title: WholeBlood_CRC305D2GENT129120_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT129120 on day 7

tag: protocol


title: WholeBlood_CRC305D2GENT154422_Day7

status: Public on Jan 07 2022

type: RNA

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT154422 on day 7

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood, PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: tissue

value: whole blood

tag: treatment

tag: day

tag: participant

tag: gender

value: male

tag: age

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

tag: recent boostrix


title: WholeBlood_CRC305D2GENT175416_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT175416 on day 3

value: BOOSTRIX


title: WholeBlood_CRC305D2GENT196124_Day2

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT196124 on day 2


title: WholeBlood_CRC305D2GENT191721_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT191721 on day 3

value: female


title: WholeBlood_CRC305D2GENT231526_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT231526 on day 2


title: WholeBlood_CRC305D2GENT238223_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT238223 on day 2


title: MMBC010011NOR

type: SRA

city: CHICAGO

first: JI

last: NIE

state: IL

department: Chemistry

country: USA

institute: The University of Chicago

library_source: genomic

data_processing:
Sequenced reads were trimmed by trimmomatic(v0.36), then mapped to targeted sites by bowtie2.
Barcode counts were called. Batch effect was corrected by combat, R sva package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes barcode counts for each sample

molecule: genomic DNA

source_name: plasma

extract_protocol:
Cell-free DNA was isolated from plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen) according to the manufacturer’s protocol.
Library construction was performed for illumina sequencing platform.

value: plasma

tag: patient diagnosis

value: healthy

tag: tissue compartment

value: cell-free DNA


title: WholeBlood_CRC305D2GENT194123_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT194123 on day 2


title: WholeBlood_CRC305D2GENT152421_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT152421 on day 7


title: blood_416 [Sample46]

type: genomic

city: Davis

first: Anita

last: Oberbauer

state: CA

address: One Shields Ave.

department: Animal Science Department

institute: University of California, Davis

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

hyb_protocol: Hybridization was performed according to the Infinium HD Super Assay documentation using the automated protocol.

scan_protocol: Scanning was performed according to the Infinium HD Super Assay documentation using the automated protocol.

data_processing:
The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.

label: C-Bio, G-Bio, A-DNP, T-DNP

organism: Bos taurus

source_name: blood from coccygeal vein in the tail

label_protocol: According to the Infinium HD Super Assay documentation (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-hd-super-assay/infinium-hd-super-assay-reference-guide-11322427-03.pdf), labels were added during allele-specific base extension.

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.

tag: mastitis

tag: metritis

tag: milk fever

tag: farm

value: A

tag: Sex


title: blood_417 [Sample47]


title: WholeBlood_CRC305D2GENT130119_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT130119 on day 7

tag: protocol


title: WholeBlood_CRC305D2GENT120415_Day3

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT120415 on day 3

tag: tissue


title: MMBC010009NOR


title: WholeBlood_CRC305D2GENT179525_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT179525 on day 2

tag: treatment


title: MMBC010008NOR


title: blood_415 [Sample45]


title: blood_414 [Sample44]


title: MMBC010007NOR


title: WholeBlood_CRC305D2GENT235222_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT235222 on day 2

tag: day


title: WholeBlood_CRC305D2GENT147122_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT147122 on day 2

tag: participant


title: blood_413 [Sample43]

value: B


title: MMBC010010NOR


title: WholeBlood_CRC305D2GENT240427_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT240427 on day 3

tag: gender


title: MMBC010005NOR


title: WholeBlood_CRC305D2GENT168322_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT168322 on day 7

tag: age


title: WholeBlood_CRC305D2GENT170426_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT170426 on day 3

tag: race


title: WholeBlood_CRC305D2GENT182524_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT182524 on day 2

tag: ethnicity


title: WholeBlood_CRC305D2GENT141520_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT141520 on day 7

tag: recent boostrix


title: WholeBlood_CRC305D2GENT243326_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT243326 on day 3


title: WholeBlood_CRC305D2GENT116118_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT116118 on day 7


title: WholeBlood_CRC305D2GENT142521_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT142521 on day 7


title: MMBC010004NOR

tag: patient diagnosis


title: blood_410 [Sample40]


title: WholeBlood_CRC305D2GENT208221_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT208221 on day 2


title: WholeBlood_CRC305D2GENT172519_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT172519 on day 7


title: WholeBlood_CRC305D2GENT133425_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT133425 on day 3


title: WholeBlood_CRC305D2GENT118117_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT118117 on day 7


title: WholeBlood_CRC305D2GENT234325_Day3

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT234325 on day 3


title: MMBC010006NOR

tag: tissue compartment


title: WholeBlood_CRC305D2GENT212321_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT212321 on day 7


title: MMBC010003NOR


title: blood_409 [Sample39]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

tag: mastitis


title: blood_9 [SampleGSM4820554]

tag: metritis


title: blood_411 [Sample41]

tag: milk fever


title: MMBC020019NOR

value: HBV


title: MMBC010002NOR


title: MMBC010001NOR


title: WholeBlood_CRC305D2GENT190527_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT190527 on day 2


title: blood_408 [Sample38]

tag: farm


title: WholeBlood_CRC305D2GENT144121_Day2

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT144121 on day 2


title: blood_412 [Sample42]

tag: Sex


title: WholeBlood_CRC305D2GENT187323_Day0

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT187323 on day 0

tag: protocol


title: blood_406 [Sample36]


title: WholeBlood_CRC305D2GENT141520_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT141520 on day 1

tag: tissue


title: blood_405 [Sample35]


title: MMBC020017NOR


title: WholeBlood_CRC305D2GENT141520_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT141520 on day 0

tag: treatment


title: MMBC020016NOR


title: WholeBlood_CRC305D2GENT183822_Day1

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT183822 on day 1

tag: day


title: WholeBlood_CRC305D2GENT163817_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT163817 on day 7

tag: participant


title: blood_404 [Sample34]


title: WholeBlood_CRC305D2GENT187323_Day3

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT187323 on day 3

tag: gender


title: WholeBlood_CRC305D2GENT187323_Day1

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT187323 on day 1

tag: age


title: WholeBlood_CRC305D2GENT172519_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT172519 on day 1

tag: race


title: blood_403 [Sample33]


title: WholeBlood_CRC305D2GENT168322_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT168322 on day 1

tag: ethnicity


title: WholeBlood_CRC305D2GENT172519_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT172519 on day 0

tag: recent boostrix


title: MMBC020015NOR

tag: patient diagnosis


title: WholeBlood_CRC305D2GENT188823_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT188823 on day 0


title: blood_402 [Sample32]


title: WholeBlood_CRC305D2GENT168322_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT168322 on day 0


title: blood_401 [Sample31]


title: MMBC020013NOR

tag: tissue compartment


title: blood_400 [Sample30]

tag: mastitis


title: WholeBlood_CRC305D2GENT192821_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT192821 on day 1


title: MMBC020014NOR


title: WholeBlood_CRC305D2GENT248518_Day1

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT248518 on day 1


title: MMBC020018NOR


title: WholeBlood_CRC305D2GENT168322_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT168322 on day 3


title: blood_398 [Sample28]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

tag: metritis


title: WholeBlood_CRC305D2GENT162816_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT162816 on day 7


title: MMBC020010NOR


title: blood_397 [Sample27]

tag: milk fever


title: MMBC020012NOR


title: blood_399 [Sample29]

tag: farm


title: MMBC020011NOR


title: blood_396 [Sample26]

tag: Sex


title: MMBC020009NOR


title: MMBC020006NOR


title: WholeBlood_CRC305D2GENT248518_Day0

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT248518 on day 0

tag: protocol


title: WholeBlood_CRC305D2GENT212321_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT212321 on day 0

tag: tissue


title: WholeBlood_CRC305D2GENT212321_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT212321 on day 1

tag: treatment


title: WholeBlood_CRC305D2GENT209820_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT209820 on day 1

tag: day


title: blood_393 [Sample23]


title: WholeBlood_CRC305D2GENT192821_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT192821 on day 0

tag: participant


title: WholeBlood_CRC305D2GENT212321_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT212321 on day 3

tag: gender


title: MMBC020008NOR


title: blood_395 [Sample25]


title: MMBC020007NOR


title: WholeBlood_CRC305D2GENT209820_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT209820 on day 0

tag: age


title: blood_394 [Sample24]


title: WholeBlood_CRC305D2GENT151320_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT151320 on day 0

tag: race


title: WholeBlood_CRC305D2GENT148517_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT148517 on day 1

tag: ethnicity


title: blood_392 [Sample22]


title: MMBC020005NOR


title: WholeBlood_CRC305D2GENT151320_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT151320 on day 3

tag: recent boostrix


title: MMBC020004NOR

tag: patient diagnosis


title: WholeBlood_CRC305D2GENT148517_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT148517 on day 0


title: WholeBlood_CRC305D2GENT076814_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT076814 on day 7


title: WholeBlood_CRC305D2GENT151320_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT151320 on day 1


title: WholeBlood_CRC305D2GENT167815_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT167815 on day 7


title: blood_391 [Sample21]


title: WholeBlood_CRC305D2GENT171722_Day0

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT171722 on day 0


title: WholeBlood_CRC305D2GENT211319_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT211319 on day 1


title: WholeBlood_CRC305D2GENT171722_Day1

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT171722 on day 1


title: WholeBlood_CRC305D2GENT145516_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT145516 on day 1


title: WholeBlood_CRC305D2GENT145516_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT145516 on day 0


title: WholeBlood_CRC305D2GENT211319_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT211319 on day 0


title: blood_390 [Sample20]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)


title: MMBC020003NOR

tag: tissue compartment


title: WholeBlood_CRC305D2GENT158720_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT158720 on day 7


title: MMBC020002NOR


title: blood_389 [Sample19]

tag: mastitis


title: WholeBlood_CRC305D2GENT211319_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT211319 on day 3


