title: SH-SY5Y SACS KO+FCCP_2


title: P2_FD-AO_EpCAM+ scRNA-seq_73

status: Public on Nov 26 2020

type: SRA

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

description: Single " P2_FD-AO EpCAM+" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

library_source: transcriptomic

data_processing:
Illumina bcl2fastq-1.8.4 software was used to demultiplex data and convert BCL files from HiSeq2500 systems running RTA versions 1.18.64 to standard FASTQ file formats for downstream analysis.
Sequenced reads were mapped to GRCh38 whole genome using STAR 2.6.1a aligner following ENCODE standard option in STAR manual.
Reads aligned to each gene were counted using featureCount.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample .

molecule: total RNA

organism: Homo sapiens

source_name: EpCAM+ cells

growth_protocol:
FD-AO EpCAM+ cells were induced from isolated CPM-high progenitor cells on day 21 and cocultured with human fetal fibroblasts for 14 days under the treatment of dexamethasone, 8-Br-cAMP, 3-Isobutyl-1-methylxanthine, KGF with and without passages (P0 and P2).
FF SFTPC+ cells were induced from isolated CPM-high progenitor cells on day 21. Briefly, CPM-high progenitor cell aggregates were formed on non-adherent cell culture plates for 2 days, followed by Matrigel-embedded three-dimensional culture for 5 days under the treatment of dexamethasone, 8-Br-cAMP, 3-Isobutyl-1-methylxanthine, KGF, Y27632, CHIR99021, and SB431542 WITHOUT co-culturing human fetal lung fibroblasts.

extract_protocol:
Single cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) .
The first-strand cDNA was synthesized and amplified on the independent chambera using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

treatment_protocol: P2 FD-AO EpCAM+ cells were treated with DMSO or 10 μM XAV-939 from day 2 to 14.

tag: culture condition

value: FD-AO

tag: cell types

value: hiPSC-derived EpCAM+ cells

tag: passage

tag: compound


title: SH-SY5Y SACS KO_1

type: protein

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: Hybridization was performed at Somalogic

scan_protocol: Agilent scanner for microarrays

data_processing: Sample data is  rst normalized to remove hybridization variation within a run followed by median normalization across all samples to remove other assay biases within the run and finally calibrated to remove assay differences between runs.

molecule: protein

source_name: SH-SY5Y SACS KO

label_protocol: Labeling was performed at Somalogic

growth_protocol: Cells were grown at 37 °C with 5% CO2 in Dulbecco’s modified Eagle’s medium, containing 10% FBS, 4.5 g/L glucose and 1% antibiotics/antimycotics; primary cells from humans were grown at 37 °C with 5% CO2 in Dulbecco’s modified Eagle’s medium, containing 10% FBS, 4.5 g/L glucose and 1% antibiotics/antimycotics.

extract_protocol: All samples (fibroblasts and cell models) were washed twice with PBS 1X and then homogenized in M-PER™ Mammalian Protein Extraction Reagent (Thermo Scientific, Rodano (MI), Italy) containing inhibitors of proteases (Roche Diagnostics, Monza (MB), Italy), following the manufacturer’s standard protocol.

treatment_protocol: Cell lines were treated with CRISPR/Cas9 gene editing to produce clones harboring a loss-of function mutation in SACS; both cell lines and primary fibroblasts were treated with 20 μM carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone (FCCP) for 2 hours to induce mitochondrial damage and fragmentation.

tag: cell line

tag: treatment

tag: mutation in sacs

value: KO


title: P2_FD-AO_EpCAM+ scRNA-seq_72


title: P2_FD-AO_EpCAM+ scRNA-seq_71


title: Ctrl2_2

source_name: Fibroblast

tag: individual

tag: cell type

value: primary fibroblasts

value: WT


title: Pt2_1


title: SH-SY5Y SACS KO_3


title: P2_FD-AO_EpCAM+ scRNA-seq_70


title: SH-SY5Y WT_1

source_name: SH-SY5Y WT


title: Pt1_1

value: Homozygous deletion  c.2187-4345_9832del


title: P2_FD-AO_EpCAM+ scRNA-seq_77


title: P2_FD-AO_EpCAM+ scRNA-seq_69


title: P2_FD-AO_EpCAM+ scRNA-seq_68


title: SH-SY5Y WT+FCCP_1

value: FCCP


title: P2_FD-AO_EpCAM+ scRNA-seq_67


title: P2_FD-AO_EpCAM+ scRNA-seq_66


title: Ctrl3_1


title: Pt3_2


title: P2_FD-AO_EpCAM+ scRNA-seq_65


title: P2_FD-AO_EpCAM+ scRNA-seq_64


title: P2_FD-AO_EpCAM+ scRNA-seq_63


title: SH-SY5Y WT_3


title: SH-SY5Y WT+FCCP_3


title: P2_FD-AO_EpCAM+ scRNA-seq_62


title: Ctrl1_1


title: P2_FD-AO_EpCAM+ scRNA-seq_61


title: Pt1_2


title: P2_FD-AO_EpCAM+ scRNA-seq_60


title: P2_FD-AO_EpCAM+ scRNA-seq_58


title: P2_FD-AO_EpCAM+ scRNA-seq_59


title: [HL]-[Blood mononuclear cells]-[02]

type: RNA

city: Bucharest

first: Loredan

middle: Stefan

last: Niculescu

address: 8, B. P. Hasdeu Street

department: Lipidomics

country: Romania

institute: Institute of Cellular Biology and Pathology "Nicolae Simionescu"

description: 52 spike-in control probes (Spike-in miRNA v2) were spoted to assure optimal labeling and hybridization.

hyb_protocol: Hybridization, blocking and washing of microarrays slides were performed using the reagents included in the miRCURY LNA microRNA Array kit 7th generation (Exiqon) accordingly to manufacturer's protocol; hybridization cassettes, gaskets and oven were from Agilent and used accordingly to Exiqon reccomended protocol.

scan_protocol: The microarrays slides were read with Innoscan 1100AL scanner (Innopsys) using the Mapix software (Innopsys) at 10 mm resolution, green laser power (532 nm, 65% gain, set at high). The raw data were obtained after image processing with Imagene software (Innopsys) using the indicated gal file from Exiqon.

data_processing: R-studio platform (limma) with quantile normalization (linear fit) were used to analyse all raw data applying the local background correction.

organism: Mesocricetus auratus

source_name: HL_Blood mononuclear cells

label_protocol: For each sample, 750 ng total RNA were labeled with Hy3 using miRCURY LNA microRNA Array Hi-Power labeling kit (Exiqon) accordingly to manufacturer's protocol.

growth_protocol: 12-14 weeks old hamsters (Mesocricetus auratus) were fed either standard chow - normolipidemic group (NL, n=3) or standard rodent chow supplemented with 3% cholesterol and 15% butter - hyperlipidemic animals (HL, n=3) for 12 weeks.

extract_protocol: Total RNA from hamsters' tissues and BMCs were extracted using Trizol reagent (Invitrogen) accordingly to manufacturer's protocol.

treatment_protocol: NL and HL hamsters were after overnight fasting and subjected to laparotomy under letal ketamine-xylazine (50-5 mg Kg-1 body) anesthesia and the vasculature cleared by perfusion with warm PBS for 5 minutes (inlet, left ventricle; outlet, right atrium). The liver, myocardium and small intestine (jejunum) were collected, PBS-cleaned and frozen in liquid nitrogen. Before the procedure, blood was collected on EDTA from the venous retro-orbital plexus (under 4-5% isoflurane anaesthesia) for BMC isolation on Histopaque gradient.

tag: age

value: 12-14 weeks

tag: gender

value: male

tag: diet

value: High-fat supplemented chow

tag: tissue

value: Blood circulating mononuclear cells, hyperlipidemic


title: [HL]-[Blood mononuclear cells]-[01]


title: Pt3_1


title: P2_FD-AO_EpCAM+ scRNA-seq_56


title: [NL]-[Blood mononuclear cells]-[01]

source_name: NL_Blood mononuclear cells

value: Regular chow

value: Blood circulating mononuclear cells, normolipidemic


title: P2_FD-AO_EpCAM+ scRNA-seq_55


title: P2_FD-AO_EpCAM+ scRNA-seq_53


title: P2_FD-AO_EpCAM+ scRNA-seq_57


title: [NL]-[Blood mononuclear cells]-[02]


title: P2_FD-AO_EpCAM+ scRNA-seq_54


title: P2_FD-AO_EpCAM+ scRNA-seq_50


title: [HL]-[Blood mononuclear cells]-[03]


title: P2_FD-AO_EpCAM+ scRNA-seq_49


title: [NL]-[Heart, left ventricle]-[03]

source_name: NL_Heart, left ventricle

value: Left ventricle of the heart, normolipidemic


title: [HL]-[Heart, left ventricle]-[03]

source_name: HL_Heart, left ventricle

value: Left ventricle of the heart, hyperlipidemic


title: [HL]-[Heart, left ventricle]-[02]


title: P2_FD-AO_EpCAM+ scRNA-seq_48


title: P2_FD-AO_EpCAM+ scRNA-seq_47


title: [HL]-[Small intestine]-[01]

source_name: HL_Small intestine

value: Small intestine, hyperlipidemic


title: [HL]-[Small intestine]-[03]


title: P2_FD-AO_EpCAM+ scRNA-seq_46


title: [NL]-[Blood mononuclear cells]-[03]


title: P2_FD-AO_EpCAM+ scRNA-seq_45


title: [NL]-[Small intestine]-[03]

source_name: NL_Small intestine

value: Small intestine, normolipidemic


title: P2_FD-AO_EpCAM+ scRNA-seq_44

value: FD-AO


title: [NL]-[Small intestine]-[02]


title: P2_FD-AO_EpCAM+ scRNA-seq_43

value: hiPSC-derived EpCAM+ cells


title: P2_FD-AO_EpCAM+ scRNA-seq_52


title: P2_FD-AO_EpCAM+ scRNA-seq_51


title: P2_FD-AO_EpCAM+ scRNA-seq_42


title: P2_FD-AO_EpCAM+ scRNA-seq_41


title: P2_FD-AO_EpCAM+ scRNA-seq_40


title: [HL]-[Liver]-[02]

value: Right lobe of the liver, hyperlipidemic


title: [NL]-[Heart, left ventricle]-[01]


title: [HL]-[Liver]-[01]


title: [HL]-[Liver]-[03]


title: P2_FD-AO_EpCAM+ scRNA-seq_39


title: P2_FD-AO_EpCAM+ scRNA-seq_38


title: [HL]-[Small intestine]-[02]


title: [NL]-[Small intestine]-[01]


title: P2_FD-AO_EpCAM+ scRNA-seq_37


title: [NL]-[Liver]-[02]

value: Right lobe of the liver, normolipidemic


title: P2_FD-AO_EpCAM+ scRNA-seq_36


title: P2_FD-AO_EpCAM+ scRNA-seq_35


title: P2_FD-AO_EpCAM+ scRNA-seq_34


title: P2_FD-AO_EpCAM+ scRNA-seq_33


title: P2_FD-AO_EpCAM+ scRNA-seq_32


title: P2_FD-AO_EpCAM+ scRNA-seq_31


title: P2_FD-AO_EpCAM+ scRNA-seq_30


title: P2_FD-AO_EpCAM+ scRNA-seq_29


title: P2_FD-AO_EpCAM+ scRNA-seq_28


title: P2_FD-AO_EpCAM+ scRNA-seq_25


title: P2_FD-AO_EpCAM+ scRNA-seq_26


title: [NL]-[Liver]-[03]


title: P2_FD-AO_EpCAM+ scRNA-seq_24


title: P2_FD-AO_EpCAM+ scRNA-seq_23


title: HighRunner_Line8_Female [Runner4]

city: Riverside

first: Sachiko

last: Haga-Yamanaka

state: CA

address: 900 University Ave.

department: Molecular, Cell and Systems Biology

country: USA

institute: University of California, Riverside

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were aligned to the mouse reference genome (GRCm38/mm10), using STAR aligner ver. 2.6.1d with an increased stringency unforgiving any of mismatches per each read (‘-outFilterMismatchNmax 0’). Any reads that map to multiple locations in the genome are not counted (‘-outFilterMultimapNmax 1’) since they cannot be assigned to any gene unambiguously.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated usingCuffdiff included in Cufflinks.
Supplementary_files_format_and_content: read count (GSE146644_Count_Female.txt.gz); RPKM (GSE146644_RPKM_Female.txt.gz)

organism: Mus musculus

source_name: High runner_female_vomeronasal organ

extract_protocol:
The VNO tissues were harvested from 3 male or 3 female mice from each of the 4 HR and 4 control lines, immediately transferred to RNA later (Sigma-Aldrich), then stored at −80˚C until use for RNA-seq. VNO tissues from the same line of mice were pooled and homogenized in Trizol Reagent (Life Technologies, Carlsbad, CA) and processed according to the manufacturer's protocol. Trizol-purified RNA samples were quantified using Qubit1 2.0 (Life Technologies). The integrity of isolated RNA was measured by the 28S/18S rRNA analysis using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA) with RNA Nano chip (Agilent Technologies, Palo Alto, CA). Samples had RNA integrity number values of at least 8.30.
RNA libraries were prepared for sequencing using the Ultra II Directional RNA Library Prep kit (NEB).

