title: Patient2_untreated_ETP-ALL_544


title: Patient2_untreated_ETP-ALL_542

status: Public on Jan 01 2021

type: SRA

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

country: USA

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

tag: who classification

value: ETP-ALL

tag: cell type

value: Peripherial blood mononuclear cells


title: Patient2_untreated_ETP-ALL_540


title: Patient2_untreated_ETP-ALL_539


title: Patient2_untreated_ETP-ALL_557


title: Patient2_untreated_ETP-ALL_537


title: Patient2_untreated_ETP-ALL_536


title: Patient2_untreated_ETP-ALL_538


title: Patient2_untreated_ETP-ALL_534


title: Patient2_untreated_ETP-ALL_576


title: Patient2_untreated_ETP-ALL_535


title: Patient2_untreated_ETP-ALL_533


title: Patient2_untreated_ETP-ALL_530


title: Patient2_untreated_ETP-ALL_532


title: Patient2_untreated_ETP-ALL_531


title: Patient2_untreated_ETP-ALL_529


title: Patient2_untreated_ETP-ALL_547


title: Patient2_untreated_ETP-ALL_549


title: Patient2_untreated_ETP-ALL_528


title: Patient2_untreated_ETP-ALL_554


title: Patient2_untreated_ETP-ALL_527


title: Patient2_untreated_ETP-ALL_525


title: Patient2_untreated_ETP-ALL_543


title: Patient2_untreated_ETP-ALL_524


title: Patient2_untreated_ETP-ALL_523


title: Patient2_untreated_ETP-ALL_541


title: Patient2_untreated_ETP-ALL_521


title: Patient2_untreated_ETP-ALL_520


title: Patient2_untreated_ETP-ALL_519


title: Patient2_untreated_ETP-ALL_522


title: Patient2_untreated_ETP-ALL_516


title: Patient2_untreated_ETP-ALL_518


title: Patient2_untreated_ETP-ALL_513


title: Patient2_untreated_ETP-ALL_514


title: Patient2_untreated_ETP-ALL_515


title: Patient2_untreated_ETP-ALL_517


title: Patient2_untreated_ETP-ALL_512


title: Patient2_untreated_ETP-ALL_508


title: Patient2_untreated_ETP-ALL_511


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title: Patient2_untreated_ETP-ALL_497


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title: Patient2_untreated_ETP-ALL_500


title: Patient2_untreated_ETP-ALL_496


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title: Patient2_untreated_ETP-ALL_510


title: Patient2_untreated_ETP-ALL_490


title: Patient2_untreated_ETP-ALL_489


title: Patient2_untreated_ETP-ALL_488


title: Patient2_untreated_ETP-ALL_485


title: Patient2_untreated_ETP-ALL_585


title: Patient2_untreated_ETP-ALL_486


title: Patient2_untreated_ETP-ALL_484


title: Patient2_untreated_ETP-ALL_480


title: Patient2_untreated_ETP-ALL_481


title: Patient2_untreated_ETP-ALL_477


title: Patient2_untreated_ETP-ALL_482


title: Patient2_untreated_ETP-ALL_478


title: Patient2_untreated_ETP-ALL_476


title: Patient2_untreated_ETP-ALL_475


title: Patient2_untreated_ETP-ALL_474


title: Patient2_untreated_ETP-ALL_505


title: Patient2_untreated_ETP-ALL_479


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title: Patient2_untreated_ETP-ALL_470


title: Patient2_untreated_ETP-ALL_473


title: Patient2_untreated_ETP-ALL_467


title: Patient2_untreated_ETP-ALL_468


title: Patient2_untreated_ETP-ALL_469


title: Patient2_untreated_ETP-ALL_487


title: Patient2_untreated_ETP-ALL_466


title: Patient2_untreated_ETP-ALL_483


title: Patient2_untreated_ETP-ALL_462


title: Patient2_untreated_ETP-ALL_461


title: Patient2_untreated_ETP-ALL_464


title: Patient2_untreated_ETP-ALL_458


title: Patient2_untreated_ETP-ALL_463


title: Patient2_untreated_ETP-ALL_460


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title: Patient2_untreated_ETP-ALL_456


title: Patient2_untreated_ETP-ALL_455


title: Patient2_untreated_ETP-ALL_454


title: Patient2_untreated_ETP-ALL_471


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title: Patient2_untreated_ETP-ALL_453


title: Patient2_untreated_ETP-ALL_452


title: Patient2_untreated_ETP-ALL_450


title: Patient2_untreated_ETP-ALL_447


title: Patient2_untreated_ETP-ALL_448


title: Patient2_untreated_ETP-ALL_446


title: Patient2_untreated_ETP-ALL_445


title: Patient2_untreated_ETP-ALL_451


title: Patient2_untreated_ETP-ALL_465


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title: Patient2_untreated_ETP-ALL_441


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title: Patient2_untreated_ETP-ALL_436


