title: 15-008-040_G4-2 reanalysis

status: Public on Jun 30 2020

type: SRA

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

country: USA

institute: National Cancer Institute

description:
15-008-040_G4-2
A3-25-5
reanalysis of GSM3728633

library_source: transcriptomic

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with TrimGalore.
Trimmed FASTQ files were aligned to hg19 using STAR.
Genomic features were quantified using FeatureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: Ensembl gene ID, Log2 counts-per-million (CPM), gene symbol, description

molecule: total RNA

organism: Homo sapiens

source_name: prostate

extract_protocol:
Total RNA was extracted from cells adhered to caps using the Qiagen RNeasy FFPE kit.
rRNA-depleted RNA was converted into cDNA and assembled into strand-specific libraries using the NEBNext Ultra II Directional RNA-Seq kit.

treatment_protocol: FFPE human prostate tissues were sectioned onto metal frame membrane slides, and regions of interest were excised onto caps using laser capture microdissection.

tag: gender

value: male

tag: patientcode

tag: regionofinterest


title: 15-492-001_G3-3 reanalysis

description:
15-492-001_G3-3
A3-41-3
reanalysis of GSM3728639


title: 15-008-040_G3-3 reanalysis

description:
15-008-040_G3-3
A3-25-3
reanalysis of GSM3728636


title: 15-008-040_G3-2 reanalysis

description:
15-008-040_G3-2
A3-25-2
reanalysis of GSM3728635


title: 15-492-001_G3-1 reanalysis

description:
15-492-001_G3-1
A3-41-1
reanalysis of GSM3728637


title: 15-008-040_G3-1 reanalysis

description:
15-008-040_G3-1
A3-25-1
reanalysis of GSM3728630


title: 15-008-040_G4-1 reanalysis

description:
15-008-040_G4-1
A3-25-4
reanalysis of GSM3728632


title: 15-492-001_G3-2 reanalysis

description:
15-492-001_G3-2
A3-41-2
reanalysis of GSM3728638


title: 15-008-040_G4-3 reanalysis

description:
15-008-040_G4-3
A3-25-6
reanalysis of GSM3728634


title: 15-008-039_IDC-2 reanalysis

description:
15-008-039_IDC-2
A3-37-5
reanalysis of GSM3728625


title: 15-008-039_ITC-1 reanalysis

description:
15-008-039_ITC-1
A3-37-6
reanalysis of GSM3728626


title: 15-008-039_IDC-1 reanalysis

description:
15-008-039_IDC-1
A3-37-4
reanalysis of GSM3728623


title: 15-008-039_ITS-3 reanalysis

description:
15-008-039_ITS-3
A3-37-3
reanalysis of GSM3728624


title: 15-008-039_ITC-2 reanalysis

description:
15-008-039_ITC-2
A3-37-7
reanalysis of GSM3728627


title: 15-008-039_ITS-5 reanalysis

description:
15-008-039_ITS-5
A3-37-9
reanalysis of GSM3728622


title: 15-008-039_IDC-4 reanalysis

description:
15-008-039_IDC-4
A3-37-10
reanalysis of GSM3728621


title: 15-008-039_ITS-4 reanalysis

description:
15-008-039_ITS-4
A3-37-8
reanalysis of GSM3728620


title: 15-008-039_ITS-2 reanalysis

description:
15-008-039_ITS-2
A3-37-2
reanalysis of GSM3728619


title: 15-008-039_ITS-1 reanalysis

description:
15-008-039_ITS-1
A3-37-1
reanalysis of GSM3728618


title: 15-008-004_G3-2 reanalysis

description:
15-008-004_G3-2
A3-16-8
reanalysis of GSM3728611


title: 15-008-004_G3-1 reanalysis

description:
15-008-004_G3-1
A3-16-6
reanalysis of GSM3728610


title: 15-008-004_G4-1 reanalysis

description:
15-008-004_G4-1
A3-16-9
reanalysis of GSM3728608


title: 11-250-14-04_G4-1 reanalysis

description:
11-250-14-04_G4-1
A2-73-5
reanalysis of GSM3728605


title: 11-250-14-04_G4-2 reanalysis

description:
11-250-14-04_G4-2
A2-73-6
reanalysis of GSM3728606


title: 11-250-14-04_G3-1 reanalysis

description:
11-250-14-04_G3-1
A2-73-2
reanalysis of GSM3728602


title: 11-250-14-04_G3-2 reanalysis

description:
11-250-14-04_G3-2
A2-73-3
reanalysis of GSM3728603


title: 15-492-001_B9-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-41-4
processed data file: HumanProstateTissue.txt

data_processing:
Base-calling was performed with CASAVA 1.9.
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HumanProstateTissue.txt: Tab-separated values, gene symbol, description, transcripts-per-million (TPM).

tag: tissue

value: prostate


title: 15-492-001_G3-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-41-2
processed data file: HumanProstateTissue.txt


title: 15-492-001_G3-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-41-1
processed data file: HumanProstateTissue.txt


title: 11-250-14-03_G3-1 reanalysis

description:
11-250-14-03_G3-1
A2-134-2
reanalysis of GSM3728599


title: 15-008-040_G4-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-25-5
processed data file: HumanProstateTissue.txt


title: 15-008-040_B9-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-25-7
processed data file: HumanProstateTissue.txt


title: 15-008-040_G4-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-25-4
processed data file: HumanProstateTissue.txt


title: 11-250-14-03_G4-1 reanalysis

description:
11-250-14-03_G4-1
A2-134-3
reanalysis of GSM3728600


title: 15-492-001_G3-3

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-41-3
processed data file: HumanProstateTissue.txt


title: 15-008-039_B9-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-12
processed data file: HumanProstateTissue.txt


title: 15-008-040_G3-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-25-1
processed data file: HumanProstateTissue.txt


title: 15-008-039_ITC-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-7
processed data file: HumanProstateTissue.txt


title: 15-008-039_LN-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-11
processed data file: HumanProstateTissue.txt


title: 15-008-040_G4-3

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-25-6
processed data file: HumanProstateTissue.txt


title: 11-250-14-04_IDC-1 reanalysis

description:
11-250-14-04_IDC-1
A2-73-4
reanalysis of GSM3728604


title: 15-008-040_G3-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-25-2
processed data file: HumanProstateTissue.txt


title: 15-008-039_ITC-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-6
processed data file: HumanProstateTissue.txt


title: 15-008-039_IDC-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-5
processed data file: HumanProstateTissue.txt


title: 15-008-039_ITS-3

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-3
processed data file: HumanProstateTissue.txt


title: 15-008-040_G3-3

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-25-3
processed data file: HumanProstateTissue.txt


title: 15-008-039_IDC-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-4
processed data file: HumanProstateTissue.txt


title: 15-008-039_IDC-4

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-10
processed data file: HumanProstateTissue.txt


title: 15-008-039_ITS-5

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-9
processed data file: HumanProstateTissue.txt


title: 15-008-039_ITS-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-2
processed data file: HumanProstateTissue.txt


title: 15-008-039_ITS-4

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-8
processed data file: HumanProstateTissue.txt


title: 15-008-015_B9-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-11-3
processed data file: HumanProstateTissue.txt


title: 15-008-039_ITS-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-37-1
processed data file: HumanProstateTissue.txt


title: 15-008-015_G5-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-11-1
processed data file: HumanProstateTissue.txt


title: 15-008-015_IDC-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-11-2
processed data file: HumanProstateTissue.txt


title: 15-008-015_IDC-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-11-5
processed data file: HumanProstateTissue.txt


title: 15-008-015_G5-3

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-11-6
processed data file: HumanProstateTissue.txt


title: 15-008-015_G5-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-11-4
processed data file: HumanProstateTissue.txt


title: 11-250-14-04_B9-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-73-1
processed data file: HumanProstateTissue.txt


title: 15-008-004_B9-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-16-7
processed data file: HumanProstateTissue.txt


title: 15-008-004_G3-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-16-8
processed data file: HumanProstateTissue.txt


title: 11-250-14-04_G4-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-73-6
processed data file: HumanProstateTissue.txt


title: 15-008-004_G4-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-16-9
processed data file: HumanProstateTissue.txt


title: 11-250-14-04_G4-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-73-5
processed data file: HumanProstateTissue.txt


title: 11-250-14-04_IDC-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-73-4
processed data file: HumanProstateTissue.txt


title: 11-250-14-04_G3-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-72-3
processed data file: HumanProstateTissue.txt


title: 15-008-004_G3-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-16-6
processed data file: HumanProstateTissue.txt


title: 11-250-14-03_G4-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-134-3
processed data file: HumanProstateTissue.txt


title: 11-250-14-04_G3-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-72-2
processed data file: HumanProstateTissue.txt


title: 11-250-14-03_B9-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-134-1
processed data file: HumanProstateTissue.txt


title: 11-250-14-03_G3-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A2-134-2
processed data file: HumanProstateTissue.txt


title: occupancy_mitoxantrone_rep1_MTX_INPUT

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

description: INPUT control for +MTX

library_source: genomic

data_processing:
Reads were mapped to hg19 whole genome using Bowtie2 v2.2.5 with preset --very-sesitive parameters.
Genome alignment were converted to BED coordinate files using bedtools bamtobed (v2.26.0)
Peaks were called using MACS v1.4 using the following parameters: macs14 -t {treatment}.bam -c {input}.bam -n {name} -f BAM -g hs --bw=500 --keep-dup all --diag
Peaks were called using SISSRs using the folllowing parameters: sissrs -i {treatment}.bed -b {input}.bed -s 3107677273
Genome_build: hg19
Supplementary_files_format_and_content: BED format, ChIP-Seq Peaks

molecule: genomic DNA

source_name: No Antibody Mitoxantrone

growth_protocol: KG-1 cells were grown up to ~9*10^5/ml. 150 ml of  cell culture was centrifuged and resuspended in 2*25ml of the same medium they grew in two falcon tubes.

extract_protocol:
Cells were cross-linked with fresh 1% formaldehyde for 10 min. and then washed with PBS and protease inhibitor cocktail. Chromatin precipitation was performed using EZ-Magna ChIP A kit (Merck-Millipore). Chromatin was fragmented with Bandelin Sano Plus HD70 sonicator in 6 15s cycles at 20% power. For each antibody three IPs with chromatin from about 2 * 10^6 cells each and 5 μg anti-Top2a antibody (3116) or 4 μg of anti-Top2b antibody (3535) were performed in 4°C for 4.5 h. Three INPUT samples for each treatment was prepared from 2.5 ul of chromatin (5%). After IP samples were treated with proteinase K for 2 h in 63°C and for additional 10 min in 90°C ChIP DNA was purified on spin columns and eluted with 30 μl of TE buffer. Samples of DNA immunoprecipitated with the same antibody were pooled together and stored in -80°C.
Samples were used to construct Illumina paired-ends libraries at Source Bioscience using their protocol and sequenced on Illumina HiSeq2000 with 50 bp read-length.

