title: E13.24H_141215_12_7


title: BM_SiglecH-Ly6CꚷDC_15

status: Public on May 10 2019

type: SRA

city: Singapore

first: Jinmiao

last: Chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description:
RMB850
single cell

library_source: transcriptomic

data_processing: Raw reads were aligned to the mouse reference genome GRCm38 from GENCODE using RSEM program version 1.2.19 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the mouse GENCODE annotation version 4.

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: primary cells

extract_protocol:
bones were removed, bone marrow was flushed out, red blood cells were lysed prior antibody staining, progenitor cells were enriched using magnetic beads prior FACS sorting, IFC capture, on-chip lysis & rt-pcr Nextera_XT Kit (Illumina, PN FC-131-1096) with dual indices (Illumina, PN FC-131-1002) was used to prepare single-cell multiplexed libraries
Cells were loaded onto C1 integrated fluidic circuits IFC (5- to 10-μm chip) for cell lysis, reverse transcription with oligo (dT) primers and amplification of cDNA on a C1 Single Cell Auto Prep System according to the mRNA-seq protocol of the manufacturer (Fluidigm). Only cells with high-quality cDNA were processed for subsequent library preparation. A Nextera_XT Kit (PN FC-131-1096; Illumina) with dual indices (PN FC-131-1002; Illumina) was used for the preparation of single-cell multiplexed libraries.

treatment_protocol: untreated

tag: tissue

value: Bone marrow

tag: strain

tag: age

value: adult 7-10 weeks

tag: cell population


title: E13.24H_141215_12_20

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

data_processing:
The 5bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
reads are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_count.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.

molecule: polyA RNA

source_name: cortical cells

extract_protocol:
The putative primary somatosensory cortex S1 was microdissected and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, fetal bovine serum was added to the mix and cells were manually dissociated via up-and-down pipetting. Cells were centrifuged 5min at 300g and the pellet was suspended in 1ml of HBSS then passed on a 70µm cell stainer. FT+ cells, gated on the top 5% brightest cells, were finally FAC-sorted on a MoFloAstrios (Beckman). FAC-sorted FT+ cells (18µl) were mixed with the C1 Suspension Reagent (2µl; Fluidigm) yielding a total of 20µl of cell suspension mix with ~500 cells/μl. The cell suspension mix was loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10- to 17-µm cells (HT-800, Fluidigm #100-57-80). cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). Single cell RNA-sequencing libraries of the cDNA were prepared using Nextera XT DNA library prep kit (Illumina). Libraries were multi-plexed and sequenced according to the manufacturer’s recommendations with paired-end reads using HiSeq2500 platform (Illumina) with an expected depth of 1M reads per single cell, and a final mapping read length of 70bp.
SMARTseq v4 kit (Clontech, # 634888)

