title: OM50 - ChD - B1/B2

description:
Library name: Sample 138
Column name in normalized_counts.csv: OM50


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-O18

status: Public on Dec 30 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain

tag: brain region

value: FC

tag: gender

value: M

tag: age

value: 9 months


title: OM49 - ChD - B1/B2

city: Rio de Janeiro

first: Eric

middle: Henrique

last: Roma

state: Rio de Janeiro

address: Av. Brasil, 4365

department: Instituto Nacional de Infectologia

country: Brazil

institute: Fundação Oswaldo Cruz

description:
Library name: Sample 137
Column name in normalized_counts.csv: OM49

library_source: transcriptomic

data_processing:
CLC Genomics Workbench software version 25 (Qiagen), with quality limit set to 0.05
miRNA counts were generated using the CLC Genomics Workbench software version 25.
Normalized counts were generated with DEseq2 package from R software environment  using Trimmed Mean of M-values (TMM) as method to normalize the miRNA-seq data.
Assembly: The generated reads were trimmed and aligned with the human mirBase v22
Supplementary files format and content: Comma-separated Values file include normalized counts for each sample
Supplementary files format and content: csv files include TMM of sequenced miRNAs for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: blood serum

extract_protocol:
miRNA from 200ul of human serum samples were extracted using the miRNeasy Serum/Plasma Advanced kit from Qiagen and stored at at -80°C until use.
Five microliters of the extracted miRNA were used for library preparation for miRNA sequencing with the QIAseq miRNA Library kit (Qiagen) following the manufacturer's recommendations. After library preparation, the quality and quantification of the libraries were assessed using the TapeStation system (Agilent, Santa Clara, USA) with the High Sensitivity DNA 1000 kit (Agilent).

tag: tissue

value: blood serum

tag: chagas disease?

value: Yes

tag: chagas disease_form

value: Chronic Chagas cardiomyopathy

tag: chronic chagas_cardiomyopathy_severity

value: moderate

value: female


title: OM44 - ChD - B1/B2

description:
Library name: Sample 136
Column name in normalized_counts.csv: OM44

value: male


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-O17


title: OM42 - ChD - B1/B2

description:
Library name: Sample 135
Column name in normalized_counts.csv: OM42


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-A7


title: OM109 - ChD - B1/B2

description:
Library name: Sample 148
Column name in normalized_counts.csv: OM109


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-N5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-N6


title: OM34 - ChD - B1/B2

description:
Library name: Sample 133
Column name in normalized_counts.csv: OM34


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-N17


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-P6


title: OM28 - ChD - B1/B2

description:
Library name: Sample 132
Column name in normalized_counts.csv: OM28


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-N18


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-M6


title: OM21 - ChD - B1/B2

description:
Library name: Sample 131
Column name in normalized_counts.csv: OM21


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-M5


title: OM15 - ChD - B1/B2

description:
Library name: Sample 128
Column name in normalized_counts.csv: OM15


title: OM20 - ChD - B1/B2

description:
Library name: Sample 130
Column name in normalized_counts.csv: OM20


title: OM6 - ChD - B1/B2

description:
Library name: Sample 127
Column name in normalized_counts.csv: OM6


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-O5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-L5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-M18


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-L6


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-M17


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-L18


title: OM209 - ChD - A

description:
Library name: Sample 124
Column name in normalized_counts.csv: OM209

value: mild


title: OM4 - ChD - B1/B2

description:
Library name: Sample 126
Column name in normalized_counts.csv: OM4


title: OM207 - ChD - A

description:
Library name: Sample 123
Column name in normalized_counts.csv: OM207


title: OM38 - ChD - B1/B2

description:
Library name: Sample 134
Column name in normalized_counts.csv: OM38


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-K6


title: OM212 - ChD - A

description:
Library name: Sample 125
Column name in normalized_counts.csv: OM212


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-L17


title: OM204 - ChD - A

description:
Library name: Sample 122
Column name in normalized_counts.csv: OM204


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-K18


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-K17


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-K5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-J6


title: OM181 - ChD - A

description:
Library name: Sample 120
Column name in normalized_counts.csv: OM181


title: OM199 - ChD - A

description:
Library name: Sample 121
Column name in normalized_counts.csv: OM199


title: OM176 - ChD - A

description:
Library name: Sample 118
Column name in normalized_counts.csv: OM176


title: OM179 - ChD - A

description:
Library name: Sample 119
Column name in normalized_counts.csv: OM179


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-J5


title: OM17 - ChD - B1/B2

description:
Library name: Sample 129
Column name in normalized_counts.csv: OM17


title: OM174 - ChD - A

description:
Library name: Sample 117
Column name in normalized_counts.csv: OM174


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-J18


title: OM159 - ChD - A

description:
Library name: Sample 116
Column name in normalized_counts.csv: OM159


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-J17


title: OM151 - ChD - A

description:
Library name: Sample 115
Column name in normalized_counts.csv: OM151


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-I6


title: OM134 - ChD - A

description:
Library name: Sample 113
Column name in normalized_counts.csv: OM134


title: OM144 - ChD - A

description:
Library name: Sample 114
Column name in normalized_counts.csv: OM144


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-I18


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-I5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-I17


title: OM125 - ChD - A

description:
Library name: Sample 112
Column name in normalized_counts.csv: OM125


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-H6


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-H5


title: OM123 - ChD - A

description:
Library name: Sample 111
Column name in normalized_counts.csv: OM123


title: OM115 - ChD - A

description:
Library name: Sample 109
Column name in normalized_counts.csv: OM115


title: OM116 - ChD - A

description:
Library name: Sample 110
Column name in normalized_counts.csv: OM116


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-H18


title: OM114 - ChD - A

description:
Library name: Sample 108
Column name in normalized_counts.csv: OM114


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-G6


title: OM106 - ChD - A

description:
Library name: Sample 107
Column name in normalized_counts.csv: OM106


title: OM93 - ChD - A

description:
Library name: Sample 106
Column name in normalized_counts.csv: OM93


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-G5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-G18


title: OM82 - ChD - A

description:
Library name: Sample 105
Column name in normalized_counts.csv: OM82


title: OM70 - ChD - A

description:
Library name: Sample 103
Column name in normalized_counts.csv: OM70


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-F6


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-G17


title: OM80 - ChD - A

description:
Library name: Sample 104
Column name in normalized_counts.csv: OM80


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-F5


title: OM67 - ChD - A

description:
Library name: Sample 102
Column name in normalized_counts.csv: OM67


title: OM64 - ChD - A

description:
Library name: Sample 101
Column name in normalized_counts.csv: OM64


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-F17


title: OM59 - ChD - A

description:
Library name: Sample 100
Column name in normalized_counts.csv: OM59


title: OM58 - ChD - A

description:
Library name: Sample 99
Column name in normalized_counts.csv: OM58


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-E5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-E6


title: OM56 - ChD - A

description:
Library name: Sample 98
Column name in normalized_counts.csv: OM56


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-E18


title: OM45 - ChD - A

description:
Library name: Sample 97
Column name in normalized_counts.csv: OM45


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-H17


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-E17


title: OM32 - ChD - A

description:
Library name: Sample 94
Column name in normalized_counts.csv: OM32


title: OM41 - ChD - A

description:
Library name: Sample 96
Column name in normalized_counts.csv: OM41


title: OM36 - ChD - A

description:
Library name: Sample 95
Column name in normalized_counts.csv: OM36


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-D6


title: OM30 - ChD - A

description:
Library name: Sample 93
Column name in normalized_counts.csv: OM30


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-D18


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-D5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-D17


title: OM19 - ChD - A

description:
Library name: Sample 91
Column name in normalized_counts.csv: OM19


title: OM26 - ChD - A

description:
Library name: Sample 92
Column name in normalized_counts.csv: OM26


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-C5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-F18


title: OM18 - ChD - A

description:
Library name: Sample 90
Column name in normalized_counts.csv: OM18


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-C6


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-C18


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-C17


title: OM235 - ChD - IND

description:
Library name: Sample 87
Column name in normalized_counts.csv: OM235

value: Indeterminate


title: OM3 - ChD - A

description:
Library name: Sample 89
Column name in normalized_counts.csv: OM3


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-B5


title: OM169 - ChD - IND

description:
Library name: Sample 86
Column name in normalized_counts.csv: OM169


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-B6


title: OM113 - ChD - IND

description:
Library name: Sample 84
Column name in normalized_counts.csv: OM113


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-B17


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-A5


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-A6


title: OM110 - ChD - IND

description:
Library name: Sample 82
Column name in normalized_counts.csv: OM110


title: OM105 - ChD - IND

description:
Library name: Sample 80
Column name in normalized_counts.csv: OM105


title: OM107 - ChD - IND

description:
Library name: Sample 81
Column name in normalized_counts.csv: OM107


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-A18


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-P4


title: OM103 - ChD - IND

description:
Library name: Sample 79
Column name in normalized_counts.csv: OM103


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-P3


title: OM102 - ChD - IND

description:
Library name: Sample 78
Column name in normalized_counts.csv: OM102


title: OM236 - ChD - IND

description:
Library name: Sample 88
Column name in normalized_counts.csv: OM236


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-P16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-P15


title: OM100 - ChD - IND

description:
Library name: Sample 77
Column name in normalized_counts.csv: OM100


title: OM98 - ChD - IND

description:
Library name: Sample 76
Column name in normalized_counts.csv: OM98


title: OM97 - ChD - IND

description:
Library name: Sample 75
Column name in normalized_counts.csv: OM97


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-O3


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-O4


title: OM95 - ChD - IND

description:
Library name: Sample 74
Column name in normalized_counts.csv: OM95


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-B18


title: OM87 - ChD - IND

description:
Library name: Sample 73
Column name in normalized_counts.csv: OM87


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-O16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-N4


title: OM167 - ChD - IND

description:
Library name: Sample 85
Column name in normalized_counts.csv: OM167


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-O15


title: OM83 - ChD - IND

description:
Library name: Sample 72
Column name in normalized_counts.csv: OM83


title: OM79 - ChD - IND

description:
Library name: Sample 71
Column name in normalized_counts.csv: OM79


title: OM111 - ChD - IND

description:
Library name: Sample 83
Column name in normalized_counts.csv: OM111


title: OM77 - ChD - IND

description:
Library name: Sample 70
Column name in normalized_counts.csv: OM77


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-A17


title: OM75 - ChD - IND

description:
Library name: Sample 69
Column name in normalized_counts.csv: OM75


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-N16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-N15


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-M4


title: OM72 - ChD - IND

description:
Library name: Sample 67
Column name in normalized_counts.csv: OM72


title: OM73 - ChD - IND

description:
Library name: Sample 68
Column name in normalized_counts.csv: OM73


title: OM66 - ChD - IND

description:
Library name: Sample 66
Column name in normalized_counts.csv: OM66


title: OM62 - ChD - IND

description:
Library name: Sample 64
Column name in normalized_counts.csv: OM62


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-M16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-M15


