title: CD49f+ HSC Subset2 SLX.15682.i711_i503


title: CD49f+ HSC Subset2 SLX.15683.i707_i517

status: Public on Sep 14 2018

type: SRA

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing:
gsnap version 2015-09-29 was used to map reads onto the human reference genome GRCh38. Parameters used: -A sam -B 5 -t 24 -n 1 -Q -N 1. The result output would be in the format of sam files.
A python HTSeq (version 0.5.3p3) was used to generate read counts text files using the output of gsnap sam files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: HTSeq counts (.csv)

molecule: total RNA

organism: Homo sapiens

source_name: cord blood derived CD49f+ haematopoietic stem cells

extract_protocol:
CD49f+ HSCs were purified by FACS from CD34+ cord blood samples obtained as in Notta et al., Science 2011. Novel HSC subsets were defined as follows:  CD49f+ Subset2 cells (CD19- CD38- CD45RA- CD90+ CD49f+ CD34hi CLEC9Alo),  HSC/MPP Subset2 (CD19- CD38- CD45RA- CD34hi CLEC9Alo). Myelo-lymphoid restricted progenitors were defined as follows: LMPP (CD19- CD38- CD34+ CD45RA+ CD10-), MLP (CD19- CD38- CD34+ CD45RA+ CD10+). Single cells were directly sorted into lysis buffer according to the Smart-seq2 protocol published by Picelli et al., Nat. Protocol 2014.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: human cord blood

tag: passages

value: fresh

tag: cell type

value: single cell CD49f+ HSC Subset2


title: CD49f+ HSC Subset2 SLX.15682.i711_i502


title: CD49f+ HSC Subset2 SLX.15682.i712_i502


title: CD49f+ HSC Subset2 SLX.15682.i712_i517


title: CD49f+ HSC Subset2 SLX.15682.i710_i502


title: CD49f+ HSC Subset2 SLX.15682.i711_i508


title: CD49f+ HSC Subset2 SLX.15682.i710_i517


title: CD49f+ HSC Subset2 SLX.15682.i711_i506


title: CD49f+ HSC Subset2 SLX.15682.i711_i505


title: HSC Subset2 [Subset2_6]

data_processing:
RNA-seq reads were aligned to hg19 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts (.txt)

source_name: cord blood derived haematopoietic stem cells

extract_protocol:
CD49f+ HSCs were purified by FACS from CD34+ cord blood samples obtained as in Notta et al., Science 2011. Novel subsets were defined as follows: CD49f+ Subset1 (CD19- CD38- CD45RA- CD90+ CD49f+ CD34lo CLEC9Ahi); CD49f+ Subset2 cells (CD19- CD38- CD45RA- CD90+ CD49f+ CD34hi CLEC9Alo), HSC/MPP Subset1 (CD19- CD38- CD45RA- CD34lo CLEC9Ahi) and HSC/MPP Subset2 (CD19- CD38- CD45RA- CD34hi CLEC9Alo). Single cell or pools of 20 cells were directly sorted into lysis buffer according to the Smart-seq2 protocol published by Picelli et al., Nat. Protocol 2014.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 20 cells HSC


title: CD49f+ HSC Subset2 SLX.15682.i710_i503


title: HSC Subset1 [Subset1_6]


title: HSC Subset1 [Subset1_5]


title: HSC Subset2 [Subset2_8]


title: HSC Subset1 [Subset1_7]


title: HSC Subset1 [Subset1_3]


title: HSC Subset2 [Subset2_3]


title: HSC Subset1 [Subset1_8]


title: HSC Subset2 [Subset2_5]


title: HSC Subset2 [Subset2_2]


title: HSC Subset2 [Subset2_4]


title: HSC Subset2 [Subset2_7]


title: HSC Subset2 [Subset2_1]


title: CD49f+ HSC Subset2 SLX.15682.i711_i517


title: HSC Subset1 [Subset1_1]


title: CD49f+ HSC [49f_subset_187]

value: single cell CD49f+ HSC


title: HSC Subset1 [Subset1_2]


title: CD49f+ HSC [49f_subset_186]


title: CD49f+ HSC [49f_subset_185]


title: CD49f+ HSC [49f_subset_183]


title: CD49f+ HSC [49f_subset_184]


title: CD49f+ HSC [49f_subset_182]


title: CD49f+ HSC [49f_subset_181]


title: CD49f+ HSC [49f_subset_180]


title: CD49f+ HSC [49f_subset_179]


title: HSC Subset1 [Subset1_4]


title: CD49f+ HSC [49f_subset_178]


title: CD49f+ HSC [49f_subset_188]


title: CD49f+ HSC [49f_subset_177]


title: CD49f+ HSC [49f_subset_175]


title: CD49f+ HSC [49f_subset_164]


title: CD49f+ HSC [49f_subset_174]


title: CD49f+ HSC [49f_subset_173]


title: CD49f+ HSC [49f_subset_162]


title: CD49f+ HSC [49f_subset_169]


title: CD49f+ HSC [49f_subset_168]


title: CD49f+ HSC [49f_subset_170]


title: CD49f+ HSC [49f_subset_165]


title: CD49f+ HSC [49f_subset_167]


title: CD49f+ HSC [49f_subset_158]


title: CD49f+ HSC [49f_subset_172]


title: CD49f+ HSC [49f_subset_166]


title: CD49f+ HSC [49f_subset_163]


title: CD49f+ HSC [49f_subset_159]


title: CD49f+ HSC [49f_subset_154]


title: CD49f+ HSC [49f_subset_156]


title: CD49f+ HSC [49f_subset_176]


title: CD49f+ HSC [49f_subset_171]


title: CD49f+ HSC [49f_subset_157]


title: CD49f+ HSC [49f_subset_160]


title: CD49f+ HSC [49f_subset_155]


title: CD49f+ HSC [49f_subset_161]


title: CD49f+ HSC [49f_subset_153]


title: CD49f+ HSC [49f_subset_152]


title: HSC/MPP Subset2 SLX.15684.i708_i504

value: single haematopoietic stem cell


title: CD49f+ HSC [49f_subset_151]


title: CD49f+ HSC [49f_subset_150]


title: CD49f+ HSC [49f_subset_149]


title: CD49f+ HSC [49f_subset_147]


title: CD49f+ HSC [49f_subset_148]


title: CD49f+ HSC [49f_subset_145]


title: CD49f+ HSC [49f_subset_144]


title: CD49f+ HSC [49f_subset_142]


title: CD49f+ HSC [49f_subset_140]


title: CD49f+ HSC [49f_subset_143]


title: CD49f+ HSC [49f_subset_138]


title: CD49f+ HSC [49f_subset_139]


title: CD49f+ HSC [49f_subset_141]


title: CD49f+ HSC [49f_subset_137]


title: CD49f+ HSC [49f_subset_136]


title: CD49f+ HSC [49f_subset_132]


title: CD49f+ HSC [49f_subset_133]


title: CD49f+ HSC [49f_subset_129]


title: CD49f+ HSC [49f_subset_131]


title: CD49f+ HSC [49f_subset_134]


title: CD49f+ HSC [49f_subset_130]


title: CD49f+ HSC [49f_subset_126]


title: CD49f+ HSC [49f_subset_125]


title: CD49f+ HSC [49f_subset_127]


title: CD49f+ HSC [49f_subset_135]


title: CD49f+ HSC [49f_subset_124]


title: CD49f+ HSC [49f_subset_146]


title: CD49f+ HSC [49f_subset_123]


title: CD49f+ HSC [49f_subset_122]


title: CD49f+ HSC [49f_subset_121]


title: CD49f+ HSC [49f_subset_119]


title: CD49f+ HSC [49f_subset_117]


title: CD49f+ HSC [49f_subset_118]


title: CD49f+ HSC [49f_subset_116]


title: CD49f+ HSC [49f_subset_120]


title: CD49f+ HSC [49f_subset_113]


title: CD49f+ HSC [49f_subset_110]


title: CD49f+ HSC [49f_subset_128]


title: CD49f+ HSC [49f_subset_112]


title: CD49f+ HSC [49f_subset_108]


title: CD49f+ HSC [49f_subset_114]


title: CD49f+ HSC [49f_subset_115]


title: HSC/MPP Subset2 SLX.15684.i708_i503


title: CD49f+ HSC [49f_subset_111]


title: CD49f+ HSC [49f_subset_109]


title: CD49f+ HSC [49f_subset_105]


title: CD49f+ HSC [49f_subset_104]


title: CD49f+ HSC [49f_subset_100]


title: CD49f+ HSC [49f_subset_101]


title: CD49f+ HSC [49f_subset_099]


title: CD49f+ HSC [49f_subset_106]


title: CD49f+ HSC [49f_subset_097]


title: CD49f+ HSC [49f_subset_102]


title: CD49f+ HSC [49f_subset_107]


title: CD49f+ HSC [49f_subset_098]


title: CD49f+ HSC [49f_subset_095]


title: CD49f+ HSC [49f_subset_096]


title: CD49f+ HSC [49f_subset_094]


title: CD49f+ HSC [49f_subset_093]


title: CD49f+ HSC [49f_subset_089]


title: CD49f+ HSC [49f_subset_087]


title: CD49f+ HSC [49f_subset_083]


title: CD49f+ HSC [49f_subset_091]


title: CD49f+ HSC [49f_subset_092]


title: CD49f+ HSC [49f_subset_085]


title: CD49f+ HSC [49f_subset_088]


title: CD49f+ HSC [49f_subset_082]


title: CD49f+ HSC [49f_subset_090]


title: CD49f+ HSC [49f_subset_084]


title: CD49f+ HSC [49f_subset_086]


title: CD49f+ HSC [49f_subset_103]


title: CD49f+ HSC [49f_subset_079]


title: CD49f+ HSC [49f_subset_078]


title: CD49f+ HSC [49f_subset_080]


title: CD49f+ HSC [49f_subset_077]


title: CD49f+ HSC [49f_subset_076]


title: CD49f+ HSC [49f_subset_073]


title: CD49f+ HSC [49f_subset_081]


title: CD49f+ HSC [49f_subset_075]


title: CD49f+ HSC [49f_subset_071]


title: CD49f+ HSC [49f_subset_070]


title: CD49f+ HSC [49f_subset_074]


title: CD49f+ HSC [49f_subset_069]


title: CD49f+ HSC [49f_subset_065]


title: CD49f+ HSC [49f_subset_072]


title: CD49f+ HSC [49f_subset_068]


title: CD49f+ HSC [49f_subset_067]


title: CD49f+ HSC [49f_subset_066]


title: CD49f+ HSC [49f_subset_064]


title: CD49f+ HSC [49f_subset_062]


