title: 20170522.A-scRNA-seq_plate1_242

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_221

status: Public on Dec 28 2023

type: SRA

city: Lausanne

first: Yun-Tsan

last: Chang

address: Avenue de Beaumont 29

department: Dermatology

country: Switzerland

institute: CHUV

description:
fluidigm C1
MF032_BE.csv

library_source: transcriptomic single cell

data_processing:
The quality control was done using fastQC (v. 0.11.7) and the adaptors and low quality bases having phred quality score less than 20 were trimmed from the ends of the reads using Trim Galore (v. 0.4.4). The T-cell receptors (TCR) were identified using TraCeR and gene expressions were quantified with Kallisto (v. 0.45.0) for cells with an identified T cell receptor as part of the TraCeR workflow. TraCeR was also used to group the cells with identified TCR into groups of clones of different sizes, which all were required to have at least one TCR monomer in common with the other cells in the same clone. The remaining cells with TCR, sharing no identical TCR monomer with each other, were considered as heterogeneous cells. The gene expression data was normalised using Scater (v. 1.10.1) using CPM (counts per million).
Assembly: GRCh37
Supplementary files format and content: Matrix table with counts for every transcript and every cell

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Capture and processing of single skin and blood T cells was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/µL onto C1 integrated fluidic circuit chips for 5–10-µm cells. All C1 capture sites were microscopically inspected to identify the sites that contained only a single cell. Empty sites and those with multiple cells were excluded from further analysis. External RNA Controls Consortium spike-in RNAs served as a control. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform. Quality control was performed using FastQC v. 0.11.7 (Babraham Bioinformatics), and the adaptors and low-quality bases with a Phred quality score <20 were trimmed from the ends of the reads using Trim Galore v. 0.4.4 (Babraham Bioinformatics)
Cells were captured and performed using the Fluidigm C1 Autoprep system. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform.

tag: tissue

value: blood

tag: patient diagnosis

value: cutaneous T-cell lymphoma

tag: cell type

value: T cells


title: 20170522.A-scRNA-seq_plate1_222

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_220

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_223

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_219

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_218

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_217

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_216

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_214

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_215

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_213

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_212

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_232

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_231

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_208

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_209

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_211

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_210

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_207

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_204

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_203

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_201

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_202

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_205

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_195

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_193

description:
fluidigm C1
MF032_BE.csv


title: 20160817.B-C1_384

description:
fluidigm C1
MF028_SL.csv

value: skin


title: 20170522.A-scRNA-seq_plate1_194

description:
fluidigm C1
MF032_BE.csv


title: 20160817.B-C1_383

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_381

description:
fluidigm C1
MF028_SL.csv


title: 20170522.A-scRNA-seq_plate1_199

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_198

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_197

description:
fluidigm C1
MF032_BE.csv


title: 20160817.B-C1_372

description:
fluidigm C1
MF028_SL.csv


title: 20170522.A-scRNA-seq_plate1_196

description:
fluidigm C1
MF032_BE.csv


title: 20170522.A-scRNA-seq_plate1_200

description:
fluidigm C1
MF032_BE.csv


title: 20160817.B-C1_371

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_368

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_366

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_382

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_361

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_374

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_379

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_375

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_378

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_376

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_370

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_373

description:
fluidigm C1
MF028_SL.csv


title: 20170522.A-scRNA-seq_plate1_206

description:
fluidigm C1
MF032_BE.csv


title: 20160817.B-C1_367

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_355

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_351

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_363

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_347

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_350

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_359

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_346

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_357

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_360

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_342

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_352

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_335

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_354

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_339

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_343

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_337

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_344

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_340

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_334

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_330

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_329

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_327

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_333

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_328

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_332

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_326

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_324

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_331

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_325

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_323

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_320

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_318

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_315

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_314

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_317

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_312

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_319

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_313

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_311

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_309

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_310

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_308

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_304

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_307

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_306

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_302

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_305

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_303

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_295

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_298

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_296

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_293

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_297

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_299

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_322

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_290

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_291

description:
fluidigm C1
MF028_SL.csv


title: 20160817.B-C1_286

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_283

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_288

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_287

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_280

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_281

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_279

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_278

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_277

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_276

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_25_L]

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16S V3-V4 sequencing of feces from patient 25 affected by limited systemic sclerosis

library_source: genomic

data_processing:
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 5
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read merging: micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clustering: micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP): micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2022sclero)
Library strategy: paired-end amplicon sequencing

molecule: genomic DNA

organism: human feces metagenome

source_name: feces

growth_protocol: Stool, skin and saliva samples were collected and stored at -80°C

extract_protocol:
Genomic DNA extraction with DNeasy PowerLyzer PowerSoil Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: sample

tag: disease type

value: limited

tag: patientid


title: 20160817.B-C1_275

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_26_L]

description: 16S V3-V4 sequencing of feces from patient 26 affected by limited systemic sclerosis


title: 20160817.B-C1_273

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_294

description:
fluidigm C1
MF028_SL.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_23_L]

description: 16S V3-V4 sequencing of feces from patient 23 affected by limited systemic sclerosis


title: Feces of a patient affected by limited (ACA) sclerodermia [F_22_L]

description: 16S V3-V4 sequencing of feces from patient 22 affected by limited systemic sclerosis


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_21_D]

description: 16S V3-V4 sequencing of feces from patient 21 affected by diffuse systemic sclerosis

value: diffuse


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_20_D]

description: 16S V3-V4 sequencing of feces from patient 20 affected by diffuse systemic sclerosis


title: 20160817.B-C1_270

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_272

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_269

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_19_D]

description: 16S V3-V4 sequencing of feces from patient 19 affected by diffuse systemic sclerosis


title: 20160817.B-C1_271

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_17_L]

description: 16S V3-V4 sequencing of feces from patient 17 affected by limited systemic sclerosis


title: 20160817.B-C1_284

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_267

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_18_D]

description: 16S V3-V4 sequencing of feces from patient 18 affected by diffuse systemic sclerosis


title: Feces of a patient affected by limited (ACA) sclerodermia [F_16_L]

description: 16S V3-V4 sequencing of feces from patient 16 affected by limited systemic sclerosis


title: 20160817.B-C1_266

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_264

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_15_D]

description: 16S V3-V4 sequencing of feces from patient 15 affected by diffuse systemic sclerosis


title: Feces of a patient affected by limited (ACA) sclerodermia [F_14_L]

description: 16S V3-V4 sequencing of feces from patient 14 affected by limited systemic sclerosis


title: 20160817.B-C1_265

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_263

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_262

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_24_D]

description: 16S V3-V4 sequencing of feces from patient 24 affected by diffuse systemic sclerosis


title: 20160817.B-C1_274

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_261

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_11_L]

description: 16S V3-V4 sequencing of feces from patient 11 affected by limited systemic sclerosis


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_12_D]

description: 16S V3-V4 sequencing of feces from patient 12 affected by diffuse systemic sclerosis


title: 20160817.B-C1_260

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_259

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_09_D]

description: 16S V3-V4 sequencing of feces from patient 9 affected by diffuse systemic sclerosis


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_10_D]

description: 16S V3-V4 sequencing of feces from patient 10 affected by diffuse systemic sclerosis


title: 20160817.B-C1_258

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_07_L]

description: 16S V3-V4 sequencing of feces from patient 7 affected by limited systemic sclerosis


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_06_D]

description: 16S V3-V4 sequencing of feces from patient 6 affected by diffuse systemic sclerosis


title: 20160817.B-C1_256

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_08_L]

description: 16S V3-V4 sequencing of feces from patient 8 affected by limited systemic sclerosis


title: 20160817.B-C1_257

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_254

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_13_L]

description: 16S V3-V4 sequencing of feces from patient 13 affected by limited systemic sclerosis


title: 20160817.B-C1_251

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_04_D]

description: 16S V3-V4 sequencing of feces from patient 4 affected by diffuse systemic sclerosis


title: Feces of a patient affected by limited (ACA) sclerodermia [F_01_L]

description: 16S V3-V4 sequencing of feces from patient 1 affected by limited systemic sclerosis


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_02_D]

description: 16S V3-V4 sequencing of feces from patient 2 affected by diffuse systemic sclerosis


title: 20160817.B-C1_248

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_247

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [F_03_D]

description: 16S V3-V4 sequencing of feces from patient 3 affected by diffuse systemic sclerosis


title: 20160817.B-C1_249

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_246

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_243

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_241

description:
fluidigm C1
MF028_SE.csv


title: Feces of a patient affected by limited (ACA) sclerodermia [F_05_L]

description: 16S V3-V4 sequencing of feces from patient 5 affected by limited systemic sclerosis


title: 20160817.B-C1_255

description:
fluidigm C1
MF028_SE.csv


title: MCC, 11

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

library_source: transcriptomic

data_processing:
Read quality was checked for each sample using FastQC.
Sequenced reads were mapped to the human genome using mapper STAR with human reference genome GRCh37.
Aligned reads were count with featureCounts program.
Further analysis were made using DESeq2, fgsea и clusterProfiler R packages, as well as MSigDB and phantasus online tools.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes matrix of raw counts for each of 12 Samples

source_name: myocardial biopsy

extract_protocol:
Total RNA was isolated from myocardial biopsy specimens with an Extract RNA kit (Evrogen, Russia)
Libraries were constructed using TruSeq Stranded mRNA library prep kit

treatment_protocol: Total RNAs were isolated from myocardial biopsy specimens of patients with chronic heart failure before cardiac contractility modulation (MCC samples) and after Optimizer implantation (MCC_OPT).

