title: aP0_1_18

description:
Sample 499
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_17

status: Public on May 02 2017

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
Sample 498
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

library_source: transcriptomic

data_processing:
[Bulk Cell RNA-seq (Sample 001-014)] Reads were aligned to Mus musculus reference genome GRCm38/mm10 with TopHat (v2.1.0) using parameter “-G”.
[Bulk Cell RNA-seq (Sample 001-014)] Reads aligned to genes were calculated using HTSeq (v 0.6.0) with parameters “-f bam -r pos -s reverse -a 30”.
[Bulk Cell RNA-seq (Sample 001-014)] Reads of biological replications were pooled together.
[Bulk Cell RNA-seq (Sample 001-014)] Gene expression levels were quantified as TPM (Transcripts Per Kilobase Million).
[Bulk Cell RNA-seq (Sample 001-014)] TPM was normalized by size factors, which were calculated using DESeq (v1.20.0).
[Single Cell RNA-seq (Sample 015-950)] Reads were aligned to Mus musculus reference genome GRCm38/mm10 with TopHat (v2.1.0) using parameter “-G”.
[Single Cell RNA-seq (Sample 015-950)] Reads aligned to genes were calculated using HTSeq (v 0.6.0) with parameters “-f bam -r pos -s no -a 30”.
[Single Cell RNA-seq (Sample 015-950)] Gene expression levels were quantified as TPM (Transcripts Per Kilobase Million).
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: P0 Gcg-Cre, Rosa-RFP+

extract_protocol:
[Bulk Cell RNA-seq (Sample 001-014)] Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490).
[Bulk Cell RNA-seq (Sample 001-014)] Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.
[Single Cell RNA-seq (Sample 015-950)] cDNA synthesis and amplification were performed following the Smart-seq2 protocol.
[Single Cell RNA-seq (Sample 015-950)] The libraries were prepared with 2 ng cDNA using the TruePrep DNA Library Prep Kit (Vazyme, TD502).

tag: tissue

value: Pancreas

tag: developmental stage

tag: strain

value: Gcg-Cre, Rosa-RFP+

tag: cell type

value: P0, Gcg-Cre, Rosa-RFP+

tag: collection method

value: FACS-sorted

tag: batch

value: α-cell P0-1


title: aP9_2_08

description:
Sample 540
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P9 Gcg-Cre, Rosa-RFP+

value: P9, Gcg-Cre, Rosa-RFP+

value: α-cell P9-2


title: aP0_1_21

description:
Sample 502
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_16

description:
Sample 497
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_15

description:
Sample 496
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_14

description:
Sample 495
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP9_2_03

description:
Sample 535
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_13

description:
Sample 494
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_12

description:
Sample 493
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_2_10

description:
Sample 512
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: manually-picked

value: α-cell P0-2


title: aP0_1_11

description:
Sample 492
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_10

description:
Sample 491
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_08

description:
Sample 489
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_09

description:
Sample 490
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_04

description:
Sample 485
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_05

description:
Sample 486
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_03

description:
Sample 484
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_07

description:
Sample 488
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_02

description:
Sample 483
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_3_07

description:
Sample 480
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: E17.5 Gcg-Cre, Rosa-RFP+

value: E17.5, Gcg-Cre, Rosa-RFP+


title: aE17.5_3_08

description:
Sample 481
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_01

description:
Sample 482
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_3_06

description:
Sample 479
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_3_04

description:
Sample 477
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_3_05

description:
Sample 478
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_3_01

description:
Sample 474
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_3_03

description:
Sample 476
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_3_02

description:
Sample 475
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_19

description:
Sample 471
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_18

description:
Sample 470
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_15

description:
Sample 467
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_17

description:
Sample 469
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_14

description:
Sample 466
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_20

description:
Sample 472
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_13

description:
Sample 465
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_16

description:
Sample 468
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_12

description:
Sample 464
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_09

description:
Sample 461
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_11

description:
Sample 463
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP0_1_06

description:
Sample 487
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_08

description:
Sample 460
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_07

description:
Sample 459
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_06

description:
Sample 458
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_04

description:
Sample 456
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_02

description:
Sample 454
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_03

description:
Sample 455
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_21

description:
Sample 473
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_01

description:
Sample 453
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_30

description:
Sample 452
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_28

description:
Sample 450
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_05

description:
Sample 457
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_29

description:
Sample 451
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_24

description:
Sample 446
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_22

description:
Sample 444
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_21

description:
Sample 443
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_25

description:
Sample 447
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_18

description:
Sample 440
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_15

description:
Sample 437
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_2_10

description:
Sample 462
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_20

description:
Sample 442
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_19

description:
Sample 441
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_23

description:
Sample 445
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_14

description:
Sample 436
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_13

description:
Sample 435
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_11

description:
Sample 433
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_12

description:
Sample 434
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_17

description:
Sample 439
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_16

description:
Sample 438
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_10

description:
Sample 432
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_09

description:
Sample 431
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_27

description:
Sample 449
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_08

description:
Sample 430
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_26

description:
Sample 448
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_04

description:
Sample 426
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_07

description:
Sample 429
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_05

description:
Sample 427
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_01

description:
Sample 423
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_02

description:
Sample 424
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_03

description:
Sample 425
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_14

description:
Sample 422
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P60 Ins1-RFP+

value: P60, Ins1-RFP+

value: β-cell P60-2


title: bP60_2_13

description:
Sample 421
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_10

description:
Sample 418
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_12

description:
Sample 420
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_11

description:
Sample 419
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_07

description:
Sample 415
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_05

description:
Sample 413
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_02

description:
Sample 410
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_04

description:
Sample 412
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_01

description:
Sample 409
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_03

description:
Sample 411
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_37

description:
Sample 406
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: β-cell P60-1


title: bP60_1_38

description:
Sample 407
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_36

description:
Sample 405
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_08

description:
Sample 416
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aE17.5_1_06

description:
Sample 428
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_39

description:
Sample 408
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_35

description:
Sample 404
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_06

description:
Sample 414
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_32

description:
Sample 401
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_33

description:
Sample 402
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_29

description:
Sample 398
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_2_09

description:
Sample 417
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_28

description:
Sample 397
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_31

description:
Sample 400
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_30

description:
Sample 399
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_34

description:
Sample 403
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_26

description:
Sample 395
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_23

description:
Sample 392
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_22

description:
Sample 391
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_25

description:
Sample 394
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_24

description:
Sample 393
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_20

description:
Sample 389
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_19

description:
Sample 388
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_18

description:
Sample 387
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_17

description:
Sample 386
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_14

description:
Sample 383
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_13

description:
Sample 382
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_12

description:
Sample 381
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_11

description:
Sample 380
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_09

description:
Sample 378
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_06

description:
Sample 375
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_07

description:
Sample 376
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_10

description:
Sample 379
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_03

description:
Sample 372
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_02

description:
Sample 371
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_04

description:
Sample 373
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_08

description:
Sample 377
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_35

description:
Sample 369
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P18 Ins1-RFP+

