title: TFEB+TFE3 KO HEK 293T, 24H 991, rep 2 TFEB_TFE3_DKO_24H_2_S35

description: TFEB+TFE3 KO HEK 293T, 24H 991, rep 2


title: WT HEK 293T, DMSO, rep 3 TFEB_TFE3_DWT_0H_DMSO_3_S3

status: Public on May 08 2023

type: SRA

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: Salk Institute for Biological Studies

description: WT HEK 293T, DMSO, rep 3

library_source: transcriptomic

data_processing:
Raw RNA sequencing reads in FASTQ files were quality-tested using FASTQC and mapped to the human reference genome (GRCh38) with STAR aligner with default parameters .
Raw or TPM (Transcripts Per Million) gene expression levels were quantified across all the exons of the top isoform in RefSeq with  analyzeRepeats.pl in HOMER
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: kidney

growth_protocol: HEK 293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was extracted from cells using the QIAGEN RNeasy Plus mini kit

tag: tissue

value: kidney

tag: cell line

tag: time

tag: genotype

value: TFEB+TFE3 WT

tag: treatment

value: DMSO


title: TFEB+TFE3 KO HEK 293T, 2H 991, rep 2 TFEB_TFE3_DKO_2H_2_S23

description: TFEB+TFE3 KO HEK 293T, 2H 991, rep 2

value: TFEB+TFE3 Knock out


title: WT HEK 293T, DMSO, rep 1 TFEB_TFE3_DWT_0H_DMSO_1_S1

description: WT HEK 293T, DMSO, rep 1


title: TFEB+TFE3 KO HEK 293T, 8H 991, rep 3 TFEB_TFE3_DKO_8H_3_S30

description: TFEB+TFE3 KO HEK 293T, 8H 991, rep 3


title: TFEB+TFE3 KO HEK 293T, 16H 991, rep 1 TFEB_TFE3_DKO_16H_1_S31

description: TFEB+TFE3 KO HEK 293T, 16H 991, rep 1


title: TFEB+TFE3 KO HEK 293T, 8H 991, rep 2 TFEB_TFE3_DKO_8H_2_S29

description: TFEB+TFE3 KO HEK 293T, 8H 991, rep 2


title: TFEB+TFE3 KO HEK 293T, DMSO, rep 2 TFEB_TFE3_DKO_0H_2_S20

description: TFEB+TFE3 KO HEK 293T, DMSO, rep 2


title: TFEB+TFE3 KO HEK 293T, 2H 991, rep 3 TFEB_TFE3_DKO_2H_3_S24

description: TFEB+TFE3 KO HEK 293T, 2H 991, rep 3


title: WT FNIP1 HEK 293T, 8H 991, rep 2 SA5WT_8H_991_2_S11

description: WT FNIP1 HEK 293T, 8H 991, rep 2

value: WT FNIP1


title: TFEB+TFE3 KO HEK 293T, DMSO, rep 1 TFEB_TFE3_DKO_0H_1_S19

description: TFEB+TFE3 KO HEK 293T, DMSO, rep 1


title: TFEB+TFE3 KO HEK 293T, 4H 991, rep 3 TFEB_TFE3_DKO_4H_3_S27

description: TFEB+TFE3 KO HEK 293T, 4H 991, rep 3


title: TFEB+TFE3 KO HEK 293T, 4H 991, rep 1 TFEB_TFE3_DKO_4H_1_S25

description: TFEB+TFE3 KO HEK 293T, 4H 991, rep 1


title: WT FNIP1 HEK 293T, 8H 991, rep 3 SA5WT_8H_991_3_S12

description: WT FNIP1 HEK 293T, 8H 991, rep 3


title: WT FNIP1 HEK 293T, 4H 991, rep 3 SA5WT_4H_991_3_S9

description: WT FNIP1 HEK 293T, 4H 991, rep 3


title: TFEB+TFE3 KO HEK 293T, 24H 991, rep 1 TFEB_TFE3_DKO_24H_1_S34

description: TFEB+TFE3 KO HEK 293T, 24H 991, rep 1


title: WT FNIP1 HEK 293T, 4H 991, rep 1 SA5WT_4H_991_1_S7

description: WT FNIP1 HEK 293T, 4H 991, rep 1


title: WT FNIP1 HEK 293T, 8H 991, rep 1 SA5WT_8H_991_1_S10

description: WT FNIP1 HEK 293T, 8H 991, rep 1


title: TFEB+TFE3 KO HEK 293T, DMSO, rep 3 TFEB_TFE3_DKO_0H_3_S21

description: TFEB+TFE3 KO HEK 293T, DMSO, rep 3


title: WT HEK 293T, 2H 991, rep 1 TFEB_TFE3_DWT_2H_991_1_S4

description: WT HEK 293T, 2H 991, rep 1


title: WT FNIP1 HEK 293T, 2H 991, rep 2 SA5WT_2H_991_2_S5

description: WT FNIP1 HEK 293T, 2H 991, rep 2


title: TFEB+TFE3 KO HEK 293T, 16H 991, rep 3 TFEB_TFE3_DKO_16H_3_S33

description: TFEB+TFE3 KO HEK 293T, 16H 991, rep 3


title: TFEB+TFE3 KO HEK 293T, 2H 991, rep 1 TFEB_TFE3_DKO_2H_1_S22

description: TFEB+TFE3 KO HEK 293T, 2H 991, rep 1


title: TFEB+TFE3 KO HEK 293T, 24H 991, rep 3 TFEB_TFE3_DKO_24H_3_S36

description: TFEB+TFE3 KO HEK 293T, 24H 991, rep 3


title: WT FNIP1 HEK 293T, 16H 991, rep 1 SA5WT_16H_991_1_S13

description: WT FNIP1 HEK 293T, 16H 991, rep 1


title: TFEB+TFE3 KO HEK 293T, 8H 991, rep 1 TFEB_TFE3_DKO_8H_1_S28

description: TFEB+TFE3 KO HEK 293T, 8H 991, rep 1


title: WT FNIP1 HEK 293T, 4H 991, rep 2 SA5WT_4H_991_2_S8

description: WT FNIP1 HEK 293T, 4H 991, rep 2


title: TFEB+TFE3 KO HEK 293T, 16H 991, rep 2 TFEB_TFE3_DKO_16H_2_S32

description: TFEB+TFE3 KO HEK 293T, 16H 991, rep 2


title: SA5 FNIP1 HEK 293T, 8H 991, rep 3 SA5_8H_991_3_S27

description: SA5 FNIP1 HEK 293T, 8H 991, rep 3

value: SA5 FNIP1


title: SA5 FNIP1 HEK 293T, 8H 991, rep 2 SA5_8H_991_2_S26

description: SA5 FNIP1 HEK 293T, 8H 991, rep 2


title: WT FNIP1 HEK 293T, 2H 991, rep 1 SA5WT_2H_991_1_S4

description: WT FNIP1 HEK 293T, 2H 991, rep 1


title: WT FNIP1 HEK 293T, 16H 991, rep 3 SA5WT_16H_991_3_S15

description: WT FNIP1 HEK 293T, 16H 991, rep 3


title: WT FNIP1 HEK 293T, 2H 991, rep 3 SA5WT_2H_991_3_S6

description: WT FNIP1 HEK 293T, 2H 991, rep 3


title: WT FNIP1 HEK 293T, 16H 991, rep 2 SA5WT_16H_991_2_S14

description: WT FNIP1 HEK 293T, 16H 991, rep 2


title: SA5 FNIP1 HEK 293T, 4H 991, rep 2 SA5_4H_991_2_S23

description: SA5 FNIP1 HEK 293T, 4H 991, rep 2


title: SA5 FNIP1 HEK 293T, 2H 991, rep 2 SA5_2H_991_2_S20

description: SA5 FNIP1 HEK 293T, 2H 991, rep 2


title: WT FNIP1 HEK 293T, DMSO, rep 3 SA5WT_0H_DMSO_3_S3

description: WT FNIP1 HEK 293T, DMSO, rep 3


title: WT FNIP1 HEK 293T, DMSO, rep 2 SA5WT_0H_DMSO_2_S2

description: WT FNIP1 HEK 293T, DMSO, rep 2


title: SA5 FNIP1 HEK 293T, 16H 991, rep 2 SA5_16H_991_2_S29

description: SA5 FNIP1 HEK 293T, 16H 991, rep 2


title: WT HEK 293T, 8H Rot, rep 3 ADWT_8H_Rot_3_S36

description: WT HEK 293T, 8H Rot, rep 3

value: AMPK WT

value: Rot


title: WT HEK 293T, 8H Rot, rep 2 ADWT_8H_Rot_2_S35

description: WT HEK 293T, 8H Rot, rep 2


title: WT HEK 293T, 8H Rot, rep 1 ADWT_8H_Rot_1_S34

description: WT HEK 293T, 8H Rot, rep 1


title: SA5 FNIP1 HEK 293T, 8H 991, rep 1 SA5_8H_991_1_S25

description: SA5 FNIP1 HEK 293T, 8H 991, rep 1


title: WT FNIP1 HEK 293T, DMSO, rep 1 SA5WT_0H_DMSO_1_S1

description: WT FNIP1 HEK 293T, DMSO, rep 1


title: SA5 FNIP1 HEK 293T, DMSO, rep 3 SA5_0H_DMSO_3_S18

description: SA5 FNIP1 HEK 293T, DMSO, rep 3


title: SA5 FNIP1 HEK 293T, DMSO, rep 1 SA5_0H_DMSO_1_S16

description: SA5 FNIP1 HEK 293T, DMSO, rep 1


title: SA5 FNIP1 HEK 293T, 16H 991, rep 1 SA5_16H_991_1_S28

description: SA5 FNIP1 HEK 293T, 16H 991, rep 1


title: WT HEK 293T, 8H Phen, rep 3 ADWT_8H_Phen_3_S24

description: WT HEK 293T, 8H Phen, rep 3

value: Phen


title: SA5 FNIP1 HEK 293T, 4H 991, rep 3 SA5_4H_991_3_S24

description: SA5 FNIP1 HEK 293T, 4H 991, rep 3


title: WT HEK 293T, 8H CCCP, rep 1 ADWT_8H_CCCP_1_S46

description: WT HEK 293T, 8H CCCP, rep 1

value: CCCP


title: WT HEK 293T, 8H 991, rep 3 ADWT_8H_991_3_S12

description: WT HEK 293T, 8H 991, rep 3


title: SA5 FNIP1 HEK 293T, 2H 991, rep 3 SA5_2H_991_3_S21

description: SA5 FNIP1 HEK 293T, 2H 991, rep 3


title: WT HEK 293T, 8H Phen, rep 1 ADWT_8H_Phen_1_S22

description: WT HEK 293T, 8H Phen, rep 1


title: WT HEK 293T, 8H 991, rep 1 ADWT_8H_991_1_S10

description: WT HEK 293T, 8H 991, rep 1


title: SA5 FNIP1 HEK 293T, DMSO, rep 2 SA5_0H_DMSO_2_S17

description: SA5 FNIP1 HEK 293T, DMSO, rep 2


title: WT HEK 293T, 8H Phen, rep 2 ADWT_8H_Phen_2_S23

description: WT HEK 293T, 8H Phen, rep 2


title: SA5 FNIP1 HEK 293T, 16H 991, rep 3 SA5_16H_991_3_S30

description: SA5 FNIP1 HEK 293T, 16H 991, rep 3


title: WT HEK 293T, 4H Phen, rep 3 ADWT_4H_Phen_3_S21

description: WT HEK 293T, 4H Phen, rep 3


title: WT HEK 293T, 8H CCCP, rep 3 ADWT_8H_CCCP_3_S48

description: WT HEK 293T, 8H CCCP, rep 3


title: SA5 FNIP1 HEK 293T, 4H 991, rep 1 SA5_4H_991_1_S22

description: SA5 FNIP1 HEK 293T, 4H 991, rep 1


title: WT HEK 293T, 8H CCCP, rep 2 ADWT_8H_CCCP_2_S47

description: WT HEK 293T, 8H CCCP, rep 2


title: WT HEK 293T, 8H 991, rep 2 ADWT_8H_991_2_S11

description: WT HEK 293T, 8H 991, rep 2


title: SA5 FNIP1 HEK 293T, 2H 991, rep 1 SA5_2H_991_1_S19

description: SA5 FNIP1 HEK 293T, 2H 991, rep 1


title: WT HEK 293T, 4H 991, rep 3 ADWT_4H_991_3_S9

description: WT HEK 293T, 4H 991, rep 3


title: WT HEK 293T, 16H CCCP, rep 2 ADWT_4H_CCCP_2_S44

description: WT HEK 293T, 16H CCCP, rep 2


title: WT HEK 293T, 4H Rot, rep 2 ADWT_4H_Rot_2_S32

description: WT HEK 293T, 4H Rot, rep 2


title: WT HEK 293T, 4H 991, rep 2 ADWT_4H_991_2_S8

description: WT HEK 293T, 4H 991, rep 2


title: WT HEK 293T, 4H Rot, rep 1 ADWT_4H_Rot_1_S31

description: WT HEK 293T, 4H Rot, rep 1


title: WT HEK 293T, 16H CCCP, rep 3 ADWT_4H_CCCP_3_S45

description: WT HEK 293T, 16H CCCP, rep 3


title: WT HEK 293T, 2H Rot, rep 3 ADWT_2H_Rot_3_S30

description: WT HEK 293T, 2H Rot, rep 3


title: WT HEK 293T, 2H 991, rep 2 ADWT_2H_Phen_2_S17

description: WT HEK 293T, 2H 991, rep 2


title: WT HEK 293T, 2H Rot, rep 2 ADWT_2H_Rot_2_S29

description: WT HEK 293T, 2H Rot, rep 2


title: WT HEK 293T, 4H Phen, rep 2 ADWT_4H_Phen_2_S20

description: WT HEK 293T, 4H Phen, rep 2


title: WT HEK 293T, 2H Rot, rep 1 ADWT_2H_Rot_1_S28

description: WT HEK 293T, 2H Rot, rep 1


