title: 12G_M_224


title: 12G_M_223

status: Public on May 19 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


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title: 12F_M_466


title: 12F_M_467


title: 12F_M_463


title: 12F_M_462


title: 12F_M_461


title: 12F_M_460


title: 12F_M_459


title: 12F_M_458


title: 12F_M_457


title: 12F_M_456


title: 12F_M_454


title: 12F_M_453


title: 12F_M_452


title: 12F_M_451


title: OU_269

type: RNA

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University

description: Prospective.Validation

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized overnight at 46C on Affymetrix U133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000.

data_processing: Probe intensities were normalized with Robust Multichip Analysis

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Prospective.Validation with Oligo dT Prime

label_protocol: RNA (50 ng) was subjected to the generation of second-strand combinational DNA (cDNA), and cRNA was amplified with a random primer (WT-Ovation FFPE RNA Amplification System V2; NuGEN, Cincinnati, Ohio). Next, the amplified cRNA was biotinylated and fragmented with the FL-Ovation cDNA Biotin Module V2 (NuGEN).

extract_protocol: Trizol (Invitrogen, Carlsbad, Calif) was used to extract RNA from core-needle tumor biopsy samples that were obtained with the Mammotome.

treatment_protocol: Patients prospectively consented to a research biopsy by vacuum-assisted core-biopsy instrument (Mammotome 8G; HH Ethicon Endosurgery, Johnson and Johnson Company) under ultrasonographic guidance for histologic examination and gene expression analysis prior to any systemic therapy, and to the future assessment of pathologic response

value: greater than 50

tag: ct

tag: cn

value: Positive

tag: er

value: Negative

tag: hg

value: wP-FEC

value: Non-pCR

value: LumA


title: OU_266

description: Prospective.Validation

value: pCR (ypT0/N0)