tag: strain background

tag: line

value: selectively bred for high voluntary wheel running activity

tag: Sex

value: female

value: vomeronasal organ


title: HighRunner_Line7_Female [Runner3]


title: Control_Line4_Female [Cont3]

source_name: control_female_vomeronasal organ

value: non-selected control


title: Control_Line5_Female [Cont4]

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were aligned to the mouse reference genome (GRCm38/mm10), using STAR aligner ver. 2.6.1d with an increased stringency unforgiving any of mismatches per each read (‘-outFilterMismatchNmax 0’). Any reads that map to multiple locations in the genome are not counted (‘-outFilterMultimapNmax 1’) since they cannot be assigned to any gene unambiguously.
Supplementary_files_format_and_content: read count (GSE146644_Count_Female.txt.gz); RPKM (GSE146644_RPKM_Female.txt.gz)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated usingCuffdiff included in Cufflinks.


title: P2_FD-AO_EpCAM+ scRNA-seq_20


title: P2_FD-AO_EpCAM+ scRNA-seq_21


title: Control_Line2_Female [Cont2]


title: P2_FD-AO_EpCAM+ scRNA-seq_18


title: Control_Line1_Female [Cont1]


title: P2_FD-AO_EpCAM+ scRNA-seq_17


title: MNase_BRM014-washout_1

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
MNase-seq reads were aligned to the genome using qAlign from the QuasR Bioconductor package version 1.26.0 (Gaidatzis et al, Bioinformatics, 2015) with default parameters, only reporting alignments for reads with a unique match to the genome.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and binsize=100. The scores in the wig file therefore represent the number of fragment midpoints per 100bp window and per million reads in the library.

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: Wild type mouse ES cell lines of 129S6/SvEvTac background were as previously described (Barisic et al., 2019). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), GlutaMAX™ Supplement (Gibco) and Non-essential amino acids (Gibco), beta-mercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). Cells were grown on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
MNase was performed as previously described (Barisic et al., 2019) with following modification: MNase-digested DNA was purified using AMPure XP beads, Purified DNA was loaded on the Agilent Bioanalyzer to determine digestion efficiency.
Libraries were prepared with NEBUltra Library Preparation Kit (NEB), using 5 PCR cycles and  500ng of starting DNA.

treatment_protocol: BRM014 and inactive analog compound were synthesised by Novartis. Powder was resuspended in DMSO to a final concentration of 10mM. Desired concentration was added directly to the tissue culture media.

tag: strain

value: mouse embryonic stem cells

tag: genotype

value: wildtype


title: MNase_BRM014-washout_2


title: P2_FD-AO_EpCAM+ scRNA-seq_19

tag: culture condition

tag: cell types


title: MNase_BRM014-10uM_2


title: [NL]-[Heart, left ventricle]-[02]

value: 12-14 weeks

value: male


title: P2_FD-AO_EpCAM+ scRNA-seq_16

tag: passage

tag: compound


title: P2_FD-AO_EpCAM+ scRNA-seq_15


title: P2_FD-AO_EpCAM+ scRNA-seq_14


title: MNase_DMSO_2

tag: treatment

value: DMSO


title: MNase_BRM014-10uM_1


title: MNase_DMSO_1


title: P2_FD-AO_EpCAM+ scRNA-seq_13


title: HighRunner_Line3_Female [Runner1]


title: P2_FD-AO_EpCAM+ scRNA-seq_27


title: DMSO_24h_Snf2hko_2

description: Snf2h knockout, DMSO control (24h)

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Paired ATAC-seq reads were first trimmed to remove adaptor sequences using cutadapt version 1.18 (Marcel Martin. EMBnet.journal, 17(1):10-12, 2011) with -a CTGTCTCTTATA -A CTGTCTCTTATA --minimum-length=10 --length=42 --overlap=1. Trimmed reads were aligned to the genome using bwa version 0.7.17 (Li and Durbin, Bioinformatics 25, 1754–1760, 2009) with default parameters, filtering out secondary alignments, and converted to bam format.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package (Gaidatzis et al, Bioinformatics 2015) version 1.26.0 with default parameters except scaling=1e6, binsize=100 and pairedAsSingle=TRUE. The scores in the wig file therefore represent the number of 5'-read ends (Tn5 insertion sites) per 100bp window and per million reads in the library.

extract_protocol:
ATAC-seq was performed according to the previously described protocol (Buenrostro et al., 2015) with modifications. Briefly, 50,000 cells were washed with cold PBS and resuspended in lysis buffer to extract nuclei. The nuclei were cold-centrifuged at 500 x g for 10 min. The nuclei pellet was incubated with transposition reaction buffer for 30 min. at 37 °C. The DNA was purified using the PCR Purification Kit (Qiagen).
The eluted transposed DNA was submitted to the PCR using Q5 High-Fidelity Polymerase (NEB). DNA was amplified with 11-12 cycles of PCR.

value: Snf2h knockout

value: unsorted


title: BRM014-10uM_24h_wt_6

description: wildtype, BRM014 treated (10uM for 24h)


title: P2_FD-AO_EpCAM+ scRNA-seq_12


title: P2_FD-AO_EpCAM+ scRNA-seq_8


title: BRM014-10uM_24h_wt_5

description: wildtype, BRM014 treated (10uM for 24h)


title: P2_FD-AO_EpCAM+ scRNA-seq_11


title: P2_FD-AO_EpCAM+ scRNA-seq_10


title: P2_FD-AO_EpCAM+ scRNA-seq_9


title: DMSO_24h_Snf2hko_1

description: Snf2h knockout, DMSO control (24h)


title: DMSO_24h_wt_6

description: wildtype, DMSO control (24h)


title: P2_FD-AO_EpCAM+ scRNA-seq_4


title: P2_FD-AO_EpCAM+ scRNA-seq_6


title: DMSO_24h_Ino80ko_2

description: Ino80 knockout, DMSO control (24h)

value: Ino80 knockout


title: P2_FD-AO_EpCAM+ scRNA-seq_7


title: Liver_6

city: Rootstown

first: Yanqiao

last: Zhang

state: OH

address: 4209 State Route 44

institute: Northeast Ohio Medical University

data_processing:
Data was provessed in the BaseSpace Sequence Hub. Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using RNA-Seq Alignment V2.02 by Illumina (Bowtie2).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated and normalized using Illumina RNA-Seq Differential Expression Version 1.0.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Liver

extract_protocol:
Total RNA was extracted using an mirVava miRNA Isolation Kit (Thermo Fisher)
TruSeq® Stranded Total RNA Library Prep kit from Illumina was used and the protocol from Illumina was followed.

value: Liver

value: 18 weeks


title: Liver_7


title: Liver_8


title: DMSO_24h_Ino80ko_1

description: Ino80 knockout, DMSO control (24h)


title: P2_FD-AO_EpCAM+ scRNA-seq_5

value: FD-AO

value: hiPSC-derived EpCAM+ cells


title: Liver_4


title: Liver_5


title: P2_FD-AO_EpCAM+ scRNA-seq_2


title: P0_FD-AO_EpCAM+ scRNA-seq_87

description: Single " P0_FD-AO EpCAM+" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.


title: P0_FD-AO_EpCAM+ scRNA-seq_86


title: Liver_3


title: P0_FD-AO_EpCAM+ scRNA-seq_85


title: DMSO_24h_wt_5

description: wildtype, DMSO control (24h)


title: Liver_2


title: Liver_1


title: P0_FD-AO_EpCAM+ scRNA-seq_84


title: P0_FD-AO_EpCAM+ scRNA-seq_83


title: P0_FD-AO_EpCAM+ scRNA-seq_82


title: P2_FD-AO_EpCAM+ scRNA-seq_3


title: P0_FD-AO_EpCAM+ scRNA-seq_81


title: BRM014-10uM_1h_wt-S_2

source_name: BRM014 treated (10uM for 1h), S cells

extract_protocol:
ATAC-seq was performed according to the previously described protocol (Buenrostro et al., 2015) with modifications. Briefly, 50,000 cells were washed with cold PBS and resuspended in lysis buffer to extract nuclei. The nuclei were cold-centrifuged at 500 x g for 10 min. The nuclei pellet was incubated with transposition reaction buffer for 30 min. at 37 °C. The DNA was purified using the PCR Purification Kit (Qiagen).
The eluted transposed DNA was submitted to the PCR using Q5 High-Fidelity Polymerase (NEB). DNA was amplified with 12 cycles of PCR.

value: S


title: BRM014-10uM_1h_wt-G2_1

source_name: BRM014 treated (10uM for 1h), G2 cells


title: BRM014-10uM_1h_wt-S_1


title: BRM014-10uM_1h_wt-G1_1

source_name: BRM014 treated (10uM for 1h), G1 cells


title: P0_FD-AO_EpCAM+ scRNA-seq_78

source_name: EpCAM+ cells


title: BRM014-10uM_1h_wt-G1_2


title: P0_FD-AO_EpCAM+ scRNA-seq_80


title: DMSO_1h_wt-G2_2

source_name: DMSO control (1h), G2 cells


title: [NL]-[Liver]-[01]

value: Regular chow

value: Right lobe of the liver, normolipidemic


title: P0_FD-AO_EpCAM+ scRNA-seq_77


title: DMSO_1h_wt-G2_1


title: DMSO_1h_wt-S_2

source_name: DMSO control (1h), S cells


title: P0_FD-AO_EpCAM+ scRNA-seq_75


title: BRM014-10uM_1h_wt-G2_2


title: P2_FD-AO_EpCAM+ scRNA-seq_1


title: DMSO_1h_wt-S_1


title: P0_FD-AO_EpCAM+ scRNA-seq_72


title: DMSO_1h_wt-G1_2

source_name: DMSO control (1h), G1 cells


title: P0_FD-AO_EpCAM+ scRNA-seq_74


title: P0_FD-AO_EpCAM+ scRNA-seq_71


title: P0_FD-AO_EpCAM+ scRNA-seq_73


title: BRM014-washout_24h_wt_2

source_name: BRM014 treated (10uM for 24h), then washout (for 24h)


title: P0_FD-AO_EpCAM+ scRNA-seq_79


title: DMSO_1h_wt-G1_1


title: P0_FD-AO_EpCAM+ scRNA-seq_76


title: P0_FD-AO_EpCAM+ scRNA-seq_70


title: BRM014-washout_24h_wt_1


title: BRM014-washout_6h_wt_1

source_name: BRM014 treated (10uM for 24h), then washout (for 6h)


title: P0_FD-AO_EpCAM+ scRNA-seq_68


title: BRM014-10uM_24h_wt_4

source_name: BRM014 treated (10uM for 24h)


title: P0_FD-AO_EpCAM+ scRNA-seq_69


title: P0_FD-AO_EpCAM+ scRNA-seq_67


title: BRM014-washout_6h_wt_2


title: BRM014-10uM_6h_wt_2

source_name: BRM014 treated (10uM for 6h)


title: P0_FD-AO_EpCAM+ scRNA-seq_63


title: P0_FD-AO_EpCAM+ scRNA-seq_65


title: BRM014-10uM_6h_wt_1


title: BRM014-10uM_3h_wt_1

source_name: BRM014 treated (10uM for 3h)


title: P0_FD-AO_EpCAM+ scRNA-seq_66


title: BRM014-10uM_3h_wt_2


title: BRM014-10uM_24h_wt_3


title: P0_FD-AO_EpCAM+ scRNA-seq_61


title: P0_FD-AO_EpCAM+ scRNA-seq_59


title: P0_FD-AO_EpCAM+ scRNA-seq_57


title: BRM014-10uM_60min_wt_4

source_name: BRM014 treated (10uM for 60min)


title: BRM014-10uM_60min_wt_3


title: P0_FD-AO_EpCAM+ scRNA-seq_60


title: BRM014-10uM_30min_wt_4

source_name: BRM014 treated (10uM for 30min)


title: P0_FD-AO_EpCAM+ scRNA-seq_58


title: DMSO_24h_wt_4

source_name: DMSO control (24h)