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-L3


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-L16


title: OM65 - ChD - IND

description:
Library name: Sample 65
Column name in normalized_counts.csv: OM65


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-M3


title: OM53 - ChD - IND

description:
Library name: Sample 61
Column name in normalized_counts.csv: OM53


title: OM57 - ChD - IND

description:
Library name: Sample 62
Column name in normalized_counts.csv: OM57


title: OM61 - ChD - IND

description:
Library name: Sample 63
Column name in normalized_counts.csv: OM61


title: OM52 - ChD - IND

description:
Library name: Sample 60
Column name in normalized_counts.csv: OM52


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-K4


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-L15


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-N3


title: OM48 - ChD - IND

description:
Library name: Sample 59
Column name in normalized_counts.csv: OM48


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-K3


title: OM47 - ChD - IND

description:
Library name: Sample 58
Column name in normalized_counts.csv: OM47


title: OM43 - ChD - IND

description:
Library name: Sample 56
Column name in normalized_counts.csv: OM43


title: OM46 - ChD - IND

description:
Library name: Sample 57
Column name in normalized_counts.csv: OM46


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-K15


title: OM35 - ChD - IND

description:
Library name: Sample 55
Column name in normalized_counts.csv: OM35


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-J4


title: OM27 - ChD - IND

description:
Library name: Sample 53
Column name in normalized_counts.csv: OM27


title: OM29 - ChD - IND

description:
Library name: Sample 54
Column name in normalized_counts.csv: OM29


title: OM24 - ChD - IND

description:
Library name: Sample 51
Column name in normalized_counts.csv: OM24


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-I3


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-I16


title: OM16 - ChD - IND

description:
Library name: Sample 48
Column name in normalized_counts.csv: OM16


title: OM25 - ChD - IND

description:
Library name: Sample 52
Column name in normalized_counts.csv: OM25


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-L4


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-J16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-I4


title: OM12 - ChD - IND

description:
Library name: Sample 45
Column name in normalized_counts.csv: OM12


title: OM11 - ChD - IND

description:
Library name: Sample 44
Column name in normalized_counts.csv: OM11


title: OM23 - ChD - IND

description:
Library name: Sample 50
Column name in normalized_counts.csv: OM23


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-H15


title: OM22 - ChD - IND

description:
Library name: Sample 49
Column name in normalized_counts.csv: OM22


title: OM7 - ChD - IND

description:
Library name: Sample 43
Column name in normalized_counts.csv: OM7


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-G3


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-J3


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-I15


title: OMG88 - nonChD

description:
Library name: Sample 41
Column name in normalized_counts.csv: OMG88

value: No


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-G16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-H4


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-J15


title: OM13 - ChD - IND

description:
Library name: Sample 46
Column name in normalized_counts.csv: OM13


title: OM14 - ChD - IND

description:
Library name: Sample 47
Column name in normalized_counts.csv: OM14


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-H3


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-K16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-H16


title: OMG80 - nonChD

description:
Library name: Sample 39
Column name in normalized_counts.csv: OMG80


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-F3


title: OMG93 - nonChD

description:
Library name: Sample 42
Column name in normalized_counts.csv: OMG93


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-G15


title: OMG72 - nonChD

description:
Library name: Sample 35
Column name in normalized_counts.csv: OMG72


title: OMG79 - nonChD

description:
Library name: Sample 38
Column name in normalized_counts.csv: OMG79


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-F16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-E15


title: OMG53 - nonChD

description:
Library name: Sample 32
Column name in normalized_counts.csv: OMG53


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-E4


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-E16


title: OMG54 - nonChD

description:
Library name: Sample 33
Column name in normalized_counts.csv: OMG54


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-G4


title: OMG50 - nonChD

description:
Library name: Sample 31
Column name in normalized_counts.csv: OMG50


title: OMG49 - nonChD

description:
Library name: Sample 30
Column name in normalized_counts.csv: OMG49


title: OMG70 - nonChD

description:
Library name: Sample 34
Column name in normalized_counts.csv: OMG70


title: OMG74 - nonChD

description:
Library name: Sample 37
Column name in normalized_counts.csv: OMG74


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-F4


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-D16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-D4


title: OMG46 - nonChD

description:
Library name: Sample 28
Column name in normalized_counts.csv: OMG46


title: OMG87 - nonChD

description:
Library name: Sample 40
Column name in normalized_counts.csv: OMG87


title: OMG45 - nonChD

description:
Library name: Sample 27
Column name in normalized_counts.csv: OMG45


title: OMG48 - nonChD

description:
Library name: Sample 29
Column name in normalized_counts.csv: OMG48


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-C4


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-D15


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-C3


title: OMG44 - nonChD

description:
Library name: Sample 26
Column name in normalized_counts.csv: OMG44


title: OMG73 - nonChD

description:
Library name: Sample 36
Column name in normalized_counts.csv: OMG73


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-F15


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-C16


title: OMG42 - nonChD

description:
Library name: Sample 25
Column name in normalized_counts.csv: OMG42


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-C15


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-E3


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-B16


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-B4


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-B3


title: OMG41 - nonChD

description:
Library name: Sample 24
Column name in normalized_counts.csv: OMG41


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-D3


title: OMG39 - nonChD

description:
Library name: Sample 22
Column name in normalized_counts.csv: OMG39


title: OMG34 - nonChD

description:
Library name: Sample 20
Column name in normalized_counts.csv: OMG34


title: OMG40 - nonChD

description:
Library name: Sample 23
Column name in normalized_counts.csv: OMG40


title: OMG36 - nonChD

description:
Library name: Sample 21
Column name in normalized_counts.csv: OMG36


title: OMG29 - nonChD

description:
Library name: Sample 16
Column name in normalized_counts.csv: OMG29


title: OMG32 - nonChD

description:
Library name: Sample 19
Column name in normalized_counts.csv: OMG32


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-A3


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-B15


title: OMG30 - nonChD

description:
Library name: Sample 17
Column name in normalized_counts.csv: OMG30


title: OMG31 - nonChD

description:
Library name: Sample 18
Column name in normalized_counts.csv: OMG31


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-P2


title: OMG28 - nonChD

description:
Library name: Sample 15
Column name in normalized_counts.csv: OMG28


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-A16


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-P14


title: OMG23 - nonChD

description:
Library name: Sample 13
Column name in normalized_counts.csv: OMG23


title: OMG26 - nonChD

description:
Library name: Sample 14
Column name in normalized_counts.csv: OMG26


title: OMG19 - nonChD

description:
Library name: Sample 12
Column name in normalized_counts.csv: OMG19


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-P1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-O2


title: OMG16 - nonChD

description:
Library name: Sample 11
Column name in normalized_counts.csv: OMG16


title: OMG15 - nonChD

description:
Library name: Sample 10
Column name in normalized_counts.csv: OMG15


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-A15


title: OMG11 - nonChD

description:
Library name: Sample 8
Column name in normalized_counts.csv: OMG11


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-O14


title: OMG12 - nonChD

description:
Library name: Sample 9
Column name in normalized_counts.csv: OMG12


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-O1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-O13


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-N2


title: OMG10 - nonChD

description:
Library name: Sample 7
Column name in normalized_counts.csv: OMG10


title: C6 - nonChD

description:
Library name: Sample 4
Column name in normalized_counts.csv: C6


title: OMG9 - nonChD

description:
Library name: Sample 6
Column name in normalized_counts.csv: OMG9


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-M2


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-P13


title: OMG8 - nonChD

description:
Library name: Sample 5
Column name in normalized_counts.csv: OMG8


title: AMB_200205_9mo_2A_3A_1_P2-2-P4-A4


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-N14


title: C1 - nonChD

description:
Library name: Sample 1
Column name in normalized_counts.csv: C1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-N13


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-M1


title: C2 - nonChD

description:
Library name: Sample 2
Column name in normalized_counts.csv: C2


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-L2


title: C5 - nonChD

description:
Library name: Sample 3
Column name in normalized_counts.csv: C5


title: 10X scRNAseq 12-16M Spine Mutant

city: Créteil

first: Céline

last: Colnot

address: 8 rue du Général Sarrail

country: France

institute: INSERM

description:
Library name: SC46_RNA
3' mRNA: read1 contains cell barcode and UMI: read2 contains transcript sequences

library_source: transcriptomic single cell

data_processing:
Fastq files were processed with the CellRanger pipeline with the default’s parameters
Reads were align against the mm10 reference genome
Filtered features barcodes matrices were used to perform data analysis
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Spine

extract_protocol:
Mice were euthanized, and the region of the vertebral column from vertebrae thoracic 11 (T11) to lumbar 2 (L2) were collected from Prss56-Nf1+/+ control and Prss56-Nf1fl/fl mutant mice at 3 months and 12-16 months of age. The vertebrae were cleaned from muscle, spinal cord, and dorsal root ganglia to avoid contamination from adjacent tissue. Before tissue processing, the collected vertebrae were observed under a fluorescent microscope to select the vertebrae with detectable tdTom+ signal. The tissues were minced using a scalpel and scissors and incubated in a digestion medium composed of 1mg/ml of Collagenase (C6885, Merck) and 2mg/ml of Dispase (D4693, Merck) in PBS for 20 min at 37°. Later 10ul/ml of 1% DNAse (WOLS02007, Serlabo, France) were added in the digestion medium and incubated for 10 min at 37°C. The supernatant was filtered and collected in sorting buffer composed of MEM-alpha and 10% FBS. The remaining tissue underwent a second step of digestion with 2ul/ml of 1% DNAse for 20 min at 37°C.  Collected cells were centrifuged at 40C for 10 min. After centrifugation, the supernatant was discarded, and the cells were resuspended in sorting buffer and incubated for 30 min with antibodies for immune and endothelial cells CD11b-BV786 (BD Biosciences 740861), CD31- BV786 (BD Biosciences 740879), CD45-BV786 (BD Biosciences 564225) on ice and protected from light. After washing, cells were resuspended in sorting buffer, and Sytox Blue (S34857, Thermo Fisher Scientific) was added to stain dead cells. Using Influx Cell Sorter, the immune, endothelial, and dead cells were sorted and discarded, while Tom+ cells were collected.
scRNA-seq libraries for the four datasets were prepared using the Chromium Single Cell Next GEM 3′ Library & Gel Bead Kit v3.1 (10x Genomics) according to the manufacturer’s instructions.

value: Spine

tag: genotype

value: Prss56Cre/Cre;R26tdTom/tdTom; Nf1fl/fl

value: 12-16 months


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-M14


title: 10X scRNAseq 3M Spine WT

description:
Library name: SC42_RNA
3' mRNA: read1 contains cell barcode and UMI: read2 contains transcript sequences

value: 3 months


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-L14


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-L13


title: 10X scRNAseq 12-16M Spine WT

description:
Library name: SC40_RNA
3' mRNA: read1 contains cell barcode and UMI: read2 contains transcript sequences


title: 10X scRNAseq 3M Spine Mutant

description:
Library name: SC39_RNA
3' mRNA: read1 contains cell barcode and UMI: read2 contains transcript sequences


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-L1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-N1


title: 5FU, Candida, Antibiotics, Sample 3

city: Farmington

first: Roberto

last: Vazquez-Munoz

state: Connecticut

address: 263 Farmington Avenue, Main building, room L6008

department: General Dentistry

institute: UConn Health

description: Library name: ADB5FUCaAb3

data_processing:
To analyze the RNA sequences, we combined the raw reads from each sample and performed a quality check using FASTQC. Next, we used Sickle to trim the reads and QC them again with FASTQC. Reads were aligned using HISAT2 against the Mus musculus (GRCm38) index. The aligned reads were then converted into binary format using Samtools, and the duplicates were removed using the tool PICARD.
The counts were calculated using the HTseq-count program, and comparisons were made between the antibiotics and non-antibiotics oropharyngeal candidiasis groups. False discovery rate-adjusted p-values ≤ 0.05 were applied to identify significantly differentially expressed (DE) genes using the DESeq2 package. Samples within a group were compared using principal component analysis and a sample-to-sample distance matrix. Finally, the R software was used to compare the two groups, and DE genes were tabulated and subjected to further downstream analysis.
Assembly: GRCm38
Supplementary files format and content: All processed files are in the COUNT file format. These files contain the raw counts per gene.