title: OU_261

description: Prospective.Validation


title: OU_271

description: Prospective.Validation


title: OU_264

description: Prospective.Validation

value: Basal


title: OU_267

description: Prospective.Validation

value: less than or equal to 50

value: LumB


title: 12F_M_450


title: OU_260

description: Prospective.Validation


title: OU_265

description: Prospective.Validation


title: OU_263

description: Prospective.Validation


title: OU_272

description: Prospective.Validation


title: OU_268

description: Prospective.Validation


title: OU_270

description: Prospective.Validation


title: OU_257

description: Prospective.Validation


title: OU_262

description: Prospective.Validation


title: OU_256

description: Prospective.Validation


title: OU_249

description: Prospective.Validation

value: wP-FEC+Trastuzumab

value: Trastuzumab


title: 12F_M_455


title: OU_258

description: Prospective.Validation


title: OU_259

description: Prospective.Validation


title: OU_253

description: Prospective.Validation


title: OU_251

description: Prospective.Validation


title: OU_254

description: Prospective.Validation


title: OU_250

description: Prospective.Validation


title: 12F_M_446


title: 12F_M_445


title: 12F_M_447


title: 12F_M_444


title: 12F_M_449


title: 12F_M_443


title: 12F_M_442


title: 12F_M_441


title: 12F_M_448


title: 12F_M_440


title: 12F_M_439


title: 12F_M_438


title: 12F_M_436


title: 12F_M_437


title: 12F_M_435


title: OU_248

description: Prospective.Validation


title: OU_242

description: Prospective.Validation


title: OU_244

description: Prospective.Validation


title: OU_245

description: Prospective.Validation


title: OU_240

description: Prospective.Validation


title: 12F_M_433


title: 12F_M_432


title: 12F_M_434


title: OU_237

description: Prospective.Validation


title: OU_239

description: Prospective.Validation


title: OU_238

description: Prospective.Validation


title: OU_236

description: Prospective.Validation


title: 12F_M_431


title: OU_232

description: Prospective.Validation


title: OU_230

description: Prospective.Validation


title: OU_231

description: Prospective.Validation


title: OU_234

description: Prospective.Validation


title: OU_229

description: Prospective.Validation


title: OU_235

description: Prospective.Validation


title: 12F_M_429


title: 12F_M_428


title: OU_233

description: Prospective.Validation


title: 12F_M_427


title: 12F_M_426


title: 12F_M_425


title: 12F_M_430


title: 12F_M_424


title: 12F_M_423


title: OU_228

description: Prospective.Validation


title: 12F_M_422


title: 12F_M_420


title: 12F_M_421


title: 12F_M_416


title: 12F_M_418


title: 12F_M_417


title: OU_227

description: Prospective.Validation


title: OU_224

description: Prospective.Validation


title: 12F_M_415


title: 12F_M_414


title: OU_225

description: Prospective.Validation


title: OU_226

description: Prospective.Validation


title: OU_217

description: Prospective.Validation


title: OU_221

description: Prospective.Validation


title: 12F_M_413


title: OU_219

description: Prospective.Validation


title: OU_222

description: Prospective.Validation


title: OU_218

description: Prospective.Validation


title: OU_220

description: Prospective.Validation


title: OU_223

description: Prospective.Validation


title: 12F_M_412


title: OU_215

description: Prospective.Validation


title: OU_216

description: Prospective.Validation


title: OU_213

description: Prospective.Validation


title: OU_212

description: Prospective.Validation


title: 12F_M_411


title: OU_214

description: Prospective.Validation


title: OU_208

description: Prospective.Validation


title: 12F_M_410


title: OU_211

description: Prospective.Validation


title: OU_209

description: Prospective.Validation


title: 12F_M_409


title: 12F_M_408


title: 12F_M_407


title: 12F_M_404


title: 12F_M_402


title: 12F_M_403


title: 12F_M_401


title: 12F_M_400


title: 12F_M_399


title: 12F_M_406


title: 12F_M_397


title: OU_204

description: Prospective.Validation

source_name: Prospective.Validation with random primer


title: 12F_M_396


title: OU_207

description: Prospective.Validation


title: OU_201

description: Prospective.Validation


title: 12F_M_395


title: OU_200

description: Prospective.Validation


title: OU_202

description: Prospective.Validation


title: OU_198

description: Prospective.Validation


title: OU_203

description: Prospective.Validation


title: OU_206

description: Prospective.Validation


title: OU_196

description: Prospective.Validation


title: 12F_M_393


title: OU_205

description: Prospective.Validation


title: 12F_M_394


title: OU_197

description: Prospective.Validation


title: OU_199

description: Prospective.Validation


title: 12F_M_398


title: OU_195

description: Prospective.Validation


title: OU_194

description: Prospective.Validation


title: OU_193

description: Prospective.Validation


title: OU_191

description: Prospective.Validation


title: 12F_M_391


title: 12F_M_390


title: 12F_M_392


title: 12F_M_388


title: 12F_M_387


title: 12F_M_389


title: 12F_M_386


title: 12F_M_385


title: 12F_M_384


title: OU_192

description: Prospective.Validation


title: 12F_M_255


title: 12F_M_254


title: 12F_M_253


title: 12F_M_252


title: 12F_M_251


title: OU_189

description: Prospective.Validation


title: OU_187

description: Prospective.Validation


title: OU_188

description: Prospective.Validation


title: 12F_M_250


title: OU_190

description: Prospective.Validation


title: OU_186

description: Prospective.Validation


title: 12F_M_249


title: OU_184

description: Prospective.Validation


title: OU_182

description: Prospective.Validation


title: 12F_M_248


title: OU_179

description: Prospective.Validation


title: 12F_M_246


title: OU_185

description: Prospective.Validation


title: OU_181

description: Prospective.Validation


title: 12F_M_244


title: OU_178

description: Prospective.Validation


title: X9.5_cKO_AF_M2

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut Street

institute: Thomas Jefferson University

description: Total RNA from Sox9cKO AF tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.75

hyb_protocol: Affymetrix Gene chips, Mouse Clariom S, were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix).

data_processing: Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the experiment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05. Inclusion cutoffs were defined at a 1.75-fold change and p-value < 0.05.

source_name: AF cKO

label_protocol: Single-stranded cDNA was generated, then fragmented and biotin-labeled using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: Sox9CTR and Sox9cKO mice were aged to 3 months, and Sox9cKO animals were injected with tamoxifen for two consecutive days to activate an Acan-CreERT2 driver. All tissues were collected 5 days following the initial injection. Genotypes were confirmed by PCR.

extract_protocol: NP and AF tissues were micro-dissected from caudal and lumbar intervertebral discs of 4 Sox9 control and 4 Sox9 conditional knock-out animals and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971) and RNA was extracted from tissue lysates using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

tag: genotype

value: Sox9 conditional knock-out mice (Sox9cKO) (AcanCreERT2Sox9fl/fl)

tag: tissue

value: annulus fibrosus (AF)

tag: Sex

value: female


title: X9.5_cKO_AF_M4


title: OU_180

description: Prospective.Validation


title: X9.5_cKO_AF_M3


title: 12F_M_242


title: 12F_M_241


title: OU_176

description: Prospective.Validation


title: OU_175

description: Prospective.Validation


title: OU_177

description: Prospective.Validation


title: X9.5_CTR_AF_C3

description: Total RNA from Sox9CTR AF tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.75

source_name: AF CTR

value: Sox9 control (Sox9CTR) (Sox9fl/fl)


