title: hpf20-29

description:
processed data file:
hpf20.txt
wei-20-i-35


title: hpf20-33

status: Public on Jun 15 2017

type: SRA

city: New York

first: wei

last: wang

state: NY

address: 100 washington square east

department: Biology

country: USA

institute: New York University

description:
processed data file:
hpf20.txt
wei-20-i-39

library_source: transcriptomic

data_processing:
For each demultiplexed single cell RNA-seq library, sequencing reads were mapped to Ciona genome (Joined-scaffold (KH), http://ghost.zool.kyotou.ac.jp/datas/JoinedScaffold.zip) using TopHat 2.0.12 (Kim et al., 2013; Trapnell et al., 2012) with parameter: --no-coverage-search. Cufflinks 2.2.0 (Trapnell et al., 2012) was used to calculate the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using KH gene models (ver.2013, http://ghost.zool.kyoto-u.ac.jp/datas/KH.KHGene.2013.gff3.zip) with default parameters.
Genome_build: Ciona genome (Joined-scaffold (KH), http://ghost.zool.kyotou.ac.jp/datas/JoinedScaffold.zip)
Supplementary_files_format_and_content: tab-delimited text files include raw FPKMs for each gene per cell

molecule: polyA RNA

organism: Ciona robusta

source_name: ScRNA-seq of FACS purified cardiopharyngeal progenitors_20hpf

extract_protocol:
Sample dissociation and FACS were performed essentially as described (Christiaen et al., 2009c; Razy-Krajka et al., 2014). Embryos and larvae were harvested at 12, 14, 16, 18 and 20hpf in 5ml borosilicate glass tubes (Fisher Scientific, Waltham, MA. Cat.No. 14-961-26) and washed with 2ml calcium- and magnesium-free artificial seawater (CMF-ASW: 449 mM NaCl, 33 mM Na2SO4, 9 mM KCl, 2.15 mM NaHCO3, 10 mM Tris-Cl pH 8.2, 2.5 mM EGTA). Embryos and larvae were dissociated in 2ml 0.2% trypsin (w/v, Sigma, T- 4799) ASW by pipetting with glass Pasteur pipettes. The dissociation was stopped by adding 2ml filtered ice cold 0.05% BSA CMF-ASW. The dissociated cells were passed through 40µm cell-strainer and collected in 5ml polystyrene round-bottom tube (Corning Life Sciences, Oneonta, New York. REF 352235). Cells were collected by centrifugation at 800g for 3 min at 4°C, followed by two rounds of washing with ice cold 0.05% BSA CMF-ASW. Cell suspensions were filtered again through a 40µm cell-strainer and stored on ice. Following dissociation, cell suspensions were used for sorting within 1 hour. The B7.5 lineage cells were labeled by Mesp>tagRFP reporter. Contaminating B-line mesenchyme cells were counter-selected using  MyoD905>EGFP as described (Christiaen et al., 2008; Razy-Krajka et al., 2014).  The TVC-specific Hand-r>tagBFP reporter was used in a 3-color FACS scheme for positive co-selection of TVC-derived cells, in order to minimize the effects of mosaicism. Dissociated cell were loaded in the BD FACS AriaTM cell sorter.  488 nm laser, FITC filter was used for EGFP; 407 nm laser, 561 nm laser, DsRed filter was used for tagRFP and Pacific BlueTM filter was used for tagBFP. The nozzle size was 100 µm. tagRFP +, tagBFP + and EGFP – cells were collected for downstream RNA sequencing analysis.
Reverse transcription and cDNA amplification were carried out using modified Smart-seq2 protocol (Picelli et al., 2013). Single cells were sorted by FACS as described above into 96-well plates and collected in 3.4 µl RT buffer (0.5 µl 10µM 3’ RT Primer ( 5' - AAG CAG TGG TAT CAA CGC AGA GTA C T30 VN - 3’), 0.5µl 10µM dNTP Mix, 0.5 µl 4U/µl RNase Inhibitor, 1 µl Maxima RT Buffer, 0,9 µl nuclease-free water) in each well. Plates were stored at -80°C  or processed immediately.  Plates were incubated at 72°C for 3min and chilled on the ice to denature the template RNA. 2µl  RT reaction mixture (0.5µl 10um TSO primer (5′-AGACGTGTGCTCTTCCGATCTNNNNNrGrGrG-3′), 0.925µl 5M Betaine, 0.4 100mM MgCl2, 0.125µl 40U/ RNAase inhibitor, 0.05µl 200 U/µl Maxima H Minus Reverse Transcriptase) were added to each well. Reverse transcription was carried out by incubating the plate at 42°C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min) and heat inactivation at 70° for 15 min. 7µl PCR amplification mixture (0.25µl 10 μM PCR primer (5′AGACGTGTGCTCTTCCGATCT-3′), 6.25µl KAPA HIFI ReadyMix, 0.5µl nuclease-free water) were added to each well. PCR amplification was carried out with a denaturation at 98 °C for 3 min, followed by 21 cycles of (98 °C for 15 s, 67 °C for 20 s, and 72 °C for 6 min) and a final extension at 72° for 5 min. PCR products were purified by adding 10µl (0.8×) Agencourt AMPureXP SPRI beads (Beckman-Coulter) to each well, followed by 5min incubation and two rounds of wash using 100µl freshly prepared  70% Ethanol at room temperature. Purified cDNA were eluted in 20µl TE. The concentration of amplified cDNA was measured across the entire plate using Picogreen assay. The concentration of amplified cDNA was in a 0.5–2 ng/μl range.  Fragment size distribution was checked for randomly selected wells with High-Sensitivity Bioanalyzer Chip (Agilent), the expected size average should be ~2 kb. For each sample, the amplified cDNA were normalized to a working concentration ranging from 0.1 to 0.2 ng/µl with TE buffer. 1.25 µl of diluted cDNA from each well were used for library preparation. Single cell libraries were prepared using the Nextera XT DNA Sample Kit (Illumina) according to manufacturer's instructions.  After library amplification, 2.5μl from each well were pooled into a single 1.5-ml microcentrifuge tube, purified using Agencourt AMPure XP beads and eluted with 30μl TE buffer.  1μl purified library was used to measure the fragment size distribution using the Agilent HS DNA BioAnalyzer chip and another 1μl of the purified library was loaded into Qubit fluorometer to estimate library concentration according to the manufacturer's instructions.  Libraries were sequenced on an Illumina HiSeq 2500 sequencer to obtain paired-end 25bp reads.