title: CD49f+ HSC [49f_subset_063]


title: CD49f+ HSC [49f_subset_059]


title: CD49f+ HSC [49f_subset_056]


title: CD49f+ HSC [49f_subset_050]


title: CD49f+ HSC [49f_subset_051]


title: CD49f+ HSC [49f_subset_058]


title: CD49f+ HSC [49f_subset_055]


title: CD49f+ HSC [49f_subset_057]


title: CD49f+ HSC [49f_subset_054]


title: CD49f+ HSC [49f_subset_053]


title: CD49f+ HSC [49f_subset_052]


title: CD49f+ HSC [49f_subset_060]


title: CD49f+ HSC [49f_subset_049]


title: CD49f+ HSC [49f_subset_046]


title: CD49f+ HSC [49f_subset_048]


title: CD49f+ HSC [49f_subset_045]


title: CD49f+ HSC [49f_subset_044]


title: CD49f+ HSC [49f_subset_047]


title: CD49f+ HSC [49f_subset_042]


title: CD49f+ HSC [49f_subset_043]


title: CD49f+ HSC [49f_subset_040]


title: CD49f+ HSC [49f_subset_039]


title: CD49f+ HSC [49f_subset_038]


title: CD49f+ HSC [49f_subset_037]


title: CD49f+ HSC [49f_subset_035]


title: CD49f+ HSC [49f_subset_036]


title: CD49f+ HSC [49f_subset_041]


title: CD49f+ HSC [49f_subset_034]


title: CD49f+ HSC [49f_subset_061]


title: CD49f+ HSC [49f_subset_032]


title: CD49f+ HSC [49f_subset_033]


title: CD49f+ HSC [49f_subset_031]


title: CD49f+ HSC [49f_subset_029]


title: CD49f+ HSC [49f_subset_028]


title: CD49f+ HSC [49f_subset_023]


title: CD49f+ HSC [49f_subset_025]


title: CD49f+ HSC [49f_subset_024]


title: CD49f+ HSC [49f_subset_026]


title: CD49f+ HSC [49f_subset_030]


title: CD49f+ HSC [49f_subset_022]


title: CD49f+ HSC [49f_subset_017]


title: CD49f+ HSC [49f_subset_013]


title: CD49f+ HSC [49f_subset_027]


title: CD49f+ HSC [49f_subset_016]


title: CD49f+ HSC [49f_subset_014]


title: CD49f+ HSC [49f_subset_020]


title: CD49f+ HSC [49f_subset_021]


title: CD49f+ HSC [49f_subset_010]


title: CD49f+ HSC [49f_subset_009]


title: CD49f+ HSC [49f_subset_007]


title: CD49f+ HSC [49f_subset_008]


title: CD49f+ HSC [49f_subset_005]


title: CD49f+ HSC [49f_subset_006]


title: CD49f+ HSC [49f_subset_012]


title: CD49f+ HSC [49f_subset_003]


title: CD49f+ HSC [49f_subset_002]


title: CD49f+ HSC [49f_subset_001]


title: CD49f+ HSC [49f_subset_018]


title: CD49f+ HSC [49f_subset_019]


title: CD49f+ HSC [49f_subset_011]


title: empty [empty_002]

tag: sample type

value: empty control


title: CD49f+ HSC [49f_subset_015]


title: CD49f+ HSC Subset1 [49f_subset1_093]

value: single cell CD49f+ HSC Subset1


title: empty [empty_003]


title: CD49f+ HSC Subset1 [49f_subset1_091]


title: CD49f+ HSC Subset1 [49f_subset1_087]


title: CD49f+ HSC Subset1 [49f_subset1_095]


title: CD49f+ HSC Subset1 [49f_subset1_090]


title: empty [empty_001]


title: CD49f+ HSC Subset1 [49f_subset1_089]


title: CD49f+ HSC Subset1 [49f_subset1_094]


title: CD49f+ HSC Subset1 [49f_subset1_085]


title: CD49f+ HSC Subset1 [49f_subset1_084]


title: CD49f+ HSC Subset1 [49f_subset1_088]


title: CD49f+ HSC Subset1 [49f_subset1_086]


title: CD49f+ HSC Subset1 [49f_subset1_083]


title: CD49f+ HSC Subset1 [49f_subset1_079]


title: CD49f+ HSC Subset1 [49f_subset1_082]


title: CD49f+ HSC Subset1 [49f_subset1_081]


title: CD49f+ HSC Subset1 [49f_subset1_078]


title: empty [empty_004]


title: CD49f+ HSC Subset1 [49f_subset1_077]


title: CD49f+ HSC Subset1 [49f_subset1_076]


title: CD49f+ HSC Subset1 [49f_subset1_075]


title: CD49f+ HSC Subset1 [49f_subset1_092]


title: CD49f+ HSC Subset1 [49f_subset1_074]


title: CD49f+ HSC Subset1 [49f_subset1_096]


title: CD49f+ HSC Subset1 [49f_subset1_073]


title: CD49f+ HSC Subset1 [49f_subset1_070]


title: CD49f+ HSC Subset1 [49f_subset1_071]


title: CD49f+ HSC Subset1 [49f_subset1_072]


title: CD49f+ HSC Subset1 [49f_subset1_067]


title: CD49f+ HSC Subset1 [49f_subset1_064]


title: CD49f+ HSC Subset1 [49f_subset1_068]


title: CD49f+ HSC Subset1 [49f_subset1_080]


title: CD49f+ HSC Subset1 [49f_subset1_066]


title: CD49f+ HSC Subset1 [49f_subset1_065]


title: CD49f+ HSC Subset1 [49f_subset1_063]


title: CD49f+ HSC Subset1 [49f_subset1_061]


title: CD49f+ HSC Subset1 [49f_subset1_062]


title: CD49f+ HSC Subset1 [49f_subset1_060]


title: CD49f+ HSC Subset1 [49f_subset1_055]


title: CD49f+ HSC Subset1 [49f_subset1_056]


title: CD49f+ HSC Subset1 [49f_subset1_057]


title: CD49f+ HSC Subset1 [49f_subset1_054]


title: CD49f+ HSC Subset1 [49f_subset1_053]


title: CD49f+ HSC Subset1 [49f_subset1_051]


title: CD49f+ HSC Subset1 [49f_subset1_050]


title: CD49f+ HSC Subset1 [49f_subset1_052]


title: CD49f+ HSC Subset1 [49f_subset1_048]


title: CD49f+ HSC Subset1 [49f_subset1_049]


title: CD49f+ HSC Subset1 [49f_subset1_069]


title: CD49f+ HSC Subset1 [49f_subset1_045]


title: CD49f+ HSC Subset1 [49f_subset1_047]


title: CD49f+ HSC Subset1 [49f_subset1_046]


title: CD49f+ HSC Subset1 [49f_subset1_058]


title: CD49f+ HSC Subset1 [49f_subset1_042]


title: CD49f+ HSC Subset1 [49f_subset1_044]


title: CD49f+ HSC Subset1 [49f_subset1_059]


title: CD49f+ HSC Subset1 [49f_subset1_035]


title: CD49f+ HSC Subset1 [49f_subset1_039]


title: CD49f+ HSC Subset1 [49f_subset1_034]


title: CD49f+ HSC Subset1 [49f_subset1_031]


title: CD49f+ HSC Subset1 [49f_subset1_040]


title: CD49f+ HSC Subset1 [49f_subset1_036]


title: CD49f+ HSC Subset1 [49f_subset1_038]


title: CD49f+ HSC Subset1 [49f_subset1_041]


title: CD49f+ HSC Subset1 [49f_subset1_032]


title: CD49f+ HSC Subset1 [49f_subset1_030]


title: CD49f+ HSC Subset1 [49f_subset1_043]


title: CD49f+ HSC Subset1 [49f_subset1_029]


title: CD49f+ HSC Subset1 [49f_subset1_028]


title: CD49f+ HSC Subset1 [49f_subset1_025]


title: CD49f+ HSC Subset1 [49f_subset1_024]


title: CD49f+ HSC Subset1 [49f_subset1_022]


title: CD49f+ HSC Subset1 [49f_subset1_023]


title: CD49f+ HSC Subset1 [49f_subset1_021]


title: CD49f+ HSC Subset1 [49f_subset1_020]


title: CD49f+ HSC Subset1 [49f_subset1_037]


title: CD49f+ HSC Subset1 [49f_subset1_019]


title: CD49f+ HSC Subset1 [49f_subset1_033]


title: CD49f+ HSC Subset1 [49f_subset1_018]


title: CD49f+ HSC Subset1 [49f_subset1_015]


title: CD49f+ HSC Subset1 [49f_subset1_014]


title: CD49f+ HSC Subset1 [49f_subset1_012]


title: CD49f+ HSC Subset1 [49f_subset1_007]


title: CD49f+ HSC Subset1 [49f_subset1_006]


title: CD49f+ HSC Subset1 [49f_subset1_010]


title: CD49f+ HSC Subset1 [49f_subset1_003]


title: CD49f+ HSC Subset1 [49f_subset1_017]


title: CD49f+ HSC Subset1 [49f_subset1_027]


title: CD49f+ HSC Subset1 [49f_subset1_008]


title: CD49f+ HSC Subset1 [49f_subset1_001]


title: CD49f+ HSC Subset1 [49f_subset1_009]


title: CD49f+ HSC Subset1 [49f_subset1_002]


title: CD49f+ HSC Subset1 [49f_subset1_026]


title: CD49f+ HSC Subset2 [49f_subset2_094]


title: CD49f+ HSC Subset2 [49f_subset2_095]


title: CD49f+ HSC Subset2 [49f_subset2_093]


title: CD49f+ HSC Subset2 [49f_subset2_092]


title: CD49f+ HSC Subset2 [49f_subset2_090]


title: CD49f+ HSC Subset1 [49f_subset1_016]


title: CD49f+ HSC Subset2 [49f_subset2_091]


title: CD49f+ HSC Subset2 [49f_subset2_089]


title: CD49f+ HSC Subset1 [49f_subset1_013]


title: CD49f+ HSC Subset2 [49f_subset2_087]


title: CD49f+ HSC Subset1 [49f_subset1_011]


title: CD49f+ HSC Subset1 [49f_subset1_004]


title: CD49f+ HSC Subset2 [49f_subset2_088]


title: CD49f+ HSC Subset2 [49f_subset2_085]


title: CD49f+ HSC Subset1 [49f_subset1_005]


title: CD49f+ HSC Subset2 [49f_subset2_086]


title: CD49f+ HSC Subset2 [49f_subset2_083]


title: CD49f+ HSC Subset2 [49f_subset2_078]