source_name: Tongue

extract_protocol:
RNA isolation from Tongue tissues was carried out using the RNeasy Kit (Qiagen) as follows: tongue samples were homogenized in 800µl of RLT buffer containing 1% βeta-mercaptoethanol (Biorad) using a tissue homogenizer. Then, 800µl of Phenol:chloroform:isoamyl-alcohol (Invitrogen) was added to the homogenate in 2 ml screw-capped tubes. Samples were centrifuged, and the aqueous phase was collected. An equal volume of 70% molecular-grade ethanol was added. Kit instructions were followed for subsequent column separation steps. DNAse treatment was performed using the TURBO DNA-free kit (Invitrogen). RNA was analyzed for quality using the Experion automated gel electrophoretic system (Biorad)
For the RNA sequencing, cDNA libraries were prepared using the TruSeq RNA kit (Illumina) and subjected to poly(A) enrichment according to the kit protocol. cDNA fragments (100 nucleotides from each end) were sequenced using the Illumina NextSeq platform.

value: Tongue

tag: Sex

tag: treatment

value: Candida-infected, Antibiotic-treated


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-K14

value: FC

value: M


title: 5FU, Candida, Antibiotics, Sample 2

description: Library name: ADB5FUCaAb2


title: 5FU, Candida, Antibiotics, Sample 1

description: Library name: ADB5FUCaAb1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-K2

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-K13


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-M13


title: 5FU, Candida, Sample 2

description: Library name: ADB5FUCa2

value: Candida-infected


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-K1


title: 5FU, Candida, Sample 3

description: Library name: ADB5FUCa3


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-J2


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-J14


title: 5FU, Candida, Sample 1

description: Library name: ADB5FUCa1


title: SD-2D-2

city: Beijing

first: Mingxin

last: Zhang

address: 2 West Yuanmingyuan Road

country: China

institute: China Agricuture University

description: Library name: Sample 4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small intestine

extract_protocol:
Intestinal crypts were isolated from small intestine samples by incubating them in PBS containing 10 mM EDTA at 4°C for 30 min. The crypt fractions were collected by pipetting and filtered through a 70 μm cell strainer (BD Biosciences).
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics)

value: Small intestine

tag: group


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-I2


title: SD 0D-2

description: Library name: Sample 2


title: SD 0D-1

description: Library name: Sample 1


title: RNA-sample-80

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description: lane8394_GTAGAGGA_TCTCTCCG_80_L001_GRCm38

data_processing:
Raw data files were processed using the Babraham Institute's standard nf_rnaseq pipeline (https://github.com/s-andrews/nextflow_pipelines/blob/master/nf_rnaseq). This pipeline processes FastQ files, performs read count QC, contamination QC, quality-/adapter trimming using Trim Galore!, and splice-aware alignments to the GRCm38 mouse genome using Hisat2. Finally, it generates an aggregate QC report.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files for read counts, annotated probe report, and differentially expressed genes.

source_name: Oocyte

growth_protocol: Oocyte samples were collected from Nlrp5 +/+, +/- and -/- mice with a C57BL6/Babr background.

extract_protocol:
Germinal vesicle oocytes were collected from 3-week old Nlrp5 female mice via collagenase digestion of dissected ovaries (30mg/ml collagenase (Sigma Aldrich), 1% Trypsin (Sigma Aldrich) in DPBS (with Magnesium and calcium), incubated at 37℃ in a thermos mixer at 550rpm for 25mins, manually disrupted intermittently using a 500ul pipette). The digest was stopped by adding equal volume of M2 medium (Sigma Aldrich). Individual oocytes were rinsed first in M2 medium, then in PBS, before being snap frozen in minimal volume of RLT+ buffer (QIAGEN) prior to library preparation.
scRNA-seq libraries were prepared according to the scM&T-seq protocol detailed in Angermueller et al., Nature Methods, 2016.

tag: cell type

value: Oocyte

tag: developmental stage

value: Germinal vesicle

value: Nlrp5 +/+


title: SD-2D-1

description: Library name: Sample 3


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-J1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-J13


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-I1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-I14


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-I13


title: RNA-sample-30

description: lane8394_TCCTGAGC_CTAAGCCT_30_L001_GRCm38

value: Nlrp5 -/-


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-H2


title: RNA-sample-29

description: lane8394_TCCTGAGC_AAGGAGTA_29_L001_GRCm38


title: RNA-sample-48

description: lane8394_TAGGCATG_TCTCTCCG_48_L001_GRCm38

value: Nlrp5 +/-


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-H14


title: RNA-sample-46

description: lane8394_TAGGCATG_CTAAGCCT_46_L001_GRCm38


title: RNA-sample-47

description: lane8394_TAGGCATG_CGTCTAAT_47_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-H1


title: RNA-sample-45

description: lane8394_TAGGCATG_AAGGAGTA_45_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-G2


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-G14


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-G13


title: RNA-sample-78

description: lane8394_GTAGAGGA_CTAAGCCT_78_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-G1


title: RNA-sample-79

description: lane8394_GTAGAGGA_CGTCTAAT_79_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-F2


title: RNA-sample-77

description: lane8394_GTAGAGGA_AAGGAGTA_77_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-F13


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-F14


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-F1


title: RNA-sample-39

description: lane8394_GGACTCCT_GCTCTAAT_39_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-E2


title: RNA-sample-40

description: lane8394_GGACTCCT_TCTCTCCG_40_L001_GRCm38


title: RNA-sample-37

description: lane8394_GGACTCCT_AAGGAGTA_37_L001_GRCm38


title: RNA-sample-31

description: lane8394_TCCTGAGC_CGTCTAAT_31_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-E13


title: RNA-sample-87

description: lane8394_GCTCATGA_CGTCTAAT_87_L001_GRCm38


title: RNA-sample-86

description: lane8394_GCTCATGA_CTAAGCCT_86_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-H13


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-E1


title: RNA-sample-85

description: lane8394_GCTCATGA_AAGGAGTA_85_L001_GRCm38


title: RNA-sample-56

description: lane8394_CTCTCTAC_TCTCTCCG_56_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-D2


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-D14


title: RNA-sample-7

description: lane8394_TAAGGCGA_CGTCTAAT_7_L001_GRCm38


title: RNA-sample-55

description: lane8394_CTCTCTAC_CGTCTAAT_55_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-D1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-D13


title: RNA-sample-53

description: lane8394_CTCTCTAC_AAGGAGTA_53_L001_GRCm38


title: RNA-sample-14

description: lane8394_CGTACTAG_CTAAGCCT_14_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-C2


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-C14


title: RNA-sample-38

description: lane8394_GGACTCCT_CTAAGCCT_38_L001_GRCm38


title: RNA-sample-15

description: lane8394_CGTACTAG_CGTCTAAT_15_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-C13


title: RNA-sample-13

description: lane8394_CGTACTAG_AAGGAGTA_13_L001_GRCm38


title: RNA-sample-62

description: lane8394_CGAGGCTG_CTAAGCCT_62_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-B2


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-C1


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-E14


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-B14


title: RNA-sample-63

description: lane8394_CGAGGCTG_CGTCTAAT_63_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-B13


title: RNA-sample-61

description: lane8394_CGAGGCTG_AAGGAGTA_61_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-B1


title: RNA-sample-72

description: lane8394_AAGAGGCA_TCTCTCCG_72_L001_GRCm38


title: RNA-sample-70

description: lane8394_AAGAGGCA_CTAAGCCT_70_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-A2


title: RNA-sample-54

description: lane8394_CTCTCTAC_CTAAGCCT_54_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-A14


title: RNA-sample-69

description: lane8394_AAGAGGCA_AAGGAGTA_69_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-A13


title: WT-48

description: SLX22109_TCCGTCTT_48_L001_non_directional_GRCm38

data_processing:
*library strategy: scPBAT-seq (single cell post bisulfite adapter tag-sequencing)
The Babraham Institute nf_scBSseq pipeline was used for processing (https://github.com/s-andrews/nextflow_pipelines/blob/master/nf_bisulfite_scBSseq), with the additional parameters --trim_galore_args="--clip_r1 9 --clip_r2 9" to account for potential mis-priming issues from the PBAT. The nf_scBSseq workflow runs an entire single-cell Bisulphite-seq processing pipeline on Fast Q files, including QC, quality-/adapter trimming using Trim Galore!, contamination QC (post trimming), alignments to the GRCm38 mouse genome using Bismark, deduplication, methylation extraction, and coverage file generation. Finally, it generates an aggregate MultiQC report
Assembly: GRCm38
Supplementary files format and content: Tab-separated values file for scPBAT-seq read count, CpG coverage, and other QC metrics (.txt)
Supplementary files format and content: Deduplicated Bismark coverage file (.deduplicated.bismark.cov.gz)

growth_protocol: Oocyte samples were collected from Nlrp5 +/+ and -/- mice with a C57BL6/Babr background.

extract_protocol:
Germinal vesicle oocytes were collected from 3-week old Nlrp5 female mice via collagenase digestion of dissected ovaries (30mg/ml collagenase (Sigma Aldrich), 1% Trypsin (Sigma Aldrich) in DPBS (with Magnesium and calcium), incubated at 37℃ in a thermos mixer at 550rpm for 25mins, manually disrupted intermittently using a 500ul pipette). The digest was stopped by adding equal volume of M2 medium (Sigma Aldrich). Individual oocytes were rinsed first in M2 medium, then in PBS, before being snap frozen in minimal volume of RLT+ buffer (QIAGEN) prior to library preparation.
scPBAT-seq libraries were prepared according to the scM&T-seq protocol detailed in Angermueller et al., Nature Methods, 2016.


title: WT-47

description: SLX22109_TAAGCGTT_47_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P2-1-O10-A1


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-P24


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-P23


title: WT-46

description: SLX22109_TCTCGGTT_46_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-P12


title: WT-45

description: SLX22109_TGGTTGTT_45_L001_non_directional_GRCm38


title: WT-44

description: SLX22109_CTTGTACT_44_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-P11


title: WT-43

description: SLX22109_GGCTACAG_43_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-O24


title: WT-41

description: SLX22109_GATCAGCG_41_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-O23


title: WT-36

description: SLX22109_TGACCACT_36_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-O12


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-O11


title: WT-33

description: SLX22109_ATCACGTT_33_L001_non_directional_GRCm38


title: RNA-sample-64

description: lane8394_CGAGGCTG_TCTCTCCG_64_L001_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-N24


title: WT-34

description: SLX22109_CGATGTTT_34_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-N11


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-N12


title: WT-7

description: SLX22109_TGCATAGT_7_L001_non_directional_GRCm38


title: WT-6

description: SLX22109_TGATACGT_6_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-N23


