title: ST-00020154-Mb

value: Peritoneum


title: DoubleNeg nuclei sample for Individual 108 [205061420154_R01C01]

status: Public on Nov 06 2024

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: nuclei samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: nuclei samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package bigmelon idat function. Data was then pre-processed using dasen function.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: DoubleNeg

label_protocol: 500 ng DNA from each nuclei sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gold Kit (Cambridge Bioscience, UK) according to the manufacturer's standard protocol.

extract_protocol: Genomic DNA was extracted from frozen nuclei aliquots using a modified proteinase K-based extraction method.

tag: cell type

value: DoubleNeg

tag: antibody combination

tag: individual id

tag: age

tag: Sex

value: M

tag: basename


title: ST-00020182-B

type: SRA

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

country: USA

institute: Oregon Health & Science University

library_source: other

data_processing:
Data was processed as part of the Adaptive Biotechnologies service.
Data was analyzed using the Adaptive Biotechnologies "immunoSeq ANALYZER 3.0" tool.
Processed data was exported from the Adaptive Biotechnologies "immunoSeq ANALYZER 3.0" tool using the "Export" function with the default option (not the v2 option).
Data can be viewed in the Adaptive Biotechnologies "immunoSeq ANALYZER 3.0" tool at this link: https://clients.adaptivebiotech.com/pub/link-2023-nc
Supplementary files format and content: Tab separated value (*.tsv) text file.  Contains sequences of templates detected, details of specific test used, multiple annotations and metrics for each template, plus metadata and metrics for each associated specimen (sample).

molecule: other

source_name: blood

extract_protocol:
Adaptive Biotechnologies human TCRB sequencing service
Adaptive Biotechnologies human TCRB sequencing service

tag: sample type

value: matched blood

tag: tissue

value: blood

tag: public patient_id

value: Male

tag: age at_diagnosis

tag: blood matched_to

value: Met


title: ST-00020154-B


title: NeuNPos nuclei sample for Individual 107 [205061420176_R03C01]

source_name: NeuNPos

value: NeuNPos

value: NeuN+

value: F


title: Total nuclei sample for Individual 106 [205061420175_R03C01]

source_name: Total

value: Total

value: unstained


title: ST-00020149-M

source_name: Peritoneum

value: metastatic tumor

value: Female


title: NeuNPos nuclei sample for Individual 118 [205862290056_R04C01]


title: DoubleNeg nuclei sample for Individual 105 [205061420172_R03C01]


title: Total nuclei sample for Individual 104 [205061420165_R06C01]


title: ST-00020142-B


title: ST-00020149-B


title: DoubleNeg nuclei sample for Individual 104 [205061420165_R08C01]


title: ST-00020131-M


title: ST-00020131-B


title: Total nuclei sample for Individual 103 [205061420154_R06C01]


title: Sox10Pos nuclei sample for Individual 102 [205061420153_R06C01]


title: ST-00020128-T

source_name: Pancreas

value: primary tumor

value: Pancreas


title: DoubleNeg nuclei sample for Individual 111 [205061420176_R06C01]


title: DoubleNeg nuclei sample for Individual 102 [205061420153_R08C01]


title: ST-00020128-B

value: Primary


title: Total nuclei sample for Individual 101 [205854150064_R05C01]


title: Sox10Pos nuclei sample for Individual 101 [205854150064_R06C01]


title: ST-00020127-T


title: NeuNPos nuclei sample for Individual 101 [205854150064_R08C01]


title: Total nuclei sample for Individual 100 [205854150065_R01C01]


title: Sox10Pos nuclei sample for Individual 100 [205854150065_R03C01]


title: ST-00020119-M

source_name: Lymph Node

value: Lymph Node


title: ST-00020119-B


title: NeuNPos nuclei sample for Individual 100 [205854150065_R02C01]


title: Sox10Pos nuclei sample for Individual 99 [205854150041_R08C01]


title: ST-00020118-B


title: DoubleNeg nuclei sample for Individual 99 [205854150041_R07C01]

value: DoubleNeg


title: ST-00020117-T


title: ST-00020116-B


title: Total nuclei sample for Individual 98 [205854150064_R03C01]

value: M


title: DoubleNeg nuclei sample for Individual 98 [205854150064_R01C01]


title: DoubleNeg nuclei sample for Individual 77 [205862290035_R01C01]


title: ST-00020112-B

value: matched blood


title: ST-00020114-T


title: ST-00020112-M

source_name: Liver

value: Liver


title: Total nuclei sample for Individual 77 [205862290035_R03C01]


title: ST-00020114-B

value: blood


title: ST-00020107-B

value: blood only


title: NeuNPos nuclei sample for Individual 77 [205862290035_R04C01]

value: NeuNPos


title: Sox10Pos nuclei sample for Individual 77 [205862290035_R02C01]


title: ST-00020123-T

value: Male


title: ST-00020123-B


title: Total nuclei sample for Individual 76 [205862290034_R01C01]


title: ST-00020127-B


title: ST-00020106-M


title: ST-00020118-M


title: NeuNPos nuclei sample for Individual 76 [205862290034_R03C01]

value: NeuN+


title: Total nuclei sample for Individual 99 [205854150041_R06C01]

value: Total


title: DoubleNeg nuclei sample for Individual 76 [205862290034_R02C01]


title: Sox10Pos nuclei sample for Individual 76 [205862290034_R04C01]


title: ST-00020117-B


title: ST-00020102-T


title: ST-00020105-B

value: Met


title: ST-00020105-M

value: metastatic tumor


title: ST-00020106-B

value: Female


title: DoubleNeg nuclei sample for Individual 75 [205862290014_R03C01]

value: F


title: NeuNPos nuclei sample for Individual 99 [205854150041_R05C01]


title: NeuNPos nuclei sample for Individual 98 [205854150064_R02C01]


title: TripleNeg nuclei sample for Individual 75 [205862290014_R05C01]

source_name: TripleNeg

value: TripleNeg


title: ST-00020102-B

value: Primary


title: ST-00020098-B


title: Total nuclei sample for Individual 75 [205862290014_R06C01]

value: unstained


title: Sox10Pos nuclei sample for Individual 74 [205862290057_R01C01]


title: Sox10Pos nuclei sample for Individual 75 [205862290014_R07C01]


title: ST-00020093-B


title: ST-00020092-M

source_name: Lower quadrant mass

value: Lower quadrant mass


title: IRF8Pos nuclei sample for Individual 74 [205862290057_R04C01]

value: M


title: ST-00020098-T

value: primary tumor

value: Pancreas


title: ST-00020092-B

value: matched blood

value: blood


title: Total nuclei sample for Individual 73 [205862290035_R05C01]


title: NeuNPos nuclei sample for Individual 73 [205862290035_R07C01]

value: NeuNPos


title: ST-00020097-B


title: ST-00020089-B

value: Male

value: blood only


title: Total nuclei sample for Individual 74 [205862290057_R03C01]

value: Total


title: ST-00020085-B


title: ST-00020078-B

value: Met


title: ST-00020077-B


title: DoubleNeg nuclei sample for Individual 73 [205862290035_R06C01]

value: DoubleNeg


title: Total nuclei sample for Individual 72 [205862290034_R08C01]


title: ST-00020087-B

value: Female


title: Sox10Pos nuclei sample for Individual 73 [205862290035_R08C01]


title: ST-00020077-T


title: Sox10Pos nuclei sample for Individual 71 [205862290015_R03C01]


title: ST-00020072-M

source_name: Omentum

value: metastatic tumor

value: Omentum


title: ST-00020076-B


title: Sox10Pos nuclei sample for Individual 72 [205862290034_R06C01]

value: F


title: TripleNeg nuclei sample for Individual 71 [205862290015_R04C01]

value: TripleNeg


title: ST-00020093-T


title: ST-00020072-B


title: ST-00020070-M

value: Liver


title: DoubleNeg nuclei sample for Individual 71 [205862290015_R07C01]

value: M


title: Total nuclei sample for Individual 71 [205862290015_R08C01]

value: unstained


title: ST-00020070-B


title: ST-00020069-B


title: ST-00020064-M

source_name: Gastric serosal

value: Gastric serosal


title: Sox10Pos nuclei sample for Individual 70 [205862290008_R07C01]


title: ST-00020069-M

value: Peritoneum


title: ST-00020064-B

value: matched blood

value: blood


title: DoubleNeg nuclei sample for Individual 70 [205862290008_R08C01]


title: IRF8Pos nuclei sample for Individual 68 [205862290072_R01C01]


title: Total nuclei sample for Individual 70 [205862290008_R06C01]