title: Patient2_untreated_ETP-ALL_432


title: Patient2_untreated_ETP-ALL_428


title: Patient2_untreated_ETP-ALL_430


title: Patient2_untreated_ETP-ALL_426


title: Patient2_untreated_ETP-ALL_431


title: Patient2_untreated_ETP-ALL_425


title: Patient2_untreated_ETP-ALL_427


title: Patient2_untreated_ETP-ALL_423


title: Patient2_untreated_ETP-ALL_424


title: Patient2_untreated_ETP-ALL_419


title: Patient2_untreated_ETP-ALL_421


title: Patient2_untreated_ETP-ALL_422


title: Patient2_untreated_ETP-ALL_420


title: Patient2_untreated_ETP-ALL_442


title: Patient2_untreated_ETP-ALL_416


title: Patient2_untreated_ETP-ALL_418


title: Patient2_untreated_ETP-ALL_414


title: Patient2_untreated_ETP-ALL_413


title: Patient2_untreated_ETP-ALL_415


title: Patient2_untreated_ETP-ALL_435


title: Patient2_untreated_ETP-ALL_412


title: Patient2_untreated_ETP-ALL_410


title: Patient2_untreated_ETP-ALL_429


title: Patient2_untreated_ETP-ALL_409


title: Patient2_untreated_ETP-ALL_411


title: Patient2_untreated_ETP-ALL_407


title: Patient2_untreated_ETP-ALL_404


title: Patient2_untreated_ETP-ALL_405


title: Patient2_untreated_ETP-ALL_406


title: Patient2_untreated_ETP-ALL_408


title: Patient2_untreated_ETP-ALL_401


title: Patient2_untreated_ETP-ALL_402


title: Patient2_untreated_ETP-ALL_417


title: Patient2_untreated_ETP-ALL_400


title: Patient2_untreated_ETP-ALL_399


title: Patient2_untreated_ETP-ALL_397


title: Patient2_untreated_ETP-ALL_396


title: Patient2_untreated_ETP-ALL_398


title: Patient2_untreated_ETP-ALL_394


title: Patient2_untreated_ETP-ALL_395


title: Patient2_untreated_ETP-ALL_393


title: Patient2_untreated_ETP-ALL_392


title: Patient2_untreated_ETP-ALL_391


title: Patient2_untreated_ETP-ALL_386


title: Patient2_untreated_ETP-ALL_390


title: Patient2_untreated_ETP-ALL_388


title: Patient2_untreated_ETP-ALL_389


title: Patient2_untreated_ETP-ALL_385


title: Patient2_untreated_ETP-ALL_403


title: Patient2_untreated_ETP-ALL_382


title: Patient2_untreated_ETP-ALL_383


title: Patient2_untreated_ETP-ALL_380


title: Patient2_untreated_ETP-ALL_384


title: Patient2_untreated_ETP-ALL_381


title: Patient2_untreated_ETP-ALL_379


title: Patient2_untreated_ETP-ALL_577


title: Patient2_untreated_ETP-ALL_375


title: Patient2_untreated_ETP-ALL_376


title: Patient2_untreated_ETP-ALL_378


title: Patient2_untreated_ETP-ALL_374


title: Patient2_untreated_ETP-ALL_369


title: Patient2_untreated_ETP-ALL_371


title: Patient2_untreated_ETP-ALL_373


title: Patient2_untreated_ETP-ALL_368


title: Patient2_untreated_ETP-ALL_370


title: Patient2_untreated_ETP-ALL_367


title: Patient2_untreated_ETP-ALL_372


title: Patient2_untreated_ETP-ALL_366


title: Patient2_untreated_ETP-ALL_365


title: Patient2_untreated_ETP-ALL_387


title: Patient2_untreated_ETP-ALL_364


title: Patient2_untreated_ETP-ALL_363


title: Patient2_untreated_ETP-ALL_362


title: Patient2_untreated_ETP-ALL_361


title: Patient2_untreated_ETP-ALL_360


title: Patient2_untreated_ETP-ALL_377


title: Patient2_untreated_ETP-ALL_357


title: Patient2_untreated_ETP-ALL_358


title: Patient2_untreated_ETP-ALL_353


title: Patient2_untreated_ETP-ALL_355


title: Patient2_untreated_ETP-ALL_354


title: Patient2_untreated_ETP-ALL_352


title: Patient2_untreated_ETP-ALL_349


title: Patient2_untreated_ETP-ALL_348


title: Patient2_untreated_ETP-ALL_350


title: Patient2_untreated_ETP-ALL_351


title: Patient2_untreated_ETP-ALL_356


title: Patient2_untreated_ETP-ALL_346


title: Patient2_untreated_ETP-ALL_343


title: Patient2_untreated_ETP-ALL_344


title: Patient2_untreated_ETP-ALL_345


title: Patient2_untreated_ETP-ALL_339


title: Patient2_untreated_ETP-ALL_340


title: Patient2_untreated_ETP-ALL_337


title: Patient2_untreated_ETP-ALL_341


title: Patient2_untreated_ETP-ALL_338


title: Patient2_untreated_ETP-ALL_336


title: Patient2_untreated_ETP-ALL_335


title: Patient2_untreated_ETP-ALL_334


title: Patient2_untreated_ETP-ALL_359


title: Patient2_untreated_ETP-ALL_331


title: Patient2_untreated_ETP-ALL_333


title: Patient2_untreated_ETP-ALL_330


title: Patient2_untreated_ETP-ALL_329


title: Patient2_untreated_ETP-ALL_347


title: Patient2_untreated_ETP-ALL_342


title: Patient2_untreated_ETP-ALL_327


title: Patient2_untreated_ETP-ALL_324


title: Patient2_untreated_ETP-ALL_319


title: Patient2_untreated_ETP-ALL_322


title: Patient2_untreated_ETP-ALL_320


title: Patient2_untreated_ETP-ALL_316


title: Patient2_untreated_ETP-ALL_317


title: Patient2_untreated_ETP-ALL_318


title: Patient2_untreated_ETP-ALL_315


title: Patient2_untreated_ETP-ALL_326


title: Patient2_untreated_ETP-ALL_312


title: Patient2_untreated_ETP-ALL_325


title: Patient2_untreated_ETP-ALL_310


title: Patient2_untreated_ETP-ALL_313


title: Patient2_untreated_ETP-ALL_321


title: Patient2_untreated_ETP-ALL_332


title: Patient2_untreated_ETP-ALL_308


title: Patient2_untreated_ETP-ALL_328


title: Patient2_untreated_ETP-ALL_307


title: Patient2_untreated_ETP-ALL_314


title: Patient2_untreated_ETP-ALL_305


title: Patient2_untreated_ETP-ALL_304


title: Patient2_untreated_ETP-ALL_309


title: Patient2_untreated_ETP-ALL_303


title: Patient2_untreated_ETP-ALL_301


title: Patient2_untreated_ETP-ALL_306


title: Patient2_untreated_ETP-ALL_296


title: Patient2_untreated_ETP-ALL_311


title: Patient2_untreated_ETP-ALL_294


title: Patient2_untreated_ETP-ALL_293


title: Patient2_untreated_ETP-ALL_302


title: Patient2_untreated_ETP-ALL_290


title: Patient2_untreated_ETP-ALL_323


title: Patient2_untreated_ETP-ALL_286


title: Patient2_untreated_ETP-ALL_300


title: Patient2_untreated_ETP-ALL_281


title: Patient2_untreated_ETP-ALL_298


title: Patient2_untreated_ETP-ALL_299


title: Patient2_untreated_ETP-ALL_297


title: Patient2_untreated_ETP-ALL_275


title: Patient2_untreated_ETP-ALL_277


title: Patient2_untreated_ETP-ALL_276


title: Patient2_untreated_ETP-ALL_279


title: Patient2_untreated_ETP-ALL_292


title: Patient2_untreated_ETP-ALL_278


title: Patient2_untreated_ETP-ALL_291


title: Patient2_untreated_ETP-ALL_287


title: Patient2_untreated_ETP-ALL_271


title: Patient2_untreated_ETP-ALL_285


title: Patient2_untreated_ETP-ALL_272


title: Patient2_untreated_ETP-ALL_273


title: Patient2_untreated_ETP-ALL_270


title: Patient2_untreated_ETP-ALL_284


title: Patient2_untreated_ETP-ALL_274


title: Patient2_untreated_ETP-ALL_289


title: Patient2_untreated_ETP-ALL_282


title: Patient2_untreated_ETP-ALL_280


title: Patient2_untreated_ETP-ALL_269


title: Patient2_untreated_ETP-ALL_266


title: Patient2_untreated_ETP-ALL_265


title: Patient2_untreated_ETP-ALL_283


title: Patient2_untreated_ETP-ALL_264


title: Patient2_untreated_ETP-ALL_295


title: Patient2_untreated_ETP-ALL_288


title: Patient2_untreated_ETP-ALL_268


title: Patient2_untreated_ETP-ALL_258


title: Patient2_untreated_ETP-ALL_267


title: Patient2_untreated_ETP-ALL_259


title: Patient2_untreated_ETP-ALL_262


title: Patient2_untreated_ETP-ALL_254


title: Patient2_untreated_ETP-ALL_257


title: Patient2_untreated_ETP-ALL_256


title: Patient2_untreated_ETP-ALL_260


title: Patient2_untreated_ETP-ALL_247


title: Patient2_untreated_ETP-ALL_251


title: Patient2_untreated_ETP-ALL_253


title: Patient2_untreated_ETP-ALL_255


title: LNCaP 1nM DHT rep3 [C3]

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LNCaP 1nM DHT

growth_protocol: ATCC-formulated Dulbecco's Modified Eagle's Medium/DMEM (ATCC, Rockville, MD) with 10% fetal bovine serum (FBS, Omega Scientific, Tarzana, CA) and 1% penicillin/streptomycin (Fisher Scientific, Chino, CA) at 370C with 5% CO2.

extract_protocol: Total RNA was extracted from cultured cells using the RNeasy Mini kit

treatment_protocol: LNCaP cells were treated by 1 nM DHT, with or without WBM extract (3 μL/mL), for 48h

tag: cell line

value: LNCaP

tag: tissue source

value: prostate gland

value: human prostate cancer cells

tag: treatment

value: 1nM DHT 48h


title: LNCaP 1nM DHT+WBM rep2 [S2]

source_name: LNCaP 1nM DHT+WBM

value: 1nM DHT+ WBM extract 48h


title: LNCaP 1nM DHT+WBM rep1 [S1]


title: Patient2_untreated_ETP-ALL_261


title: Patient2_untreated_ETP-ALL_263


title: Patient2_untreated_ETP-ALL_252


title: Patient2_untreated_ETP-ALL_250


title: Patient2_untreated_ETP-ALL_248


title: Patient2_untreated_ETP-ALL_246


title: LNCaP 1nM DHT+WBM rep3 [S3]


title: LNCaP 1nM DHT rep1 [C1]


title: LNCaP 1nM DHT rep2 [C2]


title: Patient2_untreated_ETP-ALL_242


title: Patient2_untreated_ETP-ALL_244


title: Patient2_untreated_ETP-ALL_240


title: HMLE WT

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

country: France

institute: Institut Curie

library_source: genomic

data_processing:
Library strategy: WGS
After trimming, reads were aligned to the reference genome using BWA-MEM (v 0.7.15) (Li 2013) with default parameters.
Reads that mapped to the X chromosome were retrieved using SAMtools view (v1.9) (Li et al. 2009).
Variant calling was performed using Genome Analysis Tool Kit (GATK) HaplotypeCaller (DePristo et al. 2011). GATK Best Practices for short variant discovery (https://software.broadinstitute.org/gatk/best-practices) were implemented for base quality score recalibration, indel realignment, and duplicate removal.
Heterozygous SNPs were identified using GATK SelectVariants and annotated using ANNOVAR (v20141110) (Wang et al. 2010).
Genome_build: hg19
Supplementary_files_format_and_content: The "Xchr.SNPs.pos" file lists the heterozygous positions on the X chromosome in HMLE cells.

molecule: genomic DNA

source_name: HMLE

growth_protocol: HMLE cells were cultured in DMEM:F-12/GlutaMAX supplemented with 10% FBS, 1% MEM Non-Essential Amino Acids, 1% Pen/Strep, 10 µg/ml insulin, 1 µg/mL hydrocortisone, and 10 ng/mL human epidermal growth factor (EGF).

extract_protocol:
Genomic DNA from HMLE cells was isolated using the NucleoSpin Tissue, Mini kit for DNA from cells and tissue (Macherey-Nagel, ref. 740952).
Whole Genome-Sequencing (WGS) libraries were prepared by the Institut Curie Next Generation Sequencing Core Facility using the TruSeq DNA PCR-free Library Prep Kit (Illumina, ref. 20015962-3) according to manufacturer’s instructions and sequenced on an Illumina HiSeq 2500 (PE100).

value: Immortalized human mammary epithelial cells

tag: genotype

value: WT


title: Patient2_untreated_ETP-ALL_249


title: Patient2_untreated_ETP-ALL_243


title: Patient2_untreated_ETP-ALL_241


title: Patient2_untreated_ETP-ALL_239


title: HMLE KO ML rep1

description:
raw.counts.txt
A566-A567T15

data_processing:
The human reference genome hg19 was masked with a list of informative heterozygous SNPs on the X chromosome using BEDtools maskfasta (v2.2.2).
Fastq files were aligned to the human reference genome hg19, using the gene annotation from GENCODE and the aligner STAR (v2.7.0a) with the following parameters: --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD --alignEndsType EndToEnd.
For gene expression analyses, reads overlapping exons or genes (GENCODE annotation) were counted using FeatureCounts (Subread v1.5.1) with the following parameters: -t exon -g gene_name -p -B -C.
For allele-specific analyses, PCR duplicates were removed from mapped reads using Picard tools (v1.97) with the following parameters: REMOVE_DUPLICATES=true ASSUME_SORTED=true.
Remaining reads were then split by allele using SNPsplit (v0.3.2) (options: --paired) and reads overlapping informative SNPs were quantified using SAMtools (v1.9) mpileup.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file "raw.counts.txt" contains raw counts overlapping exons and genes for non-transformed HMLE samples. VCF files contain the read counts overlapping heterozygous SNPs on the X chromosome.

growth_protocol: HMLE/HMLER cells were cultured in DMEM:F-12/GlutaMAX supplemented with 10% FBS, 1% MEM Non-Essential Amino Acids, 1% Pen/Strep, 10 µg/ml insulin, 1 µg/mL hydrocortisone, and 10 ng/mL human epidermal growth factor (EGF).

extract_protocol:
RNA was isolated with Trizol-Chloroform followed by isopropanol precipitation.
RNA-Seq Libraries for HMLE cells were prepared by the Institut Curie Next Generation Sequencing Core Facility using the TruSeq Stranded mRNA kit (Illumina, ref. 20020594-5) according to manufacturer’s instructions and sequenced on an Illumina HiSeq 2500 (PE100). RNA-Seq libraries for HMLER cells were prepared using the Swift RNA Library Kit (Swift Biosciences, ref. R1024 and R1096) according to manufacturer’s instructions and sequenced on an Illumina NovaSeq 6000 (PE100).

treatment_protocol: Cells were tripsinized, resuspended in FACS buffer (PBS 1X, 1% BSA, 5mM EDTA), and stained with FACS-grade primary antibodies against ESA or a combination of CD44 and CD24. HMLE were FACS-sorted into two populations according to their ESA positivity. In the case of HMLER, only CD44+/CD24- cells (corresponding to CSCs) were selected for subsequent analyses.

value: XIST-KO

tag: cell compartment

value: ML (ESA+)


title: HMLE KO ML rep2

description:
raw.counts.txt
A566-A567T16


title: Patient2_untreated_ETP-ALL_245


title: HMLE KO MaSC rep1

description:
raw.counts.txt
A566-A567T13

value: MaSC (ESA-)


title: HMLE WT ML rep2

description:
raw.counts.txt
A566-A567T12


title: Patient2_untreated_ETP-ALL_238


title: Patient2_untreated_ETP-ALL_237


title: Patient2_untreated_ETP-ALL_236


title: Patient2_untreated_ETP-ALL_235


title: HMLE WT MaSC rep2

description:
raw.counts.txt
A566-A567T10


title: Patient2_untreated_ETP-ALL_230


title: Patient2_untreated_ETP-ALL_231


title: Patient2_untreated_ETP-ALL_233


title: HMLE WT MaSC rep1

description:
raw.counts.txt
A566-A567T9


title: Patient2_untreated_ETP-ALL_228


title: Patient2_untreated_ETP-ALL_226


title: Patient2_untreated_ETP-ALL_227


title: Patient2_untreated_ETP-ALL_224


title: Patient2_untreated_ETP-ALL_222


title: Patient2_untreated_ETP-ALL_220


title: Patient2_untreated_ETP-ALL_216


title: Patient2_untreated_ETP-ALL_225


title: Patient2_untreated_ETP-ALL_215


title: Patient2_untreated_ETP-ALL_223


title: Patient2_untreated_ETP-ALL_219


title: HMLE KO MaSC rep2

description:
raw.counts.txt
A566-A567T14


title: Patient2_untreated_ETP-ALL_221


title: Patient2_untreated_ETP-ALL_213


title: Patient2_untreated_ETP-ALL_229


title: Patient2_untreated_ETP-ALL_218


title: Patient2_untreated_ETP-ALL_214


title: Patient2_untreated_ETP-ALL_232


title: Patient2_untreated_ETP-ALL_212


title: Patient2_untreated_ETP-ALL_211


title: 1P: sample #1 prostatectomy tissue, after treatment

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

data_processing:
Quality of sequencing data was verified using MultiQC software. Sequence alignment and quantification were performed using the STAR-RSEM pipeline. Reads overlapping exons in the annotation of Genome Reference Consortium Human Build 38 (GRCh38) were identified, and would be excluded from further downstream analysis if they failed to achieve raw read counts of at least 2 across all the libraries. The trimmed mean of M-values normalization method (TMM) (version 1.6.1) was used for calculating normalized count data.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts were generated by RSEM

source_name: Prostate tissue

growth_protocol: Tumors were macrodissected for RNA extraction.

