title: 12C_M_639


title: 12C_M_638

status: Public on May 18 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


title: 12C_M_637


title: 12C_M_641


title: 12C_M_662


title: 12C_M_635


title: 12C_M_636


title: 12C_M_633


title: 12C_M_634


title: 12C_M_631


title: 12C_M_632


title: 12C_M_630


title: 12C_M_627


title: 12C_M_640


title: 12C_M_629


title: 12C_M_625


title: 12C_M_626


title: 12C_M_628


title: 12C_M_615


title: 12C_M_616


title: 12C_M_623


title: 12C_M_618


title: 12C_M_622


title: 12C_M_620


title: 12C_M_614


title: 12C_M_617


title: 12C_M_613


title: 12C_M_612


title: 12C_M_621


title: 12C_M_619


title: 12C_M_611


title: 12C_M_610


title: 12C_M_609


title: 12C_M_608


title: 12C_M_606


title: 12C_M_607


title: 12C_M_624


title: 12C_M_604


title: 12C_M_605


title: 12C_M_603


title: 12C_M_602


title: 12C_M_601


title: 12C_M_600


title: 12C_M_597


title: 12C_M_598


title: 12C_M_599


title: 12C_M_595


title: 12C_M_593


title: 12C_M_591


title: 12C_M_592


title: 12C_M_590


title: 12C_M_589


title: 12C_M_588


title: 12C_M_594


title: 12C_M_587


title: 12C_M_586


title: 12C_M_580


title: 12C_M_584


title: 12C_M_581


title: 12C_M_582


title: 12C_M_578


title: 12C_M_583


title: 12C_M_577


title: 12C_M_579


title: 12C_M_576


title: 12C_M_596


title: 12C_M_511


title: 12C_M_508


title: 12C_M_509


title: 12C_M_507


title: 12C_M_505


title: 12C_M_510


title: 12C_M_504


title: 12C_M_585


title: 12C_M_503


title: 12C_M_501


title: 12C_M_500


title: 12C_M_499


title: 12C_M_502


title: 12C_M_496


title: 12C_M_495


title: 12C_M_494


title: 12C_M_493


title: 12C_M_490


title: 12C_M_489


title: 12C_M_488


title: 12C_M_487


title: 12C_M_486


title: 12C_M_492


title: 12C_M_485


title: 12C_M_491


title: 12C_M_484


title: 12C_M_506


title: 12C_M_482


title: 12C_M_479


title: 12C_M_483


title: 12C_M_478


title: 12C_M_480


title: 12C_M_481


title: 12C_M_477


title: 12C_M_498


title: 12C_M_476


title: 12C_M_474


title: 12C_M_497


title: 12C_M_475


title: 12C_M_473


title: 12C_M_472


title: 12C_M_470


title: 12C_M_471


title: 12C_M_469


title: 12C_M_468


title: 12C_M_467


title: 12C_M_466


title: 12C_M_465


title: 12C_M_461


title: 12C_M_455


title: 12C_M_457


title: 12C_M_456


title: 12C_M_463


title: 12C_M_459


title: 12C_M_458


title: 12C_M_453


title: 12C_M_452


title: 12C_M_454


title: 12C_M_450


title: 12C_M_447


title: 12C_M_449


title: 12C_M_446


title: 12C_M_445


title: 12C_M_444


title: 12C_M_443


title: 12C_M_442


title: 12C_M_464


title: 12C_M_439


title: 12C_M_460


title: 12C_M_440


title: 12C_M_441


title: 12C_M_436


title: 12C_M_438


title: 12C_M_437


title: 12C_M_433


title: 12C_M_429


title: 12C_M_431


title: 12C_M_428


title: 12C_M_432


title: 12C_M_451


title: 12C_M_425


title: 12C_M_448


title: 12C_M_423


title: 12C_M_427


title: 12C_M_421


title: 12C_M_424


title: 12C_M_418


title: 12C_M_420


title: 12C_M_419


title: 12C_M_415


title: 12C_M_414


title: 12C_M_413


title: 12C_M_435


title: 12C_M_411


title: 12C_M_406


title: 12C_M_409


title: 12C_M_408


title: 12C_M_405


title: 12C_M_400


title: 12C_M_397


title: 12C_M_396


title: 12C_M_398


title: 12C_M_394


title: 12C_M_393


title: 12C_M_416


title: 12C_M_417


title: 12C_M_391


title: 12C_M_395


title: 12C_M_392


title: 12C_M_390


title: 12C_M_389


title: 12C_M_412


title: 12C_M_388


title: 12C_M_385


title: 12C_M_407


title: 12C_M_404


title: 12C_M_401


title: 12C_M_319


title: 12C_M_318


title: 12C_M_384


title: 12C_M_316


title: 12C_M_399


title: 12C_M_313


title: 12C_M_314


title: 12C_M_311


title: 12C_M_308


title: 12C_M_310


title: 12C_M_309


title: 12C_M_387


title: 12C_M_302


title: 12C_M_303


title: 12C_M_386


title: 12C_M_304


title: 12C_M_301


title: 12C_M_305


title: 12C_M_300


title: 12C_M_298


title: 12C_M_297


title: 12C_M_306


title: 12C_M_295


title: 12C_M_296


title: 12C_M_315


title: 12C_M_294


title: 12C_M_299


title: 12C_M_293


title: 12C_M_288


title: 12C_M_290


title: 12C_M_286


title: 12C_M_291


title: 12C_M_289


title: 12C_M_292


title: 12C_M_287


title: 12C_M_312


title: 12C_M_285


title: 12C_M_307


title: 12C_M_284


title: 12C_M_283


title: 12C_M_281


title: 12C_M_280


title: 12C_M_279


title: 12C_M_278


title: 12C_M_277


title: 12C_M_275


title: 12C_M_274


title: 12C_M_276


title: 12C_M_273


title: 12C_M_272


title: 12C_M_271


title: 12C_M_270


title: 12C_M_269


title: 12C_M_268


title: 12C_M_267


title: 12C_M_265


title: 12C_M_266


title: 12C_M_259


title: 12C_M_262


title: 12C_M_263


title: 12C_M_264


title: 12C_M_258


title: 12C_M_260


title: 12C_M_257


title: 12C_M_282


title: 12C_M_261


title: 12C_M_255


title: 12C_M_252


title: 12C_M_254


title: 12C_M_248


title: 12C_M_251


title: 12C_M_249


title: 12C_M_247


title: 12C_M_253


title: 12C_M_244


title: 12C_M_243


title: 12C_M_242


title: 12C_M_246


title: 12C_M_239


title: 12C_M_238


title: 12C_M_256


title: 12C_M_240


title: 12C_M_241


title: 12C_M_237


title: 12C_M_235


title: 12C_M_234


title: AAV-mRNA, rep3

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description:
insertion site mapping
Splink-AAV-mRNA

data_processing:
Though paired-end files were retrieved from Miseq, only the forward reads were used for analysis; thus, only R1 files were included. FASTQ files from prepared samples were first processed for quality q>26 using BBDuk. Then, non-integrated AAV was removed with Cutadapt using a sequence unique to the AAV ITR. Next, transposon arms were trimmed out and only sequences that were trimmed were kept. After trimming 10 bases from the 5p end, reads were trimmed to a length of 30 bases and then mapped to the GRCh38 human genome using the hisat2 function. Resulting .sam files were filtered with samtools for q>=30.
.sam files were converted to .bam files using samtools view, and .bam files were converted to .bed files using bamtoBed.
Assembly: grch38
Supplementary files format and content: .txt files contain genomic coordinates and counts of detected insertion sites of the Sleeping Beauty transposon CAR transgene in T cells of a human donor (donor4003).

organism: Homo sapiens

source_name: CD8 T cell

extract_protocol:
Genomic DNA from CAR-T cells was extracted using QIAGEN's Blood Mini Kit.
First, gDNA was fragmented using NEB Ultra II FS Enzyme Mix. Then, Splinkerette adaptors were annealed by heating to 98C for 10 min and then cooling to room temp. Annealed Splinkerette adaptors were ligated to fragmented DNA using NEBNext Ultra II Ligation Master Mix. Library fragments were size selected for an approximate insert size of 150-200bp using SPRIselect magnetic beads. A two step PCR was then performed: the first PCR to amplify integrated transposon sequences (18 cycles) and the 2nd PCR to attach sequencing indeces (8 cycles). The libraries for each sample were quantified by qPCR, diluted to 2nM, and then pooled for sequencing by Miseq.
insertion site mapping

tag: treatment

value: AAV+SB100x mRNA

tag: cell type

value: CD8 T cell

tag: purity

value: Unsorted for CAR

tag: car percentage

tag: donor

value: donor 4003

tag: condition

value: in vitro CAR-Ts

tag: day stimulated after electroporation

tag: day collected after electroporation


title: MC-mRNA, rep2

description:
insertion site mapping
Splink-MC-mRNA

value: MC+SB100x mRNA


title: MC-mRNA, rep1

description:
insertion site mapping
Splink-MC-mRNA


title: MC-mRNA, rep3

description:
insertion site mapping
Splink-MC-mRNA


title: AAV-mRNA, rep2

description:
insertion site mapping
Splink-AAV-mRNA


title: 12C_M_233


title: 12C_M_250


title: 12C_M_245


title: 12C_M_232


title: AAVonly, rep3

description:
insertion site mapping
Splink-AAVonly

value: AAV


title: AAVonly, rep2

description:
insertion site mapping
Splink-AAVonly


title: 12C_M_236


title: AAVonly, rep1

description:
insertion site mapping
Splink-AAVonly


title: 12C_M_230


title: 12C_M_229


title: 12C_M_231


title: Rice-Treated, WBCs (4952-MZ-4)

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: blood

growth_protocol: Total WBCs isolated from 6ml of blood from an FPIES subject were plated into 23 wells of 12-well plates, in RPMI + 10% FBS media.

extract_protocol:
After treatment, WBCs were pipetted out of the wells, spun down and resusoended in PBS + 2% FBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells 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 retrotranscripted 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 appropiate 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.

treatment_protocol: Each well containing WBCs isolated from an FPIES subject was treated with individual homogenized foods at 1mg/ml, or with LPS or left untreated.

