title: HGCIN21

description:
raw data file: US22502676_251485063644_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_HGCIN21


title: U2932

status: Public on Apr 06 2020

type: RNA

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: DLBCL, ABC cell line

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: standard cell cultures: 1x RPMI 1640 complete with 10 or 20% FCS apart from U-HO1:80% IMDM + RPMI 1640 (at 4:1) + 20% h.i. FCS, 2 mM L-glutamine

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen.RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 50ng total RNA

treatment_protocol: cell lines were culture and harvested without treatment

tag: cell line


title: 31CBS-KO-K562-RNA-seq-2

type: SRA

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the hg19 genome assembly using Tophat, and ATAC-seq, ChIP-seq, HiC-seq  reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Chromatin structure HiC-seq was calculate and display with HOMER, Juicer and Juicebox software
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples, and peaks annotation for ATAC-seq and ChIP-seq.

growth_protocol: Human Jurkat leukemia cells and K562 cells were culture at RMPI1640 and 10% FBS media.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K4me2, H3K9/14ac and H3K27ac antibody (H3K4me3 (Millipore, #04-745), H3K4me2 (Millipore, 07-030), H3K27Ac (Abcam, #ab4729), and H3K9/14ac (Diagenode, #C15410005)).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.  HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from Jurkat T-ALL and K562 cells without any treatment

tag: cell type

value: chronic myelogenous leukemia

tag: tissue

value: peripheral blood

tag: genotype


title: Patient37_Pretreatment [FFP13.004063]

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: 200 ng fluorescent labeled RNA was hybridized to custom Agilent arrays (4x44k arrays).

scan_protocol: Agilent Technologies Scanner G2505B, Agilent Scan Control Version A.7.0.3.

data_processing: Feature Extraction software v11.5.1.1 was used to quantify fluorescent intensities, custom script were used for raw data extraction and those values were normalized by 75th percentile normalisation using DataPrint software v1.15, all by Agendia Inc. Downstream data processing was subsequently done at the Netherlands Cancer Institute, by missing data impution with knn=10 and batch correction for date of RNA extraction using ComBat from the R package sva, using all available patient material from the trial (ClinicalTrials.gov Identifier: NCT00738777). Here we deposited samples used for the Tamoxifen focused analysis described in the cited paper.

label_protocol: RNA was amplified and labeled using the lQuickAmp Labeling kit (Agilent).

extract_protocol: RNA was isolated using Qiagen RNeasy microkit according to manufacturer's specifications.

treatment_protocol:
Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment
FFPE sections of patient tumor material (10 x CF 5u gelcoat per sample) were sent to Agendia Inc.

tag: subject status

value: breast cancer patient

tag: subject id

tag: treatment

value: Pretreatment

tag: tissue/sample type

value: FFPE tumor

tag: batch

value: Batch TS


title: HGCIN18

first: Renske

middle: DM

last: Steenbergen

address: De Boelelaan 1117

department: Pathology

institute: Amsterdam UMC, location VUmc

description:
raw data file: US22502676_251485063642_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_HGCIN18

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17h in a 65°C hybridization oven (G2545A, Agilent) set to 10rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software. Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA. If intensity of a probe was <50 in both channels, it was considered missing. If a probe intensity was <50 in one of the channels, it was set to 50. Probes missing in >50% of samples probe were removed from the dataset.

source_name: cervical intraepithelial neoplasia, grade 2-3

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol: 10 micrometer frozen sections of all tissue samples were first subjected to laser capture microdissection using a Leica ASLMD microscope (Leica) to enrich for neoplastic, dysplastic or normal epithelial cells as described previously (Wilting et al., Genes, Chromosomes Cancer 2008). Total RNA was isolated from microdissected tissue samples using TRIzol Reagent according to the manufacturers’ instructions. To ensure comparable RNA integrity between specimens analysed by array, RNA pico chips were performed on an Agilent 2100 Bioanalyzer (Agilent).

tag: hpv

value: high-risk HPV-positive


title: HGCIN15

description:
raw data file: US22502676_251485063642_S01_GE2-v5_95_Feb07_1_3.txt
none
VUMC_HGCIN15

value: cervical intraepithelial neoplasia, grade 2-3


title: HGCIN24

description:
raw data file: US22502676_251485063645_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_HGCIN24


title: Patient34_Pretreatment [FFP13.004060]


title: Patient35_Pretreatment [FFP13.004061]


title: HBMEC control treated [1a]

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

data_processing: plier normalization performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)

source_name: control treated

growth_protocol: commercial human primary cell line; brain microvascular endothelial cells (HBMEC)

extract_protocol: total RNA was extracted from cultured human brain microvascular endothelial cells (HBMEC) using RNAeasy kit (Qiagen)

treatment_protocol: cultered human brain microvascular endothelial cells (HBMEC) were stimulated with growth factors (VEGF-A165, PlGF, VEGF-B186, VEGF-B167) for 6h prior to RNA extraction

value: HBMEC

value: human brain microvascular endothelial cell line (HBMEC)

value: control treated


title: HGCIN9

description:
raw data file: US22502676_251485063646_S01_GE2-v5_95_Feb07_1_4.txt
none
VUMC_HGCIN9


title: Vegfb -/- heart endothelial cells [mH_8]

hyb_protocol: performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)

organism: Mus musculus

source_name: Vegfb -/- heart endothelial cells

growth_protocol: endothelial cells isoalted from mouse hearts

extract_protocol: total RNA was extracted from isolated heart endothelial cells using RNAeasy kit (Qiagen)

treatment_protocol: not applicable

value: Vegfb -/-

tag: age

value: 12 weeks

value: heart endothelial cells


title: 31CBS-KO-K562-RNA-seq-1


title: HGCIN8

description:
raw data file: US22502676_251485063646_S01_GE2-v5_95_Feb07_1_3.txt
none
VUMC_HGCIN8


title: Vegfb -/- heart endothelial cells [mH_7]

scan_protocol: performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)


title: Patient31_Pretreatment [FFP13.004058]


title: Patient30_Pretreatment [FFP13.004057]


title: 31CBS-WT-K562-RNA-seq-2


title: HBMEC control treated [2a]

label_protocol: performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)


title: HGCIN10

description:
raw data file: US22502676_251485063646_S01_GE2-v5_95_Feb07_1_4.txt
none
VUMC_HGCIN10


title: Patient29_Pretreatment [FFP13.004056]


title: Vegfb -/- heart endothelial cells [mH_6]

data_processing: performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)


title: 31CBS-WT-K562-RNA-seq-1


title: 31CBS-inv-Jurkat-RNA-seq-2

source_name: Jurkat

value: Jurkat

value: T cell leukemia


title: HBMEC stimulated with VEGF-B186 [23a]

source_name: VEGF-B186 stimulation for 6h

value: VEGF-B186 stimulation for 6h


title: 31CBS-inv-Jurkat-RNA-seq-1


title: HGCIN7

description:
raw data file: US22502676_251485063643_S01_GE2-v5_95_Feb07_1_4.txt
none
VUMC_HGCIN7


title: HGCIN5

description:
raw data file: US22502676_251485063646_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_HGCIN5


title: Patient23_Pretreatment [FFP13.004054]


title: 31CBS-WT-Jurkat-RNA-seq-2


title: SMC_17D3

city: Cleveland

first: Xiaoxia

last: Li

state: OH

address: 9500 Euclid Ave.

department: Inflammation & Immunity

country: USA

institute: Cleveland Clinic

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

source_name: hASMC

growth_protocol: Human primary ASMCs were cultured in DMEM/F-12 supplemented with 10% FCS, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: Total RNA extracted by NucleoSpin® RNA Plus (Takara Bio, Cat#740984) from human primary ASMCs

treatment_protocol: Human primary ASMCs were untreated and treated with IL-17A (100 ng/ml), DEX (1 µg/ml) or both for 4 hours.

tag: sample type

value: Primary cell


title: HGCIN4

description:
raw data file: US22502676_251485063643_S01_GE2-v5_95_Feb07_1_4.txt
none
VUMC_HGCIN4


title: Vegfb -/- heart endothelial cells [mH_5]


title: 31CBS-WT-Jurkat-RNA-seq-1

value: peripheral blood


title: Patient51_Pretreatment [FFP13.002915]

value: breast cancer patient


title: Normal03764

description:
raw data file: US22502676_251485063645_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_Normal03764

source_name: normal cervical squamous epithelium

value: normal cervical squamous epithelium


title: wild type heart endothelial cells [mH_2]

source_name: wild type heart endothelial cells

value: wild-type


title: Normal04441

description:
raw data file: US22502676_251485063645_S01_GE2-v5_95_Feb07_1_3.txt
none
VUMC_Normal04441


title: wild type heart endothelial cells [mH_4]


title: wild type heart endothelial cells [mH_3]


title: Patient4_Pretreatment [FFP13.004048]

value: Pretreatment

value: FFPE tumor

value: Batch TS


title: wild type heart endothelial cells [mH_1]


title: HV-6

city: Wuhan

first: Jin

last: Liu

address: 185 Donghu Road

institute: wuhan university school of basic medical sciences

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 16 nt.
The clean reads were compared to the miRbase21 and Rfam database  to identify known miRNA and other non-coding RNAs.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Total clean reads were  also mapped to the Human reference genome using the bwa aligner.The mapped reads were further annotated to the repeats and exon regions based on the genome annotation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs were purchased from ScienCell Research Laboratories (Cat No: 8000, Carlsbad, USA) and cultured in ECM Medium with 5% fetal bovine serum (FBS), 1% penicillin-streptomycin and endothelial cell growth supplement (ECGS) (ScienCell) at 37°C in 5% CO2.

extract_protocol:
Total RNA from mock and HTNV-infected HUVECs was isolated with TRIzol reagent (Invitrogen, USA).
RNAs were ligated with 3’RNA adapter, and followed by 5’adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA).

treatment_protocol: HUVECs were mock-infected or HTNV-infected at a multiplicity of infection (MOI) of 1.