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-M24


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-M12


title: WT-5

description: SLX22109_TTCTGTGT_5_L001_non_directional_GRCm38


title: WT-2

description: SLX22109_TTCTGTGT_2_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-M11


title: WT-23


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-M23


title: HOM-12


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-L12


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-L24


title: HOM-11


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-L23


title: WT-22


title: HOM-10


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-K24


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-K23


title: HOM-8


title: HOM-9


title: HOM-7


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-K12


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-J24


title: HOM-6


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-K11


title: HOM-5


title: WT-8

description: SLX22109_TTGACTCT_8_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-J23


title: WT-40

description: SLX22109_ACTTGATG_40_L001_non_directional_GRCm38


title: HOM-4


title: WT-4

description: SLX22109_TTGGAGGT_4_L001_non_directional_GRCm38


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-J12


title: HOM-3


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-J11


title: HOM-2


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-I24


title: HOM-1


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-I12


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-I11


title: Ventral mesoderm, Cas7-11 + sox8 guides, Treated embryo 1

city: Dresden

first: Elias

middle: H

last: Barriga

address: ArnoldStrasse 18

department: Cluster of Excellence Physics of Life

country: Germany

institute: TU Dresden

description:
Library name: Treated Sample 1
RNA_Seq_Normalized_Counts.csv - Column name BC_S7

data_processing:
FastQC v0.12.1 and multiqc v1.14. Adapter sequences were removed, and reads with low-quality or length less than 10 bases were discarded using cutadapt v4.4 (Martin, 2011) (with the following parameters: -b CTGTCTCTTATACACATCT-b GTATCAACGCAGAGTACT -b TTTTTTTTTTTTTTTTTTTTTTTTTTTT -b AAAAAAAAAAAAAAAAAAAAA -m 10 -q 20). The rRNA sequences were filtered out with SortMeRNA v4.3.6 (Kopylova et al, 2012) using eukaryotic 18S and 28S rRNA as reference sequences. The trimmed, rRNA-depleted sequences were therefore aligned to the reference genome of X. laevis v10.1 using HISAT2 v2.2.1 with default parameters (Kim et al, 2019). SAM files were converted into BAM files, sorted via SAMtools v1.5, and transcript abundance was quantified using featureCounts v2.0.6 (Liao et al, 2014), resulting in a raw count matrix of mapped reads per gene.
Assembly: Xenopus laevis v10.1
Supplementary files format and content: csv file includes raw counts for each sample

organism: Xenopus laevis

source_name: Ventral mesoderm

extract_protocol:
mRNA libraries from ventrolateral mesoderm tissues were prepared using the Smart-seq2 protocol adapted from Macaulay et al, 2016 (https://doi.org/10.1038/nprot.2016.138). RNA quality was assessed using a HS RNA Screen Tape Analysis (Agilent Technologies).
Libraries were generated by SMART-Seq2 protocol.

value: Ventral mesoderm

value: Cas7-11 + sox8 guides

value: Gastrulating embryo injected with Cas7-11 mRNA and sox 8 guides


title: Ventral mesoderm, Cas7-11 + sox8 guides, Treated embryo 2

description:
Library name: Treated Sample 2
RNA_Seq_Normalized_Counts.csv - Column name CC_S8


title: Ventral mesoderm, Cas7-11, Control embryo 2

description:
Library name: Control Sample 2
RNA_Seq_Normalized_Counts.csv - Column name 3C_S10

value: Gastrulating embryo injected with  Cas7-11 mRNA


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-H24


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-H23


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-L11


title: Cow, PBMC, vir, 10 days, indiv5

city: Pullman

first: Massaro

middle: Wilson

last: Ueti

state: Washington

address: 3003 ADBF Washington State Univ, 3003 ADBF, Grimes Way

institute: USDA ARS Animal Disease Research Unit

description:
Library name: Cow, PBMC, vir, 10 days, indiv5
Column name in allDPC_raw.reps.txt: Bos_taurus-PBMC_10dpc_RNA-r34

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer and then mapped to the Bos taurus reference genome using HISAT2.
Tag directories were created using HOMER2 and the parameters, -flip and -sspe.
Raw read counts were then quantified using HOMER (analyzeRepeats.pl rna bosTau -strand + -count exons -d {0dpc tagDirs} {10dpc tagDirs} -raw > {raw.reps.txt}).
Assembly: GCF_002263795.2
Supplementary files format and content: allDPC_raw.reps.txt: tab-deliminated text file with raw counts for each sample

organism: Bos taurus

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA from PBMC samples stored in RNA later was extracted using the miRNeasy Micro kit (Qiagen) according to the manufacturer’s instructions. Briefly, samples were thawed in ice, the RNA later solution was removed after centrifugation, and RNA extracted according to the kit protocol. RNA samples were quantified by QubitTM 3 Fluorometer (Invitrogen), treated with DNAse I (Invitrogen), resuspended in 20 µL of EDTA TE (10mM TRIS-HCl, 0.1mM EDTA, pH 8.0 – Quality Biological) and 1 µg of RNA/sample was submitted to IGM Genomics Center at the University of California (San Diego, California, USA) for sequencing.
Strand-specific total RNA-Seq libraries from ribosomal RNA–depleted RNA were prepared using the TruSeq stranded total RNA library kit (Illumina) and sequenced using PE100 on Illumina NovaSeq 6000.

treatment_protocol: Five adult male Holstein cattle, >1.5 years of age, were infected intravenously with iRBC containing the virulent B. bovis S74-T3Bo strain. Before infection (day 0) and 10 days post-infection (day 10), blood was collected from the animals and PBMCs were isolated using Histopaque. The cells were resuspended in RNA later and stored at -80 °C until RNA extraction.

value: Peripheral blood mononuclear cells

tag: individual

tag: time

value: Day 10

tag: disease state

value: Babesia bovis


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-H12

tag: strain

value: FC


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-H11

tag: brain region

value: M


title: Cow, PBMC, vir, 10 days, indiv1

description:
Library name: Cow, PBMC, vir, 10 days, indiv1
Column name in allDPC_raw.reps.txt: Bos_taurus-PBMC_10dpc_RNA-r31


title: Cow, PBMC, vir, 0 days, indiv5

description:
Library name: Cow, PBMC, vir, 0 days, indiv5
Column name in allDPC_raw.reps.txt: Bos_taurus-PBMC_0dpc_RNA-r25

value: Day 0


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-G24

tag: gender

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-G23

tag: age


title: Cow, PBMC, vir, 0 days, indiv3

description:
Library name: Cow, PBMC, vir, 0 days, indiv3
Column name in allDPC_raw.reps.txt: Bos_taurus-PBMC_0dpc_RNA-r23


title: Cow, PBMC, vir, 0 days, indiv4

description:
Library name: Cow, PBMC, vir, 0 days, indiv4
Column name in allDPC_raw.reps.txt: Bos_taurus-PBMC_0dpc_RNA-r24


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-G11


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-G12


title: Cow, PBMC, vir, 0 days, indiv1

description:
Library name: Cow, PBMC, vir, 0 days, indiv1
Column name in allDPC_raw.reps.txt: Bos_taurus-PBMC_0dpc_RNA-r21


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-F23


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-F12


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-I23


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-F11


title: Ventral mesoderm, Cas7-11, Control embryo 1

description:
Library name: Control Sample 1
RNA_Seq_Normalized_Counts.csv - Column name 1C_S9

tag: tissue


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-E24


title: Cow, PBMC, vir, 10 days, indiv2

description:
Library name: Cow, PBMC, vir, 10 days, indiv2
Column name in allDPC_raw.reps.txt: Bos_taurus-PBMC_10dpc_RNA-r32


title: RNA-seq of sorghum bicolor: T48h Primary Roots1-NRC

city: Cold Spring Harbor

first: Sunita

last: Kumari

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Lab

description:
Library name: sbi_T2dc_PR_r1
T48h Primary Roots1-NRC

data_processing:
Adapter trimming and quality filtering were performed using Trimmomatic. Filtered reads were aligned to the Zea mays B73 v5 reference genome using STAR. Transcript assembly and quantification were performed using StringTie. Gene-level count matrices were generated for downstream differential expression. Differential expression analysis was conducted using DESeq2.
Raw reads were trimmed and filtered using Trimmomatic. Clean reads were aligned to the Sorghum bicolor BTx623 v3.1.1 reference genome using STAR. Transcript assembly and abundance estimation were performed using StringTie. Gene-level counts were exported for statistical analysis. Differential expression was performed using DESeq2.
Assembly: reference genome (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-62/plants/gff3/zea_mays/)
Supplementary files format and content: Expression_TPM_Leaves-sorghum.csv
Supplementary files format and content: Expression_TPM_Lateral-roots-sorghum.csv
Supplementary files format and content: Expression_TPM_Primary-roots-sorghum.csv

organism: Sorghum bicolor

source_name: primary root

growth_protocol: Sorghum seeds (Sorghum bicolor genotype BTx623) were germinated on rag dolls and transferred to hydroponic tanks containing full-strength Hoagland nutrient solution at 10 days after germination (10 DAG). Plants were grown under controlled environmental conditions (~28°C, 16 h light / 8 h dark). After 12 days in sufficient nitrate, plants reached the 5th leaf stage (21 DAG) and were ready for treatment.

extract_protocol:
Roots and leaves were harvested, snap-frozen in liquid nitrogen, and ground to a fine powder. Total RNA was isolated using a plant RNA extraction protocol compatible with polysaccharide- and polyphenolic-rich tissues. RNA integrity was verified on an Agilent Bioanalyzer. Each biological replicate consisted of pooled tissues from five plants.
mRNA sequencing libraries were prepared using the NEBNext RNA-seq Library Prep Kit with poly(A) selection. After cDNA synthesis, libraries were indexed, amplified, and quality-checked. Sequencing was performed on the Illumina NextSeq 2000 platform, generating paired-end reads.

treatment_protocol: At 21 DAG, sorghum plants were transferred to a nitrate-limiting nutrient solution in which Ca(NO₃)₂ and Mg(NO₃)₂ were replaced with CaCl₂ and MgSO₄. Root and leaf tissues were collected at: 0 min, 30 min, 3 hours, and 24 hours of nitrate deprivation. After 24 hours, nitrate was restored to the hydroponic solution. Recovery samples were harvested at: 24h + 30 min and 24h + 48 h.

value: nitrogen recovery control

value: 48h control

value: primary root

tag: replicate


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-D24


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-E12


title: Ex vivo peritoneal mast cells, wild-type 4

type: RNA

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

description: Gene expression in wild-type mast cells, control

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 8x60K (table 3) using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For differential gene expression FES derived output data files were further analyzed using the  Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware)

source_name: FACS-purified peritoneal mast cells, wild-type 4

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: The FACS-purified murine mast cells  were lysed using SuperAmpTM Lysis Buffer according to the instructions of the SuperAmp Preparation Kit.

treatment_protocol: The cells were isolated directly ex vivo and purified by FACS sorting of 7-AAD-negative cKIT+  ST2+ mast cells from peritoneal lavages.