title: X9.5_cKO_AF_M1


title: 12F_M_239


title: 12F_M_240


title: 12F_M_245


title: 12F_M_243


title: 12F_M_238


title: 12F_M_237


title: 12F_M_236


title: X9.5_CTR_AF_C4


title: 12F_M_235


title: 12F_M_233


title: 12F_M_234


title: 12F_M_232


title: 12F_M_229


title: 12F_M_230


title: X9.5_CTR_AF_C1


title: X9.5_cKO_NP_M3

description: Total RNA from Sox9cKO NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.75

source_name: NP cKO

value: nucleus pulposus (NP)


title: 12F_M_227


title: 12F_M_228


title: OU_172

description: Prospective.Validation

value: greater than 50


title: 12F_M_226


title: X9.5_cKO_NP_M4


title: 12F_M_225


title: X9.5_CTR_AF_C2


title: X9.5_cKO_NP_M2


title: OU_171

description: Prospective.Validation

value: Positive


title: OU_174

description: Prospective.Validation

value: Negative


title: OU_173

description: Prospective.Validation

value: wP-FEC


title: X9.5_CTR_NP_C2

description: Total RNA from Sox9CTR NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.75

source_name: NP CTR


title: 12F_M_224


title: OU_169

description: Prospective.Validation

value: Non-pCR


title: OU_170

description: Prospective.Validation

value: LumA


title: OU_167

description: Prospective.Validation


title: OU_168

description: Prospective.Validation


title: 12F_M_223


title: 12F_M_231


title: 12F_M_222


title: 12F_M_221


title: Lung, ABT-263 Infected Day 7, rep4

city: BESANCON

first: Fabrice

last: Bouilloux

address: 18 rue Alain Savary

country: France

institute: BIOMNIGENE

library_source: transcriptomic

data_processing:
The sequencing reads of each sample were trimmed and quality filtered using Trimmomatic (v0.39) with the following options: ILLUMINACLIP:3:30:10 and MAXINFO:0.5
Cleaned reads were then processed using Salmon (v1.9.0) with default parameters
Gene annotations were computed using tximport (v1.28.0)
DESeq2 (v1.12.3) was used to analyze the differential gene expression between the experimental groups.
Assembly: Mesocricetus auratus (MesAur1.0 (GCA_000349665.1)
Supplementary files format and content: RNA_counts_all.xlsx: this is an excel file that contains the resume of salmon’s estimate of the number of reads mapping to each transcript for each sample (column NumReads of quant.sh files).
Supplementary files format and content: Vh_vs_ABT-263_Fold_change.xlsx: this is an excel file that contains the results of DESeq2 analysis comparing the expression of genes between the vehicle and the ABT-263 groups.

organism: Mesocricetus auratus

source_name: Lung

extract_protocol:
Total RNAs in the tissue homogenate were extracted using the NucleoSpin RNA kit.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA library prep for Illumina® (NEB, Ipswich, USA) following manufacturer's protocols.

treatment_protocol: Animals were administered by oral gavage (200 microliters) with ABT-263 (65 mg/kg) or vehicle (DMSO) control one day before infection and then daily until the sacrifice at day 7 post-infection

tag: developmental stage

value: aged

value: Lung

value: WT

tag: treatment

tag: time of treatment

value: Day -1 (SARS-CoV-2 infection)

tag: infection

tag: time

value: day 7 post-infection


title: Lung, ABT-263 Infected Day 7, rep3


title: Lung, ABT-263 Infected Day 7, rep2


title: X9.5_CTR_NP_C1


title: Lung, ABT-263 Infected Day 7, rep1


title: X9.5_CTR_NP_C3


title: 12F_M_219


title: OU_166

description: Prospective.Validation

value: less than or equal to 50


title: 12F_M_218


title: OU_165

description: Prospective.Validation


title: X9.5_CTR_NP_C4


title: 12F_M_215


title: Lung, Vehicle Infected Day 7, rep1

value: Vehicle


title: Lung, Vehicle Infected Day 7, rep3


title: 12F_M_216


title: 12F_M_214


title: OU_164

description: Prospective.Validation

value: wP-FEC+Trastuzumab

value: Trastuzumab

value: pCR (ypT0/N0)


title: OU_162

description: Prospective.Validation

value: Basal


title: OU_161

description: Prospective.Validation

value: greater than 50

value: LumB


title: 12F_M_212


title: OU_163

description: Prospective.Validation

value: Negative

value: Positive


title: Lung, Vehicle Infected Day 7, rep2


title: X9.5_cKO_NP_M1

value: Sox9 conditional knock-out mice (Sox9cKO) (AcanCreERT2Sox9fl/fl)

value: nucleus pulposus (NP)

value: female


title: 12F_M_220


title: 12F_M_208


title: DU19-01S0004017, MSSA, scRNAseq

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

description:
DU19_01S0004017
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

library_source: transcriptomic single cell

data_processing:
Reads of scRNAseq experiments were aligned to hg38 using Cell Ranger v3.1.0 and the filtered feature-by-barcode count matrices were then processed using Seurat v4.0 [PMID: 34062119].
Assembly: hg38
Supplementary files format and content: RDS file contains the integrated data of all samples