tag: cluster


title: E13.24H_141215_12_9


title: BM_SiglecH-Ly6CꚷDC_13

description:
RMB852
single cell


title: BM_SiglecH-Ly6CꚷDC_14

description:
RMB851
single cell


title: E13.24H_141215_12_1


title: BM_SiglecH-Ly6CꚷDC_12

description:
RMB853
single cell


title: E13.24H_141215_11_38


title: BM_SiglecH-Ly6CꚷDC_10

description:
RMB855
single cell


title: E13.24H_141215_11_36


title: E13.24H_141215_11_35


title: BM_SiglecH-Ly6CꚷDC_9

description:
RMB856
single cell


title: BM_SiglecH-Ly6CꚷDC_7

description:
RMB860
single cell


title: E13.24H_141215_12_31


title: E13.24H_141215_11_33


title: BM_SiglecH-Ly6CꚷDC_5

description:
RMB862
single cell


title: BM_SiglecH-Ly6CꚷDC_16

description:
RMB848
single cell


title: E13.24H_141215_11_32


title: BM_SiglecH-Ly6CꚷDC_6

description:
RMB861
single cell


title: E13.24H_141215_11_34


title: BM_SiglecH-Ly6CꚷDC_4

description:
RMB863
single cell


title: E13.24H_141215_12_3


title: E13.24H_141215_11_28


title: BM_SiglecH-Ly6CꚷDC_3

description:
RMB864
single cell


title: BM_SiglecH-Ly6CꚷDC_2

description:
RMB865
single cell


title: E13.24H_141215_11_25


title: BM_SiglecH-Ly6CꚷDC_1

description:
RMB866
single cell


title: E13.24H_141215_11_24


title: E13.24H_141215_11_29


title: BM_SiglecH-Ly6CꚷDC_11

description:
RMB854
single cell


title: E13.24H_141215_11_39


title: E13.24H_141215_11_37


title: E13.24H_141215_11_20


title: BM_SiglecH⼮苺髞DC_43

description:
RMB913
single cell


title: E13.24H_141215_11_18


title: BM_SiglecH-Ly6CꚷDC_8

description:
RMB858
single cell


title: E13.24H_141215_11_17


title: BM_SiglecH⼮苺髞DC_42

description:
RMB914
single cell


title: BM_SiglecH⼮苺髞DC_41

description:
RMB915
single cell


title: E13.24H_141215_11_13


title: E13.24H_141215_11_12


title: BM_SiglecH⼮苺髞DC_38

description:
RMB918
single cell


title: E13.24H_141215_11_10


title: BM_SiglecH⼮苺髞DC_37

description:
RMB919
single cell


title: E13.24H_141215_11_9


title: E13.24H_141215_11_21


title: E13.24H_141215_11_2


title: E13.24H_141215_11_4


title: BM_SiglecH⼮苺髞DC_36

description:
RMB920
single cell


title: BM_SiglecH⼮苺髞DC_44

description:
RMB912
single cell


title: BM_SiglecH⼮苺髞DC_35

description:
RMB921
single cell


title: E13.24H_141215_11_7


title: E12.24H_141215_9_39


title: E12.24H_141215_9_38


title: BM_SiglecH⼮苺髞DC_32

description:
RMB924
single cell


title: BM_SiglecH⼮苺髞DC_33

description:
RMB923
single cell


title: BM_SiglecH⼮苺髞DC_30

description:
RMB926
single cell


title: BM_SiglecH⼮苺髞DC_31

description:
RMB925
single cell


title: BM_SiglecH⼮苺髞DC_40

description:
RMB916
single cell


title: E12.24H_141215_9_37


title: E12.24H_141215_9_36


title: E13.24H_141215_11_14


title: E12.24H_141215_9_35


title: BM_SiglecH⼮苺髞DC_39

description:
RMB917
single cell


title: BM_SiglecH⼮苺髞DC_28

description:
RMB928
single cell


title: BM_SiglecH⼮苺髞DC_27

description:
RMB929
single cell


title: BM_SiglecH⼮苺髞DC_29

description:
RMB927
single cell


title: BM_SiglecH⼮苺髞DC_26

description:
RMB930
single cell


title: BM_SiglecH⼮苺髞DC_25

description:
RMB931
single cell


title: E12.24H_141215_9_33


title: E12.24H_141215_9_31


title: E12.24H_141215_9_34


title: E12.24H_141215_9_30


title: BM_SiglecH⼮苺髞DC_23

description:
RMB933
single cell


title: BM_SiglecH⼮苺髞DC_24

description:
RMB932
single cell


title: E12.24H_141215_9_29


title: BM_SiglecH⼮苺髞DC_22

description:
RMB934
single cell


title: E12.24H_141215_9_28


title: E12.24H_141215_9_27


title: E12.24H_141215_9_26


title: E12.24H_141215_9_25


title: E12.24H_141215_9_23


title: BM_SiglecH⼮苺髞DC_15

description:
RMB944
single cell


title: BM_SiglecH⼮苺髞DC_20

description:
RMB936
single cell


title: BM_SiglecH⼮苺髞DC_17

description:
RMB941
single cell


title: BM_SiglecH⼮苺髞DC_19

description:
RMB938
single cell


title: BM_SiglecH⼮苺髞DC_16

description:
RMB942
single cell


title: BM_SiglecH⼮苺髞DC_18

description:
RMB939
single cell


title: E12.24H_141215_9_21


title: E12.24H_141215_9_22


title: E12.24H_141215_9_32


title: BM_SiglecH⼮苺髞DC_13

description:
RMB947
single cell


title: BM_SiglecH⼮苺髞DC_45

description:
RMB911
single cell


title: BM_SiglecH⼮苺髞DC_14

description:
RMB946
single cell


title: E12.24H_141215_9_20


title: BM_SiglecH⼮苺髞DC_21

description:
RMB935
single cell


title: BM_SiglecH⼮苺髞DC_10

description:
RMB951
single cell


title: E12.24H_141215_9_17


title: BM_SiglecH⼮苺髞DC_11

description:
RMB950
single cell


title: E12.24H_141215_9_19


title: BM_SiglecH⼮苺髞DC_12

description:
RMB949
single cell


title: E12.24H_141215_9_15


title: BM_SiglecH⼮苺髞DC_9

description:
RMB952
single cell


title: BM_SiglecH⼮苺髞DC_8

description:
RMB953
single cell


title: E12.24H_141215_9_24


title: E12.24H_141215_9_14


title: E12.24H_141215_9_11


title: E12.24H_141215_9_18


title: E12.24H_141215_9_9


title: E12.24H_141215_9_6


title: E12.24H_141215_9_40


title: E12.24H_141215_9_4


title: E12.24H_141215_9_3


title: E12.24H_141215_9_5


title: E12.24H_141215_9_2


title: E12.24H_141215_8_39


title: BM_SiglecH⼮苺髞DC_4

description:
RMB958
single cell


title: E12.24H_141215_8_38


title: BM_CD115- CDP_57

description:
RMD420
single cell


title: BM_SiglecH⼮苺髞DC_3

description:
RMB959
single cell


title: BM_CD115- CDP_56

description:
RMD423
single cell


title: BM_CD115- CDP_55

description:
RMD424
single cell


title: BM_SiglecH⼮苺髞DC_6

description:
RMB956
single cell


title: BM_SiglecH⼮苺髞DC_2

description:
RMB960
single cell


title: BM_SiglecH⼮苺髞DC_1

description:
RMB961
single cell


title: BM_CD115- CDP_58

description:
RMD418
single cell


title: BM_SiglecH⼮苺髞DC_5

description:
RMB957
single cell


title: E12.24H_141215_8_40


title: E12.24H_141215_8_37


title: BM_CD115- CDP_54

description:
RMD425
single cell


title: E12.24H_141215_8_36


title: BM_CD115- CDP_53

description:
RMD427
single cell


title: E12.24H_141215_8_33


title: E12.24H_141215_8_34


title: BM_CD115- CDP_52

description:
RMD429
single cell


title: BM_CD115- CDP_51

description:
RMD430
single cell


title: BM_CD115- CDP_50

description:
RMD432
single cell


title: BM_CD115- CDP_49

description:
RMD433
single cell


title: BM_SiglecH⼮苺髞DC_7

description:
RMB954
single cell


title: BM_CD115- CDP_48

description:
RMD434
single cell


title: E12.24H_141215_8_28


title: E12.24H_141215_8_29


title: E12.24H_141215_8_32


title: E12.24H_141215_8_31


title: BM_CD115- CDP_47

description:
RMD436
single cell


title: BM_CD115- CDP_46

description:
RMD437
single cell


title: E12.24H_141215_8_22


title: E12.24H_141215_8_21


title: E12.24H_141215_8_25


title: E12.24H_141215_8_24


title: E12.24H_141215_8_27


title: BM_CD115- CDP_44

description:
RMD439
single cell


title: E12.24H_141215_8_23


title: BM_CD115- CDP_45

description:
RMD438
single cell


title: BM_CD115- CDP_43

description:
RMD441
single cell


title: E12.24H_141215_8_20


title: E12.24H_141215_8_18


title: E12.24H_141215_8_19


title: BM_CD115- CDP_42

description:
RMD442
single cell


title: E12.24H_141215_8_16


title: BM_CD115- CDP_41

description:
RMD446
single cell


title: BM_CD115- CDP_40

description:
RMD447
single cell


title: BM_CD115- CDP_38

description:
RMD449
single cell


title: BM_CD115- CDP_39

description:
RMD448
single cell


title: BM_CD115- CDP_36

description:
RMD454
single cell


title: BM_CD115- CDP_37

description:
RMD450
single cell


title: E12.24H_141215_8_13


title: E12.24H_141215_8_10


title: E12.24H_141215_8_9


title: BM_CD115- CDP_35

description:
RMD455
single cell


title: BM_CD115- CDP_33

description:
RMD457
single cell


title: BM_CD115- CDP_34

description:
RMD456
single cell


title: BM_CD115- CDP_32

description:
RMD460
single cell


title: E12.24H_141215_8_5


title: BM_CD115- CDP_31

description:
RMD463
single cell


title: E12.24H_141215_8_4


title: E12.24H_141215_7_40


title: E12.24H_141215_8_1


title: E12.24H_141215_7_39


title: E12.24H_141215_7_38


title: BM_CD115- CDP_30

description:
RMD464
single cell


title: BM_CD115- CDP_29

description:
RMD465
single cell


title: BM_CD115- CDP_27

description:
RMD467
single cell


title: E12.24H_141215_8_14


title: BM_CD115- CDP_28

description:
RMD466
single cell


title: E12.24H_141215_7_37


title: BM_CD115- CDP_25

description:
RMD472
single cell


title: BM_CD115- CDP_22

description:
RMD478
single cell


title: BM_CD115- CDP_23

description:
RMD474
single cell


title: E12.24H_141215_7_34


title: E12.24H_141215_7_35


title: BM_CD115- CDP_21

description:
RMD479
single cell


title: BM_CD115- CDP_19

description:
RMD483
single cell


title: E12.24H_141215_7_36


title: BM_CD115- CDP_24

description:
RMD473
single cell


title: BM_CD115- CDP_26

description:
RMD469
single cell


title: E12.24H_141215_7_32


title: BM_CD115- CDP_20

description:
RMD480
single cell


title: E12.24H_141215_8_8


title: BM_SiglecH⼮苺髞DC_34

description:
RMB922
single cell


title: E12.24H_141215_7_29


title: E12.24H_141215_7_25


title: BM_CD115- CDP_18

description:
RMD485
single cell


title: E12.24H_141215_8_2


title: BM_CD115- CDP_17

description:
RMD487
single cell


title: E12.24H_141215_7_31


title: E12.24H_141215_7_27


title: E12.24H_141215_7_26


title: E12.24H_141215_7_18


title: BM_CD115- CDP_12

description:
RMD494
single cell


title: BM_CD115- CDP_13

description:
RMD493
single cell


title: BM_CD115- CDP_11

description:
RMD495
single cell


title: E12.24H_141215_7_24


title: E12.24H_141215_7_23


title: E12.24H_141215_7_22


title: BM_CD115- CDP_14

description:
RMD490
single cell


title: E12.24H_141215_7_17


title: BM_CD115- CDP_10

description:
RMD498
single cell


title: E12.24H_141215_7_20


title: BM_CD115- CDP_9

description:
RMD501
single cell


title: E12.24H_141215_7_15


title: E12.24H_141215_7_14


title: BM_CD115- CDP_16

description:
RMD488
single cell


title: BM_CD115- CDP_7

description:
RMD503
single cell


title: BM_CD115- CDP_5

description:
RMD505
single cell


title: BM_CD115- CDP_8

description:
RMD502
single cell


title: BM_CD115- CDP_4

description:
RMD506
single cell


title: E12.24H_141215_7_10


title: BM_CD115- CDP_6

description:
RMD504
single cell


title: BM_CD115- CDP_3

description:
RMD507
single cell


title: E12.24H_141215_7_11


title: E12.24H_141215_7_8


title: BM_CD115- CDP_15

description:
RMD489
single cell


title: E12.24H_141215_7_12


title: BM_CD115- CDP_2

description:
RMD508
single cell


title: E12.24H_141215_6_40


title: BM_CLP_47

description:
RMB3926
single cell


title: E12.24H_141215_7_3


title: E12.24H_141215_6_38


title: BM_CLP_44

description:
RMB3923
single cell


title: BM_CLP_42

description:
RMB3921
single cell


title: E12.24H_141215_7_1


title: E12.24H_141215_6_39


title: E12.24H_141215_6_36


title: BM_CLP_46

description:
RMB3925
single cell


title: E12.24H_141215_7_9


title: BM_CLP_48

description:
RMB3927
single cell


title: BM_CLP_45

description:
RMB3924
single cell


title: E12.24H_141215_6_35


title: BM_CLP_40

description:
RMB3919
single cell


title: BM_CLP_43

description:
RMB3922
single cell


title: E12.24H_141215_6_37


title: E12.24H_141215_6_32


title: E12.24H_141215_6_33


title: E12.24H_141215_7_4


title: BM_CLP_41

description:
RMB3920
single cell


title: E12.24H_141215_6_31


title: BM_CLP_39

description:
RMB3918
single cell


title: BM_CLP_37

description:
RMB3916
single cell


title: E12.24H_141215_6_29


title: BM_CLP_38

description:
RMB3917
single cell


title: BM_CLP_35

description:
RMB3914
single cell


title: E12.24H_141215_6_30


title: BM_CD115- CDP_1

description:
RMD509
single cell


title: BM_CLP_36

description:
RMB3915
single cell


title: BM_CLP_34

description:
RMB3913
single cell


title: E12.24H_141215_6_28


title: E12.24H_141215_6_26


title: E12.24H_141215_6_27


title: BM_CLP_32

description:
RMB3911
single cell


title: E12.24H_141215_6_34


title: E12.24H_141215_6_25


title: E12.24H_141215_6_24


title: BM_CLP_31

description:
RMB3910
single cell


title: BM_CLP_30

description:
RMB3909
single cell


title: E12.24H_141215_6_21


title: BM_CLP_29

description:
RMB3908
single cell


title: E12.24H_141215_6_18


title: E12.24H_141215_6_20


title: BM_CLP_28

description:
RMB3907
single cell


title: BM_CLP_25

description:
RMB3904
single cell


title: E12.24H_141215_6_17


title: BM_CLP_27

description:
RMB3906
single cell


title: BM_CLP_26

description:
RMB3905
single cell


title: E12.24H_141215_6_16


title: BM_CLP_24

description:
RMB3903
single cell


title: E12.24H_141215_6_15


title: E12.24H_141215_6_12


title: BM_CLP_20

description:
RMB3899
single cell


title: BM_CLP_22

description:
RMB3901
single cell


title: E12.24H_141215_6_13


title: BM_CLP_21

description:
RMB3900
single cell


title: E12.24H_141215_6_14


title: BM_CLP_33

description:
RMB3912
single cell


title: E12.24H_141215_6_9


title: BM_CLP_19

description:
RMB3898
single cell


title: E12.24H_141215_6_22


title: BM_CLP_18

description:
RMB3897
single cell


title: E12.24H_141215_6_10


title: BM_CLP_17

description:
RMB3896
single cell


title: E12.24H_141215_6_8


title: BM_CLP_16

description:
RMB3895
single cell


title: E12.24H_141215_6_6


title: BM_CLP_15

description:
RMB3894
single cell


title: BM_CLP_23

description:
RMB3902
single cell


title: E12.24H_141215_5_40


title: BM_CLP_14

description:
RMB3893
single cell


title: BM_CLP_13

description:
RMB3892
single cell


title: BM_CLP_12

description:
RMB3891
single cell


title: E12.24H_141215_5_35


title: BM_CLP_11

description:
RMB3890
single cell


title: E12.24H_141215_5_38


title: E12.24H_141215_5_36


title: E12.24H_141215_5_32


title: BM_CLP_9

description:
RMB3888
single cell


title: BM_CLP_7

description:
RMB3886
single cell


title: E12.24H_141215_5_30


title: BM_CLP_8

description:
RMB3887
single cell


title: BM_CLP_4

description:
RMB3883
single cell


title: BM_CLP_6

description:
RMB3885
single cell


title: BM_CLP_5

description:
RMB3884
single cell


title: E12.24H_141215_6_7


title: E12.24H_141215_5_29


title: BM_CLP_3

description:
RMB3882
single cell


title: BM_CLP_2

description:
RMB3881
single cell


title: E12.24H_141215_5_28


title: E12.24H_141215_6_3


title: BM_CLP_1

description:
RMB3880
single cell


title: BM_CLP_10

description:
RMB3889
single cell


title: E12.24H_141215_5_27


title: BM_GMP_51

description:
RMB4008
single cell


title: BM_GMP_50

description:
RMB4007
single cell


title: E12.24H_141215_5_26


title: BM_GMP_49

description:
RMB4006
single cell


title: E12.24H_141215_5_31


title: BM_GMP_48

description:
RMB4005
single cell


title: BM_GMP_47

description:
RMB4004
single cell


title: BM_GMP_44

description:
RMB4001
single cell


title: BM_GMP_46

description:
RMB4003
single cell


title: BM_GMP_43

description:
RMB4000
single cell


title: E12.24H_141215_5_24


title: BM_GMP_41

description:
RMB3998
single cell


title: RNA-seq_HAP1_WT_shSMARCA4shARID2_r2

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
RNA-seq on HAP1 cell line with shSMARCA4 and shARID2, replicate 2
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Reads were trimmed with Trimmomatic and aligned to the GRCh37/hg19 assembly of the human genome using Bowtie1 with the following parameters: "-q -p 6 -a -m 100-minins 0-maxins 5000-fr-sam-chunkmbs 200".
Duplicate reads were removed with Picard’s MarkDuplicates utility with standard parameters before transcript quantification with BitSeq using the Markov chain Monte Carlo method and standard parameters.
To obtain gene-level quantifications, we assigned the expression values of its highest expressed transcript to each gene.
Differential gene-level expression between each knockout and wild-type cells was performed with DESeq2 from the raw count data with a significance threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Each csv file contains read counts for each sample at gene level

organism: Homo sapiens

source_name: HAP1 cell line

growth_protocol: HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.

extract_protocol:
RNA extraction was performed with Qiagen RNeasy Mini Kit (Cat No. 74106) according to the manufacturer's instructions.
Total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

tag: library

value: RNA-seq

tag: cell line

tag: replicate

tag: knockout

value: WT

tag: perturbation


title: BM_GMP_40

description:
RMB3997
single cell


title: E12.24H_141215_5_22


title: RNA-seq_HAP1_WT_shSMARCA4shARID2_r1

description:
RNA-seq on HAP1 cell line with shSMARCA4 and shARID2, replicate 1
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: Uninfected hepatocytes 8.3

type: RNA

city: Iowa city

first: Samarchith

last: Kurup

state: Iowa

address: 51 Newton Rd

country: USA

institute: The University of Iowa

description: Gene expression in uninfected hepatocytes

hyb_protocol: Biotin-labeled ss-cDNA was then mixed with Affymetrix eukaryotic hybridization buffer, placed onto the Affymetrix GeneChip Mouse Transcriptome  Array 1.0 (Part No. 902511), and incubated at 45º C for 18 h with 60 rpm rotation

scan_protocol: GeneChips were scanned using the Affymetrix Model 3000 scanner (with 7G upgrade).

data_processing: The data were collected using Affymetrix Comand Console operating software v4.1.2 and  Affymetrix Expression Console Software Build 1.4.4.46 using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: Primary hepatocyte culture, uninfected

label_protocol: 100 ng of total RNA was converted to amplified ss-cDNA using the GeneChip WT Plus Reagent Kit (Affymetrix,Cat. #902513). Following fragmentation (fragment size ~40-70nt ), the samples were labeled with biotin.

