title: Lgr5_high_751P_06_SCBC-13

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-10

status: Public on Mar 14 2017

type: SRA

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

description: Lgr5 GFP/+ mice

library_source: transcriptomic

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
Libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse reference genome.
Gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Gencode release M8, assembly GRCm38.p4
Supplementary_files_format_and_content: Tab-separated values (.tsv) file containing gene expression values (rows) as UMI counts (MARS-Seq) for each cell (columns).

molecule: polyA RNA

organism: Mus musculus

source_name: small intestinal epithelium

growth_protocol: Lgr5::EGFP-IRES-Cre-ERT2 mice were obtained from the laboratory of Dr. Hans Clevers. Cyp1a1::H2B-YFP mice were obtained from the laboratory of Dr. Douglas J. Winton. Mice were housed and bred according to IRB Barcelona and PCB institutional guidelines.

extract_protocol:
Intestinal crypt cells were purified as previously described (Merlos-Suárez et al., 2011). Proximal small intestines (duodenum and jejunum) were dissected from age and sex-matched mice and cut open longitudinally. They were later incubated with HBSS EDTA (8 mM) for 5 min at room temperature. After this incubation, intestines were shaken vigorously to remove villi and the first supernatant was discarded. The intestines were then incubated with HBSS EDTA on ice for 15 min, after which shaking was repeated. This yielded the first crypt fraction. This process was repeated twice and after microscopic inspection of the samples the fractions enriched in crypts were kept (usually fractions 2 and 3). These fractions were then pooled together for each mouse, centrifuged at 1200 rpm for 5 min (4 ºC) and filtered through a 70 μm mesh (BD Biosciences) to further remove villi. Filtered fractions were enzymatically disaggregated by adding dispase (0.4 mg/mL, Gibco) and incubated for 20 min at 37ºC. The media was then supplemented with 5% FBS (Gibco) to neutralize dispase and the samples were filtered through a 40 μm mesh. For intestinal LRC analysis in compound mice, single cells were stained with an APC-conjugated antibody raised against EphB2 (Clone mAb 2H9, 6 µg/mL, BD). Cells were stained with DAPI (1 µg/mL, Sigma Aldrich) to exclude dead cells. The single-cell preparations of small intestinal crypts were analyzed by flow cytometry in a FACS Aria 2.0 (BD). Data was analyzed with FACSDiva software (BD) or FlowJo for EdU retention assays.
Isolation of single cells, cDNA synthesis and amplification were performed on the C1 mRNA Seq HT IFCs (Fluidigm) with the SMARTer Ultra Low RNA Kit (Clonetech). 400 capture sites on a C1 HT IFC medium chip (10-17μm). Spike-in artificial transcripts (ERCC RNA Spike-In Mix, Ambion) from The External RNA Controls Consortium were added during sample preparation as internal control to supported subsequent quality control steps (Baker et al., 2005). Quantity and quality of cDNA were assessed with a High Sensitivity DNA Chip (Agilent Technologies). Libraries were generated by Nextera XT DNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2500 (Illumina) using 100-bp mode of Truseq Rapid SBS kit v2. Sequencing was carried out as paired-end reads. Read one (12 bp) contained cell and unique molecular barcodes (Islam et al., 2014; Kivioja et al., 2012); read two (85 bp) contained the transcript sequence. Primary data analysis was carried out with the standard Illumina pipeline. Fluidigm C1 HT-Seq technology includes a two-level indexing system, which allows the multiplexed sequencing of multiple single cells and library pools. Here, we processed 10 libraries (up to 40 cells per library) of Lgr5-high cells.

treatment_protocol: For lineage tracing from the Lgr5GFP/+ model, 1 dose of diluted Tamoxifen (2 mg/kg) was used to ensure tracing from single cell conditions.

tag: cell type

value: Lgr5 intestinal stem cells (ISCs)


title: Lgr5_high_751P_06_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-04

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-02

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-01

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-30

description: Lgr5 GFP/+ mice


title: primary HSCs infected with lncRNA-shRNA3, biological rep2

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

country: China

institute: Tianjin medical university

description: lncRNA-shRNA3 2#

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts for each Sample

molecule: total RNA

growth_protocol: primary HSCs were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml)

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: primary HSCs infected with shRNA-control (n=2), lncRNA-shRNA1 (n=2) and lncRNA-shRNA3 (n=2)

tag: strain

value: Balb/c

tag: tissue

value: liver

value: primary HSCs

tag: Stage

value: day 6

tag: infection


title: Lgr5_high_751P_05_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-26

description: Lgr5 GFP/+ mice


title: primary HSCs infected with lncRNA-shRNA3, biological rep1

description: lncRNA-shRNA3 1#


title: Lgr5_high_751P_05_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-09

description: Lgr5 GFP/+ mice


title: primary HSCs infected with lncRNA-shRNA1, biological rep2

description: lncRNA-shRNA1 2#


title: primary HSCs infected with lncRNA-shRNA1, biological rep1

description: lncRNA-shRNA1 1#


title: Lgr5_high_751P_05_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-17

description: Lgr5 GFP/+ mice


title: primary HSCs infected with shRNA-control, biological rep2

description: shRNA-control 2#

value: shRNA-control


title: Lgr5_high_751P_05_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-35

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-29

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-15

description: Lgr5 GFP/+ mice


title: primary HSCs infected with shRNA-control, biological rep1

description: shRNA-control 1#


title: Lgr5_high_751P_05_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-13

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-14

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-12

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-04

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-02

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-35

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-01

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-29

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-09

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_05_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-14

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-13

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-12

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-02

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-04

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-09

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-35

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_04_SCBC-01

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-29

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-14

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-09

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-01

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-02

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-13

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-35

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-12

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-04

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_03_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-29

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-14

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-04

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L Red* rep 2, small RNA-seq

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

description: small RNAs (18-30 nt)

data_processing:
Fastq files were aligned against the dm6 Drosophila reference genome using Bowtie1
The number of unique read mapping to known microRNAs (based on miRBase) were extracted using custom scripts.
supplementary_files_format_and_content: column1:miRBase ID, column2: Unique reads count
Genome_build: Drosophila melanogaster dm6

organism: Drosophila melanogaster

source_name: adult male heads

extract_protocol: For each line, 4.5 ug of total RNA was extracted and purified from adult male heads. The biological samples were  homogenized in Trizol and Chloroform. Total RNA was finally extracted with the RNA Clean & Concentrator kit (Zymo Research) following the manufacturer’s instruction. Libraries were prepared by FASTERIS, following the standard protocol after removal of 2S RNA and polyacrilamide gel size selection (18-30 nt). Libraries were sequenced single end 1x50bp on a HiSeq2500 machine.

tag: strain background

value: Oregon-R

tag: developmental stage

value: adult

tag: Sex

value: male

tag: age

value: 4 days old

tag: genotype/variation

value: w[1118] with Fab2L transgenic insertion


title: Lgr5_high_751P_02_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-02

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L Red* rep 1, small RNA-seq

description: small RNAs (18-30 nt)


title: Lgr5_high_751P_02_SCBC-12

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L rep 2, small RNA-seq

description: small RNAs (18-30 nt)


title: Lgr5_high_751P_02_SCBC-01

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-40

description: Lgr5 GFP/+ mice


title: Oregon R, w[1118] rep 2, small RNA-seq

description: small RNAs (18-30 nt)


title: Oregon R, Fab2L White* rep 1, small RNA-seq

description: small RNAs (18-30 nt)


title: Lgr5_high_751P_01_SCBC-38

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L White* rep 2, small RNA-seq

description: small RNAs (18-30 nt)


title: Lgr5_high_751P_01_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_02_SCBC-09

description: Lgr5 GFP/+ mice


title: Oregon R, w[1118] rep 1, small RNA-seq

description: small RNAs (18-30 nt)


title: Oregon R, Fab2L rep 1, small RNA-seq

description: small RNAs (18-30 nt)


title: Lgr5_high_751P_02_SCBC-13

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L Red* rep 2, long RNA-seq

description: long RNAs (>200nt)

data_processing:
Fastq files were aligned against the dm6 Drosophila reference genome using STAR v2.5 with the following parameters: --outFilterType BySJout --outFilterMultimapN  max 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --alignIntronMin 21 --alignIntronMax 1000000 --alig  nMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical
BAM files were processed using summarizeOverlaps function from the GenomicAlignments R package (http://bioconductor.org/) to produce counts per gene matrix.
DeSeq2 (http://bioconductor.org/)  was used to calculate the expression levels in Fragments Per Kilobase of exon per Million Fragments Mapped (FPKM) per gene.
supplementary_files_format_and_content: column1:FlyBase ID, column2: FPKM
Genome_build: Drosophila melanogaster dm6

extract_protocol: For each line, 4.5 ug of total RNA was extracted and purified from adult male heads. The biological samples were  homogenized in Trizol and Chloroform. Total RNA was finally extracted with the RNA Clean & Concentrator kit (Zymo Research) following the manufacturer’s instruction. Libraries were prepared by FASTERIS, following the standard protocol without the polyA purification step and after removal of rRNA (RiboZero step). Libraries were sequenced single end 1x125bp on a HiSeq2500 machine.


title: Lgr5_high_751P_01_SCBC-36

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L rep 2, long RNA-seq

description: long RNAs (>200nt)


title: Lgr5_high_751P_01_SCBC-37

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L rep 1, long RNA-seq

description: long RNAs (>200nt)


title: Lgr5_high_751P_01_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-31