title: MMBC020001NOR


title: blood_388 [Sample18]

tag: metritis


title: MMBC040028CAC

value: HBV_Hepatocellular carcinoma


title: WholeBlood_CRC305D2GENT170426_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT170426 on day 1


title: blood_387 [Sample17]

tag: milk fever


title: WholeBlood_CRC305D2GENT191721_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT191721 on day 1


title: MMBC040027CAC


title: blood_407 [Sample37]

tag: farm


title: MMBC040026CAC


title: WholeBlood_CRC305D2GENT191721_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT191721 on day 0


title: MMBC040024CAC


title: WholeBlood_CRC305D2GENT183822_Day0

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT183822 on day 0


title: WholeBlood_CRC305D2GENT138318_Day0

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT138318 on day 0


title: WholeBlood_CRC305D2GENT169619_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT169619 on day 0


title: blood_382 [Sample12]

tag: Sex


title: blood_384 [Sample14]


title: blood_385 [Sample15]


title: MMBC040025CAC


title: WholeBlood_CRC305D2GENT150317_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT150317 on day 0

tag: protocol


title: WholeBlood_CRC305D2GENT170426_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT170426 on day 0

tag: tissue


title: WholeBlood_CRC305D2GENT138318_Day1

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT138318 on day 1

tag: treatment


title: WholeBlood_CRC305D2GENT150317_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT150317 on day 1

tag: day


title: WholeBlood_CRC305D2GENT133425_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT133425 on day 0

tag: participant


title: WholeBlood_CRC305D2GENT068718_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT068718 on day 7

tag: gender


title: blood_383 [Sample13]


title: WholeBlood_CRC305D2GENT153424_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT153424 on day 1

tag: age


title: WholeBlood_CRC305D2GENT150317_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT150317 on day 3

tag: race


title: MMBC040021CAC


title: MMBC040020CAC


title: blood_381 [Sample11]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)


title: MMBC040022CAC


title: WholeBlood_CRC305D2GENT133425_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT133425 on day 1

tag: ethnicity


title: WholeBlood_CRC305D2GENT135618_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT135618 on day 1

tag: recent boostrix


title: blood_380 [Sample10]


title: blood_377 [Sample7]


title: blood_379 [Sample9]


title: MMBC040019CAC

tag: patient diagnosis


title: MMBC040023CAC

tag: tissue compartment


title: blood_376 [Sample6]

tag: mastitis


title: blood_375 [Sample5]

tag: metritis


title: blood_378 [Sample8]

tag: milk fever


title: MMBC040018CAC


title: MMBC040017CAC


title: WholeBlood_CRC305D2GENT164719_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT164719 on day 7


title: MMBC040015CAC


title: WholeBlood_CRC305D2GENT135618_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT135618 on day 0


title: blood_374 [Sample4]

tag: farm


title: MMBC040016CAC


title: blood_386 [Sample16]

tag: Sex


title: MMBC040013CAC


title: WholeBlood_CRC305D2GENT214316_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT214316 on day 0

tag: protocol


title: MMBC040014CAC

tag: tissue


title: WholeBlood_CRC305D2GENT214316_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT214316 on day 1

tag: treatment


title: WholeBlood_CRC305D2GENT153424_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT153424 on day 0

tag: day


title: WholeBlood_CRC305D2GENT071717_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT071717 on day 7

tag: participant


title: blood_373 [Sample3]


title: blood_372 [Sample2]


title: WholeBlood_CRC305D2GENT214316_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT214316 on day 3

tag: gender


title: WholeBlood_CRC305D2GENT156423_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT156423 on day 1

tag: age


title: WholeBlood_CRC305D2GENT128617_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT128617 on day 1

tag: race


title: blood_371 [Sample1]


title: MMBC040012CAC


title: MMBC040011CAC


title: WholeBlood_CRC305D2GENT132315_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT132315 on day 3

tag: ethnicity


title: WholeBlood_CRC305D2GENT154422_Day1

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT154422 on day 1

tag: recent boostrix


title: MMBC040010CAC

tag: patient diagnosis


title: WholeBlood_CRC305D2GENT149218_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT149218 on day 0


title: WholeBlood_CRC305D2GENT128617_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT128617 on day 0


title: WholeBlood_CRC305D2GENT065716_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT065716 on day 7


title: MMBC040009CAC

tag: tissue compartment


title: WholeBlood_CRC305D2GENT121616_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT121616 on day 0


title: WholeBlood_CRC305D2GENT146217_Day0

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT146217 on day 0


title: WholeBlood_CRC305D2GENT149218_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT149218 on day 1


title: WholeBlood_CRC305D2GENT121616_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT121616 on day 1


title: WholeBlood_CRC305D2GENT156423_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT156423 on day 0


title: WholeBlood_CRC305D2GENT146217_Day1

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT146217 on day 1


title: MMBC040008CAC


title: MMBC040007CAC


title: WholeBlood_CRC305D2GENT113613_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT113613 on day 7


title: WholeBlood_CRC305D2GENT154422_Day0

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT154422 on day 0


title: WholeBlood_CRC305D2GENT147122_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT147122 on day 1


title: WholeBlood_CRC305D2GENT152421_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT152421 on day 0


title: WholeBlood_CRC305D2GENT095612_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT095612 on day 7


title: WholeBlood_CRC305D2GENT140314_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT140314 on day 3


title: MMBC040006CAC


title: m6A-RIP-Mettl3-LysM-KO-Mac IP rep2

city: New Haven

first: Xinshou

last: Ouyang

state: CT

address: 1 Gilbert street

department: Internal Medicine

institute: Yale University

hyb_protocol: 2.5 ug of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 uL 10X Blocking Agent and 1 μL of 25X Fragmentation Buffer, heated at 60C for 30 min, and combined with 25 uL 2X Hybridization buffer. 50 uL hybridization solution was dispensed into the gasket slide and assembled to the microarray slide. The slides were incubated at 65C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. The normalized intensities were used to calculate the modification percentages of the transcripts and m6A modified RNA abundances.

organism: Mus musculus

source_name: Spleen

label_protocol: the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit. The cRNAs were combined together and hybridized onto Arraystar Mouse mRNA&lncRNA Epitranscriptomic Microarray (8 x 60K, Arraystar). Raw data were acquired after array hybridization and scanning, from which two datasets named “m6A methylation level” and “m6A quantity” were extracted. In this study, the m6A quantity data were used and further subjected to principal component analysis, differentially m6A-methylated mRNAs analysis and pathway enrichment analysis.

extract_protocol: The total RNA was extracted from CD11b+F4/80+ spleen macrophages using miRNeasy mini kit  (GIAGEN).

treatment_protocol: The C57BL/6 mice were onnormal chow for 10 weeks. The total RNA was extracted from CD11b+F4/80+ cells isolated frm spleen.

tag: genotype/variation

value: KO

tag: cell type

tag: antibody

value: anti-N6-methyadenosine (m6A)


title: m6A-RIP-Mettl3-LysM-KO-Mac IP rep1


title: WholeBlood_CRC305D2GENT152421_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT152421 on day 1


title: WholeBlood_CRC305D2GENT142521_Day1

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT142521 on day 1


title: WholeBlood_CRC305D2GENT143522_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT143522 on day 0


title: WholeBlood_CRC305D2GENT131313_Day3

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT131313 on day 3


title: WholeBlood_CRC305D2GENT147122_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT147122 on day 0


title: m6A-RIP-Mettl3-LysM-WT-Mac IP rep1

value: WT


title: MMBC040005CAC


title: WholeBlood_CRC305D2GENT144121_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT144121 on day 1


title: MMBC040004CAC


title: WholeBlood_CRC305D2GENT230324_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT230324 on day 1


title: m6A-RIP-Mettl3-LysM-WT-Mac IP rep2


title: WholeBlood_CRC305D2GENT142521_Day0

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT142521 on day 0


title: m6A-RIP-Mettl3-LysM-KO-Mac input rep2


title: MMBC040003CAC


title: MMBC040002CAC


title: LIN28B_X4_eCLIP_INPUT_Rep1_Human

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner
RPKM values were calculated for all polysome samples. For eCLIP samples, read densities were calculated to identify eCLIP peaks.
eclip data processing pipeline can be requested from the following link : https://github.com/YeoLab/eclip
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: RPKM files for all polysome samples. eCLIP input normalized peaks in BED format. eCLIP reproduclible peaks in BED format. eCLIP normalized read densitied in BIGWIG format.

growth_protocol: for HEK293, standard cell culture in 10% FBS in DMEM; for mouse ESCs, cells were transitioned to feeder free conditions over 2 passage cycles and continuously maintained in 15%FBS, NEAA, NaPyr, 1000U/mL LIF in DMEM

extract_protocol:
Total and polysome derived RNA were extracted using Trizol reagent
Illumina polyA Total RNA kit

treatment_protocol: LIN28B transgenes, Sponge Construct and Controls were induced using 10ng/ml Doxycycline. Samples assayed 24-36 hours after induction.


