title: VEGFA TS1 PEACSeq 10F [T1.10F]

first: Lijia

last: Ma

address: Shilongshan Road No.18, Cloud Town, Xihu District

institute: Westlake university

description: VEGFA TS1 PEACSeq 10F

source_name: VEGFA TS1 PEACSeq 10F

tag: cell line

value: VEGFA TS1

value: GGGTGGGGGGAGTTTGCTCCTGG


title: 3D-Plasma-V1-3D_83

status: Public on Nov 13 2022

type: SRA

city: Chicoutimi

first: Luigi

last: Bouchard

state: Quebec

address: 305 rue Saint-Vallier, Pavillon des Augustines

department: Biochimie et génomique fonctionnelle

country: Canada

institute: Université de Sherbrooke

description:
83
3D-Plasma-V1-3D_83
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

library_source: transcriptomic

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with FASTX-Toolkit. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using STAR. As rRNA contamination was almost inexistant in our samples (average of 1.04±0.90% of total mapped reads based on metrics from STAR), the mapping step to the rRNA was removed to speed tup the process.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple sample (PMID : 30956140).
Samples with < 1M miRNAs reads were considered outliers and removed from the downstream analysis (differential analysis using DESeq2 package).
DESeq2 function collapseReplicates was used to combined technical replicates in the analysis for data that were extracted and sequenced twice. Technical replicate have the same ID and fastq files contains either "pilote" or "projet". Technical replicate are identified in the technical replicates column (N = 12 originally, 9 gave consent for genetic data sharing)
Assembly: GRCh37
Supplementary files format and content: tab-seperated value files include raw read counts (non-normalized) for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from either 500μl of plasma kept at −80 °C until extraction. Seventy-five μl of nuclease-free water was used to eluate total RNA which was then precipitated following the method described by Burgos et al. (PMID: 23525801). Briefly, 35 μl of cold (4°C) 7 M ammonium acetate solution (ThermoFisher Scientific, catalogue # 02002268) were added to 70μl of total RNA. This was followed by the addition of 420μl of chilled (−20°C) absolute ethanol (Commercial Alcohols, ON, Canada; catalogue # P006EAAN) and overnight precipitation at −20°C. The mix was then centrifuged at 16 000g at 4°C for 30 min. RNA pellets were then washed twice with 200 μl of cold 80% ethanol followed by centrifugation at 16 000g at 4°C for 5min. It was then dried for 30min at room temperature and 5μl of nuclease-free water was added. The total volume was used for library preparation.
Samples were randomized before library preparation. An adapted version of the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) protocol from Burgos et al. (PMID: 23525801) was used to manage low concentrated miRNA samples. In this protocol, half of the standard volumes were used for ligation (3′ and 5′ ends) of RNA sample (5μl), reverse transcription, barcoding (index 1-20: one index per sample) and PCR amplification (15 cycles) to preserve the ratio between RNA amount (which is lower in plasma samples) and the reagents. Purification and size-selection (145-160bp) of the libraries were done by migration on a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, catalogue # EC6265BOX) followed by elution in 300 μl of nuclease-free water and overnight incubation at 500 RPM at room temperature on an incubating microplate shaker (VWR, ON, Canada, catalogue #12620-930). The libraries were then precipitated according to the manufacturer's instructions (including incubation of the precipitation mix at −80°C for 30min) and were resuspended in 25 μl of 10 mM Tris-HCI pH 8.5 buffer. Library sequencing, including quality control and sample pooling, was performed at the McGill University and Génome Québec Innovation Centre (Québec, Canada). Libraries were first quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) and the average size fragment was determined using a LabChip GX II (PerkinElmer) instrument. The libraries were normalized and pooled before being denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM on an Illumina NovaSeq S1 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 1x100 cycles (single-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads. Ten samples were extracted and sequenced twice to account for batch preparation and to confirm standardization.

tag: tissue

value: Plasma

tag: Sex

value: female

tag: pregnancy status_1

value: Gestational diabetes mellitus


title: 3D-Plasma-V1-3D_90

description:
90
3D-Plasma-V1-3D_90
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Normal


title: 3D-Plasma-V1-3D_87

description:
87
3D-Plasma-V1-3D_87
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_81

description:
81
3D-Plasma-V1-3D_81
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_82

description:
82
3D-Plasma-V1-3D_82
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_80

description:
80
3D-Plasma-V1-3D_80
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_7

description:
7
3D-Plasma-V1-3D_7
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_78

description:
78
3D-Plasma-V1-3D_78
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_79

description:
79
3D-Plasma-V1-3D_79
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_74

description:
74
3D-Plasma-V1-3D_74
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_73

description:
73
3D-Plasma-V1-3D_73
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_75

description:
75
3D-Plasma-V1-3D_75
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_77

description:
77
3D-Plasma-V1-3D_77
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_76

description:
76
3D-Plasma-V1-3D_76
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_72

description:
72
3D-Plasma-V1-3D_72
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_71

description:
71
3D-Plasma-V1-3D_71
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_66

description:
66
3D-Plasma-V1-3D_66
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_6

description:
6
3D-Plasma-V1-3D_6
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_69

description:
69
3D-Plasma-V1-3D_69
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_68

description:
68
3D-Plasma-V1-3D_68
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_65

description:
65
3D-Plasma-V1-3D_65
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_86

description:
86
3D-Plasma-V1-3D_86
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_59

description:
59
3D-Plasma-V1-3D_59
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_58

description:
58
3D-Plasma-V1-3D_58
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_64

description:
64
3D-Plasma-V1-3D_64
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Other pregnancy complications


title: 3D-Plasma-V1-3D_63

description:
63
3D-Plasma-V1-3D_63
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_5

description:
5
3D-Plasma-V1-3D_5
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_57

description:
57
3D-Plasma-V1-3D_57
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_60

description:
60
3D-Plasma-V1-3D_60
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_61

description:
61
3D-Plasma-V1-3D_61
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_62

description:
62
3D-Plasma-V1-3D_62
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_55

description:
55
3D-Plasma-V1-3D_55
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_56

description:
56
3D-Plasma-V1-3D_56
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_54

description:
54
3D-Plasma-V1-3D_54
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_53

description:
53
3D-Plasma-V1-3D_53
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_70

description:
70
3D-Plasma-V1-3D_70
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_67

description:
67
3D-Plasma-V1-3D_67
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_52

description:
52
3D-Plasma-V1-3D_52
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_48

description:
48
3D-Plasma-V1-3D_48
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_4

description:
4
3D-Plasma-V1-3D_4
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_50