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Thawed PBMCs were washed with PBS/0.04% BSA. Cells were counted and 100,000-1,000,000 cells were added to a 2 mL-microcentrifuge tube. Cells were centrifuged at 300xg for 5min at 4°C. The supernatant carefully completely removed, and 0.1X lysis buffer (1x: 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 3 min incubation on ice, 1 ml of chilled wash buffer was added. The nuclei were pelted at 500 xg for 5 min at 4°C and resuspended in a chilled diluted nuclei buffer (10X Genomics) for scATAC-seq. Nuclei were counted and the concentration was adjusted to run the assay.
ScRNAseq was performed as described (10x Genomics, Pleasanton, CA), following the Single Cell 3’ Reagents Kits V3.1 User Guidelines. Cells were filtered, counted on a Countess instrument, and resuspended at a concentration of 1,000 cells/μl. The number of cells loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ Chip kit G PN-200177) was loaded to target 5,000-10,000 cells final. Reverse transcription was performed in the emulsion and cDNA was amplified following the Chromium protocol. Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit) and the library was constructed. Each library was tagged with a different index for multiplexing (Chromium i7 Multiplex Single Index Plate T Set A, PN-2000240) and quality controlled by Bioanalyzer prior to sequencing.

value: PBMC

tag: disease state

value: MSSA

value: Male


title: 12F_M_209


title: DU19-01S0004013, MRSA, scRNAseq

description:
DU19_01S0004013
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: MRSA

value: Female


title: 12F_M_211


title: DU19-01S0004015, MRSA, scRNAseq

description:
DU19_01S0004015
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_206


title: 12F_M_207


title: OU_160

description: Prospective.Validation

value: wP-FEC

value: Non-pCR

value: LumA


title: 12F_M_217


title: 12F_M_213


title: 12F_M_205


title: 12F_M_204


title: DU19-01S0004011, MRSA, scRNAseq

description:
DU19_01S0004011
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_210


title: DU19-01S0003994, MRSA, scRNAseq

description:
DU19_01S0003994
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_203


title: 12F_M_202


title: OU_157

description: Prospective.Validation


title: DU19-01S0003992, MRSA, scRNAseq

description:
DU19_01S0003992
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: OU_158

description: Prospective.Validation

value: wP-FEC+Trastuzumab

value: Trastuzumab

value: pCR (ypT0/N0)


title: OU_156

description: Prospective.Validation

value: less than or equal to 50


title: LSDS.S.SS.CX.1.2

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

description: Illumina Hiseq 2000

data_processing:
Raw RNA-seq reads were aligned to the mouse mm9 genome using TopHat2 (v2.1.0) [354] and differential gene expression analysis was conducted using Cuffdiff (v2.2.1).
Assembly: mm9

source_name: Cortex

growth_protocol: Differential 5mC and 5hmC regions across different social defeat conditions were correlated to paired RNAseq data in order to elucidate the epigenetic contribution to differences in stress response.

extract_protocol:
Brain tissue was placed in TRIzol and homogenized using a hand-held pestle homogenizer and allowed to incubate for at least 5 minutes. Chloroform was added to the homogenate in a 1:5 ratio, the tubes shaken, and allowed to incubated at room temperature for 15 minutes. Samples were centrifuged at 12,000g for 15 minutes at 4°C. The top aqueous layer was transferred to a clean tube, and the RNA was precipitated in 3M NaAc pH 5.2 (10:1 ratio), 4ml of glycogen (5mg/ml), 100% isopropanol (1:1 ratio) overnight at -37°C. The next day, samples were centrifuged at 15,000 RPM for 20 minutes at 4°C. The resulting RNA pellet was washed twice in 75% ethanol and centrifuged at 7,500g for 10 minutes at 4°C. The washed RNA pellet was dissolved in nuclease-free water. RNA was quantified by Nanodrop and quality confirmed by a gel. RTqPCR was performed using Thermo Fisher’s Super Script III First-Strand Synthesis (18080051) kit and manufactures protocol was followed.
Bulk RNA was sent to Admera Health, LLC for library construction and sequencing on an Illumina HiSeq platform.