growth_protocol: Primary hepatocyte cultures maintained in 6 well-plates

extract_protocol: The hepatocytes were detached by trypsinization (0.25% Trypsin-EDTA), FACS sorted directly into fetal calf serum. The hepatocytes were pelleted and immediately used for RNA extraction. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Co-incubated with freshly isolated Py-GFP sporozoites from mosquitoes

tag: cell type

value: Hepatocytes

tag: infection

value: uninfected


title: RNA-seq_HAP1_WT_shControl_r2

description:
RNA-seq on HAP1 cell line with shControl, replicate 2
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv

value: siControl


title: RNA-seq_HAP1_WT_shControl_r1

description:
RNA-seq on HAP1 cell line with shControl, replicate 1
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: P. yoelii infected hepatocytes 4.3

description: Gene expression in P. yoelii infected hepatocytes

source_name: Primary hepatocyte culture, 36h post infection

value: P. yoelii


title: P. yoelii infected hepatocytes 4.2


title: BM_GMP_39

description:
RMB3996
single cell


title: E12.24H_141215_5_20


title: BM_GMP_38

description:
RMB3995
single cell


title: E12.24H_141215_5_21


title: BM_GMP_37

description:
RMB3994
single cell


title: RNA-seq_HAP1_SMARCC2_r3

description:
RNA-seq on HAP1 cell line with SMARCC2 KO, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCC2_r2

description:
RNA-seq on HAP1 cell line with SMARCC2 KO, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: Uninfected hepatocytes 8.1


title: Uninfected hepatocytes 8.2


title: BM_GMP_36

description:
RMB3993
single cell


title: BM_GMP_45

description:
RMB4002
single cell


title: E12.24H_141215_5_23


title: E12.24H_141215_5_25


title: BM_GMP_42

description:
RMB3999
single cell


title: RNA-seq_HAP1_SMARCC2_r1

description:
RNA-seq on HAP1 cell line with SMARCC2 KO, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: E12.24H_141215_5_19


title: BM_GMP_35

description:
RMB3992
single cell


title: BM_GMP_33

description:
RMB3990
single cell


title: BM_GMP_34

description:
RMB3991
single cell


title: E12.24H_141215_5_17


title: BM_GMP_32

description:
RMB3989
single cell


title: BM_GMP_31

description:
RMB3988
single cell


title: E12.24H_141215_5_15


title: BM_GMP_30

description:
RMB3987
single cell


title: P. yoelii infected hepatocytes 4.1


title: BM_GMP_29

description:
RMB3986
single cell


title: BM_GMP_28

description:
RMB3985
single cell


title: E12.24H_141215_5_12


title: RNA-seq_HAP1_ARID2_SMARCA4_r2

description:
RNA-seq on HAP1 cell line with ARID2 KO and shSMARCA4, replicate 2
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCA4_shControl_r1

description:
RNA-seq on HAP1 cell line with SMARCA4 KO, with shControl, replicate 1
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: BM_GMP_27

description:
RMB3984
single cell


title: BM_GMP_25

description:
RMB3982
single cell


title: RNA-seq_HAP1_SMARCA4_ARID2_r1

description:
RNA-seq on HAP1 cell line with SMARCA4 KO and shARID2, replicate 1
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: E12.24H_141215_5_9


title: BM_GMP_22

description:
RMB3979
single cell


title: BM_GMP_26

description:
RMB3983
single cell


title: BM_GMP_21

description:
RMB3978
single cell


title: RNA-seq_HAP1_ARID2_SMARCA4_r1

description:
RNA-seq on HAP1 cell line with ARID2 KO and shSMARCA4, replicate 1
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: E12.24H_141215_5_8


title: BM_GMP_24

description:
RMB3981
single cell


title: BM_GMP_23

description:
RMB3980
single cell


title: E12.24H_141215_5_16


title: RNA-seq_HAP1_SMARCA4_shControl_r2

description:
RNA-seq on HAP1 cell line with SMARCA4 KO, with shControl, replicate 2
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: BM_GMP_20

description:
RMB3977
single cell


title: BM_GMP_19

description:
RMB3976
single cell


title: RNA-seq_HAP1_SMARCA4_ARID2_r2

description:
RNA-seq on HAP1 cell line with SMARCA4 KO and shARID2, replicate 2
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: E12.24H_141215_5_6


title: E12.24H_141215_5_5


title: RNA-seq_HAP1_ARID2_shControl_r1

description:
RNA-seq on HAP1 cell line with ARID2 KO, with shControl, replicate 1
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: BM_GMP_18

description:
RMB3975
single cell


title: BM_GMP_16

description:
RMB3973
single cell


title: E12.24H_141215_5_10


title: BM_GMP_17

description:
RMB3974
single cell


title: BM_GMP_15

description:
RMB3972
single cell


title: E12.24H_141215_5_4


title: ATAC-seq_HAP1_WT_r2_shSMARCA4

description:
ATAC-seq on HAP1 cell line with WT, shSMARCA4, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv

library_source: genomic

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: Each csv file contains read counts for each sample for each regulatory element

molecule: genomic DNA

extract_protocol: 50000 cells were resuspended in 25 µl transposase reaction mix (0.05% digitonin, 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880).

value: ATAC-seq


title: BM_GMP_14

description:
RMB3971
single cell


title: ATAC-seq_HAP1_WT_r2_shControl

description:
ATAC-seq on HAP1 cell line with WT, shControl, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_GMP_12

description:
RMB3969
single cell


title: RNA-seq_HAP1_ARID2_shControl_r2

description:
RNA-seq on HAP1 cell line with ARID2 KO, with shControl, replicate 2
baf_complex.rnaseq-synth_lethal.expression_counts.gene_level.csv


title: E14.24H_LTHT7_1_26


title: E14.24H_LTHT7_1_29


title: BM_GMP_11

description:
RMB3968
single cell


title: ATAC-seq_HAP1_WT_r4_C631

description:
ATAC-seq on HAP1 cell line with WT, clone C631, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv

tag: clone


title: BM_GMP_8

description:
RMB3965
single cell


title: BM_GMP_10

description:
RMB3967
single cell


title: BM_GMP_9

description:
RMB3966
single cell


title: E14.24H_LTHT7_1_23


title: ATAC-seq_HAP1_WT_r2_shSMARCA4shARID2

description:
ATAC-seq on HAP1 cell line with WT, shSMARCA4 and shARID2, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_GMP_7

description:
RMB3964
single cell


title: ATAC-seq_HAP1_WT_r1_shSMARCA4shARID2

description:
ATAC-seq on HAP1 cell line with WT, shSMARCA4 and shARID2, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_GMP_5

description:
RMB3962
single cell


title: E14.24H_LTHT7_1_22


title: ATAC-seq_HAP1_WT_r1_shSMARCA4

description:
ATAC-seq on HAP1 cell line with WT, shSMARCA4, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: E14.24H_LTHT7_1_18


title: BM_GMP_4

description:
RMB3961
single cell


title: ATAC-seq_HAP1_WT_r1_shControl

description:
ATAC-seq on HAP1 cell line with WT, shControl, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_GMP_1

description:
RMB3958
single cell


title: BM_GMP_3

description:
RMB3960
single cell


title: ATAC-seq_HAP1_WT_r2_shARID2

description:
ATAC-seq on HAP1 cell line with WT, shARID2, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_GMP_2

description:
RMB3959
single cell


title: BM_LMPP_64

description:
RHM695
single cell


title: BM_GMP_13

description:
RMB3970
single cell


title: ATAC-seq_HAP1_WT_r3_C631

description:
ATAC-seq on HAP1 cell line with WT, clone C631, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: E14.24H_LTHT7_1_16


title: E14.24H_LTHT7_1_21


title: E14.24H_LTHT7_1_14


title: ATAC-seq_HAP1_WT_r1_shARID2

description:
ATAC-seq on HAP1 cell line with WT, shARID2, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_LMPP_63

description:
RHM694
single cell


title: BM_LMPP_65

description:
RHM696
single cell


title: E14.24H_LTHT7_1_12


title: ATAC-seq_HAP1_WT_C631_r6

description:
ATAC-seq on HAP1 cell line with WT_C631, replicate 6
baf_complex.atacseq_peaks.raw_coverage.csv


title: BM_LMPP_62

description:
RHM693
single cell


title: BM_LMPP_60

description:
RHM691
single cell


title: BM_LMPP_59

description:
RHM690
single cell


title: BM_LMPP_58

description:
RHM689
single cell


title: ATAC-seq_HAP1_SMARCC2_6062_10_r2

description:
ATAC-seq on HAP1 cell line with SMARCC2 KO, clone 6062_10, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: BM_LMPP_61

description:
RHM692
single cell


title: ATAC-seq_HAP1_SMARCC2_6062_10_r1

description:
ATAC-seq on HAP1 cell line with SMARCC2 KO, clone 6062_10, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: E14.24H_LTHT7_1_6


title: E14.24H_LTHT7_1_7


title: E14.24H_LTHT7_1_5


title: ATAC-seq_HAP1_WT_C631_r5

description:
ATAC-seq on HAP1 cell line with WT_C631, replicate 5
baf_complex.atacseq_peaks.raw_coverage.csv


title: E14.24H_LTHT7_1_2


title: BM_LMPP_56

description:
RHM687
single cell


title: BM_LMPP_55

description:
RHM686
single cell


title: BM_LMPP_57

description:
RHM688
single cell


title: BM_LMPP_54

description:
RHM685
single cell


title: BM_LMPP_52

description:
RHM683
single cell


title: ATAC-seq_HAP1_SMARCA4_r2_shARID2

description:
ATAC-seq on HAP1 cell line with SMARCA4 KO and shARID2, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: E14.24H_LTHT7_1_1


title: KPsh-1 on dox_aKG_rep_2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Rnaseq reads were aligned to (GRCm38 - mm10) with STAR
Genome wide transcript counting was performed by HTSeq or featureCounts to generate FPKM matrix
Differential expression analysis was performed with DESeq2 package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: KPsh-1 on dox_aKG

growth_protocol: All conditions were passaged every 48 hours.  For KPsh cells analyzed off dox, cells were washed and grown without dox 8 days before collection. DMSO or dimethyl-alpha ketoglutarate were added where indicated for 72 hours.

extract_protocol:
RNA was extracted using the RNAeasy mini kit (Qiagen) per manufacturer's instructions.
RNA integrity and concentration were assessed using a BioAnalyzer (Agilent).  RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

treatment_protocol: Cells were treated with DMSO (vehicle) or dimethyl-alpha ketoglutarate for 72 hours.

value: Primary mouse PDAC cell line

tag: p53 shrna status

value: p53 shRNA ON

tag: treatment

value: 4mM DMaKG


title: BM_LMPP_50

description:
RHM681
single cell


title: ATAC-seq_HAP1_SMARCA4_r2_shControl

description:
ATAC-seq on HAP1 cell line with SMARCA4 KO and shControl, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_SMARCA4_r1_shControl

description:
ATAC-seq on HAP1 cell line with SMARCA4 KO and shControl, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_LMPP_53

description:
RHM684
single cell


title: BM_LMPP_51

description:
RHM682
single cell


title: KPsh-1 on dox_aKG_rep_1


title: BM_LMPP_49

description:
RHM680
single cell


title: KPsh-1 off dox_DMSO_rep_2

source_name: KPsh-1 off dox_DMSO

value: p53 shRNA OFF

value: DMSO (vehicle)


title: BM_LMPP_48

description:
RHM679
single cell


title: ATAC-seq_HAP1_SMARCA4_r1_shARID2

description:
ATAC-seq on HAP1 cell line with SMARCA4 KO and shARID2, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_BCL7B_4278_10_r2

description:
ATAC-seq on HAP1 cell line with BCL7B KO, clone 4278_10, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_LMPP_45

description:
RHM676
single cell


title: BM_LMPP_47

description:
RHM678
single cell


title: BM_LMPP_46

description:
RHM677
single cell


title: BM_LMPP_44

description:
RHM675
single cell


title: KPsh-1 off dox_DMSO_rep_1


title: ATAC-seq_HAP1_BCL7B_4278_10_r1

description:
ATAC-seq on HAP1 cell line with BCL7B KO, clone 4278_10, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_LMPP_43

description:
RHM674
single cell


title: ATAC-seq_HAP1_ARID2_r2_shSMARCA4

description:
ATAC-seq on HAP1 cell line with ARID2 KO and shSMARCA4, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_LMPP_41

description:
RHM672
single cell


title: KPsh-1 on dox_DMSO_rep_1

source_name: KPsh-1 on dox_DMSO


title: BM_LMPP_42

description:
RHM673
single cell


title: ATAC-seq_HAP1_ARID2_r2_shControl

description:
ATAC-seq on HAP1 cell line with ARID2 KO and shControl, replicate 2
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_GMP_6

description:
RMB3963
single cell


title: BM_LMPP_40

description:
RHM671
single cell


title: BM_LMPP_36

description:
RHM667
single cell


title: BM_LMPP_37

description:
RHM668
single cell


title: BM_LMPP_35

description:
RHM666
single cell


title: BM_LMPP_38

description:
RHM669
single cell


title: ATAC-seq_HAP1_ARID2_r1_shSMARCA4

description:
ATAC-seq on HAP1 cell line with ARID2 KO and shSMARCA4, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_ARID1B_582_5_r2