title: CD49f+ HSC Subset2 [49f_subset2_074]


title: CD49f+ HSC Subset2 [49f_subset2_082]


title: CD49f+ HSC [49f_subset_004]


title: CD49f+ HSC Subset2 [49f_subset2_096]


title: CD49f+ HSC Subset2 [49f_subset2_081]


title: CD49f+ HSC Subset2 [49f_subset2_077]


title: CD49f+ HSC Subset2 [49f_subset2_079]


title: CD49f+ HSC Subset2 [49f_subset2_080]


title: CD49f+ HSC Subset2 [49f_subset2_071]


title: CD49f+ HSC Subset2 [49f_subset2_073]


title: CD49f+ HSC Subset2 [49f_subset2_072]


title: CD49f+ HSC Subset2 [49f_subset2_070]


title: CD49f+ HSC Subset2 [49f_subset2_068]


title: CD49f+ HSC Subset2 [49f_subset2_065]


title: CD49f+ HSC Subset2 [49f_subset2_069]


title: CD49f+ HSC Subset2 [49f_subset2_064]


title: CD49f+ HSC Subset2 [49f_subset2_067]


title: CD49f+ HSC Subset2 [49f_subset2_061]


title: CD49f+ HSC Subset2 [49f_subset2_062]


title: CD49f+ HSC Subset2 [49f_subset2_063]


title: CD49f+ HSC Subset2 [49f_subset2_084]


title: CD49f+ HSC Subset2 [49f_subset2_066]


title: CD49f+ HSC Subset2 [49f_subset2_059]


title: CD49f+ HSC Subset2 [49f_subset2_058]


title: CD49f+ HSC Subset2 [49f_subset2_076]


title: CD49f+ HSC Subset2 [49f_subset2_060]


title: CD49f+ HSC Subset2 [49f_subset2_057]


title: CD49f+ HSC Subset2 [49f_subset2_075]


title: CD49f+ HSC Subset2 [49f_subset2_056]


title: CD49f+ HSC Subset2 [49f_subset2_053]


title: CD49f+ HSC Subset2 [49f_subset2_055]


title: CD49f+ HSC Subset2 [49f_subset2_052]


title: CD49f+ HSC Subset2 [49f_subset2_051]


title: CD49f+ HSC Subset2 [49f_subset2_049]


title: CD49f+ HSC Subset2 [49f_subset2_045]


title: CD49f+ HSC Subset2 [49f_subset2_048]


title: CD49f+ HSC Subset2 [49f_subset2_047]


title: CD49f+ HSC Subset2 [49f_subset2_046]


title: CD49f+ HSC Subset2 [49f_subset2_044]


title: CD49f+ HSC Subset2 [49f_subset2_050]


title: CD49f+ HSC Subset2 [49f_subset2_042]


title: CD49f+ HSC Subset2 [49f_subset2_041]


title: CD49f+ HSC Subset2 [49f_subset2_040]


title: CD49f+ HSC Subset2 [49f_subset2_043]


title: CD49f+ HSC Subset2 [49f_subset2_034]


title: CD49f+ HSC Subset2 [49f_subset2_036]


title: CD49f+ HSC Subset2 [49f_subset2_037]


title: CD49f+ HSC Subset2 [49f_subset2_032]


title: CD49f+ HSC Subset2 [49f_subset2_035]


title: CD49f+ HSC Subset2 [49f_subset2_033]


title: CD49f+ HSC Subset2 [49f_subset2_038]


title: CD49f+ HSC Subset2 [49f_subset2_030]


title: CD49f+ HSC Subset2 [49f_subset2_031]


title: CD49f+ HSC Subset2 [49f_subset2_039]


title: CD49f+ HSC Subset2 [49f_subset2_054]


title: CD49f+ HSC Subset2 [49f_subset2_029]


title: CD49f+ HSC Subset2 [49f_subset2_026]


title: CD49f+ HSC Subset2 [49f_subset2_022]


title: CD49f+ HSC Subset2 [49f_subset2_028]


title: CD49f+ HSC Subset2 [49f_subset2_027]


title: CD49f+ HSC Subset2 [49f_subset2_019]


title: CD49f+ HSC Subset2 [49f_subset2_024]


title: CD49f+ HSC Subset2 [49f_subset2_021]


title: CD49f+ HSC Subset2 [49f_subset2_025]


title: CD49f+ HSC Subset2 [49f_subset2_023]


title: CD49f+ HSC Subset2 [49f_subset2_020]


title: CD49f+ HSC Subset2 [49f_subset2_012]


title: CD49f+ HSC Subset2 [49f_subset2_018]


title: CD49f+ HSC Subset2 [49f_subset2_014]


title: CD49f+ HSC Subset2 [49f_subset2_013]


title: CD49f+ HSC Subset2 [49f_subset2_017]


title: CD49f+ HSC Subset2 [49f_subset2_016]


title: CD49f+ HSC Subset2 [49f_subset2_011]


title: CD49f+ HSC Subset2 [49f_subset2_004]


title: CD49f+ HSC Subset2 [49f_subset2_006]


title: CD49f+ HSC Subset2 [49f_subset2_009]


title: CD49f+ HSC Subset2 [49f_subset2_010]


title: CD49f+ HSC Subset2 [49f_subset2_008]


title: CD49f+ HSC Subset2 [49f_subset2_002]


title: CD49f+ HSC Subset2 [49f_subset2_007]


title: CD49f+ HSC Subset2 [49f_subset2_005]


title: CD49f+ HSC Subset2 [49f_subset2_003]


title: CD49f+ HSC Subset2 [49f_subset2_001]


title: HeyA8, pr-miR-34a rep1

status: Public on Sep 11 2018

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

country: USA

institute: Northwestern University Feinberg School of Medicine

description:
both34a.vs.controls.star.edgeR.txt
HeyA8.pre.miR.34a.5p.48hrs.rep1

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR aligner.
Raw read counts were calculated for each gene using HTSeq-counts.
In paired sets of cases and controls, the edgeR R package was used to normalize read counts and identify significantly differentially expressed genes, with associated statistics
Genome_build: hg38
Supplementary_files_format_and_content: .txt file with normalized read counts and differential expression statistics.

source_name: Derived from from Hey cells, ref: Buick, R. N., Pullano, R., and Trent, J. M. (1985). Comparative properties of five human ovarian adenocarcinoma cell lines. Cancer Res. 45: 3668 ? 3676.

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: HeyA8 cells were transfected with 10nM of indicated siRNA/premiRNA for 2 days.  Total RNA was harvested 2 days after transfection.

tag: cell line

value: Parental

value: Ovaries

tag: treatment/infection

value: Treated cells with 10nM premiR-34a (Ambion)  for 2 days

tag: genotype

value: WT


title: CD49f+ HSC Subset2 [49f_subset2_015]


title: HeyA8, pr-miR-34a rep2

description:
both34a.vs.controls.star.edgeR.txt
HeyA8.pre.miR.34a.5p.48hrs.rep2


title: HeyA8, si miR-34a Seed rep1

description:
both34a.vs.controls.star.edgeR.txt
HeyA8.si34a.seed.48hrs.rep1

value: Treated cells with 10nM si-miR-34a Seed (IDT) for 2 days


title: HeyA8, si miR-34a Seed rep2

description:
both34a.vs.controls.star.edgeR.txt
HeyA8.si34a.seed.48hrs.rep2


title: HeyA8, siNT2 (Dharmacon siRNA) rep1

description:
both34a.vs.controls.star.edgeR.txt
HeyA8.siNT2.48hrs.rep1

value: Treated cells with 10nM non-targeting siRNA # 2 (Dharmacon) for 2 days


title: HeyA8, premiR-NC rep2

description:
both34a.vs.controls.star.edgeR.txt
HeyA8.pre.miR.NC1.48hrs.rep2

value: Treated cells with 10nM non-targeting premiR-NC1( Ambion) for 2 days


title: HeyA8, premiR-NC rep1

description:
both34a.vs.controls.star.edgeR.txt
HeyA8.pre.miR.NC1.48hrs.rep1


title: HeyA8 treated with Etoposide rep 2

description:
sequenced everything above 140nts
3chemos.80hrs.HeyA8.xlsx

data_processing:
Sequenced reads were mapped to hg38 human genome using Tophat and bowtie2
raw counts were associated with genes by HTSeq
Differentially expressed genes estimated with R package EdgeR
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet of normalized counts for each gene in each sample and differential expression between treated samples and controls.  Counts for each sample were independentally normalized for each comparison.

source_name: Derived from from Hey cells, ref: Buick, R. N., Pullano, R., and Trent, J. M. (1985). Comparative properties of five human  ovarian adenocarcinoma cell lines. Cancer Res. 45: 3668 – 3676.

treatment_protocol: HeyA8 cells were plated at 50,000 cells per well in a 6-well plate; cells were treated with carboplatin (25 μg/ml), doxorubicin (50 ng/ml), or etoposide (500 nM) for 80 hours; total RNA was harvested after treatment.

value: Treated cells with Etoposide for 80 hours


title: HeyA8, siNT2 (Dharmacon siRNA) rep2

description:
both34a.vs.controls.star.edgeR.txt
HeyA8.siNT2.48hrs.rep2


title: HeyA8 treated with Carboplatinum rep 2

value: Treated cells with Carboplatinum for 80 hours


title: HeyA8 treated with Doxorubicin rep 2

value: Treated cells with Doxorubicin for 80 hours


title: HeyA8 treated with Etoposide rep 1


title: HeyA8 treated with Doxorubicin rep 1


title: HeyA8 treated with Carboplatinum rep 1


title: HeyA8 treated with water rep1

value: Treated cells with water for 80 hours


title: HeyA8 treated with water rep2


title: Derm5_Ctrl

status: Public on Aug 01 2018

city: Helsinki

first: Marja

middle: L

last: Mikkola

address: P.O.B 56 (Viikinkaari 5)

country: Finland

institute: University of Helsinki

data_processing:
Illumina bcl2fastq2 v2.17.1.14 for basecalling
The quality control of the rna-seq reads were done by AfterQC, Trimmomatic , MultiQC and FastQC
The ribosomal rRNA were filtered out using SortMeRna
The reads where aligned to mouse genome using STAR (1.5) with default parameters (GRCm38/mm10/Ensembl release 79 - March 2015) )
The gene expression was measured by counting the corresponding reads of the exons. This step was performed by htseq-count with parameters (-s reverse -t exon -i gene_id)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited gene expression count values of each samples

organism: Mus musculus

growth_protocol: 3h hanging drop culture

extract_protocol:
Qiagen micro kit was used according to manufacturer's instructions
TruSeq Stranded Total RNA with RiboZero

treatment_protocol: Fgf20 samples were incubated with 1 µg/ml rFGF20 and Ctrl samples were treated with BSA vehicle.