title: WT HEK 293T, 16H CCCP, rep 1 ADWT_4H_CCCP_1_S43

description: WT HEK 293T, 16H CCCP, rep 1


title: WT HEK 293T, 4H 991, rep 1 ADWT_4H_991_1_S7

description: WT HEK 293T, 4H 991, rep 1


title: WT HEK 293T, 2H CCCP, rep 3 ADWT_2H_CCCP_3_S42

description: WT HEK 293T, 2H CCCP, rep 3


title: WT HEK 293T, 4H Rot, rep 3 ADWT_4H_Rot_3_S33

description: WT HEK 293T, 4H Rot, rep 3


title: WT HEK 293T, 2H 991, rep 1 ADWT_2H_Phen_1_S16

description: WT HEK 293T, 2H 991, rep 1


title: WT HEK 293T, 2H 991, rep 3 ADWT_2H_Phen_3_S18

description: WT HEK 293T, 2H 991, rep 3


title: WT HEK 293T, 4H Phen, rep 1 ADWT_4H_Phen_1_S19

description: WT HEK 293T, 4H Phen, rep 1


title: WT HEK 293T, 2H CCCP, rep 2 ADWT_2H_CCCP_2_S41

description: WT HEK 293T, 2H CCCP, rep 2


title: WT HEK 293T, 16H Rot, rep 1 ADWT_16H_Rot_1_S37

description: WT HEK 293T, 16H Rot, rep 1


title: WT HEK 293T, 2H CCCP, rep 1 ADWT_2H_CCCP_1_S40

description: WT HEK 293T, 2H CCCP, rep 1


title: WT HEK 293T, 2H 991, rep 2 ADWT_2H_991_2_S5

description: WT HEK 293T, 2H 991, rep 2


title: WT HEK 293T, 2H 991, rep 3 ADWT_2H_991_3_S6

description: WT HEK 293T, 2H 991, rep 3


title: WT HEK 293T, 16H Rot, rep 3 ADWT_16H_Rot_3_S39

description: WT HEK 293T, 16H Rot, rep 3


title: WT HEK 293T, 2H 991, rep 1 ADWT_2H_991_1_S4

description: WT HEK 293T, 2H 991, rep 1


title: WT HEK 293T, 16H Rot, rep 2 ADWT_16H_Rot_2_S38

description: WT HEK 293T, 16H Rot, rep 2


title: WT HEK 293T, 16H Phen, rep 3 ADWT_16H_Phen_3_S27

description: WT HEK 293T, 16H Phen, rep 3


title: WT HEK 293T, 16H Phen, rep 1 ADWT_16H_Phen_1_S25

description: WT HEK 293T, 16H Phen, rep 1


title: WT HEK 293T, 16H CCCP, rep 2 ADWT_16H_CCCP_2_S50

description: WT HEK 293T, 16H CCCP, rep 2


title: WT HEK 293T, 16H Phen, rep 2 ADWT_16H_Phen_2_S26

description: WT HEK 293T, 16H Phen, rep 2


title: WT HEK 293T, DMSO, rep 1 ADWT_0H_DMSO_1_S1

description: WT HEK 293T, DMSO, rep 1


title: AMPK KO HEK 293T, 8H Rot, rep 3 ADKO_8H_Rot_3_S87

description: AMPK KO HEK 293T, 8H Rot, rep 3

value: AMPK Knock out


title: AMPK KO HEK 293T, 8H Rot, rep 2 ADKO_8H_Rot_2_S86

description: AMPK KO HEK 293T, 8H Rot, rep 2


title: WT HEK 293T, 16H CCCP, rep 3 ADWT_16H_CCCP_3_S51

description: WT HEK 293T, 16H CCCP, rep 3


title: WT HEK 293T, 16H 991, rep 3 ADWT_16H_991_3_S15

description: WT HEK 293T, 16H 991, rep 3


title: WT HEK 293T, 16H 991, rep 2 ADWT_16H_991_2_S14

description: WT HEK 293T, 16H 991, rep 2


title: WT HEK 293T, 16H 991, rep 1 ADWT_16H_991_1_S13

description: WT HEK 293T, 16H 991, rep 1


title: WT HEK 293T, DMSO, rep 3 ADWT_0H_DMSO_3_S3

description: WT HEK 293T, DMSO, rep 3


title: WT HEK 293T, DMSO, rep 2 ADWT_0H_DMSO_2_S2

description: WT HEK 293T, DMSO, rep 2


title: WT HEK 293T, 16H CCCP, rep 1 ADWT_16H_CCCP_1_S49

description: WT HEK 293T, 16H CCCP, rep 1


title: AMPK KO HEK 293T, 8H 991, rep 3 ADKO_8H_991_3_S63

description: AMPK KO HEK 293T, 8H 991, rep 3


title: AMPK KO HEK 293T, 4H Phen, rep 2 ADKO_4H_Phen_2_S71

description: AMPK KO HEK 293T, 4H Phen, rep 2


title: AMPK KO HEK 293T, 4H Rot, rep 1 ADKO_4H_Rot_1_S82

description: AMPK KO HEK 293T, 4H Rot, rep 1


title: AMPK KO HEK 293T, 8H Phen, rep 2 ADKO_8H_Phen_2_S74

description: AMPK KO HEK 293T, 8H Phen, rep 2


title: AMPK KO HEK 293T, 4H CCCP, rep 3 ADKO_4H_CCCP_3_S96

description: AMPK KO HEK 293T, 4H CCCP, rep 3


title: AMPK KO HEK 293T, 8H CCCP, rep 3 ADKO_8H_CCCP_3_S99

description: AMPK KO HEK 293T, 8H CCCP, rep 3


title: AMPK KO HEK 293T, 8H Phen, rep 3 ADKO_8H_Phen_3_S75

description: AMPK KO HEK 293T, 8H Phen, rep 3


title: AMPK KO HEK 293T, 8H CCCP, rep 1 ADKO_8H_CCCP_1_S97

description: AMPK KO HEK 293T, 8H CCCP, rep 1


title: AMPK KO HEK 293T, 8H CCCP, rep 2 ADKO_8H_CCCP_2_S98

description: AMPK KO HEK 293T, 8H CCCP, rep 2


title: AMPK KO HEK 293T, 4H Phen, rep 3 ADKO_4H_Phen_3_S72

description: AMPK KO HEK 293T, 4H Phen, rep 3


title: AMPK KO HEK 293T, 8H Phen, rep 1 ADKO_8H_Phen_1_S73

description: AMPK KO HEK 293T, 8H Phen, rep 1


title: AMPK KO HEK 293T, 8H Rot, rep 1 ADKO_8H_Rot_1_S85

description: AMPK KO HEK 293T, 8H Rot, rep 1


title: AMPK KO HEK 293T, 4H CCCP, rep 1 ADKO_4H_CCCP_1_S94

description: AMPK KO HEK 293T, 4H CCCP, rep 1


title: AMPK KO HEK 293T, 4H 991, rep 3 ADKO_4H_991_3_S60

description: AMPK KO HEK 293T, 4H 991, rep 3


title: AMPK KO HEK 293T, 4H Rot, rep 3 ADKO_4H_Rot_3_S84

description: AMPK KO HEK 293T, 4H Rot, rep 3


title: AMPK KO HEK 293T, 4H 991, rep 1 ADKO_4H_991_1_S58

description: AMPK KO HEK 293T, 4H 991, rep 1


title: AMPK KO HEK 293T, 8H 991, rep 1 ADKO_8H_991_1_S61

description: AMPK KO HEK 293T, 8H 991, rep 1


title: AMPK KO HEK 293T, 4H Rot, rep 2 ADKO_4H_Rot_2_S83

description: AMPK KO HEK 293T, 4H Rot, rep 2


title: AMPK KO HEK 293T, 2H Phen, rep 3 ADKO_2H_Phen_3_S69

description: AMPK KO HEK 293T, 2H Phen, rep 3


title: AMPK KO HEK 293T, 8H 991, rep 2 ADKO_8H_991_2_S62

description: AMPK KO HEK 293T, 8H 991, rep 2


title: AMPK KO HEK 293T, 2H Rot, rep3 ADKO_2H_Rot_3_S81

description: AMPK KO HEK 293T, 2H Rot, rep3


title: AMPK KO HEK 293T, 2H CCCP, rep 2 ADKO_2H_CCCP_2_S92

description: AMPK KO HEK 293T, 2H CCCP, rep 2


title: AMPK KO HEK 293T, 4H CCCP, rep 2 ADKO_4H_CCCP_2_S95

description: AMPK KO HEK 293T, 4H CCCP, rep 2


title: AMPK KO HEK 293T, 2H Rot, rep1 ADKO_2H_Rot_1_S79

description: AMPK KO HEK 293T, 2H Rot, rep1


title: AMPK KO HEK 293T, 2H Phen, rep 2 ADKO_2H_Phen_2_S68

description: AMPK KO HEK 293T, 2H Phen, rep 2


title: AMPK KO HEK 293T, 2H Rot, rep2 ADKO_2H_Rot_2_S80

description: AMPK KO HEK 293T, 2H Rot, rep2


title: AMPK KO HEK 293T, 4H Phen, rep 1 ADKO_4H_Phen_1_S70

description: AMPK KO HEK 293T, 4H Phen, rep 1


title: AMPK KO HEK 293T, 2H Phen, rep 1 ADKO_2H_Phen_1_S67

description: AMPK KO HEK 293T, 2H Phen, rep 1


title: AMPK KO HEK 293T, 2H CCCP, rep 1 ADKO_2H_CCCP_1_S91

description: AMPK KO HEK 293T, 2H CCCP, rep 1


title: AMPK KO HEK 293T, 2H CCCP, rep 3 ADKO_2H_CCCP_3_S93

description: AMPK KO HEK 293T, 2H CCCP, rep 3


title: AMPK KO HEK 293T, 2H 991, rep 3 ADKO_2H_991_3_S57

description: AMPK KO HEK 293T, 2H 991, rep 3


title: AMPK KO HEK 293T, 2H 991, rep 1 ADKO_2H_991_1_S55

description: AMPK KO HEK 293T, 2H 991, rep 1


title: AMPK KO HEK 293T, 16H Rot, rep 3 ADKO_16H_Rot_3_S90

description: AMPK KO HEK 293T, 16H Rot, rep 3


title: AMPK KO HEK 293T, 16H Phen, rep 3 ADKO_16H_Phen_3_S78

description: AMPK KO HEK 293T, 16H Phen, rep 3


title: AMPK KO HEK 293T, 16H Rot, rep 2 ADKO_16H_Rot_2_S89

description: AMPK KO HEK 293T, 16H Rot, rep 2


title: AMPK KO HEK 293T, 16H Phen, rep 2 ADKO_16H_Phen_2_S77

description: AMPK KO HEK 293T, 16H Phen, rep 2


title: AMPK KO HEK 293T, 16H Phen, rep 1 ADKO_16H_Phen_1_S76

description: AMPK KO HEK 293T, 16H Phen, rep 1


title: AMPK KO HEK 293T, 4H 991, rep 2 ADKO_4H_991_2_S59

description: AMPK KO HEK 293T, 4H 991, rep 2


title: AMPK KO HEK 293T, 16H CCCP, rep 3 ADKO_16H_CCCP_3_S102

description: AMPK KO HEK 293T, 16H CCCP, rep 3


title: AMPK KO HEK 293T, 16H CCCP, rep 1 ADKO_16H_CCCP_1_S100

description: AMPK KO HEK 293T, 16H CCCP, rep 1


title: AMPK KO HEK 293T, 16H 991, rep 3 ADKO_16H_991_3_S66

description: AMPK KO HEK 293T, 16H 991, rep 3


title: AMPK KO HEK 293T, 16H 991, rep 2 ADKO_16H_991_2_S65

description: AMPK KO HEK 293T, 16H 991, rep 2


title: AMPK KO HEK 293T, 16H 991, rep 1 ADKO_16H_991_1_S64

description: AMPK KO HEK 293T, 16H 991, rep 1


title: AMPK KO HEK 293T, DMSO, rep3 ADKO_0H_DMSO_3_S54

description: AMPK KO HEK 293T, DMSO, rep3


title: AMPK KO HEK 293T, DMSO, rep1 ADKO_0H_DMSO_1_S52

description: AMPK KO HEK 293T, DMSO, rep1


title: AMPK KO HEK 293T, DMSO, rep2 ADKO_0H_DMSO_2_S53

description: AMPK KO HEK 293T, DMSO, rep2


title: NHP_myotube-Exp2

status: Public on May 03 2023

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

description:
Diff_2
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt

data_processing:
NHP transcriptomic data were mapped to the macaca fascicularis reference genome (macFas6). Human transcriptomic data were mapped to the homo sapiens reference genome (hg38). Data were analyzed using the CHURP pipeline (https://github.com/msi-ris/CHURP). Differentially expressed transcripts were identified using DESeq2, considering differentially expressed all transcripts with q<0.05 and absolute log2FoldChange>2.
Assembly: macFas6
Assembly: hg38
Supplementary files format and content: raw_counts_mac_fas_RNAseq_new_2_for_R.txt - processed files contain tab-delimited expression counts obtained following analysis using CHURP
Supplementary files format and content: raw_counts_homo_sap_RNAseq_PLZ_MP_vs_MT.txt - processed files contain tab-delimited expression counts for human myogenic progenitors (this study) and myotubes (from GSE130592) obtained following analysis using CHURP