value: P18, Ins1-RFP+

value: β-cell P18-2


title: bP18_2_34

description:
Sample 368
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_33

description:
Sample 367
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_21

description:
Sample 390
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_31

description:
Sample 365
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_32

description:
Sample 366
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_29

description:
Sample 363
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_30

description:
Sample 364
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_28

description:
Sample 362
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_27

description:
Sample 361
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_25

description:
Sample 359
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_16

description:
Sample 385
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_05

description:
Sample 374
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_24

description:
Sample 358
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_01

description:
Sample 370
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_20

description:
Sample 354
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_22

description:
Sample 356
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_15

description:
Sample 384
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_21

description:
Sample 355
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_15

description:
Sample 349
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_14

description:
Sample 348
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_17

description:
Sample 351
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_12

description:
Sample 346
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_19

description:
Sample 353
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_16

description:
Sample 350
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_18

description:
Sample 352
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_23

description:
Sample 357
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_11

description:
Sample 345
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_10

description:
Sample 344
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_08

description:
Sample 342
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_06

description:
Sample 340
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_05

description:
Sample 339
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_26

description:
Sample 360
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_03

description:
Sample 337
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_07

description:
Sample 341
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_04

description:
Sample 338
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_02

description:
Sample 336
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_01

description:
Sample 335
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_31

description:
Sample 334
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: β-cell P18-1


title: bP18_1_30

description:
Sample 333
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_29

description:
Sample 332
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_27

description:
Sample 330
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_24

description:
Sample 327
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_25

description:
Sample 328
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_26

description:
Sample 329
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_16

description:
Sample 319
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_14

description:
Sample 317
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_17

description:
Sample 320
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_21

description:
Sample 324
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_22

description:
Sample 325
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_09

description:
Sample 343
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_18

description:
Sample 321
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_23

description:
Sample 326
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_28

description:
Sample 331
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_19

description:
Sample 322
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_13

description:
Sample 316
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_20

description:
Sample 323
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_12

description:
Sample 315
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_2_13

description:
Sample 347
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_15

description:
Sample 318
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_10

description:
Sample 313
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_08

description:
Sample 311
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_07

description:
Sample 310
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_06

description:
Sample 309
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_03

description:
Sample 306
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_02

description:
Sample 305
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_04

description:
Sample 307
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_01

description:
Sample 304
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_19

description:
Sample 295
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P15 Ins1-RFP+

value: P15, Ins1-RFP+

value: β-cell P15-2


title: bP15_2_18

description:
Sample 294
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: Pancreas


title: bP15_2_21

description:
Sample 297
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_27

description:
Sample 303
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_05

description:
Sample 308
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_24

description:
Sample 300
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_11

description:
Sample 314
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_22

description:
Sample 298
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_17

description:
Sample 293
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_16

description:
Sample 292
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_25

description:
Sample 301
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_23

description:
Sample 299
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP18_1_09

description:
Sample 312
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: jazQmycT_2

city: East Lansing

first: Gregg

middle: A

last: Howe

state: MI

address: 612 Wilson Rd

department: Plant Research Laboratory

country: USA

institute: Michigan State University

data_processing:
Illumina Casava1.8.2 software used to convert and demultiplex basecall files to FASTQ.
Reads assessed for quality and filtered with Illumina quality control tools filters and FASTX toolkit (http://hannonlab.cshl.edu /fastx_toolkit/).
RSEM v1.2.11 (Li and Dewey, BMC Bioinformatics, 2011) used to map reads to the Arabidopsis genome using the Illumina iGenomes TAIR10 index with default parameters. Transcript abundances expressed as transcripts per million (TPM; reads per kilobase of model per million mapped reads normalized to transcript coverage).
Genome_build: TAIR10
Supplementary_files_format_and_content: expression data (jQmT_expression.txt) in tab-delimited matrix table for TPM (transcripts per million) values for all samples, as determined by RSEM
Supplementary_files_format_and_content: count data (jQmT_counts.txt) in tab-delimited matrix table for read counts for all samples, as determined by RSEM

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: Plant seedlings (Col-0 wildtype, jazQ, mycT, jazQ mycT) were grown on square Petri plates containing solid medium (half-strength Linsmaier and Skoog [2.365 g/L], 0.7% phytoblend agar, 0.8% sucrose). Plates were incubated vertically in a growth chamber maintained at 21 °C for 8 d after sowing in continuous light.

extract_protocol:
For each replicate sample, approximately 200 seedlings (whole plant, including roots) per genotype were pooled and immediately frozen in liquid nitrogen and stored at -80C until processing. Wildtype and mutant seedlings were grown on the same plate to minimize plate-to-plate variation. Three independent samples (biological replicates) were sequenced per genotype. Total RNA was isolated using a Qiagen RNeasy kit with Qiagen on-column DNase treatment to remove genomic DNA. RNA integrity was assessed with a 2100 Bioanalyzer (Agilent Bioanalyzer) and all samples had an integrity score of at least 7.0.
Barcoded sequencing libraries were prepared using the Illumina RNAseq kit according to the manufacturer's instructions. Normalized libraries were sequenced on the Ilumina HiSeq 2000 platform with multiplexing of six libraries per lane.

tag: ecotype

tag: genotype

value: jazQ mycT

tag: age

value: 8 d

value: whole plant

tag: replicate


title: jazQmycT_3


title: bP15_2_15

description:
Sample 291
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_14

description:
Sample 290
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_13

description:
Sample 289
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_12

description:
Sample 288
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: mycT_3

value: mycT


title: mycT_2


title: mycT_1


title: bP15_2_26

description:
Sample 302
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_11

description:
Sample 287
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_20

description:
Sample 296
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_10

description:
Sample 286
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_09

description:
Sample 285
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: jazQ_2

description:
jazQ_rep2
GSM2083586

value: jazQ


title: jazQ_3

description:
jazQ_rep3
GSM2083587


title: jazQ_1

description:
jazQ_rep1
GSM2083585


title: bP15_2_08

description:
Sample 284
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: manually-picked


title: bP15_2_07

description:
Sample 283
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_06

description:
Sample 282
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: Col-0_2

description:
Col-0_rep2
GSM2083583

value: wildtype


title: Col-0_1

description:
Col-0_rep1
GSM2083582


title: Col-0_3

description:
Col-0_rep3
GSM2083584


title: jazQmycT_1


title: bP15_2_04

description:
Sample 280
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_03

description:
Sample 279
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_02

description:
Sample 278
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_2_01

description:
Sample 277
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C71_D11

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs

data_processing:
De-multiplexed files were created using CASAVA 1.8
Each sample was filtered using Trimmatic (http://www.usadellab.org/cms/?page=trimmomatic) with the settings LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35 and only paired matches were kept
Using the RSEM aligner and the Ensembl GRC h38 release 87 paired fastq files were aligned to the genome
Raw output from RSEM was generated with the "rsem-generate-data-matrix" function in the RSEM package.
tximport (v1.2.0) was used to import all of the genes.results files from RSEM and edgeR (v3.16.5) was used to normalize using the TMM method.
A matrix of TMM normalized counts per million was output using the edgeR cpm funciton.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: "ips17_BU3_normalized_edgeR_counts_TMM_all.txt" is a matrix of normalized counts per million of all genes and cells was output from edgeR. "rsem_results_h38_ips17_BU3_gene_fpkm_matrix.txt" and "rsem_results_h38_ips17_BU3.gene.count.matrix" are the fpkm and count matrix output from rsem.