tag: individual id

value: FPIES

tag: tissue

value: blood

value: white blood cells

value: Rice


title: 12C_M_228


title: LPS-treated, WBCs (4952-MZ-2)

description: 10x Genomics

value: LPS


title: 12C_M_227


title: AAV-mRNA, rep1

description:
insertion site mapping
Splink-AAV-mRNA


title: 12C_M_226


title: 12C_M_225


title: 12C_M_224


title: Rice-Treated, WBCs (2270-MZ-4)

description: 10x Genomics


title: Almond_Butter-Treated, WBCs (2270-MZ-5)

description: 10x Genomics

value: Almond Butter


title: Untreated, WBCs (4952-MZ-1)

description: 10x Genomics

value: untreated


title: Cow_Milk-Treated, WBCs (2270-MZ-3)

description: 10x Genomics

value: Cow Milk


title: LPS-treated, WBCs (2270-MZ-2)

description: 10x Genomics


title: 12C_M_222


title: 12C_M_220


title: MCF10A hRas 1q-loss c4 rep 2

first: Jason

last: Sheltzer

address: 300 George Street

department: Surgery

institute: Yale University

description: Breast epithelial cell line with deletion of an extra copy of chromosome 1q expressing hRASV12, biological replicate 2

library_source: transcriptomic

data_processing:
Custom Novogene QC scripts
Novogene: Remove reads containing adapters
Novogene: Remove reads containing >10% undetermined bases (N)
Novogene: Remove reads with >=50% of bases with Qscore <= 5
Hisat2 (v2.0.5) alignment to hg38
featureCounts v1.5.0-p3 to count reads mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing read counts for each sample

growth_protocol: Cells were plated and allowed to grow for 24 hours prior to extraction

extract_protocol:
Qiagen RNEeasy
In brief, mRNA was purified from total cellular RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis. Subsequently, libraries were prepared with end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Single cell derived clones with engineered chr losses were generated through a collection of ReDACT techniques

tag: cell line

value: breast epithelial

tag: genotype

value: ReDACT-CO, targeting chr1q, expressing hRASV12


title: 12C_M_223


title: MCF10A hRas 1q-loss c4 rep 1

description: Breast epithelial cell line with deletion of an extra copy of chromosome 1q expressing hRASV12, biological replicate 1


title: MCF10A hRas 1q-loss c3 rep 2

value: ReDACT-TR, targeting chr1q, expressing hRASV12


title: 12C_M_221


title: 12C_M_219


title: 12C_M_218


title: MCF10A hRas 1q-loss c2 rep 2


title: MCF10A hRas 1q-loss c2 rep 1


title: MCF10A hRas 1q-loss c1 rep 2


title: 12C_M_217


title: 12C_M_216


title: MCF10A hRas 1q-loss c3 rep 1


title: MCF10A hRas 1q-loss c1 rep 1


title: 12C_M_215


title: 12C_M_213


title: MCF10A 1q-loss c4 rep 2

description: Breast epithelial cell line with deletion of an extra copy of chromosome 1q, biological replicate 2

value: ReDACT-CO, targeting chr1q


title: 12C_M_212


title: Scrambled_Eggs-Treated, WBCs (4952-MZ-3)

description: 10x Genomics

value: Scrambled Eggs


title: 12C_M_211


title: MCF10A 1q-loss c3 rep 2

value: ReDACT-TR, targeting chr1q


title: MCF10A 1q-loss c3 rep 1

description: Breast epithelial cell line with deletion of an extra copy of chromosome 1q, biological replicate 1


title: 12C_M_210


title: 12C_M_209


title: MCF10A 1q-loss c2 rep 2


title: 12C_M_208


title: MCF10A 1q-loss c2 rep 1


title: MCF10A 1q-loss c1 rep 2


title: 12C_M_204


title: MCF10A 1q-loss c1 rep 1


title: MCF10A hRas WT rep 1

description: Wildtype breast epithelial cell line expressing hRASV12, biological replicate 1

value: WT

value: Wildtype, expressing hRASV12


title: 12C_M_205


title: MCF10A hRas WT rep 2

description: Wildtype breast epithelial cell line expressing hRASV12, biological replicate 2


title: 12C_M_202


title: MCF10A WT rep 1

description: Wildtype breast epithelial cell line, biological replicate 1

value: Wildtype


title: MCF10A WT rep 2

description: Wildtype breast epithelial cell line, biological replicate 2


title: 12C_M_206


title: 12C_M_201


title: 12C_M_200


title: 12C_M_199


title: MCF10A 1q-loss c4 rep 1


title: PBMC_5yr, LPS, Donor2

city: Tucson

first: James

last: Read

state: AZ

address: 1501 N. Campbell Avenue

institute: University of Arizona

description: 10x Genomics

data_processing:
fastq.qz files were processed with the CellRanger Toolkit (Version 6.1.1, 10x Genomics). The CellRanger count pipeline was run with default parameters.
Assembly: Human GRCh38 genome assembly (refdata-gex-GRCh38-2020-A).
Supplementary files format and content: Tab-separated values (.tsv) files and matrix (.mtx) files.

source_name: Peripheral blood

extract_protocol:
Cryopreserved CBMC/5yr PBMC samples were thawed, transfered to RPMI + 5% AB serum, and stimulated with 1ng/ml LPS or 50μl/ml Poly(I:C) or left untreated, and plates were incubated at 37oC (5% CO2) for 18 hours. Following culture, samples were re-suspended at target concentration of 2,000 cells/μl.
Single cells were processed on Chromium using the Chromium Next GEM Single Cell 3’ Kit v3.1 (4rxns, PN-1000269, 10X Genomics) on Chip G (PN-1000127, 10x Genomics) according to manufacturer’s protocol with targeted recovery of 5,000 cells per channel. Libraries were sequenced on the NovaSeq 6000 platform in a single batch.

treatment_protocol: Matched samples were cultured with Lipoloysaccharide (LPS) or Polyinosinic:polycytidylic acid (Poly(I:C)), or were culture in media only.

value: Peripheral Blood Mononuclear Cells

value: Peripheral blood

tag: sex at_birth

value: Male

tag: stimuli

value: 5 years


title: PBMC_5yr, PIC, Donor2

description: 10x Genomics


title: 12C_M_198

tag: brain region


title: PBMC_5yr, CTRL, Donor2

description: 10x Genomics

value: Unstimulated

tag: age


title: 12C_M_197

tag: strain


title: 12C_M_196


title: CBMC, PIC, Donor2

description: 10x Genomics

source_name: Umbilical cord blood

value: Cord Blood Mononuclear Cells

value: Umbilical cord blood

value: Birth


title: CBMC, LPS, Donor2

description: 10x Genomics

value: LPS


title: 12C_M_207


title: 12C_M_195


title: Untreated, WBCs (2270-MZ-1)

description: 10x Genomics

value: FPIES

value: blood

value: white blood cells

tag: treatment

value: untreated


title: CBMC, CTRL, Donor2

description: 10x Genomics

tag: cell type


title: 12C_M_194


title: PBMC_5yr, LPS, Donor1

description: 10x Genomics

value: Female


title: PBMC_5yr, PIC, Donor1

description: 10x Genomics


title: PBMC_5yr, CTRL, Donor1

description: 10x Genomics


title: CBMC, PIC, Donor1

description: 10x Genomics


title: 12C_M_203


title: 12C_M_193


title: 12C_M_191


title: 12C_M_190


title: CBMC, LPS, Donor1

description: 10x Genomics


title: CBMC, CTRL, Donor1

description: 10x Genomics


title: 12C_M_189


title: 12C_M_188


title: 12C_M_192


title: 12C_M_186


title: QJNTN24

city: West Haven

first: Sidi

last: Chen

address: 850 West Campus Drive

description: Nextera amplicon sequencing

data_processing:
For indel quantification, paired reads were mapped to the amplicon sequences using BWA-MEM with default settings (BWA-v0.7.1), sorted and indexed using Samtools, variants were called using mpileup via Samtools with a max depth of 100000, and indels were quantified using Varscan pileup2indel command and filtered (>= 2 indel reads, >=2 coverage at indel locus, indel frequency > 0.00001). Cutting efficiency was reported as the proportion of indels detected with a 75 bp window of the target cut site.
Assembly: GRCh38 Ensembl Version 96
Supplementary files format and content: Indel data is in the Varscan output format, in tab-delimitted files.
Library strategy: Nextera DNA sequencing

extract_protocol:
Genetic perturbations from CRISPR-RNP were quantified from genomic DNA (gDNA) that was extracted from T cells using QuickExtract Buffer (NEB) according to manufacturer’s recommendation. The genomic regions targeted by CRISPR-RNP were amplified by PCR (95 oC / 3 min; 36 cycles: 95 oC / 30 s, 60 oC / 30 s and 72 oC / 45 s; 72 oC / 4 min), 1 μL QuickExtract Buffer digested mixture was used as template in a 50 μL PCR reaction with DreamTaq Green 2X PCR Master Mix (Thermo Fisher Scientific) and 0.5 μM oligos.
For Nextera sequencing, 0.5 ng of PCR product was used for tagmentation and subsequently barcoded, as per manufacturer’s instructions (Illumina). The processed DNA was pooled, purified by 2 % agarose E-Gel electrophoresis, extracted from the gel via DNA Gel Extraction kit (Qiagen), and the pooled DNA was sequenced by the Illumina Novaseq platform (100 bp paired-end; Illumina).

value: culture

value: CAR-T cells

value: PDK1 gene locus


title: 12C_M_185


title: QJNTN23

description: Nextera amplicon sequencing


title: 12C_M_184


title: QJNTN21

description: Nextera amplicon sequencing

value: NTC-gRNA


title: QJNTN20

description: Nextera amplicon sequencing


title: 12C_M_183


title: 12C_M_182


title: QJNTN18

description: Nextera amplicon sequencing

value: ADA gene locus

value: ADA-gRNA


title: 12C_M_181


title: 12C_M_180


title: QJNTN17

description: Nextera amplicon sequencing


title: QJNTN15

description: Nextera amplicon sequencing


title: 12C_M_179


title: QJNTN16

description: Nextera amplicon sequencing


title: 12C_M_178


title: QJNTN14

description: Nextera amplicon sequencing


title: 12C_M_176


title: 12C_M_174


title: QJNTN13

description: Nextera amplicon sequencing


title: 12C_M_175


title: PDK1_sg13_Rep2

description: Nextera amplicon sequencing

value: T cells


title: PDK1_sg13_Rep3

description: Nextera amplicon sequencing


title: QJNTN22

description: Nextera amplicon sequencing


title: PDK1_sg13_NTC3

description: Nextera amplicon sequencing


title: PDK1_sg13_Rep1

description: Nextera amplicon sequencing


title: PDK1_sg13_NTC2

description: Nextera amplicon sequencing


title: 12C_M_171


title: QJNTN19

description: Nextera amplicon sequencing


title: PDK1_sg13_NTC1

description: Nextera amplicon sequencing


title: 12C_M_170


title: 12C_M_169


title: QJNT12

description: Nextera amplicon sequencing

source_name: ADA sg11


title: QJNT11

description: Nextera amplicon sequencing


title: 12C_M_168


title: 12C_M_167


title: QJNT10

description: Nextera amplicon sequencing


title: 12C_M_166


title: QJNT3

description: Nextera amplicon sequencing

source_name: ADA NTC sg11


title: 12C_M_165


title: QJNT2

description: Nextera amplicon sequencing


title: CAR_PDK1_OE_3

description: RNA-sequencing

data_processing:
mRNA sequencing data was aligned to the human transcriptome reference panel (GRCh38 Ensembl Version 96) and quantified from raw FASTQ files using Kallisto with the quant function and 100 bootstraps.
Assembly: GRCh38 Ensembl Version 96
Supplementary files format and content: Kallisto output files in tab-separated-value format.