title: m6A-RIP-Mettl3-LysM-KO-Mac input rep1


title: WholeBlood_CRC305D2GENT230324_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT230324 on day 0


title: WholeBlood_CRC305D2GENT090611_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT090611 on day 7


title: MMBC030022CAC

value: gastric cancer


title: MMBC040001CAC


title: LIN28B_X3_eCLIP_INPUT_Rep2_Human


title: WholeBlood_CRC305D2GENT080109_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT080109 on day 7

value: whole blood


title: WholeBlood_CRC305D2GENT075111_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT075111 on day 7

value: male


title: WholeBlood_CRC305D2GENT144121_Day0

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT144121 on day 0

value: white


title: WholeBlood_CRC305D2GENT143522_Day1

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT143522 on day 1

value: not hispanic or latino


title: WholeBlood_CRC305D2GENT077110_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT077110 on day 7

value: BOOSTRIX


title: m6A-RIP-Mettl3-LysM-WT-Mac input rep2


title: WholeBlood_CRC305D2GENT085108_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT085108 on day 7


title: WholeBlood_CRC305D2GENT058107_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT058107 on day 7


title: WholeBlood_CRC305D2GENT093106_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT093106 on day 7


title: LIN28B_X4_eCLIP_INPUT_Rep2_Human


title: WholeBlood_CRC305D2GENT094605_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT094605 on day 28

value: female


title: WholeBlood_CRC305D2GENT089610_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT089610 on day 7


title: m6A-RIP-Mettl3-LysM-WT-Mac input rep1


title: WholeBlood_CRC305D2GENT160412_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT160412 on day 7


title: MMBC030021CAC

value: plasma


title: WholeBlood_CRC305D2GENT100115_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT100115 on day 7


title: LIN28B_X3_eCLIP_INPUT_Rep1_Human


title: LIN28B_X2_eCLIP_INPUT_Rep1_Human


title: MMBC030018CAC


title: LIN28B_X1_eCLIP_INPUT_Rep2_Human


title: MMBC030020CAC


title: LIN28B_X2_eCLIP_INPUT_Rep2_Human


title: MMBC030019CAC


title: LIN28B_X1_eCLIP_INPUT_Rep1_Human


title: LIN28B_X4_eCLIP_IP_Rep2_Human

tag: barcode

value: X2A, X2B


title: MMBC030016CAC

value: cell-free DNA


title: WholeBlood_CRC305D2GENT096505_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT096505 on day 7


title: MMBC030015CAC


title: LIN28B_X4_eCLIP_IP_Rep1_Human


title: WholeBlood_CRC305D2GENT101710_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT101710 on day 7


title: WholeBlood_CRC305D2GENT098213_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT098213 on day 28


title: LIN28B_X3_eCLIP_IP_Rep2_Human


title: WholeBlood_CRC305D2GENT080109_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT080109 on day 28


title: MMBC030014CAC


title: MMBC030017CAC


title: WholeBlood_CRC305D2GENT053603_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT053603 on day 28


title: MMBC030013CAC


title: WholeBlood_CRC305D2GENT091212_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT091212 on day 28


title: WholeBlood_CRC305D2GENT085108_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT085108 on day 28


title: LIN28B_X2_eCLIP_IP_Rep2_Human

value: C01, D08fixed


title: WholeBlood_CRC305D2GENT064504_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT064504 on day 7


title: WholeBlood_CRC305D2GENT103114_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT103114 on day 7


title: LIN28B_X2_eCLIP_IP_Rep1_Human


title: WholeBlood_CRC305D2GENT057211_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT057211 on day 28


title: WholeBlood_CRC305D2GENT132315_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT132315 on day 7


title: WholeBlood_CRC305D2GENT037812_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT037812 on day 28


title: WholeBlood_CRC305D2GENT069608_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT069608 on day 7


title: WholeBlood_CRC305D2GENT059507_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT059507 on day 28


title: MMBC030011CAC


title: WholeBlood_CRC305D2GENT063607_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT063607 on day 7


title: WholeBlood_CRC305D2GENT110512_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT110512 on day 7


title: WholeBlood_CRC305D2GENT088609_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT088609 on day 7


title: LIN28B_X3_eCLIP_IP_Rep1_Human


title: LIN28B_X1_eCLIP_IP_Rep2_Human


title: MMBC030010CAC


title: MMBC030009CAC


title: MMBC030012CAC


title: AID-TRRAP-cloneAT63-IAA-24h

city: Montpellier

first: Dominique

last: Helmlinger

address: 1919 route de Mende

department: CRBM

country: France

institute: CNRS

description: Illumina TruSeq Stranded mRNA Library

data_processing:
Basecalling pipeline at Fasteris: HiSeq Control Software HD 3.4.0.38; RTA 2.7.7; bcl2fastq2.17 v2.17.1.14
Sequenced reads were trimmed for adaptor sequence using FastQ Groomer and mapped to to human genome assembly GRCh37 (hg19) using HISAT2 v2.1.0 with strand-specific information (--rna-strandness R) and otherwise default options
Reads were then counted for gene and exon features using htseq-count v0.9.1 in union mode (--mode union), reverse stranded (--stranded Reverse), and a minimum alignment quality of 10 (--minaqual 10)
Variance-mean dependence was estimated from count tables and tested for differential expression based on a negative binomial distribution, using DESeq2 v1.18.1. Pairwise comparison or one-way analysis of variance were run with a parametric fit and genotype as the source of variation (factor: ‘mutant’ or ‘control’)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited txt files wee merged into one Excel spreadsheet, in which each sheet includes Gene ID, Log2 fold-change and normalized P values (P-adj) for each DESeq2 analysis.

source_name: Adherent cells

growth_protocol: Non-confluent HCT116 cells grown in MCCOYS’5A medium (Sigma) supplemented with 10% (v/v) FBS and 100 U/ml Penicillin/Streptomycin in 5% CO2 at 37°C

extract_protocol:
RNA was extracted using TRIzol. DNA was removed by DNase I digestion, using the TURBO DNA-free™ kit. RNA was cleaned using the RNeasy Mini kit. Total RNA quality and concentration was determined using an Agilent Bioanalyzer. Transcripts were purified by polyA-tail selection.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library prep kit

treatment_protocol: NaOH at 0.01% or 3-Indoleacetic acid (IAA) (Sigma, I2886) at 0.5 mM for either 48 hours (TELO2-AID) or 24 hours (AID-TRRAP)

tag: genotype

value: TIR1 AID-TRRAP

value: IAA

tag: clone number


title: WholeBlood_CRC305D2GENT140314_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT140314 on day 7

tag: tissue

tag: protocol


title: WholeBlood_CRC305D2GENT081411_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT081411 on day 7

tag: treatment

tag: day


title: WholeBlood_CRC305D2GENT058107_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT058107 on day 28

tag: participant

tag: gender


title: MMBC030007CAC


title: WholeBlood_CRC305D2GENT040811_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT040811 on day 28

tag: age

tag: race


title: WholeBlood_CRC305D2GENT074410_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT074410 on day 7

tag: ethnicity

tag: recent boostrix


title: WholeBlood_CRC305D2GENT092606_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT092606 on day 7


title: AID-TRRAP-cloneAT29-IAA-24h

description: Illumina TruSeq Stranded mRNA Library


title: MMBC030006CAC

tag: patient diagnosis

tag: tissue compartment


title: WholeBlood_CRC305D2GENT097506_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT097506 on day 28


title: AID-TRRAP-cloneAT63-NaOH-24h

description: Illumina TruSeq Stranded mRNA Library

value: NaOH


title: WholeBlood_CRC305D2GENT052210_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT052210 on day 28


title: AID-TRRAP-cloneAT29-NaOH-24h

description: Illumina TruSeq Stranded mRNA Library


title: MMBC030005CAC


title: WholeBlood_CRC305D2GENT137419_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT137419 on day 7


title: WholeBlood_CRC305D2GENT139420_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT139420 on day 7


title: MMBC030008CAC


title: AID-TRRAP-cloneAT28-IAA-24h

description: Illumina TruSeq Stranded mRNA Library


title: MMBC030004CAC


title: WholeBlood_CRC305D2GENT093106_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT093106 on day 28


title: AID-TRRAP-cloneAT28-NaOH-24h

description: Illumina TruSeq Stranded mRNA Library


title: MMBC030003CAC


title: MMBC030002CAC


title: MMBC030001CAC


title: MMBC020017CAC

value: esophageal cancer


title: WholeBlood_CRC305D2GENT161312_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT161312 on day 7


title: UC-F(repeat)

city: Seoul

first: WEIWEI

last: GAO

address: Anam-ro

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: urine cell

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

tag: cell type

value: female urine cell

tag: passage


title: iNPC-F(repeat)

source_name: induced nephron progenitor

value: femal urine cell induced nephron progenitor cell


title: MMBC020016CAC


title: Sample 14_Human cardiac immune cells

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

data_processing:
Cell Ranger Single Cell Software Suite (10x Genomics) was used to pre-process sequenced cells, and to generate the expression matrices.
Raw base call (BCL) files from HiSeq2500 sequencer were demultiplexed into FASTQ files.
Sequencing reads were aligned to the mouse or human transcriptome using STAR aligner.
Cell barcodes and UMIs underwent filtering and correction, followed by barcode and UMI counting to generate the feature-barcode matrices.
Genome_build: mm10 (Samples 1-13); hg19 (Sample 14)
Supplementary_files_format_and_content: Cell barcodes: TSV, Genes: TSV, Counts: expression matricies, MTX

source_name: Heart immune cells

extract_protocol:
(Samples 1-13, mouse) Tissues were perfused with 20 ml of cold PBS. Tissues were chopped finely and digested, while being shaken, at 37 °C in DMEM containing collagenase I (450 U ml–1), DNase I (60 U ml–1) and hyaluronidase (60 U ml–1) enzymes and 1mM Flavopiridol. Digestions were stopped after 45 min and cells were processed into a single-cell suspension on ice. Cells were labeled with CD45 magnetic beads (Miltenyi Biotec) and subsequently fluorescently tagged antibodies to CD45, CD64, CD11b, B220, CD3, Ly6G, NK1.1, Ly6C and MHC-II. Hematopoietic cells were positively enriched using the AutoMACS instrument (Miltenyi Biotec). Live macrophages (DAPI-CD45+CD64int-hiCD11b+) were sorted on the Aria Fusion (BD Bioscience) under low pressure into DMEM containing 50% bovine serum for 10x Genomics single-cell RNA sequencing.
(Samples 14, human) Resected tissue was immediately placed into sterile, cold DMEM media supplemented with 50% fetal bovine serum. Human cardiac tissue was processed similar to mouse tissue and stained with anti-CD45 antibody. Cell sorting was performed using Aria II instrumentation (BD Bioscience). Total live immune cells were sorted by gating on DAPI-CD45+ cells. Samples were sorted directly into DMEM + 50% bovine serum for single-cell RNA sequencing submission.
(Samples 1-5) Libraries were prepared as outlined by the Chromium Single Cell 3’ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
(Sample 6-14) Libraries were prepared as outlined by the Chromium Single Cell 3’ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).