value: myocardial biopsy

tag: treatment

value: before cardiac contractility modulation


title: MCC, 15


title: MCC, 14


title: MCC, 14, optimazer

value: after cardiac contractility modulation


title: MCC, 11, optimazer


title: MCC, 15, optimazer


title: MCC, 10, optimazer


title: 20160817.B-C1_252

description:
fluidigm C1
MF028_SE.csv


title: MCC, 10


title: 20160817.B-C1_239

description:
fluidigm C1
MF028_SE.csv


title: MCC, 09, optimazer


title: 20160817.B-C1_240

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_238

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_250

description:
fluidigm C1
MF028_SE.csv


title: MCC, 09


title: MCC, 06


title: MCC, 06, optimazer


title: 20160817.B-C1_236

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_245

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_237

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_234

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_26_L]

description: 16S V3-V4 sequencing of saliva from patient 26 affected by limited systemic sclerosis

organism: human saliva metagenome

source_name: saliva


title: 20160817.B-C1_235

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_25_L]

description: 16S V3-V4 sequencing of saliva from patient 25 affected by limited systemic sclerosis


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_24_D]

description: 16S V3-V4 sequencing of saliva from patient 24 affected by diffuse systemic sclerosis


title: 20160817.B-C1_231

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_22_L]

description: 16S V3-V4 sequencing of saliva from patient 22 affected by limited systemic sclerosis


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_16_L]

description: 16S V3-V4 sequencing of saliva from patient 16 affected by limited systemic sclerosis


title: 20160817.B-C1_230

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_227

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_18_D]

description: 16S V3-V4 sequencing of saliva from patient 18 affected by diffuse systemic sclerosis


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_20_D]

description: 16S V3-V4 sequencing of saliva from patient 20 affected by diffuse systemic sclerosis


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_21_D]

description: 16S V3-V4 sequencing of saliva from patient 21 affected by diffuse systemic sclerosis


title: 20160817.B-C1_229

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_228

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_222

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_14_L]

description: 16S V3-V4 sequencing of saliva from patient 14 affected by limited systemic sclerosis


title: 20160817.B-C1_221

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_17_L]

description: 16S V3-V4 sequencing of saliva from patient 17 affected by limited systemic sclerosis


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_19_D]

description: 16S V3-V4 sequencing of saliva from patient 19 affected by diffuse systemic sclerosis


title: 20160817.B-C1_232

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_218

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_11_L]

description: 16S V3-V4 sequencing of saliva from patient 11 affected by limited systemic sclerosis


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_13_L]

description: 16S V3-V4 sequencing of saliva from patient 13 affected by limited systemic sclerosis


title: 20160817.B-C1_216

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_23_L]

description: 16S V3-V4 sequencing of saliva from patient 23 affected by limited systemic sclerosis


title: 20160817.B-C1_223

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_215

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_224

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_10_D]

description: 16S V3-V4 sequencing of saliva from patient 10 affected by diffuse systemic sclerosis


title: 20160817.B-C1_220

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_226

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_214

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_07_L]

description: 16S V3-V4 sequencing of saliva from patient 7 affected by limited systemic sclerosis


title: 20160817.B-C1_213

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_08_L]

description: 16S V3-V4 sequencing of saliva from patient 8 affected by limited systemic sclerosis


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_15_D]

description: 16S V3-V4 sequencing of saliva from patient 15 affected by diffuse systemic sclerosis


title: 20160817.B-C1_219

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_211

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_212

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_06_D]

description: 16S V3-V4 sequencing of saliva from patient 6 affected by diffuse systemic sclerosis


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_04_D]

description: 16S V3-V4 sequencing of saliva from patient 4 affected by diffuse systemic sclerosis


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_05_L]

description: 16S V3-V4 sequencing of saliva from patient 5 affected by limited systemic sclerosis


title: 20160817.B-C1_208

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_03_D]

description: 16S V3-V4 sequencing of saliva from patient 3 affected by diffuse systemic sclerosis


title: 20160817.B-C1_207

description:
fluidigm C1
MF028_SE.csv


title: CK47

city: Suita

first: Tomonori

last: Kimura

state: Osaka

address: Yamadaoka 2-2

country: Japan

institute: Osaka University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: kidney

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: kidney

value: WT

value: D-Ala

tag: time point


title: 20160817.B-C1_206

description:
fluidigm C1
MF028_SE.csv


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_02_D]

description: 16S V3-V4 sequencing of saliva from patient 2 affected by diffuse systemic sclerosis


title: 20160817.B-C1_204

description:
fluidigm C1
MF028_SE.csv


title: CK48


title: 20160817.B-C1_205

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_202

description:
fluidigm C1
MF028_SE.csv


title: CK44


title: CK46


title: CK45


title: 20160817.B-C1_203

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_199

description:
fluidigm C1
MF028_SE.csv


title: CK43


title: 20160817.B-C1_198

description:
fluidigm C1
MF028_SE.csv


title: CK42


title: CK41


title: 20160817.B-C1_196

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_195

description:
fluidigm C1
MF028_SE.csv


title: CK40


title: 20160817.B-C1_194

description:
fluidigm C1
MF028_SE.csv


title: CK38


title: CK39


title: 20160817.B-C1_197

description:
fluidigm C1
MF028_SE.csv


title: CK37


title: 20160817.B-C1_200

description:
fluidigm C1
MF028_SE.csv


title: 20160817.B-C1_193

description:
fluidigm C1
MF028_SE.csv


title: CK36

value: Vehicle


title: 20170522.A-scRNA-seq_plate1_96

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_94

description:
fluidigm C1
MF028_BLC.csv


title: CK35


title: 20170522.A-scRNA-seq_plate1_95

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_93

description:
fluidigm C1
MF028_BLC.csv


title: CK33


title: CK32


title: 20170522.A-scRNA-seq_plate1_92

description:
fluidigm C1
MF028_BLC.csv


title: 20160817.B-C1_210

description:
fluidigm C1
MF028_SE.csv


title: CK30


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_12_D]

description: 16S V3-V4 sequencing of saliva from patient 12 affected by diffuse systemic sclerosis


title: 20170522.A-scRNA-seq_plate1_90

description:
fluidigm C1
MF028_BLC.csv


title: CK29


title: 20170522.A-scRNA-seq_plate1_9

description:
fluidigm C1
MF028_BLC.csv


title: CK27


title: 20170522.A-scRNA-seq_plate1_89

description:
fluidigm C1
MF028_BLC.csv


title: CK25


title: 20170522.A-scRNA-seq_plate1_88

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_86

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_85

description:
fluidigm C1
MF028_BLC.csv


title: CK34


title: 20170522.A-scRNA-seq_plate1_91

description:
fluidigm C1
MF028_BLC.csv


title: CK31


title: CK22


title: 20170522.A-scRNA-seq_plate1_83

description:
fluidigm C1
MF028_BLC.csv


title: CK23


title: 20170522.A-scRNA-seq_plate1_84

description:
fluidigm C1
MF028_BLC.csv


title: CK21


title: 20170522.A-scRNA-seq_plate1_82

description:
fluidigm C1
MF028_BLC.csv


title: CK20


title: CK17


title: 20170522.A-scRNA-seq_plate1_8

description:
fluidigm C1
MF028_BLC.csv


title: CK19


title: 20170522.A-scRNA-seq_plate1_79

description:
fluidigm C1
MF028_BLC.csv


title: CK18


title: CK28


title: CK16


title: CK24


title: 20170522.A-scRNA-seq_plate1_78

description:
fluidigm C1
MF028_BLC.csv


title: CK26


title: 20170522.A-scRNA-seq_plate1_87

description:
fluidigm C1
MF028_BLC.csv


title: CK15


title: 20170522.A-scRNA-seq_plate1_80

description:
fluidigm C1
MF028_BLC.csv


title: CK14


title: 20170522.A-scRNA-seq_plate1_75

description:
fluidigm C1
MF028_BLC.csv


title: CK13


title: CK10


title: 20170522.A-scRNA-seq_plate1_71

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_74

description:
fluidigm C1
MF028_BLC.csv


title: CK12


title: 20170522.A-scRNA-seq_plate1_69

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_77

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_73

description:
fluidigm C1
MF028_BLC.csv


title: CK8


title: CK7


title: CK11


title: 20170522.A-scRNA-seq_plate1_67

description:
fluidigm C1
MF028_BLC.csv


title: CK6


title: 20170522.A-scRNA-seq_plate1_72

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_70

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_62

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_68

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_66

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_76

description:
fluidigm C1
MF028_BLC.csv


title: CK3


title: CK4


title: 20170522.A-scRNA-seq_plate1_63

description:
fluidigm C1
MF028_BLC.csv


title: CK2


title: 20170522.A-scRNA-seq_plate1_60

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_59

description:
fluidigm C1
MF028_BLC.csv


title: DA6_13

data_processing:
Illumina Casava1.8.2 software
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA sample prep kit following manufacturer's protocols.

