title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_E01_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_E01_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_D09_cat)

status: Public on Dec 31 2018

type: SRA

city: Cambridge

first: Sanjay

last: Prakadan

state: MA

address: 77 Massachusetts Ave, E25-356

country: USA

institute: Massachusetts Institute of Technology

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_D09_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
TopHat was used to align data
RSEM was used to generate estimates of transcripts per million reads for each single cell
Regression analysis was done as described in manuscript
Genome_build: mm10
Supplementary_files_format_and_content: Transformed, filtered RSEM TPM Matrices:
[BH.tumor.rsem.full.txt.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH4.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH4.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH5.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH5.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH7.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH7.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH8.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH8.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH9.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH9.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y

molecule: total RNA

organism: Mus musculus

source_name: Transcriptome of single CTC captured by optofluidic device

extract_protocol:
Smart-seq 2
Illumina Nextera XT

tag: cell type

tag: time point

tag: treatment status

value: treated

tag: origin

value: CTC


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_D08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_D08_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt

value: single CTC captured by optofluidic device


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_D04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_D04_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_D07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_D07_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_D05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_D05_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_D03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_D03_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_C10_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_C10_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_C09_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_C09_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_C07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_C07_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_C08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_C08_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_C04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_C04_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_B09_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_B09_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_C05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_C05_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_B08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_B08_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_E04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_E04_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_B04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_B04_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_A09_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_A09_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_B07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_B07_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_B03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_B03_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_A11_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_A11_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_A07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_A07_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_F07_S451)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_F07_S451)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_A01_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_A01_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_A08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_A08_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_F08_S452)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_F08_S452)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_A04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_A04_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_F05_S449)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_F05_S449)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_F06_S450)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_F06_S450)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_F02_S446)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_F02_S446)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_F04_S448)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_F04_S448)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_F01_S445)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_F01_S445)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_C05_S413)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_C05_S413)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_C03_S411)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_C03_S411)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_C03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_C03_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_C02_S410)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_C02_S410)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_A09_S393)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_A09_S393)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_B02_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_B02_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH9_1_A05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_1_A05_cat)
BH9.rsem.regress.txt
BH9.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_A08_S392)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_A08_S392)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_A07_S391)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_A07_S391)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_A06_S390)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_A06_S390)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_A04_S388)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_A04_S388)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_E08_S440)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_E08_S440)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_A05_S389)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_A05_S389)
BH8.rsem.regress.txt
BH8.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_A02_S386)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_A02_S386)
BH8.rsem.regress.txt
BH8.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_G08_S368)
BH7.rsem.regress.txt
BH7.rsem.full.txt