molecule: total RNA

organism: Macaca fascicularis

growth_protocol: Human (PLZ clone) and NHP (CyMN2 clone) iPSC were differentiated into myogenic progenitors using conditional expression of PAX7 coupled with small molecule treatment to control mesoderm and paraxial mesoderm specification (described in Selvaraj S et al, 2019 - PMID: 31710288). Myogenic progenitors were induced to terminally differentiate in a serum free low nutrient medium supplemented with small molecules (SDDF: 10 µM SB-431542, 10 µM LY-374973, 10 µM forskolin, and 10µM dexamethasone)

extract_protocol:
Total RNA was extracted in TRIzol reagent and column purified with DNAse treatment using the Purelink RNA mini kit as per manufacturer's instructions
RNA-seq: Dual-indexed libraries were generated using the TruSeq stranded mRNA library kit

treatment_protocol: Myogenic progenitors were terminally differentiated into myotubes upon a 5-day treatment with small molecules (SDDF: 10 µM SB-431542, 10 µM LY-374973, 10 µM forskolin, and 10µM dexamethasone)

tag: developmental stage

value: myotube

tag: cell type

value: NHP iPSC

value: control line

value: day 20


title: ChIP P-Smad2 Day2

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

country: Germany

institute: MPI Molecular Genetics

library_source: genomic

data_processing:
For ChIP-Seq, reads were trimmed to 50 bp length. The trimmed reads were aligned to the reference genome using bowtie2 (version 2.2.4) (Langmead, 2012) with the following arguments: -3 5 -I 100 -X 500 --no-discordant --no-mixed. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. For visualization, the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing CPM --extendReads 200 --smoothLength 9 -bs 3 -ignore chrM.
Assembly: mm10
Supplementary files format and content: bigWig files representing density for ChIP-Seq

molecule: genomic DNA

organism: Mus musculus

source_name: ES cells

growth_protocol: ES cells were deprived of feeder cells and cultured for 24 hours. Cells were then dissociated, and 40,000 cell/ml cell suspension was plated onto tissue culture plates in 5 µl droplets. Plates were then inverted and incubated for 24 hours. Drops containing mES cell aggregates (corresponding to differentiation day 0, or ES) were then pooled and resuspended in differentiation medium: 48% (v/v) DMEM/F12 (ThermoFisher; 11320033), 48% (v/v) Neurobasal medium (ThermoFisher; 21103049), 1% (v/v) 200 mM L-glutamine (Lonza; BE17-605E), 1% (v/v) penicillin and streptomycin, 1% (v/v) B27 (Gibco; 17504044), 0.5% (v/v) N2 (Gibco; 17502048), 0,5% (v/v) 7.5% BSA fraction V (Gibco; 15260037), 0.1 mM thioglycerol (Sigma-Aldrich; M1753) supplemented with 20 ng/ml mouse recombinant Bmp4 (R&D Systems; 5020-BP-010). To start differentiation, mESC aggregates resuspended in differentiation medium containing Bmp4 were immediately plated on plates pre-coated with fibronectin (Calbiochem; 341631). Differentiation medium supplemented with Bmp4 was refreshed every 24 hours.

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in 2.5 ml LB1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20 minutes. The cell suspension was homogenized using a douncer. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5 minutes and resuspended in 2.5 ml LB2 (10 mM Tris pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). After 10 minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5 ml LB3 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15 ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C cold room with tubes chilled in ice water. After sonication, 150 μl of Triton X-100 was added per tube, transferred to two 1.5 ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. The solubilized chromatin was then pooled and mixed thoroughly. After taking 50 μl as an input control, the chromatin was distributed into 1.5 ml aliquots, snap frozen and stored at -80°C until use.  The input was reverse-crosslinked with the addition of 50 μl 2x elution buffer (100 mM Tris pH 8, 20 mM EDTA pH 8, 2% SDS) and 13-15 hour incubation at 65°C. 100μl of TE buffer were added, and RNA was digested using 0.2 μg/ml RNase A at 37°C for 2 hours. Proteins were digested with the addition of 0.2 μg/ml proteinase K and incubation at 55°C for 2 hours. The DNA was purified with two subsequent phenol:chloroform:isoamyl alcohol (25:24:1, pH 8) extractions and a subsequent MinElute (Qiagen) purification. The input DNA was quantified using a NanoPhotometer (Implen).    For ChIP, 100 μl protein G-coated Dynal beads (Life Technologies) were washed 3x with 1 ml of blocking buffer (PBS, 0.5% BSA), resuspended in 500 μl of blocking solution containing 5 μg primary ChIP antibody (listed in the Key resources table) and rotated overnight at 4°C. Beads were then washed 3x with 1 ml of blocking buffer and resuspended in 100 μl blocking buffer. Chromatin equivalent to 5x107 cells was added and rotated overnight at 4°C. The following day, 6 washing steps (9 for T) with 1 ml RIPA buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and one washing step with 1 ml of TEN (10 mM Tris pH 8, 1 mM EDTA, 50 mM NaCl) were performed. The elution was performed in two subsequent steps using 100 μl of 1x elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and incubation at 65°C while shaking for 10 minutes each. The eluates were combined and incubated for 13-15 hours at 65°C. 200 μl of TE were added and the ChIP DNA was purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the previously described modifications (Koch, 2017). After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 14 μl of resuspension buffer (RSB, Illumina). After the addition of 1 μl primer mix (25 mM each) and 15 μl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 μl of RSB. Ligation products were then separated using a 1.5% agarose gel. Post-run staining was performed using SYBR Gold under agitation for 30 minutes. Gel slices corresponding to 250-400 bp fragment size were cut out. using a Dark Reader Transilluminator.  The gel extraction was performed using 5 gel volumes of QG buffer (Qiagen) with the addition of one gel volume of isopropanol. The MinElute (Qiagen) columns were washed once with QG buffer and twice with PE buffer, air-dried for at least 10 minutes and eluted using 21 μl of EB buffer. 19 μl of the eluate was used in the final amplification, with the addition of 1 μl primer mix and 20 μl 2x Kapa HiFi Hotstart premix. The same protocol as for the pre-amplification was used, with the exception of using 13 amplification cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips.

treatment_protocol: Crosslinking was performed directly on differentiating cells in differentiation medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH 7.8) for 10 minutes at room temperature, while shaking. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Cells were washed twice with cold PBS, scraped in cold PBS containing 0.05% Triton X-100, pelleted in aliquots of 50 million cells, snap frozen and stored at -80°C until sonication.

tag: strain

value: ES cells

value: WT

value: in vitro differentiated cardiac mesoderm progenitors


title: AMPK KO HEK 293T, 16H Rot, rep 1 ADKO_16H_Rot_1_S88

description: AMPK KO HEK 293T, 16H Rot, rep 1

value: kidney


title: NHP_myogenic-prog-Exp2

description:
D13_plus_2
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt

value: myogenic progenitor

value: day 13


title: AMPK KO HEK 293T, 2H 991, rep 2 ADKO_2H_991_2_S56

description: AMPK KO HEK 293T, 2H 991, rep 2


title: NHP_myogenic-prog-Exp1

description:
D13_plus_1
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt


title: NHP_Paraxial_Mesoderm-Exp2

description:
D6_2
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt

value: paraxial mesoderm

value: day 6


title: NHP_Paraxial_Mesoderm-Exp1

description:
D6_1
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt


title: NHP_Mesoderm-Exp1

description:
D4_1
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt

value: mesoderm

value: day 4


title: NHP_Mesoderm-Exp2

description:
D4_2
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt


title: NHP_iPSC-Exp2

description:
iPS_2
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt

value: pluripotent

value: day 0


title: NHP_iPSC-Exp1

description:
iPS_1
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt


title: AMPK KO HEK 293T, 16H CCCP, rep 2 ADKO_16H_CCCP_2_S101

description: AMPK KO HEK 293T, 16H CCCP, rep 2

value: AMPK Knock out

value: CCCP


title: ChIP-Seq PH-1: PH-1 with iron excess treatment H3K27me3 IP rep 2

city: Hangzhou

first: SUN

last: Kewei

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Further, ChIP-enriched DNA with a monoclonal anti-H3K27 me3 or polyclonal anti-H2A.Z antibody were sequenced on an Illumina NovaSeq 6000,For ChIP-seq analysis, 50 bp single-end reads of ChIP-seq were obtained, and quality was controlled using SOAPnuke(v2.1.7). The parameters were as follows: remove reads containing adapters or more than 1% of unknown nucleotides (N); delete the read if there are more than 40% bases having a quality value lower than 20.  Clean reads were mapped to the Fg reference genome by Bowtie2 (version 2.4.5) with default parameters.  The visualization of the average read coverage over 2 kb upstream and downstream of the TSS was performed by Deeptools.  BigWig files generated by Deeptools were used for visualization in Integrative Genome Viewer (version 2.8.9).  RPKM (Reads Per Kilobase per Million mapped reads) were calculated to normalized reads using bamCompare tool in Deeptools (version 2.4.1) with input DNA as a contorl.
Assembly: ASM24013v3 (reference genome of F. graminearum strain PH-1)
Supplementary files format and content: BW

organism: Fusarium graminearum PH-1

source_name: Mycelium

extract_protocol: Fresh mycelia were cross-linked with 1% formaldehyde for 15 min and then stopped with 125 mM glycine. The cultures were ground with liquid nitrogen and resuspended in lysis buffer (250 mM, HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% deoxycholate, 10 mM DTT) and 1% protease inhibitor. The DNA was sheared into ~300 bp fragments with 20 pulses of 10 s with 20 s of resting at 35% amplitude (Qsonica*sonicator, Q125, Branson, USA). After centrifugation, the supernatant was diluted with 10 × ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris–HCl, pH 8.0, and 167 mM NaCl). Samples were pre-washed with 20 μl of protein A agarose (sc-2001, Santa Cruz, CA, USA) for 1 h at 4°C. Then immunoprecipitation was performed using a monoclonal anti-H3K27 me3 (39155, Active Motif, Shanghai, China), polyclonal anti-H2A.Z (ABclonal® Technology, Wuhan, China) or monoclonal anti-GFP (ab290, Abcam, Cambridge, UK) antibody together with protein A agarose (Santa Cruz, CA, USA). A mock sample was incubated with anti-IgG antibody (MA1-10406, Invitrogen-Thermo Fisher Scientific, Waltham, MA, USA). DNA was immunoprecipitated with ethanol after washing, eluting, reversing the cross-linking, and digesting with proteinase K.