tag: genotype

value: D-ala

tag: time

value: 2 h


title: CK9


title: DA6_12


title: 20170522.A-scRNA-seq_plate1_58

description:
fluidigm C1
MF028_BLC.csv


title: DA6_15


title: CK1


title: DA6_11


title: DA6_14


title: DA6_10

value: L-ala


title: CK5


title: DA6_8


title: DA6_9


title: 20170522.A-scRNA-seq_plate1_5

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_54

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_50

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_56

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_51

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_49

description:
fluidigm C1
MF028_BLC.csv


title: DA6_4


title: DA6_7


title: DA6_6


title: 20170522.A-scRNA-seq_plate1_48

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_57

description:
fluidigm C1
MF028_BLC.csv


title: DA6_5


title: 20170522.A-scRNA-seq_plate1_45

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_46

description:
fluidigm C1
MF028_BLC.csv


title: DA6_3


title: 20170522.A-scRNA-seq_plate1_47

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_53

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_43

description:
fluidigm C1
MF028_BLC.csv


title: DA6_1


title: 20170522.A-scRNA-seq_plate1_44

description:
fluidigm C1
MF028_BLC.csv


title: 27_mRNAseq_YTTPdeltaARE_MPP3_rep3

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

country: USA

institute: National Institute on Aging

data_processing:
cutadapt trimming
STAR alignment (RNA-seq)
featureCount, gene-level extraction (RNA-seq)
Assembly: mm10
Supplementary files format and content: text file

source_name: Hematopoetic stem cells

extract_protocol:
RNA was purified with TRIzol TM Reagent (Invitrogen, 15596026) and Direct-zol RNA microprep (Zymo R2060)
RNA-seq libraries were constructed using SMARTer Standard mRNA-seq kit v2

value: Born Marrow

value: Multipotent progenitor 3

value: TPPdeltaARE

tag: age

value: Young-age


title: DA6_2


title: 20170522.A-scRNA-seq_plate1_42

description:
fluidigm C1
MF028_BLC.csv

value: blood

value: cutaneous T-cell lymphoma

value: T cells


title: 26_mRNAseq_YTTPdeltaARE_MPP3_rep2


title: 28_mRNAseq_YTTPdeltaARE_MPP3_rep4


title: 20170522.A-scRNA-seq_plate1_40

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_41

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_4

description:
fluidigm C1
MF028_BLC.csv


title: 24_mRNAseq_YWT_MPP3_rep4


title: 25_mRNAseq_YTTPdeltaARE_MPP3_rep1


title: 20170522.A-scRNA-seq_plate1_38

description:
fluidigm C1
MF028_BLC.csv


title: 23_mRNAseq_YWT_MPP3_rep3


title: 22_mRNAseq_YWT_MPP3_rep2


title: 20170522.A-scRNA-seq_plate1_39

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_37

description:
fluidigm C1
MF028_BLC.csv


title: 21_mRNAseq_YWT_MPP3_rep1


title: 17_mRNAseq_YTTPdeltaARE_HSC_rep3

value: Hematopoetic stem cells


title: 18_mRNAseq_YTTPdeltaARE_HSC_rep4


title: 20170522.A-scRNA-seq_plate1_36

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_34

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_33

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_35

description:
fluidigm C1
MF028_BLC.csv


title: 15_mRNAseq_YTTPdeltaARE_HSC_rep1


title: 16_mRNAseq_YTTPdeltaARE_HSC_rep2


title: 20170522.A-scRNA-seq_plate1_32

description:
fluidigm C1
MF028_BLC.csv


title: Saliva of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [S_09_D]

description: 16S V3-V4 sequencing of saliva from patient 9 affected by diffuse systemic sclerosis

value: diffuse


title: 14_mRNAseq_YWT_HSC_rep4


title: 20170522.A-scRNA-seq_plate1_31

description:
fluidigm C1
MF028_BLC.csv


title: 13_mRNAseq_YWT_HSC_rep3


title: 20170522.A-scRNA-seq_plate1_3

description:
fluidigm C1
MF028_BLC.csv


title: 12_mRNAseq_YWT_HSC_rep2


title: 11_mRNAseq_YWT_HSC_rep1


title: 20170522.A-scRNA-seq_plate1_30

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_29

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_28

description:
fluidigm C1
MF028_BLC.csv


title: 07_mRNAseq_MTTPdeltaARE_HSC_rep2

value: Mid-age


title: 08_mRNAseq_MTTPdeltaARE_HSC_rep3


title: 06_mRNAseq_MTTPdeltaARE_HSC_rep1


title: 20170522.A-scRNA-seq_plate1_26

description:
fluidigm C1
MF028_BLC.csv


title: 05_mRNAseq_MWT_HSC_rep5


title: 20170522.A-scRNA-seq_plate1_27

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_24

description:
fluidigm C1
MF028_BLC.csv


title: 04_mRNAseq_MWT_HSC_rep4


title: 03_mRNAseq_MWT_HSC_rep3


title: 01_mRNAseq_MWT_HSC_rep1


title: 02_mRNAseq_MWT_HSC_rep2


title: 20170522.A-scRNA-seq_plate1_23

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_22

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_21

description:
fluidigm C1
MF028_BLC.csv


title: Donor 2 SAHA/VOR scATAC-seq HIV latency reversal

city: Chapel Hill

first: Yuchao

last: Jiang

state: NC

address: 3101 McGavran-Greenberg Hall

institute: University of North Carolina at Chapel Hill

description:
10X Genomics Multiome RNA + ATAC
filtered_feature_bc_matrix_donor2.h5

data_processing:
For the 10X Genomics Multiome data, we used Cell Ranger ARC (version 2.0.0) to perform sample demultiplexing, barcode processing, peak calling, and counting of RNA and ATAC reads in single cells. Alignment was performed with the cellranger-arc count function. Cells with high percentages of mitochondrial reads, extreme RNA read counts, and/or extreme ATAC fragment counts were removed. Doublet cells, identified by scDblFinder across multiplexed samples corresponding to the treatment groups, were excluded from subsequent analysis. For read count normalization, we used sctransform by Seurat for scRNA-seq and TF-IDF by Signac for scATAC-seq.  This is followed by principal component analysis (PCA) and latent semantic indexing (LSI) for dimension reduction, respectively. We kept the top 50 principal components (PCs) from scRNA-seq and the top 2-50 LSIs from scATAC-seq. Jointly, these are used as input to construct a weighted nearest neighbor (WNN) graph, which is further used for joint UMAP visualization and clustering.  We used the Leiden clustering algorithm for community detection with the resolution parameter visualized and optimized by the clustree algorithm, which builds a tree to visualize and examine how clusters are related to each other at varying resolutions, allowing researchers to assess which clusters are distinct and which are unstable with the use of additional metrics such as the SC3 stability index. For modality-specific processing, we built the unweighted K-nearest neighbor (KNN) and the weighted shared nearest neighbor (SNN) graphs, followed by UMAP visualization and clustering identification. For scATAC-seq data, we also adopted weighted PCA by Destin weighing chromatin accessibilities by existing genomic annotations and publicly available regulomic data. We obtained the position frequency matrices and annotated 633 pairs of TFs and motifs from the JASPAR 2020 database; we further applied chromVAR to derive, for each TF, its motif score, which measures the deviation in chromatin accessibility across the set of peaks containing the corresponding motif, compared to a set of background peaks. We also constructed a pseudo-gene activity matrix, summing ATAC read counts in gene bodies and promoter regions (2Kb upstream of genes' transcription start sites), followed by sctransform normalization.
Assembly: hg38
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: Primary CD4 cells

growth_protocol: Cells were cultured in RPMI supplemented with 10% FCS, L-Glutamine, HEPES, PenStrep, and Sodium Pyruvate.

extract_protocol:
Nuclei were isolated following the 10X Genomics protocol (CG000365 • Rev C) with slight modifications. Cells were harvested, washed once with ice-cold DPBS-0.5% BSA containing 0.2 U/μl RiboLock RNase inhibitor (Thermo Fisher, cat. no. EO0382), counted and viability detected by Trypan blue (Thermo Fisher, cat. no.15250061). Dead cells were first removed using Dead Cell Removal Kit (Miltenyi Biotec, cat. No. 130-090-101). For each sample, 1×106 cells were pelleted by centrifugation at 500g, 4 °C, 5 min. The cells were resuspended in 100μl of ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM sodium chloride, 3 mM magnesium chloride, 0.01% Tween-20 (Sigma, cat. no. 655205-250ML), 0.01% nonidet P40 substitute (Sigma, cat. no. I8896), 0.01% Digitonin (Promega, cat. no. G9441), 1 U/μl RiboLock RNase inhibitor, 1% BSA and 1mM DTT) and incubated on ice for 3 min. The nuclei were then pelleted and washed with 1 mL ice-cold wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM sodium chloride, 3 mM magnesium chloride, 0.01% Tween-20, 1% BSA, 1mM DTT and 1 U/μl RiboLock RNase inhibitor) and re-suspended in diluted nuclei buffer (1X nuclei buffer, 1mM DTT, 1 U/μl RiboLock RNase inhibitor).
Construction of single cell multiome libraries was performed using a 10X Genomics Chromium controller and a single cell multiome ATAC + Gene expression kit following manufacturers protocol. Nuclei were first isolated following the 10X Genomics protocol. Then, the intact nuclei suspensions were subjected to Tn5 transposition in bulk, followed by barcoding using GEM (Gel Beads-in-Emulsion) beads. Silane magnetic beads were used to purify the barcoded products from the post GEM-RT reaction mixture. Incubation of the GEMs produces barcoded DNA from the transposed DNA (for scATAC-seq) and barcoded, full-length cDNA from poly-adenylated mRNA (for scRNA-seq). Barcoded transposed DNA and barcoded full-length cDNA were then pre-amplified by polymerase chain reaction (PCR) to facilitate library construction. The pre-amplified product was used as input for both ATAC and gene expression (GEX) library construction. P5 and P7 indexes were added to the pre-amplified transposed DNA for ATAC-seq library. cDNA amplification, enzymatic fragmentation followed by end Repair, A-tailing, adaptor Ligation, and PCR were performed to incorporate P5, P7, i7 and i5 sample indices, and TruSeq Read 2 (read 2 primer sequence) for gene expression libraries. The libraries were quantified using an Agilent Tapestation 4200 and the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen, #Q33230). Pooled samples from ATAC and RNA libraries were sequenced using paired-end, single-index (ATAC-seq) and dual index (RNA-seq) sequencing on a NextSeq 2000 instrument (Illumina). For GEX libraries, the read format was: Read 1 - 28 cycles; Read 2 - 90 cycles; i7 - 10 cycles; i5 – 10 cycles.  For ATAC libraries the read format was: Read 1 – 50 cycles; Read 2 – 49 cycles; i7 – 8 cycles, i5 – 16 cycles. Paired end reads of pooled libraries were demultiplexed prior to downstream analysis.
Paired end, dual indexing

