title: 3603_OF2A_5-3-D6-O18

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0507 [D1132]

status: Public on Dec 12 2023

type: RNA

city: Brisbane

first: Hao

last: Zhang

state: CA

address: 3260 Bayshore Blvd

department: Research and Development

country: USA

institute: CareDx, Inc.

hyb_protocol: 150 ng total RNA (in 8 μl) was hybridized to gene-specific probes at 65˚C for 16 hours and then deposited onto glass cartridges using the standard sensitivity” setting on the nCounter® Prep Station (NanoString Technologies, Seattle, WA, USA).  When total RNA yield of one sample was <150 ng, all obtained total RNA from that sample was used as input for hybridization.  Samples with low RNA concentration were vacuum concentrated to reduce the RNA sample volume to 8 μl or less before hybridization.

scan_protocol: The number of barcodes hybridized to specific RNA targets on cartridges were directly counted by the nCounter® Digital Analyzer with high fields of view setting of 280.

data_processing: Normalization of RNA loading was performed using the geometric mean of 12 internal reference genes (housekeeping genes; ABCF1, G6PD, GUSB, NRDE2, OAZ1, POLR2A, PPIA, SDHA, STK11IP, TBC1D10B, TBP, and UBB).

molecule: total RNA

organism: Homo sapiens

source_name: renal biopsy tissue

extract_protocol: Two tissue curls from the FFPE block of each biopsy sample were dissected at 16-μm thickness per curl and stored at -80°C until RNA extraction was performed with either Zymo® Quick-RNA FFPE kits by manual RNA extraction or with Zymo® Quick-RNA MagBead kit and Tecan Fluent Liquid Handler.

tag: histology diganosis of rejection

value: Mixed Rejection

tag: tissue

value: renal biopsy tissue

tag: cohort

value: Discovery cohort sample


title: 3603_OF2A_5-3-D6-P18

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: nuclear RNA + genomic DNA

library_source: transcriptomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM file were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmCT-seq

molecule: nuclear RNA

source_name: OF2A human BA46

extract_protocol: Library prepared following protocol described in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female


title: 3603_OF2A_5-5-D6-C10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0503 [D1082]

value: Antibody-mediated Rejection


title: Discovery_Sample_0499 [D1205]


title: 3603_OF2A_5-3-D6-O6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-N6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0504 [D756]

value: No Rejection


title: Discovery_Sample_0498 [D356]

value: T cell-mediated Rejection


title: 3603_OF2A_5-3-D6-N5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0501 [D338]


title: Discovery_Sample_0500 [D1369]


title: 3603_OF2A_5-3-D6-N18

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0497 [D192]


title: Discovery_Sample_0508 [D325]


title: 3603_OF2A_5-3-D6-N17

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0505 [D242]


title: Discovery_Sample_0496 [D718]


title: Discovery_Sample_0495 [D964]


title: Discovery_Sample_0502 [D936]


title: 3603_OF2A_5-3-D6-M18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-M17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-M6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0493 [D669]


title: 3603_OF2A_5-3-D6-O17

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0492 [D141]


title: Discovery_Sample_0491 [D960]


title: Discovery_Sample_0494 [D1453]


title: 3603_OF2A_5-3-D6-L6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0490 [D1093]


title: 3603_OF2A_5-3-D6-L17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-L5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0487 [D855]


title: 3603_OF2A_5-3-D6-K18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-K6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-K17

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0488 [D400]


title: 3603_OF2A_5-3-D6-M5

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-L18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-K5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0489 [D147]


title: Discovery_Sample_0484 [D1437]


title: Discovery_Sample_0485 [D952]


title: Discovery_Sample_0482 [D1076]


title: 3603_OF2A_5-3-D6-J17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-J6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0483 [D432]


title: 3603_OF2A_5-3-D6-I5

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-J5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0486 [D741]


title: 3603_OF2A_5-3-D6-J18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-I18

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0481 [D200]


title: 3603_OF2A_5-3-D6-I17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-I6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0477 [D332]


title: Discovery_Sample_0480 [D1374]


title: 3603_OF2A_5-3-D6-H18

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0479 [D1001]


title: Discovery_Sample_0478 [D055]


title: Discovery_Sample_0476 [D1024]


title: 3603_OF2A_5-3-D6-H6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-H17

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0474 [D838]


title: 3603_OF2A_5-3-D6-G6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-H5

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-G5

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-G18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-F6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0472 [D907]


title: Discovery_Sample_0470 [D1362]


title: Discovery_Sample_0471 [D1308]


title: Discovery_Sample_0469 [D258]


title: Discovery_Sample_0547 [D1367]


title: 3603_OF2A_5-3-D6-F5

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-G17

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0473 [D451]


title: 3603_OF2A_5-3-D6-F18

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0475 [D1185]


title: Discovery_Sample_0465 [D266]


title: Discovery_Sample_0466 [D288]


title: Discovery_Sample_0467 [D1318]


title: Discovery_Sample_0464 [D770]


title: 3603_OF2A_5-3-D6-F17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-E6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-E5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0463 [D156]


title: 3603_OF2A_5-3-D6-E18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-E17

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0462 [D916]


title: 3603_OF2A_5-3-D6-D6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0458 [D1056]


title: Discovery_Sample_0459 [D1480]


title: Discovery_Sample_0468 [D397]


title: 3603_OF2A_5-3-D6-D5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0460 [D1209]


title: Discovery_Sample_0457 [D260]


title: 3603_OF2A_5-3-D6-D18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-D17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-C6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-C5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0456 [D950]


title: 3603_OF2A_5-3-D6-C18

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0455 [D295]


title: 3603_OF2A_5-3-D6-C17

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0454 [D391]


title: Discovery_Sample_0453 [D892]


title: 3603_OF2A_5-3-D6-B6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0461 [D1291]


title: 3603_OF2A_5-3-D6-B18

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0452 [D440]


title: Discovery_Sample_0451 [D065]


title: Discovery_Sample_0448 [D022]


title: Discovery_Sample_0450 [D1129]


title: Discovery_Sample_0449 [D1022]


title: 3603_OF2A_5-3-D6-A6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0447 [D399]


title: Discovery_Sample_0446 [D977]


title: 3603_OF2A_5-3-D6-A17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-P4

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-A5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0444 [D120]


title: Discovery_Sample_0445 [D717]


title: 3603_OF2A_5-2-D6-P16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-B5

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-3-D6-B17

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0442 [D734]


title: 3603_OF2A_5-2-D6-O16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-P15

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0440 [D759]


title: 3603_OF2A_5-2-D6-O4

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-O15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-N4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0439 [D1065]


title: Discovery_Sample_0438 [D222]


title: Discovery_Sample_0436 [D114]


title: Discovery_Sample_0437 [D922]


title: 3603_OF2A_5-2-D6-N16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-N3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-N15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-M4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0433 [D089]


title: 3603_OF2A_5-2-D6-P3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0443 [D1035]


title: Discovery_Sample_0434 [D1030]


title: 3603_OF2A_5-2-D6-M3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0432 [D616]


title: Discovery_Sample_0441 [D350]


title: 3603_OF2A_5-2-D6-M16

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0430 [D768]


title: Discovery_Sample_0431 [D105]


title: 3603_OF2A_5-2-D6-O3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0429 [D1141]


title: Discovery_Sample_0428 [D464]


title: 3603_OF2A_5-2-D6-M15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-L3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0435 [D181]


title: 3603_OF2A_5-2-D6-L4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0427 [D1109]


title: Discovery_Sample_0425 [D914]


title: Discovery_Sample_0426 [D224]


title: 3603_OF2A_5-2-D6-L16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-K4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0424 [D881]


title: 3603_OF2A_5-2-D6-K3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0422 [D1522]


title: 3603_OF2A_5-2-D6-K16

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0421 [D619]


title: 3603_OF2A_5-2-D6-K15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-J16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-J3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-J15

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0419 [D1088]


title: Discovery_Sample_0420 [D1309]


title: Discovery_Sample_0418 [D1145]


title: 3603_OF2A_5-2-D6-I4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0417 [D1284]


title: Discovery_Sample_0415 [D1403]


title: 3603_OF2A_5-2-D6-L15

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0416 [D1353]


title: 3603_OF2A_5-2-D6-I16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-I3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-J4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0414 [D1385]


title: 3603_OF2A_5-2-D6-H3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-I15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-H16

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0413 [D1358]


title: Discovery_Sample_0412 [D965]


title: Discovery_Sample_0409 [D1340]


title: 3603_OF2A_5-2-D6-H15

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0411 [D115]


title: Discovery_Sample_0410 [D174]


title: 3603_OF2A_5-2-D6-G4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0408 [D1497]


title: Discovery_Sample_0407 [D1475]


title: 3603_OF2A_5-2-D6-G3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-G16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-G15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-F4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0406 [D351]


title: Discovery_Sample_0405 [D117]


title: Discovery_Sample_0404 [D806]


title: 3603_OF2A_5-2-D6-F3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0403 [D1050]


title: 3603_OF2A_5-2-D6-H4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0401 [D443]


title: 3603_OF2A_5-2-D6-F15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-E3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-E4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0400 [D606]


title: Discovery_Sample_0399 [D279]


title: Discovery_Sample_0398 [D829]


title: 3603_OF2A_5-2-D6-E16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-E15

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0397 [D108]


title: 3603_OF2A_5-2-D6-D16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-D3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-D4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0396 [D1465]


title: Discovery_Sample_0394 [D308]


title: 3603_OF2A_5-2-D6-D15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-C4

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-C3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0402 [D889]


title: Discovery_Sample_0392 [D1485]


title: 3603_OF2A_5-2-D6-C16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-F16

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0390 [D1113]


title: Discovery_Sample_0391 [D406]


title: 3603_OF2A_5-2-D6-C15

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0389 [D418]


title: Discovery_Sample_0388 [D731]


title: 3603_OF2A_5-2-D6-B4

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-B16

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0387 [D173]


title: 3603_OF2A_5-2-D6-B3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0386 [D879]


title: Discovery_Sample_0385 [D074]


title: 3603_OF2A_5-2-D6-A4

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0384 [D1195]


title: 3603_OF2A_5-2-D6-B15

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0395 [D810]


title: 3603_OF2A_5-2-D6-A16

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0383 [D1435]


title: 3603_OF2A_5-2-D6-A3

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0393 [D1095]


title: Discovery_Sample_0382 [D1156]


title: Discovery_Sample_0381 [D949]


title: 3603_OF2A_5-1-D6-P2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-P1

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-P14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-P13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0380 [D444]


title: Discovery_Sample_0379 [D783]


title: Discovery_Sample_0378 [D1442]


title: Discovery_Sample_0377 [D079]


title: 3603_OF2A_5-1-D6-O2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-O1