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L White* rep 1, long RNA-seq

description: long RNAs (>200nt)


title: Oregon R, Fab2L White* rep 2, long RNA-seq

description: long RNAs (>200nt)


title: Oregon R, w[1118] rep 2, long RNA-seq

description: long RNAs (>200nt)


title: Lgr5_high_751P_01_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-29

description: Lgr5 GFP/+ mice


title: Oregon R, w[1118] rep 1, long RNA-seq

description: long RNAs (>200nt)


title: Canton S, Fab2L Red* rep 3

library_source: genomic

data_processing:
Fastq files were aligned against the dm6 Drosophila reference genome using Bowtie2 with standard parameters. Uniquely aligned read pairs were extracted using custom scripts, and reads mapping to unplaced or unlocalized scaffolds were discarded. BAM files containing uniquely aligned reads were pooled within each line using Picard and sorted and indexed using SAMtools. SNPs were called using BCFtools. Structural variations (SVs) detection was carried out using the DSVD pipeline as previously described (Sievers et al., 2014). Seed-based alignment was performed using Bowtie2 with parameters -3 95 –N 1 –L 30 –k 11. Sixteen different SV types, including small insertions and deletions, inversions and complex chromosomal rearrangements, were considered. Detected events were then filtered by discordant coverage, and SVs with a weight of 1 were discarded.
supplementary_files_format_and_content: CSV files containing the common events found in the DNA-seq between Oregon-R and Canton-S that cannot be find in Fab2L.
Genome_build: Drosophila melanogaster dm6

molecule: genomic DNA

source_name: adult female

extract_protocol: For each line, gDNA was extracted and purified from 150 adult female flies using the Gentra Puregene Cell Kit (Qigen) following the manufacturer’s instructions; Libraries were prepared by FASTERIS following the standard protocol with a gel size selection at 230 bp

value: Canton-S

value: female


title: Canton S, Fab2L Red* rep 2


title: Lgr5_high_751P_01_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-24

description: Lgr5 GFP/+ mice


title: Canton S, Fab2L rep 1


title: Lgr5_high_751P_01_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-25

description: Lgr5 GFP/+ mice


title: Canton S, Fab2L rep 2


title: Canton S, Fab2L White* rep 2


title: Lgr5_high_751P_01_SCBC-35

description: Lgr5 GFP/+ mice


title: Canton S, Fab2L White* rep 3


title: Oregon R, Fab2L Red* rep 1, long RNA-seq

description: long RNAs (>200nt)


title: Lgr5_high_751P_01_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-34

description: Lgr5 GFP/+ mice


title: Canton S, Fab2L White* rep 1


title: Lgr5_high_751P_01_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-28

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L Red* rep 1

data_processing:
Fastq files were aligned against the dm6 Drosophila reference genome using Bowtie2 with standard parameters.
Uniquely aligned read pairs were extracted using custom scripts and reads mapping to unplaced or unlocalized scaffolds were discarded.
BAM files containing uniquely aligned reads were pooled within each line using Picard, and sorted and indexed using SAMtools.
Structural variations (SVs) detection was carried out using the DSVD pipeline as previously described. Seed-based alignment was performed using Bowtie2 with parameters -3 95 –N 1 –L 30 –k 11.
Sixteen different SV types, including small insertions and deletions, inversions and complex chromosomal rearrangements, were considered (see Sievers et al. 2014 for details).
Detected events were then filtered by coverage, and SVs with a weight < 10 were discarded. All remaining line-specific high-confidence SVs were annotated to genomic compartments and coding sequences. Coding sequences of PcG and trxG genes, as well as genes involved in eye pigmentation, were further inspected.
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: For the single_bp files: column1: breakpoint number; column2: chromosome name; column3: genomic position; columns4-5: the number of discordant reads (weight) that support the breakpoint
Supplementary_files_format_and_content: For the double_bp files: column1: breakpoint number, first breakpoint; column2: chromosome name for the first breakpoint;
Supplementary_files_format_and_content: For the triple_bp files: column1: breakpoint number, first breakpoint; column2: chromosome name for the first breakpoint;

growth_protocol: Oregon-R w1118 flies were raised in standard cornmeal yeast extract media at 21°C.


title: Canton S, Fab2L Red* rep 1


title: Oregon R, Fab2L rep 3


title: Oregon R, Fab2L Red* rep 2


title: Oregon R, Fab2L Red* rep 3


title: Lgr5_high_751P_01_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-14

description: Lgr5 GFP/+ mice


title: Canton S, Fab2L rep 3


title: Lgr5_high_751P_01_SCBC-16

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L rep 2


title: Oregon R, Fab2L White* rep 2


title: Lgr5_high_751P_01_SCBC-13

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L rep 1


title: Lgr5_high_751P_01_SCBC-12

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-09

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_01_SCBC-04

description: Lgr5 GFP/+ mice


title: PBT003 gliblastoma stem cells, METTL14 shRNA 2, m6A-IP

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

country: USA

institute: University of Chicago

description:
RNA-seq data of m6A-IP RNA from PBT003 gliblastoma stem cells treated with virus expressing METTL14 shRNA 2
shM14.R2.bed

data_processing:
All samples were sequenced by Illumina Hiseq 4000 with single-end 50-bp read length. The deep sequencing data were mapped to human genome version 38 (GRCh38).
Data analysis for each experiment: (1) for m6A-seq, reads were aligned to the reference genome using Tophat v2.0.14 with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene had multiple isoforms. Aligned reads were extended to 150 bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from introns in peak calling. The peak calling method was modified from published work (Dominissini et al., 2012). To call m6A peaks, the longest isoform of each gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with read counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. A Fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the FDR < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP samples in the current peak/window (a), median read counts of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c), and median read counts of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c). (2) for mRNA-seq (the input samples of m6A-seq), reads were mapped with Tophat and Cufflink (v2.2.1) was used to calculate the FPKM of each gene to represent their mRNA expression level.
Genome_build: hg38
Supplementary_files_format_and_content: m6A peak list from IP samples

organism: Homo sapiens

growth_protocol: Cells were cultured in DMEM-F12 medium supplemented with B27 and growth factors EGF and FGF.

extract_protocol:
Total RNA was extracted by Trizol (Ambion) according to the manufacturer's instructions. mRNA was then purified using Dynabeads mRNA purification kit (Ambion, Catalog # 61006).
RNA fragmentation was performed by sonication at 10 ng μl-1 in 100 μl RNase-free water using Bioruptor Pico (Diagenode) with 30 s on / 30 s off cycle for 30 cycles. 5% of the fragments was saved as input. m6A-immunoprecipitation (m6A IP) and library preparation were performed according to a published protocol (Dominissini et al., 2013). In detail, 2.5 μg affinity purified anti-m6A rabbit polyclonal antibody (Synaptic Systems; Catalog # 202003) and 20 μl Protein A beads (ThermoFisher; Catalog# 10002D) were used for each affinity pull-down. m6A antibody-bound RNAs were eluted with 100 μl elution buffer and recovered by RNA Clean and Concentrator-5 (Zymo), and subjected to RNA library preparation with TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Cells were treated with lentivurs expressing control shRNA or target (METTL3 or METTL14) shRNA for 24 hours and were cultured for another 7 days before RNA extraction.

value: Brain tumor PBT003 gliblastoma stem cells

tag: molecule purification

value: poly(dT) selected RNA, fragmented, and pulled down by m6A-antibody


title: PBT003 gliblastoma stem cells, METTL14 shRNA 1, m6A-IP

description:
RNA-seq data of m6A-IP RNA from PBT003 gliblastoma stem cells treated with virus expressing METTL14 shRNA 1
shM14.R1.bed


title: PBT003 gliblastoma stem cells, METTL3 shRNA, m6A-IP

description:
RNA-seq data of m6A-IP RNA from PBT003 gliblastoma stem cells treated with virus expressing METTL3 shRNA
shM3.R1.bed


title: PBT003 gliblastoma stem cells, control shRNA, m6A-IP

description:
RNA-seq data of m6A-IP RNA from PBT003 gliblastoma stem cells treated with virus expressing control shRNA
ShControl.R1.bed


title: Lgr5_high_751P_01_SCBC-03

description: Lgr5 GFP/+ mice


title: Oregon R, Fab2L White* rep 3


title: Lgr5_high_751P_01_SCBC-01

description: Lgr5 GFP/+ mice


title: PBT003 gliblastoma stem cells, METTL14 shRNA 2, Input

description:
RNA-seq data (input RNA) of PBT003 gliblastoma stem cells treated with virus expressing control METTL14 shRNA2
shM14.R2.bed

source_name: PBT003 gliblastoma stem cells treated with virus expressing METTL14 shRNA 2

value: poly(dT) selected RNA, fragmented


title: PBT003 gliblastoma stem cells, METTL14 shRNA 1, Input

description:
RNA-seq data (input RNA) of PBT003 gliblastoma stem cells treated with virus expressing control METTL14 shRNA1
shM14.R1.bed

source_name: PBT003 gliblastoma stem cells treated with virus expressing METTL14 shRNA 1


title: Aged stem cells 3

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Stem cells obtained from Proximal intestinal crypts from a Male Lgr5-eGFP-IRES-CreERT2 reporter mouse on C57Bl6/SV129 background, aged 20-22 months

data_processing:
Adapters and barcodes were trimmed from raw reads, which were filtered using a base quality cutoff <30 and zero 'Ns' allowed.  High quality reads were aligned to the mm10 mouse genome with annotations provided by UCSC.  Transcripts were aligned to produce FPKM.
Raw reads were thresholded at 1, log2 transformed, normalized using the DESeq algorithm, and baselined to the median of all samples.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Aged stem cells

growth_protocol: Proximal small intestines were obtained from young and aged mice, villi removed, and crypts were isolated.  RNA isolated from stem and paneth cells obtained from intestinal crypts was used for RNA sequencing

extract_protocol:
RNA was isolated using the QIAGEN Rneasy minikit.
Stem cell sample libraries were prepared using standard Illumina protocols. Paneth cells were prepared using Clonetech Smarter Pico RNA seq kit.

tag: genotype/variatation

value: Lgr5-eGFP-IRES-CreERT2 reporter mouse

value: 20-22 months

value: Proximal intestinal crypts

tag: cell subtype

value: Stem


title: Lgr5_high_751P_01_SCBC-02

description: Lgr5 GFP/+ mice

value: Lgr5 intestinal stem cells (ISCs)


title: PBT003 gliblastoma stem cells, control shRNA, Input

description:
RNA-seq data (input RNA) of PBT003 gliblastoma stem cells treated with virus expressing control shRNA
ShControl.R1.bed


title: Aged stem cells 1


title: Aged stem cells 2


title: PBT003 gliblastoma stem cells, METTL3 shRNA, Input

description:
RNA-seq data (input RNA) of PBT003 gliblastoma stem cells treated with virus expressing control METTL3 shRNA
shM3.R1.bed

source_name: PBT003 gliblastoma stem cells treated with virus expressing METTL3 shRNA


title: Young stem cells 1

description: Stem cells obtained from Proximal intestinal crypts from a Male Lgr5-eGFP-IRES-CreERT2 reporter mouse on C57Bl6/SV129 background, aged 2-3 months

source_name: Young stem cells

value: 2-3 months


title: Young stem cells 3


title: Aged paneth cells 3

description: Paneth cells obtained from Proximal intestinal crypts from a Male Lgr5-eGFP-IRES-CreERT2 reporter mouse on C57Bl6/SV129 background, aged 20-22 months

source_name: Aged paneth cells

value: Paneth


title: Aged paneth cells 2


title: Oregon R, Fab2L White* rep 1

value: Oregon-R


title: Young stem cells 2


title: Young paneth cells 3

description: Paneth cells obtained from Proximal intestinal crypts from a Male Lgr5-eGFP-IRES-CreERT2 reporter mouse on C57Bl6/SV129 background, aged 2-3 months

source_name: Young paneth cells


title: Young paneth cells 2


title: Aged paneth cells 1


title: Young paneth cells 4


title: Hep2

description: Primary hepatocytes from adult liver

data_processing:
Following removal of primers and barcodes, raw reads were aligned to the human genome Hg19 using TopHat (version 2.0.13), using transcripts provided by UCSC and Ensembl.
Transcript abundances were measured in FPKM, which were normalized to the median of all samples.
Genome_build: Hg19
Supplementary_files_format_and_content: [.txt] files with gene symbol and FPKM

source_name: Primary hepatocytes

growth_protocol: iPSC cell–derived hepatic endoderm cells were routinely generated by endoderm differentiation cultures (activin and Wnt3a in B27 supplemented RPMI medium for 6 days and KO serum and DMSO in KO media for 3 days) on matrigel coated plastic. MSC and HUVEC are cultured separately in their specifc culture media, supplied by Lonza.  Hepatic specified iPSC were dissociated with Accutase and re-plated on Matrigel after mixed with dissociated MSC and HUVEC. The liver organoids were harvested at day 0, 2,4,6 of co-culture with 50% of Hepatic Growth Medium (Lonza) and 50% of EGM Endothelial cell Growth Medium, (Lonza), supplemented with Dexamethasone, FBS, HGF and Oncostatin M.

