title: extranodal NKTL,NKTL43,FFPE Preparation

type: genomic

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL43

hyb_protocol: MIP probe annealing and hybridization to Affymetrix OncoScanCNV Arrays was performed according to manufacturer's protocols.

scan_protocol: Arrays were hybridized, washed, and stained in Affymetrix fluidics station according to manufacturer's protocols. Arrays were scanned using the Affymetrix 3000 7G scanner according to manufacturer's protocols.

data_processing:
Data is processed using Affymetrix OncoScan Console (v1.3) software.
Processed data files includes: Median Log2 Ratio
Median Log2 Ratio: log2 ratio of the normalized intensity of the sample over the normalized intensity of a reference with further correction for sample specific variation.
The reference for calculating log2 normalized intensity ratio is normal diploid  markers identified in the cancer samples. This normal diploid region is the region without any copy number gain and loss in the cancer samples, and it can be identified automatically or manually in the software (oncoscan console,v1.3).

source_name: Tumor

label_protocol: Each of the DNA samples were annealed with MIP (Molecular Inversion Probe) linear probe according to the Affymetrix OncoScanCNV protocol.

extract_protocol: Total DNA from FFPE tissue samples were extracted by using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Invitrogen™.

tag: disease

tag: type

value: AT

value: GC


title: gene_expression_MD10

status: Public on Nov 27 2021

type: RNA

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level  3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

description: Gene expression data from Homo sapiens extranodal NKTL sample

hyb_protocol: cRNA samples were hybridized for 16 hr on GeneChip® Clariom D Assay (Human) Array according to the manufacturer's instruction. GeneChips were washed and stained in using the FS450_0001 fluidics protocol.

scan_protocol: Arrays were scanned using an Affymetrix 3000 7G scanner.

data_processing: Gene expression data were normalized with the robust multi-array average (RMA) algorithm through the “oligo” package (1.48.0) in R (ver 3.6)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: extranodal NKTL,MD10,FFPE Preparation

label_protocol: Sample labeling was performed using GeneChip® Clariom D Assay (Human) Array according to the manufacturer's instruction.

extract_protocol: Total RNA from FFPE tissue samples were extracted by using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Invitrogen™.

treatment_protocol: Tissues were formalin fixed and embeded in paraffin to make FFPE tissue samples.

tag: tissue

value: extranodal NKTL

tag: tissue preparation

value: FFPE


title: gene_expression_NKTL50

description: Gene expression data from Homo sapiens EBV+ PTCL (nodal TNKL) sample

source_name: EBV+ PTCL (nodal TNKL),NKTL50,FFPE Preparation

value: EBV+ PTCL (nodal TNKL)


title: gene_expression_PTCL25

description: Gene expression data from Homo sapiens PTCL NOS sample

source_name: PTCL NOS,PTCL25,FFPE Preparation

value: PTCL NOS


title: extranodal NKTL,NKTL41,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL41

molecule: genomic DNA


title: gene_expression_LN Control 5

description: Gene expression data from Homo sapiens LN control sample

source_name: LN control,LN Control 5,FFPE Preparation

value: normal lymph node


title: gene_expression_K2

source_name: EBV+ PTCL (nodal TNKL),K2,FFPE Preparation


title: gene_expression_TW42

source_name: PTCL NOS,TW42,FFPE Preparation


title: gene_expression_NKTL65

source_name: EBV+ PTCL (nodal TNKL),NKTL65,FFPE Preparation


title: gene_expression_T242

source_name: EBV+ PTCL (nodal TNKL),T242,FFPE Preparation


title: gene_expression_NKTL59

source_name: EBV+ PTCL (nodal TNKL),NKTL59,FFPE Preparation


title: Individual #12, 1000 nM 25D, rep1

type: SRA

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
Doseresponse_Individual12_Vit25D3_24h_1000nM_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH28

library_source: transcriptomic

data_processing:
Read alignment and quantification via nf-core/rnaseq STAR-Salmon pipeline 3.0 (http://doi.org/10.5281/zenodo.4323183)
Read counts normalization via EdgeR 3.21.1 (TMM)
Differential gene expression analysis via EdgeR 3.21.1
Genome_build: hg38, Ensembl annotation version 103
Supplementary_files_format_and_content: Excel tables of normalized read counts and statistical metrics

source_name: Individual #12_1000 nM 25D_PBMC

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: treatment for 24 h with either 100 nM, 250 nM, 1000 nM, 10.000 nM 25(OH)D3 (Sigma-Aldrich), 250 nM D3 (Sigma-Aldrich) or solvent (0.1% EtOH)

tag: subject id

value: Individual #12

value: peripheral blood mononuclear cells (PBMC)

tag: treatment


title: gene_expression_TNK03

source_name: EBV+ PTCL (nodal TNKL),TNK03,FFPE Preparation


title: gene_expression_T241

source_name: extranodal NKTL,T241,FFPE Preparation


title: gene_expression_HKU-PTCL19

source_name: PTCL NOS,HKU-PTCL19,FFPE Preparation


title: Individual #12, 100 nM 25D, rep1

description:
Doseresponse_Individual12_Vit25D3_24h_100nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH31

source_name: Individual #12_100 nM 25D_PBMC


title: extranodal NKTL,NKTL36,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL36


title: Individual #12, 100 nM 25D, rep3

description:
Doseresponse_Individual12_Vit25D3_24h_100nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH33


title: extranodal NKTL,NKTL32A,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL32A


title: gene_expression_MD05

source_name: extranodal NKTL,MD05,FFPE Preparation


title: gene_expression_NKTL41

source_name: extranodal NKTL,NKTL41,FFPE Preparation


title: gene_expression_NKTL53

source_name: extranodal NKTL,NKTL53,FFPE Preparation


title: Individual #12, 100 nM 25D, rep2

description:
Doseresponse_Individual12_Vit25D3_24h_100nM_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH32


title: extranodal NKTL,NKTL27B,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL27B

source_name: Tumor


title: extranodal NKTL,NKTL23B,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL23B


title: gene_expression_TW39

source_name: extranodal NKTL,TW39,FFPE Preparation


title: extranodal NKTL,NKTL22,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL22


title: gene_expression_T114

source_name: EBV+ PTCL (nodal TNKL),T114,FFPE Preparation


title: gene_expression_LN Control 4

source_name: LN control,LN Control 4,FFPE Preparation


title: gene_expression_PTCL09

source_name: PTCL NOS,PTCL09,FFPE Preparation


title: gene_expression_PTCL11

source_name: PTCL NOS,PTCL11,FFPE Preparation


title: gene_expression_HKU-PTCL08

source_name: EBV+ PTCL (nodal TNKL),HKU-PTCL08,FFPE Preparation


title: Individual #09, 250 nM 25D, rep2

description:
VitDHiD_Individual09_Vit25D3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual9-Vit25D3-rep2

source_name: Individual #09_250 nM 25D_PBMC

value: Individual #09


title: extranodal NKTL,NKTL25,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL25


title: gene_expression_TW37

source_name: extranodal NKTL,TW37,FFPE Preparation


title: Individual #09, 250 nM D3, rep3

description:
VitDHiD_Individual09_VitD3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual9-VitD3-rep3

source_name: Individual #09_250 nM D3_PBMC

value: 250 nM D3 for 24 h


title: extranodal NKTL,NKTL24,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL24


title: Individual #09, 250 nM D3, rep1

description:
VitDHiD_Individual09_VitD3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual9-VitD3-rep1


title: extranodal NKTL,T241,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
T241


title: Individual #09, 250 nM 25D, rep3

description:
VitDHiD_Individual09_Vit25D3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual9-Vit25D3-rep3


title: Individual #09, 250 nM D3, rep2

description:
VitDHiD_Individual09_VitD3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual9-VitD3-rep2


title: extranodal NKTL,T25,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
T25


title: extranodal NKTL,NKTL16A,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL16A


title: Individual #05, EtOH, rep3

description:
Doseresponse_Individual05_EtOH_24h_0.1pct_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH24

source_name: Individual #05_EtOH_PBMC

value: Individual #05

value: 0.1% ethanol for 24 h


title: Individual #09, 250 nM 25D, rep1

description:
VitDHiD_Individual09_Vit25D3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual9-Vit25D3-rep1


title: gene_expression_A1

description: Gene expression data from Homo sapiens EBV+ PTCL (nodal TNKL) sample

source_name: EBV+ PTCL (nodal TNKL),A1,FFPE Preparation


title: gene_expression_NKTL43

description: Gene expression data from Homo sapiens extranodal NKTL sample

source_name: extranodal NKTL,NKTL43,FFPE Preparation


title: extranodal NKTL,T202,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
T202


title: gene_expression_PTCL17

description: Gene expression data from Homo sapiens PTCL NOS sample

source_name: PTCL NOS,PTCL17,FFPE Preparation


title: gene_expression_TW26

source_name: extranodal NKTL,TW26,FFPE Preparation


title: Individual #05, EtOH, rep2

description:
Doseresponse_Individual05_EtOH_24h_0.1pct_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH23


title: EBV+ PTCL (nodal TNKL),T242,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
T242


title: gene_expression_PTCL07

source_name: PTCL NOS,PTCL07,FFPE Preparation


title: gene_expression_PTCL18B

source_name: PTCL NOS,PTCL18B,FFPE Preparation


title: gene_expression_T202

source_name: extranodal NKTL,T202,FFPE Preparation


title: gene_expression_PTCL12A

source_name: PTCL NOS,PTCL12A,FFPE Preparation


title: gene_expression_TNK02

source_name: EBV+ PTCL (nodal TNKL),TNK02,FFPE Preparation


title: Individual #05, 250 nM D3, rep2

description:
VitDHiD_Individual05_VitD3_24h_250nM_Jan-Feb2019
HF257BGXC_1-1_19s003936-1-1_Carlberg_lane1-Individual5-VitD3-rep2

source_name: Individual #05_250 nM D3_PBMC


title: gene_expression_HKU-PTCL24

source_name: PTCL NOS,HKU-PTCL24,FFPE Preparation


title: gene_expression_PTCL22

source_name: PTCL NOS,PTCL22,FFPE Preparation


title: Individual #05, 250 nM D3, rep3

description:
VitDHiD_Individual05_VitD3_24h_250nM_Jan-Feb2019
HF257BGXC_1-1_19s003936-1-1_Carlberg_lane1-Individual5-VitD3-rep3


title: EBV+ PTCL (nodal TNKL),T114,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
T114