treatment_protocol: Cells were treated with 0.5 μM mitoxantrone for 1 hour

tag: cell line

tag: drug exposure

value: 60 mins

tag: drug

value: Mitoxantrone

tag: antibody


title: occupancy_mitoxantrone_rep1_nodrug_beta

description: TOP2B experimental for -MTX

source_name: Topo-2B Antibody No Mitoxantrone

treatment_protocol: Cells were left untreated for 1 hour

value: 0 mins

value: Anti-Top2Beta (3535)


title: occupancy_mitoxantrone_rep1_nodrug_INPUT

description: INPUT control for -MTX

source_name: No Antibody No Mitoxantrone


title: occupancy_mitoxantrone_rep1_MTX_beta

description: TOP2B experimental for +MTX

source_name: Topo-2B Antibody Mitoxantrone


title: occupancy_mitoxantrone_rep1_nodrug_alpha

description: TOP2A experimental for -MTX

source_name: Topo-2A Antibody No Mitoxantrone

value: Anti-Top2Alpha (3116)


title: occupancy_mitoxantrone_rep1_MTX_alpha

description: TOP2A experimental for +MTX

source_name: Topo-2A Antibody Mitoxantrone


title: occupancy_etoposide_rep2_VP16_INPUT

description: INPUT control for +VP16

source_name: No Antibody Etoposide

treatment_protocol: Cells were treated with 100 μM etoposide for 1 hour

value: Etoposide


title: occupancy_etoposide_rep2_VP16_alpha

description: TOP2A experimental for +VP16

source_name: Topo-2A Antibody Etoposide


title: occupancy_etoposide_rep2_VP16_beta

description: TOP2B experimental for +VP16

source_name: Topo-2B Antibody Etoposide


title: occupancy_etoposide_rep2_nodrug_INPUT

description: INPUT control for -VP16

source_name: No Antibody No Etoposide

treatment_protocol: Cells were treated with methanol (vehicle) for 1 hour

value: Methanol (vehicle)


title: occupancy_etoposide_rep2_nodrug_beta

description: TOP2B experimental for -VP16

source_name: Topo-2B Antibody No Etoposide


title: occupancy_etoposide_rep2_nodrug_alpha

description: TOP2A experimental for -VP16

source_name: Topo-2A Antibody No Etoposide


title: occupancy_etoposide_rep1_VP16_INPUT

description: INPUT control for +VP16


title: occupancy_etoposide_rep1_VP16_beta

description: TOP2B experimental for +VP16


title: occupancy_etoposide_rep1_VP16_alpha

description: TOP2A experimental for +VP16


title: TX701 TRV:GhSP rep1

city: Denton

first: Roisin

middle: C

last: McGarry

state: TX

address: 1511 West Sycamore

department: Dept. of Biological Sciences, BioDiscovery Institute

institute: University of North Texas

data_processing:
Read quality was checked using FastQC.
Reads were aligned to the G. hirsutum JGI reference genome sequence using the Tuxedo suite pipeline (TopHat v2.0.9 with Bowtie v2.1.0).
Reads were aligned to the Gossypium hirsutum TM-1 genome CRI assembly v1_a1 reference genome (Yang et al., 2019) using the Tuxedo suite pipeline (TopHat v2.0.9 with Bowtie v2.1.0).
Gene FPKM (fragments per kilobase of exon model per million mapped fragments) values as normalized gene expression levels were calculated with Cufflinks v2.1.1.
Cuffdiff v2.1.1 was used to determine significant differences in gene expression between pair-wise comparisons using q ≤ 0.05 where q is the Benjamini-Hochberg correction to reduce false positives.
All of the above steps were conducted in the Discovery Environment at CyVerse.
Genome_build: G. hirsutum TX JGI assembly v.1.0 and annotation v.1.1 reference genome (Saski et al., 2017).
Genome_build: Gossypium hirsutum TM-1 genome CRI assembly v1_a1 reference genome (Yang et al., 2019).
Supplementary_files_format_and_content: Processed data file is a text file from the Cuffdiff output comparing FPKM values for each coding sequence across all treatments.

organism: Gossypium hirsutum

source_name: TX701 TRV:GhSP_shoot apex at 15 dpi

growth_protocol: Cotton was germinated in a 25°C growth chamber. At 4 days post-germination, seedlings remained uninoculated or the cotyledons were infiltrated with Agrobacterium tumefasciens GV3101 pMP90 harboring viral constructs. Following inoculations, plants were covered with a dome, incubated at room temperature overnight, and returned to the same 25°C growth chamber.

extract_protocol:
At 15 days post-inoculation, apices were excised from inoculated seedlings and uninoculated controls, fixed in acetone with vacuum-infiltration, and acetone changed twice before storing at 4°C. Acetone-dried apices were trimmed to 5 mm and expanding leaves were removed. Dried samples were frozen in liquid nitrogen, homogenized using a Retsch mill (Retsch GmbH, Haan, Germany), and RNA isolated by hot borate (Wan and Wilkins, 1994) followed by column clean-up (Zymo Research, Irvine, CA, USA).
2 µg of total RNA from uninoculated, dCLCrV:GhSFT-, and TRV:GhSP-infected DP61 and TX701 plants were used to prepare Illumina TruSeq Stranded mRNA libraries (Illumina, Inc., San Diego, CA, USA) as per the manufacturer's protocols, with three biological replicates per treatment per accession.  Libraries were sequenced on a HiSeq2000 (the University of Texas Southwestern Genomics Core), and >30 million 50 bp single-end reads were obtained per replicate.

treatment_protocol: Virus construction and inoculations were as described (McGarry et al., 2016).

tag: accession

value: wild photoperiodic Texas 701 (TX701)

tag: virus inoculation

tag: genotype/variation

value: silencing GhSP

value: Shoot apex (5 mm) harvested at 15 days post-inoculation


title: TX701 TRV:GhSP rep3


title: TX701 TRV:GhSP rep2


title: occupancy_etoposide_rep1_nodrug_alpha

description: TOP2A experimental for -VP16


title: occupancy_etoposide_rep1_nodrug_INPUT

description: INPUT control for -VP16


title: TX701 dCLCrV:GhSFT rep3

source_name: TX701 dCLCrV:GhSFT_shoot apex at 15 dpi

value: over-expressing GhSFT


title: occupancy_etoposide_rep1_nodrug_beta

description: TOP2B experimental for -VP16


title: TX701 uninoculated rep3

source_name: TX701 uninoculated_shoot apex at 15 dpi

value: uninoculated control

value: wild type


title: TX701 uninoculated rep2


title: TX701 dCLCrV:GhSFT rep2


title: TX701 dCLCrV:GhSFT rep1


title: DP61 dCLCrV:GhSFT rep3

source_name: DP61 dCLCrV:GhSFT_shoot apex at 15 dpi

value: domesticated day-neutral Delta Pine 61 (DP61)


title: DP61 TRV:GhSP rep2

source_name: DP61 TRV:GhSP_shoot apex at 15 dpi


title: TX701 uninoculated rep1


title: DP61 TRV:GhSP rep3


title: DP61 TRV:GhSP rep1


title: TSML rep3

data_processing:
Read quality was checked using Fastqc.
Reads were aligned to the G. hirsutum TX JGI assembly v.1.0 and annotation v.1.1 reference genome (Saski et al., 2017) using the Tuxedo suite pipeline (TopHat v2.0.9 with Bowtie v2.1.0).
Reads were aligned to the Gossypium hirsutum TM-1 genome CRI assembly v1_a1 reference genome (Yang et al., 2019) using the Tuxedo suite pipeline (TopHat v2.0.9 with Bowtie v2.1.0).
Gene FPKM (fragments per kilobase of exon model per million mapped fragments) values as normalized gene expression levels were calculated with Cufflinks v2.1.1.
Cuffdiff v2.1.1 was used to determine significant differences in gene expression between pair-wise comparisons using q ≤ 0.05 where q is the Benjamini-Hochberg correction to reduce false positives.
Genome_build: Gossypium hirsutum TX JGI assembly v.1.0 and annotation v.1.1 reference genome (Saski et al., 2017).
Genome_build: Gossypium hirsutum TM-1 genome CRI assembly v1_a1 reference genome (Yang et al., 2019).
Supplementary_files_format_and_content: Text file of Cuffdiff output comparing FPKM values for each coding sequence across all samples.

source_name: leaves flanking the TSM meristems

growth_protocol: Plants were grown under 16 h/8 h long (L)  or 10 h/14 h short (S) days.

extract_protocol:
Total RNA was isolated using hot borate (Wan and Wilkins, 1994) followed by column-purification (Zymo Research, Irvine, CA, USA), and mRNA amplified (one-round) with TargetAmp Amplification Kit (Epicenter, Madison, WI, USA).  Amplified mRNA was quantified by bioanalyzer (Agilent, Santa Clara, CA, USA), and 125 ng used to prepare Illumina TruSeq mRNA stranded libraries (Illumina, Inc., San Diego, CA, USA).
125 ng of amplified mRNA was used to prepare Illumina TruSeq mRNA stranded libraries (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: Apices from DP61 and TX701 cotton were harvested at different developmental stages. Apices were fixed in acetone, and meristems and flanking leaves were dissected with the aid of a SMZ 1500 stereomicroscope (Nikon, Melville, NY, USA). The developmental stages from which meristems were harvested included: (1) monopodial main stem from juvenile DP61; (2) monopodial main stem from juvenile TX701; (3) adult monopodial main stem from TX701 grown under non-inductive long days (plants were not flowering); (4) monopodial lateral branches from TX701 grown under non-inductive long days (plants were not flowering); (5) adult monopodial main stem from TX701 grown under inductive short days after the transition to reproductive growth (plants had flowering sympodial branches); and (6) adult sympodial fruiting branches from TX701 grown under inductive short days (flowering sympodial branches). Abbreviations are as follows: D = DP61; T = TX701; DJ/TJ = juvenile meristems; DJL/TJL = immature leaves flanking DJ/TJ meristems; TL20/TS20 = meristem from the branch at node 20 of TX701 plants grown under long (L) or short (S) days; TL20L/TS20L = immature leaves flanking the TL20/TS20 meristems; TLM/TSM = monopodial main stem meristem from mature TX701 plants grown under long (L) or short (S) days; TLML/TSML = immature leaves flanking the TLM/TSM meristems.

value: wild photoperiodic Texs 701 (TX701)

value: leaves


title: DP61 dCLCrV:GhSFT rep2


title: TSML rep1


title: TSM rep3

source_name: monopodial main stem meristem from mature TX701 plants grown under short days

tag: growth regime

value: 10 h/14h short (S) days

value: meristem


title: DP61 uninoculated rep2

source_name: DP61 uninoculated_shoot apex at 15 dpi


title: TSML rep2


title: DP61 uninoculated rep1


title: TS20L rep3

source_name: immature leaves flanking the TS20 meristems


title: TS20L rep2


title: TS20 rep3

source_name: meristem from the branch at node 20 of TX701 plants grown under short days


title: TS20L rep1


title: TLML rep1

source_name: immature leaves flanking the TLM meristems


title: DP61 dCLCrV:GhSFT rep1


title: DP61 uninoculated rep3


title: TLML rep3


title: TL20L rep3

source_name: immature leaves flanking the TL20 meristems


title: TS20 rep2


title: TLM rep2

source_name: monopodial main stem meristem from mature TX701 plants grown under long days

value: 16 h/8 h long (L) days


title: TL20L rep2


title: TLML rep2


title: TSM rep1


title: TLM rep1


title: TL20 rep3

source_name: meristem from the branch at node 20 of TX701 grown under long days


title: TL20L rep1


title: TLM rep3


title: TL20 rep2


title: TSM rep2


title: TJL rep3

source_name: immature leaves flanking the juvenile meristems from TX701 seedlings


title: TL20 rep1


title: TJ rep3

source_name: meristems from juvenile TX701 seedlings


title: TJL rep2


title: TJL rep1


title: Seq_4th

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

description:
RMM624
Sequential group, 2 weeks after 4th dose.
processed data file: Processed_Data_AllDb.csv

data_processing:
Illumina Casava software used for basecalling.
Raw sequences were processed using the pRESTO (version 0.5.13) toolkit. The paired-ends MiSeq data firstly assembled into a full-length Ig sequence. Follow by removing the low quality reads, annotating Ig isotype (IgD, IgM and IgG), masking the primer regions and yielding the final repertoire comprised of unique sequence with at least two representative reads. The IMGT/High was used to determine germline V(D)J assignments and functionality with the Change-O (version 0.4.6) tool.
Genome_build: IMGT/High
Supplementary_files_format_and_content: Processed_Data_AllDb.csv: Comma-separated text file includes each Ig sequence, VDJ calls and length, CDR/FWR, clone assignment, germline info, sample annotation.

organism: Mus musculus

source_name: C57BL/6J (B6) Mouse B cells

extract_protocol:
RNA was extracted from sorted cells by RNeasy Micro Kit (Qiagen) and the quality of RNA was assessed by Nanodrop and quantified by Qubit Fluorometer. RNA was reverse transcribed into cDNA by 10× SMARTScribe Reverse Transcriptase (Clontech). The cDNA was purified using a MinElute PCR Purification Kit (Qiagen).
The RNA-seq library preparation was executed by NEBNext Ultra II DNA Library Prep kit following manufacturer’s instruction.