extract_protocol:
RNA was harvested using Trizol reagent. miRNAesy kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell population

value: Primary hepatocytes

tag: time


title: Young paneth cells 1

value: male


title: TkLB4

description: Human iPSC-derived liver bud at day 6

source_name: Liver buds at day 6

value: Liver bud

value: day 6


title: TkLB5

description: Human iPSC-derived liver bud at day 6


title: TkLB10

description: Human iPSC-derived liver bud at day 4

source_name: Liver buds at day 4

value: day 4


title: NHL

description: Whole human liver

source_name: Whole liver

value: Whole liver


title: TkLB9

description: Human iPSC-derived liver bud at day 4


title: TkLB6

description: Human iPSC-derived liver bud at day 6


title: TkLB7

description: Human iPSC-derived liver bud at day 4


title: TkLB11

description: Human iPSC-derived liver bud at day 2

source_name: Liver buds day 2

value: day 2


title: Base2

description: Human iPSC-derived liver bud at day 0

source_name: Liverbud at '0' time

value: day 0


title: TkHE5

description: Human hepatic-specified endoderm iPSC

source_name: Hepatic endoderm

value: Hepatic-specified endoderm iPSC


title: Base3

description: Human iPSC-derived liver bud at day 0


title: TkLB13

description: Human iPSC-derived liver bud at day 2


title: THP1-Mebendazole-3

city: London

first: Jasper

middle: de

last: de Boer

state: Greater London

address: 30 Guilford Street

department: Developmental Biology and Cancer Programme

country: United Kingdom

institute: UCL Great Ormond Street Institute of Child Health

data_processing:
Analysis performed with the BaseSpace® RNA Express app consisting of the following steps:
Alignment: Reads for each sample are aligned against the corresponding genome using the Spliced Transcripts Alignment to a Reference (STAR) software
Post-Alignment: After alignment, the BAM files are sorted, indexed, and bedGraph coverage files are created using bedtools
Read Counting: Gene expression is estimated at the gene level by counting the number of aligned reads that overlap each gene present in the annotation. The counting strategy is similar to htseq-count in the ‘union’ mode
Global Expression: The raw read counts are used as input for differential expression analysis using R and DESeq2
Pairwise Differential Expression: A new R script for the differential analysis is executed. This script loads the counts for all samples in this comparison and performs a pairwise differential expression analysis between them using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including counts for each Sample

growth_protocol: THP-1 cells (monocyte cell line) (ATCC , Manassas, VA, USA) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with PureLink® RNA Mini Kit according to manufacturers instructions
Indexed RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols

treatment_protocol: THP-1 cells were either treated with 10uM Mebendazole or Vehicle Control (DMSO) for 6 hours

tag: cell line

tag: agent

value: Mebendazole

tag: sample pair


title: THP1-Mebendazole-2


title: THP1-Mebendazole-1


title: THP1-control-2

value: DMSO


title: TkDE2

description: Human definitive endoderm iPSC

source_name: Definitive endoderm

value: Definitive endoderm iPSC


title: TkDE3

description: Human definitive endoderm iPSC


title: TkDE1

description: Human definitive endoderm iPSC


title: TkHE2

description: Human hepatic-specified endoderm iPSC


title: MSC1

description: Human MSC

source_name: Mesenchymal stem cells (MSC)

value: MSC


title: THP1-control-1


title: MSC3

description: Human MSC


title: U1 rep3

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

country: Japan

institute: Kagoshima University

data_processing:
Illumina RTA 1.18.61 software used for basecalling.
sequence reads were filtered using the Illumina chastity filter.
sequence reads were trimmed using Trimmomatic v0.32.
sequence reads were mapped using BWA-MEM algorithm of bwa v0.7.12.
mapped fragments were counted using perl script.
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

organism: Aspergillus luchuensis

source_name: U1_whole cell

extract_protocol:
Rice koji was frozen by liquid nitrogen and RNA was extracted by RNAiso (Takara Bio). The RNA was purified by SV total RNA isolation system (Promega).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: high starch degrading mutant strain U1

value: whole cell


title: U1 rep2


title: TkLB12

description: Human iPSC-derived liver bud at day 2


title: HUVEC3

description: Human HUVEC

source_name: Human umbilical vein endothelial cells (HUVEC)

value: HUVEC


title: S1-KECSTclone4

city: Stanford

first: Jonghyeob

last: Lee

state: CA

address: 279 Campus Drive, Beckman Center B300

institute: Stanford University School of Medicine

data_processing:
base-calling, alignment, filetering and peak-calling: DNAstar ArrarStar and Qseq version 12.3.1 build 53
generation of normalized abundance measurements: DNAstar ArrarStar and Qseq version 12.3.1 build 53
Genome_build: Human Genome Assembly hg19
Supplementary_files_format_and_content: Tab-delimited text file, Total Raw count

source_name: transduced ductal cell clone

growth_protocol: FACS-sorted human adult pancreatic ductal cells were infected with appropriate lentivirus. Next day, infected cells were washed twice with PBS and resuspended with 120 µl sphere culture media. 200 µl of growth factor-reduced Matrigel (BD Biosciences) was then added the mixture was placed around the bottom rim of each well of 12-well plate. After solidification at 37°C for 60 min, each well was overlaid with 2mL of sphere culture media. Media were replaced twice a week and the spheres were harvested after 2 to 3 weeks for passaging.

extract_protocol:
Spheres were harvested and washed with PBS twice and the cell pellets were snap frozen in liquid nitrogen. Total RNA was prepared with PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
RNA-Seq libraries were built using KAPA Stranded mRNA-Seq kit (KK8400, KAPA Biosystems, Wilmington, MA) according to the manufacturer’s recommendation. Barcoded libraries were multiplexed and sequenced as single-end 75bp reads on Illumina NextSeq 500 sequencer.

treatment_protocol: cells were infected with a combination of lentiviruses encoding oncogenic KRAS (K) or ERBB2 (E), or lentiCRISPRv2 encoding sgRNAs against CDKN2A, SMAD4, or TP53 (CST).

tag: cell type

value: primary adult pancreatic ductal cells

tag: mutations

value: KECST

tag: growth type

value: 3-dimensional sphere


title: S1-KECSTclone3


title: S1-KCSTclone4

value: KCST


title: S1-KCSTclone3


title: HUVEC2

description: Human HUVEC


title: Base1

description: Human iPSC-derived liver bud at day 0

value: Liver bud


title: U1 rep1

tag: tissue


title: S1-CTRL

source_name: control ductal cell

value: No


title: THP1-control-3


title: S2-KECSTclone8


title: WT rep3

source_name: WT_whole cell

tag: strain background

value: wild type


title: HUVEC1

description: Human HUVEC


title: TkUD3

description: Human iPSC

source_name: Baseline/undifferentiated iPSC

value: Baseline iPSC


title: MSC2

description: Human MSC


title: WT rep2


title: TkUD2

description: Human iPSC


title: TkUD1

description: Human iPSC


title: WT rep1


title: S2-KCTclone3

value: KCT


title: S2-KCSTclone8


title: Sample_Th17_H3K27Ac_rep1

status: Public on Mar 13 2017

city: New York

first: Rajal

last: Sharma

state: NY

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

data_processing:
Basecalls performed using CASAVA version 1.4
Read sequences were filtered by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were called using MACS with Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
Genome_build: mm9
Supplementary_files_format_and_content: Wig files generated by computing feature density over a 5 bp window across the genome. http://genome.ucsc.edu/goldenPath/help/wiggle.html

source_name: primary T cells

growth_protocol: CD4+ T cells were purified from spleen. Naïve T cells were activated with plate bound anti-CD3 and anti-CD28 plus IL6(20ng/mL), TGFb(2.5ng/mL) . The cells were cultured for 48h to 72h before harvesting for further analysis.

extract_protocol:
Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies.
ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase.  An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar.  Adaptor-modified fragments were enriched by 16 cycles of PCR amplification.  The DNA library prep was validated in Bioanalyzer for quantity and size.

tag: strain

value: primary T cells

tag: chip antibody


title: Sample_Th17_enh_input_rep1


title: Sample_Th17_H3K27Ac_rep2


title: Sample_Th17_enh_input_rep2


title: Sample_JQ1_input_rep2

extract_protocol:
Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies.
ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size.


title: Sample_Th17_H3K4me1_rep2


title: Sample_Th17_H3K4me1_rep1


title: Sample_JQ1_input_rep1


title: Sample_JQ1_Brd2_rep2

value: Brd2 (Bethyl; IHC-00612)


title: Sample_JQ1_Brd2_rep1


title: Sample_JQ1_Brd4_rep2

value: Brd4 (Bethyl; IHC-00396)


title: Sample_JQ1_Brd4_rep1


title: Sample_Th17_input_rep1


title: Sample_Th17_Brd4_rep2


title: Sample_Th17_Brd2_rep1


title: RNA LPS 4h_3

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

country: Italy

institute: Istituto Clinico Humanitas

description:
chromatin associated RNA
MacroTFs_189

data_processing:
Reads were quality filtered according to the Illumina pipeline.
Reads were mapped to the mouse mm10 genome and transcripts using TopHat 2.1.0 (PMID:23618408) and Bowtie 2.2.4 (PMID:22388286), with parameters -G --coverage-search --library-type fr-unstranded.
Transcripts abundance were obtained using Cufflinks 2.2.1 (PMID:22383036).
Genome_build: mm10 (GRCm38); transcripts from UCSC Table Browser, refGene table as of 2016-02-04.
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), gene_exp.diff.gz includes the cuffdiff output for untreated (UT) vs LPS_4h-treated cells.