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissus

value: dermis

tag: treated with

value: BSA (control) for 3hrs


title: Derm5_Fgf20

value: FGF20 (1 µg/ml) for 3hrs


title: Derm8_Fgf20


title: Derm6_Ctrl


title: Derm8_Ctrl


title: Derm6_Fgf20


title: Derm9_Fgf20


title: Derm9_Ctrl


title: Derm7_Fgf20


title: Derm7_Ctrl


title: HeyA8 treated with DMSO rep 1

value: Treated cells with DMSO for 80 hours


title: HeyA8 treated with DMSO rep 2


title: WT_1

status: Public on Jun 14 2018

city: Madrid

first: Jose Luis

last: de la Pompa

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Reads were pre-processed with a pipeline that used cutadapt v1.6 to remove Illumina adaptors and FastQC to perform quality controls after each step.
Processed reads were mapped on the transcriptome and quantified using RSEM v1.2.3.
Genome_build: Ensembl genebuild 76 (mouse assembly GRCm38)
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and batch-corrected, TMM-Normalized counts per million for each sample.

molecule: polyA RNA

source_name: Heart

growth_protocol: Experiments were conducted with WT and Bmp2 GOF mouse embryos at stage E9.5

extract_protocol:
Hearts were collected at E9.5 from WT and Bmp2GOF;Nkx2.5-Cre embryos. RNA was isolated with the Arcturus Pipopure RNA isolation kit (Applied Biosystems).
Libraries were prepared using the NEBNext Ultra RNA Library preparation kit (New England Biolabs)

value: heart


title: GOF_4


title: GOF_2


title: WT_4


title: WT_3


title: WT_2


title: GOF_1


title: GOF_3


title: ABCB5-enriched metastatic melanoma patient blood sample (D07_BB_A)

status: Public on May 11 2018

type: RNA

city: perth

first: Carlos

middle: A

last: Aya-bonilla

state: WA

address: 32 kinship street

country: Australia

institute: Telethon Kids Institute

hyb_protocol: Hybridization according to the Affymetrix® GeneChip® genome 2.0 ST array protocol (Affymetrix, US), performed at Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney, Australia).

scan_protocol: According to standard Affymetrix protocol.

data_processing:
Data was analysed using Partek Genomics Suite software version 6.5 (Partek Inc., US)
The differentially expressed gene list was generated with ANOVA p<0.05 and fold difference 2 vs respective controls in either cell type (MSCP or ABCB5 CTCs). Unsupervised two-dimensional hierarchical clustering with complete linkage was performed on differentially expressed genes using Spearman’s correlation as similarity matrix.

label: biotin

label_protocol: Labeling according to the Affymetrix® GeneChip® genome 2.0 ST array protocol (Affymetrix, US), performed at Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney, Australia).

extract_protocol:
After enrichment, RNA was isolated using RNeasy Mini Kit (Qiagen) and stored at -80oC until further use. Detailed methodology in Reid et al., 2015 (PMID 25523300)
RNA quantity and quality was analysed with a Pico Bioanalyzer chip (Agilent Technologies, US). Samples were prepared using the NuGEN Pico WTA kit (NuGEN Technologies, US).

treatment_protocol: CTCs were enriched as it follows. Whole blood from healthy donors or patients was treated with red blood cell lysing buffer and remaining cells were incubated  with immunomagnetic beads coated with antibodies against MCSP (clone 9.2.27, BD Biosciences) or ABCB5 (clone 3C2-1D12, kindly provided by Prof. Markus H Frank). Detailed methodology is described by Freeman et al., 2012 (PMID 22978632).

tag: disease state

value: metastatic melanoma

tag: gender

value: Male

tag: age

value: 60 yo

value: BRAF V600E mutation in tumor of patient

value: blood

value: ABCB5-enriched CTCs


title: ABCB5-enriched metastatic melanoma patient blood sample (A07_SW_A)

value: Female

value: 57 yo

value: BRAF WT mutation in tumor of patient


title: ABCB5-enriched Healthy Donor blood sample (G09_PR_A)

value: control

value: 59 yo


title: MCSP-enriched metastatic melanoma patient blood sample (C05_MH_M)

value: 53 yo

value: MCSP-enriched CTCs


title: ABCB5-enriched Healthy Donor blood sample (E09_DM_A)


title: MCSP-enriched Healthy Donor blood sample (F07_RA_M)

value: 54 yo


title: MCSP-enriched Healthy Donor blood sample (G07_DM_M)


title: ABCB5-enriched Healthy Donor blood sample (F09_AC_A)


title: MCSP-enriched Healthy Donor blood sample (B09_JH_M)

value: 58 yo


title: ABCB5-enriched Healthy Donor blood sample (D09_RA_A)


title: MCSP-enriched metastatic melanoma patient blood sample (F05_NP_M)

value: 81 yo

value: BRAF V600E and S607F mutation in tumor of patient


title: ABCB5-enriched metastatic melanoma patient blood sample (H05_JT_A)

value: metastatic melanoma

value: 61 yo

value: BRAF V600K mutation in tumor of patient


title: MCSP-enriched Healthy Donor blood sample (A09_PR_M)

value: Male


title: ABCB5-enriched metastatic melanoma patient blood sample (G05_MH_A)

value: BRAF V600E mutation in tumor of patient

value: blood


title: ABCB5-enriched metastatic melanoma patient blood sample (B07_GO_A)

value: ABCB5-enriched CTCs


title: ABCB5-enriched metastatic melanoma patient blood sample (C07_DeR_A)

value: Female

value: 62 yo


title: MCSP-enriched metastatic melanoma patient blood sample (E05_DeR_M)


title: MCSP-enriched metastatic melanoma patient blood sample (D05_SW_M)

value: 57 yo

value: BRAF WT mutation in tumor of patient


title: ABCB5-enriched Healthy Donor blood sample (H09_JH_A)

value: control


title: MCSP-enriched Healthy Donor blood sample (E07_MZ_M)

value: MCSP-enriched CTCs


title: MCSP-enriched metastatic melanoma patient blood sample (A05_CH_M)

value: 73 yo


title: ABCB5-enriched Healthy Donor blood sample (C09_MZ_A)


title: bmp2GOF2

status: Public on Apr 11 2018

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted illumina2bam from picard tools
Reads were pre-processed with Cutadapt 1.0, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.19 and Bowtie v0.12.9.
Data were normalized using TMM with the Bioconductor package EdgeR v3.0.8
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: NormCounts.txt. TMM Normalised counts per million reads sequenced

organism: Mus

source_name: ventricles and valves of 4 embryos

growth_protocol: Standard protocols were used to maintain the mice

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and then purified on Rneasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) And quantity were determined on the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard TrueSeq Illumina protocols

value: Heart


title: WT2

value: WT


title: bmp2GOF3


title: MCSP-enriched Healthy Donor blood sample (H07_AC_M)

value: 60 yo


title: MCSP-enriched metastatic melanoma patient blood sample (B05_JT1_M)

value: metastatic melanoma


title: bmp2GOF1


title: WT1


title: MUT2_PV

status: Public on Jan 31 2018

description:
PolyA RNA
Processed data file: Normalized_counts.txt

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Reads were pre-processed with a pipeline that used cutadapt v1.6 to remove Illumina adaptors, a Perl script to trim the first 15 bases of each read and eliminate Ovation adaptors, and FastQC to perform quality controls after each step.
Processed reads were mapped on the transcriptome and quantified using RSEM v1.2.3.
ComBat was used to correct for effects associated to different library batches.
Genome_build: GRCm38, Ensembl genebuild 70
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text file contains ENSEMBL gene Ids and batch-corrected, TMM-Normalized counts per million for each sample.

source_name: Cardiac pulmonary valve, Jag1flox;Nkx2.5-Cre mutant

growth_protocol: Experiments were conducted with WT and Jag1flox;Nkx2.5-Cre mouse embryos at stage E14.5.

extract_protocol:
Cardiac aortic and pulmonary valves were isolated by laser microdissection. RNA was isolated with the Arcturus Picopure RNA isolation kit (Applied Biosystems) and amplified with the Ovation RNA-Seq System V2 (NuGen).
cDNA was prepared using the standard Illumina TrueSeq RNA-seq library preparation kit.
Libraries for aortic valve and pulmonary valve samples were prepared as different batches.

tag: strain/background

value: Jag1flox;Nkx2.5-Cre mutant

value: heart, pulmonary valve

tag: library batch

tag: litter id


title: MUT4_PV

tag: tissue


title: MUT3_PV


title: MUT1_PV


title: WT1_PV

source_name: Cardiac pulmonary valve, WT


title: WT4_PV


title: WT3_PV


title: MUT4_AV

source_name: Cardiac aortic valve, Jag1flox;Nkx2.5-Cre mutant

value: heart, aortic valve


title: MUT3_AV


title: MUT2_AV


title: WT1_AV

source_name: Cardiac aortic valve, WT


title: WT2_AV


title: WT3_AV


title: HeyA8_siCGA_48hr_rep2_lg

status: Public on Jan 12 2018

description:
large RNA library prepared
Derived from Hey cells, ref: Buick, R. N., Pullano, R., and Trent, J. M. (1985). Comparative properties of five human ovarian adenocarcinoma cell lines. Cancer Res. 45: 3668 – 3676.

data_processing:
Sequenced reads were mapped to hg38 human genome using Tophat and bowtie2
raw counts were calculated by HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with normalized read counts for each sample comparison of interest, along with log2FoldChange values, p-values and adjusted p-values.

