title: WT TFH, biological rep1

value: wildtype


title: genomic DNA from oral tissue 6

status: Public on Apr 09 2019

type: genomic

city: Shillong

first: Srimoyee

last: Ghosh

state: Meghalaya

address: Umshing-Mawkynroh

department: Zoology

country: India

institute: North Eastern Hill University

description:
Sample 6
Normal oral tissue sample.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Oral tissue, normal

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from oral tissue samples using Qiagen DNeasy Kit according to standard instructions.

tag: tissue

value: Oral tissue

tag: disease state

value: normal

tag: gender

value: Female


title: genomic DNA from oral tissue 3

description:
Sample 3
Cancer oral tissue sample.

source_name: Oral tissue, cancer

value: cancer


title: X3_2_C_S14

type: SRA

city: Charlestown

first: Alexandra-Chloe

last: Villani

department: Medicine

country: USA

institute: MGH

library_source: transcriptomic

data_processing:
BCL2FASTQ conversion using bcl2fastq2-2.17.1.14
Aligmnent using STAR 2.6.0 with default parameters
Read QC using RNASEQC_STAR
Abundance estimation using RSEM v1.2.8
N/A
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files including raw count and RPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Sorted Murine Treg Cells

extract_protocol:
T cells were sorted according  directly in 10μL of lysis buffer consisting of TCL buffer (Qiagen) and 1% of beta-mercaptoethanol. Samples were the flash frozen and kept at -80°C prior to further processing
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Sorted Murine Treg Cells

tag: batch

tag: genotype

value: FCre x C1fl/fl

tag: treg status

value: Resting


title: genomic DNA from oral tissue 4

description:
Sample 4
Normal oral tissue sample.


title: S18_PB

city: Boston

first: Jarrett

last: Morrow

state: MA

address: 181 Longwood Ave.

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

data_processing:
The quality control pipeline included FastQC and RNA-SeQC. Adapter trimming was performed using Skewer.
STAR aligner version 2.4.0h was used to map the reads to the GRCH38 genome reference.
The Python framework HTSeq was used to produce gene-level counts with the Ensembl version 81 gene annotation.
The samples retained for analysis each had more than 7 million total reads, and greater than 70% of reads mapped to the reference genome, with less than 10% of R1 reads in the sense orientation.
Only data for genes mapped to autosomal chromosomes were retained, leaving counts for 54,243 of the 65,988 transcripts available for analysis.
Genome_build: GRCH38
Supplementary_files_format_and_content: Gene-level counts

source_name: peripheral blood

extract_protocol:
Whole blood was collected in a PaxGene RNA tube on the day of bronchoscopy.
Total RNA was extracted using the AllPrep kit (Qiagen, Valenica, CA). RNA quality was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Extracted RNA samples with RNA integrity number (RIN) greater than six and a concentration greater than or equal to 20 μg/ul were sequenced.
Libraries were QCed by quantification with picogreen, size analysis on an Agilent Bioanalyzer (Agilent, Santa Clara, CA) and qPCR quantitation against a standard curve. Paired end reads with nominal 75 bp length were generated on an Illumina HiSeq 2500 flow cell. Sequencing was performed to an average depth of 20 million reads.

value: whole blood

tag: rin

tag: age

tag: Sex

value: M

tag: race

value: AA

tag: packyears

tag: smoke

value: Current

tag: copd

value: cont

tag: bmi

tag: pctemph

tag: awt

tag: wallareapct

tag: wbc


title: S19_BAL

source_name: bronchoalveolar lavage

extract_protocol:
Bronchoalveolar lavage (BAL) was performed in two lung segments with 60ml of normal saline in each segment, and the BAL fluid obtained from each subject was pooled.
Total RNA was extracted using the AllPrep kit (Qiagen, Valenica, CA). RNA quality was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Extracted RNA samples with RNA integrity number (RIN) greater than six and a concentration greater than or equal to 20 μg/ul were sequenced.
Libraries were QCed by quantification with picogreen, size analysis on an Agilent Bioanalyzer (Agilent, Santa Clara, CA) and qPCR quantitation against a standard curve. Paired end reads with nominal 75 bp length were generated on an Illumina HiSeq 2500 flow cell. Sequencing was performed to an average depth of 20 million reads.

value: alveolar macrophage

value: NHW

value: Never


title: S18_LA

source_name: large airway

extract_protocol:
Large airway brushings were performed in the right mainstem bronchus and placed in RLT buffer (Qiagen).
Total RNA was extracted using the AllPrep kit (Qiagen, Valenica, CA). RNA quality was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Extracted RNA samples with RNA integrity number (RIN) greater than six and a concentration greater than or equal to 20 μg/ul were sequenced.
Libraries were QCed by quantification with picogreen, size analysis on an Agilent Bioanalyzer (Agilent, Santa Clara, CA) and qPCR quantitation against a standard curve. Paired end reads with nominal 75 bp length were generated on an Illumina HiSeq 2500 flow cell. Sequencing was performed to an average depth of 20 million reads.

value: bronchial epithelium


title: genomic DNA from oral tissue 2

description:
Sample 2
Normal oral tissue sample.

tag: tissue

tag: disease state

tag: gender

value: Male


title: S19_LA

tag: cell type


title: X3_1_C_S13

tag: batch

tag: genotype

tag: treg status


title: X3_1_E_S16

value: Effector


title: S18_BAL

tag: rin

tag: age

tag: Sex


title: X2_3_E_S12

value: FCre x C1fl/+


title: X2_3_C_S9


title: PDC_rep1

city: Oak Ridge

first: Xiaohan

last: Yang

state: TN

address: 1 Bethel Valley Road

department: Biosciences Division

institute: Oak Ridge National Laboratory

data_processing:
Sequenced reads were trimmed for low-quality regions and adaptor sequences using Trimmomatic v0.35 (Bolger et al. 2014) to remove trailing sequences below a phred quality score of 20 and to drop reads which are less than 20 bases long
The trimmed sequencing reads from P. trichocarpa and P. deltoides were mapped to the P. trichocarpa genome v3.0 and P. deltoides WV94 v2.1 (https://phytozome.jgi.doe.gov), respectively, using TopHat2 (Kim et al. 2013).
Novel genes were assembled and transcript abundance in RPKM (Reads Per Kilobase of transcript per Million mapped reads) was estimated using Cufflinks (Trapnell et al. 2012).
Analysis of differential gene expression was performed using Cuffdiff (Trapnell et al. 2012)
For miRNA analysis, the small RNA sequencing reads were filtered to remove adaptors and low-quality bases by FastQC (Andrews 2010). The clean reads were further selected by length between 18-30 bp for miRNA identification process. The miRDP1.3 package (Yang and Li 2011) was used for miRNA precursor prediction with size set at 250 nt. To validate the miRNAs, the secondary structure and reads distribution were evaluated to generate the final set of miRNAs (Yin et al. 2016). The precursors and mature sequences were aligned with the searching toolbox in PNRD database for annotation of miRNAs (Yi et al. 2015). To quantify the abundance of miRNA, transcripts per million value was defined as ‘counts of read mapped to miRNA*1000000’/‘reads mapped to reference genome’ (Fahlgren et al. 2007)
Genome_build: Populus trichocarpa genome v3.0 and Populus deltoides WV94 v2.1 (https://phytozome.jgi.doe.gov)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample; the fasta files include the sequences of differentially-expressed transcripts
isoform_exp_diff_sig_PD.txt: Abundance measurements of differentially-expressed transcripts
isoform_exp_diff_sig_PT.txt: Abundance measurements of differentially-expressed transcripts
isoform_exp_diff_sig_transcript_PD.fa: Sequence of differentially-expressed transcripts
isoform_exp_diff_sig_transcript_PT.fa: Sequence of differentially-expressed transcripts
miRNA_EXP_diff_sig_PD.fa: Sequence of differentially-expressed miRNAs
miRNA_EXP_diff_sig_PD.txt: Abundance measurements of differentially-expressed miRNAs
miRNA_EXP_diff_sig_PT.fa: Sequence of differentially-expressed miRNAs
miRNA_EXP_diff_sig_PT.txt: Abundance measurements of differentially-expressed miRNAs

organism: Populus deltoides

source_name: Root

growth_protocol: Inoculated cuttings were grown for three months post inoculation in a greenhouse at 15–28˚C, 12-h photoperiod at INRA-Nancy, France during summer

extract_protocol:
Total RNA was extracted from the root system of three of the eight replicates per genotype per treatment by combining a CTAB extraction method and the Spectrum™ Total Plant RNA extraction kit (Sigma) as reported in Bryan et al. (2016)
Prior to synthesizing sequencing libraries, RNA templates were quantified using a Nanodrop Spectrophotometer (Thermo Scientific) and RNA quality was determined using BioRad Experion™. Samples with a 260/280 reading between 2.0 and 2.2 and a RIN >7 were determined to be of high enough quality and the high-quality RNA samples were used for sRNA-sequencing library preparation with an Illumina TruSeq small RNA sample prep kit (Illumina, CA, USA). As specified in the Illumina protocol, small RNA fragments were selected after PCR amplification by gel purification to capture RNA approximately 20bp-170bp in length.  The Illumina TruSeq small RNA library prep workflow is considered to be stranded because adapters are ligated directionally, facilitating maintenance of strand information during analysis.

treatment_protocol: The rooted cuttings of Populus trichocarpa (genotype 101-74) and Populus deltoides (genotype 73028-62) were individually inoculated with a 1/9 (v/v) mixture of Laccaria bicolor inoculum and calcined clay (Oil Dri US Special, Damolin, Denmark). Eight replicates per genotype and treatment were carried out. L. bicolor S238N inoculum was produced by growing mycelium on an autoclaved peat-vermiculite nutrient mixture in 1-L glass jars for 2 months in the dark at 25°C and kept at 4°C before use (Duponnois and Garbaye 1991). Rhizophagus irregularis inoculum consisted of spores (200 spores per litter of calcinate clay).

value: Root

tag: treatment

value: Control


title: S17_PB

value: F

tag: race

tag: packyears

tag: smoke

value: Former

tag: copd


title: K14-Cre-BRCA1f/f-p53f/f-121918take2

type: RNA

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Primary

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

extract_protocol: Total RNA isolated using Qiagen RNeasy Kit

tag: strain

value: C57Bl6/J and 129

value: K14-Cre; p53 f/f Brca1 f/f primary tumors


title: K14-Cre-BRCA1f/f-p53f/f-121918P.10-136498T1

description: Primary

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: X2_2_E_S11

value: Sorted Murine Treg Cells


title: FVB_KPB_25L_CellLine_Regular_DH

description: Cell Line

tag: line

value: tumor cell line


title: S17_LA

tag: bmi

tag: pctemph

tag: awt

tag: wallareapct

tag: wbc


title: K14-Cre-BRCA1f/f-p53f/f-122452Primary

description: Primary

tag: tissue


title: X2_2_C_S8

tag: cell type

tag: batch

tag: genotype

tag: treg status

value: Resting


title: K14-Cre-BRCA1f/f-p53f/f-121918P9-138466T2

description: Primary


title: K14Cre-BRCA1f/f;p53f/f;138731-1primary

description: Primary


title: FVB_KPB1-B _Cell-line_ Psg9_Cristina

description: Cell Line

source_name: FVB_KPB1-B _Cell-line_ Psg9_Cristina


title: S16_PB

value: whole blood

tag: rin

tag: age

tag: Sex

value: Current

value: case


title: K14Cre-BRCA1f/f;p53f/f;138731-2-primary

description: Primary


title: K14Cre-BRCA1f/f-p53f/f-121916Primary-T.1 (possibly squamous)

description: Primary


title: X2_1_C_S7


title: K14p53BRCA1-121379-CLx1_Perou

description: Cell Line


title: X2_1_E_S10


title: X1_3_E_S6

value: FCre x C1+/+


title: S17_BAL

value: alveolar macrophage

tag: race

value: NHW

tag: packyears

tag: smoke

value: cont


title: X1_3_C_S3


title: FVB_K14Cre-p53f/f-Brca1f/f_Cell Line

description: Cell Line

tag: strain

source_name: FVB_K14Cre-p53f/f-Brca1f/f_Cell Line

tag: line


title: S16_BAL

tag: copd

tag: bmi

tag: pctemph


title: S15_PB

value: AA

tag: awt

tag: wallareapct

tag: wbc


title: S15_LA

tag: cell type

value: bronchial epithelium


title: X1_2_E_S5

tag: batch

tag: genotype

value: Effector


title: CD4+ Effector memory T cells_healthy control_rep4

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

hyb_protocol: The hybridization procedure was performed according to the “One-Color Microarray-Based Gene Expression Analysis protocol (version 6.6, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Custom Oligo Microarrays 4x44K (AMADID 014850) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System G2505C (Agilent Technologies). The Agilent Feature Extraction Software (FES) 10.7.3.1 was used to read out and process the microarray image files.

