title: CE_4_01

value: Control


title: CE_4_02

status: Public on Jul 14 2017

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (GRCm38/mm10) and the 92 ERCC spike-in sequences using TopHat (v2.1.0) with parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq”.
HTSeq (v0.6.0) was used to count the number of reads mapped to each gene with parameters “htseq-count -f bam -r pos -s no -a 30 input_bam gtf”.
TPM (Transcripts Per Million) was employed to quantify gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: The major lobes were collected from E12.5 embryos and cultured on Nuclepore Track-Etch Membranes (Whatman, 110414) in 12-well plates containing 2 ml of RPMI 1640 medium (Invitrogen, 22400) supplemented with 10% fetal bovine serum, 50 ng/ml EGF, 1×ITS-X (Gibco, 51500) and antibiotics.

extract_protocol:
After FACS sorting, single cells were manually picked up under the microscope with a mouth pipette and transferred into 4 μl of cell lysis buffer containing 0.05 μl of a 1:300,000 dilution of ERCC Spike-in RNA (Life Technologies, 4456740). The cDNA was synthesized, amplified (18 cycles) using the Smart-seq2 protocol, and purified using VAHTS DNA Clean Beads XP beads (Vazyme, N411-03).
Two nanograms of cDNA were used to prepare the sequencing libraries using the TruePrep DNA Library Prep Kit (Vazyme, TD502) with 0.4 × of the standard reaction volume. PCR amplifications were conducted in 8 cycles. Purification and size-based selection of PCR products were performed to obtain libraries with a peak size of 350 bp.

treatment_protocol: The cultures were treated for two days with 0.5 μM TPPB (Calbiochem, 508158) and/or 10 μM U0126 (Sigma, U120) or DMSO carrier as a control.

tag: embryonic day

tag: culture time

value: 2 days

tag: treatment

tag: sorting

value: EpCAM+

tag: putative cell type

value: hepatoblast/hepatocyte


title: UE_4_01

value: cholangiocyte


title: UE_3_05


title: UE_3_04


title: UE_4_02


title: UE_3_02


title: UE_3_03


title: TUE_4_05


title: Control male liver pool 2_rRNA-depleted_G138_M11

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

description: Ribosomal RNA-depleted, strand-specific library

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) mRNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene, Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; it thus excludes sequences found in an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results comparing intact females and GH-treated male mouse livers compared to sham-treated male mouse livers.

source_name: liver tissue

extract_protocol:
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was depleted of rRNA using the NEB rRNA depletion kit (NEB, Ipswich, MA, Cat# E6310). Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, Cat# E7420) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335, E7500), according to the manufacturer's instructions.

treatment_protocol: Male and female CD1 mice, 8-9 weeks of age, were purchased from Charles River Laboratories  (Crl:CD1(ICR)). Alzet osmotic pumps (model 1007D) were filled with recombinant rat GH and were implanted subcutaneously under ketamine and xylazine anesthesia. GH was infused at a rate of 25 ng/g body weight/h for 10 h or 1 d. Sham treated males were used as controls.

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

value: Sham pump

tag: Sex

value: Male

tag: age

value: 8 weeks


title: UE_4_08


title: TUE_4_04


title: TUE_4_03


title: UE_3_01


title: TUE_4_02


title: TUE_3_03


title: TUE_3_04


title: TUE_3_01


title: sHyp7h replicate-2

status: Public on Jul 15 2017

city: La Jolla

first: Joanne

last: Chory

state: California

address: 10010 N Torrey Pines RD

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
Sequenced reads were trimmed for adaptor sequence, then aligned to TAIR10 whole genome build using Tophat2 v2.0.8b (Kim et al. 2013 Genome Biology) on a Linux platform
FPKM were calculated for each sample using Cufflinks 2.1.1 (Trapnell et al. 2012 Nature Protocols) with parameters -u --compatible-hits-norm -G parameters on a Linux platform
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Arabidopsis thaliana

source_name: WT_hypocotyl_low R:FR_7h

growth_protocol: Seeds of the indicated genotype was stratified for 2 days in the cold and then was grown on 0.5x Linsmaier and Skoog medium under 16hL 8hD conditions at 22°C.

extract_protocol:
RNeasy Micro kit (Qiagen)
Truseq RNA Sample prep kit v2 Cat# RS-122-2001 and RS-122-2002 (Illumina, CA)

treatment_protocol: 5 day old white high R:FR grown seedlings were treated low R:FR or mock treated (high R:FR) for indicated times

tag: ecotype

value: Columbia

tag: genotype/variation

value: WT

tag: exposed to

value: low R:FR

tag: treatment time

tag: tissue

value: hypocotyl tissue


title: CE_3_09


title: CE_3_08


title: CE_3_07


title: CE_3_06


title: sHyp30m replicate-1

source_name: WT_hypocotyl_low R:FR_0.5h


title: TUE_4_01


title: CE_3_04


title: CE_3_05


title: CE_3_01


title: E14.5E_3_19

value: P2 gate, EpCAM+


title: CE_3_03


title: CE_3_02


title: E14.5E_3_18

extract_protocol:
After FACS sorting, single cells were manually picked up under the microscope with a mouth pipette and transferred into 4 ul of cell lysis buffer containing 0.05 ul of a 1:300,000 dilution of ERCC Spike-in RNA (Life Technologies, 4456740). The cDNA was synthesized, amplified (18 cycles) using the Smart-seq2 protocol, and purified using VAHTS DNA Clean Beads XP beads (Vazyme, N411-03).
Two nanograms of cDNA were used to prepare the sequencing libraries using the TruePrep DNA Library Prep Kit (Vazyme, TD502) with 0.4 × of the standard reaction volume. PCR amplifications were conducted in 8 cycles. Purification and size-based selection of PCR products were performed to obtain libraries with a peak size of 350 bp.


title: E14.5E_3_17


title: E14.5E_3_14


title: E14.5E_3_13


title: E14.5E_3_15


title: E14.5E_3_11


title: E14.5E_3_10


title: CE_3_10


title: E14.5E_3_12


title: TUE_3_02


title: E14.5E_3_06


title: E14.5E_3_08


title: E14.5E_3_04


title: E14.5E_3_03


title: E14.5E_3_02


title: E14.5D_3_14

value: P1 gate, DLK+


title: E14.5E_3_01


title: E14.5D_3_10


title: E14.5D_3_13


title: E14.5E_3_05


title: E14.5D_3_09


title: E14.5D_3_12


title: E14.5D_3_08


title: E14.5D_3_06


title: E14.5D_3_03


title: E14.5D_3_11


title: E14.5D_3_04


title: E14.5E_3_16


title: E14.5E_3_09


title: E14.5D_3_05


title: E14.5D_3_07


title: E14.5E_3_07


title: E14.5D_3_02


title: Male liver 3 h PCN_pool2_G95_M8

description: poly-A selected_unstranded library_PE

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
HTSeq (0.6.1p1) was used to obtain read counts for exon collapsed regions of RefSeq genes and featureCounts (1.4.6-p5) was used to obtain read counts for exon collapsed regions of lncRNAs
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9

molecule: nuclear RNA

source_name: liver nuclei

extract_protocol:
RNA was isolated from prepared liver nuclei using TriZOL LS reagent per manufacturer's protocol
NEBNext Ultra Directional RNA Sequencing for Illumina kit following poly(A) selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module

treatment_protocol: Male and female CD1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA) at 7 weeks of age. Mice were injected with 3 mg/kg TCPOBOP, 50 mg/kg PCN or vehicle (1% DMSO in corn oil) between 8:00-8:45 AM on Day 1 and tissue was collected between 11:00-11:45 AM on Day 1 (3 h) or between 11:00-11:45 AM on Day 2 (27 h). Nuclei were isolated and stored at -80C prior to RNA isolation

value: CD-1 (Charles River)

value: 50 mg/kg PCN_ 3 h

value: male

value: 7 weeks


title: Male liver 3 h vehicle_pool1_G95_M1 (control for PCN treatments)

description: poly-A selected_unstranded library_PE

value: Vehicle (1% DMSO in corn oil)_ 3 h


title: Male liver 3 h vehicle_pool3_G95_M3 (control for PCN treatments)

description: poly-A selected_unstranded library_PE


title: Male liver 3 h vehicle_pool2_G95_M2 (control for PCN treatments)

description: poly-A selected_unstranded library_PE


title: Male liver 3 h PCN_pool3_G95_M9

description: poly-A selected_unstranded library_PE


title: Male liver 3 h PCN_pool1_G95_M7

description: poly-A selected_unstranded library_PE


title: Female liver 27 h TCPOBOP_pool1_G123_M15

description: poly-A selected_stranded specific library_PE

value: 3 mg/kg TCPOBOP_27 h

value: female


title: E14.5D_3_01

value: hepatoblast/hepatocyte


title: Female liver 27 h vehicle_pool2_G123_M14

value: Vehicle (1% DMSO in corn oil)_27 h


title: Female liver 27 h vehicle_pool1_G123_M13


title: Female liver 3 h TCPOBOP_pool2_G123_M12

value: 3 mg/kg TCPOBOP_ 3 h


title: Female liver 3 h TCPOBOP_pool1_G123_M11


title: Female liver 27 h TCPOBOP_pool2_G123_M16


title: Male liver 27 h TCPOBOP_pool2_G123_M8

data_processing: Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010). HTSeq (0.6.1p1) was used to obtain read counts for exon collapsed regions of RefSeq genes, and featureCounts (1.4.6-p5) was used to obtain read counts for exon collapsed regions of lncRNAs. Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics), Genome_build: mm9.

extract_protocol: RNA was isolated from prepared liver nuclei using TriZOL LS reagent per manufacturer's protocol. NEBNext Ultra Directional RNA Sequencing for Illumina kit following poly(A) selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: Male and female CD1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA) at 7 weeks of age. Mice were injected with 3 mg/kg TCPOBOP, 50 mg/kg PCN or vehicle (1% DMSO in corn oil) between 8:00-8:45 AM on Day 1 and liver was collected between 11:00-11:45 AM on Day 1 (3 h) or between 11:00-11:45 AM on Day 2 (27 h). Nuclei were isolated and stored at -80C prior to RNA isolation

tag: mouse strain

value: liver


title: Female liver 3 h vehicle_pool2_G123_M10


title: Male liver 27 h TCPOBOP_pool1_G123_M7


title: Male liver 27 h vehicle_pool1_G123_M5


title: Male liver 27 h vehicle_pool2_G123_M6


title: Male liver 3 h vehicle_pool2 (control for TCPOBOP treatments)_G123_M2

value: Vehicle (1% DMSO in corn oil)_3 h


title: Male liver 3 h TCPOBOP_pool1_G123_M3

value: 3 mg/kg TCPOBOP_3 h


title: Male liver 3 h vehicle_pool1 (control for TCPOBOP treatments)_G123_M1

treatment_protocol: Male and female CD1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA) at 7 weeks of age. Mice were injected with 3 mg/kg TCPOBOP, 50 mg/kg PCN or vehicle (1% DMSO in corn oil) between 8:00-8:45 AM on Day 1 and liver was collected between 11:00-11:45 AM on Day 1 (3 h) or between 11:00-11:45 AM on Day 2 (27 h). Nuclei were isolated and stored at -80C prior to RNA isolation.

value: CD-1 (Charles River); treatment:Vehicle (1% DMSO in corn oil)_3 h; sex:male; age:7 weeks; tissue:liver


title: TE_2_08

description:
Single-cell_RNA-seq_Cultured_Read_Count.txt.gz
Single-cell_RNA-seq_Cultured_Normalized_TPM.txt.gz