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.

treatment_protocol: HeyA8 cells were treated with 1nM of indicated siRNAs for 2 days.  Total RNA was harvested 2 days after transfection for HeyA8 cells.

value: Ovary

value: Treated cells with 1nM siCGA/UCG for 2 days


title: HeyA8_siCGA_48hr_rep1_lg


title: HeyA8_siCAG_48hr_rep2_lg

value: Treated cells with 1nM siCAG/CUG for 2 days


title: HeyA8 R6 KO C11 pLKO-R6 100hrs (duplicate 2, lg)

status: Public on Sep 16 2017

description:
chr10:89,008,920-89,009,153
HeyA8_shR6_100hr_rep2_lg

source_name: Derived from from HEY-T30 ATCC CRL-3252

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.
sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: HeyA8 ΔshR6 clone #11 was infected with pLKO-shScr or pLKO-shR6. A pool of three 293T ΔshL3 clones was infected with either pTIP-shScr or pTIP-shL3. After selection with puromycin, the pTIP-infected 293T cells were plated with Doxycycline (100ng/uL) in duplicate at 500,000 cells per T175 flask. The pLKO-infected HeyA8 cells were plated in duplicate at 500,000 cells per flask. Total RNA was harvested 50 hours and 100 hours after plating.

value: HeyA8 (single Fas KO clone #11)

value: Ovaries

tag: infection

value: Infected with pLKO-shR6

tag: time point

value: harvested at 100hrs

value: Fas KO -/-


title: HeyA8 R6 KO C11 pLKO-R6 100hrs (duplicate 1, lg)

description:
chr10:89,008,920-89,009,152
HeyA8_shR6_100hr_rep1_lg

tag: cell line


title: HeyA8 R6 KO C11 pLKO-scr 100hrs (duplicate 1, lg)

description:
chr10:89,008,920-89,009,150
HeyA8_shSCR_100hr_rep1_lg

value: Infected with pLKO-scr


title: HeyA8_siCAG_48hr_rep1_lg

tag: treatment/infection


title: HeyA8 R6 KO C11 pLKO-scr 50hrs (duplicate 2, lg)

description:
chr10:89,008,920-89,009,147
HeyA8_shSCR_50hr_rep2_lg

value: harvested at 50hrs

tag: genotype


title: HeyA8 R6 KO C11 pLKO-R6 50hrs (duplicate 1, lg)

description:
chr10:89,008,920-89,009,148
HeyA8_shR6_50hr_rep1_lg


title: HeyA8_siScr_48hr_rep2_lg

source_name: HeyA8_nontargeting siRNA

value: Treated cells with 1nM non-targeting siScr for two days


title: HeyA8_siScr_48hr_rep1_lg

value: WT


title: WT2_PV


title: WT4_AV


title: 293T pTIP-L3 50hrs (duplicate 2, lg)

description:
chr1:172,665,726-172,665,766 deletion
293T_shL3_50hr_rep2_lg

source_name: ATCC CRL-3216

value: 293T (pool of 3 KO clones)

value: Human Embryonic kidney

value: Infected with pTIP-shL3; 100ng/uL doxycycline

value: Fas ligand KO -/-


title: 293T pTIP-scr 50hrs (duplicate 2, lg)

description:
chr1:172,665,726-172,665,766 deletion
293T_shSCR_50hr_rep2_lg

value: Infected with pTIP-scr; 100ng/uL doxycycline


title: HeyA8 R6 KO C11 pLKO-scr 100hrs (duplicate 2, lg)

description:
chr10:89,008,920-89,009,151
HeyA8_shSCR_100hr_rep2_lg


title: HeyA8 R6 KO C11 pLKO-scr 50hrs (duplicate 1, lg)

description:
chr10:89,008,920-89,009,146
HeyA8_shSCR_50hr_rep1_lg


title: 293T pTIP-scr 100hrs (duplicate 2, lg)

description:
chr1:172,665,726-172,665,766 deletion
293T_shSCR_100hr_rep2_lg


title: 293T pTIP-L3 100hrs (duplicate 2, lg)

description:
chr1:172,665,726-172,665,766 deletion
293T_shL3_100hr_rep2_lg


title: 293T pTIP-L3 50hrs (duplicate 1, lg)

description:
chr1:172,665,726-172,665,766 deletion
293T_shL3_50hr_rep1_lg


title: 503 HeyA8 KO C11 pLenti 50hrs (rep 1, lg)

description:
chr10:89,008,920-89,009,146 deletion
HeyA8_vec_50hr_rep1_lg

treatment_protocol: Cells were infected with either empty pLenti virus or pLenti-CD95L virus overnight and then treated with 3ug/mL puromycin for selection.  After selection cells were plated and total RNA harvested 50hrs after plating.

value: HeyA8 CD95 k.o. cells clone #11

value: Cells were infected with empty pLenti-GIII-CMV-RFP-2A-Puro and selected with 3 ug/mL puromycin for 2 days.  Total RNA was isolated 50hrs after puromycin selection.


title: 293T pTIP-scr 100hrs (duplicate 1, lg)

description:
chr1:172,665,726-172,665,766 deletion
293T_shSCR_100hr_rep1_lg


title: HeyA8 R6 KO C11 pLKO-R6 50hrs (duplicate 1)

description:
chr10:89,008,920-89,009,148
HeyA8_shR6_50hr_rep1_sm

source_name: Derived from from HEY-T30 ATCC CRL-3254

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol. Two small RNA-SEQ sub-libraries were generated: one containing library fragments 140-150 bp in size and one containing library fragments 150-200 bp in size (both including the sequencing adator of about 130bp).
sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

value: Infected with pLKO-shR6 harvested at 50hrs


title: HeyA8 R6 KO C11 pLKO-R6 100hrs (duplicate 2)

description:
chr10:89,008,920-89,009,153
HeyA8_shR6_100hr_rep2_sm

source_name: Derived from from HEY-T30 ATCC CRL-3259

value: HeyA8 (single Fas KO clone #11)


title: 293T pTIP-L3 100hrs (duplicate 2)

description:
chr1:172,665,726-172,665,766 deletion
293T_shL3_100hr_rep2_sm


title: HeyA8 R6 KO C11 pLKO-R6 100hrs (duplicate 1)

description:
chr10:89,008,920-89,009,152
HeyA8_shR6_100hr_rep1_sm

source_name: Derived from from HEY-T30 ATCC CRL-3258

value: Ovaries


title: HeyA8 R6 KO C11 pLKO-scr 50hrs (duplicate 1)

description:
chr10:89,008,920-89,009,146
HeyA8_shSCR_50hr_rep1_sm


title: 293T pTIP-scr 50hrs (duplicate 1, lg)

description:
chr1:172,665,726-172,665,766 deletion
293T_shSCR_50hr_rep1_lg


title: MUT1_AV

description:
PolyA RNA
Processed data file: Normalized_counts.txt

value: Jag1flox;Nkx2.5-Cre mutant

value: heart, aortic valve


title: 506 HeyA8 KO C11 FasL 50hrs (rep 2, lg)

description:
chr10:89,008,920-89,009,146 deletion
HeyA8_FasL_50hr_rep2_lg

value: Cells were infected with  pLenti-GIII-CMV-RFP-2A-Puro-CD95L and selected with 3 ug/mL puromycin for 2 days.  Total RNA was isolated 50hrs after puromycin selection.


title: 505 HeyA8 KO C11 FasL 50hrs (rep 1, lg)

description:
chr10:89,008,920-89,009,146 deletion
HeyA8_FasL_50hr_rep1_lg


title: 04 HeyA8 KO C11 pLenti 50hrs (rep 2, lg)

description:
chr10:89,008,920-89,009,146 deletion
HeyA8_vec_50hr_rep2_lg


title: HeyA8 R6 KO C11 pLKO-R6 50hrs (duplicate 2)

description:
chr10:89,008,920-89,009,149
HeyA8_shR6_50hr_rep2_sm

source_name: Derived from from HEY-T30 ATCC CRL-3255

value: Fas KO -/-


title: HeyA8 R6 KO C11 pLKO-scr 50hrs (duplicate 2)

description:
chr10:89,008,920-89,009,147
HeyA8_shSCR_50hr_rep2_sm

source_name: Derived from from HEY-T30 ATCC CRL-3253

value: Infected with pLKO-scr

value: harvested at 50hrs


title: 293T pTIP-L3 100hrs (duplicate 1)

description:
chr1:172,665,726-172,665,766 deletion
293T_shL3_100hr_rep1_sm

value: harvested at 100hrs


title: 293T pTIP-L3 50hrs (duplicate 1)

description:
chr1:172,665,726-172,665,766 deletion
293T_shL3_50hr_rep1_sm

value: 293T (pool of 3 KO clones)


title: 293T pTIP-scr 100hrs (duplicate 2)

description:
chr1:172,665,726-172,665,766 deletion
293T_shSCR_100hr_rep2_sm

value: Human Embryonic kidney


title: 293T pTIP-scr 50hrs (duplicate 1)

description:
chr1:172,665,726-172,665,766 deletion
293T_shSCR_50hr_rep1_sm


title: NT#2 (IDT siRNA) rep2

description: large RNA library prepared

source_name: Derived from from Hey cells, ref: Buick, R. N., Pullano, R., and Trent, J. M. (1985). Comparative properties of five human ovarian adenocarcinoma cell lines. Cancer Res. 45: 3668 – 3676.

treatment_protocol: HeyA8 cells were treated with 25nM of indicated siRNAs for 2 days.  Total RNA was harvested 2 days after transfection for HeyA8 cells.

value: Parental HeyA8

tag: transfection

value: Treated cells with 25nM non-targeting siRNA # 2 (IDT)

value: for 2 days

value: WT


title: 293T pTIP-L3 50hrs (duplicate 2)

description:
chr1:172,665,726-172,665,766 deletion
293T_shL3_50hr_rep2_sm

value: Infected with pTIP-shL3; 100ng/uL doxycycline

value: Fas ligand KO -/-


title: siL3 (IDT siRNA) rep2

description: large RNA library prepared

value: Treated cells with 25nM siL3 siRNA (IDT)


title: 293T pTIP-scr 50hrs (duplicate 2)

description:
chr1:172,665,726-172,665,766 deletion
293T_shSCR_50hr_rep2_sm

value: Infected with pTIP-scr; 100ng/uL doxycycline


title: siL3 (Dharmacon siRNA) rep1

description: large RNA library prepared

value: Ovaries

value: Treated cells with 25nM siL3 siRNA (Dharmacon)


title: HeyA8 R6 KO C11 pLKO-scr 100hrs (duplicate 1)

description:
chr10:89,008,920-89,009,150
HeyA8_shSCR_100hr_rep1_sm

source_name: Derived from from HEY-T30 ATCC CRL-3256

value: HeyA8 (single Fas KO clone #11)


title: NT#2 (IDT siRNA) rep1

description: large RNA library prepared


title: 293T pTIP-scr 100hrs (duplicate 1)

description:
chr1:172,665,726-172,665,766 deletion
293T_shSCR_100hr_rep1_sm


title: HeyA8 R6 KO C11 pLKO-scr 100hrs (duplicate 2)