value: Wild-type

value: Peritoneal cavity


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-E11


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-E23


title: Ex vivo peritoneal mast cells, wild-type 3

source_name: FACS-purified peritoneal mast cells, wild-type 3


title: RNA-seq of sorghum bicolor: T48h Primary Roots3-NRC

description:
Library name: sbi_T2dc_PR_r3
T48h Primary Roots3-NRC


title: RNA-seq of sorghum bicolor: T48h Primary Roots3-NR

description:
Library name: sbi_T2d_PR_r3
T48h Primary Roots3-NR

value: nitrogen recovery


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-F24


title: Cow, PBMC, vir, 0 days, indiv2

description:
Library name: Cow, PBMC, vir, 0 days, indiv2
Column name in allDPC_raw.reps.txt: Bos_taurus-PBMC_0dpc_RNA-r22


title: RNA-seq of sorghum bicolor: T48h Primary Roots2-NRC

description:
Library name: sbi_T2dc_PR_r2
T48h Primary Roots2-NRC


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-D12


title: Ex vivo peritoneal mast cells, wild-type 2

source_name: FACS-purified peritoneal mast cells, wild-type 2


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-D23


title: RNA-seq of sorghum bicolor: T48h Primary Roots2-NR

description:
Library name: sbi_T2d_PR_r2
T48h Primary Roots2-NR


title: RNA-seq of sorghum bicolor: T48h Primary Roots1-NR

description:
Library name: sbi_T2d_PR_r1
T48h Primary Roots1-NR


title: Ex vivo peritoneal mast cells, cKitCreERT2 1

description: Gene expression in mast cells affected by knock-in of CreERT2 into the c-Kit locus, control

source_name: FACS-purified peritoneal mast cells, cKitcreERT2 1


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-D11


title: RNA-seq of sorghum bicolor: T24.5h Primary Roots3-NR

description:
Library name: sbi_T1d30min_PR_r3
T24.5h Primary Roots3-NR


title: Ex vivo peritoneal mast cells, dKO 3

description: Gene expression in mast cells affected by knockout of Roquin1 and Roquin2

source_name: FACS-purified peritoneal mast cells, Mcpt5Cre Roquin1FF Roquin2FF 3

value: Mcpt5Cre Roquin1FF Roquin2FF


title: lib_nonamer_2

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

description: Library name: Nonamer library repeat 2

data_processing:
Reads were trimmed to remove adapter sequences and filtered for quality (Q > 30). UMIs were used to account for possible PCR duplicates. Reads containing CACAGTGGTAGTACT were classified as pre-recombination, and those containing CACTGTGCACAGTG were classified as post-recombination. Nonamer sequences were extracted from both sets. For each unique nonamer, its frequency was calculated as the number of reads containing that nonamer divided by the total number of reads in the respective subset (pre- or post-recombination).
Assembly: N/A
Supplementary files format and content: Tab-delimited text file containing processed read counts and RIC scores for each nonamer sequence.

source_name: v-Abl

growth_protocol: (v-Abl) pre-B cells were cultured in RPMI 1640 medium (Gibco) supplemented with 15% fetal calf serum (FBS; Sigma), 2 μM L-glutamine, sodium pyruvate, MEM non-essential amino acids (NEAA), penicillin (100 U/mL), streptomycin (100 μg/mL) (Gibco), and 50 μM 2-mercaptoethanol.  Cells were incubated at 37 °C in 5% CO2.

extract_protocol: Genomic DNA was extracted from 5 × 10? cells using the Qiagen DNeasy Blood & Tissue Kit, according to the manufacturer's instructions. Pre- and post-recombination 12?23 RSS fragments were amplified by two rounds of PCR. Sequencing libraries were prepared for Illumina next-generation sequencing and sequenced on the Illumina MiSeq platform using the MiSeq Reagent Kit v2 (Illumina), following the manufacturer's protocol.

treatment_protocol: For G1 cell cycle arrest and subsequent RAG expression, v-Abl cells were treated with Abl kinase inhibitor 3uM Imatinib (STI-571, Novartis) for 72h.

tag: cell line

value: v-Abl

value: pre-B cells

value: PMG transduced-WT-vAbl

value: Imatinib- G1 cycle arrested


title: Ex vivo peritoneal mast cells, cKitCreERT2 3

source_name: FACS-purified peritoneal mast cells, cKitcreERT2 3


title: Ex vivo peritoneal mast cells, Mcpt5Cre 2

description: Gene expression in mast cells affected by an Mcpt5Cre BAC transgene, control

source_name: FACS-purified peritoneal mast cells, Mcpt5Cre 2


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-C24


title: Ex vivo peritoneal mast cells, wild-type 1

source_name: FACS-purified peritoneal mast cells, wild-type 1


title: Ex vivo peritoneal mast cells, dKO 5

source_name: FACS-purified peritoneal mast cells, Mcpt5Cre Roquin1FF Roquin2FF 5


title: Patient 1230; RNA-Seq - mets

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

description: Library name: 1230M

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner (bwa) version 0.7.15
Non-uniquely mapped/redundant reads were discarded.
Narrow peaks were called using MACS version 2.1.2 on deduplicated bam files using the following command: macs2 callpeak --SPMR -B -q 0.01 --keep-dup 1 -g hs -f BAMPE --extsize 146 --nomodel -t {treat.bam} -c {input.bam}.
ATAC-seq: Downstream processing included alignment to hg19, peak calling, and differential accessibility analysis using the CHIPS pipeline and DESeq2.
RNA-seq: Reads were quality trimmed, aligned to the human genome with STAR, and transcript quantification and differential expression performed with Cufflinks and DESeq2.
Assembly: hg19
Supplementary files format and content: BigWig and peak text files (BED) were generated
Supplementary files format and content: fpkm_tracking

source_name: Metastasis; Liver

extract_protocol:
Using a 2 mm2 core needle, one core was extracted from frozen RP tissue blocks in the areas marked on the corresponding slide. Frozen cores were pulverized using the Covaris CryoPrep system.
ATAC-seq: Frozen tissue cores (2 mm2 core, ~20 mg) were pulverized (Covaris CryoPrep), nuclei were isolated via iodixanol density gradient, and 50,000 nuclei were subjected to Tn5 transposition using the Omni-ATAC protocol; libraries were purified, PCR-amplified, and sequenced on an Illumina platform (150 bp paired-end).
RNA-seq: Total RNA was extracted from frozen tissue using Qiagen RNeasy columns with on-column DNase digestion, and 1  g RNA was used to prepare stranded polyA+ libraries (Illumina TruSeq); libraries were barcoded, pooled, and sequenced on an Illumina HiSeq 2500 (50 bp paired-end).
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

value: Metastasis; Liver


title: Ex vivo peritoneal mast cells, cKitCreERT2 2

source_name: FACS-purified peritoneal mast cells, cKitcreERT2 12


title: RNA-seq of sorghum bicolor: T24.5h Primary Roots1-NR

description:
Library name: sbi_T1d30min_PR_r1
T24.5h Primary Roots1-NR


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-C12


title: Patient 1166; RNA-Seq - mets

description: Library name: 1166M

source_name: Metastasis; Adrenal

value: Metastasis; Adrenal


title: Patient 334; RNA-Seq - mets

description: Library name: 334M

source_name: Metastasis; Colon

value: Metastasis; Colon


title: Patient 1164; RNA-Seq - mets

description: Library name: 1164M

source_name: Metastasis; Pancreas

value: Metastasis; Pancreas


title: Ex vivo peritoneal mast cells, Mcpt5Cre 1

source_name: FACS-purified peritoneal mast cells, Mcpt5Cre  1


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-C23

value: FC

value: M


title: Ex vivo peritoneal mast cells, dKO 2

source_name: FACS-purified peritoneal mast cells, Mcpt5Cre Roquin1FF Roquin2FF 2


title: lib_nonamer_1

description: Library name: Nonamer library repeat 1


title: Ex vivo peritoneal mast cells, dKO 4

source_name: FACS-purified peritoneal mast cells, Mcpt5Cre Roquin1FF Roquin2FF 4


title: Patient 1350; RNA-Seq - mets

description: Library name: 1350M

source_name: Metastasis; Bladder

value: Metastasis; Bladder


title: Ex vivo peritoneal mast cells, Mcpt5Cre 3

source_name: FACS-purified peritoneal mast cells, Mcpt5Cre 3


title: RNA-seq of sorghum bicolor: T24h Primary Roots3-ND

description:
Library name: sbi_T1d_PR_r3
T24h Primary Roots3-ND

source_name: primary root

value: nitrogen deprivation


title: Patient 1136; RNA-Seq - mets

description: Library name: 1136M

source_name: Metastasis; Brain

value: Metastasis; Brain


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-C11

value: 9 months


title: Ex vivo peritoneal mast cells, dKO 1

source_name: FACS-purified peritoneal mast cells, Mcpt5Cre Roquin1FF Roquin2FF 1

value: Peritoneal cavity


title: Patient 344; RNA-Seq - mets

description: Library name: 344M


title: RNA-seq of sorghum bicolor: T24.5h Primary Roots2-NR

description:
Library name: sbi_T1d30min_PR_r2
T24.5h Primary Roots2-NR

value: nitrogen recovery

value: primary root


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-B24


title: Patient 1169; RNA-Seq - mets

description: Library name: 1169M


title: Patient 1168; RNA-Seq - mets

description: Library name: 1168M

source_name: Metastasis; Omentum

value: Metastasis; Omentum


title: RNA-seq of sorghum bicolor: T3h Primary Roots3-ND

description:
Library name: sbi_T3h_PR_r3
T3h Primary Roots3-ND


title: Patient 573; RNA-Seq - mets

description: Library name: 573M

source_name: Metastasis; Soft Tissue

value: Metastasis; Soft Tissue


title: Patient 968; RNA-Seq - mets

description: Library name: 968M

source_name: Metastasis; Diaphragm

value: Metastasis; Diaphragm


title: RNA-seq of sorghum bicolor: T24h Primary Roots1-ND

description:
Library name: sbi_T1d_PR_r1
T24h Primary Roots1-ND


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-B12


title: Patient 1247; RNA-Seq - mets 1

description: Library name: 1247A

source_name: Metastasis; lung

value: Metastasis; lung


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-B11


title: Patient 1247; RNA-Seq - mets 2

description: Library name: 1247B

source_name: Metastasis; lymph node

value: Metastasis; lymph node


title: Patient 1077/1284/1308; RNA-Seq - mets 3

description: Library name: 1308M

source_name: Metastasis; abdominal wall

value: Metastasis; abdominal wall


title: Patient 1120 (sample no 1124); RNA-Seq

description: Library name: 1124M


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-A24


title: RNA-seq of sorghum bicolor: T0.5h Primary Roots3-ND

description:
Library name: sbi_T30min_PR_r3
T0.5h Primary Roots3-ND


title: Patient 1120; RNA-Seq - local tumor

description: Library name: 1120T

source_name: Primary; Kidney tumor

value: Primary; Kidney tumor


title: Patient 1120; RNA-Seq - normal

description: Library name: 1120N

source_name: Normal Kidney

value: Normal Kidney


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-A23

value: FC


title: Patient 233; RNA-Seq - local tumor

description: Library name: R233T


title: RNA-seq of sorghum bicolor: T0.5h Primary Roots2-ND

description:
Library name: sbi_T30min_PR_r2
T0.5h Primary Roots2-ND


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-A12

value: M


title: RNA-seq of sorghum bicolor: T24h Primary Roots2-ND

description:
Library name: sbi_T1d_PR_r2
T24h Primary Roots2-ND


title: RNA-seq of sorghum bicolor: T0.5h Primary Roots1-ND

description:
Library name: sbi_T30min_PR_r1
T0.5h Primary Roots1-ND


title: Patient 1091 (sample no 1320); RNA-Seq - normal adjacent to mets

description: Library name: a1320N

source_name: Normal adjacent to metastasis

value: Normal adjacent to metastasis


title: Patient 1091 (sample no 1320); RNA-Seq - mets

description: Library name: a1320M

source_name: Metastasis; Ovary

value: Metastasis; Ovary


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-B23


title: Patient 256; RNA-Seq - mets

description: Library name: 256M


title: AMB_200205_9mo_2A_3A_1_P1-6-N18-A11


title: RNA-seq of sorghum bicolor: T3h Primary Roots2-ND

description:
Library name: sbi_T3h_PR_r2
T3h Primary Roots2-ND

value: nitrogen deprivation


title: Patient 1091; RNA-Seq - normal

description: Library name: a1091N


title: Patient 1014; RNA-Seq - local tumor

description: Library name: a1014T


title: RNA-seq of sorghum bicolor: T3h Primary Roots1-ND

description:
Library name: sbi_T3h_PR_r1
T3h Primary Roots1-ND


title: Patient 1091; RNA-Seq - local tumor

description: Library name: a1091T


title: Patient 1077/1284/1308; RNA-Seq - mets 1

description: Library name: 1077M

source_name: Metastasis; bone

value: Metastasis; bone


title: RNA-seq of sorghum bicolor: T0 Primary Roots3-NN

description:
Library name: sbi_T0_PR_r3
T0 Primary Roots3-NN

value: normal nitrogen


title: Patient 1014; RNA-Seq - normal

description: Library name: a1014N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-P22