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (GRCm38/mm10) and the 92 ERCC spike-in sequences using TopHat (v2.1.0) with parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq”.
HTSeq (v0.6.0) was used to count the number of reads mapped to each gene with parameters “htseq-count -f bam -r pos -s no -a 30 input_bam gtf”.
TPM (Transcripts Per Million) was employed to quantify gene expression levels.
genome build: mm10
values tab-delimited text files include read count and TPM values for each sample

value: 2 days

value: TPPB

value: EpCAM+

value: cholangiocyte


title: TE_2_10


title: TE_2_11


title: TE_2_09


title: TE_2_12


title: TE_2_06


title: TE_2_04


title: TE_2_03


title: TE_2_05


title: TE_1_09


title: TE_2_01


title: TE_1_07


title: TE_1_10


title: TE_2_07


title: TE_2_02


title: TE_1_08


title: TE_1_04


title: TE_1_05


title: TE_1_03


title: Male liver 3 h TCPOBOP_pool2_G123_M4

value: CD-1 (Charles River)


title: TE_1_01


title: TE_1_02


title: TD_2_05

value: DLK+


title: TD_2_04


title: TD_2_06


title: TD_2_02


title: CE_2_07

value: Control


title: CE_2_05


title: CE_2_06


title: CE_2_08


title: CE_2_04


title: TE_1_06


title: CE_2_03


title: CE_1_03


title: CE_1_02


title: CE_2_02


title: CE_1_04


title: CD_2_04


title: CE_2_01


title: Female liver 3 h vehicle_pool1_G123_M9

value: Vehicle (1% DMSO in corn oil)_ 3 h

value: 7 weeks


title: CE_1_01


title: CD_2_02


title: CD_2_03


title: CD_2_05


title: CD_2_01


title: CD_1_01


title: E17.5E_4_16

description:
Single-cell_RNA-seq_in_vivo_Read_Count.txt.gz
Single-cell_RNA-seq_in_vivo_Normalized_TPM.txt.gz

value: P2 gate, EpCAM+


title: E17.5E_4_15


title: E17.5E_4_14


title: E17.5E_4_13


title: TD_2_01

value: hepatoblast/hepatocyte


title: TD_2_03


title: E17.5E_4_11


title: E17.5E_4_07


title: E17.5E_4_06


title: E17.5E_4_08


title: E17.5E_4_05


title: E17.5E_4_02


title: E17.5E_3_04


title: E17.5E_4_03


title: E17.5E_3_03


title: E17.5E_3_02


title: E17.5E_4_12


title: E17.5E_3_01


title: E17.5E_4_10


title: E17.5E_1_14


title: E17.5E_1_11


title: E17.5E_1_12


title: E17.5E_1_09


title: E17.5E_4_01


title: E17.5E_1_15


title: E17.5E_4_09


title: E17.5E_1_08


title: E17.5E_1_13


title: E17.5E_1_02


title: E17.5E_1_05


title: E17.5E_1_03


title: E17.5E_1_10


title: E17.5E_1_01


title: E17.5E_1_04


title: E17.5E_1_06


title: E17.5D_4_04

value: P1 gate, DLK+


title: E17.5D_4_02


title: E17.5E_4_04


title: E17.5D_4_05


title: E17.5D_4_03


title: E17.5D_3_07


title: E17.5D_4_01


title: E17.5D_3_08


title: E17.5D_3_06


title: E17.5D_3_05


title: E17.5E_1_07


title: E17.5D_3_04


title: E17.5D_3_01


title: E17.5D_3_02


title: E17.5D_3_03


title: E17.5D_2_07


title: E17.5D_2_08


title: E17.5D_2_05


title: E17.5D_2_01


title: E17.5D_2_03


title: E17.5D_2_04


title: E17.5D_2_06


title: E17.5D_1_13


title: E17.5D_1_14


title: E17.5D_1_12


title: E17.5D_1_11


title: E17.5D_1_10


title: E17.5D_1_08


title: E17.5D_1_09


title: E17.5D_1_03


title: E17.5D_1_04


title: E17.5D_1_07


title: E17.5D_1_06


title: E17.5D_1_05


title: E17.5D_1_02


title: E15.5E_4_10


title: E15.5E_4_08


title: E15.5E_4_09


title: E17.5D_1_01


title: E15.5E_4_11


title: E17.5D_2_02


title: E15.5E_4_07


title: E15.5E_3_07


title: E15.5E_2_19


title: E15.5E_3_06


title: E15.5E_4_05


title: E15.5E_3_03


title: E15.5E_4_04


title: E15.5E_3_02


title: E15.5E_3_04


title: E15.5E_4_06


title: E15.5E_4_02


title: E15.5E_2_18


title: E15.5E_4_01


title: E15.5E_4_03


title: E15.5E_3_01


title: E15.5E_2_11


title: E15.5E_2_10


title: E15.5E_2_15


title: E15.5E_2_16


title: E15.5E_2_17


title: E15.5E_2_14


title: E15.5E_2_05


title: E15.5E_2_06


title: E15.5E_2_04


title: E15.5E_2_08


title: E15.5E_3_05


title: E15.5E_2_09


title: E15.5E_3_08


title: E15.5E_2_02


title: E15.5E_2_01


title: E15.5D_4_19


title: E15.5D_4_17


title: E15.5D_4_18


title: E15.5D_4_16


title: E15.5E_2_12


title: E15.5D_4_13


title: E15.5D_4_14


title: E15.5E_2_03


title: E15.5D_4_09


title: E15.5E_2_07


title: E15.5E_2_13


title: E15.5D_4_11


title: E15.5D_4_08


title: E15.5D_4_12


title: E15.5D_4_07


title: E15.5D_4_02


title: E15.5D_4_05


title: E15.5D_3_07


title: E15.5D_4_01


title: E15.5D_4_03


title: E15.5D_3_06


title: E15.5D_3_05


title: E15.5D_3_04


title: E15.5D_4_15


title: E15.5D_3_03


title: E15.5D_3_01


title: E15.5D_1_12


title: E15.5D_1_08


title: E15.5D_1_11


title: E15.5D_1_09


title: E15.5D_1_10


title: E15.5D_4_04


title: E15.5D_1_01


title: E15.5D_3_08


title: E15.5D_1_05


title: E15.5D_1_06


title: E15.5D_1_02


title: E15.5D_1_03


title: E15.5D_1_04


title: E14.5E_2_11


title: E15.5D_4_06


title: E15.5D_4_10


title: E14.5E_2_09


title: E14.5E_2_07


title: E14.5E_2_08


title: E14.5E_2_04


title: E14.5E_2_03


title: E14.5E_2_01


title: E14.5E_2_05


title: E15.5D_1_07


title: E14.5E_1_12


title: E15.5D_3_02


title: E14.5E_1_09


title: E14.5E_1_11


title: E14.5E_1_08


title: E14.5E_2_10


title: E14.5E_1_06


title: E14.5E_1_10


title: E14.5E_1_02


title: E14.5E_1_07


title: E14.5E_1_05


title: E14.5E_1_04


title: E14.5E_2_06


title: E14.5D_2_01


title: E14.5D_1_08


title: E14.5D_1_10


title: E14.5D_2_03


title: E14.5D_1_06


title: E14.5E_1_13


title: E14.5D_1_05


title: E14.5D_1_03


title: E14.5D_1_02


title: E14.5D_1_01


title: E13.5E_3_08


title: E13.5E_3_07


title: E14.5D_1_09


title: E13.5E_3_05


title: E13.5E_3_04


title: E13.5E_3_06


title: E14.5E_1_03


title: E14.5D_2_02


title: E14.5E_1_01


title: E14.5D_1_04


title: E13.5E_2_15


title: E13.5E_2_18


title: E13.5E_2_16


title: E13.5E_2_12


title: E13.5E_2_13


title: E13.5E_3_02


title: E14.5D_1_07


title: E13.5E_3_03


title: E13.5E_2_17


title: E13.5E_2_09


title: E13.5E_2_08


title: E13.5E_2_07


title: E13.5E_2_10


title: E13.5E_2_11


title: E13.5E_2_05


title: E13.5E_2_06


title: E13.5E_2_14


title: E13.5E_2_03


title: E13.5E_2_04


title: E14.5E_2_02


title: E13.5E_3_01


title: E13.5E_2_02


title: E13.5D_3_06


title: E13.5D_3_05


title: E13.5D_3_08


title: E13.5D_3_07


title: E13.5D_3_03


title: E13.5D_3_04


title: E13.5D_2_15


title: E13.5D_2_18


title: E13.5D_2_14


title: E13.5D_2_13


title: E13.5D_2_17


title: E13.5D_3_01


title: E13.5D_3_02


title: E13.5E_2_01


title: E13.5D_2_11


title: E13.5D_2_16


title: E13.5D_2_07


title: E13.5D_2_09


title: E13.5D_2_08


title: E13.5D_2_04


title: E13.5D_2_06


title: E13.5D_2_03


title: E13.5D_1_12


title: E13.5D_2_01


title: E13.5D_1_13


title: E13.5D_2_02


title: E13.5D_1_10


title: E13.5D_1_09


title: E13.5D_2_12


title: E13.5D_1_06


title: E13.5D_1_07


title: E13.5D_1_04


title: E13.5D_2_10


title: E12.5E_2_01


title: E12.5E_2_02


title: E13.5D_1_05


title: E12.5E_1_13


title: E12.5E_1_14


title: E12.5E_2_05


title: E13.5D_1_03


title: E12.5E_2_03


title: E13.5D_1_01


title: E12.5E_2_04


title: E12.5E_2_06


title: E12.5E_1_12


title: E13.5D_2_05


title: E12.5E_1_10


title: E12.5E_1_11


title: E13.5D_1_02


title: E12.5E_1_09


title: E13.5D_1_11


title: E12.5E_1_08


title: E12.5E_1_07


title: E13.5D_1_08


title: E12.5E_1_05


title: E12.5E_1_06


title: E12.5E_1_03


title: E12.5E_1_04


title: E12.5D_2_06


title: E12.5E_1_02


title: E12.5E_1_01


title: E12.5D_2_03


title: E12.5D_2_04


title: E12.5D_1_15


title: E12.5D_2_01


title: E12.5D_2_02


title: E12.5D_1_12


title: E12.5D_1_11


title: E12.5D_1_14


title: E12.5D_1_13


title: E12.5D_1_10


title: E12.5D_1_09


title: E12.5D_1_05


title: E12.5D_1_04


title: E12.5D_1_06


title: E12.5D_1_03


title: E12.5D_1_02


title: E12.5D_1_07


title: E11.5E_3_07


title: E11.5E_3_05


title: E11.5E_3_06


title: E12.5D_1_01


title: E11.5E_3_04


title: E11.5E_3_08


title: E12.5D_2_05


title: E11.5E_3_01


title: E11.5E_2_25


title: E11.5E_3_03


title: E11.5E_2_26


title: E11.5E_2_24


title: E11.5E_2_23


title: E12.5D_1_08


title: E11.5E_2_22


title: wt_notag_Flag_IP_2_rep1

city: Daejeon

first: Youngseo

last: Cheon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

library_source: genomic

data_processing:
The adapter sequences are trimmed by Fastqc, and we aligned the processed reads to the S. pombe ASM294v2 genome assembly using Novoalign.
The merged BAM files generated by samtools were computed by deepTools bamCompare to generate normalized bigWig files.
CENP-ACnp1 ChIP-Seq were normalized to input and Flag ChIP-Seq for Ies6-5xFlag and Iec1-5xFlag were normalized to mock (no tag).
For quantitative analysis of H3 ChIP-Seq, we calculated the ratio of IP:input in each ChIP normalized to that of the spike-in control and the fold change of IP in mutants versus wild type (wt) were computed by deepTools bamCompare.
Genome_build: SpombeASMv2
Supplementary_files_format_and_content: The bigWig files of the ChIP-Seq for Flag-tagged Ino80 subunits normalized to mock (no tag) and the ChIP-Seq for CENP-ACnp1 and H3 changes in mutants versus wild type (wt) were generated.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: Schizosaccharomyces pombe cells were grown in YES medium to mid log phase and we used 1.6×109, 4×108 and 2.4~3.2×109 cells for the the CENP-ACnp1 ChIP, H3 ChIP and Flag ChIP experiments, respectively.

extract_protocol:
For the CENP-ACnp1 ChIP and the H3 ChIP experiments, we prepared the cell extracts by disrupting the cells in lysis buffer (50 mM Hepes-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) using a standard bead-beating protocol. For the Flag ChIP experiments, we used a modified lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100) and TBS (20 mM Tris-HCl, pH 7.5, 150 mM NaCl)-based wash buffers (TBS and TBS with 0.05% Tween-20) to avoid denaturation of the M2 antibody by sodium deoxycholate. As the external spike-in control for the H3 ChIP-Seq experiments, formaldehyde-fixed S. cerevisiae cells were added to S. pombe cells in 1:8 ratio before cell disruption. We recovered the de-crosslinked DNA using a Qiagen PCR purification kit.
We constructed the ChIP-Seq libraries using 5 to 10 ng of input DNA or 1 to 10 ng of immunoprecipitated DNA with a ChIP-Seq kit (NEXTflex ChIP-Seq kit, Bioo Scientific) according to the manufacturer’s protocol.