source_name: Pool of sorted effector memory (CD45RA-CCR7-) T cells from peripheral blood of 2 healthy individuals, unstimulated

label_protocol: Sample labeling was performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis protocol (version 6.6, part number G4140-90040). Briefly, 10 ng of each total RNA samples was used for the amplification and labeling step using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: no growth, sorted unstimulated T cells

extract_protocol: Total RNA was isolated from sorted T cells using Trizol.

treatment_protocol: no treatment, unstimulated T cells

tag: gender

value: female

tag: tissue

value: blood

value: adult

tag: disease state

value: healthy


title: X1_2_C_S2

value: Sorted Murine Treg Cells

tag: treg status


title: S16_LA

tag: rin

tag: age

tag: Sex

value: F

tag: race

tag: packyears


title: CD4+ TEMRA cells_healthy control_rep2

source_name: Pool of sorted TEMRA (CD45RA+CCR7-) cells from peripheral blood of 2 healthy individuals, unstimulated

value: male


title: CD4+ TEMRA cells_liver disease_rep1

source_name: Pool of sorted TEMRA (CD45RA+CCR7-) cells from peripheral blood of 2 patients with liver disease (e.g. alcoholic liver cirrhosis), unstimulated

value: liver disease


title: CD4+ TEMRA cells_healthy control_rep1

source_name: Pool of sorted TEMRA (CD45RA+CCR7-) cells from peripheral blood of 3 healthy individuals, unstimulated


title: X1_1_E_S4


title: FVB_K14Cre-p53f/f-Brca1f/f_122452-T1_primary_SDance

description: Primary

tag: strain

value: C57Bl6/J and 129

value: K14-Cre; p53 f/f Brca1 f/f primary tumors


title: FVB_K14Cre-p53f/f-Brca1f/f_122448-T1_primary_SDance

description: Primary


title: S14_PB

value: whole blood

tag: smoke

value: Former

tag: copd

tag: bmi

tag: pctemph


title: CD4+ Effector memory T cells_healthy control_rep1

source_name: Pool of sorted effector memory (CD45RA-CCR7-) T cells from peripheral blood of 3 healthy individuals, unstimulated


title: FVB_K14Cre-p53f/f-Brca1f/f_121449-T1_primary_SDance

description: Primary


title: X1_1_C_S1

tag: cell type

value: FCre x C1+/+

value: Resting


title: FVB_K14Cre-p53f/f-Brca1f/f_122053-T1_primary_SDance

description: Primary


title: FVB_K14Cre-p53f/f-Brca1f/f_121379-T1_primary_SDance

description: Primary


title: CD4+ Effector memory T cells_liver disease_rep3

source_name: Pool of sorted effector memory (CD45RA-CCR7-) T cells from peripheral blood of 2 patients with liver disease (e.g. alcoholic liver cirrhosis), unstimulated


title: CD4+ Effectormemory T cells_liver disease_rep2

source_name: Pool of sorted effector memory (CD45RA-CCR7-) T cells from peripheral blood of 3 patients with liver disease (e.g. alcoholic liver cirrhosis), unstimulated


title: S14_LA

value: NHW

value: cont

tag: awt

tag: wallareapct

tag: wbc


title: S15_BAL

value: alveolar macrophage

value: AA


title: FVB_K14Cre-p53f/f-Brca1f/f(het)_121382_primary_GMurrow

description: Primary

tag: tissue


title: FVB_K14Cre-p53f/f-Brca1f/f_121374_primary_GMurrow

description: Primary


title: Red FAP⍺+ THY1+ R8_S13

city: Birmingham

first: Adam

last: Croft

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

data_processing:
The reads were mapped to the GRCm38 (Ensemble release 85) mouse genome using STAR alignment software version v2.5.2b. Read counts per gene were produced by the same software.
Sample normalization was performed using DESeq2 R Bioconductor package.
Genome_build: GRCm38 (Ensemble release38)
Supplementary_files_format_and_content: Normalised count data

source_name: Hind limb synovial joints

extract_protocol:
Enzymatic digestion of hind limb synovial joints, sort purification of CD45- PDPN+ live synovial cells
cDNA synthesis preformed using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (ClonTech 634890). Nextera XT Library prep kit (Illumina FC-131-1024) was used following the Fludigm C1 adapted protocol on p28 SMARTer-C1-mRNA-Sequencing-Protocol (Fludigm document PN 100-5950 B1) from ‘Tagmentation’ onwards. Libraries were pooled and sequenced paired end 75 bases each end with the NextSeq 500 system.

treatment_protocol: Day 9 serum transfer induced arthritis model.

value: synovial joints

value: Sort purified Live CD45+ PDPN+ FAPalpha+ THY1+ synovial cells


title: 175423 KPB1-B

description: Transplant

tag: line

value: tumor transplant line


title: S14_BAL


title: CD4+ Effector memory T cells_liver disease_rep1

tag: gender

value: blood

value: adult

tag: disease state


title: CD4+ Effector memory T cells_healthy control_rep3

source_name: Sorted effector memory (CD45RA-CCR7-) T cells from peripheral blood of 1 healthy individual, unstimulated

value: male

tag: age

value: healthy


title: CD4+ Effector memory T cells_liver disease_rep4

value: female

value: liver disease


title: S13_PB

value: whole blood

tag: rin

tag: Sex

value: M


title: Red FAP⍺+ THY1+ R8-7_S6


title: Red FAP⍺+ THY1+ R8_8


title: CD4+ Central memory T cells_healthy control_rep3

source_name: Sorted central memory (CD45RA-CCR7+) T cells from peripheral blood of 1 healthy individual, unstimulated


title: CD4+ Central memory T cells_healthy control_rep4

source_name: Pool of sorted central memory (CD45RA-CCR7+) T cells from peripheral blood of 2 healthy individuals, unstimulated


title: S13_LA

value: bronchial epithelium

tag: race

tag: packyears

value: Former


title: Red FAP⍺+ THY1+ R8_5

tag: strain


title: S13_BAL

source_name: bronchoalveolar lavage

value: NHW

tag: smoke

tag: copd


title: Red FAP⍺+ THY1+ R8_19


title: S12_PB

source_name: peripheral blood

value: Never

value: cont

tag: bmi

tag: pctemph


title: S12_LA

source_name: large airway

tag: cell type

tag: awt


title: Red FAP⍺+ THY1+ R8_17


title: S12_BAL

value: alveolar macrophage

tag: wallareapct

tag: wbc


title: S11_PB

value: case


title: Red FAP⍺+ THY1+ R8_16

tag: tissue

value: synovial joints

value: Sort purified Live CD45+ PDPN+ FAPalpha+ THY1+ synovial cells


title: S11_LA


title: Red FAP⍺+ THY1+ R8_14


title: CD4+ Central memory T cells_healthy control_rep2

tag: gender

value: blood


title: CD4+ Central memory T cells_healthy control_rep1

source_name: Pool of sorted central memory (CD45RA-CCR7+) T cells from peripheral blood of 3 healthy individuals, unstimulated

value: adult

tag: disease state


title: Red FAP⍺+ THY1+ R8_13


title: CD4+ Central memory T cells_liver disease_rep4

source_name: Pool of sorted central memory (CD45RA-CCR7+) T cells from peripheral blood of 2 patients with liver disease (e.g. alcoholic liver cirrhosis), unstimulated

tag: age


title: 157209K14cre P53L/L Brca1L/L mammary tumor

description: Primary

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

value: C57Bl6/J and 129

value: K14-Cre; p53 f/f Brca1 f/f primary tumors


title: CD4+ Central memory T cells_liver disease_rep2

source_name: Pool of sorted central memory (CD45RA-CCR7+) T cells from peripheral blood of 3 patients with liver disease (e.g. alcoholic liver cirrhosis), unstimulated

value: male


title: 159057 (153560 P1) K14cre P53 L/L Brca1 L/L

description: Transplant

tag: line

value: tumor transplant line


title: CD4+ Central memory T cells_liver disease_rep1

value: liver disease


title: 159053 (154160 P1) K14cre P53 L/L Brca1 L/L

description: Transplant


title: S11_BAL

tag: rin

tag: Sex

value: M


title: CD4+ Naive T cells_healthy control_rep3

source_name: Sorted naive (CD45RA+CCR7+) T cells from peripheral blood of 1 healthy individual, unstimulated

value: healthy


title: 154180 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: CD4+ Naive T cells_healthy control_rep4

source_name: Pool of sorted naive (CD45RA+CCR7+) T cells from peripheral blood of 2 healthy individuals, unstimulated

value: female


title: 156775 K14cre P53 L/L Brca1 L/L

description: Primary

source_name: 156775 K14cre P53 L/L Brca1 L/L


title: 175422 KPB1-A

description: Transplant


title: 157391 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: 155448 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: CD4+ Naive T cells_healthy control_rep2


title: Red FAP⍺+ THY1+ R8_18


title: CD4+ Central memory T cells_liver disease_rep3


title: 154160 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: 154814 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: 154140 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: CD4+ Naive T cells_healthy control_rep1

source_name: Pool of sorted naive (CD45RA+CCR7+) T cells from peripheral blood of 3 healthy individuals, unstimulated


title: S10_PB

value: whole blood

tag: race

value: AA

tag: packyears

value: Former


title: Red FAP⍺+ THY1+ R8_12

tag: strain


title: S10_LA

value: bronchial epithelium

tag: smoke

tag: copd

value: cont


title: S10_BAL

value: alveolar macrophage

tag: bmi

tag: pctemph


title: 153084 K14 cre P53 L/L Brca1 L/L

description: Primary

source_name: 153084 K14 cre P53 L/L Brca1 L/L


title: CD4+ Naive T cells_liver disease_rep4

source_name: Pool of sorted naive (CD45RA+CCR7+) T cells from peripheral blood of 2 patients with liver disease (e.g. alcoholic liver cirrhosis), unstimulated


title: Purple FAP⍺- THY1- R7_S13

source_name: Hind limb synovial joints

value: synovial joints

tag: cell type

value: Sort purified Live CD45+ PDPN+ FAPalpha- THY1- synovial cells


title: S9_PB

value: F

tag: awt

tag: wallareapct


title: Purple FAP⍺- THY1-  R7-7_S20

tag: tissue


title: S9_LA

tag: wbc


title: Purple FAP⍺- THY1- R7_S10


title: S9_BAL


title: Red FAP⍺+ THY1+ R8_11

value: Sort purified Live CD45+ PDPN+ FAPalpha+ THY1+ synovial cells


title: S8_PB

value: NHW

value: Current

value: case


title: S8_LA


title: Purple FAP⍺- THY1- R7-S15_S24


title: Green FAP⍺- THY1+ R12_S14

value: Sort purified Live CD45+ PDPN+ FAPalpha- THY1+ synovial cells


title: S8_BAL

value: M


title: 153560 K14cre P53L/L Brca1L/L mammary tumor

description: Primary

value: C57Bl6/J and 129

value: K14-Cre; p53 f/f Brca1 f/f primary tumors


title: CD4+ Naive T cells_liver disease_rep2

source_name: Pool of sorted naive (CD45RA+CCR7+) T cells from peripheral blood of 3 patients with liver disease (e.g. alcoholic liver cirrhosis), unstimulated

tag: gender

value: male

value: blood

value: adult

tag: disease state

value: liver disease


title: PP-EAE SJL/J mouse spleen_2

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

country: Japan

institute: Kindai University Faculty of Medicine

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were visualized and quantified by Affymetrix GeneChip Command Console (AGCC), and normalized by Robust Multi-array Average (RMA) using Expression Console.