source_name: Tumor


title: gene_expression_PTCL06

source_name: PTCL NOS,PTCL06,FFPE Preparation


title: gene_expression_HKU-PTCL22

source_name: PTCL NOS,HKU-PTCL22,FFPE Preparation


title: gene_expression_MD15

source_name: extranodal NKTL,MD15,FFPE Preparation


title: gene_expression_NKTL52

source_name: extranodal NKTL,NKTL52,FFPE Preparation


title: EBV+ PTCL (nodal TNKL),A1,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
A1


title: extranodal NKTL,MD15,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
MD15


title: Individual #05, 250 nM D3, rep1

description:
VitDHiD_Individual05_VitD3_24h_250nM_Jan-Feb2019
HF257BGXC_1-1_19s003936-1-1_Carlberg_lane1-Individual5-VitD3-rep1


title: gene_expression_T72

source_name: extranodal NKTL,T72,FFPE Preparation


title: gene_expression_HKU-PTCL20

source_name: PTCL NOS,HKU-PTCL20,FFPE Preparation


title: gene_expression_LN Control 3

description: Gene expression data from Homo sapiens LN control sample

source_name: LN control,LN Control 3,FFPE Preparation


title: Individual #05, 250 nM 25D, rep2

description:
VitDHiD_Individual05_Vit25D3_24h_250nM_Jan-Feb2019
HF257BGXC_1-1_19s003936-1-1_Carlberg_lane1-Individual5-Vit25D3-rep2

source_name: Individual #05_250 nM 25D_PBMC


title: extranodal NKTL,MD10,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
MD10


title: Individual #05, 250 nM 25D, rep3

description:
VitDHiD_Individual05_Vit25D3_24h_250nM_Jan-Feb2019
HF257BGXC_1-1_19s003936-1-1_Carlberg_lane1-Individual5-Vit25D3-rep3


title: gene_expression_NKTL78A

source_name: EBV+ PTCL (nodal TNKL),NKTL78A,FFPE Preparation


title: extranodal NKTL,MD05,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
MD05


title: extranodal NKTL,MD04,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
MD04


title: Individual #05, EtOH, rep1

description:
Doseresponse_Individual05_EtOH_24h_0.1pct_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH22

source_name: Individual #05_EtOH_PBMC


title: Individual #05, 10000 nM 25D, rep2

description:
Doseresponse_Individual05_Vit25D3_24h_10000nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH14

source_name: Individual #05_10000 nM 25D_PBMC


title: gene_expression_TNK05

description: Gene expression data from Homo sapiens EBV+ PTCL (nodal TNKL) sample

source_name: EBV+ PTCL (nodal TNKL),TNK05,FFPE Preparation


title: extranodal NKTL,TW39,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW39


title: Individual #05, 10000 nM 25D, rep3

description:
Doseresponse_Individual05_Vit25D3_24h_10000nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH15


title: Individual #05, 10000 nM 25D, rep1

description:
Doseresponse_Individual05_Vit25D3_24h_10000nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH13


title: Individual #05, 250 nM 25D, rep1

description:
VitDHiD_Individual05_Vit25D3_24h_250nM_Jan-Feb2019
HF257BGXC_1-1_19s003936-1-1_Carlberg_lane1-Individual5-Vit25D3-rep1


title: gene_expression_HKU-PTCL26

source_name: EBV+ PTCL (nodal TNKL),HKU-PTCL26,FFPE Preparation


title: gene_expression_TW22

description: Gene expression data from Homo sapiens extranodal NKTL sample

source_name: extranodal NKTL,TW22,FFPE Preparation


title: extranodal NKTL,TW38,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW38


title: gene_expression_PTCL21

description: Gene expression data from Homo sapiens PTCL NOS sample

source_name: PTCL NOS,PTCL21,FFPE Preparation


title: gene_expression_T85

source_name: EBV+ PTCL (nodal TNKL),T85,FFPE Preparation


title: gene_expression_TW13

source_name: extranodal NKTL,TW13,FFPE Preparation


title: gene_expression_PTCL19

source_name: PTCL NOS,PTCL19,FFPE Preparation


title: gene_expression_HKU-PTCL17

source_name: PTCL NOS,HKU-PTCL17,FFPE Preparation


title: gene_expression_HKU-PTCL07

source_name: PTCL NOS,HKU-PTCL07,FFPE Preparation


title: Individual #05, 1000 nM 25D, rep3

description:
Doseresponse_Individual05_Vit25D3_24h_1000nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH18

source_name: Individual #05_1000 nM 25D_PBMC


title: gene_expression_TW40

source_name: extranodal NKTL,TW40,FFPE Preparation


title: gene_expression_TNK09

source_name: EBV+ PTCL (nodal TNKL),TNK09,FFPE Preparation


title: gene_expression_TW33

source_name: extranodal NKTL,TW33,FFPE Preparation


title: gene_expression_TW34

source_name: extranodal NKTL,TW34,FFPE Preparation


title: gene_expression_NKTL24

source_name: extranodal NKTL,NKTL24,FFPE Preparation


title: extranodal NKTL,TW37,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW37

source_name: Tumor


title: extranodal NKTL,TW34,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW34


title: extranodal NKTL,TW29,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW29


title: extranodal NKTL,TW27,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW27


title: gene_expression_TW29

source_name: extranodal NKTL,TW29,FFPE Preparation


title: Individual #05, 100 nM 25D, rep3

description:
Doseresponse_Individual05_Vit25D3_24h_100nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH21

source_name: Individual #05_100 nM 25D_PBMC


title: gene_expression_TW07

source_name: extranodal NKTL,TW07,FFPE Preparation


title: gene_expression_HKU-PTCL29

source_name: PTCL NOS,HKU-PTCL29,FFPE Preparation


title: Individual #05, 1000 nM 25D, rep2

description:
Doseresponse_Individual05_Vit25D3_24h_1000nM_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH12


title: extranodal NKTL,TW33,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW33


title: GFP-MAB21L1  mutant form GFP-Arg51Gln replicate 2 with treatment of tetracycline for 12 hrs

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

description: GFP-Arg51Gln_Tet ON_2

data_processing:
Transcript-level quantitation was performed using Salmon (v0.8.2) against the GRCh38 Ensembl reference transcriptome (release-89)
Transcript-level counts were summarized to gene level using the bioconductor package tximport (v1.4.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: txi_counts.csv summarized gene level counts generated from tximport

source_name: HEK 293

extract_protocol:
Tetracycline for 12 hours
Total RNA extracted from two biological replicates of each cell line after 12 hrs of 1 μg/ml tetracycline treatment using the RNeasy kit (QIAGEN).
Random primed cDNA from poly(A) selected RNA was converted into an Illumina sequencing library using RNA Library Prep Kit from Illumina (E7420, NEB, USA) in conjunction with NEBNext® Multiplex Oligos for Illumina (E7335/E7500, NEB, USA).
Single-end 50-base pair (bp) reads were generated using a NextSeq 500 (Illumina Inc, SY-415-1002)

treatment_protocol: Cells were cultured  in DMEM (modified Eagle’s medium; DMEM) supplemented with 10% fetal bovine serum, 5% Lglutamine,5% penicillin/streptomycin antibiotics and 5 μg/ml blasticidin and 400 μg/ml hygromycin in 5% CO2 and normoxic conditions.

value: Tetracyline

tag: genotype

tag: tag

value: GFP


title: Individual #05, 1000 nM 25D, rep1

description:
Doseresponse_Individual05_Vit25D3_24h_1000nM_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH16


title: gene_expression_PTCL10A

source_name: PTCL NOS,PTCL10A,FFPE Preparation


title: extranodal NKTL,NKTL52,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL52


title: PTCL NOS,PTCL25,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL25


title: extranodal NKTL,NKTL13,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL13


title: PTCL NOS,PTCL22,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL22


title: Individual #05, 100 nM 25D, rep1

description:
Doseresponse_Individual05_Vit25D3_24h_100nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH17


title: Individual #05, 100 nM 25D, rep2

description:
Doseresponse_Individual05_Vit25D3_24h_100nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH20


title: extranodal NKTL,TW26,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW26


title: PTCL NOS,PTCL18B,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL18B


title: EBV+ PTCL (nodal TNKL),NKTL50,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL50


title: PTCL NOS,TW42,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
TW42


title: EBV+ PTCL (nodal TNKL),NKTL78A,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
NKTL78A


title: PTCL NOS,PTCL17,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL17


title: EBV+ PTCL (nodal TNKL),TNK10,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
TNK10


title: GFP-MAB21L1  mutant form GFP-Arg51Gln replicate 1 with treatment of tetracycline for 12 hrs

description: GFP-Arg51Gln_Tet ON_1


title: gene_expression_MD04

description: Gene expression data from Homo sapiens extranodal NKTL sample

source_name: extranodal NKTL,MD04,FFPE Preparation


title: EBV+ PTCL (nodal TNKL),TNK9,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
TNK9


title: gene_expression_PTCL15

description: Gene expression data from Homo sapiens PTCL NOS sample

source_name: PTCL NOS,PTCL15,FFPE Preparation


title: gene_expression_HKU-PTCL12

source_name: PTCL NOS,HKU-PTCL12,FFPE Preparation


title: gene_expression_NKTL13

source_name: extranodal NKTL,NKTL13,FFPE Preparation


title: PTCL NOS,PTCL15,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL15


title: PTCL NOS,PTCL21,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL21


title: gene_expression_NKTL32A


title: extranodal NKTL,MD11,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
MD11


title: GFP-MAB21L1  mutant form GFP-Arg51Leu replicate 1 with treatment of tetracycline for 12 hrs

description: GFP-Arg51Leu_Tet ON_1


title: Wild type GFP-MAB21L1 replicate 2 with treatment of tetracycline for 12 hrs

description: GFP-MAB21L1_Tet ON_2

value: WT


title: GFP-MAB21L1  mutant form GFP-Arg51Leu replicate 2 with treatment of tetracycline for 12 hrs

description: GFP-Arg51Leu_Tet ON_2


title: gene_expression_TW23

description: Gene expression data from Homo sapiens EBV+ PTCL (nodal TNKL) sample

source_name: EBV+ PTCL (nodal TNKL),TW23,FFPE Preparation


title: EBV+ PTCL (nodal TNKL),TNK6,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
TNK6


title: PTCL NOS,PTCL13A,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL13A


title: PTCL NOS,PTCL12A,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL12A


title: Wild type GFP-MAB21L1 replicate 1 with treatment of tetracycline for 12 hrs