value: umbilical cord

value: wild type

tag: htnv infection

value: HTNV infected


title: Normal02449

description:
raw data file: US22502676_251485063642_S01_GE2-v5_95_Feb07_1_4.txt
none
VUMC_Normal02449

value: HPV-negative


title: Patient50_Pretreatment [FFP13.001919]


title: Patient51_Tamoxifen [FFP13.001761]

value: Tamoxifen


title: SMC_17D2


title: HV-4


title: Normal02400

description:
raw data file: US22502676_251485063644_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_Normal02400

value: high-risk HPV-positive


title: con-5

value: mock infected


title: HV-2


title: Patient26_Tamoxifen [FFP12.003151]


title: SMC_DEX3

value: DEX


title: SMC_DEX2


title: Patient28_Tamoxifen [FFP12.003105]


title: Normal02371

description:
raw data file: US22502676_251485063646_S01_GE2-v5_95_Feb07_1_3.txt
none
VUMC_Normal02371


title: Patient24_Tamoxifen [FFP12.003103]


title: Patient26_Pretreatment [FFP12.003150]


title: con-4


title: SMC_DEX1


title: Normal02218

description:
raw data file: US22502676_251485063646_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_Normal02218


title: con-3


title: D21R6: Day 21 GRASLND shRNA 1

city: St Louis

first: Farshid

last: Guilak

state: Missouri

address: Couch Building, 3rd Floor, #3213

department: Orthopaedics

institute: Washington University in St Louis

data_processing:
Raw fastq files were trimmed with Trimmomatic-0.36
Processed reads were aligned with STAR-2.6.0c to ENSEMBL 92
Reads were counted with featureCounts
Genome_build: Homo sapiens Ensembl 92
Supplementary_files_format_and_content: tab-delimited text files include raw counts fore genes for each sample by gene symbol; tab-delimited text files include normalized counts for genes for each sample by gene symbol

source_name: Mesenchymal stem cells

growth_protocol: MSCs were digested in 0.05% Trypsin-EDTA (Gibco), and trypsin was inactivated with 1.5X volume of expansion medium. Digested cells were centrifuged at 200 x g for 5 minutes, and supernatant was aspirated. Subsequently, cells were washed in pre-warmed DMEM-high glucose (Gibco) three times, and resuspended at 5 x 105 cells/mL in complete chondrogenic medium: DMEM-high glucose (Gibco), 1% Penicillin/ streptomycin (Gibco), 1% ITS+ (Corning), 100 nM Dexamethasone (Sigma-Aldrich), 50 µg/mL ascorbic acid (Sigma-Aldrich), 40 µg/mL L-proline (Sigma-Aldrich), 10 ng/mL rhTGF-β3 (R&D Systems). Five hundred µL of the above cell mixture was dispensed into 15 mL conical tubes, and centrifuged at 200 x g for 5 minutes. Pellets were cultured at 37°C, 5% CO2 for 21 days with medium exchange every three days.

extract_protocol:
On day of harvest, pellets were rinsed once in PBS, snap frozen in liquid nitrogen, and stored at -80℃ until further processing. On day or RNA isolation, pellets were homogenized in buffer RL using a bead beater (BioSpec Products) at 2,500 oscillations per minute for 20 seconds for a total of three times. Subsequent steps were performed following manufacter's protocol (Norgen total RNA isolation kit; Norgen Biotek).
Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold Kit (Illumina)

value: day 21 mesenchymal stem cell pellets

tag: genotype/variation

value: transduced with GRASLND shRNA #1


title: SMC_173

value: Primary cell


title: D21R7: Day 21 GRASLND shRNA 2

value: transduced with GRASLND shRNA #2


title: D21PT: Day 21 scrambled shRNA 2

value: transduced with scrambled shRNA #2


title: Normal01306

description:
raw data file: US22502676_251485063643_S01_GE2-v5_95_Feb07_1_3.txt
none
VUMC_Normal01306

value: normal cervical squamous epithelium


title: SMC_171


title: SMC_UT2

value: Unt


title: SMC_UT3


title: D21BC: Day 21 scrambled shRNA 1

value: transduced with scrambled shRNA #1


title: Patient22_Tamoxifen [FFP12.003101]

value: breast cancer patient

value: FFPE tumor

value: Batch TS


title: Normal0196

description:
raw data file: US22502676_251485063643_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_Normal0196


title: Patient21_Tamoxifen [FFP12.003100]


title: SMC_172


title: SMC_UT1


title: SUMA-3

city: Lincoln

first: Qingsheng

state: NE

address: 4240 Fair Street

institute: University of Nebraska Lincoln

description: humanized-BLT mice

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were put through FastQC anaylsis for quality control. Low quality reads were trimmed or removed by Trimmomatic.
Paired and unpaired sequencing files were mapped to the reference genome using Tophat 2.1
Cufflinks 2.2 was used to estimate relative abundance of transcripts and Cuffmerge was used to combine the output.
Cuffdiff was used to determine significant differences in transcript expression between SIV & SUMA.
Genome_build: Ensembl GRch37
Supplementary_files_format_and_content: Cuffdiff abundance measurements (SIV vs. SUMA)

source_name: human CD4+ T cells

growth_protocol: Human lymphocytes derived from Hu-BLT mice spleen were further sorted through negative magnetic beads selection of human CD4+ T Cell Isolation Kit (Catalog #130-096-533, Miltenyi Biotec).

extract_protocol:
The total RNA was extracted using RNeasy Plus Mini Kit (Qiagen).
SMARTer® Stranded Total RNA-Seq Kit (Pico Input Mammalian) was used for library preparation (Clontech Laboratories, Inc).

tag: strain

value: NSG

value: human CD4+ T cells

tag: virus infection

value: HIV-1 (SUMA)


title: Normal01194

description:
raw data file: US22502676_251485063644_S01_GE2-v5_95_Feb07_1_4.txt
none
VUMC_Normal01194

value: high-risk HPV-positive


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 7_DAC treated

description:
raw data file: US22502676_251485074176_S01_GE2_107_Sep09_1_4.txt
none
FK18BT7+

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software. Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA.

source_name: primary human foreskin keratinocytes transfected with HPV18

growth_protocol: Establishment and culture of the HPV16 (FK16A and FK16B) and HPV18 (FK18A and FK18B) transformed keratinocyte cell lines was described previously (Steenbergen et al., Oncogene 1996).

extract_protocol: Total RNA was isolated using TRIzol Reagent according to the manufacturer’s instructions (ThermoFisher Scientific).

treatment_protocol: Cells were treated with either 5000nM 5-aza-2’-deoxycytidine (DAC; Sigma-Aldrich) dissolved in PBS or PBS only for 5 days. Medium with or without DAC was refreshed every day.

tag: transformation stage

value: anchorage independent

tag: timepoint

value: timepoint 7

value: 5000 nM 5-aza-2’-deoxycytidine (DAC)


title: SUMA-2

description: humanized-BLT mice

tag: cell type


title: Normal01265

description:
raw data file: US22502676_251485063642_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_Normal01265


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 8_DAC treated

description:
raw data file: US22502676_251485074150_S01_GE2_107_Sep09_1_2.txt
none
FK18BT8+

value: primary human foreskin keratinocytes transfected with HPV18

value: timepoint 8


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 6_DAC treated

description:
raw data file: US22502676_251485074174_S01_GE2_107_Sep09_1_3.txt
none
FK18BT6+

value: timepoint 6


title: Patient17_Tamoxifen [FFP12.003096]

value: Tamoxifen


title: Patient10_Tamoxifen [FFP12.003089]


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 4_DAC treated

description:
raw data file: US22502676_251485074175_S01_GE2_107_Sep09_1_2.txt
none
FK18BT4+

value: timepoint 4


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 5_DAC treated

description:
raw data file: US22502676_251485074272_S01_GE2_107_Sep09_1_4.txt
none
FK18BT5+

value: timepoint 5


title: Patient7_Tamoxifen [FFP12.003086]


title: Patient19_Tamoxifen [FFP12.003098]


title: Patient20_Tamoxifen [FFP12.003099]


title: MB-3

description: humanized-BLT mice

value: SIV (MB)


title: Embryos_30min post-wounding_exp4

city: Seattle

first: Susan

middle: M

last: Parkhurst

state: WA

address: 1100 Fairview Ave N; A1-162

department: Division of Basic Sciences

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Targets were co-hybridized to microarrays for 16 hrs at 63°C and sequentially washed at room temperature in 1 x SSC and 0.03% SDS for 2 min, 1 x SSC for 2 min, 0.2 x SSC with agitation for 20 min, and 0.05 x SSC with agitation for 10 min.

scan_protocol: Scanned on a GenePix 4000B scanner

data_processing: Each array was background subtracted and ratio values were log2 transformed.  Intra-array normalization was performed using a loess algorithm to correct for intensity-dependent ratio biasing

organism: Drosophila melanogaster

source_name: Embryos_30min post-wounding

label_protocol: Cy5- and Cy3-labeled cDNA targets were generated from 30 ug of total RNA using a reverse transcription, amino-allyl based protocol

growth_protocol: Flies were cultured on yeast-cornmeal-molasses-malt media and maintained at room temperature. For embryo collections, flies were transferred to a collection chamber and the grape juice agar plate was changed every hour. Embryos were recovered from the grape plates.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions

treatment_protocol: For laser wounded samples: embryos were collected for 0-1hr on grape juice agar plates, hand dechorionated, transferred to series 700 halocarbon oil on greneir lumox culture dishes, and laser ablated using the manual Micropoint system (Photonics). Embryos harbored an actin reporter (sGMCA) to visualized the cortical cytoskeleton. For unwounded embryos: same conditions were followed, but without wounding. After 30 minutes, embryos were recovered from the culture dish, the oil was removed with heptane and the embryos were flash frozen in liquid N2.

tag: developmental stage

value: 0-1 hrs embryos

source_name: Embryos_30min unwounded


title: SUMA-1

description: humanized-BLT mice


title: MB-1

description: humanized-BLT mice


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 3_DAC treated

description:
raw data file: US22502676_251485074149_S01_GE2_107_Sep09_1_1.txt
none
FK18BT3+

value: timepoint 3


title: Embryos_30min post-wounding_exp5


title: Patient9_Tamoxifen [FFP12.003088]

value: breast cancer patient

value: FFPE tumor

value: Batch TS


title: Patient4_Tamoxifen [FFP12.003083]


title: BF-3

description: humanized-BLT mice

value: NSG

value: human CD4+ T cells

value: SIV (BF)


title: Patient16_Tamoxifen [FFP12.003095]


title: MB-2

description: humanized-BLT mice


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 2_DAC treated

description:
raw data file: US22502676_251485074273_S01_GE2_107_Sep09_1_3.txt
none
FK18BT2+

value: extended lifespan

value: timepoint 2


title: BF-2

description: humanized-BLT mice


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 8_DAC treated

description:
raw data file: US22502676_251485074174_S01_GE2_107_Sep09_1_1.txt
none
FK18AT8+

value: primary human foreskin keratinocytes transfected with HPV18

value: anchorage independent

value: 5000 nM 5-aza-2’-deoxycytidine (DAC)


title: Embryos_0min post-wounding_exp8

treatment_protocol: For laser wounded sample: embryos were collected for 0-1hr on grape juice agar plates, hand dechorionated, transferred to series 700 halocarbon oil on greneir lumox culture dishes, and laser ablated using the manual Micropoint system (Photonics). Embryos harbored an actin reporter (sGMCA) to visualized the cortical cytoskeleton. For unwounded embryos: same conditions were followed, but without wounding. Embryos were inmediately recovered from the culture dish, oil was removed with heptane and the embryos were flash frozen in liquid N2.