title: NeuNPos nuclei sample for Individual 72 [205862290034_R05C01]

value: NeuNPos

value: NeuN+


title: NeuNPos nuclei sample for Individual 70 [205862290008_R05C01]


title: ST-00020057-B

value: Male

value: blood only


title: DoubleNeg nuclei sample for Individual 72 [205862290034_R07C01]

value: DoubleNeg


title: Sox10Pos nuclei sample for Individual 68 [205862290072_R03C01]


title: NeuNPos nuclei sample for Individual 68 [205862290072_R04C01]


title: ST-00020046-B


title: TripleNeg nuclei sample for Individual 68 [205862290072_R05C01]


title: ST-00019945-B

value: Female

value: Primary


title: Total nuclei sample for Individual 68 [205862290072_R02C01]

value: Total


title: ST-00019682-T

value: primary tumor

value: Pancreas


title: Total nuclei sample for Individual 67 [205096370002_R07C01]


title: ST-00019607-M

value: metastatic tumor


title: ST-00019682-B


title: IRF8Pos nuclei sample for Individual 67 [205096370002_R04C01]

value: M


title: NeuNPos nuclei sample for Individual 67 [205096370002_R05C01]


title: ST-00019607-B

value: Met


title: ST-00019598-T


title: DoubleNeg nuclei sample for Individual 67 [205096370002_R06C01]


title: NeuNPos nuclei sample for Individual 65 [205862290046_R01C01]

value: F


title: Total nuclei sample for Individual 65 [205862290046_R02C01]

value: unstained


title: ST-00019590-T


title: ST-00019458-B

value: matched blood


title: Total nuclei sample for Individual 64 [205862290012_R07C01]


title: ST-00019458-T


title: ST-00019945-T


title: ST-00019590-B

value: blood


title: ST-00019429-B


title: NeuNPos nuclei sample for Individual 64 [205862290012_R05C01]

value: NeuNPos


title: ST-00019429-T


title: Sox10Pos nuclei sample for Individual 65 [205862290046_R04C01]


title: Total nuclei sample for Individual 63 [205862290008_R01C01]


title: ST-00019368-B


title: Sox10Pos nuclei sample for Individual 64 [205862290012_R06C01]


title: DoubleNeg nuclei sample for Individual 62 [205862290047_R03C01]


title: ST-00019368-T


title: DoubleNeg nuclei sample for Individual 63 [205862290008_R04C01]


title: ST-00019367-B


title: IRF8Pos nuclei sample for Individual 62 [205862290047_R04C01]


title: ST-00019367-T


title: ST-00019303-B


title: Total nuclei sample for Individual 62 [205862290047_R05C01]


title: Sox10Pos nuclei sample for Individual 62 [205862290047_R07C01]


title: ST-00019194-T


title: ST-00019598-B


title: NeuNPos nuclei sample for Individual 62 [205862290047_R06C01]

value: NeuN+


title: ST-00019056-T


title: DoubleNeg nuclei sample for Individual 64 [205862290012_R04C01]


title: DoubleNeg nuclei sample for Individual 61 [205096370073_R04C01]


title: ST-00019056-B


title: NeuNPos nuclei sample for Individual 57 [205096370087_R07C01]


title: ST-00019043-T

value: Male


title: NeuNPos nuclei sample for Individual 60 [205096370075_R06C01]


title: IRF8Pos nuclei sample for Individual 57 [205096370087_R06C01]


title: ST-00019040-T


title: ST-00019043-B


title: DoubleNeg nuclei sample for Individual 57 [205096370087_R05C01]


title: ST-00019040-B


title: Total nuclei sample for Individual 56 [205097260015_R02C01]


title: ST-00019006-T


title: ST-00018988-B


title: ST-00018988-T


title: NeuNPos nuclei sample for Individual 56 [205097260015_R01C01]


title: NeuNPos nuclei sample for Individual 53 [205096370052_R01C01]


title: Total nuclei sample for Individual 53 [205096370052_R03C01]


title: ST-00018963-T


title: ST-00019194-B


title: ST-00018963-B


title: Sox10Pos nuclei sample for Individual 56 [205097260015_R03C01]


title: Total nuclei sample for Individual 51 [205097260017_R01C01]


title: IRF8Pos nuclei sample for Individual 61 [205096370073_R08C01]


title: ST-00018955-T


title: ST-00018955-B


title: Sox10Pos nuclei sample for Individual 51 [205097260017_R03C01]


title: Total nuclei sample for Individual 52 [205097260016_R03C01]


title: ST-00018893-T


title: ST-00018893-B


title: DoubleNeg nuclei sample for Individual 51 [205097260017_R02C01]


title: ST-00018848-T


title: ST-00018821-T


title: ST-00018848-B


title: Total nuclei sample for Individual 50 [205096370073_R02C01]


title: ST-00019006-B


title: Total nuclei sample for Individual 48 [205097260018_R04C01]


title: ST-00018809-B


title: DoubleNeg nuclei sample for Individual 48 [205097260018_R02C01]


title: ST-00018724-B


title: ST-00018724-T


title: Sox10Pos nuclei sample for Individual 48 [205097260018_R01C01]


title: ST-00018821-B


title: ST-00018809-T


title: NeuNPos nuclei sample for Individual 49 [205096370075_R02C01]


title: ST-00018628-T


title: ST-00018616-T


title: NeuNPos nuclei sample for Individual 51 [205097260017_R04C01]


title: Total nuclei sample for Individual 46 [205097260015_R06C01]


title: Total nuclei sample for Individual 45 [205097260029_R04C01]


title: DoubleNeg nuclei sample for Individual 50 [205096370073_R01C01]


title: ST-00018616-B


title: ST-00018628-B


title: Sox10Pos nuclei sample for Individual 47 [205097260006_R06C01]


title: ST-00018584-T


title: NeuNPos nuclei sample for Individual 50 [205096370073_R03C01]


title: NeuNPos nuclei sample for Individual 45 [205097260029_R02C01]


title: DoubleNeg nuclei sample for Individual 45 [205097260029_R01C01]


title: ST-00018426-B


title: Total nuclei sample for Individual 44 [205097260016_R08C01]


title: ST-00018360-T


title: Total nuclei sample for Individual 47 [205097260006_R07C01]


title: NeuNPos nuclei sample for Individual 44 [205097260016_R05C01]


title: ST-00018260-B


title: NeuNPos nuclei sample for Individual 47 [205097260006_R08C01]


title: ST-00018257-T


title: DoubleNeg nuclei sample for Individual 44 [205097260016_R06C01]


title: Total nuclei sample for Individual 43 [205097260018_R08C01]


title: ST-00018257-B


title: ST-00018232-M

source_name: Lung

value: Lung


title: TripleNeg nuclei sample for Individual 40 [205862290079_R03C01]

value: TripleNeg


title: Total nuclei sample for Individual 42 [205097260029_R05C01]


title: DoubleNeg nuclei sample for Individual 41 [205097260030_R07C01]

value: DoubleNeg


title: Sox10Pos nuclei sample for Individual 40 [205862290079_R01C01]


title: ST-00018236-T

value: Female


title: NeuNPos nuclei sample for Individual 40 [205862290079_R02C01]


title: Total nuclei sample for Individual 40 [205862290079_R04C01]

value: Total


title: ST-00018179-B

value: Primary


title: ST-00018179-T

value: primary tumor

value: Pancreas


title: ST-00018136-T


title: ST-00018584-B


title: DoubleNeg nuclei sample for Individual 39 [205097260030_R01C01]

value: M


title: IRF8Pos nuclei sample for Individual 40 [205862290079_R05C01]


title: ST-00018136-B


title: Total nuclei sample for Individual 38 [205096370051_R07C01]


title: ST-00018050-B

value: blood only


title: Total nuclei sample for Individual 37 [205097260049_R07C01]

value: F


title: Sox10Pos nuclei sample for Individual 37 [205097260049_R06C01]


title: ST-00017985-T


title: Total nuclei sample for Individual 36 [205096370045_R07C01]

value: unstained


title: ST-00017975-T


title: ST-00018236-B

value: matched blood


title: ST-00017985-B

value: blood


title: ST-00017975-B


title: ST-00018232-B

value: Met


title: NeuNPos nuclei sample for Individual 36 [205096370045_R08C01]

value: NeuNPos

value: NeuN+


title: ST-00017915-M

value: metastatic tumor

value: Lung


title: Total nuclei sample for Individual 229 [202073180019_R06C01]


title: ST-00017945-B

value: Male


title: TripleNeg nuclei sample for Individual 37 [205097260049_R08C01]