extract_protocol:
RNA was extracted from the paraffin samples using the MasterPure™ RNA Purification Kit (Epicenter Biotechnologies, Madison, WI, USA). RNA was then treated with 20 units DNase I (Ambion, Austin, TX, USA) for 30 min and checked for residual genomic DNA by TaqMan RT-PCR targeting ACTB. The final RNA concentration (A260:0.025) and purity (A260:A280 ratio) were measured using a NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
300 ng total RNA were sent to MedGenome Inc (Foster City, CA), where RNAseq was performed on the HiSeq-2500 platform (Illumina, San Diego, CA) after using the TruSeq RNA Access Library Prep Kit (Illumina).
Sequencing runs were performed on Illumina Hiseq 2500 in the paired read mode of 51 cycle of read 1 and 7 cycles of index with V4 Kits.

treatment_protocol: Tumor sections were placed in 2.0 mL RNase-free Eppendorf tubes. Sections were treated twice with 1.9 mL xylene for 5 min at 55 °C while rocking. The sections were washed twice with 100% ethanol.

tag: tissue

value: Prostate

tag: sample type

value: Prostatatomy

value: the combination of ezetimibe and simvastatin


title: 1B: sample #1 biopsy tissue, before treatment

value: Biopsy

value: No treatment


title: HMLE WT ML rep1

description:
raw.counts.txt
A566-A567T11


title: Patient2_untreated_ETP-ALL_210

value: ETP-ALL


title: Patient2_untreated_ETP-ALL_209

value: Peripherial blood mononuclear cells


title: case with pharyngitis by adenovirus infection [P040]

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
symptomatic pharyngitis by adenovirus infection (sAdV)
ROC_10318_R1

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the human Ensembl GRCh38.76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in at least four samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights
Genome_build: Human Ensembl GRCh38.76 primary assembly
Supplementary_files_format_and_content: raw counts at gene level

source_name: whole blood leukocyte

extract_protocol:
Total RNA was extracted from blood samples using the Tempus Spin RNA Isolation Kit and processed for globin reduction using GLOBINclear Human Kit (Thermo Fisher Scientific).
RNAseq was performed using cDNA libraries generated from 200 ng of globin reduced total RNA from each sample. Libraries were constructed with the NexteraXT library kit (Illumina, San Diego, CA) and sequenced (single end reads) on the Illumina HiSeq2500 (Illumina, San Diego, CA) to generate 20 million reads/sample.

treatment_protocol: Blood specimens were collected from study subjeccts before treatment.

tag: group

tag: gender

value: M

tag: age

tag: race

value: white


title: case with pharyngitis by group a streptococcus [P038]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10308_R1

value: F

value: black


title: case with pharyngitis by group a streptococcus [P039]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10313_R1


title: 2P: sample #2 prostatectomy tissue, after treatment


title: Patient2_untreated_ETP-ALL_203


title: case with pharyngitis by group a streptococcus [P034]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10289_R1


title: Patient2_untreated_ETP-ALL_204


title: Patient2_untreated_ETP-ALL_202


title: case with pharyngitis by group a streptococcus [P032]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10279_R1


title: Patient2_untreated_ETP-ALL_200


title: Patient2_untreated_ETP-ALL_199


title: Patient2_untreated_ETP-ALL_208


title: virus-negative control [P028]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10260_R1

value: virus-negative control


title: Patient2_untreated_ETP-ALL_207


title: Patient2_untreated_ETP-ALL_198


title: case with pharyngitis by group a streptococcus [P037]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10303_R1


title: Patient2_untreated_ETP-ALL_206


title: case with pharyngitis by group a streptococcus [P036]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10298_R1


title: Patient2_untreated_ETP-ALL_195


title: 2B: sample #2 biopsy sample, tissue treatment


title: Patient2_untreated_ETP-ALL_194


title: case with pharyngitis by adenovirus infection [P035]

description:
symptomatic pharyngitis by adenovirus infection (sAdV)
ROC_10293_R1


title: Patient2_untreated_ETP-ALL_205


title: Patient2_untreated_ETP-ALL_201


title: virus-negative control [P031]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10274_R1


title: virus-negative control [P030]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10269_R1


title: case with pharyngitis by group a streptococcus [P033]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10284_R1


title: virus-negative control [P024]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10240_R1


title: virus-negative control [P023]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10235_R1


title: control with group a streptococcus colonized [P021]

description:
asymptomatic control with group a streptococcus colonized (asGAS)
ROC_10225_R1


title: Patient2_untreated_ETP-ALL_190


title: virus-negative control [P027]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10255_R1


title: case with pharyngitis by group a streptococcus [P018]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10210_R1


title: Patient2_untreated_ETP-ALL_188


title: Patient2_untreated_ETP-ALL_197


title: case with pharyngitis by other cause [P026]

description:
symptomatic pharyngitis by other cause (sOP)
ROC_10250_R1

value: case with pharyngitis by other cause


title: Patient2_untreated_ETP-ALL_196


title: case with pharyngitis by other cause [P022]

description:
symptomatic pharyngitis by other cause (sOP)
ROC_10230_R1


title: Patient2_untreated_ETP-ALL_191


title: case with pharyngitis by group a streptococcus [P020]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10220_R1


title: Patient2_untreated_ETP-ALL_192


title: Patient2_untreated_ETP-ALL_187


title: Patient2_untreated_ETP-ALL_193


title: Patient2_untreated_ETP-ALL_186


title: virus-negative control [P017]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10205_R1


title: case with pharyngitis by other cause [P019]

description:
symptomatic pharyngitis by other cause (sOP)
ROC_10215_R1


title: virus-negative control [P016]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10200_R1


title: Patient2_untreated_ETP-ALL_183


title: control with group a streptococcus colonized [P012]

description:
asymptomatic control with group a streptococcus colonized (asGAS)
ROC_10178_R1


title: Patient2_untreated_ETP-ALL_189


title: virus-positive control [P013]

description:
asymptomatic control with positive of non-adenovirus (vCtrl)
ROC_10184_R1

value: virus-positive control


title: control with group a streptococcus colonized [P025]

description:
asymptomatic control with group a streptococcus colonized (asGAS)
ROC_10245_R1


title: Patient2_untreated_ETP-ALL_185


title: virus-positive control [P015]

description:
asymptomatic control with positive of non-adenovirus (vCtrl)
ROC_10195_R1


title: virus-negative control [P014]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10190_R1


title: Patient2_untreated_ETP-ALL_180


title: Patient2_untreated_ETP-ALL_179


title: control with group a streptococcus colonized [P006]

description:
asymptomatic control with group a streptococcus colonized (asGAS)
ROC_10143_R1


title: virus-negative control [P010]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10166_R1


title: Patient2_untreated_ETP-ALL_177


title: virus-negative control [P005]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10137_R1


title: virus-negative control [P007]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10148_R1


title: Patient2_untreated_ETP-ALL_184


title: virus-positive control [P003]

description:
asymptomatic control with positive of non-adenovirus (vCtrl)
ROC_10125_R1


title: Patient2_untreated_ETP-ALL_174


title: Patient2_untreated_ETP-ALL_182


title: Patient2_untreated_ETP-ALL_234


title: Pancreatic cancer associated fibroblasts CW5 - untreated RNA-Seq

city: Allen

first: Wei

last: Lin

state: TX

address: 1525 Evanvale Dr.

institute: Translational Genomics Research Institute

data_processing:
ChIP-seq reads were aligned to a reference genome (version hg19) using Bowtie2 with default parameters
H3K27Ac peak finding was performed using MACS (v1.4.2) and Homer with default settings.
Peak finding for each sample was performed separately with their matched input genomic DNA as a background control.
ROSE (Young lab) was then used to call and rank Super-enhancers and their associated genes
For RNAseq raw paired-end reads were trimmed using fastx-trimmer tools prior to mapping
TopHat (version 2.0.14) was used to map reads to a reference genome with parameters ‘–library-type fr-firststrand’ (for a strand-specific library) ‘—mate-std-dev #stdev’ and ‘-r #insert-distance’. The #stdev and #insert-distance were estimated from sub-sampling of samples individually
After mapping, bam files were further analyzed using Arraystudio (Omicsoft) software with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: beg files for ChIPseq data were generated using MACS (v1.4.2)
Supplementary_files_format_and_content: tab-delimited text file that include FPKM values or htseqcounts for  RNAseq samples

source_name: Isolated from a pancreatic tumor

growth_protocol: T75 flasks in DMEM medium + 20% FBS to 60-80% confluency

extract_protocol:
Total RNA was isolated using RNeasy® Midi Kit (Qiagen)
Sequencing libraries were prepared according to Illumina's instructions.

treatment_protocol: Not treated

value: Untreated


title: Pancreatic cancer associated fibroblasts PS1 - untreated RNA-Seq


title: case with pharyngitis by adenovirus infection [P011]

description:
symptomatic pharyngitis by adenovirus infection (sAdV)
ROC_10172_R1


title: Pancreatic cancer associated fibroblasts BF1 - untreated RNA-Seq


title: Patient2_untreated_ETP-ALL_181


title: virus-negative control [P009]

description:
asymptomatic control with negative of viruses tested (nCtrl)
ROC_10160_R1


title: Patient2_untreated_ETP-ALL_178


title: Patient2_untreated_ETP-ALL_217


title: Patient2_untreated_ETP-ALL_176


title: Patient2_untreated_ETP-ALL_166


title: Patient2_untreated_ETP-ALL_175


title: case with pharyngitis by group a streptococcus [P002]

description:
symptomatic pharyngitis by group a streptococcus infection (sGAS)
ROC_10119_R1


title: Patient2_untreated_ETP-ALL_173


title: Patient2_untreated_ETP-ALL_171


title: Patient2_untreated_ETP-ALL_172


title: Pancreatic cancer associated fibroblasts CW1 - untreated RNA-Seq


title: Patient2_untreated_ETP-ALL_170


title: Pancreatic cancer cells Patu899S -  untreated RNA-Seq

source_name: Pancreatic cancer cell line

growth_protocol: T75 flasks in RPMI-1640 medium + 10% FBS to 60-80% confluency


title: Pancreatic cancer associated fibroblasts CAF08 - untreated RNA-Seq

growth_protocol: T75 flasks in MSCGro medium + 20% FBS to 60-80% confluency


title: Pancreatic cancer cells Patu8902 -  untreated RNA-Seq


title: Patient2_untreated_ETP-ALL_168


title: Patient2_untreated_ETP-ALL_169


title: Pancreatic cancer cells P4057 -  untreated RNA-Seq


title: Pancreatic cancer associated fibroblasts B0010A - untreated RNA-Seq


title: Patient2_untreated_ETP-ALL_167


title: Pancreatic cancer associated fibroblasts B009B - untreated RNA-Seq


title: Pancreatic cancer cells -  MIA PaCa-2 untreated RNA-Seq


title: Patient2_untreated_ETP-ALL_160


title: Patient2_untreated_ETP-ALL_158


title: Pancreatic cancer associated fibroblasts B011C - untreated RNA-Seq


title: Patient2_untreated_ETP-ALL_159


title: control with group a streptococcus colonized [P004]

description:
asymptomatic control with group a streptococcus colonized (asGAS)
ROC_10131_R1


title: Patient2_untreated_ETP-ALL_165


title: Pancreatic cancer cells BxPC3 -  untreated RNA-Seq


title: Pancreatic cancer cells Capan1-  untreated RNA-Seq


title: Pancreatic cancer cells AsPC1 -  untreated RNA-Seq


title: Pancreatic cancer cells PANC1 -  untreated RNA-Seq


title: Pancreatic cancer cells PSN1 -  untreated RNA-Seq


title: Patient2_untreated_ETP-ALL_164


title: Patient2_untreated_ETP-ALL_156


title: Pancreatic cancer cells -THZ1 treated  RNA-Seq Replicate 2

treatment_protocol: Cells were treated with THZ1 (20nM) for 18 hours.