description:
chr10:89,008,920-89,009,151
HeyA8_shSCR_100hr_rep2_sm

source_name: Derived from from HEY-T30 ATCC CRL-3257

value: Fas KO -/-


title: siL3 (Dharmacon siRNA) rep2

description: large RNA library prepared


title: pLenti HCT116 cells rep 2

source_name: ATCC CCL-247

extract_protocol:
Cells were lysed in NP40 lysis buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% (v/v) NP40, supplemented with phosphatase inhibitors) on ice for 15 minutes. The lysate was sonicated 3 times for 30 s at 60% amplitude (Sonics, VCX130) and cleared by centrifugation at 12,000g for 20 minutes. AGO1-4 were pulled down by using 500 mg of Flag-GST-T6B peptide (Hauptmann et al., 2015) and with 60 ml anti-Flag M2 magnetic beads (Sigma-Aldrich) for 2 hrs at 4°C. The pull-down was washed 3 times in NP40 lysis buffer. During the last wash, 10% of beads were removed and incubated at 95°C for 5 minutes in 2x SDS-PAGE sample buffer. Samples were run on a 4-12% SDS-PAGE and transferred to nitrocellulose membrane. The pull-down efficiency was determined by immunoblotting against AGO1 and AGO2 (Abcam 98056 and 32381). To the remaining beads 500 µl TRIzol reagent were added and the RNA extracted according to the manufacturer’s instructions. The RNA pellet was diluted in 20 µl of water. The sample was split and half of the sample was dephosphorylated with 0.5 U/μl of CIP alkaline phosphatase at 37°C for 15 min and subsequently radiolabeled with 0.5 μCi γ-32P-ATP and 1 U/μl of T4 PNK kinase for 20 min at 37°C. The AGO1-4 interacting RNAs were visualized on a 15% urea-PAGE. The remaining RNA was taken through a small RNA library preparation as previously descried (Hafner et al., 2012). Briefly, RNA was ligated with 3’ adenylated adapters and separated on a 15% denaturing urea-PAGE. The RNA corresponding to insert size of 19-35 nt was eluted from the gel, ethanol precipitated followed by 5’ adapter ligation. The samples were separated on a 12% Urea-PAGE and extracted from the gel. Reverse transcription was performed using Superscript III reverse transcriptase and the cDNA amplified by PCR. The cDNA was sequenced on Illumina HiSeq 3000. Adapter sequences: Adapter 1 – NNTGACTGTGGAATTCTCGGGTGCCAAGG; Adapter 2 – NNACACTCTGGAATTCTCGGGTGCCAAGG, Adapter 3 –  NNACAGAGTGGAATTCTCGGGTGCCAAGG, Adapter 4 – NNGCGATATGGAATTCTCGGGTGCCAAGG, Adapter 47 – NNTCTGTGTGGAATTCTCGGGTGCCAAGG, Adapter 48 – NNCAGCATTGGAATTCTCGGGTGCCAAGG, Adapter 49 – NNATAGTATGGAATTCTCGGGTGCCAAGG, Adapter 50 – NNTCATAGTGGAATTCTCGGGTGCCAAGG. RT primer sequence: GCCTTGGCACCCGAGAATTCCA; PCR primer sequences: CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA. To identify CD95L derived small RNAs all reads (4 conditions in duplicate) after removal of the adaptor sequences were BLASTED against the CD95L ORF (derived from NM_000639.1). Only reads were considered with an evalue of less than 0.05 and 100% identity across the entire length of the read.
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol. Two small RNA-SEQ sub-libraries were generated: one containing library fragments 140-150 bp in size and one containing library fragments 150-200 bp in size (both including the sequencing adator of about 130bp).
sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Either parental or Drosha k.o. HCT116 cells were infected with pLenti or pLenti-CD95LMUTNP overnight; puromycin selection was done for 2 days and then cells were plated for 50hrs post selection before cells pellets were isolated and frozen; Ago pull-down was then done on the frozen pellets. Total time from addition of lentiviruses to freezing pellets was 122 hours.

tag: genotype/variation

value: Parental

value: colon

value: Cells infected with empty pLenti and selected with 3ug/mL puromycin for 2 days.  Cells were plated for 50hours and an Ago-pull down was performed and the small RNA (19-23nts) sequenced.


title: NT#2 (Dharmacon siRNA) rep1

description: large RNA library prepared

value: Treated cells with 25nM non-targeting siRNA # 2 (Dharmacon)


title: NT#2 (Dharmacon siRNA) rep2

description: large RNA library prepared


title: CD95LMUTNP overexpressed in HCT116 cells rep 1

value: Cells infected with pLenti-CD95LMUTNP and selected with 3ug/mL puromycin for 2 days.  Cells were plated for 50hours and an Ago-pull down was performed and the small RNA (19-23nts) sequenced.


title: pLenti HCT116 Drosha KO cells rep 2

source_name: ATCC CCL-247; Drosha KO cells provided by Narry Kim, ref: Kim Y.K., Kim B., Kim V.N. (2016). Re-evaluation of the roles of DROSHA, Export in 5, and DICER in microRNA biogenesis. Proc Natl Acad Sci U S A. 113(13):E1881-9.

value: Drosha k.o.


title: CD95LMUTNP overexpressed in HCT116 cells rep 2


title: 293T-pTIP-shL1 + Dox for 100 hrs Replicate 2

description:
large RNA library prepared
293T_shL1_100hr_rep2_lg

treatment_protocol: HeyA8 cells were infected with either pTIP-shScr or pTIP-shL1. After selection with puromycin, the pTIP-infected 293T cells were plated with Doxycycline (100ng/uL) in duplicate at 500,000 cells per T175 flask. Total RNA was harvested 100 hours after plating for pTIP infected cells.

value: Parental ATCC CRL-3216

value: human embryonic kidney

value: Infected with pTIP-shL1

tag: treatment

value: 100ng/uL doxycycline

value: harvested at 100hrs


title: 293T-pTIP-shScr + Dox for 100 hrs Replicate 2

description:
large RNA library prepared
293T_shSCR_100hr_rep2_lg

value: Infected with pTIP-scr

value: WT


title: 293T-pTIP-shL1 + Dox for 100 hrs Replicate 1

description:
large RNA library prepared
293T_shL1_100hr_rep1_lg


title: 293T-pTIP-shScr + Dox for 100 hrs Replicate 1

description:
large RNA library prepared
293T_shSCR_100hr_rep1_lg


title: siL3 (IDT siRNA) rep1

description: large RNA library prepared

value: Parental HeyA8

value: Ovaries

value: Treated cells with 25nM siL3 siRNA (IDT)

value: for 2 days


title: RBPJko3 ApoE-/-; RBPJflox/flox;Cdh5-CreERTmice

status: Public on Jun 30 2017

description: RBPJ KO induced in chd5 domain at 8 weeks old mice

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build NCBIM37.v65) And gene expression quantified using RSEM v1.16 and Bowtie v0.12.7.
Data were normalized using voom with the Bioconductor package EdgeR and limma
Differential expression were tested using lm with Bioconductor package limma
Genome_build: NCBIM37.v65
Supplementary_files_format_and_content: RBP_KOvsWT.NormCounts.csv. Voom Normalised counts

source_name: aortic arches

growth_protocol: 1 week tamoxifen treatment at 8 weeks old mice followed by 6 weeks of High Fat diet

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) And then purified on RNA-Easy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) And quantity were determined on the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols

tag: delevopmental stage

value: adult

tag: strain

value: aorta


title: RBPJko2 ApoE-/-; RBPJflox/flox;Cdh5-CreERTmice

treatment_protocol: 1 week tamoxifen treatment at 8 weeks old mice

value: RBPJ KO induced in chd5 domain at 8 weeks old mice


title: RBPJko1 ApoE-/-; RBPJflox/flox;Cdh5-CreERTmice


title: RBPwt3 ApoE-/-;RBPJflox/flox

description: ApoE mice

value: ApoE mice


title: RBPwt2 ApoE-/-;RBPJflox/flox

description: ApoE mice


title: RBPwt1 ApoE-/-;RBPJflox/flox

description: ApoE mice


title: pLenti HCT116 Drosha KO cells rep 1

value: colon

value: Cells infected with empty pLenti and selected with 3ug/mL puromycin for 2 days.  Cells were plated for 50hours and an Ago-pull down was performed and the small RNA (19-23nts) sequenced.


title: pLenti HCT116 cells rep 1

value: Parental


title: CD95LMUTNP overexpressed in HCT116 Drosha KO cells rep 1

value: Drosha k.o.

value: Cells infected with pLenti-CD95LMUTNP and selected with 3ug/mL puromycin for 2 days.  Cells were plated for 50hours and an Ago-pull down was performed and the small RNA (19-23nts) sequenced.


title: DMSO_Control_1

status: Public on Mar 31 2017

description:
Cryoinjured heart treated with DMSO
DMSO1

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the zebrafish transcriptome (Ensembl gene-build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release-75/gtf/danio_rerio/Danio_rerio.Zv9.75.gtf.gz) and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCZv9.v75
Supplementary_files_format_and_content: ROvsControl.NormCounts.csv reports TMM-normalized counts per million reads sequenced

organism: Danio rerio

source_name: apex of 3 hearts

growth_protocol: Standard protocols were used to maintain the zebrafish to adulthood

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) And then purified on Rneasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) And quantity were determined on the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols

treatment_protocol: Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h after cryoinjury of the heart

tag: developmental stage

value: AB

tag: stress

value: cryoinjury

value: control

value: Heart


title: DMSO_Control_2

description:
Cryoinjured heart treated with DMSO
DMSO2


title: RO_Treated_4

description:
Cryoinjured heart treated with RO secretase inhibitor
RO4

value: RO gamma secretase inhibitor


title: DMSO_Control_3

description:
Cryoinjured heart treated with DMSO
DMSO3


title: IGG

status: Public on Feb 16 2017

description: Chromatin IP

library_source: genomic

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

molecule: genomic DNA

source_name: breast tumor

growth_protocol: Cell lines were maintained in RPMI supplemented with 10% FBS.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-STAT1 antibody

treatment_protocol: CD95 stimulation was done with IgG and APO-1 100ngr/ml with protein-A 1ng/ml.

value: MCF-7 from NCI-60

tag: antibody

value: IgG control


title: APOI

description: Chromatin IP

value: Stat1a p91 sc-345

tag: antibody vendor

value: Santa Cruz

tag: antibody lot#


title: RO_Treated_2

description:
Cryoinjured heart treated with RO secretase inhibitor
RO2

value: adult


title: APO1-1

description: SAMPLE 1

hyb_protocol: The arrays were processed at the Northwestern University Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and 1% PS.

extract_protocol: Total RNA were extracted using Trizol according to manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using Nanodrop Spectrophotometer.