treatment_protocol: CD4 T-cells were isolated from uninfected donor peripheral blood mononuclear cells (PBMCs) using the EasySep Human CD4 T Cell Isolation Kit (StemCell Technologies, catalog # 17952) using negative selection following the manufacturers protocol. Purity of CD4+ cells were determined by flow cytometry, which showed a high purity (97.5%) CD4+T-cell population. Cells were plated at 1 million cells/mL in RPMI, 10% FBS, penicillin/streptomycin and incubated overnight at 37˚C. The cells were activated using Dynabeads Human T-Activator CD3/CD28 beads (Thermo Fisher Scientifc, Cat. No. 111.31D) for 72h at a ratio of 1:1 (beads:cells). Dynabeads were then removed and  activated cells were spin-infected with NL4-3-△6-drEFGP-IRES-thy1.2 virus at a speed of 600g for 2h. Successful infection was confirmed by measuring GFP expression by flow cytometry at 2dpi  followed by enrichment of infected cells by flow sorting using a FACSAria (BD). Enriched cells expressing GFP were kept in culture for 3 weeks, during which time viral gene expression diminished, leaving most infected cells GFP negative. The GFP negative population was then re-sorted to enrich the latently infected (GFP-) population.  Latently infected cells were then treated with the latency reversing agents (LRAs), vorinostat, prostratin or iBET151 at concentrations of 500nM along or with vehicle control (DMSO 0.05%). 24h post treatment, cells were harvested, washed and quantified for reactivation by GFP expression. The remainder of the reactivated cells were used for integrated single cell multiomic scRNA-seq/scATAC-seq library preparation.

tag: subject id

value: Donor 2

tag: cell line

value: Primary CD4 cells

value: Primary CD4 cells infected with HIV in vitro

value: SAHA/VOR


title: 20170522.A-scRNA-seq_plate1_19

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_2

description:
fluidigm C1
MF028_BLC.csv


title: Donor 2 Prostratin scATAC-seq HIV latency reversal

value: Prostratin


title: Donor 2 DMSO scATAC-seq HIV latency reversal

value: DMSO


title: Donor 2 iBET151 scATAC-seq HIV latency reversal


title: 20170522.A-scRNA-seq_plate1_18

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_17

description:
fluidigm C1
MF028_BLC.csv


title: Donor 2 SAHA/VOR scRNA-seq HIV latency reversal

molecule: nuclear RNA


title: 20170522.A-scRNA-seq_plate1_16

description:
fluidigm C1
MF028_BLC.csv


title: Donor 2 Prostratin scRNA-seq HIV latency reversal


title: Donor 2 iBET151 scRNA-seq HIV latency reversal


title: 20170522.A-scRNA-seq_plate1_13

description:
fluidigm C1
MF028_BLC.csv


title: Donor 2 DMSO scRNA-seq HIV latency reversal


title: Donor 1 SAHA/VOR scATAC-seq HIV latency reversal

description:
10X Genomics Multiome RNA + ATAC
filtered_feature_bc_matrix_donor1.h5

value: Donor 1


title: 20170522.A-scRNA-seq_plate1_14

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_11

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-scRNA-seq_plate1_25

description:
fluidigm C1
MF028_BLC.csv


title: 20170522.A-cRNA-seq_plate1_1

description:
fluidigm C1
MF028_BLC.csv


title: Donor 1 iBET151 scATAC-seq HIV latency reversal


title: Donor 1 DMSO scATAC-seq HIV latency reversal


title: 20170522.A-scRNA-seq_plate1_10

description:
fluidigm C1
MF028_BLC.csv


title: 20160817.B-C1_98

description:
fluidigm C1
MF028_BL.csv


title: Donor 1 Prostratin scRNA-seq HIV latency reversal


title: 20160817.B-C1_97

description:
fluidigm C1
MF028_BL.csv


title: Donor 1 iBET151 scRNA-seq HIV latency reversal


title: Donor 1 DMSO scRNA-seq HIV latency reversal


title: 20160817.B-C1_99

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_192

description:
fluidigm C1
MF028_BL.csv


title: Donor 1 SAHA/VOR scRNA-seq HIV latency reversal


title: 20160817.B-C1_189

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_190

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_188

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_185

description:
fluidigm C1
MF028_BL.csv


title: 20170522.A-scRNA-seq_plate1_12

description:
fluidigm C1
MF028_BLC.csv


title: 20160817.B-C1_187

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_182

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_184

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_186

description:
fluidigm C1
MF028_BL.csv


title: Donor 1 Prostratin scATAC-seq HIV latency reversal


title: 20160817.B-C1_181

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_180

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_178

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_177

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_174

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_173

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_172

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_170

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_169

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_168

description:
fluidigm C1
MF028_BL.csv


title: SNC-SCC 3S

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

institute: University of Verona

data_processing:
Basecalls performed using bcl2fastq
Starting from raw FASTQ files, quality of reads obtained from each sample was assessed using FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapters were trimmed and reads with length <18bp or >27bp were filtered out with cutadapt (1.16).
Filtered reads were aligned to the miRBase 21 using SHRiMP2 (2.2.3) with the “mirna” option activated. Mature miRNAs were assigned to the fragments based on the mapping position on the hairpin miRNAs.
The number of unique-UMI mapped fragments were counted for each mature miRNA and counts were normalized as CPM.
Supplementary_files_format_and_content: Tab-delimited text file includes normalized expression values for every microRNAs and every sample.

source_name: SNC-patient

extract_protocol:
Total RNA was extracted using a commercial RNeasy Mini Kit (Qjagen).
miRNA-seq library preparation was performed using the QIAseq miRNA kit (Qiagen).

value: mucouse

tag: histotype

value: SCC

tag: disease state

value: non malignant


title: SNC-ITAC 5P

value: sinonasal cancer

value: ITAC

value: Malignant


title: SNC-ITAC 2S


title: SNC-ITAC 1S


title: SNC-ITAC 1P


title: SNC-ITAC 4P


title: SNC-SCC 1P


title: SNC-SCC 2S


title: SNC-ITAC 4S


title: SNC-SCC 3P


title: SNC-ITAC 5S


title: SNC-SCC 4S


title: SNC-ITAC 3P


title: SNC-ITAC 2P


title: SNC-SCC 4P


title: SNC-ITAC 3S


title: SNC-SCC 1S


title: SNC-SCC 2P


title: 20160817.B-C1_167

description:
fluidigm C1
MF028_BL.csv

value: blood

value: cutaneous T-cell lymphoma

value: T cells


title: SNC-SCC 5S


title: 20160817.B-C1_175

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_164

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_163

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_162

description:
fluidigm C1
MF028_BL.csv


title: 231 Azeliragon 2uM 72h c

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

data_processing:
Illumina patforms
Reads were aligned with STAR v2.6.1d to GRCh38 human reference genome
raw count of each sample was quantified by FeatureCounts v1.5.0-p3
Differentially expressed genes were obtained using limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

growth_protocol: MDA-MB-231 cells were mantained in DMEM-F12 supplemented with 10% FBS and 2mmol/L L-Glutamine.

extract_protocol:
Tumor RNA from cells was harvested using RNeasy kit (Qiagen)
libraries were performed by Novogene (Cambridge, UK)

treatment_protocol: MDA-MB-231 cells were treated for 72h with DMSO or Azeliragon (AZ)

value: Azeliragon


title: 20160817.B-C1_151

description:
fluidigm C1
MF028_BL.csv


title: 231 DMSO 72h b


title: 20160817.B-C1_155

description:
fluidigm C1
MF028_BL.csv


title: 231 DMSO 72h c


title: 20160817.B-C1_158

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_153

description:
fluidigm C1
MF028_BL.csv


title: 231 Azeliragon 2uM 72h b


title: 20160817.B-C1_156

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_154

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_160

description:
fluidigm C1
MF028_BL.csv


title: 231 DMSO 72h a


title: TRAP.RepoGal4.ime4RNAi.34D.IP.e29.Rep2 [experiment 29]

city: Philadelphia

first: Alexandra

last: Perlegos

state: PA

address: 231 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

description: experiment 29

data_processing:
library strategy: TRAP-seq
Paired-end FASTQs were trimmed using TrimGalore
Trimmed FASTQs were mapped using STAR-2.7.3a
Mapped BAM files were filtered for primary mapped reads in properly matching pairs using samtools
Count tables were produced for RNA-seq using an in-house R script utilizing the GenomicRanges summarizeOverlaps function
Differential expression tables were produced by DESeq2 from RNA-seq count tables
m6A-IP-seq was processed with RADAR for differential peak calling. FACS sorting expeirments, counts were processed using RUV-seq (RUVr) before differential expression analysis using Deseq2.
Assembly: dm6
Supplementary files format and content: bigWig files for each condition were produced using deepTools (bamCoverage to produce bw files from BAM files with --normalizeUsing CPM)

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Drosophila crosses set up in 25 degree incubator. Male progeny collected 1-2 days post eclosion for aging to 34 D old and young 5D old and RNA extraction. For experiemnt 21 DaGal4> Control RNAi (BL35785) DaGal4> Mettl3 RNAi(BL80448). Experiment 08 and 07 ElavGal4-c155 x UAS-mcd8GFP and ElavGal4c155 x UAS-AB(2x) male flies 6D old. For experiment 25 FACS sorting ElavGal4>UAS-mcD8GFP x mCherry RNAi or ElavGal4>UAS-mcD8GFP x Ime4 RNAi for aging to 34 D old and young 5D old and FACS sorting GFP + cells. For experiment 27 FACS sorting RepoGal4>UAS-mcD8GFP x mCherry RNAi or RepoGal4>UAS-mcD8GFP x Ime4 RNAi for aging to 34 D old and young 5D old and FACS sorting GFP+ and GFP- cells. For exerpeiemnt 29 TRAP IP seq, ElavGAl4>UAS-RPL3-FLAG x mCherry RNAi, ElavGAl4>UAS-RPL3-FLAG x Ime4 RNAi, RepoGAl4>UAS-RPL3-FLAG x mCherry RNAi, RepoGAl4>UAS-RPL3-FLAG x Ime4 RNAi for aging to 34 D old and young 5D old and FLAG tag IP and RNA extraction.