value: TripleNeg


title: ST-00017915-B

value: Female


title: Sox10Pos nuclei sample for Individual 229 [202073200073_R05C01]


title: DoubleNeg nuclei sample for Individual 229 [202073200073_R08C01]

value: DoubleNeg


title: ST-00017838-T

value: primary tumor


title: NeuNPos nuclei sample for Individual 229 [202073200073_R07C01]


title: Total nuclei sample for Individual 228 [202073200073_R06C01]

value: Total


title: ST-00017762-T

value: Pancreas


title: Sox10Pos nuclei sample for Individual 228 [202073180019_R08C01]

value: M


title: ST-00017838-B

value: Primary


title: NeuNPos nuclei sample for Individual 228 [202073180019_R05C01]


title: ST-00017549-T


title: DoubleNeg nuclei sample for Individual 228 [202073180019_R07C01]


title: Total nuclei sample for Individual 227 [202073200091_R03C01]

value: unstained

value: F


title: ST-00017945-T


title: ST-00017449-T


title: Sox10Pos nuclei sample for Individual 227 [202073200091_R04C01]


title: NeuNPos nuclei sample for Individual 227 [202073200091_R02C01]


title: ST-00017449-B

value: matched blood

value: blood


title: ST-00017440-T


title: DoubleNeg nuclei sample for Individual 36 [205096370045_R05C01]


title: Sox10Pos nuclei sample for Individual 226 [202073180089_R01C01]


title: ST-00017381-T


title: ST-00017340-T


title: Total nuclei sample for Individual 225 [202073180020_R04C01]


title: ST-00017381-B


title: ST-00017340-B


title: ST-00017440-B


title: DoubleNeg nuclei sample for Individual 226 [202073180089_R04C01]


title: ST-00017310-T

source_name: Ampulla of Vater

value: Ampulla of Vater


title: NeuNPos nuclei sample for Individual 225 [202073180020_R02C01]

value: NeuNPos

value: NeuN+


title: ST-00017310-B


title: NeuNPos nuclei sample for Individual 224 [202073180021_R01C01]


title: ST-00017261-B


title: ST-00017762-B


title: ST-00017261-T


title: ST-00017549-B


title: Total nuclei sample for Individual 224 [202073180021_R02C01]


title: Total nuclei sample for Individual 223 [202073200099_R07C01]


title: ST-00017227-T


title: ST-00017227-B


title: Sox10Pos nuclei sample for Individual 223 [202073200099_R06C01]


title: Total nuclei sample for Individual 226 [202073180089_R02C01]


title: Total nuclei sample for Individual 205 [202073200073_R02C01]


title: ST-00017080-T


title: DoubleNeg nuclei sample for Individual 224 [202073180021_R03C01]


title: ST-00017080-B


title: NeuNPos nuclei sample for Individual 205 [202073200073_R01C01]


title: NeuNPos nuclei sample for Individual 226 [202073180089_R03C01]


title: DoubleNeg nuclei sample for Individual 205 [202073200073_R03C01]


title: ST-00017074-T


title: Sox10Pos nuclei sample for Individual 205 [202073200073_R04C01]


title: ST-00017074-B


title: ST-00017041-T


title: Sox10Pos nuclei sample for Individual 204 [202073200091_R06C01]


title: ST-00017041-B


title: Total nuclei sample for Individual 204 [202073200091_R08C01]


title: ST-00017003-M

value: metastatic tumor

value: Liver


title: Total nuclei sample for Individual 203 [202073180089_R05C01]


title: ST-00017034-B

value: blood only


title: NeuNPos nuclei sample for Individual 203 [202073180089_R07C01]


title: DoubleNeg nuclei sample for Individual 203 [202073180089_R06C01]


title: ST-00017003-B

value: Male

value: Met


title: Total nuclei sample for Individual 202 [202073180020_R07C01]


title: ST-00016998-T

value: primary tumor


title: ST-00016998-B


title: Sox10Pos nuclei sample for Individual 202 [202073180020_R08C01]


title: ST-00016968-T


title: ST-00016968-B


title: ST-00016911-B

value: Female


title: Total nuclei sample for Individual 201 [202073180021_R08C01]

value: Total


title: ST-00016911-T

value: Pancreas


title: NeuNPos nuclei sample for Individual 201 [202073180021_R06C01]

value: M


title: ST-00016844-T


title: ST-00016858-B

value: Primary


title: DoubleNeg nuclei sample for Individual 201 [202073180021_R05C01]

value: DoubleNeg


title: DoubleNeg nuclei sample for Individual 202 [202073180020_R06C01]

value: F


title: Sox10Pos nuclei sample for Individual 152 [204026590066_R03C01]


title: ST-00016806-T


title: ST-00016844-B

value: matched blood

value: blood


title: Sox10Pos nuclei sample for Individual 201 [202073180021_R07C01]


title: Total nuclei sample for Individual 152 [204026590066_R02C01]

value: unstained


title: NeuNPos nuclei sample for Individual 152 [204026590066_R04C01]

value: NeuNPos

value: NeuN+


title: NeuNPos nuclei sample for Individual 204 [202073200091_R05C01]


title: ST-00016806-B


title: DoubleNeg nuclei sample for Individual 152 [204026590066_R01C01]


title: ST-00016742-T


title: Total nuclei sample for Individual 151 [204026590047_R06C01]


title: ST-00016742-B


title: ST-00016623-T


title: Sox10Pos nuclei sample for Individual 151 [204026590047_R08C01]


title: NeuNPos nuclei sample for Individual 202 [202073180020_R05C01]


title: Total nuclei sample for Individual 150 [204022160046_R06C01]


title: ST-00016623-B


title: NeuNPos nuclei sample for Individual 151 [204026590047_R07C01]


title: ST-00016499-T

value: Ampulla of Vater


title: ST-00016858-T


title: NeuNPos nuclei sample for Individual 150 [204022160046_R07C01]


title: Total nuclei sample for Individual 149 [203996140032_R02C01]


title: Sox10Pos nuclei sample for Individual 149 [203996140032_R04C01]


title: ST-00016213-T


title: Sox10Pos nuclei sample for Individual 148 [203998240054_R05C01]


title: ST-00015973-B


title: ST-00015839-T


title: DoubleNeg nuclei sample for Individual 149 [203996140032_R01C01]


title: Total nuclei sample for Individual 148 [203998240054_R07C01]


title: ST-00015777-T


title: DoubleNeg nuclei sample for Individual 47 [205097260006_R05C01]


title: Sox10Pos nuclei sample for Individual 147 [203998240040_R02C01]


title: ST-00015777-B


title: DoubleNeg nuclei sample for Individual 147 [203998240040_R04C01]


title: ST-00015332-B


title: ST-00015177-B


title: NeuNPos nuclei sample for Individual 146 [204001350069_R01C01]


title: ST-00015163-B


title: Total nuclei sample for Individual 146 [204001350069_R02C01]


title: Sox10Pos nuclei sample for Individual 146 [204001350069_R04C01]


title: ST-00016499-B


title: ST-00015163-T


title: ST-00015136-T


title: NeuNPos nuclei sample for Individual 149 [203996140032_R03C01]


title: ST-00016213-B


title: ST-00016257-B

value: blood only


title: Total nuclei sample for Individual 147 [203998240040_R03C01]


title: DoubleNeg nuclei sample for Individual 146 [204001350069_R05C01]


title: Total nuclei sample for Individual 145 [204001350047_R03C01]


title: Sox10Pos nuclei sample for Individual 145 [204001350047_R01C01]


title: ST-00015114-T

value: Male


title: IRF8Pos nuclei sample for Individual 145 [204001350047_R05C01]


title: ST-00015839-B


title: ST-00014696-B


title: ST-00015136-B


title: ST-00015332-T


title: DoubleNeg nuclei sample for Individual 145 [204001350047_R02C01]


title: ST-00014550-T


title: Total nuclei sample for Individual 144 [204001350046_R04C01]


title: ST-00015114-B


title: ST-00014575-B


title: Sox10Pos nuclei sample for Individual 144 [204001350046_R05C01]


title: ST-00014550-B


title: NeuNPos nuclei sample for Individual 147 [203998240040_R01C01]


title: NeuNPos nuclei sample for Individual 144 [204001350046_R02C01]


title: DoubleNeg nuclei sample for Individual 144 [204001350046_R03C01]


title: ST-00014524-M

value: metastatic tumor

value: Liver


title: ST-00014537-T

value: primary tumor

value: Female


title: IRF8Pos nuclei sample for Individual 144 [204001350046_R01C01]