description: GFP-MAB21L1_Tet ON_1


title: PTCL NOS,PTCL9,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL9


title: GFP-MAB21L1  mutant form GFP-Arg51Gln replicate 2 without treatment of tetracycline for 12 hrs

description: GFP-Arg51Gln_Tet OFF_2


title: EBV+ PTCL (nodal TNKL),TNK3,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
TNK3


title: gene_expression_PTCL24

source_name: PTCL NOS,PTCL24,FFPE Preparation


title: PTCL NOS,PTCL7,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL7


title: PTCL NOS,PTCL6,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL6


title: PTCL NOS,PTCL3,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL3


title: GFP-MAB21L1  mutant form GFP-Arg51Gln replicate 1 without treatment of tetracycline for 12 hrs

description: GFP-Arg51Gln_Tet OFF_1


title: PTCL NOS,PTCL10A,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL10A


title: PTCL NOS,HKU-PTCL-29,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-29


title: GFP-MAB21L1  mutant form GFP-Arg51Leu replicate 2 without treatment of tetracycline for 12 hrs

description: GFP-Arg51Leu_Tet OFF_2


title: Wild type GFP-MAB21L1 replicate 2 without treatment of tetracycline for 12 hrs

description: GFP-MAB21L1_Tet OFF_2


title: EBV+ PTCL (nodal TNKL),HKU-PTCL-26,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-26


title: PTCL NOS,HKU-PTCL-27,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-27


title: PTCL NOS,PTCL1,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL1


title: gene_expression_TW27

description: Gene expression data from Homo sapiens extranodal NKTL sample

source_name: extranodal NKTL,TW27,FFPE Preparation


title: EBV+ PTCL (nodal TNKL),TNK1,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
TNK1


title: gene_expression_TW38

source_name: extranodal NKTL,TW38,FFPE Preparation


title: GFP-MAB21L1  mutant form GFP-Arg51Leu replicate 1 without treatment of tetracycline for 12 hrs

description: GFP-Arg51Leu_Tet OFF_1


title: gene_expression_T25

source_name: extranodal NKTL,T25,FFPE Preparation


title: extranodal NKTL,TW22,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW22


title: gene_expression_TW35

source_name: extranodal NKTL,TW35,FFPE Preparation


title: extranodal NKTL,TW13,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW13

source_name: Tumor


title: EBV+ PTCL (nodal TNKL),TNK4,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
TNK4


title: Wild type GFP-MAB21L1 replicate 1 without treatment of tetracycline for 12 hrs

description: GFP-MAB21L1_Tet OFF_1


title: PTCL NOS,HKU-PTCL-22,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-22


title: extranodal NKTL,TW7,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
TW7


title: PTCL NOS,HKU-PTCL-21,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-21


title: EBV+ PTCL (nodal TNKL),NKTL59,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL59


title: PTCL NOS,HKU-PTCL-20,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-20


title: extranodal NKTL,NKTL60,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL60


title: EBV+ PTCL (nodal TNKL),NKTL40,FFPE Preparation

description:
Genomic copy number data from Homo sapiens EBV+ PTCL (nodal TNKL) samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL40


title: NoT_2

city: Dallas

first: Jennifer

last: Kohler

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: UT Southwestern

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Fastq files were mapped to human genome using STAR(v2.5.3a)
Read counts were generated using featureCounts (subread)
Differential expression was performed using edgeR
Normalized read counts generated using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files that includes normalized read counts for each sample per gene

source_name: Differentiated Caco-2 BBe1 cells

growth_protocol: Caco-2 BBe1 cells used for RNA-seq experiment were seeded at a density of 100,000 cells/well onto 12-mm-diameter Transwell permeable inserts with 0.4 mm pores (Corning and grown in supplemented DMEM for 14 days to achieve full differentiation prior to use.

extract_protocol:
Total RNA from differentiated Caco-2 BBe1 cells was prepared using RNeasy Mini Kit (Qiagen, Hilden, Germany) and contaminating DNA was removed using DNA-free DNA removal kit (ThermoFisher Scientific).
mRNA libraries were prepared using the Illumina TruSeq protocol and sequenced using Illumina NextSeq 500 with read configuration as 76bp, single end. Each sample got approximately 42 million reads. Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4). Fastq files were mapped to hg19 (UCSC version from igenomes) using STAR(v2.5.3a). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR. Genes with reads of log2 counts per million (CPM) > 0 and p-values < 0.05 were considered differentially expressed. Volcano plot was made using EnhancedVolcano.

treatment_protocol: Differentiated Caco-2 BBe1 cells were then placed in serum-free media (supplemented media without HI-FBS for each cell line) for 16-18 hr. Cells were then treated with 10 ng/mL rhIL-22 to the basolateral compartment or incubated in serum-free media for 4 h.

tag: cell line

value: Caco-2 BBe1 cells

value: No Treatment group


title: NoT


title: PTCL NOS,HKU-PTCL-17,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-17

value: AT

value: GC


title: K14-4-1BB (389)_OD_n3

city: Muenster

first: Karin

last: Loser

state: NRW

address: von-Esmarch-Strasse 58

department: Dermatology Experimental Dermatology and Immunobiology of the Skin

country: Germany

institute: University of Muenster

description:
Gene expression data from eye tissue- Onset of disease High copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Onset of disease High copy number K14-4-1BB mice_Loser_15

hyb_protocol: DNA targets were hybridized for 17h at 45°C on GeneChip Mouse Transcriptome Arrays 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol (Affymetrix GeneChip Wash, Stain and Scan Kit, 900720).

scan_protocol: Subsequently, the GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing:
For microarray data analysis, the Applied Biosystem Expression Console and Transcriptome Analysis Console was used. The robust multi-array (RMA) averaging method  was applied for background correction, quantile normalization, and probe summarization.
To obtain the CHP files it was considered also the Exon level-STT expression. CHP files include  both gene- and exon-level data.

label: Biotin

organism: Mus musculus

source_name: Eye tissue-K14-4-1BB (389) - Transgenic mouse with a high copy number of 4-1BB- onset of disease in the eye (4 weeks)

label_protocol: The fragmented and biotinylated DNA targets were prepared according to the standard Applied Biosystem WT PLUS Reagent Kit protocol (Applied Biosystem GeneChip® WT PLUS Reagent Kit, 902280) from 100 ng total RNA starting material and 5.5 µg cDNA intermediate product.

growth_protocol: Mice were sacrificed with CO2 at the age of 5 months (for the C57/BL6 WT control, K14-4-1BB (355), K14-41BB (389) full blown disease ) or at 4 weeks (for the K14-4-1BB (389) onset of disease)

extract_protocol: RNA was extracted from frozen eye samples using affinity chromatographgy columns according to the manufacturer's instructions (Extractme Total RNA Kit; 7BioScience, Hartheim).

treatment_protocol: Eyes were isolated immediately after euthanization of the mice and snap frozen in liquid nitrogen.

value: Eye

tag: age

value: 4 weeks


title: K14-4-1BB (389)_OD_n4

description:
Gene expression data from eye tissue- Onset of disease High copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Onset of disease High copy number K14-4-1BB mice_Loser_16


title: extranodal NKTL,NKTL23A,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL23A

value: FFPE

value: extranodal NKTL


title: K14-4-1BB (389)_OD_n1

description:
Gene expression data from eye tissue- Onset of disease High copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Onset of disease High copy number K14-4-1BB mice_Loser_13


title: IL22_3

value: IL-22 treated group


title: IL22


title: K14-4-1BB (389)_OD_n2

description:
Gene expression data from eye tissue- Onset of disease High copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Onset of disease High copy number K14-4-1BB mice_Loser_14


title: PTCL NOS,HKU-PTCL-12,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-12

value: PTCL NOS


title: IL22_2


title: PTCL NOS,HKU-PTCL-11,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-11


title: K14-4-1BB (389)_FBD_n4

description:
Gene expression data from eye tissue- Full blown disease High copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Full blown disease High copy number K14-4-1BB mice_Loser_12

source_name: Eye tissue-K14-4-1BB (389) - Transgenic mouse with a high copy number of 4-1BB- full blown disease in the eye-5 months

value: 5 months


title: K14-4-1BB (389)_FBD_n3

description:
Gene expression data from eye tissue- Full blown disease High copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Full blown disease High copy number K14-4-1BB mice_Loser_11


title: NoT_3


title: extranodal NKTL,NKTL53,FFPE Preparation

description:
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL53


title: PTCL NOS,TTSH01,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
TTSH01


title: K14-4-1BB (389)_FBD_n2

description:
Gene expression data from eye tissue- Full blown disease High copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Full blown disease High copy number K14-4-1BB mice_Loser_10


title: ino80_21°C_Input_rep2

city: beijing

first: Danhua

last: Jiang

address: No. 1 West Beichen Road, Chaoyang District

country: China

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1.
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2.
Reads were filtered for duplicated reads by using Picard version 2.24.0 MarkDuplicates.
bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to sequencing depth using CPM.
Average ChIP-seq profiles were generated using deepTools utility plotProfile.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.bw, normalized H2A.Z coverage files.

organism: Arabidopsis thaliana

source_name: 7-day-old seedlings

growth_protocol: Seedlings grown at 21°C under short-day conditions for 7 days.

extract_protocol:
Materials were ground with liquid nitrogen into fine powder and fixed with 1% formaldehyde. After nuclei extraction, mononucleosomes were generated with micrococcal nuclease (MNase) (Sigma, N5386) digestion. Immunoprecipitation was performed with an anti-H2A.Z antibody. After antibody incubation, Protein A Dynabeads (Life Technologies,10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification.
Library was prepared with VAHTS universal DNA library prep kit for Illumina (Vazyme, ND607) according to the manufacturer’s instruction.

treatment_protocol: 7-day-old seedlings grown at 21°C under short-day conditions were further grown for an additional hour at 21°C.

tag: ecotype

value: Col

value: seedling

value: 7 days

value: 21oC for 1 hour

tag: chip antibody


title: PTCL NOS,HKU-PTCL-19,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
HKU-PTCL-19


title: PTCL NOS,TTSH02,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
TTSH02


title: gene_expression_TNK01

description: Gene expression data from Homo sapiens EBV+ PTCL (nodal TNKL) sample

source_name: EBV+ PTCL (nodal TNKL),TNK01,FFPE Preparation

value: EBV+ PTCL (nodal TNKL)


title: K14-4-1BB (389)_FBD_n1

description:
Gene expression data from eye tissue- Full blown disease High copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Full blown disease High copy number K14-4-1BB mice_Loser_9


title: ino80_21°C_Input_rep1


title: s25

city: Xi'an

first: Changhao

last: Yang

address: 169 Changlexi Road

institute: Fourth military medical university

description: microRNA expression in human blood of low blood lead group

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: Periperal Blood, Low Blood Lead Level Group