description:
50
3D-Plasma-V1-3D_50
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_46

description:
46
3D-Plasma-V1-3D_46
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_49

description:
49
3D-Plasma-V1-3D_49
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_40

description:
40
3D-Plasma-V1-3D_40
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_47

description:
47
3D-Plasma-V1-3D_47
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_43

description:
43
3D-Plasma-V1-3D_43
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_45

description:
45
3D-Plasma-V1-3D_45
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_39

description:
39
3D-Plasma-V1-3D_39
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_3

description:
3
3D-Plasma-V1-3D_3
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_44

description:
44
3D-Plasma-V1-3D_44
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_38

description:
38
3D-Plasma-V1-3D_38
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_36

description:
36
3D-Plasma-V1-3D_36
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_42

description:
42
3D-Plasma-V1-3D_42
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_34

description:
34
3D-Plasma-V1-3D_34
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_35

description:
35
3D-Plasma-V1-3D_35
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_32

description:
32
3D-Plasma-V1-3D_32
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_31

description:
31
3D-Plasma-V1-3D_31
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_29

description:
29
3D-Plasma-V1-3D_29
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_30

description:
30
3D-Plasma-V1-3D_30
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_2

description:
2
3D-Plasma-V1-3D_2
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_28

description:
28
3D-Plasma-V1-3D_28
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_51

description:
51
3D-Plasma-V1-3D_51
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_27

description:
27
3D-Plasma-V1-3D_27
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_26

description:
26
3D-Plasma-V1-3D_26
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_41

description:
41
3D-Plasma-V1-3D_41
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_25

description:
25
3D-Plasma-V1-3D_25
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_235

description:
235
3D-Plasma-V1-3D_235
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

tag: pregnancy status_2


title: 3D-Plasma-V1-3D_23

description:
23
3D-Plasma-V1-3D_23
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_232

description:
232
3D-Plasma-V1-3D_232
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_233

description:
233
3D-Plasma-V1-3D_233
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_234

description:
234
3D-Plasma-V1-3D_234
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_22

description:
22
3D-Plasma-V1-3D_22
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_229

description:
229
3D-Plasma-V1-3D_229
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_228

description:
228
3D-Plasma-V1-3D_228
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_33

description:
33
3D-Plasma-V1-3D_33
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_24

description:
24
3D-Plasma-V1-3D_24
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_230

description:
230
3D-Plasma-V1-3D_230
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_37

description:
37
3D-Plasma-V1-3D_37
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_226

description:
226
3D-Plasma-V1-3D_226
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_225

description:
225
3D-Plasma-V1-3D_225
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_231

description:
231
3D-Plasma-V1-3D_231
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_221

description:
221
3D-Plasma-V1-3D_221
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_220

description:
220
3D-Plasma-V1-3D_220
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_21

description:
21
3D-Plasma-V1-3D_21
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_222

description:
222
3D-Plasma-V1-3D_222
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_223

description:
223
3D-Plasma-V1-3D_223
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_219

description:
219
3D-Plasma-V1-3D_219
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_218

description:
218
3D-Plasma-V1-3D_218
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_217

description:
217
3D-Plasma-V1-3D_217
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_216

description:
216
3D-Plasma-V1-3D_216
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_215

description:
215
3D-Plasma-V1-3D_215
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_ss_rep3

city: Delft

first: Diederik

last: Laman Trip

address: Van der Maasweg 9

department: Bionanoscience

country: Netherlands

institute: Delft University of Technology

description: mRNA

data_processing:
Salmon tool to quantify relative transcript abundance (see methods in the article for details of our methodology)
Assembly: reference transcripts for S. cerevisiae from Ensembl (assembly R64-1-1)
Supplementary files format and content: Salmon outputs (".sf"), readable as ".csv"

organism: Saccharomyces cerevisiae

source_name: steady-state mRNA levels

extract_protocol:
RiboPure Yeast RNA extraction kit (Thermo Fischer Scientific, cat. No. AM1926) following the kit instructions
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat

tag: temperature (degrees celcius)

tag: added gsh (um)


title: 3D-Plasma-V1-3D_214

description:
214
3D-Plasma-V1-3D_214
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_227

description:
227
3D-Plasma-V1-3D_227
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_213

description:
213
3D-Plasma-V1-3D_213
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_224

description:
224
3D-Plasma-V1-3D_224
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_t3_rep3

description: 4tU-labelled mRNA

source_name: 20 min after adding 4tU


title: w303_30C_t2_rep3

description: 4tU-labelled mRNA

source_name: 10 min after adding 4tU


title: 3D-Plasma-V1-3D_211

description:
211
3D-Plasma-V1-3D_211
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_t1_rep3

description: 4tU-labelled mRNA

source_name: 5 min after adding 4tU


title: w303_30C_t0_rep3

description: 4tU-labelled mRNA

source_name: reference for 30C and no GSH, right before adding 4tU


title: 3D-Plasma-V1-3D_20

description:
20
3D-Plasma-V1-3D_20
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_210

description:
210
3D-Plasma-V1-3D_210
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_208

description:
208
3D-Plasma-V1-3D_208
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: C4-2 Ctrl-2

city: Dallas

first: Xu

last: Li

state: Texas

address: 6000 Harry Hines Blvd.

department: Molecular Biology

country: USA

institute: University of Texas Southwestern Medical Center at Dallas

data_processing:
Fastq files were quality checked using fastqc (v0.11.2)
Read from each sample were mapped to the reference genome using STAR(v2.5.3a)
Read counts were generated using featureCounts
The differential expression analysis was performed using edgeR
Assembly: Human (hg19)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Tumor cell

growth_protocol: Cells were cultured in RPMI-1640 with 10% FBS.

extract_protocol:
Cellular RNA was extracted using Qiagen RNA extraction kit (Qiagen; Cat: 74104) according to the manufacturer’s instructions.
Libraries were prepared according to TruSeq Stranded mRNA Sample Preparation Kit.

treatment_protocol: With/without Dox 0.2mg/ml treatment for 24 hours

value: prostate cancer

tag: genotype

value: Tet-O-YAP5SA C4-2

tag: treatment

value: Ctrl


title: C4-2 Dox-1

value: Dox


title: 3D-Plasma-V1-3D_209

description:
209
3D-Plasma-V1-3D_209
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: C4-2 Ctrl-1


title: 3D-Plasma-V1-3D_207

description:
207
3D-Plasma-V1-3D_207
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: C4-2 Dox-3


title: w303_30C_ss_rep2

description: mRNA


title: 3D-Plasma-V1-3D_205

description:
205
3D-Plasma-V1-3D_205
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_204

description:
204
3D-Plasma-V1-3D_204
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_t3_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_203

description:
203
3D-Plasma-V1-3D_203
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_212

description:
212
3D-Plasma-V1-3D_212
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: C4-2 Dox-2


title: 3D-Plasma-V1-3D_202

description:
202
3D-Plasma-V1-3D_202
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Xoo KACC10331, in vitro, rep3