title: Total nuclei sample for Individual 143 [203996140062_R04C01]

value: Total


title: NeuNPos nuclei sample for Individual 145 [204001350047_R04C01]

value: M


title: ST-00014524-B

value: Met


title: Sox10Pos nuclei sample for Individual 143 [203996140062_R01C01]


title: ST-00014490-T

value: Pancreas


title: NeuNPos nuclei sample for Individual 143 [203996140062_R02C01]


title: ST-00014494-T


title: ST-00014494-B

value: Primary


title: ST-00014391-T


title: ST-00014490-B

value: matched blood


title: Total nuclei sample for Individual 142 [203991540165_R06C01]

value: F


title: DoubleNeg nuclei sample for Individual 143 [203996140062_R03C01]

value: DoubleNeg


title: ST-00014391-B

value: blood


title: Sox10Pos nuclei sample for Individual 142 [203991540165_R08C01]


title: ST-00014023-T


title: DoubleNeg nuclei sample for Individual 142 [203991540165_R05C01]


title: NeuNPos nuclei sample for Individual 142 [203991540165_R07C01]

value: NeuNPos

value: NeuN+


title: ST-00014023-B


title: ST-00013971-T


title: Total nuclei sample for Individual 141 [204026590064_R05C01]

value: unstained


title: Sox10Pos nuclei sample for Individual 141 [204026590064_R06C01]


title: DoubleNeg nuclei sample for Individual 141 [204026590064_R07C01]


title: NeuNPos nuclei sample for Individual 141 [204026590064_R08C01]


title: ST-00014537-B


title: ST-00013971-B


title: ST-00013861-T

value: Male


title: ST-00013861-B


title: ST-00013544-B


title: Total nuclei sample for Individual 138 [204022160097_R04C01]


title: ST-00013415-T


title: ST-00013415-B


title: Sox10Pos nuclei sample for Individual 138 [204022160097_R02C01]


title: NeuNPos nuclei sample for Individual 138 [204022160097_R03C01]


title: DoubleNeg nuclei sample for Individual 138 [204022160097_R01C01]


title: ST-00013374-T


title: Total nuclei sample for Individual 137 [204022160062_R03C01]


title: ST-00013374-B


title: ST-00013312-B


title: Sox10Pos nuclei sample for Individual 137 [204022160062_R04C01]


title: ST-00013291-T


title: Sox10Pos nuclei sample for Individual 136 [204022160046_R03C01]


title: ST-00013291-B


title: NeuNPos nuclei sample for Individual 136 [204022160046_R02C01]


title: Total nuclei sample for Individual 136 [204022160046_R01C01]


title: ST-00013253-T


title: DoubleNeg nuclei sample for Individual 136 [204022160046_R04C01]


title: ST-00013253-B


title: NeuNPos nuclei sample for Individual 140 [204026590064_R03C01]


title: Total nuclei sample for Individual 134 [203998240054_R02C01]


title: ST-00013160-B


title: Total nuclei sample for Individual 139 [204026590047_R03C01]


title: Total nuclei sample for Individual 135 [203998240149_R01C01]


title: ST-00013158-T


title: Sox10Pos nuclei sample for Individual 134 [203998240054_R04C01]


title: ST-00013091-T


title: ST-00013158-B


title: NeuNPos nuclei sample for Individual 134 [203998240054_R03C01]


title: ST-00013091-B


title: Total nuclei sample for Individual 133 [203998240040_R07C01]


title: ST-00013084-T


title: Sox10Pos nuclei sample for Individual 133 [203998240040_R05C01]


title: ST-00013084-B


title: DoubleNeg nuclei sample for Individual 133 [203998240040_R06C01]


title: NeuNPos nuclei sample for Individual 133 [203998240040_R08C01]


title: ST-00012975-B

value: blood only


title: ST-00012968-B


title: ST-00012967-M

value: metastatic tumor

value: Liver


title: ST-00013160-T

value: primary tumor


title: Total nuclei sample for Individual 132 [203998240027_R05C01]

value: Total


title: DoubleNeg nuclei sample for Individual 132 [203998240027_R07C01]

value: M


title: ST-00012931-T


title: ST-00012967-B

value: Met


title: NeuNPos nuclei sample for Individual 132 [203998240027_R06C01]


title: ST-00012908-T

value: Pancreas

value: Female


title: Total nuclei sample for Individual 131 [204001350068_R03C01]


title: ST-00012818-T


title: Sox10Pos nuclei sample for Individual 131 [204001350068_R01C01]


title: ST-00012931-B

value: matched blood

value: Primary


title: ST-00012908-B


title: NeuNPos nuclei sample for Individual 131 [204001350068_R02C01]


title: Sox10Pos nuclei sample for Individual 132 [203998240027_R08C01]


title: IRF8Pos nuclei sample for Individual 131 [204001350068_R05C01]


title: DoubleNeg nuclei sample for Individual 131 [204001350068_R04C01]

value: DoubleNeg


title: DoubleNeg nuclei sample for Individual 134 [203998240054_R01C01]

value: F


title: ST-00012818-B

value: blood


title: ST-00012814-T


title: Total nuclei sample for Individual 130 [203998240027_R03C01]


title: ST-00012742-T


title: Sox10Pos nuclei sample for Individual 130 [203998240027_R04C01]


title: ST-00012814-B


title: ST-00012742-B


title: NeuNPos nuclei sample for Individual 130 [203998240027_R02C01]

value: NeuNPos

value: NeuN+


title: ST-00012327-T


title: Total nuclei sample for Individual 129 [203996140062_R06C01]

value: unstained


title: DoubleNeg nuclei sample for Individual 130 [203998240027_R01C01]


title: NeuNPos nuclei sample for Individual 129 [203996140062_R05C01]


title: ST-00011357-T


title: Sox10Pos nuclei sample for Individual 129 [203996140062_R08C01]


title: Total nuclei sample for Individual 128 [203996140031_R08C01]


title: Total nuclei sample for Individual 127 [203996140031_R02C01]


title: ST-00012319-T


title: ST-00012319-B


title: ST-00011353-B


title: ST-00011357-B


title: DoubleNeg nuclei sample for Individual 127 [203996140031_R04C01]


title: Total nuclei sample for Individual 97 [202073200101_R04C01]


title: ST-00011168-B

value: Male


title: ST-00010984-T


title: Sox10Pos nuclei sample for Individual 127 [203996140031_R01C01]


title: NeuNPos nuclei sample for Individual 97 [202073200101_R03C01]


title: ST-00010919-T


title: DoubleNeg nuclei sample for Individual 97 [202073200101_R01C01]


title: ST-00010984-B


title: ST-00011168-T


title: ST-00010904-T


title: Total nuclei sample for Individual 96 [202073200009_R03C01]


title: ST-00010919-B


title: ST-00010904-B


title: Sox10Pos nuclei sample for Individual 96 [202073200009_R01C01]


title: DoubleNeg nuclei sample for Individual 96 [202073200009_R04C01]


title: NeuNPos nuclei sample for Individual 127 [203996140031_R03C01]


title: NeuNPos nuclei sample for Individual 96 [202073200009_R02C01]


title: ST-00011353-M

value: metastatic tumor


title: ST-00009790-M

source_name: Pelvic nodule

value: Pelvic nodule


title: ST-00010889-B


title: Sox10Pos nuclei sample for Individual 97 [202073200101_R02C01]


title: Total nuclei sample for Individual 95 [202073200092_R05C01]


title: ST-00012327-B


title: ST-00009790-B


title: Sox10Pos nuclei sample for Individual 95 [202073200092_R08C01]


title: NeuNPos nuclei sample for Individual 95 [202073200092_R06C01]


title: ST-00009787-B

value: blood only


title: DoubleNeg nuclei sample for Individual 95 [202073200092_R07C01]


title: Total nuclei sample for Individual 94 [202073180098_R03C01]

value: Total


title: ST-00008601-T

value: primary tumor


title: Sox10Pos nuclei sample for Individual 94 [202073180098_R01C01]

value: M


title: ST-00008601-B


title: Total nuclei sample for Individual 93 [203990170071_R06C01]


title: ST-00008056-T

value: Pancreas


title: ST-00010889-T

value: Female


title: Sox10Pos nuclei sample for Individual 93 [203990170071_R08C01]


title: ST-00008108-B

value: matched blood


title: ST-00008056-B

value: Primary


title: ST-00008043-T


title: DoubleNeg nuclei sample for Individual 93 [203990170071_R07C01]

value: DoubleNeg


title: Total nuclei sample for Individual 92 [203991540165_R02C01]