source_name: Primary bone marrow-derived macrophages (BMDM) (7th day of differentiation)

growth_protocol: Bone marrow cells isolated from FVB/Hsd or C57/Bl6 mice were plated in 10 cm plates in 10ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol).

extract_protocol: Nascent 4-thio-uridine (4sU) labelled RNA was obtained adding 4sU to the cell culture medium at a final concentration of 300 mM for 45 min before harvesting the cells. The 4sU-labeled RNA was isoleted ad described (Rabani M. et al., 2011).Chromatin associated RNA was prepared as previously described (Bhatt et al., Cell 2012). Libraries were prepared from 40 ng of  RNA using the TruSeq RNA sample preparation kit (Illumina), skipping the step of either ribosomal depletion and polyA-selection.

value: bone marrow

value: macrophage

tag: days of differentiation

tag: treatment

value: LPS (10 ng/ml) for 4 hours


title: Sample_Th17_Brd2_rep2


title: RNA LPS 4h_2

description:
chromatin associated RNA
MacroTFs_187


title: RNA UT_3

description:
chromatin associated RNA
MacroTFs_188

value: No treatment


title: Sample_Th17_Brd4_rep1


title: RNA UT_2

description:
chromatin associated RNA
MacroTFs_186


title: RNA UT_1

description:
chromatin associated RNA
MacroTFs_184


title: RNApolII_Cep55_16

data_processing:
Reads quality filtered according to the Illumina pipeline.
Reads were mapped to the genome using Bowtie2 v2.2.4 (PMID:22388286). Alignments with low mapping quality (MAPQ<10) and PCR duplicates were removed.
Peak calling was performed using MACS2 v2.1.0 (PMID:18798982). Each IP was compared to input DNA. Each ChIP was compared to input DNA. Enriched regions (peaks) were filtered by q-value <= 0.01 and fold enrichment >= 4.
Peaks falling in blacklisted regions identified by the ENCODE project (The ENCODE Project Consortium, 2012) were discarded.
Genome_build: mm10 (GRCm38).
Supplementary_files_format_and_content: *.bed: list of the peaks called by MACS2 after filtering

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 10ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol).

extract_protocol: Roughly 80 x 10^6 (for Fli1, Elf1 and Pol II ChIP-seq), 40 x 10^6 (for GABP-α, Elf4 ChIP-seq) or 5 x 10^6 (for PU.1 and histone modifications ChIP-seq) cells were fixed in 1% formaldehyde for 10min and were lysed with RIPA buffer, after chromatin shearing by sonication. Lysate was immunoprecipitated with 5-10 μg of antibody. Antibodies were pre-bound overnight to 50-100 μl of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA libraries were prepared for HiSeq 2000 Illumina sequencing using a standard protocol (Garber et al., 2012) with slight modifications (Ostuni et al., 2013).

value: Adult strain BALB/c male

value: macrophage; Abelson murine leukemia virus transformed

tag: antibody

value: Pol II antibody from Santa Cruz (sc-899)


title: GABPa_WT_AAM_5h

source_name: Primary bone marrow-derived macrophages (BMDM); 7th day of differentiation

value: GABP-α antibody from Santa Cruz (sc-22810)

value: alpha amanitin 10μg/ml for 5 hours (SIGMA)


title: Input

description:
MacroTFs_139
Whole extract

value: not needed


title: RNA LPS 4h_1

description:
chromatin associated RNA
MacroTFs_185


title: ELF4_WT_LPS_4h

value: Elf4 home made antibody

value: 4h LPS treatment (10ng/ml)


title: GABPa_WT_LPS_UT


title: GABPa_WT_AAM_UT


title: ELF4_WT_AAM_5h


title: RNApolII_WT_LPS_UT


title: ELF4_WT_LPS_UT


title: Sample_Th17_input_rep2


title: WT_AAM_5h_R1

description: ATAC-seq

data_processing:
Library strategy: ATAC-seq
Reads quality filtered according to the Illumina pipeline.
Reads were mapped to the genome using Bowtie2 v2.2.4 (PMID:22388286). Alignments with low mapping quality (MAPQ<10) were removed.
PCR duplicates and reads aligned to chrM were removed with Samtools v0.1.19 (PMID:19505943).
Reads aligning to the forward strand were offset by +4 bp, and reads aligning to the reverse strand were offset −5 bp as described in Buenrostro et al. 2013 (PMID:24097267)
Genome_build: mm10 (GRCm38).
Supplementary_files_format_and_content: bigWig

source_name: Primary bone marrow-derived macrophages (BMDM)

extract_protocol: The original ATACseq protocol {Buenrostro, 2013 #118} was modified according to Lara-Astiaso et al. {Lara-Astiaso, 2014 #122}. Briefly, 50 X 103 cells were pelleted by centrifugation and re-suspended in 25 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630). Nuclei were pelleted by centrifugation for 20 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 25 µl of reaction buffer containing 1 µl of Tn5 transposase (made in house) and 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2). The reaction was incubated at 37ºC for one hour. Then 5 µl of clean up buffer (900mM NaCl, 300mM EDTA), 2ul of 5% SDS and 2 µl of Proteinase K (20 µg/µl) (New England Biolabs) were added and incubated for 30 min at 40 ºC. Tagmented DNA was isolated using SPRI beads (2x). For library amplification, two sequential PCR reactions were performed in order to enrich small tagmented DNA fragments. We used 2 µl of indexing primers and KAPA HiFi HotStart ready mix. After the first PCR, fragments smaller than 600 bp were isolated using SPRI cleanup and a second PCR was performed using the same conditions in order to obtain the final library. DNA concentration was measured with a Qubit fluorometer (Life Technologies) and library quality was analyzed using a Bioanalyzer (Agilent Technologies). Libraries where sequenced on an Illumina HiSeq 2000.

value: macrophages

tag: day of differentiation


title: ELF4_WT_AAM_UT


title: ELF1_WT_UT

value: Elf1 antibody from Santa Cruz (sc-631X)


title: WT_AAM_UT_R1

description: ATAC-seq


title: BRG1fl_NANOG_72hTAM_rep3

first: Hamish

middle: W

last: King

address: 4 Newark St

department: Blizard Institute

institute: Queen Mary University of London

data_processing:
For ATAC-seq and ChIP-seq, paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options. Non-uniquely mapping reads and reads mapping to custom “blacklist” of artificially high regions of the genome were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
Merged BAM files were used to make a genome track using DANPOS2, with the input control provided as background.
Peakcalling was performed using the DANPOS2 dpeak function using untreated and treated samples in biological triplicate with input control as background.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files representing genome coverage (with background subtracted) for merged biological triplicate were generated using DANPOS2.

source_name: Embryonic stem cells, untreated control, NANOG ChIP-seq

growth_protocol: Mouse embryonic stem cells containing a doxycycline-sensitive OCT4 transgene (ZHBTC4; (Niwa et al., 2000)) were grown on gelatin-coated plates in DMEM (Gibco, Carlsbad, CA) supplemented with 15 % FBS, 10 ng/mL leukemia-inhibitory factor, penicillin/streptomycin, beta-mercaptoethanol, l-glutamine and non-essential amino-acids.  Brg1fl/fl ESCs were previously described (Ho et al., 2011) and were maintained in DMEM KnockOut supplemented with 10 % FBS and 5 % serum replacement, plus additional factors described for ZHBTC4 ESCs.

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Farcas et al., 2012), with minor modifications. Cells were fixed for 1 h in 2 mM DSG and 12.5 min in 1 % formaldehyde. Reactions were quenched by the addition of glycine to a final concentration of 125 µM. After cell lysis and chromatin extraction, chromatin was sonicated using a BioRuptor sonicator (Diagenode), followed by centrifugation at 16,000 × g for 20 min at 4°C, and used fresh or stored at -80°C. Chromatin was quantified by denaturing chromatin 1:10 0.1 M NaOH, and measuring DNA concentration by NanoDrop and 150 µg chromatin/IP was diluted ten-fold in ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl (pH 8), 150 mM NaCl) prior to pre-clearing with prepared protein A magnetic Dynabeads (Invitrogen, Carlsbad, CA) which had been blocked for 1 h with 0.2 mg/mL BSA and 50 µg/mL yeast tRNA. Antibody-bound chromatin was isolated on protein A magnetic Dynabeads. ChIP washes were performed with low salt buffer (0.1 % SDS, 1 % Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1 % SDS, 1 % Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1 % NP40, 1 % sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)) and TE buffer (x2 washes) (10 mM Tris-HCl (pH 8.0), 1 mM EDTA).
To prepare ChIP-seq material, ChIP DNA was eluted using 1 % SDS 100 mM NaHCO3, and cross-links reversed at 65°C in the presence of 200 mM NaCl. Samples were then treated with RNase and proteinase K before being purified with ChIP DNA Clean & Concentrator™ kit (Zymo, Irvine, CA). ChIP-seq libraries were prepared using the NEBNext Ultra DNA Library Prep Kit, and sequenced as 38bp paired-end reads on Illumina NextSeq500 platform. All ChIP-seq experiments were carried out in biological triplicate.

treatment_protocol: ZHBTC4 cells were treated with 1 µg/mL doxycycline for 24 h to ablate OCT4 expression. Brg1fl/fl ESCs were treated with 4-hydroxytamoxifen for 72 h to ablate BRG1 protein levels.