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

description: In vitro rep3

data_processing:
Raw data derived from RNA-seq was filtered to a minimum phred quality score of 28 in more than 50% of gene length, using FASTX-Toolkit.
The filtered reads were processed using the BWA-MEM algorithm with default parameters.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bam2readcount.
Reads per kilobase of gene per million mapped sequence reads were calculated for normalization.
Genome_build: Xanthomonas oryzae pv. oryzae KACC10331 ASM738v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Xanthomonas oryzae pv. oryzae KACC 10331

source_name: Bacterial culture, Xoo KACC10331

growth_protocol: Xoo KACC10331 was incubated on PSA media at 30 °C for 2 days with shaking at 200 rpm. After a subculture, the final inoculation concentration was adjusted into an optical density of 0.5 at 600 nm. Cultured bacteria cells were then collected by centrifugation, and resuspended in distilled water. Leafs of the rice cultivar Dongjin at the vegetative stage were inoculated by leaf-clipping method with bacterial resuspension. Inoculated plants were grown in a greenhouse (average 30 °C for day time and 25 °C for night time) for 10 days.

extract_protocol:
In the cold room (4 °C), the infected rice tissues were segmented into about 3 cm length, and immediately centrifuged at 4 °C with 2000 ×g for 5 min in 15 mL conical tubes to collect bacterial pellets. The in planta bacterial pellets contained 1.0 × 109 to 1.5 x 109 CFU/mL, that were primarily composed of Xoo KACC10331. For RNA extraction step, the bacterial pellets were treated with 2 mL of RNAprotectTM Bacteria Reagent.
Six ibraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq2000 instrument.

tag: pathovar

value: oryzae

tag: strain

value: wild-type

tag: condition

value: in vitro


title: 3D-Plasma-V1-3D_201

description:
201
3D-Plasma-V1-3D_201
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_t2_rep2

description: 4tU-labelled mRNA


title: C4-2 Ctrl-3


title: 3D-Plasma-V1-3D_200

description:
200
3D-Plasma-V1-3D_200
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Xoo KACC10331, in vitro, rep1

description: In vitro rep1


title: w303_30C_t1_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_1

description:
1
3D-Plasma-V1-3D_1
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_t0_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_199

description:
199
3D-Plasma-V1-3D_199
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_ss_rep1

description: mRNA


title: 3D-Plasma-V1-3D_206

description:
206
3D-Plasma-V1-3D_206
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_197

description:
197
3D-Plasma-V1-3D_197
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_198

description:
198
3D-Plasma-V1-3D_198
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_19

description:
19
3D-Plasma-V1-3D_19
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_196

description:
196
3D-Plasma-V1-3D_196
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_t3_rep1

description: 4tU-labelled mRNA


title: Xoo KACC10331, in planta, rep2

description: In planta rep2

source_name: In rice, Xoo KACC10331

value: in planta


title: 3D-Plasma-V1-3D_195

description:
195
3D-Plasma-V1-3D_195
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_t2_rep1

description: 4tU-labelled mRNA


title: Xoo KACC10331, in planta, rep3

description: In planta rep3


title: 3D-Plasma-V1-3D_194

description:
194
3D-Plasma-V1-3D_194
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_193

description:
193
3D-Plasma-V1-3D_193
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-9.5 NT, biological rep 4

type: RNA

city: LOUISVILLE

first: Partha

last: Mukhopadhyay

state: KY

address: 501 S PRESTON ST

department: Division of Craniofacial Development & Anomalies

institute: University of Louisville

description: Gene (microRNA) expression data from neural tubes of GD-9.5 embryos

hyb_protocol: Follwing labeling, biotin-labelled cRNAs were hybridized for 16 hr at 48C on Affymetrix GeneChip miRNA 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400, following the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

scan_protocol: GeneChips were scanned and the  fluorescence intensities were determined using an Affymetrix GeneChip Scanner 3000.

data_processing: GeneChip image processing was perfromed employing the Affymetrix® Expression Console Software (version 1.2.1). Further processed data is not available.

label: biotin

organism: Mus musculus

source_name: Mouse embryos of gestation day 9.5

label_protocol: For microRNA (miRNA) expression profiling, the total RNA (250 ng/sample) was labelled using the FlashTag Biotin HSR labeling kit (Genisphere, Hatfield, PA).

growth_protocol: Mature male and female ICR (CD-1) mice were housed by an American Association for Accreditation of Laboratory Animal Care (AAALAC)-approved facility, in rooms at 22°C, with a 12-hour alternating light/dark cycle, and were maintained on an appropriate brand of rodent chow and water ad libitum. Timed pregnancies were obtained by overnight mating of a single mature male with two nulliparous females. The presence of a vaginal plug the following morning was considered evidence of mating, and the time designated day 0 of gestation (GD 0).

extract_protocol: Total RNA (containing miRNA) from micro-dissected GD-8.5, -9.0 and -9.5 NT tissues was isolated using the Qiagen miRNeasy mini kit (Qiagen, Inc., Germantown, MD) according to the manufacturer’s instructions.

treatment_protocol: Female mice were euthanized by carbon dioxide asphyxiation followed by cervical dislocation on GD-8.5, -9.0, and -9.5, which spans the critical period of murine NT development in ICR mice.  Embryos were dissected from decidual tissues and immediately placed in ice-cold phosphate-buffered saline (PBS).

value: neural tube

value: ICR (CD-1) mice

tag: age

value: Embryonic day 9.5


title: w303_30C_t1_rep1

description: 4tU-labelled mRNA


title: Xoo KACC10331, in vitro, rep2

description: In vitro rep2


title: GD-9.5 NT, biological rep 3


title: 3D-Plasma-V1-3D_192

description:
192
3D-Plasma-V1-3D_192
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_191

description:
191
3D-Plasma-V1-3D_191
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_30C_t0_rep1