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0376 [D754]


title: Discovery_Sample_0375 [D869]


title: Discovery_Sample_0374 [D918]


title: 3603_OF2A_5-1-D6-O13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0373 [D1409]


title: 3603_OF2A_5-1-D6-O14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-N2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-2-D6-A15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-N1

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-N14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-N13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0371 [D1197]


title: Discovery_Sample_0370 [D042]


title: Discovery_Sample_0369 [D253]


title: Discovery_Sample_0372 [D826]


title: Discovery_Sample_0368 [D310]


title: Discovery_Sample_0366 [D862]


title: Discovery_Sample_0367 [D757]


title: 3603_OF2A_5-1-D6-M14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-M13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0365 [D1448]


title: 3603_OF2A_5-1-D6-L2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-L1

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0363 [D221]


title: 3603_OF2A_5-1-D6-L14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-L13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0362 [D1372]


title: Discovery_Sample_0361 [D309]


title: 3603_OF2A_5-1-D6-K2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-K1

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0359 [D745]


title: 3603_OF2A_5-1-D6-M2

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0358 [D1015]


title: 3603_OF2A_5-1-D6-K13

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-J2

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0357 [D1143]


title: 3603_OF2A_5-1-D6-K14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-M1

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0356 [D1078]


title: Discovery_Sample_0353 [D809]


title: Discovery_Sample_0354 [D1481]


title: 3603_OF2A_5-1-D6-J13

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-J14

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0364 [D1280]


title: 3603_OF2A_5-1-D6-I2

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0352 [D330]


title: 3603_OF2A_5-1-D6-I1

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-I13

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-H2

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0349 [D1306]


title: Discovery_Sample_0350 [D1289]


title: Discovery_Sample_0346 [D945]


title: Discovery_Sample_0347 [D235]


title: 3603_OF2A_5-1-D6-J1

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-H14

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0348 [D111]


title: Discovery_Sample_0355 [D1341]


title: Discovery_Sample_0345 [D277]


title: 3603_OF2A_5-1-D6-G2

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0343 [D008]


title: Discovery_Sample_0351 [D875]


title: 3603_OF2A_5-1-D6-F1

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-G1

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-H1

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0341 [D461]


title: Discovery_Sample_0342 [D1460]


title: Discovery_Sample_0338 [D1146]


title: 3603_OF2A_5-1-D6-I14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-G14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-F2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-F13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0339 [D1068]


title: Discovery_Sample_0340 [D1297]


title: 3603_OF2A_5-1-D6-F14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-E2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-H13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0337 [D116]


title: 3603_OF2A_5-1-D6-E14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-E1

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0423 [D239]


title: Discovery_Sample_0336 [D1112]


title: 3603_OF2A_5-1-D6-G13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0335 [D1096]


title: Discovery_Sample_0334 [D311]


title: Discovery_Sample_0332 [D292]


title: 3603_OF2A_5-1-D6-D2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-E13

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-D1

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-D13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0344 [D1213]


title: 3603_OF2A_5-1-D6-D14

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0331 [D966]


title: Discovery_Sample_0330 [D699]


title: 3603_OF2A_5-1-D6-C2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-C13

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-C1

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0333 [D771]


title: Discovery_Sample_0329 [D601]


title: 3603_OF2A_5-1-D6-B2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-C14

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0324 [D525]


title: Discovery_Sample_0327 [D1013]


title: Discovery_Sample_0328 [D1393]


title: Discovery_Sample_0326 [D263]


title: Discovery_Sample_0323 [D072]


title: Discovery_Sample_0322 [D730]


title: 3603_OF2A_5-1-D6-B1

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-B14

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0325 [D886]


title: 3603_OF2A_5-1-D6-A2

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-A14

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-A1

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0319 [D1268]


title: Discovery_Sample_0320 [D231]


title: Discovery_Sample_0318 [D1033]


title: 3603_OF2A_4-6-B6-P24

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0317 [D378]


title: 3603_OF2A_5-1-D6-A13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0316 [D1471]


title: Discovery_Sample_0315 [D863]


title: Discovery_Sample_0314 [D145]


title: Discovery_Sample_0312 [D1004]


title: 3603_OF2A_4-6-B6-P23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-O23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-O12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0310 [D052]


title: Discovery_Sample_0309 [D302]


title: 3603_OF2A_4-6-B6-O11

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-P12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0313 [D499]


title: 3603_OF2A_4-6-B6-N24

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0321 [D1133]


title: 3603_OF2A_4-6-B6-O24

description: nuclear RNA + genomic DNA


title: 3603_OF2A_5-1-D6-B13

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0308 [D1031]


title: Discovery_Sample_0311 [D306]


title: Discovery_Sample_0307 [D142]


title: 3603_OF2A_4-6-B6-N12

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-N23

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0306 [D747]


title: 3603_OF2A_4-6-B6-P11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0303 [D007]


title: 3603_OF2A_4-6-B6-N11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0305 [D318]


title: 3603_OF2A_4-6-B6-M24

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-M23

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0301 [D935]


title: Discovery_Sample_0304 [D1204]


title: Discovery_Sample_0300 [D739]


title: 3603_OF2A_4-6-B6-M12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0299 [D812]


title: 3603_OF2A_4-6-B6-L12

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-L24

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-L23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-K24

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0297 [D1436]


title: Discovery_Sample_0298 [D1198]


title: 3603_OF2A_4-6-B6-K12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0296 [D327]


title: 3603_OF2A_4-6-B6-K23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-L11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0295 [D802]


title: Discovery_Sample_0294 [D796]


title: Discovery_Sample_0302 [D795]


title: Discovery_Sample_0291 [D068]


title: 3603_OF2A_4-6-B6-K11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0293 [D988]


title: 3603_OF2A_4-6-B6-J24

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-J23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-J12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0292 [D433]


title: 3603_OF2A_4-6-B6-J11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0288 [D081]


title: 3603_OF2A_4-6-B6-I24

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-M11

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-I12

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-I23

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0286 [D136]


title: Discovery_Sample_0287 [D437]


title: 3603_OF2A_4-6-B6-H24

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0285 [D344]


title: 3603_OF2A_4-6-B6-H23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-H12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0281 [D947]


title: Discovery_Sample_0283 [D1301]


title: 3603_OF2A_4-6-B6-H11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0290 [D995]


title: 3603_OF2A_4-6-B6-G24

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0280 [D1153]


title: Discovery_Sample_0279 [D932]


title: 3603_OF2A_4-6-B6-G23

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0289 [D244]


title: 3603_OF2A_4-6-B6-G12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0278 [D199]


title: 3603_OF2A_4-6-B6-G11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0277 [D934]


title: Discovery_Sample_0360 [D664]


title: 3603_OF2A_4-6-B6-F23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-F24

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-I11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0275 [D080]


title: 3603_OF2A_4-6-B6-F12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0284 [D459]


title: Discovery_Sample_0274 [D1210]


title: 3603_OF2A_4-6-B6-E24

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0282 [D1010]


title: Discovery_Sample_0273 [D252]


title: 3603_OF2A_4-6-B6-F11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0272 [D372]


title: Discovery_Sample_0271 [D794]


title: 3603_OF2A_4-6-B6-E23

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0270 [D1111]


title: 3603_OF2A_4-6-B6-D23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-D12

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-D24

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-E11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0268 [D100]


title: Discovery_Sample_0265 [D1505]


title: 3603_OF2A_4-6-B6-D11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0266 [D1261]


title: Discovery_Sample_0276 [D1072]


title: Discovery_Sample_0269 [D1405]


title: 3603_OF2A_4-6-B6-C24

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0264 [D967]


title: 3603_OF2A_4-6-B6-C23

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0267 [D608]


title: Discovery_Sample_0261 [D061]


title: Discovery_Sample_0263 [D264]


title: FRI_4h2

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

country: China

institute: Peiking University

data_processing:
Raw reads stored in the fastq format after the Illumina sequencing were first pro-cessed through in-house perl scripts. In this step, clean reads were obtained by re-moving reads containing adapter, reads containing ploy-N, and low quality reads from the raw data. Clean reads were generated with high quality that were assessed by pa-rameters of the Q20, Q30, and GC contents.
Assembly: Botrytis cinerea B05.10 reference genome (GenBank accession number: GCA_000143535.4)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Botrytis cinerea

source_name: Fludioxonil treat

growth_protocol: The B. cinerea strains, BC-2 and BC-57, used in this study, were isolated from typical gray mold symptom tomato leaves found in local greenhouses (Beijing City). Both of the B. cinerea isolates were first purified using single spore isolation and thereafter main-tained on potato dextrose agar (PDA, 200 g/L potato, 20 g/L agar, and 20 g/L dextrose). After approximately three days of dark-incubation at 23°C, B. cinerea mycelia were ob-tained from the edge of the colonies and transferred to the PDA slants and preserved at 15°C in darkness.

extract_protocol:
Mycelium of the parent fludioxonil-sensitive strain (S), laboratory fludioxo-nil-resistant strain (LR), and field fludioxonil-resistant strains were obtained as de-scribed above. All of the isolates were grown at the same time for the same amount of time (three days) under the same conditions (shaking at 23°C and 180 rpm) in PDB. The mycelium were then collected at the same time.  RNA was extracted from samples using the TRIzol method (Invitro Corp., Carlsbad, CA, USA).The RNA concentration and quality were assessed using a nanodrop and gelelectrophoresis. The samples were stored at ?80°C.
RNA sequencing was conducted by Novogene using an Illumina? (San Diego, CA, USA) based method to generate 20 million 150-bp paired-end reads per sample. The se-quencing library was prepared with the NEBNext? Ultra?RNA Library Prep Kit for Illumina?, and sequencing was performed on the NovaSeq PE150.

treatment_protocol: S (fludioxonil-sensitive), FR (fludioxonil resistance from field), and LR (fludioxonil resistance from laboratory) were routinely cultivated on PDA for three days. For each fungal strain, eight mycelium plugs (5 mm) were incubated using a 200 mL potato dextrose broth (PDB) medium for two days at 23°C and shaken at 180 rpm. The resulting mycelia were treated with or without fludioxonil. In detail, the 10 mg/L fludioxonil stock solutions were added to the PDB medium at final concentrations of 0.05 μg/mL for S, 10 μg/mL for FR, and 500 μg/mL for LR, and the same volume of acetone was added to the 200 mL PDB medium to prepare the control samples. The fludioxonil-induced and no-induced (control) samples were cultured under the same conditions (at 23°C and 180 rpm) for 4 h before RNA extraction. Six samples in total were collected for the following RNA manipulations, i.e., fludioxonil-induced and no-induced S (designated as SI_4h and S_4h), fludioxonil-induced and no-induced LR (designated as LRI_4h and LR_4h), and fludioxonil-induced and no-induced FR (designated as FRI_4h and FR_4h, respec-tively).