molecule: polyA RNA

organism: Homo sapiens

source_name: ipsc cell line C17

growth_protocol: iPSCs were transitioned to feeder-free conditions on Matrigel (Corning) in mTeSR1 (Stem Cell Technologies) and passaged with Gentle Cell Dissociation Reagent (Stem Cell Technologies). For the lung  differentiation we first induced definitive endoderm using STEMDiff definitive endoderm kit (STEMCELL Technologies) according to the accompanying protocol. After approximately 72 cells were plated in small clumps at approximately 50-150,000 cells/cm2  on Matrigel-coated plates in complete serum-free differentiation media (CSFDM) supplemented with 2μM Dorsomorphin (Stemgent), 10μM SB431542 (Tocris) for 72 hours. 10μM Y-27632 (Tocris) was added for the first 24 hours. The differentiation media was changed on day 6 to “CFKBRa”; CSFDM supplemented with 3μM CHIR99021 (Tocris), 10ng/ml rhFGF10, 10ng/ml rhKGF, 10ng/ml rhBMP4 (all from R&D Systems), 50-100nM Retinoic acid (Sigma). On day 15, cells were dissociated with 0.05% trypsin and live cells identified were sorted by flow cytometry.

extract_protocol:
Single cells enriched by FACS were captured by C1 Single-cell Auto Prep System(Fluidigm).  polyA RNA from each single cell was reverse transcribed and cDNA amplified using SMARTer kit (SMARTer Ultra Low RNA Kit for the Fluidigm C1 System,Clontech#634936)
0.25 ng of amplified cDNA was used as input for the NexteraXT kit (Illumina #FC-131-1096) and indexed with dual indices (Illumina #FC-131-2001)

tag: cell line

value: induced pluripotent stem cell line C17

tag: days in lung differentiation protocol

tag: facs selection

value: NKX2-1-GFP and Live cells (PI)


title: ips17_C74_E5


title: ips17_C77_E11


title: ips17_C72_D12


title: ips17_C8_B2


title: ips17_C81_F4


title: ips17_C70_D10


title: bP15_1_18

description:
Sample 274
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: β-cell P15-1


title: ips17_C6_A7


title: bP15_1_17

description:
Sample 273
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_16

description:
Sample 272
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C69_D6


title: bP15_2_05

description:
Sample 281
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_15

description:
Sample 271
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C65_C11


title: bP15_1_13

description:
Sample 269
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP60_1_27

description:
Sample 396
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P60, Ins1-RFP+

value: FACS-sorted

value: β-cell P60-1


title: ips17_C64_C10


title: ips17_C62_C5


title: ips17_C63_C6


title: bP15_1_12

description:
Sample 268
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_20

description:
Sample 276
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_19

description:
Sample 275
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_10

description:
Sample 266
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_11

description:
Sample 267
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_09

description:
Sample 265
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C60_B12


title: ips17_C58_B10


title: bP15_1_08

description:
Sample 264
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_07

description:
Sample 263
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_06

description:
Sample 262
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C59_B11

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs


title: ips17_C56_B5


title: ips17_C57_B6


title: bP15_1_05

description:
Sample 261
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C68_D5


title: ips17_C55_B4


title: bP15_1_14

description:
Sample 270
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C54_A12


title: bP15_1_03

description:
Sample 259
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_04

description:
Sample 260
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C53_A11


title: ips17_C52_A10


title: ips17_C51_A6


title: bP15_1_01

description:
Sample 257
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C61_C4


title: bP9_4_12

description:
Sample 256
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P9 Ins1-RFP+; expressing two or more of Pbk, Foxm1 and Cdk1

value: P9, Ins1-RFP+; proliferative cell enriched by PCR

value: β-cell P9-4


title: ips17_C50_A5


title: bP9_4_11

description:
Sample 255
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: Ins1-RFP+; expressing two or more of Pbk, Foxm1 and Cdk1


title: ips17_C4_A9


title: bP9_4_10

description:
Sample 254
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: Pancreas


title: bP9_4_09

description:
Sample 253
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_4_08

description:
Sample 252
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C48_H9


title: bP9_4_07

description:
Sample 251
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C47_H8


title: ips17_C45_H3


title: ips17_C44_H2


title: bP9_4_06

description:
Sample 250
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_4_04

description:
Sample 248
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C46_H7


title: ips17_C42_G9


title: bP9_4_03

description:
Sample 247
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_4_05

description:
Sample 249
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_4_02

description:
Sample 246
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP15_1_02

description:
Sample 258
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P15, Ins1-RFP+


title: bP9_4_01

description:
Sample 245
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C3_A1

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs


title: bP9_3_19

description:
Sample 244
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P9 Ins1-RFP+

value: P9, Ins1-RFP+

value: β-cell P9-3


title: ips17_C39_G3


title: ips17_C36_F9


title: bP9_3_17

description:
Sample 242
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C38_G2


title: ips17_C35_F8


title: bP9_3_15

description:
Sample 240
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_3_14

description:
Sample 239
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C33_F3


title: ips17_C43_H1


title: ips17_C32_F2


title: bP9_3_12

description:
Sample 237
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_3_13

description:
Sample 238
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C31_F1


title: bP9_3_11

description:
Sample 236
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C30_E9


title: ips17_C2_A2


title: bP9_3_10

description:
Sample 235
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C28_E7


title: ips17_C27_E3


title: bP9_3_09

description:
Sample 234
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_3_08

description:
Sample 233
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C37_G1


title: ips17_C26_E2


title: bP9_3_07

description:
Sample 232
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_3_16

description:
Sample 241
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_3_18

description:
Sample 243
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C34_F7


title: bP9_3_06

description:
Sample 231
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C23_D8


title: ips17_C24_D7


title: bP9_3_05

description:
Sample 230
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C22_D9


title: bP9_3_04

description:
Sample 229
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C25_E1

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs


title: bP9_3_03

description:
Sample 228
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C21_D1


title: bP9_3_02

description:
Sample 227
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C20_D2


title: bP9_3_01

description:
Sample 226
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C1_A3


title: ips17_C19_D3


title: bP9_2_23

description:
Sample 225
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: β-cell P9-2


title: bP9_2_22

description:
Sample 224
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C16_C9


title: bP9_2_19

description:
Sample 221
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ips17_C12_B7


title: ips17_C14_C2


title: ips17_C15_C1


title: bP9_2_16

description:
Sample 218
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C9_B1

source_name: ipsc cell line BU3

value: induced pluripotent stem cell line BU3

value: Live cells (PI)


title: BU3_C95_H11


title: ips17_C10_B9


title: ips17_C11_B8


title: bP9_2_13

description:
Sample 215
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_14

description:
Sample 216
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_10

description:
Sample 212
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_11

description:
Sample 213
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_08

description:
Sample 210
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C8_B2


title: BU3_C87_G4


title: BU3_C93_H4


title: bP9_2_09

description:
Sample 211
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C92_H5


title: bP9_2_07

description:
Sample 209
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_17

description:
Sample 219
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C86_G5


title: bP9_2_20

description:
Sample 222
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_06

description:
Sample 208
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_04

description:
Sample 206
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_05

description:
Sample 207
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_15

description:
Sample 217
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C85_G6

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs


title: BU3_C96_H10


title: bP9_2_01

description:
Sample 203
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_02

description:
Sample 204
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_21

description:
Sample 223
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C80_F5


title: BU3_C84_F10


title: BU3_C78_E10


title: ips17_C18_C7


title: BU3_C7_B3


title: BU3_C81_F4


title: bP9_1_21

description:
Sample 200
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: manually-picked

value: β-cell P9-1


title: BU3_C76_E12


title: BU3_C77_E11


title: ips17_C13_C3

value: induced pluripotent stem cell line C17

value: NKX2-1-GFP and Live cells (PI)


title: bP9_1_23

description:
Sample 202
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C75_E4


title: bP9_2_03

description:
Sample 205
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_20

description:
Sample 199
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_2_12

description:
Sample 214
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_19

description:
Sample 198
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C74_E5


title: BU3_C73_E6


title: BU3_C70_D10


title: bP9_1_17

description:
Sample 196
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_16

description:
Sample 195
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_22

description:
Sample 201
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C71_D11


title: BU3_C69_D6


title: bP9_1_15

description:
Sample 194
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_14

description:
Sample 193
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C68_D5


title: BU3_C6_A7


title: bP9_1_09

description:
Sample 188
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_11

description:
Sample 190
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C67_D4