value: THZ1 treated_Rep2


title: Patient2_untreated_ETP-ALL_163


title: Patient2_untreated_ETP-ALL_162


title: Patient2_untreated_ETP-ALL_153


title: Patient2_untreated_ETP-ALL_161


title: Patient2_untreated_ETP-ALL_151


title: Pancreatic cancer associated fibroblasts - triptolide treated RNA-Seq

description: Processed RNA-Seq on triptolide treated CW5

growth_protocol: T75 flasks in DMEM medium + 20 FBS to 60-80% confluency

treatment_protocol: Cells were treated with triptolide (20nM) for 18 hours.

value: Triptolide treated


title: Patient2_untreated_ETP-ALL_154


title: Patient2_untreated_ETP-ALL_150


title: Patient2_untreated_ETP-ALL_152


title: Patient2_untreated_ETP-ALL_149


title: Pancreatic cancer cells -THZ1 treated  RNA-Seq Replicate 1

value: THZ1 treated_Rep1


title: Patient2_untreated_ETP-ALL_155


title: Patient2_untreated_ETP-ALL_157


title: Patient2_untreated_ETP-ALL_147


title: Patient2_untreated_ETP-ALL_146


title: Patient2_untreated_ETP-ALL_145


title: Patient2_untreated_ETP-ALL_141


title: Patient2_untreated_ETP-ALL_148


title: Pancreatic cancer associated fibroblasts - Vehicle (DMSO) treated  RNA-Seq

treatment_protocol: Cells were treated with vehicle (DMSO) for 18 hours.

value: DMSO treated


title: Patient2_untreated_ETP-ALL_144


title: Patient2_untreated_ETP-ALL_143


title: Patient2_untreated_ETP-ALL_139


title: Patient2_untreated_ETP-ALL_137


title: Patient2_untreated_ETP-ALL_136


title: Patient2_untreated_ETP-ALL_135


title: Patient2_untreated_ETP-ALL_142


title: Patient2_untreated_ETP-ALL_140


title: Patient2_untreated_ETP-ALL_138


title: Patient2_untreated_ETP-ALL_134


title: Patient2_untreated_ETP-ALL_133


title: Pancreatic cancer cells - Vehicle (DMSO) treated  RNA-Seq Replicate 2

value: DMSO treated_Rep2


title: Pancreatic cancer cells - H3K27ac Triptolide 20 treated Input

growth_protocol: 60 mm dishes in RPMI-1640 medium + 10% FBS to 60-80% confluency

extract_protocol:
ChIP DNA was purified by the QIAquick PCR purification kit (QIAgen)
Sequencing libraries were prepared according to Illumina's instructions.

treatment_protocol: Treated with triptolide

tag: antibody

value: H3K27ac from Active Motif (Cat. #39133)

value: Triptolide treated Input


title: Pancreatic stellate cells -THZ1 treated

source_name: Isolated from normal pancreas

growth_protocol: 60 mm dishes in DMEM medium + 20 FBS to 60-80% confluency

value: THZ1 treated


title: Pancreatic cancer associated fibroblasts CW1 - H3K27ac - untreated Input

growth_protocol: 60 mm dishes in DMEM medium + 20% FBS to 60-80% confluency

value: Input


title: Pancreatic cancer cells - H3K27ac THZ1 treated Input

treatment_protocol: Treated with THZ1

value: THZ1 treated Input


title: Pancreatic stellate cells -Triptolide treated


title: Pancreatic stellate cells - Vehicle (DMSO) treated Input

value: DMSO treated Input


title: Pancreatic cancer cells -Triptolide treated  RNA-Seq Replicate 2

value: Triptolide treated_Rep2


title: Pancreatic stellate cells -Triptolide treated Input


title: Pancreatic cancer cells -Triptolide treated  RNA-Seq Replicate 1

value: Triptolide treated_Rep1


title: Pancreatic cancer cells - H3K27ac Triptolide 20 treated


title: Pancreatic cancer cells - H3K27ac - Vehicle (DMSO) treated Input

treatment_protocol: Treated with vehicle control


title: Pancreatic cancer cells - Vehicle (DMSO) treated RNA-Seq Replicate 1

value: DMSO treated_Rep1


title: Pancreatic stellate cells -THZ1 treated Input


title: Pancreatic cancer cells - H3K27ac - Vehicle (DMSO) treated


title: Pancreatic stellate cells - Vehicle (DMSO) treated


title: Pancreatic cancer cells - H3K27ac THZ1 treated


title: Pancreatic cancer associated fibroblasts CW1 - H3K27ac - untreated


title: Pancreatic cancer associated fibroblasts PS1 - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_132

value: ETP-ALL

value: Peripherial blood mononuclear cells


title: Patient2_untreated_ETP-ALL_131


title: Pancreatic cancer associated fibroblasts CAF08 - H3K27ac - untreated Input

growth_protocol: 60 mm dishes in MSCGro medium + 20% FBS to 60-80% confluency


title: Patient2_untreated_ETP-ALL_130


title: Pancreatic cancer associated fibroblasts CAF08 - H3K27ac - untreated

value: Untreated


title: Pancreatic cancer associated fibroblasts BF1 - H3K27ac - untreated


title: Pancreatic cancer associated fibroblasts PS1 - H3K27ac - untreated Input


title: Pancreatic cancer associated fibroblasts BF1 - H3K27ac - untreated Input


title: Patient2_untreated_ETP-ALL_129


title: Patient2_untreated_ETP-ALL_127


title: Pancreatic cancer associated fibroblasts B011C - H3K27ac - untreated Input


title: Pancreatic cancer associated fibroblasts B011C - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_128


title: Patient2_untreated_ETP-ALL_126


title: Pancreatic cancer associated fibroblasts B009B - H3K27ac - untreated


title: Pancreatic cancer cells PANC1 - H3K27ac - untreated Input


title: Patient2_untreated_ETP-ALL_125


title: Pancreatic cancer cells PSN1 - H3K27ac - untreated Input


title: Pancreatic cancer cells PSN1 - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_119


title: Patient2_untreated_ETP-ALL_118


title: Pancreatic cancer associated fibroblasts B0010A - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_122


title: Patient2_untreated_ETP-ALL_123


title: Pancreatic cancer associated fibroblasts B0010A - H3K27ac - untreated Input


title: Patient2_untreated_ETP-ALL_124


title: Pancreatic cancer cells PANC1 - H3K27ac - untreated


title: Pancreatic cancer cells Patu899S - H3K27ac - untreated


title: Pancreatic cancer cells Patu899S - H3K27ac - untreated Input


title: Patient2_untreated_ETP-ALL_120


title: Patient2_untreated_ETP-ALL_116


title: Pancreatic cancer cells Patu8902 - H3K27ac - untreated Input


title: Pancreatic cancer cells Patu8902 - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_115


title: Patient2_untreated_ETP-ALL_121


title: Patient2_untreated_ETP-ALL_114


title: Pancreatic cancer associated fibroblasts B009B - H3K27ac - untreated input


title: Pancreatic cancer cells P4057 - H3K27ac - untreated Input


title: Patient2_untreated_ETP-ALL_113


title: Pancreatic cancer cells P4057 - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_111


title: Patient2_untreated_ETP-ALL_117


title: Pancreatic cancer cells MIA PaCa-2 - H3K27ac - untreated Input


title: Patient2_untreated_ETP-ALL_112


title: Pancreatic cancer cells MIA PaCa-2 - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_109


title: Pancreatic cancer cells Capan1 - H3K27ac - untreated Input


title: Patient2_untreated_ETP-ALL_110


title: Patient2_untreated_ETP-ALL_107


title: Pancreatic cancer cells AsPC1 - H3K27ac - untreated Input


title: Pancreatic cancer cells Capan1 - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_106


title: Pancreatic cancer cells AsPC1 - H3K27ac - untreated


title: Patient2_untreated_ETP-ALL_104


title: Patient2_untreated_ETP-ALL_108


title: Patient2_untreated_ETP-ALL_105


title: Patient2_untreated_ETP-ALL_102


title: Patient2_untreated_ETP-ALL_099


title: 8785_Flash frozen breast tumor tissue-miRNASeq

city: Buffalo

first: Yao

last: Song

state: NY

address: Carlton House - A349, Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

data_processing:
The adapter for each read was trimmed by cutadapt (version 1.12).
The trimmed reads were aligned to hg19 by Burrows−Wheeler Aligner (version 0.7.15) with no mismatches allowed.
The miRNA profiling pipeline developed by the British Columbia Genome Sciences Centre was implemented to quantify miRNA expression.
Genome_build: hg19
Supplementary_files_format_and_content: raw count data

source_name: Flash frozen breast tumor tissue

extract_protocol:
RNA extracted using RNeasy Mini Kit (Qiagen)
NEBNext Multiplex Small RNA kit for small RNA cDNA library preparation

value: breast tumor tissue

value: Female

value: African American

tag: er

value: Negative

tag: molecule subtype

value: miRNA


title: 9048_Flash frozen breast tumor tissue-miRNASeq

value: Positive


title: 9648_Flash frozen breast tumor tissue-miRNASeq

value: Caucasian


title: 20376_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_100


title: Patient2_untreated_ETP-ALL_101


title: 9038_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_098


title: Pancreatic cancer cells BxPC3 - H3K27ac - untreated Input

value: H3K27ac from Active Motif (Cat. #39133)