tag: genotype/variation

value: Wild type

tag: developmental stage

value: Hatching larva

tag: cell type

value: Trunk ventral cells

tag: cell subtype

value: Multipotent cardiopharyngeal progenitor cells


title: hpf20-30

description:
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hpf20.txt
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title: hpf20-28

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title: hpf18-384

description:
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hpf18.txt
wei-18-iv-96

source_name: ScRNA-seq of FACS purified cardiopharyngeal progenitors_18hpf


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hpf16_p4_96_R1

source_name: ScRNA-seq of FACS purified cardiopharyngeal progenitors_16hpf

value: Late tailbud III


title: hpf18-1

description:
processed data file:
hpf18.txt
wei-18-i-1


title: hpf16-190

description:
processed data file:
hpf16.txt
hpf16_p4_95_R1


title: hpf16-189

description:
processed data file:
hpf16.txt
hpf16_p4_94_R1


title: hpf16-192

description:
processed data file:
hpf16.txt
hpf16_p4_9_R1


title: hpf16-186

description:
processed data file:
hpf16.txt
hpf16_p4_91_R1


title: hpf16-187

description:
processed data file:
hpf16.txt
hpf16_p4_92_R1


title: hpf16-188

description:
processed data file:
hpf16.txt
hpf16_p4_93_R1


title: hpf16-184

description:
processed data file:
hpf16.txt
hpf16_p4_8_R1


title: hpf16-181

description:
processed data file:
hpf16.txt
hpf16_p4_87_R1


title: hpf16-185

description:
processed data file:
hpf16.txt
hpf16_p4_90_R1


title: hpf16-179

description:
processed data file:
hpf16.txt
hpf16_p4_85_R1


title: hpf16-183

description:
processed data file:
hpf16.txt
hpf16_p4_89_R1


title: hpf18-8

description:
processed data file:
hpf18.txt
wei-18-i-16


title: hpf16-182

description:
processed data file:
hpf16.txt
hpf16_p4_88_R1


title: hpf16-177

description:
processed data file:
hpf16.txt
hpf16_p4_83_R1


title: hpf18-6

description:
processed data file:
hpf18.txt
wei-18-i-14


title: hpf16-174

description:
processed data file:
hpf16.txt
hpf16_p4_80_R1


title: hpf16-175

description:
processed data file:
hpf16.txt
hpf16_p4_81_R1


title: hpf16-172

description:
processed data file:
hpf16.txt
hpf16_p4_79_R1


title: hpf16-171

description:
processed data file:
hpf16.txt
hpf16_p4_78_R1


title: hpf16-169

description:
processed data file:
hpf16.txt
hpf16_p4_76_R1


title: hpf16-170

description:
processed data file:
hpf16.txt
hpf16_p4_77_R1


title: hpf16-180

description:
processed data file:
hpf16.txt
hpf16_p4_86_R1


title: hpf16-167

description:
processed data file:
hpf16.txt
hpf16_p4_74_R1


title: hpf16-163

description:
processed data file:
hpf16.txt
hpf16_p4_70_R1


title: hpf16-165

description:
processed data file:
hpf16.txt
hpf16_p4_72_R1


title: hpf16-178

description:
processed data file:
hpf16.txt
hpf16_p4_84_R1


title: hpf16-164

description:
processed data file:
hpf16.txt
hpf16_p4_71_R1


title: hpf16-176

description:
processed data file:
hpf16.txt
hpf16_p4_82_R1


title: hpf16-160

description:
processed data file:
hpf16.txt
hpf16_p4_68_R1


title: hpf16-158

description:
processed data file:
hpf16.txt
hpf16_p4_66_R1


title: hpf16-156

description:
processed data file:
hpf16.txt
hpf16_p4_64_R1


title: hpf16-159

description:
processed data file:
hpf16.txt
hpf16_p4_67_R1


title: hpf16-157

description:
processed data file:
hpf16.txt
hpf16_p4_65_R1


title: hpf16-152

description:
processed data file:
hpf16.txt
hpf16_p4_60_R1


title: hpf16-154

description:
processed data file:
hpf16.txt
hpf16_p4_62_R1


title: hpf16-161

description:
processed data file:
hpf16.txt
hpf16_p4_69_R1


title: hpf16-153

description:
processed data file:
hpf16.txt
hpf16_p4_61_R1


title: hpf16-151

description:
processed data file:
hpf16.txt
hpf16_p4_5_R1


title: hpf16-150

description:
processed data file:
hpf16.txt
hpf16_p4_59_R1


title: hpf16-173

description:
processed data file:
hpf16.txt
hpf16_p4_7_R1


title: hpf16-149

description:
processed data file:
hpf16.txt
hpf16_p4_58_R1


title: hpf16-148

description:
processed data file:
hpf16.txt
hpf16_p4_57_R1


title: hpf16-147

description:
processed data file:
hpf16.txt
hpf16_p4_56_R1


title: hpf16-166

description:
processed data file:
hpf16.txt
hpf16_p4_73_R1


title: hpf16-162

description:
processed data file:
hpf16.txt
hpf16_p4_6_R1


title: hpf16-146

description:
processed data file:
hpf16.txt
hpf16_p4_55_R1


title: hpf16-144

description:
processed data file:
hpf16.txt
hpf16_p4_53_R1


title: hpf16-143

description:
processed data file:
hpf16.txt
hpf16_p4_52_R1


title: hpf16-142

description:
processed data file:
hpf16.txt
hpf16_p4_51_R1


title: hpf16-141

description:
processed data file:
hpf16.txt
hpf16_p4_50_R1


title: hpf16-140

description:
processed data file:
hpf16.txt
hpf16_p4_4_R1


title: hpf16-138

description:
processed data file:
hpf16.txt
hpf16_p4_48_R1


title: hpf16-137

description:
processed data file:
hpf16.txt
hpf16_p4_47_R1


title: hpf16-135

description:
processed data file:
hpf16.txt
hpf16_p4_45_R1


title: hpf16-134

description:
processed data file:
hpf16.txt
hpf16_p4_44_R1


title: hpf16-133

description:
processed data file:
hpf16.txt
hpf16_p4_43_R1


title: hpf16-130

description:
processed data file:
hpf16.txt
hpf16_p4_40_R1


title: hpf16-129

description:
processed data file:
hpf16.txt
hpf16_p4_3_R1


title: hpf16-136

description:
processed data file:
hpf16.txt
hpf16_p4_46_R1


title: hpf16-127

description:
processed data file:
hpf16.txt
hpf16_p4_38_R1


title: hpf16-126

description:
processed data file:
hpf16.txt
hpf16_p4_37_R1


title: hpf16-131

description:
processed data file:
hpf16.txt
hpf16_p4_41_R1


title: hpf16-125

description:
processed data file:
hpf16.txt
hpf16_p4_36_R1


title: hpf16-128

description:
processed data file:
hpf16.txt
hpf16_p4_39_R1


title: hpf16-124

description:
processed data file:
hpf16.txt
hpf16_p4_35_R1


title: hpf16-123

description:
processed data file:
hpf16.txt
hpf16_p4_34_R1


title: hpf16-120

description:
processed data file:
hpf16.txt
hpf16_p4_31_R1


title: hpf16-121

description:
processed data file:
hpf16.txt
hpf16_p4_32_R1


title: hpf16-122

description:
processed data file:
hpf16.txt
hpf16_p4_33_R1


title: hpf16-119

description:
processed data file:
hpf16.txt
hpf16_p4_30_R1


title: hpf16-118

description:
processed data file:
hpf16.txt
hpf16_p4_2_R1


title: hpf16-115

description:
processed data file:
hpf16.txt
hpf16_p4_27_R1


title: hpf16-132

description:
processed data file:
hpf16.txt
hpf16_p4_42_R1


title: hpf16-168

description:
processed data file:
hpf16.txt
hpf16_p4_75_R1


title: hpf16-114

description:
processed data file:
hpf16.txt
hpf16_p4_26_R1


title: hpf16-113

description:
processed data file:
hpf16.txt
hpf16_p4_25_R1


title: hpf16-155

description:
processed data file:
hpf16.txt
hpf16_p4_63_R1


title: hpf16-106

description:
processed data file:
hpf16.txt
hpf16_p4_19_R1


title: hpf16-107

description:
processed data file:
hpf16.txt
hpf16_p4_1_R1


title: hpf16-111

description:
processed data file:
hpf16.txt
hpf16_p4_23_R1


title: hpf16-117

description:
processed data file:
hpf16.txt
hpf16_p4_29_R1


title: hpf16-108

description:
processed data file:
hpf16.txt
hpf16_p4_20_R1


title: hpf16-109

description:
processed data file:
hpf16.txt
hpf16_p4_21_R1


title: hpf16-112

description:
processed data file:
hpf16.txt
hpf16_p4_24_R1


title: hpf16-103

description:
processed data file:
hpf16.txt
hpf16_p4_16_R1


title: hpf16-102

description:
processed data file:
hpf16.txt
hpf16_p4_15_R1


title: hpf16-110

description:
processed data file:
hpf16.txt
hpf16_p4_22_R1


title: hpf16-99

description:
processed data file:
hpf16.txt
hpf16_p4_12_R1


title: hpf16-104

description:
processed data file:
hpf16.txt
hpf16_p4_17_R1


title: hpf16-101

description:
processed data file:
hpf16.txt
hpf16_p4_14_R1


title: hpf16-105

description:
processed data file:
hpf16.txt
hpf16_p4_18_R1


title: hpf16-95

description:
processed data file:
hpf16.txt
hpf16_p3_96_R1


title: hpf16-94

description:
processed data file:
hpf16.txt
hpf16_p3_95_R1


title: hpf16-97

description:
processed data file:
hpf16.txt
hpf16_p4_10_R1


title: hpf16-116

description:
processed data file:
hpf16.txt
hpf16_p4_28_R1


title: hpf16-145

description:
processed data file:
hpf16.txt
hpf16_p4_54_R1


title: hpf16-96

description:
processed data file:
hpf16.txt
hpf16_p3_9_R1


title: hpf16-98

description:
processed data file:
hpf16.txt
hpf16_p4_11_R1


title: hpf16-100

description:
processed data file:
hpf16.txt
hpf16_p4_13_R1


title: hpf16-93

description:
processed data file:
hpf16.txt
