title: CBP-1 N2 emb rep3 ChIP-seq

city: New York City

first: Lena

middle: Annika

last: Street

state: NY

address: 100 Washington Square East

department: Biology

institute: New York University

description:
CBP1_N2_Emb_LW197_SE339_BC053_average.bw
CBP1_N2_Emb_LW197_SE339_BC053_final_peaks.bed

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.2.0 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.3 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.3 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.1.1 using default parameters, specifying first strand alignment.
Resultant RNA-seq bam files were converted to sam files using samtools version 1.6. Sam files were used to generate count data using htseq-cout version 0.6.1.
Genome_build: WS220
Supplementary_files_format_and_content: BigWig files were generated by converting wiggle files using the UCSC wigToBigWig utility. Wiggle files were generated using MACS version 1.4.3, normalized according to the genome-wide mean coverage and then input subtracted. Scores represent the average coverage of each replicate at each base position.
Supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.3 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Supplementary_files_format_and_content: Counts files were generated using Htseq-counts version 0.6.1.

source_name: whole worms

growth_protocol: Embryos were isolated by bleaching gravid adults grown on plates at 20C.

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

tag: developmental stage

value: mixed embryo

tag: antibody target

tag: chip antibody (vendor, cat#, lot#)

value: SDIX LLC, SDQ3582 non-commercial cbp-1 modENCODE antibody 1

tag: antibody antigen

tag: antibody (host, clone)

value: Rabbit, polyclonal

tag: matching input


title: BC032 input N2 emb ChIP-seq (reanalysis)

status: Public on Jan 08 2019

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Caenorhabditis elegans

tag: strain

value: INPUT


title: I4_R1_001

city: Birmingham

first: Beatriz

last: Leon Ruiz

state: Alabama

address: 1825 University Blvd

department: Microbiology

institute: University of Alabama at Birmingham

library_source: transcriptomic

data_processing:
All RNA-seq analyses were performed using the Penn State Galaxy publicly available server using the tuxedo suite analysis tools. Fastq files were aligned to the mm10 reference genome using TopHat (Galaxy Tool Version 0.9; Tool Version TopHat v2.0.14 for all studies except for the glutamine studies, Galaxy Tool Version 2.1.0 and Tool Version TopHat v2.1.0) were used with default parameters.
Cufflinks, Cuffmerge, Cuffquant, and Cuffnorm were performed to define RPKM values for genes. Cufflinks (Galaxy Tool Version 2.2.2.0; Tool Version Cufflinks v2.2.1.0) was performed using default parameters for all settings except bias and multi-read correction was performed.
Cuffmerge (Galaxy Tool Version 2.2.1.0) was performed using default parameters. Cuffquant (Galaxy Tool Version 2.2.1.0; Tool Version Cuffquant v2.2.1) was performed using default parameters for all settings except bias and multi-read correction was performed.
Cuffdiff (Galaxy Tool Version 2.2.1.3; Tool Version Cuffdiff v2.2.1) was performed using default parameters (using Cuffquant output files). Cuffnorm (Galaxy Tool Version 2.2.1.1; Tool Version Cuffnorm v2.2.1) was performed using default parameters with a Cuffdiff format output.
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel Open XML Format Spreadsheet files showing RPKM values for each individual sample

molecule: total RNA

organism: Mus musculus

source_name: mLN

extract_protocol:
RNA was isolated using the RNA Isolation Kit: Rneasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols. All samples (Genewiz)

tag: cell type

value: CD11b+ mDCs

tag: treatment

value: 24H post i.n. sensitization with HDM+LPS

tag: age


title: non-stressed control WT group

status: Public on Jan 09 2019

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: non-stressed WT DRN

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

tag: background strain

tag: tissue

value: dorsal raphe nucleus (DRN)

tag: Sex

value: male

value: 10 weeks old

tag: condition

value: no stress

tag: genotype

value: WT


title: I2_R1_001


title: I1_R1_001


title: A1_R1_001


title: mouse liver RNA-seq NASH-1

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

description:
Mouse liver was harvested and immediately frozen into liquid nitrogen. RNA was extract by TRIzol. Sequencing library was constructed from 1ug of total RNA by using Illumina TruSeq RNA Library Prep Kit v2 (Cat#RS-122-2001).
DESeq2_NASH_RNA_seq.csv

data_processing:
FastQC was used to assess the sequencing quality on fastq files.
STAR was used for alignment to generate bam files.
The reads aligned to each gene feature were counted by HTSeq.
R package DESeq2 was used for differential expression analysis.
Single-cell RNA seq data was processed by Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from bulk RNA-seq, UMI count matrices from single cell RNA-seq.

source_name: liver

extract_protocol:
please see samples description
RNA libraries were prepared for sequencing using standard Illumina and 10X genomics Chromium single cell protocols

treatment_protocol: mice were fed on NASH diet (D09100301, Research Diets) for 36 weeks

value: whole liver

tag: phenotype

value: NASH


title: A3_R1_001

data_processing:
All RNA-seq analyses were performed using the Penn State Galaxy publicly available server using the tuxedo suite analysis tools. Fastq files were aligned to the mm10 reference genome using TopHat (Galaxy Tool Version 0.9; Tool Version TopHat v2.0.14 for all studies except for the glutamine studies, Galaxy Tool Version 2.1.0 and Tool Version TopHat v2.1.0) were used with default parameters.
Cufflinks, Cuffmerge, Cuffquant, and Cuffnorm were performed to define RPKM values for genes. Cufflinks (Galaxy Tool Version 2.2.2.0; Tool Version Cufflinks v2.2.1.0) was performed using default parameters for all settings except bias and multi-read correction was performed.
Cuffmerge (Galaxy Tool Version 2.2.1.0) was performed using default parameters. Cuffquant (Galaxy Tool Version 2.2.1.0; Tool Version Cuffquant v2.2.1) was performed using default parameters for all settings except bias and multi-read correction was performed.
Cuffdiff (Galaxy Tool Version 2.2.1.3; Tool Version Cuffdiff v2.2.1) was performed using default parameters (using Cuffquant output files). Cuffnorm (Galaxy Tool Version 2.2.1.1; Tool Version Cuffnorm v2.2.1) was performed using default parameters with a Cuffdiff format output.
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel Open XML Format Spreadsheet files showing PKM values for each individual sample


title: mouse liver RNA-seq chow-3

value: chow


title: mouse liver RNA-seq NASH-3


title: mouse liver RNA-seq NASH-2


title: FS-stressed D2R-KO  group

source_name: FS-stressed D2R-KO DRN

value: forced swim stress

value: D2R KO


title: low_input_rnaseq_Vd2_IGTB627_3

city: Boston

first: Maria

last: Gutierrez-Arcelus

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital, Harvard Medical School

description:
Vd2_IGTB627_3
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz

data_processing:
Low input gene expression quantification was performed with Kallisto version 0.43.1 (Bray et al, Nature Biotechnology, 2016), using the Ensembl 83 annotation. Five outlier samples with low proportion of common genes detected were removed. Normalized expression are log2(tpm+1) values.
Single-cell gene expression quantification was performed with CellRanger version 2.1.0 using human genome assembly GRCh38. Cells with <=500 genes expressed or >=20% mitochondrial gene UMIs were removed. Cells that passed the antibody barcode quality criteria were kept. Normalized expression is ln(UMI counts per 1e04 + 1).
Genome_build: low input: hg19, single-cell: GRCh38
Supplementary_files_format_and_content: tab-delimited text files including gene counts, normalized gene expression, metadata for single cell experiment
Supplementary_files_format_and_content: low_input_rnaseq_gene_counts.txt.gz:read abundance measurements
Supplementary_files_format_and_content: low_input_rnaseq_gene_normalized.txt.gz:read abundance measurements
Supplementary_files_format_and_content: single_cell_rnaseq_gene_counts.txt.gz:UMI abundance measurements
Supplementary_files_format_and_content: single_cell_rnaseq_gene_normalized.txt.gz:UMI abundance measurements
Supplementary_files_format_and_content: single_cell_rnaseq_meta_data.txt.gz:meta data for single cell rnaseq experiment

organism: Homo sapiens

extract_protocol:
Healthy individuals had blood drawn in the morning, after which cells were promptly stained and sorted. For low input RNA-seq, cells were sorted into lysis buffer in a 96-well plate and frozen for later library preparation. For single-cell RNA-seq, sorted cell-types were labeled with DNA-barcoded antibodies to tag the cell type and donor of origin.
For low-input RNA-seq we used the Smart-seq2 protocol (Picelli et al. Nature Protocols, 2014). For single-cell RNA-seq we used 10X and the CITE-seq protocol with cell hashing (Stoeckius et al. Genome Biology, 2018).


title: mouse liver RNA-seq chow-1


title: low_input_rnaseq_Vd2_IGTB615_62

description:
Vd2_IGTB615_62
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd2_IGTB430_50

description:
Vd2_IGTB430_50
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd2_IGPR999_17

description:
Vd2_IGPR999_17
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd2_IGTB430_49

description:
Vd2_IGTB430_49
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd2_IGTB615_78

description:
Vd2_IGTB615_78
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: single_cell_rnaseq_10X_CITE-seq

description:
single_cell_rnaseq_gene_counts.txt.gz
single_cell_rnaseq_gene_normalized.txt.gz
single_cell_rnaseq_meta_data.tx.gz

source_name: T cells and NK cells


title: low_input_rnaseq_Vd2_IGPR999_18

description:
Vd2_IGPR999_18
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd2_IGTB187_85

description:
Vd2_IGTB187_85
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: FS-stressed D2LR-KO  group

source_name: FS-stressed D2LR-KO DRN

value: D2LR KO


title: low_input_rnaseq_Vd2_IGTB627_4

description:
Vd2_IGTB627_4
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: mouse liver RNA-seq chow-2


title: FS-stressed WT group

source_name: FS-stressed WT DRN


title: low_input_rnaseq_Vd2_IGTB107_36

description:
Vd2_IGTB107_36
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd2_IGTB187_69

description:
Vd2_IGTB187_69
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGPR999_20

description:
Vd1_IGPR999_20
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGPR999_19

description:
Vd1_IGPR999_19
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGTB627_5

description:
Vd1_IGTB627_5
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: A2_R1_001


title: low_input_rnaseq_Vd1_IGTB615_79

description:
Vd1_IGTB615_79
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGTB627_6

description:
Vd1_IGTB627_6
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGTB430_51

description:
Vd1_IGTB430_51
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGTB430_52

description:
Vd1_IGTB430_52
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGTB187_86

description:
Vd1_IGTB187_86
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGTB107_37

description:
Vd1_IGTB107_37
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd1_IGTB187_70

description:
Vd1_IGTB187_70
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB627_2

description:
NKT_IGTB627_2
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz

source_name: iNKT

value: iNKT


title: low_input_rnaseq_NKT_IGTB430_47

description:
NKT_IGTB430_47
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB430_48

description:
NKT_IGTB430_48
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB187_68

description:
NKT_IGTB187_68
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGPR999_21

description:
NK_IGPR999_21
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz

source_name: NK

value: NK


title: low_input_rnaseq_NKT_IGPR999_16

description:
NKT_IGPR999_16
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB627_1