title: Pancreatic cancer cells BxPC3 - H3K27ac - untreated


title: 19268_Flash frozen breast tumor tissue-miRNASeq


title: 19011_Flash frozen breast tumor tissue-miRNASeq


title: 19282_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_095


title: Patient2_untreated_ETP-ALL_103


title: Patient2_untreated_ETP-ALL_096


title: Patient2_untreated_ETP-ALL_093


title: 18800_Flash frozen breast tumor tissue-miRNASeq


title: 18664_Flash frozen breast tumor tissue-miRNASeq


title: 18612_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_092


title: Patient2_untreated_ETP-ALL_090


title: 18367_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_089


title: 18268_Flash frozen breast tumor tissue-miRNASeq


title: 18313_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_087


title: Patient2_untreated_ETP-ALL_097


title: 18033_Flash frozen breast tumor tissue-miRNASeq


title: 18986_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_088


title: Patient2_untreated_ETP-ALL_094


title: Patient2_untreated_ETP-ALL_086


title: Patient2_untreated_ETP-ALL_085


title: 18534_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_084


title: Patient2_untreated_ETP-ALL_091


title: 17812_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_081


title: 17453_Flash frozen breast tumor tissue-miRNASeq


title: 17506_Flash frozen breast tumor tissue-miRNASeq


title: 18475_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_082


title: 17271_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_080


title: 17469_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_079


title: 17411_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_078


title: Patient2_untreated_ETP-ALL_076


title: 16722_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_077


title: 17074_Flash frozen breast tumor tissue-miRNASeq


title: 17098_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_083


title: 16296_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_072


title: 16823_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_073


title: Patient2_untreated_ETP-ALL_074


title: Patient2_untreated_ETP-ALL_071


title: Patient2_untreated_ETP-ALL_070


title: 16053_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_068


title: Patient2_untreated_ETP-ALL_069


title: 15362_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_066


title: Patient2_untreated_ETP-ALL_067


title: 14738_Flash frozen breast tumor tissue-miRNASeq


title: 14843_Flash frozen breast tumor tissue-miRNASeq


title: 14677_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_075


title: 16172_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_064


title: 15980_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_063


title: Patient2_untreated_ETP-ALL_062


title: 14503_Flash frozen breast tumor tissue-miRNASeq


title: 14535_Flash frozen breast tumor tissue-miRNASeq


title: 14308_Flash frozen breast tumor tissue-miRNASeq


title: 14496_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_060


title: 14302_Flash frozen breast tumor tissue-miRNASeq


title: 14994_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_061


title: Patient2_untreated_ETP-ALL_059


title: 14944_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_058


title: 14051_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_057


title: 14128_Flash frozen breast tumor tissue-miRNASeq


title: 14045_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_065


title: 13913_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_054


title: Patient2_untreated_ETP-ALL_053


title: 13240_Flash frozen breast tumor tissue-miRNASeq


title: 13014_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_051


title: 12777_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_050


title: 12694_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_049


title: Patient2_untreated_ETP-ALL_052


title: 12151_Flash frozen breast tumor tissue-miRNASeq


title: 11326_Flash frozen breast tumor tissue-miRNASeq


title: 11119_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_046


title: Patient2_untreated_ETP-ALL_044


title: Patient2_untreated_ETP-ALL_047


title: Human_Colon_5059

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v2 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on an Illumina HiSeq/NovaSeq sequencer in a paired-end, single indexing run. Sequencing for each library  targeted 25,000 mean reads per cell. Data was then processed using the Cellranger pipeline (10x genomics, v.3.0.2) for demultiplexing and alignment of sequencing reads to a pre-mRNA transcriptome references of human (GRCh38) and mouse (mm10). These custom references were created using the protocol at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references for creation of feature-barcode matrices. For mouse distal colon and human colon, both intronic and exonic reads were included. Individual single cell RNAseq libraries were aggregated using the cellranger aggr pipeline. Libraries were normalized for sequencing depth across all libraries during aggregation. Secondary analysis on the aggregated feature barcode matrix was performed using the Seurat package (v.2.3.4 for mouse distal colon and human colon and v.3.1.2 for E17.5 small intestine) within the R computing environment. For mouse distal colon and human colon, cells expressing less than 200 or more than 5000 genes were excluded from further analysis. Additionally, cells expressing >10% mitochonrial genes were excluded. For E17.5 mouse bowel, cells expressing less than 1000 or more than 9000 genes were excluded from further analysis. Additionally, cells expressing >5% mitochondrial genes were excluded.
Genome_build: Mouse distal colon and E17.5 mouse: pre-mRNA mm10, Human colon: pre-mRNA GRCh38

source_name: Nuclei from human colon muscularis tissue enriched for ENS

extract_protocol:
Mouse distal colon: Colon was removed, flushed with phosphate buffered saline, cut along the mesentery, pinned mucosal side down. Muscularis was carefully peeled from the mucosa and placed in cold O.C.T. compound in a biopsy specimen cryomold frozen in methylbutane on dry ice, and stored at -80°C. Human colon: Colons were maximally stretched and pinned. Tissue was incubated 10 minutes in 9 parts carboxygenated Krebs-Ringer solution and 1 part 4-(4-(Dimethylamino)styryl) -N-Methylpyridinium Iodide (4-Di-2-Asp) at room temperature. Tissue was transferred to ice-cold carboxygenated Krebs-Ringers solution under a fluorescence dissecting scope and fluorescent ENS was carefully dissected from muscularis by peeling away longitudinal muscle strips with forceps, placed in cold O.C.T. compound, frozen in methylbutane on dry ice, and stored at -80°C. Mouse distal colon and human colon: These pieces were sectioned at 100 microns. To isolate nuclei, frozen  sections in ice-cold lysis buffer were chopped rapidly with iridectomy scissors, transferred to a pre-cooled Dounce homogenizer on ice, homogenized, filtered through MACS SmartStrainer, centrifuged, resuspended in staining buffer with 2.5µg/mL Hoechst 33342 Trihydrochloride Trihydrate, filtered and flow sorted into 5µL staining buffer (1x phosphate-buffered saline (PBS), 1% w/v Ultrapure BSA, 0.2U/mL Protector RNase inhibitor) using a 70µm nozzle to isolate Hoechst+/mCherry+ nuclei (mouse) or Hoechst+ nuclei (human). E17.5 Mouse: E17.5 Nos1-CreERT2;ChAT-L10A-EGFP;R26R-TdTomato dams, tamoxifen treated (200 mg/kg) at E15.5 was euthanized, and pups were rapidly dissected on ice (2 TdTomato+, 3 GFP+). Full-length small intestines and colon dissociated together were used for RNA-seq. Tissue in carboxygenated 1x Hanks’ Balanced Salt Solution (HBSS) was cut into small pieces with insulin needles, and dissociated with Liberase plus DNase I, MgCl2, and CaCl2 in HBSS (37oC, 40 minutes) with repeated trituration (P1000). Dissociated cells were, passed 2-3x through 35 µm filters, pelleted in 10% fetal bovine serum (FBS)/Iscove's DMEM, resuspended in FACS buffer (0.04% w/v BSA  in HBSS, filtered again, and sorted (100µm nozzle) into 300μL FACS buffer for sequencing.
Mouse distal colon: Dataset consists of a total of 3 single-nucleus datasets generated using the 10x Genomics Chromium platform. Prior to GEM generation, sample concentration was estimated using nuclei numbers reported from FACS and a hemocytometer. Human colon: Dataset consists of a total of 16 single-nucleus datasets generated using the 10x Genomics Chromium platform.  Prior to GEM generation, sample concentration was estimated using nuclei numbers reported from FACS and a hemocytometer. Mouse E17.5 bowel: Dataset consists of one single-cell dataset, sequenced twice to improve read depth. Prior to GEM generation, the sample’s concentration (cells/ul) and viability (%) were determined by staining the cells with trypan blue and by manually counting using an inverted microscope. All: Next-generation sequencing libraries were prepared following the 10X Single Cell v2 protocol without modification. Sample quality was evaluated using Agilent’s Bioanalyzer High Sensitivity reagent kit following cDNA amplification and library construction. The completed libraries were quantified using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries were sequenced in a paired-end, single-indexed format on the Illumina HiSeq2500 or NovaSeq 6000.

value: nuclei

value: Human colon


title: Patient2_untreated_ETP-ALL_056


title: Patient2_untreated_ETP-ALL_043


title: 13558_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_048


title: Human_Colon_5047


title: Patient2_untreated_ETP-ALL_045


title: Patient2_untreated_ETP-ALL_041


title: Human_Colon_5035


title: Patient2_untreated_ETP-ALL_055


title: Human_Colon_5040


title: Human_Colon_5054


title: Patient2_untreated_ETP-ALL_042


title: Patient2_untreated_ETP-ALL_039


title: Human_Colon_4992


title: Human_Colon_5031


title: Patient2_untreated_ETP-ALL_037


title: Patient2_untreated_ETP-ALL_038


title: Human_Colon_4988


title: 10820_Flash frozen breast tumor tissue-miRNASeq


title: Patient2_untreated_ETP-ALL_036


title: Human_Colon_4950


title: Patient1_untreated_PBMC_046


title: Human_Colon_4966


title: Patient1_untreated_PBMC_045


title: Patient1_untreated_PBMC_044


title: Human_Colon_4701


title: Patient1_untreated_PBMC_042


title: Patient1_untreated_PBMC_043


title: Human_Colon_4695


title: Human_Colon_4602


title: Patient2_untreated_ETP-ALL_040


title: Human_Colon_4579


title: Human_Colon_4683


title: Patient1_untreated_PBMC_041


title: Patient1_untreated_PBMC_039


title: Patient1_untreated_PBMC_040


title: Human_Colon_4969


title: Patient1_untreated_PBMC_038


title: Patient1_untreated_PBMC_037


title: Patient1_untreated_PBMC_035


title: Pat11_1: HBEC-ALI nonCF11 rep1

city: Rotterdam

first: Rutger

last: Brouwer

address: Wytemaweg 80

department: Center for Biomics

country: Netherlands

institute: Erasmus MC

data_processing:
adapter_trimmer: zcat INPUT.fastq.gz | adapter_trimmer -a "AGATCGGAAGAG" "CTGTCTCTTATA" "AAAAAAAAAAAA" --maximum-mismatches 2 --minimum-matches 2 --minimum-bases-remaining 19 --output INPUT.tr.fastq
HISAT2 alignment: hisat2 -p 8 -x grch38_tran/genome_tran -U INPUT.tr.fastq | samtools addreplacerg -r "ID:{SAMPLEID}" -r "CN:ECB" r "LB:{SAMPLEID}" -r "SM:{SAMPLEID}" -r "PL:ILLUMINA"  -r "DS:{FULLPATH}"  - |  samtools sort     -o INPUT.BAM
samtools namesort: samtools sort -n -o INPUT.NAMESORT.BAM INPUT.BAM
htseq gene signal quantification: htseq-count -f bam -r name  --additional-attr gene_name -m union -s reverse INPUT.NAMESORT.bam Homo_sapiens.GRCh38.91.gtf
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited files with ensembl_id, gene symbol, and alignments

source_name: primary air-liquid interface culture 21 days

growth_protocol: Primary airway cells from human lungs were isolated and cultured at air-liquid interface (ALI) on permeable membranes to allow differentiation to airway epithelial cells (Methods BEGM) as described in (Stolarczyk, 2018, AJP_Lung). CF primary epithelial cells were obtained from the CF Translational Center, McGill University, Montreal, Canada where they were prepared according to a protocol approved by the Institutional Review Board of McGill University (#A08-M70-14B) using methods previously described in detail (40). Control non-CF cells were obtained from the ErasmusMC Rotterdam, Pulmonology Department, lung resection material with permission of the Ethical reviewboard of the ErasmusMC, and cultured using the same methods. In all experiments reported here CF and WT cells were expanded in KSFM + ROCKinhibitor and differentiated on 12 mm transwell with 0.4 µl pore polyester membrane inserts (Costar) in air-liquid interface culture in parallel (BEGM, LONZA), essentially as described previously. HBEC-ALI cultured for 21 days, used in all experiments, showed comparable trans-epithelial resistance (>400 Ω•cm2), differentiated epithelial morphology as shown by lateral cadherin (ECAD) and tight junction (ZO-1) staining, and 20-30% ciliated cells. In all experiments reported here, the cells were cultured on BEGM-EGF for 24 hours to achieve a basal state of EGFR signaling, previous to intervention or control in BEGM-EGF. After 24 h media were collected, an apical wash was performed, and cells were harvested for RNA isolation or lipid analysis.

extract_protocol:
For RNA isolation 12 mm Transwell inserts (Corning) were placed on ice in a 6-well plate. 300 µl TRizol (Sigma) was added directly on the insert. The cells were then scraped and transferred to a 1.5 ml tube for 5 min at room temperature, 60 µl chloroform (Sigma) was added and the tube was shaken for 15 sec. After 10 min at room temperature the tubes were centrifuged at 12,000 x g for 20 min at 4°C. 180 µl isopropanol was added to the aqueous phase for 5-10 min at room temperature and centrifuged at 12,000 x g for 10 minutes at 4°C. The RNA pellet was washed with 300 µl of 70% cold EtOH, centrifuged at 11,400 rpm for 5 min at 4°C and dissolved in 25 µl DEPC (Sigma) water. The quality of the RNA was checked using a 2100 Bioanalyser (Agilent) and the samples were stored at -80°C before analysis
Stranded sequencing libraries of poly-adenylated mRNA were prepared from 200 ng of isolated total RNA using the Stranded mRNA Prep (Illumina) according to the manufacturer’s recommendations. In short, poly-adenylated mRNA was enriched using magnetic oligo-dT beads. The enriched mRNA was then fragmented enzymatically and the first and second strand cDNA syntheses were performed. In the synthesis of the second strand, dUTPs are incorporated instead of dTTP, which will not be amplified in future PCR reactions. To the resulting double stranded cDNA, adapters were ligated and the stranded library is amplified and sequenced on an HiSeq2500 sequencer (Illumina).

