title: CRCGN009_HEPG2_24H:I03

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_I03.lxb
CRCGN009_HEPG2_24H_X2_B29_I03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H18

status: Public on Aug 28 2021

type: RNA

city: Boston

first: Stefano

last: Monti

state: MA

address: 25 Buick Street

department: Computational Medicine

country: USA

institute: Boston University

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H18.lxb
CRCGN009_HEPG2_24H_X2_B29_H18.lxb
Broad Institute Human L1000 epsilon

scan_protocol: Following treatment and lysis, the gene expression of the HepG2 and MCF10A cells was profiled using the L1000 platform, a high-throughput assay that measures the expression of ∼1,000 landmark genes and computationally infers the expression of nonmeasured transcripts.

data_processing: For each perturbation and landmark gene, we computed the change in gene expression following the perturbation using a moderated z-score procedure as described in the CMap–L1000 workflow. Differential expression values were calculated as moderated z-scores for each landmark gene and each unique perturbation (chemical and dose combination) perturbation, collapsed to a single value across replicates (Subramanian et al. 2017).

label: biotin

molecule: polyA RNA

organism: Homo sapiens

source_name: Liver Carcinogenicity

label_protocol: Each chemical perturbation for the HEPG2 screen was administered at six doses in triplicate wells per dose and chemical combination, starting from 40μM maximum dose (40 mM stock diluted 1:1,000) for NTP chemicals and 20μM for chemicals procured from Sigma-Aldrich, in series of two-fold dilutions. The sole exception to the standard dosage was 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which had a starting dose of 50 nM due to its extreme potency. Each chemical perturbation for the MCF10A was administered at three doses (100, 33, 10μM) in triplicate wells. The vehicle control used was DMSO with final dose of 14.1 mM. Four positive controls were used (vorinostat, geldanamycin, mitoxantrone, withaferin-a) each in final doses of 10, 3.33, and 1.00μM, respectively.

growth_protocol: HepG2 (ATCC® HB-8,065™), MCF10A parental and TP53-/- (Horizon, cat# HD 101-005), were used with medium RPMI1640 (10040CV; Mediatech) supplemented with 10% v/v fetal bovine serum (F4135; Sigma-Aldrich), 1× penicillin-streptomycin-glutamine (Invitrogen 10378016), and incubated at humidified 5% CO2 atmosphere at 37°C. Cell cultures were plated with 4,000 cells (45μL of growth medium) per well on 384-well plates (3707; Corning) and incubated for 24 h before treatment.

treatment_protocol: Cells were treated with 5μL of 1:100 diluted 1,000× stock compound plates to final volume of 50μL and incubated for 24 h before lysis

tag: tissue

tag: treatment


title: CRCGN009_HEPG2_24H:I19

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_I19.lxb
CRCGN009_HEPG2_24H_X2_B29_I19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:I05

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_I05.lxb
CRCGN009_HEPG2_24H_X2_B29_I05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:I02

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_I02.lxb
CRCGN009_HEPG2_24H_X2_B29_I02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:I01

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_I01.lxb
CRCGN009_HEPG2_24H_X2_B29_I01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:I12

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_I12.lxb
CRCGN009_HEPG2_24H_X2_B29_I12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H19

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H19.lxb
CRCGN009_HEPG2_24H_X2_B29_H19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H23

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H23.lxb
CRCGN009_HEPG2_24H_X2_B29_H23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:I06

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_I06.lxb
CRCGN009_HEPG2_24H_X2_B29_I06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H17

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H17.lxb
CRCGN009_HEPG2_24H_X2_B29_H17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H21

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H21.lxb
CRCGN009_HEPG2_24H_X2_B29_H21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H16

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H16.lxb
CRCGN009_HEPG2_24H_X2_B29_H16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H15

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H15.lxb
CRCGN009_HEPG2_24H_X3_B29_H15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H14

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H14.lxb
CRCGN009_HEPG2_24H_X2_B29_H14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H13

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H13.lxb
CRCGN009_HEPG2_24H_X2_B29_H13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H12

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H12.lxb
CRCGN009_HEPG2_24H_X2_B29_H12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H11

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H11.lxb
CRCGN009_HEPG2_24H_X2_B29_H11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H08

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H08.lxb
CRCGN009_HEPG2_24H_X2_B29_H08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H07

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H07.lxb
CRCGN009_HEPG2_24H_X2_B29_H07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H10

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H10.lxb
CRCGN009_HEPG2_24H_X2_B29_H10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H05

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H05.lxb
CRCGN009_HEPG2_24H_X2_B29_H05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H04

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H04.lxb
CRCGN009_HEPG2_24H_X2_B29_H04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H09

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H09.lxb
CRCGN009_HEPG2_24H_X2_B29_H09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H01

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H01.lxb
CRCGN009_HEPG2_24H_X2_B29_H01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H03

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H03.lxb
CRCGN009_HEPG2_24H_X2_B29_H03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H02

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H02.lxb
CRCGN009_HEPG2_24H_X2_B29_H02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G22

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G22.lxb
CRCGN009_HEPG2_24H_X2_B29_G22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H20

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H20.lxb
CRCGN009_HEPG2_24H_X2_B29_H20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G21

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G21.lxb
CRCGN009_HEPG2_24H_X2_B29_G21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G23

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G23.lxb
CRCGN009_HEPG2_24H_X2_B29_G23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G20

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G20.lxb
CRCGN009_HEPG2_24H_X2_B29_G20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G05

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G05.lxb
CRCGN009_HEPG2_24H_X2_B29_G05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G03

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G03.lxb
CRCGN009_HEPG2_24H_X2_B29_G03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G01

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G01.lxb
CRCGN009_HEPG2_24H_X2_B29_G01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G24

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G24.lxb
CRCGN009_HEPG2_24H_X2_B29_G24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G19

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G19.lxb
CRCGN009_HEPG2_24H_X2_B29_G19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G04

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G04.lxb
CRCGN009_HEPG2_24H_X2_B29_G04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F17

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F17.lxb
CRCGN009_HEPG2_24H_X2_B29_F17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G02

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G02.lxb
CRCGN009_HEPG2_24H_X2_B29_G02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F16

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F16.lxb
CRCGN009_HEPG2_24H_X2_B29_F16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:H06

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_H06.lxb
CRCGN009_HEPG2_24H_X2_B29_H06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F13

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F13.lxb
CRCGN009_HEPG2_24H_X2_B29_F13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F15

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F15.lxb
CRCGN009_HEPG2_24H_X2_B29_F15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F18

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F18.lxb
CRCGN009_HEPG2_24H_X2_B29_F18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F14

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F14.lxb
CRCGN009_HEPG2_24H_X2_B29_F14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F05

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F05.lxb
CRCGN009_HEPG2_24H_X2_B29_F05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:G06

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_G06.lxb
CRCGN009_HEPG2_24H_X2_B29_G06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F03

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F03.lxb
CRCGN009_HEPG2_24H_X2_B29_F03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F01

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F01.lxb
CRCGN009_HEPG2_24H_X2_B29_F01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F06

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F06.lxb
CRCGN009_HEPG2_24H_X2_B29_F06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E24

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E24.lxb
CRCGN009_HEPG2_24H_X2_B29_E24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F04

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F04.lxb
CRCGN009_HEPG2_24H_X2_B29_F04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E21

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E21.lxb
CRCGN009_HEPG2_24H_X2_B29_E21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E23

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E23.lxb
CRCGN009_HEPG2_24H_X2_B29_E23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E17

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E17.lxb
CRCGN009_HEPG2_24H_X2_B29_E17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E16

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E16.lxb
CRCGN009_HEPG2_24H_X2_B29_E16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E19

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E19.lxb
CRCGN009_HEPG2_24H_X2_B29_E19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E20

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E20.lxb
CRCGN009_HEPG2_24H_X2_B29_E20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E18

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E18.lxb
CRCGN009_HEPG2_24H_X2_B29_E18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E15

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E15.lxb
CRCGN009_HEPG2_24H_X2_B29_E15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E11

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E11.lxb
CRCGN009_HEPG2_24H_X2_B29_E11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E07

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E07.lxb
CRCGN009_HEPG2_24H_X2_B29_E07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E14

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E14.lxb
CRCGN009_HEPG2_24H_X2_B29_E14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E13

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E13.lxb
CRCGN009_HEPG2_24H_X2_B29_E13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E10

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E10.lxb
CRCGN009_HEPG2_24H_X2_B29_E10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E09

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E09.lxb
CRCGN009_HEPG2_24H_X2_B29_E09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E05