source_name: culture

extract_protocol:
Total RNA was extracted by treating cells with TRIzol Reagent (Invitrogen), then isolating RNA with the Qiagen RNA extraction kit, as per manufacturer’s instructions.
For mRNA-seq, library preparation was performed using the NEBNext® Poly(A) mRNA Magnetic Isolation module (Illumina) and NEBNext® Ultra™ II Directional RNA Library Prep Kit (Illumina), per manufacturer’s instruction. Briefly, all samples were normalized to 200 or 500 ng total RNA for fragmentation and cDNA synthesis. Double-stranded cDNA was purified using oligo-dT Sample Purification Beads, adapters were ligated to the cDNA, and samples were barcoded using the NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB).

value: alpha-CD19 CAR


title: 12C_M_164


title: 12C_M_163


title: 12C_M_177


title: CAR_PDK1_OE_1

description: RNA-sequencing


title: 12C_M_161


title: CAR_3

description: RNA-sequencing

value: Control


title: 12C_M_172


title: QJNT1

description: Nextera amplicon sequencing


title: 12C_M_160


title: CAR_PDK1_OE_2

description: RNA-sequencing


title: CAR_2

description: RNA-sequencing


title: CAR_1

description: RNA-sequencing


title: CAR_ADA_OE_3

description: RNA-sequencing

value: ADA-OE


title: 12C_M_157


title: 12C_M_159


title: 12C_M_156


title: CAR_ADA_OE_2

description: RNA-sequencing


title: 12C_M_155


title: CAR_ADA_OE_1

description: RNA-sequencing


title: 12C_M_154


title: 12C_M_153


title: 12C_M_152


title: CAR_PDK1_sg13_1

description: RNA-sequencing


title: 12C_M_162


title: 12C_M_151


title: CAR_ADA_sg11_2

description: RNA-sequencing


title: CAR_ADA_sg11_3

description: RNA-sequencing


title: 12C_M_150


title: 12C_M_173


title: 12C_M_147


title: 12C_M_149


title: 12C_M_148


title: CAR_ADA_sg11_1

description: RNA-sequencing


title: 12C_M_146


title: sgQKI+QKI7-WT 8h rep1

city: Monrovia

first: Jianjun

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to GRCh38 using the STAR aligner. The aligned reads were then assigned to genes using RSEM
Assembly: GRCh38
Supplementary files format and content: table delimited text file containing the expression of genes

molecule: polyA RNA

growth_protocol: The U2OS cells were expanded in DMEM medium with 10% FBS, 1 X penicillin-streptomycin and plasmocin prophylactic for 1-2 weeks and the cells were collected at 70-80% confluency in 150 mm dish

extract_protocol:
The total RNA was extracted at indicated time points.
KAPA Stranded mRNA-Seq Kit (Illumina Platforms) was utilized to construct library and sequencing was performed on an Illumina Nova Seq 6000.

treatment_protocol: The U2OS cells were treated  with 5 µg/mL actinomycin D and 200 µM sodium arsenite.

value: Human Bone Osteosarcoma Epithelial Cells

value: actinomycin D+sodium arsenite for 8h


title: sgQKI+QKI7-WT 4h rep2

value: actinomycin D+sodium arsenite for 4h


title: sgQKI+QKI7-WT 0h rep2

value: actinomycin D+sodium arsenite for 0h


title: sgQKI+QKI7-WT 4h rep1


title: sgQKI+QKI7-WT 0h rep1


title: sgQKI+QKI7-WT 8h rep2


title: 12C_M_145


title: sgQKI+QKI7-△KH 8h rep2


title: CAR_PDK1_sg13_3

description: RNA-sequencing


title: 12C_M_142


title: 12C_M_141


title: 12C_M_214


title: 12C_M_144


title: sgQKI+QKI7-△KH 8h rep1


title: CAR_PDK1_sg13_2

description: RNA-sequencing


title: 12C_M_140


title: sgQKI+QKI7-△KH 4h rep2


title: sgQKI+QKI7-△KH 4h rep1


title: 12C_M_138


title: 12C_M_137


title: sgQKI+QKI7-△KH 0h rep2


title: sgQKI+QKI7-△KH 0h rep1


title: 12C_M_136


title: sgQKI+EV 8h rep1

value: sgQKI+EV


title: 12C_M_135


title: sgQKI+EV 8h rep2


title: sgQKI+EV 4h rep2


title: 12C_M_143


title: sgQKI+EV 4h rep1


title: sgQKI+EV 0h rep2


title: 12C_M_132


title: 12C_M_130


title: sgQKI+EV 0h rep1


title: 12C_M_131


title: 12C_M_128


title: sgNS+EV 8h rep1

value: sgNS+EV


title: sgNS+EV 4h rep2


title: 12C_M_139


title: 12C_M_2810


title: 12C_M_2808


title: sgNS+EV 4h rep1


title: 12C_M_2807


title: sgNS+EV 0h rep1


title: 12C_M_2806


title: 12C_M_2805


title: SCR3

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

data_processing:
Reads from *.fastq files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Assembly: human reference genome (GRCh37)

source_name: human trophoblast stem cell

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (scr versus KD).
RACE

value: extravillouse trophoblast

tag: shRNA

value: shRNAscr


title: 12C_M_133


title: KD3


title: 12C_M_2803


title: 12C_M_2802


title: KD2


title: 12C_M_2809


title: sgNS+EV 8h rep2


title: KD1


title: 12C_M_2799


title: 12C_M_2801


title: Xenografted human skin equivalent - Human Alignment

city: Irvine

first: Scott

last: Atwood

address: 4340 McGaugh Hall, Ring Rd

institute: University of California, Irvine

description:
Xenograft_HSE-1_Hs_Alignment_10XGenomics
RNA from single cells

data_processing:
Transcripts from all samples were mapped to the reference genome (GRCh38) except "Xenograft_HSE-1_Mm_Alignment_10XGenomics" which was aligned to the reference genome (mm10). Cell Ranger Version 2.1.1 was used for the "Matrigel_HSE-1_10XGenomics" sample and Cell Ranger Version 3.1.0 for all other samples.
Quality control of all data sets was performed using Seurat (Version 3.2.2) and SoptSC
Processed files were analyzed with Seurat V3.2.2 and scvelo and SoptSC
Genome_build: GRCh38 for all samples except the "Xenograft_HSE-1_Mm_Alignment_10XGenomics" sample which used the mm10 genome.
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Human skin equivalent

growth_protocol: Matrigel was applied to the underside of a 1.5 square cm piece of devitalized dermis. The devitalized dermis was elevated to the air liquid interface of a 6 cm tissue culture dish that contained 4 ml of keratinocyte growth media then primary human keratinocytes were seeded on top of it. Media was changed every other day for 1 week. The human skin equivalents then had their matrigel removed and were grafted onto NSG mice for 24 days.

extract_protocol:
The xenografted tissues were dissected from the NSG mice that they were grafted on to. The tissues were then placed in dispase overnight, at 37C, until the epidermis could be peeled apart from the dermis. The epidermis was then trypsinized for 30 min, and the dermis was discarded. Epidermal cells were incubated with DNAse for 5 min, filtered over 40um cell strainer, and flow sorted for live cells for library preparation.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v3 chemistry. Libraries were sequenced on an Illumina Next-Seq6000 platform (Illumina). Cell counting, capture, library preparation, quality control, and sequencing was performed at the Genomics High Throughput Sequencing facility at the University of California, Irvine.
Single Cell 3’ v3 chemistry - 10X Genomics

treatment_protocol: Human skin equivalents consisting of an epidermal layer comprised entirely of primary human keratinocytes and a devitalized dermis from human cadavers that has matrigel applied to the underside. Human skin equivalents were first grown for 1 week to reepithelialize the tissue and then the matrigel was removed and the human skin equivalent was grafted onto NSG mice (Jackson Laboratory: 005557) for 26 days. Cells from three grafts were collected and pooled prior to sequencing. This is the same replicate as the Xenograft_HSE-1_Mm_Alignment_10XGenomics sample except it was aligned to the GRCh38 genome.

value: Human skin equivalent

value: Xenografted human skin equivalent


title: 12C_M_2798


title: Human skin equivalent containing fibroblasts - Replicate 2

description:
Fibroblast_HSE-2_10XGenomics
RNA from single cells

growth_protocol: Primary dermal fibroblasts were seeded into a 1.5 square cm piece of devitalized dermis via centrifugation. The devitalized dermis was elevated to the air liquid interface of a 6 cm tissue culture dish that contained 4 ml of keratinocyte growth media then primary human keratinocytes were seeded on top of it. Media was changed every other day for 4 weeks. Keratinocytes self-organized into a fully stratified epidermal tissue.

extract_protocol:
The tissue was placed in dispase at 37C for two hours or until the epidermis could be peeled apart from the dermis. The epidermis was then trypsinized for 30 min. The dermis was digested in collagenase for 1 hour followed by trypsin for 30 minutes. Epidermal and dermal cells were independently incubated with DNAse for 5 min, filtered over a 40um cell strainer, recombined into the same solution, and flow sorted for live cells for library preparation.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v3 chemistry. Libraries were sequenced on an Illumina Next-Seq6000 platform (Illumina). Cell counting, capture, library preparation, quality control, and sequencing was performed at the Genomics High Throughput Sequencing facility at the University of California, Irvine.
Single Cell 3’ v3 chemistry - 10X Genomics

treatment_protocol: Human skin equivalent consisting of an epidermal layer comprised entirely of primary human keratinocytes and a devitalized dermis from human cadavers that has been seeded with primary human dermal fibroblasts. No matrigel was used. This human skin equivalent was grown for 28 days prior to sequencing. Biological replicate 2.