tag: temperature

value: 30 °C

tag: chip antibody

value: anti-Flag M2 antibody (mouse monoclonal, F1804, Sigma)


title: wt_notag_Flag_IP_2_rep2


title: wt_Iec1-Flag_Flag_IP_2_rep2


title: wt_Ies6-Flag_Flag_IP_2_rep2


title: E11.5E_3_02


title: E11.5E_2_20


title: E11.5E_2_19


title: E11.5E_2_18


title: E11.5E_2_17


title: E11.5E_2_16


title: E11.5E_2_14


title: wt_Ies6-Flag_Flag_IP_2_rep1


title: cnp1-1_Iec1-Flag_Flag_IP_36C_rep2

value: 36 °C


title: E11.5E_2_12


title: E11.5E_2_10


title: cnp1-1_notag_Flag_IP_36C_rep1


title: cnp1-1_Ies6-Flag_Flag_IP_36C_rep2


title: cnp1-1_Iec1-Flag_Flag_IP_36C_rep1


title: E11.5E_2_15


title: E11.5E_2_13


title: cnp1-1_Ies6-Flag_Flag_IP_36C_rep1


title: wt_Iec1-Flag_Flag_IP_36C_rep2


title: wt_Iec1-Flag_Flag_IP_2_rep1


title: E11.5E_2_11


title: E11.5E_2_09


title: wt_Iec1-Flag_Flag_IP_36C_rep1


title: wt_notag_Flag_IP_36C_rep2


title: E11.5E_2_21


title: cnp1-1_notag_Flag_IP_36C_rep2


title: E11.5E_2_07


title: E11.5E_2_08


title: wt_Ies6-Flag_Flag_IP_36C_rep1


title: wt_Ies6-Flag_Flag_IP_36C_rep2


title: E11.5E_2_06


title: wt_notag_Flag_IP_36C_rep1


title: E11.5E_2_05


title: hrp1D_spikein_input_rep1

description: As the external spike-in control for the H3 ChIP-Seq experiments, formaldehyde-fixed wild-type S. cerevisiae (W303a) cells were added to S. pombe cells in 1:8 ratio before cell disruption.

value: none (input)


title: hrp1D_spikein_input_rep2


title: E11.5E_2_03


title: E11.5E_2_02


title: wt_spikein_input_rep2


title: hrp1D_spikein_H3_IP_rep2

value: anti-H3 antibody (rabbit polyclonal)


title: wt_spikein_input_rep1


title: E11.5E_2_04


title: hrp1D_spikein_H3_IP_rep1


title: E11.5E_2_01


title: E11.5D_3_05


title: E11.5D_3_03


title: wt_spikein_H3_IP_rep1


title: E11.5D_3_06


title: E11.5D_3_07


title: ies6D_spikein_H3_IP_rep2


title: ies6D_spikein_input_rep2


title: ies6D_spikein_H3_IP_rep1


title: E11.5D_3_04


title: E11.5D_2_13


title: tel1R-neocen_notag_Flag_IP_rep1


title: tel1R-neocen_notag_Flag_IP_rep2


title: E11.5D_2_12


title: wt_spikein_H3_IP_rep2


title: ies6D_spikein_input_rep1


title: E11.5D_3_02


title: tel1R-neocen_Ies6-Flag_Flag_IP_rep2


title: tel1R-neocen_Ies6-Flag_Flag_IP_rep1


title: E11.5D_2_08


title: E11.5D_2_07


title: E11.5D_2_09


title: wt_notag_Flag_IP_rep2


title: wt_notag_Flag_IP_rep1


title: tel1R-neocen_H3_IP_rep2


title: wt_Ies6-Flag_Flag_IP_rep1


title: tel1R-neocen_input_rep2


title: E11.5D_2_04


title: wt_Ies6-Flag_Flag_IP_rep2


title: E11.5D_3_01


title: E11.5D_2_05


title: E11.5D_2_02


title: tel1R-neocen_input_rep1


title: tel1R-neocen_H3_IP_rep1


title: E11.5D_2_11


title: tel1R-neocen_Cnp1_IP_rep1

value: anti-CENP-ACnp1 antibody (rabbit polyclonal)


title: E11.5D_2_01


title: tel1R-neocen_Cnp1_IP_rep2


title: mis18-262_input_36C_rep2


title: E11.5D_1_15


title: E11.5D_1_16


title: mis18-262_input_36C_rep1


title: E11.5D_2_06


title: E11.5D_2_10


title: E11.5D_1_12


title: E11.5D_1_13


title: E11.5D_1_14


title: mis18-262_Cnp1_IP_36C_rep1


title: wt_input_36C_rep1


title: wt_input_36C_rep2


title: E11.5D_1_11


title: mis18-262_Cnp1_IP_36C_rep2


title: wt_Cnp1_IP_36C_rep2


title: wt_Cnp1_IP_36C_rep1


title: E11.5D_2_03


title: TetR-Flag-Iec1_AHT_H3_IP_rep1

description: Anhydrotetracycline (AHT) was added to release TetR-Iec1 from bighyg and used as negative controls.


title: E11.5D_1_10


title: TetR-Flag-Iec1_AHT_H3_IP_rep2


title: E11.5D_1_05


title: E11.5D_1_07


title: E11.5D_1_06


title: E11.5D_1_09


title: TetR-Flag-Iec1_H3_IP_rep2


title: TetR-Flag_H3_IP_rep1


title: E11.5D_1_04


title: TetR-Flag-Iec1_H3_IP_rep1


title: E11.5D_1_08


title: TetR-Flag-Iec1_AHT_input_rep2


title: E11.5D_1_03


title: TetR-Flag_H3_IP_rep2


title: E11.5D_1_02


title: E11.5D_1_01


title: E10.5D_3_13


title: E10.5D_3_12


title: E10.5D_3_15


title: E10.5D_3_16


title: TetR-Flag-Iec1_AHT_Cnp1_IP_rep2


title: TetR-Flag-Iec1_AHT_input_rep1


title: E10.5D_3_11


title: TetR-Flag-Iec1_Cnp1_IP_rep1


title: E10.5D_3_14


title: TetR-Flag-Iec1_input_rep2


title: TetR-Flag-Iec1_input_rep1


title: TetR-Flag_input_rep2


title: TetR-Flag-Iec1_Cnp1_IP_rep2


title: E10.5D_3_09


title: E10.5D_3_08


title: TetR-Flag_input_rep1


title: TetR-Flag_Cnp1_IP_rep1


title: E10.5D_3_04


title: ino80-11_hrp1D_input_20C_rep2

value: 20 °C


title: E10.5D_3_06


title: E10.5D_3_05


title: TetR-Flag_Cnp1_IP_rep2


title: ino80-11_hrp1D_input_20C_rep1


title: E10.5D_3_07


title: E10.5D_3_02


title: E10.5D_3_01


title: ino80-11_hrp1D_Cnp1_IP_20C_rep1


title: ino80-11_hrp1D_Cnp1_IP_20C_rep2


title: E10.5D_3_03


title: E10.5D_3_10


title: hrp1D_input_20C_rep2


title: E10.5D_2_22


title: hrp1D_Cnp1_IP_20C_rep1


title: hrp1D_input_20C_rep1


title: TetR-Flag-Iec1_AHT_Cnp1_IP_rep1


title: E10.5D_2_21


title: E10.5D_2_19


title: E10.5D_2_17


title: ino80-11_Cnp1_IP_20C_rep1


title: wt_input_20C_rep2


title: ino80-11_Cnp1_IP_20C_rep2


title: E10.5D_2_15


title: E10.5D_2_11


title: E10.5D_2_13


title: E10.5D_2_12


title: wt_input_20C_rep1


title: ino80-11_input_20C_rep2


title: hrp1D_input_rep2


title: hrp1D_input_rep1


title: ino80-11_input_20C_rep1


title: E10.5D_2_08


title: hrp1D_Cnp1_IP_20C_rep2


title: wt_Cnp1_IP_20C_rep1


title: E10.5D_2_20


title: E10.5D_2_09


title: hrp1D_Cnp1_IP_rep2


title: E10.5D_2_07


title: hrp1D_Cnp1_IP_rep1


title: E10.5D_2_10


title: E10.5D_2_18


title: E10.5D_2_16


title: wt_Cnp1_IP_20C_rep2


title: E10.5D_2_06


title: E10.5D_2_14


title: E10.5D_2_04


title: ies6D_input_rep1


title: E10.5D_2_05


title: ies6D_Cnp1_IP_rep1


title: E10.5D_2_02


title: wt_Cnp1_IP_rep2


title: E10.5D_1_16


title: E10.5D_2_01


title: wt_input_rep1


title: E10.5D_1_14


title: ies6D_input_rep2


title: wt_Cnp1_IP_rep1


title: E10.5D_1_13


title: E10.5D_1_10


title: E10.5D_1_12


title: E10.5D_1_11


title: E10.5D_1_09


title: E10.5D_1_04


title: E10.5D_1_03


title: E10.5D_1_07


title: E10.5D_1_08


title: E10.5D_1_06


title: ies6D_Cnp1_IP_rep2


title: E10.5D_2_03


title: E10.5D_1_01


title: Chix 69_Control_Day 7

city: Storrs

first: Edan

last: Tulman

state: CT

address: 61 North Eagleville Rd

institute: University of Connecticut

data_processing:
Illumina RTA v2 was used for base-calling
Fastq data from individual chickens were mapped using the TopHat package (version 2.0.1) utilizing the Bowtie2 engine (version 2.2.5) to align reads to the Gallus gallus reference genome
BAM files were processed using Cuffdiff to calculate FPKM expression values  and differential expression
Genome_build: Gallus gallus genome (WASHUC2)
Supplementary_files_format_and_content: tab-delimited text files including FPKM values, fold change, and significance.  Each cuffdiff .txt file contains the tophat output from each chicken used to determine FPKMs and differential expression of genes between birds/within groups (Controls v. infected for each time point).

organism: Gallus gallus

source_name: Control White Leghorn Chicken

extract_protocol:
TRIzol extraction of tracheal cells/content of tracheal lumen
Total RNA was collected in TRIzol, extracted using the zymo direct-zol mini prep, and enriched using Illumina PolyA selection per product instructions
rRNA depleted RNA
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA library prep kit HT)

tag: host breed

value: White Leghorn

tag: infection

tag: infectious agent

value: Hayflick's only

tag: time

value: Day 7


title: E10.5D_1_02

tag: embryonic day

tag: culture time

tag: treatment

tag: sorting


title: wt_input_rep2


title: E10.5D_1_15

tag: putative cell type


title: Chix 67_Control_Day 7


title: WT NICD1-3

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Low quilty reads and nucleotide was trimed by using trimmomatic, and then were aligned to mouse mm9 assembly by using Bismark with Bowtie2 and speicfic opoion: -q -N 1 --score-min L,0,-0.6 --ignore-quals --quiet
Genome_build: mouse mm9
Supplementary_files_format_and_content: bedGraph, bed

source_name: WT NICD T-ALL

growth_protocol: WT and Dnmt3a knockout c-Kit+ hematopoietic progenitors were transduced with a retrovirus expressing Notch Intracellular Domain (NICD).  Cell were transplaned into lethally irradiated mcie, and mice were sacrificed when they became moribund with T-cell acute lymphoblastic leukemia (T-ALL).  At the time of euthanasia, GFP+ T-ALL blasts were purified from the bone marrow by flow cytometry for extraction of DNA

extract_protocol:
PureLink Genomic DNA Kit (Invitrogen)
PCR of MspI digested genomic DNA with Illumina adapters following bisulfite conversion EZ DNA Methylation Kit (Zymo Research)