tag: developmetnal stage


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 1_DAC treated

description:
raw data file: US22502676_251485074085_S01_GE2_107_Sep09_1_1.txt
none
FK18BT1+

value: timepoint 1


title: Embryos_0min post-wounding_exp7


title: Patient1_Tamoxifen [FFP12.003080]

tag: subject status

value: Tamoxifen


title: exosome-M2-6

city: Shanghai

first: xiaoduan

last: li

address: Changle road no. 536

institute: Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai , China.

description: Gene expression of exosome secreted by M2 macrophage induced from Thp-1 cells after 24h.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a   reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the   manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was   added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) for 17 hours at 65°C   in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with   GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief   centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan   setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green   PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to   obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were   normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as   Detected were maintained.

source_name: M2 induced from Thp-1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug 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. instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Thp-1 cells were cultured in RPMI1640+10%FBS , P6 was collected and devided into Thp-1 group and M2 group.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: the M2 group Thp-1 cells was induced by PMA (50 ng/ml) and IL-4 (20 ng/ml) for 24h, Then the culture medium was change into RPMI1640 and culture for 24h. The Thp-1 group was untreated for 24h, then change into RPMI1640 and culture for 24h.In order to isolate exosomes, we centrifuge the supernatants for two times (1000g × 10min, 3000g × 30min to deplete the cell or fragments), and then add the total exosome isolation kit (Life technology) over night, and then centrifuge for 10000g×1h.Total RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556).

tag: tissue

value: exosome


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 6_DAC treated

description:
raw data file: US22502676_251485074273_S01_GE2_107_Sep09_1_2.txt
none
FK18AT6+

value: timepoint 6

tag: treatment


title: Patient28_Pretreatment [FFP12.003079]

tag: subject id

value: Pretreatment

tag: tissue/sample type


title: exosome-M2-5


title: BF-1

description: humanized-BLT mice


title: Embryos_0min post-wounding_exp4

value: 0-1 hrs embryos


title: Embryos_30min post-wounding_exp3


title: Patient2_Tamoxifen [FFP12.003081]

value: breast cancer patient

tag: batch


title: Patient24_Pretreatment [FFP12.003077]

value: FFPE tumor


title: exosome-M2-3


title: Embryos_0min post-wounding_exp3


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 4_DAC treated

description:
raw data file: US22502676_251485074085_S01_GE2_107_Sep09_1_4.txt
none
FK18AT4+

value: timepoint 4


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 5_DAC treated

description:
raw data file: US22502676_251485074175_S01_GE2_107_Sep09_1_3.txt
none
FK18AT5+

value: timepoint 5


title: Patient21_Pretreatment [FFP12.003074]

value: Batch TS


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 7_DAC treated

description:
raw data file: US22502676_251485074272_S01_GE2_107_Sep09_1_1.txt
none
FK18AT7+

value: timepoint 7


title: Patient22_Pretreatment [FFP12.003075]


title: exosome-Thp-1-6

description: Gene expression of exosome secreted by Thp-1 cells


title: exosome-M2-1


title: Patient20_Pretreatment [FFP12.003073]


title: exosome-Thp-1-5


title: exosome-Thp-1-3


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 3_DAC treated

description:
raw data file: US22502676_251485074176_S01_GE2_107_Sep09_1_3.txt
none
FK18AT3+

value: immortal

value: timepoint 3


title: GM12878-rep2

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mahalle, Üniversite Caddesi No:27 Tuzla, Sabancı Üniversitesi

department: Mol. Bio. Genetics & Bioeng.

country: Turkey

institute: Sabanci University

description: UV irradiated cell line derived from human B lymphocytes

library_source: genomic

data_processing:
Library strategy: XR-Seq
3' adapter sequences trimmed using Cutadapt (Martin 2011) for XR-Seq reads
Reads were aligned to hg19 human genome and Mmur_3.0 mouse lemur genome with Bowtie2 version 2.3.4.1 (Langmead and Salzber 2012) with default parameters for XR-Seq reads.
Reads were aligned to hg19 human genome and Mmur_3.0 mouse lemur genome with Star version 2.6.1a (Dobin et al. 2012) with default parameters for RNA-Seq reads.
Aligned reads transformed to bed format, and sorted to remove duplicate reads
Genome_build: hg19 for human genome and Mmur_3.0 for mouse lemur
Supplementary_files_format_and_content: bed files containing regions and read counts

molecule: genomic DNA

source_name: human B lymphocytes

extract_protocol:
Samples are pooled, lysed, and immunoprecipitated with anti-TFIIH antibodies p62 (Santa Cruz Biotechnology, sc292) and p89 (XPB, Santa Cruz Biotechnology, sc293).
Ligated to adapters and processed for sequencing.

treatment_protocol: Cells grown to ~80% confluency in 15-cm plates were harvested 1 h and 5 minutes after irradiation with 20 J/m2 of UV.

tag: cell line

value: UV irradiation

tag: time point (after treatment)

value: 1 hour

tag: replicate


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 1_DAC treated

description:
raw data file: US22502676_251485074149_S01_GE2_107_Sep09_1_2.txt
none
FK18AT1+

value: primary human foreskin keratinocytes transfected with HPV18

value: 5000 nM 5-aza-2’-deoxycytidine (DAC)


title: GM12878-rep1


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 7_DAC treated

description:
raw data file: US22502676_251485074149_S01_GE2_107_Sep09_1_3.txt
none
FK16BT7+

source_name: primary human foreskin keratinocytes transfected with HPV16

value: anchorage independent


title: Patient18_Pretreatment [FFP12.003071]


title: KAH_347

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

hyb_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.

data_processing: R bioconduct was used to process the data, and RMA was used to summarize and normalize the expression values

source_name: Skin

label_protocol: Complementary DNA was prepared and biotinylated using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6).

extract_protocol: RNA was isolated from 10μm sections of formalin-fixed paraffin embedded blocks of identified skin biopsies. RNA was extracted using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek).

tag: disease

value: healthy control

tag: patient


title: exosome-Thp-1-1

value: exosome


title: Patient11_Pretreatment [FFP12.003065]

value: Pretreatment


title: Patient19_Pretreatment [FFP12.003072]


title: KAH_348

scan_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.


title: Patient3_Pretreatment [FFP12.003060]


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 5_DAC treated

description:
raw data file: US22502676_251485074150_S01_GE2_107_Sep09_1_1.txt
none
FK16BT5+

value: primary human foreskin keratinocytes transfected with HPV16


title: Patient5_Pretreatment [FFP12.003062]

value: breast cancer patient


title: HCC827/R RNA-Seq

city: Zhengzhou

first: Xiangzhen

last: Kong

address: No.1 Jianshe road

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
we aligned reads of sample A and sample B to the reference genome from NCBI, Ensembl or NCBI database using Tophat package,which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Tophat allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.Tophat build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The aligned read files were processed by scripts in house, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the transcripts.
The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).
The feference GTF annotation file was downloaded from NCBI, Ensembl or NCBI database.
Genome_build: CIRCExplorer was used to de novo assemble the mapped reads to circular RNAs

growth_protocol: They were cultured in RPMI-1640 (Hyclone, MA, USA) with 10% fetal bovine serum (Gibco, NY, USA) , 100 unit/ml of penicillin and 100 mg/ml of streptomycin.

extract_protocol:
Total RNA from the cell lines was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's protocol. The total RNA quantity and purity were measured by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number ≥8
Approximately 10 μg of total RNA was used to deplete ribosomal RNA, was fragmented into small pieces and then was reverse-transcribed to create the final cDNA library. And then the paired-end sequencing (300±50 bp) was performed on an Illumina X10 (LC Sceiences, USA) following the vendor's recommended protocol.

value: non-small-cell lung cancer cell line

tag: phenotype

value: cisplatin-resistant


title: Patient2_Pretreatment [FFP12.003059]

value: FFPE tumor


title: KAH_346


title: KAH_345


title: Patient15_Pretreatment [FFP12.003068]

value: Batch TS


title: KAH_332

value: dermatomyositis


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 4_DAC treated

description:
raw data file: US22502676_251485074273_S01_GE2_107_Sep09_1_1.txt
none
FK16BT4+

tag: transformation stage

value: timepoint 4


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 3_DAC treated

description:
raw data file: US22502676_251485074272_S01_GE2_107_Sep09_1_2.txt
none
FK16BT3+

tag: timepoint

value: timepoint 3


title: KAH_342


title: KAH_344


title: KAH_341


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 6_DAC treated

description:
raw data file: US22502676_251485074175_S01_GE2_107_Sep09_1_4.txt
none
FK16BT6+

tag: cell type

value: timepoint 6


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 8_DAC treated

description:
raw data file: US22502676_251485074085_S01_GE2_107_Sep09_1_3.txt
none
FK16BT8+

value: timepoint 8


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 2_DAC treated

description:
raw data file: US22502676_251485074150_S01_GE2_107_Sep09_1_4.txt
none
FK18AT2+

value: primary human foreskin keratinocytes transfected with HPV18

value: immortal

value: timepoint 2


title: A549/R RNA-Seq


title: HCC827 RNA-Seq

value: parental


title: Patient25_Pretreatment [FFP17.009602]

value: Batch SJ


title: A549 RNA-Seq


title: wt4.82

city: Minneapolis

first: Michael

last: Kyba

state: MN

address: 2231 6th St SE

institute: University of Minnesota

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using salmon v0.6.0.
Read assignments were performed using salmon v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include salmon count assigned raw reads for each sample.

source_name: WT

extract_protocol:
RNA from whole muscle was extracted using an RNA extraction kit (Zymo) following manufacturer’s instructions. RNA from endothelial and FAPs, i.e. CD31+ and Pdgfrα+ cells, 75,000 cells were FACS sorted from hind limb muscle, and total RNA was extracted using RNeasy Mini Kit (Qiagen).
RNAseq libraries from whole muscle were prepared using 500 ng total RNA and KAPA mRNA Hyper Prep kit following manufacturer’s instructions. cDNA from RNA from FAPs and CD31 ositive cels was synthesized using NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification kit (New England Biolabs) and libraries we generated with Nextera XT DNA Library Preparation Kit (Illumina). 50 base paired-end sequencing was performed  50 base paired end sequencing was performed on an Illumina instrument at the University of Minnesota Genomics Center.

treatment_protocol: Mice were treated with  doxyxycline contaning chow.