value: Mycelium

value: Day 2 of fresh mycelium under iron excess treatment


title: ChIP-Seq PH-1: PH-1 with iron excess treatment Input rep 1


title: ChIP-Seq PH-1: PH-1 with iron excess treatment H3K27me3 IP rep 1


title: ChIP-Seq PH-1: PH-1 with iron excess treatment H2A.Z IP rep 1


title: RNA-Seq PH-1: PH-1 at 4 dpi_rep 3

description: PH-1_4 dpi_3

data_processing:
For RNA-seq analysis, F. graminearum mycelia were collected at 3 and 4 dpi from infected wheat coleoptiles, or were collected from the CM culture with or without iron excess treatment. RNA-seq was conducted using Illumina NovaSeq 6000 (Genergy Bio, Shanghai, China) sequencing system. RNA-Seq by Expectation-Maximization (RSEM) software was used to calculate the values of fragments per kilobase of transcript per million fragments mapped (FPKM) to evaluate gene expression level. DEGs (differentially expressed genes) detection was performed with DEseq2 (Parameters: Fold Change2.00) and adjusted p value ≤ 0.05 as described.
Assembly: ASM24013v3 (reference genome of F. graminearum strain PH-1)
Supplementary files format and content: BW

extract_protocol: Strains were grown in CM for 36 h and then treated with or without 10 mM FeSO4. RNA from each strain was extracted using TaKaRa RNAiso Reagent (TaKaRa Biotechnology Co., Dalian, China). Each RNA sample was reverse transcribed using a HiScript II Q RT Kit (Vazyme, R223-01, Nanjing, China).

value: 4 d  post inoculation


title: ChIP-Seq PH-1: PH-1 with iron excess treatment H2A.Z IP rep 2


title: RNA-Seq PH-1: PH-1 at 4 dpi_rep 1

description: PH-1_4 dpi_1


title: RNA-Seq PH-1: PH-1 at 4 dpi_rep 2

description: PH-1_4 dpi_2


title: RNA-Seq PH-1: PH-1 at 3 dpi_rep 3

description: PH-1_3 dpi_3

value: 3 d  post inoculation


title: RNA-Seq PH-1: PH-1 at 3 dpi_rep 2

description: PH-1_3 dpi_2

value: WT


title: RNA-Seq PH-1: PH-1 at 3 dpi_rep 1

description: PH-1_3 dpi_1


title: RNA-Seq PH-1: deletion mutant FgSreA_CM_rep 3

description: deletion mutant FgSreA_CM_3

value: FgSreA knockout

value: Day 2 of fresh mycelium


title: RNA-Seq PH-1: deletion mutant FgSreA_FE_rep 1

description: deletion mutant FgSreA_FE_1


title: RNA-Seq PH-1: deletion mutant FgSreA_FE_rep 2

description: deletion mutant FgSreA_FE_2


title: RNA-Seq PH-1: deletion mutant FgSreA_FE_rep 3

description: deletion mutantFgSreA_FE_3


title: NHP_myotube-Exp1

description:
Diff_1
cells collected at different time points of myogenic lineage specification
raw_counts_mac_fas_RNAseq_new_2_for_R.txt

value: myotube

value: NHP iPSC

value: control line

value: day 20


title: RNA-Seq PH-1: PH-1_FE_rep 3


title: RNA-Seq PH-1: PH-1_FE_rep 1


title: RNA-Seq PH-1: PH-1_FE_rep 2


title: RNA-Seq PH-1: deletion mutant FgSreA_CM_rep 1

description: deletion mutant FgSreA_CM_1


title: RNA-Seq PH-1: PH-1_CM_rep 1


title: ChIP-Seq PH-1: PH-1 with iron excess treatment Input rep 2


title: RNA-Seq PH-1: deletion mutant FgHapX_FE_rep 3

description: deletion mutant FgHapX_FE_3

value: FgHapX knockout


title: RNA-Seq PH-1 : deletion mutant FgHapX_FE_rep 1

description: deletion mutant FgHapX_FE_1


title: RNA-Seq PH-1: PH-1_CM_rep 2


title: RNA-Seq PH-1: deletion mutant FgHapX_FE_rep 2

description: deletion mutant FgHapX_FE_2


title: RNA-Seq PH-1: deletion mutant FgHapX_CM_rep 3

description: deletion mutant FgHapX_CM_3


title: RNA-Seq PH-1: deletion mutant FgHapX_CM_rep 2

description: deletion mutant FgHapX_CM_2


title: RNA-Seq PH-1: deletion mutant FgHapX_CM_rep 1

description: deletion mutant FgHapX_CM_1


title: hum_myogenic-prog-Exp5

description:
PLZ_MP_5
cells collected at different time points of myogenic lineage specification
raw_counts_homo_sap_RNAseq_PLZ_MP_vs_MT.txt

source_name: PLZ

value: myogenic progenitor

value: PLZ

value: human iPSC

value: day 13


title: hum_myogenic-prog-Exp4

description:
PLZ_MP_4
cells collected at different time points of myogenic lineage specification
raw_counts_homo_sap_RNAseq_PLZ_MP_vs_MT.txt


title: hum_myotube-Exp2

description:
PLZ_MT_2
re-analysis of GSM3744433
raw_counts_homo_sap_RNAseq_PLZ_MP_vs_MT.txt


title: adipocyte-obese-rep48

status: Public on Apr 14 2023

type: genomic

city: London

first: William

middle: Robert

last: Scott

address: Hammersmith Hospital, Du Cane Road

department: Institute of Clinical Sciences

country: United Kingdom

institute: Imperial College London

description:
HA96
human adipocyte isolated by flotation

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human HumanMethylation450 and EPIC Beadchips using standard Illumina protocol

scan_protocol: Illumina HiScan using standard recommended Illumina scanner setting.

data_processing:
Custom R scripts. Quantile normalisation of signal intensities.
Supplementary files format and content: meth_obese_visceral_pval.bedgraph: Association between DNA methylation and obesity in visceral adipocytes (combined discovery and replication datasets); score is -log10 pvalue (negative = lower in obesity).
Supplementary files format and content: meth_obese_subcut_pval.bedgraph: Association between DNA methylation and obesity in subcutaneous adipocytes (combined discovery and replication datasets); score is -log10 pvalue (negative = lower in obesity).
Supplementary files format and content: meth_obese_visceral_effect.bedgraph: Association between DNA methylation and obesity in visceral adipocytes (combined discovery and replication datasets); score is %-methylation difference (negative = lower in obesity).
Supplementary files format and content: meth_obese_subcut_effect.bedgraph: Association between DNA methylation and obesity in subcutaneous adipocytes (combined discovery and replication datasets); score is %-methylation difference (negative = lower in obesity).

label: Cy3 and Cy5

source_name: visceral

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from human adipocytes using the Qiagen DNA/RNA/miRNA Universal Kit according to standard instructions

tag: age

tag: Sex

value: F

tag: cohort

value: discovery


title: adipocyte-obese-rep47

description:
HA95
human adipocyte isolated by flotation

value: M


title: adipocyte-obese-rep46

description:
HA94
human adipocyte isolated by flotation


title: adipocyte-obese-rep44

description:
HA92
human adipocyte isolated by flotation


title: adipocyte-obese-rep42

description:
HA90
human adipocyte isolated by flotation


title: adipocyte-obese-rep43

description:
HA91
human adipocyte isolated by flotation


title: adipocyte-obese-rep40

description:
HA88
human adipocyte isolated by flotation


title: adipocyte-obese-rep45

description:
HA93
human adipocyte isolated by flotation


title: RNA-Seq PH-1: deletion mutant FgSreA_CM_rep 2

description: deletion mutant FgSreA_CM_2

value: Mycelium


title: adipocyte-obese-rep41

description:
HA89
human adipocyte isolated by flotation


title: adipocyte-obese-rep36

description:
HA84
human adipocyte isolated by flotation


title: adipocyte-obese-rep39

description:
HA87
human adipocyte isolated by flotation


title: adipocyte-obese-rep33

description:
HA81
human adipocyte isolated by flotation


title: adipocyte-obese-rep34

description:
HA82
human adipocyte isolated by flotation


title: adipocyte-obese-rep35

description:
HA83
human adipocyte isolated by flotation


title: adipocyte-obese-rep38

description:
HA86
human adipocyte isolated by flotation


title: adipocyte-obese-rep37

description:
HA85
human adipocyte isolated by flotation


title: adipocyte-obese-rep29

description:
HA77
human adipocyte isolated by flotation


title: adipocyte-obese-rep32

description:
HA80
human adipocyte isolated by flotation


title: hum_myotube-Exp4

description:
PLZ_MT_4
re-analysis of GSM3744434
raw_counts_homo_sap_RNAseq_PLZ_MP_vs_MT.txt


title: adipocyte-obese-rep28

description:
HA76
human adipocyte isolated by flotation


title: hum_myotube-Exp1

description:
PLZ_MT_1
re-analysis of GSM3744432
raw_counts_homo_sap_RNAseq_PLZ_MP_vs_MT.txt


title: RNA-Seq PH-1: PH-1_CM_rep 3


title: adipocyte-obese-rep30

description:
HA78
human adipocyte isolated by flotation


title: adipocyte-obese-rep25

description:
HA73
human adipocyte isolated by flotation


title: hum_myogenic-prog-Exp2

description:
PLZ_MP_2
cells collected at different time points of myogenic lineage specification
raw_counts_homo_sap_RNAseq_PLZ_MP_vs_MT.txt