hpf16_p3_94_R1


title: hpf16-139

description:
processed data file:
hpf16.txt
hpf16_p4_49_R1


title: hpf16-92

description:
processed data file:
hpf16.txt
hpf16_p3_93_R1


title: hpf16-91

description:
processed data file:
hpf16.txt
hpf16_p3_92_R1


title: hpf16-87

description:
processed data file:
hpf16.txt
hpf16_p3_89_R1


title: hpf16-88

description:
processed data file:
hpf16.txt
hpf16_p3_8_R1


title: hpf16-90

description:
processed data file:
hpf16.txt
hpf16_p3_91_R1


title: hpf16-86

description:
processed data file:
hpf16.txt
hpf16_p3_88_R1


title: hpf16-80

description:
processed data file:
hpf16.txt
hpf16_p3_82_R1


title: hpf16-84

description:
processed data file:
hpf16.txt
hpf16_p3_86_R1


title: hpf16-85

description:
processed data file:
hpf16.txt
hpf16_p3_87_R1


title: hpf16-82

description:
processed data file:
hpf16.txt
hpf16_p3_84_R1


title: hpf16-83

description:
processed data file:
hpf16.txt
hpf16_p3_85_R1


title: hpf16-79

description:
processed data file:
hpf16.txt
hpf16_p3_81_R1


title: hpf16-75

description:
processed data file:
hpf16.txt
hpf16_p3_78_R1


title: hpf16-76

description:
processed data file:
hpf16.txt
hpf16_p3_79_R1


title: hpf16-74

description:
processed data file:
hpf16.txt
hpf16_p3_77_R1


title: hpf16-73

description:
processed data file:
hpf16.txt
hpf16_p3_76_R1


title: hpf16-77

description:
processed data file:
hpf16.txt
hpf16_p3_7_R1


title: hpf16-71

description:
processed data file:
hpf16.txt
hpf16_p3_74_R1


title: hpf16-67

description:
processed data file:
hpf16.txt
hpf16_p3_70_R1


title: hpf16-66

description:
processed data file:
hpf16.txt
hpf16_p3_6_R1


title: hpf16-65

description:
processed data file:
hpf16.txt
hpf16_p3_69_R1


title: hpf16-70

description:
processed data file:
hpf16.txt
hpf16_p3_73_R1


title: hpf16-89

description:
processed data file:
hpf16.txt
hpf16_p3_90_R1


title: hpf16-64

description:
processed data file:
hpf16.txt
hpf16_p3_68_R1


title: hpf16-63

description:
processed data file:
hpf16.txt
hpf16_p3_67_R1


title: hpf16-81

description:
processed data file:
hpf16.txt
hpf16_p3_83_R1


title: hpf16-58

description:
processed data file:
hpf16.txt
hpf16_p3_62_R1


title: hpf16-78

description:
processed data file:
hpf16.txt
hpf16_p3_80_R1


title: hpf16-59

description:
processed data file:
hpf16.txt
hpf16_p3_63_R1


title: hpf16-61

description:
processed data file:
hpf16.txt
hpf16_p3_65_R1


title: hpf16-56

description:
processed data file:
hpf16.txt
hpf16_p3_60_R1


title: hpf16-52

description:
processed data file:
hpf16.txt
hpf16_p3_57_R1


title: hpf16-57

description:
processed data file:
hpf16.txt
hpf16_p3_61_R1


title: hpf16-54

description:
processed data file:
hpf16.txt
hpf16_p3_59_R1


title: hpf16-55

description:
processed data file:
hpf16.txt
hpf16_p3_5_R1


title: hpf16-68

description:
processed data file:
hpf16.txt
hpf16_p3_71_R1


title: hpf16-50

description:
processed data file:
hpf16.txt
hpf16_p3_55_R1


title: hpf16-47

description:
processed data file:
hpf16.txt
hpf16_p3_52_R1


title: hpf16-72

description:
processed data file:
hpf16.txt
hpf16_p3_75_R1


title: hpf16-48

description:
processed data file:
hpf16.txt
hpf16_p3_53_R1


title: hpf16-46

description:
processed data file:
hpf16.txt
hpf16_p3_51_R1


title: hpf16-45

description:
processed data file:
hpf16.txt
hpf16_p3_50_R1


title: hpf16-69

description:
processed data file:
hpf16.txt
hpf16_p3_72_R1


title: hpf16-44

description:
processed data file:
hpf16.txt
hpf16_p3_4_R1


title: hpf16-40

description:
processed data file:
hpf16.txt
hpf16_p3_46_R1


title: hpf16-41

description:
processed data file:
hpf16.txt
hpf16_p3_47_R1


title: hpf16-60

description:
processed data file:
hpf16.txt
hpf16_p3_64_R1


title: hpf16-43

description:
processed data file:
hpf16.txt
hpf16_p3_49_R1


title: hpf16-42

description:
processed data file:
hpf16.txt
hpf16_p3_48_R1


title: hpf16-39

description:
processed data file:
hpf16.txt
hpf16_p3_45_R1


title: hpf16-38

description:
processed data file:
hpf16.txt
hpf16_p3_44_R1


title: hpf16-53

description:
processed data file:
hpf16.txt
hpf16_p3_58_R1


title: hpf16-36

description:
processed data file:
hpf16.txt
hpf16_p3_42_R1


title: hpf16-35

description:
processed data file:
hpf16.txt
hpf16_p3_41_R1


title: hpf16-49

description:
processed data file:
hpf16.txt
hpf16_p3_54_R1


title: hpf16-34

description:
processed data file:
hpf16.txt
hpf16_p3_40_R1


title: hpf16-51

description:
processed data file:
hpf16.txt
hpf16_p3_56_R1


title: hpf16-33

description:
processed data file:
hpf16.txt
hpf16_p3_3_R1


title: hpf16-37

description:
processed data file:
hpf16.txt
hpf16_p3_43_R1


title: hpf16-32

description:
processed data file:
hpf16.txt
hpf16_p3_39_R1


title: hpf16-30

description:
processed data file:
hpf16.txt
hpf16_p3_37_R1


title: hpf16-28

description:
processed data file:
hpf16.txt
hpf16_p3_35_R1


title: hpf16-29

description:
processed data file:
hpf16.txt
hpf16_p3_36_R1


title: hpf16-27

description:
processed data file:
hpf16.txt
hpf16_p3_34_R1


title: hpf16-22

description:
processed data file:
hpf16.txt
hpf16_p3_2_R1


title: hpf16-24

description:
processed data file:
hpf16.txt
hpf16_p3_31_R1


title: hpf16-21

description:
processed data file:
hpf16.txt
hpf16_p3_29_R1


title: hpf16-23

description:
processed data file:
hpf16.txt
hpf16_p3_30_R1


title: hpf16-20

description:
processed data file:
hpf16.txt
hpf16_p3_28_R1


title: hpf16-25

description:
processed data file:
hpf16.txt
hpf16_p3_32_R1


title: hpf16-26

description:
processed data file:
hpf16.txt
hpf16_p3_33_R1


title: hpf16-17

description:
processed data file:
hpf16.txt
hpf16_p3_25_R1


title: hpf16-14

description:
processed data file:
hpf16.txt
hpf16_p3_22_R1


title: hpf16-19

description:
processed data file:
hpf16.txt
hpf16_p3_27_R1


title: hpf16-18

description:
processed data file:
hpf16.txt
hpf16_p3_26_R1


title: hpf16-16

description:
processed data file:
hpf16.txt
hpf16_p3_24_R1


title: hpf16-15

description:
processed data file:
hpf16.txt
hpf16_p3_23_R1


title: hpf16-31

description:
processed data file:
hpf16.txt
hpf16_p3_38_R1


title: hpf16-7

description:
processed data file:
hpf16.txt
hpf16_p3_16_R1


title: hpf16-9

description:
processed data file:
hpf16.txt
hpf16_p3_18_R1


title: hpf16-8

description:
processed data file:
hpf16.txt
hpf16_p3_17_R1


title: hpf16-12

description:
processed data file:
hpf16.txt
hpf16_p3_20_R1


title: hpf16-5

description:
processed data file:
hpf16.txt
hpf16_p3_14_R1


title: hpf16-3

description:
processed data file:
hpf16.txt
hpf16_p3_12_R1


title: hpf16-4

description:
processed data file:
hpf16.txt
hpf16_p3_13_R1


title: hpf14-576

description:
processed data file:
hpf14.txt
hpf14-S9

source_name: ScRNA-seq of FACS purified cardiopharyngeal progenitors_14hpf

value: Late tailbud II


title: hpf16-2

description:
processed data file:
hpf16.txt
hpf16_p3_11_R1


title: hpf16-1

description:
processed data file:
hpf16.txt
hpf16_p3_10_R1


title: hpf16-6

description:
processed data file:
hpf16.txt
hpf16_p3_15_R1


title: hpf14-567

description:
processed data file:
hpf14.txt
hpf14-S91


title: hpf14-569

description:
processed data file:
hpf14.txt
hpf14-S93


title: hpf14-570

description:
processed data file:
hpf14.txt
hpf14-S94


title: hpf14-573

description:
processed data file:
hpf14.txt
hpf14-S97


title: hpf14-574

description:
processed data file:
hpf14.txt
hpf14-S98


title: hpf16-13

description:
processed data file:
hpf16.txt
hpf16_p3_21_R1


title: hpf14-572

description:
processed data file:
hpf14.txt
hpf14-S96


title: hpf14-575

description:
processed data file:
hpf14.txt
hpf14-S99


title: hpf16-11

description:
processed data file:
hpf16.txt
hpf16_p3_1_R1


title: hpf14-563

description:
processed data file:
hpf14.txt
hpf14-S88


title: hpf16-10

description:
processed data file:
hpf16.txt
hpf16_p3_19_R1


title: hpf14-565

description:
processed data file:
hpf14.txt
hpf14-S8


title: hpf14-566

description:
processed data file:
hpf14.txt
hpf14-S90


title: hpf14-562

description:
processed data file:
hpf14.txt
hpf14-S87


title: hpf14-564

description:
processed data file:
hpf14.txt
hpf14-S89


title: hpf14-561

description:
processed data file:
hpf14.txt
hpf14-S86


title: hpf14-560

description:
processed data file:
hpf14.txt
hpf14-S85


title: hpf14-558

description:
processed data file:
hpf14.txt
hpf14-S83


title: hpf14-559

description:
processed data file:
hpf14.txt
hpf14-S84


title: hpf14-557

description:
processed data file:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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title: hpf14-165