description:
ATAC-seq on HAP1 cell line with ARID1B KO, clone 582_5, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: BM_LMPP_39

description:
RHM670
single cell


title: ATAC-seq_HAP1_ARID2_r1_shControl

description:
ATAC-seq on HAP1 cell line with ARID2 KO and shControl, replicate 1
baf_complex.atacseq-synth_lethal_peaks.raw_coverage.csv


title: BM_LMPP_31

description:
RHM662
single cell


title: BM_LMPP_32

description:
RHM663
single cell


title: ATAC-seq_HAP1_ARID1B_582_5_r1

description:
ATAC-seq on HAP1 cell line with ARID1B KO, clone 582_5, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: BM_LMPP_33

description:
RHM664
single cell


title: KPsh-1 on dox_DMSO_rep_2


title: BM_LMPP_29

description:
RHM660
single cell


title: BM_LMPP_27

description:
RHM658
single cell


title: BM_LMPP_28

description:
RHM659
single cell


title: BM_LMPP_26

description:
RHM657
single cell


title: BM_LMPP_34

description:
RHM665
single cell


title: BM_LMPP_30

description:
RHM661
single cell


title: BM_LMPP_25

description:
RHM656
single cell


title: KO2-3d

city: Shanghai

first: Jing

last: Hu

address: 280 Chongqing road

country: China

institute: Shanghai Jiaotong university school of medicine

data_processing:
Basecalls performed using CASAVA version 1.7
Sequences are aligned to transcriptome with Salmon (v0.8.2)
Transcripts Per Million were calculated by Salmon(v0.8.2)by defalut parameters
Genome_build: hg38
Supplementary_files_format_and_content: comma seprated file(.csv) include TPM values for all samples

source_name: KO_3d_mesoderm-like cells

extract_protocol:
Total RNA was isolated from cells collected at differentiation day 3 using TRIzol Reagent (Invitrogen). Isolated RNA was enriched by Poly(A) tails and fragmented. Sequencing libraries were prepared according to Illumina manufacturer instruction. Paired-end RNA-seq of 2x100 base pair reads were sequenced on Illumina Hiseq2000 platform or 2x150 base pair reads were sequenced on Hiseq X-ten
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: mouse ES-derived mesoderm-like cells

tag: genotype/variation


title: KO1-3d


title: BM_LMPP_24

description:
RHM655
single cell

tag: tissue


title: WT2-3d

source_name: WT_3d_mesoderm-like cells

value: wild type


title: BM_LMPP_23

description:
RHM654
single cell

tag: strain


title: custom_0014: MM_elastin_tchal_rep1

city: RIBEIRAO PRETO

first: Tamires

middle: Aparecida

last: Bitencourt

state: SP

address: AV COSTABILE ROMANO 2221

department: BIOTECNOLOGY

country: Brazil

institute: UNAERP

description: Gene expression of mycelia growth on elastin 0.25%, and exposed to trans-chalcone

hyb_protocol: 1.65 ug of Cy-3 labeled cRNA ( specific activity >9pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume  of 55uL, containing 25x Agilent fragmentation buffer and 10x Blocking Agent following manufacture's instructions.

scan_protocol: Slides were scanned immediately after washing on Agilent DNA Microarray scanner using one color  scan setting for 1x44K  array slides ( Scan area 61x21.6mm, scan resolution 10uM, Dye channerl was set to Green, and Green PMT was set to 100%)

data_processing: The scanned  images were analysed with Agilent Feature Extraction version 10.5 using default parameters to obtain background subtracted and spatially detrended  Processed Signal intensities

organism: Trichophyton rubrum

source_name: Mycelia growth on Cove's Medium with  elastin added with 0.24ug/mL of trans-chalcone for 3,7, and 14 days replicate 1.

label_protocol: Cyanine-3 (Cy-3) labeled cRNA was prepared from 100ng RNA using  the Agilent Low input Amplification Kit (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer’s instruction, followed by purification with RNAspin Mini Isolation Kit ( GE Healthcare).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Illusta RNAspin Mini RNA Isolation Kit (GE Healthcare) following manufacture's recommendation. The RNA integrity was measured by microfluidic electrophoresis using Agilent 6000 RNA Nano chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: Mycelia of T. rubrum was  inoculated in Cove's medium with glucose and nitrate ( control), in Cove's medium with 0.25% elastin, in Cove's medium with 0.5% keratin, in control medium added with 0.24ug/mL of trans-chalcone, in keratin medium added with 0.24ug/mL of trans-chalcone, in elastin medium with 0.24ug/mL of trans-chalcone and incubated for 3, 7 and 14 days under shaking.

value: mycelia


title: BM_LMPP_22

description:
RHM653
single cell

value: Bone marrow

tag: age


title: WT1-3d


title: custom_0011: MM_keratin_tchal_rep1

description: Gene expression of mycelia growth on keratin 0.5%, and exposed to trans-chalcone

source_name: Mycelia growth on Cove's Medium with  keratin  added with 0.24ug/mL of trans-chalcone for 3,7, and 14 days replicate 1.


title: RiboZ_sstotSmarter_10ng D2

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

country: France

institute: CNRGH

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using tophat2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts values for all samples

extract_protocol: RNA libraries were prepared for sequencing according to the kit manufacturer instructions

tag: sample type

value: Mixture 25% A + 75% B (D)

tag: tissue source

value: Tissue mixture

tag: protocol

value: Kit RiboZero + SMARTer


title: BM_LMPP_21

description:
RHM652
single cell

value: adult 7-10 weeks

tag: cell population


title: BM_LMPP_20

description:
RHM651
single cell


title: RiboZ_sstotSmarter_100ng D1


title: custom_0010: MM_control_tchal_rep2

description: Gene expression of mycelia growth on glucose and nitrate, and exposed to trans-chalcone

source_name: Mycelia growth on Cove's Medium with  Glucose and Nitrate added with 0.24ug/mL of trans-chalcone for 3,7, and 14 days replicate 2.


title: custom_0012: MM_keratin_tchal_rep2

source_name: Mycelia growth on Cove's Medium with  keratin  added with 0.24ug/mL of trans-chalcone for 3,7, and 14 days replicate 2.


title: sstotRNATruseq_1ug D2

value: Kit total RNA TruSeq


title: HeLa_6hr_THZ1 0.1μM_rep3

first: Shanshan

last: Zhong

address: NO.160 Road, Pudong New District

institute: Ren Ji hospital

description: Gene expression after 100nM THZ1 treatment for 6 hours in HeLa

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2545A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_QCM_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HeLa, 6hr, THZ1 100nM, replicate 3

label_protocol: Total RNA were transcribed to double strand cDNA, then synthesized into cRNA. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug cRNA using  One-Color (24×） low input Quick-Amp Labeling Kit（Agilent） according to the manufacturer's instructions. The labeled cRNAs were purified by RNAeasy column(QIAGEN RNAeasy Mini kit) .  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: HeLa were maintained in DMEM/high glucose medium containing 10% fetal bovine serum  and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using TRIZOL (Invitrogen) after treatment with THZ1 or DMSO for 6 hours. RNA was quantified using a NanoDrop ND-2000 (Thermo Scientific).

treatment_protocol: HeLa were seeded in 6-well plates at a density of 1ⅹ106 cells each well, and then treated with 100nM THZ1 or DMSO for 6 hours.

tag: cell line

value: HeLa

value: 100nM THZ1 or DMSO for 6 hours.


title: BM_LMPP_19

description:
RHM650
single cell


title: custom_0015: MM_elastin_tchal_rep2

source_name: Mycelia growth on Cove's Medium with  elastin added with 0.24ug/mL of trans-chalcone for 3,7, and 14 days replicate 2.


title: RiboZ_sstotSmarter_100ng D2


title: HeLa_6hr_THZ1 0.1μM_rep1

source_name: HeLa, 6hr, THZ1 100nM, replicate 1


title: custom_008: MM_elastin_rep2

description: Gene expression of mycelia growth on elastin 0.25%

source_name: Mycelia growth on Cove's Medium with 0.25% of elastin for 3,7, and 14 days,  replicate 2.


title: BM_LMPP_18

description:
RHM649
single cell

source_name: Bone marrow


title: custom_009: MM_control_tchal_rep1

source_name: Mycelia growth on Cove's Medium with  Glucose and Nitrate added with 0.24ug/mL of trans-chalcone for 3,7, and 14 days replicate 1.


title: BM_LMPP_17

description:
RHM648
single cell


title: HeLa_6hr_THZ1 0.1μM_rep2

source_name: HeLa, 6hr, THZ1 100nM, replicate 2


title: RiboG_sstotSmarter_100ng D2

value: Kit RiboGone + SMARTer


title: RiboZ_sstotSmarter_10ng D1


title: HeLa_6hr_0_rep2

description: Gene expression after DMSO treatment for 6 hours in HeLa

source_name: HeLa, 6hr, 0, replicate 2

value: DMSO


title: custom_006: MM_keratin_rep3

description: Gene expression of mycelia growth on keratin 0.5%

source_name: Mycelia growth on Cove's Medium with 0.5%  of keratin  for 3,7, and 14 days,  replicate 3.


title: RiboG_sstotSmarter_100ng D1


title: custom_007: MM_elastin_rep1

source_name: Mycelia growth on Cove's Medium with 0.25%  of elastin  for 3,7, and 14 days,  replicate 1.


title: BM_LMPP_15

description:
RHM646
single cell


title: HeLa_6hr_0_rep3

description: Gene expression after DMSO treatment for 6 hours in  HeLa

source_name: HeLa, 6hr, 0, replicate 3


title: H4ac Nrd1-AA_-Rap_rep2

last: Soudet

address: 30 quai Ansermet

department: BICEL

institute: Université de Genève

description: NOTE: processed data was generated from both rep1 & rep2, and is linked to the corresponding rep1 sample records.

data_processing:
Paired-end reads were aligned to sacCer3 genome assembly using  Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) with options '-k 20 --end-to-end --sensitive -X 800'. PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments (120-200bp to visualize only proper nucleosomes and not “fragile nucleosomes” (Brahma and Henikoff, 2019; Kubik et al., 2015)) and counting of only the 3 bp at the center of fragments.
Genome_build: saccer3
Supplementary_files_format_and_content: bigWig files correspond to the mean of the 2 replicates. Normalization:cpm

organism: Saccharomyces cerevisiae

source_name: H4ac Nrd1-AA_-Rap

growth_protocol: All strains were derived from the Anchor-Away genetic backgrounds (Haruki et al. 2008). Cells were grown in YEPD medium (1% yeast extract, 1% peptone) supplemented with 2% glucose as carbon source. All strains were grown at 30°C and were not affected in growth by the different tags or deletions. Anchor-away of Nrd1-AA was induced by adding 1μg/ml of rapamycin to the medium.