treatment_protocol: Samples analysed here represent the basal state inder the culture conditions described

tag: disease state

value: Non-Cystic fibrosis

value: airway epithelium


title: Patient1_untreated_PBMC_036

tag: who classification


title: Pat11_2: HBEC-ALI nonCF11 rep2


title: Pat21_2: HBEC-ALI nonCF21 rep2


title: BCF174_3: HBEC-ALI CF rep3

value: Cystic fibrosis


title: Patient1_untreated_PBMC_034

tag: cell type


title: BCF174_2: HBEC-ALI CF rep2


title: Patient1_untreated_PBMC_032


title: Patient1_untreated_PBMC_033


title: 102-00548-B

first: William

middle: Evan

last: Johnson

address: 72 E Concord St E609

department: Division of Computational Biomedicine

institute: Boston University

data_processing:
Raw sequencing FASTQ files were assessed for data quality using FastQC. Trimmomatic was used to trim the reads (SLIDINGWINDOW:4:20 LEADING:3 TRAILING:3 MINLEN:36). Rsubread was used to align reads to human genome hg38 and to determine expression counts for each feature, using the Ensembl GRCh38.99.gtf annotations.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file containing counts for each feature

source_name: Whole Blood

extract_protocol:
We analyzed RNA-seq data from enrollment PaxGene tubes from a subset of index cases and tuberculin skin test positive (TST ≥5mm) household contacts. PaxGene tubes were sent to MedGenome (Bangalore, India) for processing.  RNA was extracted from thawed samples using the PAXgene Blood RNA kit (Cat #762164, Qiagen, Hilden, Germany)..
Library preparation and sequencing was performed as described previously (Leong S, Zhao Y, Joseph NM, et al. Existing blood transcriptional classifiers accurately discriminate active tuberculosis from latent infection in individuals from south India. Tuberculosis. 2018;109. doi:10.1016/j.tube.2018.01.002)

tag: tb status

value: LTBI

tag: Sex

value: male

tag: bmi


title: Patient1_untreated_PBMC_030

value: ETP-ALL

value: Peripherial blood mononuclear cells


title: Pat11_3: HBEC-ALI nonCF11 rep3


title: 102-00467-B

value: female


title: Patient1_untreated_PBMC_031


title: BCF174_1: HBEC-ALI CF rep1


title: Pat21_3: HBEC-ALI nonCF21 rep3


title: 102-00525-B


title: Patient1_untreated_PBMC_029


title: Patient1_untreated_PBMC_027


title: 102-00381-A

value: activeTB


title: Pat21_1: HBEC-ALI nonCF21 rep1


title: 102-00380-A


title: 102-00459-B


title: 102-00377-A


title: Patient1_untreated_PBMC_026


title: 102-00374-B0


title: Patient1_untreated_PBMC_025


title: 102-00373-B


title: Patient1_untreated_PBMC_024


title: Patient1_untreated_PBMC_023


title: Patient1_untreated_PBMC_022


title: Patient1_untreated_PBMC_021


title: Patient1_untreated_PBMC_028


title: 102-00365-B


title: 102-00361-A


title: 102-00350-B


title: Patient1_untreated_PBMC_019


title: 102-00349-A


title: Patient1_untreated_PBMC_018


title: Patient1_untreated_PBMC_017


title: 102-00347-A


title: Patient1_untreated_PBMC_016


title: 102-00343-A


title: 102-00346-A


title: Patient1_untreated_PBMC_015


title: 102-00335-A


title: 102-00341-A


title: Patient1_untreated_PBMC_012


title: Patient1_untreated_PBMC_014


title: Patient1_untreated_PBMC_013


title: 102-00332-A


title: Patient1_untreated_PBMC_011


title: 102-00323-B


title: 102-00315-A


title: 102-00311-A


title: Patient1_untreated_PBMC_010


title: Patient1_untreated_PBMC_020


title: Patient1_untreated_PBMC_009


title: 102-00310-B


title: 102-00308-B0


title: Patient1_untreated_PBMC_008


title: Patient1_untreated_PBMC_007


title: 102-00308-A0


title: Patient1_untreated_PBMC_006


title: 102-00304-B


title: Patient1_untreated_PBMC_005


title: 102-00303-A


title: Patient1_untreated_PBMC_004


title: 102-00298-B


title: Patient1_untreated_PBMC_002


title: 102-00291-B


title: Patient1_untreated_PBMC_003


title: Patient1_untreated_PBMC_001


title: 102-00290-B


title: NormalDonor5_untreated_PBMC_094

value: Normal


title: 102-00277-B


title: 102-00265-B0


title: NormalDonor5_untreated_PBMC_092


title: 102-00261-B


title: NormalDonor5_untreated_PBMC_091


title: 102-00247-B


title: 102-00374-A0


title: 102-00275-B


title: NormalDonor5_untreated_PBMC_089


title: 102-00246-B


title: NormalDonor5_untreated_PBMC_090


title: Muscle_tourniquet_60min_sample8

type: RNA

city: Mannheim

first: Ahmed

last: Jawhar

state: Badenwürttemberg

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: Universitätsmedizin Mannheim

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human HTA-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: M. vastus medialis, tourniquet, 60min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Muscle homogenates were obtained using BioMasherII Kible. Muscle extracts were prepared using RNeasy Plus Universal Mini Kit Qiagen.

treatment_protocol: Muscle biopsies of (5 × 5 × 5 mm) 125 mm3 were obtained from vastus medialis immediately after performing the surgical approach for primary total knee arthroplasty and exactly 60 min later.

value: M. vastus medialis

value: tourniquet, 60min


title: 102-00241-B


title: NormalDonor5_untreated_PBMC_087


title: Muscle_tourniquet_60min_sample3


title: Muscle_tourniquet_60min_sample9


title: Muscle_non-tourniquet_60min_sample10

source_name: M. vastus medialis, non-tourniquet, 60min

value: non-tourniquet, 60min


title: Muscle_tourniquet_60min_sample6


title: Muscle_tourniquet_60min_sample11


title: Muscle_tourniquet_60min_sample7


title: Muscle_non-tourniquet_60min_sample9


title: Muscle_non-tourniquet_60min_sample8


title: Muscle_non-tourniquet_60min_sample6


title: Muscle_tourniquet_60min_sample4


title: Muscle_non-tourniquet_60min_sample7


title: 102-00240-B


title: Muscle_tourniquet_60min_sample2


title: NormalDonor5_untreated_PBMC_093


title: Muscle_non-tourniquet_60min_sample5


title: NormalDonor5_untreated_PBMC_088


title: NormalDonor5_untreated_PBMC_086


title: 102-00227-B


title: 102-00217-B


title: NormalDonor5_untreated_PBMC_084


title: 102-00216-B


title: Muscle_tourniquet_60min_sample1


title: Muscle_non-tourniquet_60min_sample3


title: Muscle_tourniquet_60min_sample10


title: 102-00188-B


title: YAMATseq, Z.mays seedling

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

country: China

institute: Tianjin Normal University

description: pretreated RNA

data_processing:
Library strategy: YAMAT-seq
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.

organism: Zea mays

source_name: Z.mays seedling

growth_protocol: Arabidopsis thaliana, Glycine max, Hordeum vulgare, Setaria italica, Sorghum bicolor, Triticum aestivum, Zea mays plants were germinated in the soil and grown at 23 ºC under the standard long-day condition (16 hours of light followed by 8 hours of darkness). The 10-day old seedlings were collected for tRNA-seq or YAMAT-seq analysis.

extract_protocol:
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
RNA pretreatment was conducted using rtStar tRF&tiRNA pretreatment kit (Arraystar). Pretreated RNAs were purified by Phenol:Chloroform extraction and ethanol precipitation. tRNA-seq library was constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). Purification of PCR amplified cDNAs were conducted using VAHTS DNA Clean Beads (Vazyme). YAMAT-seq was performed as previously described (Shigematsu et al Nucleic Acids Res. 2017) with some modifications. The design of Y-shaped adapters followed previous study. 2 µl of 3’ adaptor (10 µM) and 2 µl of 5’ adaptor mix (10 µM) were incubated at 70ºC for 2 min and cooled at room temperature to allow 5’ and 3’ adaptors to fully anneal. Then, the Y-shaped adaptor was mixed with 2 µg pretreated RNA, 4 unit T4 Rnl2 (New England Biolabs) and 2 µl ligation buffer with total reaction of 20 µl, and incubated at 37 ºC for 2 h. Next, 1 µl RNA RT Primer (RTP, Illumina) was added to the reaction and incubated at 70 ºC for 3 min, and then immediately chilled on ice. Subsequently, reverse transcription and cDNA amplification reactions were performed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). A Universal Primer and RNA PCR Index Primers (Illumina) were used for amplifying cDNAs with 12 PCR cycles. The PCR products were purified using VAHTS DNA Clean Beads (Vazyme).

value: seedling


title: tRNAseq, Z.mays seedling

description:
pretreated RNA
tRNAseq_tRNA.xlsx

data_processing:
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.


title: Muscle_non-tourniquet_60min_sample1


title: NormalDonor5_untreated_PBMC_083


title: MCF-7 cells, siControl RNA_3

city: Wu han

first: Le

last: Wu

state: Hu bei

address: No.1,Shizishan Street · Hongshan District · Wuhan

institute: HuaZhong Agricultural university

data_processing:
Removed reads with low quality, adapter contamination and high content of unknown base N
Aligned to the hg38 whole genome using HISAT2
Quanitify gene-expression level using RSEM,which is estimate by count and RPKM value
Genome_build: hg38
Supplementary_files_format_and_content: ExpressionProfile.txt containing  RPKM values

source_name: MCF-7 cells

growth_protocol: DMEM medium with 10% FBS

extract_protocol:
RNA extraction with Qiagen kit
NA

treatment_protocol: si RNA 50 nM

tag: cell line

tag: genotype

value: control


title: NormalDonor5_untreated_PBMC_082

source_name: Blood


title: 102-00171-B


title: 102-00131-B


title: MCF-7 cells, siControl RNA_2


title: MCF-7 cells, siTRIM3_2

value: TRIM3 depletion


title: MCF-7 cells, siTRIM3_1


title: 102-00129-B0


title: NormalDonor5_untreated_PBMC_085


title: IL-21_rep3

city: Beijing

first: Ying

last: Li

address: Datun Road #15, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to filter reads.
HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to do the mapping step.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

organism: Mus musculus

source_name: OT-1 Tcells

extract_protocol:
RNA was prepared by RNeasy mini kit (Qiagen, 74104).
RNA libraries were prepared for sequencing using BGISEQ-500 protocol(version A1).