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E05.lxb
CRCGN009_HEPG2_24H_X2_B29_E05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E03

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E03.lxb
CRCGN009_HEPG2_24H_X2_B29_E03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E08

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E08.lxb
CRCGN009_HEPG2_24H_X2_B29_E08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E06

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E06.lxb
CRCGN009_HEPG2_24H_X2_B29_E06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E04

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E04.lxb
CRCGN009_HEPG2_24H_X2_B29_E04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:F02

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_F02.lxb
CRCGN009_HEPG2_24H_X2_B29_F02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E02

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E02.lxb
CRCGN009_HEPG2_24H_X2_B29_E02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D22

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D22.lxb
CRCGN009_HEPG2_24H_X2_B29_D22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E12

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E12.lxb
CRCGN009_HEPG2_24H_X2_B29_E12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D23

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D23.lxb
CRCGN009_HEPG2_24H_X2_B29_D23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D24

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D24.lxb
CRCGN009_HEPG2_24H_X2_B29_D24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D21

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D21.lxb
CRCGN009_HEPG2_24H_X2_B29_D21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D19

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D19.lxb
CRCGN009_HEPG2_24H_X2_B29_D19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E22

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E22.lxb
CRCGN009_HEPG2_24H_X2_B29_E22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D12

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D12.lxb
CRCGN009_HEPG2_24H_X2_B29_D12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D17

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D17.lxb
CRCGN009_HEPG2_24H_X2_B29_D17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D14

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D14.lxb
CRCGN009_HEPG2_24H_X2_B29_D14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D09

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D09.lxb
CRCGN009_HEPG2_24H_X2_B29_D09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D15

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D15.lxb
CRCGN009_HEPG2_24H_X2_B29_D15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D18

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D18.lxb
CRCGN009_HEPG2_24H_X2_B29_D18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D16

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D16.lxb
CRCGN009_HEPG2_24H_X2_B29_D16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D10

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D10.lxb
CRCGN009_HEPG2_24H_X2_B29_D10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D13

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D13.lxb
CRCGN009_HEPG2_24H_X2_B29_D13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D08

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D08.lxb
CRCGN009_HEPG2_24H_X2_B29_D08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D02

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D02.lxb
CRCGN009_HEPG2_24H_X2_B29_D02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D04

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D04.lxb
CRCGN009_HEPG2_24H_X2_B29_D04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C18

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C18.lxb
CRCGN009_HEPG2_24H_X2_B29_C18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D06

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D06.lxb
CRCGN009_HEPG2_24H_X2_B29_D06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D07

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D07.lxb
CRCGN009_HEPG2_24H_X2_B29_D07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C17

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C17.lxb
CRCGN009_HEPG2_24H_X2_B29_C17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C15

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C15.lxb
CRCGN009_HEPG2_24H_X2_B29_C15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D03

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D03.lxb
CRCGN009_HEPG2_24H_X2_B29_D03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D01

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D01.lxb
CRCGN009_HEPG2_24H_X2_B29_D01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C16

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C16.lxb
CRCGN009_HEPG2_24H_X2_B29_C16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C13

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C13.lxb
CRCGN009_HEPG2_24H_X2_B29_C13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C12

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C12.lxb
CRCGN009_HEPG2_24H_X2_B29_C12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D20

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D20.lxb
CRCGN009_HEPG2_24H_X2_B29_D20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C10

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C10.lxb
CRCGN009_HEPG2_24H_X2_B29_C10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C14

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C14.lxb
CRCGN009_HEPG2_24H_X2_B29_C14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:D05

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_D05.lxb
CRCGN009_HEPG2_24H_X2_B29_D05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:E01

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_E01.lxb
CRCGN009_HEPG2_24H_X2_B29_E01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C11

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C11.lxb
CRCGN009_HEPG2_24H_X2_B29_C11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C07

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C07.lxb
CRCGN009_HEPG2_24H_X2_B29_C07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C04

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C04.lxb
CRCGN009_HEPG2_24H_X2_B29_C04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C06

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C06.lxb
CRCGN009_HEPG2_24H_X2_B29_C06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C01

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C01.lxb
CRCGN009_HEPG2_24H_X2_B29_C01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B24

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B24.lxb
CRCGN009_HEPG2_24H_X2_B29_B24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C05

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C05.lxb
CRCGN009_HEPG2_24H_X2_B29_C05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C03

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C03.lxb
CRCGN009_HEPG2_24H_X2_B29_C03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B23

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B23.lxb
CRCGN009_HEPG2_24H_X2_B29_B23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B16

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B16.lxb
CRCGN009_HEPG2_24H_X2_B29_B16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B18

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B18.lxb
CRCGN009_HEPG2_24H_X2_B29_B18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B22

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B22.lxb
CRCGN009_HEPG2_24H_X2_B29_B22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B20

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B20.lxb
CRCGN009_HEPG2_24H_X2_B29_B20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B14

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B14.lxb
CRCGN009_HEPG2_24H_X2_B29_B14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C09

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C09.lxb
CRCGN009_HEPG2_24H_X2_B29_C09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B19

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B19.lxb
CRCGN009_HEPG2_24H_X2_B29_B19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B15

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B15.lxb
CRCGN009_HEPG2_24H_X2_B29_B15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B09

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B09.lxb
CRCGN009_HEPG2_24H_X2_B29_B09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C08

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C08.lxb
CRCGN009_HEPG2_24H_X2_B29_C08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B07

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B07.lxb
CRCGN009_HEPG2_24H_X2_B29_B07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A24

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A24.lxb
CRCGN009_HEPG2_24H_X2_B29_A24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:C02

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_C02.lxb
CRCGN009_HEPG2_24H_X2_B29_C02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B11

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B11.lxb
CRCGN009_HEPG2_24H_X2_B29_B11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B08

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B08.lxb
CRCGN009_HEPG2_24H_X2_B29_B08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B10

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B10.lxb
CRCGN009_HEPG2_24H_X2_B29_B10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B12

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B12.lxb
CRCGN009_HEPG2_24H_X2_B29_B12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A23

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A23.lxb
CRCGN009_HEPG2_24H_X2_B29_A23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A22

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A22.lxb
CRCGN009_HEPG2_24H_X2_B29_A22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B21

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B21.lxb
CRCGN009_HEPG2_24H_X2_B29_B21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A20

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A20.lxb
CRCGN009_HEPG2_24H_X2_B29_A20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A21

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A21.lxb
CRCGN009_HEPG2_24H_X2_B29_A21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A18

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A18.lxb
CRCGN009_HEPG2_24H_X2_B29_A18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A17

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A17.lxb
CRCGN009_HEPG2_24H_X2_B29_A17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:B13

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_B13.lxb
CRCGN009_HEPG2_24H_X2_B29_B13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A16

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A16.lxb
CRCGN009_HEPG2_24H_X2_B29_A16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A12

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A12.lxb
CRCGN009_HEPG2_24H_X2_B29_A12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A14

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A14.lxb
CRCGN009_HEPG2_24H_X2_B29_A14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A15

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A15.lxb
CRCGN009_HEPG2_24H_X2_B29_A15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:D11

description:
raw data information:
CRCGN008_HEPG2_24H_X3_B29_D11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A09

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A09.lxb
CRCGN009_HEPG2_24H_X2_B29_A09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A10

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A10.lxb
CRCGN009_HEPG2_24H_X2_B29_A10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A11

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A11.lxb
CRCGN009_HEPG2_24H_X2_B29_A11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A07

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A07.lxb
CRCGN009_HEPG2_24H_X2_B29_A07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P21.lxb
CRCGN008_HEPG2_24H_X3_B29_P21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P23.lxb
CRCGN008_HEPG2_24H_X3_B29_P23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P22.lxb
CRCGN008_HEPG2_24H_X3_B29_P22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A19

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A19.lxb
CRCGN009_HEPG2_24H_X2_B29_A19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P20.lxb
CRCGN008_HEPG2_24H_X3_B29_P20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P16.lxb
CRCGN008_HEPG2_24H_X3_B29_P16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P12.lxb
CRCGN008_HEPG2_24H_X3_B29_P12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P14.lxb
CRCGN008_HEPG2_24H_X3_B29_P14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P19.lxb
CRCGN008_HEPG2_24H_X3_B29_P19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P24.lxb
CRCGN008_HEPG2_24H_X3_B29_P24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P17.lxb
CRCGN008_HEPG2_24H_X3_B29_P17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P15.lxb
CRCGN008_HEPG2_24H_X3_B29_P15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A13

