title: Cerebella_NoCreControl_3

city: Chapel Hill

first: Jennifer

middle: Karín

last: Ocasio

state: NC

address: 115 Mason Farm Rd NRB 6131

institute: University of North Carolina at Chapel Hill

description:
no cre Gska+-, GskBff 3
Whole cerebella from 1 replicate

hyb_protocol: Samples were hydribidized to the mouse Gene 2.1 ST 24-Arrays (Affymetrix) according to manufacturer's instruction by the UNC Functional Genomics Core

scan_protocol: Affymetrix GeneChip Scanner 3000 7G Plus

data_processing:
Data were processed using the Partek Genomics Suite 6.6 and R. The microarray data was imported into Partek and adjusted for GC, normalized RMA background, and normalized quantiles between samples. The data was then imported into R and we performed differential gene expression analysis by Signficance Analysis of Microarrays (SAM) and Gene Set Analysis (GSA). We determined significant genes by comparing Gsk-3DKO and M-Cre/GSKa+/- controls with log |Fold Change| > 2 and a false discovery rate (FDR) of <0.05. We obtained a list of 68 differentially expressed genes, with 14 downregulated and 54 upregulated genes in the Gsk-3 DKO.
probe group file: MoGene-2_1-st-v1
meta-probeset file: RefSeq_mm9_030617.fa
genome_build: Mouse mm9
Probeset values from Affymetrix files analyzed in the Partek Genomics Suite

source_name: Whole cerebella, no Cre Gsk-3 intact CGNPs, control

label_protocol: Samples were prepared using the biotin-based Affymetrix HT WT Terminal Labeling and Controls Kit (#901647) by the University of North Carolina (UNC) Functional Genomics Core.

growth_protocol: Cells were dissociated from freshly harvested whole cerebella from P2 mouse pups with the indicated genotypes.

extract_protocol: Mice were genotyped to determine Cre, Gsk-3a, and Gsk-3b expression. Samples were snap frozen in a dry ice/70% ethanol slurry and stored at -80oC. RNA was isolated using the RNeasy Mini Kit (Qiagen). RNA quality and quantity were assessed by spectrophotometry, capillary gel electrophoresis, and nanodrop. Each sample contained at least 83.3 ng/ul RNA and had a RIN score 7.5 or higher.

treatment_protocol: Not applicable

value: No Cre control

tag: age

value: cerebellum


title: Cerebella_NoCreControl_4

status: Public on Aug 07 2019

type: RNA

department: Neurology

country: USA

description:
no cre Gska+-, GskBff 4
Whole cerebella from 1 replicate

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain background

tag: genotype

tag: tissue


title: Res_Kelly_shLUC_2

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console.

data_processing: Microarray data were analyzed using a custom CDF file (GPL16043) that contained the mapping information of the ERCC probes used in the spike-in RNAs. The data were analyzed with Bioconductor using the MAS5 normalization method. Briefly, all chip data were imported in R (version 3.1.3) using the affy package, converted into expression values using the expresso command, normalized to take into account the different numbers of cells and spike-ins used in the different experiments and renormalized using loess regression fitted to the spike-in probes.

organism: Homo sapiens

source_name: shLUC resistant Kelly cells

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng of total RNA (GeneChip 3' IVT Express Kit User Manual, Affymetrix).

growth_protocol: Resistant Kelly cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, in the presence of TAE684 at a concetration of 1µM.

extract_protocol: Biological duplicates (equivalent to 5 x 10e6 cells per replicate) were collected and homogenized in 1ml of TRIzol Reagent (Ambion), purified using the mirVANA miRNA isolation kit (Ambion) following the manufacturer’s instructions and re-suspended in 50 ml nuclease-free water  (Ambion). Total RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion), treated with DNA-freeTM DNase I (Ambion) and analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies) for integrity.

treatment_protocol: Cells were infected for 24 h with viral particles containing either the shBORIS or the shLUC (control) construct in the presence of polybrene (8 µg/ml), and then selected with puromycin for 48h before performing RNA extraction.