title: Human skin equivalent containing fibroblasts - Replicate 1

description:
Fibroblast_HSE-1_10XGenomics
RNA from single cells

treatment_protocol: Human skin equivalent consisting of an epidermal layer comprised entirely of primary human keratinocytes and a devitalized dermis from human cadavers that has been seeded with primary human dermal fibroblasts. No matrigel was used. This human skin equivalent was grown for 28 days prior to sequencing. Biological replicate 1.


title: 12C_M_2797


title: sgNS+EV 0h rep2


title: Human skin equivalent containing Matrigel - Replicate 2

description:
Matrigel_HSE-2_10XGenomics
RNA from single cells

growth_protocol: Matrigel was applied to the underside of a 1.5 square cm piece of devitalized dermis. The devitalized dermis was elevated to the air liquid interface of a 6 cm tissue culture dish that contained 4 ml of keratinocyte growth media then primary human keratinocytes were seeded on top of it. Media was changed every other day for 4 weeks. Keratinocytes self-organized into a fully stratified epidermal tissue.

extract_protocol:
The tissue was placed in dispase at 37C for two hours or until the epidermis could be peeled apart from the dermis. The epidermis was then trypsinized for 30 min, and the dermis was discarded. Epidermal cells were incubated with DNAse for 5 min, filtered over 40um cell strainer, and flow sorted for live cells for library preparation.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v3 chemistry. Libraries were sequenced on an Illumina Next-Seq6000 platform (Illumina). Cell counting, capture, library preparation, quality control, and sequencing was performed at the Genomics High Throughput Sequencing facility at the University of California, Irvine.
Single Cell 3’ v3 chemistry - 10X Genomics

treatment_protocol: Human skin equivalent consisting of an epidermal layer comprised entirely of primary human keratinocytes and a devitalized dermis from human cadavers that has matrigel applied to the underside. This human skin equivalent was grown for 28 days prior to sequencing. Biological replicate 2.


title: 12C_M_2795


title: SCR2


title: 12C_M_129


title: 12C_M_2794


title: 12C_M_2804


title: www39_CFA_OXY

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

description:
www39
S18

data_processing:
alignment to Rn6 genome from UCSC using hisat2 (v2.1.0) followed by samtools to sort alignments
counting using htseq-count (v0.6.1) with 'intersection-strict'
indidivual count files were compiled into single csv using R/DESeq2
Assembly: Rn6
Supplementary files format and content: CSV files. Counts from HTSEQ-COUNT.

organism: Rattus norvegicus

source_name: Brain / mPFC

growth_protocol: Adult male Sprague-Dawley rats

extract_protocol:
mRNA from tissue punches (2mm punches obtained from the mPFC region) was isolated and purified using TRIzol (Ambion, Austin, TX) and the Qiagen total RNA kit with on-column DNase (Qiagen, Venlo, Netherlands). RNA concentrations were measured on a NanoDrop.
RNA libraries were constructed using the Illumina TruSeq Stranded Total RNA library prep kit

treatment_protocol: CFA = injection of 0.1 mL in paw or saline as control; OXY = injection of 1 mg/g IP daily for 7 days or saline as control.

value: Brain / mPFC

tag: pain

value: CFA

tag: drug

value: OXY


title: SCR1


title: 12C_M_2793


title: www29_CFA_Saline

description:
www29
S17

value: Saline


title: 12C_M_2792


title: www19_Saline_OXY

description:
www19
S16


title: www09_Saline_Saline

description:
www09
S15


title: Xenografted human skin equivalent - Mouse Alignment

description:
Xenograft_HSE-1_Mm_Alignment_10XGenomics
RNA from single cells

treatment_protocol: Human skin equivalents consisting of an epidermal layer comprised entirely of primary human keratinocytes and a devitalized dermis from human cadavers that has matrigel applied to the underside. Human skin equivalents were first grown for 1 week to reepithelialize the tissue and then the matrigel was removed and the human skin equivalent was grafted onto NSG mice (Jackson Laboratory: 005557) for 26 days. Cells from three grafts were collected and pooled prior to sequencing. This is the same replicate as the Xenograft_HSE-1_Hs_Alignment_10XGenomics sample except it was aligned to the mm10 genome.


title: 12C_M_2791


title: 12C_M_2790


title: 12C_M_2800


title: ww38_CFA_OXY

description:
ww38
S14


title: ww37_CFA_OXY

description:
ww37
S10


title: 12C_M_2788


title: 12C_M_2796


title: 12C_M_2786


title: 12C_M_2785


title: ww34_CFA_OXY

description:
ww34
S16


title: 12C_M_2787


title: ww35_CFA_OXY

description:
ww35
S2


title: ww32_CFA_OXY

description:
ww32
S8


title: www33_CFA_OXY

description:
www33
S12


title: 12C_M_2783


title: 12C_M_2780


title: ww31_CFA_OXY

description:
ww31
S4


title: 12C_M_2779


title: ww28_CFA_Saline

description:
ww28
S13


title: 12C_M_2777


title: ww26_CFA_Saline

description:
ww26
S5


title: 12C_M_2778


title: ww30_CFA_Saline

description:
ww30
S1


title: 12C_M_2776


title: ww27_CFA_Saline

description:
ww27
S9


title: 12C_M_2775


title: ww23_CFA_Saline

description:
ww23
S11


title: ww24_CFA_Saline

description:
ww24
S15


title: 12C_M_2773


title: ww36_CFA_OXY

description:
ww36
S6


title: ww22_CFA_Saline

description:
ww22
S7


title: ww20_Saline_OXY

description:
ww20
S2


title: 12C_M_2774


title: 12C_M_2772


title: ww18_Saline_OXY

description:
ww18
S12


title: ww21_CFA_Saline

description:
ww21
S3


title: 12C_M_2771


title: ww17_Saline_OXY

description:
ww17
S8


title: 12C_M_2769


title: 12C_M_2784


title: ww16_Saline_OXY

description:
ww16
S4


title: 12C_M_2768


title: ww15_Saline_OXY

description:
ww15
S18


title: ww14_Saline_OXY

description:
ww14
S14


title: ww13_Saline_OXY

description:
ww13
S10


title: 12C_M_2767


title: 12C_M_2765


title: 12C_M_2763


title: 12C_M_2766


title: ww08_Saline_Saline

description:
ww08
S11


title: 12C_M_2762


title: ww10_Saline_Saline

description:
ww10
S13


title: ww07_Saline_Saline

description:
ww07
S7


title: 12C_M_2761


title: 12C_M_2760


title: ww05_Saline_Saline

description:
ww05
S17


title: ww06_Saline_Saline

description:
ww06
S3


title: 12C_M_2759


title: 12C_M_2770


title: ww03_Saline_Saline

description:
ww03
S9


title: 12C_M_2758


title: 12C_M_2757


title: ww01_Saline_Saline

description:
ww01
S1


title: 12C_M_2756


title: 12C_M_2755


title: 12C_M_2754


title: 12C_M_2753


title: ww12_Saline_OXY

description:
ww12
S6


title: 12C_M_2752


title: 12C_M_2764


title: 12C_M_2750


title: 12C_M_2751


title: 12C_M_2749


title: ww02_Saline_Saline

description:
ww02
S5


title: 12C_M_2748


title: 12C_M_2746


title: 12C_M_2747


title: 12C_M_2745


title: 12C_M_2743


title: 12C_M_2742


title: 12C_M_2740


title: 12C_M_2744


title: 12C_M_2741


title: 12627 - BM D pool2

type: RNA

first: Ruteja

middle: A

last: Barve

state: MO

address: 4515 McKinley Ave

institute: Washington University

description: Vitamin D sufficient

hyb_protocol: 25 ng of starting RNAs were amplified with NuGEN Ovation PicoSL WTAV2 kit (NuGEN Technologies Inc., San Carlos, CA) and2,500 ng of biotin-labeled cDNAs were hybridized following vendor's standard protocol

scan_protocol: Arrays were washed and stained and subsequently scanned on an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara,  CA, USA).

data_processing: CEL files (row data files) were preprocessed (RMA background subtraction and quantile normalization were applied) in Partek GS (www.partek.com). All control probe sets were removed prior to the analysis. A principal Component Analysis (PCA) was performed to check the sample quality.

label: biotin

source_name: BM of VD+ FL-HSC mice

growth_protocol: Mice (8 weeks) of both sexes, either Vitamin D deficiency diet or Vitamin D sufficiency diet

extract_protocol: Use Trizol method, and then RNA clean up with Qiagen Kit(Rneasy clean up)

treatment_protocol: Bone marrow macrophages from mice (8 weeks) of both sexes, either Vitamin D deficiency diet or Vitamin D sufficiency diet

tag: group

value: Vitamin D sufficient


title: 12630 - BM D-3

description: Vitamin D deficient

source_name: BM of VD-  FL-HSC mice

label_protocol: 25 ng of starting RNAs were amplified with NuGEN Ovation PicoSL WTAV2 kit (NuGEN Technologies Inc., San Carlos, CA) and2,500 ng of biotin-labeled cDNAs were hybridized following vendor's standard protocol

value: Vitamin D deficient


title: ORCA 93

city: Amsterdam

first: Frederike

last: Dijk

address: Meibergdreef 9

country: Netherlands

institute: AMC

description:
replicate 1
Fresh frozen tissue

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. The file "Normalized_data.txt" contains the quantile normalized signal and can be found on the series record.