extract_protocol:
The MNase- and MNase-ChIP-seq experiments were performed mainly as described in the (Weiner et al., 2015) with the following modifications. Nrd1-AA strain was inoculated overnight and diluted in the morning to OD600 of 0.2 in YEPD medium. Yeast cell culture of 100 mL was used per modification. Rapamycin treatment was performed at OD600 of 0.5 for 60 minutes on half of the culture. The cells were fixed with formaldehyde at a final concentration of 1% for 15 minutes followed glycine addition at a final concentration of 125 mM for 5 minutes. Cells were washed 2x with ddH2O , harvested in magnaLyser tubes (Roche) (100 mL cell culture/tube) and frozen at -20 °C .   Chromatin extraction was performed by breaking cells in 1 mL of Cell Breaking buffer (0.1 M Tris-HCl, pH 7.9, 20% glycerol, EDTA-free protease inhibitors) and 1 mL of acid-washed glass beads in a magnaLyser (Roche). The cell extract was then centrifuged at 19,000 g at 4 °C for 10 minutes to collect chromatin. The chromatin was resuspended in 600 uL of NP buffer (0.5 mM Spermidine, 50 mM NaCl, 1mM beta-mercaptoethanol, 0.075% NP-40, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2) per tube. The DNA concentration was measured using Qubit dsDNA BR assay kit (Invitrogen). Chromatin was diluted to 20 ug/mL using NP buffer in all conditions for comparable results.   MNase treatment was performed using 0.2 uL of MNase (ThermoScientific 100 units/uL ) / 12 ug of chromatin in 600 uL reaction mixture for 14 minutes at 37 °C. To perform all the modifications for one replicate from one cell culture the reaction was scaled 10x. The reaction was stopped by adding EDTA (final concentration 20 mM) in the reaction mixture.   For MNase-seq, equal amount of elution buffer (10 mM Tris-HCl, pH 8.0, 1% SDS, 150 mM NaCl, 5 mM DTT) was added. The further steps for MNase is same as the ones performed after MNase-ChIP elution.  For MNase-ChIP, the buffer of the MNase reaction mixture was adjusted to be compatible to FA-lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, EDTA-free protease tablet).  The following salts were added to the MNase reaction tube: 80 uL of 0.5 M HEPES-KOH, pH 7.5, 22.4 uL of 5 M NaCl,  pre-mixed with protease inhibitors. Followed by addition of detergents, 6.4 uL of 12.5% sodium deoxycholate and 80 uL of 10% Triton X-100 per 600 uL MNase reaction.   The protein-G dynabeads (ThermoFisher Scientific) were pre-incubated with the antibodies for one hour at 4 °C on a rotor, 85 uL beads/reaction. The antibodies used were anti-H3 (Abcam ab1791) 12 uL  per reaction, anti-H3K36me3 (Abcam ab9050) 6 uL  per reaction, anti-H3K18ac (abcam ab1191) 7 uL  per reaction, H4ac (Merck Millipore 06-598) 10 uL  per reaction. The beads were washed in FA-lysis buffer twice, followed by incubation with the MNase-treated chromatin for 4 hours at 4 °C on a rotor. The beads were sequentially washed with 1 mL of  FA-Lysis buffer, 1 mL FA500-lysis Buffer (FA-Lysis Buffer + 500 mM NaCl), 1 mL of Buffer III ( 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.05% sodium deoxycholate), 1 mL of Tris-EDTA pH 8.0. For elution, the beads were incubated in 150 uL of elution buffer at 65 °C for 15 minutes.   The crosslinking was reversed by incubation of the eluate at 65 °C overnight followed by addition of 150 uL of TE (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). The eluate was then treated with proteinase K (1 ug/uL final concentration) for 3 hours at 42 °C. The DNA was purified using the NucleoSpin Gel and PCR clean-up kit (Macherey-Nagel) using the SDS protocol provided in the manual. The DNA concentration was measured using Qubit dsDNA HS assay kit (Invitrogen) and the libraries were prepared using NEBnext Ultra DNA library prep kit for Illumina (NEB). Finally, samples were paired-end sequenced at the iGE3 genomics platform of the University of Geneva.
NEBnext Ultra DNA library prep kit for Illumina (NEB)

treatment_protocol: With or without 1μg/ml of rapamycin for 1h

value: Minus Rapamycin 1h (1μg/ml)

tag: chip antibody

tag: chip antibody vendor

value: Merck-Milipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: H4ac Nrd1-AA_+Rap_rep1

source_name: H4ac Nrd1-AA_+Rap

value: Plus Rapamycin 1h (1μg/ml)


title: custom_0013: MM_keratin_tchal_rep3

source_name: Mycelia growth on Cove's Medium with  keratin  added with 0.24ug/mL of trans-chalcone for 3,7, and 14 days replicate 3.


title: H3K18ac Nrd1-AA_+Rap_rep2

source_name: H3K18ac Nrd1-AA_+Rap

value: abcam


title: H4ac Nrd1-AA_-Rap_rep1


title: H4ac Nrd1-AA_+Rap_rep2


title: custom_005: MM_keratin_rep2

source_name: Mycelia growth on Cove's Medium with 0.5%  of keratin  for 3,7, and 14 days,  replicate 2.


title: custom_004: MM_keratin_rep1

source_name: Mycelia growth on Cove's Medium with 0.5%  of keratin  for 3,7, and 14 days,  replicate 1.


title: IVm (re-analysis)_miRNA-Seq

city: Yangling

first: Ming

last: Xu

state: Shaanxi

address: No. 3, Taicheng Road

department: College of Plant Protection

institute: Northwest A&F University

data_processing:
The raw data of MVm and IVm (GEO accession: GSM2807180; SRA accession: SRX3265281), released at 2017-10-10) were processed with the Illumina pipeline filter (Solexa 0.3). The resulting data was subjected to the ACGT101-miR (LC Sciences, Houston, USA) to remove adapter dimers, junk, common RNA families (rRNA, tRNA, snRNA, snoRNA), low complexity, and repeats.
The subsequent unique sequences with length of 18~25 nt were mapped to miRBase 21.0 (Kozomara & Griffiths-Jones, 2010) to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 5’ and 3’ ends and one mismatch inside of the sequence were permitted in the blast. The unmapped sequences were blasted against the V. mali genomes by Bowtie (Langmead, 2010), and the hairpin RNA structures containing sequences were predicated from the flanking sequences (up to 200 bp) using mfold (http://unafold.rna.albany.edu/?q=mfold/RNA-Folding-Form) following the parameter setting as described previously (Lee et al., 2010).
The milRNAs in MVm and IVm was normalized by transcript per million (TPM)
TargetFinder were used to predict candidate target genes of Vm-milRNA binding sites. The alignment score was set as not more than seven.
Raw sequencing reads of TMVm and TIVm (GEO accession: GSM2807182; SRA accession: SRX3265283,  released at 2017-10-10) were obtained using Illumina’s Pipeline v1.5 software.
V. mali transcripts cleaved by Vm-milRNAs were analyzed with CleaveLand3.0 (LC-BIO, Hangzhou, China).
Genome_build: Valsa mali ASM81815v1
Supplementary_files_format_and_content: Files include normalized read count (TPM) of Vm-miRNAs and degradome results

organism: Malus domestica

source_name: twig

growth_protocol: Valsa mali mycelia were cultured on PDA medium covered with a layer of cellophane at 25 ℃ in the dark.

extract_protocol:
According to the instruction of TrizolTM Reagent (Invitrogen, Carlsbad, CA), total RNA was extracted from each sample, and RNA purity was evaluated using NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) were used to assess RNA concentration and integrity.
Three repeats of control samples and inoculation samples were mixed for small RNA library construction, respectively. Three μg of total RNA per sample was used as input material for the small RNA library. Three micrograms total RNA was used for each small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England BioLabs Inc, Beverly, MA, USA) according to manufacturer’s instructions. The clustering of each index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia, San Diego, USA) following the manufacturer’s instructions.  Approximately 20 μg total RNA used for small RNA sequencing library construction were also used to construct degradome sequencing library following protocol as described (German et al., 2009). Poly(A)+ RNA was isolated and annealed with biotinylated random primers. 5’ adaptor was ligated to the annealed poly(A)+ RNAs which contain 5’-monophosphates. After reverse transcription and PCR amplification, single-end sequencing (36 bp) were performed on Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following manufacturer’s protocol.

treatment_protocol: Samples were collected at 3 days post culture and quick-freezed in liquid nitrogen. All the samples were stored at minus 80°C.

value: bark

value: inoculated with Valsa mali


title: TIVm (re-analysis)_degradome-Seq

data_processing:
Library strategy: degradome-Seq
The raw data of MVm and IVm (GEO accession: GSM2807180; SRA accession: SRX3265281), released at 2017-10-10) were processed with the Illumina pipeline filter (Solexa 0.3). The resulting data was subjected to the ACGT101-miR (LC Sciences, Houston, USA) to remove adapter dimers, junk, common RNA families (rRNA, tRNA, snRNA, snoRNA), low complexity, and repeats.
The subsequent unique sequences with length of 18~25 nt were mapped to miRBase 21.0 (Kozomara & Griffiths-Jones, 2010) to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 5’ and 3’ ends and one mismatch inside of the sequence were permitted in the blast. The unmapped sequences were blasted against the V. mali genomes by Bowtie (Langmead, 2010), and the hairpin RNA structures containing sequences were predicated from the flanking sequences (up to 200 bp) using mfold (http://unafold.rna.albany.edu/?q=mfold/RNA-Folding-Form) following the parameter setting as described previously (Lee et al., 2010).
The milRNAs in MVm and IVm was normalized by transcript per million (TPM)
TargetFinder were used to predict candidate target genes of Vm-milRNA binding sites. The alignment score was set as not more than seven.
Raw sequencing reads of TMVm and TIVm (GEO accession: GSM2807182; SRA accession: SRX3265283,  released at 2017-10-10) were obtained using Illumina’s Pipeline v1.5 software.
V. mali transcripts cleaved by Vm-milRNAs were analyzed with CleaveLand3.0 (LC-BIO, Hangzhou, China).
Genome_build: Valsa mali ASM81815v1
Supplementary_files_format_and_content: Files include normalized read count (TPM) of Vm-miRNAs and degradome results


title: custom_003: MM_control_rep3

description: Gene expression of mycelia growth on glucose and nitrate

source_name: Mycelia growth on Cove's Medium with  Glucose and Nitrate for 3,7, and 14 days, replicate 3.

value: mycelia


title: custom_001: MM_control_rep1

source_name: Mycelia growth on Cove's Medium with  Glucose and Nitrate for 3,7, and 14 days replicate 1.


title: BM_LMPP_14

description:
RHM645
single cell

value: Bone marrow


title: HeLa_6hr_0_rep1

source_name: HeLa, 6hr, 0, replicate 1


title: sstotRNATruseq_1ug D1

value: Mixture 25% A + 75% B (D)


title: BM_LMPP_16

description:
RHM647
single cell

source_name: Bone marrow


title: custom_002: MM_control_rep2

source_name: Mycelia growth on Cove's Medium with  Glucose and Nitrate for 3,7, and 14 days replicate 2.


title: H3K18ac Nrd1-AA_+Rap_rep1


title: RiboG_sstotSmarter_100ng C1

value: Mixture 75% A + 25% B (C)

value: Tissue mixture


title: H3K18ac Nrd1-AA_-Rap_rep1

source_name: H3K18ac Nrd1-AA_-Rap


title: BM_LMPP_13

description:
RHM644
single cell

value: adult 7-10 weeks


title: H3K18ac Nrd1-AA_-Rap_rep2


title: RiboZ_sstotSmarter_10ng C2

value: Kit RiboZero + SMARTer


title: RiboZ_sstotSmarter_100ng C2


title: RiboZ_sstotSmarter_100ng C1


title: 34 Fi/Fi Cre KO Tm 1ug 6h, biological rep3

city: Santiago

first: Alfredo

last: Sagredo

state: Santiago

address: Independencia Av. 1027

country: Chile

institute: University of Chile

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The affyPLM-package was used for normalization and processing http://www.bioconductor.org/packages/release/bioc/html/affyPLM.html. The default model was used. The custom chip definition file from Brainarray Version 22.0  based on Entrez ID’s was used to annotate the microarrays.

label: biotin

label_protocol: Affymetrix

extract_protocol: Total RNA was prepared from liver tissues using Trizol (Invitrogen, Carlsbad, CA, USA), and cDNA was synthesized with SuperScript III (Invitrogen) using random primers p(dN)6 (Roche).

treatment_protocol: Ern1 floxed mice were previously described and crossed with Mx1-cre transgenic mice to generate a conditional KO animal (IRE1αcKO). Deletion was induced by injection of polyinosinic-polycytidylic acid (Poly (I:C)) which efficiently delete the floxed gene in the liver and bone marrow. 5-6 weeks old mice were intraperitoneally (i.p) injected 3 times with 250 µg of poly(I:C) each time with 2 day intervals to induce the Cre expression. Mice were used for experiments at least 2-3 weeks after the final poly (I:C) injection. DMSO or 50 mg/Kg etoposide or 1 mg/Kg tunicamycin or were i.p. injected and 6 h later mice were sacrificed.