value: Heart

value: 12 years old

value: Congenital cardiomyopathy; male


title: ESC-NPC_BG01(repeat)

value: nephron progenitor cell derived from ESC-BG01


title: WholeBlood_CRC305D2GENT038709_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT038709 on day 28

value: whole blood

value: white

value: not hispanic or latino


title: WholeBlood_CRC305D2GENT087409_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT087409 on day 7

value: BOOSTRIX

value: male


title: WholeBlood_CRC305D2GENT094605_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT094605 on day 7

value: female


title: WholeBlood_CRC305D2GENT096505_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT096505 on day 28


title: WholeBlood_CRC305D2GENT055209_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT055209 on day 28


title: WholeBlood_CRC305D2GENT039708_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT039708 on day 28


title: WholeBlood_CRC305D2GENT054105_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT054105 on day 28


title: WholeBlood_CRC305D2GENT050208_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT050208 on day 28


title: WholeBlood_CRC305D2GENT064504_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT064504 on day 28


title: WholeBlood_CRC305D2GENT108813_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT108813 on day 7


title: TELO2-AID-cloneTAY620-IAA-48h

description: Illumina TruSeq Stranded mRNA Library

value: TIR1 TELO2-AID


title: MMBC020015CAC

value: plasma

value: cell-free DNA


title: TELO2-AID-cloneTAY620-NaOH-48h

description: Illumina TruSeq Stranded mRNA Library

value: NaOH


title: MMBC020014CAC

value: esophageal cancer


title: LIN28B_X1_eCLIP_IP_Rep1_Human

tag: barcode


title: TELO2-AID-cloneTAY615-IAA-48h

description: Illumina TruSeq Stranded mRNA Library

tag: genotype

value: IAA


title: TELO2-AID-cloneTAY615-NaOH-48h

description: Illumina TruSeq Stranded mRNA Library

tag: clone number


title: MMBC020012CAC

tag: tissue


title: TELO2-AID-cloneH8-NaOH-48h

description: Illumina TruSeq Stranded mRNA Library


title: WholeBlood_CRC305D2GENT083408_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT083408 on day 7

tag: protocol


title: TELO2-AID-cloneH8-IAA-48h

description: Illumina TruSeq Stranded mRNA Library

tag: treatment


title: WholeBlood_CRC305D2GENT165310_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT165310 on day 7

tag: day


title: MMBC020011CAC


title: WholeBlood_CRC305D2GENT047207_Day28

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT047207 on day 28

tag: participant


title: WholeBlood_CRC305D2GENT127417_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT127417 on day 7

tag: gender


title: MMBC020010CAC


title: WholeBlood_CRC305D2GENT119308_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT119308 on day 7

tag: age


title: WholeBlood_CRC305D2GENT107511_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT107511 on day 7

tag: race


title: WholeBlood_CRC305D2GENT049503_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT049503 on day 28

tag: ethnicity


title: WholeBlood_CRC305D2GENT043707_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT043707 on day 28

tag: recent boostrix


title: WholeBlood_CRC305D2GENT072715_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT072715 on day 7


title: TbPOLIE RNAi induced (+D) rep 2

city: CLEVELAND

first: Bibo

last: Li

state: OH

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease

institute: CLEVELAND STATE University

data_processing:
Base-calling using NovaSeq 6000 for Illumina sequencing
Raw reads were first processed with Novogene Perl Scripts (removing reads with low quality,  with adapters, and containing poly-N; calculating Q20, Q30 and GC contents).
Clean reads were mapped to T. brucei Lister 427 genome TriTrypDB-45_TbruceiLister427_2018_Genome.fasta and its annotation TriTrypDB-45_TbruceiLister427_2018.gff Idownloaded from the TriTryp DB) using HISAT2.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (1.18.0)

molecule: polyA RNA

organism: Trypanosoma brucei brucei

source_name: culcured cells

growth_protocol: Bloodstream T. brucei cells were cultured in HMI9 medium with 10% FBS. All cells were maintained with medium containing 2 µg/ml G418, 4 µg/ml Hygromycin, and 2 µg/ml of Phleomycin.

extract_protocol:
Total RNA was isolated and purified through RNeasy columns (Qiagen). RNA samples were run on a BioAnalyzer 2100 (Agilent Technologies) using the Agilent RNA 6000 nano kit to verify the RNA quality before sent to Novogene, where RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) using 1 μg poly(A) RNA according to manufacturer’s protocol and index codes were added to attribute sequences to each sample.

treatment_protocol: 100 ng/ml doxycycline (to induce TbPOLIE RNAi) for 30 hrs

tag: strain

value: lister 427

tag: genotype/variation

value: TbPOLIE+Myc/+ RNAi

value: TbPOLIE-myc (endogenous tagging)

value: +doxycycline


title: WholeBlood_CRC305D2GENT070307_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT070307 on day 7


title: MMBC020009CAC

tag: patient diagnosis

tag: tissue compartment


title: TbPOLIE RNAi induced (+D) rep 1


title: WholeBlood_CRC305D2GENT079714_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT079714 on day 7


title: WholeBlood_CRC305D2GENT175416_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT175416 on day 7


title: WholeBlood_CRC305D2GENT044706_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT044706 on day 28


title: blood_369 [SampleGSM5058787]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

tag: mastitis

tag: metritis

tag: milk fever

tag: farm

value: D

tag: Sex


title: WholeBlood_CRC305D2GENT106510_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT106510 on day 7

tag: tissue

value: whole blood

tag: protocol

tag: treatment


title: TbPOLIE RNAi uninduced (-D) rep 2

value: -doxycycline


title: WholeBlood_CRC305D2GENT157309_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT157309 on day 7

tag: day

tag: participant

tag: gender

value: white

value: not hispanic or latino


title: blood_370 [SampleGSM5058788]


title: MMBC020008CAC


title: WholeBlood_CRC305D2GENT046502_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT046502 on day 28

value: BOOSTRIX

tag: age

tag: race

tag: ethnicity


title: MMBC020007CAC


title: blood_368 [SampleGSM5058786]

value: female


title: blood_367 [SampleGSM5058785]


title: WholeBlood_CRC305D2GENT120415_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT120415 on day 7

value: male

tag: recent boostrix


title: blood_366 [SampleGSM5058784]


title: MMBC020006CAC

value: plasma

tag: patient diagnosis


title: WholeBlood_CRC305D2GENT060113_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT060113 on day 28


title: AvL1-RNA-Rep1

city: Woods Hole

first: Irina

last: Arkhipova

state: MA

address: 7 MBL St

department: Josephine Bay Paul Center

institute: Marine Biological Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (cutadapt v1.9.2), and masked for short sequences (<15nt) or low-quality scores (<20), then mapped to reference genome using TopHat v2.1.1, with default parameters and --max-intron-length 100
Prediction of protein-coding genes in AvL1 strain: BRAKER, a combination of GeneMark-ET and AUGUSTUS, was used to predict protein-coding genes in the AvL1 genome using aligned RNA-Seq data. TopHat aligments were used to generate UTR training examples for AUGUSTUS to train UTR parameters and predict genes. This procedure was done with --softmasking enabled, after masking the genome with RepeatMasker. Total predictions comprised 74,569 gene models, saved as fasta and GFF-format.
Prediction of protein-coding genes in Av reference genome (MBL) was taken from Flot et al. Nature 2013.
Aligned sequence reads were counted by genomic feature with HTSeq-count, using Tophat RNA-seq alignment output bam file and gene annotation gff file.
Supplementary_files_format_and_content: read counts

organism: Adineta vaga

source_name: whole animal

extract_protocol:
RNA was harvested using Trizol reagent. PolyA selection.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: whole animal


title: WholeBlood_CRC305D2GENT078509_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT078509 on day 7


title: MMBC020005CAC

tag: tissue compartment

value: cell-free DNA


title: Av-RNA-Rep3

value: MBL


title: blood_365 [SampleGSM5058783]

tag: mastitis

tag: metritis


title: MMBC020004CAC

value: esophageal cancer


title: WholeBlood_CRC305D2GENT111215_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT111215 on day 7


title: MMBC020003CAC


title: Av-RNA-Rep2


title: WholeBlood_CRC305D2GENT131313_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT131313 on day 7


title: WholeBlood_CRC305D2GENT035407_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT035407 on day 28


title: Av-RNA-Rep1


title: AvL1-RNA-Rep2


title: MMBC020002CAC


title: blood_363 [SampleGSM5058781]

tag: milk fever

tag: farm


title: Av input DNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence (cutadapt v1.9.2), and masked for short sequences (<15nt) or low-quality scores (<20), then mapped to reference genome using Bowtie2, with default parameters
Aligned sequence reads processed with MACS2 using default parameters
Supplementary_files_format_and_content: bed files with called peaks

extract_protocol:
Lysates were sonicated (Covaris S220) and inmunoprecipitated with antibody.
DNA was prepared using NEBNext Ultra II DNA Library Prep Kit (NEB)

tag: tissue

tag: chip antibody


title: blood_361 [SampleGSM5058779]

tag: Sex


title: blood_362 [SampleGSM5058780]


title: MMBC010014CAC

value: colon cancer


title: MMBC020001CAC


title: blood_360 [SampleGSM5058778]


title: WholeBlood_CRC305D2GENT099713_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT099713 on day 7