tag: strain/background

tag: immunization strategy

value: Sequential

tag: time point

value: 2 weeks after 4th dose

tag: cell type

value: Dengue-specific B cells


title: DJ rep3

source_name: meristems from juvenile DP61 seedlings


title: Seq_2nd

description:
RMM621
Sequential group, 2 weeks after 2nd dose.
processed data file: Processed_Data_AllDb.csv

value: 2 weeks after 2nd dose


title: TJ rep2


title: Tetra_2nd

description:
RMM620
Tetravalent group, 2 weeks after 2nd dose.
processed data file: Processed_Data_AllDb.csv

value: Tetravalent


title: Seq_1st

description:
RMM619
Sequential group, 2 weeks after 1st dose.
processed data file: Processed_Data_AllDb.csv

value: 2 weeks after 1st dose


title: DJL rep3

source_name: immature leaves flanking the juvenile meristems from DP61 seedlings


title: TS20 rep1


title: DJL rep2


title: TJ rep1


title: TY52

city: Qingdao

first: Jing

last: Lv

state: China

address: No.11, Keyuan Jingsi Road, Laoshan District

country: China

institute: CAAS

data_processing:
Raw data (raw reads) in fastq format were cleaned by removing  adaptor sequences, reads containing poly-N sequences, and low-quality  reads.
The clean reads were mapped directly to the reference tobacco genome available from the 2017 genome website(ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/edwards_et_al_2017/annotation/).
The expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) was calculated based on the length of the gene and read counts mapped to the gene.
DEGs of both conditions were identified by the DEGSeq R package (v1.20.0).
The P-values were adjusted using the Benjamini and Hochberg method. A corrected P-value of 0.005 and a log2(fold change) of 1 were set as the threshold for significant differential expression.
Genome_build: Nicotiana_tabacum_Edwards2017_Scf.fa
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Nicotiana tabacum

source_name: axillary shoot

extract_protocol:
Total RNA was isolated from 100 mg of shoot tissue using a reagent kit (Invitrogen, Germany) following the manufacturer's instructions
The RNAeSeq library was constructed using a NEBNext® Ultra™ RNA Library Prep Kit (Illumina,NEB, USA) following the manufacturer's recommendations, and index cards were added to attribute sequences to different samples.

treatment_protocol: The flowering head and two leaves below the flag leaf were removed by topping

value: axillary shoot

tag: treatment

value: topped plants after 5 days


title: TY53


title: TY42

value: topped plants after 3 days


title: DJ rep1


title: Tetra_4th

description:
RMM625
Tetravalent group, 2 weeks after 4th dose.
processed data file: Processed_Data_AllDb.csv


title: TY12

value: topped plants after 1 day


title: DJ rep2


title: TY13


title: Seq_3rd

description:
RMM623
Sequential group, 2 weeks after 3rd dose.
processed data file: Processed_Data_AllDb.csv

value: 2 weeks after 3rd dose


title: Tetra_3rd

description:
RMM622
Tetravalent group, 2 weeks after 3rd dose.
processed data file: Processed_Data_AllDb.csv


title: NY2

value: control (untopped)


title: TY41


title: TY51


title: TY43


title: Lib7

city: Helsinki

first: Petri

last: Auvinen

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

description: small RNA

data_processing:
The reads in SOLiD colorspace format were mapped to human genome(GRC37) using SOLiD small RNA pipeline (RNA2MAP) with default parameters.
Genome_build: GRCh37, miRBase v17
Supplementary_files_format_and_content: csv files report miRNA normalized counts

source_name: CIN1/ condyloma

extract_protocol:
Total RNA from altogether four 20-micrometer sections from FFPE tissue samples were harvested using the RecoverAll total RNA isolation kit (Ambion)
Small RNA fragments of ~18–25nt were enriched from total RNA preparations (ca. 6 mg) from HPK IA cells, HPK II cells and ten tissue samples by flashPAGE system (Ambion). All of the enriched small RNA fractions (30-60 ng)  was used for preparing the libraries and subsequently ligated to adaptors in the SOLiDTM Total RNA-Seq kit (Ambion). Next, small RNAs were reverse transcribed into cDNA libraries, size selected using PAGE gel, and amplified with PCR primers introducing barcode sequences. The libraries were prepared for emulsion PCR (emPCR) according to SOLiD sequencing instructions followed by sequencing using the SOLiD 4 instrument (Life Technologies, Carlsbad, CA).

value: FFPE Tissue from HPV-infected cervical epithelium (CIN1/ condyloma )


title: DJL rep1

value: domesticated day-neutral Delta Pine 61 (DP61)

value: leaves


title: Lib6

description: small RNA

source_name: adenocarcinoma in situ

value: FFPE Tissue from HPV-infected cervical epithelium (adenocarcinoma in situ)


title: Lib5

description: small RNA

source_name: squamous cell carcinoma

value: FFPE Tissue from HPV-infected cervical epithelium (squamous cell carcinoma)


title: Lib3

description: small RNA

source_name: normal cervical squamous epithelium

value: FFPE Tissue from HPV-infected cervical epithelium (normal cervical squamous epithelium)


title: TY11


title: Lib12

description: small RNA

source_name: normal cervical columnar epithelium

value: FFPE Tissue from HPV-infected cervical epithelium (normal cervical columnar epithelium)


title: NY1


title: Lib1

description:
HPK IA and HPK II cells established by transfection of primary human foreskin keratinocytes with HPV 16, together with CaSki epidermoid cervical carcinoma cells and SiHa human cervical tumor cells were cultured in DMEM (Sigma-Aldrich Inc., Saint Louis, MO) supplemented with 10% fetal bovine serum and penicillin/streptomycin at 37°C and 5% CO2 in a humidified incubator.
small RNA

source_name: HPK IA

extract_protocol:
Total RNA from cultured cells was isolated using the mirVana RNA isolation kit (Ambion, Austin, TX).
Small RNA fragments of ~18–25nt were enriched from total RNA preparations (ca. 6 mg) from HPK IA cells, HPK II cells and ten tissue samples by flashPAGE system (Ambion). All of the enriched small RNA fractions (30-60 ng)  was used for preparing the libraries and subsequently ligated to adaptors in the SOLiDTM Total RNA-Seq kit (Ambion). Next, small RNAs were reverse transcribed into cDNA libraries, size selected using PAGE gel, and amplified with PCR primers introducing barcode sequences. The libraries were prepared for emulsion PCR (emPCR) according to SOLiD sequencing instructions followed by sequencing using the SOLiD 4 instrument (Life Technologies, Carlsbad, CA).

value: HPV 16 immortalized cell line HPK IA


title: Tetra_1st

description:
RMM618
Tetravalent group, 2 weeks after 1st dose.
processed data file: Processed_Data_AllDb.csv

value: Dengue-specific B cells


title: Lib8

description: small RNA

value: FFPE Tissue from HPV-infected cervical epithelium (CIN1/ condyloma)


title: NY3


title: Lib11

description: small RNA

value: FFPE Tissue from HPV-infected cervical epithelium (CIN2)


title: Lib4

description: small RNA


title: Lib9

description: small RNA


title: FGF3_Palbo..S88

first: Ofir

last: Cohen

state: Massachusetts

address: 415 Main St, Cambridge, MA 02142

department: Cancer Program

institute: Broad Institute

description:
FGFR.Rescue.seq.tpm.normalized.QC.csv
FGFR.Rescue.seq.counts.QC.csv

data_processing:
mRNA-seq libraries were sequenced on an Illumina NextSeq 500 sequencer, V2 75 cycle kits
Reads were mapped with STAR aligner (Dobin et al. 2013)
Genome_build: hg19 of the human genome and build 12 of the GENCODE human genome annotation

source_name: Breast Cancer

growth_protocol: T47D cells were infected de novo with lentivirus encoding FGFR1, FGFR2 mutants, FGF3  and controls  in the pLX307 plasmid.  Cells were plated in 96-well plates in for 48 hours.

extract_protocol:
Plates with cell lysates were thawed and purified with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics). The RNA captured beads were air-dried and processed immediately for RNA secondary structure denaturation (72˚C for three minutes) and cDNA synthesis. We performed SMART-Seq2 following the published protocol
Smart-seq 2

treatment_protocol: Cell were then treated with DMSO, fulvestrant (100 nM), palbociclib (1 uM), FIIN-3 (100 nM), and trametinib (500 nM) as single agent and in combinations for 24 hours