value: Fi/Fi Cre KO

tag: agent

value: Tunicamycin

tag: doses

value: 1 ug/g

tag: time point

value: 6 hrs


title: BM_LMPP_12

description:
RHM643
single cell


title: 35 Fi/Fi Cre KO Tm 1ug 6h, biological rep3


title: BM_LMPP_10

description:
RHM641
single cell


title: H3K36me3 Nrd1-AA_+Rap_rep2

source_name: H3K36me3 Nrd1-AA_+Rap

tag: strain background

tag: treatment


title: BM_LMPP_9

description:
RHM640
single cell

tag: tissue


title: H3K36me3 Nrd1-AA_+Rap_rep1

tag: genotype/variation


title: BM_LMPP_11

description:
RHM642
single cell

tag: strain

tag: age


title: H3K36me3 Nrd1-AA_-Rap_rep1

source_name: H3K36me3 Nrd1-AA_-Rap

value: Minus Rapamycin 1h (1μg/ml)


title: RiboZ_sstotSmarter_10ng C1

tag: sample type

tag: tissue source


title: sstotRNATruseq_1ug C1

tag: protocol

value: Kit total RNA TruSeq


title: MNase-seq Nrd1-AA_+Rap_rep2

source_name: MNase-seq Nrd1-AA_+Rap

value: Plus Rapamycin 1h (1μg/ml)


title: RiboG_sstotSmarter_100ng B2

value: Human Brain Reference RNA (B)

value: Normal brain tissue mixture

value: Kit RiboGone + SMARTer


title: MNase-seq Nrd1-AA_+Rap_rep1


title: BM_LMPP_7

description:
RHM638
single cell

tag: cell population


title: sstotRNATruseq_1ug B2


title: H3K36me3 Nrd1-AA_-Rap_rep2

tag: chip antibody

value: abcam


title: MNase-seq Nrd1-AA_-Rap_rep2

source_name: MNase-seq Nrd1-AA_-Rap


title: BM_LMPP_6

description:
RHM637
single cell

value: Bone marrow


title: MNase-seq Nrd1-AA_-Rap_rep1


title: 33 Fi/Fi Cre KO Tm 1ug 6h, biological rep1


title: RiboZ_sstotSmarter_100ng B2


title: 32 Fi/Fi Cre KO Eto 50ug 6h, biological rep3

value: Etoposide

value: 50 ug/g


title: BM_LMPP_8

description:
RHM639
single cell


title: 30 Fi/Fi Cre KO Eto 50ug 6h, biological rep1


title: 31 Fi/Fi Cre KO Eto 50ug 6h, biological rep2


title: ATAC-seq Nrd1-AA_drpd3_+Rap

data_processing:
Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) with default options from the Galaxy server (Afgan et al., 2018). PCR duplicates were removed from the analysis. DeepTools 2.0 (Ramirez et al., 2016) was then used through the bamCoverage function with size selection of fragments (0-120bp, 0-120bp and 120-200bp for TBP-ChEC, ATAC-seq and Sth1-ChEC respectively) and counting of only the 3bp at the center of fragments.
Genome_build: saccer3
Supplementary_files_format_and_content: bigWig files with cpm normalization.

source_name: ATAC-seq Nrd1-AA_drpd3_+Rap

extract_protocol:
The experiment was performed after combining the protocols from (Buenrostro et al., 2013; Buenrostro et al., 2015; Schep et al., 2015) and (Au - Grbesa et al., 2017). The yeast strains were inoculated the day before in YEPD. Culture was diluted to OD600 of 0.2 and it was allowed to reach an OD600 of 0.4. Then, half of the culture is treated with Rapamycin for 1h at 30°C. 1 mL of the cell culture was harvested from all conditions and strains. Cells were washed twice in 1 mL sorbitol buffer (1.4 M Sorbitol, 40 mM HEPES-KOH, pH 7.5, 0.5 mM; MgCl2) and were resuspended in 190 uL of sorbitol buffer and 10 uL of 10 mg/mL Zymolyase (20T Zymolyase, AMSIO) and incubated at 30 °C shaking at 200 rpm for 30 minutes. The cells were washed twice in sorbitol buffer and then the nuclei were incubated in 95 uL of 1x TD buffer and 5 uL of the TD enzyme (Illumina). The reaction was incubated at 37 °C at 500 rpm for 30 minutes. DNA was then extracted with 3x SPRI beads (AmpureXP Beckman Coulter) and was eluted in 28 uL 10 mM Tris-HCl, pH 8.0. Initial PCR amplification was performed with 4 uL of transposed DNA to check the transpositions and cycles required. Final amplification was performed with NEBNext High-Fidelity 2x PCR Master Mix (NEB) using Nextera Primers (Illumina). 12 cycles were performed.The size selection was performed by sequential SPRI beads precipitation. First, the DNA was mixed by pipetting in 0.5x beads followed by incubation for 5 minutes at room temperature. The supernatant was used for next DNA precipitation with 2.5x SPRI beads after which the supernatant was discarded and the beads were washed with 70% ethanol twice before the DNA was extracted using 28 uL of 10 mM Tris-HCl, pH 8.0.  The DNA concentration was measured and the samples were paired-end sequenced at iGE3 genomics platform of the University of Geneva.
NEBnext Ultra DNA library prep kit for Illumina (NEB)

value: Nrd1-AA drpd3


title: BM_LMPP_4

description:
RHM635
single cell

value: adult 7-10 weeks


title: 28 Fi/Fi Cre KO untreat, biological rep2

value: Untreatment


title: ATAC-seq Nrd1-AA_drpd3_-Rap

source_name: ATAC-seq Nrd1-AA_drpd3_-Rap


title: ATAC-seq Nrd1-AA_+Rap

source_name: ATAC-seq Nrd1-AA_+Rap


title: RiboG_sstotSmarter_100ng B1


title: 29 Fi/Fi Cre KO untreat, biological rep3

value: Fi/Fi Cre KO


title: BM_LMPP_5

description:
RHM636
single cell


title: 26 Fi/Fi Cre WT Tm1ug 6h, biological rep3

value: Fi/Fi Cre WT

value: Tunicamycin


title: BM_LMPP_2

description:
RHM633
single cell


title: RiboZ_sstotSmarter_100ng B1

value: Kit RiboZero + SMARTer


title: BM_LMPP_3

description:
RHM634
single cell


title: RiboZ_sstotSmarter_10ng B1


title: ATAC-seq Nrd1-AA_-Rap

source_name: ATAC-seq Nrd1-AA_-Rap

value: Minus Rapamycin 1h (1μg/ml)


title: sstotRNATruseq_1ug A2

value: Universal Human Reference RNA (A)

value: Tissue mixture

value: Kit total RNA TruSeq


title: BM_LMPP_1

description:
RHM632
single cell


title: 25 Fi/Fi Cre WT Tm1ug 6h, biological rep2

value: 1 ug/g

value: 6 hrs


title: STH1-ChEC Nrd1-AA_drpd3_+Rap_rep2

data_processing:
library strategy: Chromatin endogenous cleavage (ChEC)-seq
Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) with default options from the Galaxy server (Afgan et al., 2018). PCR duplicates were removed from the analysis. DeepTools 2.0 (Ramirez et al., 2016) was then used through the bamCoverage function with size selection of fragments (0-120bp, 0-120bp and 120-200bp for TBP-ChEC, ATAC-seq and Sth1-ChEC respectively) and counting of only the 3bp at the center of fragments.
Genome_build: saccer3
Supplementary_files_format_and_content: bigWig files corresponding to the mean of rep1 and rep2. cpm normalization.

source_name: STH1-ChEC Nrd1-AA_drpd3_+Rap

extract_protocol:
The experiment was performed as described in (Zentner et al., 2015) after some modifications. The yeast strains were cultured the day before in YEPD medium. They were diluted to OD600 of 0.2 in YEPD medium in the morning. The 60 mins rapamycin treatment was performed at OD600 of 0.4. For each condition, 50 mL cell culture was harvested at room temperature.  The cells were washed twice in 1 mL of Buffer A (15 mM Tris-HCl pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine and protease inhibitor tablet (Sigma-Aldrich). Cells were resuspended in 594 uL of buffer A and 6 uL of 10% digitonin (0.1% final concentration) were added to permeabilize the cells during 5min at 30 °C. Then CaCl2 was added (final concentration 5 mM) to activate the MNase cleavage. 200 uL were collected at 30s for SPT15-MNase or 20s for STH1-MNase and were immediately mixed with 200 uL of 2X Stop solution (400 mM NaCl, 20 mM EDTA, 4 mM EGTA, 1% SDS). The cells were treated with Proteinase K (0.4 ug/uL final concentration) and incubated at 55 °C for 30 minutes. The DNA was extracted using phenol:chloroform:isoamyl extraction, followed by precipitation by adding 30 ug glycogen, 500 uL of 100% ethanol and incubated at -20 °C for one hour. RNAse treatment was performed by adding 34.5 uL of Tris, pH 8.0 and 10 ug of RNAse per reaction. For size selection of DNA fragments, 75 uL of solid phase reversible immobilization beads (SPRI, AmpureXP Beckman Coulter) were added in 25 uL of RNAse treated DNA and the reaction was mixed by pipetting up and down 10 times. The beads were incubated at room temperature for 5 minutes. The tubes were placed in the magnetic rack and supernatant was transferred to the new tube containing 10 mM Tris and 0.2 M NaCl for each reaction. The DNA was extracted with phenol:chloroform:isoamyl solution and precipitated with 100% ethanol. The pellets were washed with 70% ethanol and resuspended in 29 uL of Tris, pH 8.0. DNA concentration was measured using Qubit dsDNA HS assay kit (Invitrogen) using 4 uL sample. The rest 25 uL was used to prepare sequencing libraries using NEBnext Ultra DNA library prep kit for Illumina (NEB). The samples were sequenced in the paired-end mode at the iGE3 genomics sequencing platform in Geneva.
NEBnext Ultra DNA library prep kit for Illumina (NEB)

value: Plus Rapamycin 1h (1μg/ml)

tag: sample group

value: Nrd1-AA drpd3 STH1-ChEC


title: RiboG_sstotSmarter_100ng A2

value: Kit RiboGone + SMARTer


title: 22 Fi/Fi Cre WT Eto50ug 6h, biological rep3

value: Etoposide

value: 50 ug/g


title: 23 Fi/Fi Cre WT Eto50ug 6h, biological rep4


title: Acta2 high

city: San Francisco

first: Tatsuya

last: Tsukui

state: CA

address: 555 Mission Bay Blvd South, 282

department: Medicine

institute: UCSF

data_processing:
The raw reads were aligned against the mouse refseq genes (UCSC, http/hgdownload.cse.ucsc.edu/goldenPath/mm9/ database/) using BWA 0.6.2 which uses the 25_1 mapping parameter. We generated unique gene counts by excluding reads that mapped to contigs of more than one gene. Reads mapping to several contigs within an isogroup were only counted once.
Genome_build: mm9

source_name: Transferred fibroblasts purified based on high Acta2 expression from host lungs

extract_protocol:
Total RNA of purified donor fibroblasts was isolated by using RNeasy mini kit (Qiagen).
Whole transcriptome of purified transferred cells was amplified and acquired by SAGE as described previously with minor differences (GSE42564 and GSE110533). Purified total RNA was dissolved in lysis buffer (1% LiDS, 100 mM Tris-HCl pH 7.5, 500 mM LiCl, 10 mM EDTA, 5 mM DTT) and mRNA was trapped on Dynabeads M270 streptavidin (Thermo Fisher Scientific) labeled with biotinylated oligo-dT-containing DNA adapters as described previously (GSE110533). On-beads reverse transcription and second strand synthesis was performed by adding RT mix (1x First-strand buffer, 0.5 mM dNTP, 2.5 µM DTT, 1U/µl RNaseIn Plus (Promega),  1.2 µM SMART-LNA oligo (Exiqon), 20U/µl Superscript II (Thermo Fisher)) and incubating 37ºC for 1 hour, 70ºC for 10 min, and hold at 4 ºC. Then, whole transcriptome was amplified using PrimeSTAR DNA polymerase (Takara) by performing below program; 98 ºC 2min, 18 cycles of [98 ºC 20 sec, 60 ºC 15 sec, 68 ºC 4 min], 68 ºC 4 min, and hold at 4 ºC. SAGE libraries were constructed by using each amplified whole transcripts as described previously (GSE42564).
3'SAGE

treatment_protocol: The host mice were instilled with bleomycin. Donor fibroblasts were purified from untreated Col-GFP or Col-GFP/Acta2-mKO1 double transgenic mice. Donor fibroblasts were transferred intratracheally into the host mice 7 days after the bleomycin treatment. Donor cells were purified from the host lungs on day 2, 4, or 7 after the transfer.