tag: protocol

tag: treatment

tag: day


title: H3K9me3_ChIP-seq_Av

value: H3K9me3 (Diagenode Cat. #15410056)


title: MMBC010013CAC


title: blood_359 [SampleGSM5058777]


title: H3K4me3_ChIP-seq_Av

value: H3K4me3 (Diagenode Cat. #15410003)


title: H3K27me3_ChIP-seq_Av

value: H3K27me3 (Diagenode Cat. #15410195)


title: AvL1 input DNA


title: MMBC010012CAC


title: WholeBlood_CRC305D2GENT036705_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT036705 on day 28

tag: participant

tag: gender

tag: age


title: WholeBlood_CRC305D2GENT073508_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT073508 on day 7

tag: race

tag: ethnicity

tag: recent boostrix


title: WholeBlood_CRC305D2GENT067112_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT067112 on day 28


title: MMBC010011CAC

tag: patient diagnosis

tag: tissue compartment


title: WholeBlood_CRC305D2GENT082306_Day7

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT082306 on day 7


title: WholeBlood_CRC305D2GENT112214_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT112214 on day 7


title: WholeBlood_CRC305D2GENT159414_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT159414 on day 7


title: H3K27me3_ChIP-seq_AvL1

tag: strain


title: blood_364 [SampleGSM5058782]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

tag: mastitis

tag: metritis

tag: milk fever

value: D


title: MMBC010010CAC

tag: tissue


title: blood_356 [SampleGSM5058774]

tag: farm

tag: Sex


title: MMBC010009CAC


title: blood_355 [SampleGSM5058773]


title: H3K4me3_ChIP-seq_AvL1

tag: chip antibody


title: H3K9me3_ChIP-seq_AvL1


title: MMBC010008CAC


title: blood_354 [SampleGSM5058772]


title: NGSB71

city: Tao-Yuan

first: Ian Yi-Feng

last: Chang

state: Type below ...

address: 259 Wen-Hwa 1st Road, Kwei-Shan

department: Molecular Medicine Research Center

country: Taiwan

institute: CHANG GUNG UNIVERSITY

data_processing:
Raw fastq data were submitted to irweb.irepertoire.com for data analysis.
1) separate reads based on barcode (5'-NNN-BARCODE(6bp)-READS-3') in Read 1 (de-multiplex-script.zip provided by irpertoire.com)
2) map reads to TRA/TRB VDJ sequences
3) assign TRA/TRB reads to correct patients
Genome_build: N/A
Supplementary_files_format_and_content: Text file in comma-separated values (csv) format. The identified sequence and frequencies of TCRA or TCRB sequences. The patient ID are included in the file names.

source_name: Peripheral Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated following the standard procedure, and total RNA from PBMCs was extracted using TRIzol reagent
A multiplex PCR amplification reaction was used to amplify the TCR immune repertoire. Human TCRα and TCRβ libraries were prepared using the HTAI-M and HTBI-M Kits (iRepertoire, Inc.) according to the manufacturer’s instructions and sequenced on the Illumina MiSeq platform.
Equal concentrations of each library with different barcodes were pooled and sequenced using the Illumina Paired-End Sequencing Kit (MiSeq, Illumina).

tag: disease

value: healthy

tag: tcra

tag: tcrb

tag: run

value: blood


title: MMBC010007CAC


title: blood_353 [SampleGSM5058771]


title: WholeBlood_CRC305D2GENT063607_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT063607 on day 28

value: whole blood

tag: protocol

tag: treatment

tag: day

tag: participant

tag: gender

tag: age

tag: race

value: white


title: NGSB69


title: WholeBlood_CRC305D2GENT105712_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT105712 on day 7

value: BOOSTRIX

tag: ethnicity

value: not hispanic or latino

tag: recent boostrix


title: WholeBlood_CRC305D2GENT075111_Day28

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT075111 on day 28

tag: tissue

value: male


title: blood_352 [SampleGSM5058770]

tag: mastitis

tag: metritis

tag: milk fever

tag: farm

value: female


title: WholeBlood_CRC305D2GENT059507_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT059507 on day 7


title: WholeBlood_CRC305D2GENT045406_Day28

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT045406 on day 28


title: WholeBlood_CRC305D2GENT098213_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT098213 on day 7


title: blood_351 [SampleGSM5058769]

tag: Sex


title: blood_358 [SampleGSM5058776]


title: MMBC010003CAC

value: plasma

tag: patient diagnosis

tag: tissue compartment


title: blood_357 [SampleGSM5058775]


title: MMBC010006CAC

value: cell-free DNA


title: WholeBlood_CRC305D2GENT166413_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT166413 on day 7

tag: protocol


title: MMBC010004CAC


title: MMBC010005CAC


title: WholeBlood_CRC305D2GENT109116_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT109116 on day 7

tag: treatment


title: blood_350 [SampleGSM5058768]


title: NGSB68

tag: disease

tag: tcra

tag: tcrb

tag: run


title: WholeBlood_CRC305D2GENT092606_Day28

description: Whole blood gene expression of PLACEBOD2 treated participant CRC305D2GENT092606 on day 28

tag: day

tag: participant

tag: gender

tag: age

tag: race


title: NGSB67

tag: tissue


title: NGSB66


title: NGSB52


title: blood_349 [SampleGSM5058767]

tag: mastitis

tag: metritis

tag: milk fever


title: blood_348 [SampleGSM5058766]

tag: farm

tag: Sex


title: MMBC010001CAC

tag: patient diagnosis

tag: tissue compartment


title: blood_347 [SampleGSM5058765]


title: 3ECKO

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina high-throughput sequencing results initially exist as Raw image Data files and are transformed bybcl2fastq software into Sequenced Reads, which are called Raw Data or Raw Reads
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count and RPKM values for each Sample

source_name: Brain endothelial cell

extract_protocol:
Collect total RNA with Trizol reagent and 2ug of total RNA was used to construct  sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

tag: strain

tag: developmental stage

tag: genotype


title: blood_346 [SampleGSM5058764]


title: NGSB46

tag: disease

tag: tcra

tag: tcrb

tag: run


title: WholeBlood_CRC305D2GENT061711_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT061711 on day 7

tag: protocol

tag: treatment

tag: day

tag: participant

tag: gender

tag: age

tag: ethnicity

tag: recent boostrix


title: WholeBlood_CRC305D2GENT077110_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT077110 on day 28

tag: tissue

tag: race


title: MMBC010002CAC

tag: patient diagnosis

tag: tissue compartment


title: NGSA74

tag: Sex


title: blood_344 [SampleGSM5058762]

tag: mastitis

tag: metritis

tag: milk fever

tag: farm


title: WholeBlood_CRC305D2GENT097506_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT097506 on day 7

tag: protocol


title: NGSB41

tag: disease

tag: tcra

tag: tcrb

tag: run


title: WholeBlood_CRC305D2GENT091212_Day7

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT091212 on day 7

tag: treatment

tag: day

tag: participant

tag: gender

tag: age


title: WholeBlood_CRC305D2GENT034305_Day28

description: Whole blood gene expression of BOOSTRIX treated participant CRC305D2GENT034305 on day 28

tag: tissue

tag: race

tag: ethnicity

tag: recent boostrix


title: P6wDay1

city: Tianjin

first: Linlin

last: Liu

address: Weijin Road 97

institute: Nankai university

description:
P6wDay_FRAL20H000344-1a
processed data file: tmp_why_1029

data_processing:
trim-galore to get clean raw reads
FastQC to evaluate the quality of the clean data
Hisat2(version, 2-2.1.0,parameters:-p 20 -x mm10 -1 fq1 -2 fq2 -S  sample.sam  ) to align genome
Using samtools to convert sam files to bam files
featurecounts to get raw counts and RSEM to get FPKM files
Genome_build: mm10
Supplementary_files_format_and_content: csv

source_name: P6w PGCs

extract_protocol:
Cells were harvested and total RNA extracted using RNeasy Mini kit (Qiagen), according to the manufacturers’ instruction, including a DNAse digestion. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system and the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform.

tag: cell type

value: Separated from day1 aggregates(P6w)

tag: strain

tag: experiment type

value: bulk RNA-seq


title: NGSB62

tag: Sex


title: NGSA68

tag: disease


title: blood_341 [SampleGSM5058759]

tag: mastitis

tag: metritis

tag: milk fever

tag: farm


title: MEF_2

description:
MEFDay_FRAL20H000343-2a
processed data file: tmp_why_1029

value: Separated from day1 aggregates(MEF)


title: 4WT

tag: developmental stage

tag: genotype


title: Plantaris

city: Kumamoto

first: Shin

last: Fujimaki

address: Honjo 2-2-1

department: IMEG

country: Japan

institute: Kumamoto University

data_processing:
The raw fastq files were processed using the CellRanger 6.0.1 (10X Genomics) and mapped to a mouse reference dataset (gex-mm10-2020-A).
For alignment and creating the barcode matrices, the command “cellranger count” was run with default parameters, except for adding the include-intron option for counting intronic reads.
Two individual data for single nuclei isolated from GAS and PLA were integrated by running the command “cellranger aggr” without normalization.
The expression of transcripts was analyzed using the Loupe Browser (10X Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files including sample-ID associated with the library and raw read counts in each nucleus.

source_name: Plantaris muscle

extract_protocol:
Gastrocnemius and plantaris muscles were collected and thoroughly minced into small pieces. Miced muscles were homogenized using bead crasher and filtered  to remove the debris. Nuclei were labelled with PI and purified by sorting followed by loading on 10X Chromium.
All libraries were prepared by the 10X Chromium system using the Chromium NextGEM Single Cell 3' Kit v3.1 according to the manufacturer’s protocol. RNA-seq was commercially commisioned to Macrogen Japan.