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A13.lxb
CRCGN009_HEPG2_24H_X2_B29_A13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P08.lxb
CRCGN008_HEPG2_24H_X3_B29_P08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P05.lxb
CRCGN008_HEPG2_24H_X3_B29_P05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P13.lxb
CRCGN008_HEPG2_24H_X3_B29_P13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P10.lxb
CRCGN008_HEPG2_24H_X3_B29_P10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P03.lxb
CRCGN008_HEPG2_24H_X3_B29_P03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P18.lxb
CRCGN008_HEPG2_24H_X3_B29_P18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P11.lxb
CRCGN008_HEPG2_24H_X3_B29_P11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P09.lxb
CRCGN008_HEPG2_24H_X3_B29_P09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P07.lxb
CRCGN008_HEPG2_24H_X3_B29_P07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN009_HEPG2_24H:A08

description:
raw data information:
CRCGN009_HEPG2_24H_X1_B29_A08.lxb
CRCGN009_HEPG2_24H_X2_B29_A08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O24.lxb
CRCGN008_HEPG2_24H_X3_B29_O24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O23.lxb
CRCGN008_HEPG2_24H_X3_B29_O23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P02.lxb
CRCGN008_HEPG2_24H_X3_B29_P02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P01.lxb
CRCGN008_HEPG2_24H_X3_B29_P01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O19.lxb
CRCGN008_HEPG2_24H_X3_B29_O19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P06.lxb
CRCGN008_HEPG2_24H_X3_B29_P06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:P04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_P04.lxb
CRCGN008_HEPG2_24H_X3_B29_P04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O16.lxb
CRCGN008_HEPG2_24H_X3_B29_O16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O18.lxb
CRCGN008_HEPG2_24H_X3_B29_O18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O22.lxb
CRCGN008_HEPG2_24H_X3_B29_O22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O13.lxb
CRCGN008_HEPG2_24H_X3_B29_O13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O11.lxb
CRCGN008_HEPG2_24H_X3_B29_O11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O21.lxb
CRCGN008_HEPG2_24H_X3_B29_O21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O15.lxb
CRCGN008_HEPG2_24H_X3_B29_O15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N22.lxb
CRCGN008_HEPG2_24H_X3_B29_N22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O09.lxb
CRCGN008_HEPG2_24H_X3_B29_O09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O07.lxb
CRCGN008_HEPG2_24H_X3_B29_O07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O12.lxb
CRCGN008_HEPG2_24H_X3_B29_O12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O17.lxb
CRCGN008_HEPG2_24H_X3_B29_O17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O14.lxb
CRCGN008_HEPG2_24H_X3_B29_O14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N16.lxb
CRCGN008_HEPG2_24H_X3_B29_N16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N20.lxb
CRCGN008_HEPG2_24H_X3_B29_N20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N17.lxb
CRCGN008_HEPG2_24H_X3_B29_N17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N24.lxb
CRCGN008_HEPG2_24H_X3_B29_N24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N21.lxb
CRCGN008_HEPG2_24H_X3_B29_N21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O20.lxb
CRCGN008_HEPG2_24H_X3_B29_O20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N12.lxb
CRCGN008_HEPG2_24H_X3_B29_N12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N23.lxb
CRCGN008_HEPG2_24H_X3_B29_N23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N09.lxb
CRCGN008_HEPG2_24H_X3_B29_N09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N19.lxb
CRCGN008_HEPG2_24H_X3_B29_N19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N14.lxb
CRCGN008_HEPG2_24H_X3_B29_N14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N13.lxb
CRCGN008_HEPG2_24H_X3_B29_N13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N15.lxb
CRCGN008_HEPG2_24H_X3_B29_N15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N18.lxb
CRCGN008_HEPG2_24H_X3_B29_N18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N07.lxb
CRCGN008_HEPG2_24H_X3_B29_N07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N10.lxb
CRCGN008_HEPG2_24H_X3_B29_N10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N11.lxb
CRCGN008_HEPG2_24H_X3_B29_N11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O08.lxb
CRCGN008_HEPG2_24H_X3_B29_O08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N08.lxb
CRCGN008_HEPG2_24H_X3_B29_N08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N01.lxb
CRCGN008_HEPG2_24H_X3_B29_N01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M22.lxb
CRCGN008_HEPG2_24H_X3_B29_M22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M20.lxb
CRCGN008_HEPG2_24H_X3_B29_M20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M19.lxb
CRCGN008_HEPG2_24H_X3_B29_M19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:O10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_O10.lxb
CRCGN008_HEPG2_24H_X3_B29_O10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N06.lxb
CRCGN008_HEPG2_24H_X3_B29_N06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N05.lxb
CRCGN008_HEPG2_24H_X3_B29_N05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N02.lxb
CRCGN008_HEPG2_24H_X3_B29_N02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M12.lxb
CRCGN008_HEPG2_24H_X3_B29_M12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M16.lxb
CRCGN008_HEPG2_24H_X3_B29_M16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M24.lxb
CRCGN008_HEPG2_24H_X3_B29_M24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M06.lxb
CRCGN008_HEPG2_24H_X3_B29_M06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M18.lxb
CRCGN008_HEPG2_24H_X3_B29_M18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M14.lxb
CRCGN008_HEPG2_24H_X3_B29_M14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M15.lxb
CRCGN008_HEPG2_24H_X3_B29_M15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M11.lxb
CRCGN008_HEPG2_24H_X3_B29_M11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M17.lxb
CRCGN008_HEPG2_24H_X3_B29_M17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M08.lxb
CRCGN008_HEPG2_24H_X3_B29_M08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M09.lxb
CRCGN008_HEPG2_24H_X3_B29_M09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:N03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_N03.lxb
CRCGN008_HEPG2_24H_X3_B29_N03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M21.lxb
CRCGN008_HEPG2_24H_X3_B29_M21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M10.lxb
CRCGN008_HEPG2_24H_X3_B29_M10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M05.lxb
CRCGN008_HEPG2_24H_X3_B29_M05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M23.lxb
CRCGN008_HEPG2_24H_X3_B29_M23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L20.lxb
CRCGN008_HEPG2_24H_X3_B29_L20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L19.lxb
CRCGN008_HEPG2_24H_X3_B29_L19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M07.lxb
CRCGN008_HEPG2_24H_X3_B29_M07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M04.lxb
CRCGN008_HEPG2_24H_X3_B29_M04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M03.lxb
CRCGN008_HEPG2_24H_X3_B29_M03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L15.lxb
CRCGN008_HEPG2_24H_X3_B29_L15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L24.lxb
CRCGN008_HEPG2_24H_X3_B29_L24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L21.lxb
CRCGN008_HEPG2_24H_X3_B29_L21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L22.lxb
CRCGN008_HEPG2_24H_X3_B29_L22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M02.lxb
CRCGN008_HEPG2_24H_X3_B29_M02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L18.lxb
CRCGN008_HEPG2_24H_X3_B29_L18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:M01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_M01.lxb
CRCGN008_HEPG2_24H_X3_B29_M01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L23.lxb
CRCGN008_HEPG2_24H_X3_B29_L23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L11.lxb
CRCGN008_HEPG2_24H_X3_B29_L11.lxb
Broad Institute Human L1000 epsilon


title: LiMTx_1

type: SRA

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

library_source: transcriptomic

data_processing:
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
We trimmed all reads to 44 bases and aligned to mm9/hg19 with Bowtie version 1.0.0 (Allowed up to 3 mismatches, but required unique best matches.)
Used R scripts to count tags that aligned to the exons of UCSC RefSeq gene models and calculate FPKM values.
Genome_build: mm9 and hg19

molecule: total RNA

organism: Mus musculus

source_name: mouse LiM progenitor cells engrafted in FRGN mouse liver

extract_protocol:
RNA lysis buffer is TRIzol reagent
RNA libraries were prepared with standard Illumina protocols

tag: cell type

value: FACS sorted host derived tdTomato+ cells from engraftment

tag: passage number

tag: diagnosis

value: normal

tag: age

value: Adult

tag: genotype

value: ROSAmT/mG


title: LiMTx_2

value: mouse LiM progenitor cells engrafted in FRGN mouse liver


title: mHC_3

source_name: uncultured mouse hepatocytes

value: uncultured mouse hepatocytes

value: uncultured,FAH+


title: mHC_2


title: LiMTx_3


title: mHC_1


title: CRCGN008_HEPG2_24H:L16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L16.lxb
CRCGN008_HEPG2_24H_X3_B29_L16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L17.lxb
CRCGN008_HEPG2_24H_X3_B29_L17.lxb
Broad Institute Human L1000 epsilon