tag: cell type

value: WT NICD T-ALL blasts

tag: passages

value: Freshly isolated from moribund mice

tag: strain


title: Chix 66_Control_Day 7

value: Control


title: Chix 65_Control_Day 7


title: Chix 63_Infected_Day 7

source_name: Infected White Leghorn Chicken

value: Infected

value: M. gallisepticum Rlow


title: WT NICD1-2


title: WT NICD1-1


title: E10.5D_1_05

value: hepatoblast/hepatocyte


title: Chix 62_Infected_Day 7


title: Chix 61_Infected_Day 7


title: CD4CD8 CONTROL2

source_name: Control CD4+ CD8+ thymocytes

value: Normal DP thymocytes


title: Chix 60_Infected_Day 7


title: Chix 49_Control_Day 5

value: Day 5


title: Chix 47_Control_Day 5


title: Chix 48_Control_Day 5


title: Chix 43_Infected_Day 5


title: Chix 46_Control_Day 5


title: CD4CD8 CONTROL1


title: Chix 45_Control_Day 5


title: 3aKO NICD2-1

source_name: Dnmt3a-null NICD T-ALL

value: Dnmt3a-null NICD T-ALL blasts


title: Chix 44_Infected_Day 5


title: 3aKO NICD1-3


title: Chix 41_Infected_Day 5


title: 3aKO NICD1-2


title: Chix 40_Infected_Day 5


title: Chix 68_Control_Day 7


title: Chix 42_Infected_Day 5


title: Chix 64_Infected_Day 7


title: Chix 29_Control_Day 3

value: Day 3


title: CD4CD8 CONTROL3


title: Chix 28_Control_Day 3


title: Chix 27_Control_Day 3


title: 9 WT_1-1

data_processing:
Low quilty reads and nucleotide was trimed by using trimmomatic, and then were aligned to mouse mm9 assembly by using STAR
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

growth_protocol: WT and Dnmt3a knockout c-Kit+ hematopoietic progenitors were transduced with a retrovirus expressing Notch Intracellular Domain (NICD).  Cell were transplaned into lethally irradiated mcie, and mice were sacrificed when they became moribund with T-cell acute lymphoblastic leukemia (T-ALL).  At the time of euthanasia, GFP+ T-ALL blasts were purified from the bone marrow by flow cytometry for extraction of RNA

extract_protocol:
NucleoSpin RNA XS Kit (Machery-Nagel)
SMARTer kit (Clontech), HiSeq 1x50 (Illumina )


title: PbKin- AL mouse3

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

data_processing:
RNA-seq reads were mapped to the reference genome with TopHat software
Differentially expressed genes were selected using P. berghei genome annotations from Ensembl (Genome Assembly: May 2010) and Cufflinks tool
Genome_build: Genome Assembly: May 2010 (http://protists.ensembl.org/Plasmodium_berghei/Info/Annotation/#assembly)
Supplementary_files_format_and_content: Processed data file contains FPKM values for P. berghey genome annotations from Ensembl () using Cufflinks

organism: Plasmodium berghei

source_name: Blood stages

growth_protocol: Plasmodium berghei parasites were propagated in BALB/c mice

extract_protocol:
The total mRNA was extracted using the Trizol reagent and Magnetic mRNA Isolation Kit (NEB) according to manufacturer instructions
First strand cDNA was synthesized with Random Hexamer primers and SuperScript III Reverse Transcriptase (Life Technologies), following the manufacturer’s instructions. The DNA/RNA hybrids were purified using Agencourt AMPure XP beads and the 2nd strand was synthesized using dUTP nucleotide mix, DNA Polymerase I (E. coli) and RNAse H (NEB) by 2.5 hours of incubation at 16°C. CDNA was fragmented to approximately 200 nucleotides using Covaris S220 System. The fragments were end-repaired, TA-tailed and ligated to Illumina adaptors with index barcodes using NEBNext kits according to manufacturer instructions. Excess adaptors were removed with 2 rounds of clean up with 50μl of Agencourt AMPure XP beads (Beckman Coulter). Final libraries were eluted in 30μl water, visualized on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR. A pool of the indexed libraries was sequenced on an Illumina HiSeq2000, with 100bp paired-end reads.

treatment_protocol: BALB/c mice were on a moderate dietary restriction protocol (food intake decreased by 30-40%) prior and during P. berghei infection

tag: mouse stain

value: BALB/c

tag: dietary regiment

value: control

tag: parasite line

value: KIN mutant

tag: age (hours post invasion)


title: 8 WT_1-1


title: Chix 26_Control_Day 3


title: 3aKO_1-3


title: 3aKO_2-1


title: PbWT DR mouse1

value: dietary restriction

value: wild type


title: PbWT AL mouse3


title: PbKin- DR mouse3


title: 3aKO_1-2


title: PbKin- DR mouse2


title: Chix 25_Control_Day 3

value: White Leghorn

value: Hayflick's only


title: PbKin- AL mouse1


title: Chix 24_Infected_Day 3


title: WT_2-3

value: WT NICD T-ALL blasts


title: PbWT DR mouse3


title: Control_3

value: Freshly isolated from moribund mice


title: Chix 22_Infected_Day 3


title: Chix 20_Infected_Day 3


title: 3aKO_1-1


title: PbWT AL mouse2


title: LPS DC+MSK inh.+C5a  donor 6

city: Amsterdam

first: Anouk

last: Zaal

state: NH

address: Plesmanlaan 125

department: Immunopathology

country: Netherlands

institute: Sanquin Research

data_processing:
The RNA library was sequenced on an Illumina HiSeq 2000 platform (single read 50bp+7bp index)
The single read sequence reads (~7-13 million reads per sample) were mapped against the human genome (NCBI build 37) using Tophat 2.0.6 software.
The readcounts (raw counts) were determined using HTseq-count (Ensemble version 75)
To identify statistically relevant differences in mRNA expression the “DESeq2” (v1.4.5) package in R (v3.1) [29] was used and the readcounts obtained from HTseq-count.
The cpm normalization used by DESeq2 is counts per million x size factor, where size factor is computed by library size. These normalized counts were subsequently subjected to a Wald test with a Benjamini-Hochberg (false discovery rate, FDR) correction for multiple testing and additionally yields a log2 fold change for each comparison. Four pairwise comparisons were made: (1) unstimulated moDC vs LPS-stimulated moDC, (2) unstimulated moDC vs C5a-stimulated moDC, (2) LPS-stimulated moDC vs LPS-stimulated moDC plus C5a, and (3) LPS-stimulated moDC vs LPS-stimulated moDC plus C5a in the presence of the MSKII inhibitor.
Genome_build: NCBI build 37
Supplementary_files_format_and_content: tab-delimited raw count matrix

organism: Homo sapiens

source_name: monocytes

growth_protocol: Human monocyte-derived dendritic cells of 4 independent donors were generated by culturing monocytes in Cellgro DC serum-free medium supplemented with Penicillin/Streptomycin (100U/mL), GM-CSF (1000IU/mL) and IL-4 (800IU/mL) for 6-7 days at 37˚C, 5% CO2. Prior to stimulation, moDC were plated for 2 hours at a concentration of 2.0x10^6 cells/well.

extract_protocol:
RNA was harvested using peqGold Trifast reagent (Peqlab, Erlangen, Germany). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: human monocyte-derived dendritic cells (moDC) were stimulated for 2 hours in the absence and presence of LPS (50ng/mL) and C5a (10nM). In case of stimulation with both LPS and C5a, the two compounds were added simultaneously. In case of LPS stimulated moDC, also conditions were included in which the MSK inhibitor SB-747561 (1μM) was added 30 minutes prior to TLR stimulation.

value: monocyte-derived dendritic cells

tag: stimulation

tag: donor


title: Chix 23_Infected_Day 3

tag: host breed

tag: infection

value: Infected


title: Chix 8_Control_Day 1

value: Control

tag: infectious agent

tag: time

value: Day 1


title: LPS DC+MSK inh.  donor 6


title: Control_2

value: Normal DP thymocytes


title: Chix 21_Infected_Day 3

value: M. gallisepticum Rlow


title: Control_1


title: PbKin- DR mouse1


title: Chix 7_Control_Day 1


title: LPS DC donor 6

value: 50ng/ml LPS


title: Chix 9_Control_Day 1


title: PbKin- AL mouse2


title: PbWT AL mouse1


title: GH infusion_14d male liver pool 3_polyA-selected_G96_M7

description: poly-A selected RNA, unstranded library

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene. Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; this counting thus excludes sequence reads that map to an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results comparing cGH-treated male mouse livers to sham-treated male mouse livers; The raw sequencing data for the sham-treated controls is found in GEO series GSE66140, samples GSM1612771, GSM1612772, and GSM1612773.

extract_protocol:
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was polyA-selected and sequencing libraries were prepared using the Illumina TruSeq RNA library preparation kit (Illumina, cat# RS-122-2001), according to the manufacturer's instructions.

treatment_protocol: Male CD1 mice, 8–9 weeks of age, were purchased from Charles River Laboratories  (Crl:CD1(ICR)). Alzet osmotic pumps (model 1007D) were filled with recombinant rat GH and were implanted subcutaneously under ketamine and xylazine anesthesia. GH was infused at a rate of 25 ng/g body weight/h for either 10 h or 14 d.

value: Crl:CD1(ICR) (Charles River, strain code #022)

value: Continuous GH 14 days

tag: Sex

value: Male

tag: age

value: 8-9 weeks


title: Chix 5_Infected_Day 1


title: MethylC-seq on 6 pooled L. albipes social adult females

city: Griffin

first: Brendan

middle: G.

last: Hunt

state: GA

address: 125 Redding Building, Griffin Campus, 1109 Experiment Street

department: Entomology

institute: University of Georgia

description: MethylC–seq

data_processing:
Data were mapped to the Dufourea novaeangliae v1.1 genome, the Lasioglossum albipes OGSv5.42 genome, and the Neodiprion lecontei v1.0 genome respectively
MethylC-seq analysis were performed as described in Glastad et al. (In submission) : Variation in DNA methylation is not consistently reflected by CpG depletion or sociality in Hymenoptera
Genome_build: Dufourea novaeangliae v1.1 genome (http://hymenopteragenome.org/beebase/sites/hymenopteragenome.org.beebase/files/data/consortium_data/Dufourea_novaeangliae.fa.gz), the Lasioglossum albipes OGSv5.42 genome (http://hymenopteragenome.org/beebase/sites/hymenopteragenome.org.beebase/files/data/consortium_data/Lalb_v2.fa.gz), and the Neodiprion lecontei v1.0 genome (Nlec1.0)
Supplementary_files_format_and_content: tab delimited text file, <scaffold> <position> <fraction methylated reads> <number of methylated reads> <number of unmethylated reads> <Benjamini-Hochberg corrected binomial test result>

organism: Lasioglossum albipes

source_name: genomic DNA

extract_protocol: Genomic DNA was extracted from individual whole bodies of these three species using a standard phenol-chloroform protocol, then pooled for bisulfite conversion and sequencing of a single library per species.

tag: collection method

value: caught as adult in Rimont and Aillac, France

tag: tissue

value: 6 pooled whole-bodies

value: adult


title: LPS DC+C5a donor 6

tag: cell type

value: 50ng/ml LPS+10nM C5a


title: E18.5#2

description:
Bulk-cell_RNA-seq_Read_Count.txt.gz
Bulk-cell_RNA-seq_Pooled_Normalized_TPM.txt.gz

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (GRCm38/mm10) using TopHat (v2.1.0) with parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq1 input_fastq2”.
HTSeq (v0.6.0) was used to count the number of reads mapped to each gene with parameters “htseq-count -f bam -r pos -s reverse -a 30 input_bam gtf”.
Reads of two biological replicates were pooled.
TPM (Transcripts Per Million) was employed to quantify gene expression levels.
TPM data was normalized by size factors calculated on all genes.
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and TPM values for each sample

extract_protocol:
Total RNA from about 200,000 DLK+ cells was extracted with the RNeasy Micro Kit (Qiagen, 74004). Poly(A) RNA was purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490).
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB, #E7420) according to the manufacturer’s instructions.

value: hepatoblast/hepatocyte

tag: cell marker

value: DLK+


title: Chix 3_Infected_Day 1

value: White Leghorn


title: Chix 2_Infected_Day 1

value: Infected


title: ChIP_SKOV-3_H3K27ac

city: Leuven

first: Hana

last: Imrichova

address: Herestraat, 49

country: Belgium

institute: KU Leuven

data_processing:
Sequence reads were mapped to the reference genome (hg19-Gencode v18) using Bowtie2 2.1.0
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Narrow peaks were called by MACS2 algorithm (MACS version 2.1.0.20150603), using q-value < 0.001.