value: 12 weeks

value: Plantaris muscle


title: blood_345 [SampleGSM5058763]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)


title: NGSB32

tag: tcra

tag: tcrb

tag: run


title: Gastrocnemius

source_name: Gastrocnemius muscle

tag: age

tag: tissue

value: Gastrocnemius muscle


title: Sample 13_Parabiosis lung macrophages_donor_25wks

source_name: Lung macrophages

value: Lung

value: CD45.1 & CD45.2 pooled

value: 32 weeks

tag: treatment

value: Mice paired at 7 weeks for a 25 week time period


title: MMBC020013CAC

tag: patient diagnosis

value: esophageal cancer

tag: tissue compartment


title: Sample 12_Parabiosis lung macrophages_host_25wks

tag: strain


title: TbPOLIE RNAi uninduced (-D) rep 1

value: lister 427

tag: genotype/variation

value: TbPOLIE+Myc/+ RNAi

value: TbPOLIE-myc (endogenous tagging)

value: -doxycycline


title: NGSA51

tag: disease

value: healthy

tag: Sex

value: female

value: blood


title: Sample 11_Parabiosis lung macrophages_donor_5wks

value: Mice paired at 7 weeks for a 5 week time period


title: blood_338 [SampleGSM5058756]

tag: mastitis

tag: metritis

value: E


title: Sample 9_Parabiosis heart macrophages_donor_25wks

source_name: Heart macrophages

value: Heart


title: blood_342 [SampleGSM5058760]

tag: milk fever

tag: farm

value: D


title: NGSA57

value: male


title: Sample 10_Parabiosis lung macrophages_host_5wks

value: Lung

tag: genotype

value: 12 weeks


title: MEF_1

description:
MEFDay_FRAL20H000343-1a
processed data file: tmp_why_1029

tag: cell type

value: Separated from day1 aggregates(MEF)

tag: experiment type

value: bulk RNA-seq


title: NGSA49

tag: tcra

tag: tcrb

tag: run


title: NGSA81

tag: age

tag: tissue


title: P6wDay

description:
P6wDay_FRAL20H000344-2a
processed data file: tmp_why_1029

value: Separated from day1 aggregates(P6w)


title: blood_340 [SampleGSM5058758]


title: CD63_2

description:
CD63D_FRAL20H000342-2a
processed data file: tmp_why_1029

value: Separated from day1 aggregates(Cd63+)


title: Sample 8_Parabiosis heart macrophages_host_25wks

value: CD45.1 & CD45.2 pooled

value: 32 weeks

tag: treatment

value: Mice paired at 7 weeks for a 25 week time period


title: Gonad_2

description:
GonadDay11_FRAL202386995-1a
processed data file: tmp_why_1029

value: Separated from day1 aggregates(Gonad)

tag: strain


title: blood_343 [SampleGSM5058761]

value: female


title: Sample 6_Parabiosis heart macrophages_host_5wks


title: blood_339 [SampleGSM5058757]


title: CD63_1

description:
CD63D_FRAL20H000342-1a
processed data file: tmp_why_1029


title: Sample 5_Mouse brain macrophages

source_name: Brain macrophages

value: Brain

value: 20 weeks

value: Pulsed with tamoxifen at P21


title: Sample 7_Parabiosis heart macrophages_donor_5wks

value: Heart

value: Mice paired at 7 weeks for a 5 week time period


title: NGSA46

value: healthy

value: blood


title: Gonad_1

description:
GonadD12_FRAL202386996-1a
processed data file: tmp_why_1029


title: NGSA16


title: blood_337 [SampleGSM5058755]

value: E


title: NGSA37

value: male


title: NGSA31


title: Sample 4_Mouse kidney macrophages

source_name: Kidney macrophages

value: Kidney


title: E13.5_2

description:
E13-5-1-2_L5_I353
processed data file: counts_why_2.csv

source_name: E13.5 gonadal somatic cells

value: Separated from E13.5 female gonads

value: bulk RNA-seq


title: blood_335 [SampleGSM5058753]

source_name: blood from coccygeal vein in the tail


title: Sample 3_Mouse lung macrophages

value: Lung


title: E13.5_1

description:
E13-5-1-2_L5_I352
processed data file: counts_why_2.csv


title: CRC01706

value: colon cancer


title: Sample 2_Mouse liver macrophages

source_name: Liver macrophages

value: Liver


title: blood_333 [SampleGSM5058751]


title: blood_334 [SampleGSM5058752]


title: Sample 1_Mouse heart macrophages


title: blood_332 [SampleGSM5058750]


title: blood_336 [SampleGSM5058754]


title: CRC01704


title: E12.5_2

description:
E12-5-1-2_L5_I351
processed data file: counts_why_2.csv

source_name: E12.5 gonadal somatic cells

value: Separated from E12.5 female gonads


title: blood_331 [SampleGSM5058749]

value: female


title: CRC01703


title: P6w_2

description:
P6w-2_L1_I359
processed data file: counts_why_2.csv

source_name: P6w ovary somatic cells

value: Separated from P6w ovary


title: E12.5_1

description:
E12-5-1-2_L5_I350
processed data file: counts_why_2.csv


title: P6w_1

description:
P6w-1_L1_I358
processed data file: counts_why_2.csv


title: blood_330 [SampleGSM5058748]


title: CRC01705


title: KO NCX rep4

city: Boston

first: Hye Ji

last: Cha

address: 1 Blackfan Circle

institute: Boston Children’s Hospital

data_processing:
Single-end 100bp reads were generated using Illumina HiSeq 2500 sequencing platform.
Sequencing reads were mapped to the mm10 mouse reference genome using STAR (v2.5.4a).
Raw counts were produced using Htseq.
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: APP/APLP1/APLP2 -/-_Neocortex

extract_protocol:
Total RNA was extracted from the neocortex and hippocampus, separately, using RNeasy Plus Universal Kit or RNeasy Plus Mini kit (Qiagen), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Neocortex

value: APP/APLP1/APLP2 -/-

value: 3 months


title: CRC01702


title: KO NCX rep3


title: KO NCX rep2


title: CRC01701


title: blood_328 [SampleGSM5058746]


title: CRC01608


title: KO NCX rep1


title: V580_D8_3

description:
V580D83
processed data file: index_fpkm_all_mef

source_name: GSCLCs induced from ESCs

value: derived from ESCs


title: blood_327 [SampleGSM5058745]


title: WT NCX rep5

source_name: wild type_Neocortex

value: wild type


title: V580_D8_2

description:
V580D82
processed data file: index_fpkm_all_mef


title: blood_326 [SampleGSM5058744]


title: CRC01607

source_name: Peripheral Blood

value: blood


title: V580_D8_1

description:
V580D81
processed data file: index_fpkm_all_mef


title: blood_325 [SampleGSM5058743]

value: E


title: WT NCX rep4


title: CRC01605

value: male


title: WT NCX rep3


title: V580_D6_3

description:
V580D63
processed data file: index_fpkm_all_mef


title: CRC01604


title: WT NCX rep2


title: KO NCX rep5


title: blood_324 [SampleGSM5058742]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)


title: CRC01606


title: blood_323 [SampleGSM5058741]


title: V580_D6_2

description:
V580D62
processed data file: index_fpkm_all_mef


title: CRC01603


title: V580_D6_1

description:
V580D61
processed data file: index_fpkm_all_mef


title: E16.5_2

description:
E16-5-2_L1_I355
processed data file: counts_why_2.csv

source_name: E16.5 gonadal somatic cells

value: Separated from E16.5 female gonads


title: blood_329 [SampleGSM5058747]


title: E16.5_1

description:
E16-5-1_L5_I354
processed data file: counts_why_2.csv


title: WT NCX rep1


title: blood_322 [SampleGSM5058740]


title: CRC01602


title: KO HP rep5

source_name: APP/APLP1/APLP2 -/-_Hippocampus

value: Hippocampus


title: blood_321 [SampleGSM5058739]


title: V580_D4_3

description:
V580D43
processed data file: index_fpkm_all_mef

value: bulk RNA-seq


title: V580_D4_2

description:
V580D42
processed data file: index_fpkm_all_mef


title: blood_320 [SampleGSM5058738]


title: CRC01601


title: KO HP rep4


title: CRC01509


title: blood_319 [SampleGSM5058737]


title: V580_D4_1

description:
V580D41
processed data file: index_fpkm_all_mef


title: V580_D10_3

description:
V580D103
processed data file: index_fpkm_all_mef


title: CRC01508


title: blood_318 [SampleGSM5058736]


title: CRC01507


title: V580_D10_2

description:
V580D102
processed data file: index_fpkm_all_mef


title: V580_D10_1

description:
V580D101
processed data file: index_fpkm_all_mef


title: KO HP rep1


title: CRC01506


title: blood_316 [SampleGSM5058734]


title: blood_317 [SampleGSM5058735]


title: WT HP rep5

source_name: wild type_Hippocampus


title: CRC01505


title: WT HP rep4


title: blood_315 [SampleGSM5058733]


title: CRC01504


title: V580_48h_1

description:
V580_481
processed data file: index_fpkm_all_mef


title: WT HP rep3


title: V580_48h_2

description:
V580_482
processed data file: index_fpkm_all_mef


title: blood_314 [SampleGSM5058732]


title: WT HP rep2


title: V580_24h_2

description:
V580_242
processed data file: index_fpkm_all_mef


title: KO HP rep3


title: V580_24h_1

description:
V580_241
processed data file: index_fpkm_all_mef


title: CRC01502


title: blood_312 [SampleGSM5058730]

value: A


title: CRC01501

value: colon cancer


title: KO HP rep2


title: NSP-844

city: Durham

first: Benjamin

last: Alman

state: NC

address: Levine Science Research Center,308 Research Drive

institute: Duke university

description:
SP_NSP_SP-844_NSP-844.genes.tsv
SP_NSP_SP-844_NSP-844.matrix.mtx
SP_NSP_SP-844_NSP-844.barcodes.tsv
barcodes.tsv and its four samples:  barcode-1 SP844, barcode-2 NSP844, barcode-4 SP, barcode-5 NSP (barcode-3 does not correspond to any sample in this study).