tag: inducible gene

value: WT

tag: tissue type

value: Whole Muscle

tag: group name


title: 3569.8


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 1_DAC treated

description:
raw data file: US22502676_251485074174_S01_GE2_107_Sep09_1_4.txt
none
FK16BT1+

value: primary human foreskin keratinocytes transfected with HPV16

value: timepoint 1

value: 5000 nM 5-aza-2’-deoxycytidine (DAC)


title: 1576.81


title: KAH_324


title: Patient53_Tamoxifen [FFP17.009562]

tag: subject status

value: breast cancer patient

value: Tamoxifen

value: FFPE tumor


title: KAH_302

value: dermatomyositis


title: KAH_307


title: 696.77


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 8_DAC treated

description:
raw data file: US22502676_251485074149_S01_GE2_107_Sep09_1_4.txt
none
FK16AT8+

value: anchorage independent

tag: treatment


title: 693.78


title: Patient8_Pretreatment [FFP17.009600]

tag: subject id

value: Pretreatment


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 2_DAC treated

description:
raw data file: US22502676_251485074176_S01_GE2_107_Sep09_1_2.txt
none
FK16BT2+


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 7_DAC treated

description:
raw data file: US22502676_251485074085_S01_GE2_107_Sep09_1_2.txt
none
FK16AT7+

value: timepoint 7


title: KAH_313


title: Patient54_Tamoxifen [FFP17.009563]

tag: tissue/sample type


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 6_DAC treated

description:
raw data file: US22502676_251485074176_S01_GE2_107_Sep09_1_1.txt
none
FK16AT6+

value: timepoint 6


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 5_DAC treated

description:
raw data file: US22502676_251485074174_S01_GE2_107_Sep09_1_2.txt
none
FK16AT5+

value: timepoint 5


title: Patient92_Tamoxifen [FFP17.009598]

tag: batch


title: KAH_308


title: KAH_328


title: KAH_305


title: Patient94_Pretreatment [FFP17.009560]


title: KAH_343


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 4_DAC treated

description:
raw data file: US22502676_251485074150_S01_GE2_107_Sep09_1_3.txt
none
FK16AT4+

value: immortal

value: timepoint 4


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 3_DAC treated

description:
raw data file: US22502676_251485074273_S01_GE2_107_Sep09_1_4.txt
none
FK16AT3+

value: timepoint 3


title: 692.75


title: Patient92_Pretreatment [FFP17.009559]

value: Batch SJ


title: KAH_335


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 2_DAC treated

description:
raw data file: US22502676_251485074175_S01_GE2_107_Sep09_1_1.txt
none
FK16AT2+

value: timepoint 2


title: Patient91_Pretreatment [FFP17.009558]


title: 562.73

value: Whole Muscle


title: 694.74

value: WT


title: 202.72


title: PDGWT9

value: PDGWT

value: PDGFRa+ FAP


title: PDGWT11


title: Patient52_Tamoxifen [FFP17.009561]

value: breast cancer patient

value: Tamoxifen


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 1_DAC treated

description:
raw data file: US22502676_251485074272_S01_GE2_107_Sep09_1_3.txt
none
FK16AT1+

value: primary human foreskin keratinocytes transfected with HPV16

value: timepoint 1

value: 5000 nM 5-aza-2’-deoxycytidine (DAC)


title: Patient1_Pretreatment [FFP12.003058]

value: Pretreatment

value: FFPE tumor

value: Batch TS


title: Patient89_Tamoxifen [FFP17.009595]


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 8_untreated

description:
raw data file: US22502676_251485074150_S01_GE2_107_Sep09_1_2.txt
none
FK18BT8-

value: primary human foreskin keratinocytes transfected with HPV18

value: anchorage independent

value: timepoint 8

value: no treatment


title: KAH_340

value: dermatomyositis


title: KAH_337


title: PDGDUX14

value: PDGDUX


title: PDGWT10

value: WT


title: Patient90_Tamoxifen [FFP17.009596]

value: Batch SJ


title: PDGDUX13

value: PDGFRa+ FAP


title: Patient87_Pretreatment [FFP17.009554]

value: breast cancer patient


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 2_untreated

description:
raw data file: US22502676_251485074273_S01_GE2_107_Sep09_1_3.txt
none
FK18BT2-

value: extended lifespan

value: timepoint 2


title: Patient90_Pretreatment [FFP17.009557]


title: KAH_330


title: KAH_331


title: Patient89_Pretreatment [FFP17.009556]


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 5_untreated

description:
raw data file: US22502676_251485074272_S01_GE2_107_Sep09_1_4.txt
none
FK18BT5-

value: timepoint 5


title: KAH_303


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 7_untreated

description:
raw data file: US22502676_251485074176_S01_GE2_107_Sep09_1_4.txt
none
FK18BT7-

value: timepoint 7


title: Patient88_Pretreatment [FFP17.009555]

value: Pretreatment


title: KAH_318


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 4_untreated

description:
raw data file: US22502676_251485074175_S01_GE2_107_Sep09_1_2.txt
none
FK18BT4-

value: timepoint 4


title: PDGDUX15


title: Patient86_Tamoxifen [FFP17.009592]

value: Tamoxifen

value: FFPE tumor


title: PDGDUX12


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 6_untreated

description:
raw data file: US22502676_251485074174_S01_GE2_107_Sep09_1_3.txt
none
FK18BT6-

value: primary human foreskin keratinocytes transfected with HPV18

value: anchorage independent

value: timepoint 6


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 3_untreated

description:
raw data file: US22502676_251485074149_S01_GE2_107_Sep09_1_1.txt
none
FK18BT3-

value: timepoint 3

value: no treatment


title: KAH_312

value: dermatomyositis


title: KAH_309


title: Patient83_Tamoxifen [FFP17.009590]

value: Batch SJ


title: CD31WT2

value: WT

value: CD31+ Endothelial cells


title: KAH_327


title: Patient82_Tamoxifen [FFP17.009589]

value: breast cancer patient


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 8_untreated

description:
raw data file: US22502676_251485074174_S01_GE2_107_Sep09_1_1.txt
none
FK18AT8-

value: timepoint 8


title: Patient85_Pretreatment [FFP17.009552]


title: Patient86_Pretreatment [FFP17.009553]


title: CD31DUX8


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 7_untreated

description:
raw data file: US22502676_251485074272_S01_GE2_107_Sep09_1_1.txt
none
FK18AT7-


title: KAH_306


title: CD31DUX7


title: KAH_326


title: CD31DUX6


title: Patient83_Pretreatment [FFP17.009550]


title: Patient82_Pretreatment [FFP17.009549]


title: Patient76_Tamoxifen [FFP17.009585]


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 5_untreated

description:
raw data file: US22502676_251485074175_S01_GE2_107_Sep09_1_3.txt
none
FK18AT5-

value: timepoint 5


title: KAH_323


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 6_untreated

description:
raw data file: US22502676_251485074273_S01_GE2_107_Sep09_1_2.txt
none
FK18AT6-


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 3_untreated

description:
raw data file: US22502676_251485074176_S01_GE2_107_Sep09_1_3.txt
none
FK18AT3-

value: immortal


title: KAH_321


title: KAH_338


title: KAH_333


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 2_untreated

description:
raw data file: US22502676_251485074150_S01_GE2_107_Sep09_1_4.txt
none
FK18AT2-

value: timepoint 2


title: KAH_316


title: CD31DUX5


title: Mixed-Ly6g high captures (Cell Hashing)_ADT

city: Cincinnati

first: H. Leighton

last: Grimes

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

data_processing:
The 10x Genomics libraries were each sequenced to a depth of 373 and 455-million reads, respectively. The 10x Genomics libraries were aligned to the mouse genome (mm10), with unique molecular index quantified (UMI) gene counts obtained using the Cell Ranger workflow (v2.1.0), from the automated filtered cell barcode output. Using the default filtered cellular barcodes, the associated sparse-filtered matrix files were processed in AltAnalyze and ICGS as previously described to obtain normalized gene counts (counts per ten thousands UMIs) and initial predicted cell populations (PMID: 29183737).
The antibody derived tag (ADT)-linked library for each 10x Genomics capture was sequenced with the same 10x Genomics sample. To obtain ADT UMIs for each cellular barcode, each ADT barcode was supplied as input in the CITE-Seq-Counts python program with the Undetermined fastqs files. Prior to visualization in the software SeqGeq (FlowJo Inc.), normalization was performed on the ADT counts using CLR transformation in Excel using the equation: LN(([adt count value]+1)/mean([all adt count values for antibody])).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file and HDF5
Supplementary_files_format_and_content: clusters.Gfi1-WT.txt: Cell Clusters: cellHarmony assigned clusters for GMP-P and Ly6g high sorted Gfi1 WT cells
Supplementary_files_format_and_content: clusters.Gfi1-Het.txt: Cell Clusters: cellHarmony assigned clusters for GMP-P and Ly6g high sorted Gfi1+/- cells
Supplementary_files_format_and_content: clusters.Gfi1-K403R-Het.txt: Cell Clusters: cellHarmony assigned clusters for GMP-P and Ly6g high sorted Gfi1-K403R-Het cells
Supplementary_files_format_and_content: clusters.Gfi1-R412X-Het.txt: Cell Clusters: cellHarmony assigned clusters for GMP-P and Ly6g high sorted Gfi1-R412X-Het cells
Supplementary_files_format_and_content: clusters.Gfi1-R412X-Irf8.txt: Cell Clusters: cellHarmony assigned clusters for GMP-P and Ly6g high sorted Gfi1-R412X-R412X cells
Supplementary_files_format_and_content: clusters.Gfi1-R412X-R412X.h5.txt: Cell Clusters: cellHarmony assigned clusters for GMP-P and Ly6g high sorted Gfi1-R412X Irf8+/- cells
Supplementary_files_format_and_content: RNA.Gfi1-WT.h5: RNA: mRNA UMI counts for GMP-P and Ly6g high sorted Gfi1 WT cells
Supplementary_files_format_and_content: RNA.Gfi1-Het.h5: RNA: mRNA UMI counts for GMP-P and Ly6g high sorted Gfi1+/- cells
Supplementary_files_format_and_content: RNA.Gfi1-K403R-Het.h5: RNA: mRNA UMI counts for GMP-P and Ly6g high sorted Gfi1-K403R-Het cells
Supplementary_files_format_and_content: RNA.Gfi1-R412X-Het.h5: RNA: mRNA UMI counts for GMP-P and Ly6g high sorted Gfi1-R412X-Het cells
Supplementary_files_format_and_content: RNA.Gfi1-R412X-Irf8.h5: RNA: mRNA UMI counts for GMP-P and Ly6g high sorted Gfi1-R412X-R412X cells
Supplementary_files_format_and_content: RNA.Gfi1-R412X-R412X.h5: RNA: mRNA UMI counts for GMP-P and Ly6g high sorted Gfi1-R412X Irf8+/- cells
Supplementary_files_format_and_content: ADT.Gfi1-WT.txt: ADT: Antibody UMI counts for GMP-P and Ly6g high sorted Gfi1 WT cells
Supplementary_files_format_and_content: ADT.Gfi1-Het.txt: ADT: Antibody UMI counts for GMP-P and Ly6g high sorted Gfi1+/- cells
Supplementary_files_format_and_content: ADT.Gfi1-K403R-Het.txt: ADT: Antibody UMI counts for GMP-P and Ly6g high sorted Gfi1-K403R-Het cells
Supplementary_files_format_and_content: ADT.Gfi1-R412X-Het.txt: ADT: Antibody UMI counts for GMP-P and Ly6g high sorted Gfi1-R412X-Het cells
Supplementary_files_format_and_content: ADT.Gfi1-R412X-Irf8.txt: ADT: Antibody UMI counts for GMP-P and Ly6g high sorted Gfi1-R412X-R412X cells
Supplementary_files_format_and_content: ADT.Gfi1-R412X-R412X.txt: ADT: Antibody UMI counts for GMP-P and Ly6g high sorted Gfi1-R412X Irf8+/- cells