title: mLiM_1

source_name: mouse hepatocytes in LiM

value: mouse hepatocytes in LiM

value: cultured in LiM


title: CRCGN008_HEPG2_24H:L09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L09.lxb
CRCGN008_HEPG2_24H_X3_B29_L09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L07.lxb
CRCGN008_HEPG2_24H_X3_B29_L07.lxb
Broad Institute Human L1000 epsilon


title: mLiM_2


title: mYAC_3

source_name: mouse hepatocytes in YAC

value: mouse hepatocytes in YAC

value: cultured in YAC


title: CRCGN008_HEPG2_24H:L14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L14.lxb
CRCGN008_HEPG2_24H_X3_B29_L14.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L10.lxb
CRCGN008_HEPG2_24H_X3_B29_L10.lxb
Broad Institute Human L1000 epsilon


title: mYAC_1


title: CRCGN008_HEPG2_24H:L08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L08.lxb
CRCGN008_HEPG2_24H_X3_B29_L08.lxb
Broad Institute Human L1000 epsilon


title: mYAC_2


title: CRCGN008_HEPG2_24H:L06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L06.lxb
CRCGN008_HEPG2_24H_X3_B29_L06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L02.lxb
CRCGN008_HEPG2_24H_X3_B29_L02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L04.lxb
CRCGN008_HEPG2_24H_X3_B29_L04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L05.lxb
CRCGN008_HEPG2_24H_X3_B29_L05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K24.lxb
CRCGN008_HEPG2_24H_X3_B29_K24.lxb
Broad Institute Human L1000 epsilon


title: Kidney, ISCH_ANESTH_3

city: Paris

first: Pierre

last: Galichon

address: 4 rue de la Chine

department: Hopital Tenon - Urgences Nephrologiques et Transplantation Renale

country: France

institute: Assistance Publique - Hopitaux de Paris

data_processing:
Reads of 100 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.
After quality control performed with FastQC, reads were mapped to the mm10 genome using STAR software.
Tables of counts were thus generated with HTSeq.
The normalization and differential expression analysis were performed with the R package edgeR, for the genes annotated in the reference genome.
We filter out very lowly expressed genes and normalized data according to the library size (sequencing depth) and the RNA composition (dispersion).  The differentially expressed genes were estimated using a GLM approach (General Linear Model), negative binomial distribution and a quasi-likelihood F-test.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from kidneys with Trizol reagent (Invitrogen) according to manufacturer’s instruction. RNA quantification was performed with a Qubit fluorimeter (ThermoFisher Scientific) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The TruSeq mRNA stranded kit from Illumina was used for library preparation with 700 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies).

treatment_protocol: 20 minutes renal ischemia by clamping the renal pedicle and sacrifice for kidney procurement after 24 hours

value: Kidney

tag: strain

tag: Sex

value: male

tag: group

value: ISCHEMIA conscious


title: Kidney, ISCH_CONCIOUS_3

value: ISCHEMIA anesthesia


title: Kidney, ISCH_CONCIOUS_1


title: CRCGN008_HEPG2_24H:K23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K23.lxb
CRCGN008_HEPG2_24H_X3_B29_K23.lxb
Broad Institute Human L1000 epsilon


title: Kidney, ISCH_ANESTH_2


title: Kidney, ISCH_CONCIOUS_4


title: Kidney, ISCH_CONCIOUS_2


title: Kidney, ISCH_ANESTH_1


title: Kidney, CTL_2

value: CONTROL


title: Kidney, CTL_3


title: Kidney, CTL_1


title: Kidney, ISCH_ANESTH_4


title: CRCGN008_HEPG2_24H:K18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K18.lxb
CRCGN008_HEPG2_24H_X3_B29_K18.lxb
Broad Institute Human L1000 epsilon


title: Kidney, CTL_4


title: CRCGN008_HEPG2_24H:K21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K21.lxb
CRCGN008_HEPG2_24H_X3_B29_K21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:L01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_L01.lxb
CRCGN008_HEPG2_24H_X3_B29_L01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K15.lxb
CRCGN008_HEPG2_24H_X3_B29_K15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K20.lxb
CRCGN008_HEPG2_24H_X3_B29_K20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K19.lxb
CRCGN008_HEPG2_24H_X3_B29_K19.lxb
Broad Institute Human L1000 epsilon


title: mLiM_3


title: 26046_Sua7_ssl2-N230I_ChIp-exo_replicate2

city: Pittsburgh

first: Tingting

last: Zhao

state: PA

address: 4200 Fifth Ave

institute: University of Pittsburgh

library_source: genomic

data_processing:
Quality control on TSS sequencing library FASTQ files was performed to remove reads with low quality using fastq_quality_filter in the FASTX-Toolkit package with parameters ‘fastq_quality_filter -v -q 20 -p 75’. Cutadapt was then used to remove the 6 nucleotide 5’ linker with parameter of ‘cutadapt -u 6’. The resulting reads were trimmed from 3’ end to 35 nucleotides long with parameter of ‘cutadapt -l 35 --minimum-length=35’. Trimmed reads were mapped to the S. cerevisiae R64-1-1 (SacCer3) genome using Bowtie with allowance of no more than two mismatches with suppression of non-uniquely mapped reads ‘bowtie -p3 -v2 -m1 -q --sam --un’, reported in sam files. Uniquely mapped reads were then extracted from sam files using SAMtools and output in bam format ‘samtools view -F 4 -S -b’. Bam files were then sorted and converted into bed files by SAMtools ‘samtools sort -o’, and BEDTools ‘bedtools bamtobed -cigar’. Customized commands were then used on bed files to identify the genomic coordinate of the 5’ end of each uniquely mapped read ‘awk 'BEGIN{FS=OFS="\t"} $6=="+" {$3=$2+1} $6=="-" {$2=$3-1} {print}'’. BEDTools was then used to determine pileup (TSS coverage) across the genome with parameters of ‘bedtools genomecov -g R64.new.genome -i -bg -strand -’ and ‘bedtools genomecov -g R64.new.genome -i -bg -strand +’, resulting in stranded bedGraph files. FASTQ files of individual library were directly processed or contacted by strains/mutants to generate begraph files for correlation analysis. For each of 5979 selected yeast promoters, TSS usage was examined within 401-nt wide window, spanning 250 nt upstream and 150 nt downstream of the previously annotated median TSS. Using customized bash and R scripts, TSS coverage from the bedGraph files of a library or a mutant were assigned into the defined windows to generate a 401×5979 TSS count table, with each row representing one of the 5979 promoters in the same order as the promoter annotation file, each column represents a promoter position, and the number in each cell representing 5’ ends mapping to that position. These count tables were stored in csv files. Using customized R script and the count table of a library or a mutant, an expression-spread-median file containing promoter expression, median TSS position of the promoter, TSS spread of the promoter was generated. The median TSS position was defined as the actual TSS containing the 50th percentile of the promoter window. The spread of TSS, which measures the width of the middle 80% of TSS distribution, was calculated by subtracting positions of 10th percentile and 90th percentile of TSS counts in 401-nt promoter window and adding 1. The positions of 10th percentile and 90th percentile of TSS counts in each promoter window were also stored in this expression-spread-median file. The streamlined codes to generate bedGraph files, the prompter annotation file and the customized scripts to generate count tables and expression-spread-median files can be found on Github account TingtingSsl2, under repository of “Ssl2_scanning”.
ChIP-exo data processing was performed as described by Rossi et al. in Nature Communications, 2018 and Qiu et al. in Genome Biology, 2020. Briefly, ChIP-exo libraries were sequenced on a NextSeq 500 in paired-end mode to generate 40 (read1) x 36 bp (read2) reads. Reads passing Q30 quality threshold were then aligned to the sacCer3 genome using the BWA-MEM alignment algorithm (v0.7.9a) with default parameters. After alignment, PCR duplicates were removed using Picard and SAMtools assuming unique combinations of read1 and read2 were PCR duplicates. Using ScriptManager v0.12, BAM files of a library were assigned into two 401×5979 matrices and saved in CDT files, which stores counts of 5’ position of protein binding on top and bottom strands, respectively. The same as in TSS-seq data analysis, each row of 401×5979 matrix representing one of 5979 promoters and each column representing a position in the 401-nt promoter window. These 401×5979 matrices were also saved in csv format. Matrices from the same mutant were combined into a single matrix by adding counts in library matrices at the same dimension and saved in csv files. Similar to TSS-seq analysis, the customized R script and the matrix of a library or a mutant were used to generate an expression-spread-median file containing promoter expression, median 5’ position of protein binding, the binding site of the spread of the promoter and saved in txt files.
Genome_build: S. cerevisiae R64-1-1 (SacCer3)
Supplementary_files_format_and_content: Each TSS-seq raw fastq file generates two begraph files. Each paired ChIP-exo fastq file generates two cdt files, one TOP strand cdt file and one BOTTOM cdt file.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cell

growth_protocol: Yeast cell cultures were grown in duplicates and cells were harvested at mid-log phase at a density of 1X107 cells/mL, as determined by cell counting. For S. cerevisiae TSS-seq, cells collected from 50 mL of S. cerevisiae culture and 5 mL of S. pombe culture (serving as potential spike-in) were mixed and total RNA was extracted.