tag: strain

value: mycelia


title: FRI_4h3


title: FRI_4h1


title: 3603_OF2A_4-6-B6-C11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0259 [D053]


title: Discovery_Sample_0260 [D1274]


title: Discovery_Sample_0262 [D723]


title: 3603_OF2A_4-6-B6-C12

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-E12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0258 [D872]


title: FR_4h3

source_name: Control


title: Discovery_Sample_0257 [D823]


title: Discovery_Sample_0256 [D1183]


title: 3603_OF2A_4-6-B6-B24

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0255 [D112]


title: FR_4h2


title: 3603_OF2A_4-6-B6-B23

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-B12

description: nuclear RNA + genomic DNA


title: FR_4h1


title: Discovery_Sample_0254 [D706]


title: Discovery_Sample_0253 [D1486]


title: LRI_4h3


title: Discovery_Sample_0251 [D1377]


title: 3603_OF2A_4-6-B6-B11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0249 [D088]


title: Discovery_Sample_0250 [D1060]


title: LRI_4h2


title: Discovery_Sample_0252 [D819]


title: 3603_OF2A_4-6-B6-A23

description: nuclear RNA + genomic DNA


title: LRI_4h1


title: 3603_OF2A_4-6-B6-A24

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-6-B6-A12

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0248 [D343]


title: Discovery_Sample_0247 [D409]


title: Discovery_Sample_0246 [D957]


title: Discovery_Sample_0245 [D1174]


title: LR_4h3


title: Discovery_Sample_0244 [D1085]


title: Discovery_Sample_0243 [D285]


title: Discovery_Sample_0242 [D160]


title: 3603_OF2A_4-6-B6-A11

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0241 [D236]


title: 3603_OF2A_4-5-B6-P9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0239 [D743]


title: SI_4h3


title: Discovery_Sample_0238 [D814]


title: 3603_OF2A_4-5-B6-P22

description: nuclear RNA + genomic DNA


title: SI_4h2


title: SI_4h1


title: Discovery_Sample_0237 [D353]


title: Discovery_Sample_0236 [D598]


title: S_4h3


title: Discovery_Sample_0235 [D1066]


title: 3603_OF2A_4-5-B6-P10

description: nuclear RNA + genomic DNA


title: S_4h2


title: Discovery_Sample_0234 [D1431]


title: 3603_OF2A_4-5-B6-O9

description: nuclear RNA + genomic DNA


title: LR_4h1


title: LR_4h2


title: S_4h1


title: Discovery_Sample_0232 [D194]


title: Discovery_Sample_0233 [D897]


title: Discovery_Sample_0231 [D877]


title: Discovery_Sample_0230 [D1361]


title: 3603_OF2A_4-5-B6-O22

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-5-B6-O21

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0240 [D1285]


title: Discovery_Sample_0228 [D1005]


title: Lm7210 Hi-C

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
The Juicer pipeline release 1.6 (UGER scripts) with options “-s DpnII” was used to map reads back to the final assemblies and construct contact maps before visualization.
Supplementary files format and content: Multi-resolution contact maps from the Juicer pipeline in .hic format.

molecule: genomic DNA

organism: Lemna minor

source_name: whole frond

growth_protocol: Sterile cultures were obtained from the Rutgers Duckweed Stock Cooperative and cultivated in 50 mL Schenk and Hildebrandt (SH) medium with 1% sucrose at pH 5.6 at 23°C under a 16 hour photoperiod of approximately 30 μmol/m2/s per second of white fluorescent light. For HMW DNA extraction, culture flasks were covered in foil and grown in the dark for up to 2 weeks prior to harvest to deplete excess carbohydrates. Cultures were then flash frozen in liquid N2 and stored at -80ºC.

extract_protocol: For Lg7742a, Lj8627 and Wa8730, approximately 10g of tissue per sample was sent to Dovetail Genomics and Hi-C libraries were prepared using their in-house protocol with the DpnII enzyme. For Lm7210 and Lt9434, the Arima-HiC Kit was used to prepare libraries as previously described (Abramson et al. 2021). The resulting libraries were sequenced on an Illumina NextSeq 500 (PE 150bp).

value: whole frond

tag: genotype


title: Discovery_Sample_0227 [D1456]


title: Discovery_Sample_0226 [D1150]


title: 3603_OF2A_4-5-B6-O10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0225 [D449]


title: Wa8730 WGBS 1

data_processing:
Adapter sequences were removed and reads were hard-trimmed with Trimmomatic v0.35 with options “HEADCROP:5 TRAILING:3 MINLEN:25”. Technical and biological replicates were merged, and reads were aligned to the genomes using Bismark v0.23.1 with options “-N 1 -L 20 --maxins 1200”. Reads were deduplicated and methylated cytosines were called using “bismark_methylation_extractor --CX --bedGraph --ignore_r2 2 --comprehensive” and a genome-wide cytosine report was generated with coverage2cytosine, and separate bigWig coverage tracks were derived for CpG, CHG, and CHH contexts. Profiles over genomic regions were calculated with deepTools 3.5.1 computeMatrix with options “scale-regions --skipZeros -bs 100 -m 2000 -b 2000 -a 2000” and plotted in R.
Supplementary files format and content: BigWig coverage tracks for each cytosine context.

organism: Wolffia australiana

extract_protocol:
High molecular weight (HMW) DNA extractions were performed using a modified CTAB prep followed by a high-salt low-ethanol starch cleanup (Pacific Biosciences) as follows:  4 g frozen tissue was ground three times under liquid N2 with a mortar and pestle and transferred to 20 mL pre-warmed lysis buffer (100 mM Tris-HCl pH 9.0, 2% w/v CTAB, 1.4 M NaCl, 20 mM EDTA, 2% PVP-10, 1% 2-mercaptoethanol, 0.1% sarkosyl, 100ug/mL Proteinase K), briefly vortexed, and then incubated at 65ºC for 1 hour with periodic mixing by gentle inversion. The lysate was extracted with 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) and then 1 vol. of chloroform:isoamyl alcohol in phase-lock gel tubes. HMW DNA was precipitated from the aqueous phase in a 50 mL falcon tube by the addition of 0.1 vol. 3M NaOAc pH 5.2 followed by 0.7 vol. Isopropanol. After gentle swirling but no inversion mixing, precipitated salt in the upper phase was pipetted off and HMW DNA was hooked out with a bent pasteur pipette, washed by dipping in 70% EtOH, air-dried for 2 minutes, and resuspended in 200 uL Tris-Cl pH 8.5 (EB). The DNA solution was treated with 2 uL 20 mg/mL RNase A at 37ºC for 20 minutes followed by 2 uL 50 mg/mL Proteinase K at 50ºC for 30 minutes. 194 uL EB, 100 uL 5M NaCl, and 2 uL 0.5 M EDTA were added and organic solvent extractions were performed as before (1x P:C:IA and 1x C:IA). 0.3 vol. EtOH was added followed by centrifugation at 16,000 x g for 15 minutes to precipitate carbohydrates. The supernatant was poured into a new tube and 1.7 vol. of EtOH was added to precipitate HMW DNA, followed by hooking with a pasteur pipette, a 70% EtOH wash, drying, and resuspension in 50 uL EB.
WGBS libraries were prepared for Sp9509, Lg7742a, Lj8627 and Wa8730 as described previously (Parent et al. 2021) for Arabidopsis embryos, except that DNA from the HMW extraction methods described above was used. Libraries were sequenced on a NextSeq 500 (PE 151) or a HiSeq 2500 (PE 108)


title: 3603_OF2A_4-5-B6-P21

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-5-B6-N9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0223 [D148]


title: Discovery_Sample_0224 [D1349]


title: Discovery_Sample_0222 [D466]


title: Lj8627 small RNA 3

data_processing:
Sequencing adapters were trimmed using skewer v0.2.2 and 4nt randomer sequences were removed from both ends of each read with fastp v0.20.1 with options “--trim_front1 4 --trim_tail1 4 --length_required 10 --length_limit 35 --disable_adapter_trimming --trim_poly_g -q 20 --unqualified_percent_limit 10”. Reads mapping perfectly to annotated structural RNAs and organelles were removed, and those remaining were aligned to the genomes with ShortStack v4.0.0 using options “--mincov 0.5 --mmap f --dn_mirna --knownRNAs <miRBase 22.1 mature plant sequences>”. Separate ShortStack runs with merged biological replicates were performed for microRNA discovery, and microRNAs identified by ShortStack were annotated by top BLAST hit of the mature sequence to miRBase 22.1. Alignments were split by size class and bigWig coverage tracks computed with deepTools “bamCoverage --binSize 1 --normalizeUsing CPM”.
Supplementary files format and content: BigWig coverage tracks of merged replicates for each size class of 20nt - 24nt small RNA.
Supplementary files format and content: Small RNA clusters annotated by ShortStack 4 (GFF3) for merged replicates.

organism: Lemna japonica

extract_protocol:
RNA was extracted from 3 biological replicates of 100mg of frozen tissue for each accession using the Quick-DNA/RNA Miniprep kit (Zymo) following manufacturer’s instructions with the following modifications: frozen tissue was ground under LN2 with a mortar and pestle and resuspended in the Shield solution. It was refrozen in LN2, thawed, and treated with Proteinase K, and frozen again after the addition of lysis buffer. After thawing, samples were centrifuged at full speed, RT for 3 min. to remove debris, and the manufacturer’s protocol was followed as described. Afterwards, samples were DNase treated, enriched for RNAs 17-200 nt in length, and concentrated using the RNA Clean & Concentrator kit (Zymo).
Libraries were prepared with the NEXTflex Small RNA-Seq Kit v3 (Perkin Elmer) following manufacturer instructions and sequenced on a NextSeq 500 (SE 75).


title: Lj8627 small RNA 2


title: 3603_OF2A_4-5-B6-N21

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0229 [D006]


title: Discovery_Sample_0219 [D1020]


title: Discovery_Sample_0218 [D240]


title: Lj8627 small RNA 1


title: Discovery_Sample_0221 [D1106]


title: Lj8627 transcriptome pool 1

data_processing:
Long-read (LR) cDNA libraries were aligned with uLTRA v0.0.4  with parameters “--ont or --isoseq, --max_intron 10000, –use_NAM_seeds” and exon hints from ab_initio_preds.
Short-read cDNA evidence was aligned with HISAT2 v2.2.1 with options “--dta --max-intronlen 10000 --rna-strandness <orientation>”.
Coverage was calculated over 1bp bins with deeptools v3.5.2 “bamCoverage --samFlagExclude 2304 --ignoreDuplicates --binSize 1 --normalizeUsing CPM”.
Supplementary files format and content: Coverage of spliced alignments of reads to their respective reference assemblies.