extract_protocol:
For m6A-IP seq flies were flash frozen and head tissue was collected into cold RNAse free tubes. Total RNA was extracted from 200 Drosophila Heads per replicate using Trizol/ chloroform extraction. PolyA+ mRNA was obtained using NEBNext Poly(A) mRNA Magnetic Isolation Module. PolyA+ RNA was fragmented using the NEB Next Magnesium Fragmentation Module (NEB, E6150S) for 4 minutes at 95 °C for a 250 ng sample of polyA+ RNA, and RNA was repurified using the Zymo RNA clean & concentrator -5 kit (Zymo, R1013). 10% of the fragmented polyA+ RNA was saved as an input control for sequencing. M6A -immunoprecipitation was done using the EpiMark N6-Methyladenosine Enrichment kit protocol with some minor alteration. 30ul of protein G magnetic beads (NEB, #S1430) were washed and resuspended in IP buffer (150mM NaCl, 10mM Tris-HCL, 0.1% NP-40). 4ul of synaptic systems antibody (SYS, 202003) was conjugated to protein G-magnetic beads (NEB, S1430S) for 2 hours at 4°C. Beads/ antibody were washed twice in IP buffer. ~1μg PolyA+ RNA was incubated with beads/antibody in IP buffer supplemented with 0.1% SUPERase-In RNase Inhibitor (Thermo Fisher; AM2696) for 2 hours at 4°C. After incubation, RNA/beads/antibody are washed twice in IP buffer, twice in low salt IP buffer (50mM NaCl, 10mM Tris-HCL, 0.1% NP-40), and twice in high salt IP buffer (500mM NaCl, 10mM Tris-HCL, 0.1% NP-40). RNA is eluted from beads with 25μl of RLT buffer twice and elution was pooled and concentrated using Zymo RNA clean and concentrator kit-5 (R1015). Library preparation and sequencing was done by Admera Health. Total RNA was extracted from brains using trizol/chloroform and Zymo RNA clean and concentrator kit-5 (R1015). The RNA-seq libraries from brains were prepared using the Tru-seq stranded mRNA library prep. Library preparation and sequencing was done by Admera Health, and sequenced using illumina HiSeq with 40M paired end reads (2x150bp). Biological replicates were done for each experimental condition and genotype as indicated. For FACS sorting Brains (10–15 per replicate) from young (5days old) and old (34days old) males were dissected, collected into a tube with cold Schneider's medium (SM) containing 45μM actinomycin D, and washed twice in PBS. Next, we added 300μL of dissociating solution, which included Papain diluted in PBS (Worthington PAP2, LK003178) and liberase (2.5 mg/ml). Brains were dissociated at 25°C using a shaker at 1000rpm for 20 min and vigorous pipetting every 5min, and passing through 25G 5/8 needle 7x. Dissociated tissue was filtered through 40μm cell strainers and sorted on an BD FACS Aria II SORP with a 100μm nozzle into a 96 well plate at the sorting facility of the University of Pennsylvania. Dead cells were excluded by staining with 4,6-diamidino-2-phenylindole (DAPI). GFP+ cells gates were set according to the fluorescence profile of GFP- brain tissue, and nuclear stain Syto60. Desired glia or neuronal populations (~500 cells per replicate) were directly sorted into 10X lysis buffer (Takara 635013) plus RNAse inhibitor for library preparations using SMART-seq v4. For TRAP IP fly brains (30 brains/sample) were dissected and stored in buffer ( 10mM Hepes, 150 mM KCl, 5mM MgCl2, 100ug/ml Cyclohexamide, 1x protease inhibitor, Rnase inhibitor) in -80 until samples were ready to process. Protein G Magnetic beads were coated with 4 ug of anti-flag antibody, and resuspended in reaction buffer (10mM Hepes, 150 mM KCl, 5mM MgCl2, 100ug/ml Cyclohex, 1x protease inhibitor (Sigma, 11873580001), + 0.1% triton x-100, Rnase inhibitor (Thermo Fisher, AM2696). Samples with brain tissue were homogenized in lysis buffer (reaction buffer + 0.5% triton-x). 20% of sample was saved as input control and RNA extraction using zymo clean and concentrator kit -5. The rest of the sample was added to antibody plus beads, and incubated for 4 hr at 4°C. Beads + RNA was washed and RNA was extracted from beads using zymo clean and concentrator kit -5. Libraries were made using SMARTer Stranded Total RNA-Seq Kit V4 for IPed and input RNA, and sequenced with 40M paired end reads (2x150bp).
For experiment 21 and 08, m6A-IPseq libraries were made using SMARTer Stranded Total RNA-Seq Kit V3 without rRNA depletion (takarabio, 634486) for IPed and input RNA. Experiment 07 brain RNA-seq libraries were prepared using the Tru-seq stranded mRNA library prep. Experiment 25, 27, and 29 FACS sorting and TRAP-seq libraries were made using SMART-Seq V4 + NexteraXT Library Preparation. All libraries were sequenced using illumina Illumina NovaSeq 6000 with 40M paired end reads (2x150bp).

treatment_protocol: Drosophila progeny were collected and anesthetized. Tissue was collected in basal conditions, at young 5D or aged conditions 34D. For AB conditions, flies were collected after 6D of UAS-AB expression.

value: brain

tag: sample type

value: IP


title: TRAP.RepoGal4.ime4RNAi.34D.IP.e29.Rep4 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.ime4RNAi.34D.IP.e29.Rep1 [experiment 29]

description: experiment 29


title: 20160817.B-C1_150

description:
fluidigm C1
MF028_BL.csv


title: Yeast SIR4 deletion

type: RNA

city: Fukui-city

first: Takahito

last: Ayano

state: Fukui

address: 3-9-1, Bunkyo

department: Graduate school engineering

institute: University of Fukui

hyb_protocol: Following fragmentation, 7.5μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G System.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using default analysis settings.

label: biotin

organism: Saccharomyces cerevisiae

source_name: SIR4 deleted yeast strain

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (GeneChip®  3’ IVT Express Kit user Manual, 2010, Affymetrix).

growth_protocol: Yeast cells were grown at 30ºC in 5ml YPD until exponential phase (optimal density of 0.7).

extract_protocol: Total RNA was extracted by acid phenol-chloroform extraction.

treatment_protocol: Deletion strains were constructed by homologous recombination utilizing a KanMX gene.

tag: tag

value: SIR4 deletion


title: Yeast SIR3 deletion

source_name: SIR3 deleted yeast strain

value: SIR3 deletion


title: 20160817.B-C1_161

description:
fluidigm C1
MF028_BL.csv

tag: tissue


title: TRAP.RepoGal4.ime4RNAi.34D.Input.e29.Rep4 [experiment 29]

description: experiment 29

value: Input


title: Yeast SIR2 deletion

source_name: SIR2 deleted yeast strain

value: SIR2 deletion


title: TRAP.RepoGal4.ime4RNAi.34D.Input.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_149

description:
fluidigm C1
MF028_BL.csv

tag: patient diagnosis


title: Yeast BY4742 Wt

source_name: Wild type yeast strain

value: Wild type


title: TRAP.RepoGal4.ime4RNAi.34D.IP.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_152

description:
fluidigm C1
MF028_BL.csv

tag: cell type


title: 20160817.B-C1_148

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_146

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_159

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.ime4RNAi.34D.Input.e29.Rep2 [experiment 29]

description: experiment 29


title: 20160817.B-C1_144

description:
fluidigm C1
MF028_BL.csv


title: 231 Azeliragon 2uM 72h a


title: 20160817.B-C1_147

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_143

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_141

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.ime4RNAi.5D.IP.e29.Rep1 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.ime4RNAi.5D.Input.e29.Rep4 [experiment 29]

description: experiment 29


title: 20160817.B-C1_140

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_139

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_138

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.ime4RNAi.5D.IP.e29.Rep2 [experiment 29]

description: experiment 29


title: 20160817.B-C1_137

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.ime4RNAi.5D.Input.e29.Rep2 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.ime4RNAi.5D.Input.e29.Rep1 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.ime4RNAi.5D.Input.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_136

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.34D.IP.e29.Rep3 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.mcherryRNAi.34D.IP.e29.Rep4 [experiment 29]

description: experiment 29


title: 20160817.B-C1_135

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.34D.IP.e29.Rep2 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.mcherryRNAi.34D.IP.e29.Rep1 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.ime4RNAi.5D.IP.e29.Rep3 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.ime4RNAi.34D.Input.e29.Rep1 [experiment 29]

description: experiment 29


title: 20160817.B-C1_134

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.34D.Input.e29.Rep4 [experiment 29]

description: experiment 29


title: 20160817.B-C1_131

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.34D.Input.e29.Rep2 [experiment 29]

description: experiment 29


title: 20160817.B-C1_129

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.34D.Input.e29.Rep1 [experiment 29]

description: experiment 29


title: 20160817.B-C1_145

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_130

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_133

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.5D.IP.e29.Rep4 [experiment 29]

description: experiment 29


title: 20160817.B-C1_127

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_126

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.5D.IP.e29.Rep2 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.mcherryRNAi.34D.Input.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_125

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.5D.IP.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_132