label: biotin

source_name: Spleen from SJL/J mouse with PP-EAE at the disease peak

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

growth_protocol: Mice were given standard laboratory rodent chow and water ad libitum.

extract_protocol: Brains and spleens were homogenized in TRI-Reagent (Molecular Research Center) using the Kinematica Polytron homogenizer (Kinematica).  Total RNA was extracted with an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions from brain and spleen homogenate.  DNase treatment was performed during RNA isolation with an RNase-Free DNase Set (Qiagen).  All samples were purified to an absorbance ratio (A260/A280) between 1.9 and 2.1

treatment_protocol: To induce PP-EAE, 5-week-old female SJL/J mice and A.SW mice were sensitized in the base of the tail with 100 nmol of MOG92-106 peptide (DEGGYTCFFRDHSYQ) in complete Freund’s adjuvant (CFA).  On day -1 prior to MOG injection, 5 mg curdlan (a Th17 inducer produced by Alcaligenes faecalis var. myxogenes) in PBS was injected for SJL/J mice intraperitoneally.

value: Spleen

value: SJL/J mouse

tag: treatment

value: Subcutaneous injection of myelin oligodendrocyte glycoprotein 92-106 on day 0 and intraperitoneal injection of cardlan on day -1


title: 152940 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: PP-EAE SJL/J mouse spleen_3


title: CD4+ Naive T cells_liver disease_rep3

value: female

tag: age


title: 152547 K14cre P53 Brca1 primary

description: Primary

source_name: 152547 K14cre P53 Brca1 primary


title: 152904 K14 cre P53 Brca1 primary

description: Primary

source_name: 152904 K14 cre P53 Brca1 primary


title: Control SJL/J mouse spleen_2

source_name: Spleen from control SJL/J mouse

value: No treatment


title: 152906 K14 cre P53 Brca1primary

description: Primary

source_name: 152906 K14 cre P53 Brca1primary


title: 152455 K14 cre P53 L/L Brca1 L/L

description: Primary

source_name: 152455 K14 cre P53 L/L Brca1 L/L


title: Control SJL/J mouse spleen_1


title: 152437 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: S7_PB

source_name: peripheral blood

value: whole blood

tag: rin

tag: Sex

value: F

value: Former


title: Purple FAP⍺- THY1- R7_6

value: synovial joints

value: Sort purified Live CD45+ PDPN+ FAPalpha- THY1- synovial cells


title: S7_BAL

source_name: bronchoalveolar lavage

value: alveolar macrophage

tag: race

value: NHW

tag: packyears

value: case


title: Control SJL/J mouse spleen_3

tag: strain


title: S7_LA

source_name: large airway

value: bronchial epithelium

tag: smoke

tag: copd


title: 151884 K14 cre P53 L/L Brca1 L/L

description: Primary

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

value: C57Bl6/J and 129

source_name: 151884 K14 cre P53 L/L Brca1 L/L

value: K14-Cre; p53 f/f Brca1 f/f primary tumors


title: 151591 K14 cre P53 L/L Brca1L/L

description: Primary

source_name: 151591 K14 cre P53 L/L Brca1L/L


title: PP-EAE A.SW mouse spleen_3

source_name: Spleen from A.SW mouse with PP-EAE at the disease peak

value: A.SW mouse

value: Subcutaneous injection of myelin oligodendrocyte glycoprotein 92-106 on day 0


title: Green FAP⍺- THY1+ R12_5

value: Sort purified Live CD45+ PDPN+ FAPalpha- THY1+ synovial cells


title: Green FAP⍺- THY1+ R12_S10


title: Green FAP⍺- THY1+ R12_6


title: Green FAP⍺- THY1plus R12_21


title: PP-EAE A.SW mouse spleen_2

value: Spleen


title: S6_LA

value: AA

value: Current

value: cont

tag: bmi

tag: pctemph


title: Blue FAP⍺+ THY1- R6_S14

tag: cell type

value: Sort purified Live CD45+ PDPN+ FAPalpha+ THY1- synovial cells


title: S6_PB

value: whole blood

value: F

tag: awt

tag: wallareapct


title: Green FAP⍺- THY1+ R12_13

tag: tissue

value: synovial joints


title: 152422 K14 cre P53 L/L Brca1L/L

description: Primary

source_name: 152422 K14 cre P53 L/L Brca1L/L


title: S6_BAL

value: alveolar macrophage

tag: wbc


title: S5_PB

value: M

value: NHW


title: Blue FAP⍺+ THY1- R6_S13


title: 151363 K14 cre P53 Brca1 primary

description: Primary

source_name: 151363 K14 cre P53 Brca1 primary


title: PP-EAE A.SW mouse spleen_1


title: 151241 K14cre P53L/L Brca1L/L mammary tumor

description: Primary


title: 149722K14 Cre P53 Brca1 primary

description: Primary

source_name: 149722K14 Cre P53 Brca1 primary


title: S5_BAL

value: case


title: 150484 K14 P53 Brca1primary

description: Primary

value: C57Bl6/J and 129

source_name: 150484 K14 P53 Brca1primary


title: 150481 K14 Cre P53 Brca1 primary

description: Primary

source_name: 150481 K14 Cre P53 Brca1 primary

value: K14-Cre; p53 f/f Brca1 f/f primary tumors


title: Blue FAP⍺+ THY1- R6_8

source_name: Hind limb synovial joints


title: Green FAP⍺- THY1+ R12_S12


title: Blue FAP⍺+ THY1- R6_7


title: PP-EAE SJL/J mouse spleen_1

source_name: Spleen from SJL/J mouse with PP-EAE at the disease peak

value: SJL/J mouse

value: Subcutaneous injection of myelin oligodendrocyte glycoprotein 92-106 on day 0 and intraperitoneal injection of cardlan on day -1


title: Blue FAP⍺+ THY1- R6_6


title: S4_LA

value: bronchial epithelium

value: Former


title: S4_PB


title: S5_LA


title: Blue FAP⍺+ THY1- R6_5


title: S4_BAL


title: KPB1-B CC 219 24hr Carbo/Tax

description: Transplant

tag: sample type

value: Reference

source_name: KPB1-B CC 219 24hr Carbo/Tax

value: Carboplatin; Paclitaxel

tag: time

value: 24 hours

tag: line

value: tumor transplant line


title: PP-EAE SJL/J mouse brain_3

source_name: Brain from SJL/J mouse with PP-EAE at the disease peak

value: Brain

tag: treatment


title: PP-EAE SJL/J mouse brain_1


title: KPB1-B CC196 10day Carbo/Tax

description: Transplant

source_name: KPB1-B CC196 10day Carbo/Tax

value: 10 days


title: KPB1-B CC 217 24hr Carbo/Tax

description: Transplant

source_name: KPB1-B CC 217 24hr Carbo/Tax


title: Control A.SW mouse spleen_3

source_name: Spleen from control A.SW mouse

value: Spleen

value: A.SW mouse

value: No treatment


title: Control A.SW mouse spleen_1


title: Control A.SW mouse spleen_2


title: PP-EAE SJL/J mouse brain_2


title: Blue FAP⍺+ THY1- R6_21

value: synovial joints

value: Sort purified Live CD45+ PDPN+ FAPalpha+ THY1- synovial cells


title: KPB1-B CC 216 24hr Carbo/Tax

description: Transplant

value: C57Bl6/J and 129

source_name: KPB1-B CC 216 24hr Carbo/Tax


title: S3_PB

source_name: peripheral blood

value: whole blood

tag: rin

tag: age

tag: Sex

value: F

value: AA

value: Current

value: cont


title: KPB1-B CC 204 10day Carbo/Tax

description: Transplant

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

tag: strain

value: Reference

source_name: KPB1-B CC 204 10day Carbo/Tax


title: Control SJL/J mouse brain_3

source_name: Brain from control SJL/J mouse

value: SJL/J mouse


title: Control SJL/J mouse brain_2


title: S3_LA

source_name: large airway

value: bronchial epithelium

tag: race

tag: packyears

tag: smoke


title: Blue FAP⍺+ THY1- R6_20


title: S3_BAL

source_name: bronchoalveolar lavage

value: alveolar macrophage

tag: copd

tag: bmi

tag: pctemph


title: Orthotopic_shControl_5aza_3 RNA-Seq

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Raw reads were mapped to the reference mouse genome assembly.
Tophat was used for mapping, and rpkm values were calculated with Cufflink.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

source_name: Orthotopic_shControl_5aza_3 RNA-Seq

growth_protocol: Bladder tumors were dissociated into single cells as described in this study. Cells were resuspended in 80 μl DMEM containing 50% Matrigel (BD Bioscience) and then submucosally injected with 29-gauge insulin syringes into the anterior aspect of the bladder dome. The abdominal incisions and skin were then closed with a 4-0 nylon suture, and the surgical site was disinfected with alcohol. For orthotopic transplantation of tumor organoids, bladder tumor organoids were selected, resuspended in 50% organoid medium and 50% Matrigel and then transplanted into recipient mice.

extract_protocol:
Total RNAs were extracted using Trizol reagent.
Libraries were made following the instructions of Illumina TruSeq RNA sample prep kit v2.

treatment_protocol: For BBN-induced bladder carcinogenesis, 0.1% concentration of BBN (TCI) was dissolved in drinking water, and BBN-containing water was provided to mice ad libitum for 4 to 6 months in a dark bottle. BBN-containing water was changed twice a week. Bladders were collected and analyzed after 4 to 6 months of BBN administration. For orthotopic transplantation of bladder tumors, bladder tumors were dissociated into single cells as described above. Cells were resuspended in 80 μl DMEM containing 50% Matrigel (BD Bioscience) and then submucosally injected with 29-gauge insulin syringes into the anterior aspect of the bladder dome. The abdominal incisions and skin were then closed with a 4-0 nylon suture, and the surgical site was disinfected with alcohol. For orthotopic transplantation of tumor organoids, bladder tumor organoids were selected, resuspended in 50% organoid medium and 50% Matrigel and then transplanted into recipient mice.

tag: agent

tag: shRNA

value: shControl


title: S2_PB

tag: cell type

value: NHW

value: Former

tag: awt

tag: wallareapct

tag: wbc


title: Orthotopic_shControl_5aza_2 RNA-Seq

source_name: Orthotopic_shControl_5aza_2 RNA-Seq


title: PP-EAE A.SW mouse brain_3

source_name: Brain from A.SW mouse with PP-EAE at the disease peak

tag: tissue

value: Brain

value: A.SW mouse

tag: treatment

value: Subcutaneous injection of myelin oligodendrocyte glycoprotein 92-106 on day 0


title: S2_LA

tag: rin

tag: age


title: PP-EAE A.SW mouse brain_2

tag: strain


title: Orthotopic_shControl_5aza_1 RNA-Seq

source_name: Orthotopic_shControl_5aza_1 RNA-Seq


title: Control SJL/J mouse brain_1

value: No treatment


title: S2_BAL

tag: Sex

tag: race


title: KPB1-B CC 194 24hr Carbo/Tax

description: Transplant

value: C57Bl6/J and 129

tag: sample type

source_name: KPB1-B CC 194 24hr Carbo/Tax

value: Carboplatin; Paclitaxel

tag: time

value: 24 hours

tag: line

value: tumor transplant line


title: KPB1-B CC 198 10day Carbo/Tax

description: Transplant

source_name: KPB1-B CC 198 10day Carbo/Tax

value: 10 days


title: ASCs_Yy1_iKo_RNAseq

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

country: China

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
For ChIP-seq data, sequenced reads were mapped to mm9 genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20. For RNA-seq data, sequenced reads were mapped to mm9 genome using TOPHAT2.
Peaks were called using MACS2 (v2.1.0), a p-value of 10^-4 was used as the cutoff and gene expression level was quantified by Cufflinks v2.2.1, then differential express genes (DEGs) were identified with following criterias: 1) FPKM value larger than 1 in at least one stage; 2) the absolute value of log2(Fold change) is greater or equal to 2 by comparing FPKM value in wildtype and knocKout SCs.
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: [ChIP-Seq] MACS2-generated peak file.
[RNA-Seq] Cufflinks-generated FPKMs.