extract_protocol:
Frozen whole frond tissue (100-150 mg) was lysed with Bashing Beads (Zymo) and total RNA was extracted with the ZR Plant RNA MiniPrep kit (Zymo) following manufacterer's instructions. DNase treatment was performed on-column.
Polyadenylated RNA was enriched from total RNA with the Dynabeads mRNA Purification Kit (Life Technologies). Indexed, directional RNA-seq libraries were prepared with ScriptSeq v2 reagents (Epicentre) according to the manufacturer’s instructions.

treatment_protocol: To provide broad transcriptional evidence for annotation, RNA samples were collected from fronds of Lg7742a and Lj8627 grown under a diverse set of conditions: variable daylength, nutrient stress, temperature stress, high NaCl, high pH, UV damage, and exogenous hormone exposure. Samples from all conditions were pooled, polyA enriched or rRNA depleted, and strand-specific cDNA libraries were prepared and sequenced on Illumina and Oxford Nanopore Technologies instruments.


title: 3603_OF2A_4-5-B6-M9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0217 [D688]


title: Discovery_Sample_0220 [D1041]


title: Discovery_Sample_0215 [D191]


title: Discovery_Sample_0216 [D1493]


title: Discovery_Sample_0214 [D1206]


title: 3603_OF2A_4-5-B6-M22

description: nuclear RNA + genomic DNA


title: Lj8627 Hi-C


title: 3603_OF2A_4-5-B6-N10

description: nuclear RNA + genomic DNA


title: Lj8627 WGBS 2


title: Discovery_Sample_0213 [D213]


title: Lj8627 WGBS 1


title: Discovery_Sample_0210 [D1184]


title: Discovery_Sample_0211 [D579]


title: 3603_OF2A_4-5-B6-M10

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-5-B6-M21

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0212 [D159]


title: Lg7742a small RNA 3

organism: Lemna gibba


title: Discovery_Sample_0209 [D032]


title: 3603_OF2A_4-5-B6-L9

description: nuclear RNA + genomic DNA


title: Lg7742a small RNA 2


title: 3603_OF2A_4-5-B6-N22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0207 [D048]


title: Discovery_Sample_0208 [D832]


title: 3603_OF2A_4-5-B6-L21

description: nuclear RNA + genomic DNA


title: Lg7742a small RNA 1


title: Discovery_Sample_0205 [D348]


title: Lg7742a Hi-C


title: 3603_OF2A_4-5-B6-L22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0203 [D1404]


title: Discovery_Sample_0204 [D1388]


title: Lg7742a WGBS 2


title: 3603_OF2A_4-5-B6-K9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0201 [D205]


title: 3603_OF2A_4-5-B6-L10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0200 [D876]


title: Discovery_Sample_0202 [D300]


title: Discovery_Sample_0199 [D857]


title: Discovery_Sample_0197 [D1138]


title: 3603_OF2A_4-5-B6-K22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0198 [D375]


title: 3603_OF2A_4-5-B6-K21

description: nuclear RNA + genomic DNA


title: gas_M2

city: Shanghai

first: Kong

last: Xingxing

address: Songhu Road 2005

department: School of Life Sciences

institute: Fudan University

data_processing:
The sequencing data was filtered with trim-galore (v0.6.6) by removing reads containing sequencing adapter and reads with low-quality base, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome (Macaca_fascicularis_5.0) using STAR (v2.7.8a). Then expression level of gene was calculated by RSEM (v1.3.3).
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

organism: Macaca fascicularis

source_name: non-lean

extract_protocol:
Total RNA was extracted from the skeletal muscle tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces using fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The double stranded PCR products were heated denatured and circularized by the splint oligo sequence to get the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 150) bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Gastrocnemius muscle

tag: treatment

value: high fat diet


title: gas_M1

source_name: lean

value: chow diet


title: Discovery_Sample_0206 [D858]


title: Discovery_Sample_0195 [D1315]


title: 3603_OF2A_4-5-B6-K10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0193 [D1468]


title: 3603_OF2A_4-5-B6-J9

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-5-B6-J22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0191 [D204]


title: Discovery_Sample_0192 [D697]


title: Discovery_Sample_0190 [D767]


title: Lg7742a WGBS 1


title: 3603_OF2A_4-5-B6-J10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0186 [D250]


title: Discovery_Sample_0188 [D1495]


title: Discovery_Sample_0196 [D178]


title: Wild type Sciatic Sample 6

city: Bar Harbor

first: George

middle: C

last: Murray

state: ME

address: 600 Main St.

department: Research

institute: The Jackson Laboratory

description: Column AD

data_processing:
nf-core RNASeq pipline v3.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Quality was assessed using FASTQC
Trimmed sequence reads were mapped to GRCm38/mm10 using Star
Read count extraction and normalization were performed using RSEM
Assembly: GRCm38 - mm10
Supplementary files format and content: tab-delimited text files include RSEM expected counts, TPM, and FPKM values for each Sample

organism: Mus musculus

source_name: sciatic nerve

extract_protocol:
Tissues were lysed and homogenized in TRIzol Reagent (ThermoFisher) using a Pellet Pestle Motor (Kimbal), then RNA was isolated using the miRNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step.  RNA concentration and quality were assessed using the Nanodrop 2000/Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Nano and Pico Assay (Agilent Technologies).
Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturer’s instructions.
Libraries were sequenced 150 bp paired-end on an Illumina NovaSeq 6000 using the S4 Reagent Kit v1.5.

value: sciatic nerve

value: F

value: WT


title: Wild type Sciatic Sample 7

description: Column AG

value: M


title: Wild type Sciatic Sample 5

description: Column AC


title: 3603_OF2A_4-5-B6-I9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0187 [D066]


title: C3-PMP22 Sipa1l2 -/- Sciatic Sample 8

description: Column AB

value: C3-PMP22 Sipa1l2-/-


title: Discovery_Sample_0184 [D1009]

value: renal biopsy tissue


title: Discovery_Sample_0194 [D121]

value: Discovery cohort sample


title: 3603_OF2A_4-5-B6-I22

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: C3-PMP22 Sciatic Sample 8

description: Column AF


title: Discovery_Sample_0183 [D207]


title: C3-PMP22 Sipa1l2 -/- Sciatic Sample 7

description: Column AA


title: C3-PMP22 Sciatic Sample 7

description: Column AE


title: Discovery_Sample_0182 [D118]


title: Discovery_Sample_0181 [D883]


title: Discovery_Sample_0180 [D749]


title: 3603_OF2A_4-5-B6-I21

description: nuclear RNA + genomic DNA

value: Female


title: Discovery_Sample_0189 [D969]

value: Antibody-mediated Rejection


title: 3603_OF2A_4-5-B6-J21

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0185 [D1389]


title: 3603_OF2A_4-5-B6-I10

description: nuclear RNA + genomic DNA


title: Sipa1l2-/- Sciatic Sample 9

description: Column Z


title: Discovery_Sample_0178 [D661]

value: No Rejection


title: C3-PMP22 Sipa1l2 -/- Sciatic Sample 6

description: Column W


title: Discovery_Sample_0175 [D1354]

value: T cell-mediated Rejection


title: C3-PMP22 Sciatic Sample 6

description: Column X


title: 3603_OF2A_4-5-B6-H22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0176 [D1086]


title: Discovery_Sample_0177 [D025]


title: 3603_OF2A_4-5-B6-H9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0174 [D1044]


title: 3603_OF2A_4-5-B6-H21

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0170 [D704]


title: Discovery_Sample_0171 [D170]


title: Discovery_Sample_0173 [D1058]


title: Sipa1l2-/- Sciatic Sample 8

description: Column V


title: Discovery_Sample_0168 [D107]


title: C3-PMP22 Sciatic Sample 5

description: Column U


title: 3603_OF2A_4-5-B6-H10

description: nuclear RNA + genomic DNA


title: Wild type Sciatic Sample 4

description: Column Y


title: Sipa1l2-/- Sciatic Sample 7

description: Column T


title: Discovery_Sample_0179 [D673]


title: Discovery_Sample_0166 [D401]


title: 3603_OF2A_4-5-B6-G22

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-5-B6-G9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0169 [D1454]


title: Wild type Sciatic Sample 3

description: Column S


title: 3603_OF2A_4-5-B6-G21

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0167 [D940]


title: Wild type Sciatic Sample 2

description: Column R


title: 3603_OF2A_4-5-B6-G10

description: nuclear RNA + genomic DNA


title: Sipa1l2-/- Sciatic Sample 6

description: Column Q


title: Discovery_Sample_0172 [D1190]

value: Mixed Rejection


title: 3603_OF2A_4-5-B6-F9

description: nuclear RNA + genomic DNA


title: C3-PMP22 Sciatic Sample 4

description: Column P


title: Discovery_Sample_0164 [D942]


title: Discovery_Sample_0163 [D218]


title: Discovery_Sample_0165 [D853]


title: Discovery_Sample_0159 [D611]


title: Discovery_Sample_0160 [D1292]


title: Discovery_Sample_0161 [D357]


title: Discovery_Sample_0158 [D1189]


title: Discovery_Sample_0157 [D613]


title: 3603_OF2A_4-5-B6-F21

description: nuclear RNA + genomic DNA


title: C3-PMP22 Sciatic Sample 3

description: Column O


title: C3-PMP22 Sipa1l2 -/- Sciatic Sample 5

description: Column M


title: 3603_OF2A_4-5-B6-E9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0153 [D882]


title: Discovery_Sample_0156 [D299]


title: C3-PMP22 Sipa1l2 -/- Sciatic Sample 4

description: Column L


title: Discovery_Sample_0155 [D807]


title: 3603_OF2A_4-5-B6-E22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0152 [D707]


title: C3-PMP22 Sciatic Sample 2

description: Column N


title: Discovery_Sample_0151 [D954]


title: Discovery_Sample_0150 [D1434]


title: 3603_OF2A_4-5-B6-E21

description: nuclear RNA + genomic DNA


title: C3-PMP22 Sipa1l2 -/- Sciatic Sample 3

description: Column J


title: 3603_OF2A_4-5-B6-E10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0148 [D753]


title: C3-PMP22 Sipa1l2 -/- Sciatic Sample 2

description: Column I


title: Discovery_Sample_0147 [D016]