tag: strain

value: OT-1 mice

tag: tissue

value: Lymph nodes

tag: teatment

value: Differentiated with IL-21 for 3 days


title: NormalDonor5_untreated_PBMC_080


title: MCF-7 cells, siControl RNA_1


title: PD-1Ab21_rep3

value: Differentiated with PD-1Ab21 for 3 days


title: NormalDonor5_untreated_PBMC_077


title: NormalDonor5_untreated_PBMC_078


title: NormalDonor5_untreated_PBMC_081


title: 102-00088-B

value: LTBI


title: NormalDonor5_untreated_PBMC_076


title: IL-21_rep1


title: Naive_rep3

value: Untreated


title: Adult Patient 9

city: Richmond

first: Maren

middle: Lydia

last: Smith

state: Virginia

address: 1217 E Marshall St

department: Pharmacology and Toxicology

institute: Virginia Commonwealth University

data_processing:
Illumina software used for basecalling.
Sequence reads were mapped to GRC38.91 using STAR v2.6.
Count data was generated from STAR produced BAM files using HTSeq v0.61p1.
Count data was corrected for batch effects using ComBat (Johnson et al. PMID: 16632515) and transformed to positive whole numbers.
Genome_build: GRC38.91
Supplementary_files_format_and_content: Tab-deliminted text files countaining count values for each sample after batch correction by ComBat and transformation to positive, whole numbers.

source_name: whole blood

extract_protocol:
Whole blood (2 mL) was collected from study participants in Tempus Blood RNA tubes at the time of diagnosis or flareup. RNA was extracted from blood using the Tempus Spin RNA Isolation Kit (Thermo Fisher), and polyA enrichment was conducted using the NEBNEXT Poly(A) mRNA magnetic isolation kit (New England BioSciences).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole blood

value: ANCA-associated vasculitis

tag: rna-cluster

value: Adult Endotype B

tag: anca status

value: MPO


title: NormalDonor5_untreated_PBMC_079

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

value: Normal

value: Peripherial blood mononuclear cells


title: PD-1Ab_rep3

value: Differentiated with PD-1Ab for 3 days


title: PD-1Ab_rep1


title: Adult Patient 11

value: NEGATIVE


title: Naive_rep2


title: 102-00042-B

tag: age

value: female


title: IL-21_rep2


title: PD-1Ab21_rep1


title: NormalDonor5_untreated_PBMC_073


title: Adult Patient 7


title: IL-15_rep2

value: Differentiated with IL-15 for 4 days


title: PD-1Ab21_rep2


title: Adult Patient 10


title: IL-2_rep1

value: Differentiated with IL-2 for 4 days


title: MCF-7 cells, siTRIM3_3

value: TRIM3 depletion


title: Muscle_non-tourniquet_60min_sample2

value: M. vastus medialis

tag: group

value: non-tourniquet, 60min


title: RAW-Rv3722c-3

city: Wuhan

first: Yingying

last: Lei

state: China

address: NO. 1 shizishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
BGIMega software
Alignment was done by hisat2 and samtools
Readcounts was generated by stringtie
Differencial analysis and normalized abundance measurements was done by deseq2
Genome_build: grcm38
Supplementary_files_format_and_content: Count matrix was generated by stringtie

source_name: leukemia cells of monocyte macrophage

growth_protocol: Two cell lines were cultured in DMEM for 24h and harvest  for RNA isolation by TriZol protocol

extract_protocol:
RNA was harvested using Trizol reagent. VAHTS Universal V6 RNA-seq Library Prep Kit for MGI (Vazyme, NRM604) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard MGI protocols

treatment_protocol: 5×105 cells were seeded into 6-well plates and grown to 80–90% confluence. HEK293T cells were transfected using calcium phosphtate precipitation.

tag: cell name

value: ATCC TIB-71TM

value: Rv3722c overexpression


title: Naive_rep1

value: OT-1 mice

value: Lymph nodes

value: Untreated


title: Adult Patient 8

value: whole blood

value: ANCA-associated vasculitis

value: Adult Endotype B


title: RAW-Rv3722c-2


title: IL-15_rep3


title: PD-1Ab_rep2


title: IL-2_rep2


title: NormalDonor5_untreated_PBMC_074

value: Normal

value: Peripherial blood mononuclear cells


title: NormalDonor5_untreated_PBMC_075


title: NormalDonor5_untreated_PBMC_072


title: RAW-Vector-3

value: Vector control


title: Adult Patient 6

value: Adult Endotype A

value: MPO


title: Activated_rep1

value: Activated by OVA peptide


title: Adult Patient 5


title: RAW-Vector-2


title: RAW-Vector-1


title: Activated_rep2


title: Adult Patient 4


title: Adult Patient 1

value: Adult Other


title: Activated_rep3


title: NormalDonor5_untreated_PBMC_070


title: IL-15_rep1

value: Differentiated with IL-15 for 4 days


title: Adult Patient 3


title: IL-2_rep3

value: Differentiated with IL-2 for 4 days


title: NormalDonor5_untreated_PBMC_069


title: Pediatric Patient 30

value: Endotype B


title: RAW-Rv3722c-1

value: ATCC TIB-71TM

value: Rv3722c overexpression


title: Adult Patient 2


title: NormalDonor5_untreated_PBMC_071


title: NormalDonor5_untreated_PBMC_066


title: NormalDonor5_untreated_PBMC_068


title: HFD3.2-F2XXA

city: Shenzhen

first: Jin

last: Xin

state: Guangdong

address: Beishan road

institute: BGI

data_processing:
Filtering and trimming the reads using Trimmomatic v0.38 with parameters “HEADCROP:9 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50 AVGQUAL:20”.
Clean reads were mapped to the Mus musculus genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6 ) using Hisat2 v2-2.1.0 with default parameters.
The reads of each sample were then assembled into transcripts and compared with reference gene models using StringTie v1.3.4d.
Merging the 31 transcripts to obtain a consensus transcript using StringTie-Merge program.
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
DEG analysis was performed using Ballgown v2.12.0.
Gene-set enrichment analysis (GSEA) was performed on genes ranked by their differential expression Signal2Noise using GSEA software (4.3.0 from Broad Institute). KEGG pathway database were downloaded from https://www.kegg.jp/kegg .bin/search_pathway_text?map=mmu&keyword=&mode=1&viewImage=truehttps://www.kegg.jp/kegg .

source_name: hippocampus

extract_protocol:
A phenol-chloroform extraction
RNA libraries were prepared for sequencing using standard BGI-500 protocols

value: hippocampus

tag: mouse group

value: HFD-F


title: NormalDonor5_untreated_PBMC_067

first: Birgit

last: Knoechel

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute


title: HFD3.2-F4XXA


title: HFD2.5-F2XYA


title: HFD3.2-F1XXA


title: HFD2.2-F4XYA


title: Pediatric Patient 27

value: whole blood

tag: disease state

value: Other


title: Pediatric Patient 28

value: ANCA-associated vasculitis


title: Pediatric Patient 29


title: NormalDonor5_untreated_PBMC_065

tag: who classification

value: Normal


title: NormalDonor5_untreated_PBMC_062

tag: cell type

value: Peripherial blood mononuclear cells


title: HFD2.5-F1XYA


title: NormalDonor5_untreated_PBMC_064


title: HFD2.5-C1XXA

value: HFD-C


title: Pediatric Patient 22

value: Endotype A


title: HFD2.3-C3XYA


title: HFD1.5-C3XXA


title: NormalDonor5_untreated_PBMC_063


title: HFD3.3-C2XYA


title: HFD3.2-C1XYA


title: Pediatric Patient 26

value: NEGATIVE


title: NormalDonor5_untreated_PBMC_060


title: HFD1.5-C2XXA


title: HFD1.5-C2XYA


title: HFD2.2-C2XXA


title: NormalDonor5_untreated_PBMC_059


title: Muscle_non-tourniquet_60min_sample4

value: M. vastus medialis

value: non-tourniquet, 60min


title: Pediatric Patient 17


title: FFD3.2-C5XXA

value: FFD-C


title: HFD2.2-F1XYA


title: HFD3.2-F3XXA


title: FFD2.2-C2XXA


title: NormalDonor5_untreated_PBMC_061


title: Pediatric Patient 21


title: FFD1.3-C2XXA


title: HFD1.5-C1XYA


title: Pediatric Patient 18


title: FFD2.2-C2XYA


title: Pediatric Patient 13

value: MPO


title: NormalDonor5_untreated_PBMC_054


title: FD2.2-C4XYA

value: FD-C


title: Pediatric Patient 12

value: Endotype B


title: NormalDonor5_untreated_PBMC_057


title: Pediatric Patient 16


title: NormalDonor5_untreated_PBMC_056


title: FFD1.3-C1XYA


title: Pediatric Patient 11


title: Pediatric Patient 15


title: NormalDonor5_untreated_PBMC_055


title: NormalDonor5_untreated_PBMC_058


title: Pediatric Patient 14


title: FFD2.2-C1XYA


title: FFD1.1-C3XYA


title: FD1.2-C3XXA


title: Pediatric Patient 8


title: FD2.2-C5XYA


title: FD2.2-C3XXA


title: FFD1.1-C2XXA


title: FD2.2-C1XXA


title: Pediatric Patient 6


title: FD2.1-C4XXA


title: NormalDonor5_untreated_PBMC_052


title: FD2.1-C1XYA


title: NormalDonor5_untreated_PBMC_053


title: NormalDonor5_untreated_PBMC_051


title: Pediatric Patient 4


title: CD2.5X-F4XXA

value: CD-F


title: FD1.2-C1XYA

value: hippocampus


title: NormalDonor5_untreated_PBMC_050


title: NormalDonor5_untreated_PBMC_048


title: CD2.6-F2XXA


title: CD2.5X-F1XXA


title: Pediatric Patient 3


title: Pediatric Patient 5


title: 17614_Flash frozen breast tumor tissue-miRNASeq

value: breast tumor tissue

tag: gender

value: Female

tag: race

value: African American

tag: er

value: Negative

tag: molecule subtype

value: miRNA


title: CD2.6-F1XYA


title: CD1.5-F2XYA


title: CD1.5-F1XYA


title: CD2.6-F2XYA


title: NormalDonor5_untreated_PBMC_046

value: Normal

value: Peripherial blood mononuclear cells


title: CD2.2-C2XYA

value: CD-C


title: NormalDonor5_untreated_PBMC_049


title: CD2.1-C3XXA


title: NormalDonor5_untreated_PBMC_044


title: CD2.1-C1XYA


title: Pediatric Patient 1

value: whole blood

value: ANCA-associated vasculitis


title: CD2.5-C4XXA


title: NormalDonor5_untreated_PBMC_045


title: CD1.1-C4XYA


title: CCF 702_RNA-seq

city: Cleveland

first: Briana

last: Prager

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

data_processing:
Single-end reads were trimmed to 75 bp using BBDuk from the BBMap toolset to match the sample format from GSE101638.
Trim Galore was used to trim adaptors and remove low quality reads.
Reads were quantified against Gencode v29 using Salmon with correction for fragment-level GC bias, positional bias and sequence-specific biases.
Transcripts were summarized to gene level and processed to transcripts per million (TPM) using the R/Bioconductor package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: meningioma_TPM.csv

source_name: Meningioma tissue

growth_protocol: First-passage arachnoid granulation cells were grown in DMEM supplemented with 7% FBS and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted flash frozen, pulverized tissue using the miRNeasy mini kit (Qiagen, cat #217004) in accordance with the manufacturer protocols.
Libraries were prepared and sequenced by Genewiz. Stranded RNA library preparation was performed with ribosomal RNA depletion according to instructions from the manufacturer (Epicentre).
Paired-end sequencing was performed on the Illumina HiSeq 2500 with single-end read configuration.