value: Brg1fl/fl (BRG1 conditional)

tag: ChIP

value: NANOG

value: Cell Signalling (#8822)

tag: replicate

tag: passage


title: BRG1fl_NANOG_72hTAM_rep2

tag: cell line


title: BRG1fl_NANOG_72hTAM_rep1


title: RNApolII_WT_2


title: PU1_WT_AAM_UT

value: bone marrow

value: PU.1 home made antibody


title: BRG1fl_BRG1_72hTAM_rep3

source_name: Embryonic stem cells, untreated control, BRG1 ChIP-seq


title: BRG1fl_NANOG_UNT_rep1


title: BRG1fl_NANOG_UNT_rep2


title: BRG1fl_NANOG_UNT_rep3


title: BRG1fl_BRG1_72hTAM_rep2


title: BRG1fl_BRG1_72hTAM_rep1


title: BRG1fl_BRG1_UNT_rep2


title: BRG1fl_BRG1_UNT_rep1


title: FLI1_WT_UT

value: macrophage

value: Fli1 antibody from Santa Cruz (sc-356X)


title: ZHBTC4_SS18_24hDOX_rep3

source_name: Embryonic stem cells, untreated control, SS18 ChIP-seq

value: ZHBTC4 (OCT4 conditional)

value: Cell Signalling (#21792)


title: ZHBTC4_SS18_24hDOX_rep2


title: ZHBTC4_SS18_UNT_rep2


title: ZHBTC4_SS18_UNT_rep3


title: BRG1fl_nucRNA_UNT_rep3 (RNA-Seq)

data_processing:
RNA-seq reads were initially aligned against the rRNA genomic sequence (GenBank: BK000964.3) using bowtie2 to filter out rRNA fragments, prior to alignment using the STAR RNA-seq aligner (Dobin et al., 2012). To improve mapping of nascent, intronic sequences, reads which failed to map using STAR were aligned against the genome using bowtie2.
Biological triplicate read counts were determined using custom scripts for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered on size (>200bp), gene body and TSS mappability, unique TSS and TTS, so as to remove poorly mappable and highly similar transcripts.
The final set of 20,633 genes were used for differential analysis using DESeq2 (Love et al., 2014), with default settings and a significance threshold of padj < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: [.bw] Stranded bigWig files representing genome coverage for merged biological triplicate
Supplementary_files_format_and_content: [.txt] ReadCounts and DESeq2 results

source_name: Embryonic stem cells, untreated control, nucRNA-seq

extract_protocol:
1 × 10e7 cells were resuspended in 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05 % NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT)  for 1 min at room temperature to isolate nuclei. Nuclei were centrifuged at 1,000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer. Nuclei were then resuspended in 1mL of TriZOL reagent (ThermoScientific) according to the manufacturer’s protocol. Nuclear RNA was treated with the TURBO DNA-free Kit (ThermoScientific) and depleted for rRNA using the NEBNext rRNA Depletion Kit (NEB).
RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA-seq kit (NEB) and libraries were sequenced on the Illumina NextSeq500 with 80bp paired-end reads.

value: untreated control


title: BRG1fl_nucRNA_72hTAM_rep1 (RNA-Seq)

source_name: Embryonic stem cells, tamoxifen-treated, nucRNA-seq

value: tamoxifen-treated


title: ZHBTC4_nucRNA_24hDOX_rep3 (RNA-Seq)

source_name: Embryonic stem cells, doxycycline-treated, nucRNA-seq

value: doxycycline-treated


title: BRG1fl_nucRNA_72hTAM_rep3 (RNA-Seq)


title: BRG1fl_nucRNA_72hTAM_rep2 (RNA-Seq)


title: BRG1fl_nucRNA_UNT_rep2 (RNA-Seq)


title: ZHBTC4_nucRNA_24hDOX_rep2 (RNA-Seq)


title: BRG1fl_nucRNA_UNT_rep1 (RNA-Seq)


title: ZHBTC4_nucRNA_24hDOX_rep1 (RNA-Seq)


title: ZHBTC4_nucRNA_UNT_rep3 (RNA-Seq)


title: ZHBTC4_nucRNA_UNT_rep2 (RNA-Seq)


title: ZHBTC4_nucRNA_UNT_rep1 (RNA-Seq)


title: BRG1fl_BRG1_UNT_rep3


title: BRG1fl_SOX2_72hTAM_rep3 (ChIP-Seq)

source_name: Embryonic stem cells, tamoxifen-treated, SOX2 ChIP-seq

value: Cell Signalling (#23064)


title: BRG1fl_Input_UNT_rep1 (ChIP-Seq)

source_name: Embryonic stem cells, untreated control, sonicated control

value: untreated control, sonicated control


title: BRG1fl_SOX2_72hTAM_rep1 (ChIP-Seq)


title: BRG1fl_SOX2_UNT_rep2 (ChIP-Seq)

source_name: Embryonic stem cells, untreated control, SOX2 ChIP-seq


title: ZHBTC4_SS18_24hDOX_rep1


title: BRG1fl_SOX2_72hTAM_rep2 (ChIP-Seq)


title: BRG1fl_SOX2_UNT_rep3 (ChIP-Seq)


title: BRG1fl_OCT4_72hTAM_rep3 (ChIP-Seq)

source_name: Embryonic stem cells, tamoxifen-treated, OCT4 ChIP-seq

value: Cell Signalling (#5677)


title: ZHBTC4_SS18_UNT_rep1


title: BRG1fl_SOX2_UNT_rep1 (ChIP-Seq)


title: BRG1fl_OCT4_UNT_rep3 (ChIP-Seq)

source_name: Embryonic stem cells, untreated control, OCT4 ChIP-seq


title: BRG1fl_OCT4_72hTAM_rep2 (ChIP-Seq)


title: BRG1fl_OCT4_UNT_rep2 (ChIP-Seq)


title: BRG1fl_OCT4_UNT_rep1 (ChIP-Seq)


title: BRG1fl_OCT4_72hTAM_rep1 (ChIP-Seq)


title: ZHBTC4_Input_UNT_rep1 (ChIP-Seq)


title: ZHBTC4_BRG1_24hDOX_rep3 (ChIP-Seq)

source_name: Embryonic stem cells, doxycycline-treated, BRG1 ChIP-seq


title: ZHBTC4_BRG1_24hDOX_rep1 (ChIP-Seq)


title: ZHBTC4_BRG1_24hDOX_rep2 (ChIP-Seq)


title: ZHBTC4_BRG1_UNT_rep1 (ChIP-Seq)


title: ZHBTC4_BRG1_UNT_rep3 (ChIP-Seq)


title: ZHBTC4_NANOG_24hDOX_rep3 (ChIP-Seq)

source_name: Embryonic stem cells, doxycycline-treated, NANOG ChIP-seq


title: ZHBTC4_BRG1_UNT_rep2 (ChIP-Seq)


title: ZHBTC4_NANOG_24hDOX_rep1 (ChIP-Seq)


title: ZHBTC4_NANOG_24hDOX_rep2 (ChIP-Seq)


title: ZHBTC4_NANOG_UNT_rep3 (ChIP-Seq)


title: ZHBTC4_NANOG_UNT_rep2 (ChIP-Seq)


title: PU1_WT_AAM_5h

value: alpha amanitin 10μg/ml for 5 hours (SIGMA)


title: ZHBTC4_NANOG_UNT_rep1 (ChIP-Seq)


title: ZHBTC4_SOX2_24hDOX_rep2 (ChIP-Seq)

source_name: Embryonic stem cells, doxycycline-treated, SOX2 ChIP-seq


title: ZHBTC4_SOX2_24hDOX_rep3 (ChIP-Seq)


title: ZHBTC4_SOX2_UNT_rep3 (ChIP-Seq)


title: ZHBTC4_SOX2_24hDOX_rep1 (ChIP-Seq)


title: ZHBTC4_SOX2_UNT_rep1 (ChIP-Seq)


title: ZHBTC4_SOX2_UNT_rep2 (ChIP-Seq)


title: ZHBTC4_OCT4_24hDOX_rep2 (ChIP-Seq)

source_name: Embryonic stem cells, doxycycline-treated, OCT4 ChIP-seq


title: ZHBTC4_OCT4_24hDOX_rep3 (ChIP-Seq)


title: ZHBTC4_OCT4_24hDOX_rep1 (ChIP-Seq)


title: ZHBTC4_OCT4_UNT_rep2 (ChIP-Seq)


title: ZHBTC4_OCT4_UNT_rep3 (ChIP-Seq)


title: ZHBTC4_OCT4_UNT_rep1 (ChIP-Seq)


title: BRG1fl_ATAC_72hTAM_rep2 (ATAC-Seq)

data_processing:
Library strategy: ATAC-seq
For ATAC-seq and ChIP-seq, paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options. Non-uniquely mapping reads and reads mapping to custom “blacklist” of artificially high regions of the genome were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
Merged BAM files were used to make a genome track using DANPOS2, with the Tn5 control provided as background.
Peakcalling was performed using the DANPOS2 dpeak function using untreated and treated samples in biological triplicate with Tn5 gDNA control digestion as background.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files representing genome coverage (with background subtracted) for merged biological triplicates were generated using DANPOS2.

source_name: Embryonic stem cells, tamoxifen-treated, ATAC-seq

extract_protocol:
Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al., 2013). Briefly, 5 × 106 cells were harvested, washed with PBS and nuclei were isolated using 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05 % NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT)  for 1 min at room temperature. Nuclei were centrifuged at 1,000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer (10mM NaCl, 10mM Tris (pH 7.4), 3mM MgCl2), to remove as much of contaminating cytoplasmic and mitochondrial material as possible. Nuclei were then counted, and 5×104 nuclei were resuspended in Tn5 reaction buffer (10mM TAPS, 5mM MgCl2, 10% dimethylformamide) and 2 µl of Tn5 transposase (25µM) made in house according to the previously described protocol (Picelli et al., 2014). Nuclei were then incubated for 30 min at 37°C, before isolation and purification of tagmented DNA using QiaQuick MinElute columns (Qiagen). To control for sequence bias of the Tn5 transposase, an ATAC “input” sample was generated, by tagmenting genomic DNA from ESCs with Tn5 for 30 min at 55°C.
ATAC-seq libraries were prepared by PCR amplification using custom made Illumina barcodes previously described (Buenrostro et al., 2013) and the NEBNext® High-Fidelity 2X PCR Master Mix with 8-10 cycles. Libraries were purified with two rounds of AMPure XP bead cleanup (1.5X beads:sample), followed by quantification by qPCR using SensiMix SYBR (Bioline) and KAPA Library Quantification DNA standards (KAPA Biosystems). ATAC-seq libraries were sequenced on Illumina NextSeq500 using 80bp paired-end reads in biological triplicate.