description:
NKT_IGTB627_1
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB107_34

description:
NKT_IGTB107_34
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB615_61

description:
NKT_IGTB615_61
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB107_33

description:
NKT_IGTB107_33
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB627_8

description:
NK_IGTB627_8
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB187_71

description:
NK_IGTB187_71
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB430_54

description:
NK_IGTB430_54
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGPR999_22

description:
NK_IGPR999_22
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB615_64

description:
NK_IGTB615_64
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB187_87

description:
NK_IGTB187_87
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB430_53

description:
NK_IGTB430_53
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB615_80

description:
NK_IGTB615_80
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB107_39

description:
NK_IGTB107_39
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGPR999_15

description:
NKT_IGPR999_15
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGPR999_23

description:
MAIT_IGPR999_23
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz

source_name: MAIT

value: MAIT


title: low_input_rnaseq_MAIT_IGPR999_24

description:
MAIT_IGPR999_24
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB627_9

description:
MAIT_IGTB627_9
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NK_IGTB107_40

description:
NK_IGTB107_40
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB615_77

description:
NKT_IGTB615_77
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_NKT_IGTB187_84

description:
NKT_IGTB187_84
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB430_56

description:
MAIT_IGTB430_56
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB627_10

description:
MAIT_IGTB627_10
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB615_65

description:
MAIT_IGTB615_65
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB107_41

description:
MAIT_IGTB107_41
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGPR999_26

description:
CD8_IGPR999_26
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGPR999_25

description:
CD8_IGPR999_25
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB187_72

description:
MAIT_IGTB187_72
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB107_42

description:
MAIT_IGTB107_42
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB430_55

description:
MAIT_IGTB430_55
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB627_11

description:
CD8_IGTB627_11
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB187_73

description:
CD8_IGTB187_73
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB430_58

description:
CD8_IGTB430_58
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB615_82

description:
CD8_IGTB615_82
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB430_57

description:
CD8_IGTB430_57
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_Vd2_IGTB107_35

description:
Vd2_IGTB107_35
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB107_44

description:
CD8_IGTB107_44
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGTB627_14

description:
CD4_IGTB627_14
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGTB627_13

description:
CD4_IGTB627_13
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB107_43

description:
CD8_IGTB107_43
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_MAIT_IGTB615_81

description:
MAIT_IGTB615_81
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGTB615_67

description:
CD4_IGTB615_67
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGPR999_28

description:
CD4_IGPR999_28
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGTB187_90

description:
CD4_IGTB187_90
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGTB430_60

description:
CD4_IGTB430_60
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGTB187_74

description:
CD4_IGTB187_74
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGTB107_46

description:
CD4_IGTB107_46
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB627_12

description:
CD8_IGTB627_12
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD8_IGTB187_89

description:
CD8_IGTB187_89
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGTB107_45

description:
CD4_IGTB107_45
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: low_input_rnaseq_CD4_IGPR999_27

description:
CD4_IGPR999_27
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: I3: Extracted RNA cultured isolated human islets

city: Leiden

first: Eelco

last: de Koning

address: Albinusdreef 2

country: Netherlands

institute: LUMC

data_processing:
Paired end reads obtained by automated CEL-seq were aligned to the transcriptome containing all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. Reads mapping to multiple loci were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: pan_counttable_def.xls: Column separated data file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples. Column name indicates the sample number. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: cultured pancreatic islets

extract_protocol:
Samples for RNA extraction were re-suspended in RLT buffer (Qiagen), and extractions were carried out using the RNeasy Mini or Micro RNA Extraction Kit (Qiagen).
For mRNA sequencing, 10ng of RNA per sample was processed using the CEL-Seq protocol (Hashimshony et al., 2012), and 75 bp paired end sequencing was carried out on an Illumina Nextseq. Next, Read 1 was aligned with the hg19 RefSeq human transcriptome (available from UCSC genome browser (Kent et al., 2002)) using Burrows-Wheeler Alignment (Li et al., 2010) with default parameters. Read 2 contained a barcode that identified the sample-of-origin for that read. The CEL-Seq method sequences only a short stretch of the 3′ end of a transcript, and yields one read per transcript. Reads-per-million (RPM) normalization was used per sample and only genes with more than 10 RPM in 4 or more samples were accepted for subsequent analysis.

value: cultured pancreatic islets


title: EndoC_BH1_RNA_seq

city: Farmington

first: Michael

last: Stitzel

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
EndoC-ßH1 RNA Pol2 ChIA-PET libraries were generated and sequenced reads were processed and analyzed according to the protocol in (Li et al., 2017b). ChIA-PET interactions were identified using ChIA-PET2 (Li et al., 2017a) using the “bridge linker mode” option. ChIA-PET and Hi-C loops were further filtered using the Bioconductor package InteractionSet_1.8.0 (Lun et al., 2016) to retain only those in which both interacting sites (anchors) overlapped OCRs. ChIA-PET anchors were annotated to the nearest gene.
Hi-C libraries were generated as described in (Rao et al., 2014) and analyzed using the Juicer Tools version 1.75 pipeline (Durand et al., 2016a). We sequenced 6,065,763,792 Hi-C read pairs in EndoC-ßH1 cells, yielding 1,909,699,446 Hi-C contacts; we also sequenced 6,009,242,588 Hi-C read pairs in islet cells, yielding 1,516,995,339 Hi-C contacts. Loci were assigned to A and B compartments at 500 kB resolution. Loops were annotated using HiCCUPS at 5kB and 10kB resolutions with default Juicer parameters. This yielded a list of 9,100 loops in EndoC-ßH1 cells and 2,580 loops in Islet cells.
EndoC-ßH1 ATAC-seq libraries were prepared as previously described (Varshney et al., 2017) and sequenced on an Illumina NextSeq 500 with 2 x 125 bp cycles. Paired-end ATAC-seq reads were quality trimmed using Trimmomatic version 0.33 (Bolger et al., 2014) and parameters “TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”. Trimmed reads were aligned to human genome (hg19) using BWA version 0.7.12 (Li, 2013), specifically using the bwa mem –M option. Duplicate reads were removed using “MarkDuplicates” from Picard-tools version 1.95 (The Broad Institute, 2013). After preprocessing and quality filtering, peaks were called on alignments with MACS version 2.1.0 (Zhang et al., 2008) using the parameters “-g 'hs' --nomodel --keep-dup all --broad --broad-cutoff 0.05 -f BAMPE”. Peaks located in blacklisted regions of the genome were removed.
Total RNA was extracted and purified from EndoC using Trizol as previously described (Varshney et al., 2017). All sequencing was performed on an Illumina NextSeq 500 with 2 x 101 bp cycles. Paired-end RNA-seq reads were trimmed using Trimmomatic with the same parameters as used for ATAC-seq reads. Trimmed reads were aligned to human genome (hg19) using STAR version 2.53 (Dobin et al., 2012) with default parameters and expression levels of all genes were determined using QoRTs version 1.2.42 (Hartley and Mullikin, 2015) with default parameters and Gencode v19 transcript annotations.
Total RNA was extracted and purified from 2 x 106 EndoC-ßH1 cells using Trizol (Life Technologies). RNA quality was confirmed with Bioanalyzer 2100 (Agilent);  EndoC- ßH1 cells RNA RIN scores were > 9.0. miRNA libraries were prepared at the NIH Intramural Sequencing Core (NISC) from 1 µg total RNA using Illumina’s TruSeq Small RNA Library Kit according to the manufacturer’s guidelines, except a 10% acrylamide gel was used for better separation of library from adapters. Libraries were pooled in groups of about 8 for gel purification. Single-end 51 base sequencing was performed on Illumina HiSeq 2500 sequencers in Rapid Mode using version 2 chemistry.  Data was processed using RTA version 1.18.64 and CASAVA 1.8.2. All resulting data was processed with miRquant 2.0 (Kanke et al., 2016).
CTCF, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K79me2, H3K4me3, H3K9me3 ChIP-seq was performed as previously described (Stitzel et al., 2010) and sequenced on an Illumina HiSeq 2500 using 2 x 100 bp cycles. Harmonized ChromHMM states for EndoC-ßH1 and NIH Roadmap cells/tissues were determined as previously described (Varshney et al., 2017).
Genome_build: Human genome GRch37/hg19, and Gencode v19 reference gene annotations
Supplementary_files_format_and_content: Tab delimited text or BED files. HiC files contain HiCCUPS loop locations. ChIAPET file contains RNA Pol2 loop locations. ChromHMM file contains chromatin position and chromatin state annotation information as determined by ChromHMM algorithm (this file is meant to be a "summary" processed data file representing the amalgamation of all 13 ChIP-seq samples). ATACseq file contains broad peak positions as determined by MACS2 software. RNAseq file contains raw counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values for each gene. miRNA file contains reads per million mapped miRNA (RPMMM) values for each miRNA.

source_name: Pancreas

growth_protocol: EndoC-ßH1 cells provided by EndoCells/INSERM were cultured and passaged as previously described (Ravassard et al., 2011). Briefly, cells were seeded at a density of approximately 600,000 cells/cm2 on tissue culture-treated plates pre-coated overnight with extracellular matrix (Sigma) and fibronectin (Sigma) in EndoC-ßH1 complete medium. Cells were passaged approximately every 7 days. Cells were harvested at various passages and distinct sites (e.g., NHGRI, JAX-GM) for karyotyping, genotyping, ATAC-seq, ChIP-seq, RNA-seq, Hi-C, and Pol2 ChIA-PET analyses.

tag: cell line

value: EndoC-BH1 human pancreatic beta cell line

tag: biomaterial provider

value: Not applicable

tag: unos id

tag: ethnicity


title: I1: Extracted RNA cultured isolated human islets


title: I4: Extracted RNA cultured isolated human islets


title: EndoC_BH1_ATAC_seq

extract_protocol: EndoC-ßH1 ATAC-seq libraries were prepared as previously described (Varshney et al., 2017) and sequenced on an Illumina NextSeq 500 with 2 x 125 bp cycles.


title: E3: Extracted RNA islet-depleted pancreatic exocrine tissue


title: E1: Extracted RNA islet-depleted pancreatic exocrine tissue


title: low_input_rnaseq_CD4_IGTB430_59

description:
CD4_IGTB430_59
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: E2: Extracted RNA islet-depleted pancreatic exocrine tissue


title: P2: Extracted RNA fetal pancreas 18 weeks

source_name: Whole pancreas

tag: developmental stage

value: fetal

value: Whole pancreas


title: P1: Extracted RNA fetal pancreas 9 weeks


title: P4: Extracted RNA fetal pancreas 10 weeks


title: F2: Extracted RNA from ALDH high cells from 7-day expanded fetal pancreatic organoids

source_name: Organoids derived from fetal pancreatic tissue

value: ALDH high cells


title: F3: Extracted RNA from ALDH high cells from 7-day expanded fetal pancreatic organoids

value: Organoids derived from fetal pancreatic tissue


title: low_input_rnaseq_CD4_IGTB615_83

description:
CD4_IGTB615_83
low_input_rnaseq_gene_counts.txt.gz
low_input_rnaseq_gene_normalized.txt.gz


title: A2: Extracted RNA from ALDH high cells from 7-day expanded adult pancreatic organoids

source_name: Organoids derived from adult pancreatic tissue

value: adult


title: A3: Extracted RNA from ALDH high cells from 7-day expanded adult pancreatic organoids

value: Organoids derived from adult pancreatic tissue


title: F1: Extracted RNA from ALDH high cells from 7-day expanded fetal pancreatic organoids


title: A1: Extracted RNA from ALDH high cells from 7-day expanded adult pancreatic organoids


title: I2: Extracted RNA cultured isolated human islets


title: E4: Extracted RNA islet-depleted pancreatic exocrine tissue


title: IC:PBS6_2

city: New Haven

first: Andrew

last: Wang

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University School of Medicine

description: BMDMs stimulated first with Poly I:C then with PBS for 6 hours.