molecule: polyA RNA

source_name: muscle

growth_protocol: Fresly isolated SCs were grown in growth medium containing F10, 20% FBS and 1% pen/strep.

extract_protocol:
Chromatin from activated SCs were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies.
Purified RNAs were fragmented and the cDNA were synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added.
ChIP-seq and RNA-seq libraries were constructed according to the standard illumina pair-end sequencing procedure.

value: Adult muscle satellite cells

tag: protocol

value: Activated satellite cells cultured for 36 Hrs


title: PP-EAE A.SW mouse brain_1


title: KPB1-B CC 193 24hr Carbo/Tax

description: Transplant

value: Reference

source_name: KPB1-B CC 193 24hr Carbo/Tax


title: S1_PB

value: whole blood

value: F

tag: packyears

tag: smoke

value: Current

tag: copd

value: case

tag: bmi

tag: pctemph


title: Blue FAP⍺+ THY1- R6_17

source_name: Hind limb synovial joints

value: synovial joints

tag: cell type

value: Sort purified Live CD45+ PDPN+ FAPalpha+ THY1- synovial cells


title: S1_LA

value: bronchial epithelium

value: NHW

tag: awt

tag: wallareapct

tag: wbc


title: ASCs_Wt_RNAseq


title: S1_BAL

value: alveolar macrophage

tag: rin

tag: age


title: Orthotopic_shSHH_5aza_1 RNA-Seq

source_name: Orthotopic_shSHH_5aza_1 RNA-Seq

tag: strain

tag: agent

tag: shRNA

value: shSHH


title: Orthotopic_shSHH_5aza_2 RNA-Seq

source_name: Orthotopic_shSHH_5aza_2 RNA-Seq


title: Orthotopic_shSHH_5aza_3 RNA-Seq

source_name: Orthotopic_shSHH_5aza_3 RNA-Seq


title: FISCs_Yy1_iKo_RNAseq

value: Freshly isolated satellite cells


title: Orthotopic_shBMPR_5aza_3 RNA-Seq

source_name: Orthotopic_shBMPR_5aza_3 RNA-Seq

value: shBMPR


title: FISCs_Wt_RNAseq


title: Peripheral whole blood_ health _lncRNA_mRNA_rep6

city: Beijing

first: Yu-Jin

last: Zhu

address: FuXing Road, Haidian District

institute: Chinese PLA General Hospital

description:
Peripheral whole blood_ health _ rep6
mRNA lncRNA

data_processing:
in-house perl scripts
Bowtie v2.0.6
TopHat v2.0.9.
Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010)
Cuffdiff (v2.1.1) was used to calculate FPKMs
Genome_build: hg19
Supplementary_files_format_and_content: excel,FPKM

source_name: Peripheral whole blood

growth_protocol: 2ml Peripheral blood was isolated from each sample and saved

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNaseH-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

tag: condition

value: control


title: Orthotopic_shBMPR_5aza_2 RNA-Seq

source_name: Orthotopic_shBMPR_5aza_2 RNA-Seq


title: Orthotopic_shBMPR_5aza_1 RNA-Seq

source_name: Orthotopic_shBMPR_5aza_1 RNA-Seq


title: Peripheral whole blood_ health _lncRNA_mRNA_rep5

description:
Peripheral whole blood_ health _ rep5
mRNA lncRNA

treatment_protocol: 2ml Peripheral blood was isolated from each sample and saved


title: Peripheral whole blood_ health _lncRNA_mRNA_rep4

description:
Peripheral whole blood_ health _ rep4
mRNA lncRNA


title: Control A.SW mouse brain_3

source_name: Brain from control A.SW mouse

tag: tissue

value: Brain

value: A.SW mouse

tag: treatment

value: No treatment


title: KPB1-B CC 192 24hr Carbo/Tax

description: Transplant

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

value: C57Bl6/J and 129

tag: sample type

value: Reference

source_name: KPB1-B CC 192 24hr Carbo/Tax

value: Carboplatin; Paclitaxel

tag: time

value: 24 hours

tag: line

value: tumor transplant line


title: Orthotopic_DMSO_5 RNA-Seq

source_name: Orthotopic_DMSO_5 RNA-Seq

value: DMSO


title: KPB1-B CC 186 Untreated

description: Transplant

source_name: KPB1-B CC 186 Untreated

value: 0 days


title: KPB1-B CC 189 Untreated

description: Transplant

source_name: KPB1-B CC 189 Untreated


title: KPB1-B 175438 10 day Carbo/Tax

description: Transplant

source_name: KPB1-B 175438 10 day Carbo/Tax

value: 10 days


title: KPB1-B 175436 10 day Carbo/Tax

description: Transplant

source_name: KPB1-B 175436 10 day Carbo/Tax


title: KPB1-B 175437 10 day Carbo/Tax

description: Transplant

source_name: KPB1-B 175437 10 day Carbo/Tax


title: KPB1-B CC 191 24hr Carbo/Tax

description: Transplant

source_name: KPB1-B CC 191 24hr Carbo/Tax


title: Control A.SW mouse brain_1


title: Orthotopic_DMSO_4 RNA-Seq

source_name: Orthotopic_DMSO_4 RNA-Seq


title: Peripheral whole blood_Neu _lncRNA_mRNA_rep5

description:
Peripheral whole blood_Neu _ rep5
mRNA lncRNA

value: eosinophilic asthma


title: Peripheral whole blood_Neu _lncRNA_mRNA_rep6

description:
Peripheral whole blood_Neu _ rep6
mRNA lncRNA


title: Orthotopic_DMSO_3 RNA-Seq

source_name: Orthotopic_DMSO_3 RNA-Seq


title: KPB1-B 173336 TB 24 hr Carbo/Tax

description: Transplant

source_name: KPB1-B 173336 TB 24 hr Carbo/Tax


title: KPB1-B CC 203 10day Carbo/Tax

description: Transplant

source_name: KPB1-B CC 203 10day Carbo/Tax


title: Orthotopic_DMSO_2 RNA-Seq

source_name: Orthotopic_DMSO_2 RNA-Seq


title: Peripheral whole blood_Neu _lncRNA_mRNA_rep4

description:
Peripheral whole blood_Neu _ rep4
mRNA lncRNA

source_name: Peripheral whole blood


title: Peripheral whole blood_Neu _lncRNA_mRNA_rep3

description:
Peripheral whole blood_Neu _ rep3
mRNA lncRNA


title: Orthotopic_DMSO_1 RNA-Seq

source_name: Orthotopic_DMSO_1 RNA-Seq


title: Peripheral whole blood_Neu _lncRNA_mRNA_rep2

description:
Peripheral whole blood_Neu _ rep2
mRNA lncRNA


title: Orthotopic_5aza_2 RNA-Seq

source_name: Orthotopic_5aza_2 RNA-Seq


title: Peripheral whole blood_Neu _lncRNA_mRNA_rep1

description:
Peripheral whole blood_Neu _ rep1
mRNA lncRNA


title: Control A.SW mouse brain_2

source_name: Brain from control A.SW mouse


title: SK-N-AS_P3_sample1_rep3

city: Chiba

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute

hyb_protocol: Sample preparations were performed on SurePrint G3 Human GE 8x60K V2 microarrays per Agilent Technologies’ recommendations.

scan_protocol: Data acquisition was performed on an Agilent SureScan microarray scanner.

data_processing: Differential expressions of microarray data were calculated by the LIMMA package in R. Replicates underwent background correction by the “normexp” method with an offset of 32, and scale-normalized for replicate spots between arrays. After a linear model fit for each gene was determined, statistical evaluations and differential expressions were compiled via the method of empirical Bayes, with fold changes calculated based on difference in responses between control and treat groups. Spots with matching RefSeq mRNA, ncRNA and Ensemble accessions were filtered and retained for subsequent analyses.

label_protocol: RNA Spike-In Kit

growth_protocol: SK-N-AS cells were maintained in 1:1 MEM/Ham's F-12 supplemented with 10% FBS (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) and cultured in a humidified atmosphere at 37°C with 5% carbon dioxide.

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Cells were plated in a 6-well microtiter plate for overnight attachment prior to treatment of 50 nM polyamide 3 (P3) or 0.05% DMSO.

value: brain

tag: cell line

value: SK-N-AS


title: SK-N-AS_DMSO_sample1_rep3


title: Peripheral whole blood_Eos _lncRNA_mRNA_rep12

description:
Peripheral whole blood_Eos _ rep12
mRNA lncRNA


title: SK-N-AS_P3_sample1_rep2


title: Orthotopic_5aza_1 RNA-Seq

source_name: Orthotopic_5aza_1 RNA-Seq


title: KPB1-B 173336 TA 24 hr Carbo/Tax

description: Transplant

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

source_name: KPB1-B 173336 TA 24 hr Carbo/Tax


title: KPB1-A CC180 10day Carbo/Tax

description: Transplant

source_name: KPB1-A CC180 10day Carbo/Tax


title: KPB1-A CC179 10day Carbo/Tax

description: Transplant

source_name: KPB1-A CC179 10day Carbo/Tax


title: SK-N-AS_DMSO_sample1_rep2


title: SK-N-AS_P3_sample1_rep1


title: KPB1-A CC178 10day Carbo/Tax

description: Transplant

source_name: KPB1-A CC178 10day Carbo/Tax


title: SiHA_P2_sample1_rep2

data_processing: Differential expressions of microarray data were calculated by the LIMMA package in R. Replicates underwent background correction by the “normexp” method with an offset of 20, and scale-normalized for replicate spots between arrays. After a linear model fit for each gene was determined, statistical evaluations and differential expressions were compiled via the method of empirical Bayes, with fold changes calculated based on difference in responses between control and treat groups. Spots with matching RefSeq mRNA, ncRNA and Ensemble accessions were filtered and retained for subsequent analyses.

growth_protocol: SiHA cells were maintained in Eagle's MEM supplemented with 10% FBS (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) and cultured in a humidified atmosphere at 37°C with 5% carbon dioxide.

treatment_protocol: Cells were plated in a 6-well microtiter plate for overnight attachment prior to treatment of 50 nM polyamide 2 (P2) or 0.05% DMSO.

value: cervix

value: SiHA


title: BBN_4 RNA-Seq

source_name: BBN_4 RNA-Seq


title: KPB1-A CC177 10day Carbo/Tax

description: Transplant

source_name: KPB1-A CC177 10day Carbo/Tax


title: SK-N-AS_DMSO_sample1_rep1


title: KPB1-A CC 266 24hr Carbo/Tax

description: Transplant

source_name: KPB1-A CC 266 24hr Carbo/Tax


title: Peripheral whole blood_Eos _lncRNA_mRNA_rep11

description:
Peripheral whole blood_Eos _ rep11
mRNA lncRNA


title: SiHA_DMSO_sample2_rep2


title: SiHA_DMSO_sample2_rep1


title: BBN_3 RNA-Seq

source_name: BBN_3 RNA-Seq


title: Peripheral whole blood_Eos _lncRNA_mRNA_rep10

description:
Peripheral whole blood_Eos _ rep10
mRNA lncRNA


title: Blue FAP⍺+ THY1- R6_S10

source_name: Hind limb synovial joints

value: synovial joints

value: Sort purified Live CD45+ PDPN+ FAPalpha+ THY1- synovial cells


title: BBN_1 RNA-Seq

source_name: BBN_1 RNA-Seq


title: KPB1-A CC 17424hr Carbo/Tax

description: Transplant

source_name: KPB1-A CC 17424hr Carbo/Tax


title: tumor_bearing_mouse_2 [mouse_t_2_3]