treatment_protocol: CD95 stimulation was done with IgG and Apo-1 100ngr/ml with protein-A 1ngr/ml. Multiplicity of infection (MOI) for the CD95 knockdown and PLKO control particles (Sigma) was 3

value: anti-Apo-1 (anti-CD95 agonistig antibody)


title: Atlantic_timepoint2_treatment4

status: Public on Jun 21 2016

city: Ste-Anne-de-Bellevue

first: Martina

last: Stromvik

state: Quebec

address: 21,111 Lakeshore Rd

department: Department of Plant Science

country: Canada

institute: McGill University

description: processed data file: atlantic_time2_annotated_gene_exp.diff.gz

data_processing:
Alignment with TopHat (-p 5 --library-type=fr-unstranded)
Transcript assembly with CuffLinks (--library-type=fr-unstranded --multi-read-correct --frag-bias-correct)
Assembly of reference transcriptome, per experiment, with CuffMerge
Differential expression analysis with CuffDiff (--multi-read-correct --frag-bias-correct). FPKM were calculated for all genes calculated as follow: exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Gene annotation added through custom perl script that took information from S. tuberosum ITAG1.0 gtf file (ftp://ftp.solgenomics.net/genomes/Solanum_tuberosum/annotation/ITAG1.0/).
Genome_build: S. tuberosum reference genome v3_2.1.10
Supplementary_files_format_and_content: gene_exp.diff, contains FPKM information for control samples vs. treatment, as well as a statistical test to determine whether each gene is differentially expressed between groups

organism: Solanum tuberosum

growth_protocol: Plants were propagated in the field at the Potato Research Centre of Agriculture and Agri-Food Canada in New Brunswick. Plants were fertilized with 150 kg ha^-1 of P2O2 and K2O at planting. Hand cut 50g seed-pieces were hand-planted and imidaclorpid was applied to control for Colorado potato beetle. At each sampling, the apical leaflet of the last fully expanded leaf (usually the fourth leaf from the top of the plant) was sampled from each of 15 randomly selected plants in each plot and placed into 50 ml Falcon tubes. The tube was immediately placed in liquid N, and stored at -80 ˚C until RNA extraction.

extract_protocol:
Leaf tissue was ground to a powder in liquid N using a mortar and pestle. Samples were pre-extracted in 1 ml Hot Borate Buffer (Wan & Wilkins 1994). The lysate supernatant (200 ul) was used for RNA extraction with the Biomek NXP Laboratory Automation Workstation (Beckman Coulter) using the RNAdvance Tissue Kit (Agencourt) according to the manufacturer’s instructions for liquid samples.
Libraries were generated using the TruSeq RNA kit (Illumina). Messenger RNA was purified from 1 g of total RNA using oligo-dT beads. The mRNA enriched fraction was reverse transcribed to generate cDNA fragments that were sheared to yield ~200 bp fragments. Following end-repair, 3’ end adenylation steps, and index ligation, a PCR amplification step was performed. A separate index was used for each N treatment-variety-replicate combination for a total of 24 indices.

treatment_protocol: The experiment included two fertilizer N rates in a randomized complete block design with four blocks. The control groups had no added ammonium nitrate. The treatment groups were fertilized with 180 kg ha^-1 of ammonium nitrate at planting.

tag: cultivar

value: Atlantic

tag: treated with

value: 180 kg N ha-1 N-fertilizer

tag: sampling date/time point

value: Foliar; apical leaflet of the last fully expanded leaf (usually the 4th leaf from the top of the plant)


title: smallRNA-seq_mGC_E15.5_M

status: Public on Oct 10 2016

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Small RNA-seq libraries were trimmed using trim_galore (v0.4.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default settings. Small RNA-seq libraries were trimmed to remove poor quality reads, adaptor and barcodes sequences. Trimmed data were mapped using Bowtie against the mouse GRCm38 genome build. miRNA in mapped small RNA-seq data were quantitated using the  RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/). For piRNA analysis, small RNA-seq data processing was performed using the freely available piRNA pipeline piPipes (https://github.com/bowhan/piPipes) (Han et al., 2015).
Genome_build: GRCm38
Supplementary_files_format_and_content: Quantitated small RNA-seq data file is tab delimited and contains the following columns: (1) miRNA name; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-7) log2 RPM values for each sample

source_name: Primordial germ cell (PGC)

extract_protocol:
RNA was isolated using TriReagent (Sigma) and treated with DNAseI (Ambion DNA-free DNA Cat #1311027) using manufacturers instructions
Small RNA Sequencing libraries were generated using the Illumina TruSeq Small RNA Library Preparation Kit (RS-200-0012) with the following modifications. 100ng – 1µg total RNA input material was used. cDNA samples were run on 10% Novex PAGE gels for purification and the gel piece between the 145bp and 160bp marker was excised and cDNA was eluted from the gel in freshly prepared 0.3M NaCl by rotation overnight at 4˚C. The cDNA was precipitated in EtOH overnight from the supernatant the cDNA was resuspended in 10µl EB buffer and the library was quantified using the High-Sensitivity DNA chips on the Agilent Bioanalyzer. High-throughput sequencing of all libraries was carried out with a single-end protocol on a HiSeq 2000 instrument (Illumina).

tag: background strain

tag: cell type

value: Primordial germ cell (PGC)

value: Wild-type


title: Atlantic_timepoint2_treatment2

tag: tissue


title: Atlantic_timepoint2_treatment3


title: Atlantic_timepoint2_control4

value: 0 kg N ha-1 N-fertilizer


title: smallRNA-seq_E14_mESC

source_name: Embryonic stem cell (ESC)

value: Embryonic stem cell (ESC)

tag: genotype


title: RussetBurbank_timepoint2_treatment4

description: processed data file: russetBurbank_time2_annotated_gene_exp.diff.gz

value: Russet Burbank


title: Atlantic_timepoint2_treatment1


title: Atlantic_timepoint2_control3


title: Atlantic_timepoint2_control1


title: RussetBurbank_timepoint2_treatment2


title: RussetBurbank_timepoint2_treatment3


title: RO_Treated_3

description:
Cryoinjured heart treated with RO secretase inhibitor
RO3

value: AB

value: cryoinjury


title: Atlantic_timepoint2_control2


title: RussetBurbank_timepoint2_treatment1


title: CD95LMUTNP overexpressed in HCT116 Drosha KO cells rep 2

value: Drosha k.o.

tag: cell line

value: colon

tag: treatment/infection

value: Cells infected with pLenti-CD95LMUTNP and selected with 3ug/mL puromycin for 2 days.  Cells were plated for 50hours and an Ago-pull down was performed and the small RNA (19-23nts) sequenced.


title: RussetBurbank_timepoint2_control4


title: IgG3-2

description: SAMPLE 4

scan_protocol: The arrays were processed at the Northwestern University Genomics Core (Illinois) according to manufacturer’s protocol.

value: MCF-7 from NCI-60

tag: treatment

value: IgG control


title: RussetBurbank_timepoint2_control3


title: RussetBurbank_timepoint2_control2


title: Shepody_timepoint2_treatment4

description: processed data file: shepody_time2_annotated_gene_exp.diff.gz

value: Shepody


title: RussetBurbank_timepoint2_control1


title: Shepody_timepoint2_treatment3


title: Shepody_timepoint2_control4


title: Atlantic_timepoint1_control4

description: processed data file: atlantic_time1_annotated_gene_exp.diff.gz


title: Atlantic_timepoint1_control1


title: IgG3-1

description: SAMPLE 2

label_protocol: The arrays were processed at the Northwestern University Genomics Core (Illinois) according to manufacturer’s protocol.


title: Atlantic_timepoint1_treatment4


title: Shepody_timepoint2_control2


title: Atlantic_timepoint1_control2


title: Atlantic_timepoint1_control3


title: Shepody_timepoint2_control1


title: RussetBurbank_timepoint1_treatment1

description: processed data file: russetBurbank_time1_annotated_gene_exp.diff.gz


title: RussetBurbank_timepoint1_treatment3


title: Shepody_timepoint2_treatment1


title: APO-1-2

description: SAMPLE 3

value: anti-Apo-1 (anti-CD95 agonistig antibody)


title: Shepody_timepoint2_treatment2


title: Atlantic_timepoint1_treatment1

value: Atlantic


title: RussetBurbank_timepoint1_control4


title: Atlantic_timepoint1_treatment2

value: 180 kg N ha-1 N-fertilizer


title: Atlantic_timepoint1_treatment3

value: Foliar; apical leaflet of the last fully expanded leaf (usually the 4th leaf from the top of the plant)


title: RussetBurbank_timepoint1_control3


title: Shepody_timepoint1_treatment4

description: processed data file: shepody_time1_annotated_gene_exp.diff.gz


title: RussetBurbank_timepoint1_treatment2


title: Shepody_timepoint2_control3


title: Shepody_timepoint1_treatment1


title: Shepody_timepoint1_treatment2


title: RussetBurbank_timepoint1_treatment4


title: RussetBurbank_timepoint1_control1


title: Shepody_timepoint1_control2


title: Shepody_timepoint1_control3


title: Shepody_timepoint1_control1


title: Shepody_timepoint1_treatment3


title: Jag1WT-TnT_1

status: Public on Feb 12 2016

description: WT sibling from Jag1 experient

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Data were batch corrected with Bioconductor package ComBat.R
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: D4NFKOvsWT.D4T2KOvsWT.NormCounts.csv. TMM Normalised counts per million reads sequenced
Supplementary_files_format_and_content: NINFKOvsWT.NormCounts.csv.  TMM Normalised counts per million reads sequenced
Supplementary_files_format_and_content: J1andJ2andJ12.NormCounts.txt. TMM Normalized counts per million reads sequenced

source_name: heart ventricles from 4 embryos

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) And then purified on Rneasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) And quantity were determined on the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

tag: age

tag: genotype/variation

value: WT

value: Heart


title: Jag1WT-TnT_3

description: WT sibling from Jag1 experient

tag: developmental stage


title: Jag1KO-TnT_1

description: Jag1 KO in Tnt domain

value: Jag1flox; TnT-Cre


title: Jag1KO-TnT_2

description: Jag1 KO in Tnt domain


title: Jag1WT-TnT_2

description: WT sibling from Jag1 experient


title: Notch1WT-Nfat_2

description: WT sibling from Notch1 Nfat experiment

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Data were batch corrected with Bioconductor package ComBat.R
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: D4NFKOvsWT.D4T2KOvsWT.NormCounts.csv. TMM Normalised counts per million reads sequenced
Supplementary_files_format_and_content: NINFKOvsWT.NormCounts.csv.  TMM Normalised counts per million reads sequenced

source_name: whole hearts of 8 embryos


title: OTII_CD103+CD11b+_3

status: Public on Mar 28 2016

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

data_processing:
reads were aligned to Mouse Ensembl genes using the STAR version 2.3.0 software
Differential expression was determined by use of the Cufflinks software with default settings
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM

source_name: naïve OT-II CD4 T cells

extract_protocol:
1. Naive OT-II CD4 T cell extraction: peripheral lymphnodes and spleens were dissected on ice and mechanically disrupted in RPMI/10% FBS. Naïve CD4 T cells were pre-enriched by negative selection using biotinylated antibodies against CD8α, CD25, CD11c, CD11b, TER-119, NK1.1, and B220 and anti-biotin MACS beads (Miltenyi Biotec) and sorted as Aqua–CD11c–CD8α–MHCII–Vα2+CD4+CD25–CD62hiCD44lo. 2. Mesenteric lymphnodes from eight week old male C57Bl6 mice reared in the SPF facility of Rockefeller University were dissected into cold HBSS supplemented with Mg2+ and Ca2+, finely chopped and incubated in 400 U/ml Collagenase D (Roche) in HBSS for 25 min at 37°C, 5% CO2. Collagenase was quenched on ice by addition of final 10% FCS. Single cell suspensions were extracted from connective tissue by taking up and resuspending the digests five times. Mesenteric dendritic cells were pre-enriched using anti-CD11c MACS beads (Miltenyi Biotec) and LS MACS Separation Columns (Miltenyi Biotec). Cells were sorted using FACS Aria cell sorter flow cytometer (Becton Dickinson).Dendritic were sorted as Aqua–CD45+Lin–(CD3–B220–NK1.1–CD19–) CD11chi, and the subpopulations further as MHCIIintCD8α+CD11blo, MHCIIintCD8α–CD11b+, MHCIIhiCD103+CD11b– and MHCIIhiCD103+CD11b+. 3. After 24 h of co-culture with DCs, OT-II cells were sorted as Aqua-CD11c–CD8α–MHCII–Vα2+CD4+. RNA from sorted cell pellets was extracted and column-purified using the Arcturus PicoPure RNA Isolation kit (Applied Biosystems). Genomic DNA was removed by on-column digest with DNAse I (Qiagen), according to the PicoPure RNA Isolation kit manual.
RNA libraries were prepared using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech Laboratories) and sequenced using 50 base pair paired end reading on a HiSeq 2500 instrument (Illumina).

treatment_protocol: Sorted and Cell TraceTM stained naïve OT-II cells were cultured for24h in flat bottom 96 well plates OT-II in the presence of sorted mLN DC subpopulations, 1 μg/ml anti-IL4 and 1 μg/ml anti-IFN-γ antibody in RPMI/10 % FBS. Antigen was provided as 1 μg/ml of OT-II peptide (chicken OVA323-339, amino acid sequence ISQAVHAAHAEINEAGR, made by the Rockefeller University Proteomics Resource Center). Cells were co-cultured at a 5:1 T cell/DC ratio (100,000 to 20,000 or 50,000 to 10,000).

tag: strain

value: C57BL/6 CD45.1 OT-II

tag: organ

value: spleen and  lymphnodes

value: CD4 T cells


title: OTII_CD103+CD11b+_2


title: Notch1WT-Nfat_1

description: WT sibling from Notch1 Nfat experiment


title: OTII_CD103+CD11b+_1


title: Shepody_timepoint1_control4

value: 0 kg N ha-1 N-fertilizer


title: Notch1KO-Nfat_3

description: Notch1 KO in Nfat domain

value: Notch1flox; Nfatc1-Cre


title: RussetBurbank_timepoint1_control2

value: Russet Burbank


title: OTII_CD103+CD11b-_1


title: Notch1KO-Nfat_2

description: Notch1 KO in Nfat domain


title: Notch1KO-Nfat_1

description: Notch1 KO in Nfat domain


title: OTII_CD103+CD11b-_3


title: Dll4WT-Tie2_3

description: WT sibling from Dll4 Tie2 Experiment

source_name: whole hearts of 9 embryos


title: Dll4WT-Tie2_1

description: WT sibling from Dll4 Tie2 Experiment


title: Jag1KO-TnT_3

description: Jag1 KO in Tnt domain


title: Dll4WT-Nfat_2

description: WT sibling from Dll4 Nfat experiment


title: Dll4WT-Nfat_4

description: WT sibling from Dll4 Nfat experiment


title: HeyA8 R6 KO C11 pLKO-R6 50hrs (duplicate 2, lg)

description:
chr10:89,008,920-89,009,149
HeyA8_shR6_50hr_rep2_lg

source_name: Derived from from HEY-T30 ATCC CRL-3252

value: HeyA8 (single Fas KO clone #11)

value: Ovaries

tag: infection

value: Infected with pLKO-shR6

tag: time point

value: harvested at 50hrs

value: Fas KO -/-


title: Dll4WT-Nfat_3

description: WT sibling from Dll4 Nfat experiment


title: Dll4WT-Nfat_1

description: WT sibling from Dll4 Nfat experiment


title: Dll4KO-Tie2_3

description: Dll4 KO in Tie2 domain

value: Dll4flox; Tie2-Cre


title: Dll4KO-Tie2_2

description: Dll4 KO in Tie2 domain


title: Dll4KO-Tie2_1

description: Dll4 KO in Tie2 domain


title: Dll4KO-Nfat_3

description: Dll4 KO in Nfat domain

value: Dll4flox; Nfatc1-Cre


title: Dll4KO-Nfat_2

description: Dll4 KO in Nfat domain

value: embryo


title: Dll4KO-Nfat_4

description: Dll4 KO in Nfat domain


title: 293T pTIP-L3 100hrs (duplicate 1, lg)

description:
chr1:172,665,726-172,665,766 deletion
293T_shL3_100hr_rep1_lg

source_name: ATCC CRL-3216

value: 293T (pool of 3 KO clones)

value: Human Embryonic kidney

value: Infected with pTIP-shL3; 100ng/uL doxycycline

value: harvested at 100hrs

value: Fas ligand KO -/-


title: Dll4WT-Tie2_2

description: WT sibling from Dll4 Tie2 Experiment

value: WT

value: Heart


title: Jag2KO-TnT_2

description:
Jag2 KO in Tnt domain
TnTJ2_KO2

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Data were batch corrected with Bioconductor package ComBat.R
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: MFng.NormCounts.txt.  TMM Normalized counts per million reads sequenced
Supplementary_files_format_and_content: J1andJ2andJ12.NormCounts.txt. TMM Normalized counts per million reads sequenced

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) And then purified on Rneasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) And quantity were determined on the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using NEBNext Ultra kit for Illumina

treatment_protocol: No treatment applied

value: Jag2flox; TnT-Cre

value: heart venticle


title: Jag1Jag2KO-TnT_1

description:
Double Jag1 and Jag2 KO in Tnt domain
TJ1J2_KO1

value: Jag1flox; Jag2flox; TnT-Cre


title: Jag1Jag2WT-TnT_2

description:
WT sibling from double Jag1-Jag2 KO experient
TJ1J2_WT2


title: Tie2-MFng_WT2

description:
WT sibling from MFngGOF experient
MFT2_WT2

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Data were batch corrected with Bioconductor package ComBat.R
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: MFng.NormCounts.txt.  TMM Normalized counts per million reads sequenced


title: Jag2KO-TnT_1

description:
Jag2 KO in Tnt domain
TnTJ2_KO1


title: Jag2WT-TnT_2

description:
WT sibling from Jag2 experient
TnTJ2_WT2


title: Tie2-MFng_WT3

description:
WT sibling from MFngGOF experient
MFT2_WT3


title: Jag1Jag2KO-TnT_2

description:
Double Jag1 and Jag2 KO in Tnt domain
TJ1J2_KO2


title: Tie2-MFng_WT4

description:
WT sibling from MFngGOF experient
MFT2_WT4


title: Jag1Jag2WT-TnT_1

description:
WT sibling from double Jag1-Jag2 KO experient
TJ1J2_WT1


title: Jag1Jag2KO-TnT_3

description:
Double Jag1 and Jag2 KO in Tnt domain
TJ1J2_KO3


title: Tie2-MFng_WT1

description:
WT sibling from MFngGOF experient
MFT2_WT1


title: Tie2-MFng_GOF4

description:
MFng overexpression in Tie2 domain
MFT2_GOF4

value: MFng; Tie2-Cre


title: Tie2-MFng_GOF1

description:
MFng overexpression in Tie2 domain
MFT2_GOF1


title: Tie2-MFng_GOF3

description:
MFng overexpression in Tie2 domain
MFT2_GOF3


title: Tie2-MFng_GOF2

description:
MFng overexpression in Tie2 domain
MFT2_GOF2


title: Jag2KO-TnT_3

description:
Jag2 KO in Tnt domain
TnTJ2_KO3


title: Jag2WT-TnT_1

description:
WT sibling from Jag2 experient
TnTJ2_WT1


title: MibWT-TnT_3

status: Public on Aug 10 2015

description:
WT sibling from Mib Experiment
Mib1WTTnT3

data_processing:
Illumina RTA software v 1.13.48.0
Illumina2bam v:0.03
SamToFastq.jar v1.86
Reads were pre-processed with Cutadapt 1.2.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build mm9.ensGenesV65) And genome, Using RSEM v1.16 and Bowtie2 v0.12.7.
Data were normalized using Voom with the Bioconductor package EdgeR-limma
Differential expression were tested using Voom and LM with the Bioconductor package EdgeR-limma
Genome_build: mm9 (ENSEMBL V65)
Supplementary_files_format_and_content: Mib1KO.Norm.Counts.txt. Voom-normalized counts per million reads sequenced

source_name: heart ventricles of E14.5 embryos

growth_protocol: Standard procedures were used to breed mice

extract_protocol:
Total RNA was extracted with QIAzol Lysis Reagent and then purified on RNeasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) and quantity were determined on the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq single-end


title: MibKO-TnT_4

description:
Mib1 KO in Tnt domain
Mib1KOTnT4

value: Mib1flox; TnT-Cre


title: MibWT-TnT_1

description:
WT sibling from Mib Experiment
Mib1WTTnT1


title: MibWT-TnT_4

description:
WT sibling from Mib Experiment
Mib1WTTnT4


title: MibKO-TnT_1

description:
Mib1 KO in Tnt domain
Mib1KOTnT1


title: MibWT-TnT_2

description:
WT sibling from Mib Experiment
Mib1WTTnT2


title: Dll4KO-Nfat_1

description: Dll4 KO in Nfat domain


title: MibKO-TnT_3

description:
Mib1 KO in Tnt domain
Mib1KOTnT3


title: MibKO-TnT_2

description:
Mib1 KO in Tnt domain
Mib1KOTnT2


title: OTII_CD103+CD11b-_2

value: C57BL/6 CD45.1 OT-II

value: spleen and  lymphnodes

value: CD4 T cells