value: Col-GFP and Acta2-mKO1 (C57BL/6)


title: 21 Fi/Fi Cre WT Eto50ug 6h, biological rep2


title: STH1-ChEC Nrd1-AA_drpd3_+Rap_rep1

value: Nrd1-AA drpd3


title: 24 Fi/Fi Cre WT Tm1ug 6h, biological rep1


title: STH1-ChEC Nrd1-AA_drpd3_-Rap_rep2

source_name: STH1-ChEC Nrd1-AA_drpd3_-Rap


title: Day 4

source_name: Transferred fibroblasts purified from host lungs

value: Col-GFP (C57BL/6)


title: Acta2 low

source_name: Transferred fibroblasts purified based on low Acta2 expression from host lungs


title: RiboZ_sstotSmarter_100ng A1


title: Day 7


title: RiboZ_sstotSmarter_100ng A2


title: RiboG_sstotSmarter_100ng A1


title: STH1-ChEC Nrd1-AA_+Rap_rep2

source_name: STH1-ChEC Nrd1-AA_+Rap

value: Nrd1-AA STH1-ChEC


title: Day 2


title: STH1-ChEC Nrd1-AA_drpd3_-Rap_rep1


title: sstotRNATruseq_1ug A1


title: 27 Fi/Fi Cre KO untreat, biological rep1

value: Fi/Fi Cre KO

value: Untreatment


title: STH1-ChEC Nrd1-AA_-Rap_rep2

source_name: STH1-ChEC Nrd1-AA_-Rap

value: Minus Rapamycin 1h (1μg/ml)


title: ssmRNATruseq_100ng D1

value: Mixture 25% A + 75% B (D)

value: Kit mRNA TruSeq


title: 20 Fi/Fi Cre WT Eto50ug 6h, biological rep1

value: Fi/Fi Cre WT


title: Untreated

source_name: Lung fibroblasts purified from untreated mice


title: 17 Fi/Fi Cre WT untreat, biological rep1


title: 19 Fi/Fi Cre WT untreat, biological rep3


title: STH1-ChEC Nrd1-AA_-Rap_rep1


title: ssmRNATruseq_100ng D2

value: Tissue mixture


title: 16 KO IRE1 Tm 1ug 16h, biological rep2

source_name: 16 KO IRE1 Tm 1ug 16h, biological rep2

value: KO IRE

value: Tunicamycin

value: 1 ug/g

value: 16 hrs


title: TBP-ChEC Nrd1-AA_drpd3_+Rap_rep2

source_name: TBP-ChEC Nrd1-AA_drpd3_+Rap

value: Plus Rapamycin 1h (1μg/ml)

value: Nrd1-AA drpd3 TBP-ChEC


title: RiboZ_sstotSmarter_10ng A1

value: Universal Human Reference RNA (A)

value: Kit RiboZero + SMARTer


title: ssmRNATruseq_1ug D1


title: STH1-ChEC Nrd1-AA_+Rap_rep1


title: 18 Fi/Fi Cre WT untreat, biological rep2

value: 6 hrs


title: 15 KO IRE1 Tm 1ug 16h, biological rep1

source_name: 15 KO IRE1 Tm 1ug 16h, biological rep1


title: TBP-ChEC Nrd1-AA_drpd3_+Rap_rep1

value: Nrd1-AA drpd3


title: ssmRNATruseq_1ug D2


title: TBP-ChEC Nrd1-AA_drpd3_-Rap_rep2

source_name: TBP-ChEC Nrd1-AA_drpd3_-Rap


title: TBP-ChEC Nrd1-AA_drpd3_-Rap_rep1


title: 14 KO IRE1 Eto 50ug 16h, biological rep2

value: Etoposide

value: 50 ug/g


title: TBP-ChEC Nrd1-AA_+Rap_rep2

source_name: TBP-ChEC Nrd1-AA_+Rap

value: Nrd1-AA TBP-ChEC


title: ssmRNATruseq_100ng C2

value: Mixture 75% A + 25% B (C)


title: ssmRNATruseq_1ug C1

value: Kit mRNA TruSeq


title: BM-MSC_patient6

city: Warsaw

first: Anna

last: Burdzińska

address: Nowogrodzka 59

department: Department of Immunology, Transplantology and Internal Medicine

country: Poland

institute: Medical University of Warsaw

description: Gene expression data from mesenchymal stromal cells

hyb_protocol: Following fragmentation, 5,5 μg of ssDNA were hybridized for 20 hr at 48 degrees Cent. to the GeneChip™ Human Gene 2.1 ST Array Strip (Affymetrix) in the Affymetrix GeneATlas hybridization Oven.   scan protocol  GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

scan_protocol: The array strips were scanned using the Affymetrix GeneAtlas Scanner.

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 beta software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

source_name: Bone marrov derived mesenchymal stromal cells

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 10 ng total RNA using GeneChip™ WT Pico Kit, according to the standard protocol provided by Affymetrix.

growth_protocol: Cells were cultured in standard growth medium composed of Dulbecco’s modified Eagle’s medium with low glucose supplemented with 10% fetal bovine serum and 1.5% (v/v) antibiotic–antimycotic solution.

extract_protocol: RNA was isolated using a RNeasy Mini-Kit with on-column DNase digestion (Qiagen) according to the manufacturer’s instructions.

value: Bone Marrow

tag: patient

tag: gender

value: F

tag: cell type


title: ssmRNATruseq_1ug C2

value: Tissue mixture


title: BM-MSC_patient5

value: Bone marrov derived mesenchymal stromal cells


title: TBP-ChEC Nrd1-AA_-Rap_rep2

source_name: TBP-ChEC Nrd1-AA_-Rap

value: Minus Rapamycin 1h (1μg/ml)


title: 10 WT IRE1 Tm 1ug 16h, biological rep3

source_name: 10 WT IRE1 Tm 1ug 16h, biological rep3

value: WT IRE1

tag: agent

value: Tunicamycin

tag: doses

value: 1 ug/g

value: 16 hrs


title: TBP-ChEC Nrd1-AA_+Rap_rep1

tag: strain background

value: Plus Rapamycin 1h (1μg/ml)


title: BM-MSC_patient2


title: 11 KO IRE1 untreat, biological rep1

source_name: 11 KO IRE1 untreat, biological rep1

value: KO IRE

value: Untreatment

tag: time point


title: ssmRNATruseq_100ng B2

value: Human Brain Reference RNA (B)

value: Normal brain tissue mixture


title: 12 KO IRE1 untreat, biological rep2

source_name: 12 KO IRE1 untreat, biological rep2


title: ssmRNATruseq_100ng C1


title: 9 WT IRE1 Tm 1ug 16h, biological rep2

source_name: 9 WT IRE1 Tm 1ug 16h, biological rep2


title: ASC_patient5

source_name: Adipose tissue derived mesenchymal stromal cells

tag: tissue

value: Fat


title: RNA-seq Nrd1-AA_drpd3_+Rap_rep2

data_processing:
Single-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) with options '-k 20 --end-to-end --sensitive -X 800'. PCR duplicates were removed from the analysis. BigWig coverage files were generated using Bam2wig function. Differential expression analysis was performed using the R/Bioconductor package DEseq on mRNA annotations Ensembl (Saccharomyces_cerevisiae.EF4.65.gtf).
Genome_build: saccer3
Supplementary_files_format_and_content: bigWig files of Watson and Crick Strands. Each file corresponds to the mean of rep1 and rep2.

source_name: RNA-seq Nrd1-AA_drpd3_+Rap

extract_protocol:
RNAs were extracted using Glass-beads and TRIzol (Invitrogen).
ribodep stranded RNA (Illumina)

tag: genotype/variation

value: Nrd1-AA drpd3

tag: treatment


title: ASC_patient4

value: Adipose tissue derived mesenchymal stromal cells


title: 8 WT IRE1 Tm 1ug 16h, biological rep1

source_name: 8 WT IRE1 Tm 1ug 16h, biological rep1


title: 7 WT IRE1 Eto 50ug 16h, biological rep4

source_name: 7 WT IRE1 Eto 50ug 16h, biological rep4

value: Etoposide

value: 50 ug/g


title: 6 WT IRE1 Eto 50ug 16h, biological rep3

source_name: 6 WT IRE1 Eto 50ug 16h, biological rep3


title: RNA-seq Nrd1-AA_drpd3_+Rap_rep1


title: ssmRNATruseq_100ng B1

value: Kit mRNA TruSeq


title: ASC_patient3

value: F


title: 5 WT IRE1 Eto 50ug 16h, biological rep2

source_name: 5 WT IRE1 Eto 50ug 16h, biological rep2


title: ASC_patient2


title: TBP-ChEC Nrd1-AA_-Rap_rep1

value: Minus Rapamycin 1h (1μg/ml)

value: Nrd1-AA TBP-ChEC


title: RNA-seq Nrd1-AA_drpd3_-Rap_rep2

source_name: RNA-seq Nrd1-AA_drpd3_-Rap


title: 13 KO IRE1 Eto 50ug 16h, biological rep1


title: ssmRNATruseq_100ng A2

value: Universal Human Reference RNA (A)

value: Tissue mixture


title: Nxf1 Input

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

data_processing:
Reads were adaptor and quality trimmed, removing bases with a Q<15 from the 5’ end of the read, Q<20 from the 3’ end of the read and also if the average quality in a 4 nts window falls below 15. Trimmed reads greater than 36 nts were retained.
Reads were  mapped to hg19 using BWA MEM version 0.7.17-r1188 (http://bio-bwa.sourceforge.net/) with the options `-M –k 25`.
Alignments were filtered to remove reads mapping to more than one location, other non-primary alignments, alignments that are not “proper-paired” and alignments with an alignment score < 30. PCR duplicates were removed using Picard MarkDuplicates
Coverage tracks were generated using genomecov from Bedtools, scaling depths to counts per million, and converted to Bigwig using BedGraphToBigWig from UCSC Kent utils.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files showing read depth in counts per million

extract_protocol:
Cell pellets were lysed in ChIP Lysis Buffer 1 (50 mM HEPES-NaOH pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100, protease inhibitors SigmaFAST) and rotated at 4°C for 5 minutes. Nuclei were then pelleted via centrifugation (3000 x g, 5 minutes at 4°C), and resuspended in ChIP Buffer 2 (10 mM Tris-HCl pH 7.3, 200 mM NaCl, 0.5 mM EGTA, 1 mM EDTA, protease inhibitors SigmaFAST), before rotation at room temperature for 10 mins. Nuclei were pelleted via centrifugation (1500 x g, 5 minutes at 4°C) and resuspended in ChIP Lysis Buffer 3 (10 mM Tris-HCl pH 7.3, 200 mM NaCl, 0.5 mM EGTA, 1 mM EDTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, protease inhibitors SigmaFAST). Samples were sonicated using a Bioruptor (High, 20 x [30s-ON/30s-OFF]) to generate chromatin fragments of 250-300 nts, and cleared by centrifugation (16100 x g, 15 minutes, 4°C). Lysate concentrations were measured by Bradford assay, and equal concentrations of chromatin were incorporated into the IPs. IPs were carried out overnight at 4°C using 5 µg of FLAG antibody (Sigma). 100 µL blocked protein-G Dynabeads were then added to the samples and incubated for 2 hours at 4°C. Following incubation, beads were washed with 4 x 0.5 mL RIPA Wash Buffer (50 mM HEPES-NaOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP40, 0.7% Na-deoxycholate, 0.1% N-lauroylsarcosine) and once with 0.5 mL ChIP Final Wash Buffer (10 mM Tris-HCl pH7.3, 1 mM EDTA, 50 mM NaCl). Complexes were eluted by adding 200 µL of ChIP Elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) and incubated at 65°C for 30 minutes. NaCl was added to a final concentration of 200 mM and cross-links were reversed overnight at 65°C. Samples were then treated with RNase A (0.2 mg/mL) for 2 hours at 37°C, followed by proteinase K (0.2 mg/mL) for 2 hours at 55°C. DNA was purified via phenol-chloroform extraction and ethanol precipitation, and then resuspended in water.
Library construction was using the standard ChIP-seq protocol of Novogene (Beijing, China)

treatment_protocol: Three 15-cm dishes were seeded per ChIP condition with 5 x 106 cells/dish. Near endogenous expression of the FLAG-tagged proteins was induced for 48 hours in the stable cell lines by addition of tetracycline at 5 ng/mL for Nxf1, and 10 ng/mL for Chtop, and Alyref. Protein-DNA complexes were cross-linked in vivo by incubating the cells with 20 mL PBS-formaldehyde (1%).