data_processing:
Cell Ranger v3 cellranger mkfastq  was first used to demultiplex cellular barcodes to produce raw 3’ end read profiles for individual cells
cellranger count was then used to performed alignment, filtering, barcode counting, and UMI (unique molecular identifier) counting, producing a feature-barcode matrix per sample
Genome_build: mm10
Supplementary_files_format_and_content: tar.gz file including barcodes.tsv, genes.tsv, matrix.mtx generated by cellranger for all samples

source_name: Primary mouse UPS cellls

growth_protocol: Tumors from autochthonous mouse model UPS driven by oncogenic KrasG12D and homozygous p53 deletions are digested into single cells and sorted for the SP and NSP populations using flow cytometry.  Cells isolated by flow-cytometry activated cell sorting (FACS).

extract_protocol:
RNA preparation was performed using 10x Genomics kit following manufacture's instruction (Cat #PN-1000077)
Libraries were prepared according to instructions from 10x Genomics and Illumina
Single-cell RNA sequencing

treatment_protocol: No treatment

value: mixed

tag: disease state

value: mouse model of undifferentiated pleomorphic sarcoma (UPS)

tag: cell population

value: NSP

value: No treatment


title: SP-844

value: SP


title: blood_311 [SampleGSM5058729]

tag: Sex

value: female


title: E12.5_GC_3

description:
E12_5GC3
processed data file: index_fpkm_all_mef

source_name: Separated from E12.5 female gonads

value: Separated from  mice


title: CRC01305

tag: disease


title: blood_310 [SampleGSM5058728]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

tag: mastitis

tag: metritis


title: E12.5_GC_2

description:
E12_5GC2
processed data file: index_fpkm_all_mef


title: CRC01304


title: 840-SP

description:
840-SP.features.tsv
840-SP.matrix.mtx
840-SP.barcodes.tsv


title: CRC01303


title: 840-NSP

description:
840-NSP.features.tsv
840-NSP.matrix.mtx
840-NSP.barcodes.tsv


title: E12.5_GC_1

description:
E12_5GC1
processed data file: index_fpkm_all_mef


title: blood_308 [SampleGSM5058726]

tag: milk fever

tag: farm


title: Con_48h_2

description:
Con_482
processed data file: index_fpkm_all_mef

tag: cell type

value: derived from ESCs


title: NSP


title: Con_48h_1

description:
Con_481
processed data file: index_fpkm_all_mef

tag: experiment type


title: CRC01503

tag: tcra


title: CRC01302

tag: tcrb


title: blood_307 [SampleGSM5058725]


title: blood_313 [SampleGSM5058731]


title: Con_24h_2

description:
Con_242
processed data file: index_fpkm_all_mef


title: WT HP rep1

tag: genotype

value: wild type

value: 3 months


title: blood_306 [SampleGSM5058724]


title: CRC01204

tag: age

tag: run

value: blood


title: blood_305 [SampleGSM5058723]


title: blood_309 [SampleGSM5058727]


title: Vc_48h_1

description:
C_481
processed data file: index_fpkm_all_mef


title: Con_24h_1

description:
Con_241
processed data file: index_fpkm_all_mef


title: Vc_48h_2

description:
C_482
processed data file: index_fpkm_all_mef


title: blood_304 [SampleGSM5058722]


title: blood_303 [SampleGSM5058721]


title: blood_302 [SampleGSM5058720]


title: blood_301 [SampleGSM5058719]


title: CRC01301

value: male

tag: tissue


title: CRC01202


title: AM580_48h_2

description:
A580_482
processed data file: index_fpkm_all_mef

tag: strain


title: blood_300 [SampleGSM5058718]


title: CRC01107


title: CRC01203


title: Vc_24h_1

description:
C_241
processed data file: index_fpkm_all_mef


title: CRC01201


title: Vc_24h_2

description:
C_242
processed data file: index_fpkm_all_mef


title: AM580_48h_1

description:
A580_481
processed data file: index_fpkm_all_mef


title: CRC01106


title: blood_299 [SampleGSM5058717]


title: SP

description:
SP_NSP_SP-844_NSP-844.genes.tsv
SP_NSP_SP-844_NSP-844.matrix.mtx
SP_NSP_SP-844_NSP-844.barcodes.tsv
barcodes.tsv and its four samples:  barcode-1 SP844, barcode-2 NSP844, barcode-4 SP, barcode-5 NSP (barcode-3 does not correspond to any sample in this study).

tag: disease state

tag: treatment


title: CRC01104

tag: Sex


title: CRC01105

tag: disease


title: blood_298 [SampleGSM5058716]

tag: mastitis


title: AM580_24h_1

description:
A580_241
processed data file: index_fpkm_all_mef


title: AM580_24h_2

description:
A580_242
processed data file: index_fpkm_all_mef


title: CRC01103


title: blood_297 [SampleGSM5058715]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

tag: metritis


title: sgRNAseq of CRISPR TF transduced ESCs on day 12 post-transduction

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description:
genome-integrated sgRNAs
Day12_CRISPR_TF_transduced_cells

data_processing:
Library strategy: sgRNA-seq
Sequences flanking the 20 nucleotide sgRNA sequence were trimmed using cutadapt.
Remaining 20 nucleotide sgRNA sequence reads were aligned to a library index generated by 17820 sgRNA sequences using bowtie.
Genome_build: mm10
Supplementary_files_format_and_content: TXT: tab-delimited text file containing output of featurecounts for Refseq genes.

source_name: Embryonic stem cells

growth_protocol: 3 x 10^6 ESC cells were distributed to 5 12-well dishes (Thermo Scientific) with 5 x 10^5 mESC cells per well. 4 h after cells were plated, the media was replaced with 8 µL of 100x concentrated library lentivirus mixed in 1 mL ESC medium with 1x polybrene (EMD Millipore). 16 h later, the virus solution was removed, cells were washed 1 time with PBS1X, and cells were split 1:2 to 10 12-well plates.

extract_protocol:
In a 15 ml conical tube, we added 6 ml of NK Lysis Buffer (50 mM Tris (Boston BioProducts), 50 mM EDTA (Ambion), 1% SDS (Invitrogen), pH 8), and 30 μl of 20 mg/ml Proteinase K (Qiagen) to 9 million cells (>500 coverage) and incubated at 55°C overnight. 30 μl of 10 mg/ml RNAse A (Qiagen, diluted in NK Lysis Buffer to 10 mg/ml and then stored at 4 °C) was added to the lysed sample, which was then inverted 25 times and incubated at 37°C for 30 minutes. Samples were cooled on ice before the addition of 2 ml of pre-chilled 7.5M ammonium acetate (Sigma) to precipitate proteins. After adding ammonium acetate, the samples were vortexed at high speed for 20 seconds and then centrifuged at ≥ 4,000 x g for 10 minutes. After the spin, a tight pellet was visible in each tube and the supernatant was carefully decanted into a new 15 ml conical tube. 6 ml 100% isopropanol was added to the tube, inverted 50 times and centrifuged at ≥4,000 x g for 10 minutes. Genomic DNA was visible as a small white pellet in each tube. The supernatant was discarded, 6 ml of freshly prepared ice-cold 70% ethanol was added, the tube was inverted 10 times, and then centrifuged at ≥4,000 x g for 1 minute. The supernatant was discarded by pouring; the tube was briefly spun, and the remaining ethanol was removed using a P200 pipette. After air-drying for 10-30 minutes, the DNA changed appearance from a milky white pellet to slightly translucent. At this stage, 500 μl of 1x TE buffer (Sigma) was added, the tube was incubated at 65°C for 1 hour and at room temperature overnight to fully resuspend the DNA. The next day, the gDNA samples were vortexed briefly. The gDNA concentration was measured using a Nanodrop (Thermo Scientific).
5 PCR1 reactions were used for 52 µg of DNA for >500x coverage. Per PCR tube, 10.4 µg of genomic DNA was used in 100 µL volume with 0.4 µL Taq-B Polymerase (Enzymatics), 10X Taq buffer (Enzymatics), 10 mM dNTPs (NEB), 10 µM Fwd (5’ GAGGGCCTATTTCCCATGATTC) and Rvs (5’ GTTGCGAAAAAGAACGTTCACGG) using the following PCR protocol: Denaturation 94 °C for 30s, 25 cycles of 94 °C for 10s, 55 °C for 30s, 68 °C for 45s, final elongation 68 °C for 2 min. For the addition of Illumina barcodes, 5 staggered forward primers and 1 reverse primer with specific barcodes containing Illumina adaptors were mixed to obtain 10 µM primer mix. 2 PCR2 reactions were used per timepoint with 5 µL of PCR1 product amplified with 25 µL Q5 High Fidelity 2X Master Mix (NEB), 5 µL of 10 µM primer mix in 50 µL volume using the following PCR protocol: Denaturation 98 °C for 30s, 10 cycles of 98 °C for 10s, 65 °C for 30s, 72 °C for 45s, final elongation 72 °C for 5 min. All samples were pooled in equimolar ratio and PCR purified pooled sample with QIAquick PCR Purification Kit (Qiagen). The purified sample was then run on a 2% E-Gel and the correct size band was extracted for PCR2 (250-270 bp) and purified with QIAquick Gel Extraction Kit (Qiagen). The pooled library was then quantified with a Low-Range Quantitative ladder on 2% E-Gel. Libraries were then sequenced on Illumina MiSeq v3 for 150 cycles single end at the genomics core facility at NYU.