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_190

description:
190
3D-Plasma-V1-3D_190
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_18

description:
18
3D-Plasma-V1-3D_18
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_189

description:
189
3D-Plasma-V1-3D_189
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-9.5 NT, biological rep 2


title: GD-9.5 NT, biological rep 1


title: w303_5C_t7_GSH_rep3

description: 4tU-labelled mRNA

source_name: 96 hrs after adding 4tU


title: 3D-Plasma-V1-3D_187

description:
187
3D-Plasma-V1-3D_187
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Xoo KACC10331, in planta, rep1

description: In planta rep1


title: w303_5C_ss_GSH_rep3

description: mRNA


title: 3D-Plasma-V1-3D_188

description:
188
3D-Plasma-V1-3D_188
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-9.0 NT, biological rep 4

description: Gene (microRNA) expression data from neural tubes of GD-9.0 embryos

source_name: Mouse embryos of gestation day 9.0

value: Embryonic day 9.0


title: GD-9.0 NT, biological rep 3


title: 3D-Plasma-V1-3D_184

description:
184
3D-Plasma-V1-3D_184
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Plasma


title: 3D-Plasma-V1-3D_186

description:
186
3D-Plasma-V1-3D_186
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: female


title: GD-9.0 NT, biological rep 2


title: w303_5C_t5_GSH_rep3

description: 4tU-labelled mRNA

source_name: 24 hrs after adding 4tU


title: 3D-Plasma-V1-3D_183

description:
183
3D-Plasma-V1-3D_183
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_185

description:
185
3D-Plasma-V1-3D_185
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_180

description:
180
3D-Plasma-V1-3D_180
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t3_GSH_rep3

description: 4tU-labelled mRNA

source_name: 6 hrs after adding 4tU


title: 3D-Plasma-V1-3D_17

description:
17
3D-Plasma-V1-3D_17
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Gestational diabetes mellitus


title: GD-8.5 NT, biological rep 4

description: Gene (microRNA) expression data from neural tubes of GD-8.5 embryos

source_name: Mouse embryos of gestation day 8.5

value: Embryonic day 8.5


title: 3D-Plasma-V1-3D_178

description:
178
3D-Plasma-V1-3D_178
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Normal


title: 3D-Plasma-V1-3D_179

description:
179
3D-Plasma-V1-3D_179
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Other pregnancy complications


title: GD-8.5 NT, biological rep 3


title: 3D-Plasma-V1-3D_177

description:
177
3D-Plasma-V1-3D_177
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_175

description:
175
3D-Plasma-V1-3D_175
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_174

description:
174
3D-Plasma-V1-3D_174
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t1_GSH_rep3

description: 4tU-labelled mRNA

source_name: 1.5 hrs after adding 4tU


title: w303_5C_t2_GSH_rep3

description: 4tU-labelled mRNA

source_name: 3 hrs after adding 4tU


title: w303_5C_t6_GSH_rep3

description: 4tU-labelled mRNA

source_name: 48 hrs after adding 4tU


title: 3D-Plasma-V1-3D_173

description:
173
3D-Plasma-V1-3D_173
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

source_name: Plasma


title: GD-8.5 NT, biological rep 1


title: w303_5C_t0_GSH_rep3

description: 4tU-labelled mRNA

source_name: reference for 5C and with GSH, right before adding 4tU


title: 3D-Plasma-V1-3D_176

description:
176
3D-Plasma-V1-3D_176
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_171

description:
171
3D-Plasma-V1-3D_171
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_170

description:
170
3D-Plasma-V1-3D_170
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_ss_GSH_rep2

description: mRNA

source_name: steady-state mRNA levels


title: w303_5C_t4_GSH_rep3

description: 4tU-labelled mRNA

source_name: 12 hrs after adding 4tU


title: GD-9.0 NT, biological rep 1

description: Gene (microRNA) expression data from neural tubes of GD-9.0 embryos


title: 3D-Plasma-V1-3D_16

description:
16
3D-Plasma-V1-3D_16
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_169

description:
169
3D-Plasma-V1-3D_169
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t7_GSH_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_168

description:
168
3D-Plasma-V1-3D_168
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_167

description:
167
3D-Plasma-V1-3D_167
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t6_GSH_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_166

description:
166
3D-Plasma-V1-3D_166
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_165

description:
165
3D-Plasma-V1-3D_165
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t5_GSH_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_164

description:
164
3D-Plasma-V1-3D_164
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female primitive endoderm cell at E4.5 biological rep 2

city: Boston

first: Ruslan

last: Sadreyev

state: MA

address: 185 Cambridge St

institute: Harvard Medical School/ Mass General Hospital

hyb_protocol: Biotinylated, fragmented cRNA was hybridized to Affymetrix mouse expression arrays 430 2.0 according to the manufacturer's instructions.

scan_protocol: Affymetrix mouse expression arrays 430 2.0 were scanned according to Affymetrix protocols by the Harvard Partners Center for Genomics and Genetics (HPCGG).

data_processing: The data were analyzed using R Bioconductor Affy package, with RMA applied as summarization and normalization method

label_protocol: After the initial qPCR characterization, selected cDNAs were further amplified and in vitro transcribed into biotin-labeled cRNA and fragmented.

growth_protocol: E3.5 embryos of C57BL/6 strain were flushed from uteri and used directly for single-cell analysis or cultured in potassium simplex optimization medium with amino acids (KSOM+AA medium; Millipore; MR-121-D) overnight (37°C, 5% CO2) to be processed on E4.25 and E4.5.

extract_protocol: ICM cells were isolated by trypsin-EDTA treatment, picked into lysis buffer, cDNA synthesized and amplified using the V1V3 protocol  [Kurimoto, K. et al., Nucleic acids research 34, e42 (2006); Kurimoto, K., Yabuta, Y., Ohinata, Y. and Saitou, M., Nature protocols 2, 739-752 (2007)].