title: BRM014-10uM_30min_wt_3


title: DMSO_24h_wt_3


title: P0_FD-AO_EpCAM+ scRNA-seq_56


title: P0_FD-AO_EpCAM+ scRNA-seq_64


title: BRM014-washout_60min_wt_2

source_name: BRM014 treated (10uM for 60min), then washout (for 60min)


title: P0_FD-AO_EpCAM+ scRNA-seq_55


title: BRM014-washout_60min_wt_1


title: BRM014-washout_30min_wt_2

source_name: BRM014 treated (10uM for 60min), then washout (for 30min)


title: P0_FD-AO_EpCAM+ scRNA-seq_52


title: P0_FD-AO_EpCAM+ scRNA-seq_51


title: HighRunner_Line6_Female [Runner2]

source_name: High runner_female_vomeronasal organ

value: selectively bred for high voluntary wheel running activity

value: female

value: vomeronasal organ


title: P0_FD-AO_EpCAM+ scRNA-seq_50


title: P0_FD-AO_EpCAM+ scRNA-seq_53


title: BRM014-washout_30min_wt_1

value: mouse embryonic stem cells

value: wildtype


title: BRM014-washout_15min_wt_2

source_name: BRM014 treated (10uM for 60min), then washout (for 15min)


title: P0_FD-AO_EpCAM+ scRNA-seq_54


title: BRM014-washout_15min_wt_1


title: P2_FD-AO_EpCAM+ scRNA-seq_22


title: BRM014-10uM_60min_wt_2


title: P0_FD-AO_EpCAM+ scRNA-seq_49


title: P0_FD-AO_EpCAM+ scRNA-seq_62


title: BRM014-10uM_60min_wt_1


title: P0_FD-AO_EpCAM+ scRNA-seq_48


title: BRM014-10uM_30min_wt_1


title: BRM014-10uM_30min_wt_2


title: [HL]-[Heart, left ventricle]-[01]

source_name: HL_Heart, left ventricle

value: 12-14 weeks

value: male

value: High-fat supplemented chow

value: Left ventricle of the heart, hyperlipidemic


title: P0_FD-AO_EpCAM+ scRNA-seq_45

source_name: EpCAM+ cells


title: P0_FD-AO_EpCAM+ scRNA-seq_46


title: P0_FD-AO_EpCAM+ scRNA-seq_44


title: BRM014-10uM_20min_wt_1

source_name: BRM014 treated (10uM for 20min)

value: unsorted


title: P0_FD-AO_EpCAM+ scRNA-seq_43


title: P0_FD-AO_EpCAM+ scRNA-seq_47


title: P0_FD-AO_EpCAM+ scRNA-seq_42


title: BRM014-10uM_10min_wt_1

source_name: BRM014 treated (10uM for 10min)


title: DMSO_60min_wt_1

source_name: DMSO control (60min)

value: DMSO


title: BRM014-10uM_10min_wt_2


title: P0_FD-AO_EpCAM+ scRNA-seq_40


title: BRM014-10uM_24h_wt_1


title: P0_FD-AO_EpCAM+ scRNA-seq_39


title: BRM014-10uM_24h_wt_2


title: P0_FD-AO_EpCAM+ scRNA-seq_38


title: BRM014-1uM_24h_wt_2

source_name: BRM014 treated (1uM for 24h)


title: P0_FD-AO_EpCAM+ scRNA-seq_37


title: BRM014-1uM_24h_wt_1


title: inactive-10uM_24h_wt_2

source_name: inactive compound-treated (10uM for 24h)


title: P0_FD-AO_EpCAM+ scRNA-seq_36


title: BRM014-10uM_20min_wt_2


title: P0_FD-AO_EpCAM+ scRNA-seq_35


title: P0_FD-AO_EpCAM+ scRNA-seq_34


title: inactive-10uM_24h_wt_1


title: P0_FD-AO_EpCAM+ scRNA-seq_33


title: DMSO_24h_wt_1


title: P0_FD-AO_EpCAM+ scRNA-seq_32


title: HighRunner_Line6_Male [Runner2]

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were aligned to the mouse reference genome (GRCm38/mm10), using STAR aligner ver. 2.6.1d with an increased stringency unforgiving any of mismatches per each read (‘-outFilterMismatchNmax 0’). Any reads that map to multiple locations in the genome are not counted (‘-outFilterMultimapNmax 1’) since they cannot be assigned to any gene unambiguously.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated usingCuffdiff included in Cufflinks.
Supplementary_files_format_and_content: read count (GSE146644_Count.txt.gz); RPKM (GSE146644_RPKM.txt.gz)

source_name: High Runner_Vomeronasal organ


title: HighRunner_Line7_Male [Runner3]


title: HighRunner_Line8_Male [Runner4]


title: P0_FD-AO_EpCAM+ scRNA-seq_29


title: P0_FD-AO_EpCAM+ scRNA-seq_31


title: P0_FD-AO_EpCAM+ scRNA-seq_41


title: HighRunner_Line3_Male [Runner1]


title: P0_FD-AO_EpCAM+ scRNA-seq_30


title: DMSO_60min_wt_2


title: P0_FD-AO_EpCAM+ scRNA-seq_28


title: Control_Line4_Male [Cont3]

source_name: control_Vomeronasal organ

value: non-selected control


title: Control_Line2_Male [Cont2]


title: Control_Line5_Male [Cont4]


title: Control_Line1_Male [Cont1]


title: P0_FD-AO_EpCAM+ scRNA-seq_26

value: FD-AO


title: P0_FD-AO_EpCAM+ scRNA-seq_27

value: hiPSC-derived EpCAM+ cells


title: P0_FD-AO_EpCAM+ scRNA-seq_25


title: DMSO_24h_wt_2


title: P0_FD-AO_EpCAM+ scRNA-seq_22


title: P0_FD-AO_EpCAM+ scRNA-seq_21


title: single-cell data from microdissected mouse renal inner medulla

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

description: scIM

data_processing:
R1 contains cell barcode (bp 1-12) and UMI (bp 13-20). R2 is the biological read.
Generation of digital expression matrix (DGE) from raw fastq files were obtained using the Dropseq toolkit version 1.12.
Seurat objects were generated in R using the Seurat package version 2.3.1. using a lower gene number (nGene) cutoff of 200 and an upper cutoff of 5000. Data were then log-normalized and scaled according to the number of unique molecular identifiers (UMIs). All single-cell data samples were merged into one Seurat object. Clustering was performed using highly variable genes (Seurat parameters: x.low.cutoff = 0.0125, x.high.cutoff=Inf, y.cutoff=0.5) on all cells using Seurat’s default settings. TSNE plots were generated using 30 principal components from PCA with highly variable genes, a perplexity of 30 and a resolution of 0.6. All other parameters were at default levels.
Genome_build: mm9
Supplementary_files_format_and_content: Compressed text files containing the DGEs.

source_name: mouse renal inner medulla

extract_protocol:
Mouse kidneys were perfused with 4°C PBS at 10ml/min using a total volume of 30ml to remove blood and to cool the organ. Then, the whole organ or microdissected parts of the kidney were thoroughly minced and digested using a cold protease-based protocol (protease from Bacillus licheniformis, 10mg/ml, Sigma P5380). The tissue digestion comprised 4 digestion steps in total including different trituration and shaking steps of the tissue suspension (see Adam et al., 2017 for a step-by-step protocol). The final cell suspension was fixated in 80% methanol as previously published (Alles et al., 2017). So fixated cells were stored at -80°C. Before the Dropseq run, cells were pelleted at 3000g and resuspended in PBS/0.01%BSA + Ribolock (1U/µl) + Vanadyl Ribonucleoside Complex (VRC, New England Biolabs, S1402S, 10mM final concentration) to avoid RNA degradation, centrifuged and resuspended again in PBS/0.01%BSA + Ribolock + VRC and passed through a 35µm strainer. Cells were then counted and subjected to Dropseq and library preparation as previously published (Alles et al., 2017).
Libraries were constructed as described in Alles et al., 2017 and sequenced on Illumina NextsSeq 500 sequencers

value: wild type

value: kidney

tag: kidney region

value: inner medulla


title: P0_FD-AO_EpCAM+ scRNA-seq_20


title: P0_FD-AO_EpCAM+ scRNA-seq_24


title: P0_FD-AO_EpCAM+ scRNA-seq_19


title: IGG_PAX6_3

city: Seville

first: Villalba

last: Leticia

address: Avda. Manuel Siurot s/n

country: Spain

institute: FISEVI

data_processing:
Basecalls performed automatically by MiSeq Control Software using Real-Time Analysis
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie for Illumina (Galaxy Version 1.1.2) with default parameters
Peaks were called using MACS Model-based Analysis for ChIP-Seq (version 1.0.0) with default parameters
BETA-minus: Targets prediction with binding only (version 1.0.0), PAVIS and PAPST 1.0 tools, were used to assign the ChIP-seq peak data to the neighboring genes (annotation) with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated using MACS Model-based Analysis for ChIP-Seq (version 1.0.0); Columns: Chr peak; Start peak; End peak; -10*log10(pvalue)

source_name: Enteric precursor cells

growth_protocol: Enteric precursor cells were extracted from ganglionic bowels of 7 days aged CD-1 mice. Bowels were dissected and incubated in a solution of 0.26 mg/ml trypsin collagenase, 5 mg/ ml dispase, 0.28 mg/ml hyaluronidase, 3.3 μg/ml elastase, and 0.6 mg/ml collagenase in phosphate-buffered saline for up to 30 minutes at 37 °C. Digested tissue was triturated and washed, and the cells were cultured in Dulbecco’s modified Eagle medium (1 mg/ml glucose) containing 100 U/ml penicillin, 100 g/ml streptomycin, supplemented with 2 mmol/l l-glutamine (Gibco Life Technologies, Carlsbad, CA), 0.05 mmol/l 2-mercaptoethanol, 1% (volume/volume) N1 (Sigma Aldrich, Poole, Dorset, UK), 10% (volume/volume) human serum, 20 ng/ml basic fibroblast growth factor, 20 ng/ml epidermal growth factor, and 10 ng/ml glial cell–derived neurotrophic factor (Peprotech, London, UK).

extract_protocol:
Cells were fixed with 1%  formaldehyde and was sonicated in a Bioruptor System (Diagenode, USA). ChIP assay was performed with the Magna Chip Hisens Kit (Millipore,USA) according to manufacturer’s instructions and using the Anti-Pax6 antibody (Millipore, USA). 10% of samples volume/reaction was kept as controls (input) before immunoprecipitation. Mouse IgG (Diagenode) was used as negative control (IgG).
ChIP, input and IGG samples were processed with the ChIP-Seq DNA sample prep kit (Illumina, USA), following the manufacturer’s instructions. Size-selection was then performed by agarose gel electrophoresis to isolate fragments with size between 200 and 300bp. Afterwards, purified libraries were amplified by PCR and size range was subsequently checked in the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent, USA). Quantification was performed in the 7500-Real Time PCR System (Applied Biosystems) with the Library Quantification Kit (Kapa Biosystems). After proper dilutions, 4 nM libraries were processed, to obtain pools at a final concentration of 8 pM following the instructions of the Miseq Reagent kit V2. (50 cycles) (Illumina, USA).