label: Cy 3

source_name: Ovarian adenocarcinoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with RNABee, followed by DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: ovary

tag: gender

value: Female

tag: histological subtype

value: undifferentiated adenocarcinoma

tag: figo

value: IV

tag: differentiation grade

tag: type i or type ii

value: type II (highgrade serous, undiff)

tag: overall survival (mnths)


title: ORCA 91

description:
replicate 1
Fresh frozen tissue

tag: tissue

value: enodometrioid adenocarcinoma

value: IA

value: type I (grade I serous and others)


title: ORCA 90

description:
replicate 1
Fresh frozen tissue

value: serous adenocarcinoma

value: IIIC


title: ORCA 92

description:
replicate 1
Fresh frozen tissue


title: ORCA 94

description:
replicate 1
Fresh frozen tissue


title: 12632 - BM D- pool2

description: Vitamin D deficient


title: 12628 - BM D-1

description: Vitamin D deficient


title: ORCA 95

description:
replicate 1
Fresh frozen tissue


title: ORCA 89

description:
replicate 1
Fresh frozen tissue


title: 12623 - BM D1

description: Vitamin D sufficient


title: 12629 - BM D-2

description: Vitamin D deficient


title: 12624 - BM D2

description: Vitamin D sufficient


title: ORCA 88

description:
replicate 1
Fresh frozen tissue

value: IIc


title: 12631 - BM D- pool1

description: Vitamin D deficient


title: 12626 - BM D pool1

description: Vitamin D sufficient


title: ORCA 87

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2739


title: 12C_M_2738


title: 12625 - BM D3

description: Vitamin D sufficient


title: ORCA 86

description:
replicate 1
Fresh frozen tissue

value: IIIB


title: ORCA 85

description:
replicate 1
Fresh frozen tissue

value: IIIA


title: 12C_M_2736


title: 12C_M_2735


title: 12C_M_2734


title: ORCA 84

description:
replicate 1
Fresh frozen tissue


title: ORCA 83

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2733


title: ORCA 82

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2737


title: ORCA 78

description:
replicate 1
Fresh frozen tissue


title: ORCA 74

description:
replicate 1
Fresh frozen tissue

value: IIC


title: ORCA 75

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2731


title: 12C_M_2727


title: 12C_M_2724


title: 12C_M_2732


title: 12C_M_2725


title: ORCA 72

description:
replicate 1
Fresh frozen tissue


title: ORCA 77

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2726


title: 12C_M_2730


title: ORCA 79

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2729


title: 12C_M_2728


title: ORCA 80

description:
replicate 1
Fresh frozen tissue

value: mucinous adenocarcinoma


title: ORCA 73

description:
replicate 1
Fresh frozen tissue


title: ORCA 70

description:
replicate 1
Fresh frozen tissue


title: ORCA 69

description:
replicate 1
Fresh frozen tissue


title: ORCA 68

description:
replicate 1
Fresh frozen tissue


title: ORCA 67

description:
replicate 1
Fresh frozen tissue


title: ORCA 66

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2720


title: 12C_M_2721


title: 12C_M_2723


title: 12C_M_2722


title: 12C_M_2719


title: 12C_M_2718


title: ORCA 63

description:
replicate 1
Fresh frozen tissue


title: ORCA 64

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2717


title: ORCA 65

description:
replicate 1
Fresh frozen tissue


title: ORCA 62

description:
replicate 1
Fresh frozen tissue


title: ORCA 60

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2715


title: ORCA 58

description:
replicate 1
Fresh frozen tissue


title: ORCA 61

description:
replicate 1
Fresh frozen tissue

value: IC


title: 12C_M_2716


title: 12C_M_2714


title: 12C_M_2712


title: 12C_M_2709


title: ORCA 57

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2711


title: 12C_M_2713


title: ORCA 59

description:
replicate 1
Fresh frozen tissue


title: ORCA 55

description:
replicate 1
Fresh frozen tissue


title: ORCA 71

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2708


title: ORCA 54

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2707


title: ORCA 51

description:
replicate 1
Fresh frozen tissue


title: ORCA 52

description:
replicate 1
Fresh frozen tissue

value: clear cell adenocarcinoma


title: ORCA 53

description:
replicate 1
Fresh frozen tissue

value: ovary


title: 12C_M_2704


title: 12C_M_2705


title: ORCA 50

description:
replicate 1
Fresh frozen tissue

value: Female


title: ORCA 49

description:
replicate 1
Fresh frozen tissue


title: ORCA 47

description:
replicate 1
Fresh frozen tissue

value: undifferentiated adenocarcinoma


title: ORCA 48

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2702


title: 12C_M_2700


title: 12C_M_2701


title: 12C_M_2699


title: ORCA 44

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2698


title: ORCA 45

description:
replicate 1
Fresh frozen tissue

value: IV


title: ORCA 43

description:
replicate 1
Fresh frozen tissue

value: type II (highgrade serous, undiff)


title: 12C_M_2697


title: 12C_M_2706


title: ORCA 42

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2696


title: P50_retina_OIR+AFLx2_rep2

city: Cambridge

first: Jesus Eduardo

last: Rojo Arias

address: Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: Retina of P50 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13 and 15 replicate 2

hyb_protocol: 5.5 ug of biotinylated and fragmented single-stranded cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Whole Transcriptome Arrays according to the GeneChip® WT PLUS Reagent Kit User Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The scanned images were processed with the Transcriptome Analysis Console (TAC) Software (Affymetrix) using default parameters to obtain background subtracted and summarized probe sets.
The data were analyzed with the Agilent GeneSpring GX software version 13.0 using Affymetrix default analysis settings and GC-RMA. No baseline transformation was done.
The normalized_data_matrix.txt contains the normalized light intensity readings of the microarray for all transcripts, with chromosomal locations included and is being used for identification of differentially regulated transcripts.

label: proprietary DNA labeling reagent (GeneChipTM WT PLUS Reagent Kit)

label_protocol: Biotinylated cDNA samples were prepared according to the GeneChip WT PLUS Reagent Kit (902280) protocol from 250 ng total RNA.

growth_protocol: Mice were housed in standard conditions. OIR mice were subjected to 75% oxygen from postnatal day 6 to postnatal day 11. OIR+AFLx2 mice were treated with Aflibercept at 25 mg per kg body weight on postnatal day 13 and 15. OIR+AFLx3 mice were treated with Aflibercept at 25 mg per kg body weight on postnatal day 13, 15 and 17.

extract_protocol: Total RNA was isolated from whole retinas as follows. Mice were sacrificed at P50 by an overdose of ketamine and xylazine. Eyes were immediately removed from their orbits and retinal cups were promptly dissected in PBS at 37°C. After dissection, both retinas of a single normoxic, OIR, OIR+AFLx2 or OIR+AFLx3 mouse were pooled together and warm PBS was replaced by 750 µl TRIzol (Thermo Fisher Scientific, MA, USA). Next, retinal tissues were disrupted by 10 rounds of aspiration/ejection through 18G and 23G needles and incubated at RT for 5 min. Thereafter, 150 µl chloroform (Merck, Darmstadt, Germany) were added, samples were vortexed at maximum speed for 15 seconds, incubated at RT for 15 min, and centrifuged at 12 000 g for 20 min at 4°C. After centrifugation, the aqueous phase was collected, 1.5 µl RNA-grade glycogen (Thermo Fisher Scientific, MA, USA) and 375 µl isopropanol (Merck, Darmstadt, Germany) were added. Samples were subsequently vortexed 15 seconds at maximum speed and centrifuged at 12000 g for 20 min at 4°C. The supernatant was discarded, and pellets were washed twice in 1 ml 75% ethanol in molecular biology-grade water, air-dried for 10-20 min and re-suspended in 20 µl RNAse-free water.

treatment_protocol: Aflibercept was administered to OIR mice intra-peritoneally at 25 mg per kg body weight on postnatal days 13 and 15 (OIR+AFLx2) or on postnatal days 13, 15 and 17 (OIR+AFLx3).

tag: developmental stage

value: Postnatal day 50

value: oxygen-induced retinopathy mouse treated with 25 mg per kg body weight AFL on P13 and P15

value: Retina


title: P50_retina_OIR+AFLx2_rep1

description: Retina of P50 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13 and 15 replicate 1


title: P50_retina_OIR+AFLx2_rep3

description: Retina of P50 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13 and 15 replicate 3


title: P50_retina_OIR+AFLx3_rep3

description: Retina of P50 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13, 15 and 17 replicate 3

value: oxygen-induced retinopathy mouse treated with 25 mg per kg body weight AFL on P13, P15 and P17


title: 12C_M_2703

tag: brain region


title: P50_retina_OIR+AFLx3_rep1

description: Retina of P50 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13, 15 and 17 replicate 1


title: P50_retina_OIR_rep3

description: Retina of P50 mouse subjected to the OIR protocol replicate 3

value: oxygen-induced retinopathy mouse


title: P50_retina_OIR_rep2

description: Retina of P50 mouse subjected to the OIR protocol replicate 2


title: Mouse NAc, biol replicate 1, snATACseq

city: Boston

first: Parth

last: Bhatia

state: Massachusetts

address: 230 South Huntington Avenue, Apt 1

department: Neurology

institute: Brigham and Women's Hospital

description:
Sample1
NAc_snATAC_GEO_Submission.rds
Metadata_to_submit_NAc.csv

library_source: genomic single cell

data_processing:
After sequencing, Illumina BCL files were mapped the mouse reference genome (GRCm38) using the Cellranger ATAC v1.1.0 pipeline using default settings.
Assembly: mm10
Supplementary files format and content: Seurat object containing raw and normalized counts from filtered cells annotated by cell type along with meta data provided separately as csv file.