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs


title: bP9_1_12

description:
Sample 191
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C66_C12


title: BU3_C65_C11


title: bP9_1_10

description:
Sample 189
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C64_C10


title: BU3_C60_B12


title: bP9_1_08

description:
Sample 187
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_07

description:
Sample 186
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C61_C4


title: bP9_1_13

description:
Sample 192
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C63_C6


title: BU3_C59_B11


title: bP9_1_06

description:
Sample 185
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C58_B10


title: bP9_1_04

description:
Sample 183
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C57_B6


title: bP9_2_18

description:
Sample 220
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_03

description:
Sample 182
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_02

description:
Sample 181
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C56_B5


title: BU3_C55_B4


title: BU3_C53_A11


title: bP9_1_01

description:
Sample 180
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C52_A10


title: bP3_2_18

description:
Sample 177
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P3 Ins1-RFP+

value: P3, Ins1-RFP+

value: β-cell P3-2


title: bP3_2_19

description:
Sample 178
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: FACS-sorted


title: BU3_C51_A6


title: bP3_2_20

description:
Sample 179
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_16

description:
Sample 175
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_17

description:
Sample 176
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C48_H9

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs


title: BU3_C4_A9


title: BU3_C50_A5


title: bP9_1_05

description:
Sample 184
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C45_H3


title: BU3_C46_H7


title: BU3_C47_H8


title: BU3_C44_H2


title: bP3_2_12

description:
Sample 171
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_15

description:
Sample 174
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_10

description:
Sample 169
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_09

description:
Sample 168
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_08

description:
Sample 167
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C42_G9


title: BU3_C49_A4


title: bP3_2_07

description:
Sample 166
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C40_G7


title: bP3_2_14

description:
Sample 173
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_06

description:
Sample 165
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C41_G8


title: bP3_2_04

description:
Sample 163
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_13

description:
Sample 172
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_03

description:
Sample 162
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP9_1_18

description:
Sample 197
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_05

description:
Sample 164
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C38_G2


title: BU3_C37_G1


title: bP3_2_02

description:
Sample 161
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C36_F9


title: BU3_C35_F8


title: BU3_C34_F7


title: bP3_1_17

description:
Sample 159
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: β-cell P3-1


title: bP3_2_11

description:
Sample 170
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_2_01

description:
Sample 160
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C43_H1

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs


title: BU3_C32_F2


title: bP3_1_16

description:
Sample 158
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C31_F1


title: bP3_1_15

description:
Sample 157
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_1_14

description:
Sample 156
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_1_12

description:
Sample 154
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C2_A2


title: BU3_C39_G3


title: bP3_1_13

description:
Sample 155
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_1_11

description:
Sample 153
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_1_09

description:
Sample 151
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C30_E9


title: BU3_C3_A1


title: bP3_1_07

description:
Sample 149
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C29_E8


title: BU3_C23_D8


title: bP3_1_06

description:
Sample 148
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_1_04

description:
Sample 146
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_1_05

description:
Sample 147
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C19_D3


title: bP3_1_03

description:
Sample 145
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C20_D2


title: BU3_C25_E1


title: BU3_C26_E2


title: BU3_C18_C7


title: BU3_C24_D7


title: bP3_1_02

description:
Sample 144
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_1_01

description:
Sample 143
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C16_C9


title: bP0_3_09

description:
Sample 142
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P0 Ins1-RFP+; expressing two or more of Pbk, Foxm1 and Cdk1

value: P0, Ins1-RFP+; proliferative cell enriched by single-cell RT-qPCR

value: β-cell P0-3


title: bP0_3_08

description:
Sample 141
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: Pancreas

value: Ins1-RFP+; expressing two or more of Pbk, Foxm1 and Cdk1


title: BU3_C15_C1

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs


title: BU3_C14_C2


title: bP3_1_10

description:
Sample 152
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP0_3_07

description:
Sample 140
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP3_1_08

description:
Sample 150
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C12_B7


title: BU3_C22_D9


title: bP0_3_06

description:
Sample 139
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C21_D1


title: BU3_C11_B8


title: PB-Gbx2

city: Hefei

first: Manman

last: Wang

address: No 111, Jiu Long Road

institute: anhui university

data_processing:
Illumina Hiseq3000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to m38 whole genome using STAR software
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the expression values of this transcript expressed in FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) for each Sample ...

source_name: empty vector-transfected control 46C embryonic stem cells

growth_protocol: ESCs were routinely maintained on gelatin-coated plates in the conventional mouse ESC medium

extract_protocol:
RNA was harvested using Trizol reagent.TruSeq® RNA LT Sample Prep Kit v2  was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Inner cell mass of pre-implantation embryo

tag: passages


title: bP0_3_05

description:
Sample 138
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C10_B9


title: bP0_3_03

description:
Sample 136
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP0_3_02

description:
Sample 135
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: S3 HeLa cells CF25Im KD

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
CASAVA or MiSeq Reporter demultiplexing
Custom trimming and filitering to remove poly(A) tails (See Routh et al)
Mapping of processed reads to hg19 with HiSat2
Custom Scripts to extract poly(A) site and frequency (see Routh et al)
Genome_build: hg19
Supplementary_files_format_and_content: BEDGraph (4 tab-delimted columns: chromosome number \t start coordinate \t end coordinate \t read count)

source_name: HeLa Cells in culture

extract_protocol:
TRIzol Extraction from cells in culture
Poly(A)-ClickSeq (PAC-seq) libraries where generated using oligo-dT primers carrying partial p7 Illumina adaptors in RT-PCR reactions supplemented with azido-terminating nucleotides (AzVTPs). Azido-blocked cDNAs covering the junction of the 3'UTR and poly(A) tails were thus generated and were 'click-ligated' to p5 Illumina sequencing adaptors using the 'ClickSeq' methodology. These cDNA libraries were amplified by PCR to fill-in the Indexing sequences and the rest of the p7 adaptor.

value: HeLa

tag: treatment

value: CF25Im KD


title: S2 HeLa cells CF25Im KD


title: hCMEC 2

city: West Lafayette

first: Xiaoping

last: Bao

state: Indiana

address: 480 Stadium Mall Drive

department: Chemical Engineering

institute: Purdue University

data_processing:
Casava1.8 software used for basecalling
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2
the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Primary Cardiac Microvascular Endothelial Cells

growth_protocol: hPSC-derived endocardial endothelial cells were generated from day 20 hPSC-derived epicardial cells by treatment of VEGF from day 20-25 and A83-01 from day 25 to 30.