treatment_protocol: 50 ng/µL Zeocin (Invivogen) was added to each well 24h later and transduced cells were maintained with Zeocin selection. To maintain 50-70% confluency throughout the screen, cells were transferred to 6-well plates (Thermo Fisher) on day 2 and selected for 3 additional days for a total of 5 days of selection. The first time point was obtained on day 5 post-selection. The second and third timepoints were taken on day 8 and day 12 while growing in ESC medium containing 50 ng/µL Zeocin.

value: Ainv15(iNgn2 Tubb3::GFP)

value: Embryonic stem cells


title: sgRNAseq of CRISPR TF transduced ESCs on day 8 post-transduction

description:
genome-integrated sgRNAs
Day8_CRISPR_TF_transduced_cells


title: CRC01102


title: sgRNAseq of CRISPR TF transduced ESCs on day 5 post-transduction

description:
genome-integrated sgRNAs
Day5_CRISPR_TF_transduced_cells


title: blood_296 [SampleGSM5058714]

tag: milk fever


title: V580_D6_single_cell

description:
V580-D6-10XSC3_S130
processed data file: sample.count

value: 10x single cell RNA-seq


title: Intermediate progenitors - full_length_Notch_Rep2

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

institute: The Gurdon Institute

description:
pTa1_NotchFL_unlog.bedgraph
pTa1_NotchFL_unlog.bedgraph.bw

data_processing:
Library strategy: DamID-seq
Fastq-files were processed with the damidseq_pipeline (Marshall and Brand, Bioinformatics, 2015), with bins=300, RPM normalization and otherwise default parameters.
For transcripton factor data, each Dam-fusion sample was normalized to each Dam-only sample from the same cell-type, resulting in a matrix of n1 Dam-fusion x n2 Dam-only. All normalizations were then averaged and backtransformed ("unlog") to generate a final average .bedgraph file.
For chromatin accessibility data, Dam-only files from a each experimental condition were averaged and provided as .bedgraph files.
Peaks were called using MACS2 (broad peaks), and only peaks present in all replicates at FDR<10^-5 were considered.
Peaks from all samples were merged and then k-means clustered to generate pHespTa1_NotchRbpj_clus8_FDR5.allPeak.bed
Genome_build: mm10
Supplementary_files_format_and_content: .bedgraph files are tracks at gatc-fragment resolution, of averaged transcription factor or chromatin accessibility DamID. Scores represent normalised fold enrichment of transcription factor DamID vs Dam-only; for chromatin accessibility scores represent read density.
Supplementary_files_format_and_content: .bw files are browser-readable versions of the .bedgraph files
Supplementary_files_format_and_content: .bed files contain peak coordinates

source_name: Intermediate progenitors E13-14

extract_protocol:
After dissection of electroporated cortex, gDNA was extracted using the QiAmp DNA Micro kit. The gDNA was digested with DpnI, adaptors were ligated and then digested with DpnII and amplified by PCR (Marshall et al, Nat Protoc, 2016).
After gDNA extraction and DamID, DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed with AlwI digestion. Sonicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified (see Marshall et al., Nat Protoc, 2016).

value: mouse embryonic cortex

tag: stage of electroporation-dissection

tag: dam-fusion protein

value: mouse full-length Notch

value: IPC


title: sgRNAseq of Maxiprep of CRISPR TF library replicate 2

description:
genome-integrated sgRNAs
Maxiprep_CRISPR_TF_library_rep2

tag: cell type


title: blood_295 [SampleGSM5058713]

data_processing:
The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.

tag: farm

value: A


title: LV14_GFP_MOI0.2_72h_2

city: Seville

first: Anabel

last: Rojas

state: Seville

address: Avda. Américo Vespucio

department: Stem Cell

country: Spain

institute: CABIMER

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Gene 2.0 ST Array of Affymetrix

scan_protocol: GeneChips were scanned using the Scanner 3000 7G of Affymetrix

data_processing: The data were analyzed with Affimetrix GeneChip® Human Gene 2.0ST Array. Differentially expressed genes were defined as those for which the nominal P was 0.05

label: biotin

source_name: Hepatic Stellate Cells(LX2) infected with Ad-GFP during 72 hours

label_protocol: Biotinylated cDNA were prepared according to the GeneChip® Human Gene 2.0 ST Array of Affymetrix  protocol

growth_protocol: 2x105 cells were cultured in DMEM supplemented with 10% fetal bovine serum in a 10-cm plate

extract_protocol: Total RNA was isolated using Rneasy Plus Micro Kit following manufacturer instruction.

treatment_protocol: Cells were infected with Adenovirus-hGata4 and Adenovirus-GFP as a control at MOI 100 during  72 hours

tag: cell line

value: Active Hepatic Stellate Cells


title: sgRNAseq of Maxiprep of CRISPR TF library replicate 1

description:
genome-integrated sgRNAs
Maxiprep_CRISPR_TF_library_rep1

tag: genotype

value: No treatment


title: CRC01101

value: colon cancer

tag: age

tag: tcra

tag: tcrb


title: CRC01003

tag: run

tag: tissue


title: LV17_G4_MOI0.2_72h_1

source_name: Hepatic Stellate Cells  (LX2) infected with Ad-G4 during 72 hours


title: LV18_G4_MOI0.2_72h_3

source_name: Hepatic Stellate Cells (LX2) infected with Ad-G4 during 72 hours


title: blood_294 [SampleGSM5058712]

city: Davis

first: Anita

last: Oberbauer

address: One Shields Ave.

institute: University of California, Davis

source_name: blood from coccygeal vein in the tail

value: female


title: LV15_GFP_MOI0.2_72h_3

source_name: Hepatic Stellate Cells (LX2) infected with Ad-GFP during 72 hours


title: Intermediate progenitors - full_length_Notch_Rep1


title: LV16_G4_MOI0.2_72h_1


title: CRC01002


title: LV13_GFP_MOI0.2_72h_1


title: blood_293 [SampleGSM5058711]


title: Radial glia cells - full_length_Notch_Rep3

description:
pHes5_NotchFL_unlog.bedgraph
pHes5_NotchFL_unlog.bedgraph.bw

source_name: Radial glia cells E13-14

value: RGC


title: Radial glia cells - full_length_Notch_Rep4


title: CRC00901


title: CRC01001


title: Radial glia cells - full_length_Notch_Rep2


title: CRC00801


title: Radial glia cells - full_length_Notch_Rep1


title: blood_291 [SampleGSM5058709]


title: PCC6803_WT_24h_rep2

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture, at 4% NaCl for 24h

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis sp. 6803 substrain PCC-M (Trautmann et al., 2012) was used for the experiment. Axenic cells were grown photoautotrophically at 29°C in glass tubes containing liquid BG11 medium (Rippka et al., 1979, TES-buffered at pH 8). If not stated differently, cultures were aerated with CO2-enriched air (5% CO2 [v/v]) and kept under continuous illumination of 150 µmol photons m-2 s-1 (warm light, Osram L58 W32/3).

extract_protocol: Synechocystis 6803 cells were collected by rapid filtration on hydrophilic polyethersulfone filters (Pall Supor 800 Filter, 0.8 µm). Filters covered with cells were dissolved in 1 ml PGTX (Pinto et al., 2009; BMC Mol Biol 10: 79) and RNA was extracted as described (Hein et al., 2013; RNA Biol 10: 852–864).

treatment_protocol: Control cells were cultured in NaCl-free BG11 medium. Short-term salt shock experiments were performed by adding crystalline NaCl to a final concentration of 4% into the suspension of control cultures at time point zero. Subsequently, cells were harvested at defined time points.

value: WT

tag: treatment


title: CRC00705

tag: Sex


title: blood_290 [SampleGSM5058708]


title: blood_289 [SampleGSM5058707]


title: Neurons - Dam-only_Rep3

description:
pND1_floxDam.bedgraph
pND1_floxDam.bedgraph.bw

data_processing:
Fastq-files were processed with the damidseq_pipeline (Marshall and Brand, Bioinformatics, 2015), with bins=300, RPM normalization and otherwise default parameters.
For transcripton factor data, each Dam-fusion sample was normalized to each Dam-only sample from the same cell-type, resulting in a matrix of n1 Dam-fusion x n2 Dam-only. All normalizations were then averaged and backtransformed ("unlog") to generate a final average .bedgraph file.
For chromatin accessibility data, Dam-only files from a each experimental condition were averaged and provided as .bedgraph files.
Peaks were called using MACS2 (broad peaks), and only peaks present in all replicates at FDR<10^-5 were considered.
Peaks from all samples were merged and then k-means clustered to generate pHespTa1_NotchRbpj_clus8_FDR5.allPeak.bed
Genome_build: mm10
Supplementary_files_format_and_content: .bedgraph files are tracks at gatc-fragment resolution, of averaged transcription factor or chromatin accessibility DamID. Scores represent normalised fold enrichment of transcription factor DamID vs Dam-only; for chromatin accessibility scores represent read density.
Supplementary_files_format_and_content: .bw files are browser-readable versions of the .bedgraph files
Supplementary_files_format_and_content: .bed files contain peak coordinates

source_name: Neurons E13-16

extract_protocol:
After dissection of electroporated cortex, gDNA was extracted using the QiAmp DNA Micro kit. The gDNA was digested with DpnI, adaptors were ligated and then digested with DpnII and amplified by PCR (Marshall et al, Nat Protoc, 2016).
After gDNA extraction and DamID, DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed with AlwI digestion. Sonicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified (see Marshall et al., Nat Protoc, 2016).
DamID-seq

value: Dam-only

value: Neurons


title: CRC00703

tag: disease

value: blood


title: blood_292 [SampleGSM5058710]

tag: mastitis


title: PCC6803_WT_24h_rep1

value: cells from liquid culture, at 4% NaCl for 24h


title: CRC00702


title: Neurons - Dam-only_Rep2


title: blood_288 [SampleGSM5058706]

tag: metritis


title: PCC6803_WT_2h_rep1

source_name: cells from liquid culture, at 4% NaCl for 2h