tag: Stage

tag: cell type

value: primitive endoderm

tag: xist expression

value: Xist+


title: single female primitive endoderm cell at E4.25 biological rep 1


title: GD-8.5 NT, biological rep 2

description: Gene (microRNA) expression data from neural tubes of GD-8.5 embryos


title: single male epiblast cell at E4.5 biological rep 1

source_name: single male epiblast cell at E4.5

value: epiblast

value: Xist-

value: male


title: 3D-Plasma-V1-3D_163

description:
163
3D-Plasma-V1-3D_163
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t3_GSH_rep2

description: 4tU-labelled mRNA


title: single female primitive endoderm cell at E4.5 biological rep 1


title: w303_5C_t4_GSH_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_159

description:
159
3D-Plasma-V1-3D_159
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_162

description:
162
3D-Plasma-V1-3D_162
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_161

description:
161
3D-Plasma-V1-3D_161
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female epiblast cell at E4.5 biological rep 1

source_name: single female epiblast cell at E4.5


title: 3D-Plasma-V1-3D_158

description:
158
3D-Plasma-V1-3D_158
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_157

description:
157
3D-Plasma-V1-3D_157
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female epiblast cell at E4.25 (Xist-) biological rep 4

source_name: single female epiblast cell at E4.25


title: 3D-Plasma-V1-3D_15

description:
15
3D-Plasma-V1-3D_15
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female epiblast cell at E4.5 biological rep 2


title: w303_5C_t2_GSH_rep2

description: 4tU-labelled mRNA


title: w303_5C_t0_GSH_rep2

description: 4tU-labelled mRNA


title: w303_5C_t1_GSH_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_156

description:
156
3D-Plasma-V1-3D_156
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_ss_GSH_rep1

description: mRNA


title: 3D-Plasma-V1-3D_154

description:
154
3D-Plasma-V1-3D_154
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_155

description:
155
3D-Plasma-V1-3D_155
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female epiblast cell at E4.25 (Xist-) biological rep 2


title: 3D-Plasma-V1-3D_153

description:
153
3D-Plasma-V1-3D_153
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_152

description:
152
3D-Plasma-V1-3D_152
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female epiblast cell at E4.5 biological rep 3


title: single female epiblast cell at E4.25 (Xist-) biological rep 1


title: w303_5C_t7_GSH_rep1

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_151

description:
151
3D-Plasma-V1-3D_151
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_150

description:
150
3D-Plasma-V1-3D_150
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_160

description:
160
3D-Plasma-V1-3D_160
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_14

description:
14
3D-Plasma-V1-3D_14
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female epiblast cell at E4.25 (Xist+) biological rep 2


title: 3D-Plasma-V1-3D_149

description:
149
3D-Plasma-V1-3D_149
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t6_GSH_rep1

description: 4tU-labelled mRNA


title: single female epiblast cell at E4.25 (Xist+) biological rep 1


title: w303_5C_t5_GSH_rep1

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_148

description:
148
3D-Plasma-V1-3D_148
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_147

description:
147
3D-Plasma-V1-3D_147
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female epiblast cell at E4.25 (Xist-) biological rep 3


title: 3D-Plasma-V1-3D_146

description:
146
3D-Plasma-V1-3D_146
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_145

description:
145
3D-Plasma-V1-3D_145
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: single female epiblast cell at E3.5 biological rep 1

source_name: single female epiblast cell at E3.5


title: w303_5C_t1_GSH_rep1

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_142

description:
142
3D-Plasma-V1-3D_142
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t3_GSH_rep1

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_141

description:
141
3D-Plasma-V1-3D_141
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_140

description:
140
3D-Plasma-V1-3D_140
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_143

description:
143
3D-Plasma-V1-3D_143
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_ss_noGSH_rep3

description: mRNA


title: w303_5C_t0_GSH_rep1

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_139

description:
139
3D-Plasma-V1-3D_139
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t6_noGSH_rep3

description: 4tU-labelled mRNA


title: w303_5C_t7_noGSH_rep3

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_137

description:
137
3D-Plasma-V1-3D_137
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_144

description:
144
3D-Plasma-V1-3D_144
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_13

description:
13
3D-Plasma-V1-3D_13
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_135

description:
135
3D-Plasma-V1-3D_135
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_138

description:
138
3D-Plasma-V1-3D_138
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_136

description:
136
3D-Plasma-V1-3D_136
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_134

description:
134
3D-Plasma-V1-3D_134
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t5_noGSH_rep3

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_133

description:
133
3D-Plasma-V1-3D_133
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-9.5 NT, biological rep 4

description: Gene (messenger RNA) expression data from neural tubes of GD-9.5 embryos

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Genome (MG) 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400, following the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

data_processing: GeneChip image processing was perfromed employing the Affymetrix® Expression Console Software (version 1.2.1), and Robust Multi-chip Average, with GC-content background correction (GC-RMA) pre-processing, and 'per gene normalization' were performed  with the GeneSpring v7.2 (Silicon Genetics, Inc., Redwood City, CA).

source_name: Mouse embryos of gestation day 9.5

label_protocol: For messenger RNA (mRNA) expression profiling, the RNA (100 ng/sample) was first reverse transcribed to double-stranded (ds) cDNA, fragmented and labelled using the Biotin labelling kit.


title: GD-9.5 NT, biological rep 3


title: GD-9.5 NT, biological rep 1


title: w303_5C_t3_noGSH_rep3

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_131

description:
131
3D-Plasma-V1-3D_131
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_130

description:
130
3D-Plasma-V1-3D_130
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t2_noGSH_rep3

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_12

description:
12
3D-Plasma-V1-3D_12
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-9.0 NT, biological rep 4

description: Gene (messenger RNA) expression data from neural tubes of GD-9.0 embryos


title: w303_5C_t1_noGSH_rep3

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_129

description:
129
3D-Plasma-V1-3D_129
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_127

description:
127
3D-Plasma-V1-3D_127
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_128

description:
128
3D-Plasma-V1-3D_128
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_132

description:
132
3D-Plasma-V1-3D_132
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t0_noGSH_rep3

description: 4tU-labelled mRNA

source_name: reference for 5C and no GSH, right before adding 4tU


title: GD-9.0 NT, biological rep 2

source_name: Mouse embryos of gestation day 9.0


title: 3D-Plasma-V1-3D_125

description:
125
3D-Plasma-V1-3D_125
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-9.5 NT, biological rep 2


title: w303_5C_t4_noGSH_rep3

description: 4tU-labelled mRNA


title: w303_5C_ss_noGSH_rep2

description: mRNA


title: GD-9.0 NT, biological rep 3


title: 3D-Plasma-V1-3D_126

description:
126
3D-Plasma-V1-3D_126
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-8.5 NT, biological rep 4

description: Gene (messenger RNA) expression data from neural tubes of GD-8.5 embryos


title: 3D-Plasma-V1-3D_123

description:
123
3D-Plasma-V1-3D_123
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_122

description:
122
3D-Plasma-V1-3D_122
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-8.5 NT, biological rep 3


title: w303_5C_t7_noGSH_rep2

description: 4tU-labelled mRNA

source_name: 96 hrs after adding 4tU


title: w303_5C_t6_noGSH_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_124

description:
124
3D-Plasma-V1-3D_124
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_11

description:
11
3D-Plasma-V1-3D_11
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t5_noGSH_rep2

description: 4tU-labelled mRNA

source_name: 24 hrs after adding 4tU


title: 3D-Plasma-V1-3D_119

description:
119
3D-Plasma-V1-3D_119
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Sample_SARS-CoV-2_2-72h