title: BRG1fl_ATAC_72hTAM_rep3 (ATAC-Seq)


title: E14_Tn5Control (ATAC-Seq)

source_name: Embryonic stem cell genomic DNA, Tn5 tagmented


title: BRG1fl_ATAC_UNT_rep3 (ATAC-Seq)

source_name: Embryonic stem cells, untreated control, ATAC-seq


title: BRG1fl_ATAC_UNT_rep2 (ATAC-Seq)


title: BRG1fl_ATAC_72hTAM_rep1 (ATAC-Seq)


title: BRG1fl_ATAC_UNT_rep1 (ATAC-Seq)


title: ZHBTC4_ATAC_24hDOX_rep3 (ATAC-Seq)

source_name: Embryonic stem cells, doxycycline-treated, ATAC-seq


title: ZHBTC4_ATAC_UNT_rep2 (ATAC-Seq)


title: ZHBTC4_ATAC_UNT_rep3 (ATAC-Seq)


title: ZHBTC4_ATAC_UNT_rep1 (ATAC-Seq)


title: MPC_S3_SPOPwt

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description: Barcode: ACAGTG

data_processing:
Reads (FASTQ files) were mapped to the mouse reference genome sequence (mm10/GRCm38 http://hgdownload.cse.ucsc.edu/downloads.html - mouse) using STAR v2.4.0j
The resulting BAM files were subsequently converted into mapped-read format (MRF) using RSEQtools(Habegger et al., 2011).
Quantification of gene expression was performed via RSEQtools using GENCODE as reference gene–annotation set  (http://www.gencodegenes.org/mouse_releases/9.html). Expression levels (RPKM) were estimated by counting all nucleotides mapped to each gene and were normalized by the total number of mapped nucleotides (per million) and the gene length (per kb).
ComBat(Johnson et al., 2007) was used to remove the batch effect for the downstream gene expression analysis.
Differential expression analysis were performed using the Mann-Whitney Wilcoxon test after transforming the RPKMs via log2(RPKM + 1) from mouse samples. Multiple-hypothesis testing was considered by using Benjamini-Hochberg (FDR) correction.
Genome_build: mm10
Supplementary_files_format_and_content: First column represents the gene name, and second represents the expression level (RPKM) for each gene.

source_name: mouse SPOPwt organoids

growth_protocol: Cell growth was measured in a 96 well format by using PicoGreen (Invitrogen, P7581). For “organoid formation assay” 10 single cells were plated per well (total of 48) on day 1. Number of formed organoids was counted on day 7 as well as day 14 post plating. Size of organoid was measured on day 14 with cellSens software by Olympus.

extract_protocol:
RNA extraction of cell pellets as well as frozen cores from fresh frozen tissue was done as described by manufacture using the automated Maxwell®16 system (Promega, AS1280 and AS1270). cDNA synthesis was transcribed by using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, #4374966). Quantitative PCR was done on the Roche Light Cycler 480.
Organoids (5 pairs from model A and one pair from model B of SPOP mutant and controls) were prepared for RNA sequencing using TruSeq RNA Library Preparation Kit v2. RNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent Technologies). Each sample was then sequenced with the HiSeq 2500 to generate 2×51-bp paired-end reads.

treatment_protocol: Prostate tissue was extracted from euthanized mice and digested as previously described (Lukacs et al., 2010). Cells were plated in Matrigel (Corning, BD 356231) and covered by mouse media containing 5-50ng/ml EGF. Media and culture condition as previously described (Karthaus et al., 2014). Inducible organoid systems: Mouse prostate cells were virally infected with a CreERT2 construct and selected with puromycin (Line_A) or generated from a mouse containing transgenic TMPRSS2-CreERT2 construct (Line_B, (Gao et al., 2016)). CreERT2 was activated by adding 1μM 4-Hydroxytamoxifen (Sigma-Aldrich, T176) into the media over night. Either GFP or sham (for control cells) sorting was performed on the BD FACSAria – II. Noninducible organiod system: Organoid lines with Cre expression under the control Probasin 24 promoter were generated by taking tissue from PbCre negative (Control) and PbCre;R26F133V  (SPOPmut) mice.

value: prostate organoid

tag: genotype/variation

value: SPOPwt


title: MPC_S5_SPOPwt

description: Barcode: TAGCTT


title: MPC_S4_SPOPwt

description: Barcode: CCGTCC


title: MPC_S2_SPOPwt

description: Barcode: CCGTCC


title: MPC_S1_SPOPwt

description: Barcode: ACAGTG


title: MPC_S0_SPOPwt

description: Barcode: CTTGTA


title: MPC_S4_SPOPmut

description: Barcode: GTCCGC

source_name: mouse SPOPmut organoids

value: SPOPmut


title: MPC_S5_SPOPmut

description: Barcode: ATCACG


title: MPC_S2_SPOPmut

description: Barcode: GTCCGC


title: ngr1_KO_pyx2

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The first 6 and last 20 nucleotides for each read were trimmed to remove lower-scoring base reads. Trimming was performed using the FASTX toolkit. Sequences were aligned using Tophat v.2.0.8  to the latest reference UCSC human genome and transcript annotation (mm10), and only reads that mapped to a unique location within the genome were considered for further analysis.
Tophat alignments were processed using Cufflinks v2.1.1 software to calculate differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. Cuffdiff output format.

source_name: pyramidotomized cortex

extract_protocol:
GFP+ Corticospinal motor neurons from crym-GFP transgenic wild type and ngr1-/- mice were harvested via laser capture microdissection from flash frozen brains, cut on a cryostat. RNA was harvested with QIAGEN Rneasy Micro kit (cat#74004). 500pg of total RNA was processed with Clontech's SMARTer Ultra Low Kit (cat# 634888) was used for the construction of sequencing libraries.
Covaris AFA system was used prior to standard Illumina protocols.

value: crym-GFP+ corticospinal motor neurons

tag: age

value: post natal day 56

tag: genotype


title: ngr1_crym_FB2

source_name: intact cortex

value: crym-GFP+/FB+ corticospinal motor neurons


title: ngr1_crym_FB3


title: 106_Myd88-E_100uM_noEGF

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

description: PTEC-TERT1 cells treated with Myd88-E (100uM) for 6h in the absence of exogeneous EGF

data_processing:
Base-calling, filtering, QC, and alignment was handled automatically by IonTorrent Server Suite (version 4.0.2)
Amplicon coverage is reported by IonTorrent Server Suite (version 4.0.2) as a tab-delimited file, which was converted into GCT format by in-house scripts.
Genome_build: hg19
Supplementary_files_format_and_content: GCT format, with amplicon counts for pathway reporter genes in each sample

growth_protocol: PTEC-TERT1 (Evercyte GmbH, Austria) were cultured according to the manufacturer’s instructions in PTEC medium [DMEM/F12 without phenol red (Invitrogen 110390-021) containing 1% Pen/Strep (Gibco: 15140-122), 10 mM Hepes (Gibco: 15630-056) , 5.0 µg/ml human insulin (Gibco: 41400-045), 5.0 µg/ml human transferrin (Gibco: 41400-045), 8.65 ng/ml sodium selenite (Gibco: 41400-045), 0.1µM hydrocortisone (Sigma H6909), 10 ng/ml human recombinant Epidermal Growth Factor (R&D Systems : 236-EG-200), 3.5µg/ml ascorbic acid (SIGMA : A4544 powder), 25 ng/ml prostaglandin E1(SIGMA : P5515), 3.2 pg/ml Triiodo-L-thyronine (Sigma T-5516) and 100 µg/ml Geneticin (Gibco: 10131-027)].

extract_protocol:
Cell were harvested 6h after ASO addition by removing the culture medium. Cell lysates in 50 µl RLT buffer (QIAGEN, Hombrechtikon, Switzerland) were immediately frozen and stored at -80°C.
10 ng of total RNA from each time point and biological replicate was reverse transcribed to cDNA and amplified by limited PCR according to the protocol supplied with the Ion AmpliSeq™ RNA Library Kit (Life Technologies, Carlsbad, USA, Catalog number 4482335). After primer digestion, adapters and barcodes were ligated to the amplicons followed by magnetic bead purification. The purified library was amplified, purified and stored at -20°C. Amplicon size and DNA concentration was measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer's guide.

treatment_protocol: For ASO toxicity assessment, PTEC-TERT1 were seeded into 96-well plates (Falcon, 353219) at a density of 40 000 and 20 000 cells/well respectively in PTEC medium and grown until confluence prior to treatment with ASOs. ASOs were dissolved in PBS and added to the cell culture at a final concentration of 10, 30 or 100 µM in a final volume of 100 µl. Medium was changed, stored at -20ᵒC for cytokine analysis and refreshed along with AONs every 3 days. PBS served as vehicle control.

tag: cell type

value: PTEC-TERT1 cells

tag: antisense oligonucleotides (asos)

tag: concentration

tag: exogeneous egf

value: FALSE


title: ZHBTC4_ATAC_24hDOX_rep2 (ATAC-Seq)

value: ZHBTC4 (OCT4 conditional)


title: ngr1_KO_pyx1

tag: strain

tag: tissue


title: ngr1_crym_FB1


title: ngr1_KO_control3

value: GFP- cortical tissue


title: 107_Myd88-E_100uM_EGF

description: PTEC-TERT1 cells treated with Myd88-E (100uM) for 6h in the presence of exogeneous EGF

value: TRUE


title: 103_PCSK9-B_100uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-B (100uM) for 6h in the presence of exogeneous EGF


title: 105_Myd88-E_100uM_EGF


title: ngr1_KO_pyx3


title: 101_Scramble-A_100uM_EGF

description: PTEC-TERT1 cells treated with Scramble-A (100uM) for 6h in the presence of exogeneous EGF

value: Scramble-A


title: 102_PCSK9-D_100uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-D (100uM) for 6h in the presence of exogeneous EGF


title: ZHBTC4_ATAC_24hDOX_rep1 (ATAC-Seq)

value: doxycycline-treated


title: ngr1_KO_control1


title: 100_Vehicle_100uM_EGF

description: PTEC-TERT1 cells treated with Vehicle (100uM) for 6h in the presence of exogeneous EGF

value: Vehicle


title: ngr1_KO_control2


title: 098_PCSK9-D_100uM_EGF


title: MPC_S3_SPOPmut

description: Barcode: ATGTCA


title: MPC_S1_SPOPmut

description: Barcode: ATGTCA


title: 099_PCSK9-B_100uM_EGF


title: 096_Vehicle_100uM_EGF


title: MPC_S0_SPOPmut

description: Barcode: GCCAAT


title: 095_Myd88-E_100uM_EGF


title: ngr1_KO_crym2


title: 094_PCSK9-C_100uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-C (100uM) for 6h in the presence of exogeneous EGF


title: 104_PCSK9-C_100uM_EGF


title: ngr1_KO_crym1


title: WT_pyx3

value: wild type


title: 093_PCSK9-B_100uM_EGF


title: 092_Scramble-A_100uM_EGF


title: 091_Vehicle_100uM_EGF


title: WT_pyx2


title: 087_PCSK9-D_100uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-D (100uM) for 6h in the absence of exogeneous EGF


title: 089_PCSK9-C_100uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-C (100uM) for 6h in the absence of exogeneous EGF


title: WT_pyx1


title: ngr1_KO_crym3


title: 085_Vehicle_100uM_noEGF

description: PTEC-TERT1 cells treated with Vehicle (100uM) for 6h in the absence of exogeneous EGF


title: 086_Scramble-A_100uM_noEGF

description: PTEC-TERT1 cells treated with Scramble-A (100uM) for 6h in the absence of exogeneous EGF