tag: lentivirus

tag: replicate

value: Palbo


title: FGF3_Palbo..S87


title: parental_Palbo..S97

value: parental


title: FGF3_Fulv.Palbo.FIIN3..S93


title: FGF3_Palbo.FIIN.3..S89


title: Lib10

description: small RNA


title: FGF3_control..S86

value: control


title: FGFR2_K660N_Fulv.Palbo.FGF2.FIIN.3..S82


title: FGFR2_K660N_Fulv.Palbo.FGF2.Tram..S84


title: FGF3_Fulv.Palbo.Tram..S95

value: Fulv+Palbo+Tram


title: FGFR2_K660N_Palbo.FGF2.FIIN.3..S77


title: Lib2

source_name: HPK II

value: HPV 16 immortalized cell line HPK II


title: FGF3_FIIN.3..S92


title: FGFR2_K660N_Palbo.FGF2..S76


title: parental_FIIN.3..S8


title: parental_Palbo..S98


title: FGFR2_K660N_Palbo..S74


title: FGF3_Fulv.Palbo.FIIN3..S94


title: parental_Palbo.FGF2..S99


title: FGFR2_N550K_Fulv.Palbo.FGF2.Tram..S71


title: FGFR2_K660N_Fulv.Palbo.FGF2.FIIN.3..S81


title: FGFR2_K660N_Palbo..S73


title: parental_Fulv.Palbo.FGF2.FIIN.3..S9


title: FGF3_control..S85


title: parental_FIIN.3..S7


title: FGFR2_N550K_FIIN.3..S68


title: FGFR2_N550K_Fulv.Palbo.FGF2.FIIN.3..S69


title: FGFR2_K660N_Fulv.Palbo.FGF2.Tram..S83


title: FGFR2_N550K_Palbo.FGF2.FIIN.3..S66


title: FGFR2_N550K_Palbo.FGF2.FIIN.3..S65


title: FGFR2_K660N_FIIN.3..S80


title: FGFR2_N550K_Palbo..S62


title: FGFR2_K660N_FIIN.3..S79


title: FGFR2_K660N_Palbo.FGF2..S75


title: FGFR2_M538I_Fulv.Palbo.FGF2.Tram..S60


title: FGFR2_N550K_Palbo..S61


title: FGFR2_M538I_FIIN.3..S56


title: FGFR2_N550K_Palbo.FGF2..S64


title: FGFR2_M538I_Fulv.Palbo.FGF2.Tram..S59


title: FGFR2_M538I_Fulv.Palbo.FGF2.FIIN.3..S58


title: FGFR2_M538I_Palbo.FGF2..S51


title: parental_Palbo.FGF2.FIIN.3..S5


title: FGFR2_N550K_FIIN.3..S67


title: FGFR2_M538I_FIIN.3..S55


title: FGFR2_M538I_Palbo.FGF2.FIIN.3..S54


title: FGFR2_M538I_Fulv.Palbo.FGF2.FIIN.3..S57


title: FGFR2_WT_Fulv.Palbo.FGF2.Tram..S48


title: FGFR2_WT_Palbo.FGF2.FIIN.3..S42


title: FGFR2_M538I_Palbo.FGF2..S52


title: FGFR2_N550K_Fulv.Palbo.FGF2.FIIN.3..S70


title: FGFR2_N550K_Fulv.Palbo.FGF2.Tram..S72


title: FGFR2_M538I_Palbo..S50


title: FGFR2_M538I_Palbo.FGF2.FIIN.3..S53


title: FGFR2_M538I_Palbo..S49


title: FGFR2_WT_Palbo.FGF2..S40


title: FGFR2_WT_Fulv.Palbo.FGF2.Tram..S47


title: FGFR2_WT_Palbo..S38


title: FGFR1_Fulv.Palbo.FGF2.Tram..S36


title: FGFR2_WT_FIIN.3..S44


title: FGFR2_WT_FIIN.3..S43


title: FGFR1_Fulv.Palbo.FGF2.FIIN.3..S34


title: FGFR2_WT_Fulv.Palbo.FGF2.FIIN.3..S45


title: FGFR2_WT_Palbo.FGF2.FIIN.3..S41


title: FGFR1_FIIN.3..S32


title: FGFR2_WT_Palbo.FGF2..S39


title: FGFR2_WT_Palbo..S37


title: FGFR1_Fulv.Palbo.FGF2.Tram..S35


title: FGFR1_FIIN.3..S31


title: FGFR1_Palbo.FGF2.FIIN.3..S30


title: parental_Palbo.FGF2..S3


title: FGFR1_Fulv.Palbo.FGF2.FIIN.3..S33


title: FGFR1_Palbo.FGF2.FIIN.3..S29


title: FGF3_Fulv.Palbo.Tram..S288


title: FGF3_Fulv.Palbo.FIIN3..S286


title: FGF3_FIIN.3..S284


title: FGF3_control..S277


title: FGFR2_K660N_Fulv.Palbo.FGF2.FIIN.3..S274


title: FGFR2_K660N_Palbo.FGF2.FIIN.3..S269


title: FGFR2_K660N_Palbo.FGF2.FIIN.3..S270


title: FGF3_Fulv.Palbo.Tram..S287


title: FGF3_Palbo.FIIN.3..S281


title: FGFR2_K660N_Palbo.FGF2..S267


title: FGFR2_K660N_Palbo..S266


title: FGFR2_K660N_Palbo.FGF2..S268


title: FGFR1_Palbo.FGF2..S28


title: FGF3_Palbo..S279


title: FGF3_Palbo..S280


title: FGF3_Fulv.Palbo.FIIN3..S285


title: FGF3_FIIN.3..S283


title: FGF3_control..S278


title: FGFR2_K660N_Fulv.Palbo.FGF2.Tram..S275


title: FGFR2_K660N_Fulv.Palbo.FGF2.FIIN.3..S273


title: FGF3_Palbo.FIIN.3..S282


title: FGFR2_N550K_Fulv.Palbo.FGF2.FIIN.3..S261


title: FGFR2_N550K_FIIN.3..S260


title: FGFR2_N550K_Fulv.Palbo.FGF2.Tram..S264


title: FGFR2_K660N_FIIN.3..S272


title: FGFR2_K660N_Fulv.Palbo.FGF2.Tram..S276


title: FGFR2_K660N_Palbo..S265


title: FGFR1_Palbo.FGF2..S27


title: FGFR2_N550K_Fulv.Palbo.FGF2.Tram..S263


title: FGFR2_N550K_Fulv.Palbo.FGF2.FIIN.3..S262


title: FGFR2_K660N_FIIN.3..S271


title: FGFR2_N550K_Palbo.FGF2.FIIN.3..S258


title: FGFR2_N550K_Palbo.FGF2..S255


title: FGFR2_M538I_Fulv.Palbo.FGF2.Tram..S252


title: FGFR2_N550K_Palbo..S253


title: FGFR1_Palbo..S25


title: FGFR2_M538I_FIIN.3..S248


title: FGFR2_N550K_Palbo..S254


title: FGFR2_N550K_Palbo.FGF2..S256


title: FGFR2_N550K_FIIN.3..S259


title: FGFR2_N550K_Palbo.FGF2.FIIN.3..S257


title: FGFR1_Palbo..S26


title: FGFR2_M538I_Fulv.Palbo.FGF2.Tram..S251


title: FGFR2_M538I_Fulv.Palbo.FGF2.FIIN.3..S250


title: FGFR2_M538I_Fulv.Palbo.FGF2.FIIN.3..S249


title: FGFR2_WT_Fulv.Palbo.FGF2.Tram..S240


title: FGFR2_M538I_FIIN.3..S247


title: FGFR2_WT_Palbo.FGF2..S231


title: FGFR2_WT_Palbo.FGF2.FIIN.3..S233


title: FGFR2_WT_FIIN.3..S235


title: FGFR2_WT_Fulv.Palbo.FGF2.FIIN.3..S237


title: FGFR2_WT_Palbo..S230


title: GFP_Fulv.Palbo.FGF2.Tram..S23

value: GFP


title: FGFR2_M538I_Palbo.FGF2..S244


title: FGFR2_M538I_Palbo.FGF2.FIIN.3..S246


title: FGFR2_M538I_Palbo.FGF2.FIIN.3..S245


title: FGFR2_WT_Palbo..S229


title: FGFR2_M538I_Palbo.FGF2..S243


title: FGFR1_Fulv.Palbo.FGF2.Tram..S228


title: FGFR2_WT_Fulv.Palbo.FGF2.Tram..S239


title: FGFR2_M538I_Palbo..S241


title: FGFR2_M538I_Palbo..S242


title: GFP_Fulv.Palbo.FGF2.Tram..S24


title: FGFR2_WT_Fulv.Palbo.FGF2.FIIN.3..S238


title: FGFR2_WT_FIIN.3..S236


title: FGFR1_FIIN.3..S224


title: FGFR1_Palbo.FGF2.FIIN.3..S221


title: FGFR1_FIIN.3..S223


title: FGFR2_WT_Palbo.FGF2..S232


title: FGFR2_WT_Palbo.FGF2.FIIN.3..S234


title: FGFR1_Palbo.FGF2.FIIN.3..S222


title: FGFR1_Fulv.Palbo.FGF2.FIIN.3..S226


title: FGFR1_Fulv.Palbo.FGF2.FIIN.3..S225


title: FGFR1_Palbo.FGF2..S220


title: FGFR1_Palbo..S218


title: FGFR1_Palbo.FGF2..S219


title: GFP_Fulv.Palbo.FGF2.Tram..S216


title: GFP_Fulv.Palbo.FGF2.FIIN.3..S213


title: GFP_Fulv.Palbo.FGF2.FIIN.3..S21


title: GFP_Fulv.Palbo.FGF2.Tram..S215


title: GFP_Palbo..S206


title: GFP_Palbo.FGF2..S208


title: parental_Fulv.Palbo.FGF2.Tram..S203


title: FGFR1_Palbo..S217


title: parental_Fulv.Palbo.FGF2.FIIN.3..S202


title: parental_Fulv.Palbo.FGF2.Tram..S204


title: GFP_Palbo..S205


title: GFP_FIIN.3..S211


title: GFP_FIIN.3..S212


title: GFP_Fulv.Palbo.FGF2.FIIN.3..S214


title: GFP_Palbo.FGF2.FIIN.3..S210


title: GFP_Palbo.FGF2.FIIN.3..S209


title: FGFR1_Fulv.Palbo.FGF2.Tram..S227


title: parental_Fulv.Palbo.FGF2.FIIN.3..S201


title: GFP_Palbo.FGF2..S207


title: parental_FIIN.3..S199


title: parental_Palbo.FGF2.FIIN.3..S197


title: parental_Palbo.FGF2..S195


title: parental_Palbo..S194


title: parental_FIIN.3..S200


title: GFP_FIIN.3..S20


title: parental_Palbo..S193


title: parental_Palbo.FGF2.FIIN.3..S198


title: parental_Palbo.FGF2..S196


title: FGF3_Fulv.Palbo.Tram..S191


title: FGF3_FIIN.3..S187


title: GFP_FIIN.3..S19


title: FGF3_Palbo.FIIN.3..S185


title: FGF3_Fulv.Palbo.FIIN3..S190


title: FGF3_Palbo.FIIN.3..S186


title: FGF3_Fulv.Palbo.FIIN3..S189


title: FGF3_Palbo..S183


title: FGF3_FIIN.3..S188


title: FGF3_control..S182


title: FGF3_Palbo..S184


title: FGFR2_K660N_Fulv.Palbo.FGF2.FIIN.3..S178


title: FGF3_control..S181


title: FGFR2_K660N_FIIN.3..S175


title: GFP_Palbo.FGF2.FIIN.3..S18


title: FGFR2_K660N_Palbo.FGF2.FIIN.3..S174


title: FGFR2_K660N_Fulv.Palbo.FGF2.Tram..S179


title: FGFR2_K660N_Fulv.Palbo.FGF2.FIIN.3..S177


title: FGFR2_K660N_FIIN.3..S176


title: FGFR2_K660N_Palbo.FGF2.FIIN.3..S173


title: FGFR2_K660N_Palbo.FGF2..S172


title: FGFR2_K660N_Palbo..S170


title: Liver_Fibroblasts_IFNg_RNA_3

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: SMART-seq sample of Liver GP38posCD31neg cells

data_processing:
Adapter trimming with trimmomatic (version 0.32) with settings: SLIDINGWINDOW:4:1 MAXINFO:16:0.40 MINLEN:30
Genome alignment using HISAT (2.1.0) with default parameters
Filtered reads to primary alignments (excluding secondary alignments) to exons (defined by Ensembl, genome-build GRCm38.p6 in the GENCODE Basic set)  using the GenomicAlignments package in R (3.2.3)
Counted reads in genes over all samples using the package GenomicAlignments in R (3.2.3)
Normalized to counts per million (CPM) and transformed to log2(CPM) using Limma Voom in R
Regressed out immune cell signatures using Limma removeBatchEffect in R
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of read counts (CSV), read counts of each gene for each sample
Supplementary_files_format_and_content: Matrix of log2(CPM) values (CSV), log2(CPM) after regressing out immune signatures of each gene

molecule: polyA RNA

source_name: Murine structural cells

growth_protocol: C57BL/6J mice, bred and maintained under specific pathogen free conditions at the Insti-tute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences in Vienna, Austria. 8 to 12 week old mice (males only) were used for the steady state characterization

extract_protocol:
Organs were digested with Accumax and structural cells isolated using FACS
For each individual assay, a maximum of 200 cells were sort-purified and deposited in 96-well plates con-taining 4 μl lysis buffer (1:20 solution of RNase Inhibitor (Clontech) in 0.2% v/v Triton X-100 (Sigma-Aldrich)), spun down, and immediately frozen at -80ºC. Reverse transcription and PCR were performed as described (Picelli et al., 2014). Library preparation was conducted on 1 ng of cDNA using the Nextera XT DNA Sample Preparation Kit (Illumina) followed by SPRI (Beckman Coulter) size selection. Sequencing was performed by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50-bp single-end configuration.

treatment_protocol: For the cytokine treatment experiments, mice were intravenously injected with 100 μg/kg of the following recombinant cytokines: IFN alpha, IFN beta, IL-3, IL-6, TGF-beta or TNF (all from Biolegend) and sacrificed 2 hours after cytokine injection.