title: Discovery_Sample_0162 [D1441]


title: Discovery_Sample_0146 [D919]


title: 3603_OF2A_4-5-B6-F22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0154 [D110]


title: Discovery_Sample_0144 [D1398]


title: Sipa1l2-/- Sciatic Sample 5

description: Column K


title: Discovery_Sample_0145 [D788]


title: 3603_OF2A_4-5-B6-F10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0143 [D1364]


title: C3-PMP22 Sciatic Sample 1

description: Column H


title: 3603_OF2A_4-5-B6-D22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0149 [D953]


title: C3-PMP22 Sipa1l2 -/- Sciatic Sample 1

description: Column F


title: 3603_OF2A_4-5-B6-D21

description: nuclear RNA + genomic DNA


title: Sipa1l2-/- Sciatic Sample 4

description: Column G


title: Discovery_Sample_0142 [D1324]


title: Discovery_Sample_0138 [D1444]


title: Discovery_Sample_0139 [D392]


title: Discovery_Sample_0140 [D941]


title: Discovery_Sample_0141 [D1037]


title: 3603_OF2A_4-5-B6-D10

description: nuclear RNA + genomic DNA


title: Sipa1l2-/- Sciatic Sample 3

description: Column E


title: 3603_OF2A_4-5-B6-C9

description: nuclear RNA + genomic DNA


title: Sipa1l2-/- Sciatic Sample 2

description: Column D


title: 3603_OF2A_4-5-B6-D9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0136 [D1188]


title: Sipa1l2-/- Sciatic Sample 1

description: Column C


title: Discovery_Sample_0135 [D426]


title: 3603_OF2A_4-5-B6-C22

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0134 [D817]


title: 3603_OF2A_4-5-B6-C21

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0132 [D515]


title: Wild type Sciatic Sample 1

description: Column B


title: Discovery_Sample_0133 [D272]


title: Discovery_Sample_0131 [D1355]


title: Discovery_Sample_0130 [D751]


title: Discovery_Sample_0129 [D847]


title: 3603_OF2A_4-5-B6-C10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0128 [D720]


title: 3603_OF2A_4-5-B6-B9

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0127 [D1168]


title: Discovery_Sample_0126 [D442]


title: Discovery_Sample_0137 [D001]


title: 3603_OF2A_4-5-B6-B22

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-5-B6-B21

description: nuclear RNA + genomic DNA


title: RNAseq_PB_treated_rep1

city: Chengdu, Cihna

first: Xiangmeng

last: Luo

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description: RNAseq_tumor_organoid_PB_vs_Veh_result_all_submitted_data.csv

data_processing:
Transcriptome sequencing was conducted using the Illumina NovaSeq 6000 platform with 150 bp paired-end sequencing. After removing the adapters, ploy-N, and low-quality reads, clean data were aligned against the reference mouse genome (mm10) using STAR_2.6.0a. Following this, raw counts were normalized and significance scores as well as log2-fold change values were calculated using the DESeq2 (v.1.26.0).
Assembly: mm10
Supplementary files format and content: csv files include counts and DESeq2 normalized data

source_name: Esophageal tumor organoids, Trp53-/-;Myc OE; sgCdkn2a; sgTgfbr2, treated with pinaverium bromide

growth_protocol: Isolate about 1.5 cm of esophageal tissue and wash it with a PBS buffer solution containing antibiotics (Gibco, Cat# 15240096)about five times. Transfer the tissue to a new 15ml centrifuge tube and minced with fine scissors. Add 0.25% Trypsin-EDTA (GIBCO, Cat#  2152925) and incubate at 37°C for about 1 hour, then add serum-containing DMEM medium to stop digestion. Filter the mixture through a 70-μm cell strainer (JET BIOFIL, Cat#CSS-013-070), centrifuge at 400 g for 5 minutes, discard the supernatant, resuspend the bottom cells with Matrigel (Corning, Cat# 354230) on ice. Add 30 μL of the mixture to each well of a 48-well plate and supplemented with 200 μl complete medium containing 1 x B27 (GIBCO, Cat# A3582801), 1 x N2 (GIBCO, Cat# 17502048), EGF (R&D, final 50 ng/mL), FGF10 (Peprotech, Cat# 100-26-1000, final 200 ng/mL), Y27632 (Abmole Bioscience, final 10 μM), A83-01 (Peprotech, Cat# 9094360, final 2 μM), R-spodin 1 (Peprotech, Cat# 120-38-1000, final 250 ng/ml), Noggin (Peprotech, Cat# 120-10C-250, final 100 ng/mL), 10% Wnt-3A conditioned medium, Nicotinamide (Sigma, Cat # N0636, 1mM), N-acetylcysteine (Sigma, Cat# A9165, 1mM), Glutamax (Peprotech, Cat# 35050-061, 2 mM), and 1 x Penicil-lin/Streptomycin (GIBCO, Cat# 15140-122) in DMEM-F12 (Cat# 8121062).

extract_protocol:
RNA was extracted with Trizol libraries were prepared for sequencing using standard Illumina protocols
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

treatment_protocol: TCMT mouse tumor organoids were dissociated in TrypLE and seeded into 96-well plates (1000 cells per well). After 72h culturing, organoids were treated with 2μM pinaverium bromide or 10μM candidate FDA- approved drugs.

tag: cell type

value: Esophageal tumor organoids

value: Trp53-/-;Myc OE; sgCdkn2a; sgTgfbr2

value: treated with 2μM pinaverium bromide


title: RNAseq_Veh_treated_rep3

source_name: Esophageal tumor organoids, Trp53-/-;Myc OE; sgCdkn2a; sgTgfbr2, treated with DMSO

value: treated with DMSO


title: RNAseq_PB_treated_rep2


title: Discovery_Sample_0122 [D1424]


title: Discovery_Sample_0124 [D959]


title: 3603_OF2A_4-5-B6-B10

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-5-B6-A9

description: nuclear RNA + genomic DNA


title: RNAseq_PB_treated_rep3


title: RNAseq_Veh_treated_rep1


title: RNAseq_Veh_treated_rep2


title: Discovery_Sample_0118 [D1128]


title: 3603_OF2A_4-5-B6-A22

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-5-B6-A21

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0120 [D1038]


title: RNAseq_sgTgfbr2_tumor_organoids_rep2

description: RNAseq_tumor_organoid_sgTgfbr2_vs_sgScr_result_all_submitted_data.csv

source_name: Esophageal tumor organoids, Trp53-/-;Myc OE; sgCdkn2a; sgTgfbr2


title: RNAseq_sgTgfbr2_tumor_organoids_rep1


title: Discovery_Sample_0119 [D1455]


title: Discovery_Sample_0117 [D911]


title: Discovery_Sample_0125 [D234]


title: Discovery_Sample_0116 [D1423]


title: 3603_OF2A_4-5-B6-A10

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0114 [D365]


title: Discovery_Sample_0113 [D232]


title: Discovery_Sample_0115 [D891]


title: 3603_OF2A_4-4-B6-P8

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0123 [D1489]


title: Discovery_Sample_0112 [D1426]


title: Discovery_Sample_0121 [D797]


title: Discovery_Sample_0111 [D1334]


title: 3603_OF2A_4-4-B6-P20

description: nuclear RNA + genomic DNA


title: RNAseq_sgScr_tumor_organoids_rep1

source_name: Esophageal tumor organoids, Trp53-/-;Myc OE; sgCdkn2a

value: Trp53-/-;Myc OE; sgCdkn2a


title: 3603_OF2A_4-4-B6-P7

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0110 [D151]


title: Discovery_Sample_0109 [D895]


title: RNAseq_sgScr_tumor_organoids_rep3


title: RNAseq_sgTgfbr2_2_premalignant_organoids_rep2

description: RNAseq_premelignant_organoid_sgTgfbr2_vs_sgScr_result_all_submitted_data.csv

source_name: Esophageal premalignant organoids, Trp53-/-;Myc OE; sgCdkn2a; sgTgfbr2

value: Esophageal premalignant organoids


title: Discovery_Sample_0107 [D390]


title: Discovery_Sample_0106 [D884]


title: Discovery_Sample_0104 [D1196]


title: 3603_OF2A_4-4-B6-O8

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0105 [D1087]


title: RNAseq_sgTgfbr2_2_premalignant_organoids_rep1


title: RNAseq_sgTgfbr2_1_premalignant_organoids_rep2


title: 3603_OF2A_4-4-B6-O7

description: nuclear RNA + genomic DNA


title: RNAseq_sgTgfbr2_1_premalignant_organoids_rep1


title: Discovery_Sample_0103 [D321]


title: 3603_OF2A_4-4-B6-O20

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0101 [D004]


title: 3603_OF2A_4-4-B6-P19

description: nuclear RNA + genomic DNA


title: RNAseq_sgScr_tumor_organoids_rep2


title: RNAseq_sgScr_premalignant_organoids_rep3

source_name: Esophageal premalignant organoids, Trp53-/-;Myc OE; sgCdkn2a


title: Discovery_Sample_0099 [D230]


title: 3603_OF2A_4-4-B6-O19

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0098 [D1492]


title: Discovery_Sample_0108 [D056]


title: Discovery_Sample_0097 [D1104]


title: Discovery_Sample_0096 [D790]


title: RNAseq_sgScr_premalignant_organoids_rep1


title: 3603_OF2A_4-4-B6-N8

description: nuclear RNA + genomic DNA


title: RNAseq_sgScr_premalignant_organoids_rep2


title: 3603_OF2A_4-4-B6-N7

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0100 [D1003]


title: Discovery_Sample_0093 [D1094]


title: Discovery_Sample_0095 [D1384]


title: Discovery_Sample_0094 [D262]


title: SCC mix HASH

city: Stanford

first: Ansuman

middle: T

last: Satpathy

address: 240 Pasteur Drive

institute: Stanford University

description:
Hmix
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Libraries were processed using Cell Ranger count v6.0.0.
Assembly: mm10
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz contain both GEX and HTO data.