title: adipocyte-obese-rep26

description:
HA74
human adipocyte isolated by flotation


title: adipocyte-control-rep48

description:
HA72
human adipocyte isolated by flotation


title: adipocyte-control-rep45

description:
HA69
human adipocyte isolated by flotation


title: adipocyte-obese-rep27

description:
HA75
human adipocyte isolated by flotation


title: adipocyte-control-rep42

description:
HA66
human adipocyte isolated by flotation


title: adipocyte-control-rep40

description:
HA64
human adipocyte isolated by flotation


title: adipocyte-control-rep44

description:
HA68
human adipocyte isolated by flotation


title: adipocyte-control-rep47

description:
HA71
human adipocyte isolated by flotation


title: adipocyte-control-rep43

description:
HA67
human adipocyte isolated by flotation


title: adipocyte-control-rep41

description:
HA65
human adipocyte isolated by flotation


title: adipocyte-obese-rep31

description:
HA79
human adipocyte isolated by flotation


title: adipocyte-control-rep39

description:
HA63
human adipocyte isolated by flotation


title: adipocyte-control-rep38

description:
HA62
human adipocyte isolated by flotation


title: adipocyte-control-rep37

description:
HA61
human adipocyte isolated by flotation


title: adipocyte-control-rep34

description:
HA58
human adipocyte isolated by flotation


title: adipocyte-control-rep36

description:
HA60
human adipocyte isolated by flotation


title: adipocyte-control-rep35

description:
HA59
human adipocyte isolated by flotation


title: adipocyte-control-rep32

description:
HA56
human adipocyte isolated by flotation


title: adipocyte-control-rep31

description:
HA55
human adipocyte isolated by flotation


title: adipocyte-control-rep29

description:
HA53
human adipocyte isolated by flotation


title: adipocyte-control-rep27

description:
HA51
human adipocyte isolated by flotation


title: adipocyte-control-rep26

description:
HA50
human adipocyte isolated by flotation


title: adipocyte-control-rep28

description:
HA52
human adipocyte isolated by flotation


title: adipocyte-control-rep25

description:
HA49
human adipocyte isolated by flotation


title: adipocyte-obese-rep23

description:
HA47
human adipocyte isolated by flotation

source_name: subcutaneous


title: adipocyte-obese-rep24

description:
HA48
human adipocyte isolated by flotation


title: adipocyte-obese-rep22

description:
HA46
human adipocyte isolated by flotation


title: adipocyte-control-rep33

description:
HA57
human adipocyte isolated by flotation


title: adipocyte-obese-rep20

description:
HA44
human adipocyte isolated by flotation


title: adipocyte-obese-rep21

description:
HA45
human adipocyte isolated by flotation


title: adipocyte-obese-rep17

description:
HA41
human adipocyte isolated by flotation


title: adipocyte-obese-rep12

description:
HA36
human adipocyte isolated by flotation


title: adipocyte-obese-rep16

description:
HA40
human adipocyte isolated by flotation


title: adipocyte-obese-rep15

description:
HA39
human adipocyte isolated by flotation


title: adipocyte-control-rep46

description:
HA70
human adipocyte isolated by flotation


title: adipocyte-obese-rep13

description:
HA37
human adipocyte isolated by flotation


title: adipocyte-obese-rep10

description:
HA34
human adipocyte isolated by flotation


title: adipocyte-obese-rep11

description:
HA35
human adipocyte isolated by flotation


title: adipocyte-control-rep30

description:
HA54
human adipocyte isolated by flotation


title: adipocyte-obese-rep18

description:
HA42
human adipocyte isolated by flotation


title: adipocyte-obese-rep8

description:
HA32
human adipocyte isolated by flotation


title: adipocyte-obese-rep9

description:
HA33
human adipocyte isolated by flotation


title: adipocyte-obese-rep4

description:
HA28
human adipocyte isolated by flotation


title: adipocyte-obese-rep7

description:
HA31
human adipocyte isolated by flotation


title: adipocyte-obese-rep5

description:
HA29
human adipocyte isolated by flotation


title: adipocyte-obese-rep6

description:
HA30
human adipocyte isolated by flotation


title: adipocyte-obese-rep2

description:
HA26
human adipocyte isolated by flotation


title: adipocyte-obese-rep19

description:
HA43
human adipocyte isolated by flotation


title: adipocyte-obese-rep1

description:
HA25
human adipocyte isolated by flotation


title: adipocyte-control-rep23

description:
HA23
human adipocyte isolated by flotation


title: adipocyte-control-rep24

description:
HA24
human adipocyte isolated by flotation


title: adipocyte-control-rep21

description:
HA21
human adipocyte isolated by flotation


title: adipocyte-control-rep20

description:
HA20
human adipocyte isolated by flotation


title: adipocyte-control-rep18

description:
HA18
human adipocyte isolated by flotation


title: adipocyte-control-rep19

description:
HA19
human adipocyte isolated by flotation


title: adipocyte-control-rep17

description:
HA17
human adipocyte isolated by flotation


title: adipocyte-control-rep16

description:
HA16
human adipocyte isolated by flotation


title: adipocyte-control-rep14

description:
HA14
human adipocyte isolated by flotation


title: adipocyte-control-rep12

description:
HA12
human adipocyte isolated by flotation


title: adipocyte-obese-rep14

description:
HA38
human adipocyte isolated by flotation


title: adipocyte-obese-rep3

description:
HA27
human adipocyte isolated by flotation


title: adipocyte-control-rep13

description:
HA13
human adipocyte isolated by flotation


title: adipocyte-control-rep9

description:
HA9
human adipocyte isolated by flotation


title: adipocyte-control-rep7

description:
HA7
human adipocyte isolated by flotation


title: adipocyte-control-rep8

description:
HA8
human adipocyte isolated by flotation


title: adipocyte-control-rep4

description:
HA4
human adipocyte isolated by flotation


title: adipocyte-control-rep2

description:
HA2
human adipocyte isolated by flotation


title: adipocyte-control-rep5

description:
HA5
human adipocyte isolated by flotation


title: adipocyte-control-rep3

description:
HA3
human adipocyte isolated by flotation


title: adipocyte-control-rep6

description:
HA6
human adipocyte isolated by flotation


title: adipocyte-control-rep1

description:
HA1
human adipocyte isolated by flotation


title: adipocyte-control-rep22

description:
HA22
human adipocyte isolated by flotation


title: adipocyte-obese-rep96

description:
HA192
human adipocyte isolated by flotation

value: replication


title: adipocyte-obese-rep90

description:
HA186
human adipocyte isolated by flotation


title: adipocyte-obese-rep95

description:
HA191
human adipocyte isolated by flotation


title: adipocyte-obese-rep91

description:
HA187
human adipocyte isolated by flotation


title: adipocyte-obese-rep94

description:
HA190
human adipocyte isolated by flotation


title: adipocyte-obese-rep93

description:
HA189
human adipocyte isolated by flotation


title: adipocyte-obese-rep92

description:
HA188
human adipocyte isolated by flotation


title: adipocyte-obese-rep89

description:
HA185
human adipocyte isolated by flotation


title: adipocyte-control-rep15

description:
HA15
human adipocyte isolated by flotation


title: adipocyte-obese-rep87

description:
HA183
human adipocyte isolated by flotation


title: adipocyte-obese-rep88

description:
HA184
human adipocyte isolated by flotation


title: adipocyte-control-rep11

description:
HA11
human adipocyte isolated by flotation


title: adipocyte-control-rep10

description:
HA10
human adipocyte isolated by flotation


title: adipocyte-obese-rep85

description:
HA181
human adipocyte isolated by flotation


title: adipocyte-obese-rep84

description:
HA180
human adipocyte isolated by flotation


title: adipocyte-obese-rep83

description:
HA179
human adipocyte isolated by flotation


title: adipocyte-obese-rep82

description:
HA178
human adipocyte isolated by flotation


title: adipocyte-obese-rep80

description:
HA176
human adipocyte isolated by flotation


title: adipocyte-obese-rep81

description:
HA177
human adipocyte isolated by flotation


title: adipocyte-obese-rep79

description:
HA175
human adipocyte isolated by flotation


title: adipocyte-obese-rep78

description:
HA174
human adipocyte isolated by flotation


title: adipocyte-obese-rep77

description:
HA173
human adipocyte isolated by flotation


title: adipocyte-obese-rep74

description:
HA170
human adipocyte isolated by flotation


title: adipocyte-obese-rep75

description:
HA171
human adipocyte isolated by flotation


title: adipocyte-obese-rep73

description:
HA169
human adipocyte isolated by flotation


title: adipocyte-control-rep96

description:
HA168
human adipocyte isolated by flotation


title: adipocyte-control-rep91

description:
HA163
human adipocyte isolated by flotation


title: adipocyte-control-rep86

description:
HA158
human adipocyte isolated by flotation


title: adipocyte-control-rep94

description:
HA166
human adipocyte isolated by flotation


title: adipocyte-control-rep90

description:
HA162
human adipocyte isolated by flotation


title: adipocyte-control-rep85

description:
HA157
human adipocyte isolated by flotation


title: adipocyte-control-rep92

description:
HA164
human adipocyte isolated by flotation


title: adipocyte-control-rep93

description:
HA165
human adipocyte isolated by flotation


title: adipocyte-obese-rep86

description:
HA182
human adipocyte isolated by flotation


title: adipocyte-control-rep88

description:
HA160
human adipocyte isolated by flotation


title: adipocyte-control-rep87

description:
HA159
human adipocyte isolated by flotation


title: adipocyte-control-rep84

description:
HA156
human adipocyte isolated by flotation


title: adipocyte-control-rep79

description:
HA151
human adipocyte isolated by flotation


title: adipocyte-control-rep80

description:
HA152
human adipocyte isolated by flotation


title: adipocyte-control-rep81

description:
HA153
human adipocyte isolated by flotation


title: adipocyte-control-rep77

description:
HA149
human adipocyte isolated by flotation


title: adipocyte-control-rep78

description:
HA150
human adipocyte isolated by flotation


title: adipocyte-control-rep82

description:
HA154
human adipocyte isolated by flotation


title: adipocyte-control-rep74

description:
HA146
human adipocyte isolated by flotation


title: adipocyte-control-rep73

description:
HA145
human adipocyte isolated by flotation


title: adipocyte-obese-rep72

description:
HA144
human adipocyte isolated by flotation


title: adipocyte-obese-rep76

description:
HA172
human adipocyte isolated by flotation


title: adipocyte-obese-rep71

description:
HA143
human adipocyte isolated by flotation


title: adipocyte-control-rep95

description:
HA167
human adipocyte isolated by flotation


title: adipocyte-obese-rep70

description:
HA142
human adipocyte isolated by flotation


title: adipocyte-obese-rep68

description:
HA140
human adipocyte isolated by flotation


title: adipocyte-control-rep89

description:
HA161
human adipocyte isolated by flotation


title: adipocyte-control-rep75

description:
HA147
human adipocyte isolated by flotation


title: adipocyte-obese-rep69

description:
HA141
human adipocyte isolated by flotation


title: adipocyte-obese-rep67

description:
HA139
human adipocyte isolated by flotation


title: adipocyte-obese-rep65

description:
HA137
human adipocyte isolated by flotation


title: adipocyte-obese-rep66

description:
HA138
human adipocyte isolated by flotation


title: adipocyte-obese-rep60

description:
HA132
human adipocyte isolated by flotation


title: adipocyte-obese-rep59

description:
HA131
human adipocyte isolated by flotation


title: adipocyte-obese-rep64

description:
HA136
human adipocyte isolated by flotation


title: adipocyte-obese-rep62

description:
HA134
human adipocyte isolated by flotation


title: adipocyte-obese-rep63

description:
HA135
human adipocyte isolated by flotation


title: adipocyte-obese-rep58

description:
HA130
human adipocyte isolated by flotation


title: adipocyte-obese-rep57

description:
HA129
human adipocyte isolated by flotation


title: adipocyte-obese-rep53

description:
HA125
human adipocyte isolated by flotation


title: adipocyte-obese-rep56

description:
HA128
human adipocyte isolated by flotation


title: adipocyte-obese-rep54

description:
HA126
human adipocyte isolated by flotation


title: adipocyte-control-rep76

description:
HA148
human adipocyte isolated by flotation


title: adipocyte-obese-rep49

description:
HA121
human adipocyte isolated by flotation


title: adipocyte-obese-rep51

description:
HA123
human adipocyte isolated by flotation


title: adipocyte-obese-rep50

description:
HA122
human adipocyte isolated by flotation


title: adipocyte-control-rep72

description:
HA120
human adipocyte isolated by flotation


title: adipocyte-control-rep69

description:
HA117
human adipocyte isolated by flotation


title: adipocyte-control-rep83

description:
HA155
human adipocyte isolated by flotation


title: adipocyte-control-rep71

description:
HA119
human adipocyte isolated by flotation


title: adipocyte-control-rep68

description:
HA116
human adipocyte isolated by flotation


title: adipocyte-control-rep66

description:
HA114
human adipocyte isolated by flotation


title: adipocyte-control-rep65

description:
HA113
human adipocyte isolated by flotation


title: adipocyte-obese-rep61

description:
HA133
human adipocyte isolated by flotation


title: adipocyte-control-rep64

description:
HA112
human adipocyte isolated by flotation


title: adipocyte-control-rep62

description:
HA110
human adipocyte isolated by flotation


title: adipocyte-control-rep60

description:
HA108
human adipocyte isolated by flotation


title: adipocyte-control-rep59

description:
HA107
human adipocyte isolated by flotation


title: adipocyte-control-rep61

description:
HA109
human adipocyte isolated by flotation


title: adipocyte-obese-rep55

description:
HA127
human adipocyte isolated by flotation


title: adipocyte-obese-rep52

description:
HA124
human adipocyte isolated by flotation


title: adipocyte-control-rep56

description:
HA104
human adipocyte isolated by flotation


title: adipocyte-control-rep55

description:
HA103
human adipocyte isolated by flotation


title: adipocyte-control-rep58

description:
HA106
human adipocyte isolated by flotation


title: adipocyte-control-rep53

description:
HA101
human adipocyte isolated by flotation


title: adipocyte-control-rep51

description:
HA99
human adipocyte isolated by flotation


title: adipocyte-control-rep52

description:
HA100
human adipocyte isolated by flotation


title: adipocyte-control-rep70

description:
HA118
human adipocyte isolated by flotation


title: adipocyte-control-rep50

description:
HA98
human adipocyte isolated by flotation


title: adipocyte-control-rep54

description:
HA102
human adipocyte isolated by flotation


title: adipocyte-control-rep49

description:
HA97
human adipocyte isolated by flotation


title: Blood_Platelets VUMC-P-PH-001-162-TR2910

status: Public on Apr 10 2023

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Assembly: hg19
Supplementary files format and content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