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified using mirVanaTM  PARISTM (Cat#AM1556, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: Fresh peripheral blood was drawn from healthy volunteers in each group, then total RNA was extracted for further analysis.

tag: subject group

value: Low Blood Lead Level

value: whole blood


title: K14-4-1BB (355)_n3

description:
Gene expression data from eye tissue- Low copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Low copy number K14-4-1BB mice_Loser_7

source_name: Eye tissue-K14-4-1BB (355) - Transgenic mouse with a low copy number of 4-1BB-5 months


title: PTCL NOS,PTCL16B,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL16B


title: PTCL NOS,PTCL11,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL11


title: K14-4-1BB (355)_n2

description:
Gene expression data from eye tissue- Low copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Low copy number K14-4-1BB mice_Loser_6


title: Col_21°C_Input_rep1

value: wild type


title: s75

description: microRNA expression in human blood of high blood lead group

source_name: Periperal Blood, High Blood Lead Level Group

value: High Blood Lead Level


title: MCF-7 cells, B2_G1_100 nM treated

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

data_processing:
Quality Control Check:  FastQC (It analyzes fastq data and check whether data has any problems before doing any further analysis.)
Data Trimming Steps:  fastp (It trims the adapters and low quality reads from the fastq files.)
Quality Control Check:  FastQC (Re-assess the filtered reads prior to successive mapping.)
Read Alignment:  HISAT2 (Mapping the reads against the reference genome file.)
Genome Build:  Ensemble Homo sapiens GRCh38 genome ()
Sam to Bam Conversion:  Samtools (The mapped output files (sam files) were converted into binary files (bam files).)
Quantification of Reads:  featureCounts (Quantification of mapped reads.)
Differential Gene Expression Analysis:  DESeq2 (It was carried out on count data for normalization, visualization and differential gene expression analysis.)
Genome_build: Homo sapiens GRCh38 (gtf)
Supplementary_files_format_and_content: Excel file includes read count values

source_name: MCF-7 cells, G1_100 nM treated

growth_protocol: MCF-7 cells were grown in a humidified chamber maintained at 37⁰C and 5% CO2. The growth medium was Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% FBS (heat-inactivated) and 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Total RNA was isolated using RNA extraction reagent prepared in-house.
Standard library preparation

treatment_protocol: 0.2 million MCF-7 cells were seeded in 35mm dishes. After 48 hours of seeding, the cells were washed with DPBS and treated with 100 nM or 1 μM concentration of G1. The control group was treated with 0.1% of ethanol. After 48 hours of treatment, the cells were washed with DPBS to remove the debris.

value: Treated with 100 nM G1 for 48 hours

tag: cell type

value: Breast cancer cells

value: Wild type


title: ino80_21°C_H2A.Z_rep2

value: anti-H2A.Z antibody


title: MCF-7 cells, C4_G1_1 μM treated

source_name: MCF-7 cells, G1_1 uM treated

value: Treated with 1 uM G1 for 48 hours


title: MCF-7 cells, B3_G1_100 nM treated


title: MCF-7 cells, C1_G1_1 μM treated


title: K14-4-1BB (355)_n1

description:
Gene expression data from eye tissue- Low copy number K14-4-1BB mice
Eye_Gene expression data from eye tissue- Low copy number K14-4-1BB mice_Loser_5

value: Eye


title: MCF-7 cells, C2_G1_1 μM treated


title: ino80_21°C_H2A.Z_rep1


title: PTCL NOS,PTCL19,FFPE Preparation

description:
Genomic copy number data from Homo sapiens PTCL NOS samples by Affymetrix OncoScan CNV FFPE Assay
sample name:
PTCL19

value: FFPE

value: PTCL NOS

value: AT

value: GC


title: Fmr1KO 2

city: Athens

first: Oshri

last: Avraham

state: GA

address: 120 Cedar St

department: Cellular Biology

institute: University of Georgia

description: single nuclei

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Quantification and statistical analysis were done with Partek Flow package (https://www.partek.com/partek-flow/).
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: mtx

source_name: DRG

extract_protocol:
Whole DRG’s were dissociated with enzyme mix (Papain, Collagenase) to a single cell suspension, washed in 1X PBS+0.2%BSA solution, passed through a 70-micron cell strainer and FACS sorted using live/dead staining.
single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3′ Gel Bead and Library Kit (10x Genomics). polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform.  Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform (https://www.10xgenomics.com/single-cell/). libraries were then constructed using standard instrutions of the 10x plaform.

tag: strain

value: FVB

value: Dorsal root ganglion

value: 28–30-day old


title: MCF-7 cells, A3_Ethanol treated_Vehicle control

source_name: MCF-7 cells, Ethanol treated

value: Treated with Ethanol for 48 hours


title: C57/BL6_n3

description:
Gene expression data from eye tissue- Wild type control
Eye_Gene expression data from eye tissue- Wild type control_Loser_3

source_name: Eye tissue-C57/BL6 mouse - Wild type control-5 months

value: wildtype

value: 5 months


title: Col_21°C_Input_rep2

value: Col

value: wild type

value: seedling

value: 7 days

value: 21oC for 1 hour


title: Col_21°C_H2A.Z_rep1

value: anti-H2A.Z antibody


title: WT 2

description: single cell


title: MCF-7 cells, A2_Ethanol treated_Vehicle control

value: Breast cancer cells

value: Wild type


title: Col_21°C_H2A.Z_rep2


title: Fmr1KO 1

description: single nuclei


title: C57/BL6_n1

description:
Gene expression data from eye tissue- Wild type control
Eye_Gene expression data from eye tissue- Wild type control_Loser_1

value: Eye


title: C57/BL6_n2

description:
Gene expression data from eye tissue- Wild type control
Eye_Gene expression data from eye tissue- Wild type control_Loser_2


title: MCF-7 cells, A1_Ethanol treated_Vehicle control


title: WT 1

description: single cell


title: tub_rep2

status: Public on Nov 26 2021

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Alignment with BWA
Filtering of duplicated and not valid reads
Differential accessibility analysis, PCA and clustering with DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: BED format, differentially accesible ATACseq peaks

organism: Drosophila melanogaster

source_name: wing imaginal discs

growth_protocol: Flies were allowed to lay eggs on standard fly food for two days.

extract_protocol:
Samples were lysed in Lysis Buffer and Lysates were centrifuged at 500g for 5 minutes at 4ºC to isolate the nuclei.
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

treatment_protocol: Larvae were kept at 17ºC for 7 days and then transfer at 31º for two days before dissection

value: Expressing GFP under the tub-Gal4, tub-Gal80 driver

value: wing imaginal discs


title: tub_rep1


title: Cdk_rep2

value: Expressing Cdk1-RNAi under the tub-Gal4, tub-Gal80 driver


title: KELLY cells, ChIP_input

city: Houston

first: H. Courtney

last: Hodges

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: Input control DNA

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis. Fragments were extended to 200 bp, Reads within coding regions were counted using bedtools.
Bigwig files were created by extending fragments to 200 bp, with intermediate files created using bedtools 2.28.0. All bigWig files are unscaled and require scaling before comparison across samples.
Genome_build: hg38
Supplementary_files_format_and_content: Unscaled bigWig files of genome-wide coverage

source_name: KELLY cells

growth_protocol: KELLY cells were cultured in 10% FBS DMEM medium using standard approaches.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with formaldehyde, and protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were transduced with lentiviral vectors expressing either wild-type IWS1-FLAG (WT), or mutant disrupting TIM3 (M3) and selected using 1 ug/ml puromycin.

value: KELLY cells

tag: marker

value: WT IWS1-FLAG

value: WT

tag: chip antibody vendor

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: fzr_rep1

value: Expressing fzr under the tub-Gal4, tub-Gal80 driver

tag: tissue


title: Cdk_rep1


title: KELLY cells, ChIP_WT_rep1

description: anti-FLAG ChIP in KELLY cells expressing WT IWS1-FLAG

value: Anti-FLAG

value: Millipore Sigma


title: MCF-7 cells, B1_G1_100 nM treated

value: Treated with 100 nM G1 for 48 hours


title: KELLY cells, ChIP_M3_rep2

description: anti-FLAG ChIP in KELLY cells expressing M3 IWS1-FLAG

value: M3 IWS1-FLAG

value: M3 mutant


title: KELLY cells, ChIP_M3_rep1


title: R371CMSA

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were mapped to the hg38 human reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and geneSCF (Subhash et.al. 2016), respectively.
Statistical and downstream bioinformatics analyses were performed within the R environment.
Gene expression heatmaps were produced with GENE-E (Broad Institute).
Genome_build: hg38