data_processing:
fastq files aligned with Tophat2
aligned files assembled with Cufflinks
assembled files merged with Cuffmerge
quantified using Cuffquant
normalized using Cuffnorm
Genome_build: mm9
Supplementary_files_format_and_content: .txt files with FPKMs in supplementary file

molecule: polyA RNA

source_name: BMDM

growth_protocol: Bone marrow derived macrophages (BMDMs) were prepared from male animals 6-12 weeks of age. Animals were euthanized by CO2 asphyxiation and femurs and tibias were isolated. The bone marrow cells were and grown in macrophage growth medium (RPMI 1640 supplemented with 10% FBS (Gibco), 1% penicillin-streptomycin (Gibco), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco), 0.01 M HEPES (AmericanBio), and 30% L929-conditioned media as a source of CSF-1), and plated on petri dishes. Macrophage growth medium was supplemented on day 3. Cells were plated for use on day 6.

extract_protocol:
For cell culture experiments, at the indicated times after stimulation, media was removed from the wells and cells were washed twice with PBS. RLT (Qiagen) was added to lyse cells and RNA extraction was performed using Qiagen RNAeasy kits as per manufacturer’s instructions.
For RNA Sequencing library preparation, on-column DNAse digestion was performed as per manufacturer’s instructions. Sequencing libraries were constructed following Illumina Tru-seq stranded mRNA protocol.  Paired-end sequencing performed with Next-seq 500 with 76 bp reads from each end.

treatment_protocol: For sequential stimuli, cells were first stimulated with 100 ng/mL Poly I:C (InvivoGen), 5 ng/mL LPS derived from Escherichia coli 055:B5 (Sigma-Aldrich), or 100U/mL recombinant IFN beta (R&D Systems). 24 hours or at the indicated time after initial stimulation, the media was removed and cells were washe    age growth media, and then the media was replaced with Poly I:C or LPS. 2-DG was used at 2.5 mg/mL and added with the second stimulation.

value: Bone marrow derived macrophages


title: PBS:LPS6_2

description: BMDMs stimulated first with PBS then with LPS for 6 hours.


title: PBS:LPS6_1


title: IC:LPS6_2

description: BMDMs stimulated first with Poly I:C then with LPS for 6 hours.


title: IC:LPS6_1


title: IC:PBS6_1


title: IC:LPS2_2

description: BMDMs stimulated first with Poly I:C then with LPS for 2 hours.


title: IC:LPS2_1


title: P3: Extracted RNA fetal pancreas 14 weeks


title: IC:PBS2_1

description: BMDMs stimulated first with Poly I:C then with PBS for 2 hours.


title: PBS:LPS2_2

description: BMDMs stimulated first with PBS then with LPS for 2 hours.


title: PBS:PBS2

description: BMDMs stimulated first with PBS then with PBS for 2 hours.


title: PBS:LPS2_1


title: PBS:PBS6

description: BMDMs stimulated first with PBS then with PBS for 6 hours.


title: IC:PBS2_2


title: VS-5-fast

city: Copenhagen OE

first: Hjalte

middle: Christian Reeberg

last: Sass

address: Blegdamsvej 9

department: Department of Otorhinolaryngology, Head and Necksurgery & Audiology

country: Denmark

institute: Copenhagen University Hospital Rigshospitalet

description:
PCTho-Ext-05-PC-27-1a-A-100339-1554-miRNA-1_02Xgain-a1
Tumor miRNA expression related to vestibular schwannoma growth.

hyb_protocol: The labeled samples were hybridized to GeneChip miRNA 4.0 (Affymetrix Inc, USA) containing probes for small-coding RNAs (miRNA, snoRNA and scaRNA).

scan_protocol: Arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450, and the arrays were scanned in the Affymetrix GeneArray® 3000 scanner to generate fluorescent images, as described in the Affymetrix Gene Chip® protocol.

data_processing:
Cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software (AGCC) (Affymetrix, Santa Clara, CA, USA). The CEL files were RMA (Robust Multi-array Average) normalized using Partek Genomics Suite 6.5 and the probes representing the human RNAs (2.578 Human mature miRNA, 2.025 Human pre–miRNA, 1.996 Human snoRNA, CDBox RNA, H/ACA Box RNA and scaRNA) were used for group comparison analysis.
The original image scanning files (cell files) were analysed in the statistical environment R with the packages affy, pcaGoPromoter46 and targetscan.Hs.eg.dk from Bioconductor. Only human annotated miRNAs (n=847) were used for further analyses. Principal Component Analysis (PCA) was performed by the function pca.

label: FlashTag™ Biotin HSR RNA

source_name: Vestibular schwannoma. A benign tumor located at the 8th cranial nerve

label_protocol: 250ng RNA from each tumor sample was labeled using the FlashTag™ Biotin HSR RNA Labeling kit from Affymetrix (Genisphere Inc., USA) according to manufacturers instructions.

extract_protocol: Total RNA extraction using Trizol according to standard procedures.

value: Vestibular Schwannoma

value: Male

tag: tumor size

tag: tumor growth rate (ccm/year)


title: VS-6-fast

description:
PCTho-Ext-06-PC-060557-2103-2-miRNA-1_02Xgain-a1
Tumor miRNA expression related to vestibular schwannoma growth.


title: VS-7-fast

description:
PCTho-Ext-07-PC-2-240572-3096-miRNA-1_02Xgain-a1_2
Tumor miRNA expression related to vestibular schwannoma growth.

value: Female


title: VS-2-slow

description:
PCTho-Ext-02-PC-16-1a-A-miRNA-1_02Xgain-a1
Tumor miRNA expression related to vestibular schwannoma growth.


title: VS-3-slow

description:
PCTho-Ext-03-PC-3-070851-0653-miRNA-1_02Xgain-a1
Tumor miRNA expression related to vestibular schwannoma growth.


title: VS-1-slow

description:
PCTho-Ext-01-PC-8-1a-A-miRNA-1_02Xgain-a1
Tumor miRNA expression related to vestibular schwannoma growth.


title: VS-8-fast

description:
PCTho-Ext-08-PC-31A-1a-A-160862-1039-miRNA-1_02Xgain-a1
Tumor miRNA expression related to vestibular schwannoma growth.


title: Testis wild type rep3

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: After exported from BeadStudio, data were normalized using quantile normalization

label: biotin

source_name: P0 Testis

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted with the QIAGEN RNeasy microkit followed by DNAse I treatment in accordance with the manufacturer instructions.

tag: strain

value: FVBN

value: Testis

value: Wild type


title: Testis KO rep3

value: DMXL2 tm1a/tm1a (Knockout)


title: Testis wild type rep2


title: VS-4-slow

description:
PCTho-Ext-04-PC-4-260178-2203-miRNA-1_02Xgain-a1
Tumor miRNA expression related to vestibular schwannoma growth.


title: Testis wild type rep1


title: Ovary wild type rep3

source_name: P0 Ovary

value: Ovary


title: Testis KO rep1


title: Testis KO rep2


title: Ovary KO rep3


title: Ovary wild type rep2


title: Ovary KO rep2


title: Ovary wild type rep1


title: 9394274018_E

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: peripheral Treg cells

extract_protocol: Qiagen RNAeasy kits (Qiagen)

tag: genotype/variation

value: Prdm1+/+CD4-Cre+, Control


title: 9394274018_F


title: Ovary KO rep1


title: BC_86

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: 0.85 microgram of biotin-labeled cRNA was hybridized to Illumina HumanRef8 V1 at 55 °C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's GenomeStudio software.

data_processing: Data were normalized by Bioconductor lumi pipeline with loess normalization

source_name: Breast Cancer surgical specimen

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanRef8_V1 arrays

growth_protocol: Tumor were collected upon surgical resection and stored in liquid nitrogen

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

value: frozen breast tumor

tag: disease free survival (months)

tag: prognosis (1=dfs < 60 months,  0= dfs > 60 months)

tag: er status (1=er+,  0=er-)


title: 9394274018_A


title: BC_83

tag: tissue


title: BC_79


title: BC_76


title: 9394274034_A

description: WT iTreg conc.


title: 9394274034_B

description: KO iTreg conc.


title: BC_80


title: 9394274018_B


title: BC_77


title: BC_85


title: BC_82


title: BC_68


title: BC_71


title: BC_75


title: BC_78


title: BC_66


title: BC_81


title: BC_72


title: BC_67


title: BC_69


title: BC_70


title: BC_73


title: BC_74


title: BC_64


title: BC_65


title: BC_84


title: BC_3


title: BC_1


title: BC_6


title: BC_16


title: BC_31


title: BC_19


title: BC_15


title: BC_26


title: BC_33


title: BC_9


title: BC_11


title: BC_22


title: BC_30


title: BC_18


title: BC_14


title: BC_10


title: BC_32


title: BC_13


title: BC_24


title: BC_2


title: BC_56


title: BC_52


title: BC_58


title: BC_17


title: BC_57


title: BC_37


title: BC_53


title: BC_23


title: BC_7


title: BC_55


title: BC_51


title: BC_44


title: BC_42


title: BC_29


title: BC_43


title: BC_47


title: BC_5


title: BC_36


title: BC_45


title: BC_4


title: BC_38


title: BC_41


title: BC_34


title: BC_50


title: BC_54


title: BC_49


title: BC_21


title: BC_46


title: BC_28


title: BC_40


title: BC_35


title: BC_48


title: BC_27


title: BC_20


title: BC_39


title: BC_25


title: BC_8


title: BC_12


title: SE140 input N2 emb ChIP-seq (reanalysis)

source_name: whole worms

value: mixed embryo

tag: antibody target

value: INPUT

tag: chip antibody (vendor, cat#, lot#)


title: BC_63


title: H4K16ac N2 emb rep1 ChIP-seq

description:
H4K16ac_N2_Emb_SE143_SE146_SE256_average.bw
H4K16ac_N2_Emb_SE143_SE146_SE256_final_peaks.bed

value: Millipore, 07-329

tag: antibody antigen

value: KLH-conjugated linear peptide corresponding to 10 amino acids from the N-terminal region of human Histone H4 acetylated on Lysine 16

tag: antibody (host, clone)

value: Rabbit, polyclonal

tag: matching input


title: SE139 input N2 emb ChIP-seq (reanalysis)


title: H4K16ac N2 emb rep2 ChIP-seq


title: BC_61


title: BC_62


title: BC_60


title: D14-1054

city: Cambridge

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the mouse genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample
Supplementary_files_format_and_content: raw count

source_name: WT1 AM 50nM VD3

growth_protocol: Fresh AMs were isolated from mice in the lavage.