value: Enteric precursor cells

value: ganglionic gut

tag: chip antibody

value: Mouse IgG (Diagenode)

tag: pool number


title: IGG_PAX6_4

tag: cell type

tag: age


title: P0_FD-AO_EpCAM+ scRNA-seq_18


title: P0_FD-AO_EpCAM+ scRNA-seq_16


title: P0_FD-AO_EpCAM+ scRNA-seq_14


title: P0_FD-AO_EpCAM+ scRNA-seq_15


title: P0_FD-AO_EpCAM+ scRNA-seq_23


title: P0_FD-AO_EpCAM+ scRNA-seq_12


title: Input_PAX6_16


title: P0_FD-AO_EpCAM+ scRNA-seq_11


title: P0_FD-AO_EpCAM+ scRNA-seq_13


title: Input_PAX6_14


title: single-cell data from microdissected mouse whole kidney_2

source_name: mouse whole kidney

value: whole kidney


title: Input_PAX6_15


title: Input_PAX6_13


title: P0_FD-AO_EpCAM+ scRNA-seq_17


title: IGG_PAX6_2


title: Input_PAX6_9


title: Input_PAX6_8


title: P0_FD-AO_EpCAM+ scRNA-seq_6


title: Input_PAX6_6


title: P0_FD-AO_EpCAM+ scRNA-seq_7


title: Input_PAX6_11


title: Input_PAX6_12


title: P0_FD-AO_EpCAM+ scRNA-seq_9


title: single-cell data from microdissected mouse whole kidney_1


title: single-cell data from microdissected mouse renal cortex

description: scCortex

source_name: mouse renal cortex

value: cortex


title: single-cell data from microdissected mouse renal outer medulla

description: scOM

source_name: mouse renal outer medulla

value: outer medulla


title: P0_FD-AO_EpCAM+ scRNA-seq_10


title: Input_PAX6_7


title: P0_FD-AO_EpCAM+ scRNA-seq_5


title: Input_PAX6_4


title: P0_FD-AO_EpCAM+ scRNA-seq_8


title: P0_FD-AO_EpCAM+ scRNA-seq_4


title: P0_FD-AO_EpCAM+ scRNA-seq_2


title: P0_FD-AO_EpCAM+ scRNA-seq_3


title: P0_FD-AO_EpCAM+ scRNA-seq_1


title: Input_PAX6_3


title: LI3_22_S22_R1_001

city: Galveston

first: Kathryn

last: Cunningham

state: Texas

address: 301 University blvd, route 0615

department: Pharmacology and Toxicology

institute: UTMB

data_processing:
Illumina Casava1.7 software used for basecalling.
Data quality control was done using CLC Genomics Workbench 12.0.2 (QIAGEN) using “QC for sequencing reads” workflow.
Reads were mapped to the University of California at Santa Cruz transcript set (updated February, 2017) (Tyner et al., 2017) using Bowtie2 version 2.1.0 (Langmead and Salzberg, 2012)
Gene expression level was estimated using RNA-Seq by Expectation Maximization (v1.2.15) (Li and Dewey, 2011)
Differentially expressed genes were identified using Fisher’s exact test in the Empirical Analysis of Digital Gene Expression Data in the R program (v3) (Robinson et al., 2010)
Genome_build: Rattus norvegicus The University of California at Santa Cruz transcript set (updated February, 2017)
Supplementary_files_format_and_content: Tab-delimited text files include expected_count  TPM     FPKM

organism: Rattus norvegicus

source_name: Medial Prefrontal Cortex

extract_protocol:
RNA from mPFC was isolated with TRIzol then purified with QIAGEN RNeasy column, resuspended in RNase free H2O
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HI and LI rats were defined as falling within the upper and lower quartiles of premature responses in the 1-CSRT task (n = 4-6/phenotype), respectively.

value: Sprague-Dawley

value: Medial prefrontal cortex homogenate

tag: group

value: low (LI) motor impulsivity

value: Male


title: KARYO-034_2_IGO_05737_X_44

city: New York

first: Xiaoli

last: Mi

state: NY

address: 1275 York Ave

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Alignment-free quantification of transcript abundance was performed with kallisto v0.43.0 on GENCODE annotation v25, accounting for hexamer bias and using 100 bootstrap iterations to quantify the technical uncertainty.
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcript abundances are stored in abundance.tsv file, while values from bootstrap are stored in the compressed abundance.h5 file. Information about the configuration is stored in run_info.json

source_name: Blood

extract_protocol:
RNA extraction by Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were from patients treated with selinexor

tag: timepoint

value: drug

tag: matched

value: yes

tag: drug reponse


title: IGG_PAX6_1

tag: tissue


title: LI4_23_S23_R1_001

tag: strain

tag: Sex


title: LI1_20_S20_R1_001


title: Input_PAX6_5


title: ChIP-Seq_PAX6_16

value: Anti-PAX6 Antibody (Millipore, USA)


title: KARYO-034_1_IGO_05737_X_43

value: baseline


title: ChIP-Seq_PAX6_15


title: HI3_18_S18_R1_001

value: high (HI)  motor impulsivity


title: HI2_17_S17_R1_001


title: HI4_19_S19_R1_001


title: HI1_8_S16_R1_001


title: KARYO-031_1_IGO_05737_X_38


title: Input_PAX6_2


title: KARYO-031_2_IGO_05737_X_39


title: KARYO-029_2_IGO_05737_X_36

value: no


title: ChIP-Seq_PAX6_14


title: ChIP-Seq_PAX6_12


title: KARYO-030_IGO_05737_X_37


title: ChIP-Seq_PAX6_13


title: KARYO-028_2_IGO_05737_X_34


title: ChIP-Seq_PAX6_10


title: ChIP-Seq_PAX6_11


title: KARYO-026_2_IGO_05737_X_31


title: ChIP-Seq_PAX6_9


title: KARYO-026_1_IGO_05737_X_30


title: KARYO-021_2_IGO_05737_X_27


title: KARYO-020_IGO_05737_X_25


title: ChIP-Seq_PAX6_8


title: ChIP-Seq_PAX6_7


title: ChIP-Seq_PAX6_6


title: KARYO-018_2_IGO_05737_X_22


title: ChIP-Seq_PAX6_5


title: LI2_21_S21_R1_001


title: ChIP-Seq_PAX6_4


title: KARYO-018_1_IGO_05737_X_21


title: KARYO-016_1_IGO_05737_X_19


title: KARYO-015_1_IGO_05737_X_17


title: ChIP-Seq_PAX6_2


title: KARY0-012_1_IGO_05737_X_15


title: KARYO-007_2_IGO_05737_X_10


title: KARYO-010_IGO_05737_X_14


title: KARYO-005_2_IGO_05737_X_8


title: KARYO-002_2_IGO_05737_X_4


title: RNA_BRM014-10uM_24h_Snf2hko_2

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
RNA-seq reads were aligned to the genome using STAR (Dobin et al., Bioinformatics, 2012, doi:10.1093/bioinformatics/bt-s635, version 2.7.3a), with parameters --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1. These parameters report alignments for reads with up to 20 best matches to the genome and report no more than a single, randomly selected alignment per read.
Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from mouse GENCODE, version M24) were counted using the qCount function from the QuasR Bioconductor package version 1.26.0 (Gaidatzis et al, Bioinformatics, 2015) with default parameters.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: matrix table with raw alignment counts per gene (rows) for all samples (columns)

source_name: embryonic stem cells

extract_protocol:
RNA for RNA-seq was purified using RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared from purified RNA for at least two biological replicates using TruSeq stranded Total RNA Library Prep (Illumina).

value: mouse embryonic stem cells

tag: genotype


title: KARYO-003_2_IGO_05737_X_6


title: RNA_BRM014-10uM_24h_Ino80ko_1


title: RNA_BRM014-10uM_24h_Ino80ko_2


title: KARYO-001_2_IGO_05737_X_2


title: RNA_BRM014-10uM_24h_wt_4

value: wildtype


title: RNA_BRM014-10uM_24h_wt_3


title: KARYO-001_1_IGO_05737_X_1


title: RNAseq_rep3

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

data_processing:
Reads were mapped using STAR
The QuasR::qCount function was used for calculation of gene levels in R
Reads Per Kilobase of exon per Megabase of library size (RPKM) values were calculated using the 'rpkm' function of the R/Bioconductor package EdgeR
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: 2 csv files are provided: a GeneCount table containing raw counts per gene, and an rpkm table containing RPKM values for each gene.

growth_protocol: Cells were grown in Dulbecco's modified eagle medium (DMEM) with 10% (v/v) fetal bovine serum.

extract_protocol:
Total RNA was isolated with the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. 10µg of the purified RNA was treated with Turbo DNAse (Ambion) and then cleaned with RNeasy Mini Kit. DNase-treated RNA was resuspended in EB buffer (Qiagen).
Total RNA-seq Illumina ScriptSeq with Complete Gold according to manufacturer’s instructions

value: wt

tag: transgene

value: Stable and unique insertion of a 5xUAS followed by Luciferase sequence in the first intron of NCOA5 (Stielow et al. EMBO Rep. 2008)


title: RNAseq_rep2


title: RNA_DMSO_24h_Ino80ko_2

value: DMSO


title: RNA_DMSO_24h_Snf2hko_1


title: ChIP-Seq_PAX6_3

value: Enteric precursor cells

value: ganglionic gut


title: KARYO-019_2_IGO_05737_X_24


title: ChIP-Seq_PAX6_1


title: RNA_DMSO_24h_Ino80ko_1


title: RNA_BRM014-10uM_24h_Snf2hko_1


title: Input_PAX6_1


title: RNA_DMSO_24h_wt_4


title: RNA_DMSO_24h_Snf2hko_2


title: RNA_DMSO_24h_wt_3


title: Input_PAX6_10


title: RNA_BRM014-washout_24h_wt_2


title: C7-143_rep2

city: shanghai

first: Ming

last: Zhao

address: 130 Meilong Road, Xuhui District

country: China

institute: East China University of Science and Technology

description: Finally evolurioanry strain for producing β-carotene

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S288C whole genome using HISAT2 software
Genome_build: Saccharomyces cerevisiae S288C
Supplementary_files_format_and_content: xlxs file include count and FPKM and count values for each Sample

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisia-S288C

growth_protocol: Yeast strains were cultured in YPD (yeast peptone dextrose) broth medium (10 g/L yeast extract, 20 g/L peptone, and 20 g/L glucose) at 30°C.

extract_protocol:
Cells were grown in YPD medium to exponential phase (OD600~3) for transcriptomic analyses. A 50 mL aliquot of each yeast culture was then centrifuged at 8,000 × g for 2 min at room temperature. After removal of the supernatant, the cell pellets were frozen in liquid nitrogen, and total RNA was extracted using the QIAGEN RNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0

tag: overexpress protein

value: spCas9-NG, HMG1, CrtE, CrtYB, Crt I


title: C5-63_rep2

description: Processed evolurioanry strain for producing β-carotene


title: RNA_BRM014-washout_24h_wt_1


title: RNAseq_rep1


title: C5-63_rep3


title: C7-143_rep3


title: C3-06_rep3


title: C5-63_rep1


title: RNA_BRM014-washout_6h_wt_2


title: C3-06_rep2


title: TPC-1-shFAM60A_replicate3

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

description: Gene expression data from TPC-1 cells transfected with FAM60A shRNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Robust multi-array average (RMA) using a non-linear correction based upon a convolution model.

label: biotin

source_name: cells transfected with FAM60A shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: TPC-1 cells were maintained in RPMI1640.The media were supplemented with 10% fetal bovine serum in an incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from control and RNAi DLD1 was prepared with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with control-shRNA-expressing lentivirus or FAM60A-shRNA-expressing lentivirus.

tag: cell line

value: PTC cells

value: FAM60A1 knockdown


title: TPC-1-shFAM60A_replicate2


title: MRL/lpr-kideny 3

city: Sapporo

first: Md.

middle: Abdul

last: Masum

state: Hokkaido

address: Kita 18, nishi 9

department: Basic Veterinary Sciences

institute: Faculty of Veterinary Medicine

description: Gene expression in 6 months of age

hyb_protocol: Gene Expression Hybridization Kit (Agilent) was used, and 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 25x fragmentation buffer and 10x GE blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μL of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE (G4852A) for 17 hours at 65°C.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Ver.12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Kidney from MRL/lpr 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were confired by NanoDrop Spectrophotometer (Thermo Scientific).

growth_protocol: All experimental mice were maintained under specific pathogen-free conditions.

extract_protocol: Total RNA from cells was purified using RNeasy Mini Kit (Qiagen)  following the manufacturer's recommendations. RNA samples were examined for RNA integrity on a Bioanalyzer 2100 II (Agilent Technologies).

treatment_protocol: Kidneys from experimental mice were collected after deep euthanasia.