source_name: Brain

extract_protocol:
Isolation of NAc nuclei was performed according to the ‘non- gradient’ nuclear isolation protocol we described previously (Yang et al., 2022) with minor modifications. Briefly, bilateral NAc were dissected from 1 mm coronal sections using 14 g tissue biopsy punches (centered on 1.6 AP, 0.9 ML, 􀀀4.4 DV) and frozen on dry ice (Renthal et al., 2007). Each sample included NAc pooled from two mice. Nuclei from two biological replicates were isolated separately; they were thawed in homogenization buffer (73 mM NaCl, 0.5 mM CaCl2, 10 mM MgCl2,5 mM Tris-HCl pH 7.5, 1 % BSA, and 0.1 U/μl RNase inhibitor (Promega)) and transferred to a total of 5 mL of homogenization buffer in a Dounce homogenizer for 10 strokes with the tight pestle. Tween 20 (0.01 %), NP40 (0.01 %), and Digitonin (0.001 %) was then added and 5 additional strokes with the tight pestle were performed. The homogenate was then passed through a 40 μM filter and diluted 1:1 with mogenization buffer without detergent. Nuclei were then centrifugated at 500 g for 10 min at 4C and resuspended in 1×PBS, 0.04 % BSA, and 0.1 U/μL RNAse inhibitor and quantified using a hemocytometer.
Approximately 10,000 nuclei in total from two biological replicate were added to a 10x Genomics ATAC-seq chip. Biological replicates were processed independently according to the manufacturer's structions. Library fragment distribution was confirmed using an Agilent Tapestation and libraries were sequenced on an Illumina Nextseq 550 using a 75 cycle high output kit.
10X Genomics ATAC assay

value: Nucleus accumbens

value: Brain

tag: age

value: 8 weeks old


title: ORCA 41

description:
replicate 1
Fresh frozen tissue

value: serous adenocarcinoma

value: IIIC


title: Mouse NAc, biol replicate 2, snATACseq

description:
Sample2
NAc_snATAC_GEO_Submission.rds
Metadata_to_submit_NAc.csv

tag: strain


title: ORCA 40

description:
replicate 1
Fresh frozen tissue

value: enodometrioid adenocarcinoma

value: type I (grade I serous and others)


title: P50_retina_OIR+AFLx3_rep2

description: Retina of P50 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13, 15 and 17 replicate 2

tag: treatment


title: P50_retina_normoxia_rep3

description: Retina of P50 normoxic mouse replicate 3

value: normoxic mouse


title: ORCA 39

description:
replicate 1
Fresh frozen tissue

value: ovary

value: Female


title: P50_retina_normoxia_rep2

description: Retina of P50 normoxic mouse replicate 2


title: P50_retina_OIR_rep1

description: Retina of P50 mouse subjected to the OIR protocol replicate 1


title: P50_retina_normoxia_rep1

description: Retina of P50 normoxic mouse replicate 1


title: ORCA 38

description:
replicate 1
Fresh frozen tissue


title: CRAC_Rpb1_Top1AIDTop2AID_IAA_R2

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor was clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (martin M. embnet.journal, 2011) and the resulting insert  quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
Assembly: R64
Supplementary files format and content: Bigwig files providing coverage for all samples. All values are normalized to 10,000,000 reads or to S. pombe spike-in
Library strategy: CRAC-seq

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae culture

growth_protocol: For all datasets, 2L of yeast cells expressing an HTP-tagged version of target protein were grown at 30°C to OD600=0.6 in conditional media.

extract_protocol:
Cells were broken and extracts were prepared as described in the original publication.
Library construction is described in Candelli et al., EMBO J, 2018 and in the associated manuscript.

treatment_protocol: For the IAA condition, cells were treated with 5 mM Indole-3-acetic acid (IAA) for 1h before processing. Cells were crosslinked for 50 seconds using a W5 UV crosslinking unit (UVO3).

value: as w303, Top1-AID Top2-AID

tag: cell cycle phase

value: Asynchronous

tag: tagged protein


title: 12C_M_2691

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.


title: ORCA 37

description:
replicate 1
Fresh frozen tissue

value: undifferentiated adenocarcinoma

value: IV

value: type II (highgrade serous, undiff)


title: 12C_M_2693


title: 12C_M_2692


title: 12C_M_2690


title: 12C_M_2689


title: ORCA 35

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2695


title: ORCA 36

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2694


title: CRAC_Rpb1_Top1AIDTop2AID_IAA_R1


title: CRAC_Rpb1_Top1AIDTop2AID_noIAA_R2


title: ORCA 33

description:
replicate 1
Fresh frozen tissue


title: CRAC_Rpb1_Top1AIDTop2AID_noIAA_R1


title: 12C_M_2688


title: ORCA 34

description:
replicate 1
Fresh frozen tissue


title: ORCA 32

description:
replicate 1
Fresh frozen tissue


title: Dam-Pc

city: Beijing

first: Tao

last: He

address: Summer Palace Road No. 5

country: China

institute: Peking university

data_processing:
DamID-seq reads were aligned to the dmel-r6.41 genome using Bowtie2 version 2.3.5.1.
To create DamID-seq coverage plots, the locations of the mapped DamID-seq reads were extended to 300 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: dmel-all-chromosome-r6.41
Supplementary files format and content: bedgraph format files (log2 ratio compared with Dam control）
Library strategy: DamID-seq

organism: Drosophila melanogaster

source_name: Wing imaginal disc

extract_protocol: Drosophila wing discs of indicated genotypes were collected, and DNA were extracted using the DNeasy Tissue kit.

value: Wing imaginal disc

tag: cell line

value: tissue

tag: cell type

value: epithelial cell

tag: genotype

value: nub-Gal4, UAS-Dam-Pc


title: Dam-Pc+Stx

value: nub-Gal4, UAS-Dam-Pc, UAS-Stx-HA


title: 12C_M_2686

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

source_name: C57BL/6J Male P56 Mouse Brain


title: 12C_M_2687


title: 12C_M_2685


title: ORCA 31

description:
replicate 1
Fresh frozen tissue

tag: gender


title: Dam-Ctr

value: nub-Gal4, UAS-Dam


title: ORCA 30

description:
replicate 1
Fresh frozen tissue

tag: histological subtype

value: serous adenocarcinoma

value: IIIC


title: 12C_M_2684


title: ORCA 29

description:
replicate 1
Fresh frozen tissue

tag: figo


title: 12C_M_2683


title: 12C_M_2682


title: ORCA 27

description:
replicate 1
Fresh frozen tissue

value: clear cell adenocarcinoma

value: IC

tag: differentiation grade

value: type I (grade I serous and others)


title: ORCA 28

description:
replicate 1
Fresh frozen tissue

value: ovary

value: Female

value: mucinous adenocarcinoma

tag: type i or type ii


title: 12C_M_2681


title: ORCA 26

description:
replicate 1
Fresh frozen tissue

tag: overall survival (mnths)


title: 12C_M_2680


title: 12C_M_2679


title: 12C_M_2678


title: ORCA 25

description:
replicate 1
Fresh frozen tissue

tag: tissue


title: 12C_M_2677


title: ORCA 24

description:
replicate 1
Fresh frozen tissue


title: ORCA 22

description:
replicate 1
Fresh frozen tissue

value: enodometrioid adenocarcinoma

value: IIC


title: ORCA 23

description:
replicate 1
Fresh frozen tissue

value: IV


title: Human skin equivalent containing Matrigel - Replicate 1

description:
Matrigel_HSE-1_10XGenomics
RNA from single cells

extract_protocol:
The tissue was placed in dispase at 37C for two hours or until the epidermis could be peeled apart from the dermis. The epidermis was then trypsinized for 30 min, and the dermis was discarded. Epidermal cells were incubated with DNAse for 5 min, filtered over 40um cell strainer, and flow sorted for live cells for library preparation.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry. Libraries were sequenced on an Illumina Next-Seq4000 platform (Illumina). Cell counting, capture, library preparation, quality control, and sequencing was performed at the Genomics High Throughput Sequencing facility at the University of California, Irvine.
Single Cell 3’ v2 chemistry - 10X Genomics

treatment_protocol: Human skin equivalent consisting of an epidermal layer comprised entirely of primary human keratinocytes and a devitalized dermis from human cadavers that has matrigel applied to the underside. This human skin equivalent was grown for 28 days prior to sequencing. Biological replicate 1.

value: Human skin equivalent


title: 12C_M_2675


title: GEX mel7_scexpTIL_1

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

data_processing:
The scRNA-Seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count (10X Genomics, version 4.0.0). Filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used and processed using the Seurat R package version 4.0.1.
For live-sorted cells from expanded TILs data (5`GEX), we defined and removed low-quality cells containing more than 10% of mitochondrial reads.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression raw count with Gene Symbol mapping for filtered non-apoptotic cells in tab-separted format

source_name: melanoma

extract_protocol:
TILs were expanded from melanoma tumors following conventional pre-REP and REP conditions as previously described (Gannon et al., Cytotherapy, 2020). Some expanded TILs were cryopreserved in 90% human serum + 10% DMSO for latter studies. The day of the assay, the product of expansion was thawed and TILs undergone overnight recovery in R8 medium supplemented with 3000 IU/mL IL-2 (Proleukin) or fresh TILs were directly used. TILs were resuspended in PBS + 0.04% BSA and DAPI (Invitrogen) staining was performed.
Live cells were sorted with a BD FACS Melody sorter and manually counted to assess viability with Trypan blue. Live TILs were resuspended at a density of 600-1200 cells µL-1 with a viability of >90% and subjected to a 10X Chromium instrument for single-cell analysis. The standard protocol of 10X Genomics was followed and the reagents for the Chromium Single Cell 5’ Library and V(D)J library (v1.0 or v1.1 Chemistry) were used. 15’000 cells were loaded per sample. Using a microfluidic technology, single-cell were captured and lysed, mRNA was reverse transcribed to barcoded cDNA using the provided reagents (10X Genomics). 14 PCR cycles were used to amplify cDNA and the final material was divided into two fractions: first fraction was target-enriched for TCRs and V(D)J library was obtained according to manufacturer protocol (10X Genomics). The second fraction was processed for 5’ gene expression library following the manufacturer’s instruction (10X Genomics). Barcoded V(D)J libraries and GEX libraries were pooled and sequenced by an Illumina HiSeq 4000 sequencer.