tag: seq

value: RNA

value: WT


title: OU_155

description: Prospective.Validation

value: greater than 50

value: Negative


title: LSDS.S.SS.CX.1.1

description: Illumina Hiseq 2000


title: OU_159

description: Prospective.Validation

value: Positive

value: LumB


title: LSDS.S.RR.CX.4

description: Illumina Hiseq 2000


title: 12F_M_201

tag: brain region


title: DU19-01S0003989, MRSA, scRNAseq

description:
DU19_01S0003989
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: PBMC

tag: age


title: DU19-01S0003987, MRSA, scRNAseq

description:
DU19_01S0003987
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: LSDS.S.RR.CX.2

description: Illumina Hiseq 2000

tag: strain


title: DU19-01S0003978, MRSA, scRNAseq

description:
DU19_01S0003978
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: DU19-01S0003549, MRSA, scRNAseq

description:
DU19_01S0003549
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_200


title: 12F_M_199


title: LSDS.C.CX.RS.1R

description: Illumina Hiseq 2000


title: LSDS.C.CX.RS.2.4

description: Illumina Hiseq 2000


title: 12F_M_198


title: 12F_M_197


title: OU_153

description: Prospective.Validation

tag: ct


title: ASDS.S.CX.1

description: Illumina Hiseq 2000


title: 12F_M_196


title: DU19-01S0003527, MSSA, scRNAseq

description:
DU19_01S0003527
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: MSSA


title: 12F_M_195


title: ASDS.C.CX.3

description: Illumina Hiseq 2000


title: DU19-01S0003515, MSSA, scRNAseq

description:
DU19_01S0003515
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: Male


title: OU_154

description: Prospective.Validation

tag: cn


title: OU_149

description: Prospective.Validation

tag: er


title: OU_152

description: Prospective.Validation

tag: hg

value: Basal


title: DU19-01S0003509, MSSA, scRNAseq

description:
DU19_01S0003509
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: Female


title: ASDS.S.CX.2

description: Illumina Hiseq 2000

tag: genotype


title: 12F_M_194


title: ASDS.C.CX.1

description: Illumina Hiseq 2000


title: CSDS6.SR.CX.4

description: Illumina Hiseq 2000


title: DU19-01S0003507, MSSA, scRNAseq

description:
DU19_01S0003507
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

tag: tissue


title: DU19-01S0003542, MRSA, scRNAseq

description:
DU19_01S0003542
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: MRSA

tag: Sex


title: OU_148

description: Prospective.Validation

value: wP-FEC

value: Non-pCR


title: OU_150

description: Prospective.Validation

value: wP-FEC+Trastuzumab

value: Trastuzumab


title: OU_151

description: Prospective.Validation

value: less than or equal to 50

value: LumA


title: DU19-01S0003492, MSSA, scRNAseq

description:
DU19_01S0003492
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: CSDS6.SR.CX.3

description: Illumina Hiseq 2000

value: RNA

value: WT


title: OU_146

description: Prospective.Validation

value: greater than 50


title: OU_145

description: Prospective.Validation

value: Positive

value: Negative


title: OU_144

description: Prospective.Validation


title: OU_147

description: Prospective.Validation


title: CSDS6.SS.CX.1

description: Illumina Hiseq 2000


title: CSDS6.SS.CX.2

description: Illumina Hiseq 2000


title: 12F_M_192


title: DU19-01S0003466, MSSA, scRNAseq

description:
DU19_01S0003466
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: PBMC


title: 12F_M_127


title: DU19-01S0003482, MSSA, scRNAseq

description:
DU19_01S0003482
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: MSSA


title: 12F_M_126


title: 12F_M_125


title: DU19-01S0003462, MSSA, scRNAseq

description:
DU19_01S0003462
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: CSDS6.C.CX.4

description: Illumina Hiseq 2000


title: CSDS6.C.CX.2

description: Illumina Hiseq 2000


title: DU19-01S0003464, MSSA, scRNAseq

description:
DU19_01S0003464
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_193


title: 12F_M_124


title: OU_142

description: Prospective.Validation


title: CSDS.SS.CX.4

description: Illumina Hiseq 2000


title: OU_143

description: Prospective.Validation

value: pCR (ypT0/N0)


title: 12F_M_123


title: DU19-01S0003453, MSSA, scRNAseq

description:
DU19_01S0003453
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: CSDS.SS.CX.3

description: Illumina Hiseq 2000


title: OU_140

description: Prospective.Validation

value: LumB


title: BWJ0023, Control, scRNAseq

description:
BWJ0023
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: Control

value: Female


title: BMI0102, Control, scRNAseq

description:
BMI0102
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: Male


title: CSDS.SR.CX.4

description: Illumina Hiseq 2000


title: BMI0101, Control, scRNAseq

description:
BMI0101
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: CSDS.SR.CX.2