extract_protocol:
Qiagen RNeasy Micro Kit
KAPA mRNA HyperPrep Kit

treatment_protocol: WT AMs were treated with or without 50nM VD3 (Sigma) in vitro for 24 hours in complete RMPI1640.

tag: genotype/varation

value: WT

tag: agent

value: 50 nM Vitamin D3

tag: cell type

value: alveolar macropahges (AM)


title: D14-5843

source_name: WT2 4wk

tag: age

value: 4 weeks old


title: D18-150030

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the mouse genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample
Supplementary_files_format_and_content: raw count
Supplementary_files_format_and_content: normalized file

source_name: LPS2 plus VD3

treatment_protocol: WT AMs were treated with 100ng/mL LPS or LPS plus 50nM VD3 (Sigma) in vitro for 4 hours in complete RMPI1640.

value: LPS plus 50 nM Vitamin D3

value: alveolar macropahges


title: D18-150026

source_name: Control 2

value: Control


title: D14-1053

source_name: WT1 AM w/o VD3


title: D14-5846

source_name: WT2 AM w/o VD3


title: D14-5835

source_name: KO2 10wk

value: VDR knockout

value: 10 weeks old


title: D14-5845

source_name: KO2 4wk


title: D14-1051

source_name: WT1 10wk


title: D14-1052

source_name: KO1 10wk


title: D18-150027

source_name: LPS 2

value: LPS


title: D18-150029

source_name: LPS1 plus VD3


title: D14-5834

source_name: WT2 10wk


title: D15-2642

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the mouse genome by bowtie 2
DNA Binding peaks were called and analyzed by Homer
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: anti-VDR in AM w 50nM VD3

growth_protocol: Fresh AMs were isolated from mice in the lavage and cultured to expand in complete RPMI1640 supplementary with 30ng/mLrecombinent GM-CSF.

extract_protocol:
Chromatin was cross-linked and then fragmented with micrococcal nuclease based on the SimpleChIP® Plus Enzymatic Chromatin IP Kit (CST #9005) and immunoprecipated using indicated antibodies. ChIP DNA was then prepared for sequencing
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645)

treatment_protocol: AMs were treated with or without 50nM VD3 (Sigma) in vitro for 24 hours in complete RMPI1640.

tag: antibody

value: anti-VDR


title: D18-150025

source_name: Control 1


title: D15-2641

source_name: anti-VDR in AM wo VD3


title: D15-2638

source_name: IgG

value: IgG


title: D14-5844

source_name: KO1 4wk


title: D18-4691

source_name: LPS 1


title: LAS96 input N2 Control RNAi emb ChIP-seq

source_name: whole worms

tag: developmental stage

value: mixed embryo


title: LAS95 input N2 DPY-27 RNAi emb ChIP-seq

tag: strain

value: INPUT


title: BC_59

source_name: Breast Cancer surgical specimen

value: frozen breast tumor


title: LAS94 input N2 Control RNAi emb ChIP-seq


title: LAS80 input GW638 emb ChIP-seq


title: D14-5847

source_name: WT3 AM 50nM VD3


title: LAS79 input N2 DPY-27 RNAi emb ChIP-seq


title: PHA-4 N2 DPY-27 RNAi emb rep2 ChIP-seq

description:
PHA4_OP37_Emb_DPY27RNAi_LAS01_LAS08_LW107_average.bw
PHA4_OP37_Emb_DPY27RNAi_LAS01_LAS08_LW107_final_peaks.bed

value: Abcam, ab290

value: Recombinant full length protein corresponding to GFP


title: D14-5842

source_name: WT1 4wk

value: WT


title: CBP1 N2 DPY-27 RNAi emb rep2 ChIP-seq

description:
CBP1_N2_Emb_DPY27RNAi_LAS87_LAS88_average.bw
CBP1_N2_Emb_DPY27RNAi_LAS87_LAS88_final_peaks.bed

value: SDIX LLC, SDQ3582 non-commercial cbp-1 modENCODE antibody 1

value: Rabbit, polyclonal


title: RNA Pol II GW638 emb rep2 ChIP-seq

description:
RNAPolII_GW638_Emb_LAS91_LAS92_average.bw
RNAPolII_GW638_Emb_LAS91_LAS92_final_peaks.bed

value: Abcam, ab817

value: RNA polymerase II CTD repeat YSPTSPS. Immunogen:Wheat germ RNA Polymerase II

value: Mouse, monoclonal


title: PHA-4 N2 DPY-27 RNAi emb rep1 ChIP-seq


title: H3K9me3 N2 DPY-27 RNAi emb rep2 ChIP-seq

description:
H3K9me3_N2_Emb_DPY27RNAi_LAS72_LAS78_LAS85_average.bw
H3K9me3_N2_Emb_DPY27RNAi_LAS72_LAS78_LAS85_final_peaks.bed

value: Abcam, ab8898

value: Human Histone H3 aa 1-100 (N terminal) (tri methyl K9) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: CAPG1 GW638 emb rep2 ChIP-seq

description:
CAPG1_GW638_Emb_LAS81_LAS83_average.bw
CAPG1_GW638_Emb_LAS81_LAS83_final_peaks.bed


title: PHA-4 N2 Control RNAi emb rep2 ChIP-seq

description:
PHA4_OP37_Emb_ControlRNAi_LAS22_LAS23_LW106_average.bw
PHA4_OP37_Emb_ControlRNAi_LAS22_LAS23_LW106_final_peaks.bed


title: CAPG1 GW638 emb rep1 ChIP-seq


title: PHA-4 N2 Control RNAi emb rep1 ChIP-seq


title: H3K9me3 N2 DPY-27 RNAi emb rep3 ChIP-seq


title: RNA Pol II GW638 emb rep1 ChIP-seq


title: H3K27me2 N2 DPY-27 RNAi emb rep2 ChIP-seq

description:
H3K27me2_N2_Emb_DPY27RNAi_LAS73_LAS86_average.bw
H3K27me2_N2_Emb_DPY27RNAi_LAS73_LAS86_final_peaks.bed

value: Abcam, ab24684

value: Histone H3 aa 1-100 (N terminal) (di methyl K27) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: H3K27me2 N2 DPY-27 RNAi emb rep1 ChIP-seq


title: H3K9me3 N2 Control RNAi emb rep2 ChIP-seq

description:
H3K9me3_N2_Emb_ControlRNAi_LAS89_LAS90_average.bw
H3K9me3_N2_Emb_ControlRNAi_LAS89_LAS90_final_peaks.bed


title: H3K9me3 N2 Control RNAi emb rep1 ChIP-seq


title: CBP1 N2 DPY-27 RNAi emb rep1 ChIP-seq


title: LAS93 input N2 DPY-27 RNAi emb ChIP-seq


title: EndoC_BH1_miRNA_seq

source_name: Pancreas

extract_protocol: Total RNA was extracted and purified using Trizol (Life Technologies). miRNA libraries were prepared at the NIH Intramural Sequencing Core (NISC) from 1 µg total RNA using Illumina’s TruSeq Small RNA Library Kit according to the manufacturer’s guidelines, except a 10% acrylamide gel was used for better separation of library from adapters. Libraries were pooled in groups of about 8 for gel purification. Single-end 51 base sequencing was performed on Illumina HiSeq 2500 sequencers in Rapid Mode using version 2 chemistry.  Data was processed using RTA version 1.18.64 and CASAVA 1.8.2. All resulting data was processed with miRquant 2.0 (Kanke et al., 2016).

tag: cell line

value: EndoC-BH1 human pancreatic beta cell line

tag: biomaterial provider

value: Not applicable

tag: Sex

tag: unos id

tag: ethnicity


title: CRFK cell infected by CPV_VTE034

city: Chaingmai

first: Soulasack

last: Vanamahaxay

state: chaingmai

address: 155m2 Maehia Dormitory

department: Veterinary Medicine

country: Thailand

institute: ChaingMai University

description: The data was paired end sequence read

data_processing:
Libraries are fed into Illumina machines
Tophat v.2.0.12 using for mapping to a reference genome
Using HTSeq software for data quantification
cufflinks v2.1.1 is use to Novel gene predicton
For differential expression analysis used by DEGSeq v.1.12.0; DESeq v.1.10.1 and edgeR v.3.0.8
GOSeq, topGO, hmmscan softwares to be analy GO Enrichment
KOBAS software is using for KEGG Enrichment analysis
Protein-Protein interaction using by BLAST v2.2.28 for analysis
Plant:iTAK; Animal:AnmalTFDB softwares are using for the Transcription Factor Analysis

organism: Felis catus

source_name: CrFK Feline Kidney Cell line

growth_protocol: CRFK monolayer is cultivated in 25 ml tissue culture flasks (T-25) containing DMEM supplemented with 5% FBS, antibiotic and antifungal in 5% CO2 incubator at 37°C

extract_protocol:
After three-day, CRFK cell and virus-infected cell are harvest. The supernatant containing CRFK and  viruses is centrifuged at 800x g for 5 min and then total RNAs will be extracted byThe Direct-zol™ RNA MiniPrep Plus Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The 70% confluent of CRFK cells are infected with 0.5 ml CPV isolated form Vientiane, Lao PDR. Virus inoculated cell cultures are kept at 37°C for 72 h in a 5% CO2 atmosphere

value: Kidney Cells

tag: treatment group

value: Infeted by CPV


title: CRFK cell_02

description: The data was paired end sequence read

value: Control


title: CRFK cell_01

description: The data was paired end sequence read


title: CRFK cell infected by CPV_C22

description: The data was paired end sequence read


title: H3K9me3 N2 DPY-27 RNAi emb rep1 ChIP-seq

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.2.0 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.3 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.3 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.1.1 using default parameters, specifying first strand alignment.
Resultant RNA-seq bam files were converted to sam files using samtools version 1.6. Sam files were used to generate count data using htseq-cout version 0.6.1.
Genome_build: WS220
Supplementary_files_format_and_content: BigWig files were generated by converting wiggle files using the UCSC wigToBigWig utility. Wiggle files were generated using MACS version 1.4.3, normalized according to the genome-wide mean coverage and then input subtracted. Scores represent the average coverage of each replicate at each base position.
Supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.3 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Supplementary_files_format_and_content: Counts files were generated using Htseq-counts version 0.6.1.

value: mixed embryo

tag: antibody target

tag: chip antibody (vendor, cat#, lot#)


title: EndoC_BH1_ChIA_PET

extract_protocol: EndoC-ßH1 RNA Pol2 ChIA-PET libraries were generated and sequenced reads were processed and analyzed according to the protocol in (Li et al., 2017b).