value: melanoma

tag: patient

value: expanded TILs


title: VDJ mel10_scexpTIL_1

data_processing:
The scTCR-Seq reads were aligned to the GRCh38 reference genome (refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0) and quantified using cellranger vdj (10X Genomics, version 4.0.0).
Assembly: GRCh38
Supplementary files format and content: csv file ("all_contig_annotations.csv" output from Cellranger) containing the mapping of unique cells to TCR

extract_protocol:
TILs were generated in the GMP manufacturing facilities of the Centre of Thérapies Expérimentales (CTE) of the Centre Hospitalier Universitaire Vaudois (CHUV) under specific conditions previously described (Gannon et al., Cytotherapy, 2020). Some TILs of the infusion product were cryopreserved in 90% human serum + 10% DMSO for translational studies. The day of the assay, the samples of the infused T cell product were thawed and TILs undergone overnight recovery in R8 medium supplemented with 3000 IU/mL IL-2 (Proleukin) or fresh TILs were directly used. TILs were resuspended in PBS + 0.04% BSA and DAPI (Invitrogen) staining was performed.
Live cells were sorted with a BD FACS Melody sorter and manually counted to assess viability with Trypan blue. Live TILs were resuspended at a density of 600-1200 cells µL-1 with a viability of >90% and subjected to a 10X Chromium instrument for single-cell analysis. The standard protocol of 10X Genomics was followed and the reagents for the Chromium Single Cell 5’ Library and V(D)J library (v1.0 or v1.1 Chemistry) were used. 15’000 cells were loaded per sample. Using a microfluidic technology, single-cell were captured and lysed, mRNA was reverse transcribed to barcoded cDNA using the provided reagents (10X Genomics). 14 PCR cycles were used to amplify cDNA and the final material was divided into two fractions: first fraction was target-enriched for TCRs and V(D)J library was obtained according to manufacturer protocol (10X Genomics). The second fraction was processed for 5’ gene expression library following the manufacturer’s instruction (10X Genomics). Barcoded V(D)J libraries and GEX libraries were pooled and sequenced by an Illumina HiSeq 4000 sequencer.
scTCR-seq


title: GEX mel10_scexpTIL_1


title: ORCA 21

description:
replicate 1
Fresh frozen tissue

value: type II (highgrade serous, undiff)


title: VDJ mel7_scexpTIL_1


title: VDJ mel8_scexpTIL_1


title: 12C_M_2676

first: Joseph

tag: brain region


title: GEX mel8_scexpTIL_1


title: VDJ mel9_scexpTIL_1


title: GEX mel9_scexpTIL_1


title: ORCA 20

description:
replicate 1
Fresh frozen tissue

tag: age

value: undifferentiated adenocarcinoma


title: ORCA 19

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2674

tag: strain


title: 12C_M_2673


title: 12C_M_2672


title: ORCA 17

description:
replicate 1
Fresh frozen tissue


title: EL_input_sh4-UBAP2L_1

first: En-Ching

last: Luo

address: 9500 Gilman St

institute: UCSD

data_processing:
RNA-sequencing reads were trimmed using cutadapt (v1.4.0) of adaptor sequences, and mapped to repetitive elements (RepBase v18.04) using the STAR (v2.4.0i). Reads did not map to repetitive elements were then mapped to the human genome (hg19). Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
Differential expression was calculated using DESeq2 version 1.10.1
The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.
Genome_build: Homo sapiens UCSC hg19

source_name: hPSC cortical neuron

growth_protocol: H1 human pluripotent stem cells (hPSCs) were edited by CRISPR-Cas9 to generate KO and WT FMR1 clones. Details are described in a separate study (Kosmaczewski et al., in preparation). All hPSCs were maintained in mTeSR medium (Stem Cell Technologies) supplemented with 5 µM XAV939 (Stemgent), grown on Geltrex-coated plates (Life Technologies) and passaged with TrypLE Express (Life Technologies) plus Y27632 ROCK inhibitor (Stemgent). For knockdown experiments, hPSCs were transduced in suspension with lentivirus for UPBAP2L-shRNA3, UPBAP2L-shRNA4, or non-targeting shRNA. Two days post-transduction, cells were selected and then maintained with 5 µg/mL puromycin. Excitatory cortical neurons were generated as described (Nehme et al., 2018). Briefly, on day 1, hPSCs expressing doxycycline-inducible Ngn2 were seeded at 40,000 cells/cm2 and 8 hours later, Ngn2 expression was induced with doxycycline in KSR media supplemented with patterning molecules. On day two, media was changed to a 50:50 mix of KSR and N2 with Zeocin at 5 µg/ml (Thermo Fisher) to select for cells expressing Ngn2. On day three, media was changed to N2 plus B27 with Zeocin. On day four, cells were re-plated and then maintained in NBM plus B27 and neurotrophic factors. Doxycyclin was maintained in the media throughout the differentiation process. On day 14, neurons were treated with 100 µg/ml cycloheximide (Sigma) for 3 minutes, washed with ice-cold PBS plus cycloheximide, spun down, aspirated and flash frozen.

extract_protocol:
Total and polysome derived RNA were extracted using Trizol reagent
Strand-specific RNA sequencing libraries were prepared from 0.5-3 µg total RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina).

treatment_protocol: Polysome cells were treated with cycloheximide (CHX) at 100 µg/ml for 5 min at 37°C.

value: hPSC cortical neuron


title: EL_poly_scramble_2


title: EL_input_sh3-UBAP2L_1


title: EL_poly_sh3-UBAP2L_1


title: 12C_M_2670

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: EL_input_scramble_2


title: ORCA 16

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2669


title: 12C_M_2668


title: EL_poly_sh4-UBAP2L_1


title: EL_poly_scramble_1


title: ORCA 15

description:
replicate 1
Fresh frozen tissue

value: serous adenocarcinoma


title: ORCA 14

description:
replicate 1
Fresh frozen tissue

value: IA


title: 12C_M_2667


title: 12C_M_2666


title: Sam3_3

city: Chongqing

first: Yanxi

address: 2 Tiansheng Street

department: College of Animal Medicine

institute: Southwest University

data_processing:
illumina Casava 1.8 software used for basecalling
Alignment analysis of the reference genome was performed on the filtered clean reads using HISAT2.
CIRI2 According to the comparison results of bwa (Heng Li, 2013), look for PCC (paired chiastic clipping) signal, PEM (pair end mapping) signal, GTAG shear site information preliminarily determine junction reads. Then, based on the results of the global alignment (Dynamic Programming alignment) and the supporting number of reads of circRNA, the candidate circRNA is filtered by the reference genome annotation information. Finally, based on the results of CIRI 2 identification and bwa comparison results, the length of circRNA and the expression level were corrected using CIRI AS().
Density statistics were performed on the reads from all alignments of each sample to each chromosome on the genome, and the distribution of reads on each chromosome was viewed with circos mapping.
Supplementary files format and content: tab-delimited text files

organism: Sus scrofa

source_name: PK-15 cells, SVA infection

growth_protocol: PK-15 cells were maintained in DMEM supplemented with 5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Total rna extraction kit (TianGen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
The total RNA samples were subjected to quality detection, rRNA was removed, double-stranded DNA was synthesized, the ends were repaired, sequencing joints were connected, fragment selection, degradation of second-strand cDNA, PCR enrichment, and computer sequencing after library quality inspection.
circRNA-seq

treatment_protocol: PK-15 cells were infected with the SVA-CH-CQ strain (moi = 1).

value: PK-15  cells

value: Porcine Kidney-15

tag: treatment

value: SVA-infected


title: Sam3_1


title: Sam3_2


title: Sam1_3

source_name: PK-15 cells

value: SVA-noninfected


title: EL_input_scramble_1


title: EL_pol_wt_2


title: ORCA 18

description:
replicate 1
Fresh frozen tissue

value: ovary

value: Female

value: IIIC


title: Sam1_2


title: ORCA 12

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2665


title: EL_pol_wt_1


title: 12C_M_2664


title: Sam1_1


title: ORCA 11

description:
replicate 1
Fresh frozen tissue

value: IIIB


title: skin, 4 hpb, scRNAseq

first: Zhaoyang

last: Wang

address: Shuangqing Road 30

institute: Tsinghua University

description: 10x Genomics

data_processing:
Cellranger pipeline The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
Seurat pipeline The other clustering method is Seurat 3.0(R package). Cells whose gene number was less than 200, or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormal and filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE and UMAP.
Enrichment Analysis GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testing adjustment, using top 20 markers gene of cluster. The results were visualized using R package.
PPI(protein-protein interaction) Protein-protein interaction was obtained from STRING database with combine_score >=400. For each cluster, the interaction of top 20 marker genes was extracted from the database and the results were visualized using Cytoscape software, respectively.
Transcription Factor Prediction Transcription Factors were predicted within 2000 bp upstream and 500 bp downstream of TSS for top 20 marker genes of each cluster using TFBSTools and JASPAR database. The gene and TF network for each cluster was visualized using Cytoscape software.
GSEA assay(Gene Set Enrichment Analysis) GSEA was performed by using GSEA software version 2.2.2.4, which uses predefined gene sets from the Molecular Signatures Database (MSigDB v6.2).All genes detected in all cells of one sample were used. Gene expression data was calculated by mean umi count of gene in one cluster and the rest cluster, respectively. The minimum and maximum criteria for selection of gene sets from the collection were 0 and 500 genes, respectively.
Single-cell trajectories Analysis Single-cell trajectories were built with Monocle (R package) that introduced pseudotime. Genes were filtered by the following criteria: Expressed in more than 10 cells; The average expression value was greater than 0.1; Qval was less than 0.01 in different analysis.
Cell Cycle Phase Cell Cycle Phase (human and mouse only) was assigned by Seurat 3.0 and the same parameters were used.
WGCNA Weighted correlation network analysis(WGCNA) was performed by The WGCNA R software package. According to above clustering result, every cluster was divided into sub-clusters, and average expression of gene in a sub-cluster was calculated. Parameters were default.
Cell Type Annotation Cell type was annotated by singleR (https://bioconductor.org/packages/devel/bioc/html/SingleR.html). Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently. For human, Blueprint_Encode or HPCA was used, and for mouse, ImmGen or Mouse.RNAseq.
Assembly: mm 10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: The skin of mouse footpads at 4 hours post mosquito bites

extract_protocol:
Ten Aedes aegypti mosquitoes were used to bite the two hind footpads of each of eight mice in two groups (0 h and 4 h). Footpads from each group were pooled together after collection. Control mice were not bitten, and the footpads were digested at 37 °C for 1 h using a mixed digestive solution containing type I and type II collagenases (1 mg/mL each). After dead cells and red blood cells were removed, flow cytometry was performed to sort CD45+ immunocytes for single-cell sequencing.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) strategy (performed by CapitalBi reading o Technology, Beijing).