extract_protocol:
RNA of hPSC-derived and primary cardiac endothelial cells was harvested using Trizol reagent. NuGEN Ovation RNA Library Prep was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard NuGEN protocols

value: Heart

value: Human Adult


title: PB

source_name: Gbx2-overexpressed 46C embryonic stem cells


title: bP0_3_01

description:
Sample 134
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H9 EEC 2

source_name: hPSC-derived Endocardial Endothelial Cells

value: day 30 from hPSC


title: H13 EEC 2


title: BU3_C17_C8

value: induced pluripotent stem cell line BU3

value: Live cells (PI)


title: bP0_2_29

description:
Sample 133
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: P0 Ins1-RFP+

value: P0, Ins1-RFP+

value: β-cell P0-2


title: hCMEC 1


title: aP0_3_16

description:
Sample 950
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: Pancreas

value: P0, Gcg-Cre, Rosa-RFP+; Gcg+, Ghrl+

value: manually-picked

value: α-cell P0-3


title: S1 HeLa cells CF25Im KD


title: aP0_3_15

description:
Sample 949
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P0, Gcg-Cre, Rosa-RFP+; Gcg+, Ins1+


title: H13 EEC 1


title: aE17.5_4_08

description:
Sample 948
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: E17.5, Gcg-Cre, Rosa-RFP+; Gcg+, Ins1+


title: bP60_3_30

description:
Sample 946
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P60, Ins1-RFP+; Ins1+, Gcg+

value: β-cell P60-3


title: C1 HeLa cells mock

value: mock


title: H9 EEC 1


title: C2 HeLa cells mock

value: HeLa


title: aP60_5_13

description:
Sample 942
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P60, Gcg-Cre, Rosa-RFP+

value: FACS-sorted

value: α-cell P60-5


title: aP60_5_15

description:
Sample 944
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_5_16

description:
Sample 945
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_5_11

description:
Sample 940
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ST_22DAP_biorep1

city: Madison

first: Marisa

middle: S

last: Otegui

state: WI

address: 1525 Linden Dr.

department: Botany

institute: University of Wisconsin-Madison

description:
ST_22DAP_expressions_of_biorep.xlsx
AL_ST_at18and22DAP_averageTPM.xlsx

data_processing:
The quality of all sequencing reads were checked using software fastqc. We trimmed away any polyA sequence and any adapter sequences as well as low quality bases (quality score < 20) at the beginning and end of all reads.
The RNA-sequencing data were aligned to the maize B73 version 3 genome (B73 RefGen_v3) (Hubbard et al., 2002) and the version 3.26 gene model (Maize gene model AGP3.26, 2015) using RSEM version 1.2.15 (Li and Dewey, 2011). The RSEM program first used Bowtie2 version 2.2.3 (Langmead and Salzberg, 2012) to align the RNA-sequencing reads to exons and SAMtools version 0.1.19-44428cd (Li et al., 2009) to sort the aligned reads, and then estimated the gene expression levels. We also provided the fragment-length mean and standard deviation (300bp and 33bp, respectively) of the RNAseq data to RSEM for alignment as well. All other parameters were left as default in RSEM.
TPM was chosen as the measurement for relative gene expression levels. To increase the accuracy of our reported TPM and reduce variation caused by difference in sequencing depth, we used the average TPM of all available biological replicates as the TPM of a gene if and only if all biological replicates have TPM>0. Otherwise, the gene was treated as not expressed, i.e. TPM=0.
Genome_build: B73 RefGen_v3
Supplementary_files_format_and_content: excel files containing estimated expressions of each gene in individual biological replicate of all tissues collected; one excel file containing averaged gene expressions (TPM) for all tissues we collected

organism: Zea mays

source_name: starchy endosperm cells

growth_protocol: Maize (Zea mays, inbred B73) were grown in a greenhouse under a 14-hour-light/10-hour-dark photoperiod, supplemental lighting (700 μmol m-2 s-1), and average temperature of 28°C during the light period and 21°C during the dark period.

extract_protocol:
Kernels from two biological replicate plants were collected at 18DAP and 22DAP, respectively. The kernels were stored at -80°C until tissue extraction. The aleurone cell layer and starchy endosperm excised by mechanical peeling after defrosting, and carefully rinsed using distilled water before further processing for RNA-sequencing. For constructing and sequencing RNA-seq libraries, RNA from the collected aleurone and starchy endosperm samples. Starchy endosperm tissue and aleurone peels were mechanically dissected, frozen in liquid nitrogen, and ground in NTES buffer (20 mM Tris-HCl, pH 8.0, 100 mM NaCl, 10 mM EDTA, and 1% SDS) to avoid starch solubilization. Nucleic acids were extracted three times using Tris-buffered phenol/chloroform (1:1), pH 8, followed by 10,000g centrifugation. The RNA present in the aqueous phase was later purified using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. One microgram of total RNA was reversely transcribed to the first strand of the cDNA using oligo(dT) in a 20-mL reaction volume using AMV transcriptase (Promega). RNA quality was checked using Agilent Bioanalyzer for one of each pair of biological replicates and all RNA samples had RNA integrity number >=7.6 which is close to Illumina’s recommendation of RNA integrity number >=8.
RNA-Seq libraries were made according to the TruSeq RNA protocol; 1mg of total RNA was used for all of libraries (mean size approximately 300bp, standard deviation approximately 30bp).

value: starchy endosperm cells

value: 22 day after pollination

tag: inbred line


title: AL_22DAP_biorep2

description:
AL_22DAP_expressions_of_biorep.xlsx
AL_ST_at18and22DAP_averageTPM.xlsx

source_name: aleurone cells

value: aleurone cells


title: aP60_5_10

description:
Sample 939
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: AL_22DAP_biorep1


title: aP60_5_07

description:
Sample 936
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_5_09

description:
Sample 938
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ST_18DAP_biorep1

description:
ST_18DAP_expressions_of_biorep.xlsx
AL_ST_at18and22DAP_averageTPM.xlsx

value: 18 day after pollination


title: aP60_5_08

description:
Sample 937
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ST_22DAP_biorep2


title: aE17.5_4_07

description:
Sample 947
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: E17.5, Gcg-Cre, Rosa-RFP+; Gcg+, Ppy+, Sst+


title: aP60_5_05

description:
Sample 934
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: AL_18DAP_biorep2

description:
AL_18DAP_expressions_of_biorep.xlsx
AL_ST_at18and22DAP_averageTPM.xlsx


title: C3 HeLa cells mock


title: aP60_5_04

description:
Sample 933
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: AL_18DAP_biorep1


title: aP60_5_02

description:
Sample 931
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: ST_18DAP_biorep2


title: aP60_5_14

description:
Sample 943
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_5_12

description:
Sample 941
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_15

description:
Sample 928
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: α-cell P60-4


title: aP60_5_03

description:
Sample 932
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_12

description:
Sample 925
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: manually-picked


title: aP60_4_13

description:
Sample 926
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_14

description:
Sample 927
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_11

description:
Sample 924
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_5_06

description:
Sample 935
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_08

description:
Sample 921
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_09

description:
Sample 922
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_10

description:
Sample 923
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_03

description:
Sample 916
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_05

description:
Sample 918
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_06

description:
Sample 919
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_04

description:
Sample 917
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_02

description:
Sample 915
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_01

description:
Sample 914
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_3_14

description:
Sample 912
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: α-cell P60-3


title: aP60_5_01

description:
Sample 930
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: bP0_3_04

description:
Sample 137
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: Pancreas

value: Ins1-RFP+; expressing two or more of Pbk, Foxm1 and Cdk1

value: P0, Ins1-RFP+; proliferative cell enriched by single-cell RT-qPCR

value: β-cell P0-3


title: aP60_3_15

description:
Sample 913
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_4_16

description:
Sample 929
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BU3_C13_C3

description:
Rsem counts with ensembl gene IDs
Rsem fpkm values with ensebl gene IDs
TMM normalized CPM values with NCBI gene IDs

value: induced pluripotent stem cell line BU3

value: Live cells (PI)