description: Illumina Hiseq 2000


title: BMI0095, Control, scRNAseq

description:
BMI0095
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: BMI0099, Control, scRNAseq

description:
BMI0099
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: CSDS.C.CX.3

description: Illumina Hiseq 2000


title: 12F_M_119


title: 12F_M_120


title: 12F_M_118


title: 12F_M_121


title: BMI0094, Control, scRNAseq

description:
BMI0094
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_117


title: 12F_M_122


title: BMI0093, Control, scRNAseq

description:
BMI0093
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: mC.LSDS.S.SS.CX.R.2

description: Illumina Hiseq 2000

data_processing:
Data mapping and processing was performed as previously described [18]. Briefly, bowtie2 (v2.3.5.1) [351] was used to map pair-end reads to the mm9 reference genome followed by MACS2 peak calling (v 2.1.2) [352]. Technical replicates were combined using the bedtools (v2.28.0)   “window” function with a 300bp extension applied up and downstream of the peak. Only the common peaks in all the replicates were considered for further analysis. Peaks were then annotated to their corresponding genes using HOMER (Hypergeometric Optimization of Motif EnRichment) (v4.11.1) [353] and the flag “-annStat” was added to annotate these peaks to genomic features. Raw RNA-seq reads were aligned to the mouse mm9 genome using TopHat2 (v2.1.0) [354] and differential gene expression analysis was conducted using Cuffdiff (v2.2.1).
Assembly: mm9

extract_protocol:
In brief, 5mg of genomic DNA was sonicated to 300-400 base pairs and 5hmC containing fragments were glucosylated (T4 phage ß-glucosyltransferase enzyme and UDP-6-N3-glucose). The glucosylated fragments were purified and then biotinylated (disulfide biotin linker) and pulled down with Dynabeads MyOne Streptavidin C1 beads. The 5hmC fragments were released from the beads using dithiothreitol and purified for a final time. DNA fragments were eluted in nuclease-free water and quantified by Qubit. 5mC: 3mg of genomic DNA was sonicated to 300-400 base pairs using a Covaris focused ultrasonicator. The DNA fragments were then subjected to end repair, A-tailing, adaptor ligation and USER digestion using the NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs, E7645S) according to the manufacturer’s protocol. Following USER digestion and purification, DNA was denatured for 10 minutes at 95°C and immunoprecipitated overnight at 4°C with 4mL of either 5mC antibody (Active Motif, 39649) or IgG antibody (Sigma 12-371) in IP buffer (500mM Tris-HCl, pH 7.4, 750mM NaCl and 0.25% TritonX). The mixture was then incubated with Protein G coated Dynabeads for at least 2 hours at 4°C, washed with ice cold IP buffer and finally washed in ice cold high salt (300mM NaCl) IP buffer. After the final washing, the beads were treated with 200mL digest buffer (1X TE Buffer, pH 7.4, 0.25% SDS, 0.25% Proteinase K (2.5mg/mL)) and shaken at 1000rpm for 2 hours at 55°C. The methylated DNA was recovered by phenol:chloform:isoamyl alcohol (25:24:1) extraction followed by precipitation in 3X volume of 100% ethanol supplemented with 3mL glycogen(5mg/mL) and 15mL NaAC pH 5.2 overnight at -20°C. The next day, the DNA was pelleted and washed with 75% ethanol and dissolved in nuclease-free water. Illumina indexes were added, PCR enriched and purified using the NEBNext Ultra II DNA Library Prep kit for Illumina following the manufacturer’s protocol.
The NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs, E7645S) was used per the manufacturer’s protocol for enriched and unenriched genomic DNA. An Agilent 2100 Bioanalyzer was used to confirm purity and fragmentation size of the final libraries. Libraries were sequenced pair-end (150bp) on an Illumina HiSeq platform by Admera Health, LLC.

value: ChIP

tag: chip antibody

value: 5mC antibody (Active Motif, 39649)


title: 12F_M_116


title: BMI0040, Control, scRNAseq

description:
BMI0040
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: mC.LSDS.S.RR.CX.4

description: Illumina Hiseq 2000


title: mC.LSDS.S.SS.CX.R.1

description: Illumina Hiseq 2000


title: OU_139

description: Prospective.Validation

value: wP-FEC

value: Non-pCR


title: 12F_M_115


title: CSDS.C.CX.2

description: Illumina Hiseq 2000


title: mC.LSDS.S.RR.CX.2

description: Illumina Hiseq 2000


title: BMI0037, Control, scRNAseq

description:
BMI0037
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: AS18-00669, Control, scRNAseq

description:
AS18_00669
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_113