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

data_processing:
All  processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops). The following steps are provided as an overview on the internal workings of inDrops.py. FASTQ files and processing steps are provided for mouse only.
inDrops.py first filters reads  for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 12 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene.
Subsequent steps are performed using the output of inDrops.py to generate the final normalized counts files provided here. Individual cell barcodes were filtered for: i) total counts > 600; ii) mitochondrial gene content <15.  Counts were total counts normalized as described in methods, and combined into a single genes x cells normalized filtered matrix per species. Putative cell doublets were identified using Scrublet (Wolock et al., 2018) and removed from further analysis. The resulting count matrixes are provided as mouse_counts_normalized_15939x28205.mtx and human_counts_normalized_54773x41861.mtx
Genome_build: GRCm38/91 (mouse) and GRCh38/81 (human)
Supplementary_files_format_and_content: human_counts_normalized_54773x41861.mtx contains filtered normalized counts from human samples.  human_cell_metadata_54773x25.tsv contains per-cell meta data for human samples, such as cell subset labels, xy coordinates for scatterplot shown in the publication, percentage of mitochondrial counts, total counts.  gene_names_human_41861.tsv contains the list of human gene names.  mouse_counts_normalized_15939x28205.mtx contains filtered normalized counts from mouse samples.  mouse_cell_metadata_15939x12.tsv contains per-cell meta data for mouse samples, such as cell subset labels, xy coordinates for scatterplot shown in the publication, percentage of mitochondrial counts, total counts.  gene_names_mouse_28205.tsv contains the list of mouse gene names.  human_*_raw_counts.tsv.gz contain unfiltered raw counts from human samples prior to normalization; one file per sequencing library.  mouse_*_raw_counts.tsv.gz contain unfiltered raw counts from mouse samples prior to normalization; one file per sequencing library.

source_name: lung tumor

extract_protocol:
Single cell suspensions were obtained from lung tissue of C57BL/6 male mice which were perfused with PBS. Small tissue pieces were generated from perfused lungs using scissors and digested (RPMI containing 0.2 mg/ml collagenase type I, Worthington Biochemical Corporation) for 15min at 37°C while shaking (700rpm). Digested lung tissue was gently meshed through 70µM cell strainers using a plunger. Single cell suspensions were then stained with a fluorescent conjugated antibody specific to CD45 (clone 30-F11, Biolegend) for 45min at 4°C. The cells were washed with staining buffer (PBS containing 0.5% BSA and 2 mM EDTA) and CD45+ live cells were sorted on a FACS Aria cell sorter (BD) into FBS containing tubes which were kept on ice until the cells were further processed for scRNASeq. 7-aminoactinomycin (7AAD, Sigma) positivity was used to exclude dead cells.
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols.

treatment_protocol: Murine KP1.9 lung adenocarcinoma tumor cells were injected into C57BL/6 male mice intravenously (2.5x105 cells in 100µl PBS) to develop orthotopic tumors in the lung. The tumor cell line was derived from lung tumor nodules of a C57BL/6 KrasLSL-G12D/WT;p53Flox/Flox (KP) mouse and was kindly provided by Dr. Zippelius (University Hospital Basel, Switzerland). Mice were analyzed for tumor phenotypes 4 weeks post-tumor initiation.

tag: gender

value: M

tag: treatment received prior to surgery (1= treated; 0=untreated)

tag: tumor cell line injected

value: KP1.9 lung adenocarcinoma tumor cells from lung tumor nodules of a C57BL/6 KrasLSL-G12D/WT;p53Flox/Flox male mouse

tag: age at injection of tumor cell line (weeks)

tag: purification

value: RBC-depletion; CD45+ cells

tag: age at sacrifice (weeks)


title: tumor_bearing_mouse_2 [mouse_t_2_4]


title: KPB1-B 173337 TA 24 hr Carbo/Tax

description: Transplant

value: C57Bl6/J and 129

value: Reference

source_name: KPB1-B 173337 TA 24 hr Carbo/Tax


title: tumor_bearing_mouse_2 [mouse_t_2_1]


title: BBN_2 RNA-Seq

source_name: BBN_2 RNA-Seq


title: tumor_bearing_mouse_2 [mouse_t_2_2]


title: KPB1-A CC 268 24hr Carbo/Tax

description: Transplant

source_name: KPB1-A CC 268 24hr Carbo/Tax

value: Carboplatin; Paclitaxel

value: 24 hours


title: KPB1-A CC 172 24hr Carbo/Tax

description: Transplant

source_name: KPB1-A CC 172 24hr Carbo/Tax

value: tumor transplant line


title: ME180_P2_sample2_rep1

growth_protocol: ME180 cells were maintained in RPMI1640 supplemented with 10% FBS (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) and cultured in a humidified atmosphere at 37°C with 5% carbon dioxide.


title: KPB1-A CC 173 24hr Carbo/Tax

description: Transplant

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

source_name: KPB1-A CC 173 24hr Carbo/Tax


title: SiHA_P2_sample1_rep1


title: tumor_bearing_mouse_1 [mouse_t_1_3]


title: ME180_P2_sample1_rep1


title: KPB1-A CC 171 24hr Carbo/Tax

description: Transplant

source_name: KPB1-A CC 171 24hr Carbo/Tax


title: ME180_DMSO_sample2_rep1


title: MCIXC_P3_sample1_rep3

growth_protocol: MC-IXC cells were maintained in 1:1 MEM/Ham's F-12 supplemented with 10% FBS (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) and cultured in a humidified atmosphere at 37°C with 5% carbon dioxide.

value: MC-IXC


title: SiHA_DMSO_sample1_rep1


title: KPB1-A 175431 10 day Carbo/Tax

description: Transplant

source_name: KPB1-A 175431 10 day Carbo/Tax

value: 10 days


title: tumor_bearing_mouse_1 [mouse_t_1_2]


title: ME180_DMSO_sample1_rep1


title: KPB1-A CC 167 Untreated

description: Transplant

source_name: KPB1-A CC 167 Untreated

value: 0 days


title: KPB1-A 173327 TB 24 hr Carbo/Tax

description: Transplant

source_name: KPB1-A 173327 TB 24 hr Carbo/Tax


title: MCIXC_P3_sample1_rep2

value: brain


title: ME180_P2_sample2_rep2


title: KPB1-A CC 166 Untreated

description: Transplant

source_name: KPB1-A CC 166 Untreated


title: KPB1-A 175432 10 day Carbo/Tax

description: Transplant

source_name: KPB1-A 175432 10 day Carbo/Tax


title: KPB1-A 175433 10 day Carbo/Tax

description: Transplant

source_name: KPB1-A 175433 10 day Carbo/Tax


title: tumor_bearing_mouse_1 [mouse_t_1_5]


title: ME180_DMSO_sample1_rep2


title: MCIXC_P3_sample1_rep1


title: MCIXC_DMSO_sample1_rep3


title: MCIXC_DMSO_sample1_rep2


title: KPB1-A 173326 TB 24hr Carbo/Tax

description: Transplant

source_name: KPB1-A 173326 TB 24hr Carbo/Tax


title: KPB1-A 173327 TA 24hr Carbo/Tax

description: Transplant

source_name: KPB1-A 173327 TA 24hr Carbo/Tax


title: KPB1-A CC 168 Untreated

description: Transplant

source_name: KPB1-A CC 168 Untreated


title: 285 KPB1A 6 Day Carbo/Tax

description: Transplant

source_name: 285 KPB1A 6 Day Carbo/Tax

value: 6 days


title: MCIXC_DMSO_sample1_rep1


title: KPB1-A 173326 TA 24hr Carbo/Tax

description: Transplant

source_name: KPB1-A 173326 TA 24hr Carbo/Tax


title: patient_7_blood [human_p7b1]

source_name: blood

extract_protocol:
3-4 ml of blood were withdrawn in a K2EDTA vacutainer and stored on ice. Upon delivery to the Klein laboratory where scRNAseq was performed, 10µl of 0.5M EDTA were added per ml of blood and cells were resuspended by inverting the tube 3-5 times. Blood was kept on ice at all times prior to red blood cell (RBC) removal. RBC removal was performed using the ErythroClear kit (Stemcell Technologies, cat. no. 01738). 100 ul of blood were transferred to a 1.5-ml tube prefilled with 500 ul of 1xPBS with 0.1% w/v BSA and mixed by pipetting up-and-down. 170 ul of ErythroClear bead suspension were transferred to a separate 1.5-ml tube, placed on a magnet for 1 min, and the unbound storage solution discarded. Beads were resuspended in 100 ul of 1xPBS with 0.1% w/v BSA by vortexing vigorously, then gently mixed with the cell suspension and left at room temperature for 1 min. The tube was placed on a magnet for 3 min. The RBC-depleted unbound fraction was carefully pipetted out and into another tube, pelleted by centrifugation at 450 x g for 5 min at 4 °C, and resuspended to a final concentration of 100k/ml in 1xPBS with 0.1% w/v BSA and 15% v/v OptiPrep.
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols, with modifications summarized in Table S6 of Zilionis et al., 2019 (related to this GEO record).

value: F

tag: tissue diagnosis

value: NSC

tag: histology-reduced (who categories based on diagnosis reported in surgical pathology report)

value: Adeno

tag: status (a=alive; d=deceased)

value: a

tag: age at surgery (years)

tag: tumor stage, ajcc 8th edition

tag: type of surgery

value: LUL lobectomy

tag: pd-l1 expression (rpkm)

value: Not tested

value: RBC-depletion


title: patient_7_tumor [human_p7t2]

source_name: lung tumor

extract_protocol:
Human lung tumor tissue was dissociated for single cell RNA sequencing using the Tumor Dissociation kit by Miltenyi Biotec (cat. no. 130-095-929). Briefly, the tissue was placed in a petri dish on ice and cut into small pieces of 2-4 mm. The pieces were infused with the RPMI/enzyme mix (Miltenyi Biotec), transferred to a gentleMACS C tube containing RPMI/enzyme mix, attached to the sleeve of the gentleMACS Octo Dissociator and run using the “37_h-TDK2” program. After termination of the program, the cells were spun down at 300 x g for 10 min at 4°C, resuspended in RPMI-2% FBS, passed through a 70µm strainer and centrifugation was repeated. The cell pellet was treated with 1 ml ACK solution for 7 min at room temperature, the lysis stopped with 4 ml RPMI-2% FBS. After centrifugation, the cells were resuspended in 1 ml of RPMI-2 % FBS and passed through a cell strainer to obtain a single-cell suspension. Immediately before transcriptome barcoding using the inDrop platform, cells were pelleted at 300 x g for 5 min at 4°C in a swing-bucket rotor, gently resuspended in 1x PBS with 0.1% w/v BSA, manually counted on a hemocytometer and diluted to 100 k cells/ml. The final cell suspension included 15% v/v OptiPrep (Sigma-Aldrich, cat. no. D1556).
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols, with modifications summarized in Table S6 of Zilionis et al., 2019 (related to this GEO record).


title: 284 KPB1A 6 Day Carbo/Tax

description: Transplant

tag: strain

value: C57Bl6/J and 129

tag: sample type

source_name: 284 KPB1A 6 Day Carbo/Tax

tag: treatment


title: patient_6_blood [human_p6b1]

value: M

value: LUL wedge


title: patient_7_tumor [human_p7t1]


title: KELLY_P3_sample1_rep3

growth_protocol: Kelly cells were maintained in RPMI1640 supplemented with 10% FBS (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) and cultured in a humidified atmosphere at 37°C with 5% carbon dioxide.

tag: tissue

tag: cell line

value: Kelly


title: KELLY_P3_sample1_rep2


title: KELLY_P3_sample1_rep1


title: 282 KPB1A 6 Day Carbo/Tax

description: Transplant

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

value: Reference

source_name: 282 KPB1A 6 Day Carbo/Tax

value: Carboplatin; Paclitaxel

tag: time

tag: line

value: tumor transplant line


title: patient_6_tumor [human_p6t2]

tag: gender

tag: treatment received prior to surgery (1= treated; 0=untreated)


title: CHP134_P3_sample1_rep3

growth_protocol: CHP-134 cells were maintained in RPMI1640 supplemented with 10% FBS (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) and cultured in a humidified atmosphere at 37°C with 5% carbon dioxide.