title: zebrafish3 FAIRE-seq

city: Durham

first: John

last: Rawls

state: North Carolina

address: Duke University 213 Research Drive, Box 3580 DUMC CARL Building 327

institute: Duke University

description:
processed data file:
AIEC_danrer7_Q.01_merge_peaks.bed

library_source: genomic

data_processing:
Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2(v2.0.9) with default conditions using Galaxy(0.5)
Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotations(Ensemble genes 71) using Galaxy(0.0.5)
bigWig files were generated using bamCoverage (Galaxy verion 2.2.3.0) and read normalized
Genome_build: danRer7
Supplementary_files_format_and_content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information

molecule: genomic DNA

organism: Danio rerio

source_name: Intestinal Epithelial Cells_FAIRE-seq

growth_protocol: TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets

extract_protocol:
To isolate zebrafish IECs, intestines were dissected, splayed, and washed extensively with ice-cold 1x PBS with care taken to remove as much intestine associated fascia, adipocytes, and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 (DR1; 30 mM EDTA, 1.5 mM DTT, 0.5x Complete protease inhibitors (Roche), in 1x PBS) for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 (DR2; 30 mM EDTA, 0.5x Complete protease inhibitors (Roche), in PBS) and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C, washed once with 13 ml of cold 1X PBS, and re-suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE, and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE, freshly isolated intestinal epithelial cells were directly fixed for 5-10 minutes in 10 ml of 1-3% w/v Formaldehyde solution (in 1x PBS) at room temperature and gentle rocking. Glycine (2.5M) was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without dissociating the pellet. Fixed and washed cell pellets were flash frozen and stored at -80°C. Cells were lysed in 2 ml Lysis Buffer A (10 mMTris-HCl (pH8.0), 2% (vol/vol) Triton X-100, 1% SDS, 100 mM NaCl and 1 mM EDTA) and sonicated using a Branson Sonifier 450D equipped with a microtip for 6-13 cycles (1 second burst, 0.5 second pause, for 30 seconds/cycle at 70% intensity) allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent.
UNC Highthrough-put Sequencing Core performed TruSeq library preperation.

value: TL

value: Zebrafish Adult Intestinal Epithelial Cells


title: zebrafish2 FAIRE-seq


title: aP60_3_09

description:
Sample 907
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P60, Gcg-Cre, Rosa-RFP+


title: aP60_3_12

description:
Sample 910
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_3_13

description:
Sample 911
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: zebrafish1 FAIRE-seq


title: aP60_3_10

description:
Sample 908
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_3_11

description:
Sample 909
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: zIEC3 mRNA

source_name: Intestinal Epithelial Cells_RNA-seq


title: aP60_4_07

description:
Sample 920
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_3_08

description:
Sample 906
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: zIEC2 mRNA


title: aP60_3_07

description:
Sample 905
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_3_06

description:
Sample 904
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: zebrafish4 FAIRE-seq


title: zIEC1 mRNA


title: aP60_3_04

description:
Sample 902
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: HeLa_500ng_PACSeq

treatment_protocol: New samples are PACseq libraries of serially diluted samples of the same original sample of HeLa total cellular RNA. Serial dilutions were performed to establish the minimal requirement for starting RNA in PACseq.

value: HeLa

value: mock

tag: dilution


title: H6_D3

city: Chicago

first: Lauren

middle: Elizabeth

last: Blake

state: Illinois

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
50 bp single-end RNA-seq reads from each species were trimmed and mapped to the appropriate genome (hg19 or panTro3) using Tophat2 (version 2.0.11) (Kim et al. 2013). We kept only reads that mapped uniquely.
The number of reads falling into orthologous meta-exons across 30,030 Ensembl genes from hg19, panTro3 and rheMac3 (Blekhman et al. 2010) was determined using featureCounts within SubRead (version 1.4.4) (Liao et al. 2014).
Genome_build: hg19 & panTro3
Supplementary_files_format_and_content: RNA-seq counts for orthologous genes for all individuals

source_name: iPSC-derived definitive endoderm cells

growth_protocol: Feeder free cultures were initially maintained on Growth Factor Reduced Matrigel using Essential 8 Medium (E8) as previously described. After 10 passages in E8, all cell lines were transitioned to iDEAL feeder free medium that was prepared in house (Marinho et al. 2015). Cell culture was conducted at 37°C, 5% CO2, and atmospheric O2.

extract_protocol:
RNA was extracted using the ZR-Duet DNA/RNA MiniPrep kit (Zymo) with the addition of an on column DNAse I treatment step prior to RNA elution.
Samples were pooled together in 4 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit v2.  50 bp sing-end RNA-seq libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.

treatment_protocol: To produce definitive endoderm and intermediate cell types, we followed a recently published three-day protocol that systematically identified and targeted pathways involved in cell fate decisions, at critical junctures in endoderm development (Loh et al. 2014) with minimal modification. At 12 hours prior to initiating differentiation, iPSC lines at 70-90% confluence were seeded at a density of 50,000 cells/cm2. Basal medial for differentiations consisted of 50/50 IMDM/F12 basal media supplemented with 0.5 mg/mL human albumin, 0.7 g/mL Insulin, 15 g/mL holo-Transferrin and 1% v/v chemically defined lipid concentrate. For differentiation, basal media was supplemented with the following: day 1 (Primitive streak induction) media included 100 ng/mL Activin A, 50 nM PI-103 (PI3K inhibitor), 2 nM CHIR99021 (Wnt agonist), days 2-3 media included 100 ng/mL Activin A and 250 nM LDN-193189 (BMP inhibitor). Two separate batches of differentiation were performed, resulting in replicates for a subset of samples. Cell culture was conducted at 37°C, 5% CO2, and atmospheric O2.

tag: Sex

value: Female

tag: population

value: Caucasian


title: H5B_D3

value: Male


title: H4_D3


title: aP60_3_03

description:
Sample 901
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: Kc_HiC-seq_rep1

city: Cambridge

first: Rob

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

data_processing:
library strategy: HiC-seq
Paired end HiC reads were aligned against Drosophila genome BDGB release 5 with HiCUP (v0.5.7) (http://www.bioinformatics.babraham.ac.uk/projects/hicup/). Mapping and read filtering with HiCUP was performed using bowtie2 (v 2.2.6) and the default HiCUP parameters.
Genome_build: dm3 (Drosophila genome BDGB release 5)
Supplementary_files_format_and_content: HiC interactions of both replicates were combined and binned at 10kb resolution, which are provided in WT12_bin10kb_raw_interactions.txt.gz. Interactions were then normalised uding GOTHiC (v1.6.0) R package, however as HiCUP already filteres undigested fragments the filterdist was set to 0 and we set removeDiagonal = FALSE in the internal binomialHiC function. The reported normalised interaction counts in WT12_bin10kb_normalised_interactions.txt.gz are observed/expected counts. HiC segements were identified on chr2L, chr2R, chr3L, chr3R, chr4 and chrX from the normalised contact matrices using HiCseg (v1.1) R package , however 10% of the lowest linear portion of log-likelihood segment borders were removed. The WT12_bin10kb_HiCseg.bed.gz file contains the identified borders.
Supplementary_files_format_and_content: Kc_rep1rep2_bin10kb_raw_interactions.txt.gz; extended bed file with 2 locations and raw counts in 7th column
Supplementary_files_format_and_content: Kc_rep1rep2_bin10kb_normalised_interactions.txt.gz; extended bed file with 2 locations and normalised observed/expected counts in 7th column

organism: Drosophila melanogaster

source_name: HiC Kc cells

growth_protocol: Kc cells were grown to 80-90% confluence in Schneider’s Drosophila medium with 5%FBS and antibiotics (Pen-Strep) in 100 mm cell culture plates.