source_name: Bone marrow

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with TotalSeq antibodies and fluorchome-conjugated antibodies for FACS-sorting, then 10,000 cells per sample were loaded in each lane of a Chromium Controller Instrument (10x Genomics).
The 10x Genomics single cell 3’ v2 assay protocol was followed as described until the cDNA amplification step. The cDNA amplification mix was modified to include 1 mL of a 2 mM dilution of ADT PCR additive primer (5’-CCTTGGCACCCGAGAATT*C*C-3’ where * indicates a phosphorotioate bond) and 1 mL of a 2 mM dilution of HTO PCR additive primer (5’-GTGACTGGAGTTCAGACGTGTGC*T*C-3’ where * indicates a phosphorotioate bond) when applicable, replacing 1-2 mL of water. An 0.6X SPRI selection was performed, and the resulting supernatant was set aside (contains ADTs and HTOs) while the beads (mRNA-derived cDNA) were processed according to the standard 10x Genomics single cell 3’ v2 assay protocol. The ADTs and HTOs were further processed according to the CITE-Seq protocol (New York Genome Center, https://cite-seq.com/protocol/). The final pooled library was comprised of 90% mRNA-derived library and 10% ADT library or 85% mRNA-derived library, 10% ADT library, and 5% HTO library prior to sequencing.

tag: strain

value: Bone marrow derived Modified GMP

tag: genotype

value: Ly6g high captures of mixed genotypes, with different cell hashing ADTs

tag: cdna synthesis

tag: library prep


title: Patient78_Pretreatment [FFP17.009547]

value: Pretreatment

value: FFPE tumor


title: Gfi1-R412X-Het and Irf8+/- 10x CITE-Seq_ADT

description:
Male GMP mRNA
clusters.Gfi1-R412X-R412X.h5.txt
ADT.Gfi1-R412X-R412X.txt

value: Gfi1-R412X-Het and Irf8+/-

value: 10x Genomics single cell 3’ v2 assay protocol


title: KAH_339

tag: disease

tag: patient


title: Mixed-Ly6g high captures (Cell Hashing)_mRNA

tag: sequencing parameters

value: 455 million reads


title: Patient76_Pretreatment [FFP17.009545]


title: Gfi1-R412X-R412X 10x CITE-Seq_ADT

description:
Male GMP mRNA
clusters.Gfi1-R412X-Irf8.txt
ADT.Gfi1-R412X-Irf8.txt


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 7_untreated

description:
raw data file: US22502676_251485074149_S01_GE2_107_Sep09_1_3.txt
none
FK16BT7-

value: primary human foreskin keratinocytes transfected with HPV16

tag: transformation stage

value: anchorage independent

tag: timepoint

value: timepoint 7

value: no treatment


title: Patient77_Pretreatment [FFP17.009546]

value: Batch SJ


title: KAH_329

value: dermatomyositis


title: Patient74_Pretreatment [FFP17.009543]

value: breast cancer patient


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 8_untreated

description:
raw data file: US22502676_251485074085_S01_GE2_107_Sep09_1_3.txt
none
FK16BT8-

tag: cell type

value: timepoint 8


title: KAH_334


title: Gfi1-R412X-Het and Irf8+/- 10x CITE-Seq_mRNA

description:
Male GMP mRNA
clusters.Gfi1-R412X-R412X.h5.txt
RNA.Gfi1-R412X-R412X.h5

value: 432 million reads


title: KAH_310


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 6_untreated

description:
raw data file: US22502676_251485074175_S01_GE2_107_Sep09_1_4.txt
none
FK16BT6-

value: timepoint 6


title: Patient73_Tamoxifen [FFP17.009582]

value: Tamoxifen


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 4_untreated

description:
raw data file: US22502676_251485074273_S01_GE2_107_Sep09_1_1.txt
none
FK16BT4-

value: timepoint 4


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 1_untreated

description:
raw data file: US22502676_251485074149_S01_GE2_107_Sep09_1_2.txt
none
FK18AT1-

value: primary human foreskin keratinocytes transfected with HPV18

value: immortal

value: timepoint 1


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 5_untreated

description:
raw data file: US22502676_251485074150_S01_GE2_107_Sep09_1_1.txt
none
FK16BT5-

value: timepoint 5


title: KAH_322


title: KAH_301


title: Gfi1-R412X-Het 10x CITE-Seq_ADT

description:
Male GMP mRNA
clusters.Gfi1-R412X-Het.txt
ADT.Gfi1-R412X-Het.txt

value: Bone marrow derived Modified GMP

value: 10x Genomics single cell 3’ v2 assay protocol


title: Gfi1-R412X-R412X 10x CITE-Seq_mRNA

description:
Male GMP mRNA
clusters.Gfi1-R412X-Irf8.txt
RNA.Gfi1-R412X-Irf8.h5

value: 373 million reads


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 3_untreated

description:
raw data file: US22502676_251485074272_S01_GE2_107_Sep09_1_2.txt
none
FK16BT3-

value: primary human foreskin keratinocytes transfected with HPV16

value: anchorage independent

value: timepoint 3


title: KAH_325

value: dermatomyositis


title: Gfi1-R412X-Het 10x CITE-Seq_mRNA

description:
Male GMP mRNA
clusters.Gfi1-R412X-Het.txt
RNA.Gfi1-R412X-Het.h5

value: 395 million reads


title: Gfi1-K403R 10x CITE-Seq_ADT

description:
Female GMP mRNA
clusters.Gfi1-K403R-Het.txt
ADT.Gfi1-K403R-Het.txt


title: Patient69_Pretreatment [FFP17.009539]

value: breast cancer patient

value: Pretreatment

value: FFPE tumor

value: Batch SJ


title: Patient73_Pretreatment [FFP17.009542]


title: Patient72_Pretreatment [FFP17.009541]


title: Gfi1-K403R 10x CITE-Seq_mRNA

description:
Female GMP mRNA
clusters.Gfi1-K403R-Het.txt
RNA.Gfi1-K403R-Het.h5

value: 449 million reads


title: Gfi1+/- 10x CITE-Seq_mRNA

description:
Male GMP mRNA
clusters.Gfi1-Het.txt
RNA.Gfi1-Het.h5

value: 429 million reads


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 2_untreated

description:
raw data file: US22502676_251485074176_S01_GE2_107_Sep09_1_2.txt
none
FK16BT2-

value: immortal

value: timepoint 2

value: no treatment


title: Patient71_Tamoxifen [FFP17.009580]

value: Tamoxifen


title: Patient79_Pretreatment [FFP17.009548]


title: KAH_314


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 8_untreated

description:
raw data file: US22502676_251485074149_S01_GE2_107_Sep09_1_4.txt
none
FK16AT8-

value: timepoint 8


title: Patient70_Tamoxifen [FFP17.009579]


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 7_untreated

description:
raw data file: US22502676_251485074085_S01_GE2_107_Sep09_1_2.txt
none
FK16AT7-

value: timepoint 7


title: Patient68_Pretreatment [FFP17.009538]


title: Patient66_Pretreatment [FFP17.009536]


title: KAH_315


title: KAH_320


title: Gfi1 wild-type 10x CITE-Seq_ADT

description:
Male GMP mRNA
clusters.Gfi1-WT.txt
ADT.Gfi1-WT.txt

value: Bone marrow derived Modified GMP

value: Wild-type

value: 10x Genomics single cell 3’ v2 assay protocol


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 6_untreated

description:
raw data file: US22502676_251485074176_S01_GE2_107_Sep09_1_1.txt
none
FK16AT6-

value: primary human foreskin keratinocytes transfected with HPV16

value: anchorage independent

value: timepoint 6


title: Patient64_Pretreatment [FFP17.009535]

value: breast cancer patient

value: Pretreatment


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 1_untreated

description:
raw data file: US22502676_251485074174_S01_GE2_107_Sep09_1_4.txt
none
FK16BT1-

value: timepoint 1


title: KAH_311

value: dermatomyositis


title: Gfi1+/- 10x CITE-Seq_ADT

description:
Male GMP mRNA
clusters.Gfi1-Het.txt
ADT.Gfi1-Het.txt


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 4_untreated

description:
raw data file: US22502676_251485074085_S01_GE2_107_Sep09_1_4.txt
none
FK18AT4-

value: primary human foreskin keratinocytes transfected with HPV18

value: timepoint 4


title: Gfi1 wild-type 10x CITE-Seq_mRNA

description:
Male GMP mRNA
clusters.Gfi1-WT.txt
RNA.Gfi1-WT.h5

value: 446 million reads


title: Patient63_Pretreatment [FFP17.009534]

value: FFPE tumor

value: Batch SJ


title: KAH_319


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 5_untreated

description:
raw data file: US22502676_251485074174_S01_GE2_107_Sep09_1_2.txt
none
FK16AT5-

value: timepoint 5

value: no treatment


title: Patient68_Tamoxifen [FFP17.009577]

value: Tamoxifen


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 4_untreated

description:
raw data file: US22502676_251485074150_S01_GE2_107_Sep09_1_3.txt
none
FK16AT4-

value: immortal


title: KAH_336


title: 31CBS-inv-Jurkat-HIC-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the hg19 genome assembly using Tophat, and ATAC-seq, ChIP-seq, HiC-seq  reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Chromatin structure HiC-seq was calculate and display with HOMER, Juicer and Juicebox software
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples, and peaks annotation for ATAC-seq and ChIP-seq.