title: OU_138

description: Prospective.Validation

value: LumA


title: 12F_M_114


title: OU_137

description: Prospective.Validation

value: less than or equal to 50


title: OU_141

description: Prospective.Validation


title: mC.LSDS.C.RS.CX.2

description: Illumina Hiseq 2000

value: WT


title: OU_133

description: Prospective.Validation

value: greater than 50


title: OU_136

description: Prospective.Validation

value: Positive


title: OU_130

description: Prospective.Validation


title: OU_131

description: Prospective.Validation

value: Negative


title: OU_132

description: Prospective.Validation

value: Basal


title: OU_135

description: Prospective.Validation


title: mC.LSDS.C.RS.CX.1

description: Illumina Hiseq 2000


title: 12F_M_112


title: AS17-02129, Control, scRNAseq

description:
AS17_02129
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: PBMC


title: AS17-00144, Control, scRNAseq

description:
AS17_00144
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_111


title: 12F_M_110


title: mC.ASDS.S.CX.1

description: Illumina Hiseq 2000


title: OU_128

description: Prospective.Validation


title: AS14-03700, Control, scRNAseq

description:
AS14_03700
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: AS14-00902, Control, scRNAseq

description:
AS14_00902
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_109


title: mC.ASDS.C.CX.3

description: Illumina Hiseq 2000


title: AS13-08590, Control, scRNAseq

description:
AS13_08590
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: mC.ASDS.C.CX.1

description: Illumina Hiseq 2000


title: 12F_M_108


title: mC.ASDS.S.CX.2

description: Illumina Hiseq 2000


title: AS11-18755, Control, scRNAseq

description:
AS11_18755
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_107


title: AS13-13951, Control, scRNAseq

description:
AS13_13951
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_106


title: mC.6CSDS.SS.CX.2

description: Illumina Hiseq 2000


title: mC.6CSDS.SR.CX.3

description: Illumina Hiseq 2000


title: AS11-12162, Control, scRNAseq

description:
AS11_12162
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_105


title: OU_129

description: Prospective.Validation


title: OU_126

description: Prospective.Validation


title: OU_125

description: Prospective.Validation


title: OU_122

description: Prospective.Validation


title: OU_124

description: Prospective.Validation


title: OU_121

description: Prospective.Validation


title: OU_127

description: Prospective.Validation

value: pCR (ypT0/N0)


title: 12F_M_104


title: mC.6CSDS.SR.CX.4

description: Illumina Hiseq 2000


title: OU_123

description: Prospective.Validation


title: OU_119

description: Prospective.Validation


title: 12F_M_103


title: mC.6CSDS.C.CX.4

description: Illumina Hiseq 2000


title: mC.6CSDS.C.CX.2

description: Illumina Hiseq 2000


title: AS10-21035, Control, scRNAseq

description:
AS10_21035
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: AS09-13278, Control, scRNAseq

description:
AS09_13278
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: mC.CSDS.SS.CX.4

description: Illumina Hiseq 2000


title: AS08-09890, Control, scRNAseq

description:
AS08_09890
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: mC.CSDS.SS.CX.3

description: Illumina Hiseq 2000


title: 12F_M_101


title: mC.6CSDS.SS.CX.1

description: Illumina Hiseq 2000


title: AS11-07881, Control, scRNAseq

description:
AS11_07881
MRSA-MSSA-CTRL-all-combine-20210908.Rdata


title: 12F_M_100


title: OU_118

description: Prospective.Validation


title: mC.CSDS.SR.CX.4

description: Illumina Hiseq 2000


title: DU19-01S0004017, MSSA, scATACseq

description:
DU19_01S0004017
Staph_scATAC_integration.tar

library_source: genomic single cell

data_processing:
Reads of scATAC-seq experiments were aligned to the GRCh38 (hg38) human reference genome using cellranger-atac software (10x Genomics; version 1.2 or 1.0). The resulting fragment files were processed using ArchR [PMID: 33633365].
Assembly: hg38
Supplementary files format and content: tar file contains the integrated data of all samples

extract_protocol:
Thawed PBMCs were washed with PBS/0.04% BSA. Cells were counted and 100,000-1,000,000 cells were added to a 2 mL-microcentrifuge tube. Cells were centrifuged at 300xg for 5min at 4°C. The supernatant carefully completely removed, and 0.1X lysis buffer (1x: 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 3 min incubation on ice, 1 ml of chilled wash buffer was added. The nuclei were pelted at 500 xg for 5 min at 4°C and resuspended in a chilled diluted nuclei buffer (10X Genomics) for scATAC-seq. Nuclei were counted and the concentration was adjusted to run the assay.
ScATAC-seq was performed immediately after nuclei isolation and following the Chromium Single Cell ATAC Reagent Kits V1.1 User Guide (10x Genomics, Pleasanton, CA). Transposition was performed in 10 ul at 37°C for 60 min on at least 1,000 nuclei, before loading of the Chromium Chip H (PN-2000180). Barcoding was performed in the emulsion (12 cycles) following the Chromium protocol. After post GEM cleanup, libraries were prepared following the protocol and were indexed for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000427). Each library was assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit).