tag: tissue/sample type

value: Meningioma tissue


title: CD1.1-C1XXA

tag: strain


title: CD2.5X-F2XXA

tag: tissue


title: NormalDonor5_untreated_PBMC_047

city: Boston


title: CCF 3590_RNA-seq


title: WT1_1

city: shanghai

first: chen

last: xue

address: Nanchen Road381 room305

department: College of Life Science

institute: shanghai university

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to mm9 whole genome using HISAT2
Sequence reads were mapped to mouse genome (mm9) by using bowtie 2 with default settings, and reads mapped to multiple positions (MAPQ < 10) were discarded.
Gene expression levels were measured by RPKM (reads per kilobase of exon per million reads) by RSEM.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes fpkm values for each Sample

source_name: WT_lymphoid CD4 positive T cells

growth_protocol: Pten f/f Pf4-Cre mice and littermate control Pten f/f mice growth normally

extract_protocol:
Lymphoid CD4 positive T cells were sorted by FACS. RNA was isolated from the T cell pellet by Trizol Reagent (Invitrogen), and the quality was determined by Bioanalyzer 2100 (Agilent). The 23S and 16S rRNA were depleted with MicrobExpress kit (Ambion). Genomic DNA was removed by two digestions using Amplification grade DNAse 1 (Invitrogen). The RNA was sheared and reverse transcribed by random primers to obtain cDNA.
The library quality was determined by Bioanalyzer 2100 (Agilent).RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2. Then, the library was used for sequencing including making DNA NanoBalls (DNBs).

treatment_protocol: no treatment

tag: strain background

tag: genotype/variation

value: control Pten f/f

value: Lymph node

tag: cells

value: CD4+ T cells


title: KO3_1

source_name: KO_lymphoid CD4 positive T cells

value: Pten f/f Pf4-Cre


title: CCF 471_RNA-seq


title: CCF 3255_RNA-seq


title: WT3_1


title: NormalDonor5_untreated_PBMC_042


title: WT2_1


title: KO1_1


title: Shoot, salt rep2

description: pretreated RNA

data_processing:
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by tRanalyzer, a self-designed pipeline for quantifications of tsRNAs and tRNAs.
Genome_build: TAIR10, TIGR7
Supplementary_files_format_and_content: Each excel format file includes four sheets. The tRNAID sheet includes the IDs, genomic coordinates and unique sequences of tRNAs. tRNA_expression sheet shows tRNA abundances. tRFs_from_each_tRNA sheet shows the abundance of tRFs from each tRNA. Each_tRF sheet shows the abundance of each tRF species.

organism: Oryza sativa

source_name: Shoot, salt treated

growth_protocol: Arabidopsis thaliana plants were germinated in the soil and grown at 23 ºC under the standard long-day condition (16 hours of light followed by 8 hours of darkness). Oryza sativa seeds were germinated at 30ºC for 2 d. Uniformly germinated seeds were transferred to Yoshida’s nutrient solution and grown at 28ºC under long-day condition (14 hours of light followed by 10 hours of darkness). Yoshida’s solution were replaced every 3 d with pH adjusted to 5.5.

extract_protocol:
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
RNA pretreatment was conducted using rtStar tRF&tiRNA pretreatment kit (Arraystar). Pretreated RNAs were purified by Phenol:Chloroform extraction and ethanol precipitation. Pretreated RNAs were subjected to small RNA-seq library construction using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). Purification of PCR amplified cDNAs were conducted using VAHTS DNA Clean Beads (Vazyme).
tRNA-seq

treatment_protocol: In salt treatment, Oryza sativa seedlings were transferred to 300 mM NaCl solution for 8 h. In cold treatment, Oryza sativa seedlings were transferred to a cold room at 4ºC under continuous light for 8 h. The control and stress treated seedlings were collected and immediately frozen in liquid nitrogen and stored at -80ºC before RNA extraction.

tag: treatment

value: salt


title: DI 98_RNA-seq


title: CD1.1-C5XYA

tag: age

value: hippocampus


title: CD2.5-C3XXA


title: CCF 3706_RNA-seq


title: NormalDonor5_untreated_PBMC_043


title: CCF 556_RNA-seq


title: Shoot, control rep1

description: pretreated RNA

source_name: Shoot, control

value: control


title: Shoot, cold rep1

description: pretreated RNA

source_name: Shoot, cold treated

value: cold


title: AG02_RNA-seq

source_name: Arachnoid granulation cell model

value: Arachnoid granulation cell model


title: CCF 3622_RNA-seq


title: NormalDonor5_untreated_PBMC_036


title: NormalDonor5_untreated_PBMC_039


title: NormalDonor5_untreated_PBMC_035


title: Root, control rep1

description: pretreated RNA

source_name: Root, control


title: Root, control rep2

description: pretreated RNA


title: Root, cold rep2

description: pretreated RNA

source_name: Root, cold treated


title: CCF 66_RNA-seq


title: DI 134_RNA-seq


title: Shoot, salt rep1

description: pretreated RNA


title: Panicle rep1

description: pretreated RNA

source_name: Panicle


title: Shoot, control rep2

description: pretreated RNA


title: NormalDonor5_untreated_PBMC_038


title: NormalDonor5_untreated_PBMC_032


title: muscle, Double_mutants_rep1

first: jing

last: zhao

address: Qiuyue Road

institute: IRCBC

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to dme with cellranger count by default parameter (version 3.0.0) . The count files were used as input to Seurat for downstream analysis.
Genome_build: Dme_6.19
Supplementary_files_format_and_content: output from Cellranger; output from Seurat

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: muscle, Double_mutants

growth_protocol: Flies were cultured in standard media at 25ºC with 60% humidity unless otherwise specified. The control (WT) line used was 5905 (FlyBase ID FBst0005905, w1118). The given genotype male flies were collected at the third day of eclosion

extract_protocol:
Nuclei isolated by Nuclei isolation kit(SIGMA, SLBZ5331 )
sNuc-seq libraries were prepared according to instructions of 10X single cell  library  kit v2 (Chromiun, 120234).

treatment_protocol: Flies were harvested at the given age.

value: muscle

value: Day 3

tag: genotype


title: muscle, WT_rep3

source_name: muscle, WT


title: Shoot, cold rep2

description: pretreated RNA


title: AG01_RNA-seq


title: NormalDonor5_untreated_PBMC_037

source_name: Blood

value: Normal


title: UCSF 9889_ChIP

data_processing:
FASTQ reads were trimmed to remove low quality reads and adaptors with Trim Galore.
Uniquely mapped reads were aligned to the human reference genome h19/GRCh37 with the Burrows-Wheeler Aligner to generate BAMs.
BAMs were sorted and indexed with SAMtools.
PCR duplicates were removed using PicardTools.
Peaks were called using the MACS2 callleak function on the ChIP-seq BAM file using the following parameters: BAMPE for paired-end reads, scaling to the larger dataset, the default log2 fold change enrichment of 2 vs. input and a p-value cutoff of 1e-5.
Bigwig tracks were generated using the DeepTools (v3.1.2)24 bamCoverage command with RPKM normalization
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs

extract_protocol:
5–10 mg of flash-frozen primary meningioma tumors was pulverized, crosslinked using 1.5% formaldehyde and sonicated to fragment sizes of 200-800 bp. Samples were incubated overnight with 5 μg H3K27ac antibody per ChIP experiment (Active Motif; 39133).
Enriched DNA was quantified by using PicoGreen (Invitrogen) and ChIP libraries were amplified and barcoded by using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to the manufacturer’s recommendations. Following library amplification, DNA fragments were agarose gel (1.0%) size selected (<1 kb), analyzed using a Bioanalyzer (Agilent Technologies)
Samples were sequenced at Genewiz by using Illumina HiSeq 2500 150-bp paired-end reads.

tag: patient sex

value: M

tag: tumor grade

tag: chip antibody

value: H3K27ac antibody (Active Motif; 39133)


title: NormalDonor5_untreated_PBMC_041

tag: who classification

tag: cell type

value: Peripherial blood mononuclear cells


title: AG03_RNA-seq


title: Root, salt rep2

description: pretreated RNA

source_name: Root, salt treated


title: NormalDonor5_untreated_PBMC_030


title: KO2_1


title: NormalDonor5_untreated_PBMC_040


title: UCSF 9673_ChIP

value: F


title: Root, salt rep1

description: pretreated RNA


title: NormalDonor5_untreated_PBMC_029


title: NormalDonor5_untreated_PBMC_034


title: UCSF 9387_INP

value: Meningioma tissue


title: Panicle rep2

description: pretreated RNA


title: NormalDonor5_untreated_PBMC_033


title: muscle, Double_mutants_rep2


title: muscle, WT_rep2


title: UCSF 9889_INP


title: UCSF 9387_ChIP


title: Root, cold rep1

description: pretreated RNA


title: NormalDonor5_untreated_PBMC_031


title: UCSF 9253_INP


title: SCAP at k, biological rep1

city: Jinan

first: Junqing

last: Liu

address: No.44-1 Wenhua Road West

institute: Shandong University

description: Gene expression data from SCAP after osteogenic differentiation for 7 days.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on GeneChip miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing: The data were analyzed with Expression Console ™ Software 1.3 using Affymetrix default analysis settings and global scaling as normalization method.The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: dental (apical papilla)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color  Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Then cells were cultured in α-minimum essential medium (HyClone, Logan, UT, United States) supplemented with 20% fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA), 100 U/ml penicillin and 100 μg/ml streptomycin (HyClone) at 37°C in a 5% CO2 incubator.  The medium was changed every 3 days.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (AM1561 ) following the manufacturer's instructions.

treatment_protocol: For osteogenic differentiation, when cells reached 80% confluence, the medium was changed to osteogenic medium containing 10 mM β-glycerolphosphate (Sigma-Aldrich, St. Louis, MO, USA), 10 nM dexamethasone (Sigma-Aldrich) and 50 μg/mL L-ascorbic acid (Sigma-Aldrich). The osteogenic medium was changed every 3 days.

value: osteogenic differentiation for 7 days


title: UCSF 9673_INP


title: muscle, WT_rep1


title: NormalDonor5_untreated_PBMC_024


title: reC3_EN_rep3

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.8.2 software used for basecalling.
Illumina reads were aligned to a minimal set of coding sequences of the TAIR 10 release of the Arabidopsis thaliana genome (http://www.arabidopsis.org/) using BLAT (Kent, 2002) in protein space. The minimal transcriptome was obtained as described in Gowik et al. (2011) and contains 22,079 protein coding genes.
The best BLAT hit for each read was determined by (i) lowest e-value and (ii) highest bit score.
Raw read counts were transformed to reads per million (rpm) to normalize for the number of reads available at each sampling stage
Means of rpm of biological triplicate group (drought stage) were calculated.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel sheet (SupplementalData.xlsx) file including Arabidopsis Gene Identifier (AGI) and TAIR10_short_description, raw counts and rpm for each sample, mean rpm for biological triplicates.

organism: Talinum fruticosum

source_name: Leaf

growth_protocol: Talinum triangulare plants were grown well-watered for 28 days and then subjected to drought treatment

extract_protocol:
Mature leaves of T. triangulare were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the GeneMatrix Universal RNA Purification Kit (EURx Ltd.). Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 150 bp read length) on an Illumina HiSeq 2000 platform.

value: leaf

tag: water-limitation

value: 12 d drought + 2 d re-watered

tag: time

value: End of the night

tag: zeitgeber time

tag: photosynthetic mode


title: NormalDonor5_untreated_PBMC_028


title: NormalDonor5_untreated_PBMC_027


title: reC3_EN_rep1


title: SCAP at k, biological rep2