tag: organ

value: Liver

tag: condition

value: IFNg

tag: age

value: 8 to 12 weeks

tag: strain


title: LargeIntestine_Epithelium_PBS_RNA_1

description: SMART-seq sample of LargeIntestine EPCAMpos cells

value: LargeIntestine

value: EPCAMpos

value: PBS


title: Liver_Fibroblasts_IFNg_RNA_1


title: Liver_Fibroblasts_IFNg_RNA_2


title: Lung_Fibroblasts_PBS_RNA_3

description: SMART-seq sample of Lung GP38posCD31neg cells

value: Lung


title: GFP_Palbo.FGF2.FIIN.3..S17

tag: cell line


title: LargeIntestine_Epithelium_TNF_RNA_1

value: TNF


title: LargeIntestine_Epithelium_IFNg_RNA_3


title: LargeIntestine_Epithelium_IFNg_RNA_1


title: FGFR2_N550K_Fulv.Palbo.FGF2.FIIN.3..S165


title: FGFR2_N550K_Fulv.Palbo.FGF2.Tram..S168


title: LargeIntestine_Epithelium_IFNg_RNA_2


title: FGFR2_N550K_FIIN.3..S163


title: FGFR2_K660N_Palbo..S169


title: FGFR2_N550K_Fulv.Palbo.FGF2.FIIN.3..S166


title: Liver_Epithelium_PBS_RNA_2

description: SMART-seq sample of Liver EPCAMpos cells


title: FGFR2_K660N_Palbo.FGF2..S171


title: LargeIntestine_Epithelium_PBS_RNA_2


title: FGFR2_N550K_Fulv.Palbo.FGF2.Tram..S167


title: LargeIntestine_Endothelium_IL6_RNA_1

description: SMART-seq sample of LargeIntestine GP38negCD31pos cells


title: Spleen_Epithelium_IL6_RNA_3

description: SMART-seq sample of Spleen EPCAMpos cells

value: Spleen


title: FGFR2_N550K_FIIN.3..S164


title: Spleen_Endothelium_TGFb_RNA_2

description: SMART-seq sample of Spleen GP38negCD31pos cells

value: TGFb


title: Spleen_Epithelium_IFNg_RNA_3


title: LargeIntestine_Epithelium_TNF_RNA_2


title: LargeIntestine_Fibroblasts_PBS_RNA_1

description: SMART-seq sample of LargeIntestine GP38posCD31neg cells


title: FGFR2_N550K_Palbo..S158


title: LargeIntestine_Endothelium_IL3_RNA_1


title: FGFR2_N550K_Palbo..S157


title: FGFR2_N550K_Palbo.FGF2.FIIN.3..S162


title: Spleen_Epithelium_TNF_RNA_1


title: LargeIntestine_Endothelium_TGFb_RNA_1


title: FGFR2_N550K_Palbo.FGF2.FIIN.3..S161


title: FGFR2_N550K_Palbo.FGF2..S160


title: Spleen_Fibroblasts_TGFb_RNA_2

description: SMART-seq sample of Spleen GP38posCD31neg cells


title: Spleen_Epithelium_TGFb_RNA_2


title: Lung_Epithelium_TNF_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells


title: GFP_Palbo.FGF2..S16


title: FGFR2_N550K_Palbo.FGF2..S159


title: Spleen_Fibroblasts_IFNg_RNA_1


title: FGFR2_M538I_Fulv.Palbo.FGF2.Tram..S156


title: FGFR2_M538I_Fulv.Palbo.FGF2.Tram..S155


title: FGFR2_M538I_FIIN.3..S152


title: FGFR2_M538I_Fulv.Palbo.FGF2.FIIN.3..S154


title: FGFR2_M538I_FIIN.3..S151


title: Lung_Epithelium_IL6_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells


title: Lung_Epithelium_PBS_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: FGFR2_M538I_Palbo..S146


title: FGFR2_M538I_Palbo..S145


title: FGFR2_M538I_Palbo.FGF2.FIIN.3..S150


title: GFP_Palbo.FGF2..S15


title: Spleen_Epithelium_PBS_RNA_2


title: Spleen_Fibroblasts_IL6_RNA_3


title: Spleen_Fibroblasts_IL3_RNA_3


title: Liver_Fibroblasts_PBS_RNA_2


title: FGFR2_WT_Fulv.Palbo.FGF2.FIIN.3..S142


title: FGFR2_M538I_Palbo.FGF2.FIIN.3..S149


title: FGFR2_M538I_Palbo.FGF2..S148


title: Lung_Fibroblasts_IL3_RNA_2


title: LargeIntestine_Fibroblasts_IL6_RNA_2


title: FGFR2_WT_FIIN.3..S140


title: FGFR2_WT_Fulv.Palbo.FGF2.Tram..S144


title: Spleen_Endothelium_TNF_RNA_3


title: LargeIntestine_Endothelium_TGFb_RNA_3


title: Liver_Endothelium_IL6_RNA_3

description: SMART-seq sample of Liver GP38negCD31pos cells


title: Spleen_Endothelium_IL6_RNA_3


title: FGFR2_WT_Palbo.FGF2.FIIN.3..S138


title: Lung_Endothelium_IL3_RNA_1

description: SMART-seq sample of Lung GP38negCD31pos cells


title: FGFR2_WT_Fulv.Palbo.FGF2.Tram..S143


title: FGFR2_WT_Palbo.FGF2.FIIN.3..S137


title: Liver_Endothelium_TNF_RNA_3


title: Spleen_Endothelium_TGFb_RNA_3


title: FGFR2_WT_Fulv.Palbo.FGF2.FIIN.3..S141


title: FGFR2_WT_Palbo.FGF2..S136


title: Lung_Epithelium_TNF_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: GFP_Palbo..S14


title: FGFR2_WT_FIIN.3..S139


title: Liver_Epithelium_TNF_RNA_3


title: FGFR2_WT_Palbo.FGF2..S135


title: LargeIntestine_Endothelium_IL3_RNA_2


title: Liver_Endothelium_IL6_RNA_1


title: Spleen_Epithelium_IFNg_RNA_2


title: Liver_Endothelium_PBS_RNA_1


title: FGFR2_WT_Palbo..S134


title: Lung_Fibroblasts_IFNa_RNA_1

value: IFNa


title: GFP_Palbo..S13

value: Palbo


title: FGFR1_Fulv.Palbo.FGF2.Tram..S132


title: FGFR1_Fulv.Palbo.FGF2.Tram..S131


title: Lung_Endothelium_TNF_RNA_3


title: FGFR2_WT_Palbo..S133


title: Lung_Endothelium_TGFb_RNA_3


title: FGFR1_Fulv.Palbo.FGF2.FIIN.3..S129


title: FGFR1_FIIN.3..S127


title: FGFR1_Fulv.Palbo.FGF2.FIIN.3..S130


title: FGFR1_Palbo.FGF2.FIIN.3..S126


title: Spleen_Endothelium_IFNa_RNA_1


title: Lung_Fibroblasts_TGFb_RNA_3


title: Liver_Endothelium_IL3_RNA_1


title: Liver_Endothelium_PBS_RNA_3


title: FGFR1_Palbo..S122


title: FGFR1_Palbo.FGF2..S124


title: FGFR1_Palbo.FGF2..S123


title: Liver_Epithelium_IFNg_RNA_1


title: FGFR1_Palbo..S121


title: FGFR1_Palbo.FGF2.FIIN.3..S125


title: Lung_Endothelium_IL3_RNA_3


title: Liver_Epithelium_IFNa_RNA_3


title: parental_Fulv.Palbo.FGF2.Tram..S12

value: parental


title: Liver_Epithelium_TGFb_RNA_2


title: GFP_Fulv.Palbo.FGF2.Tram..S119


title: Liver_Endothelium_PBS_RNA_2


title: Liver_Epithelium_IFNg_RNA_3


title: FGFR1_FIIN.3..S128


title: LargeIntestine_Endothelium_IFNa_RNA_2


title: Lung_Epithelium_TGFb_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: GFP_Fulv.Palbo.FGF2.FIIN.3..S117


title: GFP_FIIN.3..S116


title: Lung_Endothelium_IFNg_RNA_1


title: GFP_FIIN.3..S115


title: Lung_Epithelium_IFNg_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: GFP_Palbo.FGF2.FIIN.3..S114


title: LargeIntestine_Endothelium_TNF_RNA_1


title: GFP_Palbo.FGF2.FIIN.3..S113


title: Spleen_Endothelium_TNF_RNA_1


title: GFP_Palbo.FGF2..S111


title: Lung_Epithelium_TGFb_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: Spleen_Fibroblasts_PBS_RNA_2


title: GFP_Fulv.Palbo.FGF2.Tram..S120


title: parental_Fulv.Palbo.FGF2.Tram..S11


title: Spleen_Endothelium_IL3_RNA_2


title: parental_Fulv.Palbo.FGF2.Tram..S108


title: GFP_Fulv.Palbo.FGF2.FIIN.3..S118


title: GFP_Palbo..S109


title: parental_Fulv.Palbo.FGF2.Tram..S107


title: LargeIntestine_Endothelium_IFNg_RNA_1


title: LargeIntestine_Endothelium_IFNa_RNA_1


title: Liver_Fibroblasts_TNF_RNA_2


title: parental_Fulv.Palbo.FGF2.FIIN.3..S106


title: Spleen_Endothelium_IL3_RNA_1


title: Spleen_Endothelium_IFNg_RNA_3


title: Spleen_Endothelium_IFNa_RNA_2


title: GFP_Palbo..S110


title: Lung_Fibroblasts_TNF_RNA_2


title: parental_FIIN.3..S103


title: parental_Fulv.Palbo.FGF2.FIIN.3..S105


title: LargeIntestine_Fibroblasts_IFNa_RNA_3


title: LargeIntestine_Fibroblasts_IFNg_RNA_2


title: LargeIntestine_Epithelium_TGFb_RNA_2


title: Spleen_Epithelium_IL6_RNA_1


title: parental_Fulv.Palbo.FGF2.FIIN.3..S10


title: Spleen_Endothelium_IL6_RNA_2


title: Liver_Fibroblasts_IFNa_RNA_1


title: parental_Palbo..S1


title: Lung_Fibroblasts_IFNa_RNA_3


title: parental_Fulv.FGF2.Tram..S97


title: Liver_Endothelium_IL3_RNA_2


title: FGF3_Fulv.Palbo..S96

value: Fulv+Palbo


title: FGF3_Fulv.Tram..S94

value: Fulv+Tram


title: parental_FIIN.3..S104


title: FGF3_Fulv.Tram..S93


title: FGF3_Fulv.FIIN.3..S92


title: FGF3_Fulv.FIIN.3..S91


title: Liver_Endothelium_IFNg_RNA_3


title: Spleen_Epithelium_PBS_RNA_1


title: FGF3_Fulv.Palbo..S95


title: parental_Fulv.Palbo.FGF2..S99


title: Lung_Fibroblasts_IL6_RNA_3


title: parental_Palbo.FGF2.FIIN.3..S101


title: parental_FIIN.3.FGF2..S9


title: parental_Fulv.FGF2.Tram..S98


title: Liver_Fibroblasts_IL6_RNA_3


title: Spleen_Epithelium_IFNg_RNA_1


title: Spleen_Fibroblasts_TNF_RNA_1


title: Lung_Endothelium_TNF_RNA_1


title: FGF3_DMSO..S86

value: DMSO


title: Lung_Endothelium_IL6_RNA_1


title: Liver_Fibroblasts_TGFb_RNA_2


title: Liver_Endothelium_TNF_RNA_2


title: Lung_Endothelium_TGFb_RNA_1


title: Liver_Endothelium_IL3_RNA_3


title: LargeIntestine_Endothelium_PBS_RNA_2


title: FGF3_FIIN.3..S89


title: FGF3_FIIN.3..S90


title: FGFR2_K660N_FIIN.3.FGF2..S82


title: FGF3_Fulv..S88

value: Fulv


title: FGFR2_K660N_FIIN.3.FGF2..S81


title: parental_Fulv.FGF2..S8


title: Liver_Fibroblasts_IL3_RNA_2

value: Liver


title: FGFR2_K660N_Fulv.FGF2..S79


title: LargeIntestine_Fibroblasts_TNF_RNA_2


title: FGFR2_K660N_Fulv.FGF2.FIIN.3..S84


title: FGFR2_K660N_Fulv.FGF2.FIIN.3..S83


title: Liver_Endothelium_TGFb_RNA_2


title: FGFR2_K660N_FGF2..S77


title: Spleen_Epithelium_TNF_RNA_3


title: Lung_Fibroblasts_PBS_RNA_1


title: Spleen_Fibroblasts_IFNg_RNA_2

value: IFNg


title: Lung_Epithelium_PBS_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells

value: 8 to 12 weeks


title: Spleen_Epithelium_IL6_RNA_2


title: FGFR2_K660N_DMSO..S74


title: FGFR2_K660N_Fulv..S75


title: FGFR2_N550K_Fulv.FGF2.FIIN.3..S72


title: FGFR2_K660N_Fulv.FGF2..S80


title: FGFR2_N550K_FIIN.3.FGF2..S70


title: parental_Fulv.FGF2..S7


title: Liver_Fibroblasts_PBS_RNA_3


title: LargeIntestine_Endothelium_IL6_RNA_2

value: LargeIntestine


title: FGFR2_K660N_FGF2..S78


title: Lung_Fibroblasts_IL3_RNA_1


title: Lung_Endothelium_PBS_RNA_3


title: FGFR2_N550K_Fulv.FGF2..S67


title: FGFR2_K660N_Fulv..S76


title: Lung_Fibroblasts_IL6_RNA_1


title: FGFR2_N550K_FGF2..S66


title: FGFR2_N550K_FGF2..S65


title: FGFR2_N550K_Fulv..S63


title: LargeIntestine_Fibroblasts_TNF_RNA_1


title: Liver_Epithelium_PBS_RNA_3

value: EPCAMpos


title: FGFR2_K660N_DMSO..S73


title: Spleen_Fibroblasts_IL6_RNA_2


title: LargeIntestine_Epithelium_IFNa_RNA_1


title: FGFR2_M538I_Fulv.FGF2.FIIN.3..S60


title: FGFR2_N550K_Fulv.FGF2.FIIN.3..S71


title: FGFR2_M538I_Fulv.FGF2.FIIN.3..S59


title: LargeIntestine_Endothelium_TNF_RNA_2


title: Liver_Fibroblasts_IL6_RNA_1


title: Spleen_Epithelium_IL3_RNA_3


title: LargeIntestine_Fibroblasts_IFNa_RNA_2


title: Liver_Epithelium_IL3_RNA_3


title: Liver_Epithelium_TGFb_RNA_3


title: FGFR2_N550K_FIIN.3.FGF2..S69


title: FGFR2_N550K_Fulv.FGF2..S68


title: FGFR2_M538I_FGF2..S54


title: LargeIntestine_Fibroblasts_IFNa_RNA_1


title: Lung_Epithelium_IFNg_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: LargeIntestine_Fibroblasts_IFNg_RNA_1


title: LargeIntestine_Fibroblasts_IL6_RNA_1


title: LargeIntestine_Epithelium_IL3_RNA_1


title: Spleen_Epithelium_IFNa_RNA_3


title: Lung_Epithelium_IFNg_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells


title: FGFR2_N550K_Fulv..S64


title: FGFR2_M538I_Fulv..S52


title: Lung_Epithelium_TNF_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: Spleen_Fibroblasts_TNF_RNA_3


title: FGFR2_N550K_DMSO..S62


title: FGFR2_N550K_DMSO..S61


title: Lung_Endothelium_IL3_RNA_2


title: Spleen_Endothelium_PBS_RNA_2

value: PBS


title: Lung_Endothelium_IFNa_RNA_1

value: Lung


title: Spleen_Fibroblasts_IFNa_RNA_2


title: FGFR2_WT_Fulv.FGF2.FIIN.3..S47


title: parental_FGF2..S6


title: Lung_Epithelium_IL3_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: FGFR2_WT_FIIN.3.FGF2..S45


title: FGFR2_WT_Fulv.FGF2..S44


title: LargeIntestine_Epithelium_IL6_RNA_2


title: FGFR2_M538I_FIIN.3.FGF2..S57


title: Lung_Endothelium_PBS_RNA_1


title: FGFR2_M538I_FIIN.3.FGF2..S58


title: Liver_Endothelium_TGFb_RNA_3


title: FGFR2_M538I_Fulv.FGF2..S56


title: FGFR2_M538I_Fulv.FGF2..S55


title: Spleen_Epithelium_TNF_RNA_2

value: TNF


title: FGFR2_WT_Fulv.FGF2..S43


title: FGFR2_M538I_FGF2..S53


title: FGFR2_WT_FGF2..S42


title: Spleen_Endothelium_IL6_RNA_1

value: Spleen


title: Lung_Fibroblasts_TGFb_RNA_1

value: TGFb


title: FGFR2_WT_FGF2..S41


title: LargeIntestine_Epithelium_IFNa_RNA_2

value: IFNa


title: FGFR2_M538I_Fulv..S51


title: FGFR2_M538I_DMSO..S50


title: parental_FGF2..S5


title: Lung_Epithelium_IFNa_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: FGFR2_N550K_Fulv.FIIN.3..S384


title: LargeIntestine_Fibroblasts_TGFb_RNA_2


title: Spleen_Epithelium_IL3_RNA_2


title: FGFR2_WT_Fulv.FGF2.FIIN.3..S48


title: FGFR2_WT_FIIN.3.FGF2..S46


title: FGFR2_N550K_FIIN.3..S382


title: FGFR2_N550K_FIIN.3..S381


title: Lung_Endothelium_IFNg_RNA_3


title: FGFR2_N550K_Fulv.FIIN.3..S380


title: Spleen_Epithelium_IFNa_RNA_1


title: Spleen_Fibroblasts_TGFb_RNA_1


title: Liver_Epithelium_TGFb_RNA_1


title: Lung_Epithelium_IL6_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: LargeIntestine_Epithelium_IL3_RNA_2


title: Spleen_Epithelium_IFNa_RNA_2


title: FGFR2_N550K_FIIN.3..S378


title: Liver_Fibroblasts_IL3_RNA_3


title: Lung_Endothelium_TGFb_RNA_2


title: parental_Fulv..S4


title: FGFR2_WT_Fulv..S40


title: FGFR2_WT_Fulv..S39


title: Spleen_Endothelium_TGFb_RNA_1


title: Spleen_Fibroblasts_PBS_RNA_1


title: LargeIntestine_Fibroblasts_IL3_RNA_1


title: FGFR2_N550K_FIIN.3..S373


title: FGFR2_K660N_Fulv.Palbo.FGF2..S371


title: FGFR2_K660N_Fulv.Palbo.FGF2..S372


title: Lung_Epithelium_IFNa_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: FGFR2_WT_DMSO..S37


title: Lung_Epithelium_IFNa_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells


title: FGFR2_WT_DMSO..S38


title: FGFR2_N550K_Fulv.FIIN.3..S383


title: FGFR2_N550K_Fulv.FIIN.3..S379


title: FGFR2_N550K_FIIN.3..S377


title: FGFR2_K660N_Fulv.FGF2.Tram..S369


title: FGFR2_K660N_Fulv.FGF2.FIIN.3..S368


title: FGFR2_N550K_Fulv.FIIN.3..S376


title: FGFR2_K660N_FIIN.3.FGF2..S365


title: LargeIntestine_Epithelium_IFNa_RNA_3


title: Liver_Fibroblasts_IL3_RNA_1


title: FGFR2_N550K_FIIN.3..S374


title: FGFR2_N550K_Fulv.FIIN.3..S375


title: Lung_Epithelium_IL3_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells


title: Liver_Endothelium_TGFb_RNA_1


title: FGFR2_K660N_Fulv.FGF2.Tram..S370


title: Lung_Fibroblasts_IL3_RNA_3


title: Liver_Epithelium_TNF_RNA_1


title: Spleen_Endothelium_TNF_RNA_2


title: FGFR2_K660N_FGF2..S362


title: FGFR2_K660N_FGF2..S361


title: Liver_Fibroblasts_IFNa_RNA_3


title: LargeIntestine_Epithelium_IL6_RNA_1


title: Lung_Endothelium_IL6_RNA_2


title: FGFR2_K660N_Fulv.FGF2.FIIN.3..S367


title: FGFR2_K660N_FIIN.3.FGF2..S366


title: Spleen_Fibroblasts_IL3_RNA_1


title: Liver_Epithelium_IL6_RNA_2


title: FGFR2_K660N_Fulv.FGF2..S364


title: FGFR2_N550K_Fulv.Palbo.FGF2..S360


title: FGFR1_Fulv.FGF2.FIIN.3..S36


title: FGFR2_N550K_Fulv.FGF2.Tram..S357


title: Lung_Fibroblasts_IFNg_RNA_2


title: FGFR2_K660N_Fulv.FGF2..S363


title: Lung_Endothelium_IFNa_RNA_3


title: Liver_Fibroblasts_TGFb_RNA_1


title: FGFR2_N550K_FIIN.3.FGF2..S354


title: FGFR2_N550K_FIIN.3.FGF2..S353


title: Liver_Endothelium_IFNa_RNA_2


title: Spleen_Fibroblasts_IL3_RNA_2


title: Spleen_Epithelium_TGFb_RNA_1


title: FGFR2_N550K_Fulv.Palbo.FGF2..S359


title: FGFR2_N550K_Fulv.FGF2..S352


title: Spleen_Endothelium_IFNg_RNA_2


title: FGFR2_N550K_FGF2..S350


title: FGFR2_N550K_Fulv.FGF2..S351


title: FGFR2_N550K_Fulv.FGF2.Tram..S358


title: Lung_Fibroblasts_IFNg_RNA_1


title: FGFR2_N550K_FGF2..S349


title: LargeIntestine_Endothelium_IFNg_RNA_2


title: Liver_Epithelium_IFNa_RNA_1


title: Liver_Epithelium_IL6_RNA_3


title: FGFR2_M538I_Fulv.Palbo.FGF2..S348


title: Spleen_Epithelium_IL3_RNA_1


title: FGFR2_N550K_Fulv.FGF2.FIIN.3..S355


title: Lung_Endothelium_PBS_RNA_2


title: LargeIntestine_Fibroblasts_PBS_RNA_2


title: Liver_Epithelium_IL3_RNA_1


title: FGFR2_N550K_Fulv.FGF2.FIIN.3..S356


title: LargeIntestine_Epithelium_TGFb_RNA_3


title: LargeIntestine_Fibroblasts_IFNg_RNA_3


title: Lung_Fibroblasts_PBS_RNA_2


title: Lung_Fibroblasts_TNF_RNA_1


title: FGFR1_Fulv.FGF2.FIIN.3..S35


title: Liver_Epithelium_IFNg_RNA_2


title: FGFR2_M538I_FIIN.3.FGF2..S341


title: Liver_Fibroblasts_PBS_RNA_1


title: Lung_Endothelium_IFNg_RNA_2


title: FGFR2_M538I_Fulv.Palbo.FGF2..S347


title: FGFR2_M538I_Fulv.FGF2.Tram..S346


title: FGFR2_M538I_Fulv.FGF2..S340


title: FGFR2_M538I_Fulv.FGF2.Tram..S345


title: LargeIntestine_Endothelium_PBS_RNA_1


title: FGFR2_M538I_Fulv.FGF2.FIIN.3..S344


title: LargeIntestine_Fibroblasts_IL3_RNA_2


title: FGFR2_M538I_Fulv.FGF2.FIIN.3..S343


title: Spleen_Endothelium_IFNa_RNA_3


title: Liver_Epithelium_PBS_RNA_1


title: FGFR2_WT_Fulv.FGF2.Tram..S334


title: Spleen_Endothelium_IFNg_RNA_1


title: Liver_Endothelium_IL6_RNA_2


title: Liver_Epithelium_IL6_RNA_1


title: FGFR2_M538I_FIIN.3.FGF2..S342


title: FGFR2_WT_Fulv.FGF2.Tram..S333


title: FGFR2_WT_Fulv.FGF2.FIIN.3..S332


title: FGFR2_M538I_FGF2..S337


title: Lung_Epithelium_PBS_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: FGFR2_WT_Fulv.Palbo.FGF2..S336


title: FGFR2_WT_Fulv.FGF2.FIIN.3..S331


title: Liver_Endothelium_TNF_RNA_1


title: Lung_Fibroblasts_IFNg_RNA_3


title: FGFR2_M538I_FGF2..S338


title: Liver_Epithelium_IFNa_RNA_2


title: Spleen_Epithelium_PBS_RNA_3


title: Liver_Endothelium_IFNa_RNA_1


title: FGFR2_M538I_Fulv.FGF2..S339


title: FGFR2_WT_FIIN.3.FGF2..S329


title: FGFR2_WT_FIIN.3.FGF2..S330


title: FGFR1_FIIN.3.FGF2..S33


title: FGFR2_WT_Fulv.Palbo.FGF2..S335


title: FGFR1_FIIN.3.FGF2..S34


title: FGFR2_WT_Fulv.FGF2..S328


title: Liver_Endothelium_IFNg_RNA_2


title: FGFR2_WT_Fulv.FGF2..S327


title: LargeIntestine_Epithelium_TGFb_RNA_1


title: Lung_Epithelium_IL6_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: LargeIntestine_Endothelium_TGFb_RNA_2