source_name: Thrombocytes

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

tag: classification group

value: PostCapillary

value: Thrombocytes


title: Blood_Platelets VUMC-P-PH-001-146-TR2940


title: adipocyte-control-rep67

description:
HA115
human adipocyte isolated by flotation


title: Blood_Platelets VUMC-P-PH-001-139-TR2985


title: Blood_Platelets VUMC-P-PH-001-136-TR2982


title: Blood_Platelets VUMC-P-PH-001-137-TR2983


title: Blood_Platelets VUMC-P-PH-001-157-TR2944


title: Blood_Platelets VUMC-P-PH-001-147-TR2941


title: Blood_Platelets VUMC-P-PH-001-128-TR2968


title: Blood_Platelets VUMC-P-PH-001-130-TR2970


title: adipocyte-control-rep63

description:
HA111
human adipocyte isolated by flotation


title: adipocyte-control-rep57

description:
HA105
human adipocyte isolated by flotation


title: Blood_Platelets VUMC-P-PH-001-135-TR2981


title: Blood_Platelets VUMC-P-PH-001-124-TR2964


title: Blood_Platelets VUMC-P-PH-001-133-TR2973


title: Blood_Platelets VUMC-P-PH-001-121-TR2917


title: Blood_Platelets Vumc-P-PH-001-097-TR2583

value: PreCapillary


title: Blood_Platelets Vumc-P-PH-001-094-TR2580


title: Blood_Platelets Vumc-P-PH-001-092-TR2579


title: Blood_Platelets Vumc-P-PH-001-083-TR2575


title: Blood_Platelets Vumc-P-PH-001-105-TR2567


title: Blood_Platelets Vumc-P-PH-001-081-TR2573


title: Blood_Platelets Vumc-P-PH-001-080-TR2572


title: Blood_Platelets Vumc-P-PH-001-078-TR2571


title: Blood_Platelets Vumc-P-PH-001-077-TR2570


title: Blood_Platelets Vumc-P-PH-001-076-TR2569


title: Blood_Platelets Vumc-P-PH-001-072-TR2559


title: Blood_Platelets Vumc-P-PH-001-070-TR2558


title: Blood_Platelets Vumc-P-PH-001-067-TR2556


title: Blood_Platelets Vumc-P-PH-001-066-TR2555


title: Blood_Platelets Vumc-P-PH-001-064-TR2553


title: Blood_Platelets Vumc-P-PH-001-062-TR2551


title: Blood_Platelets Vumc-P-PH-001-063-TR2552


title: Blood_Platelets Vumc-P-PH-001-059-TR2549


title: Blood_Platelets Vumc-P-PH-001-057-TR2547


title: Blood_Platelets Vumc-P-PH-001-058-TR2548


title: Blood_Platelets Vumc-P-PH-001-050-TR1460


title: Blood_Platelets Vumc-P-PH-001-041-TR1422


title: Blood_Platelets Vumc-P-PH-001-042-TR1423


title: Blood_Platelets Vumc-P-PH-001-053-TR1461


title: Blood_Platelets Vumc-P-PH-001-039-TR1421


title: Blood_Platelets Vumc-P-PH-001-037-TR1420


title: Blood_Platelets Vumc-P-PH-001-036-TR1419


title: Blood_Platelets Vumc-P-PH-001-034-TR1512-seq2


title: Blood_Platelets Vumc-P-PH-001-030-TR1415


title: Blood_Platelets Vumc-P-PH-001-031-TR2545


title: Blood_Platelets Vumc-P-PH-001-035-TR1418


title: Blood_Platelets Vumc-P-PH-001-028-TR1410


title: Blood_Platelets Vumc-P-PH-001-026-TR1408


title: Blood_Platelets Vumc-P-PH-001-029-TR1434


title: Blood_Platelets Vumc-P-PH-001-023-TR1407


title: Blood_Platelets Vumc-P-PH-001-027-TR1409


title: Blood_Platelets Vumc-P-PH-001-022-TR1511


title: Blood_Platelets Vumc-P-PH-001-020-TR1509


title: Blood_Platelets Vumc-P-PH-001-019


title: Blood_Platelets Vumc-P-PH-001-018-TR1413


title: Blood_Platelets Vumc-P-PH-001-017-TR1507


title: Blood_Platelets Vumc-P-PH-001-060-TR2550


title: Blood_Platelets Vumc-P-PH-001-014-TR1459


title: Blood_Platelets Vumc-P-PH-001-012-TR1506


title: Blood_Platelets Vumc-P-PH-001-011-TR1458


title: Blood_Platelets Vumc-P-PH-001-013-TR1400


title: Blood_Platelets Vumc-P-PH-001-016-TR1404


title: Blood_Platelets Vumc-P-PH-001-010-TR1505-seq2


title: Blood_Platelets Vumc-P-PH-001-009-TR1397


title: Blood_Platelets Vumc-P-PH-001-005-TR1503


title: Blood_Platelets Vumc-P-PH-001-007-TR1395


title: Blood_Platelets Vumc-P-PH-001-002-TR1391


title: Blood_Platelets Vumc-P-PH-001-003-TR1392


title: Blood_Platelets Vumc-P-PH-001-033-TR1417


title: Blood_Platelets Vumc-P-PH-001-006-TR1457


title: Blood_Platelets TR4541-PPH-VUMC


title: Blood_Platelets TR4539-PPH-VUMC


title: Blood_Platelets TR4540-PPH-VUMC


title: Blood_Platelets TR4538-PPH-VUMC


title: Blood_Platelets TR4534-PPH-VUMC


title: Blood_Platelets TR4532-PPH-VUMC


title: Blood_Platelets TR4531-PPH-VUMC


title: Blood_Platelets TR4208-PPH-VU


title: Blood_Platelets TR4007-PPH-VUMC


title: Blood_Platelets TR3912-PPH-VUMC


title: Blood_Platelets TR3911-PPH-VUMC


title: Blood_Platelets TR3909-PPH-VUMC


title: Blood_Platelets TR3910-PPH-VUMC


title: Blood_Platelets TR3907-PPH-VUMC


title: Blood_Platelets TR3908-PPH-VUMC


title: Blood_Platelets TR3903-PPH-VUMC


title: Blood_Platelets TR3905-PPH-VUMC


title: Blood_Platelets TR3902-PPH-VUMC


title: Blood_Platelets TR3904-PPH-VUMC


title: Blood_Platelets Vumc-P-PH-001-008-TR1504


title: Blood_Platelets TR3876-PPH-VUMC


title: Blood_Platelets TR4533-PPH-VUMC


title: Naïve_Bach2-/-_HiC_rep1

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
Fastq files were pre-processed into single end reads in a custom workflow with vsearch to overlap or blunt end join R1 and R1, seqkit to remove PCR duplicates. Processed fastq reads were then mapped to the mouse reference, GRCm38 with bwa mem with the following flags, (-M, -K 10000000, -5) and converted into bam files with samtools. Intragenic contacts have been extracted with a custom C script that generated three column table (region1, region2, chromsome_name). The following table can be quantised into any bin sizes. Depending on the downstream analysis different bin sizes have been used, 50 Kb for differential looping and TAD’s, 100 Kb for A/B calling. An Rscript using `data.table` package was used to quantise raw contacts table into binned table with the following columns (chromsome_name, region1, region2, IF), where IF is an interaction frequency. A/B compartments were called with HiTC R package. TADs have been called with SpectralTAD and Armatus. For differential loops analysis, multiHiCcompare R package was used including cyclic loess joint normalisation and differential loops calling. Each end of the loop has been annotated with a gene, using in house script, where gene was assigned to either end of the loop if the overlap was no more then 25 from the end of the loop. This ensures that genes in the middle of the loops were not retained.
Assembly: mm10
Supplementary files format and content: Differential loops and hic track files.
Supplementary files format and content: bed files are bigInteract files (https://genome.ucsc.edu/goldenPath/help/interact.html) that contain differential loops.

source_name: Spleen

extract_protocol: Hi-C was performed as per Rao (Rao et al., 2014), with the following adjustments: Step 2 - cells were fixed with 1.5% formaldehyde for 10 min at RT. Step 7 - the nuclei extraction buffer contained 0.4% Igepal. Step 12 - restriction digestion was performed overnight with 400U Mbo1 (NEB) in NEB buffer 2.1. Steps 28-35 were skipped. Step 54 - 2.5ul NEBNext Adapter for Illumina (cat # E7370) was used in place of Illumina indexed adapter, with ligation at 20C for 15 min, followed by addition of 3U USER enzyme and further incubation at 37C for 15min. Step 60 - samples were incubated at 95C for 10 min in a thermocycler, and beads were removed before final library amplification with NEBNext Multiplex Oligos for Illumina (cat # E7335S).

value: Spleen

value: CD8+ T cells


title: CD4+CD8+_SATB1m1Anu/m1Anu_HiC_rep2

source_name: Thymus

value: Thymus

value: Satb1 m1Anu/m1Anu

value: CD4+CD8+ thymocytes


title: Blood_Platelets TR3918-PPH-VUMC


title: CD4+CD8+_SATB1m1Anu/m1Anu_HiC_rep1


title: Blood_Platelets TR3906-PPH-VUMC


title: Blood_Platelets TR3901-PPH-VUMC


title: Effector_WT_HiC_rep3

value: WT


title: Effector_WT_HiC_rep4


title: Naïve_Satb1_HiC_rep1


title: Blood_Platelets TR3900-PPH-VUMC


title: Blood_Platelets TR3899-PPH-VUMC


title: adr-1(-);adr-2(-) OP50 biol rep3

status: Public on Apr 01 2023

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

description:
Sample 18_GSF3253
WTvadr1adr2diffexp2.csv

data_processing:
Reads were aligned to C. elegans reference genome using STAR (v.2.7.6a)
Differential gene expression analysis was performed using Feature counts and DeSeq2
Assembly: C. elegans WS275
Supplementary files format and content: .csv files include DeSeq2 analysis with normalized read counts

organism: Caenorhabditis elegans

growth_protocol: After hatching, L1 was plated to grow upto 42 hours to obtain L4 stage worms

extract_protocol:
Worms were collected in Trizol (Invitogen) and purified using TURBO Dnase(Ambion) followed by Rneasy extraction kit (Qiagen)
Poly-A selected mRNA library preparation was done using KAPA stranded library preparation kit

treatment_protocol: L4 worms were exposed to Pseudomonas aeruginosa strain PA14 or OP50 for 7 hours

value: Whole worm

value: Exposed to OP50 for 7 hours at L4 stage


title: Blood_Platelets TR3897-PPH-VUMC


title: Blood_Platelets TR3898-PPH-VUMC


title: Blood_Platelets TR3874-PPH-VUMC


title: Blood_Platelets TR4530-PPH-VUMC


title: Blood_Platelets TR3873-PPH-VUMC


title: adr-1(-) OP50 biol rep3

description:
Sample 16_GSF3253
WTvadr1diffexp2.csv


title: Naïve_Bach2-/-_HiC_rep2


title: Memory_WT_HiC_rep1


title: Naïve_Satb1_HiC_rep2


title: adr-2(-) OP50 biol rep2

description:
Sample 13_GSF3253
WTvadr2diffexp2.csv


title: Effector_WT_HiC_rep1


title: adr-1(-) OP50 biol rep2

description:
Sample 12_GSF3253
WTvadr1diffexp2.csv


title: adr-1(-);adr-2(-) OP50 biol rep2

description:
Sample 14_GSF3253
WTvadr1adr2diffexp2.csv


title: Effector_WT_HiC_rep2


title: adr-2(-) OP50 biol rep1

description:
Sample 9_GSF3253
WTvadr2diffexp2.csv


title: CD4+CD8+_WT_HiC_rep2


title: Naïve_WT_HiC_rep1


title: Naïve_WT_HiC_rep2


title: CD4+CD8+_WT_HiC_rep1


title: adr-2(-) OP50 biol rep3

description:
Sample 17_GSF3253
WTvadr2diffexp2.csv


title: ADR-1 dsRBD1 mutant PA14 biol rep1

description:
Sample 3_GSF3037
N2PA14vs114PA14diffexp.csv

value: adr-1(-) + dsRBD1(KKK-EAA)

value: Exposed to Pseudomonas aeruginosa strain PA14 for 7 hours at L4 stage


title: adr-1(-) PA14 biol rep1

description:
Sample 2_GSF3037
N2PA14vsadr1PA14diffexp.csv


title: N2 PA14 biol rep1

description:
Sample 1_GSF3037
N2PA14vsadr1PA14diffexp.csv
N2PA14vs114PA14diffexp.csv

value: Wildtype


title: N2 OP50 biol rep2

description:
Sample 11_GSF3253
WTvadr1diffexp2.csv
WTvadr2diffexp2.csv
WTvadr1adr2diffexp2.csv


title: A375 cell, control,6 days [SA-SPLICE19-2_S2]

status: Public on Mar 13 2023

city: Melbourne

first: David

last: Goode

state: Victoria

address: 305 Grattan Street

department: Research Division

institute: Peter MacCallum Cancer Centre

description:
HTSeq_matrix_new.xlsx
edgeR_normalised_read.csv

data_processing:
Read quality was assessed using FastQC v0.11.6.
Reads were aligned to the GRCh37.73 (hg19) version of the human genome using Hisat 2.0.4.
Bam files were sorted and index using Picard v2.17.3 and samtools v1.18.
Aligned reads in the BAM files and the GRCh37 GTF annotation file from Ensembl were input to HTSeq v0.11.2 with default settings for read quantification of genes.
Gene counts from HTSeq were normalised with the Trimmed Mean of M-values (TMM) method using edgeR.
Differential alternative splicing analysis was performed with rMATS (v.4.1.0) to detect five categories of splicing events including skipped exon (SE), intron retention (RI), mutually exclusive exons (MXE), alternative 5’ splice site (A5SS) and alternative 3’ splice site (A3SS).
Assembly: hg19
Supplementary files format and content: Single combined csv file containing gene counts of all samples.
Supplementary files format and content: csv file containing normalised gene counts from edgeR

growth_protocol: A375 and CHL1 cell lines were obtained from American Type Culture Collection. A375 cell line were grown in RPMI-1640 Media (Gibco) and CHL1 cell line were grown in DMEM (Gibco). Media were supplemented with 10% (vol/vol) fetal bovine serum (FBS) (Gibco), 2 mM GlutaMAX-I L-alanyl-L-glutamine dipeptide (Gibco), 100 μg/mL penicillin/streptomycin (Gibco), and buffered with 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES).

extract_protocol:
total RNA was isolated using the RNeasy Mini kit (QIAGEN) following the manufacturer’s instructions.
Approximately 1 μg of RNA was used for library preparation according to standard protocols (TruSeq RNA; Illumina).

treatment_protocol: Four different culture conditions with two replicates each were grown: (i) DMSO alone added for 72 hours (control), (ii) 1µM of palbociclib added for 72 hours (CDK4/6i_72hr), (iii) 1µM of palbociclib added for 6 days (CDK4/6i_6d) and (iv) 500nM of GSK3326595 added for 72 hours (PRMT5i_72hr).