description:
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title: hpf14-163

description:
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title: hpf14-158

description:
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title: hpf14-156

description:
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title: hpf14-157

description:
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hpf14-S241


title: hpf14-160

description:
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hpf14-S244


title: hpf14-181

description:
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hpf14-S263


title: 15-100 DG dissociated 101-DG-4

city: Davis

first: Rayna

middle: Michelle

last: Harris

state: CA

address: 1 Shields Ave

institute: University of California Davis

data_processing:
Raw reads were downloaded from the Amazon cloud server to the Stampede Cluster at the Texas Advanced Computing Facility for processing and analysis.
RNA quality was checked using the bioinformatic program FASTQC.
Low quality reads and adapter sequences were removed using the program Cutadapt.
To explore gross patterns at the whole transcriptome level, we used a Kallisto for read counting and mapping.
We used DESeq2 for gene expression normalization and quantification
We used the a rank-based gene ontology analysis of gene expression data using the R package GO MWU
Statistics on the principal component analyses were conduct in R
Genome_build: Gencode MV11 mouse transcriptome
Supplementary_files_format_and_content: kallisto count files

molecule: total RNA

organism: Mus musculus

source_name: DG

extract_protocol:
RNA from CA1, CA3, and from DG was isolated using the Maxwell 16 LEV RNA Isolation Kit (Promega).
NA libraries were prepared by the Genomic Sequencing and Analysis Facility at the University of Texas at Austin using the Illumina HiSeq platform.

treatment_protocol: One sample was designated for the control homogenized processing and the other for the cellular dissociation treatment . The homogenized tissue sample was placed prepared using the Maxwell 16 LEV RNA Isolation Kit (Promega). The sample was incubated for 75 minutes in aCSF containing 1 mg/ml pronase at RT, then vortexed and centrifuged. The incubation was determined by replacing aCSF containing pronase with aCSF. Sample was then vortexed, centrifuged, and gently triturated by 200-μl pipette tip twenty times in aCSF containing 1% FBS. The sample was centrifuged used as input for the Maxwell 16 LEV RNA Isolation Kit (Promega).

tag: strain

tag: treatment

value: dissociated


title: hpf14-154

description:
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hpf14.txt
hpf14-S239


title: hpf14-170

description:
processed data file:
hpf14.txt
hpf14-S253


title: hpf14-153

description:
processed data file:
hpf14.txt
hpf14-S238


title: 15-100 CA3 dissociated 101-CA3-1


title: 15-100 CA1 dissociated 101-CA1-2


title: hpf14-150

description:
processed data file:
hpf14.txt
hpf14-S235


title: hpf14-152

description:
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hpf14.txt
hpf14-S237


title: hpf14-161

description:
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hpf14.txt
hpf14-S245


title: hpf14-162

description:
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hpf14.txt
hpf14-S246


title: hpf14-149

description:
processed data file:
hpf14.txt
hpf14-S234


title: hpf14-159

description:
processed data file:
hpf14.txt
hpf14-S243


title: 15-100 DG control 100-DG-2

value: control


title: hpf14-155

description:
processed data file:
hpf14.txt
hpf14-S23


title: hpf14-180

description:
processed data file:
hpf14.txt
hpf14-S262


title: 15-100 CA3 control 100-CA3-1


title: 15-100 CA1 control 100-CA1-2


title: 15-100 CA1 control 100-CA1-1


title: hpf14-151

description:
processed data file:
hpf14.txt
hpf14-S236


title: 15-100 DG dissociated 101-DG-3


title: 15-100 CA3 dissociated 101-CA3-4


title: 15-100 CA1 dissociated 101-CA1-1


title: 15-100 DG control 100-DG-3


title: hpf14-143

description:
processed data file:
hpf14.txt
hpf14-S229


title: hpf14-141

description:
processed data file:
hpf14.txt
hpf14-S227


title: hpf14-140

description:
processed data file:
hpf14.txt
hpf14-S226


title: hpf14-148

description:
processed data file:
hpf14.txt
hpf14-S233


title: hpf14-139

description:
processed data file:
hpf14.txt
hpf14-S225


title: 15-100 CA1 dissociated 101-CA1-3


title: hpf14-147

description:
processed data file:
hpf14.txt
hpf14-S232


title: 15-100 CA3 control 100-CA3-4


title: NS1_L132A_L133A_rep1

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

description: single-end demultiplexed

data_processing:
Fastq files for each sample were aligned to hg38 genome (Release 23 Gencode, GRCh38.p3) using STAR  with following options --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outReadsUnmapped Fastx --outSAMstrandField All. Each sample was evaluated according to a variety of both pre- and post-alignment QC measures with Picard tools. To assess batch effects in data set we used hierarchical clustering (average linkage algorithm with 1 minus the Pearson correlation coefficient as the dissimilarity measure) and principal component analysis. Aligned reads were quantified using quant3p script (github.com/ctlab/quant3p) to account for specifics of 3' sequencing: higher dependency on good 3' annotation and lower level of sequence specificity close to 3' end. Actual read contings were carried out by HTSeq with enriched genome annotation and alignment with fixed multimapper flags. For analysis, two or three replicates from each condition were used, due to presence of outliers for some conditions.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited file that includes raw count data for each sample and tab delimited file with barcode annotations.