tag: genetics

value: MRL/MpJ-Fas lpr/lpr

tag: gender

value: Female

value: 6 months

value: kidney


title: TPC-1-shControl_replicate3

description: Gene expression data from TPC-1 cells transfected with control shRNA

source_name: cells transfected with control shRNA

value: control


title: TPC-1-shControl_replicate1


title: MRL/lpr-kideny 1

description: Gene expression in 6 months of age

source_name: Kidney from MRL/lpr 1


title: TPC-1-shFAM60A_replicate1


title: MRL/MpJ-kidney 2

description: Gene expression in 6 months of age

source_name: Kidney from MRL/MpJ 2

value: MRL/MpJ


title: MRL/MpJ-kidney 3

description: Gene expression in 6 months of age

source_name: Kidney from MRL/MpJ 3


title: C0_rep3

description: Original stain for producing β-carotene


title: MRL/lpr-kideny 2

description: Gene expression in 6 months of age

source_name: Kidney from MRL/lpr 2


title: RNA_BRM014-washout_6h_wt_1

value: mouse embryonic stem cells

tag: treatment


title: C7-143_rep1


title: C0_rep1

description: Original stain for producing β-carotene


title: TPC-1-shControl_replicate2


title: C0_rep2

description: Original stain for producing β-carotene


title: Two body lengths per second sample 2

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

description:
FG1902_08
Group3_vs_ctrl.xlsx
Group3_vs_group2.xlsx

data_processing:
Image analysis and base calling were done by the Illumina pipeline (Rta Version 3.3.3).
Reads were aligned to the seabream reference genome using TopHat (version 2.0.13) (Trapnell et al., 2009).
The resulting files were filtered using SAMtools (version 1.2 using htslib 1.2.1) (Li et al., 2009) to exclude secondary alignment of reads.
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.6.1p1) (Anders and Huber, 2014).
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel.
Genome_build: Saurata_v1.refseq.fasta from http://biocluster.her.hcmr.gr; ef9ef3fa43ce084a6b52808d0f20ce0c-Saurata_0817.gff3
Supplementary_files_format_and_content: Microsoft Office Excel files (.xlsx) with the following columns: id; Note; Sample #; Sample #; Sample #; Sample #; Sample #; Sample #; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj

organism: Sparus aurata

source_name: white skeletal muscle

extract_protocol:
Skeletal white muscle was dissected from each individual, and stored in RNAlater (Ambion) at -80ºC till RNA extraction. Total RNA was isolated from homogenized samples (TissueRuptor, Qiagen) using the miRNeasy mini kit according to the manufacturer’s instructions (Qiagen), and analyzed with an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent). A transcriptome library for each sample was prepared from 0.5 microgram total RNA, using the TruSeq Stranded mRNA Library Prep following the manufacturer’s instructions (Illumina Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Control fish (group 1) were kept at minimal water flow for 8 months, whereas fish in group 2 were exposed to 8-months swimming exercise at one body length per second and fish in group 3 were exposed to 8-months swimming exercise at two body lengths per second.

value: white skeletal muscle

tag: origin of specimen

value: commercial seabream farm (Culmar, Alicante, Spain)


title: Two body lengths per second sample 3

description:
FG1902_09
Group3_vs_ctrl.xlsx
Group3_vs_group2.xlsx

value: swimming exercise at two body lengths per second


title: BY47419_rep1

description: Original stain


title: RNA_BRM014-washout_30min_wt_2

value: wildtype


title: Two body lengths per second sample 1

description:
FG1902_07
Group3_vs_ctrl.xlsx
Group3_vs_group2.xlsx


title: C3-06_rep1


title: RNA_BRM014-washout_30min_wt_1


title: rBMSCs, 5% CBM-CS-2

city: Shanghai

first: Mengmeng

last: Li

address: 1295 Dingxi Road

institute: Shanghai Institute of Ceramics, Chinese Academy of Sciences

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 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: OryCun2.0 (GCF_000003625.3)
Supplementary_files_format_and_content: tab-delimited text file includes counts and FPKM values for each Sample

organism: Oryctolagus cuniculus

source_name: Bone marrow mesenchymal stem cells

extract_protocol:
rBMSCs grown on scaffolds were collected by trypsin enzyme digesting technique, and RNA was then harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: breed

value: New Zealand white

value: cultured on Calcium Silicate scaffolds treated with 5% bacteria medium

value: post natal day 8 weeks

tag: cell type

value: Rabbit bone marrow mesenchymal stem cells (rBMSCs)


title: RNA_BRM014-washout_1h_wt_2


title: BY47419_rep2

description: Original stain

value: his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0


title: BY47419_rep3

description: Original stain


title: rBMSCs, 5% CBM-CS-3

tag: age


title: One body length per second sample 3

description:
FG1902_06
Group2_vs_ctrl.xlsx
Group3_vs_group2.xlsx

value: swimming exercise at 1 body length per second

tag: group


title: rBMSCs, M-CS-3

value: cultured on Calcium Silicate scaffolds treated with Medium


title: One body length per second sample 2

description:
FG1902_05
Group2_vs_ctrl.xlsx
Group3_vs_group2.xlsx


title: rBMSCs, 5% CBM-CS-1


title: RNA_inactive-10uM_24h_wt_2


title: MRL/MpJ-kidney 1

description: Gene expression in 6 months of age

source_name: Kidney from MRL/MpJ 1

value: Female


title: One body length per second sample 1

description:
FG1902_04
Group2_vs_ctrl.xlsx
Group3_vs_group2.xlsx


title: rBMSCs, M-CS-1


title: rBMSCs, M-CS-2


title: RNA_inactive-10uM_24h_wt_1


title: RNA_BRM014-washout_1h_wt_1


title: rBMSCs, CS-3

value: cultured on Calcium silicate scaffolds untreated


title: Minimal flow sample 3

description:
FG1902_03
Group2_vs_ctrl.xlsx
Group3_vs_ctrl.xlsx

value: minimal water flow

value: 1 (control)


title: rBMSCs, CS-2


title: Minimal flow sample 2

description:
FG1902_02
Group2_vs_ctrl.xlsx
Group3_vs_ctrl.xlsx


title: Minimal flow sample 1

description:
FG1902_01
Group2_vs_ctrl.xlsx
Group3_vs_ctrl.xlsx


title: RNA_inactive-10uM_1h_wt_2


title: RNA_inactive-10uM_1h_wt_1


title: NIH-3T3_dCas9TET_gRNA3_rep3

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

description: Bisulfite-converted

data_processing:
Base calling was performed with RTA v3.4.4 . Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate FastQ reads.
Paired-end FastQ files were trimmed for adapters and quality scores using TrimGalore v0.6.4_dev, default parameters, with --paired enabled.
Alignments to the mouse mm10 genome were performed using Bismark v0.22.3 under default settings.
Alignments were de-duplicated under default parameters using the deduplicate_bismark script within Bismark v0.22.3.
Methylation calls were performed with bismark_methylation_extractor script within Bismark v0.22.3, with --paired-end --gzip --comprehensive enabled.
Final Bismark coverage files for CpG context cytosines were generated with the bismark2bedGraph script within Bismark v0.22.3, under default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Files are Bismark coverage files, similar to BED files. They have the following columns: chromosome, start, end, methylation percent, number of Cs, number of Ts. Data is for CpGs only, in both strands (not merged).

source_name: NIH-3T3 cells

growth_protocol: NIH-3T3 cells (ATCC) were thawed and maintained in DMEM medium (Gibco) supplemented with 10% Premium Fetal Bovine Serum (Wisent) and 1X Penicillin-Streptomycin-Glutamine (Gibco). Cells were grown in a humidified incubator of 5% carbon dioxide at 37⁰C and cultured in 100mmx20mm tissue culture dishes (Corning) and harvested or passaged by trypsinization (Gibco) upon reaching 80-90% confluency.

extract_protocol:
Genomic DNA was extracted from 70% confluent cell culture dishes by removing cell culture media, washing cells once with 10 mL phosphate buffered saline,  addition of 400 µL DNA lysis buffer (100mM Tris, pH 7.5, 150 mM NaCl, 0.5% SDS, 10 mM EDTA), and collection by cell scraping. The mixtures were then incubated for 30 minutes with RNAse A at 37 °C, followed by 4 hours with proteinase K at 65 °C. This was followed by phenol-chloroform extraction, precipitation in ethanol ovenight at -20 °C, washing once with 70% ethanol, and resuspension in 50 µL PCR-grade water.
WGBS was performed by the Centre d'expertise et de services Génome Québec at McGill University. Genomic DNA was quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies). 2x151bp paired-end libraries were generated using the NEBNext® Enzymatic Methyl-seq Kit (New England BioLabs, NEB).  Adapters were purchased from NEB. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) and average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM on an Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 5% level.

treatment_protocol: Lentiviral particles derived from plasmids for dCas9 (pLV hUbC-dCas9-T2A-GFP, Addgene #53191), gRNA (pLenti-puro backbone), Cre recombinase (pLenti6/V5-DEST backbone), and/or dCas9-TET (Fuw-dCas9-Tet1CD-P2A-BFP, Addgene #108245) were incubated sequentially with 80,000 NIH-3T3 cells plated 24 hours before. For dCas9 gRNA3/gRNAscr cells, dCas9 expressing cells were first isolated by flow cytometry (GFP positive) and, after expansion and incubation with gRNA virus, selected with 10 µg/mL puromycin. For dCas9-TET gRNA3/gRNAscr cells, dCas9-TET expressing cells were first selected by flow cytometry (BFP positive) and, after expansion and incubation with gRNA virus, selected with 1 µg/mL puromycin.

value: dCas9-TET, gRNA 3 (by lentivirus)


title: NIH-3T3_dCas9TET_gRNA3_rep2

description: Bisulfite-converted


title: NIH-3T3_dCas9TET_gRNAscr_rep2

description: Bisulfite-converted

value: dCas9-TET, gRNA scr (by lentivirus)


title: NIH-3T3_dCas9TET_gRNAscr_rep3

description: Bisulfite-converted


title: NIH-3T3_dCas9TET_gRNAscr_rep1

description: Bisulfite-converted


title: RNA_DMSO_24h_wt_1

value: mouse embryonic stem cells

value: DMSO


title: NIH-3T3_dCas9TET_gRNA3_rep1

description: Bisulfite-converted


title: Manji_S7

city: London

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

institute: Western University

data_processing:
RNA sequencing reads were pre-processed with the sequence-grooming tool cutadapt version 0.4.1(MARTIN 2011) with the following quality trimming and filtering parameters (`--phred33 --length 36 -q 5 --stringency 1 -e 0.1`). Each set of paired-end reads was mapped against the C. albicans SC5314 haplotype A, version A22 downloaded from the Candida Genome Database (CGD) (www.candidagenome.org) using HISAT2 version 2.0.4. SAMtools was then used to sort and convert SAM files. The read alignments and C. albicans SC5314 genome annotation were provided as input into StringTie v1.3.3 (PERTEA et al. 2015) which returned gene abundances for each sample. We imported gene abundances into R and conducted differential analysis of gene count data using the DESeq2 R package (Love et al. 2014).
Genome_build: C. albicans CAI4 haplotype A, version A22
Supplementary_files_format_and_content: Tab-delimited gene abundances files

organism: Candida albicans

source_name: Met28 Activation

extract_protocol:
Total RNA isolation was performed as previously described (Tebbji et al, PloSGenetics 2014)
Libraries were prepared according to Illumina's mRNASeq stranded library preparation kit

treatment_protocol: growth in SC-GlcNac medium and untreated

value: wild type with Met28 activation


title: NIH-3T3_dCas9_gRNAscr_Cre_rep3

description: Bisulfite-converted

value: dCas9, gRNA scr, Cre (by lentivirus)


title: NIH-3T3_dCas9_gRNAscr_Cre_rep2

description: Bisulfite-converted


title: Manji_S8


title: RNA_BRM014-10uM_24h_wt_2

value: wildtype


title: NIH-3T3_dCas9_gRNAscr_Cre_rep1

description: Bisulfite-converted


title: RNA_BRM014-10uM_24h_wt_1


title: Manji_S6

source_name: Met4 activation

treatment_protocol: growth in SC-GlcNac medium and treated with α-pheromone

value: wild type with Met4 activation


title: Manji_S5


title: Manji_S2

source_name: Wildtype CAI5

value: wild type


title: NIH-3T3_dCas9_gRNA3_Cre_rep3

description: Bisulfite-converted

value: dCas9, gRNA 3, Cre (by lentivirus)


title: RNA_BRM014-10uM_6h_wt_1


title: rBMSCs, CS-1

value: New Zealand white

value: post natal day 8 weeks

value: Rabbit bone marrow mesenchymal stem cells (rBMSCs)


title: RNA_BRM014-10uM_6h_wt_2


title: PA14 mutS::Tna

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

description:
Non-evolved PA14 mutS::Tn.
processed data file: ProcessedDataMatrix.xlsx

data_processing:
Reads were trimmed for adaptor sequences and mapped to the PA14 whole genome using a Stampy pipeline with default parameters.
Genome_build: NC_008463.1 (PA14)
Supplementary_files_format_and_content: ProcessedDataMatrix.xlsx file is a data matrix that contains raw unique gene reads.

organism: Pseudomonas aeruginosa

source_name: RNA derived from liquid culture in LB (OD600=0.4-0.6)

growth_protocol: Cells were grown in LB to an OD600 =0.4-0.6.

extract_protocol:
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction.
The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina).

treatment_protocol: Directly after cultivation, the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C.