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_123

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_122

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.5D.IP.e29.Rep1 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.mcherryRNAi.5D.Input.e29.Rep4 [experiment 29]

description: experiment 29


title: 20160817.B-C1_121

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.5D.Input.e29.Rep3 [experiment 29]

description: experiment 29


title: TRAP.RepoGal4.mcherryRNAi.5D.Input.e29.Rep2 [experiment 29]

description: experiment 29


title: 20160817.B-C1_124

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_120

description:
fluidigm C1
MF028_BL.csv


title: TRAP.ElavGal4.ime4RNAi.34D.IP.e29.Rep4 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.ime4RNAi.34D.IP.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_118

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_119

description:
fluidigm C1
MF028_BL.csv


title: TRAP.ElavGal4.ime4RNAi.34D.IP.e29.Rep1 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.ime4RNAi.34D.Input.e29.Rep4 [experiment 29]

description: experiment 29


title: 20160817.B-C1_116

description:
fluidigm C1
MF028_BL.csv


title: TRAP.ElavGal4.ime4RNAi.34D.Input.e29.Rep2 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.ime4RNAi.34D.Input.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_113

description:
fluidigm C1
MF028_BL.csv


title: TRAP.ElavGal4.ime4RNAi.34D.Input.e29.Rep1 [experiment 29]

description: experiment 29


title: 20160817.B-C1_111

description:
fluidigm C1
MF028_BL.csv


title: TRAP.ElavGal4.ime4RNAi.5D.IP.e29.Rep4 [experiment 29]

description: experiment 29


title: 20160817.B-C1_108

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_106

description:
fluidigm C1
MF028_BL.csv


title: TRAP.ElavGal4.ime4RNAi.5D.IP.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_105

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_104

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_102

description:
fluidigm C1
MF028_BL.csv


title: TRAP.RepoGal4.mcherryRNAi.5D.Input.e29.Rep1 [experiment 29]

description: experiment 29


title: 20160817.B-C1_101

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_96

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_117

description:
fluidigm C1
MF028_BL.csv


title: TRAP.ElavGal4.ime4RNAi.5D.Input.e29.Rep2 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.mcherryRNAi.34D.IP.e29.Rep4 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.ime4RNAi.5D.Input.e29.Rep1 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.ime4RNAi.5D.Input.e29.Rep4 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.ime4RNAi.5D.IP.e29.Rep2 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.ime4RNAi.5D.IP.e29.Rep1 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.ime4RNAi.5D.Input.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_115

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_100

description:
fluidigm C1
MF028_BL.csv


title: 20160817.B-C1_114

description:
fluidigm C1
MF028_BL.csv


title: TRAP.ElavGal4.mcherryRNAi.34D.IP.e29.Rep3 [experiment 29]

description: experiment 29


title: 20160817.B-C1_95

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_94

description:
fluidigm C1
MF028_BE.csv


title: Input rep1, B104-1-1

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to mm10 reference genome by Bowtie2.
PCR duplicates were removed by Samtools.
Peaks were called by MACS2.
Assembly: mm10
Supplementary files format and content: ChIP-seq narrowPeak files

extract_protocol:
Genomic DNA of NIH/3T3 cells, B104-1-1 cells were all prepared using Monarch Genomic DNA Purification Kit (NEB, T3010S). All the DNA samples were harshly treated with RNase A (NEB, T3018L) again prior to library construction to get rid of any RNA contaminants.
The ChIP-seq grade antibody H3K4me3 (1 µg/ µl) was provided by the iDeal ChIP-seq Kit for Histones, while H3K9me3 (D4W1U, Rabbit mAb, #13969, 1:50 dilution) and H3K27me3 (C36B11, Rabbit mAb, #9733, 1:50 dilution) antibodies were purchased separately at Cell Signaling. The immunoprecipitated DNA was further proceeded with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S) for library preparation, followed by sequencing at NextSeq 2000 as paired-end 75 bp mode.


title: Input rep2, NIH/3T3


title: TRAP.ElavGal4.mcherryRNAi.34D.IP.e29.Rep2 [experiment 29]

description: experiment 29


title: H3K4me3 IP rep2, B104-1-1

tag: antibody


title: TRAP.ElavGal4.mcherryRNAi.34D.Input.e29.Rep4 [experiment 29]

description: experiment 29


title: H3K4me3 IP rep1, B104-1-1


title: TRAP.ElavGal4.ime4RNAi.34D.IP.e29.Rep2 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.mcherryRNAi.34D.Input.e29.Rep3 [experiment 29]

description: experiment 29


title: H3K9me3 IP rep2, B104-1-1


title: 20160817.B-C1_90

description:
fluidigm C1
MF028_BE.csv


title: TRAP.ElavGal4.mcherryRNAi.34D.Input.e29.Rep2 [experiment 29]

description: experiment 29


title: H3K9me3 IP rep2, NIH/3T3


title: H3K9me3 IP rep1, B104-1-1


title: H3K27me3 IP rep1, B104-1-1


title: TRAP.ElavGal4.mcherryRNAi.34D.Input.e29.Rep1 [experiment 29]

description: experiment 29


title: TRAP.ElavGal4.mcherryRNAi.5D.IP.e29.Rep3 [experiment 29]

description: experiment 29


title: Input rep2, B104-1-1


title: 20160817.B-C1_89

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_9

description:
fluidigm C1
MF028_BE.csv


title: H3K4me3 IP rep2, NIH/3T3


title: H3K27me3 IP rep2, B104-1-1


title: 20160817.B-C1_92

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_85

description:
fluidigm C1
MF028_BE.csv


title: H3K27me3 IP rep2, NIH/3T3


title: Input rep1, NIH/3T3


title: TRAP.ElavGal4.mcherryRNAi.5D.IP.e29.Rep2 [experiment 29]

description: experiment 29


title: 20160817.B-C1_88

description:
fluidigm C1
MF028_BE.csv


title: TRAP.ElavGal4.mcherryRNAi.34D.IP.e29.Rep1 [experiment 29]

description: experiment 29


title: H3K27me3 IP rep1, NIH/3T3


title: Ear skin, Spleen, Blood; RNA,HTO

city: Wuerzburg

first: Georg

last: Gasteiger

address: Versbacher Strasse 9

department: Institute of Systems Immunology

country: Germany

institute: University Wuerzburg

description:
Hashtag-derived oligonucleotide (HTO)
barcodes.tsv.gz
matrix.mtx.gz
features.tsv.gz

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Lymphocytes

extract_protocol:
Skin:Liberase (0,245mg/ml) +DNAse (20ng/ml) in DMEM for 90' @37C, Spleen: Collagenase D (0,5mg/ml) + DNAse (20ng/ml) in DMEM for 30' @ 37C, then red blood cell lysis buffer for 2'@RT
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Lymphocytes

value: Ear skin, Spleen, Blood

tag: library type

value: HTO

tag: antibodies/tags

value: Hashtag2_TotalA / Memory skin rechallenge; Hashtag3_TotalA / Memory control skin rechallenge; Hashtag4_TotalA / Naive Challenge skin; Hashtag5_TotalA / Naive control spleen;  Hashtag6_TotalA / Naive control blood

tag: strain

value: 12-22 weeks old

tag: Sex

value: male


title: TRAP.ElavGal4.mcherryRNAi.5D.Input.e29.Rep4 [experiment 29]

description: experiment 29

tag: genotype

tag: treatment


title: TRAP.ElavGal4.mcherryRNAi.5D.IP.e29.Rep1 [experiment 29]

description: experiment 29


title: Ear skin, Spleen, Blood; RNA,ADT

description:
Antibody-derived oligonucleotide (ADT)
barcodes.tsv.gz
matrix.mtx.gz
features.tsv.gz

value: ADT

value: CD45_TotalA, CD45.1_TotalA, CD45.2_TotalA, CD11b_TotalACD25_TotalA, CD27_TotalA, CD49a_TotalA, CD49b_TotalA, CD62L_TotalA, CD69_TotalA, CD127_TotalA, CD160_TotalA, CD200r_TotalA, CX3CR1_TotalA, Cxcr6_TotalA, KLRG1_TotalA, NK1.1_TotalA, NKp46_TotalA

tag: age


title: 20160817.B-C1_91

description:
fluidigm C1
MF028_BE.csv

value: blood

value: cutaneous T-cell lymphoma

value: T cells


title: Ear skin, Spleen, Blood; RNA,GEX

description:
barcodes.tsv.gz
matrix.mtx.gz
features.tsv.gz

value: GEX


title: H3K4me3 IP rep1, NIH/3T3

value: IP


title: Liver, ORX_IH, mice 5

city: Quebec

first: Vincent

last: Joseph

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Université Laval / IUCPQ

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
18Lv_ORX-IHNS.1959

data_processing:
Base calling was performed with RTA v3. The bcl2fastq2 v2.20 program was then used to demultiplex samples and generate fastq reads
Reads were trimmed using fastp v0.23.2. Quality check was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.9 and MultiQC v1.12
The quantification was performed with Kallisto v0.46.1
Raw reads data table was imported in Qlucore and normalized using the trimmed mean of M-values (TMM)
The 9Lv sham sample did not pass QC so is not represented in the processed data files.
Assembly: GRCm39
Supplementary files format and content: csv data file includes raw counts for each samples
Supplementary files format and content: csv data file inclucudes TMM normalized counts for each sample

source_name: Liver

extract_protocol:
total RNA was extraction from frozen liver samples using EasyPure® RNA Kit, Libraries were generated from 250 ng of total RNA
mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs.