value: F


title: Sox10Pos nuclei sample for Individual 92 [203991540165_R04C01]


title: ST-00007646-T


title: ST-00008043-B

value: blood


title: NeuNPos nuclei sample for Individual 92 [203991540165_R01C01]

value: NeuNPos


title: DoubleNeg nuclei sample for Individual 92 [203991540165_R03C01]


title: Total nuclei sample for Individual 91 [203990170071_R04C01]


title: ST-00007599-B


title: Sox10Pos nuclei sample for Individual 91 [203990170071_R02C01]


title: ST-00007613-T


title: NeuNPos nuclei sample for Individual 91 [203990170071_R03C01]

value: NeuN+


title: ST-00007595-M

value: Liver


title: ST-00007595-B

value: Met


title: Total nuclei sample for Individual 90 [203991400080_R07C01]

value: unstained


title: ST-00007613-B

value: Male


title: ST-00007590-B


title: DoubleNeg nuclei sample for Individual 94 [202073180098_R04C01]


title: Sox10Pos nuclei sample for Individual 90 [203991400080_R05C01]


title: NeuNPos nuclei sample for Individual 90 [203991400080_R08C01]


title: NeuNPos nuclei sample for Individual 93 [203990170071_R05C01]


title: ST-00007585-B


title: Total nuclei sample for Individual 89 [203991400080_R02C01]


title: ST-00007402-M

source_name: Mesocolon

value: metastatic tumor

value: Mesocolon


title: DoubleNeg nuclei sample for Individual 90 [203991400080_R06C01]


title: ST-00007402-B


title: ST-00007646-B


title: Sox10Pos nuclei sample for Individual 89 [203991400080_R01C01]


title: NeuNPos nuclei sample for Individual 89 [203991400080_R03C01]


title: ST-00007398-B

value: blood only


title: Sox10Pos nuclei sample for Individual 88 [203990170060_R05C01]

value: M


title: Total nuclei sample for Individual 88 [203990170060_R08C01]

value: Total


title: ST-00007389-M


title: ST-00007389-B


title: DoubleNeg nuclei sample for Individual 88 [203990170060_R06C01]


title: ST-00007386-B


title: DoubleNeg nuclei sample for Individual 89 [203991400080_R04C01]


title: ST-00007382-B


title: NeuNPos nuclei sample for Individual 88 [203990170060_R07C01]


title: ST-00007381-B


title: ST-00007382-M

value: Peritoneum


title: ST-00008108-T

value: primary tumor

value: Pancreas

value: Female


title: ST-00007386-M


title: Total nuclei sample for Individual 87 [203990170060_R03C01]

value: F


title: Sox10Pos nuclei sample for Individual 87 [203990170060_R04C01]


title: ST-00007585-T


title: DoubleNeg nuclei sample for Individual 87 [203990170060_R01C01]

value: DoubleNeg


title: NeuNPos nuclei sample for Individual 87 [203990170060_R02C01]

value: NeuNPos


title: ST-00007380-M

source_name: Gallbladder

value: Gallbladder


title: ST-00007380-B

value: matched blood

value: blood


title: ST-00007377-M


title: Total nuclei sample for Individual 86 [203990170057_R07C01]

value: unstained


title: NeuNPos nuclei sample for Individual 86 [203990170057_R06C01]

value: NeuN+


title: Sox10Pos nuclei sample for Individual 86 [203990170057_R05C01]


title: ST-00007377-B

value: Male

value: Met


title: DoubleNeg nuclei sample for Individual 86 [203990170057_R08C01]

source_name: DoubleNeg


title: ST-00007313-B

source_name: blood

value: Primary


title: ST-00007313-T


title: Total nuclei sample for Individual 85 [203990170057_R01C01]

value: M


title: ST-00007307-T


title: Sox10Pos nuclei sample for Individual 85 [203990170057_R02C01]


title: DoubleNeg nuclei sample for Individual 85 [203990170057_R03C01]


title: ST-00007303-B


title: ST-00007307-B


title: ST-00007303-T


title: Total nuclei sample for Individual 84 [203990170027_R06C01]

value: Total


title: NeuNPos nuclei sample for Individual 85 [203990170057_R04C01]

source_name: NeuNPos


title: ST-00007302-T


title: ST-00007302-B


title: NeuNPos nuclei sample for Individual 84 [203990170027_R08C01]


title: Total nuclei sample for Individual 83 [203986510071_R07C01]

source_name: Total


title: ST-00007298-T


title: ST-00007300-B


title: ST-00007298-B


title: Sox10Pos nuclei sample for Individual 83 [203986510071_R06C01]


title: ST-00007300-T


title: DoubleNeg nuclei sample for Individual 83 [203986510071_R05C01]


title: ST-00007288-M

source_name: Peritoneum

value: metastatic tumor

value: Peritoneum


title: NeuNPos nuclei sample for Individual 83 [203986510071_R08C01]


title: Total nuclei sample for Individual 82 [203991390017_R05C01]


title: ST-00007296-B


title: ST-00007296-T

source_name: Pancreas

value: primary tumor

value: Pancreas


title: Sox10Pos nuclei sample for Individual 82 [203991390017_R07C01]


title: NeuNPos nuclei sample for Individual 82 [203991390017_R06C01]


title: DoubleNeg nuclei sample for Individual 82 [203991390017_R08C01]


title: ST-00007279-B


title: ST-00007288-B

value: Female


title: ST-00007276-B

value: blood only


title: Sox10Pos nuclei sample for Individual 81 [203986510071_R03C01]


title: ST-00007279-T


title: DoubleNeg nuclei sample for Individual 81 [203986510071_R04C01]

value: DoubleNeg


title: ST-00007267-T


title: ST-00007267-B


title: Sox10Pos nuclei sample for Individual 84 [203990170027_R07C01]


title: Total nuclei sample for Individual 80 [203991390017_R01C01]


title: ST-00007266-T


title: ST-00007266-B


title: DoubleNeg nuclei sample for Individual 84 [203990170027_R05C01]


title: NeuNPos nuclei sample for Individual 81 [203986510071_R02C01]

value: NeuNPos


title: ST-00007257-T


title: Sox10Pos nuclei sample for Individual 80 [203991390017_R02C01]


title: DoubleNeg nuclei sample for Individual 80 [203991390017_R03C01]


title: ST-00007257-B

value: matched blood


title: DoubleNeg nuclei sample for Individual 79 [203990170158_R03C01]


title: Total nuclei sample for Individual 78 [204022160053_R03C01]

value: F


title: ST-00007239-B

value: blood


title: ST-00007239-T


title: Sox10Pos nuclei sample for Individual 66 [203991460077_R06C01]


title: DoubleNeg nuclei sample for Individual 69 [203991460087_R03C01]


title: TripleNeg nuclei sample for Individual 66 [203991460077_R03C01]

value: TripleNeg


title: DoubleNeg nuclei sample for Individual 66 [203991460077_R05C01]


title: ST-00007223-B

value: Male


title: ST-00007234-B


title: ST-00007216-T


title: ST-00007216-B


title: ST-00007223-T


title: ST-00007234-T


title: DoubleNeg nuclei sample for Individual 59 [203991460087_R05C01]


title: DoubleNeg nuclei sample for Individual 58 [203991460086_R07C01]


title: ST-00007208-T


title: Total nuclei sample for Individual 58 [203991460086_R06C01]

value: unstained


title: ST-00007208-B

value: Primary


title: NeuNPos nuclei sample for Individual 55 [203991460086_R02C01]

value: NeuN+

value: M


title: NeuNPos nuclei sample for Individual 80 [203991390017_R04C01]


title: Total nuclei sample for Individual 55 [203991460086_R03C01]

value: Total


title: DoubleNeg nuclei sample for Individual 55 [203991460086_R01C01]


title: Total nuclei sample for Individual 79 [203990170158_R01C01]


title: ST-00007206-T


title: ST-00007256-T


title: NeuNPos nuclei sample for Individual 54 [203991460058_R06C01]


title: ST-00007206-B


title: ST-00007256-B


title: ST-00007203-T


title: Total nuclei sample for Individual 35 [202073200101_R05C01]


title: ST-00007203-B


title: Sox10Pos nuclei sample for Individual 35 [202073200101_R06C01]


title: Total nuclei sample for Individual 59 [203991460087_R07C01]


title: NeuNPos nuclei sample for Individual 35 [202073200101_R08C01]


title: ST-00007195-B


title: DoubleNeg nuclei sample for Individual 35 [202073200101_R07C01]


title: Sox10Pos nuclei sample for Individual 34 [203265000097_R08C01]