value: adrenal


title: K14-a_157391_vs_FVB_v1.0

hyb_protocol: described in Herschkowitz et al., 2012, PNAS, 109:2778-2783

data_processing: Gene expression was calculated as log2 Cy5/Cy3 ratios, keeping only probes with Lowess normalized intensity values greater than 10 in both Cy5 and Cy3 channels.

source_name: FVB Qiagen DNA Reference

extract_protocol: Genomic DNA was extracted using a DNeasy blood and tissue kit (Qiagen #69504), labeled with a Sure Tag DNA kit (Agilent #5190-4240), and hybridized to 244K CGH microarrays (Agilent #G4415A) as previously described.

value: FVB

source_name: Mammary Tumor

value: Mammary Tumor

tag: genotype

value: K14-Cre; P53 F/F BRCA1 F/F


title: K14-a_153084_vs_FVB_v1.0

label_protocol: described in Herschkowitz et al., 2012, PNAS, 109:2778-2783


title: KELLY_DMSO_sample1_rep1

value: brain


title: K14-a_154160_vs_FVB_v1.0


title: 271 KPB1A 3 Day Carbo/Tax

description: Transplant

source_name: 271 KPB1A 3 Day Carbo/Tax

value: 3 days


title: patient_6_tumor [human_p6t1]

tag: tissue diagnosis

value: NSC

value: Adeno

value: a

tag: purification


title: CHP134_P3_sample1_rep2


title: 283 KPB1A 6 Day Carbo/Tax

description: Transplant

source_name: 283 KPB1A 6 Day Carbo/Tax

value: 6 days


title: KELLY_DMSO_sample1_rep3


title: 273 KPB1A 3 Day Carbo/Tax

description: Transplant

value: C57Bl6/J and 129

source_name: 273 KPB1A 3 Day Carbo/Tax


title: KELLY_DMSO_sample1_rep2


title: 265 KPB1A Untreated

description: Transplant

source_name: 265 KPB1A Untreated

value: 0 days


title: 275 KPB1A 3 Day Carbo/Tax

description: Transplant

source_name: 275 KPB1A 3 Day Carbo/Tax


title: K14-a_154180_vs_FVB_v1.0


title: patient_5_tumor [human_p5t2]

value: F

tag: histology-reduced (who categories based on diagnosis reported in surgical pathology report)

tag: status (a=alive; d=deceased)

value: RLL wedge

value: Not tested


title: K14-a_157209_vs_FVB_v1.0

value: Reference


title: K14-a_152437_vs_FVB_v1.0


title: K14-a_149722_vs_FVB_v1.0


title: K14-a_152906_vs_FVB_v1.0


title: 274 KPB1A 3 Day Carbo/Tax

description: Transplant

source_name: 274 KPB1A 3 Day Carbo/Tax

value: Carboplatin; Paclitaxel

value: tumor transplant line


title: patient_5_tumor [human_p5t1]

tag: age at surgery (years)

tag: tumor stage, ajcc 8th edition

value: RBC-depletion


title: patient_4_tumor [human_p4t3]

value: M

tag: type of surgery

value: LUL wedge

tag: pd-l1 expression (rpkm)


title: patient_4_blood [human_p4b1]


title: K14-a_152940_vs_FVB_v1.0

tag: strain

value: FVB

tag: sample type

value: Mammary Tumor

value: K14-Cre; P53 F/F BRCA1 F/F


title: CaSki_P2_sample2_rep1

data_processing: Differential expressions of microarray data were calculated by the LIMMA package in R. Replicates underwent background correction by the “normexp” method with an offset of 20, and scale-normalized for replicate spots between arrays. After a linear model fit for each gene was determined, statistical evaluations and differential expressions were compiled via the method of empirical Bayes, with fold changes calculated based on difference in responses between DMSO and KR12 treatments. Spots with matching RefSeq mRNA, ncRNA and Ensemble accessions were filtered and retained for subsequent analyses.

growth_protocol: CaSki cells were maintained in RPMI1640 supplemented with 10% FBS (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) and cultured in a humidified atmosphere at 37°C with 5% carbon dioxide.

tag: tissue

value: cervix

value: CaSki


title: 235 KPB1B 6 Day Carbo/Tax

description: Transplant

source_name: 235 KPB1B 6 Day Carbo/Tax

tag: treatment

value: 6 days


title: 261 KPB1A Untreated

description: Transplant

value: C57Bl6/J and 129

source_name: 261 KPB1A Untreated

tag: time


title: K14-a_153560_vs_FVB_v1.0


title: CaSki_DMSO_sample2_rep1

tag: cell line


title: CHP134_DMSO_sample1_rep2

value: adrenal


title: K14-a_151591_vs_FVB_v1.0


title: patient_4_tumor [human_p4t2]

tag: gender

value: NSC

value: Adeno

value: a


title: CaSki_P2_sample1_rep1


title: patient_4_tumor [human_p4t1]

tag: treatment received prior to surgery (1= treated; 0=untreated)

value: Not tested


title: patient_3_blood [human_p3b1]

value: F

value: RUL lobectomy

value: Negative


title: patient_3_tumor [human_p3t3]


title: 234 KPB1B 6 Day Carbo/Tax

description: Transplant

value: Reference

source_name: 234 KPB1B 6 Day Carbo/Tax

value: Carboplatin; Paclitaxel

tag: line

value: tumor transplant line


title: K14-a_150484_vs_FVB_v1.0

value: FVB

value: Mammary Tumor

tag: genotype


title: 232 KPB1B 6 Day Carbo/Tax

description: Transplant

source_name: 232 KPB1B 6 Day Carbo/Tax


title: FVB_K14Cre-p53f/f-Brca1f/f_122448_primary_CGH_GMurrow

value: K14-Cre; P53 F/F BRCA1 F/F


title: 233 KPB1B 6 Day Carbo/Tax

description: Transplant

source_name: 233 KPB1B 6 Day Carbo/Tax


title: 262 KPB1A Untreated

description: Transplant

source_name: 262 KPB1A Untreated

value: 0 days


title: CaSki_DMSO_sample1_rep1

value: cervix

value: CaSki


title: CaSki_DMSO_sample2_rep2


title: CHP134_DMSO_sample1_rep1

value: adrenal


title: K14-a_151363_vs_FVB_v1.0


title: CHP134_DMSO_sample1_rep3


title: K14-a_152455_vs_FVB_v1.0


title: CHP134_P3_sample1_rep1


title: FVB_K14Cre-p53f/f-Brca1f/f_121918_primary_CGH_GMurrow


title: NNBC12

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

description:
microRNA
FFP308

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
MiRNA prediction and the assessment of copy number were performed using the miRDeep2 Package
Conserved miRNAs were annotated based on miRBase release 21.
Genome_build: AZBK00000000.1

organism: Anguilla anguilla

source_name: liver

extract_protocol:
PureLink MiRNA Isolation Kit (Invitrogen)
NEBNext Small RNA Library Prep Set for Illumina

value: liver

tag: location

value: Gironde Estuary


title: 229 KPB1B 3 Day Carbo/Tax

description: Transplant

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

value: C57Bl6/J and 129

source_name: 229 KPB1B 3 Day Carbo/Tax

value: 3 days


title: patient_3_tumor [human_p3t2]

source_name: lung tumor

value: F

tag: tissue diagnosis

value: NSC

tag: histology-reduced (who categories based on diagnosis reported in surgical pathology report)

value: Adeno

value: a


title: patient_3_tumor [human_p3t1]

tag: status (a=alive; d=deceased)

tag: age at surgery (years)

value: RUL lobectomy

value: Negative

tag: purification

value: RBC-depletion


title: FVB_K14Cre-p53f/f-Brca1f/f_121382_primary_CGH_GMurrow

source_name: FVB Qiagen DNA Reference

value: FVB

value: Reference

source_name: Mammary Tumor

value: Mammary Tumor


title: NNBC9

description:
microRNA
FFP303


title: patient_2_tumor [human_p2t2]

value: Squamous

tag: tumor stage, ajcc 8th edition

value: ypT4 N1Mx

tag: type of surgery

value: L pneumonectomy

tag: type of treatment

value: Chemo and XRT

tag: pd-l1 expression (rpkm)

value: Positive


title: patient_2_blood [human_p2b1]

source_name: blood

extract_protocol:
3-4 ml of blood were withdrawn in a K2EDTA vacutainer and stored on ice. Upon delivery to the Klein laboratory where scRNAseq was performed, 10µl of 0.5M EDTA were added per ml of blood and cells were resuspended by inverting the tube 3-5 times. Blood was kept on ice at all times prior to red blood cell (RBC) removal. RBC removal was performed by ACK lysis. 2 ml of blood were transferred into a 50-ml tube prefilled with 20 ml of ACK lysis buffer (Lonza, cat. no. 10-548E or Stemcell, cat. no. 07800) and the tube was rotated for 10 min, protected from light. ACK lysis was performed at room temperature, all other steps were performed on ice. After stopping lysis by topping the tube with ice-cold 1xPBS, the cells were pelleted by centrifugation at 450 x g for 5 min at 4 °C in a swing-bucked rotor and the supernatant decanted. The cells were then resuspended in 1x PBS with 0.1% w/v BSA and transferred into a 15-ml tube. The cell suspension was underlaid with two layers of OptiPrep solution in 1xPBS, 5 ml of 15% v/v and 2 ml of 47% v/v, and centrifuged for 15 min at 800 x g in a swing-bucket rotor with the break turned off. RBC-depleted blood cells were retrieved from the interface between the two layers of OptiPrep, counted, and diluted to a final concentration of 100k/ml in 1xPBS with 0.1% w/v BSA and 15% v/v OptiPrep.
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols, with modifications summarized in Table S6 of Zilionis et al., 2019 (related to this GEO record).


title: ASCs_Input_C57_Chipseq

library_source: genomic

source_name: muscle

tag: cell type

value: Adult muscle satellite cells

tag: protocol

value: Activated satellite cells cultured for 36 Hrs

tag: chip antibody


title: NNBC8

description:
microRNA
FFP302

tag: tissue

value: liver

value: Gironde Estuary


title: NNBC7

description:
microRNA
FFP301


title: patient_2_tumor [human_p2t1]

tag: gender

value: F

value: NSC

tag: treatment received prior to surgery (1= treated; 0=untreated)


title: NNBC10

description:
microRNA
FFP304


title: patient_1_blood [human_p1b3]

value: M

value: a

value: pT2a N1Mx

value: RLL lobectomy

value: Not tested


title: 223 KPB1B 3 Day Carbo/Tax

description: Transplant

tag: strain

value: C57Bl6/J and 129

tag: sample type

value: Reference

source_name: 223 KPB1B 3 Day Carbo/Tax

tag: treatment

value: Carboplatin; Paclitaxel

tag: time

value: 3 days

tag: line

value: tumor transplant line


title: NNBC6

description:
microRNA
FFP215

tag: location

value: Arcachon Bay


title: 215 KPB1B Untreated

description: Transplant

source_name: 215 KPB1B Untreated

value: 0 days


title: 214 KPB1B Untreated

description: Transplant

source_name: 214 KPB1B Untreated


title: 222 KPB1B 3 Day Carbo/Tax

description: Transplant

source_name: 222 KPB1B 3 Day Carbo/Tax


title: 221 KPB1B 3 Day Carbo/Tax

description: Transplant

source_name: 221 KPB1B 3 Day Carbo/Tax


title: 211 KPB1B Untreated

description: Transplant

source_name: 211 KPB1B Untreated


title: 213 KPB1B Untreated

description: Transplant

source_name: 213 KPB1B Untreated


title: NNBC5

description:
microRNA
FFP213


title: Mutant replicate 3

city: Seattle

first: Sumita

last: Jain

state: WA

address: 1959 NE Pacific Street, HSB D-652

department: Periodontics

institute: University of Washington

description:
adapters: TAATCG
SJ20B

data_processing:
FASTQ files were trimmed using bbduk (BBMap 36.92).
Trimmed FASTQ reads were aligned to the P. gingivalis 33277 genome (NC_010729.1) using Bowtie v1.2.
Alignments processed (sorted, etc.) with samtools (1.3.1).
Reads were counted with htseq-count from HTSeq-0.6.1p1 in Python3.
Counts were analyzed in R using limma (3.30.11) and edgeR (3.16.5).
Various extract, transform, and load operations were performed in ad hoc scripts (bash, Dart and Python).
The full pipeline including parameters used is available on request.
Supplementary_files_format_and_content: Table (tab-separated-values) of expression values (from all 6 samples) in log2 space derived from read counts using the packages edgeR and limma in R.
Genome_build: NC_010729.1 Porphyromonas gingivalis ATCC 33277 DNA, complete genome. Annotation from GCF_000010505.1_ASM1050v1_genomic.gff.