tag: transgenic construct

tag: antibody

tag: replicate

tag: cell line


title: RNA-seq Nrd1-AA_drpd3_-Rap_rep1


title: Nxf1 ChIP rep1

value: FLAG


title: RNA-seq Nrd1-AA_+Rap_rep2

source_name: RNA-seq Nrd1-AA_+Rap

value: Plus Rapamycin 1h (1μg/ml)


title: ssmRNATruseq_1ug B1

tag: sample type

tag: tissue source

tag: protocol


title: BM-MSC_patient1

value: Bone Marrow

tag: patient

value: Bone marrov derived mesenchymal stromal cells


title: ssmRNATruseq_100ng A1


title: ssmRNATruseq_1ug A1


title: 4 WT IRE1 Eto 50ug 16h, biological rep1

source_name: 4 WT IRE1 Eto 50ug 16h, biological rep1

value: WT IRE1

value: 16 hrs


title: BM-MSC_patient4

tag: gender

value: M


title: RNA-seq Nrd1-AA_+Rap_rep1


title: Chtop Input

source_name: Chtop-IN

value: FLAG-Chtop


title: ssmRNATruseq_1ug B2

value: Human Brain Reference RNA (B)

value: Normal brain tissue mixture


title: 1 WT IRE1 untreat, biological rep1

source_name: 1 WT IRE1 untreat, biological rep1


title: ssmRNATruseq_1ug A2


title: RNA-seq Nrd1-AA_-Rap_rep2

source_name: RNA-seq Nrd1-AA_-Rap


title: MVm_miRNA-Seq

organism: Cytospora mali

source_name: mycelia of axenic culture

value: mycelia

value: mycelia cultured on PDA medium


title: Chtop ChIP rep 2


title: Chtop ChIP rep 1


title: mRNATruseq_1ug C2

value: Mixture 75% A + 25% B (C)

value: Kit mRNA TruSeq


title: BM-MSC_patient3

source_name: Bone marrov derived mesenchymal stromal cells

tag: cell type


title: ASC_patient1

value: Fat

value: F

value: Adipose tissue derived mesenchymal stromal cells


title: Nfat5-2-siRNA 2 (500 mOsm)

city: Karise

first: Rune

middle: Nørgaard

last: Rasmussen

address: Vesterled 4

department: Drug transporters in ADME

country: Denmark

institute: Southern University of Denmark

data_processing:
Alignment was performed with Hisat 2.0.5
Read count was performed using featureCounts v1.5.1
Genome_build: CFA 3.1

organism: Canis lupus familiaris

source_name: Madin-Darby Canine Kidney (MDCK) I cells

growth_protocol: MDCK I cells  were cultured using DMEM/F-12 containing 1 % penicillin-streptomycin, 2 mM L-glutamine and 10 % FBS in an atmosphere of 5 % CO2- 95 % O2 at 37 °C at a density of 7.6 x 10.000 in non-coated 24 well plates for a total of 144 h.  The cells was treated with different compounds in the last 24 h of the cultivation,

extract_protocol:
RNA was isolated using Nucleospin® RNA/Protein  following the protocol of the manufactor.
The library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: MDCK I cells treated with siRNA and cultivated in isosmotic (300 mOsm) and hyperosmotic (raffinose; 500 mOsm) culture medium were used for RNA-sequencing. Briefly, siRNA (100 nM final concentration) and 1.5 μl Lipofectamine® RNAiMAX in a total volume of 100 μl serum free medium were prepared following the manufactures protocol and added to each well (24 well plate, well area 1.9 cm2) and incubated at room temperature for approximately 20 min. Then, 400 μl cells suspension with a concentration of 427,500 MDCK I cells per ml (90,000 MDCK I cells per cm2) in normal growth medium was added. The cells were incubated at 37°C 5% CO2 over night. The next day, the medium containing siRNA was removed and exchange with normal growth medium over night, whereafter raffinose (200 mOsm) supplemented normal growth medium (total osmolality of 500 mOsm) was added for 24 h. To control cells Slc22a6-siRNA (Neg-siRNA) was used under both cells treated with normal growth medium (300 mOsm) and raffinose supplemented normal growth medium (500 mOsm) as Slc22a6 is not expressed in MDCK I cells  After 24 h, the cellular uptake of either [3H]-ibuprofen (50 nM, 1 μCi/ml) 1 or [3H]-taurine (99 nM, 1 μCi/ml) was measured. When transfecting with siRNA against Tmem184b, the medium was not changed the day after transfection. Instead the cells were treated with raffinose supplemented growth medium (500 mOsm) for 24 h resulting in a total cultivation time of 48 h

tag: passage

value: Raffinose (500 mOsm) + Nfat5-2-siRNA


title: Alyref Input rep 2

value: FLAG-Alyref


title: Nfat5-2-siRNA 1 (500 mOsm)


title: Alyref Input rep 1


title: Nxf1 ChIP rep2

value: FLAG


title: RNA-seq Nrd1-AA_-Rap_rep1

value: Minus Rapamycin 1h (1μg/ml)


title: 3 WT IRE1 untreat, biological rep3

source_name: 3 WT IRE1 untreat, biological rep3

value: WT IRE1

tag: agent


title: 2 WT IRE1 untreat, biological rep2

source_name: 2 WT IRE1 untreat, biological rep2

value: 16 hrs


title: Nfat5-1-siRNA 2 (500 mOsm)

value: Raffinose (500 mOsm) + Nfat5-1-siRNA


title: mRNATruseq_1ug B1


title: mRNATruseq_1ug C1

value: Tissue mixture


title: Alyref ChIP rep 2


title: Nfat5-1-siRNA 1 (500 mOsm)


title: TMVm_degradome-Seq


title: mRNATruseq_1ug B2

value: Human Brain Reference RNA (B)


title: Alyref ChIP rep 1


title: Neg-siRNA 2 (500 mOsm)

value: Raffinose (500 mOsm) + Neg-siRNA


title: mRNATruseq_1ug D1

value: Mixture 25% A + 75% B (D)


title: H_sgPTTG3P

city: Taipei

first: JOU-HO

last: SHIH

state: Please Select

address: 128 Sec. 2, Academia Rd. Nankang, Taipei

country: Taiwan

institute: Institute of Biomedical Sciences, Academia Sinica

data_processing:
The RNA-seq reads of knockdown groups were first processed with Trimmomatic (Trimmomatic-0.38) to eliminate the adapter contamination.
The qualified reads from knockdown groups were aligned to the reference genome by STAR (STAR_2.6.1d).
The qualified reads of knockdown groups were conducted with RSEM (RSEM-1.3.1). Gene expression quantification were conducted with FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: H1299 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted from  cell lines by NucleoSpin RNA XS (Macherey Nagel, Duren, Germany).
A total amount of 3 μg RNA per sample was used as in put material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out. using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H. Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: sgPTTG3P knockdown


title: 6_NC218_LO: Non-sphere-forming primary glioma cells cocultured with Large Oncosomes

city: Planegg-Martinsried

first: Andrea

last: Terrasi

address: Großhaderner Strasse 9

department: Biomedical Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45¬∞C on GeneChip Gene 2.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for gene annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/genecodeg.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Therefore, the expression levels of Ensembl genes specific for 18642 unique mRNAs were obtained.

source_name: LO High cocultured primary GBM derived cells

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100-250 nanograms of total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

growth_protocol: Primary patients' derived glioma cells were washed twice with HBSS (Gibco-Invitrogen, Thermo Fisher Scientific, Waltham, MA USA) and coltured with neurocult (NC) media (Stem Cells)

extract_protocol: Total RNA was purified from LO or mock-treated glioma cocultures using Master Pure RNA purification kit (Epicentre Biotechnologies, Illumina; Madison, WI, USA) followed by DNA digestion with DNase I.

treatment_protocol: Total RNA was extracted from cultures and 300ng of DNA-free total RNA were reverse transcribed using the SuperScript II Reverse Transcriptase and random hexamers (both from Thermo Fisher Scientific).

value: primary human non-sphere-forming glioma cells

tag: cocultured

value: LO High


title: 5_NC218_UNTR: Untreated non-sphere-forming primary glioma cells

source_name: untreated primary GBM derived cells

value: mock


title: Neg-siRNA 1 (500 mOsm)


title: Neg-siRNA 2 (300 mOsm)

value: Control (300 mOsm) + Neg-siRNA


title: Reaggregation comparison, Re-aggregated clusters

city: Cambridge

first: Adrian

last: Veres

state: Massachusetts

address: 7 Divinity Ave

institute: Harvard University

description:
Veres2019_analysis_data.tar
Misc.Reagg_comparison.processed_counts.tsv.gz
Misc.Reagg_comparison.cell_metadata.tsv
Misc.Reagg_comparison.raw_indrops_counts.tsv.gz

data_processing:
All processing steps from raw fastq files to count matrices were performed using the custom pipeline for inDrops data analysis (www.github.com/indrops/indrops) using the the following parameters specified in the YAML file: [trimmomatic arguments]: LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "30". [output_arguments]: filter_alignments_to_softmasked_regions: True. All other parameters were used as in the default_parameters file in the repository github.com/indrops/indrops, commit hash 8a9167.
Genome_build: GRCh38.88
Supplementary_files_format_and_content: '*.raw_indrops_counts.*' files are the raw, unfiltered output from the Indrops processing pipeline. The first column indicates the barcode label using the Indrops pipeline nomenclature, all folllowing columns are UMIFM counts as defined in Klein et al. (2015). The gene corresponding to each column is listed in the header line.
Supplementary_files_format_and_content: '*.processed_counts.*' are filtered counts files, removing undetected genes and filtering cells using the thresholds described in the methods section of Veres et al. 2019. The first column indicates the cell label, all following columns are UMIFM counts for the gene indicated in the header row.
Supplementary_files_format_and_content: '*.cell_metadata.*' files contain metadata associated for all filtered cells in the each dataset. The first row is a header detailing the type of data in each column. These include TSNE coordinates, cluster label annotations and pseudotime values (as appropriate).
Supplementary_files_format_and_content: code_analysis_files.tar is a tarball of all files (primarily loom-formatted) used in generating the analysis, with the accompanying code at https://github.com/meltonlab/scbeta_indrops

source_name: in vitro differentiated pluripotent stem cell

growth_protocol: Human embryonic and pluripotent stem cells were maintained and differentiated as described in the methods of (Veres et al. 2018). Differentiation was carried out using step-wise protocols aimed at gradually producing beta cells in vitro.

extract_protocol:
Differentiated clusters were prepared for single cell RNA sequencing as follows: 1-2 mL suspension culture was sampled from the spinner flask, dissociated with TrypLE Express (5-15 minutes at 37 °C), quenched with cold PBS + 1% BSA and gently dispersed with a P1000 pipette. Cells were then centrifuged (300 rpm, 3 min), resuspended in cold PBS+1% BSA and filtered through a 70 µm mesh filter. Centrifugation, resuspension and filtering was repeated a total of 3 times. Cells were then counted and resuspended to the working dilution for inDrops (100,000 cells/mL) in 1X PBS with 13% Optiprep (Sigma; D1556).
Single cell RNA sequencing was carried out using the inDrops platform, as previously described (Klein 2015, Zilionis 2016). Most samples were run using ‘inDrops v2’ barcoded hydrogel beads (1 Cell Bio, Harvard Single Cell Core), and one experiment used ‘inDrops v3’ beads (Harvard Single Cell Core). Following the inDrops protocol, each biological sample was split into several aliquots of 1000-3000 cells after encapsulation. At least two library aliquots were prepared separately from each sample, indexing using recommended index sequences, pooled and sequencing on a NextSeq 500 (Illumina).

tag: experiment

value: Reaggregation comparison

value: SC-beta protocol v4

tag: Stage

value: Stage 6


title: Re-processed human islets data from GSE84133

source_name: Human pancreatic islets

value: Human pancreatic islets


title: H_control

tag: genotype/variation

value: sgRNA control


title: Neg-siRNA 1 (300 mOsm)

tag: treatment