title: EndoC_BH1_ChIP_seq_H3K4me3_SE

extract_protocol: CTCF, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K79me2, H3K4me3, H3K9me3 ChIP-seq was performed as previously described (Stitzel et al., 2010)

tag: chip antibody


title: EndoC_BH1_ChIP_seq_H3K9me3


title: EndoC_BH1_ChIP_seq_H3K27ac_SE


title: EndoC_BH1_ChIP_seq_H3K9me2


title: EndoC_BH1_ChIP_seq_CTCF_SE

value: CTCF


title: EndoC_BH1_ChIP_seq_Input_SE

value: none (Input)


title: EndoC_BH1_ChIP_seq_H3K4me3


title: EndoC_BH1_ChIP_seq_H3K79me2


title: Islet_ADAC418_HiC

growth_protocol: The single human pancreatic islet sample used in this study was obtained from the National Disease Research Interchange (NDRI). The islet was shipped overnight from the distribution center. On receipt, we pre-warmed the islet to 37 °C in shipping media for 1–2 h before harvest; ∼50,000 islet equivalents (IEQs) were harvested for Hi-C.

extract_protocol: Hi-C libraries were generated as described in (Rao et al., 2014) and analyzed using the Juicer Tools version 1.75 pipeline (Durand et al., 2016a).

tag: tissue

value: Human pancreatic islet

value: NDRI

value: female

value: Caucasian


title: EndoC_BH1_ChIP_seq_H3K4me1


title: EndoC_BH1_ChIP_seq_Input


title: EndoC_BH1_ChIP_seq_H3K36me3


title: EndoC_BH1_ChIP_seq_H3K27ac


title: EndoC_BH1_ChIP_seq_H3K27me3


title: EndoC_BH1_HiC


title: POOL2__pMPRA1__HepG2__rep7

first: Martha

middle: L.

last: Bulyk

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

data_processing:
We used cutadapt to remove adapters from the raw reads and trim bases with a Phred score < 20.
We then counted barcodes if they exactly matched an 11-bp barcode in the design index as well as the constant upstream 6 bp.
All scripts used for subsequent data analysis of processed files can be found at https://github.com/kmattioli/2018__lncRNA_promoter_MPRA
Genome_build: hg19
Supplementary_files_format_and_content: Barcode sequence and count per replicate

source_name: HepG2 cell line

extract_protocol:
RNA from transiently transfected K562, HeLa, and HepG2 was precipitated by phenol-chloroform extraction according to standard protocols. DNase treatment (Worthington) was followed by cDNA synthesis with SuperScript III First-Strand Synthesis System (Invitrogen).
cDNA was subject to library amplification and libraries were cleaned up with AMPure beads (0.6x, 1.6x, 1.0x).
plasmid sequencing and RNA-seq

treatment_protocol: K562 cells were transiently transfected for 48 hours with a ratio of 1:1 with Xtreme Gene HP (Roche), HeLa and HepG2 both with 3:1 Xtreme Gene HP according to the manufacturer protocol. 4x10e6 K562 cells in 6 cm dish, 1.6x10e6 HeLa or HepG2 cells in 10 cm dish were seeded 12-16 hours prior to the transfection. Cells were counted before the transfection and per 1 x 10e6 cells, 5 µg oligopool were transfected. Media was not changed and transfection efficiency was microscopically determined by GFP expression 48 hours post transfection.

tag: sample type

value: GFP-RNA


title: POOL2__pMPRA1__HepG2__rep6


title: POOL2__pMPRA1__HepG2__rep5


title: POOL2__pMPRA1__HepG2__rep4


title: POOL2__pMPRA1__K562__rep1

source_name: K562 cell line


title: POOL2__pMPRA1__K562__rep3


title: POOL2__pMPRA1__HepG2__rep8


title: POOL2__pMPRA1__K562__rep2


title: POOL2__pMPRA1__HepG2__rep3


title: POOL2__pMPRA1__HepG2__rep2


title: POOL2__pMPRA1__K562__rep4


title: POOL1__pNoCMVMPRA1__K562__rep3


title: POOL1__pNoCMVMPRA1__K562__rep2


title: POOL2__pMPRA1__HepG2__rep1


title: POOL1__pNoCMVMPRA1__K562__rep4


title: POOL1__pNoCMVMPRA1__HepG2__rep3


title: POOL1__pNoCMVMPRA1__HepG2__rep4


title: POOL1__pNoCMVMPRA1__K562__rep1


title: POOL1__pNoCMVMPRA1__HepG2__rep2


title: POOL1__pNoCMVMPRA1__HeLa__rep2

source_name: HeLa cell line


title: POOL1__pMPRA1__K562__rep3


title: POOL1__pNoCMVMPRA1__HeLa__rep1


title: POOL1__pNoCMVMPRA1__HeLa__rep4


title: POOL1__pNoCMVMPRA1__HepG2__rep1


title: POOL1__pNoCMVMPRA1__HeLa__rep3


title: POOL1__pMPRA1__K562__rep4


title: POOL1__pMPRA1__HepG2__rep12


title: POOL1__pMPRA1__HepG2__rep3


title: POOL1__pMPRA1__K562__rep1


title: POOL1__pMPRA1__HepG2__rep2


title: POOL1__pMPRA1__HepG2__rep1


title: POOL1__pMPRA1__HeLa__rep4


title: POOL1__pMPRA1__HepG2__rep10


title: POOL1__pMPRA1__HepG2__rep11


title: POOL1__pMPRA1__HepG2__rep8


title: POOL1__pMPRA1__HepG2__rep7


title: POOL1__pMPRA1__HepG2__rep6


title: POOL1__pMPRA1__HepG2__rep4


title: POOL1__pMPRA1__HepG2__rep5


title: POOL1__pMPRA1__K562__rep2


title: POOL1__pMPRA1__HeLa__rep2


title: POOL1__pMPRA1__HeLa__rep3


title: POOL1__pMPRA1__HepG2__rep9


title: vehicle_cel (miRNA-seq)

city: Campinas

first: Silas

middle: Pinto

last: Silva

state: Sao Paulo

address: Rua Monteiro Lobato 255

department: Biochemistry and Tissue Biology

country: Brazil

institute: University of Campinas

description: Control Worms

data_processing:
For the analysis, reads were pre-processed by the Fastx Tool Kit, the adapter was trimmed, and reads with minimum length of 18 bp were selected and aligned against the ce10 C. elegans genome (UCSC) using Bowtie2
miRNA expression was counted using Bedtools based on the miRbase database, release 20
The data was normalized by the total number of reads generated per sample. MiRNAs that changed at least 2-fold when comparing the enoxacin and vehicle groups were subjected to centroid hierarchical clustering using Cluster 3.0 and a heatmap was drawn using Java TreeView
Genome_build: ce10
Supplementary_files_format_and_content: miRNA counts (normalized)

source_name: whole worm

extract_protocol:
Total RNA was extracted using TRIzol reagent following the manufacturer’s instructions (Life Technologies)
RNA quality was determined by the 2100 Bioanalyzer (Agilent), and all samples had RNA integrity number (RIN) above 9. For each group, 10 µg of total RNA were enriched for small RNA using PureLink miRNA Isolation Kit (Invitrogen), followed by miRNA library preparation using SOLiD Total RNA-Seq Kit, according to manufacturer's recommendations (Life Technologies).

value: Day 1

tag: agent

value: vehicle


title: POOL1__pMPRA1__HeLa__rep1


title: S15 ControlBMDM_LPSstimulated_rep1

city: Oxford

first: Laurienne

last: Edgar

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S15

data_processing:
Base calls provided by the Illumina Real-Time Analysis (RTA) software were subsequently converted into BAM format (Illumina2bam) before de-multiplexing (BamIndexDecoder) into individual, sample-specific BAM files via Illumina2bam tools (1.17.3 https://github.com/wtsi-npg/illumina2bam).
Raw BAM files were merged. Reads were aligned to the mouse genome (GRCm38/mm10) using STAR (v.2.5.3a 69) in gene counting mode (--quantMode GeneCounts) with Gencode (v.M16) annotations (from which megatranscript Gm20388 was removed to avoid overlapping intervening genes).
Counts were loaded into R (v.3.3.3 70) and analyzed with edgeR (v.3.16.5 71) after removing transcripts with fewer than 0.5 mapped reads per million sequenced in all samples (13,568 transcripts retained).
Genome_build: mm10
Supplementary_files_format_and_content: The edgeR function cpm was used to log-normalize counts (Processed Data File Attached). This data was used to produce heat maps, other plots and perform downstream analysis for publication.

source_name: Bone Marrow Derived Macrophage

growth_protocol: Bone marrow differentiated into bone marrow derived macrophages (BMDM) on non-tissue culture treated petri-dishes in complete 5 mmol/L glucose DMEM media (supplemented with 10% FBS, 2% penicillin -  streptomycin and 2 mmol/L glutamine) plus 20% L929 cell conditioned media for differentiation. After differentiation for 7 days, BMDM positively selected through adhesion and plated at a density of 2 x10^5 cell/mL in complete 5 mmol/L glucose DMEM media.

extract_protocol:
Cells were lysed and RNA isolated using mirVana mRNA/miRNA isolation kit (ThermoFisher Scientific, UK), according to manufacturer's instructions.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, UK) using both Sciclone and Zephyr liquid handling robotics (PerkinElmer, UK). Library concentrations were quantified with the Qubit Fluoro-metric Quantitation system (Life Technologies, UK) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, USA).

treatment_protocol: Cells were stimulatded in complete 5 mmol/L glucose DMEM media with 10 ng/mL recombinant murine interferon-y (IFNy) plus 100 ng/mL lipopolysaccharide (LPS) for 6 hours, or left unstimulated and used as controls.

tag: cell typle

value: Bone Marrow Derived Macrophage

tag: phenotype

value: Wild-type control

tag: treatment

value: Male

tag: stimulation

value: 100 ng/mL LPS + 10 ng/mL IFNγ


title: S22 DiabeticBMDM_LPSstimulated_rep6

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S22

value: Diabetic

value: Streptozotocin (STZ) induction of diabetes

tag: strain


title: S18 DiabeticBMDM_LPSstimulated_rep4

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S18


title: S24 ControlBMDM_LPSstimulated_rep6

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S24


title: S19 ControlBMDM_LPSstimulated_rep3

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S19


title: S20 ControlBMDM_LPSstimulated_rep4

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S20


title: S17 DiabeticBMDM_LPSstimulated_rep3

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S17


title: S10 DiabeticBMDM_unstimulated_rep6

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S10

value: Unstimulated


title: S13 DiabeticBMDM_LPSstimulated_rep1

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S13


title: S9 DiabeticBMDM_unstimulated_rep5

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S9


title: S8 ControlBMDM_unstimulated_rep4

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S8


title: S4 ControlBMDM_unstimulated_rep2

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S4


title: S7 ControlBMDM_unstimulated_rep3

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S7


title: S2 DiabeticBMDM_unstimulated_rep2

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S2


title: S6 DiabeticBMDM_unstimulated_rep4

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S6


title: S5 DiabeticBMDM_unstimulated_rep3

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S5


title: S23 ControlBMDM_LPSstimulated_rep5

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S23


title: S1 DiabeticBMDM_unstimulated_rep1

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S1


title: enoxacin_cel (miRNA-seq)

description: Treated Worms

tag: age

value: enoxacin


title: S21 DiabeticBMDM_LPSstimulated_rep5

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S21


title: S11 ControlBMDM_unstimulated_rep5

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S11


title: S12 ControlBMDM_unstimulated_rep6

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S12


title: S3  ControlBMDM_unstimulated_rep1

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S3


title: S16 ControlBMDM_LPSstimulated_rep2

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S16


title: S14 DiabeticBMDM_LPSstimulated_rep2

description:
LEdgar_BMDM_RNA-seq Normalised Counts
S14


title: Freshly isolated lung squamous cell carcinoma, replicate 3

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

description:
Lung squamous cell carcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Podoplanin as cell surface marker.
sample name in processed data file:
SCC-3

data_processing:
Read mapping and abundance  estimation was performed using RSEM v1.2.31 (Li and Dewey, 2011) running  STAR v2.5 (Dobin and Gingeras, 2015) against the Mus musculus Ensembl  86 transcriptome (GRCm38), with the following non-default command line  arguments: "--star --forward-prob 0"
Gene-level read count estimates were rounded to integer values and used by DESeq2 (Love et al., 2014) to assess differential expression between replicate groups using the "DESeq2" function with default settings.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene-level raw count estimates from RSEM v1.2.31 based on Ensembl v86 mouse transcriptome.