extract_protocol:
Total RNA was extracted by a phenol-chloroform method originally described by Steven Hahn et.al with slight modification. Briefly, 50mL cultured yeast cells were harvested and suspended in 450uL AE (10 mM Tris-Cl; 0.5 mM EDTA, pH 9.0.) and 1% SDS solutions. Followed by immediate addition of 450uL AE-equilibrated phenol and vortex. After 65 ˚C incubation, the above mixture was transferred on sandy dry ice for 60 seconds and then moved on water ice. After spinning at 10,000rpm for 3 minutes at 4 ˚C, the aqueous layer was transferred to a tube containing 300uL AE-equilibrated phenol and 300uL of chloroform. Followed by 15 seconds of vortex and 2 minutes of spinning at 10,000, 4 ˚C. The supernatant was again transferred to another tube containing 450uL chloroform. Vertex 15 seconds and spinning 2 minutes at 10,000 rpm. The aqueous layer was carefully transferred to the third tube containing 50uL DEPC treated NaOAc and filled by 100% EtOH till the top. After 5-10 seconds of vortex, the tube was frozen at -20 ˚C for 1-2 hours. Spinning 10,000 rpm for 20 minutes at 4 ˚C. The supernatant was discarded and the pellet was washed with 75% EtOH twice and air dried. The pellet was then dissolved in 30-40uL RNase-free water and measured for concentration.
100 μg of the isolated total RNA was treated with 30 U of DNase I (QIAGEN) and purified using RNeasy Mini Kit (QIAGEN). A Ribo-Zero Gold rRNA Removal Kit (Illumina) was used to deplete rRNAs from 5 μg of DNase-treated RNAs. The rRNA-depleted RNA was purified by ethanol precipitation and resuspended in 10 μL of nuclease-free water. To remove RNA transcripts carrying a 5’ monophosphate moiety (5’-P), 2 μg of rRNA-depleted RNA were treated with 1 U Terminator 5’-Phosphate-Dependent Exonuclease (Epicentre) in the 1x Buffer A in the presence of 40 U RNaseOUT in a 50 μL reaction at 30 ˚C for 1 h. Samples were extracted with acid phenol-chloroform pH 4.5 (ThermoFisher Scientific), and RNA was recovered by ethanol precipitation and resuspended in 30 μL of nuclease-free water. Next, to remove 5’-terminal phosphates, RNA was treated with 1.5 U CIP (NEB) in 1x NEBuffer 3 in the presence of 40 U RNaseOUT in a 50 μL reaction at 37 ˚C for 30 min. Samples were extracted with acid phenol-chloroform and RNA was recovered by ethanol precipitation and resuspended in 30 μL of nuclease-free water. To convert 5’-capped RNA transcripts to 5’-monophosphate RNAs ligatable to 5’ adaptor, CIP-treated RNAs were mixed with 12.5 U CapClip (Cellscript) and 40 U RNaseOUT in 1X CapClip reaction buffer in a 40 μLreaction and incubated at 37 ˚C for 1 h. RNAs were extracted with acid phenol-chloroform, recovered by ethanol precipitation and resuspended in 10 μL of nuclease-free water. To ligate the 5’ adapter, the CapClip-treated RNA products were combined with 1 μM 5’ adapter oligonucleotide s1086 (5’-GUUCAGAGUUCUACAGUCCGACGAUCNNNNNN-3’), 1X T4 RNA ligase buffer, 40 U RNaseOUT, 1 mM ATP, 10% PEG 8000 and 10 U T4 RNA ligase 1 in a 30 μL reaction. The mixtures were incubated at 16°C for 16 h and the reactions were stopped by adding 30 μL of 2X RNA loading dye. The mixtures were separated by electrophoresis on 10% 7 M urea slab gels in 1X TBE buffer and incubated with SYBR Gold nucleic acid gel stain. RNA products migrating above the 5’ adapter oligo were recovered from the gel as described34, purified by ethanol precipitation and resuspended in 10 μL of nuclease-free water. To generate first strand cDNA, 5’-adaptor-ligated products were mixed with 0.3 μL of 100 μM s1082 oligonucleotide (5’-GCCTTGGCACCCGAGAATTCCANNNNNNNNN3’, N=A/T/G/C) containing a randomized 9-nt sequence at the 3’ end, incubated at 65 °C for 5 min, and cooled to 4 °C. A solution containing 4 μL of 5X First-Strand buffer, 1 μL (40 U) RNaseOUT, 1 μL of 10 mM dNTP mix, 1 μL of 100 mM DTT, 1 μL (200 U) of SuperScript III Reverse Transcriptase and 1.7 μL of nuclease-free water was added to the mixture. Reactions were incubated at 25 °C for 5 min, 55 °C for 60 min, 70 °C for 15 min, and cooled to 25 °C. 10 U RNase H was added, the mixtures were incubated 20 min at 37 °C and 20 μL of 2X DNA loading solution (PippinPrep Reagent Kit, Sage Science) were added. Nucleic acids were separated by electrophoresis on 2% agarose gel (PippinPrep Reagent Kit, external Marker B) to collect species of ~90 to ~550 nt. cDNA was recovered by ethanol precipitation and resuspended in 20 μL of nuclease-free water. To amplify cDNA, 9 μL of gel-isolated cDNA was added to the mixture containing 1X Phusion HF reaction buffer, 0.2 mM dNTPs, 0.25 μM Illumina RP1 primer (5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’), 0.25 μM Illumina index primers RPI3-RPI16 (index primers have the same sequences on 5' and 3' ends, but different on 6-nt sequence that serves as a barcode (underlined); RPI3: 5'-CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3'), and 0.02 U/μL Phusion HF polymerase in 30 μL reaction. PCR was performed with an initial denaturation step of 10 s at 98 °C, amplification for 12 cycles (denaturation for 5 s at 98 °C, annealing for 15 s at 62 °C and extension for 15 s at 72°C), and a final extension for 5 min at 72 °C. Amplified cDNAs were isolated by electrophoresis on 2% agarose gel (PippinPrep Reagent Kit, external Marker B) and products of ~180 to ~550 nt were collected. cDNA was recovered by ethanol precipitation and resuspended in 13 μL of nuclease-free water. Barcoded libraries were pooled and sequenced on an Illumina NextSeq platform in high output mode using custom primer s1115 (5’-CTACACGTTCAGAGTTCTACAGTCCGACGATC-3’).

value: ssl2 N230I

tag: tag

value: SUA7 TAP-epitope

tag: molecule

value: chromatin


title: CRCGN008_HEPG2_24H:K22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K22.lxb
CRCGN008_HEPG2_24H_X3_B29_K22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K17.lxb
CRCGN008_HEPG2_24H_X3_B29_K17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K16.lxb
CRCGN008_HEPG2_24H_X3_B29_K16.lxb
Broad Institute Human L1000 epsilon


title: 26044_Sua7_rpb1-E1103G_ChIp-exo_replicate2

value: rpb1 E1103G


title: CRCGN008_HEPG2_24H:K14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K14.lxb
CRCGN008_HEPG2_24H_X3_B29_K14.lxb
Broad Institute Human L1000 epsilon


title: 26045_Sua7_SSL2-PAM-(WT)_ChIp-exo_replicate2

value: SSL2 PAM (WT)


title: CRCGN008_HEPG2_24H:K05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K05.lxb
CRCGN008_HEPG2_24H_X3_B29_K05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K04.lxb
CRCGN008_HEPG2_24H_X3_B29_K04.lxb
Broad Institute Human L1000 epsilon