title: 097_Scramble-A_100uM_EGF


title: 083_PCSK9-B_100uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-B (100uM) for 6h in the absence of exogeneous EGF


title: 084_PCSK9-C_100uM_noEGF


title: WT_control2


title: 082_Scramble-A_100uM_noEGF


title: WT_crym3


title: 079_PCSK9-C_100uM_noEGF


title: WT_control1


title: 081_Vehicle_100uM_noEGF


title: 077_PCSK9-D_100uM_noEGF


title: 078_PCSK9-B_100uM_noEGF


title: 090_Myd88-E_100uM_noEGF


title: 076_Scramble-A_100uM_noEGF


title: 088_PCSK9-B_100uM_noEGF


title: 075_Vehicle_100uM_noEGF


title: WT_crym1


title: WT_control3


title: Memory_Input_rep2

first: Howard

middle: Y

state: California

address: 269 Campus Drive

institute: Stanford University

data_processing:
Reads were aligned to mm10 by BWA
Reads with low quality (MAPQ < 30) were filtered out. If multiple reads were mapped to the exact same location, only one read was kept.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: KLRG1loIL7Rhi memory CD8 T cells

extract_protocol:
Splenocytes were isolated and specific CD8 T cell subsets were sorted by FACS
ATAC-seq library was constructed by Nextera DNA Sample Prep Kit (Illumina). For ChIP-seq library, DNA was end-repaired using End-it End-repair kit (Epicentre) and then added an “A” base to the 3’ end of DNA fragments using Klenow (NEB). Then DNA was ligated with adaptors using quick DNA ligase (NEB) at 25°C for 15 min followed by size selection of 200-400 bp using AMPure SPRI beads (Beckman Coulter). The adaptor ligated DNA was amplified using NEBNext High-Fidelity 2X PCR master mix (NEB).

treatment_protocol: OT1 transfer and Lm-OVA infection for 8 days or >60 days

value: six to seven weeks

value: Spleen


title: WT_crym2


title: 072_PCSK9-C_30uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-C (30uM) for 6h in the presence of exogeneous EGF


title: 071_PCSK9-D_30uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-D (30uM) for 6h in the presence of exogeneous EGF


title: 070_Myd88-E_30uM_EGF

description: PTEC-TERT1 cells treated with Myd88-E (30uM) for 6h in the presence of exogeneous EGF


title: 067_Myd88-E_30uM_noEGF

description: PTEC-TERT1 cells treated with Myd88-E (30uM) for 6h in the absence of exogeneous EGF


title: MP_Input_rep2

source_name: KLRG1loIL7Rhi memory precursor CD8 T cells


title: 069_PCSK9-C_30uM_EGF


title: 068_PCSK9-D_30uM_EGF


title: 066_PCSK9-C_30uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-C (30uM) for 6h in the absence of exogeneous EGF


title: 065_PCSK9-D_30uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-D (30uM) for 6h in the absence of exogeneous EGF


title: 064_Myd88-E_30uM_noEGF


title: TE_Input_rep2

source_name: KLRG1hiIL7Rlo terminal effector CD8 T cells


title: 062_PCSK9-D_30uM_noEGF


title: MP_Input_rep1


title: TE_Input_rep1


title: 061_Scramble-A_30uM_noEGF

description: PTEC-TERT1 cells treated with Scramble-A (30uM) for 6h in the absence of exogeneous EGF


title: 074_PCSK9-C_30uM_EGF


title: 073_Myd88-E_30uM_EGF


title: 060_Vehicle_30uM_noEGF

description: PTEC-TERT1 cells treated with Vehicle (30uM) for 6h in the absence of exogeneous EGF


title: 058_PCSK9-B_30uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-B (30uM) for 6h in the presence of exogeneous EGF


title: 059_Myd88-E_30uM_EGF


title: 056_Vehicle_30uM_EGF

description: PTEC-TERT1 cells treated with Vehicle (30uM) for 6h in the presence of exogeneous EGF


title: 055_PCSK9-B_30uM_EGF


title: Memory_Input_rep1


title: Memory_H3K27ac_rep2


title: Memory_H3K27ac_rep1


title: TN_Input_rep1

source_name: naive CD8 T cells


title: 052_PCSK9-B_30uM_EGF


title: 051_Scramble-A_30uM_EGF

description: PTEC-TERT1 cells treated with Scramble-A (30uM) for 6h in the presence of exogeneous EGF


title: 049_PCSK9-B_30uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-B (30uM) for 6h in the absence of exogeneous EGF


title: 054_Scramble-A_30uM_EGF


title: MP_H3K27ac_rep2


title: 050_Vehicle_30uM_EGF


title: 053_Vehicle_30uM_EGF


title: TN_Input_rep2


title: 080_Myd88-E_100uM_noEGF

description: PTEC-TERT1 cells treated with Myd88-E (100uM) for 6h in the absence of exogeneous EGF


title: 048_Scramble-A_30uM_noEGF


title: 047_Vehicle_30uM_noEGF


title: 046_PCSK9-C_30uM_noEGF


title: TE_H3K27ac_rep2


title: 057_Scramble-A_30uM_EGF


title: TN_H3K27ac_rep2


title: TN_H3K27ac_rep1


title: MP_H3K27ac_rep1


title: 044_Vehicle_30uM_noEGF


title: 045_Scramble-A_30uM_noEGF


title: Memory_H3K4me1_rep2


title: 043_Myd88-E_30uM_noEGF


title: 042_PCSK9-C_30uM_noEGF


title: 041_PCSK9-B_30uM_noEGF


title: 063_PCSK9-B_30uM_noEGF


title: 039_Scramble-A_30uM_noEGF


title: 038_Vehicle_30uM_noEGF


title: MP_H3K4me1_rep2


title: 037_Myd88-E_10uM_EGF

description: PTEC-TERT1 cells treated with Myd88-E (10uM) for 6h in the presence of exogeneous EGF


title: 036_Scramble-A_10uM_noEGF

description: PTEC-TERT1 cells treated with Scramble-A (10uM) for 6h in the absence of exogeneous EGF


title: 035_Vehicle_10uM_noEGF

description: PTEC-TERT1 cells treated with Vehicle (10uM) for 6h in the absence of exogeneous EGF


title: 034_Myd88-E_10uM_EGF


title: TE_H3K27ac_rep1


title: 033_PCSK9-C_10uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-C (10uM) for 6h in the presence of exogeneous EGF


title: 031_PCSK9-D_10uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-D (10uM) for 6h in the presence of exogeneous EGF


title: 032_PCSK9-B_10uM_EGF

description: PTEC-TERT1 cells treated with PCSK9-B (10uM) for 6h in the presence of exogeneous EGF


title: TE_H3K4me1_rep1


title: TE_H3K4me1_rep2


title: MP_H3K4me1_rep1


title: 029_Vehicle_10uM_EGF

description: PTEC-TERT1 cells treated with Vehicle (10uM) for 6h in the presence of exogeneous EGF


title: TN_H3K4me1_rep2


title: 028_PCSK9-C_10uM_EGF


title: 030_Scramble-A_10uM_EGF

description: PTEC-TERT1 cells treated with Scramble-A (10uM) for 6h in the presence of exogeneous EGF


title: 027_PCSK9-B_10uM_EGF


title: Memory_H3K4me1_rep1


title: 024_Vehicle_10uM_EGF


title: 025_Scramble-A_10uM_EGF


title: 023_Myd88-E_10uM_EGF


title: Memory_H3K4me3_rep2


title: 026_PCSK9-D_10uM_EGF


title: 022_PCSK9-C_10uM_EGF


title: 021_PCSK9-B_10uM_EGF


title: Memory_H3K4me3_rep1


title: MP_H3K4me3_rep2


title: 020_PCSK9-D_10uM_EGF


title: 017_Myd88-E_10uM_noEGF

description: PTEC-TERT1 cells treated with Myd88-E (10uM) for 6h in the absence of exogeneous EGF


title: 016_PCSK9-C_10uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-C (10uM) for 6h in the absence of exogeneous EGF


title: 018_Vehicle_10uM_EGF


title: TE_H3K4me3_rep2


title: 015_PCSK9-B_10uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-B (10uM) for 6h in the absence of exogeneous EGF


title: 014_PCSK9-D_10uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-D (10uM) for 6h in the absence of exogeneous EGF


title: TE_H3K4me3_rep1


title: 011_Myd88-E_10uM_noEGF


title: 012_Vehicle_10uM_noEGF


title: 013_Scramble-A_10uM_noEGF


title: TN_H3K4me3_rep2


title: TN_H3K4me3_rep1


title: TN_H3K4me1_rep1


title: 010_PCSK9-C_10uM_noEGF


title: Memory_ATAC-seq_rep2


title: 009_PCSK9-B_10uM_noEGF


title: 007_Scramble-A_10uM_noEGF


title: 008_PCSK9-D_10uM_noEGF


title: Memory_ATAC-seq_rep1


title: 005_Myd88-E_10uM_noEGF


title: 040_PCSK9-D_30uM_noEGF

description: PTEC-TERT1 cells treated with PCSK9-D (30uM) for 6h in the absence of exogeneous EGF


title: 003_PCSK9-B_10uM_noEGF


title: 004_PCSK9-C_10uM_noEGF


title: MP_ATAC-seq_rep2


title: MP_ATAC-seq_rep1


title: MP_H3K4me3_rep1


title: 019_Scramble-A_10uM_EGF


title: 001_Scramble-A_10uM_noEGF


title: 002_PCSK9-D_10uM_noEGF


title: TE_ATAC-seq_rep2


title: TE_ATAC-seq_rep1


title: PF 221BsrDsRed, biological replicate 1

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

data_processing:
FASTQ sequence files were analyzed with FastQC, and reads with an average Q>20 retained (other settings default)
Indexed genome file of  Trypanosoma brucei 427 genome built with bowtie2-build (default settings)
Filtered FASTQ files aligned to built genome with Bowtie2 (with settings -I 145, -X 155 [also used -I 145, -X 170], --n-ceil L,0,0  and -S. All other settings default)
NucFrag (hpatterton@sun.ac.za) was used to find dyad positions from the paired reads, dyad data files generated of the number of dyads present at every position in each chromosome
Remove_tandem_repeats (hpatterton@sun.ac.za) was used to write the value "-1"at each dyad position located on a tandem repeat sequence, to discriminate from nucleosome free regions in downstream analyses
In each experiment, the average dyad density on each chromosome was normalized to that of the most dense chromosome, to allow inter-chromosome comparisons
BigWig files were generated with the genome sequence (TriTrypDB-9.0_TbruceiLister427_Genome.fasta) and annotation file (TriTrypDB-9.0_TbruceiLister427.gff) of version 9.0 of the TriTrypDB.
Genome_build: TriTrypDB V9.0
Supplementary_files_format_and_content: One bigwig file for each sample. Displays the normalised average nucleosome dyad density along each chromosome. We assumed that the average nucleosome density per chromosome are comparable within a sample. Dyad density is defined as the number of assigned dyads per corresponding number of basepair. Max = Maximum average dyad density observed for the 11 chromosomes in a sample  Avei = Average dyad density observed for chromosome i in a sample   = number of dyads of chromosome/chromosome size in base pairs  For each chromosome i (i=1 to 11), and for every dyad position j (j=1 to N, the size of chromosome i)  Normalized density NormDensi,j = DyadDensi,j × Max/Avei  Thus, the total number of dyads observed per unit length of a chromosome are comparable between different chromosomes of the same sample

organism: Trypanosoma brucei

source_name: Procyclic form (PF)

growth_protocol:
Cells were cultured in SDM-79 medium supplemented with 10% foetal calf serum, 5 µg/ml hemin and appropriate drugs (20 mg/ml neomycin, 25 mg/ml hygromycin, 20 mg/ml blasticidin) at 27°C, as previously described (Brun et al. 1979, PMID: 43092; Povelones et al. 2012, PMID: 23133390).  Cells were grown to a density of 1 x 107 cells per ml and harvested.
See Sample section.