extract_protocol:
Cells from 6 plates were harvested into sterile 50 ml centrifuge tubes. The cells were collected by centrifugation at 1200 rpm for 5 min at 4 ◦C.  The cells were re-suspended in 10 ml fresh medium and the cell concentration was determined using a haemocytometer. A cell concentration to 1 x10E8 was resuspended in 45 ml of fresh medium. The cells were then fixed by adding 1.25 ml 37% formaldehyde solution and incubating them with gentle shaking in a platform
shaker at room temperature for 10 min. The reaction was stopped by adding 2.5 ml 2.5M glycine and further incubation at room temperature for 5 min followed by 15 min on ice. The cross-linked cells were divided into 4 x 15 ml falcon tubes (~12.3 ml per tube). The cells were then collected at 1500 rpm for 10 min at 4 ◦C. The supernatant was discarded and the fixed cells were flash frozen in liquid nitrogen then stored at -80◦C.  Restriction enzyme digestion: The cells were thawed on ice (~2.0 x10E7 cells) and 500 μl of lysis buffer (10 mM Tris-Cl, pH 8.0; 10 mM NaCl, 0.2% Igepal CA360) and 50 ul of protease inhibitor cocktail (Sigma) were added. Cells were lysed with 15 strokes of a Dounce homogeniser using the tight pestle (Pestle A). The cell suspension was transferred to a microcentrifuge tube and spun at 5000 rpm at room temperature for 5 min. The supernatant was discarded and the pellet washed twice with 0.5 ml of ice-cold 1.20x NEBuffer 3, 5000 rpm, 5 min, at room temperature. The pellet was then resuspended in 500 μl of ice-cold 1.20x NEBuffer 3 and add 7.5 ul of 20% SDS.  This was incubated at 37◦C with shaking at 900 rpm for 1h. 50 μl of 20% Triton X-100 was added and further incubated at 37◦C, 900 rpm for 1h. A 50 μl aliquot was taken and stored at -20 °C to serve as undigested control. 45 μl of 1.20x NEBuffer 3 was then added to the remaining lysate. 400 U (8 μl) of 50U/μl Dpn II was then added and the digestion reaction was incubated at 37◦C with shaking at 900 rpm overnight. Blunt ending fragments with Klenow enzyme: The restriction enzyme reaction was incubated at 65°C for 20 min to inactive Dpn II. The inactivated reaction was dispensed into five 100μl aliquots in fresh microfuge tubes. Tube 1 was designated as a 3C control and Tubes 2-5 were used as Hi-C samples. To the Hi-C samples 0.35 μl each of 10 mM dCTP, dGTP and dTTP and 8.75 µl of 0.4 mM biotin-14-dATP and 5 µl of 5U/µl Klenow enzyme (DNA Polymerase I, NEB M210S) was added and then incubated at 37°C for 45 min.  Ligation: Two hundred ul of 10 mM Tris-HCl with 1%SDS to each blunt-ended reactions and the 3C control tube. This was then transferred to a fresh 50 ml tube containing 700 µl 10x T4 DNA Ligase Buffer (NEB) and 5894 µl molecular biology grade water. Then 106 ul 20% Triton X-100 was added and the mixture Incubated for 1 h at 37 C with gentle shaking. After which 10000U ligase was added and then incubated for 18h at 16◦C followed by 30 min at room temperature.   De-crosslinking and DNA purification: Thirty μl of 10 mg/ml PK (300 μg final) was added to the reaction and incubated at 65◦C overnight. Then 10 μl of 30 mg/ml RNase A (SIGMA) was added and the reaction was incubated at 37◦C for 45 min. Seven ml phenol-chloroform-isoamyl alcohol (PCI) was added and mixed vigorously by vortexing. The mixture was transferred to a 50 ml Phase Lock Gel (5 Prime, 2302860) and centrifuged at 2200 xg for 15 min at room termperature. The aqueous phase was transferred to a fresh 50 ml tube and 7 ml of distilled water, 1.5 ml 3M NaAcetate pH 5.2, and 35 ml 100% ice-cold ethanol were added. The mixture was incubated at -80◦C for 1 h then centrifuged at 2200 xg, 4◦C, for 45 minutes. The pellet was washed with 10 ml 70% ethanol at 2200 xg at 4°C for 15 min and the pellet dried at at room temperature for 10-15 min. The pellet was then re-suspended in 150 μl of 10 mM Tris-HCl pH 8.0 and allowed to dissolve overnight at 4°C. The purified DNA was then transferred to a microcentrifuge tube at stored at -20°C.   Re-purification of DNA: A 150 μl volume of 10 mM Tris-HCl pH 8.0 was added to the dissolved pellet and 300 μl PCI was added to each tube. These were then mixed and centrifuged at 13,200 rpm for 5 min at room temperature in a Phase Lock tube. PCI purification was then repeated on the aqueous phase. After which the DNA was precipitated by adding 30 µl 3M NaAcetate, pH 5.2 and 2.5 volumes of ice-cold 100% ethanol. The mixture was incubated at -80◦C for at least 45 min then centrifuged for 20 min at 13000 rpm at 4◦C. The pellet was washed with with 0.5 ml of ice-cold 70% and air-dried briefly.  The pellet was then resuspended in 25 μl l TLE Buffer (10 mM Tris-Cl pH 8.0, 0.1 mM EDTA). The Hi-C DNA preparations were pooled into a single tube and the concentration measured using a Qubit photometer.  Removal of biotin from unligated ends and shearing of Hi-C DNA: For every 5 μg of Hi-C DNA preparation, the following were added: 1 µl 10 mg/ml BSA, 10 µl 10X NEBuffer 2, 1 µl 10mM dGTP, 1.67 µl (5U) T4 DNA polymerase and water to a total volume of 100 µl. Incubate mixture at 12 °C for 2 hr and stop reaction by adding 2 µl 0.5 M EDTA pH 8.0. DNA was then purified by adding 1 vol of PCI and centrifuging the mixture at 13200 rpm for 5 min at room temperature in a Phase Lock tube. The DNA in the aqueous phase was precipitated by adding 10 μl 3M NaAcetate, pH 5.2 and 2.5 vol ice-cold 100% ethanol. The mixture was incubated at -80◦C for at least 30 min then centrifuged for 20 min at 13000 rpm at 4◦C. The pellet was washed with 0.5 ml of ice-cold 70% ethanol. And the pellet dissolved and pooled in a total volume of 100 μl of water. Hi-C DNA preparation was sheared at 4°C for 20 min in 30 sec pulses at low setting using a Bioruptor sonicator (Diagenode).
One and a half ug sheared DNA was end repaired, poly-A tailed and adapter ligated using the TruSeq Kit (Illumina). The adapter ligated Hi-C library was run in a 1.5% agarose gel in 0.5X TBE at 50V for 2 h. The gel was stained with Sybr Gold and DNA fragments ~250 to 750 bp in size were cut out and purified using a Qiagen Gel Extraction Kit. The DNA was eluted with 50 µl of TLE buffer and the final volume adjusted to 300 µl with water. Biotin tagged size selected Hi-C DNA was purified using Dynabeads MyOne Streptavidin Beads (Invitrogen). One hundred fifty µl of resuspended beads were prepared according to manufacturer’s instructions. These were then re-suspended in 300 µl 2x Binding Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl) and combined with 300 μl of repaired Hi-C DNA. The biotin-labelled Hi-C DNA was allowed to bind the streptavidin beads by incubating the mixture at room temperature for 15 min in a rotator. The beads were then washed in 400 µl 1x binding buffer followed by a single wash with 100µl 1x ligase buffer. The beads were then re-suspended in 50µl 1x ligase buffer and submitted to the Eastern Sequencing and Informatics (EASIH) for library preparation and 76-bp paired-end sequencing on an Illumina GAIIx sequencer.