title: ST-00007185-T


title: ST-00007185-B


title: Total nuclei sample for Individual 33 [203259750084_R07C01]


title: ST-00007183-B


title: NeuNPos nuclei sample for Individual 33 [203259750084_R08C01]


title: ST-00007180-B


title: ST-00007179-B


title: Total nuclei sample for Individual 32 [203265000112_R02C01]


title: DoubleNeg nuclei sample for Individual 33 [203259750084_R06C01]


title: ST-00007178-T


title: Total nuclei sample for Individual 31 [203265000092_R04C01]


title: ST-00007175-T


title: ST-00007178-B


title: Sox10Pos nuclei sample for Individual 31 [203265000092_R01C01]


title: ST-00007195-T


title: ST-00007175-B


title: NeuNPos nuclei sample for Individual 31 [203265000092_R02C01]


title: Total nuclei sample for Individual 30 [203265000125_R06C01]


title: ST-00007174-B


title: Total nuclei sample for Individual 34 [203265000097_R07C01]


title: ST-00007193-T


title: ST-00007193-B


title: ST-00007168-T


title: DoubleNeg nuclei sample for Individual 34 [203265000097_R06C01]


title: ST-00007183-T


title: NeuNPos nuclei sample for Individual 34 [203265000097_R05C01]


title: NeuNPos nuclei sample for Individual 30 [203265000125_R07C01]


title: ST-00007165-B


title: ST-00007168-B


title: ST-00007165-T


title: DoubleNeg nuclei sample for Individual 30 [203265000125_R08C01]


title: Sox10Pos nuclei sample for Individual 33 [203259750084_R05C01]


title: Total nuclei sample for Individual 29 [202073200009_R07C01]


title: Sox10Pos nuclei sample for Individual 29 [202073200009_R05C01]


title: ST-00007164-B


title: ST-00007147-B


title: DoubleNeg nuclei sample for Individual 29 [202073200009_R08C01]


title: ST-00007164-T


title: ST-00007147-T


title: Total nuclei sample for Individual 28 [203265000136_R01C01]


title: NeuNPos nuclei sample for Individual 29 [202073200009_R06C01]


title: ST-00007146-B


title: ST-00007120-T


title: Sox10Pos nuclei sample for Individual 28 [203265000136_R04C01]


title: NeuNPos nuclei sample for Individual 28 [203265000136_R02C01]


title: Sox10Pos nuclei sample for Individual 30 [203265000125_R05C01]


title: DoubleNeg nuclei sample for Individual 28 [203265000136_R03C01]


title: Total nuclei sample for Individual 27 [203265000097_R04C01]


title: ST-00007120-B


title: ST-00007099-T


title: ST-00007099-B


title: NeuNPos nuclei sample for Individual 27 [203265000097_R02C01]


title: ST-00007085-T


title: ST-00007085-B


title: Sox10Pos nuclei sample for Individual 27 [203265000097_R03C01]


title: Total nuclei sample for Individual 26 [203265020080_R01C01]


title: Sox10Pos nuclei sample for Individual 26 [203265020007_R01C01]


title: ST-00007071-B


title: DoubleNeg nuclei sample for Individual 27 [203265000097_R01C01]


title: ST-00007071-T


title: ST-00007067-T


title: NeuNPos nuclei sample for Individual 26 [203265020007_R03C01]


title: Total nuclei sample for Individual 25 [203265020067_R05C01]


title: ST-00007146-T


title: ST-00007067-B


title: Total nuclei sample for Individual 24 [203265000125_R02C01]


title: ST-00005813-T


title: ST-00006625-T


title: NeuNPos nuclei sample for Individual 25 [203265020067_R07C01]


title: ST-00006625-B


title: Sox10Pos nuclei sample for Individual 24 [203265000125_R04C01]


title: NeuNPos nuclei sample for Individual 24 [203265000125_R03C01]


title: ST-00005813-B


title: DoubleNeg nuclei sample for Individual 24 [203265000125_R01C01]


title: ST-00005536-B


title: ST-00005536-T


title: Total nuclei sample for Individual 23 [203265000136_R07C01]


title: Sox10Pos nuclei sample for Individual 23 [203265000136_R05C01]


title: ST-00003662-B


title: DoubleNeg nuclei sample for Individual 23 [203265000136_R06C01]


title: NeuNPos nuclei sample for Individual 23 [203265000136_R08C01]


title: ST-00003635-T


title: Total nuclei sample for Individual 22 [203265020007_R05C01]


title: ST-00003635-B


title: Sox10Pos nuclei sample for Individual 22 [203265020007_R08C01]


title: TGFb_THZ1_4186

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

library_source: transcriptomic

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the human genome assembly GRCh38.
Assembly: GRCh38
Supplementary files format and content: TSV count matrices

molecule: total RNA

source_name: normal human lung fibroblast

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: normal human lung fibroblast

tag: treatment


title: Total nuclei sample for Individual 21 [203265020067_R03C01]


title: TGFb_THZ1_4185


title: Sox10Pos nuclei sample for Individual 21 [203265020067_R01C01]


title: Sox10Pos nuclei sample for Individual 25 [203265020067_R06C01]


title: TGFb_THZ1_4184


title: DoubleNeg nuclei sample for Individual 22 [203265020007_R06C01]


title: TGFb_4183

value: TGFb


title: TGFb_4182


title: NeuNPos nuclei sample for Individual 21 [203265020067_R02C01]


title: TGFb_4181


title: DoubleNeg nuclei sample for Individual 21 [203265020067_R04C01]


title: Total nuclei sample for Individual 20 [203265020080_R05C01]


title: Sox10Pos nuclei sample for Individual 20 [203265020080_R06C01]


title: ST-00003662-T

value: primary tumor

value: Pancreas


title: NeuNPos nuclei sample for Individual 20 [203265020080_R04C01]


title: THZ1_4176


title: DMSO_4174

value: DMSO


title: Sox10Pos nuclei sample for Individual 19 [203265020007_R02C01]


title: Total nuclei sample for Individual 19 [203265020080_R02C01]


title: DMSO_4173


title: DMSO_4172


title: Sox10Pos nuclei sample for Individual 18 [203265020076_R06C01]


title: AML3_OTX015_rep3

city: Huddinge

first: Andreas

last: Lennartsson

state: Stockholm

address: Halsovagan 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description:
AML2_AML3_counts_enhancers.csv
AML2_AML3_counts_promoters.csv
AML2_AML3_counts_symbols.csv

data_processing:
MOIRAI pipeline (Hasegawa et al., 2024)
TagDust2 was used for adapter trimming.
STAR was used for read mapping to hg38
Assembly: hg38
Supplementary files format and content: Matrix tables of raw counts for enhancers,promoters, and gene symbols

source_name: cancer cell line

extract_protocol:
Qiagen RNAeasy
RNA extraction of the BET-treated cell lines for library preparation was performed as previously described. The CAGE libraries were prepared using the CAGE protocol (PMID: 21938627).

value: Myeloid leukemia cell


title: Total nuclei sample for Individual 18 [203265020076_R04C01]


title: AML3_OTX015_rep2


title: NeuNPos nuclei sample for Individual 18 [203265020076_R07C01]

value: NeuNPos


title: DoubleNeg nuclei sample for Individual 18 [203265020076_R05C01]

value: DoubleNeg


title: AML3_OTX015_rep1


title: AML3_JQ1_rep3


title: Total nuclei sample for Individual 16 [203259750084_R02C01]


title: AML3_JQ1_rep1


title: NeuNPos nuclei sample for Individual 17 [203265020076_R02C01]


title: AML3_DMSO_rep3

value: Vehicle


title: AML3_JQ1_rep2


title: Sox10Pos nuclei sample for Individual 16 [203259750084_R01C01]


title: Sox10Pos nuclei sample for Individual 17 [203265020076_R03C01]


title: Total nuclei sample for Individual 17 [203265020076_R01C01]


title: THZ1_4177


title: NeuNPos nuclei sample for Individual 16 [203259750084_R04C01]


title: THZ1_4175


title: AML3_DMSO_rep1


title: AML2_OTX015_rep3


title: AML3_DMSO_rep2


title: Sox10Pos nuclei sample for Individual 15 [203265000092_R08C01]


title: AML2_OTX015_rep1


title: NeuNPos nuclei sample for Individual 15 [203265000092_R05C01]


title: AML2_OTX015_rep2


title: DoubleNeg nuclei sample for Individual 15 [203265000092_R07C01]


title: Total nuclei sample for Individual 14 [202073200092_R02C01]