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

value: colon

tag: disease state

value: Chrohn's Disease


title: KELLY cells, ChIP_WT_rep2


title: R347IMSA

value: ileum


title: R347CMSA


title: R286CMSA


title: R292CMSA


title: R292IMSA


title: R276CMSA


title: IS444

value: Healthy


title: fzr_rep2


title: IS430


title: IS437


title: IS418


title: IS322


title: IS283


title: IS399


title: IS253


title: IS243


title: IS238


title: IS_238


title: IMSA343


title: IMSA256


title: IM451


title: IMSA286


title: IM442


title: IM445


title: IM449


title: R308CMSA


title: IM448


title: IM438


title: IM432


title: IM425


title: IM409


title: IM421


title: IM385


title: IM397


title: IMSA276


title: IM382


title: IM376


title: IM374


title: IM372


title: gene_expression_HKU-PTCL27

description: Gene expression data from Homo sapiens PTCL NOS sample

source_name: PTCL NOS,HKU-PTCL27,FFPE Preparation

value: PTCL NOS

tag: tissue preparation

value: FFPE


title: IM364


title: IM356


title: IM340


title: IM348


title: IM316


title: IM332


title: IM310


title: IM320


title: IM354


title: IM311


title: IM412


title: IM305


title: IM404


title: IM297


title: IM309


title: IM390


title: IM300


title: IM296


title: IM293


title: IM381


title: CS424


title: CS415


title: R316IMSA


title: CS405


title: CS396


title: CS361


title: IM330


title: ciPTEC CTNS-/-, 3

city: Rome

first: Francesco

last: Bellomo

address: Viale di S. Paolo, 15

department: Genetic and Rare Diseases

institute: Bambino Gesù Children's Hospital, IRCCS

data_processing:
SOAPnuke 1.5.2 software was used to filter reads (to remove reads with adaptors; to remove reads in which unknown bases are more than 10%; to remove low quality reads.
Clean reads were mapped to reference genome using HISAT2 v2.0.4
StringTie v1.0.4 was used to reconstruct transcripts and Cufflinks v2.2.1 tools were used to compare reconstructed transcripts to reference annotation.
Gene expression level was calculate with RSEM v1.2.12
Based on the gene expression level, DEGs between experimental groups were identified by using DESeq2 algorithms
Genome_build: Clean reads were mapped to the human GRCh38/hg38 build reference genome using Bowtie2 v2.2.5
Supplementary_files_format_and_content: expected_count  FPKM

source_name: conditionally immortalized proximal tubular epithelial cells

growth_protocol: Cells were cultured in DMEM–HAM’s F12 containing FCS (10%), penicillin (100 U/ml), streptomycin (100 U/ml), insulin (5 μg/ml), transferrin (5 μg/ml), selenium (5 ng/ml), hydrocortisone (36 ng/ml), epithelial growth factor (10 ng/ml), and tri-iodothyronine (40 pg/ml) in a humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Beijing Genomics perfomed total RNA extraction from cell pellet using a standard phenol cholorform extraction approach.
DNB-Seq standardized library construction was performed by Beijing Genomics using their proprietary technology. DNB-Seq - PE100
Oligo-dT, non stranded - BGI kit

treatment_protocol: Cells were collected and snap-frozen in liquid nitrogen

value: epithelial cell line immortalized with SV40-ts58

value: CTNS-/-

tag: source

value: Urine

value: kidney


title: ciPTEC CTNS-/-, 2

tag: genotype


title: CS351


title: CS350


title: ciPTEC CTNS-/-, 1


title: CS343


title: CS339


title: ciPTEC CTNS+/+, 2

value: wild type


title: ciPTEC CTNS+/+, 1


title: ciPTEC CTNS+/+, 3


title: CS338


title: CS331


title: CS330


title: CS335


title: CS327


title: CS328


title: CS322


title: CS317


title: CS388


title: CS315


title: CS344


title: CS308


title: SAMPLE 59_Control_5dpi_Skeletal muscle

city: Henan

first: Ruonan

last: Liang

address: No.100 Kexue Avenue

institute: Zhengzhou Univerisity

data_processing:
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target -Ct_ꞵ-actin)
For the normalization it uses the  housekeeping genes: ꞵ-actin
The transcription levels of relevant genes were normalized to ꞵ-actin, and were calculated by the 2^-delta deltaCt method
The normalization uesd z-score
Fold Change worksheet reports test/control (i.e., CVA2 infected mice/ culture supernatant of RD cells treated mice) ratios.

label: SYBR Green

source_name: Control_5dpi_Skeletal muscle

label_protocol: Reverse transcription (RT) was performed with Hifair® Ⅱ 1st Strand cDNA Synthesis SuperMix (Yeasen BioTechnologies) following the Manufacturer’s instructions.. Each cDNA was initially denatured at 95 °C for 5 min, and then amplified for 40 cycles of 10 s at 95°C, 30 s at 60°C using Quantagene q225 (Kubo Technoloty Co., Ltd., Beijing, China)

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen), and cDNA was generated by reverse transcription by using a kit (Yeasen)

value: BALB/c

tag: sample group

value: Control

tag: treatment

value: Culture supernatant of RD cells

tag: time point

value: Skeletal muscle


title: SAMPLE 57_Control_5dpi_Skeletal muscle


title: SAMPLE 58_Control_5dpi_Skeletal muscle


title: SAMPLE 62_Test_5dpi_Skeletal muscle

source_name: Test_5dpi_Skeletal muscle

value: Test


title: SAMPLE 61_Test_5dpi_Skeletal muscle


title: CS306


title: SAMPLE 54_Test_5dpi_Heart

value: Heart


title: CS301

value: colon


title: SAMPLE 56_Test_5dpi_Heart


title: CS292


title: SAMPLE 55_Test_5dpi_Heart


title: CS293


title: SAMPLE 63_Test_5dpi_Skeletal muscle


title: SAMPLE 53_Test_5dpi_Heart


title: SAMPLE 51_Control_5dpi_Heart


title: SAMPLE 52_Control_5dpi_Heart


title: CS288


title: SAMPLE 50_Control_5dpi_Heart


title: SAMPLE 64_Test_5dpi_Skeletal muscle


title: CS290


title: SAMPLE 60_Control_5dpi_Skeletal muscle


title: SAMPLE 49_Control_5dpi_Heart


title: CS277


title: CS270


title: CS266


title: CS261


title: SAMPLE 46_Test_5dpi_Lung

value: Lung


title: SAMPLE 48_Test_5dpi_Lung


title: SAMPLE 47_Test_5dpi_Lung


title: CS259


title: SAMPLE 45_Test_5dpi_Lung


title: CS257


title: CS219


title: CMUC439

value: Ulcerative colitis


title: SAMPLE 44_Control_5dpi_Lung


title: CMUC431


title: SAMPLE 42_Control_5dpi_Lung


title: CMUC428


title: CS256

value: Healthy


title: CMUC427


title: SAMPLE 43_Control_5dpi_Lung


title: SAMPLE 38_Test_5dpi_Brain

value: Brain


title: SAMPLE 37_Test_5dpi_Brain


title: CMUC419


title: SAMPLE 36_Control_5dpi_Brain


title: SAMPLE 34_Control_5dpi_Brain


title: SAMPLE 39_Test_5dpi_Brain


title: SAMPLE 35_Control_5dpi_Brain


title: CMUC383


title: CMUC379


title: CMUC435


title: CMUC380


title: CMUC377


title: CMUC89


title: SAMPLE 41_Control_5dpi_Lung


title: SAMPLE 40_Test_5dpi_Brain


title: SAMPLE 29_Test_3dpi_Skeletal muscle

source_name: Test_3dpi_Skeletal muscle


title: SAMPLE 30_Test_3dpi_Skeletal muscle


title: SAMPLE 33_Control_5dpi_Brain


title: SAMPLE 31_Test_3dpi_Skeletal muscle


title: SAMPLE 32_Test_3dpi_Skeletal muscle


title: CMUC363


title: CMUC366


title: CMUC360


title: CMUC365


title: CMUC368


title: CMUC346


title: CMUC352


title: SAMPLE 27_Control_3dpi_Skeletal muscle

source_name: Control_3dpi_Skeletal muscle


title: SAMPLE 28_Control_3dpi_Skeletal muscle


title: CMUC334


title: SAMPLE 26_Control_3dpi_Skeletal muscle


title: SAMPLE 24_Test_3dpi_Heart


title: CMUC333


title: CMUC331


title: CMUC394


title: CMUC323


title: SAMPLE 20_Control_3dpi_Heart


title: SAMPLE 22_Test_3dpi_Heart


title: CMUC324


title: SAMPLE 19_Control_3dpi_Heart


title: SAMPLE 17_Control_3dpi_Heart


title: SAMPLE 18_Control_3dpi_Heart


title: CMUC313


title: CMUC314


title: SAMPLE 25_Control_3dpi_Skeletal muscle


title: CMUC301


title: CMUC299


title: SAMPLE 15_Test_3dpi_Lung


title: SAMPLE 23_Test_3dpi_Heart


title: SAMPLE 16_Test_3dpi_Lung


title: SAMPLE 14_Test_3dpi_Lung


title: CMUC295


title: CMUC291


title: SAMPLE 12_Control_3dpi_Lung


title: SAMPLE 21_Test_3dpi_Heart


title: CMUC285


title: SAMPLE 10_Control_3dpi_Lung


title: SAMPLE 11_Control_3dpi_Lung


title: CMUC234


title: CMUC231


title: SAMPLE 9_Control_3dpi_Lung


title: CMUC208


title: SAMPLE 7_Test_3dpi_Brain


title: SAMPLE 8_Test_3dpi_Brain


title: CMUC200


title: SAMPLE 6_Test_3dpi_Brain


title: CMUC199


title: SAMPLE 5_Test_3dpi_Brain


title: CMUC307


title: CMUC192


title: CMUC110


title: SAMPLE 4_Control_3dpi_Brain


title: SAMPLE 13_Test_3dpi_Lung


title: SAMPLE 3_Control_3dpi_Brain


title: CMSA316

value: Chrohn's Disease


title: CMSA256


title: SAMPLE 1_Control_3dpi_Brain


title: SAMPLE 2_Control_3dpi_Brain


title: CMCD88


title: CMCD72


title: CMCD426


title: CMCD71


title: CMCD422


title: CMCD76


title: CMCD403


title: CMCD398


title: CNVS-NORM-110033912-cfDNA-WGBS-Rep1

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
Paired-end FASTQ files were mapped to the human (hg19), lambda, pUC19 and viral genomes using bwa-meth (V 0.2.0), with default parameters , then converted to BAM files using SAMtools (V 1.9)
Duplicated reads were marked by Sambamba (V 0.6.5), with parameters “-l 1 -t 16 --sort-buffer-size 16000 --overflow-list-size 10000000”.
Reads with low mapping quality, duplicated, or not mapped in a proper pair were excluded using SAMtools view with parameters -F 1796 -q 10.
Reads were stripped from non-CpG nucleotides and converted to BETA files using wgbstools (V 0.1.0) .
BETA files were computationally reduced to 450K using wgbstools (V 0.1.0) to generate the summary file blood_450k.csv.gz.
Genome_build: hg19
Supplementary_files_format_and_content: beta files were generated using wgbstools (https://github.com/nloyfer/wgbs_tools) with default parameteres
Supplementary_files_format_and_content: bigwig files were generated from beta files using wgbstools beta2bw with default parameteres

source_name: Peripheral blood

extract_protocol:
DNA was extracted using the DNeasy Blood and Tissue kit (#69504 Qiagen; Germantown, MD) according to the manufacturer’s instructions, and stored at -20°C for bisulfite conversion and whole genome sequencing.
Up to 75 ng of sheared gDNA was subjected to bisulfite conversion using the EZ-96 DNA Methylation Kit (Zymo Research; Irvine, CA), with liquid handling on a Hamilton MicroLab STAR (Hamilton; Reno, NV). Dual indexed sequencing libraries were prepared using Accel-NGS Methyl-Seq DNA library preparation kits (Swift BioSciences; Ann Arbor, MI) and custom liquid handling scripts executed on the Hamilton MicroLab STAR. Libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA). Four uniquely dual indexed libraries, along with 10% PhiX v3 library (Illumina; San Diego, CA), were pooled and clustered on a Illumina NovaSeq 6000 S2 flow cell followed by 150-bp paired-end sequencing.