source_name: ovarian cancer cell line

growth_protocol: The cell lines were grown to ~85% confluence per 15-cm dish.

extract_protocol:
A total of 20 million cells per sample were collected, yielding ~20 fractions of chromatin. Chromatin was extracted using the MagnaChIP-seq kit (millipore).Sonication was performed for 12 cycles, 30 sec pulses using the biorupter
Anti-histone H3 acetyl K27 antibody (ab4729, Abcam) antibody was used for ChIP. Per sample, 5–30 ng of precipitated DNA or input was used to perform library preparation according to the Illumina TruSeq DNA Sample preparation guide. In brief, the immunoprecipitated DNA was end-repaired, A-tailed and ligated to diluted sequencing adapters (1/100). After PCR amplification (15–18 cycles) and bead purification (Agencourt AmpureXp, Analis), the libraries were sequenced using the HiSeq 2500 (Illumina).

tag: cell line

value: ovarian

tag: antibody

value: H3K27ac (ab4729, abcam)

tag: used medium

value: McCoy’s 5a minimal essential medium supplemented with FBS


title: PbWT DR mouse2

tag: mouse stain

value: BALB/c

tag: dietary regiment

value: dietary restriction

tag: parasite line

value: wild type


title: Chix 6_Control_Day 1

value: Control

value: Hayflick's only

value: Day 1


title: Chix 4_Infected_Day 1

value: M. gallisepticum Rlow


title: imDC+C5a  donor 6

value: monocyte-derived dendritic cells

tag: stimulation

value: 10nM C5a

tag: donor


title: LPS DC donor 5

value: 50ng/ml LPS


title: LPS DC+MSK inh.  donor 5


title: E17.5#2

value: hepatoblast/hepatocyte


title: Chix 1_Infected_Day 1

tag: host breed

tag: infection


title: E18.5#1

value: DLK+


title: LPS DC+C5a donor 5

value: 50ng/ml LPS+10nM C5a


title: imDC  donor 6

value: no stimulation


title: Embryo with Coloboma 7

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.18, with Bowtie 1.1.1 for alignment. RSEM was run with option “--forward-prob 0” to take into account that the RNA-seq libraries were strand-specific
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

organism: Danio rerio

source_name: embryo with coloboma

growth_protocol: embryos were produced from natural pair matings of double zic2 heterozygous carriers and allowed to develop in embryo medium at 29C until ~25 hours post fertilization.

extract_protocol:
Illustra RNA spin mini RNA isolation kit (GE healthcare).
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol

tag: genotype background

value: zic2aGBT133/+; zic2bUW1127/+  incross

tag: developmental stage

value: ~ 25 hpf

tag: embryo phenotype

value: embryo with coloboma


title: ChIP_COLO-205_H3K27ac

source_name: colon cancer cell line

value: colon

value: H3K27ac (ab4729, abcam)

value: RPMI supplemented with FBS


title: LPS DC+MSK inh.+C5a  donor 5


title: E16.5#2

source_name: Liver

tag: age


title: imDC  donor 5


title: Embryo with Coloboma 4


title: Embryo with Coloboma 6


title: E17.5#1


title: BPA F_2

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

data_processing:
base call files were processed and deconvoluted using bcl2fastq
fastq files were subjected to QC analysis using FASTQC and adapter sequences were trimmed using cutadapt.
RNA-Seq reads were aligned to hg38 genome using HISAT2 aligner. Parameters: --rna-strandedness FR -q -x <hisat_indexes> -1 <read1.fastq> -2 <read2.fastq> -S <alignment.sam> 2> <summary.txt>
SAM files were converted to sorted and indexed BAM files using SAMtools
BAM files were uploaded to Qlucore Omic Explorer along with the GTF known genes file from UCSC. Read counts were calculated using a modified TMM algorithm which incorporates a normalisation, a correction for transcript length and a log transformation. Normalised read counts were subjected to ANOVA analysis in Omics Explorer.
Genome_build: hg38
Supplementary_files_format_and_content: matrix table of normalised abundance measurements - exported from Omics Explorer

source_name: MCF-7_Bisphenol A

growth_protocol: MCF-7 cells were seeded into 96-well plates with DMEM medium containing 10% FBS at a density of 20,000 cells per well

extract_protocol:
RNA was extracted from cells in culture wells using the RNAdvance Cell V2 kit (Agencourt), which incorporates magentic bead technology for high-throughput processing.
Libraries were prepared using 100ng total RNA using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). RNA was pooled from up to 3 replicate wells for each sample. Ribosomal RNA was removed using the rRNA Depletion kit (Human/Mouse/Rat; New England Biolabs). Briefly, RNA was converted to double stranded cDNA, end repaired, dA-tailed then adaptors were ligated. After USER digestion of second strand DNA (to maintain strandedness), the cDNA library was PCR amplified using indexed PCR adapter-primers (15 cycles). Cleaned libraries were assessed for size distribution using Bioanalyser 2100 High Sensitivity DNA chips, and were quantified using NEBNext Library Quant Kit (New England Biolabs). Libraries were pooled together and sequenced across 2 lanes of a Rapid Run Flowcell with Illumina HiSeq2500; 2x 100 PE.

treatment_protocol: After 24 h of steroid deprivation in hormone free medium (charcoal stripped FBS), the cells were stimulated with test substances for 48 h in triplicate in three independent experiments.

value: Breast cancer cell line

tag: exposure time

tag: experimental group

value: Bisphenol A

tag: replicate

tag: tmm factor


title: imDC+C5a  donor 5

tag: cell type


title: GlyD_2

tag: cell line

value: Glyphosate


title: Embryo with Coloboma 5


title: LPS DC+MSK inh.+C5a  donor 4


title: LPS DC+MSK inh.  donor 4


title: E2H_2

value: Estradiol


title: ChIP_DU-145_H3K27ac

source_name: prostate cancer cell line

tag: tissue

value: prostate

tag: antibody

tag: used medium

value: Eagle minimal essential medium supplemented with FBS


title: Neg_2

value: Negative


title: LPS DC+C5a donor 4

value: monocyte-derived dendritic cells

tag: stimulation


title: E15.5#2

value: hepatoblast/hepatocyte

tag: cell marker

value: DLK+


title: E15.5#1


title: Embryo with Coloboma 3


title: Normal Embryo 7

source_name: normal embryo

value: normal embryo


title: E14.5#2


title: E16.5#1


title: LPS DC donor 4

value: 50ng/ml LPS

tag: donor


title: Normal Embryo 6

value: zic2aGBT133/+; zic2bUW1127/+  incross

value: ~ 25 hpf


title: BAF G_1

source_name: MCF-7_Bisphenol AF

value: Bisphenol AF


title: E13.5#2


title: imDC+C5a  donor 4

value: 10nM C5a


title: BPA F_1


title: Normal Embryo 4


title: Normal Embryo 3


title: E13.5#1


title: imDC  donor 4

value: no stimulation


title: ChIP_OVCAR-3_H3K27ac

value: ovarian

value: H3K27ac (ab4729, abcam)

value: RPMI 1640 medium supplemented with FBS


title: GlyD_1

value: Breast cancer cell line

value: Glyphosate


title: BPA F_3

value: Bisphenol A


title: LPS DC+MSK inh.+C5a  donor 2


title: E12.5#2


title: LPS DC+MSK inh.  donor 2


title: LPS DC+C5a donor 2

value: 50ng/ml LPS+10nM C5a


title: GlyD_3


title: E12.5#1


title: E2H_3

value: Estradiol


title: E11.5#2

value: hepatoblast/hepatocyte


title: imDC+C5a  donor 2

value: monocyte-derived dendritic cells


title: BAF G_2


title: imDC  donor 2


title: E10.5#2

value: DLK+


title: E10.5#1


title: E2H_1


title: Neg_1

value: Negative


title: MethylC-seq on 30 pooled N. lecontei adult females

description: MethylC–seq

organism: Neodiprion lecontei

tag: collection method

value: caught as larvae in Spooner, Wisconsin and reared to adulthood in the Linnen Lab (University of Kentucky)

value: 30 pooled whole-bodies, eggs removed

value: adult


title: MethylC-seq on 4 pooled D. novaeangliae adult females

description: MethylC–seq

organism: Dufourea novaeangliae

value: caught as adult near Lake Ontario

value: 4 pooled whole-bodies


title: SMC1A ChIP-Seq - Replicate 1

status: Public on Jul 13 2017

city: Quebec

first: Steve

last: Bilodeau

state: Quebec

address: 2260 boul. Henri-Bourassa

country: Canada

institute: Centre de recherche du CHU de Québec-Université Laval

description:
SMC1A-Rep1
SMC1A ChIP-Seq - Replicate 1, using a pool of WCE Replicate 1 and WCE replicate 2 as input controls.

data_processing:
All datasets were analyzed with the ChIP-Seq pipeline developed at the McGill University and Génome Québec Innovation Centre (https://bitbucket.org/mugqic/mugqic_pipelinest) (version 2.2.0)
All samples were processed using Trimmomatic 0.33 with the following parameters: LEADING=30, TRAILING=30, SLIDINGWINDOW=4:30, MINLEN=30. Reads were mapped against the hg19 build of the human reference genome using BWA 0.7.12 with default parameters and MACS2 2.1.0 with default parameters was used for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files were generated with MACS2 2.1.0 with default parameters. The enrichment ratio of each replicate were calculated  with the 2 control files available for each cell line.

source_name: SMC1A ChIP-Seq

growth_protocol: The GM12878 cell line was obtained from the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research Institute (Catalog ID: GM12878) and cultured in RPMI 1640 medium (Fisher, MT10040CV) supplemented with 15% fetal bovine serum (Invitrogen, qualified 12483020),  2mM L-glutamine (Gibco, 25030-081), 1X MEM non-essential amino acids (Cellgro, 25-0250) and 1X Penicillin/Streptomycin (Gibco, 15170-063).

extract_protocol:
ChIP-Seq experiments were performed in duplicates as described previously (Fournier et al., 2016). Briefly, 50 million cells were crosslinked for 10 minutes with 1% formaldehyde and quenched with 125mM glycine for 5 min. Then cells were washed with PBS, pelleted, flash frozen and stored at -80°C.  Sonicated DNA fragments were immunoprecipitated with antibodies directed against NIPBL (Bethyl Laboratories, A301-779A), SMC1A (Bethyl Laboratories, A300-055A) and MED1 (Bethyl Laboratories, A300-793A).
The TruSeq DNA sample prep kit with indexing adapters was used according to the manufacturer's recommendations (Illumina)

treatment_protocol: No treatment.

value: LCL from B-Lymphocyte

tag: chip antibody

value: SMC1A (Bethyl, A300-055A)


title: WCE - Replicate 1

source_name: WCE


title: MED1 ChIP-Seq - Replicate 2

description:
MED1-Rep2
MED1 ChIP-Seq - Replicate 2, using a pool of WCE Replicate 1 and WCE replicate 2 as input controls.

source_name: MED1 ChIP-Seq

value: MED1 (Bethyl, A300-793A)


title: MED1 ChIP-Seq - Replicate 1

description:
MED1-Rep1
MED1 ChIP-Seq - Replicate 1, using a pool of WCE Replicate 1 and WCE replicate 2 as input controls.


title: SMC1A ChIP-Seq - Replicate 2

description:
SMC1A-Rep2
SMC1A ChIP-Seq - Replicate 2, using a pool of WCE Replicate 1 and WCE replicate 2 as input controls.


title: LPS DC donor 2

value: 50ng/ml LPS


title: NIPBL ChIP-Seq - Replicate 1

description:
NIPBL-Rep1
NIPBL ChIP-Seq - Replicate 1, using a pool of WCE Replicate 1 and WCE replicate 2 as input controls.

source_name: NIPBL ChIP-Seq

value: NIPBL (Bethyl, A301-779A)


title: MV4;11_JQ1-PA_RNA-seq Rep 3

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: Replicate 3

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using tophat2 and bowtie2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genes with a false discovery rate below 0.05 and a fold‐change greater than 2 were considered significantly differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of normalised expression values for all Samples

molecule: polyA RNA

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with 20% fetal calf serum, penicillin (100 units/mL) and streptomycin (100 ug/mL)

extract_protocol:
RNA was prepared using the Qiagnen RNeasy kit
TruSeq RNA Sample Preparation protocol (Illumina)

treatment_protocol: Cell lines were grown in 0.1% DMSO, 500nM JQ1 or 500nM JQ1–PA

tag: tissue source

value: peripheral blood

value: macrophage

tag: treated with


title: MV4;11_JQ1-PA_RNA-seq Rep 1

description: Replicate 1


title: MV4;11_JQ1_RNA-seq Rep 3

description: Replicate 3


title: MV4;11_JQ1-PA_RNA-seq Rep 2

description: Replicate 2


title: Neg_3

value: Breast cancer cell line


title: MV4;11_JQ1_RNA-seq Rep 2

description: Replicate 2


title: MV4;11_JQ1_RNA-seq Rep 1

description: Replicate 1


title: E11.5#1

tag: age

value: hepatoblast/hepatocyte


title: MV4;11_DMSO_RNA-seq Rep 2

description: Replicate 2

value: DMSO


title: MV4;11_DMSO_RNA-seq Rep 3

description: Replicate 3


title: MV4;11_DMSO_RNA-seq Rep 1

description: Replicate 1


title: MV411_input

description: Minput

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using bwa 0.6.2-r126
Peak-calling was performed using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bed files from MACS2 for each sample

source_name: MV4;11 cell line

growth_protocol: MV4;11 cells were grown in RPMI-1640 supplemented with 20% FBS, penicillin (100 U/mL), streptomycin (100 µg/mL). K562 cells were grown in MEM medium supplemented with 1% pyruvate, 1% NAA and 10% FBS.