value: melanoma cell

value: Control


title: A375 cell, CDK4/6 inhibition,6 days [SA-SPLICE19-3_S3]

value: CDK4/6 inhibition


title: N2 OP50 biol rep3

description:
Sample 15_GSF3253
WTvadr1diffexp2.csv
WTvadr2diffexp2.csv
WTvadr1adr2diffexp2.csv


title: N2 OP50 biol rep1

description:
Sample 7_GSF3253
WTvadr1diffexp2.csv
WTvadr2diffexp2.csv
WTvadr1adr2diffexp2.csv


title: adr-1(-) OP50 biol rep1

description:
Sample 8_GSF3253
WTvadr1diffexp2.csv


title: A375 cell, control,6 days [SA-SPLICE19-1_S1]


title: N2 PA14 biol rep2

description:
Sample 4_GSF3037
N2PA14vsadr1PA14diffexp.csv
N2PA14vs114PA14diffexp.csv


title: A375 cell, CDK4/6 inhibition,6 days [SA-SPLICE19-4_S4]


title: A375 cell, PRMT5 inhibition,72 hours [A375-CTX-72hr-2_S6]

value: PRMT5 inhibition


title: ADR-1 dsRBD1 PA14 biol rep2

description:
Sample 6_GSF3037
N2PA14vs114PA14diffexp.csv


title: adr-1(-);adr-2(-) OP50 biol rep1

description:
Sample 10_GSF3253
WTvadr1adr2diffexp2.csv


title: A375 cell, PRMT5 inhibition,72 hours [A375-CTX-72hr-1_S3]


title: A375 cell, CDK4/6 inhibition,72 hours [A375-PD991-72hr-1_S2]


title: A375 cell, CDK4/6 inhibition,72 hours [A375-PD991-72hr-2_S5]


title: PM2.5-treated worms in day 5

status: Public on Feb 22 2023

city: Beijing

first: Zinan

last: Li

address: #16 Hepingli Middle Street

institute: Beijing center for disease prevention and control

data_processing:
Clean reads were obtained by processing raw reads in Fastq format through in-house perl scripts to remove reads containing adapter and ploy-N as well as low quality reads.
During the mapping process, C elegans genome used as reference genome and gene model annotation files were downloaded from Genomics Institute of University of California, Santa Cruz (UCSC)’s website (http://hgdownload.soe.ucsc.edu/downloads.html#nematodes) directly. The index of the reference genome was built using Bowtie (v2.2.3) and clean reads were aligned to the reference genome for mapping by using TopHat (v2.0.12).
Quantification of gene expression level was achieved by using HTSeq v0.6.1 to count the reads numbers uniquely mapped to each gene.
Fragment per kilobase of exon per million fragment (FPKM) values of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ce11
Supplementary files format and content: Excel file includes RPKM values for each Sample

source_name: whole organism

extract_protocol:
Total RNA was extracted using Trizol reagent. A total amount of 3 µg RNA per sample which passed through the quality test was used as input 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. The library quality was assessed on the Aillient Bioanalyzer 2100 system.

value: whole organism

value: Wild-type


title: A375 cell, control,72 hours [A375-DMSO-72hr-2_S4]


title: sham-treated worms in day 5

value: sham


title: adr-1(-) PA14 biol rep2

description:
Sample 5_GSF3037
N2PA14vsadr1PA14diffexp.csv


title: TRLG104-14_prism_R3_250K [Prism, 250K nuclei, ATAC-seq]

status: Public on Feb 09 2023

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

institute: University College London

data_processing:
ATAC-seq: Reads obtained for each library were mapped using Bowtie2 (v2.4.1) with the parameters --very-sensitive and  -k 10 (Langmead and Salzberg, 2012) and peak calling for open chromatin region was performed using Generich (v0.6) available at https://github.com/jsh58/Genrich using ATAC model (-j), keeping unpaired alignments (-y), removing PCR duplicates (-r) and excluding reads mapped to mitochondria (-e MT). At this step, we pooled biological and technical replicates together as Generich analyses each replicate separately and then combined them by summarising p-values using Fisher’s method.
ATAC-seq: pybed tools was used to generate a set of unified peaks from the peaks called at each stage, classify peaks according to the activity during development and perform intersection with masked repetitive regions and conserved regions, as well as assigning peaks to genes
ATAC-seq: tab-delimited file containing peak intensities

organism: Paracentrotus lividus

source_name: Whole larvae

extract_protocol:
ATAC-seq: ATAC-seq was performed following the Omni-ATAC protocol using Digitonin (Promega) in addition to NP40 and Tween in the cell lysis buffer  (Corces et al., 2017). Sea urchin eggs were fertilised in filtered sea water with 2 mM of Paraminobenzoic acid (Sigma) to prevent hardening of the fertilisation envelope. The fertilization envelope was then removed by repeated filtration on a nylon net (70 µM). Embryos at the appropriate stage were collected and washed in NaCl 0,55M twice then dissociated in Calcium-Magnesium artificial sea water by energetic pipetting. For each time point, different numbers of nuclei were tested, typically 50,000, 150,000 and 250,000. The integrity of the nuclei was checked on a microscope after staining the nuclei with Hoechst.
ATAC-seq: After tagmentation the libraries were purified with a Zymo DNA clean up kit then a QPCR was performed on an aliquot  of the eluted libraries using the Ad1 and Ad2.x primers and the corresponding Ct was determined for each sample (Buenrostro et al. 2013). The libraries were then amplified at Ct+ 2 cycles. The quality of the libraries was checked on a 2% agarose gel to verify the size of the fragments and the nucleosome phasing.

value: Whole larvae

tag: Stage

value: Prism

value: Whole organism

value: Normal embryonic development


title: TRLG103-29_Pluteus_R2_150K [Pluteus, 150K nuclei, ATAC-seq]

value: Pluteus

value: WT


title: TRLG92-23-prism_R1_150K [Prism, 150K nuclei, ATAC-seq]


title: TRLG111-16_prism_R1_sucrose_150K [Prism, sucrose 150K nuclei, ATAC-seq]


title: TRLG89-9-G_R1_150K [Gastrula, 150K nuclei, ATAC-seq]

source_name: Whole embryo

value: Whole embryo

value: Gastrula


title: TRLG91-22-prism_R1_50K [Prism, 50K nuclei, ATAC-seq]


title: TRLG88-21-G_R1_50K [Gastrula, 50K nuclei, ATAC-seq]


title: TRLG90-3-G_R1_150K [Gastrula, 150K nuclei, ATAC-seq]


title: TRLG110-6_G_R1_sucrose_150K [Gastrula, sucrose 150K, ATAC-seq]


title: TRLG100-27_G_R2_50K [Gastrula, 50K nuclei, ATAC-seq]


title: TRLG98-11-LB_R2_150K [Late Blastula, 150K nuclei, ATAC-seq]

value: Late Blastula


title: TRLG97-26-LB_R2_50K [Late Blastula, 50K nuclei, ATAC-seq]


title: TRLG102-13_G_R2_250K [Gastrula, 250K nuclei, ATAC-seq]


title: TRLG101-28_G_R2_150K [Gastrula, 150K nuclei, ATAC-seq]


title: TRLG99-12-LB_R2_250K [Late Blastula, 250K nuclei, ATAC-seq]


title: TRLG87-2-LB_R1_150K [Late Blastula, 150K nuclei, ATAC-seq]


title: TRLG109-5_LB_R1_sucrose_150K [Late Blastula, sucrose 150K, ATAC-seq]


title: TRLG96-4-EB_R2_reaction_double [Early Blastula, double reaction, ATAC-seq]

value: Early Blastula


title: TRLG85-20-LB_R_150K [Late Blastula, 150K nuclei, ATAC-seq]


title: A375 cell, control,72 hours [A375-DMSO-72hr-1_S1]

value: melanoma cell


title: TRLG94-32-EB_R2_100K [Early Blastula, 100K nuclei, ATAC-seq]


title: TRLG95-25-EB_R2_250 [Early Blastula, 250K nuclei, ATAC-seq]


title: TRLG82-30-EB_R1_100K [Early Blastula, 100K nuclei, ATAC-seq]


title: TRLG83-19-EB_R1_150K [Early Blastula, 150K nuclei, ATAC-seq]


title: TRLG107-7_16-cell_R1 [16_cells, ATAC-seq]


title: RM_pos_rep3

status: Public on Feb 08 2023

city: San Francisco

first: Joel

last: Ernst

address: 1001 Potrero Ave

institute: UC, San Francisco

data_processing:
FastQC2 (v0.11.9) was used to generate quality-control reports of individual FASTQ files
Read were then aligned to the Mus musculus (house mouse) genome assembly GRCm38 (mm10) with the splice-aware STAR aligner using ‘GeneCounts’ quant mode with the Ensembl gene transfer format file (indexes were built using ‘—sjdbOverhang 50’ and the gtf file)
Assembly: GRCm38, mm10
Supplementary files format and content: raw_counts_names.tsv, tab delimited, counts

source_name: Lung

extract_protocol:
Total RNA was extracted from using RNeasy Plus Mini Kit (QIAGEN)
libraries were prepared by polyA selection using oligo-dT beads (Life Technologies)

value: Lung

value: infected


title: RM_neg_rep3

value: bystander


title: RM_neg_rep4


title: RM_pos_rep4


title: RM_pos_rep2


title: RM_pos_rep1


title: N_pos_rep4

value: N


title: N_neg_rep4


title: RM_neg_rep1


title: TRLG84-1-EB_R1_reaction_double [Early Blastula, double reaction, ATAC-seq]


title: N_neg_rep3


title: RM_neg_rep2


title: TRLG86-8-LB_R1_100K [Late Blastula, 100K nuclei, ATAC-seq]


title: N_pos_rep2


title: DC_pos_rep4


title: N_neg_rep2


title: N_pos_rep1


title: N_neg_rep1


title: DC_neg_rep4


title: DC_pos_rep3


title: DC_neg_rep3


title: DC_neg_rep1


title: DC_neg_rep2


title: AM_pos_rep4

value: AM


title: DC_pos_rep1


title: AM_neg_rep4


title: AM_pos_rep3


title: DC_pos_rep2


title: AM_neg_rep2


title: AM_neg_rep1


title: N_pos_rep3


title: AM_pos_rep2


title: AM_pos_rep1


title: CM_Doxorubicin_2

status: Public on Jan 29 2023

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Illumina BaseSpace FASTQ Generation | Version: 1.0.0
Illumina BaseSpace RNA-Seq Alignment | Version: 2.0.2; Incorporates STAR Aligner (Version: 2.6.1a) and Salmon Quantification (Version 0.11.2)
RNA-seq Differential Expression | Version 1.0.1
Assembly: Mus_musculus (UCSC mm10)
Supplementary files format and content: Doxo RNA_seq normalized counts.txt

source_name: heart

extract_protocol:
MX1gfp mice injected with vehicle or Doxorubicin were anaesthetized using isoflurane vaporizing system, and anesthesia was maintained using a nose cone throughout the surgical procedure. Following anesthesia, thoracic cavities were opened to expose the heart. Descending aorta was severed to allow exsanguination, and 7 mL EDTA buffer was immediately injected into the right ventricle. Ascending aorta was clamped using a hemostat, and the heart was removed from the mice then transferred to a 60 mm dish containing EDTA buffer. The heart was again injected  with 10 mL EDTA buffer into the left ventricle at 2 to 3 mm above apex. Next, the heart was transferred to a 60 mm dish containing perfusion buffer and injected with 3 mL of perfusion buffer through the same perforation on the left ventricle. Lastly, the heart was transferred to a 60 mm dish containing collagenase buffer, and heart digestion was achieved by continuously injecting collagenase buffer through the same perforation at the flow rate approximately 2 mL/min until the heart turned pale and flaccid and the injected perforation was enlarged. The atria and ventricles were gently separated and then the ventricles (with septum) were transferred to a new 60 mm dish containing 3 mL fresh collagenase buffer. The digested tissues were pulled into 1 mm pieces using fine-tip forceps, and cardiac cells were dissociated by gentle trituration, and then the enzyme activity was neutralized by adding 5 mL stop buffer. The single cell suspension was filtered through a 70 µm strainer, and the myocytes were settled by gravity for 20 min in a 50 mL tube. Direct-zol RNA miniprep kit (Zymo Research) was used to total RNA for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were interperitoneally injected with 100 microliters of sterile phosphate buffered saline (vehicle control) or 100 microliters of Doxorubicin dissolved in sterile phosphate buffered saline to a concentration of 25 mg of Doxorubicin per kg of total body weight

value: heart

value: primary cardiomyocytes

value: 25mg/kg Doxorubicin


title: CM_Doxorubicin_3


title: CM_Doxorubicin_1


title: CM_control_3

value: vehicle (phosphate buffered saline, PBS)


title: FLL361-H2O2-3

status: Public on Jan 23 2023

city: Loma Linda

first: Yuetan

last: Dou

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

description:
H2O2
0.25 mM of hydrogen peroxide stressed for 15 min

data_processing:
NextSeq 550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
RNA-seq fastq files were trimmed with trimmomatic, aligned to P. gingivalis W83 genome, and reads were qunatified with cutfflinks. Gene differential expression was analyzed using cuffdiff with FPKM threshold of 1.
Assembly: P. gingivalis W83
Supplementary files format and content: .csv file, with all genes reads in one file, includes FPKM values.