title: AML2_JQ1_rep3


title: AML2_JQ1_rep2


title: Sox10Pos nuclei sample for Individual 14 [202073200092_R04C01]


title: NeuNPos nuclei sample for Individual 14 [202073200092_R03C01]


title: AML2_JQ1_rep1


title: DoubleNeg nuclei sample for Individual 14 [202073200092_R01C01]


title: Total nuclei sample for Individual 12 [202073200108_R06C01]


title: Sox10Pos nuclei sample for Individual 12 [202073180098_R06C01]


title: Hippocampus_nucleus_mTLE non-HS4

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_E13-12.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt

data_processing:
(tRFs) Quality control of the small RNA-seq raw reads was performed using FastQC (Andrews S, 2010). Adapters were removed using Cutadapt (1.18; (Martin, EMBnet.journal. 2011)) with default settings for single end reads. Trimmed reads were aligned to the hg19 pre-tRNA and mature tRNA (https://github.com/sararselitsky/tDRmapper) with tDRmapper (Selitsky and Sethupathy, BMC Bioinformatics. 2015). All fragments >14 nt and <40 nt were included to further analysis. Only sequences counted >99 times were considered to be expressed.
(tRFs) Differentially expressed (DE) tRFs were identified with DESeq (Anders and Huber, Genome Biol. 2010) R package (R version 4.0.3). Data (only DE tRFs) was visualized with a clustering heatmap (gplots R package) using correlation distance, and principal component analysis (all detected tRFs; PCA; stats R package).
(miRNAs) Following trimming of low-quality bases and adapter sequences with FASTQ-MCF (version 0.0.13), processed reads were mapped using Bowtie. MiRNA alignment was performed against the human reference from miRBase (release v21).
(miRNAs) For differential expression analysis, count data for miRNAs were analysed for differential expression in R using the Bioconductor package EdgeR version 3.12.1 (Robinson et al., Bioinformatics. 2010) with the trimmed mean of M-values (TMM) normalisation method (Robinson and Oshlack., Genome Biol. 2010). Adjusted P-values for multiple testing were calculated using the Benjamini-Hochberg false discovery rate (FDR) and only genes with an FDR < 0.05 were considered significantly differentially expressed.
(miRNAs) IsomiRs analysis was performed using the IsomiRage Java tool (Muller et al., Front Bioeng Biotechnol. 2014). Briefly, .map bowtie output files were used as inputs for the Isomirage pipeline that returned a table containing the number of reads for each isoform in each biological sample. Significant changes in isoform expression were detected using EdgeR, as described above.
Assembly: GRCh37/hg19
Supplementary files format and content: Tab-delimited text files contain raw read counts of different samples, list of differentially expressed genes.
Supplementary files format and content: countTable_edgeR.txt files (The order of the samples (sample IDs) is specified in the file name starting with "guide" for each group of samples for all the comparisons. The unique sample IDs are consecutively ordered as per the guide, for e.g., first with CTL (control samples IDs) and W4 (test tissue samples, mTLE+HS IDs) in this condition. )

source_name: Hippocampus

extract_protocol:
Complete details can be found on in our recent study (Vangoor et al., MedRxiv. 2021). Briefly, sub cellular fractionation was performed isolating pure cytosolic and nuclei cell compartments. Isolated cytoplasmic and nuclei samples were stored in Qiazol (Qiagen) at -80oC until RNA extraction was performed. Total RNA was extracted using miRNeasy kit (Qiagen), according to manufacturer’s protocol.
For small RNA library construction and sequencing, small RNAs of <200 nucleotides were purified using the miRVana microRNA isolation kit (Ambion, Life Technologies). 100 ng of small RNA was prepared for sequencing using the TruSeq Small RNA preparation kit (Illumina, San Diego, California, USA). Small RNA sequencing was performed on an Illumina HiSeq 4000 sequencer at the Beijing Genomics Institute (BGI) (Hongkong, China).

value: Hippocampus

tag: cell compartment

value: Nucleus

tag: disease state

value: mTLE non-HS

tag: fraction

value: Small RNAs


title: Hippocampus_nucleus_mTLE non-HS3

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_E05-33.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt

value: Female


title: NeuNPos nuclei sample for Individual 13 [202073180069_R03C01]

value: NeuN+

value: F


title: Hippocampus_nucleus_mTLE non-HS2

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_E05-35.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt

value: Male


title: NeuNPos nuclei sample for Individual 12 [202073180098_R08C01]

value: M


title: DoubleNeg nuclei sample for Individual 13 [202073180069_R01C01]


title: Hippocampus_nucleus_control9

description:
file category:  Hippocampus(Hip)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_nucleus_CTL_vs_mTLE non-HS(W0)_isomiRs_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_S06-062.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt

value: Postmortem controls


title: Hippocampus_nucleus_mTLE non-HS5

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_E14-07.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt


title: AML2_DMSO_rep1


title: Hippocampus_nucleus_control8

description:
file category:  Hippocampus(Hip)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_nucleus_CTL_vs_mTLE non-HS(W0)_rawcounttable_isomiRs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_S09-007.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt


title: Sox10Pos nuclei sample for Individual 11 [202073200098_R03C01]


title: Hippocmapus_nucleus_mTLE non-HS1

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_E06-13.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt


title: NeuNPos nuclei sample for Individual 11 [202073200098_R02C01]


title: Hippocampus_nucleus_control3

description:
file category:  Hippocampus(Hip)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_nucleus_CTL_vs_mTLE non-HS(W0)_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_C05-93.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt


title: Total nuclei sample for Individual 10 [202073180069_R06C01]

value: Total

value: unstained


title: Hippocampus_nucleus_control2

description:
file category:  Hippocampus(Hip)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_nucleus_CTL_vs_mTLE non-HS(W0)_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_C04-05.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt


title: Hippocampus_nucleus_control1

description:
file category:  Hippocampus(Hip)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_nucleus_CTL_vs_mTLE non-HS(W0)_guide_ordered IDs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_nuc_C02-05.txt
tRFs processed data file (normalized counts):  Hip_nuc_counttable.txt
tRFs processed data file (significant  genes):  Hip_nuc_deseq.txt


title: NeuNPos nuclei sample for Individual 10 [202073180069_R07C01]


title: Total nuclei sample for Individual 13 [202073180069_R02C01]


title: Sox10Pos nuclei sample for Individual 10 [202073180069_R05C01]


title: AML2_DMSO_rep2


title: AML2_DMSO_rep3


title: Hippocampus_cytoplasm_mTLE non-HS3

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_E05-33.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt

value: Cytoplasm


title: Hippocampus_cytoplasm_mTLE non-HS4

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_E13-12.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt


title: Hippocampus_cytoplasm_mTLE non-HS5

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_E14-07.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt


title: DoubleNeg nuclei sample for Individual 10 [202073180069_R08C01]


title: Sox10Pos nuclei sample for Individual 13 [202073180069_R04C01]


title: Total nuclei sample for Individual 11 [202073200098_R04C01]


title: Sox10Pos nuclei sample for Individual 9 [202073180078_R04C01]


title: NeuNPos nuclei sample for Individual 9 [202073180078_R02C01]


title: DoubleNeg nuclei sample for Individual 9 [202073180078_R03C01]


title: Total nuclei sample for Individual 9 [202073180078_R01C01]


title: Hippocampus_cytoplasm_control8

description:
file category:  Hippocampus(Hip)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_cytoplasm_CTL_vs_mTLE non-HS(W0)_rawcounttable_isomiRs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_S09-007.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt


title: Hippocampus_cytoplasm_control9

description:
file category:  Hippocampus(Hip)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_cytoplasm_CTL_vs_mTLE non-HS(W0)_isomiRs_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_S06-062.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt


title: Total nuclei sample for Individual 8 [202073180015_R07C01]


title: Hippocampus_cytoplasm_mTLE non-HS2

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_E05-35.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt


title: Hippocmapus_cytoplasm_mTLE non-HS1

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_E06-13.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt


title: Hippocampus_cytoplasm_control2

description:
file category:  Hippocampus(Hip)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_cytoplasm_CTL_vs_mTLE non-HS(W0)_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_C04-05.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt


title: Sox10Pos nuclei sample for Individual 8 [202073180015_R05C01]


title: Hippocampus_cytoplasm_control3

description:
file category:  Hippocampus(Hip)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_cytoplasm_CTL_vs_mTLE non-HS(W0)_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_C05-93.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt


title: Total nuclei sample for Individual 6 [202073200110_R01C01]


title: Total nuclei sample for Individual 7 [202073200098_R06C01]


title: NeuNPos nuclei sample for Individual 6 [202073200110_R03C01]


title: Cortex_nucleus_mTLE non-HS17_pre

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_nuc_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E15-07_Pre.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

source_name: Cortex

value: Cortex


title: NeuNPos nuclei sample for Individual 8 [202073180015_R08C01]

value: NeuNPos


title: Sox10Pos nuclei sample for Individual 6 [202073200110_R04C01]


title: NeuNPos nuclei sample for Individual 7 [202073200098_R05C01]


title: Cortex_nucleus_mTLE non-HS15_pre

description:
file category:  Cortex(Cx)_Nucleus(nuc)_PREvsPOST
processed data file names description (miRNAs):  Cx_nucleus_PRE_vs_POST_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_nuc_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E15-06_Post.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: DoubleNeg nuclei sample for Individual 8 [202073180015_R06C01]

value: DoubleNeg


title: Cortex_nucleus_mTLE non-HS17_post

description:
file category:  Cortex(Cx)_Nucleus(nuc)_PREvsPOST
processed data file names description (miRNAs):  Cx_nucleus_isomiRs_PRE_vs_POST_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_nuc_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E15-06_Pre.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_mTLE+HS14