city: Quebec

first: Patrick

last: PROVOST

state: QUEBEC

address: 2705 , Boulevard Laurier, Bloc T

department: Centre Hospitalier de l'Université Laval (CHUL) - Microbiology, Infectious diseases, Immunology

institute: CRCHU of Québec City - Université LAVAL

data_processing:
The samples were diluted to a final concentration of 8 pM and cluster generation was performed on the illumina cBot using TruSeq Rapid SR Cluster kit (#GD-402-4001, Illumina), following manufacturer's instructions
Sequencing was performed on illumina NextSeq 500 using TruSeq Rapid SBS kits (#FC-402-4002, Illumina), according to the manufacturer's instructions
Raw sequences were generated as clean reads from Illumina Nextseq by real-time base calling and quality filtering. The clean reads were recorded in FASTQ format, containing the read information, sequences and quality encoding
Subsequently, the 3’ adapter sequence was trimmed from the clean reads and the reads with lengths shorter than 8 nt were discarded. As the 5’-adaptor was also used as the sequencing primer site, the 5’-adaptor sequence is not present in the sequencing reads. The trimmed reads were recorded in FASTA format
The trimmed reads (length ³ 8 nt) were aligned to the human pre-miRNA in miRBase 21, using novoalign software.
Assembly: miRBase 21
Supplementary files format and content: trimmed reads/tags data, FA files

growth_protocol: The lung adenocarcinoma-derived Calu-3 epithelial cell line (ATCC® HTB-55™, Bur-lington, Ontario, Canada), was cultured in Minimum Essential Medium (α-MEM) sup-plemented with 10% fetal bovine serum, 1 mM L-glutamine, 100 units/mL penicillin, and 100 µg/mL streptomycin, incubated at 37 °C in a humidified atmosphere contain-ing 5% CO2 and passaged every 2 days.

extract_protocol:
Total RNA was extracted from Calu-3 infected and non-infected cells at the 24 h, 48 h and 72 h time points, using RNA Easy kit (Qiagen, Cat. #74106, Toronto, Ontario, Canada) following the manufacturer’s recommendations. All RNA samples were treated with DNase I, quantified with the NanoDrop™ 2000 Spectrophotometer (Thermo Scientific™, Cat #ND-2000) and kept at -80°C for subsequent experiments
Total RNA of each sample was used to prepare the miRNA sequencing library which included the following steps: 1) 3'-adapter ligation with T4 RNA ligase 2 (truncated); 2) 5'-adapter ligation with T4 RNA ligase; 3) cDNA synthesis with RT primer; 4) PCR amplification; 5) extraction and purification of ~130-150 bp PCR amplified fragments (correspond to ~8-15 nt small RNAs) from the PAGE gel. After the completed libraries were quantified with Agilent 2100 Bioanalyzer, the DNA fragments in the libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ and finally sequenced for 50 cycles on Illumina Nextseq according to the manufacturer’s instruction
RNA 16-30nt library

value: lung epithelial cells

tag: infection

value: SARS-CoV-2 infected

tag: time


title: GD-9.0 NT, biological rep 1

tag: tissue

value: neural tube


title: 3D-Plasma-V1-3D_118

description:
118
3D-Plasma-V1-3D_118
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

tag: Sex


title: Sample_SARS-CoV-2_1-72h

tag: cell line


title: w303_5C_t4_noGSH_rep2

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_120

description:
120
3D-Plasma-V1-3D_120
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

tag: pregnancy status_1


title: 3D-Plasma-V1-3D_114

description:
114
3D-Plasma-V1-3D_114
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: GD-8.5 NT, biological rep 2

source_name: Mouse embryos of gestation day 8.5

value: ICR (CD-1) mice


title: GD-8.5 NT, biological rep 1


title: 3D-Plasma-V1-3D_116

description:
116
3D-Plasma-V1-3D_116
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Sample_SARS-CoV-2_3-72h


title: w303_5C_t2_noGSH_rep2

description: 4tU-labelled mRNA

tag: temperature (degrees celcius)


title: 3D-Plasma-V1-3D_113

description:
113
3D-Plasma-V1-3D_113
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_112

description:
112
3D-Plasma-V1-3D_112
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_115

description:
115
3D-Plasma-V1-3D_115
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t3_noGSH_rep2

description: 4tU-labelled mRNA

source_name: 6 hrs after adding 4tU

tag: added gsh (um)


title: Sample_Mock_2-72h

value: untreated (control)


title: Sample_SARS-CoV-2_3-24h


title: Sample_Mock_3-72h


title: 3D-Plasma-V1-3D_121

description:
121
3D-Plasma-V1-3D_121
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t1_noGSH_rep2

description: 4tU-labelled mRNA

source_name: 1.5 hrs after adding 4tU


title: 3D-Plasma-V1-3D_110

description:
110
3D-Plasma-V1-3D_110
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_111

description:
111
3D-Plasma-V1-3D_111
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_10

description:
10
3D-Plasma-V1-3D_10
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_109

description:
109
3D-Plasma-V1-3D_109
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Sample_SARS-CoV-2_2-24h


title: 3D-Plasma-V1-3D_117

description:
117
3D-Plasma-V1-3D_117
technical replicate
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t0_noGSH_rep2

description: 4tU-labelled mRNA


title: Sample_SARS-CoV-2_1-24h


title: 3D-Plasma-V1-3D_107

description:
107
3D-Plasma-V1-3D_107
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t7_noGSH_rep1

description: 4tU-labelled mRNA


title: w303_5C_ss_noGSH_rep1

description: mRNA


title: 3D-Plasma-V1-3D_106

description:
106
3D-Plasma-V1-3D_106
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Sample_Mock_3-24h


title: Sample_Mock_1-72h


title: w303_5C_t6_noGSH_rep1

description: 4tU-labelled mRNA

source_name: 48 hrs after adding 4tU


title: 3D-Plasma-V1-3D_103

description:
103
3D-Plasma-V1-3D_103
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

source_name: Plasma


title: Sample_Mock_2-24h


title: 3D-Plasma-V1-3D_105

description:
105
3D-Plasma-V1-3D_105
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Sample_Mock_1-24h


title: 3D-Plasma-V1-3D_101

description:
101
3D-Plasma-V1-3D_101
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: w303_5C_t4_noGSH_rep1

description: 4tU-labelled mRNA


title: w303_5C_t5_noGSH_rep1

description: 4tU-labelled mRNA


title: 3D-Plasma-V1-3D_104

description:
104
3D-Plasma-V1-3D_104
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Dissociated cells, poly-A captured, bulk sequenced, rep8