value: cell-free DNA

tag: height

tag: weight

tag: age

tag: Sex

value: F

tag: race

value: black


title: CMCD357


title: CNVS-NORM-110036152-cfDNA-WGBS-Rep1

tag: cell type

value: white


title: CNVS-NORM-110033746-cfDNA-WGBS-Rep1


title: CNVS-NORM-110036138-cfDNA-WGBS-Rep1


title: CNVS-NORM-110033907-cfDNA-WGBS-Rep1


title: CNVS-NORM-110036059-cfDNA-WGBS-Rep1

value: M


title: CNVS-NORM-110033745-cfDNA-WGBS-Rep1


title: CNVS-NORM-110033933-cfDNA-WGBS-Rep1


title: CNVS-NORM-110033750-cfDNA-WGBS-Rep1


title: CMCD337


title: CNVS-NORM-110033727-cfDNA-WGBS-Rep1


title: CNVS-NORM-110033633-cfDNA-WGBS-Rep1


title: CNVS-NORM-110033577-cfDNA-WGBS-Rep1


title: CMCD335


title: CMCD327


title: CNVS-NORM-110036107-cfDNA-WGBS-Rep1


title: CNVS-NORM-110033397-cfDNA-WGBS-Rep1


title: CMCD294


title: CNVS-NORM-110033253-cfDNA-WGBS-Rep1


title: CMCD287


title: CNVS-NORM-110032789-cfDNA-WGBS-Rep1


title: CMCD286


title: CNVS-NORM-110032739-cfDNA-WGBS-Rep1


title: CMCD282


title: CNVS-NORM-110029979-cfDNA-WGBS-Rep1


title: CNVS-NORM-110029639-cfDNA-WGBS-Rep1


title: CMCD275


title: CNVS-NORM-110027054-cfDNA-WGBS-Rep2


title: CMCD198


title: CMCD259


title: CMCD227


title: CNVS-NORM-110000264-cfDNA-WGBS-Rep1


title: CNVS-NORM-110000263-cfDNA-WGBS-Rep1


title: CNVS-NORM-110036152-WBC-WGBS-Rep1

value: White blood cells


title: CMCD203


title: CMCD240


title: CMCD211


title: CNVS-NORM-110036059-WBC-WGBS-Rep1


title: CMCD174


title: CNVS-NORM-110027051-cfDNA-WGBS-Rep1


title: CNVS-NORM-110036138-WBC-WGBS-Rep1


title: CNVS-NORM-110036107-WBC-WGBS-Rep1


title: CNVS-NORM-110033933-WBC-WGBS-Rep1


title: CNVS-NORM-110033912-WBC-WGBS-Rep1


title: CMCD161


title: CMCD196


title: CNVS-NORM-110033907-WBC-WGBS-Rep1


title: CMCD159


title: CMCD152


title: CMCD154


title: CMCD147


title: CMCD270


title: CNVS-NORM-110033750-WBC-WGBS-Rep1


title: CNVS-NORM-110033746-WBC-WGBS-Rep1


title: CNVS-NORM-110033745-WBC-WGBS-Rep1


title: CNVS-NORM-110033727-WBC-WGBS-Rep1


title: CMCD140


title: CM317


title: CNVS-NORM-110033633-WBC-WGBS-Rep1


title: CNVS-NORM-110033397-WBC-WGBS-Rep1


title: CNVS-NORM-110032789-WBC-WGBS-Rep1


title: CNVS-NORM-110033577-WBC-WGBS-Rep1


title: CNVS-NORM-110032739-WBC-WGBS-Rep1


title: CNVS-NORM-110033253-WBC-WGBS-Rep1


title: CNVS-NORM-110027054-WBC-WGBS-Rep1


title: CNVS-NORM-110029639-WBC-WGBS-Rep1


title: CNVS-NORM-110000263-WBC-WGBS-Rep1


title: CNVS-NORM-110027051-WBC-WGBS-Rep1


title: CNVS-NORM-110000264-WBC-WGBS-Rep1


title: Cleave-seq rep1 with XRN2 KD

city: Wuhan

first: Yu

last: Zhou

state: Hubei

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

description: polyA+ RNA-seq of RNAs with 5' phosphorylation rep1 in XRN2-KD cells

data_processing:
Reads of total RNA-seq were mapped to hg19 and Gencode v19 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.04. Reads of poly(A)+ RNA-seq were mapped to hg19 and ENSEMBL v75 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 10. Reads of nanopore were mapped to hg19 using minimap2 with parameters -ax splice -k 14 -uf --secondary=no. Reads of SLAM-seq were preprocessed to remove adapters, 3’poly(A) runs of read 2, 5’poly(A) runs of read 1 with cutadapt (v1.18) and corrected by fastp (v0.20.0). Then, these reads were mapped to hg19 and ENSEMBL v75 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 10. For each mapped pair, 5’ end of read1 was fetched and taken as the putative poly(A) site. Reads of poly(A)- RNA-seq and Cleave-seq were trimmed adapter and mapped as that of SLAM-seq. For each mapped pair of Cleave-seq, 5’ end of read1 was fetched and taken as the putative cleavage site.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig of coverage signals for rRNA-depleted RNA-seq, Bedgraph of normalized coverage (cpm) in genome for poly(A) RNA-seq, poly(A)- RNA-seq, and Cleave-seq, and Bed format file for mapped Nanopore long reads.

molecule: polyA RNA

source_name: Cleave-seq rep1 with XRN2 KD

growth_protocol: HeLa cells were maintained in DMEM (Gibco) supplemented with 10% FBS (Hyclone) and 100 U penicillin/streptomycin (Gibco) at 37°C with 5% CO2.

extract_protocol:
RNA from the lysates of different cellular fractionations or total RNA was extracted by TRIZOL reagent.
Libraries of the RNA-seq were prepared according to NEB's protocol of the NEBNext® Ultra™ II directional RNA library prep kits. Libraries of the SLAM-seq were prepared according to Lexogen's instructions of QuantSeq 3'mRNA-seq library prep kit REV for Illumina. Nanopore libraries were prepared and sequenced according to Oxford's instructions for direct RNA sequencing.

treatment_protocol: For RNA metabolic labeling, three hours just before the 4-thiouridine was added into the medium, fresh medium was exchanged. Then, s4U (Sigma) was added to the medium at a final concentration of 1 mM and the cells were placed back into the incubator for another 30 mins.

tag: cell line

value: HeLa

tag: genotype/variation

value: XRN2 KD


title: KELLY cells, PROseq_M3_rep1

description:
Nascent RNA
PRO-seq in KELLY cells expressing M3 IWS1-FLAG
PROseq_M3_F.bigWig
PROseq_M3_R.bigWig

data_processing:
Library strategy: PRO-seq
FASTQ read pairs were trimmed to 41 bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases. R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2, with those reads not mapping to the spike genome serving as input to the primary genome alignment step.
Annotated transcription start sites were obtained from human (GRCh38.99) GTFs from Ensembl. Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “–“ strands were swapped to generate bedGraphs representing 3’ end position at single nucleotide resolution.
PRO-seq signal in each sample was depth normalized and bedGraph files merged to generate bigWig files binned at 10 bp.
Genome_build: hg38
Supplementary_files_format_and_content: Depth normalized bigWig files of genome-wide coverage.

extract_protocol:
Cells in log growth were washed 2x with ice cold PBS and resuspended in 250uL of wash buffer (10 mM Tris-Cl, pH 8.0 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 10 % (v/v) Glycerol) supplemented with 10 l SUPERase-In RNase inhibitor per 50 mL. Subsequently, 10mL of permeabilization buffer ((10 mM Tris-Cl, pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 0.1 % (v/v) Igepal CA-630, 0.5 mM DTT, 0.05 % (v/v) Tween-20, 10 % (v/v) Glycerol) supplemented with 1 inhibitor tablet (EDTA-free) and 10 l SUPERase-In RNase inhibitor per 50 mL) was added to the cells and samples were incubated on ice for 5 min. Cells were pelleted and washed 1x with wash buffer before they were resuspended in freezing buffer ((50 mM Tris-Cl, pH 8.0, 40 % (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT) supplemented with 10 ul SUPERase-In RNase inhibitor per 50 mL) and snap frozen in liquid nitrogen.
Aliquots of frozen (-80°C) permeabilized cells were thawed on ice and pipetted gently to fully resuspend. Aliquots were removed and permeabilized cells were counted using a Luna II, Logos Biosystems instrument. For each sample, 1 million permeabilized cells were used for nuclear run-on, with 50,000 permeabilized Drosophila S2 cells added to each sample for normalization. 2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 40uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/uL SuperaseIN (Thermo), 1% sarkosyl).  Run-on reactions were performed at 37°C.  Adenylated 3' adapter was prepared using the 5' DNA adenylation kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB, per manufacturer’s instructions with 15% PEG-8000 final) and incubated at 16°C overnight.  180uL of betaine blocking buffer (1.42g of betaine brought to 10mL with binding buffer supplemented to 0.6 uM blocking oligo (TCCGACGATCCCACGTTCCCGTGG/3InvdT/)) was mixed with ligations and incubated 5 min at 65°C and 2 min on ice prior to addition of streptavidin beads.  After T4 polynucleotide kinase (NEB) treatment, beads were washed once each with high salt, low salt, and blocking oligo wash (0.25X T4 RNA ligase buffer (NEB), 0.3uM blocking oligo) solutions and resuspended in 5' adapter mix (10 pmol 5' adapter, 30 pmol blocking oligo, water). Fragments were then barcoded with Illumina primers and amplified using standard Illumina protocols.

value: KELLY cells

tag: marker

value: M3 IWS1-FLAG

value: M3 mutant


title: Nuclear matrix poly(A)- RNA-seq rep2

description: polyA- RNA-seq of nuclear matrix

source_name: Nuclear matrix poly(A)- RNA-seq

value: WT

tag: fraction

value: nuclear matrix


title: Nuclear matrix poly(A)- RNA-seq rep1

description: polyA- RNA-seq of nuclear matrix


title: ChIP T in vitro generated notochord cells.