source_name: Jurkat

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K4me2, H3K9/14ac and H3K27ac antibody (H3K4me3 (Millipore, #04-745), H3K4me2 (Millipore, 07-030), H3K27Ac (Abcam, #ab4729), and H3K9/14ac (Diagenode, #C15410005)).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.  HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: Jurkat

value: T cell leukemia

tag: tissue

value: peripheral blood


title: CeA_IP_rep2

city: Berkeley

first: Chenyan

last: Ma

state: CA

address: 230E Li Ka Shing Center

institute: UC Berkeley

data_processing:
Sequenced reads were trimmed for adaptor sequences and index sequences
Alignment and abundance calculation were done using RSEM (RNA-Seq by Expectation-Maximization) software.
Gene expression analysis was performed with DESeq software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene ID and TPM values fore each sample; csv files includes p-values and fold changes averaged from two repeats between IP and input group, calculated by DESeq software .

source_name: brain CeA region

extract_protocol:
CeA was rapidly dissected on ice. For each repeat, tissues from 4-5 mice were pooled, homogenized, and immunoprecipitation with FLAG and HA antibodies
RNA libraries were prepared for sequencing using Illumina Nextera Library Prep Kits

treatment_protocol: Cre-inducible retrograde HSV expressing the large ribosomal subunit protein Rpl10a fused with FLAG/hemagglutinin (HA) tag (HSV-LSL-FlagHA-L10a) were injected into the LC and PB region of Gad2-Cre mice

tag: strain background

tag: genotype/variation

value: brain

value: LC/PB projecting GABAergic neurons

tag: ip antibody

value: FLAG and HA antibodies


title: CeA_input_rep2


title: Lemur-(6-4)PP-rep2

description: UV irradiated cell line derived from primary mouse lemur fibroblasts

organism: Microcebus murinus

source_name: primary mouse lemur fibroblasts

value: mouse lemur fibroblasts

tag: treatment

value: UV irradiation

tag: time point (after treatment)

value: 5 minutes

tag: replicate


title: Bone, Piezo1/2 DKO_2

city: Boston

first: Taifeng

last: Zhou

state: Massachusetts

address: 188 Longwood Avenue, REB514B

department: Developmental biology

institute: Harvard University

data_processing:
Basecalling (Ion Torrent S5)
Alignment (Torrent mapping alignment program)
Quantification (Ion Torrent Ampliseq RNA plugin, unique mapping mode)
Count Normalizaiton (Transcriptome Analysis Console)
Genome_build: Genome_build: AmpliSeq Mouse Transcriptome V1 Reference (based on GRCm38)
Supplementary_files_format_and_content: Count Normalized

source_name: bone tissue

extract_protocol:
Using Rneasy Mini Kit according to the handbook.
Using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit according to the manufacturer’s protocols.

tag: age

tag: strain

tag: genotype

value: Piezo1/2 DKO

value: bone


title: 31CBS-WT-Jurkat-HIC-seq

first: Huacheng

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 3_untreated

description:
raw data file: US22502676_251485074273_S01_GE2_107_Sep09_1_4.txt
none
FK16AT3-

value: primary human foreskin keratinocytes transfected with HPV16

value: timepoint 3


title: Patient65_Tamoxifen [FFP17.009574]

first: Wilbert

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

data_processing: Feature Extraction software v11.5.1.1 was used to quantify fluorescent intensities, custom script were used for raw data extraction and those values were normalized by 75th percentile normalisation using DataPrint software v1.15, all by Agendia Inc. Downstream data processing was subsequently done at the Netherlands Cancer Institute, by missing data impution with knn=10 and batch correction for date of RNA extraction using ComBat from the R package sva, using all available patient material from the trial (ClinicalTrials.gov Identifier: NCT00738777). Here we deposited samples used for the Tamoxifen focused analysis described in the cited paper.

extract_protocol: RNA was isolated using Qiagen RNeasy microkit according to manufacturer's specifications.

tag: subject status

value: breast cancer patient

tag: subject id

tag: tissue/sample type

value: FFPE tumor

tag: batch

value: Batch SJ


title: KAH_317

tag: disease

value: dermatomyositis

tag: patient


title: KAH_304


title: Lemur-(6-4)PP-rep1

value: 5 minustes


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 2_untreated

first: Renske

address: De Boelelaan 1117

institute: Amsterdam UMC, location VUmc

description:
raw data file: US22502676_251485074175_S01_GE2_107_Sep09_1_1.txt
none
FK16AT2-

tag: cell type

tag: transformation stage

value: immortal

tag: timepoint

value: timepoint 2

value: no treatment


title: CD31WT1

tag: inducible gene

value: WT

tag: group name

value: CD31+ Endothelial cells


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 1_untreated

description:
raw data file: US22502676_251485074272_S01_GE2_107_Sep09_1_3.txt
none
FK16AT1-

value: timepoint 1

tag: treatment


title: Male GMP mRNA

description: Male GMP mRNA

data_processing:
The two 10x Genomics libraries (male and female) were each sequenced to a depth of 689 and 676-million reads, respectively. The 10x Genomics libraries were aligned to the mouse genome (mm10), with unique molecular index quantified (UMI) gene counts obtained using the Cell Ranger workflow. For the male GMP-P analysis Cell Ranger v2.1.0 identified 6,796 cellular barcodes with 101,403 mean reads per cell (18,687 UMIs) corresponding to 3,483 median genes expressed per cell, according to its automatic filtering options. Similar results were obtained for the female capture (156,102 mean reads per cell, median UMI counts of 21,202 and a median of 3,787 genes detected). Using the default filtered cellular barcodes, the associated sparse-filtered matrix files were processed in AltAnalyze and ICGS as previously described to obtain normalized gene counts (counts per ten thousands UMIs) and initial predicted cell populations (PMID: 29183737).
For the "mRNA" R1 R2 I1 fastq files – Read 1 is technical and Read 2 is biological. On Read 1, the barcode is from bp 1-16 and the UMI is from bp 17-26. I1 (Index 1) is technical, and contains the demultiplexed index for each specific read.
The antibody derived tag (ADT)-linked library was sequenced to greater 300 million reads (~10% of the total CITE-Seq reads) in which FASTQ files were generated by GENEWIZ using the i7 primer sequence. To obtain ADT UMIs for each cellular barcode, each ADT barcode was supplied as input in the CITE-Seq-Counts python program. Prior to visualization in the software SeqGeq (FlowJo Inc.), normalization was performed on the ADT counts using CLR transformation in Excel using the equation: LN(([adt count value]+1)/mean([all adt count values for antibody])).
For the "ADT" R1 R2 fastq files – Read 1 is technical and Read 2 is biological. On Read 1, the barcode is from bp 1-16 and the UMI is from bp 17-26. On Read 2, the ADTs are from bp 1-15.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file
[GMP-P_CITE-Seq-ADT-UMI.txt]  ADT: Antibody UMI counts for GMP-P sorted cells
[GMP-P_CITE-Seq-ADT-CLR.txt]  ADT: Antibody CLR normalized UMI for GMP-P sorted cells
[GMP-P_CITE-Seq-clusters.txt]  RNA: Cell-populations for GMP-P sorted cells
[Combined-counts.txt]  RNA: Gene UMI counts for GMP-P sorted cells

source_name: Bone marrow (mRNA)

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with TotalSeq antibodies and fluorchome-conjugated antibodies for FACS-sorting, then 10,000 cells per sample were loaded in each lane of a Chromium Controller Instrument (10x Genomics).
The 10x Genomics single cell 3’ v2 assay protocol was followed as described until the cDNA amplification step. The cDNA amplification mix was modified to include 1 mL of a 2 mM dilution of ADT PCR additive primer (5’-CCTTGGCACCCGAGAATT*C*C-3’ where * indicates a phosphorotioate bond), replacing 1 mL of water. An 0.6X SPRI selection was performed, and the resulting supernatant was set aside (contains ADTs) while the beads (mRNA-derived cDNA) were processed according to the standard 10x Genomics single cell 3’ v2 assay protocol. The final pooled library was comprised of 90% mRNA-derived library and 10% ADT library prior to sequencing.

tag: gender

value: male

value: Bone marrow derived Modified GMP

tag: cdna synthesis

tag: library prep

tag: sequencing parameters

value: 150bp Paired-End, 689 million reads


title: Patient62_Pretreatment [FFP17.009533]

value: Pretreatment


title: Bone, Piezo1 CKO_2

tag: age

tag: strain

tag: genotype

value: Piezo1 CKO

tag: tissue

value: bone


title: Lemur-CPD-rep2

value: mouse lemur fibroblasts

value: UV irradiation

tag: time point (after treatment)

value: 1 hour

tag: replicate


title: Patient61_Pretreatment [FFP17.009532]

tag: subject status

value: breast cancer patient

tag: subject id

tag: tissue/sample type

value: FFPE tumor

tag: batch

value: Batch SJ


title: Bone, Piezo1/2 DKO_1

value: Piezo1/2 DKO


title: Female GMP mRNA

description: Female GMP mRNA

value: female

tag: cell type

value: 10x Genomics single cell 3’ v2 assay protocol

value: 150bp Paired-End, 676 million reads


title: TuYV_SHR_P19_IP

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

description:
Immunoprecipitated RNA
Infected by TuYV

data_processing:
Basecalling pipeline for SS samples : HiSeq Control Software 2.2.38 ; RTA 1.18.61.0 ; CASAVA-1.8.2. Basecalling pipeline for TuYV samples : HiSeq Control Software 3.3.76 ; RTA 2.7.6 ; bcl2fastq2.17 v2.17.1.14
FASTQ file generation and demultiplexing and adapter removal was done by Fasteris.
Small RNA reads were filtered to 17-30nt long reads for analysis. Reads with identical sequence were grouped using the processReads function from the ncPRO-seq pipeline and aligned against A.thaliana’s genome (TAIR10) using bowtie2 (options : -k 100 --score-min L,0,0). For sRNA libraries from plants containing SucSUL transgene or infected by TuYV, the transgene or the virus sequences were included in the bowtie2 index as extra-chromosome.
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample, tab-delimited text files including distinct sequences and reads count values.