title: 26043_Sua7_rpb1-H1085Y_ChIp-exo_replicate2

value: rpb1 H1085Y


title: 26035_Sua7_ssl2-N230D_ChIp-exo_replicate1

value: ssl2 N230D


title: 26042_Sua7_RPB1-WT_ChIp-exo_replicate2

value: RPB1 WT


title: CRCGN008_HEPG2_24H:K02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K03.lxb
CRCGN008_HEPG2_24H_X3_B29_K03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K01.lxb
CRCGN008_HEPG2_24H_X3_B29_K01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:K06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_K06.lxb
CRCGN008_HEPG2_24H_X3_B29_K06.lxb
Broad Institute Human L1000 epsilon


title: 26033_Sua7_SSL2-PAM-(WT)_ChIp-exo_replicate1


title: 26032_Sua7_rpb1-E1103G_ChIp-exo_replicate1


title: CRCGN008_HEPG2_24H:J23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J23.lxb
CRCGN008_HEPG2_24H_X3_B29_J23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:J24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J24.lxb
CRCGN008_HEPG2_24H_X3_B29_J24.lxb
Broad Institute Human L1000 epsilon


title: 26047_Sua7_ssl2-N230D_ChIp-exo_replicate2


title: CRCGN008_HEPG2_24H:J22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J22.lxb
CRCGN008_HEPG2_24H_X3_B29_J22.lxb
Broad Institute Human L1000 epsilon


title: 26050_Ssl2_ssl2-N230I_ChIp-exo_replicate2

value: SSL2 TAP-epitope


title: CRCGN008_HEPG2_24H:J19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J19.lxb
CRCGN008_HEPG2_24H_X3_B29_J19.lxb
Broad Institute Human L1000 epsilon


title: 26030_Sua7_RPB1-WT_ChIp-exo_replicate1


title: 26031_Sua7_rpb1-H1085Y_ChIp-exo_replicate1


title: 26049_Ssl2_ssl2-N230D_ChIp-exo_replicate2


title: CRCGN008_HEPG2_24H:J20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J20.lxb
CRCGN008_HEPG2_24H_X3_B29_J20.lxb
Broad Institute Human L1000 epsilon


title: 26048_Ssl2_SSL2-PAM-(WT)_ChIp-exo_replicate2


title: CRCGN008_HEPG2_24H:J12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J12.lxb
CRCGN008_HEPG2_24H_X3_B29_J12.lxb
Broad Institute Human L1000 epsilon


title: 26041_Ssl2_rpb1-E1103G_ChIp-exo_replicate2


title: CRCGN008_HEPG2_24H:J11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J11.lxb
CRCGN008_HEPG2_24H_X3_B29_J11.lxb
Broad Institute Human L1000 epsilon


title: 26040_Ssl2_rpb1-H1085Y_ChIp-exo_replicate2


title: CRCGN008_HEPG2_24H:J09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J09.lxb
CRCGN008_HEPG2_24H_X3_B29_J09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:J08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J08.lxb
CRCGN008_HEPG2_24H_X3_B29_J08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:J07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J07.lxb
CRCGN008_HEPG2_24H_X3_B29_J07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:J21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J21.lxb
CRCGN008_HEPG2_24H_X3_B29_J21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:J10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J10.lxb
CRCGN008_HEPG2_24H_X3_B29_J10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:J05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J05.lxb
CRCGN008_HEPG2_24H_X3_B29_J05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:J06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J06.lxb
CRCGN008_HEPG2_24H_X3_B29_J06.lxb
Broad Institute Human L1000 epsilon


title: 26038_Ssl2_ssl2-N230I_ChIp-exo_replicate1


title: 26036_Ssl2_SSL2-PAM-(WT)_ChIp-exo_replicate1


title: 26037_Ssl2_ssl2-N230D_ChIp-exo_replicate1


title: 26034_Sua7_ssl2-N230I_ChIp-exo_replicate1


title: 26028_Ssl2_rpb1-H1085Y_ChIp-exo_replicate1


title: 26029_Ssl2_rpb1-E1103G_ChIp-exo_replicate1


title: CRCGN008_HEPG2_24H:J03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:J04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J04.lxb
CRCGN008_HEPG2_24H_X3_B29_J04.lxb
Broad Institute Human L1000 epsilon


title: 26039_Ssl2_RPB1-WT_ChIp-exo_replicate2


title: CRCGN008_HEPG2_24H:J02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J02.lxb
CRCGN008_HEPG2_24H_X3_B29_J02.lxb
Broad Institute Human L1000 epsilon


title: 26027_Ssl2_RPB1-WT_ChIp-exo_replicate1


title: CRCGN008_HEPG2_24H:J01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_J01.lxb
CRCGN008_HEPG2_24H_X3_B29_J01.lxb
Broad Institute Human L1000 epsilon


title: VV1567_rpb1_H1085Y_TSS-seq_bioreplicate_2

data_processing:
Library strategy: TTS-seq
Quality control on TSS sequencing library FASTQ files was performed to remove reads with low quality using fastq_quality_filter in the FASTX-Toolkit package with parameters ‘fastq_quality_filter -v -q 20 -p 75’. Cutadapt was then used to remove the 6 nucleotide 5’ linker with parameter of ‘cutadapt -u 6’. The resulting reads were trimmed from 3’ end to 35 nucleotides long with parameter of ‘cutadapt -l 35 --minimum-length=35’. Trimmed reads were mapped to the S. cerevisiae R64-1-1 (SacCer3) genome using Bowtie with allowance of no more than two mismatches with suppression of non-uniquely mapped reads ‘bowtie -p3 -v2 -m1 -q --sam --un’, reported in sam files. Uniquely mapped reads were then extracted from sam files using SAMtools and output in bam format ‘samtools view -F 4 -S -b’. Bam files were then sorted and converted into bed files by SAMtools ‘samtools sort -o’, and BEDTools ‘bedtools bamtobed -cigar’. Customized commands were then used on bed files to identify the genomic coordinate of the 5’ end of each uniquely mapped read ‘awk 'BEGIN{FS=OFS="\t"} $6=="+" {$3=$2+1} $6=="-" {$2=$3-1} {print}'’. BEDTools was then used to determine pileup (TSS coverage) across the genome with parameters of ‘bedtools genomecov -g R64.new.genome -i -bg -strand -’ and ‘bedtools genomecov -g R64.new.genome -i -bg -strand +’, resulting in stranded bedGraph files. FASTQ files of individual library were directly processed or contacted by strains/mutants to generate begraph files for correlation analysis. For each of 5979 selected yeast promoters, TSS usage was examined within 401-nt wide window, spanning 250 nt upstream and 150 nt downstream of the previously annotated median TSS. Using customized bash and R scripts, TSS coverage from the bedGraph files of a library or a mutant were assigned into the defined windows to generate a 401×5979 TSS count table, with each row representing one of the 5979 promoters in the same order as the promoter annotation file, each column represents a promoter position, and the number in each cell representing 5’ ends mapping to that position. These count tables were stored in csv files. Using customized R script and the count table of a library or a mutant, an expression-spread-median file containing promoter expression, median TSS position of the promoter, TSS spread of the promoter was generated. The median TSS position was defined as the actual TSS containing the 50th percentile of the promoter window. The spread of TSS, which measures the width of the middle 80% of TSS distribution, was calculated by subtracting positions of 10th percentile and 90th percentile of TSS counts in 401-nt promoter window and adding 1. The positions of 10th percentile and 90th percentile of TSS counts in each promoter window were also stored in this expression-spread-median file. The streamlined codes to generate bedGraph files, the prompter annotation file and the customized scripts to generate count tables and expression-spread-median files can be found on Github account TingtingSsl2, under repository of “Ssl2_scanning”.
ChIP-exo data processing was performed as described by Rossi et al. in Nature Communications, 2018 and Qiu et al. in Genome Biology, 2020. Briefly, ChIP-exo libraries were sequenced on a NextSeq 500 in paired-end mode to generate 40 (read1) x 36 bp (read2) reads. Reads passing Q30 quality threshold were then aligned to the sacCer3 genome using the BWA-MEM alignment algorithm (v0.7.9a) with default parameters. After alignment, PCR duplicates were removed using Picard and SAMtools assuming unique combinations of read1 and read2 were PCR duplicates. Using ScriptManager v0.12, BAM files of a library were assigned into two 401×5979 matrices and saved in CDT files, which stores counts of 5’ position of protein binding on top and bottom strands, respectively. The same as in TSS-seq data analysis, each row of 401×5979 matrix representing one of 5979 promoters and each column representing a position in the 401-nt promoter window. These 401×5979 matrices were also saved in csv format. Matrices from the same mutant were combined into a single matrix by adding counts in library matrices at the same dimension and saved in csv files. Similar to TSS-seq analysis, the customized R script and the matrix of a library or a mutant were used to generate an expression-spread-median file containing promoter expression, median 5’ position of protein binding, the binding site of the spread of the promoter and saved in txt files.
Genome_build: S. cerevisiae R64-1-1 (SacCer3)
Supplementary_files_format_and_content: Each TSS-seq raw fastq file generates two begraph files. Each paired ChIP-exo fastq file generates two cdt files, one TOP strand cdt file and one BOTTOM cdt file.