organism: Homo sapiens

source_name: Cell line A549

extract_protocol: mRNA was prepared using Dynabeads mRNA kit (Invitrogen) and fragmented by heat. For cDNA synthesis, custom oligo-dT primers were used with a barcode and an adapter-linker sequence (CAG ACG TGT GCT CTT CCG ATC T—XXXXXXXX-T15) and with the Affinity Script enzyme (Agilent). After first strand synthesis, samples were pooled together based on ACTB qPCR values. RNA-DNA hybrids was degraded using consecutive acid-alkali treatment. A second sequencing linker (AGA TCG GAA GAG CGT CGT GTAG) was then ligated using T4 ligase (NEB). The mixture was then PCR enriched for 12 cycles and purified to yield final strand specific RNA-seq libraries as previously described55. Libraries were sequenced using a HiSeq 2500 (Illumina) using 50bp x 25bp pair-end sequencing.

tag: cell line

tag: hour post infection

tag: infectious agent

value: hRSV NS1 L132A/L133A


title: NS1_1_118_rep3

description: single-end demultiplexed

value: hRSV NS1 1-118


title: hpf14-145

description:
processed data file:
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hpf14-S230


title: hpf14-146

description:
processed data file:
hpf14.txt
hpf14-S231


title: hpf14-144

description:
processed data file:
hpf14.txt
hpf14-S22


title: hpf14-135

description:
processed data file:
hpf14.txt
hpf14-S221


title: hpf14-137

description:
processed data file:
hpf14.txt
hpf14-S223


title: NS1_1_118_rep1

description: single-end demultiplexed


title: 15-100 CA1 control 100-CA1-3


title: NS1_WT_rep3

description: single-end demultiplexed

value: hRSV WT


title: hpf14-133

description:
processed data file:
hpf14.txt
hpf14-S21


title: hpf14-134

description:
processed data file:
hpf14.txt
hpf14-S220


title: NS1_Y125A_rep2

description: single-end demultiplexed

value: hRSV NS1 Y125A


title: hpf14-142

description:
processed data file:
hpf14.txt
hpf14-S228


title: NS1_Y125A_rep1

description: single-end demultiplexed


title: hpf14-138

description:
processed data file:
hpf14.txt
hpf14-S224


title: NS1_L132A_L133A_rep2

description: single-end demultiplexed


title: hpf14-131

description:
processed data file:
hpf14.txt
hpf14-S218


title: NS1_1_118_rep2

description: single-end demultiplexed


title: NS1_WT_rep1

description: single-end demultiplexed


title: hpf14-132

description:
processed data file:
hpf14.txt
hpf14-S219


title: mock_rep2

description: single-end demultiplexed

value: mock


title: mock_rep1

description: single-end demultiplexed


title: hpf14-136

description:
processed data file:
hpf14.txt
hpf14-S222


title: hpf14-130

description:
processed data file:
hpf14.txt
hpf14-S217


title: hpf14-129

description:
processed data file:
hpf14.txt
hpf14-S216


title: PrimaryAstrocytes_non_activated_rep1

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
mRNA
Processed data file: raw.txt
Processed data file: fpkm.txt

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite and differential gene expression was carried out using the edgeR package v3.6.8 using duplicates to compute within-group dispersion. FDR < 0.05 and log2 fold change greater than 0.5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: fpkm.txt: Tab-delimited text file includes fpkm normalized table.

source_name: cerebellum

growth_protocol: The growth protocols have been described in our study (Santos et al.)

extract_protocol:
in vitro derivation from human iPSC.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: primary astrocytes