extract_protocol:
MNase digestion of permeabilised cells: 5 x 107 cells/sample were harvested, permeabilised with digitonin and digested with MNase.  Mono-nucleosomal DNA (~150 bp) was gel-purified as described previously (Cole et al. 2012, PMID: 25348398).
Mono-nucleosomal DNA was repaired using the NEB PreCR Repair Mix. Following Illumina protocol: T4 polynucleotide kinase was used to add a 5'-phosphate to the DNA and then Klenow enzyme was used to add a 3'dA. The Illumina paired-end adaptor was ligated to the nucleosomal DNA. Indices were added to the DNA during PCR according to Illumina kit instructions.

value: Procyclic form T. brucei Lister 427 221BsrDsRed cell line.

value: Blasticidin resistance gene and DsRed gene in silent VSG221 ES, T7 polymerase and tetracycline repressor genes in tubulin array linked with neomycin and hygromycin resistance genes (Hughes et al. PMID:17431399).


title: BF RYT3, biological replicate 1

source_name: Bloodstream form (BF)

growth_protocol:
Neomycin resistance marker containing RYT3 cells were cultured in HMI-9 medium with 15% foetal calf serum and appropriate drugs (2 µg/ml neomycin, 2.5 µg/ml phleomycin, 5 µg/ml hygromycin, 5 µg/ml blasticidin), and incubated with 5% CO2 at 37°C as previously described (Hirumi et al. 1989, PMID 2614608; Povelones et al. 2012, PMID: 23133390).  Cells were grown to a density of 1 x 106 cells per ml and harvested.
See Sample section.

value: Bloodstream form T. brucei Lister 427 RYT3 cell line.

value: Blasticidin resistance gene in active VSGT3 ES, puromycin resistance gene and eGFP gene in silent VSG221 ES, T7 polymerase and tetracycline repressor genes in tubulin array linked with a neomycin resistance gene (Hughes et al. PMID:17431399)


title: BF RYT3, biological replicate 2


title: TN_ATAC-seq_rep2


title: PF Amt WT, biological replicate 2

growth_protocol:
Cells were cultured in SDM-79 medium supplemented with 10% foetal calf serum, 5 µg/ml hemin at 27°C, as previously described (Brun et al. 1979, PMID: 43092; Povelones et al. 2012, PMID: 23133390).  Cells were grown to a density of 1 x 10^7 cells per ml and harvested.
See Sample section.

value: Procyclic form T. brucei Lister 427 Amsterdam wild-type cell line.

value: Wild type


title: PF 221BsrDsRed, biological replicate 2


title: TN_ATAC-seq_rep1


title: BF HNI_VO2, biological replicate 2

growth_protocol:
Neomycin resistance marker containing BF HNI_VO2 cells were cultured in HMI-9 medium with 15% foetal calf serum and 2 µg/ml neomycin, and incubated with 5% CO2 at 37°C as previously described (Hirumi et al. 1989, PMID 2614608; Povelones et al. 2012, PMID: 23133390).  Cells were grown to a density of 1 x 106 cells per ml and harvested.
See Sample section.

value: Bloodstream form T. brucei Lister 427 HNI_VO2 cell line.

value: Neomycin resistance gene in active VSGVO2 ES, hygromycin resistance gene in silent VSG221 ES (Rudenko et al. PMID: 9763292).


title: PF Amt WT, biological replicate 1


title: 006_Vehicle_10uM_noEGF

value: PTEC-TERT1 cells

value: FALSE


title: BF HNI_VO2, biological replicate 1


title: Input_for_Bach1&MafK

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

institute: Tohoku university school of medicine

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using bwa version 0.7.10
bwa data (bam) were merged for each experiment
peaks were called using MACS2 version 2.1.0 with " macs2 callpeak -t  -c  -f BAM -n  -B -q 0.01 -g mm  --nomodel  --shiftsize 100" setting
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using bam2bigwig.sh from BAM files

source_name: pre-pro B cells

growth_protocol: Cells were cultured on TC-non-trreated plastic dosh (CORNING) in RPMI-1640 medium (Sigma-Aldrich) supplemented  with 5ug/ml IL7, 10ug/ml, Flt3L and SCF, 10% FBS and penicilli/streptmycin

extract_protocol:
Ebf1 deficient cells were fixed 1% formaldehyde, followed by quenching with 125mM of glycine. The cells were washed with ice-cold PBS and were lysed. The crosslinked chromatin was shared with a Bioruptor Sonicator (CosmoBio) and target protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 1~3 ng of ChIP DNA with the use of Ovation Ultralow DR Multiplex System (Nugen). The DNA libraries were clonally amplified on a flow cell and sequenced on HiSeq2500 (HiSeq Control Software v2.2.38, Illumina) with 51-mer paired-end sequence. Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.61, Illumina).

treatment_protocol: no treatment

value: progenitor cells

tag: chip antibody

tag: vendor (antibody)

tag: catalog#  (antibody)

tag: lot#  (antibody)


title: Fall'12 Day 42 Control Ross Heart Fat 1211

city: Newark

first: Carl

last: Schmidt

state: DE

address: 601 Sincock Ln

institute: University of Delaware

data_processing:
Bowtie
TopHat
Cufflinks
Genome_build: Gallus gallus ver 4

organism: Gallus gallus

source_name: Cardiac Adipose Tissue

growth_protocol: Birds were raised following grower standards outlined by our AACUC protocol (#(27)03-12-14R). Briefly, birds were raised on litter with ad libitum access to feed and water. First week house temperature: 35 degrees C with 5 degrees C decrease each week until 25 degrees celsius was reached. The house was maintained this temperature through completion of the trial at day 42 (typical market age). The house received 23 hours of light and 1 hour of dark for the entirety of the study. Necropsies were performed on Day 21, Day 22, Day 26, Day 32 and Day 42.

extract_protocol:
Birds were euthanized via cervical dislocation and necropsied on each day listed above. Abdominal adipose tissue and cardiac adipose tissue samples were collected and flash frozen with liquid nitrogen.
Libraries were constructed using the Illumina Stranded RNA-seq kit according to manufacturers instructions.

treatment_protocol: First week house temperature: 35 degrees C with 5 degrees C decrease each week until 25 degrees celsius was reached. The house maintained this temperature through completion of the trial at day 42 (typical market age).

value: Cardiac Adipose

tag: breed/line

value: Ross

tag: gender

value: male

tag: age of collection

value: Day 42 posthatch


title: MafK_ChIPseq

value: Santa Cruz


title: Fall'13 Day 42 Control Ross Heart Fat 1207


title: Fall'12 Day 42 Control Ross Heart Fat 1208


title: Bach1_ChIPseq

value: House made


title: Fall'13 Day 42 Control Ross Heart Fat 1205


title: Fall'12 Day 42 Control Ross Heart Fat 1210


title: Fall'13 Day 42 Control Ross Heart Fat 1204


title: Bach2_ChIPseq_rep2

value: Bach2 (Bach2N2)


title: Input_for_Bach2


title: Bach2_ChIPseq_rep1


title: Fall'13 Day 42 Control Ross Heart Fat 1206


title: Fall'12 Day 42 Control Ross Ab Fat 1199

source_name: Abdominal Adipose Tissue

value: Abdominal Adipose


title: Fall'12 Day 42 Control Ross Ab Fat 1202


title: Input replicate 1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description:
Input_rep_1
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

data_processing:
Quality control was done using FASTQC.
Removal of low quality reads and adapters was done by trim_galore.
Alignment was done with bowtie2-2.0.0-beta6 with parameters -p 6 -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000.
Duplicate reads were removed with Samtools' rmdup function.
Peak calling was performed with Macs2 callpeak function.
Coverage vectors were extracted with deeptools' bamCoverage function.
Additional processing was done in R/BioConductor. Peaks separated by less then 2 kb were stitched together.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Coverage vectors from bamCoverage are stored as bigwig files.
Supplementary_files_format_and_content: Genomic intervals of binding peaks are stored as BED format files.

source_name: HeLa (Kyoto), Input

growth_protocol: Hela Kyoto (HK) cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (FCS; Sigma) and 1% penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol:
HeLa Kyoto cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclear lysates were subjected to chromatin shearing to an average size of 150 bp. Histone-DNA complexes were isolated with GFP-antibody.
All libraries were prepared with the MicroPlex library preparation kit v2 (order no C05010012) following manufacturer's instructions.

tag: cell line

value: HeLa (Kyoto)

tag: transfected plasmid

value: pIRESneo-EGFP

value: GFP (Abcam, ab290, lot GR278073-1)


title: Fall'13 Day 42 Control Ross Ab Fat 1198


title: GFP replicate 1

description:
GFP-rep_1
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP ChIP


title: Fall'13 Day 42 Control Ross Ab Fat 1197


title: Fall'12 Day 42 Control Ross Heart Fat 1209


title: Fall'13 Day 42 Control Ross Ab Fat 1196


title: GFP-H3.3 replicate 1

description:
GFP-H3.3_rep_1
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP-H3.3 ChIP


title: Fall'13 Day 42 Control Illinois Heart Fat 1114

value: Illinois


title: Fall'12 Day 42 Control Ross Ab Fat 1200


title: Fall'13 Day 42 Control Illinois Heart Fat 1112