growth_protocol: Lung ADC and SCC primary cells were cultured in N2 B27 medium containing EGF (10 ng/ml) and FGF2 (20 ng/ml)

extract_protocol:
Lung ADC and SCC tumor cells were isolated by flow-cytometry using Sca-1 and Podoplanin as cell surface markers, respectively. RNA was isolated from primary lung tumors using "MagMAX-96 total RNA isolation kit" (ThermoFisher) or from primary cells using "RNeasy Mini Kit " (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung tumor

tag: tumor type

value: squamous cell carcinoma

tag: cell preparation

value: freshly isolated

tag: genotype

value: KRasG12D; Fbw7f/f


title: Freshly isolated lung adenocarcinoma, replicate 2

description:
Lung adenocarcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Sca-1 as cell surface marker.
sample name in processed data file:
ADC-2

source_name: Freshly isolated lung adenocarcinoma

value: adenocarcinoma


title: Freshly isolated lung adenocarcinoma, replicate 1

description:
Lung adenocarcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Sca-1 as cell surface marker.
sample name in processed data file:
ADC-1


title: Freshly isolated lung adenocarcinoma, replicate 3

description:
Lung adenocarcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Sca-1 as cell surface marker.
sample name in processed data file:
ADC-3


title: Freshly isolated lung squamous cell carcinoma, replicate 2

description:
Lung squamous cell carcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Podoplanin as cell surface marker.
sample name in processed data file:
SCC-2


title: Cultured lung adenocarcinoma, replicate 2

description:
Lung adenocarcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Sca-1 as cell surface marker. Cells were cultured in N2 B27 medium containing EGF (10 ng/ml) and FGF2 (20 ng/ml). RNAseq was done using Illumina
sample name in processed data file:
ADC-P16B

source_name: Cultured lung adenocarcinoma

value: cultured


title: Cultured lung squamous cell carcinoma, replicate 2

description:
Lung squamous cell carcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Podoplanin as cell surface marker. Cells were cultured in N2 B27 medium containing EGF (10 ng/ml) and FGF2 (20 ng/ml). RNAseq was done using Illumina
sample name in processed data file:
SCC-P5B

source_name: Cultured lung squamous cell carcinoma


title: Cultured lung squamous cell carcinoma, replicate 1

description:
Lung squamous cell carcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Podoplanin as cell surface marker. Cells were cultured in N2 B27 medium containing EGF (10 ng/ml) .and FGF2 (20 ng/ml). RNAseq was done using Illumina
sample name in processed data file:
SCC-P5A


title: Freshly isolated lung squamous cell carcinoma, replicate 1

description:
Lung squamous cell carcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Podoplanin as cell surface marker.
sample name in processed data file:
SCC-1


title: MN1 CTL + ATRA 3

city: Frankfurt am Main

last: Rieger

address: Theodor-Stern-Kai 7

country: Germany

institute: Universitätsklinikum Frankfurt/DKFZ

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178473-LR-27309

data_processing:
The resulting FASTQ files were aligned to the mm10 draft of the mouse genome and counts per gene were estimated using STAR (v. 2.5.3).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with the per gene read count as reads per million (RPM) output from STAR (v.2.5.3)

source_name: MN1 CTL + ATRA

growth_protocol: Cells were grown in DMEM + 15 % FCS + mIL3 10 ng/ml, hIL6 10 ng/ml and mSCF 100 ng/ml.

extract_protocol:
RNA extraction was performed using Qiagen Rneasy protocol as recommended by the manufacturer.
The library was prepared using Illumina's TruSeq Stranded Total RNA Library Prep kit and sequenced on an Ilumina HiSeq 4000 (San Diego, CA, USA) system using a 100-bp paired-end approach.

treatment_protocol: Lsd1 KO was induced by treatment with 4-hydroxy-tamoxifen (0.1µM) for 72 hrs. ATRA treatment was performed at 1 µM.

tag: strain background

tag: cell type

value: MN1-transformed myeloid progenitor cells

tag: treated with

value: 1 µM ATRA


title: MN1 KO W/O ATRA 3

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178474-LR-27309

source_name: MN1 KO W/O ATRA

value: 4-hydroxy-tamoxifen (0.1µM) for 72 hrs (to induce Lsd1 KO)


title: MN1 KO + ATRA 3

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178476-LR-27309

source_name: MN1 KO + ATRA


title: MN1 KO + ATRA 2

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178477-LR-27309


title: MN1 KO + ATRA 1

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178475-LR-27309


title: MN1 KO W/O ATRA 2

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178455-LR-27309


title: MN1 CTL W/O ATRA 2

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178469-LR-27309

source_name: MN1 CTL W/O ATRA


title: MN1 CTL + ATRA 2

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178472-LR-27309


title: H9M KO + ATRA 3

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178467-LR-27308

source_name: H9M KO + ATRA

value: Hoxa9/Meis1-transformed myeloid progenitor cells


title: MN1 CTL + ATRA 1

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178471-LR-27309


title: MN1 CTL W/O ATRA 3

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178470-LR-27309


title: H9M KO W/O ATRA 3

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178465-LR-27308

source_name: H9M KO W/O ATRA


title: H9M KO + ATRA 2

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178464-LR-27308


title: H9M KO + ATRA 1

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178466-LR-27308


title: H9M KO W/O ATRA 1

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178461-LR-27308


title: H9M CTL + ATRA 1

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178460-LR-27308

source_name: H9M CTL + ATRA


title: H9M CTL W/O ATRA 3

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178462-LR-27308

source_name: H9M CTL W/O ATRA


title: H9M CTL + ATRA 3

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178459-LR-27308


title: N2 L1-L3 rep4 RNA-seq

city: New York City

first: Lena

last: Street

address: 100 Washington Square East

institute: New York University

source_name: whole worms

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

tag: developmental stage


title: H9M CTL W/O ATRA 2

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178457-LR-27308


title: H9M CTL + ATRA 2

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178458-LR-27308


title: Cultured lung adenocarcinoma, replicate 1

description:
Lung adenocarcinoma cells were isolated from KRasG12D; Fbw7f/f mice by flow-cytometry using Sca-1 as cell surface marker. Cells were cultured in N2 B27 medium containing EGF (10 ng/ml) and FGF2 (20 ng/ml). RNAseq was done using Illumina
sample name in processed data file:
ADC-P16A


title: MN1 KO W/O ATRA 1

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178456-LR-27309


title: N2 L1-L3 rep3 RNA-seq


title: MN1 CTL W/O ATRA 1

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178468-LR-27309


title: X;V L1-L3 rep4 RNA-seq


title: N2 L1-L3 rep2 RNA-seq


title: H9M CTL W/O ATRA 1

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178454-LR-27308


title: N2 L1-L3 rep1 RNA-seq


title: H9M KO W/O ATRA 2

description:
processed data file: GeneCountDataMatrix_Final.txt
AS-178463-LR-27308


title: X;II L1-L3 rep4 RNA-seq


title: X;II L1-L3 rep3 RNA-seq


title: X;II L1-L3 rep2 RNA-seq


title: X;II L1-L3 rep1 RNA-seq


title: SE169 input CB428 emb ChIP-seq (reanalysis)

value: mixed embryo

tag: antibody target

value: INPUT

tag: chip antibody (vendor, cat#, lot#)


title: SE245 input N2 L3 ChIP-seq (reanalysis)


title: SE210 input N2 MxEmb ChIP-seq (reanalysis)


title: CJ44 input N2 emb ChIP-seq (reanalysis)


title: LW192 input N2 L3 ChIP-seq (reanalysis)


title: SE176 input N2 MxEmb ChIP-seq (reanalysis)


title: CJ19 input N2 MxEmb ChIP-seq (reanalysis)


title: SEA181 input CB428 emb ChIP-seq


title: SEA152 input X;V L3 ChIP-seq


title: SEA150 input X;V L3 ChIP-seq


title: SE364 input X;V L3 ChIP-seq


title: X;V L1-L3 rep3 RNA-seq


title: X;V L1-L3 rep2 RNA-seq


title: SE248 input N2 emb ChIP-seq


title: SE197 input N2 emb ChIP-seq


title: X;V L1-L3 rep1 RNA-seq


title: LW99 input N2 Control RNAi emb ChIP-seq


title: LW68 input N2 DPY-27 RNAi emb ChIP-seq


title: LW89 input N2 Control RNAi emb ChIP-seq


title: LW69 input N2 DPY-27 RNAi emb ChIP-seq


title: LW205 input N2 Control RNAi emb ChIP-seq


title: LW127 input N2 emb ChIP-seq (reanalysis)


title: LW76 input N2 Control RNAi emb ChIP-seq


title: LW55 input N2 Control RNAi emb ChIP-seq


title: LW77 input N2 DPY-27 RNAi emb ChIP-seq


title: LW144 input CB428 emb ChIP-seq


title: LW111 input N2 DPY-27 RNAi emb ChIP-seq


title: LW102 input N2 DPY-27 RNAi emb ChIP-seq


title: LW145 input CB428 emb ChIP-seq


title: LW101 input N2 DPY-27 RNAi emb ChIP-seq


title: CJ120 input N2 DPY-27 RNAi emb ChIP-seq


title: LW110 input N2 Control RNAi emb ChIP-seq


title: LW180 input N2 Control RNAi emb ChIP-seq


title: CJ21 input CB428 emb ChIP-seq


title: SE346 input N2 emb ChIP-seq


title: IgG N2 L3 rep2 ChIP-seq

description:
IgG_N2_L3_LW187_SE268_average.bw
IgG_N2_L3_LW187_SE268_final_peaks.bed

value: IgG

value: Abcam, ab46540

tag: antibody antigen

value: Native, mouse whole IgG

tag: antibody (host, clone)

value: Rabbit, polyclonal

tag: matching input


title: IgG N2 L3 rep1 ChIP-seq


title: H3K27ac X;V L3 rep2 ChIP-seq

description:
H3K27ac_15eh1_L3_SE351_SE352_average.bw
H3K27ac_15eh1_L3_SE351_SE352_final_peaks.bed