value: untreated


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_G07_S367)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_G03_S363)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_G01_S361)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_G02_S362)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_F06_S354)
BH7.rsem.regress.txt
BH7.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_A03_S387)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_A03_S387)
BH8.rsem.regress.txt
BH8.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_G05_S365)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_F07_S355)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_F03_S351)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_F01_S349)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_F02_S350)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_F04_S352)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E06_S342)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E07_S343)
BH7.rsem.regress.txt
BH7.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH8_FvS_F_C01_S409)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH8_FvS_F_C01_S409)
BH8.rsem.regress.txt
BH8.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E08_S344)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E02_S338)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E05_S341)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E01_S337)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_D08_S332)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_D07_S331)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_D06_S330)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_D05_S329)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_D04_S328)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_F05_S353)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_D02_S326)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_D03_S327)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_C08_S320)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_D01_S325)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_C07_S319)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_C05_S317)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_C04_S316)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_C02_S314)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_B06_S306)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_B05_S305)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A04_S292)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A01_S289)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A03_S291)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A02_S290)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E06_S54)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E04_S52)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E03_S51)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_E02_S50)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_B08_S20)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A08_S8)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A02_S2)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A04_S4)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_H04_S88)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_C06_S318)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_C03_S315)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_H03_S87)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_H01_S85)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_G07_S79)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_B07_S307)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_G06_S78)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_B01_S301)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A07_S295)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_G04_S76)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_96h_A06_S294)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_G05_S77)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_G07_S175)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_G03_S75)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_G04_S172)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_G02_S170)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_F07_S163)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_G05_S173)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_F08_S164)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_F06_S162)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_G01_S169)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_F05_S161)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_F04_S160)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_G03_S171)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_H06_S90)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_G08_S80)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_F01_S157)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_E07_S151)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_72h_G02_S74)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_E06_S150)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_E04_S148)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_E05_S149)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_D08_S140)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_E02_S146)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_D01_S133)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_D06_S138)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_D05_S137)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_E01_S145)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_D03_S135)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_D04_S136)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_C07_S127)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_C05_S125)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_C01_S121)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_C02_S122)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_B07_S115)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_F03_S159)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_B05_S113)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_B04_S112)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_F02_S158)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_B01_S109)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_B03_S111)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_A06_S102)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_A08_S104)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_E03_S147)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_A05_S101)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_A02_S98)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_G05_S269)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_H05_S281)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_H01_S277)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_H06_S282)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_G04_S268)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_H07_S283)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_A03_S99)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_A04_S100)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_H08_S284)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_H02_S278)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_G06_S270)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_G03_S267)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_F07_S259)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_G01_S265)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_G02_S266)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_F04_S256)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_F03_S255)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_B06_S114)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_F05_S257)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_F06_S258)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_F01_S253)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_E06_S246)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_48h_C03_S123)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_F02_S254)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_E08_S248)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_E07_S247)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_G07_S271)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_G08_S272)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_E05_S245)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_E04_S244)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_E03_S243)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_D05_S233)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_D06_S234)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_E02_S242)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_E01_S241)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_D08_S236)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_D01_S229)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_H04_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_G06_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_H03_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_G05_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_D03_S231)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_96h_G01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_G03_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_96h_G02_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_96h_H01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_G01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_H09_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_G09_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_96h_C03_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_96h_A02_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_96h_E02_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_96h_H03_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_D04_S232)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_G08_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_H08_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_F09_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH7_0h_D07_S235)
BH7.rsem.regress.txt
BH7.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_F07_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_F06_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_E06_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_F04_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_E08_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_E05_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_E04_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_E03_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_E01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_D08_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_D05_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_D06_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_D04_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_C06_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_C03_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_D03_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_C07_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_B08_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_B05_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_A09_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_A06_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_C05_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_C08_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_A03_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_G11_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_H11_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_D09_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_E02_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_C09_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_E11_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_C10_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_C11_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_0h_G01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_B01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_B04_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_E10_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_C01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_D01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_0h_F01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_0h_B01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_F05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_F05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_0h_F02_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_B01_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_A12_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_G05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_G05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_72h_A05_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_F07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_F07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_F01_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_F01_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_D07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_D07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_D01_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_D01_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_C07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_C07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_C05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_C05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_B06_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_B06_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_C04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_C04_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


description:
CTCs from a murine model of small cell lung cancer (BH5_24_48h_E06_cat)
BH5.rsem.regress.txt
BH5.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_B04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_B04_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_B05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_B05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_B01_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_B01_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_F03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_F03_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_F02_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_F02_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_B03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_B03_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_A04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_A04_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_C07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_C07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_A08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_A08_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_D07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_D07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_E03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_E03_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_96h_E03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_96h_E03_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_C03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_C03_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_E06_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_E06_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_E02_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_E02_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_D08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_D08_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_A05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_A05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_A04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_A04_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_F02_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_F02_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_D05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_D05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_D01_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_D01_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_C05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_C05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_C01_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_C01_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_B08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_B08_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_72h_A07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_72h_A07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_H06_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_H06_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_G06_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_G06_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_G02_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_G02_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_B08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_B08_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_B05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_B05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_G07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_G07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_F02_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_F02_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_48h_E06_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_48h_E06_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_E02_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_E02_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_D08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_D08_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_E08_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_E08_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_E01_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_E01_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_C05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_C05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_D05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_D05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_B07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_B07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_B06_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_B06_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_C03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_C03_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_C06_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_C06_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_D04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_D04_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_F07_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_F07_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_B05_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_B05_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_A04_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_A04_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_A03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_A03_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_A02_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_A02_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: CTCs from a murine model of small cell lung cancer, treated with JQ1 (BH4_0h_D03_cat)