city: Philadelphia

first: Ariel

middle: A

last: Hippen

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Cell Ranger (cellranger count version 6.1.2) was used to generate single-cell feature counts for each single-cell sample.
STAR (STAR version 2.7.10) was used to generate gene counts for each bulk sample.
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A provided with Cell Ranger)
Supplementary files format and content: gene count matrix (matrix_XXX.mtx.gz), features table (features_XXX.tsv.gz), barcodes table (barcodes_XXX.tsv.gz)
Supplementary files format and content: gene count matrix (XXX_STAR.tsv.gz)

molecule: polyA RNA

source_name: ovarian tumor

extract_protocol:
Tumor samples were cut into 1mm chunks, and a portion were flash frozen. The remaining fresh tissue chunks were dissociated using the Miltenyi Biotech Human Tumor Dissociation Kit and digested overnight. The dissociated tissue was filtered through a 100 micrometer nylon mesh and red blood cells removed using ACK Lysis Buffer. Dissociated cells were suspended in Dulbecco’s Phosphate Buffered Saline and cryopreserved.
Single cell library preparation was performed using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Pooled single cell library preparation was performed using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 with feature barcode technology for cell surface protein. Bulk sequencing library preparation used either the Illumina TruSeq Stranded Total RNA protocol and the RiboZero Gold kit, or the Illumina TruSeq Stranded mRNA protocol.  All libraries were sequenced on an Illumina NovaSeq 6000.

tag: disease state

value: high-grade serous ovarian cancer (HGSOC)

value: ovarian tumor


title: Dissociated cells, poly-A captured, bulk sequenced, rep4


title: HES-2, Naïve, rep1 [RRBS]

city: Jerusalem

first: Michal

last: Gropp

address: Hadassah Ein-Kerem

country: Israel

institute: Hadassah Medical Center

library_source: genomic

data_processing:
Quality control was applied to FASTQ files and included: extracting residual adapters, trimming low quality bases and filtering out short reads. Quality control was performed with FASTQC version V0.11 and trim_galore.
Filtered reads were mapped to the genome with Bismark Bisulfite Mapper and Methylation Caller version V0.20 followed by Bismark Methylation Extractor and coverage2cytosine utility.
Methylation percentages were calculated per each tile per each sample, limited to tiles exhibiting minimal coverage of six. Mean Methylation percentage per sample was then calculated for autosomal chromosomes. All calculations were performed with custom R scripts.
Assembly: GRCh38
Supplementary files format and content: RRBS_MethylationTable.txt is a tab delemeted text table of tile based methylation levels. Rows are genomic tiles, recurring in all samples. Columns are samples.

molecule: genomic DNA

growth_protocol: LN-hPSCs were cultured on mouse LN111, 3-D Culture Matrix Laminin I (CULTREX, TREVIGEN, a final concentration of ~ 8 microgram/ cm2), in a medium composed of DMEM/F12, B27 supplement, N2 supplement, L-glutamine, penicillin, streptomycin, and supplemented daily with 20 ng/ml FGF2. Conventional/primed hPSCs were cultured on Mitomycin C-treated mouse embryonic fibroblasts in a medium composed of DMEM/F12, 20% KSR, non-essential amino acids, mM 2-mercaptoethanol, L-glutamine, penicillin, streptomycin, and supplemented daily with 10 ng/ml FGF2. Naïve hPSC cultures were established from hPSCs cultured on mTeSR and maintained following the 5iLFA protocol (Theunissen et al., 2014). All hPSCs were maintained in 5% CO2, 5% O2 incubator.

extract_protocol:
hPSCs were detached from the matrix or MEFs by treatment with Collagenase type IV. Genomic DNA was extracted.
RRBS library was prepared as described (Boyle et al., 2012). Bisulfite conversion of RRBS library was performed using the EpiTect DNA Bisulfite Kit (Qiagen) following manufacturer's protocols.

value: human pluripotent stem cells

tag: genotype

value: WT, 46,XX

tag: treatment

value: 5iLFA naive culture conditions


title: w303_5C_t3_noGSH_rep1

description: 4tU-labelled mRNA


title: TwKOastro 5

city: Berkeley

first: Olesia

last: Ignatenko

state: CA

address: Morgan Hall

institute: UC Berkeley

data_processing:
Soapnuke (1.6.7)
Trimmomatic (0.39)
kallisto (v0.45.1)
sleuth (0.30.0)
Genome_build: mm10
Supplementary_files_format_and_content: xls, ensemble_id, gene_symbol, log2(FC), p-value, q-value, description, transcript abundance

source_name: purified astroyctes

growth_protocol: Mice were maintained in a vivarium with 12-h light:dark cycle at 22°C and allowed access to food and water ad libitum.

extract_protocol:
RNA was extracted using RNA-binding columns (NucleoSpin)
RNA sequencing was done in the BGI Genomics, China. mRNA was enriched by Oligo dT selection, and reverse transcription was done using random N6 primer. End repair and adaptor ligation were followed by PCR amplification of the library.

treatment_protocol: Mice were euthanised with CO2, cortices were dissected and tissue was dissociated using an enzymatic kit (Miltenyi Biotec), astrocytes were purified using ACSA-2 magnetic beads (Miltenyi Biotec)

value: cortex

tag: developmetnal stage

value: adult

tag: purification method

value: magnetic beads, ACSA-2 antibody

tag: genotype/variation

value: Twnk knockout


title: w303_5C_t2_noGSH_rep1

description: 4tU-labelled mRNA

source_name: 3 hrs after adding 4tU


title: Primed hPSCs

description: Genomics 10X

library_source: transcriptomic single cell

data_processing:
FASTQ files were first processed with 10X Genomics Cell Ranger-6.1.2(Zheng et al., 2017) to create count matrices.
Count matrices were next analyzed with R package Seurat-4.0.6 (Hao et al., 2021). Cells were retained if expressed at least 500 genes, no more than 7000 genes and mitochondrial content being less than 5-10%. Genes were retained if expressed by at least 100 cells.
LN-hPSC and primed hPSC Seurat objects were then integrated using Seurat anchor-based workflow.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz is a filtered count sparse matrix from Cell Ranger.
Supplementary files format and content: barcodes.tsv.gz is a tsv formatted list of cell IDs which are column names for the count matrix.
Supplementary files format and content: features.tsv.gz is a tsv formatted list of gene IDs which are row names for the count matrix.