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

data_processing:
Reads were mapped to chromosomes 1-19, X, Y and M of the mouse mm10 genome using bowtie version 1.1.2 (Langmead et al. 2009), providing the options ‘ -y -m 1 -S -I 100 -X 500’
The mapping information of the paired-end reads was used to elongate each fragment to its original size using a custom pearl script, with the result stored as a BED file
Reads were then sorted and deduplicated such that only one fragment with the same starting and end position was retained
For visualization, wiggle files were generated with BEDTools version 2.23.0
Bigwig files were generated from wiggle files.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing read density for ChIP-Seq

source_name: in vitro differentiated ES cells

growth_protocol: In vitro generation of notochord cells was performed following a modification of a previously published protocol (Winzi et al 2011).Embryonic stem cells were seeded on 6cm plates and passaged two times until confluence. Cells were trypsinized and resuspended in 2ml ES+LIF. mEFs were depleted from single cell suspensions by sequential plating on 0.1% gelatin (Sigma G1393) coated 6 well plates (Corning 3335) in 25min, 20min and 15min intervals. After feeder freeing, cells were resuspended in 1ml NotoDiff medium (Knock Out Knockout Dulbecco’s Modified Eagle’s Medium with sodium

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Sigma Aldrich) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in LB1 (50mM Hepes pH7.5, 140mM NaCl, 1mM EDTA pH8, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20 minutes. The cell suspension was homogenized using a douncer with a tight pestle with 3x 15 strokes, with short resting times on ice in between. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5 minutes and resuspended in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 10mM Tris pH 8) per cell pellet. After 10 minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5ml LB3 (1mM EDTA pH8, 0.5mM EGTA, 10mM Tris pH8, 100mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 12 cycles of 10s on/50s off in a 4°C coldroom with tubes chilled in ice water. After sonication, 150ul of triton X-100 was added per tube, transferred to two 1.5ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. The solubilized chromatin was then pooled and mixed thoroughly. After taking 50ul as an input control, the chromatin was distributed into 1.5ml aliquots, snap frozen and stored at -80C until use. The input was reverse-crosslinked with the addition of 50ul 2x elution buffer (100mM Tris pH8, 20mM EDTA pH8, 2% SDS) and overnight (13h-15h) incubation at 65°C. The next day, 100ul of TE buffer were added to dilute the SDS of the elution buffer and RNA was digested using RNase A at a 0.2ug/ml final concentration at 37°C for 2 hours. Proteins were digested with the addition of 0.2ug/ml proteinase K and incubation at 55°C for 2 hours. The DNA was purified with two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH8) isolations and subsequent MinElute (Qiagen) purification. Purification was performed according to manufacturer’s recommendations, except that the columns were washed 2x with PE and air dried for at least 10 minutes before elution with EB. The input DNA was quantified using a NanoPhotometer (Implen) and the shearing was verified by running 600ng of DNA on a 1.5% agarose gel. For sonication to be considered successful and sonicated chromatin to be usable for ChIP, the bulk DNA of the input had to be located between 100bp-500bp. For ChIP, 50µl of protein-coated Dynal beads (Life Technologies) were washed 3x using 1ml of blocking solution (PBS containing 0.5% BSA), resuspended in 500µl of blocking solution together with approximately 2.5µg antibody and rotated overnight at 4°C. The antibody used was a goat polyclonal anti-T (R&D, AF2085). The next day, three further washes using 1ml blocking buffer were performed and the beads were resuspended in 100µl blocking buffer. Chromatin equivalent to approximately 10x106 cells was added and rotated overnight at 4°C. The following day, 9 washing steps were performed using 1ml RIPA buffer (50mM Hepes pH7.6, 500mM LiCl, 1mM EDTA pH8, 1% NP-40, 0.7% Na-Deoxycholate) containing 1x complete protease inhibitors without EDTA and finally with 1ml of TEN (10mM Tris pH8, 1mM EDTA pH8, 50mM NaCl). The immunoprecipate was eluted in two subsequent steps using 15µL of 1x elution buffer (50mM Tris pH8, 10mM EDTA pH8, 1% SDS) and incubation at 65°C while shaking for 10 minutes each. The eluates were combined and incubated overnight (13h-15h) at 65°C under agitation. The next day, 200µl of TE were added to dilute the SDS of the elution buffer and the ChIPs were purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-Seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the following modifications. After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 15µl of resuspension buffer (RSB, Illumina). After the addition of 1µl primer mix (25mM each, Primer 1: 5’- AATGATACGGCGACCACCGA*G-3’; Primer2: 5’- CAAGCAGAAGACGGCATACGA*G-3’) and 15µl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21µl of RSB. Libraries were directly amplified for 18 cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS bioanalyzer chips.

treatment_protocol: Crosslinking was performed directly on differentiating cells in growth medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH7.8) for 10 minutes at room temperature, with the dishes placed on a shaker. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Dishes were placed on ice or in a 4°C cold room and washed twice with cold PBS. Cells were scraped and washed off using cold PBS, containing 0.05% Triton X-100 to break the surface tension. Cells were pooled in aliquots of ~30-50x106 in Eppendorf tubes, snap frozen and stored at -80°C until sonication.

value: ES-derived Noto+ cells

tag: strain

value: C57BL/6N X SV129

tag: chip antibody


title: Cleave-seq rep1 in control

description: polyA+ RNA-seq of RNAs with 5' phosphorylation rep1 in control cells

source_name: Cleave-seq rep1 in control


title: Cleave-seq rep2 with XRN2 KD

description: polyA+ RNA-seq of RNAs with 5' phosphorylation rep2 in XRN2-KD cells

source_name: Cleave-seq rep2 with XRN2 KD


title: KELLY cells, RNA_IWS1_WT_rep2

description: mRNA in KELLY cells expressing WT IWS1-FLAG

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using HISAT2 v2.1.0.
Fragments with read qualities greater than 10 were considered for further analysis. Of these, reads mapping to the coding strand of exonic regions were counted using htseq, with gene definitions obtained from the refGene table of RefSeq genes in the UCSC Table Browser.
The table of all counts was processed using DESeq2, using default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including total numbers of reads overlapping each transcript for each sample.

extract_protocol:
RNA was extracted from cells at 50% confluency using TRIzol reagent and mRNA enriched by poly(dT) capture. RNA was fragmented, converted to DNA, then size-selected for 200-400 bp DNA fragments before PCR amplification.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

value: WT IWS1-FLAG


title: KELLY cells, RNA_IWS1_WT_rep1


title: KELLY cells, RNA_IWS1_M3_rep1

description: mRNA in KELLY cells expressing M3 IWS1-FLAG


title: KELLY cells, RNA_IWS1_M3_rep2


title: KELLY cells, PROseq_WT_rep2

description:
Nascent RNA
PRO-seq in KELLY cells expressing WT IWS1-FLAG
PROseq_WT_F.bigWig
PROseq_WT_R.bigWig


title: CNVS-NORM-110029979-WBC-WGBS-Rep1


title: KELLY cells, PROseq_WT_rep1


title: HMN171244_NI

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

description:
bulk RNA library
bulk_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt

data_processing:
Fastqs were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in single-end mode (-q 20 --phred33)
Reads were pseudoaligned to GRCh38 and the IAV reference transcriptome using kallisto's quant function (Bray et al.) in single-end mode
Quantification estimates were obtained from abundance.h5 files using the R package tximport (Soneson et al.)
Genome_build: GRCh38.p12 and influenza A virus (A/California/04/09)
Supplementary_files_format_and_content: bulk_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt includes counts from abundance estimates scaled by library size

source_name: PBMCs

growth_protocol: All samples were obtained from BioIVT. Blood was collected utilizing a standard protocol from 90 male African- (AFR) and European-American (EUR) donors between the ages of 21 – 69 using a sodium heparin anticoagulant from the same collection site in the United States. A signed, written consent was obtained from each participant. Briefly, PBMCs were extracted from whole blood using a density gradient, washed with HBSS, reconstituted in CryoStor CS10 to a concentration of 10 million (M) cells/ml, and subsequently cryopreserved.

extract_protocol:
Cells were collected, washed, and stored in Qiazol prior to RNA extraction.
RNA libraries were prepared for sequencing using TM3’seq, a 3’-enriched library preparation protocol (https://www.g3journal.org/content/10/1/143).

treatment_protocol: Per individual for each condition, 1 million (M) PBMCs were plated at a concentration of 1M/ml and infected with either mock-conditioned media (negative control) or Cal/04/09 IAV at an MOI of 0.5. After 30 minutes of IAV infection, the virus was washed from PBMC cultures, cells were replated, and cells were then incubated for 6hr at 37C in 5% CO2 and 20% O2.

value: peripheral blood mononuclear cells

value: mock


title: Cleave-seq rep2 in control

description: polyA+ RNA-seq of RNAs with 5' phosphorylation rep2 in control cells

source_name: Cleave-seq rep2 in control


title: KELLY cells, PROseq_M3_rep2


title: HMN171241_NI


title: HMN171241_flu

value: flu-infected


title: HMN171244_flu


title: HMN171240_flu


title: HMN171238_NI


title: HMN171242_NI


title: HMN171240_NI


title: HMN171239_flu


title: HMN171242_flu


title: HMN171243_NI


title: HMN171239_NI


title: HMN171243_flu


title: KELLY cells, PROseq_WT_rep3


title: HMN171238_flu


title: HMN171236_flu


title: HMN171237_NI


title: HMN171236_NI


title: HMN171235_NI


title: HMN171237_flu


title: HMN171235_flu


title: HMN171234_flu


title: HMN171232_NI


title: HMN171234_NI


title: HMN171233_NI


title: Nuclear matrix Nanopore direct RNA-seq

description: Nanopore RNA-seq of nuclear matrix

data_processing:
Reads of total RNA-seq were mapped to hg19 and Gencode v19 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.04. Reads of poly(A)+ RNA-seq were mapped to hg19 and ENSEMBL v75 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 10. Reads of nanopore were mapped to hg19 using minimap2 with parameters -ax splice -k 14 -uf --secondary=no. Reads of SLAM-seq were preprocessed to remove adapters, 3’poly(A) runs of read 2, 5’poly(A) runs of read 1 with cutadapt (v1.18) and corrected by fastp (v0.20.0). Then, these reads were mapped to hg19 and ENSEMBL v75 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 10.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file of coverage signals for rRNA-depleted RNA-seq, bedGraph file of normalized coverage (cpm) in genome for polyA RNA-seq, and Bed format file for mapped Nanopore long reads.