molecule: protein

source_name: SCC31, SCC35, SCC40

extract_protocol:
Tumors were dissociated according to the Miltenyi gentleMACS protocol. Single-cell suspensions were hashed using TotalSeq-C anti-mouse Hashtag antibodies and sorted for live cells using propidium iodine.
Libraries were constructed using 10x Chromium Single Cell 5’ V(D)J v1.1 Kit with Feature Barcode technology

tag: cell line

value: SCC31, SCC35, SCC40


title: Discovery_Sample_0102 [D1447]


title: SCC40 HASH

description:
H40
Hashtag-derived oligonucleotide (HTO)


title: Discovery_Sample_0092 [D793]


title: 3603_OF2A_4-4-B6-N20

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-4-B6-N19

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0091 [D596]


title: SCC37 HASH

description:
H37
Hashtag-derived oligonucleotide (HTO)


title: Discovery_Sample_0090 [D067]


title: 3603_OF2A_4-4-B6-M8

description: nuclear RNA + genomic DNA


title: SCC35 HASH

description:
H35
Hashtag-derived oligonucleotide (HTO)


title: Discovery_Sample_0089 [D012]


title: Discovery_Sample_0088 [D1282]


title: 3603_OF2A_4-4-B6-M7

description: nuclear RNA + genomic DNA


title: SCC32 HASH

description:
H32
Hashtag-derived oligonucleotide (HTO)


title: Discovery_Sample_0086 [D859]


title: 3603_OF2A_4-4-B6-M20

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0085 [D1310]


title: Discovery_Sample_0087 [D268]


title: Discovery_Sample_0084 [D152]


title: 3603_OF2A_4-4-B6-M19

description: nuclear RNA + genomic DNA


title: SCC31 HASH

description:
H31
Hashtag-derived oligonucleotide (HTO)


title: SCC mix GEX

description:
Gmix
polyA RNA

library_source: transcriptomic single cell

molecule: polyA RNA


title: Discovery_Sample_0083 [D1103]


title: 3603_OF2A_4-4-B6-L8

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0080 [D1092]


title: Discovery_Sample_0081 [D982]


title: SCC40 GEX

description:
G40
polyA RNA


title: Discovery_Sample_0079 [D1466]


title: Discovery_Sample_0078 [D150]


title: Discovery_Sample_0077 [D1371]


title: 3603_OF2A_4-4-B6-L19

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-4-B6-L20

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0076 [D744]


title: SCC35 GEX

description:
G35
polyA RNA


title: Discovery_Sample_0075 [D1325]


title: Discovery_Sample_0082 [D714]


title: Discovery_Sample_0074 [D103]


title: Discovery_Sample_0072 [D1000]


title: 3603_OF2A_4-4-B6-K8

description: nuclear RNA + genomic DNA


title: SCC31 GEX

description:
G31
polyA RNA


title: Discovery_Sample_0073 [D1335]


title: 3603_OF2A_4-4-B6-K7

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0071 [D1130]


title: 3603_OF2A_4-4-B6-L7

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0067 [D099]


title: Discovery_Sample_0068 [D352]


title: SCC37 GEX

description:
G37
polyA RNA


title: Discovery_Sample_0069 [D1008]


title: Discovery_Sample_0070 [D867]


title: SCC35 Mif KO mix2 HASH

description:
Hmix2
Hashtag-derived oligonucleotide (HTO)

source_name: SCC35 Mif KO control 18, SCC35 Mif KO 24

extract_protocol:
Tumors were dissociated according to the Miltenyi gentleMACS protocol. Single-cell suspensions were hashed using TotalSeq-C anti-mouse Hashtag antibodies and sorted for live cells using propidium iodine.
Libraries were constructed using 10x Chromium Single Cell 5’ v2 Kit Dual Index with Feature Barcode technology.


title: 3603_OF2A_4-4-B6-K20

description: nuclear RNA + genomic DNA


title: SCC35 Mif KO mix1 HASH

description:
Hmix1
Hashtag-derived oligonucleotide (HTO)

source_name: SCC35 Mif KO control 15, SCC35 Mif KO control 18, SCC35 Mif KO 19


title: Discovery_Sample_0066 [D1422]

source_name: renal biopsy tissue


title: 3603_OF2A_4-4-B6-K19

description: nuclear RNA + genomic DNA

source_name: OF2A human BA46


title: 3603_OF2A_4-4-B6-J8

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0065 [D1506]


title: SCC35 Mif KO 24 HASH

description:
HKO24
Hashtag-derived oligonucleotide (HTO)

source_name: SCC35 Mif KO 24

value: SCC35 Mif KO 24


title: SCC32 GEX

description:
G32
polyA RNA


title: Discovery_Sample_0064 [D1137]


title: 3603_OF2A_4-4-B6-J7

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0063 [D201]


title: SCC35 Mif KO 19 HASH

description:
HKO19
Hashtag-derived oligonucleotide (HTO)

source_name: SCC35 Mif KO 19

value: SCC35 Mif KO 19


title: SCC35 Mif KO control 18 HASH

description:
HC18
Hashtag-derived oligonucleotide (HTO)

source_name: SCC35 Mif KO control 18

value: SCC35 Mif KO control 18


title: Discovery_Sample_0062 [D943]

value: renal biopsy tissue

value: Discovery cohort sample


title: SCC35 Mif KO control 15 HASH

description:
HC15
Hashtag-derived oligonucleotide (HTO)

source_name: SCC35 Mif KO control 15

value: SCC35 Mif KO control 15


title: 3603_OF2A_4-4-B6-J20

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Discovery_Sample_0061 [D1338]

value: No Rejection


title: SCC35 Mif KO mix2 GEX

description:
Gmix2
polyA RNA

value: SCC35 Mif KO control 18, SCC35 Mif KO 24


title: 3603_OF2A_4-4-B6-I8

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-4-B6-J19

description: nuclear RNA + genomic DNA


title: SCC35 Mif KO mix1 GEX

description:
Gmix1
polyA RNA

value: SCC35 Mif KO control 15, SCC35 Mif KO control 18, SCC35 Mif KO 19


title: Discovery_Sample_0059 [D1276]


title: Discovery_Sample_0057 [D1100]

value: Antibody-mediated Rejection


title: Discovery_Sample_0060 [D825]


title: Discovery_Sample_0058 [D1496]

value: T cell-mediated Rejection


title: SCC35 Mif KO 24 GEX

description:
GKO24
polyA RNA


title: 3603_OF2A_4-4-B6-I20

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0053 [D1397]


title: 3603_OF2A_4-4-B6-I7

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0054 [D050]


title: SCC35 Mif KO 19 GEX

description:
GKO19
polyA RNA


title: Discovery_Sample_0055 [D1169]

value: Mixed Rejection


title: Discovery_Sample_0050 [D1432]


title: 3603_OF2A_4-4-B6-I19

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0052 [D1073]


title: Discovery_Sample_0049 [D939]


title: Discovery_Sample_0056 [D149]


title: SCC35 Mif KO control 15 GEX

description:
GC15
polyA RNA


title: Discovery_Sample_0051 [D137]


title: Discovery_Sample_0047 [D1452]


title: 3603_OF2A_4-4-B6-H8

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-4-B6-H7

description: nuclear RNA + genomic DNA


title: TPT, DP thymocyte, 8 weeks, rep4

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

data_processing:
Raw sequence reads were trimmed using Trimmomatic v0.33
aligned to the mm10 genome assembly from iGenomes using STAR
Aligned reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78
DESeq2 was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups within an nf-Core Differential Abundance workflow
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: thymus

extract_protocol:
RNA isolation was performed using  RNeasy mini kits (QIAGEN) following the manufacturer’s protocol.
RNA-seq libraries were constructed using Nugen’s Ovation Ultralow Library systems following the manufacturer's protocol

value: thymus

value: primary cells

value: CD4+CD8+ thymocyte

value: 8 weeks

value: VavCre E2aF/F

value: Transplanted with WT bone marrow


title: Discovery_Sample_0044 [D143]

value: renal biopsy tissue


title: Discovery_Sample_0046 [D1484]

value: Discovery cohort sample


title: Discovery_Sample_0045 [D827]


title: 3603_OF2A_4-4-B6-H19

description: nuclear RNA + genomic DNA


title: TPT, DP thymocyte, 8 weeks, rep2


title: Discovery_Sample_0041 [D015]


title: Discovery_Sample_0042 [D990]


title: Discovery_Sample_0043 [D653]


title: TPT, DP thymocyte, 8 weeks, rep3


title: Discovery_Sample_0040 [D614]


title: SCC35 Mif KO control 18 GEX

description:
GC18
polyA RNA

value: SCC35 Mif KO control 18


title: 3603_OF2A_4-4-B6-G8

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3603_OF2A_4-4-B6-H20

description: nuclear RNA + genomic DNA

value: Female


title: TPT, DP thymocyte, 8 weeks, rep1


title: VcKO, DP thymocyte, 8 weeks, rep3


title: Discovery_Sample_0037 [D013]


title: Discovery_Sample_0038 [D1182]


title: Discovery_Sample_0036 [D866]


title: Discovery_Sample_0035 [D210]


title: VcKO, DP thymocyte, 8 weeks, rep2


title: R00966NM_IDPN4w

city: Hospitalet de Llobregat

first: Jordi

last: Llorens

state: Catalunya

address: Feixa Llarga s/n

department: Ciències Fisiològiques

country: Spain

institute: Universitat de Barcelona

data_processing:
RNAseq reads were mapped to the rat reference genome (Rnor6.0) with STAR/2.5.3a with ENCODE parameters
Genes were quantified with RSEM/1.3.0 with default parameters
The gene annotation file was Rnor6.0.92
Supplementary files format and content: Raw counts (text file)

organism: Rattus norvegicus

source_name: Vestibular ganglion

extract_protocol:
Vestibular ganglia were quickly dissected in ice-cold PBS. Both ganglia from each animal were pooled and stored at -80C. Total RNA was extracted using the Qiagen RNeasy mini kit and protocol.
RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2014) with some modifications. Briefly, reverse transcription of the total RNA input material of 1.8 µl (6-11 ng, in function of the sample availability) was performed using SuperScript II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3′), template-switching oligonucleotides (1 µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (2x) (Roche) and 100 nM IS PCR primer (5′-AAG CAG TGG TAT CAA CGC AGA GT-3′) with 8 cycles of PCR amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), the product size distribution and the quantity were assessed with a Bioanalyzer High Sensitivity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitivity DNA Kit.

treatment_protocol: Subchronic ototoxicity rats were given 20 mM of 3,3'-iminodipropionitrile (CAS# 111-94-4; >98%) in the drinking water for 4 weeks; control rats received plain drinking water.