value: PA14 mutS::Tn

tag: media

value: LB

tag: replica

value: Replica 1


title: PA14 mutS::Tnb

value: Replica 2


title: NIH-3T3_dCas9_gRNA3_Cre_rep2

description: Bisulfite-converted


title: WBN6-6b

description:
Single-colony-derived clone isolated from the 45th passage of WBN6 culture.
processed data file: ProcessedDataMatrix.xlsx

tag: culture number

tag: clone number


title: Manji_S1

source_name: Wildtype CAI4


title: RNA_DMSO_24h_wt_2

source_name: embryonic stem cells

tag: strain

tag: tissue


title: WBN6-6a


title: RNA_BRM014-10uM_3h_wt_2

tag: genotype


title: RNA_BRM014-10uM_3h_wt_1


title: NIH-3T3_dCas9_gRNA3_Cre_rep1

description: Bisulfite-converted


title: LJ17W8I01

city: Québec

first: Kyle

last: Wellband

state: QC

address: 1030 avenue de la Médecine

department: Institut de biologie intégrative et des systèmes

institute: Université Laval

data_processing:
Raw reads were quality and adaptor trimmed using fastp v0.19.9 by clipping the first and last base, detecting and removing Illumina sequencing adaptors, requiring 40% of bases with a phred quality >= 25, and a minimum length of 100 bp
Trimmed reads were mapped to the ICSASG_v2 Atalatic Salmon genome using bwa-meth v0.2.2 requiring a mapping quality >= 10
Reads for individuals sequenced across multiple lanes were merged into one file per individual using samtools v1.8
Optical and PCR duplicates were identified and removed using MarkDuplicates in Picard Tools v2.23.1
Pileup of C and T base sequencing coverage of CpG sites were calculated and written to bedGraph or methylKit R format files using MethylDackel v0.4.0
CpG sites with underlying allelic variation (C/T SNPs) were removed from methylation count files using bedtools v2.26.0
Genome_build: ICSASG_v2; GCF_000233375.1
Supplementary_files_format_and_content: bedGraph format of methylation status for merged CpG-context cytosines (plus and minus strands combined) as output by MethylDackel with columns: chromosome, start, end, methylation percent, coverage methylated bases (C), coverage unmethylated bases (T)
Supplementary_files_format_and_content: Juvenile liver samples only: methylKit R format methylation file for merged CpG-context cytosines (plus and minus strands combined) as output by MethylDackel with columns: CpG name (chromosome and position concatenated with a "."), chromosome, position, strand, total covarage, proportion of methylated bases (C), proportion of unmethylated bases (T)

organism: Salmo salar

source_name: liver

extract_protocol:
DNA was extracted from sperm and liver tissues using a salt-based DNA extraction protocol
WGBS libraries were constructed using the NEB Ultra II library prep kit followed by bisulfite treatment at the McGill and Genome Québec Innovation Centre

value: liver

value: WILD

value: juvenile


title: LJ17W8I02


title: NIH-3T3_Untreated_rep3

description: Bisulfite-converted


title: NIH-3T3_Untreated_rep2

description: Bisulfite-converted


title: RNA_BRM014-10uM_1h_wt_2

value: mouse embryonic stem cells


title: RNA_BRM014-10uM_1h_wt_1


title: LJ17W5I02


title: WBN6-3b


title: NIH-3T3_Untreated_rep1

description: Bisulfite-converted


title: WBN6-3a


title: WBN6-2b


title: LJ17W5I01


title: RNA_BRM014-10uM_30min_wt_2


title: WBN6-2a


title: input_uninfected_H3K4me1_3

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

description:
H3K4me1_MEMORY_INPUT_AMC
H3K4me1_MEMORY_INPUT_AMC.tagdir.tar.gz
H3K4me1_MEMORY_INPUT_AMC.bedgraph
H3K4me1_MEMORY_INPUT_AMC.tdf.gz

data_processing:
Raw sequence data were assessed for quality and content using FastQC
Sequences were aligned to the Mus musculus genome (mm10) using bowtie2 with parameters --very-sensitive -p 30 --no-discordant --no-unal . The bowtie2 alignment outputs were stored as sorted, indexed bam files generated using samtools.
Samples were pooled as detailed and converted into tag directories using Homer software (http://homer.ucsd.edu/homer/; v4.10)
Alignments were converted to bedgraph format using Homer script makeUCSCfile.
Wig format outputs were converted to TDF format for viewing in IGV  using igvtools v2.3.93 (parameters: toTDF -z 7 -f p98)
Genome_build: mm10
Supplementary_files_format_and_content: Three types of processed file are provided for each sample pool.  Firstly, a tarred gzip archive of the Homer derived tag counts. Secondly, the tags were converted into bedgraph format, prior to conversion to wiggle format. Thirdly, the wiggle format files were coverted to a comcpressed TDF format more suitable for IGV viewing.

source_name: flow sorted bone marrow inflammatory monocytes

growth_protocol: C57Bl/6J mice were bred and housed in individually ventilated cages under specific pathogen free conditions (22°C, 50% humidity) at the University of Edinburgh, UK. Since we have previously shown that mosquito transmission resets expression of the large sub-telomeric multi-gene families that control malaria parasite virulence, and in turn shapes the host immune response during the pathogenic blood-stage of infection (Spence, P.J., et al., Vector transmission regulates immune control of Plasmodium virulence. Nature, 2013. 498(7453): p. 228-31), we transmitted Plasmodium chabaudi chabaudi AJ 96AJ15 (obtained from the European Malaria Reagent Repository (malariaresearch.eu)) through Anopheles stephensi mosquitoes (strain SD500, reared in house at the University of Edinburgh) according to our published protocol: Spence, P.J., et al., Mosquito transmission of the rodent malaria parasite Plasmodium chabaudi. Malar J, 2012. 11: p. 407. Mice were injected intravenously with 200 P. chabaudi AJ sporozoites, which, following 52 hours development in the liver, establish a severe acute blood-stage infection (hyperparasitaemia, severe anaemia, hypothermia and prostration) lasting approximately 2 weeks. Thereafter > 50 % of mice remain chronically infected (verified after 40 days by quantitative PCR). Chronic P. chabaudi AJ infection was then drug treated using 100 mg/kg chloroquine diphosphate salt (Sigma, dissolved in water) administered by oral gavage daily for 10 days. Memory responses of once-malaria infected mice were assessed 30 days after the start of chloroquine treatment and compared to uninfected age-matched control mice that received an identical chloroquine regimen.

extract_protocol:
Chromatin was immunoprecipitated using the True MicroChIP kit (Diagenode) with a modified protocol: cells were lysed before chromatin shearing using a Bioruptor Pico Sonicator (Diagenode; 5 cycles: 30 seconds ON - 30 seconds OFF; fragments 100 - 300 bp). 10 % of sheared chromatin was kept as input control and 90 % was immunoprecipitated using antibodies against either H3K27ac, H3K4me1 or H3K9me (all Diagenode) over night at 4 ̊C. The next morning Protein A coated beads (Diagenode) were added and, following a 6 hour incubation at 4 ̊C, unbound chromatin fragments were removed by thorough washing. ChIP and input DNA was then decrosslinked from proteins and purified using MicroChip DiaPure columns (Diagenode).
Sequencing libraries were prepared using the MicroPlex v2 Library preparation kit (Diagenode) according to manufacturers instructions. Library amplification was monitored in real time using a Lightcycler 480 (Roche) to determine optimal cycle number. Amplified libraries were quantified using Qubit (dsDNA HS assay) and fragment quality and size distribution assessed by Bioanalyser (DNA HS Kit). Following equimolar pooling, libraries were purified using AMPure XP beads and quantity and quality of the library pool confirmed. Pooled libraries were sequenced by Edinburg Genomics, University of Edinburgh (UK) on HiSeq 4000 (75 bp paired end reads) or NovaSeq S1 (100 bp paired end reads, both Illumina).

treatment_protocol: 30 days after chloroquine treatment of once-P. chabaudi AJ malaria infected mice and uninfected age-matched controls, bone marrow cells from both femurs and tibias (pooled from two mice) were stained with antibodies and gently fixed in PBS with 1 % paraformaldehyde (Alpha Aesar) and 10 % FBS for exactly 10 minutes at room temperature. Fixation was quenched with 125 mM Glycine (Sigma). 50,000 bone marrow inflammatory monocytes (Lineage- Ly6G- cKit- CD135- CD11b+ Ly6C+) were then flow-sorted into polypropylene tubes with IMDM supplemented with 5 % FBS and 8 mM L-Glutamine. We flow-sorted multiple replicates from one biological sample, which were then chromatin-immunoprecipitated using three different antibodies. Sorted monocytes were pelleted by centrifugation and washed in HBSS (Gibco) with protease inhibitors (complete ULTRA Tablets Protease Inhibitor Cocktail, Roche) and 5 mM sodium butyrate (Alpha Aesar). Cell pellets were stored at - 80 ̊C.

tag: infection

value: uninfected age-matched

tag: chip antibody

value: not immunoprecipitated:input

tag: tag


title: LJ17W2I02


title: uninfected_H3K4me1_3

description:
H3K4me1_MEMORY_ChIP_AMC
H3K4me1_MEMORY_ChIP_AMC.tagdir.tar.gz
H3K4me1_MEMORY_ChIP_AMC.bedgraph
H3K4me1_MEMORY_ChIP_AMC.tdf.gz


title: WBN5-5b

description:
Single-colony-derived clone isolated from the 45th passage of WBN5 culture.
processed data file: ProcessedDataMatrix.xlsx


title: LJ17W2I01


title: RNA_DMSO_1h_wt_2

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

value: wildtype

value: DMSO


title: input_uninfected_H3K27ac_3

description:
H3K27ac_MEMORY_INPUT_AMC
H3K27ac_MEMORY_INPUT_AMC.tagdir.tar.gz
H3K27ac_MEMORY_INPUT_AMC.bedgraph
H3K27ac_MEMORY_INPUT_AMC.tdf.gz


title: RNA_DMSO_1h_wt_1


title: WBN5-3b


title: LJ17W1I02


title: LJ17W1I01


title: Oct4_BRM014-10uM_24h_2

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
ChIP-seq reads were aligned to the genome using qAlign from the QuasR Bioconductor package version 1.26.0 (Gaidatzis et al, Bioinformatics, 2015) with default parameters, only reporting alignments for reads with a unique match to the genome.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and binsize=100. The scores in the wig file therefore represent the number of alignments per 100bp window and per million reads in the library.

extract_protocol:
ChIP was carried out as previously described (Barisic et al., 2019) with following modifications: (1) chromatin was sonicated for ~20 cycles of 30s using a Diagenode Bioruptor Pico, with 30s breaks in between cycles, (2) protein A/G magnetic Dynabeads Magnetic beads (Thermo Fisher Scientific) were used, (3) DNA was purified using either AMPure XP beads.
Immunoprecipitated DNA and input DNA were submitted to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, input sample were amplified using 5 PCR cycles, IP sample using 12 cycles.

treatment_protocol: BRM014 compound was synthesised by Novartis. Powder was resuspended in DMSO to a final concentration of 10mM. Desired concentration was added directly to the tissue culture media.