value: Kc cells


title: HeLa_125ng_PACSeq


title: aP60_3_01

description:
Sample 899
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: manually-picked


title: H2_D3


title: HeLa_2ug_PACSeq


title: aP60_2_16

description:
Sample 898
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: α-cell P60-2


title: aP60_3_02

description:
Sample 900
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: α-cell P60-3


title: oxidized rep2 miseq

city: Farmington

first: Gordon

middle: G.

last: Carmichael

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

description:
RNA-seq (second strand)
Processed data file: DESeq2_miseq_output.txt
Processed data file: base_call_miseq.txt

data_processing:
Raw reads are trimmed using Cutadapt v1.12 to first read-through sequences for both R1 and R2 as many of the inserts can be shorter than 75bp.
A simple custom python script is used to remove PCR duplicates by comparing R2 randomer sequences in combination with actual RNA 3' end sequences.
Cutadapt is used to remove randomer and linker from R2.
Tophat 2.1.1 is used to align to hg19 with GTF of chrUn supplied, -T option is used so that reads are only mapped to chrUn. Samtools 0.1.19 is used to sort alignment files. It is also used to randomly sample alignment files if the total reads of a sample is significantly more than others to generate a smaller alignment file for subsequent analysis.
All alignment files are converted to BED files using Samtools. Read 3' single base count data is generated with a simple in-house python script. The count data files are used for DESeq2 (Bioconductor version 3.4) analysis. The DESeq2 output is then filtered and bases of interest are determined.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_count.txt files (raw read 3' end base counts) are tab-delimited single-base count data calculated from .BED (converted from alignment .BAM files) for each sample. The 3' end base of each fragment that is sequenced is the base of interest, thus ending position counts from .BED files are taken and summed for each position within the 18S and 28S rRNA region within chrUn (position 109078-118417).
Supplementary_files_format_and_content: In this case, only + strands are counted since the 18S and 28S of the chrUn we use are transcribed in sense direction. hg19 base position numbers are converted to numbers corresponding to base positions within each rRNA gene.
Supplementary_files_format_and_content: Each experimental set (i.e. MiSeq or NextSeq) has one DESeq2 output file generated by feeding all count.txt files of control and oxidized replicates to DESeq2 for normalization and statistical calculations.
Supplementary_files_format_and_content: Log2 fold change and adjusted p-values from DESeq2 output (normalized abundance measurements) are used to filter for the final base calls and are saved in the tab-delimited base_call.txt files (normalized abundance measurements filtered by log2 fold change and adjusted p values).

source_name: PA1 cell line

extract_protocol:
Total RNA extraction using PureLink® RNA Mini Kit (ThermoFisher Scientific, 12183025) and PureLink® DNase Set (ThermoFisher Scientific, 12185010) following kit protocols.
Processed RNAs 3' are first ligated to a preadenylated and 3' blocked DNA linker. RT primer (includes a 6-base randomers) is then annealed with the ligation product. Then a 5' RNA linker is ligated. RT is subsequently performed followed by PCR amplification with Illumina compatible primers (adapter+barcodes included) to generate the final sequencing library.

value: PA1 (ATCC, CRL-1572)

tag: passage

tag: sample type

value: oxidized


title: H1A_D3


title: H1B_D3


title: aP60_2_15

description:
Sample 897
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

tag: cell type

tag: collection method


title: oxidized rep1 miseq


title: Kc_HiC-seq_rep2


title: aP60_2_14

description:
Sample 896
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

tag: batch


title: H5A_D3


title: H5B_D2

source_name: iPSC-derived endoderm progenitor cells


title: aP60_3_05

description:
Sample 903
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H6_D2


title: aP60_2_12

description:
Sample 894
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H5A_D2


title: HeLa_1ug_PACSeq


title: aP60_2_13

description:
Sample 895
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: non-oxidation control rep1 miseq

value: non-oxidized control


title: HeLa_250ng_PACSeq


title: H3_D3


title: aP60_2_10

description:
Sample 892
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H3_D2


title: AML MLL-AF9 patient_2

city: Montreal

first: Magalie

last: Celton

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: IRIC

data_processing:
the fastq files obtained from MiSeq and HiSeq were concatenated
Pair-end sequences were mapped to human reference genome (GRCH37/hg19) using  Bismark v0.10.1 and Bowtie 2 v2.2.5 as alignment
Bismark-methyaltion-extractor used for methylation calls extraction
PCR duplicate were removed using a Perl script provided by Krueger and Andrews,2011
Levels of methylation were calculated usting R packeage MethylKit v0.9.2 (Akalin et al., 2012)
Data were filtered with a number reads minimal of 8
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FreqC  values corresponding to the percentage of methylation for all sequenced cytosines for each sample:
Supplementary_files_format_and_content: chrBase  Identifiant: chromosome  chr  chromosome  base  position in the chromosome   strand  Forward (F) or Reverse (R) strand of DNA   coverage  numbers of reads  freqC  number of methylated cytosines/  Total of cytosines (methylated + unmethylated)  freqT  number of unmethylated cytosines/  Total of cytosines (methylated + unmethylated)

source_name: cord blood cells

growth_protocol: Human CD34+ cord blood cells were positively selected (CD34  cells). Cells were transduced with a retrovirus containing GFP and the human MLL-AF9 fusion gene and were maintained for  in vitro culture for 80-90 days (CD34-MLL-AF9 cells).  Transduced cells were expanded in myeloid promoting culture with 15% FSC +IL3 +SCF for 4 weeks. After ~30 days of expansion cells (10 x106/mouse) from each donor sample were injected into multiple NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) immunodeficient mice. Mice were analyzed after ~20-24 weeks and the bone marrow was harvested (Model AML MLL_AF9 samples).

extract_protocol:
Genomic DNA was isolated from the cell pellets using the PureLink Genomic DNA Mini Kit.
Methyl-seq libraries were prepared for sequencing using Agilent SureSelextXT Human Methyl-seq Target enrichment system protocols

value: Fresh cord blood collect from one adult AML patient used to isolate CD34+ and monocyte


title: aP60_2_11

description:
Sample 893
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H2_D2


title: H4_D2


title: H1B_D2


title: CD34-MLL-AF9_R2

value: CD34+ transduced with a retrovirus containing human MLL-AF9 fusion gene


title: non-oxidation control rep2 miseq


title: aP60_2_08

description:
Sample 890
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H1A_D2


title: aP60_2_09

description:
Sample 891
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_2_07

description:
Sample 889
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_2_05

description:
Sample 887
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: AML MLL-AF9 patient_1


title: aP60_2_06

description:
Sample 888
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: CD34-MLL-AF9 _R1


title: CD34_R1

value: CD34+ cells enriched cord blood cells from one single healthy donors


title: aP60_2_03

description:
Sample 885
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: AML MLL-AF9 patient_3


title: H5B_D1

source_name: iPSC-derived primitive streak cells


title: H5A_D1


title: H4_D1


title: H3_D1


title: aP60_2_02

description:
Sample 884
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz