H_ArcC5KO_F2

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

value: 5 months

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: Connective tissue surrounding a capsule implanted in a young mouse - rep2


title: In-vitro Day-10 Cultured human myoblasts with young serum  - Rep. 1.1


title: Control subjects gut microbiota Replicate 2

description: Biological replicate 2 of control subjects, untreated, without UFs


title: Connective tissue surrounding a capsule implanted in a young mouse - rep1


title: T5C_ArcC5KO_F2


title: In-vitro Day-10 Cultured human myoblasts with control - Rep. 2

description:
In-vitro Day-10 Cultured human myoblasts with control
htseq_invitro.csv


title: T5H_ArcC5KO_M2


title: In-vitro Day-10 Cultured human myoblasts with control - Rep. 1


title: Uterine fibroids patients gut microbiota Replicate 42

description: Biological replicate 42 of 42.uterine fibroids patients gut microbiota

source_name: Uterine fibroids patient fecal microbiota

value: Uterine fibroids


title: Control subjects gut microbiota Replicate 1

description: Biological replicate 1 of control subjects, untreated, without UFs


title: Connective tissue surrounding a capsule implanted in an old mouse - rep6

value: connective tissue surrounding a capsule implanted in an old mouse

value: 22 months


title: T5C_ArcC5KO_M2


title: In-vitro Day-10 Cultured human myoblast with aged serum  - Rep. 3.2

description:
In-vitro Day-10 Cultured human myoblast with aged serum
htseq_invitro.csv

value: Old

value: Primary myoblasts isolated from skeletal muscle


title: Connective tissue surrounding a capsule implanted in an old mouse - rep5


title: Uterine fibroids patients gut microbiota Replicate 41

description: Biological replicate 41 of 42.uterine fibroids patients gut microbiota

value: fecal microbiota

value: Internal reference (synthetic oligos)


title: In-vitro Day-10 Cultured human myoblast with aged serum  - Rep. 3.1


title: T5H_C5KO_F2

value: WT mice with C5ar1 knocked out (constitutive KO)


title: Connective tissue surrounding a capsule implanted in an old mouse - rep4


title: T5C_C5KO_F2


title: T5H_C5KO_M2


title: In-vitro Day-10 Cultured human myoblast with aged serum  - Rep. 2.2


title: Uterine fibroids patients gut microbiota Replicate 40

description: Biological replicate 40 of 42.uterine fibroids patients gut microbiota


title: In-vitro Day-10 Cultured human myoblast with aged serum  - Rep. 2.1


title: Uterine fibroids patients gut microbiota Replicate 39

description: Biological replicate 39 of 42.uterine fibroids patients gut microbiota


title: T5C_C5KO_M2


title: Uterine fibroids patients gut microbiota Replicate 38

description: Biological replicate 38 of 42.uterine fibroids patients gut microbiota


title: In-vitro Day-10 Cultured human myoblast with aged serum  - Rep. 1.2


title: Connective tissue surrounding a capsule implanted in an old mouse - rep2


title: Connective tissue surrounding a capsule implanted in an old mouse - rep3


title: Uterine fibroids patients gut microbiota Replicate 37

description: Biological replicate 37 of 42.uterine fibroids patients gut microbiota


title: T5H_Arc_F2

value: Arc

value: Arctic mouse model of AD


title: Control subjects gut microbiota Replicate 3

description: Biological replicate 3 of control subjects, untreated, without UFs

value: Control


title: In-vitro Day-10 Cultured human myoblast with aged serum  - Rep. 1.1


title: Uterine fibroids patients gut microbiota Replicate 36

description: Biological replicate 36 of 42.uterine fibroids patients gut microbiota


title: T5C_Arc_F2

value: Female


title: Encapsulated human myoblasts implanted in an old mouse - rep10

source_name: Encapsulated human skeletal myoblasts

value: myoblasts from a capsule implanted in an old mouse

tag: implantation recipient mouse strain

tag: implantation recipient mouse age

value: old; 22 months


title: Encapsulated human myoblasts implanted in an old mouse - rep9


title: T5H_Arc_M2

value: Male


title: Connective tissue surrounding a capsule implanted in an old mouse - rep1


title: Uterine fibroids patients gut microbiota Replicate 34

description: Biological replicate 34 of 42.uterine fibroids patients gut microbiota