title: FGFR1_Fulv.Palbo.FGF2..S324


title: Lung_Epithelium_TGFb_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells


title: Spleen_Fibroblasts_IL6_RNA_1


title: Spleen_Endothelium_IL3_RNA_3


title: FGFR1_Fulv.Palbo.FGF2..S323


title: Liver_Epithelium_TNF_RNA_2


title: FGFR2_WT_FGF2..S325


title: Lung_Endothelium_IFNa_RNA_2


title: FGFR1_Fulv.FGF2.Tram..S322


title: Liver_Fibroblasts_IFNa_RNA_2


title: Lung_Fibroblasts_IFNa_RNA_2


title: FGFR1_Fulv.FGF2..S32


title: FGFR1_Fulv.FGF2.FIIN.3..S319


title: FGFR1_Fulv.FGF2.FIIN.3..S320


title: FGFR1_Fulv.FGF2.Tram..S321


title: Liver_Endothelium_IFNa_RNA_3


title: Spleen_Endothelium_PBS_RNA_1


title: FGFR2_WT_FGF2..S326


title: FGFR1_FIIN.3.FGF2..S317


title: FGFR1_Fulv.FGF2..S316


title: Liver_Endothelium_IFNg_RNA_1


title: Lung_Endothelium_IL6_RNA_3


title: Lung_Fibroblasts_TGFb_RNA_2


title: FGFR1_FGF2..S314


title: LargeIntestine_Fibroblasts_TGFb_RNA_1


title: Lung_Endothelium_TNF_RNA_2


title: Liver_Fibroblasts_TNF_RNA_1


title: GFP_Fulv.Palbo.FGF2..S311

value: GFP


title: Spleen_Fibroblasts_TNF_RNA_2


title: FGFR1_Fulv.FGF2..S31


title: Spleen_Fibroblasts_IFNa_RNA_1


title: Liver_Epithelium_IL3_RNA_2


title: Lung_Epithelium_IL3_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: FGFR1_FIIN.3.FGF2..S318


title: GFP_Fulv.FGF2.Tram..S309


title: GFP_Fulv.FGF2.Tram..S310


title: GFP_Fulv.FGF2.FIIN.3..S308


title: Liver_Fibroblasts_TGFb_RNA_3


title: GFP_Fulv.FGF2.FIIN.3..S307


title: Liver_Fibroblasts_IL6_RNA_2


title: GFP_FIIN.3.FGF2..S306


title: FGFR1_Fulv.FGF2..S315


title: GFP_Fulv.FGF2..S304


title: Lung_Fibroblasts_IL6_RNA_2


title: GFP_FGF2..S302


title: Thymus_Fibroblasts_SteadyState_RNA_1

description: SMART-seq sample of Thymus GP38posCD31neg cells

treatment_protocol: For the infection experiments, mice were intravenously infected with 2x106 focus-forming units of lym-phocytic choriomeningitis virus (LCMV) strain Clone 1343 and sacrificed 8 days after infection.