organism: Porphyromonas gingivalis

source_name: PG0686-deletion mutant of Pg W88

growth_protocol: Anaerobic condotions (80% N2, 10% H2, 10%CO2)

extract_protocol:
Briefly, RNA were harvested by Qiagen RNA kit. ribosomal RNA was removed from 2 µg of total RNA by using RiboMinus Transcriptome Isolation Kit (Life Technologies, Carlsbad, CA).
The first- and the second- strand cDNA synthesis, the RNA-seq barcode ligation, and other steps of libraries construction were performed by using Nextflex RNA-Seq kit according to the protocol of manufacturer (Bioo Scientific, Austin, TX).

treatment_protocol: Treatment group treated by 0.25 mM of hydrogen peroxide

value: PG0686-deletion mutant of Pg W83

tag: growing condition

value: anaerobic

value: hydrogen peroxide stress


title: CM_control_2


title: FLL361-H2O2-2

source_name: PG0686-deletion mutant of Pg W87


title: CM_control_1


title: FLL361-H2O2-1

source_name: PG0686-deletion mutant of Pg W86


title: FLL361-3

source_name: PG0686-deletion mutant of Pg W85

value: control


title: FLL361-1

source_name: PG0686-deletion mutant of Pg W83


title: FLL361-2

source_name: PG0686-deletion mutant of Pg W84


title: PgW83-H2O2-1

source_name: Wild-type strain Pg W86

value: Key stone oral pathogen Porphyromonas gingivalis W83


title: PgW83-H2O2-2

source_name: Wild-type strain Pg W87


title: PgW83-2

source_name: Wild-type strain Pg W84


title: AM_neg_rep3


title: PgW83-1

source_name: Wild-type strain Pg W83


title: PgW83-3

source_name: Wild-type strain Pg W85


title: ovCHA018

status: Public on Jan 09 2023

city: Daejeon

first: Jung Kyoon

last: Choi

address: 291, Daehak-ro, Yuseong-gu

department: Department of Bio and Brain Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Single-cell RNA transcriptome analysis

data_processing:
All raw files of fastq format were mapped to the reference genome GRCh38 using the Cell Ranger Single Cell v.4.0.0 software (10x Genomics).
Both Seurat v.3.2.3 and scanpy v.1.7.2 methods were used for preprocessing.
In cell filtering steps, we applied cutoff standards with cell counts for a gene greater than 3, a number of RNA features between 200 and 10000, and a mitochondrial percentage less than 20%.
The maximum count for RNA was set to 100000.
We performed the normalization, dimensionality reduction, and clustering with the default setting.
All count values were transformed to a log scale.
For initial cell type annotation, we used SingleR R package v.1.4.0 with combined references of Blueprint Encode and Human Primary Cell Atlas data.
Defining tumor cells was done by the prediction of aneuploid cells using CopyKAT v.0.1.2 with the segmentation parameter to 1 and minimum gene counts per segment to 25.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files representing: UMI counts (Ovarian_Cancer_raw_UMI_matrix.txt); normalized data (Ovarian_Cancer_normalized_log2CPM_matrix.txt)

extract_protocol:
The resected tissues were cut into blocks approximately 1cm in diameter. The premixed tumor dissociation working solution (Miltenyi Biotec, Germany) was added to minced tissue. The tissue and working solution were gently digested in the C tube (Miltenyi Biotec, Germany). The Gentle MACS tissue dissociator was running the h_tumor_02 program (Miltenyi Biotec, Germany). To prepare the single-cell suspension of tissue, the mixed-enzyme solution was pre-warmed in a 37°C hybridization incubator for 30min. The enzymatic digestion was stopped by diluting the enzyme solution with a medium containing penicillin-streptomycin and FBS. The solution was filtered through a 70μm Strainer filter (Life Technologies, USA). The solution was overlaid with the Ficoll-Paque plus (GE Healthcare, Sweden) using a serological pipette at the lowest speed setting. The centrifuge was done for the sample in the desired swing-out rotor at 400 x g and 20 °C for 30min. Using an Eppendorf pipette, the entire lymphocyte layer was aspirated, transferred to a fresh tube, and washed. Cell freezing medium was added to resuspend the single cells pellet and stored in liquid nitrogen.
Each cell suspension was subjected to 5' single-cell RNA sequencing using Single Cell 5’ Library and Gel Bead Kit V1, Single Cell A Chip Kit, and i7 Multiplex Kit (10x Genomics, USA) with a cell recovery target of 7000 except 5000, following the manufacturer’s instructions. Gene expression libraries were sequenced on an Illumina HiSeq 2500, NovaSeq 6000, and HiSeq X Ten platforms.

tag: patient id

tag: tumor stage

value: II

tag: tissue type

value: Ovarian cancer

tag: region

value: Ovary


title: ovCHA017

description: Single-cell RNA transcriptome analysis


title: ovCHA066

description: Single-cell RNA transcriptome analysis

value: III


title: ovCHA107

description: Single-cell RNA transcriptome analysis


title: ovCHA070

description: Single-cell RNA transcriptome analysis

value: IV


title: ovCHA034

description: Single-cell RNA transcriptome analysis


title: ovCHA039

description: Single-cell RNA transcriptome analysis

value: I


title: ovCHA110

description: Single-cell RNA transcriptome analysis


title: 210715_combinatorial_S9

status: Public on Jan 05 2023

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
Custom SHARE-seq pipeline
Scanpy v1.7.2
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: Raw count matrix generated by SHARE-seq pipeline (csv) and annotated processed data generated by Scanpy (h5ad). Map of cells to transcription factor ORFs produced by a custom Python script (csv)

source_name: H1 human embryonic stem cells

extract_protocol:
RNA was extracted using SHARE-seq
single-cell RNA-Seq libraries were prepared using SHARE-seq. Cells were mapped to their respective transcription factor perturbations by PCR amplifying the transcription factor and cell barcodes from the cDNA prior to tagmentation
RNA-Seq, other (amplicon)

value: H1 human embryonic stem cells

tag: differentiation protocol

value: overexpression of a library with 10 transcription factors in combinations

tag: time point

value: 7 days


title: PgW83-H2O2-3

source_name: Wild-type strain Pg W88


title: 210715_combinatorial_S4


title: 210715_combinatorial_S3


title: 210715_combinatorial_S2


title: 210715_combinatorial_S7


title: 210715_TFmap_S3

description: TF mapping results for 210715_combinatorial_S5, 210715_combinatorial_S7, 210715_combinatorial_S8, 210715_combinatorial_S9


title: C049

status: Public on Jan 19 2023

type: RNA

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from human leukocytes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering none NA.

source_name: leukocytes, whole blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: A total of 0.5 - 1.5 mL of whole blood were used for white blood cells (WBC) RNA extraction using the QIAamp RNA Blood Mini kit (Qiagen).

treatment_protocol: Whole blood samples were collected during hospitalization (average of 14 days after symptoms) or from volunteers (average of 9 days after symptoms). Whole blood was collected in an EDTA-containing tube as storage in maximum 6 hours for RNA extraction and plasma separation.

tag: gender

value: Female

tag: age (yr)

tag: group

value: Mild

tag: comorbidity

value: Systemic Arterial Hypertension; Diabetes mellitus; Hyperlipidemia


title: 210715_combinatorial_S1

tag: cell type


title: 210715_TFmap_S2

description: TF mapping results for 210715_combinatorial_S3, 210715_combinatorial_S4, 210715_combinatorial_S6


title: 210715_combinatorial_S6


title: C098

description: Gene expression from human leukocytes

value: Male

value: Severe

value: No


title: 210715_TFmap_S1

description: TF mapping results for 210715_combinatorial_S1, 210715_combinatorial_S2


title: C143

description: Gene expression from human leukocytes

value: Obesity; Asthma


title: Control_siRNA

status: Public on Jan 03 2023

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Demultiplexed mRNA seq reads were  mapped  to  the  mm10 version of the mouse reference genome using STAR methods (v2.7.3a)  and  subsequent analyses  were  performed  using  samtools  (v1.6)  and  BEDtools  (v  2.29.2).
Per-transcript expression was quantified as RPKMs using featureCounts from the subread(v.1.6.3) package.
Bigwig files were generated using deeptools (v.3.5.0) with the following parameters -bs 50 --normalizeUsing CPM
Assembly: mm10
Supplementary files format and content: Bigwig files

growth_protocol: 3T3-L1 cells (ATCC CL-173) were cultured in full medium (DMEM (FisherScientific 11995) supplemented with 10% FBS (Sigma F0926), 1x GlutaMAX (FisherScientific 35050), 1x Penicillin-Streptomycin (FisherScientific 15140)). 293T cells were grown in full medium on plates coated with 0.001% poly-L-lysine (Sigma P4832).

extract_protocol:
RNA was extracted with RNeasy Plus Mini Kit (Qiagen 74136)
Samples are run on the Agilent 2100 Bioanalyzer to determine level of degradation thus ensuring only high quality RNA is used (RIN Score 8 or higher). The Qubit fluorometer is used to determine the concentration prior to staring library prep. 4 µg of total DNAse treated RNA are then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with Ampure XP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using SBS v3 reagents."

treatment_protocol:
Adipocyte differentiatiton: Cells were grown to 100% confluence and then maintained for two days prior to initiating differentiation. Differentiation was induced by treatment with full medium supplemented with 0.5mM IBMX (Sigma I7018), 1μM dexamethasone (Sigma D1881), 5μg/ml insulin (Sigma I5500), 5μM troglitazone (Sigma T2573). Cells were treated with this differentiation medium for three days.
siRNA knockdown: 6 wells of 3T3-L1 cells at approximately 60% confluency were transfected with 30pmol of the indicated Dharmacon siRNAs using Lipofectamine RNAiMAX transfection reagent (FisherScientific 13-778-075) according to the manufacturer’s instructions. 48h post transfection, cells were treated with differentiation medium as described above for three days prior to harvesting for RNA extraction.
CRISPR editing: 6 wells of 293T cells (ATTC CRL-3216) at approximately 50% confluency were transfected with 3.3μg LentiCRISPR V2 (Addgene plasmid #52961) containing an sgRNA targeting exon 2, exon 3, or exon 17 of Med1, together with 2μg psPAX2-GAG-Pol-Rev (Addgene plasmid #12260), 0.85μg pAdVAntage (Promega E1711), and 1.3μg pCMV-VSV-G (Addgene plasmid #8454) using Lipofectamine 3000 transfection reagent FisherScientific L3000015) according to the manufacturer’s instructions. A LentiCRISPR V2  plasmid  containing  a  non-targeting  sgRNA  was  transfected  as  a  control. At  48-and  72-hours  post-transfection,  culture  medium containing  virus  was  collected  and passed  through  a  45μm  PVDF filter  onto  6  wells of 3T3-L1  cells  at  approximately  50%  confluency.  48h  after  the  second  addition  of  virus, infected 3T3-L1cells were selected using 2μg/ml puromycin (FisherScientific A11138), expanded, and frozen for future  use.  Med1  knockout and  Med1ΔIDR  cell  lines  were validated  by  probing  cell  extracts  for  MED1  protein  expression  using  an  antibody (Invitrogen, PA5-36200) that binds to an epitope located in Med1ΔIDR too and is found in the N-terminal domain of MED1.

tag: cell line

value: mouse fibroblast

tag: genotype

value: Control SiRNA

tag: treatment

value: adipogenic differentiation

tag: time

value: Day 3


title: C121

description: Gene expression from human leukocytes

value: Cardiopathy


title: Nontarget_gRNA

value: Nontarget gRNA


title: WT_undiff

value: Untreated Day 0

value: Day 0


title: ovCHA004

description: Single-cell RNA transcriptome analysis

value: III

value: Ovarian cancer

value: Ovary


title: 210715_combinatorial_S8

value: H1 human embryonic stem cells

value: overexpression of a library with 10 transcription factors in combinations

value: 7 days


title: 210715_combinatorial_S5


title: Nelfb_siRNA

value: Nelfb Knockdown


title: WT_diff

value: WT Day 3


title: Iws1_siRNA

value: Iws1 Knockdown


title: Med1_siRNA

value: mouse fibroblast

value: Med1 Knockdown


title: Ctr9_siRNA

value: Ctr9 Knockdown

value: adipogenic differentiation


title: Med1_delIDR_3

value: Med1_IDR deletion

value: Day 3


title: Spt6_siRNA

value: Spt6 Knockdown


title: Med1_KO_1


title: Med1_KO_2


title: Med1_delIDR_2