organism: Porphyromonas gingivalis ATCC 33277

source_name: RNA from bacterial cell culture

growth_protocol:
P. gingivalis 33277 were obtained from our culture collection. P. gingivalis strains were grown on blood agar plates containing 5% sheep’s blood, and in TYHK broth (30 g/liter Trypticase soy broth, 5 g/liter yeast extract, and 1 mg/liter vitamin K3). Following sterilization by autoclaving, filter-sterilized hemin was added to TYHK broth, just prior to inoculation, to a final concentration of 1 μg/ml. TYHK agar plates were used for growth of P. gingivalis on solid medium as well. All anaerobic strains were grown in an anaerobic growth chamber (5% H 2 , 5% CO 2 , 90% N 2 ) at 37°C.
Antibiotics were added to to mutant strains at the following concentrations: erythromycin (erm), 5 μg/ml.

extract_protocol:
RNA was purified from P. gingivalis cultures that were treated with Trizol (Invitrogen) to facilitate cell lysis. Briefly, a fully grown 3 ml culture was spun and the pellet brought up in 900 μl Trizol, mixed with 200 μl chloroform and the sample spun for 15 minutes. The upper aqueous layer was transferred to a new tube, an equal volume of isopropanol added, mixed well and frozen in a -80C freezer. The next day, the samples were thawed, spun, pellet washed washed with 70% ethanol, and re-suspended in water. 20 μg of this sample, containing crude RNA, was subjected to DNase treatment using RQ1 DNase (Promega). The sample was again subjected to Trizol and chloroform treatment, spun and the upper aqueous layer was concentrated using Zymo Clean and Concentrator kit (Zymo Research), according to manufacturer’s instructions.
Illumina ScriptSeq kit with RiboZero

treatment_protocol: Wildtype 33277 was mutagenized by using conjugation to transfer the mariner transposon-containing plasmid pSAM_Bt from E. coli SM10-lambda-pir to P. gingivalis 33277.

tag: genotype

value: transposon mutant


title: Mutant replicate 2

description:
adapters: CATGGC
SJ16B_S6


title: FVB_MMTV_Pymt_103575_CGH_Perou

value: FVB

value: Mammary Tumor

value: MMTV-PyMT


title: patient_1_blood [human_p1b1]

tag: tissue diagnosis

value: NSC

tag: histology-reduced (who categories based on diagnosis reported in surgical pathology report)

value: Squamous

tag: status (a=alive; d=deceased)

tag: age at surgery (years)

tag: tumor stage, ajcc 8th edition

tag: purification

value: RBC-depletion


title: patient_1_blood [human_p1b2]

value: M

value: a

value: pT2a N1Mx

tag: type of surgery

tag: pd-l1 expression (rpkm)


title: Mutant replicate 1

description:
adapters: GGTAGC
SJ12B-R


title: FVB_MMTV_Pymt_103430_CGH_cn_Perou

tag: tissue


title: ASCs_Yy1_C57_ChIPseq

tag: cell type

value: Adult muscle satellite cells

tag: protocol

value: Activated satellite cells cultured for 36 Hrs

tag: chip antibody

value: YY1 (rabbit polyclonal antibody; Santa Cruz Biotechnology, SC-1703, Lot#B1115)


title: FVB_K14Cre-p53f/f-Brca1f/f_121374_primary_CGH_GMurrow

tag: strain

tag: sample type

value: Reference

value: K14-Cre; P53 F/F BRCA1 F/F


title: IRF5_3

first: Matthias

last: Stephan

address: 1100 Fairview Ave. N., Thomas Research Buildin

institute: Fred Hutchinson Cancer Research Institute

hyb_protocol: The ligated RNA were co-incubated with miRNA capture probeset, miRNA reporter codeset in hybridization buffer following the protocol provided by NanoString. The hybridation happened in 65 °C for at least 12 hours.

scan_protocol: All samples were read on nCounter Analysis System (NanoString Technologies).

data_processing: Raw data was processed and checked for quality using the R/Bioconductor package NanoStringQCPro (Nickles D, Sandmann T, Ziman R and Bourgon R (2017). NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data. R package version 1.10.0.). Expression values were normalized to the geometric mean of housekeeping genes and log2-transformed using nSolver 4.0 software (NanoString Technologies). FDR for ratio data was calculated from the p-values returned by the t-test using the Benjamini-Yekutieli method.

source_name: F4/80+, CD11b+ peritoneal macrophage isolated from ovarian tumor mouse received 2 i.p. doses of  nanoparticles carrying 30 microgram mIRF5 mRNA treatment.

label_protocol: Ligation master mix (provided by NanoString) was added to the mRNA solution and incubated under 48 °C for 5min to allow ligation, followed with purification to remove unligated molecules.

growth_protocol: ID8 cells were injected to adult C57BL/6J mice 7 weeks before treatment

extract_protocol: Peritoneal cells were first isolated through peritoneal lavage, followed with FACS isolation of F4/80+, CD11b+ peritoneal macrophage

treatment_protocol: After 7 weeks of tumor innoculation, mice received 2 doses of i.p. injection (day 1 and day 5) of either (1) PBS, or (2) nanoparticles carrying 30 microgram of mIRF5 mRNA.

tag: treatment

value: Nanoparticles carrying mIRF5 mRNA

value: F4/80+, CD11b+ peritoneal macrophage


title: NNBC4

description:
microRNA
FFP208

source_name: liver

value: liver

tag: location

value: Arcachon Bay


title: NNBC3

description:
microRNA
FFP207


title: patient_1_tumor [human_p1t4]

tag: gender

value: RLL lobectomy

tag: treatment received prior to surgery (1= treated; 0=untreated)

value: Not tested


title: IRF5_2


title: IRF5_1


title: patient_1_tumor [human_p1t3]

tag: tissue diagnosis

value: NSC

tag: histology-reduced (who categories based on diagnosis reported in surgical pathology report)


title: FVB_MMTV_Pymt_103574_CGH_cn_Perou

value: FVB

value: Mammary Tumor

tag: genotype

value: MMTV-PyMT


title: NNBC1

description:
microRNA
FFP202


title: Wild-type replicate 2

description:
adapters: CACTCA
SJ15A_S5

growth_protocol: P. gingivalis 33277 were obtained from our culture collection. P. gingivalis strains were grown on blood agar plates containing 5% sheep’s blood, and in TYHK broth (30 g/liter Trypticase soy broth, 5 g/liter yeast extract, and 1 mg/liter vitamin K3). Following sterilization by autoclaving, filter-sterilized hemin was added to TYHK broth, just prior to inoculation, to a final concentration of 1 μg/ml. TYHK agar plates were used for growth of P. gingivalis on solid medium as well. All anaerobic strains were grown in an anaerobic growth chamber (5% H 2 , 5% CO 2 , 90% N 2 ) at 37°C.

value: wildtype


title: NNBC2

description:
microRNA
FFP204


title: PBS_3

source_name: F4/80+, CD11b+ peritoneal macrophage isolated from ovarian tumor mouse received 2 i.p. doses of PBS treatment

value: PBS


title: patient_1_tumor [human_p1t2]

value: M

value: Squamous

tag: status (a=alive; d=deceased)

value: a

tag: age at surgery (years)

tag: tumor stage, ajcc 8th edition

value: pT2a N1Mx


title: Wild-type replicate 3

description:
adapters: CTCAGA
SJ19A_S9


title: Wild-type replicate 1

description:
adapters: GTTTCG
SJ11A-R


title: patient_1_tumor [human_p1t1]

tag: type of surgery

tag: pd-l1 expression (rpkm)

tag: purification

value: RBC-depletion


title: PBS_1

tag: cell type


title: cerk1/3E-rep1

status: Public on Apr 08 2019

first: Ben-Qiang

last: Gong

address: No. 135, Xingang Xi Road, Guangzhou

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Data processing steps were conducted by the Biomarker Technologies company (Beijing, China).
Briefly, Illumina software used for basecalling.
Clean reads were trimmed for adaptor sequence, and masked for low-complexity sequence, then mapped to TAIR10 whole genome.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated from counts.
Finally, we analyzed the processed data from Biomaker company.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

organism: Arabidopsis thaliana

source_name: plant seedlings

growth_protocol: Arabidopsis seeds were germinated on ½×MS medium supplemented with 0.05% MES, 0.5% sucrose and 0.8% phytoagar, and were grown in a plant growth chamber (Ningbo Saifu, China) with 75 μmol m-2s-1 light intensity under photoperiods of 16 hr light at 23°C and 8 hr dark at 20°C for 10 days.

extract_protocol:
Total RNA was extracted using the RNAiso Plus reagent (Takara Bio, Japan).
A total amount of 1 μg RNA per sample was used for RNA-seq library construction according to the Biomarker Technologies company (Beijing, China).

treatment_protocol: Arabidopsis seedlings were treated with or without 100 nM flg22.

tag: tissue

value: plant seedlings

tag: age

value: post germination 10 days

value: no treatment


title: PBS_2

value: F4/80+, CD11b+ peritoneal macrophage

tag: strain


title: cerk1/3E-rep2

tag: treatment


title: cerk1/3D-rep1


title: cerk1/3A-rep2


title: cerk1/3A-rep1


title: 264 KPB1A Untreated

description: Transplant

source_name: common reference RNA (consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female day 1 pups.  Reference to original publication PMID:17493263)

extract_protocol: Total RNA isolated using Qiagen RNeasy Kit

value: C57Bl6/J and 129

tag: sample type

value: Reference

source_name: 264 KPB1A Untreated

tag: time

value: 0 days

tag: line

value: tumor transplant line


title: cerk1/WT-rep1


title: cerk1+mock

value: treatment with sterile water


title: cerk1+flg22

value: treatment with 100 nM flg22


title: WT+flg22

value: wild type


title: WT+mock


title: ECr/VCr atl2 2.2

city: New Haven

first: Elena

last: Gonzalo Gil

state: Connecticut

address: 25 York street

institute: Yale University School of Medicine

data_processing:
The reads were trimmed for quality using fastxtrimmer.  The trimmed reads were aligned to the reference human genome (UCSC v. hg19) using bwa mem.
The peaks were called using the MACS2 peak-caller.
Genome_build: hg19
Supplementary_files_format_and_content: peaks xls file generated by MACS2

source_name: peripheral blood

growth_protocol: CD4+ T cells obtained after positive selection from total PBMCs were activated with anti-CD3/CD28 in presence of IL-2 for 3 days.

extract_protocol:
50,000 cells were lysed and transpositions were performed using transposase mixture (Nextera DNA library prep kit, Illumina), supplemented with 0.01% digitonin (Promega). Transposition reactions were incubated for 30 min at 37°C in a ThermoMixer with agitation at 300rpm.  DNA was purified using the MinElute Reaction Cleanup kit (Qiagen)
libraries were amplified using NEBnext PCR master mix with Illumina primers for ATACseq according to Illumina's instructions

value: activated CD4+ T cells

tag: activation time

value: 3 days

tag: activation protocol

value: anti-CD3/CD28 in presence of IL2


title: ECr/VCr atl2 2.1


title: Control 2.6


title: ECr/VCr atl2 2.3


title: Control 2.5


title: Control 2.2


title: Control 2.1


title: ECr/VCr atl2 2.4


title: Ctrl 8

data_processing:
The reads were trimmed for quality using custome Perl scripts.  The trimmed reads were aligned to the reference genome hg19 using TopHat2 (ver. 2.1.1).
The aligned reads were used with UCSC hg19 reference annotation file to generate gene abundance estimates and differential gene expression using cuffdiff.
The results were visualized using R and cummeRbund.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM matrix

growth_protocol: 1x106 CD4+ T cells  were activated with anti-CD3/CD28 in presence of IL-2 for 3 days.