tag: antibody

value: OCT4 (CST C30A3C1)


title: LJ17S5I02

tag: treatment

value: SAS


title: WBN5-3a


title: Oct4_BRM014-10uM_24h_1


title: input_uninfected_H3K27ac_4


title: uninfected_H3K27ac_4

description:
H3K27ac_MEMORY_ChIP_AMC
H3K27ac_MEMORY_ChIP_AMC.tagdir.tar.gz
H3K27ac_MEMORY_ChIP_AMC.bedgraph
H3K27ac_MEMORY_ChIP_AMC.tdf.gz


title: LJ17S4I02


title: WBN5-2b


title: input_memory_H3K27ac_4

description:
H3K27ac_MEMORY_INPUT_AJ
H3K27ac_MEMORY_INPUT_AJ.tagdir.tar.gz
H3K27ac_MEMORY_INPUT_AJ.bedgraph
H3K27ac_MEMORY_INPUT_AJ.tdf.gz

value: 30 days after drug cure of chronic mosquito transmitted P. chabaudi AJ


title: WBN5-2a


title: uninfected_H3K27ac_3


title: Oct4_BRM014-10uM_2h_2


title: memory_H3K27ac_4

description:
H3K27ac_MEMORY_ChIP_AJ
H3K27ac_MEMORY_ChIP_AJ.tagdir.tar.gz
H3K27ac_MEMORY_ChIP_AJ.bedgraph
H3K27ac_MEMORY_ChIP_AJ.tdf.gz


title: LJ17S4I01


title: RNA_BRM014-10uM_30min_wt_1


title: WBN4-5b

description:
Single-colony-derived clone isolated from the 45th passage of WBN4 culture.
processed data file: ProcessedDataMatrix.xlsx


title: LJ17S5I01


title: Oct4_BRM014-10uM_30min_2


title: Oct4_BRM014-10uM_2h_1


title: WBN5-5a


title: WBN4-5a


title: uninfected_H3K9me3

description:
H3K9me3_MEMORY_ChIP_AMC
H3K9me3_MEMORY_ChIP_AMC.tagdir.tar.gz
H3K9me3_MEMORY_ChIP_AMC.bedgraph
H3K9me3_MEMORY_ChIP_AMC.tdf.gz


title: Oct4_BRM014-10uM_30min_1


title: WBN4-4b


title: Oct4_DMSO_24h_2


title: LJ17S3I01


title: LJ17S3I02


title: input_memory_H3K27ac_3


title: input_uninfected_H3K9me3

description:
H3K9me3_MEMORY_INPUT_AMC
H3K9me3_MEMORY_INPUT_AMC.tagdir.tar.gz
H3K9me3_MEMORY_INPUT_AMC.bedgraph
H3K9me3_MEMORY_INPUT_AMC.tdf.gz


title: WBN4-4a


title: LJ17S2I02


title: Oct4_DMSO_24h_1


title: memory_H3K27ac_3


title: LJ17S2I01


title: WBN4-1a


title: WBN2-4b

description:
Single-colony-derived clone isolated from the 45th passage of WBN2 culture.
processed data file: ProcessedDataMatrix.xlsx


title: memory_H3K9me3

description:
H3K9me3_MEMORY_ChIP_AJ
H3K9me3_MEMORY_ChIP_AJ.tagdir.tar.gz
H3K9me3_MEMORY_ChIP_AJ.bedgraph
H3K9me3_MEMORY_ChIP_AJ.tdf.gz


title: input_memory_H3K9me3

description:
H3K9me3_MEMORY_INPUT_AJ
H3K9me3_MEMORY_INPUT_AJ.tagdir.tar.gz
H3K9me3_MEMORY_INPUT_AJ.bedgraph
H3K9me3_MEMORY_INPUT_AJ.tdf.gz


title: Rest_BRM014-10uM_24h_2

value: REST (Santa Cruz, Cat. # H-290)


title: A18W09

source_name: sperm

value: sperm

value: adult


title: A18W10


title: Rest_BRM014-10uM_2h_2


title: bulk RNA-seq from microdissected IM 5

data_processing:
Provided FASTQ files were aligned using STAR and the mm9 genome.
Reads were then counted using featureCounts34 with -p -t exon -O -g gene_id -s 0.
Raw count values were then transformed to TPM (transcript per million) values.
Genome_build: mm9
Supplementary_files_format_and_content: TPM

source_name: mouse renal inner medulla

extract_protocol:
Kidneys were harvested from sacrificed mice and immediately put into ice-cold PBS. Total RNA was then extracted using phenol/chloroform.
Total RNA was sent to Novogene on dry ice. Novogene performed paired-end RNA-sequencing according to their cmpany guidelines (https://en.novogene.com/next-generation-sequencing-services/gene-regulation/mrna-sequencing-service/). Paired-end Illumina libraries were sequenced on Illumina Novaseq 6000.

value: wild type

value: kidney

tag: kidney region

value: inner medulla


title: Rest_BRM014-10uM_24h_1


title: bulk RNA-seq from microdissected IM 4


title: WBN2-4a

value: PA14 mutS::Tn

value: LB

value: Replica 1


title: Rest_BRM014-10uM_2h_1

value: mouse embryonic stem cells


title: bulk RNA-seq from microdissected IM 3


title: WBN2-3b

value: Replica 2


title: Rest_BRM014-10uM_30min_2


title: WBN2-3a


title: bulk RNA-seq from microdissected IM 2


title: A18W07

value: WILD


title: A18W05


title: Rest_BRM014-10uM_30min_1

value: wildtype


title: A18W04


title: bulk RNA-seq from microdissected IM 1


title: Rest_DMSO_24h_2

value: DMSO


title: WBN4-1b


title: WBN2-1a


title: A18W03


title: bulk RNA-seq from microdissected OM 4

source_name: mouse renal outer medulla

value: outer medulla


title: bulk RNA-seq from microdissected OM 5


title: A18W08


title: A18W02


title: WBN1-6b

description:
Single-colony-derived clone isolated from the 45th passage of WBN1 culture.
processed data file: ProcessedDataMatrix.xlsx


title: Input_BRM014-10uM_24h_2


title: WBN1-6a


title: Rest_DMSO_24h_1


title: A18S09

value: SAS


title: A18S10


title: WBN2-1b


title: bulk RNA-seq from microdissected OM 3


title: Input_BRM014-10uM_2h_2


title: Input_BRM014-10uM_24h_1


title: Input_BRM014-10uM_2h_1


title: A18S07


title: WBN1-4b


title: bulk RNA-seq from microdissected OM 2


title: A18S08


title: WBN1-1b


title: WBN1-4a


title: bulk RNA-seq from microdissected cortex 5

source_name: mouse renal cortex

value: cortex


title: Input_BRM014-10uM_30min_2


title: A18S05


title: bulk RNA-seq from microdissected OM 1


title: Input_BRM014-10uM_30min_1


title: e49-51hr_faire_rep3

city: Milwaukee

first: Ronald

middle: J

last: Nowling

state: WI

address: 1025 N Broadway

institute: Milwaukee School of Engineering

description:
AaegL3_faire_seq_peaks.narrowPeak
AaegL5_faire_seq_peaks.narrowPeak

data_processing:
FAIRE-Seq reads were cleaned with trimmomatic (CROP:85 HEADCROP:15 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50)
Aligned to the AaegL3.5 and AaegL 5.2 reference genomes using BWA backtrack
Alignments were filtered with SAMtools to remove reads with mapping qualities < 10
Peaks were called with MACS2 (--nomodel -p 0.01 --extsize 550 -g 1.24e9)
Genome_build: AaegL3.5; AaegL5.2
Supplementary_files_format_and_content: peak text files

organism: Aedes aegypti

source_name: Whole embryos

growth_protocol: Mosquitoes were maintained in an insectary at 26°C, ~80% humidity, under a 12 hr light and 12 hr dark cycle with 1 hr crepuscular periods at the beginning and end of each light cycle. Mosquito larvae were fed a suspension of dried beef liver powder, while adults were provided cotton soaked with 10% sugar solution. An artificial membrane blood feeding system was utilized to deliver a sheep blood meal to females.  Females deposited eggs on paper toweling during two hour eggs collections.  Eggs were maintained in the insectary for an additional 49 hrs.

extract_protocol:
Nuclei were pelleted, resuspended in FAIRE lysis buffer FAIRE Lysis Buffer (2% Triton X-100, 1% SDS, 100mM NaCl, 10mM Tris-Cl pH 8, 1mM EDTA) and subjected to bead beating with 0.5 mm glass beads.  Chromatin was sonicated using a Branson 250 ultrasonifier outfitted with a microtip to an average fragment size of 300-500 bp and then phenol-chloroform extracted.  900 ng of FAIRE-enriched DNA was prepared at the University of Notre Dame Genomics and Bioinformatics Core Facility for sequencing on an Illumina HiSeq 2000 sequencer at the BGI Americas Corporation (Cambridge, MA).
FAIRE DNA Illumina libraries were prepared using the TruSeq kit (Illumina) per the manufacturer’s guidelines.
Next-generation Illumina Sequencing (HiSeq 50 bp paired-end sequencing) with a Illumina HiSeq 2000 (BGI Americas Corporation, Cambridge, MA) was used to generate ~150 million reads for each of three replicate FAIRE DNA preparations.

treatment_protocol: FAIRE was performed using a modified version of the Drosophila melanogaster embryonic tissue protocol (McKay and Lieb, Dev Cell 27:306-318).  Samples were crosslinked for 15 min at 60° C, quenched with glycine, and rinsed with buffer A at 4° C.  The nuclei were homogenized with a pestle, and the lysate was passed through Miracloth to remove debris.

value: Liverpool-IB12 (LVP-IB12)

tag: developmental stage

value: 49-51 hrs after egg laying

value: whole embryo


title: A18S04

value: sperm

value: adult


title: bulk RNA-seq from microdissected cortex 3

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

value: wild type

value: kidney


title: Input_DMSO_24h_2

city: Basel


title: e49-51hr_faire_rep2


title: bulk RNA-seq from microdissected cortex 4


title: A18S02


title: e49-51hr_faire_rep1


title: A18S03


title: bulk RNA-seq from microdissected cortex 1


title: WBN1-1a

value: PA14 mutS::Tn

value: LB


title: K562-Mock-H4ac

status: Public on Nov 25 2020

city: Quebec City

first: Deepthi

last: Sudarshan

state: Quebec

address: 9 Rue Mc Mahon

data_processing:
the single-end reads were mapped on the human genome build hg18 using bowtie version 0.12.8.
The read alignments in sam format were then converted to bam files using samtools (Langmead et al., 2009)
Samtools was then successively utilized to remove duplicated reads, sort, and index bam files
Peak calling was performed using MACS version 1.4.0 by comparing EPC (1-581), PHF1 and EPC-PHF1 ChIP-seq signals to the control signal (Zhang et al., 2008).
We identified intersection between two sets of peaks in hg18 coordinates using bedtools “intersect” function (Quinlan and Hall, 2010)
We identified significant changes in H4ac and H3K27me3 ChIP-seq read counts at EPC-PHF1 bound regions using DESeq
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files were generated using bedtools

source_name: K562 from ATCC

growth_protocol: RPMI, 10% FBS, 1ug/ml Puromycin

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: No Treatment

tag: cell type

value: lymphoblast from chronic myelogenous leukemia (CML)

tag: growth conditions

value: normal growth conditions

value: Histone H4 hyperacetylated (Penta), Rabbit Polyclonal, Millipore, Cat# 06-946, RRID:AB_310310

value: Insertion of Tag only at the AAVS1 locus by Zinc finger Nuclease,puromycin selection


title: K562-EPC1-PHF1-H3K27me3

value: H3K27me2/me3, Mouse monoclonal, Active Motif, Cat#39535, RRID:AB_2793246

value: Insertion of EPC1-PHF1 construct at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: K562-Mock-H3K27me3

value: Insertion of Tag only at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: K562-EPC1-PHF1-FLAG

value: FLAG M2 , Mouse monoclonal, Sigma-Aldrich ,Cat# F1804, RRID:AB_262044


title: K562-PHF1-FLAG

value: Insertion of PHF1 construct at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: K562-EPC1(1-581)-H4ac

value: Insertion of EPC1(1-581aa)construct at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: K562-EPC1-PHF1-H4ac


title: K562-PHF1-H4ac


title: K562-EPC1(1-581)-FLAG


title: K562-Mock-FLAG


title: MM2_PGK.TINCR_rep2

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

institute: European Institute of Oncology

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each interference condition (shLuc and shKMT2D) for each MM patient.
Genome_build: hg19
Supplementary_files_format_and_content: A tab delimited file with normalized read counts for all samples

molecule: polyA RNA

source_name: metastasis of cutaneous melanoma

extract_protocol:
total RNA was extracted with qiagen RNeasy mini kit (cat# 74106) according to manufacturer protocol
libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 1µg of total RNA

treatment_protocol: Cells isolated from secondary PDXs were infected with lentiviral vector expressing TINCR full length cDNA or empty vector, selected in purumycin and then harvested for further analysis

value: metastasis of cutaneous melanoma

value: patient derived xenograft cells

tag: passage

tag: melanoma mutation

tag: infected shrna


title: MM2_PGK.TINCR_rep1


title: MM13_PGK.TINCR_rep1


title: MM2_EmptyVector_rep2

value: Empty Vector


title: MM2_EmptyVector_rep1


title: MM13_PGK.TINCR_rep2


title: bulk RNA-seq from microdissected cortex 2

city: Hannover

value: wild type

value: cortex


title: MM13_EmptyVector_rep2


title: Input_DMSO_24h_1

value: mouse embryonic stem cells

value: wildtype

value: DMSO


title: WM902B_shTINCR_rep2_RPF

data_processing:
Library strategy: Ribo-Seq
Basecalls performed using CASAVA version 1.9
The reads were clipped for 3’ adapter sequences quality filtered (Phred quality score 33 ) using Fastx tool kit (Ref) and the reads longer than 25 bp were kept for further analysis
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential translation efficiency of mRNAs was calculated with xtail R package , using ribosome protected fragments (RPF) and total RNA (totRNA) read counts for two biological replicas for each interference condition (shSCR and shTINCR) .
Genome_build: hg19
Supplementary_files_format_and_content: list of differentially translated mRNAs between two conditions (shTINCR vs shSCR)