value: Vestibular ganglion

value: male Long-Evans

value: Subchronic ototoxicity


title: 3603_OF2A_4-4-B6-G20

description: nuclear RNA + genomic DNA


title: VcKO, DP thymocyte, 8 weeks, rep1


title: 3603_OF2A_4-4-B6-G19

description: nuclear RNA + genomic DNA


title: R00966LF_IDPN4w


title: Discovery_Sample_0033 [D045]


title: Discovery_Sample_0034 [D1375]


title: Discovery_Sample_0039 [D1121]

value: Antibody-mediated Rejection


title: 3603_OF2A_4-4-B6-F8

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-4-B6-F7

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-4-B6-G7

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-4-B6-F20

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0032 [D1207]


title: WT (V), DP thymocyte, 8 weeks, rep2


title: R00968RF_Control

value: Control


title: Discovery_Sample_0031 [D1287]

value: No Rejection


title: 3603_OF2A_4-4-B6-F19

description: nuclear RNA + genomic DNA


title: R00965NM_Control


title: WT (V), DP thymocyte, 8 weeks, rep1

value: thymus


title: LcKO, DP thymocyte 4 weeks, rep3

value: primary cells

value: 4 weeks

value: LckCre E2aF/F


title: Discovery_Sample_0029 [D106]


title: R00965LF_Control


title: 3603_OF2A_4-4-B6-E8

description: nuclear RNA + genomic DNA


title: LcKO, DP thymocyte 4 weeks, rep2

value: CD4+CD8+ thymocyte


title: Discovery_Sample_0048 [D607]


title: Postnatal day 16 female oocyte, γ-irradiation 2

city: Athens

first: Claudia

last: Baumann

state: GA

address: 501 DW Brooks Drive

department: College of Veterinary Medicine - Physiology and Pharmacology

institute: University of Georgia

data_processing:
Data retrieved from RNA-Seq on DNBseq platform was filtered by removing reads mapped to rRNA and low-quality, adaptor-polluted and high content of unknown base (N) reads
Mapped clean reads to reference genome using HISAT2, using paramters --phred33 --sensitive --no-discordant --no-mixed -I 1 -X1000
Novel coding transcripts were merged with reference transcripts to obtain the complete reference, and then Bowtie2 was used to map clean reads to this reference (Bowtie2 parameter: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X1000 --nomixed --no-discordant -p 1 -k 200)
Gene expression level was calculated for each sample by the RSEM software (RSEM parameter: -p 8 --forward-prob 0.5 --paired-end)
Assembly: mm10
Supplementary files format and content: xls excel file with the transcript expression data of all four libraries

source_name: GV oocyte

extract_protocol:
The oocytes were recovered from the ovaries by follicle puncture and cumulus oocyte complexes were transferred to minimal essential medium (MEM) supplemented with 3mg/ml bovine serum albumin (Sigma Aldrich, St. Louis, MO) and milrinone (Sigma; 1 μg/ml) to prevent meiotic resumption. Surrounding cumulus cells were removed by gentle pipetting followed by several rinses in fresh medium. Oocytes were cultured for specified periods of time and maintained at 37°C in MEM/BSA plus milrinone under 5% CO2, 5%O2 and balanced N2.
For RNA-seq, oocytes are denuded in Tyrode’s solution (Sigma) and transferred to microcentrifuge tubes containing 3 μl of lysis buffer. Isolation of mRNA was conducted using oligo(dT)

treatment_protocol: For the irradiated oocyte group, oocytes were washed and transferred to a micro drop of Embryomax M2 medium (Sigma, cat# MR-015-D) supplemented with milrinone under mineral oil and subjected to a non-lethal dose of γ-irradiation (5 Gy; 140 Rad/min for 3.57 min) using a Mark I 68A Cesium-137 gamma irradiator (JL Shepherd and Associates, San Fernando, CA).

value: GV oocyte

value: γ-irradiation


title: 3603_OF2A_4-4-B6-E7

description: nuclear RNA + genomic DNA


title: WT (V), DP thymocyte, 8 weeks, rep3

value: 8 weeks


title: Discovery_Sample_0028 [D878]

value: renal biopsy tissue

value: Discovery cohort sample


title: R00966RF_IDPN4w


title: Postnatal day 16 female oocyte, γ-irradiation 1


title: 3603_OF2A_4-4-B6-E20

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Postnatal day 16 female oocyte, control 2

value: control


title: WT (L), DP thymocyte, 4 weeks, rep2


title: 3603_OF2A_4-4-B6-E19

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0026 [D763]


title: Discovery_Sample_0027 [D946]


title: Postnatal day 16 female oocyte, control 1


title: 3603_OF2A_4-4-B6-D8

description: nuclear RNA + genomic DNA


title: WT (L), DP thymocyte, 4 weeks, rep1


title: 3603_OF2A_4-4-B6-D7

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0025 [D1445]

value: T cell-mediated Rejection


title: Discovery_Sample_0030 [D594]


title: VcKO, DP thymocyte, 4 weeks, rep3

value: VavCre E2aF/F


title: Lepr-cKO 2wpc ipsi [SLRKO2wpc138i]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.5 was used to align the reads to the GRCm38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes
Assembly: GRCm38 version 97
Supplementary files format and content: Tab-delimited gene counts

source_name: sciatic nerve endoneurium

extract_protocol:
Tissues were microdissected in ice-cold PBS and stored at -80°C in 1ml TRIZOL (Thermofisher). RNA was extracted using the illustra RNAspin Mini RNA isolation kit from GE Healthcare (25-0500-70). RNA-sequencing was performed  at the NGS- Integrative Genomics (NIG) Core Unit Institute of Human Genetics of University Medical Center Göttingen (UMG).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: sciatic nerve endoneurium

tag: strain background

value: injured 2wpc


title: 3603_OF2A_4-4-B6-D20

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0024 [D997]

value: Antibody-mediated Rejection


title: Lepr-cKO 2wpc ipsi [SLRKO2wpc135i]


title: VcKO, DP thymocyte, 4 weeks, rep2

value: thymus

value: primary cells


title: WT (L), DP thymocyte, 4 weeks, rep3

value: 4 weeks


title: Discovery_Sample_0022 [D102]


title: VcKO, DP thymocyte, 4 weeks, rep1

value: CD4+CD8+ thymocyte


title: Lepr-cKO 2wpc ipsi [SLRKO2wpc128i]


title: Lepr-cKO 2wpc ipsi [SLRKO2wpc126i]


title: LcKO, DP thymocyte 4 weeks, rep1

value: LckCre E2aF/F


title: Discovery_Sample_0021 [D1327]

value: No Rejection


title: 3603_OF2A_4-4-B6-C8

description: nuclear RNA + genomic DNA


title: Lepr-cKO 2wpc ipsi [SLRKO2wpc125i]


title: Discovery_Sample_0023 [D024]


title: Discovery_Sample_0020 [D1390]


title: 3603_OF2A_4-4-B6-C7

description: nuclear RNA + genomic DNA


title: WT (V), DP thymocyte, 4 weeks, rep2


title: Lepr-cKO 2wpc contra [SLRKO2wpc138c]

value: control 2wpc


title: 3603_OF2A_4-4-B6-C20

description: nuclear RNA + genomic DNA


title: WT (V), DP thymocyte, 4 weeks, rep1


title: Lepr-cKO 2wpc contra [SLRKO2wpc136c]


title: 3603_OF2A_4-4-B6-D19

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0019 [D981]

value: renal biopsy tissue


title: M0: 3hrs, Unstim

city: Los Angeles

first: Katherine

middle: M

last: Sheu

address: 611 Charles E Young Dr E

institute: UCLA

description:
BD Rhapsody
Library 13

data_processing:
Raw fastq files were processed using the BD Rhapsody™ Targeted Analysis Pipeline (version v1.0) 23 hosted on Seven Bridges Genomics. Distribution-Based Error Correction (DBEC)-adjusted UMI counts (molecules per cell) were used in the downstream analysis. Multiplets, cells with undetermined barcodes, and cells with less than 80 features were removed from the analysis. (Due to the highly multiplexed nature of the experiments, fastq files also include data not described in the paper. Users should refer to supplementary file 'samptag.all_cellannotations_metadata.txt' to extract the relevant cells after processing. Processed and subsetted data is available on the manuscript's associated Zenodo repository.)
Assembly: mm10
Supplementary files format and content: Comma-separated values files for mRNA counts
Supplementary files format and content: Comma-separated values Sample Tag files for cell identities

source_name: macrophages

growth_protocol: Macrophages were obtained either via differentiation of immortalized myeloid progenitors (HoxB4 iMPs). Differentiation was performed in DMEM/10% FBS + 30% L929 supernatant for a total of 10 days: iMPs were initially thawed into 10cm non-adherent petri dishes for 3 days. On day 0 of differentiation, cells were then washed once and transferred into differentiation media (DMEM/10% FBS, 30% L929 supernatant, 1% PS, 1% L-Glut, b-Me (1:1000)). Cells were replated into 6cm plates with new media on day 7, at a density of ~20k cells/cm2.

extract_protocol:
Cells were washed once with cold PBS after 0.25, 0.5, 1, 3, 5, or 8hrs of stimulation and lifted into suspension by incubating at 37C for 5 minutes with Accutase, which resulted in cell viability typically >85%. Cells were centrifuged at 4C, 400g for 5 minutes, and resuspended in PBS + 2% FBS for the Rhapsody scRNAseq assay. Cells were hash-tagged with anti-CD45-hashtags (BD Rhapsody # 633793) and loaded onto the cartridge following manufacturer’s instructions (BD Rhapsody # 633771), with the following modifications, which helped ensure sufficient cell viability for the subsequent steps: Incubation with hashtags was performed for 30mins on ice, instead of 20mins at room temperature; only two washes were performed after hashtag incubation to minimize cell loss. Each cartridge was then loaded with a total of ~36k cells across 12 hash-tagged samples (~3k cells/sample).
Libraries were prepared according to manufacturer’s instructions (BD Rhapsody # 633771) and sequenced 2x100 on Novaseq 6000.

treatment_protocol: On day 10, the iMP-derived macrophages (iMPDMs) were stimulated with 100ng/mL lipopolysaccharide (LPS, Sigma Aldrich), 10ng/mL murine TNF, and 50μg/mL low molecular weight polyinosine-polycytidylic acid (Poly(I:C)), 100nM synthetic CpG ODN 1668 (CpG), 500U/ml IFNβ, or media only Untreated control. For polarized macrophages, cells were incubated in 50ng/ml IFNγ or 50ng/ml IL4 for 24 hours prior to stimulation on day 10.

value: macrophages

value: iMPDMs

value: includes multiple


title: Lepr-cKO 2wpc contra [SLRKO2wpc135c]


title: 3603_OF2A_4-4-B6-B8

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Lepr-cKO 2wpc contra [SLRKO2wpc128c]


title: WT (V), DP thymocyte, 4 weeks, rep3


title: Discovery_Sample_0017 [D752]

extract_protocol: Two tissue curls from the FFPE block of each biopsy sample were dissected at 16-μm thickness per curl and stored at -80°C until RNA extraction was performed with either Zymo® Quick-RNA FFPE kits by manual RNA extraction or with Zymo® Quick-RNA MagBead kit and Tecan Fluent Liquid Handler.