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and digested with micrococcal nuclease to mononucleosomes, then incubated with the clickable molecule with/without competitor. Chem-precipitation was performed with pre-clicked biotin-tetrazine conjugated beads
NEBNext ChIP-seq library prep master mix set

tag: clickable molecule

tag: competitor molecule


title: MV411_JQ1-TCO+JQ1


title: WCE - Replicate 2


title: MV411_JQ1-TCO


title: K562_input

description: Kinput

source_name: K562 cell line

value: bone marrow


title: MV411_IBET-TCO

value: IBET–TCO


title: K562_IBET-TCO+IBET

value: IBET


title: K562_JQ1-TCO+JQ1


title: MV411_input_rep2

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and digested with micrococcal nuclease to mononucleosomes, then immunoprecipitated with antibody
NEBNext ChIP-seq library prep master mix set


title: K562_JQ1-TCO


title: MV4;11_input_DNA

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then chem-precipitation was performed with pre-clicked JQ1 biotin conjugated beads
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)


title: MV4;11_JQ1–PA click-seq


title: NIPBL ChIP-Seq - Replicate 2

description:
NIPBL-Rep2
NIPBL ChIP-Seq - Replicate 2, using a pool of WCE Replicate 1 and WCE replicate 2 as input controls.


title: K562_input_rep2


title: K562_input_rep1


title: MV411_BRD4_rep2

value: anti-BRD4 (E2A7X, Cell Signalling)


title: MV4;11_input DNA

description: input

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)


title: K562_BRD4_rep1


title: BAF G_3

tag: exposure time

tag: experimental group

value: Bisphenol AF

tag: replicate


title: K562_BRD4_rep2

tag: cell line


title: MV4;11_C/EBPα_ChIP

description: C/EBPalpha

value: anti-C/EBPα (EP709Y, Abcam)


title: K562_IBET-TCO

tag: tissue


title: MV4;11_C/EBPβ_ChIP

description: C/EBPbeta

value: anti-C/EBPβ (E299, Abcam)


title: MV411_BRD4_rep1


title: MV411_IBET-TCO+IBET


title: RNA_VSG_rep2

city: Duarte

first: Juan

last: Du

state: CA

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

description:
RNA_FPKM.txt
RNA-DEseq-ShamvsVSG.txt

data_processing:
[FAIRE-seq] Illumina Casava software was used for basecalling.
[FAIRE-seq] Sequenced reads were aligned to the mouse mm9 reference genome using bowtie1 and only reads that could be mapped to single genomic location were retained (Langmead, Trapnell et al. 2009). Mapped reads were filtered to exclude improperly paired reads and PCR duplicates. Wiggle tracks were generated and viewed on the UCSC genome browser (Kent, Sugnet et al. 2002).
[FAIRE-seq] To identify accessible chromatin sites from FAIRE-seq reads, F-seq was used with default parameters and a 250 bp feature length (Boyle, Guinney et al. 2008). Irreproducible discovery rate (IDR) framework were then used to find reproducible peaks between two replicates (Li, Brown et al. 2011). A union set of chromatin sites among different conditions are generated by mergeBed function from BEDTools (Quinlan and Hall 2010).
[FAIRE-seq] To access the global chromatin accessibility across different conditions, the normalized read counts (Hicks and Irizarry 2015) for each sites were obtained. To identify chromatin sites with variable accessibility between different conditions, we input the read counts at each sites into DESeq2 (Du, Leung et al. 2016).
[RNA-seq] Illumina Casava software was used for basecalling.
[RNA-seq] Sequenced reads were aligned to the mouse mm9 reference genome with TopHat2 (Hsu, Kent et al. 2006).
[RNA-seq] Transcript expression was quantified by HTSeq (Anders, Pyl et al. 2015), and DESeq2 was utilized to identify differentially expressed genes. The common genes that are differentially expressed in Control vs Sham and Sham vs VSG groups are defined as reversible genes.
[RNA-seq] Transcript abundance was quantified by fragments per kilobase of exon per million fragments mapped (FPKM) using Cufflinks (Trapnell, Williams et al. 2010).
Genome_build: mm9
Supplementary_files_format_and_content: [FAIRE-seq] bigWig files: aligned and filtered FAIRE-seq data
Supplementary_files_format_and_content: [FAIRE-seq] narrowPeaks files: reproducible peaks identified from FAIRE-seq data
Supplementary_files_format_and_content: [FAIRE-seq] bed files: identified variable chromatin peak files (4 files)
Supplementary_files_format_and_content: [RNA-seq] tab-delimited text files: include FPKM values for each Sample
Supplementary_files_format_and_content: [RNA-seq] tab-delimited text files: include DESeq2 results

growth_protocol: C57BL/6J wild-type male mice were purchased from the Jackson Laboratory (Bar Harbor, ME). Mice were maintained in a pathogen-free animal facility under a standard 12h:12h light/dark cycle and fed standard rodent chow and water ad libitum. All procedures followed the NIH guidelines and the study was approved by the City of Hope Institutional Animal Care and Use Committee (IACUC). Mice of 8 weeks’ old received 60 kcal% saturated HFD (Research Diets, New Brunswick, NJ, D12492) for 14 weeks, and were then randomly subdivided into two bodyweight matched groups (VSG and Sham), respectively, prior to gastric surgery. The mice were maintained on HFD 14 weeks after surgery except the recovery during the immediate postoperative period. The mice in Control group were maintained on normal chow for 28 weeks.

extract_protocol:
[FAIRE-seq] Formaldehyde Isolation of Regulatory Elements (FAIRE) was performed as described previously (Leung, Parks et al. 2014).
[FAIRE-seq] FAIRE DNA was barcoded and sequenced on the HiSeq 2500 to generate 100 × 100-bp paired-end reads.
[RNA-seq] RNA was extracted from the same livers used for FAIRE using TRIzol (Invitrogen). RNA was poly(A)-enriched (Illumina TruSeq RNA Library Prep).
[RNA-seq] PolyA RNA was sequenced with Illumina protocols on a HiSeq 2500 to generate 50-bp reads.

treatment_protocol: VSG surgery: The lateral about 80% of the stomach was resected, leaving a tubular gastric remnant in continuity with the esophagus superiorly and the pylorus and duodenum inferiorly as previous reported (Ryan, Tremaroli et al. 2014). The sham procedure involved analogous isolation of the stomach followed by manually applying pressure with blunt forceps along a vertical line between the esophageal sphincter and the pylorus. Mice consumed liquid diet (Osmolite One Cal) for the first 4 postoperative days. Then all animals transitioned onto regular chow pellets of the designated diet as indicated by the study.

tag: strain

tag: gender

value: male

tag: diet

value: HFD

tag: surgery

value: VSG

value: liver


title: RNA_VSG_rep1

description:
RNA_FPKM.txt
RNA-DEseq-ShamvsVSG.txt


title: GATA6_CHIP

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

data_processing:
Samples were sequenced on Illumina HiSeq 2000
Alignment to the Human genome build hg19 was performed using Bowtie2 with option -k 1
Peak calling was done using MACS2 2.1.0 with FDR 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bdg files were generated using MACS2

source_name: hES-Derived Definitive Endoderm cells

growth_protocol: H1 hESCs containing dox-inducible Avi-tagged hGATA6 and BirA transgenes were differentiated into definitive endoderm by treatment with Activin A (4 days), and BMP4 and bFGF (first two days) in RPMI 1640 medium

extract_protocol:
Cells were crosslinked for 10 minutes with 1% formaldehyde, which was quenched with 125mM glycine.  The cells were washed 3X with ice cold PBS+protease inhibitors+PMSF, and scraped into tubes.  Chromatin was sheared in a Diagenode Bioruptor Pico to 150-600bp fragments.  Input chromatin was saved for "input sample" and the remainder of the chromatin was pulled down using streptavidin beads.  Bound chromatin and input DNA samples had the crosslinks reversed, the DNA was purified by phenol/chloroform extraction and ethanol precipitation, and the purified DNA samples were submitted to Beijing Genomics Institute for Library Generating and Sequencing.
Library generated by Beijing Genomics Institute

treatment_protocol: Cells were treated with 1ug/mL doxycycline for 24 hours prior to harvest

tag: passage

value: Between 40-50

tag: line

tag: pulldown method

value: Magnetic Streptavidin Beads


title: GATA6_INPUT

value: Input - N/A


title: MV4;11_JQ1 click-seq

tag: tissue source

value: peripheral blood


title: RNA_Sham_rep1

description:
RNA_FPKM.txt
RNA-DEseq-CtlvsSham.txt
RNA-DEseq-ShamvsVSG.txt

value: Sham


title: RNA_Sham_rep2


title: MV411_input_rep1

tag: chip antibody


title: RNA_Ctl_rep2

description:
RNA_FPKM.txt
RNA-DEseq-CtlvsSham.txt

value: Ctl

value: NoSurgery


title: RNA_Ctl_rep1

description:
RNA_FPKM.txt
RNA-DEseq-CtlvsSham.txt


title: FAIRE_Ctl_rep2

description:
FAIRE_Ctl.bw
FAIRE_Ctl_Peaks.npf
FAIRE_reversible_ShamUp.bed
FAIRE_reversible_ShamDown.bed


title: FAIRE_VSG_rep1

description:
FAIRE_VSG.bw
FAIRE_VSG_Peaks.npf
FAIRE_ShamvsVSG_ShamUp.bed
FAIRE_ShamvsVSG_VSGUp.bed
FAIRE_reversible_ShamUp.bed
FAIRE_reversible_ShamDown.bed


title: FAIRE_VSG_rep2


title: FAIRE_Sham_rep1

description:
FAIRE_Sham.bw
FAIRE_Sham_Peaks.npf
FAIRE_ShamvsVSG_ShamUp.bed
FAIRE_ShamvsVSG_VSGUp.bed
FAIRE_reversible_ShamUp.bed
FAIRE_reversible_ShamDown.bed


title: FAIRE_Sham_rep2


title: FAIRE_Ctl_rep1


title: KO_3

city: San Francisco

first: Jeremy

last: Reiter

address: 555 Mission Bay Blvd South

institute: University of California, San Francisco

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed of any presence of the Illumina adapter, then mapped to GRCm38.78 whole genome using rna-STAR
Unique alignments were aggregated across all isoforms on a per-gene basis, using only reads mapping to exons, using rna-STAR.
Normalization and differential expression estimation was performed using DESeq: Anders S and Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology, 11, pp. R106.
Genome_build: GRCm38.78 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include raw per-gene values for each sample

source_name: fibro/adipogenic progenitors (FAPs)

extract_protocol:
Total RNA from purified FAPs was isolated using the Qiagen RNAeasy Micro Kit
The TruSeq Stranded Total RNA Library Prep Kit (Ilumina) was used to generate the library according the manufactor's instructions
RNA-Seq, platform Illumina 2500 SE 50bp RNAseq