extract_protocol:
Total RNA was extracted from activated CD4+ T cells using the RNeasy mini kit (Qiagen).
For the RNAseq library preparation, mRNA was purified from total RNA with oligo-dT beads and sheared by incubation at 94 degrees.  Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries. The cDNA library was then end-repaired, and A-tailed, adapters ligated, and second-strand digestion was performed by U-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs were quantified by qRT-PCR and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer.


title: Ctrl 15


title: cerk1/3D-rep2

tag: genotype


title: Ctrl 22


title: Ctrl 13


title: Atl2-S


title: At2-M


title: Atl2


title: TIN2

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

data_processing:
Read file QC :Total reads were analysed with FastQC and visually inspected to make sure each sequenced sample met the adequate quality standards.
Adapter clipping, quality trimming and filtering :Cutadapt and Trimmomatic were used to remove Illumina adapters, filter reads shorter than 20 bases, and discard the ones with more than 30 Ns.
Genome alignment :Filtered reads were mapped to the yeast genome with TopHat2 (RNA-seq) and Bowtie2 (ChIP-seq) using the yeast R64 (sacCer3) genome as reference
Read count extraction :Raw read counts were extracted with the featureCounts tool from the R package Rsubread using the yeast R64 (sacCer3) genome annotation as a reference.
Genome_build: R64 (sacCer3)
Supplementary_files_format_and_content: Tab-delimited text file containing raw read count matrix
Supplementary_files_format_and_content: RPKM-normalised coverage bigWig tracks for the individual ChIP-seq datasets.

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: For RNA-seq: cells were grown overnight to saturation at 25ºC, then diluted to an OD600 of 0.2 approximately, and let grow at 34 ºC for almost 5 h until they reached an OD600 of 0.5-0.6. For ChIP-seq: cells were incubated for 2 h at 34 ºC.

extract_protocol:
Yeast total RNA was extracted from the liquid cultures with the standard acid-phenol method, followed by NaAc and EtOh precipitation. Immunoprecipitated DNA was extracted with the phenol method, and cleaned with purification and concentration columns.
RNA-seq: The ribosomal RNA-depleted fraction was used to construct libraries for sequencing with the NEBNext Ultra Directional RNA Library Prep Kit (Illumina). Libraries were sequenced in a HiSeq 2500 system (Ilumina). ChIP-seq: immunoprecipitated DNA and Input DNA were used to construct sequencing libraries with the NEBNext Ultra DNA Library Prep Kit for Illumina. Libraries were sequenced in a HiSeq 2500 system (Illumina).

treatment_protocol: Cells were heat shocked by shifting from 25ºC to 34ºC for 4-5 hours.

tag: genotype/variation

value: ts mutant  ten1-31

tag: chip sample

value: Input DNA


title: WIN2

value: WT


title: cerk1/WT-rep2

value: plant seedlings


title: WIN1


title: TS22

tag: chip antibody

value: anti-phospho Ser2 RNAPII (3E10)

value: IP DNA


title: WS21


title: TR12

value: anti-Rpb1 (8W16G)


title: WS22


title: TS21


title: Ctrl 16


title: WR12


title: WR11


title: WT3

description: rRNA depleted Total RNA


title: WT1

description: rRNA depleted Total RNA


title: TEN3

description: rRNA depleted Total RNA


title: TEN1

description: rRNA depleted Total RNA


title: WT2

description: rRNA depleted Total RNA


title: TEN2

description: rRNA depleted Total RNA


title: Atl2-D


title: TIN1


title: TR11


title: NNBC11

description:
microRNA
FFP305

value: liver

tag: location

value: Gironde Estuary


title: genomic DNA from nevus sample 1581

first: Nancy

last: Thomas

address: 405 Mary Ellen Jones Building

department: Dermatology

description: nevus sample

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: BeadArrays were imaged with the HiScan system using standard recommended Illumina scanner setting

data_processing: GenomeStudio M Module software

source_name: nevus sample

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from FFPE melanocytic samples using a proteinase K-based DNA lysis protocol

value: nevus

tag: disease state

value: Nevus


title: genomic DNA from nevus sample 1537

description: nevus sample


title: genomic DNA from nevus sample 1395

description: nevus sample


title: genomic DNA from nevus sample 1393

description: nevus sample


title: genomic DNA from nevus sample 1391

description: nevus sample


title: genomic DNA from nevus sample 1403

description: nevus sample


title: genomic DNA from nevus sample 1375

description: nevus sample


title: genomic DNA from nevus sample 1399

description: nevus sample


title: genomic DNA from nevus sample 1385

description: nevus sample


title: genomic DNA from nevus sample 1398

description: nevus sample


title: genomic DNA from nevus sample 1394

description: nevus sample


title: genomic DNA from nevus sample 1566

description: nevus sample


title: genomic DNA from nevus sample 1397

description: nevus sample


title: genomic DNA from nevus sample 1383

description: nevus sample


title: genomic DNA from nevus sample 1389

description: nevus sample


title: genomic DNA from nevus sample 1388

description: nevus sample


title: genomic DNA from nevus sample 1386

description: nevus sample


title: genomic DNA from nevus sample 1381

description: nevus sample


title: genomic DNA from nevus sample 1400

description: nevus sample


title: genomic DNA from nevus sample 1377

description: nevus sample


title: genomic DNA from nevus sample 1355

description: nevus sample


title: genomic DNA from nevus sample 1390

description: nevus sample


title: genomic DNA from nevus sample 1356

description: nevus sample


title: genomic DNA from nevus sample 1379

description: nevus sample


title: genomic DNA from nevus sample 1387

description: nevus sample


title: genomic DNA from nevus sample 1357

description: nevus sample


title: genomic DNA from nevus sample 1392

description: nevus sample


title: genomic DNA from nevus sample 1353

description: nevus sample


title: genomic DNA from nevus sample 1380

description: nevus sample


title: genomic DNA from nevus sample 1351

description: nevus sample


title: genomic DNA from nevus sample 1350

description: nevus sample


title: genomic DNA from nevus sample 1347

description: nevus sample


title: genomic DNA from nevus sample 1326

description: nevus sample


title: genomic DNA from nevus sample 1335

description: nevus sample


title: genomic DNA from nevus sample 1343

description: nevus sample


title: genomic DNA from nevus sample 1342

description: nevus sample


title: genomic DNA from nevus sample 1311

description: nevus sample


title: genomic DNA from nevus sample 1325

description: nevus sample


title: genomic DNA from nevus sample 1330

description: nevus sample


title: genomic DNA from nevus sample 1319

description: nevus sample


title: genomic DNA from nevus sample 1337

description: nevus sample


title: genomic DNA from nevus sample 1333

description: nevus sample


title: genomic DNA from nevus sample 1346

description: nevus sample


title: genomic DNA from nevus sample 1310

description: nevus sample


title: genomic DNA from nevus sample 1327

description: nevus sample


title: genomic DNA from nevus sample 1305

description: nevus sample


title: genomic DNA from nevus sample 858

description: nevus sample


title: genomic DNA from nevus sample 1324

description: nevus sample


title: genomic DNA from nevus sample 1317

description: nevus sample


title: genomic DNA from nevus sample 860

description: nevus sample


title: genomic DNA from nevus sample 1323

description: nevus sample


title: genomic DNA from nevus sample 864

description: nevus sample


title: genomic DNA from nevus sample 1308

description: nevus sample


title: genomic DNA from nevus sample 1318

description: nevus sample


title: genomic DNA from nevus sample 1312

description: nevus sample


title: genomic DNA from nevus sample 1334

description: nevus sample


title: genomic DNA from nevus sample 1322

description: nevus sample


title: genomic DNA from nevus sample 1329

description: nevus sample


title: Nintedanib_2uM_IPF [small RNA-seq]

city: Kaohsiung

first: Wei An

last: Chang

address: No.100, Shihcyuan 1st Rd., Sanmin Dist., Kaohsiung City 80708, Taiwan (R.O.C.)

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
TRIMMOMATIC v0.36 was used to clip the 3' adaptor sequence, trim low quality bases and discard reads shorter than 18 nucleotides.
BOWTIE v1.1.0 was used to align qualified reads on the reference genome sequence.
MiRDeep2 was used to estimate expression levels of known miRNAs, and also identifies novel miRNAs.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: excel files include miRNA ID, precursor miRNA ID, raw reads count and RPM values for each samples

source_name: Fibroblasts

growth_protocol: Human IPF lung fibroblasts (Disease Human Lung Fibroblasts, Idiopathic Pulmonary Fibrosis. Catalog No. CC-7231), purchased from Lonza Inc. (Walkersville, MD, USA), were incubated at 37°C in a 5% CO2-containing incubator in FGM™-2 Fibroblast Growth Medium-2 Bulletkit™ (Lonza, Catalog No. CC-3132) containing 0.5 mL human fibroblast growth factor-basic (hFGF-B), 0.5 mL insulin, 10 mL fetal bovine serum, and 0.5 mL GA-1000. The medium was changed every 2-3 days and the cells were passaged at 80-90% confluence for the following experiments.

extract_protocol:
total RNAs from Ctrl_IPF fibroblasts, Nintedanib_2uM_IPF fibroblasts and Nintedanib_4uM_IPF fibroblasts were extracted by Trizol Reagent according to the manufacturer’s instructions.
All RNA Sample preparation procedures were carried out according to the official Illumina protocol.  Agilent's SureSelect Strand-Specific RNA Library Preparation Kitwere used for library construction followed by AMPure XP Beads size selection.  The sequence was directly determined using Illumina's sequencing-by-synthesis (SBS) technology. Sequencing data (FASTQ files) were generated by Welgene's pipeline based on Illumina's basecalling program bcl2fastq v2.2.0.

treatment_protocol: Nintedanib (BIBF1120, Catalog No. S1010), purchased from Selleckchem (Houston, TX, USA), was dissolved in dimethyl sulfoxide (DMSO) (Sigma Chemical Co., St. Louis, MO, USA) to obtain various concentrations. The reagents were stored at -20°C until use in the experiments. In nintedanib-treated cultures, cells were treated with 1 μM, 2 μM, and 4 μM nintedanib for 24 h, 48 h, and 72 h. In control cultures, cells were treated with the carrier solvent (0.1% DMSO).

tag: source subject age

tag: gender

value: male

value: Lung

tag: cell line

value: Diseased Human Lung Fibroblasts, Idiopathic Pulmonary Fibrosis (DHLF-IPF)

value: 2uM Nintedanib


title: genomic DNA from nevus sample 1344

description: nevus sample

tag: tissue


title: Nintedanib_4uM_IPF [small RNA-seq]

value: 4uM Nintedanib


title: pCre-pTm-R2

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software v1.8 was used for base calling.
Raw fastq files were analyzed using Kallisto 0.43.0 ( -t 20 --single -l 300 -s 100 -b 100)
Kallisto output was used to test transcripts for expression differences using the Sleuth Wald test.
Files were compiled using R.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated files represent the adjusted q value for each condition and the beta value estimated by Sleuth

source_name: Splenic basophils

growth_protocol: Basophil isolation from female McpteCre +/- or -/-  DNMAML+/+ mice on B6 background from spleen, by digestion and flow sorting

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Diretional RNA-seq libraries were prepared from 25ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Naïve or day 14 T. muris infection (200 eggs), with IL-3 complex treatment on d-5 and d-2 before harvest to expand basophil numbers.

value: Mcpt8Cre+/+ DNMAML+/+

tag: condtion

value: d14 Trichuris muris infection IL-3c

tag: Sex

value: female

tag: background strain


title: pCre-pTm-R1


title: mCre-pTm-R2

value: Mcpt8Cre+/- DNMAML+/+