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Plants were grown in 12/12 light/dark conditions using a hydroponics system (Gibeaut et al., 1997)

extract_protocol:
Total RNA and P19 bound sRNA isolations were done using Tri-Reagent or equivalents and CHCl3 according the manufacturer’s instructions. 0.5 µl Glycogen (Thermo Fisher Scientific, Waltham, MA) and an aliquot (1:10 of the total water phase volume) of 5 M potassium acetate pH 5.6 was added and RNA was precipitated on ice by adding 1 volume of isopropanol for 1 hour. The pelleted RNA was washed twice with ice cold 80% (v/v) Ethanol, resuspended in ultrapure H2O or 50% (v/v) formamide containing LMW loading buffer for total RNA or IP’s, respectively
Extracted RNA was processed into sequencing libraries using adapted Illumina protocols and sequenced at Fasteris (http://www.fasteris.com, Switzerland) using the Illumina HiSeq sequencer

tag: ecotype

value: Columbia-0 wild type expressing pSHR:FLAG-HA-P19

value: roots

tag: development stage

value: full mature root system (include lateral root) 5 weeks post germination


title: Bone, Piezo1 CKO_1


title: Bone, Wild type_2

value: Wild type


title: Lemur-CPD-rep1

tag: treatment


title: Male and Female GMP ADT

description: Male and Female GMP ADT

data_processing:
Library strategy: CITE-seq
The two 10x Genomics libraries (male and female) were each sequenced to a depth of 689 and 676-million reads, respectively. The 10x Genomics libraries were aligned to the mouse genome (mm10), with unique molecular index quantified (UMI) gene counts obtained using the Cell Ranger workflow. For the male GMP-P analysis Cell Ranger v2.1.0 identified 6,796 cellular barcodes with 101,403 mean reads per cell (18,687 UMIs) corresponding to 3,483 median genes expressed per cell, according to its automatic filtering options. Similar results were obtained for the female capture (156,102 mean reads per cell, median UMI counts of 21,202 and a median of 3,787 genes detected). Using the default filtered cellular barcodes, the associated sparse-filtered matrix files were processed in AltAnalyze and ICGS as previously described to obtain normalized gene counts (counts per ten thousands UMIs) and initial predicted cell populations (PMID: 29183737).
For the "mRNA" R1 R2 I1 fastq files – Read 1 is technical and Read 2 is biological. On Read 1, the barcode is from bp 1-16 and the UMI is from bp 17-26. I1 (Index 1) is technical, and contains the demultiplexed index for each specific read.
The antibody derived tag (ADT)-linked library was sequenced to greater 300 million reads (~10% of the total CITE-Seq reads) in which FASTQ files were generated by GENEWIZ using the i7 primer sequence. To obtain ADT UMIs for each cellular barcode, each ADT barcode was supplied as input in the CITE-Seq-Counts python program. Prior to visualization in the software SeqGeq (FlowJo Inc.), normalization was performed on the ADT counts using CLR transformation in Excel using the equation: LN(([adt count value]+1)/mean([all adt count values for antibody])).
For the "ADT" R1 R2 fastq files – Read 1 is technical and Read 2 is biological. On Read 1, the barcode is from bp 1-16 and the UMI is from bp 17-26. On Read 2, the ADTs are from bp 1-15.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file
[GMP-P_CITE-Seq-ADT-UMI.txt]  ADT: Antibody UMI counts for GMP-P sorted cells
[GMP-P_CITE-Seq-ADT-CLR.txt]  ADT: Antibody CLR normalized UMI for GMP-P sorted cells
[GMP-P_CITE-Seq-clusters.txt]  RNA: Cell-populations for GMP-P sorted cells
[Combined-counts.txt]  RNA: Gene UMI counts for GMP-P sorted cells

molecule: other

source_name: Bone marrow (ADT)

tag: gender

value: pooled male and female

value: Bone marrow derived Modified GMP

tag: cdna synthesis

value: 10x Genomics single cell 3’ v2 assay protocol and the CITE-Seq protocol


title: Bone, Wild type_1

value: bone


title: TuYV_WER_P19_IP

description:
Immunoprecipitated RNA
Infected by TuYV

value: Columbia-0 wild type expressing pWER:FLAG-HA-P19


title: Lemur-rna-rep2

description: Cell line derived from primary mouse lemur fibroblasts

data_processing:
3' adapter sequences trimmed using Cutadapt (Martin 2011) for XR-Seq reads
Reads were aligned to hg19 human genome and Mmur_3.0 mouse lemur genome with Bowtie2 version 2.3.4.1 (Langmead and Salzber 2012) with default parameters for XR-Seq reads.
Reads were aligned to hg19 human genome and Mmur_3.0 mouse lemur genome with Star version 2.6.1a (Dobin et al. 2012) with default parameters for RNA-Seq reads.
Aligned reads transformed to bed format, and sorted to remove duplicate reads
Genome_build: hg19 for human genome and Mmur_3.0 for mouse lemur
Supplementary_files_format_and_content: bed files containing regions and read counts

extract_protocol:
Total RNA was isolated from one 10 cm plate of exponentially growing NHF1 or Lemur cells using Trizol (Invitrogen) and the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
The library preparation and strand-specific paired-end sequencing (2 × 150 bp) on a HiSeq 4000 platform (Illumina) was performed by Novogene Co., Ltd.

value: mouse lemur fibroblasts


title: TuYV_SHR_P19_Input

description: Infected by TuYV


title: Lemur-rna-rep1


title: Patient60_Pretreatment [FFP17.009531]

value: breast cancer patient

value: Pretreatment


title: Patient59_Pretreatment [FFP17.009530]

value: FFPE tumor

value: Batch SJ


title: CD31WT3

tag: inducible gene

value: WT

tag: group name

value: CD31+ Endothelial cells


title: Patient54_Pretreatment [FFP17.009527]


title: Patient55_Pretreatment [FFP17.009528]


title: ADF_90ng_5M

status: Public on Apr 05 2020

city: Ramat-Gan

first: Ofir

last: Hakim

address: Max and Anna Webb

country: Israel

institute: Bar-Ilan University

description: 90ng used for library preparation. Total number of reads:5M.

data_processing:
Sequenced reads were aligned to the TAIR10 Arabidopsis genome using bowtie.
SAM file was converted to BED using sam2bed python script.
Reads were assigned to restriction enzyme sites using bedtools intersect with -c parameter.
For raw data, the intersection resulted with a sgr file.
for pScore, pValue was calculated using a custom code available in Github: https://github.com/HakimLab/4SEE.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph

source_name: Seedling

growth_protocol: All plants were grown in growth room under cool white LED light ~100 LUX for 16 hr/day at 22C. Surface sterilized seeds were sowed on agar-coated floats on 1/8 Murashige and Skoog (MS).

extract_protocol:
Frozen tissue was grinded in liquid nitrogen using mortar and pestle, and transferred into Nuclear Isolation Buffer 1 (10 mM HEPES pH=7.5, 0.4 M sucrose, 5 mM KCl, 5mM MgCl2, 5 mM EDTA, supplemented with 0.2 mM Spermine, 0.5 mM Spermidine and 0.6% Triton X-100) and incubated on a rotator at 4ºC for 30 min. The sample was then passed through 40µm mesh and centrifuged (2500g at 4°C). The pellet was resuspended with Nuclear Isolation Buffer 2 (10 mM HEPES pH=7.5, 0.25 M sucrose, 5 mM KCl, 5mM MgCl2 and 5 mM EDTA). The debris was further reduced by two rounds of gentle centrifugation at 300g at 4°C for 15 sec and collecting the supernatant. The supernatant was further centrifuged for 10 min, at 2000g at 4°C and the resulting nuclei pellet was re-suspended with NIB2. For crosslinking, the sample was incubated with 1% formaldehyde at room temperature for 10 min and neutralized with125mM glycine for 5 minutes at room temperature. 10^6 crosslinked nuclei were washed twice with Csp6I RE buffer (Thermo, #ER0211) and resuspended in 1.2X Csp6I RE 1.2X. SDS was added to a final concentration of 0.3% (v/v). After 30 minutes incubation at 65°C, triton X- 100 was added to final concentration of 1.8% and the sample was incubated for 1h in 37°C. 150 units of restriction enzyme Csp6I (Thermo, #ER0211) were added and the sample was incubated overnight at 37°C. Inactivation of Csp6I was achieved by incubating the samples at 65°C for 25 minutes. Ligation reaction was then done in 1.5ml of 1X ligase buffer with 25 units T4 ligase (Roche, #EL0011) and incubated over-night at 4°C followed by 30 minutes incubation at RT. To reverse the crosslinks the sample was supplemented with 50µg proteinase K (Invitrogene, #25530049) and incubated overnight at 65°C, followed by incubation with 150 µg RNAse (Thermo, EN0551) for 45 min at 37°C. The resulting proximity-ligated DNA was extracted by phenol-chloroform followed by ethanol precipitation and dissolved in 20 µl TE buffer. For generating DNA circles, DNA was then digested over-night with DpnII (NEB, #R0543T) at 37°C.  DNA was purified using Expin DNA clean up kit (GeneAll, 112-102) and DNA concentration was determined by Nanodrop 2000 (Thermo Scientific).Ligation junctions were amplified by inverse PCR with viewpoint primers and Phusion hot-start high fidelity Taq (Thermo, #F-549) and the following thermal cycles conditions: 30 sec at 98°C ; 25 cycles of 98°C for 10 sec, 60°C for 30 sec and 72°C for 2 min; 72°C for 5min. PCR products were purified on Expin columns. 30, 120, and twice 60 ng (in total four amplified libraries) DNA templates from SALK and ADF8p:NTF/ACT2p:BirA lines were amplified separately with primer-specific barcodes. For further varying the template amounts, the sequenced tags from these libraries were combined.
Libraries for Illumina sequencing were prepared using NEBNext Ultra II system (NEB, #E7645, #E7103) and sequenced on a NextSeq platform (Illumina). For multiplexing several samples on the same sequencing lane, 4-letter barcodes were added to the primers used for inverse PCR.
4C-seq

tag: strain/background


title: ADF_90ng_50K

description: 90ng used for library preparation. Total number of reads:50K.


title: ADF_90ng_500K

description: 90ng used for library preparation. Total number of reads:500K.


title: ADF_90ng_250K

description: 90ng used for library preparation. Total number of reads:250K.


title: ADF_90ng_2.5M

description: 90ng used for library preparation. Total number of reads:2.5M.


title: ADF_90ng_10M

description: 90ng used for library preparation. Total number of reads:10M.


title: Patient53_Pretreatment [FFP17.009526]

city: Amsterdam

last: Zwart


title: ADF_60ng_5M

description: 60ng used for library preparation. Total number of reads:5M.


title: ADF_90ng_100K

description: 90ng used for library preparation. Total number of reads:100K.


title: ADF_90ng_1M

description: 90ng used for library preparation. Total number of reads:1M.


title: ADF_60ng_2.5M

description: 60ng used for library preparation. Total number of reads:2.5M.


title: ADF_60ng_500K

description: 60ng used for library preparation. Total number of reads:500K.


title: ADF_60ng_50K

description: 60ng used for library preparation. Total number of reads:50K.


title: TuYV_WER_P19_Input

description: Infected by TuYV


title: ADF_30ng_500K

description: 30ng used for library preparation. Total number of reads:500K.


title: ADF_30ng_50K

description: 30ng used for library preparation. Total number of reads:50K.


title: ADF_60ng_100K

description: 60ng used for library preparation. Total number of reads:100K.


title: ADF_60ng_1M

description: 60ng used for library preparation. Total number of reads:1M.


title: ADF_60ng_250K

description: 60ng used for library preparation. Total number of reads:250K.