title: T5C_Arc_M2

value: 5 months


title: P2336_N715-S522

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Reads were demultiplexed according to the Nextera XT dual indexes.
Libraries were inspected with the FastQC suite to assess the quality of the reads.
Paired-end reads were aligned to the human reference genome and gene expression was quantified with the GEMTools 1.7.0 RNASeq pipeline.
Genome_build: Assembly GRCh38, Gencode release 27
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

source_name: HeLa (ATCC CCL-2)

growth_protocol: All the cell lines used in this article has been authenticated by StemElite ID (Promega). HeLa (ATCC CCL-2), Huh7 and A549 cell lines were grown in Dulbecco's Modified Eagle Medium—DMEM, high glucose, GlutaMAX-I, with pyruvate (Gibco)—supplemented with 10% fetal bovine serum (FBS, Hyclone) and penicillin-streptomycin (Sigma) in a 37°C humidified incubator with ~5% CO2.

extract_protocol:
Prior to the sorting, HeLa cells were trypsinized and resuspended in PBS with 5 mM EDTA. Then, cells were sorted on a SY3200 cell sorter (Sony Biotechnology)into 96-well plate which contained 3 μL of lysis Buffer. The plate was previously prepared with the lysis buffer and stored at -70°C. After the sorting, the plate was immediately frozen in carbonic ice and sent for RNA sequencing.
Full-length single cell RNA sequencing libraries are prepared using the Smart-seq2 protocol (Picelli et al., Nat. Protoc. 2014) with minor modifications. Briefly, freshly harvested cells were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 23 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity are assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent Technologies). 150 pg of the amplified cDNA were fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit. Sequencing of Nextera libraries was carried out on a Illumina HiSeq2500 v4.

treatment_protocol: To assay the extreme metabolic conditions cells were grown for at least two weeks (chronic adaptation) in DMEM, no glucose, no glutamine, no phenol Red (Gibco), and supplemented with 4.5 g/l of D-(+)-Glucose (Sigma) or with 2 mM L-glutamine (Gibco). We used 10 mM of non-metabolizable D-(+)-Galactose (Sigma) to maintain the osmotic pressure when glucose was removed.

value: epitheloid cervix carcinoma cell line

value: HeLa (ATCC CCL-2)


title: P2336_N715-S521


title: P2336_N715-S520


title: Encapsulated human myoblasts implanted in an old mouse - rep8


title: Uterine fibroids patients gut microbiota Replicate 33

description: Biological replicate 33 of 42.uterine fibroids patients gut microbiota

value: Uterine fibroids

source_name: Internal reference provided by the manufacturer


title: Encapsulated human myoblasts implanted in an old mouse - rep7


title: T5H_WT_F2

source_name: hippocampus

value: WT

value: Wild type


title: Encapsulated human myoblasts implanted in an old mouse - rep6


title: T5C_WT_F2


title: Uterine fibroids patients gut microbiota Replicate 32

description: Biological replicate 32 of 42.uterine fibroids patients gut microbiota


title: Encapsulated human myoblasts implanted in an old mouse - rep5


title: P2336_N715-S517


title: T5H_WT_M2


title: P2336_N715-S516


title: Uterine fibroids patients gut microbiota Replicate 31

description: Biological replicate 31 of 42.uterine fibroids patients gut microbiota


title: Encapsulated human myoblasts implanted in an old mouse - rep4


title: T5C_WT_M2

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: Uterine fibroids patients gut microbiota Replicate 30

description: Biological replicate 30 of 42.uterine fibroids patients gut microbiota


title: P2336_N715-S515


title: Encapsulated human myoblasts implanted in an old mouse - rep3


title: T5H_ArcC5GFAP_F1

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: P2336_N715-S513