source_name: Nuclear matrix Nanopore direct RNA-seq

growth_protocol: HeLa cells  were maintained in DMEM (Gibco) supplemented with 10% FBS (Hyclone) and 100 U penicillin/streptomycin (Gibco) at 37°C with 5% CO2.

extract_protocol:
RNA from the lysates of different cellular fractionations  or total RNA was extracted by TRIZOL reagent.
Libraries of the RNA-seq were prepared according to NEB's protocol of the NEBNext® Ultra™ II directional RNA library prep kits. Libraries of the SLAM-seq were prepared according to Lexogen's instructions of QuantSeq 3'mRNA-seq library prep kit REV for Illumina. Naropore libraries were prepared and sequenced according to Oxford's instructions for direct RNA sequencing.
RNA-seq, SLAM-seq, Nanopore direct RNA-seq


title: pig_PG_Mo_H3K4me3_CR_rep2

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

institute: Tsinghua University

data_processing:
Library strategy: CUT&RUN
Basecalls performed using CASAVA version 1.8
All STEM-seq datasets were firstly treated with cutadapt v1.11 (Martin, 2011) and the low-quality reads and adaptors were removed before mapping. Then all filtered reads were aligned to different genomes (rat, rn6; cow, bosTau8; pig, susScr11) using Bismark (v0.7.0；bowtie2 2.1.0) (Krueger and Andrews, 2011) with default parameters. Multi-mapped reads and PCR duplicates were removed also with the Bismark. The unique mapped reads were used for CpG methylation calling with bismark_methylation_extractor. For every single CpG site, only the CpG sites that were covered at least 3 times were used for further analysis. The spiked-in Lamda DNA (1:200) was used for conversation rate calculation.
All RNA-seq datasets were mapped to the different genomes (rat: rn6; cow: bosTau8; pig: susScr11). All genomes were downloaded from UCSC (citation) by Tophat v2.1.1 (Trapnell et al., 2009). Gene expression was then calculated according to refFlat database by cufflinks 2.2.1 (Trapnell et al., 2012).
All reads were firstly processed by TrimGalore (v.0.6.4) with default parameters to remove the poor qualitied reads and also the adapters. Then the filtered reads were mapped to different genomes (rat: Rn6; cow: bosTau8; pig: susScr11) by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. All multiple mapped reads as well as the duplicates were removed with MarkDuplicates.jar. Then all unique mapped reads were used for the downstream RPKM (reads per kilobase per million of sequenced reads) calculation. The Pearson correlation was generated for each sample with two biological replicates with 10 kb bins. The replicates with good reproducibility were pooled for downstream analysis.
Supplementary_files_format_and_content: The cov txt files contains the chr, start positon, methylated CG count, unmethylated CG count. The txt files for FPKM contain gene names and the FPKM value for all stages.

organism: Sus scrofa

source_name: Morula

extract_protocol: CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), mammalian oocytes and early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ overnight on a thermomixer at 400 rpm. The next day, after washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 3 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system (Illumina) according to the manufacturer’s protocol.

tag: developmental stage

value: Morula


title: HMN171231_NI


title: pig_PG_Mo_H3K4me3_CR_rep1


title: HMN171231_flu


title: pig_PG_Mo_H3K27me3_CR_rep1


title: pig_PG_Mo_H3K27me3_CR_rep2


title: HMN171230_NI


title: HMN171228_flu


title: HMN171229_NI


title: pig_PG_Mo_Smartseq_rep4

data_processing:
Basecalls performed using CASAVA version 1.8
All STEM-seq datasets were firstly treated with cutadapt v1.11 (Martin, 2011) and the low-quality reads and adaptors were removed before mapping. Then all filtered reads were aligned to different genomes (rat, rn6; cow, bosTau8; pig, susScr11) using Bismark (v0.7.0；bowtie2 2.1.0) (Krueger and Andrews, 2011) with default parameters. Multi-mapped reads and PCR duplicates were removed also with the Bismark. The unique mapped reads were used for CpG methylation calling with bismark_methylation_extractor. For every single CpG site, only the CpG sites that were covered at least 3 times were used for further analysis. The spiked-in Lamda DNA (1:200) was used for conversation rate calculation.
All RNA-seq datasets were mapped to the different genomes (rat: rn6; cow: bosTau8; pig: susScr11). All genomes were downloaded from UCSC (citation) by Tophat v2.1.1 (Trapnell et al., 2009). Gene expression was then calculated according to refFlat database by cufflinks 2.2.1 (Trapnell et al., 2012).
All reads were firstly processed by TrimGalore (v.0.6.4) with default parameters to remove the poor qualitied reads and also the adapters. Then the filtered reads were mapped to different genomes (rat: Rn6; cow: bosTau8; pig: susScr11) by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. All multiple mapped reads as well as the duplicates were removed with MarkDuplicates.jar. Then all unique mapped reads were used for the downstream RPKM (reads per kilobase per million of sequenced reads) calculation. The Pearson correlation was generated for each sample with two biological replicates with 10 kb bins. The replicates with good reproducibility were pooled for downstream analysis.
Supplementary_files_format_and_content: The cov txt files contains the chr, start positon, methylated CG count, unmethylated CG count. The txt files for FPKM contain gene names and the FPKM value for all stages.

extract_protocol: The RNA libraries for mammalian oocytes and preimplantation embryos were prepared using Smart-seq2 method as previously reported (Picelli et al., 2014).


title: HMN171228_NI


title: HMN171230_flu


title: HMN171227_flu


title: HMN171225_NI


title: pig_PG_Mo_Smartseq_rep1


title: HMN171225_flu


title: HMN171224_NI


title: HMN171229_flu


title: HMN171226_flu


title: pig_PG_Mo_Smartseq_rep2


title: HMN171233_flu


title: HMN171226_NI


title: HMN171232_flu


title: porcine_PG_Bl_Smartseq_rep3

source_name: embryo

extract_protocol: RNA library preparation and sequencing  The RNA libraries for mammalian oocytes and preimplantation embryos were prepared using Smart-seq2 method as previously reported (Picelli et al., 2014).


title: HMN171223_NI


title: porcine_PG_Bl_Smartseq_rep2


title: HMN171224_flu


title: HMN171227_NI


title: porcine_PG_Bl_Smartseq_rep1


title: pig_PG_Mo_Smartseq_rep3


title: HMN171222_flu


title: HMN171222_NI


title: HMN171221_NI


title: porcine_PG_8C_Smartseq_rep2

value: parthenogenetically activated 8-cell embryo


title: HMN171221_flu


title: porcine_PG_8C_Smartseq_rep1


title: HMN171219_NI


title: HMN171220_flu


title: porcine_PG_4C_Smartseq_rep2

value: parthenogenetically activated 4-cell embryo


title: HMN171220_NI


title: HMN171218_NI


title: porcine_PG_4C_Smartseq_rep1


title: HMN171217_flu


title: HMN171218_flu


title: HMN171216_flu


title: HMN171217_NI


title: HMN171215_flu


title: porcine_IVM_MII_Smarseq_rep2

source_name: oocyte

value: In vitro matured mataphase II oocyte


title: porcine_PG_2C_Smarseq_rep1

value: parthenogenetically activated 2-cell embryo


title: HMN171215_NI


title: porcine_IVM_MII_Smarseq_rep1


title: HMN171223_flu


title: HMN83580_flu


title: porcine_FGO_Smartseq_rep2

value: full_grown oocyte


title: HMN83579_NI


title: HMN83579_flu


title: HMN83578_NI


title: HMN83578_flu


title: porcine_CC_H3K4me3_CR

data_processing:
Library strategy: Cut&Run
Basecalls performed using CASAVA version 1.8
All STEM-seq datasets were firstly treated with cutadapt v1.11 (Martin, 2011) and the low-quality reads and adaptors were removed before mapping. Then all filtered reads were aligned to different genomes (rat, rn6; cow, bosTau8; pig, susScr11) using Bismark (v0.7.0；bowtie2 2.1.0) (Krueger and Andrews, 2011) with default parameters. Multi-mapped reads and PCR duplicates were removed also with the Bismark. The unique mapped reads were used for CpG methylation calling with bismark_methylation_extractor. For every single CpG site, only the CpG sites that were covered at least 3 times were used for further analysis. The spiked-in Lamda DNA (1:200) was used for conversation rate calculation.
All RNA-seq datasets were mapped to the different genomes (rat: rn6; cow: bosTau8; pig: susScr11). All genomes were downloaded from UCSC (citation) by Tophat v2.1.1 (Trapnell et al., 2009). Gene expression was then calculated according to refFlat database by cufflinks 2.2.1 (Trapnell et al., 2012).
All reads were firstly processed by TrimGalore (v.0.6.4) with default parameters to remove the poor qualitied reads and also the adapters. Then the filtered reads were mapped to different genomes (rat: Rn6; cow: bosTau8; pig: susScr11) by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. All multiple mapped reads as well as the duplicates were removed with MarkDuplicates.jar. Then all unique mapped reads were used for the downstream RPKM (reads per kilobase per million of sequenced reads) calculation. The Pearson correlation was generated for each sample with two biological replicates with 10 kb bins. The replicates with good reproducibility were pooled for downstream analysis.
Supplementary_files_format_and_content: The cov txt files contains the chr, start positon, methylated CG count, unmethylated CG count. The txt files for FPKM contain gene names and the FPKM value for all stages.

source_name: cumulus cell

extract_protocol: CUT&RUN library preparation and sequencing  CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), mammalian oocytes and early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ overnight on a thermomixer at 400 rpm. The next day, after washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 3 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system (Illumina) according to the manufacturer’s protocol.

value: cumulus cell

tag: antibody


title: HMN83577_NI


title: HMN171219_flu


title: SIGAG8: DKO1 10X scRNA-seq

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

data_processing:
Demutiplexing with CASAVA
Processing with Cellranger
Genome_build: Mm10

source_name: kidney

growth_protocol: Mice were housed in SPF conditions

extract_protocol:
Kidneys were taken and a single cell suspension produced following treatment with liberase, kidneys from up to 6 mice were combinded into one pool
10x libraries were made according to manufactuers protocols with each cell pool split over 2 lanes of 10x

treatment_protocol: Mice were given Methanol prior to sample collection

tag: genotype

tag: tissue

value: kidney


title: HMN171216_NI

tag: treatment


title: SIGAH8: DKO2 10X scRNA-seq