description:
CTCs from a murine model of small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH4_0h_D03_cat)
BH4.rsem.regress.txt
BH4.rsem.full.txt


title: E12_diencephalon

city: Farmington

first: James

middle: YH

last: Li

state: CT

address: 263 Farmington Ave

department: Genetics and Genome Sciences

institute: UCHC

data_processing:
The raw reads were processed to molecule counts using the CellRanger (version 1.3.0) pipeline with default setting
The raw UMI counts from Cell Ranger was processed by the Seurat R package (version 1.4.0.9).
The count matrix without filtering was uploaded.
Genome_build: mm10
Supplementary_files_format_and_content: raw UMI counts in csv format

source_name: Diencephalon

extract_protocol:
Brains of Gbx2creER/+ embryos were dissected in ice-cold phosphate buffered saline. Under a fluorescent dissecting microscope, the thalamus, which was labeled by enhanced green fluorescent protein expressed from the Gbx2 locus, together with surrounding tissues, were dissected. Tissues from four animals were pooled, cut into pieces smaller than 1 mm in dimension, and transferred to ice-cold MACS Tissue Storage Solution (Miltenyi Biotec, Somerville, MA).
For cell dissociation, the storage solution was exchanged with RPMI 1640 Medium (Thermo-Fisher); tissue was pelleted and digested with 500 µl of pre-warmed Accumax (Innovative Cell Technologies) in a 1.5-ml tube at 37˚C for 5-10 min. At the end of digestion, the tissue pieces were dissociated by gentle trituration with a wide-bore pipet tip. The cell suspension was added to a 100-µm cell strainer (Corning, Corning, NY), and it was collected and transferred to 1.5 ml of ice-cold Resuspension Buffer (Lebovitz L15 medium with 2% FBS, 25 mM HEPES, 2 mM EDTA).
After single cell suspension, the 10X Genomics Chromium Single Cell Kit v1 (PN-120233) was used to create libraries.

tag: strain

value: Outbred (CD1)

tag: tissue

value: Diencephalon

tag: age

value: Embryonic day 12.5

tag: genotype

value: wild type

tag: Sex

value: pooled males and females


title: HSC: Thpo 92

city: Southampton

first: Patrick

middle: S

last: Stumpf

state: Hampshire

address: University Road

department: Faculty of Medicine

country: United Kingdom

institute: University of Southampton

data_processing:
Raw reads were trimmed to a length of 75 bases using the FASTX-toolkit (v. 0.0.14) and to a minimum base-call quality score of 20, while retaining only reads of length >36 or a minimum overall percentage of high quality scores in 80% of bases.
Single-end reads were aligned to the Mus musculus genome (mm10) using Bowtie 2.
Differentially expressed genes (DEGs) between Thpo treatment groups were determined using Cufflinks v2.2.1 tool cuffdiff following the merging of alignment files using the tool cuffmerge and quantification using the tool cuffquant.
In order to reduce the number of spurious results due to low overall expression within either population, a minimum expression threshold was imposed to exclude DEGs that were absent in >50% of cells. Cells with less than 375 expressed genes were considered of low quality and removed.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed output files of cufflinks tool cuffdiff in original file format.

source_name: bone marrow

extract_protocol:
For single cell RNA sequencing, CD41+ CD150+CD48-LSK cells from control and Thpo-treated mice were sorted into SFEM medium, centrifuged and re-suspended at a cell concentration of 600 cells per µl. Single cells were loaded on to C1 Single-Cell Auto Prep IFC (5-10µm diameter) for messenger RNA sequence using the Fluidigm C1 system. Cell viability of the loaded cells was assessed using LIVE/DEAD Viability/cytotoxicity Kit (Life Technologies) and imaging.
Cells were lysed and whole transcriptome amplified cDNA was prepared using SMARTer Ultra Low RNA Kit for Fluidigm C1 system (Clonetech). Harvested cDNA samples were quantitated using Qubit. Illumina libraries were constructed using Illumina Nextera XT DNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol. Libraries were cleaned using Agencourt AMPure XP beads and pooled for sequencing.