tag: age

value: fetal


title: hpf14-128

description:
processed data file:
hpf14.txt
hpf14-S215


title: PrimaryAstrocytes_non_activated_rep2


title: PrimaryAstrocytes_activated_rep2


title: hpf14-127

description:
processed data file:
hpf14.txt
hpf14-S214


title: hpf14-126

description:
processed data file:
hpf14.txt
hpf14-S213


title: PrimaryAstrocytes_activated_rep1


title: hpf14-125

description:
processed data file:
hpf14.txt
hpf14-S212


title: iPS_NPC2_non-activated_rep2

source_name: skin biopsy

value: induced pluripotent stem cells-derived neural precursor cells

tag: genotype

value: neurotypical


title: iPS_NPC2_activated_rep2


title: iPS_NPC2_non-activated_rep1


title: NS1_WT_rep2

description: single-end demultiplexed


title: hpf14-124

description:
processed data file:
hpf14.txt
hpf14-S211

value: Wild type


title: hpf14-121

description:
processed data file:
hpf14.txt
hpf14-S209


title: iPS_NPC1_non-activated_rep2


title: hpf14-122

description:
processed data file:
hpf14.txt
hpf14-S20


title: iPS_NPC2_activated_rep1


title: hpf14-123

description:
processed data file:
hpf14.txt
hpf14-S210


title: iPS_NPC1_non-activated_rep1


title: iPS_NPC1_activated_rep2


title: iPS_NPC1_activated_rep1


title: hpf14-120

description:
processed data file:
hpf14.txt
hpf14-S208


title: hpf14-118

description:
processed data file:
hpf14.txt
hpf14-S206


title: hiPSC_Astrocytes3_non-activated_rep1

value: induced pluripotent stem cells-derived astrocytes


title: hiPSC_Astrocytes3_non-activated_rep2


title: hpf14-119

description:
processed data file:
hpf14.txt
hpf14-S207

value: Trunk ventral cells


title: hiPSC_Astrocytes3_activated_rep2


title: hpf14-117

description:
processed data file:
hpf14.txt
hpf14-S205

value: Multipotent cardiopharyngeal progenitor cells


title: hpf14-116

description:
processed data file:
hpf14.txt
hpf14-S204


title: hiPSC_Astrocytes3_activated_rep1


title: hpf14-114

description:
processed data file:
hpf14.txt
hpf14-S202


title: hpf14-115

description:
processed data file:
hpf14.txt
hpf14-S203


title: hiPSC_Astrocytes2_non-activated_rep2


title: hpf14-113

description:
processed data file:
hpf14.txt
hpf14-S201


title: hiPSC_Astrocytes2_non-activated_rep1

description:
mRNA
Processed data file: raw.txt
Processed data file: fpkm.txt


title: hpf14-111

description:
processed data file:
hpf14.txt
hpf14-S1


title: hpf14-112

description:
processed data file:
hpf14.txt
hpf14-S200


title: hiPSC_Astrocytes2_activated_rep1


title: hiPSC_Astrocytes1_non-activated_rep2


title: hiPSC_Astrocytes1_non-activated_rep1


title: hpf14-109

description:
processed data file:
hpf14.txt
hpf14-S199


title: hiPSC_Astrocytes1_activated_rep2


title: hpf14-107

description:
processed data file:
hpf14.txt
hpf14-S197


title: hpf14-105

description:
processed data file:
hpf14.txt
hpf14-S195


title: hpf14-104

description:
processed data file:
hpf14.txt
hpf14-S194


title: hpf14-103

description:
processed data file:
hpf14.txt
hpf14-S193


title: hpf14-108

description:
processed data file:
hpf14.txt
hpf14-S198


title: hiPSC_Astrocytes1_activated_rep1


title: hpf14-100

description:
processed data file:
hpf14.txt
hpf14-S190


title: hpf14-95

description:
processed data file:
hpf14.txt
hpf14-S186


title: hpf14-99

description:
processed data file:
hpf14.txt
hpf14-S18


title: hpf14-101

description:
processed data file:
hpf14.txt
hpf14-S191


title: hpf14-92

description:
processed data file:
hpf14.txt
hpf14-S183


title: hpf14-93

description:
processed data file:
hpf14.txt
hpf14-S184


title: hpf14-91

description:
processed data file:
hpf14.txt
hpf14-S182


title: hpf14-96

description:
processed data file:
hpf14.txt
hpf14-S187


title: hpf14-90

description:
processed data file:
hpf14.txt
hpf14-S181


title: hpf14-89

description:
processed data file:
hpf14.txt
hpf14-S180


title: hpf14-87

description:
processed data file:
hpf14.txt
hpf14-S179


title: hpf14-88

description:
processed data file:
hpf14.txt
hpf14-S17


title: hpf14-86

description:
processed data file:
hpf14.txt
hpf14-S178


title: hpf14-110

description:
processed data file:
hpf14.txt
hpf14-S19


title: hpf14-106

description:
processed data file:
hpf14.txt
hpf14-S196


title: hpf14-85

description:
processed data file:
hpf14.txt
hpf14-S177


title: hpf14-84

description:
processed data file:
hpf14.txt
hpf14-S176


title: hpf14-83

description:
processed data file:
hpf14.txt
hpf14-S175


title: hpf14-97

description:
processed data file:
hpf14.txt
hpf14-S188


title: hpf14-82

description:
processed data file:
hpf14.txt
hpf14-S174


title: hpf14-81

description:
processed data file:
hpf14.txt
hpf14-S173


title: hpf14-98

description:
processed data file:
hpf14.txt
hpf14-S189


title: hpf14-102

description:
processed data file:
hpf14.txt
hpf14-S192


title: hpf14-79

description:
processed data file:
hpf14.txt
hpf14-S171


title: hpf14-76

description:
processed data file:
hpf14.txt
hpf14-S169


title: hpf14-94

description:
processed data file:
hpf14.txt
hpf14-S185


title: hpf14-75

description:
processed data file:
hpf14.txt
hpf14-S168


title: hpf14-74

description:
processed data file:
hpf14.txt
hpf14-S167


title: hpf14-77

description:
processed data file:
hpf14.txt
hpf14-S16


title: hpf14-78

description:
processed data file:
hpf14.txt
hpf14-S170


title: hpf14-73

description:
processed data file:
hpf14.txt
hpf14-S166


title: hpf14-67

description:
processed data file:
hpf14.txt
hpf14-S160


title: hpf14-68

description:
processed data file:
hpf14.txt
hpf14-S161


title: hpf14-62

description:
processed data file:
hpf14.txt
hpf14-S156


title: hpf14-72

description:
processed data file:
hpf14.txt
hpf14-S165


title: hpf14-70

description:
processed data file:
hpf14.txt
hpf14-S163


title: hpf14-59

description:
processed data file:
hpf14.txt
hpf14-S153


title: hpf14-69

description:
processed data file:
hpf14.txt
hpf14-S162


title: hpf14-66

description:
processed data file:
hpf14.txt
hpf14-S15


title: hpf14-63

description:
processed data file:
hpf14.txt
hpf14-S157


title: hpf14-65

description:
processed data file:
hpf14.txt
hpf14-S159


title: hpf14-60

description:
processed data file:
hpf14.txt
hpf14-S154


title: hpf14-80

description:
processed data file:
hpf14.txt
hpf14-S172