value: Liver

value: ORX-IH


title: H3K9me3 IP rep1, NIH/3T3


title: TRAP.ElavGal4.mcherryRNAi.5D.Input.e29.Rep3 [experiment 29]

description: experiment 29

value: brain

value: Input


title: Liver, ORX_IH, mice 4

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
8Lv_ORX_IHNS.1959


title: 20160817.B-C1_80

description:
fluidigm C1
MF028_BE.csv


title: TRAP.ElavGal4.mcherryRNAi.5D.Input.e29.Rep2 [experiment 29]

description: experiment 29


title: Liver, ORX_IH, mice 2

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
6Lv_ORX_IHNS.1959


title: 20160817.B-C1_78

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_75

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_76

description:
fluidigm C1
MF028_BE.csv


title: TRAP.ElavGal4.mcherryRNAi.5D.Input.e29.Rep1 [experiment 29]

description: experiment 29


title: Liver, ORX_IH, mice 1

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
5Lv_ORX_IHNS.1959


title: RepoGal4.ime4RNAi.34D.GFP+.e27.Rep3 [experiment 27]

description: experiment 27

value: Repo GFP+ cells (500)


title: Liver, ORX_Nx, mice 3

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
3Lv_ORX_NxNS.1959

value: ORX-Nx


title: Liver, ORX_Nx, mice 4

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
4Lv_ORX_NxNS.1959


title: Liver, ORX_Nx, mice 1

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
1Lv_ORX_NxNS.1959


title: Liver, ORX_Nx, mice 5

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
17Lv_ORX-NXNS.1959


title: RepoGal4.ime4RNAi.34D.GFP-.e27.Rep3 [experiment 27]

description: experiment 27

value: Repo GFP- cells (500)


title: 20160817.B-C1_83

description:
fluidigm C1
MF028_BE.csv


title: Liver, Sham_IH, mice 5

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
20_Lv_Sham_IHNS.1959

value: Sham-IH


title: 20160817.B-C1_74

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_72

description:
fluidigm C1
MF028_BE.csv


title: Liver, Sham_IH, mice 3

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
15Lv_Sham_IHNS.1959


title: Liver, Sham_IH, mice 4

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
16Lv_Sham_IHNS.1959


title: Liver, Sham_IH, mice 2

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
14Lv_Sham_IHNS.1959


title: Liver, ORX_IH, mice 3

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
7Lv_ORX_IHNS.1959


title: 20160817.B-C1_71

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_82

description:
fluidigm C1
MF028_BE.csv


title: Liver, Sham_IH, mice 1

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
13Lv_Sham_IHNS.1959


title: Liver, ORX_Nx, mice 2

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
2Lv_ORX_NxNS.1959


title: Liver, Sham_Nx, mice 5

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
19Lv_Sham_NxNS.1959

value: Sham-Nx


title: 20160817.B-C1_70

description:
fluidigm C1
MF028_BE.csv


title: Liver, Sham_Nx, mice 3

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
11Lv_Sham_NxNS.1959


title: Liver, Sham_Nx, mice 4

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
12Lv_Sham_NxLNS.1959


title: RepoGal4.ime4RNAi.34D.GFP-.e27.Rep1 [experiment 27]

description: experiment 27


title: 20160817.B-C1_7

description:
fluidigm C1
MF028_BE.csv


title: RepoGal4.ime4RNAi.34D.GFP+.e27.Rep1 [experiment 27]

description: experiment 27


title: RepoGal4.mcherryRNAi.34D.GFP-.e27.Rep3 [experiment 27]

description: experiment 27


title: 20160817.B-C1_69

description:
fluidigm C1
MF028_BE.csv


title: Lymphocytes, ear-skin, spleen, salivary gland (GEX)

description: polyA RNA

data_processing:
Single cell sequencing data analysis. Data for the cDNA library fraction were demultiplexed using Cell Ranger software and aligned to mouse mm10 reference genome. The resulting gene expression matrix were analyzed using Seurat standard workflow. After log transformation with the command LogNormalize and scaling with ScaleData, basic QC has been performed. Viable cells have been selected by filtering for cells with UMI count superior at 1,000 and a percentage of UMI mapped to mitochondrial genes inferior to 8. Cells were then assigned to appropriate samples by demultiplexing the hashtags antibodies. To demultiplex hashtags, for each cell HTODemux function in Seurat package was used as described. Cross-sample doublet cell detection was performed based on hashtag signal. Only cells that were classified as ‘singlet’ were retained and used for downstream analysis. Variable genes were identified by the function VariableFeatures with an n value of 2,000. Dimensions of the data were reduced first using a principal component analysis (PCA) on variable genes, and then a uniform manifold approximation and projection (UMAP) on the 15 first PC dimensions. Cells were also assigned to clusters with the functions FindNeighbors on the same 15 PC dimensions and then FindClusters with a resolution of 0.5. Cluster specific gene signatures have been analyzed with the function FindAllMarkers from Seurat with arguments: only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25.
Analysis of human skin single cell mRNA sequencing data. Data published by Alkon et al. (GSE180885) were downloaded and transcriptomes obtained from non-lesional skin sample were subset and analyzed using Seurat standard workflow (see above,).
Score calculation with Seurat. Scores were calculated using the Seurat function AddModuleScore with default settings. Unbiased core Trm and core circulating T cells signature were derived from the published data of Milner et al. dataset (Milner et al., 2020)(see gene list in supp table). Scores for human skin NK cells were calculated… see supp table.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: ear-skin, spleen, salivary gland

extract_protocol:
Spleen: Collagenase D (0,5mg/ml) + DNAse (20ng/ml) in DMEM for 30' @ 37C, then red blood cell lysis buffer for 2'@RT, Skin:Liberase (0,245mg/ml) +DNAse (20ng/ml) in DMEM for 90' @37C, Salivary gland: Collagenase D (1mg/m) + DNAse (20ng/ml) + CaCl2 (1:100) in 2% FCS DMEM  for 30'/120rpm@37C; after digestion, lymphocytes were enriched using  Percoll-based density gradient
scRNA-seq, cell hashing and CITE-seq. ILC1s and NK cells were sorted as individual, hash-tagged populations before pooling into one reaction. Before sorting, cells were labeled with oligonucleotide-tagged antibodies for cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq). Immediately after sorting, Library was performed according to the manufacturer’s instructions. Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. It was then sequenced on a NovaSeq 6000 S2 flow cell with 100 cycles (28-10-10-90).
CITE-seq

value: ear-skin, spleen, salivary gland

value: Lymphocytes

value: 8-12 weeks old

value: male


title: Lymphocytes, ear-skin, spleen, salivary gland (HTO)

description: Hashtags

value: skin day 8 = #A301; skin day 25 = #A302; salivary gland = #A303; spleen day 8 = #A304, spleen day 25 = #A305


title: RepoGal4.ime4RNAi.34D.GFP+.e27.Rep2 [experiment 27]

description: experiment 27


title: Liver, Sham_Nx, mice 1

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
9Lv_Sham_NxNS.1959


title: 20160817.B-C1_68

description:
fluidigm C1
MF028_BE.csv

value: blood

value: cutaneous T-cell lymphoma

value: T cells


title: 20160817.B-C1_67

description:
fluidigm C1
MF028_BE.csv


title: B cell line rep2 F

data_processing:
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to hg19 or mm9 reference genome by Bowtie2.
PCR duplicates were removed by Samtools.
Mutation calling was performed by VarScan.
Assembly: hg19/mm9
Supplementary files format and content: text files include 6mA modification levels

source_name: B cell line

extract_protocol:
Mitochondrial DNA of HepG2 cells, mouse brain and mouse liver were prepared using Mitochondrial DNA Purification Kit (Abcam, ab288088). NIH/3T3 and B104-1-1 cells were both purchased from ATCC (CRL-1658; CRL-1887), and cultured in DMEM (Gibco, 11965092) with 10% FBS (Gibco, 26140079). NIH/3T3 from ECACC were purchased from Sigma (93061524-1VL), but only used in sex determination. Genomic DNA of NIH/3T3 cells, B104-1-1 cells, 4-month-old male C57BL/6J mouse whole testis, 4-month-old male C57BL/6J mouse whole brain, and 2.5-month-old female C57BL/6J mouse whole brain were all prepared using Monarch Genomic DNA Purification Kit (NEB, T3010S). All the DNA samples were harshly treated with RNase A (NEB, T3018L) again prior to libraries construction to get rid of any RNA contaminants.
For mammalian gDNAs, antibody enrichment was performed prior to libraries construction: 50~100 μg RNA-free DNA was diluted by TE buffer (Invitrogen, AM9849) with 0.1 M NaOH and sonicated to 100~300 nt length. The fragmentated DNA was immunoprecipitated using 25 μg anti-6mA antibody (Sigma, ABE572 or Abcam, ab151230) by gently rotating at 4℃ overnight. Pierce Protein A Magnetic Beads (Thermo Scientific, 88845) were washed and used to pulldown antigen-antibody complex. Subsequentially, the beads were treated by proteinase K (NEB, P8111S) and the 6mA-enriched DNA were then purified with DNA Clean & Concentrator Kit-25 (Zymo research, D4033). The fragmented DNA was mixed with 15% (mass percentage) spike-in probes (Supplementary Table 1) and then spited into three in the proportion of 3:4:1, each for mutation group, demethylation control and high-fidelity control. For the demethylation control, DNA fragments was denatured and then incubated at 37 ℃ for 4 hours in a 300 μL reaction containing 50 mM HEPE 7.0, 60 mM KCl, 75 μM ammonium iron (II) sulfate hexahydrate, 2 mM L-asorbic acid, 300 μM α-ketoglutarate and 2.4 μM FTO purified protein. The demethylation reaction was then treated with proteinase K (NEB, P8111S) and cleaned up by Oligo Clean & Concentrator Kits (Zymo research, D4061).
OTHER: DRM-Seq

value: WT

value: Mutation + demethylation group

value: B cell line


title: B cell line rep2 B

value: Mutation group


title: RepoGal4.mcherryRNAi.34D.GFP+.e27.Rep3 [experiment 27]

description: experiment 27

value: brain

value: Repo GFP+ cells (500)


title: RepoGal4.mcherryRNAi.34D.GFP-.e27.Rep2 [experiment 27]