value: MSSA


title: AS11-07049, Control, scRNAseq

description:
AS11_07049
MRSA-MSSA-CTRL-all-combine-20210908.Rdata

value: Control


title: OU_117

description: Training

source_name: Training with random primer


title: OU_120

description: Prospective.Validation


title: OU_116

description: Validation

source_name: Validation with random primer


title: 12F_M_99


title: DU19-01S0004015, MRSA, scATACseq

description:
DU19_01S0004015
Staph_scATAC_integration.tar

value: MRSA


title: OU_114

description: Validation

value: LumB


title: mC.CSDS.SR.CX.2

description: Illumina Hiseq 2000

value: ChIP


title: DU19-01S0004013, MRSA, scATACseq

description:
DU19_01S0004013
Staph_scATAC_integration.tar

value: Female


title: 12F_M_102


title: mC.CSDS.C.CX.3

description: Illumina Hiseq 2000

value: 5mC antibody (Active Motif, 39649)


title: 12F_M_98


title: 12F_M_97


title: OU_113

description: Training

value: wP-FEC

value: Non-pCR


title: mC.CSDS.C.CX.2

description: Illumina Hiseq 2000


title: DU19-01S0004011, MRSA, scATACseq

description:
DU19_01S0004011
Staph_scATAC_integration.tar


title: 12F_M_96


title: 12F_M_95


title: DU19-01S0003994, MRSA, scATACseq

description:
DU19_01S0003994
Staph_scATAC_integration.tar

value: Male


title: hmC.LSDS.S.SS.CX.1.1

description: Illumina Hiseq 2000

value: WT


title: OU_112

description: Validation

value: greater than 50


title: OU_115

description: Training

value: Positive

value: LumA


title: hmC.LSDS.S.SS.CX.1.2

description: Illumina Hiseq 2000


title: DU19-01S0003992, MRSA, scATACseq

description:
DU19_01S0003992
Staph_scATAC_integration.tar


title: OU_111

description: Validation

value: Negative


title: DU19-01S0003989, MRSA, scATACseq

description:
DU19_01S0003989
Staph_scATAC_integration.tar

value: PBMC


title: hmC.LSDS.S.RR.CX.4

description: Illumina Hiseq 2000


title: DU19-01S0003987, MRSA, scATACseq

description:
DU19_01S0003987
Staph_scATAC_integration.tar


title: hmC.LSDS.C.CX.RS.2.4

description: Illumina Hiseq 2000


title: hmC.LSDS.S.RR.CX.2

description: Illumina Hiseq 2000


title: 12F_M_93


title: 12F_M_92


title: DU19-01S0003978, MRSA, scATACseq

description:
DU19_01S0003978
Staph_scATAC_integration.tar


title: hmC.LSDS.C.CX.RS.1R

description: Illumina Hiseq 2000


title: OU_110

description: Validation


title: 12F_M_94


title: 12F_M_91


title: 12F_M_90


title: DU19-01S0003549, MRSA, scATACseq

description:
DU19_01S0003549
Staph_scATAC_integration.tar


title: DU19-01S0003542, MRSA, scATACseq

description:
DU19_01S0003542
Staph_scATAC_integration.tar


title: hmC.ASDS.S.CX.2

description: Illumina Hiseq 2000


title: 12F_M_89


title: hmC.ASDS.S.CX.1

description: Illumina Hiseq 2000


title: DU19-01S0003527, MSSA, scATACseq

description:
DU19_01S0003527
Staph_scATAC_integration.tar


title: hmC.ASDS.C.CX.3

description: Illumina Hiseq 2000


title: DU19-01S0003515, MSSA, scATACseq

description:
DU19_01S0003515
Staph_scATAC_integration.tar


title: OU_107

description: Validation

value: less than or equal to 50


title: OU_108

description: Validation


title: OU_109

description: Training


title: OU_103

description: Training


title: OU_106

description: Validation


title: OU_105

description: Validation


title: 12F_M_87


title: 12F_M_86


title: DU19-01S0003507, MSSA, scATACseq

description:
DU19_01S0003507
Staph_scATAC_integration.tar

value: MSSA


title: DU19-01S0003509, MSSA, scATACseq

description:
DU19_01S0003509
Staph_scATAC_integration.tar


title: OU_104

description: Training


title: hmC.6CSDS.SR.CX.4

description: Illumina Hiseq 2000