value: 5' capped RNA


title: VV1557_rpb1_H1085Y_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:I23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I23.lxb
CRCGN008_HEPG2_24H_X3_B29_I23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I24.lxb
CRCGN008_HEPG2_24H_X3_B29_I24.lxb
Broad Institute Human L1000 epsilon


title: VV1413_rpb1_H1085Y_TSS-seq_bioreplicate_1


title: VV1414_rpb1_H1085Y_TSS-seq_bioreplicate_2


title: CRCGN008_HEPG2_24H:I22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I22.lxb
CRCGN008_HEPG2_24H_X3_B29_I22.lxb
Broad Institute Human L1000 epsilon


title: VV1566_rpb1 E1103G_TSS-seq_bioreplicate_2


title: VV1556_rpb1_E1103G_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:I19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I20.lxb
CRCGN008_HEPG2_24H_X3_B29_I20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I18.lxb
CRCGN008_HEPG2_24H_X3_B29_I18.lxb
Broad Institute Human L1000 epsilon


title: VV1565_RPB1_WT_TSS-seq_bioreplicate_2


title: VV1411_rpb1_E1103G_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:I17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I17.lxb
CRCGN008_HEPG2_24H_X3_B29_I17.lxb
Broad Institute Human L1000 epsilon


title: VV1564_ssl2_Y750_TSS-seq_bioreplicate_2

value: ssl2 Y750


title: CRCGN008_HEPG2_24H:I16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I16.lxb
CRCGN008_HEPG2_24H_X3_B29_I16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I14.lxb
CRCGN008_HEPG2_24H_X3_B29_I14.lxb
Broad Institute Human L1000 epsilon


title: VV1563_ssl2_R636C_TSS-seq_bioreplicate_2

value: ssl2 R636C


title: CRCGN008_HEPG2_24H:I15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I15.lxb
CRCGN008_HEPG2_24H_X3_B29_I15.lxb
Broad Institute Human L1000 epsilon


title: VV1554_ssl2_Y750_TSS-seq_bioreplicate_1


title: VV1412_rpb1_E1103G_TSS-seq_bioreplicate_2


title: CRCGN008_HEPG2_24H:I21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I21.lxb
CRCGN008_HEPG2_24H_X3_B29_I21.lxb
Broad Institute Human L1000 epsilon


title: VV1553_ssl2_R636C_TSS-seq_bioreplicate_1


title: VV1562_ssl2_D522V_TSS-seq_bioreplicate_2

value: ssl2 D522V


title: VV1417_ssl2_R636C_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:I13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I13.lxb
Broad Institute Human L1000 epsilon


title: VV1552_ssl2_D522V_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:I10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I10.lxb
CRCGN008_HEPG2_24H_X3_B29_I10.lxb
Broad Institute Human L1000 epsilon


title: VV1555_RPB1_WT_TSS-seq_bioreplicate_1


title: VV1418_ssl2_R636C_TSS-seq_bioreplicate_2


title: CRCGN008_HEPG2_24H:I11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I11.lxb
CRCGN008_HEPG2_24H_X3_B29_I11.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I09.lxb
CRCGN008_HEPG2_24H_X3_B29_I09.lxb
Broad Institute Human L1000 epsilon


title: VV1560_ssl2_N230I_TSS-seq_bioreplicate_2


title: CRCGN008_HEPG2_24H:I06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I06.lxb
CRCGN008_HEPG2_24H_X3_B29_I06.lxb
Broad Institute Human L1000 epsilon


title: VV1416_ssl2_N230D_TSS-seq_bioreplicate_2


title: CRCGN008_HEPG2_24H:I07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I07.lxb
CRCGN008_HEPG2_24H_X3_B29_I07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I08.lxb
CRCGN008_HEPG2_24H_X3_B29_I08.lxb
Broad Institute Human L1000 epsilon


title: VV1561_ssl2_N230D_TSS-seq_bioreplicate_1


title: VV1551_ssl2_N230D_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:I02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I02.lxb
CRCGN008_HEPG2_24H_X3_B29_I02.lxb
Broad Institute Human L1000 epsilon


title: VV1415_ssl2_N230D_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:I03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I03.lxb
CRCGN008_HEPG2_24H_X3_B29_I03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I05.lxb
CRCGN008_HEPG2_24H_X3_B29_I05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I04.lxb
CRCGN008_HEPG2_24H_X3_B29_I04.lxb
Broad Institute Human L1000 epsilon


title: VV1550_ssl2_N230I_TSS-seq_bioreplicate_1


title: VV1546_SSL2_WT_TSS-seq_bioreplicate_1

value: SSL2 WT


title: VV1559_ssl2_L225P_TSS-seq_bioreplicate_2

value: ssl2 L225P


title: CRCGN008_HEPG2_24H:H21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H21.lxb
CRCGN008_HEPG2_24H_X3_B29_H21.lxb
Broad Institute Human L1000 epsilon


title: VV1548_SSL2_WT_TSS-seq_bioreplicate_1


title: VV1549_ssl2_L225P_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:H24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H24.lxb
Broad Institute Human L1000 epsilon


title: VV1421_SSL2_WT_TSS-seq_bioreplicate_2


title: CRCGN008_HEPG2_24H:H23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H23.lxb
CRCGN008_HEPG2_24H_X3_B29_H23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I01.lxb
CRCGN008_HEPG2_24H_X3_B29_I01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H19.lxb
CRCGN008_HEPG2_24H_X3_B29_H19.lxb
Broad Institute Human L1000 epsilon


title: VV1422_SSL2_WT_TSS-seq_bioreplicate_2


title: VV1547_SSL2_WT_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:H20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H20.lxb
CRCGN008_HEPG2_24H_X3_B29_H20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:I12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_I12.lxb
CRCGN008_HEPG2_24H_X3_B29_I12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H17.lxb
CRCGN008_HEPG2_24H_X3_B29_H17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H16.lxb
CRCGN008_HEPG2_24H_X3_B29_H16.lxb
Broad Institute Human L1000 epsilon


title: VV1419_SSL2_WT_TSS-seq_bioreplicate_1


title: VV1558_SSL2_WT_TSS-seq_bioreplicate_1


title: CRCGN008_HEPG2_24H:H18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H18.lxb
CRCGN008_HEPG2_24H_X3_B29_H18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H22.lxb
CRCGN008_HEPG2_24H_X3_B29_H22.lxb
Broad Institute Human L1000 epsilon


title: org_2

source_name: cirrhotic liver organoid

value: cirrhotic liver organoid

value: cultured in high wnt organoid media

value: Alcoholic Steatohepatitis

value: 61 year

value: Male


title: org_1

value: 63 year


title: VV1420_SSL2_WT_TSS-seq_bioreplicate_2


title: cirrho_YAC_1

source_name: cirrhotic liver cells

value: cirrhotic liver cells

value: cultured in YAC


title: CRCGN008_HEPG2_24H:H15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H15.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H13.lxb
CRCGN008_HEPG2_24H_X3_B29_H13.lxb
Broad Institute Human L1000 epsilon


title: org_3

value: End stage liver disease

value: 62 year

value: Female


title: cirrho_LiM_1

value: cultured in LiM


title: Donor 2_CD73- memory CD4 T cells (RNAseq)

city: Palo Alto

first: Fengqin

last: Fang

state: CA

address: 3801 Miranda Avenue

department: Rheumatology&Immunology

institute: Stanford University

description: total RNA with ribosomal RNA depleted

data_processing:
Sequencing reads were mapped to human genome hg19 using STAR (Alexander Dobin 2013).
RPKM values were called using HOMER (http://homer.salk.edu/homer/motif/) analyzeRepeats.pl program.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM text file

source_name: Peripheral blood

growth_protocol: Directly sorted from human peripheral blood

extract_protocol:
RNA extraction was performed using RNeasy Plus (Qiagen) from the samples reported in this research. Ribosomal RNA was removed from each RNA extraction using Ribo-Zero Gold rRNA Removal kit (Illumina).
The RNA-seq libraries were constructed by TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: no treatment