treatment_protocol: For in vivo stimulation of Thpo signaling, recombinant human Thpo (PEG-rHuMGDF; donated from Kyowa Hakko Kirin Co., Ltd.) was administered intravenously daily. Mice were treated with either 100μg/kg (i.v.) PEG-rHuMGDF or human IgG Fc fragment (Jackson Immunoresearch).

value: WT

tag: treatment

value: Thpo 100μg/kg (i.v.)

value: bone marrow

value: hematopoietic stem cell (HSC)

tag: facs gate

value: Lin- Sca1+ cKit+ CD41+ CD150+ CD48-


title: HSC: Thpo 93


title: HSC: Thpo 89


title: HSC: Thpo 91


title: HSC: Thpo 95


title: HSC: Thpo 96


title: HSC: Thpo 88


title: HSC: Thpo 87


title: HSC: Thpo 86


title: HSC: Thpo 90


title: HSC: Thpo 94


title: HSC: Thpo 85


title: HSC: Thpo 84


title: HSC: Thpo 83


title: HSC: Thpo 82


title: HSC: Thpo 79


title: HSC: Thpo 81


title: HSC: Thpo 75


title: HSC: Thpo 74


title: HSC: Thpo 76


title: HSC: Thpo 78


title: HSC: Thpo 77


title: HSC: Thpo 73


title: HSC: Thpo 72


title: HSC: Thpo 71


title: HSC: Thpo 70


title: HSC: Thpo 68


title: HSC: Thpo 67


title: HSC: Thpo 80


title: HSC: Thpo 65


title: HSC: Thpo 63


title: HSC: Thpo 66


title: HSC: Thpo 55


title: HSC: Thpo 59


title: HSC: Thpo 58


title: HSC: Thpo 54


title: HSC: Thpo 62


title: HSC: Thpo 51


title: HSC: Thpo 64


title: HSC: Thpo 50


title: HSC: Thpo 57


title: HSC: Thpo 60


title: HSC: Thpo 53


title: HSC: Thpo 52


title: HSC: Thpo 49


title: HSC: Thpo 46


title: HSC: Thpo 45


title: HSC: Thpo 48


title: HSC: Thpo 47


title: HSC: Thpo 44


title: HSC: Thpo 69


title: HSC: Thpo 43


title: HSC: Thpo 42


title: HSC: Thpo 41


title: HSC: Thpo 61


title: HSC: Thpo 39


title: HSC: Thpo 56


title: HSC: Thpo 38


title: HSC: Thpo 37


title: HSC: Thpo 35


title: HSC: Thpo 36


title: HSC: Thpo 33


title: HSC: Thpo 32


title: HSC: Thpo 31


title: HSC: Thpo 28


title: HSC: Thpo 30


title: HSC: Thpo 27


title: HSC: Thpo 29


title: HSC: Thpo 25


title: HSC: Thpo 23


title: HSC: Thpo 40


title: HSC: Thpo 18


title: HSC: Thpo 21


title: HSC: Thpo 17


title: HSC: Thpo 22


title: HSC: Thpo 24


title: HSC: Thpo 20


title: HSC: Thpo 19


title: HSC: Thpo 16


title: HSC: Thpo 13


title: HSC: Thpo 15


title: HSC: Thpo 12


title: HSC: Thpo 10


title: HSC: Thpo 14


title: HSC: Thpo 11


title: HSC: Thpo 9


title: HSC: Thpo 34


title: HSC: Thpo 8


title: HSC: Thpo 26


title: HSC: Thpo 5


title: HSC: Thpo 6


title: HSC: Thpo 7


title: HSC: Thpo 4


title: HSC: Thpo 2


title: HSC: Control 94

value: control


title: HSC: Control 91


title: HSC: Thpo 1


title: HSC: Control 92


title: HSC: Control 93


title: HSC: Control 85


title: HSC: Control 87


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title: H1.1001200124

city: Stanford

first: Qingyun

state: CA

address: 299 Campus Drive

department: Neurobiology

institute: Stanford University

description: Single_myeloid_1922_cells_processed_data.csv

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
To filter out cells with low sequencing quality, three criteria, namely the number of total reads, the number of total detected genes and correlation coefficient between ERCC spike-ins input and corresponding read counts, were each evaluated based on the distributions of the data. The distribution of the total reads (in logarithmic scale) was fitted by a truncated Cauchy distribution, and data points in two tails of the estimated distribution were considered as outliers and eliminated. Fitting and elimination were then applied to the remaining data. This process was run iteratively until the estimated distribution became stable. The threshold was set to the value where the cumulative distribution function of the estimated distribution reaches 0.05. Similarly, cells with small numbers of detected genes, and poor correlation coefficients for ERCC (low sequencing accuracy) were dropped. After filtering, 1816 cells, out of 1922, were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing all 1922 cells and mapped gene counts (including counts for ERCC spike-ins)