description: experiment 27

value: Repo GFP- cells (500)


title: 20160817.B-C1_66

description:
fluidigm C1
MF028_BE.csv


title: B cell line rep1 H

value: Control group


title: RepoGal4.mcherryRNAi.34D.GFP-.e27.Rep1 [experiment 27]

description: experiment 27


title: RepoGal4.mcherryRNAi.34D.GFP+.e27.Rep2 [experiment 27]

description: experiment 27


title: B cell line rep1 F


title: 20160817.B-C1_65

description:
fluidigm C1
MF028_BE.csv


title: B cell line rep1 B


title: Liver, Sham_Nx, mice 2

description:
raw_counts_liver_All.csv
Liver_All TMM.csv
10Lv_Sham_NxNS.1959

value: Liver

value: Sham-Nx


title: RepoGal4.mcherryRNAi.34D.GFP+.e27.Rep1 [experiment 27]

description: experiment 27


title: 20160817.B-C1_64

description:
fluidigm C1
MF028_BE.csv


title: N cell line rep2 F

source_name: N cell line

value: N cell line


title: N cell line rep2 B


title: B cell line rep2 H


title: Lymphocytes, ear-skin, spleen, salivary gland (ADT)

description: Antibody-tags

value: ear-skin, spleen, salivary gland

value: Lymphocytes

value: 8-12 weeks old

value: skin day 8 = CD45+; skin day 20 = CD45.1+


title: RepoGal4.ime4RNAi.5D.GFP-.e27.Rep3 [experiment 27]

description: experiment 27


title: N cell line rep2 H


title: RepoGal4.ime4RNAi.5D.GFP+.e27.Rep3 [experiment 27]

description: experiment 27


title: 20160817.B-C1_63

description:
fluidigm C1
MF028_BE.csv

value: blood

value: cutaneous T-cell lymphoma


title: 20160817.B-C1_61

description:
fluidigm C1
MF028_BE.csv

value: T cells


title: 20160817.B-C1_62

description:
fluidigm C1
MF028_BE.csv


title: RepoGal4.mcherryRNAi.5D.GFP-.e27.Rep3 [experiment 27]

description: experiment 27


title: N cell line rep1 H

value: WT


title: Mouse testis rep2 H

source_name: testis

value: testis


title: N cell line rep1 B

value: Mutation group


title: RepoGal4.mcherryRNAi.5D.GFP+.e27.Rep3 [experiment 27]

description: experiment 27

value: brain


title: Mouse testis rep1 H


title: 20160817.B-C1_60

description:
fluidigm C1
MF028_BE.csv


title: N cell line rep1 F

value: Mutation + demethylation group


title: Mouse testis rep1 F


title: RepoGal4.mcherryRNAi.5D.GFP-.e27.Rep2 [experiment 27]

description: experiment 27

value: Repo GFP- cells (500)


title: 20160817.B-C1_6

description:
fluidigm C1
MF028_BE.csv


title: Mouse testis rep2 B


title: RepoGal4.mcherryRNAi.5D.GFP+.e27.Rep2 [experiment 27]

description: experiment 27

value: Repo GFP+ cells (500)


title: 20160817.B-C1_58

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_47

type: genomic

city: Boston

first: Patrick

middle: T

last: Griffin

state: MA

address: 77 Avenue Louis Pasteur

department: Harvard Medical School, Dept. of Genetics

institute: Patrick Griffin

hyb_protocol: standard protocols

scan_protocol: standard protocols

data_processing:
Raw methylation data were processed by the methylsuite series of packages. Packages used include: methylcheck (v.0.7.9), methylprep (v.1.6.0).
Average Beta

label: Cy3, Cy5

source_name: whole blood

label_protocol: standard protocols

extract_protocol: see: https://doi.org/10.1101/2021.10.25.465725 for detailed extraction protocols

value: male


title: Mouse_Sample_46


title: Mouse testis rep1 B


title: 20160817.B-C1_57

description:
fluidigm C1
MF028_BE.csv

data_processing:
The quality control was done using fastQC (v. 0.11.7) and the adaptors and low quality bases having phred quality score less than 20 were trimmed from the ends of the reads using Trim Galore (v. 0.4.4). The T-cell receptors (TCR) were identified using TraCeR and gene expressions were quantified with Kallisto (v. 0.45.0) for cells with an identified T cell receptor as part of the TraCeR workflow. TraCeR was also used to group the cells with identified TCR into groups of clones of different sizes, which all were required to have at least one TCR monomer in common with the other cells in the same clone. The remaining cells with TCR, sharing no identical TCR monomer with each other, were considered as heterogeneous cells. The gene expression data was normalised using Scater (v. 1.10.1) using CPM (counts per million).
Assembly: GRCh37
Supplementary files format and content: Matrix table with counts for every transcript and every cell

extract_protocol:
Capture and processing of single skin and blood T cells was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/µL onto C1 integrated fluidic circuit chips for 5–10-µm cells. All C1 capture sites were microscopically inspected to identify the sites that contained only a single cell. Empty sites and those with multiple cells were excluded from further analysis. External RNA Controls Consortium spike-in RNAs served as a control. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform. Quality control was performed using FastQC v. 0.11.7 (Babraham Bioinformatics), and the adaptors and low-quality bases with a Phred quality score <20 were trimmed from the ends of the reads using Trim Galore v. 0.4.4 (Babraham Bioinformatics)
Cells were captured and performed using the Fluidigm C1 Autoprep system. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform.


title: RepoGal4.ime4RNAi.5D.GFP-.e27.Rep2 [experiment 27]

description: experiment 27


title: Mouse_Sample_48


title: Mouse_Sample_44


title: 20160817.B-C1_52

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_43


title: Mouse_Sample_45


title: RepoGal4.ime4RNAi.5D.GFP+.e27.Rep2 [experiment 27]

description: experiment 27


title: RepoGal4.ime4RNAi.5D.GFP+.e27.Rep1 [experiment 27]

description: experiment 27


title: 20160817.B-C1_5

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_41


title: Mouse_Sample_40


title: RepoGal4.ime4RNAi.5D.GFP-.e27.Rep1 [experiment 27]

description: experiment 27


title: Mouse_Sample_39


title: Mouse_Sample_38


title: 20160817.B-C1_49

description:
fluidigm C1
MF028_BE.csv


title: RepoGal4.mcherryRNAi.5D.GFP-.e27.Rep1 [experiment 27]

description: experiment 27


title: 20160817.B-C1_48

description:
fluidigm C1
MF028_BE.csv


title: RepoGal4.mcherryRNAi.5D.GFP+.e27.Rep1 [experiment 27]

description: experiment 27


title: 20160817.B-C1_47

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_35


title: Mouse_Sample_37


title: Mouse_Sample_34


title: ElavGal4.ime4RNAi.34D.GFP+.e25.Rep3 [experiment 25]

description: experiment 25

value: Elav GFP+ cells (500)


title: 20160817.B-C1_44

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_32


title: 20160817.B-C1_43

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4.ime4RNAi.5D.GFP+.e25.Rep3 [experiment 25]

description: experiment 25


title: Mouse_Sample_42


title: Mouse_Sample_33


title: Mouse_Sample_31


title: Mouse_Sample_30


title: Mouse_Sample_28


title: ElavGal4.mcherryRNAi.34D.GFP+.e25.Rep3 [experiment 25]

description: experiment 25


title: ElavGal4.mcherryRNAi.5D.GFP+.e25.Rep3 [experiment 25]

description: experiment 25


title: Mouse_Sample_27


title: Mouse_Sample_29


title: 20160817.B-C1_40

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4.ime4RNAi.34D.GFP+.e25.Rep2 [experiment 25]

description: experiment 25


title: Mouse_Sample_26


title: Mouse_Sample_36


title: Mouse_Sample_25


title: 20160817.B-C1_4

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4.mcherryRNAi.34D.GFP+.e25.Rep2 [experiment 25]

description: experiment 25


title: 20160817.B-C1_39

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_23


title: Mouse_Sample_22


title: Mouse_Sample_20


title: 20160817.B-C1_38

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4.mcherryRNAi.5D.GFP+.e25.Rep1 [experiment 25]

description: experiment 25


title: Mouse_Sample_21


title: ElavGal4.mcherryRNAi.5D.GFP+.e25.Rep2 [experiment 25]

description: experiment 25


title: Mouse_Sample_19


title: Mouse_Sample_18


title: 20160817.B-C1_36

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_37

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4.ime4RNAi.5D.GFP+.e25.Rep2 [experiment 25]

description: experiment 25


title: Mouse_Sample_17


title: ElavGal4.ime4RNAi.34D.GFP+.e25.Rep4 [experiment 25]

description: experiment 25


title: 20160817.B-C1_42

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_15


title: Mouse_Sample_16


title: ElavGal4.ime4RNAi.34D.GFP+.e25.Rep1 [experiment 25]

description: experiment 25


title: Mouse_Sample_14


title: 20160817.B-C1_33

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_24

value: female


title: ElavGal4.mcherryRNAi.34D.GFP+.e25.Rep4 [experiment 25]

description: experiment 25


title: Human_Sample_952

data_processing:
SeSAMe R package was used to obtain beta values and p values from raw data .idat files.
Average Beta


title: Mouse_Sample_13


title: ElavGal4.mcherryRNAi.34D.GFP+.e25.Rep1 [experiment 25]

description: experiment 25


title: Human_Sample_950


title: 20160817.B-C1_32

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_12


title: ElavGal4.ime4RNAi.5D.GFP+.e25.Rep1 [experiment 25]

description: experiment 25


title: 20160817.B-C1_30

description:
fluidigm C1
MF028_BE.csv


title: Human_Sample_945


title: 20160817.B-C1_31

description:
fluidigm C1
MF028_BE.csv


title: Human_Sample_955