value: Discovery cohort sample


title: M0: 5hrs, 3hrs

description:
BD Rhapsody
Library 12


title: Discovery_Sample_0016 [D307]

value: T cell-mediated Rejection


title: 3603_OF2A_4-4-B6-B7

description: nuclear RNA + genomic DNA

extract_protocol: Library prepared following protocol described in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn


title: Discovery_Sample_0015 [D791]


title: Lepr-cKO 2wpc contra [SLRKO2wpc126c]

value: sciatic nerve endoneurium


title: 3603_OF2A_4-4-B6-B19

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0018 [D962]

value: Antibody-mediated Rejection


title: 3603_OF2A_4-4-B6-C19

description: nuclear RNA + genomic DNA


title: Lepr control 2wpc ipsi [SLRKO2wpc131i]

value: Leprfl/fl

value: injured 2wpc


title: 3603_OF2A_4-4-B6-B20

description: nuclear RNA + genomic DNA


title: C57BL/6 WT & Nfkbia m/m: 8hrs

description:
BD Rhapsody
Library 10

value: BMDMs


title: Discovery_Sample_0014 [D762]


title: M0: 8hrs, 0.5hrs

description:
BD Rhapsody
Library 11


title: Discovery_Sample_0013 [D906]


title: Lepr-cKO 2wpc contra [SLRKO2wpc125c]


title: Lepr control 2wpc ipsi [SLRKO2wpc147i]


title: 3603_OF2A_4-4-B6-A7

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-4-B6-A8

description: nuclear RNA + genomic DNA


title: NOD Aire GW/+: 8hrs

description:
BD Rhapsody
Library 9

value: NOD/ShiLtJ


title: M0: 8hrs, 0.25hrs

description:
BD Rhapsody
Library 7


title: 3603_OF2A_4-4-B6-A20

description: nuclear RNA + genomic DNA


title: M1(IFNg): 8hrs, 0.5hrs

description:
BD Rhapsody
Library 6


title: Lepr control 2wpc ipsi [SLRKO2wpc144i]


title: Discovery_Sample_0011 [D1126]


title: Lepr control 2wpc ipsi [SLRKO2wpc130i]


title: Discovery_Sample_0010 [D467]


title: 3603_OF2A_4-4-B6-A19

description: nuclear RNA + genomic DNA


title: M1(IFNg): 5hrs, 3hrs

description:
BD Rhapsody
Library 5


title: 3603_OF2A_4-3-B6-P6

description: nuclear RNA + genomic DNA


title: Lepr control 2wpc ipsi [SLRKO2wpc123i]


title: M1(IFNg): 24hrs, 1hr

description:
BD Rhapsody
Library 4


title: 3603_OF2A_4-3-B6-P5

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0008 [D976]


title: M0: 3hrs, 1hr

description:
BD Rhapsody
Library 8


title: Lepr control 2wpc contra [SLRKO2wpc147c]


title: Discovery_Sample_0012 [D270]


title: 3603_OF2A_4-3-B6-P18

description: nuclear RNA + genomic DNA


title: Lepr control 2wpc contra [SLRKO2wpc130c]


title: Discovery_Sample_0006 [D180]


title: M2(IL4): 1hr; M0 Unstim, M1 Unstim, M2 Unstim

description:
BD Rhapsody
Library 3


title: M2(IL4): 8hrs, 0.5hrs

description:
BD Rhapsody
Library 2


title: Discovery_Sample_0007 [D1135]

value: Mixed Rejection


title: M2(IL4): 5hrs, 3hrs

description:
BD Rhapsody
Library 1


title: Lepr control 2wpc contra [SLRKO2wpc123c]


title: 3603_OF2A_4-3-B6-P17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-3-B6-O6

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0009 [D043]


title: 210329_Tfh_Bob1KO_3

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

country: Japan

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

data_processing:
Illumina NovaSeq Sysyem software v1.6 used for basecalling
Sequence reads were trimmed for adaptor sequence/low-quality sequence and poly-A/T tail using cutadapt v1.2.1 and PRINSEQ v0.19.2.
Trimmed sequence reads were mapped to GRCm38/mm10 using TopHat v2.0.13.
Read count extraction and normalization were performed using Cufflinks v 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol:
Total RNA was extracted from FACS sorted Tfh cells by using Trizol reagent. 0.7 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing following manufacturer's protocols.

treatment_protocol: FoxP3-GFP-Bob1 floxed mice and FoxP3-GFP-CD4 conditional Bob1 KO mice were immunized by intraperitoneal administration of 100 ug of NP49-CGG in complete Freund's adjuvant. Spleens were collected these immunized mice at day 7. Single-cell suspensions from spleens were labeled with fluorophore-labeld antibodies and FACS sorted Tfh cells (CD3+CD4+CXCR5+PD-1+GFP-) using FACSAria II and III.

value: spleen

value: CD4+ Tfh cells

value: NP-CGG in CFA i.p. day 7


title: Lepr control 2wpc contra [SLRKO2wpc120c]

value: control 2wpc


title: 3603_OF2A_4-3-B6-O5

description: nuclear RNA + genomic DNA


title: 210329_Tfh_Bob1KO_2


title: 3603_OF2A_4-3-B6-O18

description: nuclear RNA + genomic DNA


title: Discovery_Sample_0005 [D593]

data_processing: Normalization of RNA loading was performed using the geometric mean of 12 internal reference genes (housekeeping genes; ABCF1, G6PD, GUSB, NRDE2, OAZ1, POLR2A, PPIA, SDHA, STK11IP, TBC1D10B, TBP, and UBB).

value: No Rejection

value: renal biopsy tissue


title: Lepr-cKO 4wpc ipsi [KO-176Sni]

value: injured 4wpc


title: Lepr control 2wpc contra [SLRKO2wpc131c]


title: Discovery_Sample_0002 [D589]


title: Lepr-cKO 4wpc ipsi [KO-177Sni]


title: Discovery_Sample_0004 [D421]


title: Lepr-cKO 4wpc ipsi [KO-175Sni]


title: Discovery_Sample_0003 [D320]


title: 3603_OF2A_4-3-B6-N6

description: nuclear RNA + genomic DNA

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM file were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmCT-seq

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: 3603_OF2A_4-3-B6-O17

description: nuclear RNA + genomic DNA


title: 210329_Tfh_WT_3

value: WT


title: Lepr-cKO 4wpc ipsi [KO-169Sni]

value: sciatic nerve endoneurium


title: P23-45_t5_control

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

data_processing:
Live basecalling and demultiplexing on the PromethION 24 device in high accuracy mode using the Guppy software.
Identification and orientation of full-length reads using Pychopper (v2.5.0)  and adapters were removed using Cutadapt (v2.7).
eads were mapped against the reference genomes of Thermus thermophilus HB8 (NC_006461.1) and phage P23-45 (OP542242) using minimap2. For mapping against the phage genome, the second long terminal repeat was omitted (mapping region [1...83630])
Peak calling using termseq-peaks scripts.
Assembly: GenBank accession OP542242 (phage P23-45) and NC_006461.1 (T. thermophilus HB8)
Supplementary files format and content: Narrowpeak files generated by peak calling

organism: Thermus thermophilus HB8

source_name: bacterial

growth_protocol: Thermus thermophilus strain HB8 was grown until exponential phase and infected with P23-45. A culture sample was taken 5 minutes post-infection.

extract_protocol:
Total RNA was extracted using the TRIzol method, followed by Dnase I treatment. The enriched sames were subjected to an enrichment procedure based on streptavidin beads to enrich for primary RNA transcripts. For the control samples the enrichment steps were omitted.
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In paralel, the control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded according to the Oxford Nanopore Technologies cDNA-PCR protocol (SQK-PCS109 combined with SQK-PBK004). The amplified cDNA samples were pooled together in a final library.

tag: infection

value: P23-45 bacteriophage

value: bacterial

value: no enrichment


title: Discovery_Sample_0001 [D880]

value: Antibody-mediated Rejection

value: Discovery cohort sample


title: Lepr-cKO 4wpc contra [KO-179Snc]

value: control 4wpc


title: 3603_OF2A_4-3-B6-N5

description: nuclear RNA + genomic DNA


title: P23-45_40min_input_gp96_replica1

description:
P23-45_40min_input_gp96_1
Replica 1

data_processing:
The adapters and low-quality sequences were eliminated by the Skoltech Genomics Core Facility.
ChIP-seq reads were aligned to P23-45 genome with the second long terminal repeat ommited ([1...83630] of the GenBank accession OP542242) using bowtie2 (version 2.4.1).
Samtools (version 1.10) software was used to convert .sam files to .bam format and to filter the reads. Filtering was performed using the following parameters: -F 4 (to remove all unmapped reads), -f 2 (to keep only the reads mapped in a proper pair), -q 1 (to skip the alignments with mapQuality < 1).
BedGraph files were generated using  MACS2 (version 2.2.7.1) with default settings.
Assembly: GenBank accession OP542242
Supplementary files format and content: bedGraph

growth_protocol: Bacterial cells were grown in an orbital shaker at 70°C in liquid medium (0.8% tryptone, 0.4% NaCl, 0.2% yeast extract, 0.5 mM MgSO4, and 0.5 mM CaCl2 in “Vittel” mineral water). Cells were grown until an optical density at 600 nm of around 0.2 and infected with P23-45 bacteriophage at a multiplicity of infection 10. At 5, 20, and 40 min post infection 200 ml of cells were collected.

extract_protocol:
Infected cells were fixed with 1% formaldehyde for 20 minutes. The cross-linking reaction was stopped by the addition of dry glycine up to the final concentration of 0.5 M. Cells were incubated for 20 min with agitation. The cells were harvested by centrifugation and washed twice with ice-cold TBS (10 mM Tris-HCl pH 7.6, 150 mM NaCl). The cells were lysed and DNA was sheared by sonication to an average size of 200 – 500 bp. Immunoprecipitation was performed using corresponding antibodies and Sera-Mag SpeedBeads Protein A/G Sepharose magnetic beads (GEHealth).
DNA libraries were generated by the Skoltech Genomics Core Facility using Swift Accel-NGS 1S Kit (Swift Biosciences) following the manufacturer’s instructions.

tag: chip antibody


title: 210329_Tfh_WT_1

value: spleen


title: P23-45_t5_enriched

value: enriched for primary RNAs


title: 210329_Tfh_WT_2

value: CD4+ Tfh cells

value: NP-CGG in CFA i.p. day 7


title: 3603_OF2A_4-3-B6-N18

description: nuclear RNA + genomic DNA