value: 9 months


title: Patient 638; RNA-Seq - local tumor

description: Library name: R638T


title: RNA-seq of sorghum bicolor: T0 Primary Roots1-NN

description:
Library name: sbi_T0_PR_r1
T0 Primary Roots1-NN

value: primary root


title: Patient 638; RNA-Seq - normal

description: Library name: R638N


title: RNA-seq of sorghum bicolor: T48h Lateral Roots 3-NRC

description:
Library name: sbi_T2dc_LR_r3
T48h Lateral Roots 3-NRC

source_name: lateral root

value: nitrogen recovery control

value: 48h control

value: lateral root


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-P21


title: Patient 1058 (sample no 1189); RNA-Seq - mets

description: Library name: 1189M

source_name: Metastasis; Spine

value: Metastasis; Spine


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-P9


title: Patient 957 (sample no 1131); RNA-Seq - mets

description: Library name: 1131M

source_name: Metastasis; Lung

value: Metastasis; Lung


title: Patient 1058; RNA-Seq - local tumor

description: Library name: 1058T


title: RNA-seq of sorghum bicolor: T48h Lateral Roots 2-NRC

description:
Library name: sbi_T2dc_LR_r2
T48h Lateral Roots 2-NRC


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-O9


title: Patient 957; RNA-Seq - local tumor

description: Library name: R957T


title: RNA-seq of sorghum bicolor: T48h Lateral Roots 1-NRC

description:
Library name: sbi_T2dc_LR_r1
T48h Lateral Roots 1-NRC


title: Patient 957; RNA-Seq - normal

description: Library name: R957N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-O22


title: RNA-seq of sorghum bicolor: T0 Primary Roots2-NN

description:
Library name: sbi_T0_PR_r2
T0 Primary Roots2-NN

source_name: primary root


title: RNA-seq of sorghum bicolor: T48h Lateral Roots 3-NR

description:
Library name: sbi_T2d_LR_r3
T48h Lateral Roots 3-NR

value: nitrogen recovery


title: Patient 962; RNA-Seq - mets

description: Library name: R962M


title: Patient 962; RNA-Seq - normal

description: Library name: R962N

value: Primary; Kidney tumor


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-O21


title: RNA-seq of sorghum bicolor: T48h Lateral Roots 2-NR

description:
Library name: sbi_T2d_LR_r2
T48h Lateral Roots 2-NR


title: Patient 962; RNA-Seq - local tumor

description: Library name: R962T


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-O10


title: RNA-seq of sorghum bicolor: T48h Lateral Roots 1-NR

description:
Library name: sbi_T2d_LR_r1
T48h Lateral Roots 1-NR


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-N9


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-P10


title: Patient 716; RNA-Seq - local tumor

description: Library name: R716T


title: Patient 1247; INPUT - mets 2

description: Library name: IN1247B

value: Metastasis; lymph node

tag: antibody

value: none (input)


title: Patient 1058; RNA-Seq - normal

description: Library name: 1058N

value: Normal Kidney


title: Patient 716; RNA-Seq - mets

description: Library name: R716M

source_name: Metastasis; adrenal

value: Metastasis; adrenal


title: RNA-seq of sorghum bicolor: T24.5h Lateral Roots 2-NR

description:
Library name: sbi_T1d30min_LR_r2
T24.5h Lateral Roots 2-NR

tag: genotype


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-N22

value: FC

value: M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-N21


title: Patient 1247; INPUT - mets 1

description: Library name: IN1247A

value: Metastasis; lung


title: RNA-seq of sorghum bicolor: T24.5h Lateral Roots 1-NR

description:
Library name: sbi_T1d30min_LR_r1
T24.5h Lateral Roots 1-NR


title: Patient 638; INPUT - local tumor

description: Library name: IN638T


title: Patient 638; INPUT - normal

description: Library name: IN638N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-N10


title: Patient 1226; RNA-Seq - mets

description: Library name: 1226M


title: Patient 1226; RNA-Seq - normal

description: Library name: 1226N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-M9


title: RNA-seq of sorghum bicolor: T24h Lateral Roots 2-ND

description:
Library name: sbi_T1d_LR_r2
T24h Lateral Roots 2-ND

value: nitrogen deprivation


title: Patient 964; INPUT - mets

description: Library name: IN964M

source_name: Metastasis; Pancreas

value: Metastasis; Pancreas


title: Patient 1014; INPUT - normal

description: Library name: IN1014N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-M22

value: 9 months


title: RNA-seq of sorghum bicolor: T24h Lateral Roots 1-ND

description:
Library name: sbi_T1d_LR_r1
T24h Lateral Roots 1-ND


title: RNA-seq of sorghum bicolor: T24.5h Lateral Roots 3-NR

description:
Library name: sbi_T1d30min_LR_r3
T24.5h Lateral Roots 3-NR


title: RNA-seq of sorghum bicolor: T24h Lateral Roots 3-ND

description:
Library name: sbi_T1d_LR_r3
T24h Lateral Roots 3-ND


title: Patient 716; RNA-Seq - normal

description: Library name: R716N


title: Patient 968; INPUT - mets

description: Library name: IN968M

value: Metastasis; Diaphragm


title: Patient 573; INPUT - mets

description: Library name: IN573M

value: Metastasis; Soft Tissue


title: Patient 354; INPUT - mets

description: Library name: IN354M

source_name: Metastasis; Bone

value: Metastasis; Bone


title: Patient 1014; INPUT - local tumor

description: Library name: IN1014T


title: RNA-seq of sorghum bicolor: T3h Lateral Roots 3-ND

description:
Library name: sbi_T3h_LR_r3
T3h Lateral Roots 3-ND

value: lateral root


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-M21


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-M10


title: Patient 344; INPUT - mets

description: Library name: IN344M

source_name: Metastasis; Brain

value: Metastasis; Brain


title: Patient 334; INPUT - mets

description: Library name: IN334M

source_name: Metastasis; Colon

value: Metastasis; Colon


title: RNA-seq of sorghum bicolor: T3h Lateral Roots 2-ND

description:
Library name: sbi_T3h_LR_r2
T3h Lateral Roots 2-ND


title: Patient 1358; INPUT - mets

description: Library name: IN1358M

source_name: Metastasis; Soft Tissue


title: Patient 256; INPUT - mets

description: Library name: IN256M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-L9


title: Patient 1320; INPUT - normal

description: Library name: IN1320N

source_name: Normal adjacent to metastasis (ovary)

value: Normal adjacent to metastasis (ovary)


title: Patient 1350; INPUT - mets

description: Library name: IN1350M

source_name: Metastasis; Bladder

value: Metastasis; Bladder


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-L22


title: Patient 1301/1319M; INPUT - mets 2

description: Library name: IN1319M

source_name: Metastasis; Adrenal

value: Metastasis; Adrenal

value: none (input)


title: RNA-seq of sorghum bicolor: T3h Lateral Roots 1-ND

description:
Library name: sbi_T3h_LR_r1
T3h Lateral Roots 1-ND


title: Ex vivo peritoneal mast cells, cKitCreERT2 4

description: Gene expression in mast cells affected by knock-in of CreERT2 into the c-Kit locus, control

source_name: FACS-purified peritoneal mast cells, cKitcreERT2 4

value: Peritoneal cavity


title: RNA-seq of sorghum bicolor: T0.5h Lateral Roots 3-ND

description:
Library name: sbi_T30min_LR_r3
T0.5h Lateral Roots 3-ND


title: Patient 1301/1319; INPUT - mets 1

description: Library name: IN1301M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-L21

value: FC


title: RNA-seq of sorghum bicolor: T0.5h Lateral Roots 1-ND

description:
Library name: sbi_T30min_LR_r1
T0.5h Lateral Roots 1-ND


title: Patient 1169; INPUT - mets

description: Library name: IN1169M


title: RNA-seq of sorghum bicolor: T0.5h Lateral Roots 2-ND

description:
Library name: sbi_T30min_LR_r2
T0.5h Lateral Roots 2-ND


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-K9

value: M


title: Patient 1136; INPUT - mets

description: Library name: IN1136M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-K22


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-L10


title: RNA-seq of sorghum bicolor: T0 Lateral Roots 3-NN

description:
Library name: sbi_T0_LR_r3
T0 Lateral Roots 3-NN

value: normal nitrogen


title: Patient 1174; INPUT - mets

description: Library name: IN1174M


title: Patient 1077/1284/1308; INPUT - mets 3

description: Library name: IN1308M

source_name: Metastasis; abdominal wall

value: Metastasis; abdominal wall


title: Patient 1168; INPUT - mets

description: Library name: IN1168M

source_name: Metastasis; Omentum

value: Metastasis; Omentum


title: RNA-seq of sorghum bicolor: T0 Lateral Roots 1-NN

description:
Library name: sbi_T0_LR_r1
T0 Lateral Roots 1-NN


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-K21

value: 9 months


title: Patient 1077/1284/1308; INPUT - mets 1

description: Library name: IN1077M

source_name: Metastasis; bone

value: Metastasis; bone


title: RNA-seq of sorghum bicolor: T0 Lateral Roots 2-NN

description:
Library name: sbi_T0_LR_r2
T0 Lateral Roots 2-NN

source_name: lateral root


title: Patient 1164; INPUT - mets

description: Library name: IN1164M

value: Metastasis; Pancreas


title: RNA-seq of sorghum bicolor: T48h Leaves 3-NRC

description:
Library name: sbi_T2dc_leaves_r3
T48h Leaves 3-NRC

source_name: leaves

value: nitrogen recovery control

value: 48h control

value: leaves


title: Patient 1120 (sample no 1124); INPUT - mets

description: Library name: IN1124M

source_name: Metastasis; lung

value: Metastasis; lung


title: Patient 1022; INPUT - mets

description: Library name: IN1022M

source_name: Metastasis; Diaphragm

value: Metastasis; Diaphragm


title: Patient 1077/1284/1308; INPUT - mets 2

description: Library name: IN1284M

source_name: Metastasis; soft tissue

value: Metastasis; soft tissue


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-J9


title: RNA-seq of sorghum bicolor: T48h Leaves 2-NRC

description:
Library name: sbi_T2dc_leaves_r2
T48h Leaves 2-NRC


title: Patient 1120; INPUT - normal

description: Library name: IN1120N

source_name: Normal Kidney

value: Normal Kidney


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-J22


title: Patient 233; INPUT - local tumor

description: Library name: IN233T

source_name: Primary; Kidney tumor

value: Primary; Kidney tumor

value: none (input)


title: Patient 1230; INPUT - mets

description: Library name: IN1230M

source_name: Metastasis; Liver

value: Metastasis; Liver


title: Patient 1166; INPUT - mets

description: Library name: IN1166M

value: Metastasis; Adrenal


title: RNA-seq of sorghum bicolor: T48h Leaves 1-NRC

description:
Library name: sbi_T2dc_leaves_r1
T48h Leaves 1-NRC

value: nitrogen recovery control (NRC)


title: Patient 1091 (sample no 1320); INPUT - mets

description: Library name: IN1320M

source_name: Metastasis; Ovary

value: Metastasis; Ovary


title: Patient 233; INPUT - normal

description: Library name: IN233N


title: Patient 1091; INPUT - local tumor

description: Library name: IN1091T


title: RNA-seq of sorghum bicolor: T48h Leaves 3-NR

description:
Library name: sbi_T2d_leaves_r3
T48h Leaves 3-NR

value: nitrogen recovery


title: Patient 1091; INPUT - normal

description: Library name: IN1091N


title: Patient 1058 (sample no 1189); INPUT - mets

description: Library name: IN1189M

source_name: Metastasis; Spine

value: Metastasis; Spine


title: RNA-seq of sorghum bicolor: T48h Leaves 2-NR

description:
Library name: sbi_T2d_leaves_r2
T48h Leaves 2-NR


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-J10

value: FC

value: M

value: 9 months


title: Patient 1058; INPUT - local tumor

description: Library name: IN1058T


title: Patient 957 (sample no 1131) ; INPUT - mets

description: Library name: IN1131M

source_name: Metastasis; Lung

value: Metastasis; Lung


title: RNA-seq of sorghum bicolor: T24.5h Leaves 3-NR

description:
Library name: sbi_T1d30min_leaves_r3
T24.5h Leaves 3-NR

value: leaves


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-I9


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-K10


title: Patient 957; INPUT - local tumor

description: Library name: IN957T


title: Patient 1120; INPUT - local tumor

description: Library name: IN1120T


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-I21


title: Patient 957; INPUT - normal

description: Library name: IN957N


title: RNA-seq of sorghum bicolor: T24.5h Leaves 2-NR

description:
Library name: sbi_T1d30min_leaves_r2
T24.5h Leaves 2-NR


title: Patient 951; INPUT - mets

description: Library name: IN951M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-I10


title: Patient 951; INPUT - local tumor

description: Library name: IN951T


title: Patient 951; INPUT - normal

description: Library name: IN951N


title: RNA-seq of sorghum bicolor: T24.5h Leaves 1-NR

description:
Library name: sbi_T1d30min_leaves_r1
T24.5h Leaves 1-NR

value: nitrogen recovery (NR)


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-H9


title: Patient 962; INPUT - mets

description: Library name: IN962M


title: RNA-seq of sorghum bicolor: T24h Leaves 3-ND

description:
Library name: sbi_T1d_leaves_r3
T24h Leaves 3-ND

value: nitrogen deprivation


title: Patient 1058; INPUT - normal

description: Library name: IN1058N


title: Patient 962; INPUT - normal

description: Library name: IN962N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-H22


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-I22


title: RNA-seq of sorghum bicolor: T24h Leaves 2-ND

description:
Library name: sbi_T1d_leaves_r2
T24h Leaves 2-ND


title: Patient 1226; INPUT - local tumor

description: Library name: IN1226T


title: Patient 962; INPUT - local tumor

description: Library name: IN962T


title: Patient 716; INPUT - mets

description: Library name: IN716M

source_name: Metastasis; adrenal

value: Metastasis; adrenal


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-H10


title: RNA-seq of sorghum bicolor: T3h Leaves 3-ND

description:
Library name: sbi_T3h_leaves_r3
T3h Leaves 3-ND


title: Patient 716; INPUT - normal

description: Library name: IN716N

value: Normal Kidney


title: Patient 638; HIF2a ChIP-Seq - local tumor

description: Library name: HIF638T

value: Primary; Kidney tumor

value: HIF2α antibody, abcam, ab199


title: RNA-seq of sorghum bicolor: T24h Leaves 1-ND

description:
Library name: sbi_T1d_leaves_r1
T24h Leaves 1-ND


title: Patient 1226; INPUT - normal

description: Library name: IN1226N

value: none (input)


title: RNA-seq of sorghum bicolor: T3h Leaves 2-ND

description:
Library name: sbi_T3h_leaves_r2
T3h Leaves 2-ND


title: Patient 1226; INPUT - mets

description: Library name: IN1226M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-G9


title: Patient 716; INPUT - local tumor

description: Library name: IN716T


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-G22


title: Patient 638; HIF2a ChIP-Seq - normal

description: Library name: HIF638N


title: RNA-seq of sorghum bicolor: T3h Leaves 1-ND

description:
Library name: sbi_T3h_leaves_r1
T3h Leaves 1-ND


title: Patient 1247; HIF2a ChIP-Seq - mets 2

description: Library name: HIF1247B

value: Metastasis; soft tissue


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-G21


title: Patient 1247; HIF2a ChIP-Seq - mets 1

description: Library name: HIF1247A

value: Metastasis; lung


title: Patient 1091 (sample no 1320); HIF2a ChIP-Seq.- normal from site of ovarian mets

description: Library name: HIF1320N

source_name: Normal from site of mets

value: Normal from site of mets


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-G10


title: Patient 1014; HIF2a ChIP-Seq - local tumor

description: Library name: HIF1014T


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-H21


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-F9


title: Patient 964; HIF2a ChIP-Seq -mets

description: Library name: HIF964M

source_name: Metastasis; Pancreas

value: Metastasis; Pancreas


title: RNA-seq of sorghum bicolor: T0.5h Leaves 1-ND

description:
Library name: sbi_T30min_leaves_r1
T0.5h Leaves 1-ND

value: nitrogen deprivation (ND


title: Patient 1014; HIF2a ChIP-Seq - normal

description: Library name: HIF1014N


title: Patient 968; HIF2a ChIP-Seq - mets

description: Library name: HIF968M

value: Metastasis; Diaphragm


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-F22

value: FC

value: M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-F21

value: 9 months


title: RNA-seq of sorghum bicolor: T0h Leaves 2-NN

description:
Library name: sbi_T0_leaves_r2
T0h Leaves 2-NN

value: normal nitrogen

value: leaves


title: Patient 256; HIF2a ChIP-Seq - mets

description: Library name: HIF256M

source_name: Metastasis; Soft Tissue

value: Metastasis; Soft Tissue


title: Patient 573; HIF2a ChIP-Seq - mets

description: Library name: HIF573M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-F10


title: Patient 354; HIF2a ChIP-Seq - mets

description: Library name: HIF354M

source_name: Metastasis; Bone

value: Metastasis; Bone


title: RNA-seq of sorghum bicolor: T0h Leaves 3 -NN

description:
Library name: sbi_T0_leaves_r3
T0h Leaves 3 -NN


title: Patient 1358; HIF2a ChIP-Seq - mets

description: Library name: HIF1358M


title: RNA-seq of sorghum bicolor: T0.5h Leaves 3-ND

description:
Library name: sbi_T30min_leaves_r3
T0.5h Leaves 3-ND

value: nitrogen deprivation


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-E9


title: Patient 344; HIF2a ChIP-Seq - mets

description: Library name: HIF344M

source_name: Metastasis; Brain

value: Metastasis; Brain


title: Patient 1350; HIF2a ChIP-Seq - mets

description: Library name: HIF1350M

source_name: Metastasis; Bladder

value: Metastasis; Bladder

value: HIF2α antibody, abcam, ab199


title: RNA-seq of sorghum bicolor: T0h Leaves 1-NN

description:
Library name: sbi_T0_leaves_r1
T0h Leaves 1-NN

source_name: leaves

value: normal nitrogen (NN)


title: Patient 1169; HIF2a ChIP-Seq - mets

description: Library name: HIF1169M


title: WT_m6A_rep2

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

description: Library name: WT_m6A_rep2

data_processing:
Basecalls performed using Illuminal CASAVA software.
Cutadapt was used to remove the first 9 bases and N’s on both ends of reads. Reads with minimum of 25 bases were kept. Reads were aligned to human genome (hg19) using STAR. Duplicated reads were marked and removed by Picard. The bam files were transformed into bed12 format by bedtools, and then shifted to 200nt by a custom script and transformed back to bed6 format. Macs2 bdgopt sub-command was used to normalize each sample to a 10 million total reads.
exomePeak was used to call m6A enriched peaks by combining both replicates with default parameters.
Assembly: mm9
Supplementary files format and content: bigWig file
Library strategy: MeRIP-seq

source_name: mouse tissue

extract_protocol:
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara-Clontech, 634413), according to the manufacturer’s instructions.

value: mouse tissue

value: NUP93 Wild type


title: RNA-seq of sorghum bicolor: T48h Leaves 1-NR

description:
Library name: sbi_T2d_leaves_r1
T48h Leaves 1-NR

value: nitrogen recovery


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-E22


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-J21


title: Patient 1168; HIF2a ChIP-Seq - mets

description: Library name: HIF1168M

source_name: Metastasis; Omentum

value: Metastasis; Omentum


title: Patient 1164; HIF2a ChIP-Seq  mets

description: Library name: HIF1164M

value: Metastasis; Pancreas


title: RNA-seq of sorghum bicolor: T0.5h Leaves 2-ND

description:
Library name: sbi_T30min_leaves_r2
T0.5h Leaves 2-ND


title: Patient 1136; HIF2a ChIP-Seq - mets

description: Library name: HIF1136M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-E21

value: FC


title: Patient 1077/1284/1308; HIF2a ChIP-Seq - mets 1

description: Library name: HIF1077M

source_name: Metastasis; abdominal wall

value: Metastasis; abdominal wall


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-D9

value: M

value: 9 months


title: Patient 233; HIF2a ChIP-Seq - local tumor

description: Library name: HIF233T

value: Primary; Kidney tumor


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-D22


title: RW_input_rep2

description: Library name: RW_input_rep2


title: Patient 1091; HIF2a ChIP-Seq - normal

description: Library name: HIF1091N

source_name: Normal Kidney

value: Normal Kidney


title: WT_input_rep2

description: Library name: WT_input_rep2


title: WT_m6A_rep1

description: Library name: WT_m6A_rep1


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-E10


title: Patient 1091; HIF2a ChIP-Seq - local tumor

description: Library name: HIF1091T

source_name: Primary; Kidney tumor


title: Patient 1077/1284/1308; HIF2a ChIP-Seq - mets 2

description: Library name: HIF1284M

source_name: Metastasis; soft tissue

value: Metastasis; soft tissue


title: Patient 1077/1284/1308; HIF2a ChIP-Seq - mets 3

description: Library name: HIF1308M

source_name: Metastasis; bone

value: Metastasis; bone


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-C9


title: WT_input_rep1

description: Library name: WT_input_rep1


title: Patient 1120 (sample no 1124M); HIF2a ChIP-Seq - mets

description: Library name: HIF1124M

source_name: Metastasis; lung

value: Metastasis; lung


title: Patient 1120; HIF2a ChIP-Seq - local tumor

description: Library name: HIF1120T


title: Patient 1058; HIF2a ChIP-Seq - normal

description: Library name: HIF1058N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-C22