source_name: Brain myeloid cell

extract_protocol:
For the E14.5 stage, whole brains were dissected out from timed embryos, and collected into 1ml PBS with 1% fetal bovine serum (added 10ul Ambion DNase I, 2ul RNase inhibitor) on ice. The sample was passed through a 26G needle 5-10 times to create single cell suspension. Cells were spun down (500g) at 4˚C for 5min, and suspended in 1ml PBS for FACS staining. Single live cells in the cKit-CD45+ gate were sorted into 96-well plates for library preparation.  For P7 and P60 stages, cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR), olfactory bulb (OB) and choroid plexus (CP) were dissected out. Tissues from the same region were pooled from multiple mice (3-8 depending on the ages and regions) into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia (myeloid cells) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+ (microglia) or CD45hiCD11b+ (myeloid cells) gate were sorted into 96-well plates for library preparation.
Sequencing libraries were prepared following the published Smart-seq2 protocol with the aid of liquid handling robotics (Picelli et al. Nature Protocols. 2014). Briefly, plates with sorted cells were thawed on ice and incubated at 72˚C for 3 min in order to anneal RNAs to the Oligo-dT30VN primer. After that, 6ul reverse transcription mixture (95U SMARTScribe™ Reverse Transcriptase (100U/ul, Clontech 639538), 10U RNase inhibitor (40U/ul), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Exiqon, Rnase free HPLC purified)) was added into each well, and RT was performed at 42˚C for 90 min, followed by 70˚C, 5 min. To amplify cDNA, 15ul PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/ul, New England BioLabs M0262S)) was added, and the following PCR program was used: (1) 37˚C 30 min; (2)95˚C 3 min; (3) 21 cycles of 98˚C 20 sec, 67˚C 15 sec, 72˚C 4 min; (4) 72˚C 5 min. Amplified cDNA samples were then purified with PCRClean DX beads (0.7:1 ratio, Aline C-1003-50), and resuspended in 20ul EB buffer. cDNA quality was examined with a Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000 bp) following the manufacture’s instruction. Samples with sufficient amount of cDNA content (>0.05ng/ul) and normal peaks on the quantification graphs were retained for library preparation. To make libraries, all samples were first diluted down to 0.15ng/ul (only if higher than 0.15ng/ul) in 384-well plates using Mantis Liquid Handler (Formulatrix) and Mosquito X1 (TTP Labtech) with customized scripts. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6ul (1.2ul Tagment enzyme mix, 0.4ul diluted cDNA) at 55˚C, 10 min. Neutralization buffer was added 0.4ul per well and incubated at room temperature for 5 min to stop the reaction. Then 0.8ul Illumina Nextera XT 384 Indexes (0.4ul each, 5uM from 4 sets of 96 indexes) and 1.2ul PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72˚C 3 min; (2) 95˚C 30 sec; (3) 10 cycles of 95˚C 10 sec, 55˚C 30 sec, 72˚C 1 min; (4) 72˚C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nextseq sequencing.

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