growth_protocol: LN-hPSCs were cultured on mouse LN111, 3-D Culture Matrix Laminin I (CULTREX, TREVIGEN, a final concentration of ~ 8 microgram/ cm2), in a medium composed of DMEM/F12, B27 supplement, N2 supplement, L-glutamine, penicillin, streptomycin, and supplemented daily with 20 ng/ml FGF2.  Conventional/primed hPSCs were cultured on Mitomycin C-treated mouse embryonic fibroblasts in a medium composed of DMEM/F12, 20% KSR, non-essential amino acids, mM 2-mercaptoethanol, L-glutamine, penicillin, streptomycin, and supplemented daily with 10 ng/ml FGF2.

extract_protocol:
HES-2-LN-hPSCs were dissociated into single-cell suspensions by treatment with Accutase. HES-2-primed hPSCs were first detached from the MEFs by treatment with Collagenase type IV, and further dissociated into single-cell suspensions by Accutase. Dissociated cells were filtered, centrifuged, and re-suspended in DMEM/F12 containing 10% FCS. To achieve cell viability of ˃ 90%, nonviable cells were removed using Dead Cell Removal kit. Viable cells were quantified after staining with Trypan Blue.
Single-cell 3’ gene expression libraries were generated from samples containing 8,000 cells (with predicted recovery of 5,000 cell), using Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics), according to manufacturer’s instructions.

value: Convenional  culture conditions


title: Dissociated cells, poly-A captured, bulk sequenced, rep6


title: Dissociated cells, poly-A captured, bulk sequenced, rep7


title: TwKOastro 4


title: LN-hPSCs

description: Genomics 10X


title: w303_5C_t1_noGSH_rep1

description: 4tU-labelled mRNA


title: Dissociated cells, poly-A captured, bulk sequenced, rep5


title: Dissociated cells, poly-A captured, bulk sequenced, rep3


title: w303_5C_t0_noGSH_rep1

description: 4tU-labelled mRNA


title: HES-2, Naïve, rep0 [RRBS]


title: 3D-Plasma-V1-3D_108

description:
108
3D-Plasma-V1-3D_108
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Plasma

value: female

value: Gestational diabetes mellitus

tag: pregnancy status_2

value: Other pregnancy complications


title: TwKOastro 3


title: HES-2, LN, rep2 [RRBS]

tag: cell type

value: Culture on LN111 in defined conditions


title: 3D-Plasma-V1-3D_100

description:
100
3D-Plasma-V1-3D_100
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Normal


title: Dissociated cells, poly-A captured, bulk sequenced, rep2


title: w303_1C_ss_GSH_rep3

description: mRNA

source_name: steady-state mRNA levels


title: HES-2, LN, rep1 [RRBS]


title: Dissociated cells, poly-A captured, bulk sequenced, rep1


title: HES-2, LN, rep0 [RRBS]


title: Dissociated cells, ribo-depleted, bulk sequenced, rep8


title: TwKOastro 1


title: TwKOastro 2


title: Control 6

value: control


title: w303_1C_t5_GSH_rep3

description: 4tU-labelled mRNA


title: w303_1C_t3_GSH_rep3

description: 4tU-labelled mRNA


title: HES-2, Conventional, rep1 [RRBS]


title: Control 5


title: Dissociated cells, ribo-depleted, bulk sequenced, rep6

value: high-grade serous ovarian cancer (HGSOC)


title: HES-2, Conventional, rep2 [RRBS]


title: Control 4


title: Dissociated cells, ribo-depleted, bulk sequenced, rep5

value: ovarian tumor


title: w303_1C_t2_GSH_rep3

description: 4tU-labelled mRNA

source_name: 12 hrs after adding 4tU


title: Dissociated cells, ribo-depleted, bulk sequenced, rep4


title: w303_1C_t0_GSH_rep3

description: 4tU-labelled mRNA

source_name: reference for 1C and with GSH, right before adding 4tU


title: Control 3


title: HES-1, Naïve, rep0 [RRBS]

value: human pluripotent stem cells


title: Control 2


title: Dissociated cells, ribo-depleted, bulk sequenced, rep3


title: HES-1, Naïve, rep1 [RRBS]

value: WT, 46,XX


title: w303_1C_ss_GSH_rep2

description: mRNA


title: w303_1C_t4_GSH_rep3

description: 4tU-labelled mRNA


title: Dissociated cells, ribo-depleted, bulk sequenced, rep2


title: Control 1


title: HES-1, LN, rep2 [RRBS]


title: Dissociated cells, ribo-depleted, bulk sequenced, rep1


title: Dissociated cells, ribo-depleted, bulk sequenced, rep7


title: w303_1C_t5_GSH_rep2

description: 4tU-labelled mRNA


title: HES-1, LN, rep0 [RRBS]


title: HES-2, Conventional, rep0 [RRBS]


title: Tissue chunks, ribo-depleted, bulk sequenced, rep8


title: w303_1C_t1_GSH_rep3

description: 4tU-labelled mRNA


title: w303_1C_t4_GSH_rep2

description: 4tU-labelled mRNA


title: w303_1C_t3_GSH_rep2

description: 4tU-labelled mRNA


title: Tissue chunks, ribo-depleted, bulk sequenced, rep7


title: HES-1, Conventional, rep2 [RRBS]


title: HES-1, Conventional, rep1 [RRBS]


title: w303_1C_t2_GSH_rep2

description: 4tU-labelled mRNA


title: Tissue chunks, ribo-depleted, bulk sequenced, rep6


title: w303_1C_t1_GSH_rep2

description: 4tU-labelled mRNA


title: KO_L24_1

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

country: China

institute: Zhejiang University

description: WT_KO_All expression gene.txt

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) using Bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow-derived monocyte are cultured in DMEM medium plus M-CSF for 5 days to generate BMDMs.

extract_protocol:
Total RNA was extracted from treated BMDMs using TRIzol reagent (Invitrogen) according to manufacturer’s protocol.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.

treatment_protocol: BMDMs  are treated with LPS (100ng/ml) for 12h, 24h.

tag: stain

value: bone marrow

tag: age

tag: time point


title: WT_L24_1

description: WT_KO_All expression gene.txt

tag: tissue

value: WT


title: KO_L12_1

description: WT_KO_All expression gene.txt


title: HES-1, Conventional, rep0 [RRBS]


title: Tissue chunks, ribo-depleted, bulk sequenced, rep5


title: WT_L0_1

description: WT_KO_All expression gene.txt


title: HES-1, LN, rep1 [RRBS]


title: Tissue chunks, ribo-depleted, bulk sequenced, rep4