value: mixed background

value: tibialis anterior muscle

tag: cell type

value: FAPs

tag: injury time point

value: 3 days post glycerol injury

tag: genotype

value: FAP-no cilia


title: KO_2


title: Ctrl_3

value: FAP-ctrl


title: Ctrl_1


title: Ctrl_5


title: Ctrl_4


title: Ctrl_2


title: KO_1


title: JQ1-PA click-seq Rep 2

tag: clickable molecule


title: JQ1–TCO click-seq Rep 2


title: JQ1–TCO click-seq Rep 1


title: Hepatitis B virus infected patient 5

city: Chengdu

first: Dan

last: Xie

state: Sichuan

address: #17 Renmin Road

department: West China Hospital

institute: Sichuan University

description: 5hmC capture sequencing of cell free DNA

data_processing:
bcl-fastq base-calling
bowtie2 2.2.5 alignment
samtools 0.1.19 filtering
bedtools for reads counting and rpkm calculation
N/A
Genome_build: hg19
Supplementary_files_format_and_content: rpkm matrix

molecule: other

source_name: Hepatitis B virus infected patient 5

growth_protocol: not applicable

extract_protocol:
Samples for healthy subjects were obtained from Stanford blood center. HCC and BrCa patients were recruited in a Stanford University Institutional Review Board-approved protocol. LuCa, PaCa, GBM, GaCa and CoCa patients were recruited in a Sichuan University Institutional Review Board-approved protocol. Blood was collected into EDTA-coated Vacutainers. Plasma was collected from the blood samples after centrifugation at 1,600 × g for 10 min at 4 °C and 16,000 × g at 10 min at 4 °C. cfDNA was extracted using the Circulating Nucleic Acid Kit (Qiagen). Whole blood genomic DNA was extracted using the DNA Mini Kit (Qiagen) and fragmented using dsDNA Fragmentase (NEB) into average 300 bp. DNA was quantified by Qubit Fluorometer (Life Technologies). Cell-free RNA was extracted using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Norgen). The extracted cell-free RNA was further digested using Baseline-ZERO DNases (Epicentre) and depleted using Ribo-Zero rRNA Removal Kit (Epicentre) according to a protocol from Clontech.
cfDNA (10 ng) or fragmented genomic DNA (1 µg) spiked with amplicons (0.001 pg of each amplicon per 10 ng DNA) was end repaired, 3’-adenylated and ligated to DNA Barcodes (Bioo Scientific) using KAPA Hyper Prep Kit (Kapa Biosystems) according to the manufacturer’s instructions. Ligated DNA was incubated in a 25 µl solution containing 50 mM HEPES buffer (pH 8), 25 mM MgCl2, 100 µM UDP-6-N3-Glc (Active Motif), and 12.5 U βGT (Thermo) for 2 hr at 37 °C. After that, 2.5 μL DBCO-PEG4-biotin (Click Chemistry Tools, 20 mM stock in DMSO) was directly added to the reaction mixture and incubated for 2 hr at 37 °C. Next, 10 µg sheared salmon sperm DNA (Life Technologies) was added into the reaction mixture and the DNA was purified by Micro Bio-Spin 30 Column (Bio–Rad). The purified DNA was incubated with 0.5 µL M270 Streptavidin beads (Life Technologies) pre-blocked with salmon sperm DNA in buffer 1 (5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl and 0.2% Tween 20) for 30 min. The beads were subsequently undergone three 5-min washes each with buffer 1, buffer 2 (buffer 1 without NaCl), buffer 3 (buffer 1 with pH 9) and buffer 4 (buffer 3 without NaCl). All binding and washing were done at room temperature with gentle rotation. Beads were then resuspended in water and amplified with 14 (cfDNA) or 9 (blood genomic DNA) cycles of PCR amplification using Phusion DNA polymerase (NEB). The PCR products were purified using AMPure XP beads. Separate input libraries were made by direct PCR from ligated DNA without labeling and capture. Pair-end 75 bp sequencing was performed on the NextSeq instrument.

treatment_protocol: not applicable

tag: sample name

value: blood

tag: target molecule

value: cell-free DNA


title: Hepatitis B virus infected patient 6

source_name: Hepatitis B virus infected patient 6


title: Hepatitis B virus infected patient 7

source_name: Hepatitis B virus infected patient 7


title: Hepatitis B virus infected patient 4

source_name: Hepatitis B virus infected patient 4


title: Hepatitis B virus infected patient 2

source_name: Hepatitis B virus infected patient 2


title: Hepatitis B virus infected patient 3

source_name: Hepatitis B virus infected patient 3


title: triple_plusrap_Rpb1

city: Boston

first: Natalia

last: Petrenko

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

description: Chip-seq of Rpb1 subunit of Pol II

data_processing:
map using Bowtie in Galaxy (Penn State). Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 .
Sam-to-Bam using Galaxy
Bam-to-Bed using Galaxy
MACS using Galaxy to create a shifted raw tag count at every bp in a wiggle file and save as bigwig. All libraries have an average fragment size of 200-300, except srb4_minusrap_Rpb1 and srb4_plusrap_Rpb1, which are 80-200
for plotting, normalize to # of sequenced reads
Genome_build: sacCer3
Supplementary_files_format_and_content: every processed file contains a shifted raw tag count at every bp in a bigwig file. SGR files are made from Bed files and can be visualized via Integrated Genome Browser

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae_NP86

extract_protocol:
as described in Fan, X., Lamarre-Vincent, N., Wang, Q., and Struhl, K. (2008). Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucl. Acids Res. 36, e125.
as described in Wong, K.-H., Jin, Y., and Moqtaderi, Z. (2013). Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol Chapter 7, Unit 7.11.


title: triple_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: Breast cancer 3

source_name: Breast cancer 3


title: Hepatitis B virus infected patient 1

source_name: Hepatitis B virus infected patient 1


title: Breast cancer 4

source_name: Breast cancer 4


title: Colon cancer 4

source_name: Colon cancer 4


title: Colon cancer 3

source_name: Colon cancer 3


title: rpb1-AA_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_NP2


title: triple_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: Breast cancer 2

source_name: Breast cancer 2


title: Breast cancer 1

source_name: Breast cancer 1


title: triple_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: Colon cancer 2

source_name: Colon cancer 2


title: Colon cancer 1

source_name: Colon cancer 1


title: sin4-AA_plusrap_Rpb1_3

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_KHW257


title: Gastric cancer 4

source_name: Gastric cancer 4


title: rpb1-AA_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: sin4-AA_minusrap_Rpb1_3

description: Chip-seq of Rpb1 subunit of Pol II


title: Gastric cancer 5

source_name: Gastric cancer 5


title: rpb1-AA_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: rpb1-AA_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: Gastric cancer 3

source_name: Gastric cancer 3


title: srb4_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_YJ104


title: med7-AA_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_YJ66


title: srb4_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: Glioblastoma 4

source_name: Glioblastoma 4


title: rgr1-AA_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_KHW258


title: rgr1-AA_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: sin4-AA_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: sin4-AA_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: Gastric cancer 2

source_name: Gastric cancer 2


title: Gastric cancer 1

source_name: Gastric cancer 1


title: Glioblastoma 2

source_name: Glioblastoma 2


title: Glioblastoma 3

source_name: Glioblastoma 3


title: gal11-AA_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_YJ78


title: rdr1/2/6 under control (dsur)

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

data_processing:
17nt RNA sequences obtained from SOLiD sequencing were mapped on Arabidopsis reference genome. If sequence tags are mapped on more than 6 loci, then the sequences are removed. Mapped tag no. of each sample was adjusted to 50 million.
Genome_build: TAIR10 Arabidopsis genome annotation was used.
Supplementary_files_format_and_content: Tag no. was displayed as variablestep in wiggle (WIG) format file.  The position of AGI-annotated genes was shown in BED file.

growth_protocol: Arabidopsis rdr1/2/6 and wild-type plants were grown on MS medium at 22 ºC in the cycle of 16hr light / 8hr dark condition for 2 weeks as described previously (Matsui et al. 2008, Plant Cell Physiol, 49: 1135-1149).

extract_protocol: rRNAs were removed from 100 μg of total RNA twice using RiboMinus Plant Kit for RNA-Seq (Life Technologies). The rRNA-depleted RNAs were ligated with 200 pmol of 5'-end RNA (adaptor 1) by T4 RNA ligase (Takara) at 37 °C for 30 min. 5’ RNA adaptor includes EcoP15I site and P2 site for SOLiD sequencing. Only uncapped RNAs can be ligated to 5’ RNA adaptor at this step. The adaptor-ligated RNAs were subjected to synthesis of single-stranded cDNAs using 100 pmol of RT primer (primer 1) that containing EcoP15I site and random hexamer by SuperScript III (Life Technologies). The single-stranded cDNAs were amplified to double-stranded cDNAs by PCR (94 ˚C, 3 min; (94 ˚C 30 sec; 55 ˚C, 30 sec; 72 ˚C, 8 min) ×10 cycles), using biotin-labled 1st PCR forward primer (primer 2) and 1st PCR reverse primer (primer 3). The PCR products were digested by EcoP15I (NEB) at 37 °C for 16 hr. 　The 5’-end fragments were recovered by biotin capture beads (Takara) and ligated with 3’-end dsDNA adaptor (adaptor 2) at 16 °C for 2 hr. The 3’ adaptor-ligated cDNAs were purified and amplified by PCR {94 ˚C, 3 min; (94 ˚C, 30 sec; 55 ˚C, 30 sec; 72 ˚C, 30 min) ×10 cycles} using 2nd PCR forward primer and reverse primer (primers 4 and 5).  Finally, PCR products (120-130 bp) were recovered and subjected to SOLiD sequencing. Adaptors: 1. 5'-end RNA adaptor: 5'-CTGCTGTACGGCCAAGGCGCAGCAGGG-3', 2. 3’-end dsDNA adaptor 5'-NNTAGTGGCTGACGGGTATCTCTCCTTTCG CCTCCGCATCACC-3', Primers: 1. RT primer: 5’-GTCTCTAGCCTGCAGGATCGATCTATCAGCAGNNNNNNNN-3', 2. Biotin-labled 1st PCR forward primer: 5’-Biotin-CTGCTGTACGGCCAAGGCGCAGCA-3', 3. 1st PCR reverse primer: 5'-GTCTCTAGCCTGCAGGATCGAT-3', 4. 2nd PCR forward primer: 5'-CTGCCCCGGGTTCCTCATTCTCT******CTGCTGTACGGCCAAGGCGCA-3 (******* ：　barcode sequence), 5. 2nd PCR reverse primer:5'-CCACTACGCCTCCGCTTTCC-3'

treatment_protocol: Two-week-old plants were subjected to drought stress treatment as described previously (Matsui et al. 2008, Plant Cell Physiol, 49: 1135-1149).

tag: application

value: 5' end-seq of uncapped RNA

tag: stress

tag: genotype/variation


title: rdr1/2/6 under drought stress (dsur)

value: 2 hr drought


title: wild-type under drought stress (dsur)

source_name: wild-type

tag: stess

value: wild-type


title: med7-AA_plusrap_Rpb1_3

description: Chip-seq of Rpb1 subunit of Pol II

tag: strain


title: med7-AA_minusrap_Rpb1_3

description: Chip-seq of Rpb1 subunit of Pol II


title: Pancreatic cancer 7

source_name: Pancreatic cancer 7

tag: tissue


title: wild-type under control (dsur)


title: srb10-AA_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_KHW256


title: Pancreatic cancer 6

source_name: Pancreatic cancer 6


title: Pancreatic cancer 5

source_name: Pancreatic cancer 5


title: srb6-AA_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_YJ65


title: rdr1/2/6 under control

data_processing:
Adaptor sequences  (downstream of 26 nt color code) were eliminated from  the SOLiD sequence data. They were mapped on Arabidopsis genome, using bowtie software (Langmead et al., 2009). We used the following two-step normalization for data analysis of smRNAs. 1) smRNAs mapped on annotated genes were counted and normalized independently for rdr1/2/6 and WT by adjusting a slope of linear approximate equation between control and drought stress conditions. We used top 10% highly-expressed smRNA loci for the normalization. 2) We used tag numbers mapped on miRNA loci by adjusting a slope of linear approximate equation between rdr1/2/6 and WT, because accumulation of miRNAs is thought to be less affected by loss of RDR1/2/6.
Genome_build: TAIR10 Arabidopsis genome annotation was used.
Supplementary_files_format_and_content: Tag no. was displayed as variablestep in wiggle (WIG) format file.  The position of AGI-annotated genes was shown in BED file.