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE+HS(W4)_isomiRs_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E11-17.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: mTLE+HS


title: Total nuclei sample for Individual 5 [202073180078_R07C01]


title: Cortex_nucleus_mTLE non-HS16_pre

description:
file category:  Cortex(Cx)_Nucleus(nuc)_PREvsPOST
processed data file names description (miRNAs):  Cx_nucleus_isomiRs_PRE_vs_POST_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_nuc_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E15-02_Pre.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_mTLE non-HS15_post

description:
file category:  Cortex(Cx)_Nucleus(nuc)_PREvsPOST
processed data file names description (miRNAs):  Cx_nucleus_PRE_vs_POST_guide_ordered IDs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_nuc_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E15-02_Post.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Hippocampus_cytoplasm_control1

description:
file category:  Hippocampus(Hip)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Hip_cytoplasm_CTL_vs_mTLE non-HS(W0)_guide_ordered IDs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Hip_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Hip_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Hip_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Hip_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Hip_cyt_C02-05.txt
tRFs processed data file (normalized counts):  Hip_cyt_counttable.txt
tRFs processed data file (significant  genes):  Hip_cyt_deseq.txt

value: Hippocampus


title: NeuNPos nuclei sample for Individual 5 [202073180078_R08C01]


title: Sox10Pos nuclei sample for Individual 5 [202073180078_R05C01]


title: Cortex_nucleus_mTLE+HS13

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE+HS(W4)_rawcounttable_isomiRs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E07-28.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: Nucleus


title: DoubleNeg nuclei sample for Individual 5 [202073180078_R06C01]


title: Cortex_nucleus_mTLE+HS11

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE+HS(W4)_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E08-17.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: NeuNPos nuclei sample for Individual 4 [202073200108_R07C01]


title: Sox10Pos nuclei sample for Individual 4 [202073200108_R05C01]


title: Cortex_nucleus_mTLE+HS10

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE+HS(W4)_guide_ordered IDs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E06-21.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_mTLE+HS9

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E05-03.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_mTLE non-HS7

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E07-24.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: mTLE non-HS


title: DoubleNeg nuclei sample for Individual 6 [202073200110_R02C01]


title: Cortex_nucleus_mTLE non-HS16_post

description:
file category:  Cortex(Cx)_Nucleus(nuc)_PREvsPOST
processed data file names description (miRNAs):  Cx_nucleus_PRE_vs_POST_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_nuc_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E15-07_Post.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: Small RNAs


title: Total nuclei sample for Individual 3 [202073180015_R02C01]


title: NeuNPos nuclei sample for Individual 3 [202073180015_R04C01]


title: Cortex_nucleus_mTLE non-HS6

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E07-21.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: Female


title: Cortex_nucleus_mTLE non-HS3

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E05-33.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Sox10Pos nuclei sample for Individual 3 [202073180015_R01C01]


title: Cortex_nucleus_mTLE non-HS2

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E05-35.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: DoubleNeg nuclei sample for Individual 4 [202073200108_R08C01]


title: DoubleNeg nuclei sample for Individual 3 [202073180015_R03C01]


title: Cortex_nucleus_control7

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_S11-028.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Total nuclei sample for Individual 2 [202073200110_R07C01]


title: Cortex_nucleus_control6

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE non-HS(W0)_isomiRs_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_S10-109.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_control5

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE non-HS(W0)_rawcounttable_isomiRs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_S12_002.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: DoubleNeg nuclei sample for Individual 2 [202073200110_R06C01]


title: Total nuclei sample for Individual 1 [202073200108_R04C01]


title: NeuNPos nuclei sample for Individual 2 [202073200110_R05C01]

value: NeuN+


title: Total nuclei sample for Individual 4 [202073180098_R05C01]

value: F


title: Cortex_nucleus_mTLE non-HS8

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E11-18.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_mTLE+HS12

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE+HS(W4)_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E06-19.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: Male


title: Cortex_nucleus_mTLE non-HS1

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_E06_13.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_control3

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE non-HS(W0)_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_C05-93.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_control4

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_nucleus_CTL_vs_mTLE non-HS(W0)_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_S02-071.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Sox10Pos nuclei sample for Individual 1 [202073200108_R02C01]


title: NeuNPos nuclei sample for Individual 1 [202073200108_R03C01]


title: Cortex_cytoplasm_mTLE non-HS17_post

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_PREvsPOST
processed data file names description (miRNAs):  Cx_cytoplasm_isomiRs_PRE_vs_POST_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_cyt_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E15-06_Pre.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_cytoplasm_mTLE non-HS17_pre

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_cyt_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E15-07_Pre.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_nucleus_control1

description:
file category:  Cortex(Cx)_Nucleus(nuc)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_nucleus(nuc)_CTL_vs_mTLE non-HS(W0)_guide_ordered IDs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_nuc_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_nuc_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_nuc_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_nuc_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_nuc_C02-05.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Sox10Pos nuclei sample for Individual 2 [202073200110_R08C01]


title: DoubleNeg nuclei sample for Individual 1 [202073200108_R01C01]


title: Cortex_cytoplasm_mTLE non-HS16_pre

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_PREvsPOST
processed data file names description (miRNAs):  Cx_cytoplasm_isomiRs_PRE_vs_POST_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_cyt_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E15-02_Pre.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: PbIMC1gckD, KD 2

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

country: China

institute: China Medical University

data_processing:
Reads counts were obtained with HTSeq v0.9.1. Differential expression analysis of genes between the PbIMC1gcKD parasites cultured in both [+] and [-] TMP conditions were determined using the DESeq R package (1.18.0). The p-values were adjusted using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR). Genes with an adjusted P value <0.05 found by DESeq were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: readscount values for each Sample

organism: Plasmodium berghei

source_name: gamete

growth_protocol: activated gametocytes from PbIMC1gcKD [+]/[-] TMP parasite were maintained in gametocyte activation buffer

extract_protocol:
activated gametocytes from PbIMC1gcKD [+]/[-] TMP parasite were purified with 48% Nycodenz and activated in gametocyte activation buffer at 25℃ for 15 min
mRNA was enriched using poly-T oligo-attached magnetic beads. Reverse transcription was performed with SuperScript II (Invitrogen) using random primers. The reaction was then treated with RNaseH to remove the RNA template and cleaned using DNA Clean and Concentrator Kit (Zymo Research). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced using the Illumina platform.
RNA-seq raw data were initially filtered by fastq to obtain high-quality, clean data. Adapter trimming was performed using cutadapt version 1.13 (http://cutadapt.readthedocs.io/en/stable/guide.html). Processed reads were aligned to the P. berghei ANA genome (assembly PlasmoDB-67) with Hisat2 v2.0.4 [108] and deduplicated according to UMI using UMI-tools (v1.0.0)

value: gamete

tag: cell line

value: Plasmodium berghei ANKA

tag: genotype

value: PbIMC2g knockdown

value: mock treatment


title: Cortex_cytoplasm_mTLE non-HS16_post

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_PREvsPOST
processed data file names description (miRNAs):  Cx_cytoplasm_PRE_vs_POST_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_cyt_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E15-07_Post.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: Cytoplasm


title: PbIMC1gckD, KD 1

tag: cell type

value: PbIMC1g knockdown


title: PbIMC1gckD, control 1

value: WT

value: trimethoprim treatment


title: Cortex_cytoplasm_mTLE+HS14

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE+HS(W4)_isomiRs_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E11-17.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: Cortex

value: mTLE+HS