title: ADF_30ng_5M

description: 30ng used for library preparation. Total number of reads:5M.


title: ADF_60ng_10M

description: 60ng used for library preparation. Total number of reads:10M.


title: ADF_30ng_250K

description: 30ng used for library preparation. Total number of reads:250K.


title: ADF_270ng_5M

description: 270ng used for library preparation. Total number of reads:5M.


title: ADF_30ng_10M

description: 30ng used for library preparation. Total number of reads:10M.


title: ADF_30ng_100K

description: 30ng used for library preparation. Total number of reads:100K.


title: ADF_270ng_500K

description: 270ng used for library preparation. Total number of reads:500K.


title: ADF_270ng_250K

description: 270ng used for library preparation. Total number of reads:250K.


title: ADF_270ng_10M

description: 270ng used for library preparation. Total number of reads:10M.


title: ADF_240ng_50K

description: 240ng used for library preparation. Total number of reads:50K.


title: ADF_240ng_5M

description: 240ng used for library preparation. Total number of reads:5M.


title: ADF_240ng_500K

description: 240ng used for library preparation. Total number of reads:500K.


title: ADF_30ng_2.5M

description: 30ng used for library preparation. Total number of reads:2.5M.


title: ADF_240ng_2.5M

description: 240ng used for library preparation. Total number of reads:2.5M.


title: ADF_240ng_10M

description: 240ng used for library preparation. Total number of reads:10M.


title: ADF_240ng_250K

description: 240ng used for library preparation. Total number of reads:250K.


title: ADF_240ng_1M

description: 240ng used for library preparation. Total number of reads:1M.


title: ADF_270ng_50K

description: 270ng used for library preparation. Total number of reads:50K.


title: ADF_240ng_100K

description: 240ng used for library preparation. Total number of reads:100K.


title: ADF_210ng_5M

description: 210ng used for library preparation. Total number of reads:5M.


title: ADF_30ng_1M

description: 30ng used for library preparation. Total number of reads:1M.


title: ADF_210ng_500K

description: 210ng used for library preparation. Total number of reads:500K.


title: ADF_210ng_50K

description: 210ng used for library preparation. Total number of reads:50K.


title: ADF_210ng_250K

description: 210ng used for library preparation. Total number of reads:250K.


title: ADF_210ng_2.5M

description: 210ng used for library preparation. Total number of reads:2.5M.


title: ADF_270ng_2.5M

description: 270ng used for library preparation. Total number of reads:2.5M.


title: sh2-3

city: Beijing

first: Liming

address: dongdan Si Tiao

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to human genome hg19 using Tophat (version 2.0.8b)
Cufflinks (V2.2.1) was used to estimate normalized expression values for each gene (FPKM, expected number of Fragments Per Kilo base of transcript sequence per Million base pairs sequenced)
Differential  expression gene was determined by Cuffdiff package (v2.2.1).
Genome_build: human genome hg19 (EMBL)
Supplementary_files_format_and_content: tab-delimited text files including FPKM for each sample.

growth_protocol: All the cells were grown in DMEM (Dulbecco’s Modified Eagle Medium) supplemented with 10% FBS and 100  U/ml penicillin-streptomycin

extract_protocol:
Total RNAs isolated from shPRMT1 (sh1 and sh2) or shGFP MDA-MB-231 cells using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: breast cancer cells

tag: genotype/variation

value: PRMT1 knockdown


title: sh2-2


title: ADF_210ng_1M

description: 210ng used for library preparation. Total number of reads:1M.


title: ADF_270ng_100K

description: 270ng used for library preparation. Total number of reads:100K.


title: ADF_270ng_1M

description: 270ng used for library preparation. Total number of reads:1M.


title: sh1-3


title: sh2-1


title: sh1-2


title: shGFP-3

value: Harboning control shRNA


title: sh1-1


title: ADF_180_5M

description: 180 used for library preparation. Total number of reads:5M.


title: shGFP-2


title: ADF_180_50K

description: 180 used for library preparation. Total number of reads:50K.


title: shGFP-1


title: ADF_180_500K

description: 180 used for library preparation. Total number of reads:500K.


title: NJP ganglia, replicate 3

first: Sara

last: Prescott

address: 240 Longwood Avenue

institute: Harvard Medical School

description: 10X Genomics v3 chemistry

data_processing:
FASTQS were made using cellranger mkfastq (parameters: --barcode-mismatches 1 --ignore-dual-index). Each Illumina NextSeq High Output flow cell was processed separately.
Alignment, filtering, barcode counting, and UMI counting were performed using cellranger count (Cell Ranger 3.0.2). Default parameters were used, and reads were aligned to a mm10 (Ensembl 84) reference transcriptome from the pre-built Cell Ranger reference package (1.1.0). The 3' end of the Glp1r locus was extended by 4kb to include the complete UTR.
Genome_build: mm10 (Ensembl 84)
Supplementary_files_format_and_content: Cell Ranger outputs

source_name: Nodose jugular petrosal superganglion

extract_protocol:
NJP ganglia were acutely harvested from adult male C57BL/6J mice (10 animals per replicate), and dissociated (75 min, 37ºC, nutation, 1 ml dissociation solution per 10 mice). Dissociation solution is Dulbecco's Modified Eagle's Medium containing liberase (55 mg/ml, Roche 05401135001) and DNAse (0.004%, Worthington, LS002007). Cells were pelleted (3 min, 300g, 4ºC), suspended (0.2% ovomucoid, 0.004% DNAse, PBS, 200 ml), triturated with a P200 pipette tip, filtered through a 100 µm mesh cell strainer, diluted (300 ml PBS passed also through the strainer), and pelleted again (3 min, 300g, 4ºC). Cells were re-suspended (1 ml, PBS-Ca2+/Mg2+, which is PBS supplemented with calcium and magnesium) and loaded onto a Percoll gradient (Sigma-Aldrich, P1644) in a 14 ml round-bottom tube with three layers: 2 ml 55% Percoll in PBS-Ca2+/Mg2+ (bottom), 2 ml 25% Percoll in PBS-Ca2+/Mg2+ (middle) and 1 ml dissociated cells (top). After centrifugation (20 min, 800g, 4ºC), the cell-enriched fraction (~1 ml) was collected at the 25%-55% Percoll interface, diluted (4 ml PBS) and centrifuged (8 min, 800g, 4ºC). The cell pellet was re-suspended (20 µl PBS-Ca2+/Mg2+), and aliquots removed for cell counting and viability analysis.
Cells (10,000 per sample) were individually encapsulated in small droplets using a 10X Genomics platform. Single-cell cDNA was prepared using the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry), following the manufacturer's protocol, and sequenced on an Illumina NextSeq High Output platform. Replicates 1-3 were prepared in parallel, multiplexed and sequenced on two  Illumina NextSeq High Output flow cells. Replicate 4 was prepared separately using the same protocol, and sequenced separately as a single Illumina NextSeq High Output flow cell.
whole single cell RNA-seq

tag: Sex

value: male

tag: developmental stage

value: adult

value: NJP ganglia

tag: chromium i7 sample index

tag: strain

tag: age

value: 8 weeks old

tag: number of pooled biological replicates


title: ADF_180_250K

description: 180 used for library preparation. Total number of reads:250K.


title: ADF_180_2.5M

description: 180 used for library preparation. Total number of reads:2.5M.


title: NJP ganglia, replicate 4

description: 10X Genomics v3 chemistry

tag: cell type


title: shDis3l2, EBd12

first: Aref

last: Ebrahimi

state: MA

address: 1 Joslin Pl

department: Islet Cell and Regenerative Biology

institute: Harvard Medical School - Joslin

data_processing:
Quality control of the reads by fastqc
Mouse index built by Subread
Reads aligned by Subread
Gene quantification raw counts by FeatureCounts
Voom/Limma for differential expression
Genome_build: Ensembl v88 - GRCm38

molecule: polyA RNA

source_name: EB differentiated cells

growth_protocol: Undifferentiated mESCs were grown in LIF/2i condition

extract_protocol:
Cells were lyzed by Trizol, RNA was extracted by chloroform and precipitated by isopropanol.
Illumina

treatment_protocol: mESCs differentiation was induced by LIF/2i removal and hanging drop formation at the presence of serum to form embryoid bodies (EBs)

value: ESC-derived EB differentiated cells

tag: day


title: NJP ganglia, replicate 2

description: 10X Genomics v3 chemistry


title: ADF_150ng_5M

description: 150ng used for library preparation. Total number of reads:5M.


title: ADF_210ng_10M

description: 210ng used for library preparation. Total number of reads:10M.


title: ADF_180_1M

description: 180 used for library preparation. Total number of reads:1M.


title: NJP ganglia, replicate 1

description: 10X Genomics v3 chemistry


title: ADF_180_100K

description: 180 used for library preparation. Total number of reads:100K.


title: ADF_150ng_50K

description: 150ng used for library preparation. Total number of reads:50K.


title: ADF_180_10M

description: 180 used for library preparation. Total number of reads:10M.


title: shDis3l2, EBd8


title: ADF_150ng_500K

description: 150ng used for library preparation. Total number of reads:500K.


title: shLacZ, EBd12

value: shLacZ


title: shDis3l2, EBd10


title: ADF_150ng_250K

description: 150ng used for library preparation. Total number of reads:250K.


title: ADF_150ng_2.5M

description: 150ng used for library preparation. Total number of reads:2.5M.


title: Patient56_Tamoxifen [FFP17.009565]

tag: subject status

tag: subject id

value: Tamoxifen

tag: tissue/sample type

tag: batch


title: shLacZ, EBd8


title: ADF_150ng_1M

description: 150ng used for library preparation. Total number of reads:1M.


title: ADF_150ng_10M

description: 150ng used for library preparation. Total number of reads:10M.


title: shLacZ, EBd6


title: shDis3l2, EBd6


title: ADF_120ng_50K

description: 120ng used for library preparation. Total number of reads:50K.


title: shLacZ, EBd10


title: shDis3l2, EBd2


title: ADF_120ng_250K

description: 120ng used for library preparation. Total number of reads:250K.


title: shLacZ, EBd2


title: shDis3l2, 2i

source_name: mESC

value: Undifferentiated mouse ESCs


title: ADF_120ng_1M

description: 120ng used for library preparation. Total number of reads:1M.


title: ADF_120ng_2.5M

description: 120ng used for library preparation. Total number of reads:2.5M.


title: ADF_120ng_500K

description: 120ng used for library preparation. Total number of reads:500K.


title: ADF_120ng_10M

description: 120ng used for library preparation. Total number of reads:10M.


title: ADF_120ng_100K

description: 120ng used for library preparation. Total number of reads:100K.


title: RT5_WT


title: RT5_ADF


title: ADF_120ng_5M

description: 120ng used for library preparation. Total number of reads:5M.