value: Footpad skin

value: CD45+ immunocytes

tag: condition

value: 4h post mosquito bite


title: skin, 0 min, scRNAseq

description: 10x Genomics

source_name: The skin of mouse footpads without mosquito bites

value: no mosquito bite


title: ORCA 10

description:
replicate 1
Fresh frozen tissue

value: type II (highgrade serous, undiff)


title: EL_inp_ko_2


title: EL_pol_ko_1


title: ORCA 9

description:
replicate 1
Fresh frozen tissue

value: undifferentiated adenocarcinoma


title: ORCA 13

description:
replicate 1
Fresh frozen tissue

value: IC


title: ORCA 7

description:
replicate 1
Fresh frozen tissue


title: IPMK KO Treg, biological rep2

city: Seoul

first: Hyungyu

last: Min

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Regulatory T cells

growth_protocol: FACS-sorted cells

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Unstimulated

value: spleen

value: IPMK cKO

value: Regulatory T cells


title: ORCA 6

description:
replicate 1
Fresh frozen tissue

value: serous adenocarcinoma


title: ORCA 5

description:
replicate 1
Fresh frozen tissue


title: 12C_M_2659

city: La Jolla


title: 12C_M_2658


title: IPMK KO Treg, biological rep3


title: ORCA 4

description:
replicate 1
Fresh frozen tissue

value: enodometrioid adenocarcinoma

value: type I (grade I serous and others)


title: EL_inp_ko_1

value: hPSC cortical neuron


title: EL_pol_ko_2


title: WT Treg, biological rep2

value: wild type


title: 12C_M_2663


title: 12C_M_2657


title: 12C_M_2662


title: ORCA 3

description:
replicate 1
Fresh frozen tissue

value: ovary

value: Female

value: IIC


title: WT Treg, biological rep1


title: MWJ-3

description: Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age).  Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 12.5 and placental discs were isolated. Dissected placental disc tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Rnor_6.0) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Assembly: rat reference genome (Rnor_6.0)

source_name: rat junctional zone

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Rnor_6.0) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (wild type versus null).
RACE

tag: gestation day


title: 12C_M_2656


title: MWJ-2


title: EL_inp_wt_2


title: PCDH-V-3

city: Shanghai

first: Linjun

last: Shi

address: No. 639, Zhizaoju Road, Shanghai, China

institute: Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University, School of Medicine

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

growth_protocol: Leuk-1 cells were cultured in keratinocyte serum-free medium (cat. No.10744, GIBCO, USA),

extract_protocol:
Total RNA was extracted from cell by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We manipulated IFITM4P expression via the stable transduction of Leuk-1 cells with lentiviral vectors carrying cDNA encoding the full length of IFITM4P protein

tag: cell line

tag: transduced with

value: vector


title: 12C_M_2655


title: MWJ-1


title: 12C_M_2660


title: 12C_M_2661


title: ORCA 1

description:
replicate 1
Fresh frozen tissue

value: IIIC


title: EL_inp_wt_1


title: 12C_M_2654


title: MWJ-4


title: PCDH-V-2


title: IPMK KO Treg, biological rep1

tag: genotype

tag: cell type


title: MNJ-3


title: 12C_M_2653


title: 12C_M_2652


title: RA_Patient_4_RNA_R1

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

description:
patient 4
DK21229_04_5GE_S4

data_processing:
Basecalls and mapping performed using Cell Ranger v6.
Assembly: GRCh38

source_name: synovium

extract_protocol:
Synovium samples from four RA patients were obtained. Single-cell suspensions were prepared as previously described (PMID: 29996944). CD4+ T cells were magnetically sorted by MojoSort Mouse CD4 T Cell Isolation Kit, and susequently CD3+ CD4+ T cells were sorted by a FACS sorter.
Sorted cells were immediately subjected to 10X Chromium controler to prepare libraries. Libraries were prepared using Chromium Next GEM Single Cell 5'Kit v2 and Single-Cell Human TCR Amplificication Kit according to the protocol.

value: synovium

value: helper T cell


title: MNJ-2

first: Khursheed

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center


title: PCDH-IF-3


title: PCDH-V-1


title: ORCA 2

description:
replicate 1
Fresh frozen tissue

tag: gender

tag: histological subtype

value: IB

value: type II (highgrade serous, undiff)


title: RA_Patient_3_TCR_R1

description:
patient 3
DK21229_03_VDJ_S3


title: WT Treg, biological rep3

value: spleen


title: MNJ-1


title: PCDH-IF-2


title: 12C_M_2651


title: RA_Patient_2_TCR_R1

description:
patient 2
DK21229_02_VDJ_S2


title: WT-d12C

description:
this sample is actually KO-d12C sample, it was mislabeled
Rat TS cells were maintained in stem state medium (RPMI-1640 containing 20% FBS, 50 µm 2-mercaptoethanol, 1 mM sodium pyruvate, 100 µm penicilin and streptomycin, 25 ng/ml fibroblast growth factor 4, 1 µg/ml heparin and 70% embrynic fibroblast-conditioned medium. Differentiation was induced by the removal of FGF4, heparin and embrynic fibroblast-conditioned medium, and cells were cultured in RPMI medium containing 1% FBS for 12 days.

source_name: rat trophoblast stem cells

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Rnor_6.0) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (null versus wild type).
RACE

value: trophoblast cell

value: Holtzman Sprague-Dawley


title: PCDH-IF-1


title: h55_8_3

city: Jinan

first: Xueyang

last: Jin

state: Shandong Province

address: No. 44 West Wenhua Road

institute: Shandong University

data_processing: tab-delimited text files include RPKM values for each Sample ...

organism: Candida albicans

growth_protocol: C. albicans SC5314 cells (2E5 cells/mL) were prepared in RPMI 1640 medium and treated with 8 µM of H55. The non-H55 treatment cells served as control. After 6 hours, cells were harvested respectively. Samples were washed carefully three times with PBS.

extract_protocol:
RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild-type

value: treated with 8 μM H55


title: 12C_M_2649


title: RA_Patient_2_RNA_R1

description:
patient 2
DK21229_02_5GE_S2


title: WT-d12B

last: Iqbal

description: Rat TS cells were maintained in stem state medium (RPMI-1640 containing 20% FBS, 50 µm 2-mercaptoethanol, 1 mM sodium pyruvate, 100 µm penicilin and streptomycin, 25 ng/ml fibroblast growth factor 4, 1 µg/ml heparin and 70% embrynic fibroblast-conditioned medium. Differentiation was induced by the removal of FGF4, heparin and embrynic fibroblast-conditioned medium, and cells were cultured in RPMI medium containing 1% FBS for 12 days.


title: MNJ-4


title: 12C_M_2647


title: h55_8_2


title: RA_Patient_4_TCR_R1

description:
patient 4
DK21229_04_VDJ_S4


title: RA_Patient_1_TCR_R1

description:
patient 1
DK21229_01_VDJ_S1


title: WT-d12A


title: 12C_M_2646


title: h55_8_1


title: RA_Patient_1_RNA_R1

description:
patient 1
DK21229_01_5GE_S1


title: KO-d12B


title: 12C_M_2644


title: contr_2

value: without drug treatment


title: RA_Patient_3_RNA_R1

description:
patient 3
DK21229_03_5GE_S3


title: contr_3


title: KO-d12A


title: 12C_M_2643


title: 12C_M_2642


title: 12C_M_2650


title: contr_1


title: WT 1-1 +hep d6

status: Public on May 17 2023

first: Philip

middle: Leo Stefan Maria

last: Gordts

department: CMM

description: Sample 15

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

source_name: MEF

growth_protocol: MEFS (mouse embryonic fibroblasts) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: MEF

value: fibroblast

value: WT

value: adipogenic differentiation + heparin

tag: time

value: Day 0


title: KO2 -1 D6

description: Sample 14

value: NDST1 Knockout

value: adipogenic differentiation

value: Day 5


title: KO 1-1 d6

description: Sample 13


title: WT2-1 +hep d3

description: Sample 10


title: WT 1-1 d6

description: Sample 11


title: WT 1-1 +hep d3

description: Sample 9


title: KO 1-1 d3

description: Sample 7


title: KO2 -1 D3

description: Sample 8


title: Del-c11.8-Rad21-ChIP

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: Rad21 ChIP-seq experiment in Patski cells with a Xi-deletion of a CTCF boundary upstream of Car5b

data_processing:
Rad21 ChIP-seq paired-end reads were mapped using SNPsplit to an N-masked C57BL6/J reference genome (mm10) where the M. spretus SNP locus was substituted with an N to reduce mapping bias. SNPs were based on Sanger data for mouse species M. spretus compared to the mm10 B6 reference assembly.
Uniquely mapped paired-end reads were  segregated to its parental allele of origin (genome 1 for BL6 and genome 2 for spretus) if either end of the read pair contained at least one SNP particular to one of the parental strains. Enrichment profiles were produced using allelic reads.
Assembly: mm10

organism:
Mus musculus
Mus spretus

source_name: Patski cells

growth_protocol: Standard cell culturing protocol using 10% FBS in DMEM.

extract_protocol:
ChIP was performed using fixed chromatin from Patski cells. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit.
Sequencing libraries were prepared each from three or  four pooled independent ChIP samples from Patski cells using the Illumina Truseq ChIP sample prep kit. Size selection of the library was done by two-step Ampure bead purification and purification of DNA in the 300-600bp range.

value: Fibroblasts derived from hybrid embryonic kidney

tag: chip antibody

value: a rabbit monoclonal antibody for Rad21 (Abcam ab217678)


title: Pat-WT-Rad21-ChIP

description: Rad21 ChIP-seq experiment in wild-type Patski cells


title: KO-d12C

description:
this sample is actually WT-d12C sample, it was mislabeled
Rat TS cells were maintained in stem state medium (RPMI-1640 containing 20% FBS, 50 µm 2-mercaptoethanol, 1 mM sodium pyruvate, 100 µm penicilin and streptomycin, 25 ng/ml fibroblast growth factor 4, 1 µg/ml heparin and 70% embrynic fibroblast-conditioned medium. Differentiation was induced by the removal of FGF4, heparin and embrynic fibroblast-conditioned medium, and cells were cultured in RPMI medium containing 1% FBS for 12 days.


title: WT 1-1 d3

description: Sample 5


title: KO 1-1 d0

description: Sample 3


title: KO2 -1 D0

description: Sample 4


title: WT 1-1 d0

description: Sample 1


title: WT2-1 d0

description: Sample 2


title: 2aOKO-OL-Ribo-TRAP

city: Singapore

first: Vetrivel

last: Sengottuvel

address: 8 College Road

department: Cardiovascular and Metabolic Disorders

country: Singapore

institute: Duke NUS Medical School

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Excel sheet include raw counts as well as normalized counts in separate sheets for each sample.

extract_protocol:
Single cell suspension from mouse brain tissue was prepared using Papain based Neural Tissue Dissociation Kit from Miltenyi Biotech. Total oligodendrocyte lineage cells were sorted based on GFP fluorescence signal using BD FACSAria II SORP Sorter (BD Biosciences).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, single cells gel bead-in-emulsion (GEM) was generated using the isolated GFP positive cells. Barcoding, reverse transcription, cDNA amplification and subsequent library construction was performed according to manufacturers instructions.

value: Brain

value: Oligodendrocyte lineage


title: WT2-1 +hep d6

description: Sample 16


title: 2afl/fl-OL-Ribo-TRAP

description: 10X Genomics