extract_protocol: smRNAs were extracted from plants using mirVana miRNA Isolation Kit (Life Technologies). smRNA libraries for SOLiD sequencing were constructed according to the protocol of SOLiD Total RNA-Seq Kit (Life Technologies). First, smRNAs were ligated with 5’ adapter and 3’ adapter to generate cDNAs. cDNAs were separated in 8M urea, 7.5% acrylamide gel and 60-80 nt cDNAs were recovered. The cDNAs were amplified by 12-15 cycles of PCR using barcode primers (Life technologies) and subjected to SOLiD sequencing.


title: Glioblastoma 1

source_name: Glioblastoma 1


title: Pancreatic cancer 4

source_name: Pancreatic cancer 4


title: Pancreatic cancer 3

source_name: Pancreatic cancer 3


title: WT_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II

data_processing:
map using Bowtie in Galaxy (Penn State).  Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 .
Sam-to-Bam using Galaxy
Bam-to-Bed using Galaxy (Concatenate the two  kin28-AA_minusrap_Gal11 files).
MACS using Galaxy to create a shifted raw tag count at every bp in a wiggle file and save as bigwig.  All libraries have an average fragment size of 200-300, except the Srb4 libraries, which are 80-200
for plotting, normalize to # of sequenced reads
Genome_build: sacCer3
Supplementary_files_format_and_content: every processed file contains a shifted raw tag count at every bp in a bigwig file

source_name: Saccharomyces cerevisiae_HHY168

extract_protocol:
Genomic DNA extraction protocol as described in Fan, X., Lamarre-Vincent, N., Wang, Q., and Struhl, K. (2008). Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucl. Acids Res. 36, e125. Antibodies used in this study include 9E10 anti-Myc antibodies from Santa Cruz and 8WG16 antibodies from Covance.
Library construction as described in Wong, K.-H., Jin, Y., and Moqtaderi, Z. (2013). Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol Chapter 7, Unit 7.11.


title: wild-type under control


title: gal11-AA_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: tbp-AA_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_KHW76


title: wild-type under drought stress

value: drought


title: WT_plusrap_Rbp1_2

description: Chip-seq of Rpb1 subunit of Pol II

data_processing:
map using Bowtie in Galaxy (Penn State).  Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 .
Sam-to-Bam using Galaxy
Bam-to-Bed using Galaxy
MACS using Galaxy to create a shifted raw tag count at every bp in a wiggle file and save as bigwig.  All libraries have an average fragment size of 200-300, except the Srb4 libraries, which are 80-200
for plotting, normalize to # of sequenced reads
Genome_build: sacCer3
Supplementary_files_format_and_content: every processed file contains a shifted raw tag count at every bp in a bigwig file.  SGR files are made from Bed files and can be visualized via Integrated Genome Browser


title: tbp-AA_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: ATACseq doxcycline rep2

city: Toronto

first: Peter

middle: B

last: Dirks

state: ON

address: 686 Bay St

department: Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Neurosurgery

institute: The Hospital for Sick Children

description: G523NS-ASCL1 KO-pBAC-ASCL1

data_processing:
ATAC-seq reads were aligned to the hg19 genome
Reads were further filtered for duplicates, unmapped contigs, random contigs, overlaps with the ENCODE blacklist, and low quality mappings with samtools and bedtools 2.23
Peaks were called using MACS2 v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files as per the standard MACS2 output format

source_name: genetic knockout of ASCL1 overexpressing ASCL1

growth_protocol: Cells were cultured adherently for 14 days

extract_protocol:
50,000 cells were lysed for nuclei and was incubated with transposase reaction mix for 30 min at 37 degrees.
Libraries were prepared according to Nextera DNA Sample Prep kit. Briefly, library fragments were amplified using 1x NEBnext PCR master mix. Libraries were purified using Qiagen PCR cleanip kit. Libraries were amplified for a total of 13 cycles. Libraries were selected for 240-360bp size fragments.

treatment_protocol: 1 μg/mL doxycycline

value: glioblastoma tumor

tag: derived cell line

value: knockout ASCL1


title: ATACseq doxcycline rep1

description: G523NS-ASCL1 KO-pBAC-ASCL1


title: WT_minusrap_Rbp1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: Pancreatic cancer 2

source_name: Pancreatic cancer 2


title: WT_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: rdr1/2/6 under drought stress


title: rgr1-AA_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_KHW258


title: Pancreatic cancer 1

source_name: Pancreatic cancer 1


title: rgr1-AA_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: Hepatocellular cancer 17

source_name: Hepatocellular cancer 17


title: Hepatocellular cancer 18

source_name: Hepatocellular cancer 18


title: srb10-AA_plusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: srb4-AA_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_YJ104


title: E14.5#1

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

institute: Peking University

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (GRCm38/mm10) using TopHat (v2.1.0) with parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq1 input_fastq2”.
HTSeq (v0.6.0) was used to count the number of reads mapped to each gene with parameters “htseq-count -f bam -r pos -s reverse -a 30 input_bam gtf”.
Reads of two biological replicates were pooled.
TPM (Transcripts Per Million) was employed to quantify gene expression levels.
TPM data was normalized by size factors calculated on all genes.
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and TPM values for each sample

source_name: Liver

extract_protocol:
Total RNA from about 200,000 DLK+ cells was extracted with the RNeasy Micro Kit (Qiagen, 74004). Poly(A) RNA was purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490).
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB, #E7420) according to the manufacturer’s instructions.

tag: age

value: hepatoblast/hepatocyte

tag: cell marker

value: DLK+


title: srb6-AA_minusrap_Rpb1_2

description: Chip-seq of Rpb1 subunit of Pol II


title: ATACseq control rep1

description: G523NS-ASCL1 KO-pBAC-ASCL1

source_name: genetic knockout of ASCL1


title: tbp-AA_plusrap_Rbp1

description: Chip-seq of Rpb1 subunit of Pol II


title: tbp-AA_minusrap_Rbp1

description: Chip-seq of Rpb1 subunit of Pol II


title: Hepatocellular cancer 16

source_name: Hepatocellular cancer 16


title: ASCL1 ChIPseq doxcycline input

data_processing:
ChIP-seq reads were aligned to the hg19 genome and trimmed to positions 6-65 using bowtie2
Alignments were filtered to keep only reads mapping in a concordant pair with samtools 1.3.1
Reads were further filtered for duplicates, unmapped contigs, random contigs, overlaps with the ENCODE blacklist, and low quality mappings with samtools and bedtools 2.23
Peaks were called using MACS2 v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files as per the standard MACS2 output format

source_name: G523NS-ASCL1 KO-pBAC-ASCL1

growth_protocol: Cells were cultured adherently for 18 hrs

extract_protocol:
Lysates were clarified from sonicated nuclei and ASCL1-DNA complexes were isolated with antibody.
Libraries were prepared according to NEBNext ChIP-Seq library preparation protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were selected with Ampure beads. Library was validated by Bioanalzyer and Kapa qPCR assay and sequenced on an Illumina HiSeq 2500 platform, using a Rapid Run mode flowcell to generate paired end reads of 100 bases.

treatment_protocol: 1 ?g/mL doxycycline

tag: tumor

value: glioblastoma


title: Hepatocellular cancer 15

source_name: Hepatocellular cancer 15


title: gal11-AA_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_YJ78


title: ASCL1 ChIPseq negative control input


title: sin4-AA_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_KHW257


title: med7-AA_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_YJ66


title: srb4-AA_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: med7-AA_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: srb10-AA_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_KHW256


title: ASCL1 ChIPseq doxcycline rep3


title: ATACseq control rep2

description: G523NS-ASCL1 KO-pBAC-ASCL1


title: Hepatocellular cancer 13

source_name: Hepatocellular cancer 13


title: Hepatocellular cancer 12

source_name: Hepatocellular cancer 12


title: srb10-AA_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: srb6-AA_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II

source_name: Saccharomyces cerevisiae_YJ65


title: ASCL1 ChIPseq negative control rep3


title: ASCL1 ChIPseq negative control rep2


title: ASCL1-KO DOX treatment rep3

data_processing:
The quality of the sequence data is assessed using FastQC v.0.11.2
Adaptors are trimmed using using Trim Galore v0.4.0 and Cutadapt v1.8.
The trimmed reads are also screened for presence of rRNA and mtRNA/DNA sequences using FastQ-Screen v.0.4.3
To assess the read distribution and confirm the strandedness of the alignments we use the RseQC package v2.3.7
The raw trimmed reads are aligned to the reference genome using Tophat v. 2.0.11
Tophat alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Raw gene counts are loaded and sample-normalized using DESeq v.1.18.0
Two-condition differential expression was done with the edgeR R package, v.3.8.6
Genome_build: UCSC hg19
Supplementary_files_format_and_content: htsqct_tmp.txt file contain raw read counts for genes
Supplementary_files_format_and_content: AllData.txt file contains output from EdgeR analysis and includes logFC, logCPM, LR, Pvalue, FDR, and RPKMs for each gene and for each sample

growth_protocol: Cells were cultured adherently for 7 days

extract_protocol:
Cells were harvested using Accutase and RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: knockout


title: Hepatocellular cancer 8

source_name: Hepatocellular cancer 8


title: ASCL1 ChIPseq negative control rep1


title: Hepatocellular cancer 9

source_name: Hepatocellular cancer 9


title: gal11-AA_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: ASCL1-KO DOX treatment rep1


title: Prmt5i_3

city: Houston

first: Margarida

last: Almeida Santos

state: Texas

address: 1515 Holcombe Blvd Mail code 1000

department: Epigenetics and Molecular Carcinogenesis

institute: UT MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to the mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on July 17, 2015) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.16.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

source_name: MLL-ENL/NrasG12D cells

growth_protocol: Mouse MLL-ENL/NrasG12D cells were kindly provided by I. Zuber and were cultured in RPMI-1640 (Gibco-Invitrogen) supplemented with 10% FBS, 100 U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol:
Cells were spun down and washed once with cold PBS, then RNA isolated with a QIAGEN RNeasy kit (Cat# 74104) according to the manufacturer’s protocol.
RNA-Seq sequencing libraries were made from MLL-ENL/RasG12D cells following Illumina TruSeq Stranded mRNA kit according to the manufacturer’s protocol.

treatment_protocol: The PRMT5 inhibitor was dissolved in DMSO at the concentration of 5 mM and the cells were treated with the compound at the final concentration of 5 μM. The cells for control were treated with equal concentration of DMSO. The cells were treated again on Day 2. At the end of each treatment period, cells were counted using the Nexcelom Cellometer and AOPI staining. Relative proliferation rates were calculated by normalizing to the rate of DMSO-treated cells.

value: MLL-fusion  leukemia cells

tag: treatment

value: PRMT5 inhibitor-treated


title: Hepatocellular cancer 6

source_name: Hepatocellular cancer 6


title: Hepatocellular cancer 5

source_name: Hepatocellular cancer 5


title: Prmt5i_2

tag: cell type


title: ASCL1-KO control treatment rep3 #2


title: Hepatocellular cancer 7

source_name: Hepatocellular cancer 7


title: DMSO_3

value: DMSO Control


title: Hepatocellular cancer 4

source_name: Hepatocellular cancer 4


title: ASCL1-KO DOX treatment rep2


title: ASCL1-KO control treatment rep2 #2


title: ASCL1-KO control treatment rep1 #2


title: ASCL1 ChIPseq doxcycline rep1


title: Hepatocellular cancer 10

source_name: Hepatocellular cancer 10


title: sin4-AA_plusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: Hepatocellular cancer 11

source_name: Hepatocellular cancer 11


title: Hepatocellular cancer 2

source_name: Hepatocellular cancer 2


title: ASCL1 ChIPseq doxcycline rep2

source_name: G523NS-ASCL1 KO-pBAC-ASCL1


title: srb6-AA_minusrap_Rpb1

description: Chip-seq of Rpb1 subunit of Pol II


title: DMSO_1