value: Resting memory CD4 T cells

tag: cell subset

value: no treatment

tag: disease state

value: Healthy donor


title: cirrho_YAC_3


title: CRCGN008_HEPG2_24H:H14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H14.lxb
CRCGN008_HEPG2_24H_X3_B29_H14.lxb
Broad Institute Human L1000 epsilon


title: Donor 3_CD73+ memory CD4 T cells (RNAseq)

description: total RNA with ribosomal RNA depleted


title: cirrho_LiM_4


title: CRCGN008_HEPG2_24H:H11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H11.lxb
CRCGN008_HEPG2_24H_X3_B29_H11.lxb
Broad Institute Human L1000 epsilon


title: cirrho_LiM_3


title: CRCGN008_HEPG2_24H:H06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H06.lxb
CRCGN008_HEPG2_24H_X3_B29_H06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H05.lxb
CRCGN008_HEPG2_24H_X3_B29_H05.lxb
Broad Institute Human L1000 epsilon


title: cirrho_YAC_2


title: cirrho_LiM_2


title: CRCGN008_HEPG2_24H:H12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H12.lxb
CRCGN008_HEPG2_24H_X3_B29_H12.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H09.lxb
CRCGN008_HEPG2_24H_X3_B29_H09.lxb
Broad Institute Human L1000 epsilon


title: Donor 1_CD73+ memory CD4 T cells (RNAseq)

description: total RNA with ribosomal RNA depleted


title: CRCGN008_HEPG2_24H:H08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H08.lxb
CRCGN008_HEPG2_24H_X3_B29_H08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H10.lxb
CRCGN008_HEPG2_24H_X3_B29_H10.lxb
Broad Institute Human L1000 epsilon


title: Donor 2_CD73- memory CD4 T cells (ATACseq)

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie2, duplicate fragments were then removed using Picard.
peaks alled using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files

extract_protocol:
Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.


title: Donor 1_CD73- memory CD4 T cells (RNAseq)

description: total RNA with ribosomal RNA depleted


title: CRCGN008_HEPG2_24H:G24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G24.lxb
CRCGN008_HEPG2_24H_X3_B29_G24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H03.lxb
CRCGN008_HEPG2_24H_X3_B29_H03.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H07.lxb
CRCGN008_HEPG2_24H_X3_B29_H07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H04.lxb
CRCGN008_HEPG2_24H_X3_B29_H04.lxb
Broad Institute Human L1000 epsilon


title: Donor 2_CD73+ memory CD4 T cells (RNAseq)

description: total RNA with ribosomal RNA depleted


title: CRCGN008_HEPG2_24H:H02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H02.lxb
CRCGN008_HEPG2_24H_X3_B29_H02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:G22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G22.lxb
CRCGN008_HEPG2_24H_X3_B29_G22.lxb
Broad Institute Human L1000 epsilon


title: Donor 3_CD73- memory CD4 T cells (ATACseq)


title: Donor 3_CD73- memory CD4 T cells (RNAseq)

description: total RNA with ribosomal RNA depleted


title: Donor 3_CD73+ memory CD4 T cells (ATACseq)


title: CRCGN008_HEPG2_24H:G20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G20.lxb
CRCGN008_HEPG2_24H_X3_B29_G20.lxb
Broad Institute Human L1000 epsilon


title: Donor 1_CD73- memory CD4 T cells (ATACseq)


title: kpn_IMP1

city: Kunming

first: Yanbing

last: Ma

state: Yunnan

address: NO.935 Jiaoling Road

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Novel gene and gene structure analysing: Rockhopper was used to identify novel genes, operon, TSS, TTS and Cis-natural antisense transcripts. It can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can aid with elucidation of bacterial transcriptomes. Then, we extract upstream 700bp sequence of Transcription Start Site for predicting promoter using TDNN.(Time-DelayNeural Network);   Predict UTR: According to the information of Transcription Start Site(Transcription terminal Site) and Translation start site(Translation terminal site), we extracted 5’UTR(3’UTR) sequences. Then, RBSfinder and TransTermH were used to predict SD sequence and terminator sequence respectively.  Analysis of sRNA:  Rockhopper was used to identify new intergenic region transcripts, and Blastx was compared with the nr library to annotate the newly predicted transgenic regions, and the unmarked transcripts were used as candidate non-coding sRNAs. RNA fold and Inta RNA were used to predict secondary structure and target gene respectively.
Quantification of gene expression level: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels .
Genome_build: Klebsiella pneumoniae reference genome
Supplementary_files_format_and_content: gene_fpkm.txt includes FPKM values for each Sample

organism: Klebsiella pneumoniae

growth_protocol: Klebsiella pneumoniae strain (kpn0507) was cultured and amplified in lysogeny broth (LB) medium at 37°C for 5 hours

extract_protocol:
RNA was extracted by RNAprep Pure Bacteria Kit (TIANGEN BIOTECH, BEIJING, Cat#DP430)
Total RNA was used as input material for the RNA sample preparations. mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U, In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: kpn1,kpn2 and kpn3 were treated with PBS, kpn_IMP1, kpn_IMP2 and kpn_IMP3 were treated with Imipenem.

value: imipenem


title: CRCGN008_HEPG2_24H:G06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G06.lxb
CRCGN008_HEPG2_24H_X3_B29_G06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:G21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G21.lxb
CRCGN008_HEPG2_24H_X3_B29_G21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:G23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G23.lxb
CRCGN008_HEPG2_24H_X3_B29_G23.lxb
Broad Institute Human L1000 epsilon


title: kpn_IMP2


title: kpn_IMP3


title: CRCGN008_HEPG2_24H:G05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G05.lxb
CRCGN008_HEPG2_24H_X3_B29_G05.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:H01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_H01.lxb
CRCGN008_HEPG2_24H_X3_B29_H01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:G04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G04.lxb
CRCGN008_HEPG2_24H_X3_B29_G04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:G19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G19.lxb
CRCGN008_HEPG2_24H_X3_B29_G19.lxb
Broad Institute Human L1000 epsilon


title: kpn3

value: control


title: kpn1


title: Donor 1_CD73+ memory CD4 T cells (ATACseq)


title: kpn2


title: CRCGN008_HEPG2_24H:G03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G03.lxb
CRCGN008_HEPG2_24H_X3_B29_G03.lxb
Broad Institute Human L1000 epsilon


title: mouse_MeCP2_T158M_RNA-seq_rep3

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

data_processing:
We cleaned the paired-end reads by Trimimomatic (version 0.36). After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
The genome sequence and gene annotation of human (GRCh38) and mouse (GRCm38) were downloaded from GENCODE. Cleaned reads were mapped to the genome sequence by HISAT (version 2.1.0) with default parameters. Number of reads that were mapped to each gene was calculated with the htseq-count script in HTSeq (version 0.9.1)
EdgeR was used to identify genes that were differentially expressed between control and experiment samples. Genes with at least two-fold change in expression and had a FDR < 0.05 were considered differentially expressed genes (DEGs).
The barcode regions in the iCLIP reads are filtered by FASTX-Toolkit.The demultiplexing and adapter trimming are performed by Flexbar. Only trimmed reads with at least 15 nt are kept for further analysis.
The individual FASTQ files for each sample are mapped to human reference genome (GRCh38) by STAR. The technical duplicates are removed using UMI-tools.
After deduplication, the crosslink events are transformed from the mapped reads by extracting the position upstream of the 5’end of the reads with BEDTools.
The crosslink sites with significantly enriched crosslink events are identified by PureCLIP and post-processed by custom scripts.
Genome_build: human (GRCh38) and mouse (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, log2Fold change and FDR for each gene.
Supplementary_files_format_and_content: bed files include the chromosome, start/end position and strand of each binding site.
Supplementary_files_format_and_content: bigWig files were generated by bedtools and bedGraphToBigWig, the scores represent the read coverage on the genome.

source_name: mouse cerebral cortex

growth_protocol: HEK293T cells were maintained in Dulbecco's Modified Eagle's medium supplemented with 10% fetal bovine serum.

extract_protocol:
For RNA-seq, total RNAs were isolated using TRIzol (Invitrogen, USA).
RNA-seq libraries were prepared according to the manufacturer’s instructions (Illumina). iCLIP-seq libraries were prepared as previously described (Buchbender et al., Methods, 2019).

treatment_protocol: Mouse cerebral cortex tissues were obtained from 6-week-old male mice.

value: MeCP2 T158M

value: mouse cerebral cortex


title: CRCGN008_HEPG2_24H:F23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F23.lxb
CRCGN008_HEPG2_24H_X3_B29_F23.lxb
Broad Institute Human L1000 epsilon