value: Thymus


title: Thymus_Fibroblasts_SteadyState_RNA_2


title: Thymus_Fibroblasts_LCMVd8_RNA_2


title: GFP_FGF2..S301


title: FGFR1_FGF2..S313


title: GFP_Fulv.Palbo.FGF2..S312


title: Spleen_Epithelium_TGFb_RNA_3


title: Thymus_Endothelium_SteadyState_RNA_1

description: SMART-seq sample of Thymus GP38negCD31pos cells


title: Thymus_Endothelium_SteadyState_RNA_2


title: parental_Fulv..S3

value: parental


title: Thymus_Fibroblasts_LCMVd8_RNA_1


title: Thymus_Fibroblasts_SteadyState_RNA_3


title: Thymus_Endothelium_LCMVd8_RNA_1


title: Thymus_Endothelium_LCMVd8_RNA_2


title: parental_Fulv.Palbo.FGF2..S300


title: Thymus_Epithelium_SteadyState_RNA_2

description: SMART-seq sample of Thymus EPCAMpos cells


title: Thymus_Epithelium_SteadyState_RNA_1


title: GFP_Fulv.FGF2..S303


title: Thymus_Fibroblasts_LCMVd8_RNA_3


title: parental_Fulv.FGF2.Tram..S297


title: parental_Fulv.Palbo.FGF2..S299


title: Thymus_Epithelium_SteadyState_RNA_3


title: GFP_FIIN.3.FGF2..S305


title: Thymus_Epithelium_LCMVd8_RNA_2


title: parental_Fulv.FGF2.Tram..S298


title: parental_Fulv.FGF2.FIIN.3..S296


title: Thymus_Epithelium_LCMVd8_RNA_1


title: parental_FIIN.3.FGF2..S294


title: FGFR1_FGF2..S30


title: parental_Fulv.FGF2..S292


title: Spleen_Fibroblasts_SteadyState_RNA_2


title: Spleen_Fibroblasts_LCMVd8_RNA_3


title: Spleen_Fibroblasts_SteadyState_RNA_3


title: Spleen_Fibroblasts_SteadyState_RNA_1


title: parental_Fulv.FGF2..S291


title: Spleen_Fibroblasts_LCMVd8_RNA_2


title: FGFR1_FGF2..S29


title: parental_FGF2..S289


title: Spleen_Fibroblasts_LCMVd8_RNA_1


title: parental_FGF2..S290


title: FGF3_Fulv.Palbo..S288

value: Fulv+Palbo


title: Spleen_Endothelium_SteadyState_RNA_1


title: Spleen_Endothelium_SteadyState_RNA_3


title: FGF3_Fulv.Tram..S286

value: Fulv+Tram


title: Spleen_Endothelium_SteadyState_RNA_2


title: parental_Fulv.FGF2.FIIN.3..S295


title: FGF3_Fulv.FIIN.3..S283


title: FGF3_FIIN.3..S282


title: Spleen_Endothelium_LCMVd8_RNA_3


title: Spleen_Endothelium_LCMVd8_RNA_2


title: FGF3_Fulv.Tram..S285


title: Spleen_Epithelium_SteadyState_RNA_1


title: FGF3_Fulv.FIIN.3..S284


title: parental_FIIN.3.FGF2..S293


title: Spleen_Epithelium_SteadyState_RNA_2


title: Spleen_Epithelium_SteadyState_RNA_3


title: FGF3_Fulv..S280

value: Fulv


title: Spleen_Epithelium_LCMVd8_RNA_1


title: FGFR1_Fulv..S28


title: Spleen_Epithelium_LCMVd8_RNA_2


title: Spleen_Epithelium_LCMVd8_RNA_3


title: FGF3_Fulv..S279


title: FGF3_Fulv.Palbo..S287


title: SmallIntestine_Fibroblasts_SteadyState_RNA_3

description: SMART-seq sample of SmallIntestine GP38posCD31neg cells

value: SmallIntestine


title: SmallIntestine_Fibroblasts_SteadyState_RNA_1


title: FGF3_DMSO..S277

value: DMSO


title: Spleen_Endothelium_LCMVd8_RNA_1

value: 8 to 12 weeks


title: FGFR2_K660N_Fulv..S276


title: FGFR2_K660N_DMSO..S274


title: FGFR2_K660N_DMSO..S273


title: SmallIntestine_Fibroblasts_SteadyState_RNA_2


title: FGFR2_K660N_Fulv..S275


title: SmallIntestine_Endothelium_SteadyState_RNA_3

description: SMART-seq sample of SmallIntestine GP38negCD31pos cells


title: FGFR2_K660N_Fulv.Palbo.FGF2..S272

description:
FGFR.Rescue.seq.tpm.normalized.QC.csv
FGFR.Rescue.seq.counts.QC.csv


title: FGF3_FIIN.3..S281


title: SmallIntestine_Fibroblasts_LCMVd8_RNA_3


title: FGFR2_K660N_Fulv.Palbo.FGF2..S271


title: SmallIntestine_Endothelium_SteadyState_RNA_2


title: FGFR2_K660N_Fulv.FGF2.Tram..S270


title: FGFR1_Fulv..S27


title: SmallIntestine_Endothelium_LCMVd8_RNA_1


title: FGFR2_K660N_Fulv.FGF2.Tram..S269


title: SmallIntestine_Endothelium_LCMVd8_RNA_2


title: FGFR2_K660N_Fulv.FGF2.FIIN.3..S268


title: FGF3_DMSO..S278


title: FGFR2_K660N_Fulv.FGF2.FIIN.3..S267


title: FGFR2_K660N_FIIN.3.FGF2..S265


title: SmallIntestine_Endothelium_LCMVd8_RNA_3


title: SmallIntestine_Epithelium_SteadyState_RNA_1

description: SMART-seq sample of SmallIntestine EPCAMpos cells


title: SmallIntestine_Epithelium_SteadyState_RNA_3


title: SmallIntestine_Fibroblasts_LCMVd8_RNA_2


title: SmallIntestine_Epithelium_SteadyState_RNA_2


title: SmallIntestine_Fibroblasts_LCMVd8_RNA_1


title: FGFR2_N550K_Fulv..S264


title: SmallIntestine_Epithelium_LCMVd8_RNA_1


title: FGFR2_K660N_FIIN.3.FGF2..S266


title: FGFR2_N550K_DMSO..S262


title: SmallIntestine_Epithelium_LCMVd8_RNA_3


title: FGFR2_N550K_Fulv..S263


title: Skin_Fibroblasts_SteadyState_RNA_3

description: SMART-seq sample of Skin GP38posCD31neg cells

value: Skin


title: FGFR2_N550K_DMSO..S261


title: FGFR2_N550K_Fulv.Palbo.FGF2..S260


title: Skin_Fibroblasts_SteadyState_RNA_2


title: SmallIntestine_Epithelium_LCMVd8_RNA_2

value: EPCAMpos


title: FGFR1_DMSO..S26


title: FGFR2_N550K_Fulv.Palbo.FGF2..S259


title: Skin_Fibroblasts_SteadyState_RNA_1


title: Skin_Fibroblasts_LCMVd8_RNA_1


title: FGFR2_N550K_Fulv.FGF2.Tram..S258


title: Skin_Fibroblasts_LCMVd8_RNA_3


title: FGFR2_N550K_Fulv.FGF2.Tram..S257


title: Skin_Fibroblasts_LCMVd8_RNA_2


title: FGFR2_N550K_Fulv.FGF2.FIIN.3..S256


title: Skin_Endothelium_SteadyState_RNA_2

description: SMART-seq sample of Skin GP38negCD31pos cells


title: Skin_Endothelium_SteadyState_RNA_1


title: FGFR2_N550K_FIIN.3.FGF2..S253


title: FGFR2_M538I_Fulv..S252


title: SmallIntestine_Endothelium_SteadyState_RNA_1


title: FGFR2_N550K_FIIN.3.FGF2..S254


title: FGFR2_N550K_Fulv.FGF2.FIIN.3..S255


title: Skin_Endothelium_SteadyState_RNA_3


title: Skin_Endothelium_LCMVd8_RNA_2


title: FGFR2_M538I_Fulv..S251


title: Skin_Endothelium_LCMVd8_RNA_3


title: FGFR2_M538I_DMSO..S250


title: FGFR1_DMSO..S25


title: Skin_Epithelium_SteadyState_RNA_3

description: SMART-seq sample of Skin EPCAMpos cells


title: Skin_Endothelium_LCMVd8_RNA_1


title: FGFR2_M538I_Fulv.Palbo.FGF2..S248


title: Skin_Epithelium_SteadyState_RNA_1

description: SMART-seq sample of Skin EPCAMpos cells


title: Skin_Epithelium_SteadyState_RNA_2

description: SMART-seq sample of Skin EPCAMpos cells


title: FGFR2_M538I_Fulv.Palbo.FGF2..S247


title: FGFR2_M538I_DMSO..S249


title: FGFR2_M538I_Fulv.FGF2.Tram..S246


title: Skin_Epithelium_LCMVd8_RNA_1

description: SMART-seq sample of Skin EPCAMpos cells


title: Skin_Epithelium_LCMVd8_RNA_3

description: SMART-seq sample of Skin EPCAMpos cells


title: Skin_Epithelium_LCMVd8_RNA_2

description: SMART-seq sample of Skin EPCAMpos cells


title: FGFR2_M538I_Fulv.FGF2.FIIN.3..S244


title: FGFR2_M538I_Fulv.FGF2.Tram..S245


title: Lymphnode_Fibroblasts_SteadyState_RNA_3

description: SMART-seq sample of Lymphnode GP38posCD31neg cells

value: Lymphnode


title: FGFR2_M538I_Fulv.FGF2.FIIN.3..S243


title: Lymphnode_Fibroblasts_SteadyState_RNA_1


title: Lymphnode_Fibroblasts_SteadyState_RNA_2


title: FGFR2_M538I_FIIN.3.FGF2..S242


title: Lymphnode_Fibroblasts_LCMVd8_RNA_1


title: Lymphnode_Endothelium_SteadyState_RNA_1

description: SMART-seq sample of Lymphnode GP38negCD31pos cells


title: FGFR2_WT_Fulv..S240


title: FGFR2_WT_DMSO..S237


title: Lymphnode_Fibroblasts_LCMVd8_RNA_3


title: FGFR2_M538I_FIIN.3.FGF2..S241


title: FGFR2_WT_Fulv.Palbo.FGF2..S236


title: FGFR2_WT_Fulv..S239


title: Lymphnode_Endothelium_LCMVd8_RNA_2


title: Lymphnode_Endothelium_SteadyState_RNA_2


title: FGFR2_WT_Fulv.Palbo.FGF2..S235


title: Lymphnode_Endothelium_LCMVd8_RNA_1


title: FGFR2_WT_DMSO..S238


title: Lymphnode_Endothelium_SteadyState_RNA_3


title: Lymphnode_Epithelium_SteadyState_RNA_1

description: SMART-seq sample of Lymphnode EPCAMpos cells


title: FGFR2_WT_Fulv.FGF2.Tram..S234


title: Lymphnode_Fibroblasts_LCMVd8_RNA_2


title: FGFR2_WT_Fulv.FGF2.Tram..S233


title: FGFR2_WT_Fulv.FGF2.FIIN.3..S232


title: Lymphnode_Epithelium_SteadyState_RNA_2


title: FGFR2_WT_Fulv.FGF2.FIIN.3..S231


title: Lymphnode_Epithelium_LCMVd8_RNA_1


title: Lymphnode_Epithelium_SteadyState_RNA_3


title: GFP_Fulv.FGF2.FIIN.3..S23


title: FGFR2_WT_FIIN.3.FGF2..S229


title: Lymphnode_Epithelium_LCMVd8_RNA_2


title: FGFR1_Fulv..S228


title: Lung_Fibroblasts_SteadyState_RNA_1

description: SMART-seq sample of Lung GP38posCD31neg cells

value: Lung


title: FGFR1_Fulv..S227


title: Lung_Fibroblasts_SteadyState_RNA_3


title: Lung_Fibroblasts_LCMVd8_RNA_1


title: FGFR1_DMSO..S226


title: Lung_Fibroblasts_LCMVd8_RNA_3


title: Lung_Fibroblasts_SteadyState_RNA_2


title: FGFR1_Fulv.FGF2.Tram..S222


title: FGFR1_Fulv.Palbo.FGF2..S224


title: FGFR1_Fulv.FGF2.Tram..S221


title: Lung_Fibroblasts_LCMVd8_RNA_2


title: Lung_Endothelium_SteadyState_RNA_2


title: Lung_Endothelium_SteadyState_RNA_1


title: Lung_Endothelium_SteadyState_RNA_3


title: FGFR1_Fulv.FGF2.FIIN.3..S220


title: FGFR1_Fulv.FGF2.FIIN.3..S219


title: GFP_FIIN.3.FGF2..S22


title: Lung_Endothelium_LCMVd8_RNA_2


title: FGFR1_FIIN.3.FGF2..S217


title: FGFR1_FIIN.3.FGF2..S218


title: Lung_Endothelium_LCMVd8_RNA_3


title: Lung_Epithelium_SteadyState_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: Lung_Epithelium_SteadyState_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells


title: GFP_Fulv..S215


title: GFP_Fulv..S216


title: GFP_DMSO..S213


title: Lung_Epithelium_SteadyState_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: GFP_DMSO..S214


title: GFP_Fulv.Palbo.FGF2..S211


title: GFP_Fulv.Palbo.FGF2..S212


title: Lung_Epithelium_LCMVd8_RNA_2

description: SMART-seq sample of Lung EPCAMpos cells


title: Lung_Epithelium_LCMVd8_RNA_1

description: SMART-seq sample of Lung EPCAMpos cells


title: Lung_Epithelium_LCMVd8_RNA_3

description: SMART-seq sample of Lung EPCAMpos cells


title: GFP_Fulv.FGF2.Tram..S210


title: GFP_FIIN.3.FGF2..S21


title: Liver_Fibroblasts_SteadyState_RNA_3

description: SMART-seq sample of Liver GP38posCD31neg cells

value: Liver


title: Liver_Fibroblasts_SteadyState_RNA_2


title: Liver_Fibroblasts_SteadyState_RNA_1


title: GFP_Fulv.FGF2.FIIN.3..S208


title: GFP_Fulv.FGF2.Tram..S209


title: Liver_Fibroblasts_LCMVd8_RNA_2


title: Lung_Endothelium_LCMVd8_RNA_1


title: GFP_Fulv.FGF2.FIIN.3..S207


title: Liver_Endothelium_SteadyState_RNA_1


title: GFP_FIIN.3.FGF2..S206


title: Liver_Fibroblasts_LCMVd8_RNA_1


title: Liver_Endothelium_SteadyState_RNA_3


title: GFP_FIIN.3.FGF2..S205


title: parental_Fulv..S203


title: Liver_Fibroblasts_LCMVd8_RNA_3


title: parental_Fulv..S204


title: parental_DMSO..S202


title: parental_DMSO..S201


title: Liver_Endothelium_SteadyState_RNA_2


title: Liver_Endothelium_LCMVd8_RNA_1


title: Liver_Endothelium_LCMVd8_RNA_3


title: Liver_Endothelium_LCMVd8_RNA_2


title: parental_Fulv.Palbo.FGF2..S200


title: parental_DMSO..S2


title: GFP_Fulv.FGF2..S20


title: Liver_Epithelium_LCMVd8_RNA_1

description: SMART-seq sample of Liver EPCAMpos cells


title: parental_Fulv.FGF2.Tram..S198


title: parental_Fulv.Palbo.FGF2..S199


title: parental_Fulv.FGF2.Tram..S197


title: parental_Fulv.FGF2.FIIN.3..S196


title: Liver_Epithelium_SteadyState_RNA_2


title: Liver_Epithelium_SteadyState_RNA_1


title: Liver_Epithelium_LCMVd8_RNA_3


title: parental_FIIN.3.FGF2..S194


title: LargeIntestine_Fibroblasts_SteadyState_RNA_2

description: SMART-seq sample of LargeIntestine GP38posCD31neg cells

value: LargeIntestine


title: Liver_Epithelium_LCMVd8_RNA_2


title: LargeIntestine_Fibroblasts_SteadyState_RNA_1


title: LargeIntestine_Fibroblasts_SteadyState_RNA_3


title: FGF3_Fulv.Palbo..S192


title: LargeIntestine_Fibroblasts_LCMVd8_RNA_1


title: parental_FIIN.3.FGF2..S193


title: LargeIntestine_Fibroblasts_LCMVd8_RNA_3


title: parental_Fulv.FGF2.FIIN.3..S195


title: FGF3_Fulv.Tram..S190


title: FGF3_Fulv.Tram..S189


title: FGF3_Fulv.FIIN.3..S188


title: LargeIntestine_Fibroblasts_LCMVd8_RNA_2


title: GFP_Fulv.FGF2..S19


title: Liver_Epithelium_SteadyState_RNA_3


title: LargeIntestine_Endothelium_SteadyState_RNA_2

description: SMART-seq sample of LargeIntestine GP38negCD31pos cells


title: LargeIntestine_Endothelium_SteadyState_RNA_3


title: FGF3_Fulv.FIIN.3..S187


title: LargeIntestine_Endothelium_LCMVd8_RNA_1


title: LargeIntestine_Endothelium_LCMVd8_RNA_3


title: FGF3_FIIN.3..S186


title: FGF3_FIIN.3..S185


title: LargeIntestine_Epithelium_SteadyState_RNA_3

description: SMART-seq sample of LargeIntestine EPCAMpos cells


title: FGF3_DMSO..S182


title: FGFR2_K660N_Fulv.FGF2..S180


title: LargeIntestine_Epithelium_SteadyState_RNA_1


title: FGF3_DMSO..S181


title: FGF3_Fulv.Palbo..S191


title: LargeIntestine_Epithelium_LCMVd8_RNA_1


title: LargeIntestine_Epithelium_LCMVd8_RNA_2


title: FGFR2_K660N_FGF2..S178


title: Kidney_Fibroblasts_SteadyState_RNA_1

description: SMART-seq sample of Kidney GP38posCD31neg cells

value: Kidney


title: Kidney_Fibroblasts_SteadyState_RNA_3


title: GFP_FGF2..S18


title: LargeIntestine_Endothelium_SteadyState_RNA_1


title: FGFR2_K660N_FGF2..S177


title: Kidney_Fibroblasts_SteadyState_RNA_2


title: Kidney_Fibroblasts_LCMVd8_RNA_1


title: FGFR2_K660N_Fulv..S176


title: Kidney_Fibroblasts_LCMVd8_RNA_2


title: FGFR2_K660N_Fulv..S175


title: FGFR2_K660N_DMSO..S174


title: LargeIntestine_Endothelium_LCMVd8_RNA_2


title: Kidney_Endothelium_SteadyState_RNA_1

description: SMART-seq sample of Kidney GP38negCD31pos cells


title: FGF3_Fulv..S184


title: FGFR2_K660N_DMSO..S173


title: Kidney_Endothelium_SteadyState_RNA_2


title: LargeIntestine_Epithelium_SteadyState_RNA_2


title: Kidney_Endothelium_LCMVd8_RNA_1


title: Kidney_Endothelium_LCMVd8_RNA_3


title: GFP_FGF2..S17


title: Kidney_Endothelium_LCMVd8_RNA_2


title: FGFR2_K660N_Fulv.FGF2..S179


title: FGFR2_K660N_Fulv.FGF2.Tram..S169


title: Kidney_Epithelium_SteadyState_RNA_3

description: SMART-seq sample of Kidney EPCAMpos cells


title: Kidney_Epithelium_SteadyState_RNA_1


title: FGFR2_N550K_Fulv.FGF2..S167


title: Kidney_Epithelium_SteadyState_RNA_2


title: FGFR2_N550K_FGF2..S166


title: Kidney_Epithelium_LCMVd8_RNA_1


title: FGFR2_N550K_FGF2..S165


title: Kidney_Endothelium_SteadyState_RNA_3


title: FGFR2_N550K_Fulv..S164


title: Heart_Fibroblasts_SteadyState_RNA_3

description: SMART-seq sample of Heart GP38posCD31neg cells

value: Heart


title: FGFR2_K660N_Fulv.Palbo.FGF2..S172

description:
FGFR.Rescue.seq.tpm.normalized.QC.csv
FGFR.Rescue.seq.counts.QC.csv


title: Kidney_Epithelium_LCMVd8_RNA_3


title: FGFR2_K660N_Fulv.Palbo.FGF2..S171


title: FGFR2_N550K_Fulv..S163


title: Heart_Fibroblasts_SteadyState_RNA_2


title: FGFR2_N550K_DMSO..S162


title: FGFR2_N550K_Fulv.Palbo.FGF2..S160


title: FGFR2_N550K_DMSO..S161


title: Heart_Fibroblasts_SteadyState_RNA_1


title: Heart_Fibroblasts_LCMVd8_RNA_2


title: GFP_Fulv..S16

value: GFP


title: FGFR2_K660N_Fulv.FGF2.Tram..S170