value: Abcam, ab4729

value: Human Histone H3 aa 1-100 (acetyl K27) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: H3K4me3 X;V L3 rep1 ChIP-seq

description:
H3K4me3_15eh1_L3_SE349_SE350_average.bw
H3K4me3_15eh1_L3_SE349_SE350_final_peaks.bed

value: Abcam, ab8580

value: Human Histone H3 aa 1-100 (tri methyl K4) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: H3K27ac X;V L3 rep1 ChIP-seq


title: H3K4me3 X;V L3 rep2 ChIP-seq


title: PHA-4 N2 DPY-27 RNAi emb rep3 ChIP-seq

description:
PHA4_OP37_Emb_DPY27RNAi_LAS01_LAS08_LW107_average.bw
PHA4_OP37_Emb_DPY27RNAi_LAS01_LAS08_LW107_final_peaks.bed

value: Abcam, ab290

value: Recombinant full length protein corresponding to GFP


title: PHA-4 N2 Control RNAi emb rep3 ChIP-seq

description:
PHA4_OP37_Emb_ControlRNAi_LAS22_LAS23_LW106_average.bw
PHA4_OP37_Emb_ControlRNAi_LAS22_LAS23_LW106_final_peaks.bed


title: DPY-27 X;V L3 rep1 ChIP-seq

description:
DPY27_15eh1_L3_SEA149_SEA151_average.bw
DPY27_15eh1_L3_SEA149_SEA151_final_peaks.bed

value: Covance Research Products Inc, JL00001_DPY27


title: PQN-85 N2 DPY-27 RNAi emb rep3 ChIP-seq

description:
PQN85_N2_Emb_DPY27RNAi_LW87_LW91_LW93_average.bw
PQN85_N2_Emb_DPY27RNAi_LW87_LW91_LW93_final_peaks.bed


title: PQN-85 N2 DPY-27 RNAi emb rep2 ChIP-seq


title: PQN-85 N2 DPY-27 RNAi emb rep1 ChIP-seq


title: PQN-85 N2 Control RNAi emb rep3 ChIP-seq

description:
PQN85_N2_Emb_ControlRNAi_LW183_LW88_LW83_average.bw
PQN85_N2_Emb_ControlRNAi_LW183_LW88_LW83_final_peaks.bed


title: LW179 input N2 DPY-27 RNAi emb ChIP-seq


title: PQN-85 N2 Control RNAi emb rep2 ChIP-seq


title: LW100 input N2 Control RNAi emb ChIP-seq


title: DPY-27 X;V L3 rep2 ChIP-seq


title: MDT-15 N2 emb rep2 ChIP-seq

description:
MDT15_N2_Emb_LW189_SE340_average.bw
MDT15_N2_Emb_LW189_SE340_final_peaks.bed

value: SDIX LLC, SDQ4097


title: MDT-15 N2 emb rep1 ChIP-seq


title: CBP-1 N2 emb rep2 ChIP-seq

description:
CBP1_N2_Emb_LW197_SE339_BC053_average.bw
CBP1_N2_Emb_LW197_SE339_BC053_final_peaks.bed

value: SDIX LLC, SDQ3582 non-commercial cbp-1 modENCODE antibody 1


title: CBP-1 N2 emb rep1 ChIP-seq


title: RNA Pol II CB428 emb rep2 ChIP-seq

description:
RNAPolII_CB428_Emb_CJ18_CJ37_average.bw
RNAPolII_CB428_emb_CJ18_CJ37_final_peaks.bed

value: Covance Research Products Inc, MMS-126R

value: RNA Polymerase II purified from wheat germ extract

value: Mouse, monoclonal


title: RNA Pol II CB428 emb rep1 ChIP-seq

value: mixed embryo

value: Millipore, 17-672


title: RNA Pol II N2 emb rep2 ChIP-seq

description:
RNAPolII_N2_Emb_CJ22_LW124_average.bw
RNAPolII_N2_Emb_CJ22_LW124_final_peaks.bed

value: Abcam, ab817

value: RNA polymerase II CTD repeat YSPTSPS. Immunogen:Wheat germ RNA Polymerase II


title: CJ119 input N2 DPY-27 RNAi emb ChIP-seq

value: INPUT


title: RNA Pol II N2 emb rep1 ChIP-seq


title: AMA1 N2 DPY-27 RNAi emb rep1 ChIP-seq

description:
AMA1_N2_Emb_DPY27RNAi_CJ106_CJ108_average.bw
AMA1_N2_Emb_DPY27RNAi_CJ106_CJ108_final_peaks.bed

value: Rabbit, polyclonal


title: H4K20me1 N2 DPY-27 RNAi emb rep2 ChIP-seq

description:
H4K20me1_N2_Emb_DPY27RNAi_LW176_LW178_average.bw
H4K20me1_N2_Emb_DPY27RNAi_LW176_LW178_final_peaks.bed

value: Abcam, ab9051

value: Human Histone H4 aa 1-100 (mono methyl K20) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: H4K20me1 N2 DPY-27 RNAi emb rep1 ChIP-seq


title: H4K20me1 N2 Control RNAi emb rep2 ChIP-seq

description:
H4K20me1_N2_Emb_ControlRNAi_LW175_LW177_average.bw
H4K20me1_N2_Emb_ControlRNAi_LW175_LW177_final_peaks.bed


title: H4K20me1 N2 Control RNAi emb rep1 ChIP-seq


title: H4panAc CB428 emb rep2 ChIP-seq

description:
H4panAc_CB428_Emb_LW132_LW135_average.bw
H4panAc_CB428_emb_LW132_LW135_final_peaks.bed

value: Lake Placid Biologicals, AR-0109-50

value: Peptide containing the amino terminal region of tetrahymena histone variant hv1 acetylated at multiple lysines


title: IgG CB428 emb rep1 ChIP-seq

description:
IgG_CB428_Emb_CJ102_SE267_average.bw
IgG_CB428_emb_CJ102_SE267_final_peaks.bed

value: IgG

value: Abcam, ab46540

value: Native, mouse whole IgG


title: IgG CB428 emb rep2 ChIP-seq


title: H4panAc CB428 emb rep1 ChIP-seq


title: H4panAc N2 emb rep2 ChIP-seq

description:
H4panAc_N2_Emb_SE205_SE206_LAS63_average.bw
H4panAc_N2_Emb_SE205_SE206_LAS63_final_peaks.bed


title: PQN-85 N2 Control RNAi emb rep1 ChIP-seq


title: H4panAc N2 emb rep1 ChIP-seq


title: H3K27me2 N2 emb rep2 ChIP-seq

description:
H3K27me2_N2_Emb_LW212_LW227_average.bw
H3K27me2_N2_Emb_LW212_LW227_final_peaks.bed

value: Abcam, ab24684

value: Histone H3 aa 1-100 (N terminal) (di methyl K27) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: H3K27me2 CB428 emb rep1 ChIP-seq

description:
H3K27me2_CB428_Emb_LW210_LW207_average.bw
H3K27me2_CB428_Emb_LW210_LW207_final_peaks.bed


title: H3K27me2 CB428 emb rep2 ChIP-seq


title: H3K27me2 N2 emb rep1 ChIP-seq


title: H3K27me1 N2 DPY-27 RNAi emb rep2 ChIP-seq

description:
H3K27me1_N2_Emb_DPY27RNAi_LW170_LW243_average.bw
H3K27me1_N2_Emb_DPY27RNAi_LW170_LW243_final_peaks.bed

value: Active Motif, 61015

value: peptide containing monomethyl Lys27 of human Histone H3


title: H3K27me1 N2 DPY-27 RNAi emb rep1 ChIP-seq

value: mixed embryo

value: Mouse, monoclonal


title: H3K27me1 CB428 emb rep1 ChIP-seq

description:
H3K27me1_CB428_Emb_LW155_LW158_average.bw
H3K27me1_CB428_emb_LW155_LW158_final_peaks.bed


title: H3K27me1 N2 emb rep2 ChIP-seq

description:
H3K27me1_N2_Emb_LW157_LW160_average.bw
H3K27me1_N2_Emb_LW157_LW160_final_peaks.bed


title: H3ac N2 emb rep1 ChIP-seq

description:
H3acetyl_N2_Emb_SE211_SE271_average.bw
H3acetyl_N2_Emb_SE211_SE271_final_peaks.bed

value: Millipore, 06-599

value: Linear peptide corresponding to human Histone H3 acetylated at the N-terminus


title: H3ac N2 emb rep2 ChIP-seq


title: H3ac CB428 emb rep2 ChIP-seq

description:
H3acetyl_CB428_Emb_LW134_LW137_average.bw
H3acetyl_CB428_emb_LW134_LW137_final_peaks.bed


title: AMA1 N2 DPY-27 RNAi emb rep2 ChIP-seq


title: H3K27me1 CB428 emb rep2 ChIP-seq


title: H3K27me1 N2 emb rep1 ChIP-seq


title: H4K16ac CB428 emb rep2 ChIP-seq

description:
H4K16ac_CB428_Emb_CJ23_LW229_average.bw
H4K16ac_CB428_emb_CJ23_LW229_final_peaks.bed

value: Active Motif, 39167

value: peptide including acetyl-lysine 16 of histone H4


title: H3K27ac N2 DPY-27 RNAi emb rep1 ChIP-seq

description:
H3K27ac_N2_Emb_DPY27RNAi_LW214_LW216_average.bw
H3K27ac_N2_Emb_DPY27RNAi_LW214_LW216_final_peaks.bed

value: Abcam, ab4729

value: Human Histone H3 aa 1-100 (acetyl K27) conjugated to Keyhole Limpet Haemocyanin (KLH)

value: Rabbit, polyclonal


title: H3K27ac N2 DPY-27 RNAi emb rep2 ChIP-seq


title: H3K27ac CB428 emb rep2 ChIP-seq

description:
H3K27ac_CB428_Emb_LW202_SEA192_average.bw
H3K27ac_CB428_emb_LW202_SEA192_final_peaks.bed


title: H3K27ac CB428 emb rep1 ChIP-seq


title: H3K27ac N2 emb rep3 ChIP-seq

description:
H3K27ac_N2_Emb_LW201_LW204_LW215_average.bw
H3K27ac_N2_Emb_LW201_LW204_LW215_final_peaks.bed


title: H3K27ac N2 emb rep2 ChIP-seq


title: H3K27ac N2 emb rep1 ChIP-seq


title: H4K16ac CB428 emb rep1 ChIP-seq

value: Millipore, 07-329

value: KLH-conjugated linear peptide corresponding to 10 amino acids from the N-terminal region of human Histone H4 acetylated on Lysine 16


title: H3 CB428 emb rep2 ChIP-seq

description:
H3_CB428_Emb_LW133_LW136_average.bw
H3_CB428_Emb_LW133_LW136_final_peaks.bed

value: Abcam, ab1791

value: Human Histone H3 aa 100 to the C-terminus conjugated to Keyhole Limpet Haemocyanin (KLH)


title: H3ac CB428 emb rep1 ChIP-seq


title: H3K4me1 CB428 emb rep2 ChIP-seq

description:
H3K4me1_CB428_Emb_LW161_LW164_average.bw
H3K4me1_CB428_Emb_LW161_LW164_final_peaks.bed

value: Abcam, ab8895

value: Human Histone H3 aa 1-100 (mono methyl K4) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: H3 CB428 emb rep1 ChIP-seq


title: H3K4me1 CB428 emb rep1 ChIP-seq


title: glp-4_PVD_C

city: Houston

first: Natalia

middle: V

last: Kirienko

state: TX

address: 6100 Main St. MS140

department: BioSciences

institute: Rice University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data were analyzed with GC-RMA in the R programming language, using the Bioconductor package gcrma. Analysis was performed using default settings.