source_name: primary melanoma cell line WM902B

extract_protocol:
Ribosome prtotected fragments were prepared by sucrose gradient centrifugation and RNAseI digestion using to Riboprofile Trueseq Illumina Kit
Ribo Profile (Mammalian) Trueseq Library Prep Kit (Illumina). The libraries were prepared in two biological replicates for each condition

treatment_protocol: The cells were treated with 100ug/ml cycloheximide for 5 min

tag: cell line

value: primary melanoma cell line

value: shTINCR

tag: molecule subtype

value: ribosome protected RNA fragments (RPF)


title: WM902B_shTINCR_rep1_torRNA

value: polyA RNA


title: WM902B_shTINCR_rep1_RPF


title: WM902B_shSCR_rep1_totRNA

value: shSCR


title: WM902B_shTINCR_rep2_totRNA


title: K562-PHF1-H3K27me3

value: lymphoblast from chronic myelogenous leukemia (CML)

value: normal growth conditions

value: H3K27me2/me3, Mouse monoclonal, Active Motif, Cat#39535, RRID:AB_2793246


title: WM902B_shSCR_rep1_RPF


title: K562-EPC1(1-581)-H3K27me3

value: Insertion of EPC1(1-581aa)construct at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: RNAseq_PM1

description:
Sample 16
hg18

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each interference condition (shLuc and shKMT2D) for each MM patient.
Genome_build: hg19( samples 1-9); hg18( Samples 10-22)
Supplementary_files_format_and_content: list of differentially expressed genes between two conditions (shTINCR vs shSCR, samples 1-4) ; tab delimited text file containing  normalized read counts for each gene ( samples 5-22)

source_name: Primary cutaneous  melanoma

value: Primary cutaneous melanoma specimen


title: RNAseq_MM5

description:
Sample 15
hg18

value: Metastatic melanoma clinical specimen


title: RNAseq_MM4

description:
Sample 14
hg18


title: RNAseq_MM2

description:
Sample 12
hg18


title: RNAseq_NV3

description:
Sample 22
hg18

source_name: Benign Nevus

value: Benign Nevus  specimen


title: RNAseq_PM2

description:
Sample 17
hg18


title: RNAseq_PM3

description:
Sample 18
hg18


title: RNAseq_NV1

description:
Sample 20
hg18

value: Benign Nevus specimen


title: RNAseq_PM4

description:
Sample 19
hg18


title: RNAseq_MM1

description:
Sample 11
hg18


title: RNAseq_WM902B_shTINCR_tumors_rep3

description:
Sample 10
hg19

source_name: mouse tumor  derived from  shTINCR expressing  WM902B cells

value: primary melanoma cell line derived xenograft tumors


title: RNAseq_WM902B_shSCR_tumors_rep3

description:
Sample 7
hg19

source_name: mouse tumor  derived from  shSCR expressing  WM902B cells


title: RNAseq_WM902B_shTINCR_tumors_rep2

description:
Sample 9
hg19


title: RNAseq_WM902B_shSCR_tumors_rep2

description:
Sample 6
hg19


title: RNAseq_WM902B_shSCR_tumors_rep1

description:
Sample 5
hg19


title: MM13_EmptyVector_rep1

value: metastasis of cutaneous melanoma

value: patient derived xenograft cells

value: Empty Vector


title: WM902B_shSCR_rep2_totRNA

value: primary melanoma cell line


title: RNAseq_WM902B_shTINCR_rep2

description:
Sample 4
hg19

value: shTINCR


title: RNAseq_WM902B_shTINCR_rep1

description:
Sample 3
hg19


title: RNAseq_WM902B_shSCR_rep2

description:
Sample 2
hg19


title: RNAseq_WM902B_shSCR_rep1

description:
Sample 1
hg19


title: RNAseq_NV2

description:
Sample 21
hg18


title: RNA_seq-B6xSPRET-B_cell-DS39200

first: Matthew

middle: T

last: Maurano

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU School of Medicine

data_processing:
Trimmed to remove low-quality sequence or adapter contamination using the trimmomatic tool (Parameters: TOPHRED33 ILLUMINACLIP: TruSeq3-PE2.fa:2:5:5:1:true MAXINFO:27:0.95 TRAILING:20 MINLEN:27')
Reads were mapped with Burrows-Wheeler Aligner to the mouse reference assembly and the strain-specific genome (Parameters: bwa aln -n 0.04 -l 32 -t 2 -Y)
Alignments were post-processed with a custom Python script using pysam to retain only properly-paired or single-end reads mapping  uniquely to the autosomes and chrX with a mapping quality of at least 20. Paired end reads were required to have an inferred template length of less than 500 bp.
Duplicate reads were flagged on a per-library basis using Samblaster
Mapped tags were converted to BED format using awk and bedops
DNase I hypersensitive sites were identified using hotspot2
RNA-seq eads were mapped to the mm10 reference and strain-specific genomes in parallel using STAR
Transcript counts were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: bed.gz file containing DHS hotspots
Supplementary_files_format_and_content: bigWig files indicate DHS density
Supplementary_files_format_and_content: tsv file containing count data for Gencode M10 transcripts
Supplementary_files_format_and_content: bigWig indicating RNA-seq read denisty

source_name: B cell

extract_protocol:
Whole liver (all lobes), both kidneys and all lobes of the lungs were rapidly dissected from sacrificed mice. Tissues were minced in 2 mm square pieces and resuspended in 5 mL of homogenization buffer per tissue. Nuclei were released using 5-10 strokes in a Dounce homogenizer with a loose-fitting type-A pestle and the resulting homogenate was filtered through a 120µm filter. Marrow was obtained from femurs of 8 week old female mice. B cells were isolated using an AutoMACS (Miltenyi Biotech) to deplete CD43 and Mac-1/CD11b markers. Nuclei were extracted by resuspending cells in buffer A supplemented with 0.015% detergent (IGEPAL-CA630) (Sigma) and incubating for 5-10 minutes on ice.
Fresh nuclei were digested with DNase I for 3 minutes. Fragments <250 bp were recovered by sucrose ultracentrifugation, end-repaired and ligated with adapters compatible with the Illumina sequencing platform. Libraries were amplified using minimal PCR cycles based on a trial qPCR amplification. Total RNA was isolated using the mirVana miRNA Isolation Kit with phenol (AM1560). Spike-in controls were mixed in (Ambion-ERCC Mix, Cat no. 4456740) and Illumina sequencing libraries were made using the RNA TruSeq Stranded total RNA (Illumina).

tag: strain

value: B cell


title: RNAseq_MM3

description:
Sample 13
hg18


title: RNA_seq-B6xC3H-Liver-DS38822

source_name: Liver

tag: tissue

value: Liver


title: RNA_seq-B6xC3H-Kidney-DS38815

source_name: Kidney

value: Kidney


title: RNA_seq-B6xC3H-Lung-DS38808

source_name: Lung

value: Lung


title: RNA_seq-B6xSPRET-Liver-DS38323


title: RNAseq_WM902B_shTINCR_tumors_rep1

description:
Sample 8
hg19

source_name: mouse tumor  derived from  shTINCRexpressing  WM902B cells


title: RNA_seq-B6xSPRET-Lung-DS38309


title: RNA_seq-B6xSPRET-Kidney-DS38305


title: DNAse_seq-B6xC3H-B_cell-DS38900A


title: WM902B_shSCR_rep2_RPF

value: shSCR

value: ribosome protected RNA fragments (RPF)


title: DNAse_seq-B6xSPRET-B_cell-DS39204A


title: DNAse_seq-B6xSPRET-Liver-DS38327C


title: DNAse_seq-B6xC3H-B_cell-DS38899A


title: DNAse_seq-B6xSPRET-B_cell-DS39205A


title: DNAse_seq-B6xC3H-Lung-DS38811A


title: DNAse_seq-B6xSPRET-Kidney-DS39287A


title: DNAse_seq-B6xSPRET-Liver-DS38327A


title: DNAse_seq-B6xC3H-Lung-DS38812A


title: DNAse_seq-B6xSPRET-Liver-DS38327B


title: DNAse_seq-B6xSPRET-Liver-DS38318B


title: DNAse_seq-B6xSPRET-Liver-DS38318A


title: DNAse_seq-B6xSPRET-Lung-DS38311A


title: DNAse_seq-B6xSPRET-Kidney-DS37591B


title: DNAse_seq-B6xSPRET-Kidney-DS37591A


title: DNAse_seq-B6xSPRET-Liver-DS37603A


title: DNAse_seq-B6xC3H-B_cell-DS38898A


title: DNAse_seq-B6xSPRET-Kidney-DS37590B


title: DNAse_seq-B6xSPRET-Kidney-DS37590A


title: RNA_seq-B6xCAST-B_cell-DS35975


title: DNAse_seq-B6xSPRET-Lung-DS37582B


title: DNAse_seq-B6xSPRET-Lung-DS37582A


title: DNAse_seq-B6xC3H-Kidney-DS38819A


title: DNAse_seq-B6xPWK-Kidney-DS37496B


title: RNA_seq-B6xPWK-B_cell-DS37551


title: DNAse_seq-B6xPWK-Kidney-DS37496A


title: DNAse_seq-B6xPWK-Kidney-DS37495B


title: DNAse_seq-B6xPWK-Kidney-DS37495A


title: DNAse_seq-B6xSPRET-Lung-DS38311B


title: DNAse_seq-B6xPWK-Lung-DS37487A


title: DNAse_seq-B6xSPRET-Liver-DS37603B


title: DNAse_seq-B6xPWK-Lung-DS37487B


title: DNAse_seq-B6xPWK-B_cell-DS36871C


title: DNAse_seq-B6xPWK-B_cell-DS36871A


title: DNAse_seq-B6xPWK-B_cell-DS36871B


title: DNAse_seq-B6xPWK-B_cell-DS36870A


title: DNAse_seq-B6xPWK-B_cell-DS36869A


title: DNAse_seq-B6xPWK-B_cell-DS36870B


title: DNAse_seq-B6xCAST-Liver-DS36791D


title: DNAse_seq-B6xPWK-B_cell-DS36869B


title: DNAse_seq-B6xCAST-Lung-DS36795A


title: DNAse_seq-B6xCAST-Liver-DS36791A


title: DNAse_seq-B6xCAST-Liver-DS36784A


title: DNAse_seq-B6xCAST-Liver-DS36791C


title: DNAse_seq-B6xCAST-Kidney-DS36778D


title: DNAse_seq-B6xCAST-Kidney-DS36777B


title: DNAse_seq-B6xCAST-Kidney-DS36777D


title: DNAse_seq-B6xCAST-Kidney-DS36777C


title: DNAse_seq-B6xCAST-Kidney-DS36778B


title: DNAse_seq-B6xCAST-Kidney-DS36777A


title: DNAse_seq-B6xCAST-Kidney-DS36778A


title: DNAse_seq-B6xCAST-Kidney-DS36776D


title: DNAse_seq-B6xCAST-Kidney-DS36776C


title: DNAse_seq-B6xCAST-Lung-DS36795B


title: DNAse_seq-B6xPWK-Lung-DS36657C


title: DNAse_seq-B6xPWK-Lung-DS36657A


title: DNAse_seq-B6xPWK-Lung-DS36655B


title: DNAse_seq-B6xCAST-Kidney-DS36776A


title: DNAse_seq-B6xPWK-Liver-DS36648B


title: DNAse_seq-B6xPWK-Lung-DS36655A


title: DNAse_seq-B6xPWK-Kidney-DS36649A


title: DNAse_seq-B6xCAST-Kidney-DS36778C


title: DNAse_seq-B6xPWK-Liver-DS36641A


title: DNAse_seq-B6xCAST-Liver-DS36791B


title: DNAse_seq-B6xPWK-Liver-DS36648A


title: DNAse_seq-B6xPWK-Liver-DS36636B


title: DNAse_seq-B6xPWK-Liver-DS36636A


title: DNAse_seq-B6xCAST-B_cell-DS35992B


title: DNAse_seq-B6xCAST-B_cell-DS35993A


title: DNAse_seq-B6xCAST-B_cell-DS35993C


title: DNAse_seq-B6xCAST-B_cell-DS35992A


title: DNAse_seq-B6xPWK-Kidney-DS36635B


title: DNAse_seq-B6xPWK-Kidney-DS36635A


title: DNAse_seq-B6xCAST-B_cell-DS35986A


title: DNAse_seq-B6xCAST-B_cell-DS35986C


title: DNAse_seq-B6xCAST-B_cell-DS35978B


title: DNAse_seq-B6xCAST-Kidney-DS36776B


title: DNAse_seq-B6xCAST-B_cell-DS35993B