title: Patient 957 (sample no 1131); HIF2a ChIP-Seq - mets

description: Library name: HIF1131M

source_name: Metastasis; Lung

value: Metastasis; Lung


title: RW_m6A_rep1

description: Library name: RW_m6A_rep1


title: Patient 1120; HIF2a ChIP-Seq - normal

description: Library name: HIF1120N

value: HIF2α antibody, abcam, ab199


title: RW_m6A_rep2

description: Library name: RW_m6A_rep2


title: Patient 1091 (sample no 1320); HIF2a ChIP-Seq - mets

description: Library name: HIF1320M

source_name: Metastasis; Ovary

value: Metastasis; Ovary


title: Patient 233; HIF2a ChIP-Seq - normal

description: Library name: HIF233N


title: Patient 1058; HIF2a ChIP-Seq - local tumor

description: Library name: HIF1058T


title: Patient 957; HIF2a ChIP-Seq - normal

description: Library name: HIF957N


title: Patient 957; HIF2a ChIP-Seq - local tumor

description: Library name: HIF957T


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-D10


title: Patient 1058 (sample no 1189); HIF2a ChIP-Seq - mets

description: Library name: HIF1189M

source_name: Metastasis; Spine

value: Metastasis; Spine


title: Total_heto_rep3

description: Library name: Total_heto_rep3

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to mm9 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Assembly: mm9
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

extract_protocol:
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by KAPA Stranded mRNA- Seq Kit (96rxn, KK8421), according to the manufacturer’s instructions.

value: mouse tissue


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-C10


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-B9


title: Patient 951; HIF2a ChIP-Seq - normal

description: Library name: HIF951N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-D21


title: Total_homo_rep3

description: Library name: Total_homo_rep3


title: Total_heto_rep1

description: Library name: Total_heto_rep1


title: Patient 962; HIF2a ChIP-Seq - normal

description: Library name: HIF962N


title: RW_input_rep1

description: Library name: RW_input_rep1


title: Patient 1226; HIF2a ChIP-Seq -mets

description: Library name: HIF1226M

source_name: Metastasis; adrenal

value: Metastasis; adrenal


title: Total_WT_rep3

description: Library name: Total_WT_rep3

value: Nup93 Wild type


title: Total_heto_rep2

description: Library name: Total_heto_rep2


title: Patient 951; HIF2a ChIP-Seq - local tumor

description: Library name: HIF951T


title: Total_homo_rep2

description: Library name: Total_homo_rep2


title: Patient 951; HIF2a ChIP-Seq - mets

description: Library name: HIF951M


title: Patient 716; HIF2a ChIP-Seq - local tumor

description: Library name: HIF716T


title: Patient 962; HIF2a ChIP-Seq - mets

description: Library name: HIF962M


title: Patient 1226; HIF2a ChIP-Seq - local tumor

description: Library name: HIF1226T


title: Patient 716; HIF2a ChIP-Seq - mets

description: Library name: HIF716M


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-B21


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-B22


title: Total_WT_rep2

description: Library name: Total_WT_rep2


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-A9


title: Patient 962; HIF2a ChIP-Seq - local tumor

description: Library name: HIF962T


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-B10


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-C21


title: Patient 968; H3K27ac ChIP-Seq - mets

description: Library name: K27968M

source_name: Metastasis; Diaphragm

value: Metastasis; Diaphragm

value: H3K27ac anitbody, Diagenode C15410196


title: Patient 716; HIF2a ChIP-Seq - noemal

description: Library name: HIF716N


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-A22

value: FC


title: Total_WT_rep1

description: Library name: Total_WT_rep1


title: Total_homo_rep1

description: Library name: Total_homo_rep1


title: Patient 964; H3K27ac ChIP-Seq - mets

description: Library name: K27964M

source_name: Metastasis; Pancreas

value: Metastasis; Pancreas


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-A10

value: M

value: 9 months


title: Patient 1226; HIF2a ChIP-Seq - normal

description: Library name: HIF1226N

value: Normal Kidney


title: AMB_200205_9mo_2A_3A_1_P1-5-N9-A21


title: Patient 962; H3K27ac ChIP-Seq - mets

description: Library name: K27962M


title: Patient 957; H3K27ac ChIP-Seq - local tumor

description: Library name: K27957T

value: Primary; Kidney tumor


title: Patient 962; H3K27ac ChIP-Seq - local tumor

description: Library name: K27962T


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-P8


title: Patient 716; H3K27ac ChIP-Seq - local tumor

description: Library name: K27716T


title: Patient 951; H3K27ac ChIP-Seq - mets

description: Library name: K27951M


title: Patient 957; H3K27ac ChIP-Seq - normal

description: Library name: K27957N


title: Nuclear_homo_rep3

description: Library name: Nuclear_homo_rep3

molecule: nuclear RNA


title: Patient 951; H3K27ac ChIP-Seq - normal

description: Library name: K27951N


title: Patient 962; H3K27ac ChIP-Seq - normal

description: Library name: K27962N


title: Nuclear_homo_rep1

description: Library name: Nuclear_homo_rep1


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-P7


title: Nuclear_heto_rep2

description: Library name: Nuclear_heto_rep2


title: Patient 716; H3K27ac ChIP-Seq - mets

description: Library name: K27716M


title: Nuclear_homo_rep2

description: Library name: Nuclear_homo_rep2


title: Patient 716; H3K27ac ChIP-Seq - normal

description: Library name: K27716N


title: Nuclear_heto_rep3

description: Library name: Nuclear_heto_rep3


title: oTr-48h-Arg 2

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Library name: oTr-48h-Arg 2

data_processing:
Raw fastq files were aligned to Sus scrofa Sscrofa11.1 genome and Ovis aries Oar3.1 genome assemblies using HISAT2 v.2.2.1.
Data were quantitated at a protein-coding mRNA level using Partek Flow bioinformatics software (https://www.partek.com/partek-flow/), with normalization by total read count (fragments per kilobase of transcript per million mapped reads, FPKM), and 75% distribution.
Differential gene expression was calculated using DESeq2. Genes were classified as differentially expressed (DEGs) if they met the following criteria: average FPKM>1 in at least one group, false discovery rate (q-value or FDR) <0.05, and ≥1.3-fold change in expression.
Assembly: Oar_v3.1 for Ovis aries; and Sscrofa11.1 for Sus scrofa
Supplementary files format and content: FPKM values

organism: Ovis aries

source_name: oTr1 Cells

extract_protocol:
The RNA from pTr2 and oTr1 cells was extracted by TRIzol following the mannual.
For RNA sequencing (RNA-seq) of pTr2 and oTr1 cells treated with or without arginine, total RNA (350 ng per samples) was used to generate sequencing libraries using the TruSeq Stranded Total RNA with Ribo-zero Plus kit (Illumina), following the manufacturer’s instruction.

value: oTr1 Cells

value: ovine trophectoderm cells

value: wildtype

value: 0.2 mM Arginine


title: Patient 951; H3K27ac ChIP-Seq - local tumor

description: Library name: K27951T


title: Nuclear_WT_rep2

description: Library name: Nuclear_WT_rep2


title: Nuclear_WT_rep3

description: Library name: Nuclear_WT_rep3


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-P19


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-P20


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-O8


title: oTr-48h-Arg 3

description: Library name: oTr-48h-Arg 3


title: oTr-48h-Arg 1

description: Library name: oTr-48h-Arg 1


title: Patient 638; H3K27ac ChIP-Seq - tumor

description: Library name: K27638T


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-O7


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-O20


title: oTr-48h-Ctrl 3

description: Library name: oTr-48h-Ctrl 3

value: 0 mM Arginine


title: Patient 573; H3K27ac ChIP-Seq - mets

description: Library name: K27573M

source_name: Metastasis; Soft Tissue

value: Metastasis; Soft Tissue


title: Nuclear_heto_rep1

description: Library name: Nuclear_heto_rep1

value: mouse tissue


title: Patient 354; H3K27ac ChIP-Seq - mets

description: Library name: K27354M

source_name: Metastasis; Bone

value: Metastasis; Bone


title: Patient 344; H3K27ac ChIP-Seq - mets

description: Library name: K27344M

source_name: Metastasis; Brain

value: Metastasis; Brain


title: oTr-48h-Ctrl 1

description: Library name: oTr-48h-Ctrl 1


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-N8


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-O19


title: oTr-48h-Ctrl 2

description: Library name: oTr-48h-Ctrl 2


title: oTr-0h-Ctrl 3

description: Library name: oTr-0h-Ctrl 3


title: Nuclear_WT_rep1

description: Library name: Nuclear_WT_rep1

source_name: mouse tissue

value: Nup93 Wild type


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-N7


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-N20


title: Patient 233; H3K27ac ChIP-Seq - local tumor

description: Library name: K27233T

value: H3K27ac anitbody, Diagenode C15410196


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-N19

value: FC


title: Patient 233; H3K27ac ChIP-Seq - normal

description: Library name: K27233N


title: oTr-0h-Ctrl 1

description: Library name: oTr-0h-Ctrl 1


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-M8


title: WT noTx 11

city: Birmingham

first: Pi-Ling

last: Chang

state: Alabama

address: 1675 University Blvd

department: Nutrition Sciences

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used to convert the bcl images to FASTQ files.
Raw sequence reads were trimmed with Trim Galore version 0.6.5 using parameters --trim-n --trim1 --nextseq 20
Trimmed reads were aligned to the reference genome with STAR version 2.7.5a using paramters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the aligned BAM files with HTSeq-count version 0.11.3 using parameters -m union -r pos -t exon -i gene_id -a 10 - s no -f bam
Assembly: Gencode GRCm38 p6 Release M24
Supplementary files format and content: tab-delimited Excel file containing raw transcript abundances for each sample and Ensembl ID#

source_name: Epidermis

growth_protocol: Not applicable

extract_protocol: Briefly, dorsal skins taken from euthanized mice were rinsed several times with DEPC water, followed by the addition of TRIzol™ Reagent (Thermo Fisher Scientific, Waltham, MA). The epidermis was scraped with a razor blade and transferred to tubes containing TRIzol™ Reagent. Total RNA isolated was sent to the UAB Genomic Core facility, analyzed for RNA integrity prior to RNA-seq.

treatment_protocol: WT, OPN-null and tg(K14-OP) male mice at 10 weeks of age were shaved 48 h prior to UVB exposure at 180 mJ/cm2. Dorsal skins of euthanized mice were harvested 24 h after UVB exposure.

value: Epidermis

value: WT

value: noTx


title: Patient 1358; H3K27ac ChIP-Seq - mets

description: Library name: K271358M


title: Patient 638; H3K27ac ChIP-Seq - normal

description: Library name: K27638N

source_name: Normal Kidney

value: Normal Kidney


title: Patient 1350; H3K27ac ChIP-Seq - mets

description: Library name: K271350M

source_name: Metastasis; Bladder

value: Metastasis; Bladder