source_name: glp-4, PVD (liq), 12h

label_protocol: Affymetrix standard protocol

growth_protocol: glp-4 worms were synchronized by hypochlorite treatment. Arrested L1s were plated on 10 cm NGM plates seeded with E. coli OP50 and grown at 15°C overnight then shifted to 25°C for 44h until they reached sterile young adult stage.

extract_protocol: RNA was extracted using TRI Reagent (Molecular Research Center) according to manufacturer's instructions and purified using an RNeasy column (Qiagen).

treatment_protocol: Animals were grown until young adult stage. Afterward, worms were incubated for 12 hours at 25°C in 6-well plates with liquid S basal media + E. coli with media control or pyoverdine (PVD). A cohort of glp-4 worms that remaind on 10 cm NGM plates served as an additional control

tag: media

value: S basal, E. coli OP50

value: Pyoverdine (PVD)

tag: tissue

value: Whole organism


title: glp-4_PVD_A

tag: treatment


title: H3K4me1 N2 DPY-27 RNAi emb rep2 ChIP-seq

description:
H3K4me1_N2_Emb_DPY27RNAi_LW172_LW244_average.bw
H3K4me1_N2_Emb_DPY27RNAi_LW172_LW244_final_peaks.bed

tag: strain

value: mixed embryo


title: glp-4_Basal_C

source_name: glp-4, S basal (liq), 12h

value: S basal


title: H4K16ac N2 emb rep3 ChIP-seq

description:
H4K16ac_N2_Emb_SE143_SE146_SE256_average.bw
H4K16ac_N2_Emb_SE143_SE146_SE256_final_peaks.bed


title: 201 ALS

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description: Total RNA from human induced astrocytes (iAstrocytes) from 3 ALS patients carrying C9orf72 mutations and 3 non-affected donors was used to investigate the role of astrocyte-derived EVs (ADEVs) in ALS astrocyte toxicity by analysis of miRNA content.

hyb_protocol: Labelled miRNA molecules were applied to Affymetrix miRNA 4 arrays and hybridised at 48C with rotation at 60 rpm for 18 hours as per the Affymetrix protocol

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: Data were normalised using Qlucore and Transcriptome Analysis Console 4 software.

label_protocol: Biotinylation of miRNA carried out according to Affymetrix Flash Tag protocol

extract_protocol:
isolation protocol: Astrocyte derived extracellular vesicles were isolated via ultracentrifugation.
Direct-Zol RNA mini-prep kit was used for RNA extraction according to manufacturers' instructions.

tag: patient group

value: fALS due to mtC9ORF72

tag: rna source


title: glp-4_Basal_A


title: glp-4_Basal_B


title: H3K4me1 N2 DPY-27 RNAi emb rep1 ChIP-seq


title: 183 ALS

source_name: Astrocyte derived extracellular vesicles


title: 170 Control

value: Non-ALS

value: Astrocyte derived extracellular vesicles


title: 78 ALS


title: glp-4_PVD_B


title: glp-4_NGM_B

source_name: glp-4, NGM (agar), 8h

value: NGM, E. coli OP50


title: TaD27-RNAi rep2

city: Taian

first: Fang

address: No. 61 Dai Zong Street

country: China

institute: Shandong Agricultural University

data_processing:
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre).
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers.
Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters.
The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).
Removing reads containing adapters;  removing reads containing more than 10% of unknown nucleotides (N); removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Triticum aestivum

source_name: Axillary bud primordia

extract_protocol:
Axillary bud were removed, flash frozen by Liquid Nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 3-week old


title: TaD27-RNAi rep1


title: TaD27-RNAi rep3


title: KN rep3


title: KN rep2


title: H3K4me1 N2 Control RNAi emb rep1 ChIP-seq

description:
H3K4me1_N2_Emb_ControlRNAi_LW171_LW173_average.bw
H3K4me1_N2_Emb_ControlRNAi_LW171_LW173_final_peaks.bed

value: Rabbit, polyclonal


title: H3K4me1 N2 emb rep1 ChIP-seq

description:
H3K4me1_N2_Emb_LW166_LAS53_average.bw
H3K4me1_N2_Emb_LW166_LAS53_final_peaks.bed


title: H3K4me3 N2 DPY-27 RNAi emb rep3 ChIP-seq

description:
H3K4me3_N2_Emb_DPY27RNAi_LW71_LW73_LW75_average.bw
H3K4me3_N2_Emb_DPY27RNAi_LW71_LW73_LW75_final_peaks.bed

value: Abcam, ab8580

value: Human Histone H3 aa 1-100 (tri methyl K4) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: 155 Control


title: KN rep1


title: H3K4me3 N2 DPY-27 RNAi emb rep1 ChIP-seq


title: H3K4me3 N2 DPY-27 RNAi emb rep2 ChIP-seq


title: H3K4me1 N2 Control RNAi emb rep2 ChIP-seq


title: H3K4me3 N2 Control RNAi emb rep2 ChIP-seq

description:
H3K4me3_N2_Emb_ControlRNAi_LW74_LW193_average.bw
H3K4me3_N2_Emb_ControlRNAi_LW74_LW193_final_peaks.bed


title: AG08620 Control


title: H3K4me3 CB428 emb rep2 ChIP-seq

description:
H3K4me3_CB428_Emb_SE175_SEA201_SE186_average.bw
H3K4me3_CB428_Emb_SE175_SEA201_SE186_final_peaks.bed


title: H3K4me3 CB428 emb rep3 ChIP-seq

value: Abcam, ab12209

value: Mouse, monoclonal


title: H3K4me3 N2 Control RNAi emb rep1 ChIP-seq


title: Control_ChIPseq_input

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

description: Agambiae_genes_and_promoters_ChIP_rpkm_counts.txt

data_processing:
We mapped reads for various histone modifications and the input to A.gambiae PEST strain genome version 4.3 using Bowtie v2.2.9 with default parameters except for --no-mixed
Reads were trimmed 5 bases from each read 5’ end (--trim5 5). Mapped reads were sorted and deduplicated using SAMtools v.1.6. We applied a quality threshold of 10 in MAPQ score. All libraries were downsampled (SAMtools) to the same number of reads (9M) for further downstream analysis
We conducted peak calling using MACS2 (v.2.1.1) [61] “callpeak” module with -t and -c options and default parameters, except for -g 2.73e8 --keep-dup all -B --SPMR -q 0.01 –nomodel
To quantitative compare histone modification profiles between infected and control mosquito tissues, we used diffReps software. ChIP-seq data for infected and control and the corresponding inputs were provided with -tr, -co, --btr and --bco options. Due to the lack of biological replicates, the statistical test used was G-test (-me gt). Rest of parameters were set as default except for --window 1000
We performed annotation of MACS2 peaks and diffReps regions to genomic features (TSSs, exons, introns, and intergenic regions) using the annotatePeaks.pl module in HOMER (v.3.12)
We mapped RNA paired directional reads to A.gambiae PEST strain genome version 4.3 using TopHat v2.0.13. We aligned reads using the option of library type set as first-strand for directional RNA-seq
Quantification and differential gene expression analysis was conducted using HTSeq/DESeq2 packages
Genome_build: AgamP4.3 (VectorBase)
Supplementary_files_format_and_content: Tracks of ChIP-seq signal, normalized and input corrected, per histone and condition (bw). The bedGraph files were built with MACS2 “bdgcmp" module (-m ppois) and bigwig files using bedGraphToBigWig tool
Supplementary_files_format_and_content: RNA-seq mapped reads coverage was obtained in bigwig format (_coverage.bw) using bamCoverage tool
Supplementary_files_format_and_content: Counts of normalized (RPKM) and input corrected ChIP-seq reads per histone and condition (txt). The counts were obtained using bedtools intersect -c

organism: Anopheles gambiae

source_name: mosquito midgut

growth_protocol: Three- to five-day-old female A.gambiae mosquitoes were sourced from an outbred colony established in 2008 and repeatedly replenished with F1 from wild-caught mosquito females collected in Kou Valley (11°23'14"N, 4°24'42"W), 30 km from Bobo-Dioulasso, south-western Burkina Faso (West Africa). Mosquitoes were maintained under standard insectary conditions (27 ± 2°C, 70 ± 5% relative humidity, 12:12 LD)

extract_protocol:
Dissection of mosquito midguts and salivary glands was performed in situ on adult females at 7 days post-blood meal. To determine infection levels, mosquito guts were dissected 7 days after blood feeding and were stained with 2% Mercurochrome before microscopic examination. Tissues were maintained in ice-cold Schneider’s insect culture medium (Sigma-Aldrich) and fresh tissues were immediately processed for chromatin and RNA analyses
Chromatin immunoprecipitation was performed in mosquito as previously described by us in Gomez-Diaz et al. Antibodies to histone modifications used in this study were anti-H3K9ac (Millipore #07-352), antiH3K4me3 (Abcam ab8580), anti-H3K27ac (Abcam ab4729), and anti-H3K9me3 (Abcam ab8898).ChIP-seq libraries were prepared following the procedure in Bowman et al., and using the HiFi Kapa Sybr library preparation kit (KapaBiosystems). To obtain the quantity needed to perform ChIP-seq, the samples were pooled, resulting in one biological replicate for infected mosquito midguts and one biological replicate of uninfected tissues. ChIP-seq libraries were sequenced at the HudsonAlpha Institute for Biotechnology using an Illumina HiSeq2000 sequencer.

treatment_protocol: Females were fed through membranes on gametocyte-infected blood from malaria patients. To eliminate transmission-blocking factors, venous blood was collected and the serum was replaced by a non-immune AB serum to avoid transmission of human blocking factors

value: midgut and salivary gland

tag: Sex

value: female

tag: time

value: 7 days post-blood meal

tag: infection status

value: Control

tag: replicate


title: H3K4me3 CB428 emb rep1 ChIP-seq

tag: developmental stage

value: Wako Chemicals, 305-34819


title: H3K4me3 N2 emb rep2 ChIP-seq

description:
H3K4me3_N2_Emb_SE180_SE255_average.bw
H3K4me3_N2_Emb_SE180_SE255_final_peaks.bed

value: mixed embryo

tag: antibody target

value: Millipore, 07-473

value: Synthetic peptide corresponding to residues surrounding and including trimethlyated Lys 4 of Histone H3


title: Control_ChIPseq_H3K27ac


title: Control_ChIPseq_H3K9me3


title: H3K4me3 N2 emb rep1 ChIP-seq

tag: chip antibody (vendor, cat#, lot#)


title: glp-4_NGM_C

value: Whole organism


title: Control_ChIPseq_H3K4me3


title: Control_ChIPseq_H3K9ac