tag: tae response

value: resistant

tag: treatment

value: short hairpin RNA Luciferase

tag: cell line

value: Neuroblastoma Kelly cells


title: Bcl11b-KO_Treg_Input_rep1

type: SRA

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

description: Input DNA

library_source: genomic

data_processing:
The quality of sequenced reads (50 bp; paired-end) was measured using FastQC , and low quality portions of the sequenced reads were trimmed using Trim Galore (version 0.4.2; with Cutadapt (version 1.12).
The trimmed reads were mapped to the mouse genome (reference assembly mm10) using HISAT2 (version 2.1.0).
The mapped reads were sorted by genomic positions using Samtools (version 1.3) , and duplicated mapped reads were removed using Sambamba (version 0.6.5).
Biological replicates for each conditions were merged and the genomic binding sites (peaks) of a given protein were identified using HOMER (version 4.10.1) with a FDR-adjusted p-value cutoff of 0.001
The peaks overlapped with the blacklisted regions that show anomalous, unstructured, and high signal/read counts were discarded.
To identify reliable target genes of a given protein, peaks located 20 kb outside of the gene’s transcription start sites were removed.
To identify common (or specific) peaks between given conditions, the identified peaks in each condition were merged.
Merged peaks were used to define common or specific peaks using HOMER (getDifferentialPeaks) with default parameters.
Deeptools (version 2.5.3-2-503c71b) was used to draw heatmaps
Genome_build: mm10
Supplementary_files_format_and_content: BED format (peak positions)

molecule: genomic DNA

source_name: Bcl11b deficient Treg cells

growth_protocol: Single cell supensions were prepared from drainig lymphnodes and spleen. Respective cell population were sorted using BD Moflo-XDP cell sorter and fixed.

extract_protocol:
Sheared Chromatin were cleared  and protein-DNA complexes were isolated with antibody-magnetic bead complex.
ChIP-seq library for each sample were prepared according to manufacturer (NEXTFLEX® ChIP-Seq Kit 5143-01) protocols. Briefly,purified immunoprecipitated DNA were end-repaired and size selected for 200–400-bp fragments with Agencourt AMPure XP beads (A63880) followed by Adenylation, barcoded adaptor-ligation and PCR amplification (15 cycles). Size distribution and concentration of each library was checked using Agilent Bioanalyzer. Equivalent amounts of barcoded libraries were pooled and sequenced using HiSeq 2500 (Illumina) instruments.

tag: strain

tag: cell type

value: Sorted CD4+YFP+ cells

value: Bcl11b f/f  Foxp3-IRES-YFP-Cre

tag: antibody

value: Input DNA


title: Cerebella_MCreControl_5

description:
cg1724 P1 #7 Gska+-, GskBff x M1Cre
Whole cerebella from 1 replicate

source_name: Whole cerebella, Gsk-3 beta only deleted CGNPs, control

value: Math1-Cre control


title: Res_Kelly_TAE_2

source_name: TAE resistant Kelly cells

growth_protocol: Sensitive and resistant Kelly cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

treatment_protocol: Cells were incubated for 24 h in the presence of DMSO (sensitive), the ALK inhibitor TAE684 at 1µM, or the BET inhibitor JQ1 at 2.5µM (resistant) before performing RNA extraction.


title: Cerebella_NoCreControl_5

description:
cg1724 P1 #9 Gska+-, no cre
Whole cerebella from 1 replicate


title: Cerebella_MCreControl_3

description:
M1Cre Gska+-, GskBff 3
Whole cerebella from 1 replicate


title: Res_Kelly_shBORIS_2

source_name: sh BORIS resistant Kelly cells

value: short hairpin RNA BORIS


title: Cerebella_MCreControl_4

description:
M1Cre Gska+-, GskBff 4
Whole cerebella from 1 replicate


title: RIP-INPUT 2hpf rep1

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

library_source: transcriptomic

data_processing:
Reads were aligned to the zv9 genome assembly using TopHat v2.1.1.
MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed.
Genome_build: zv9
Supplementary_files_format_and_content: Ybx1 binding sites in two biological replicates.

organism: Danio rerio

source_name: RIP-INPUT 2hpf

extract_protocol:
Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-BisSeq library construction.
RNA was extracted and subjected to library construction using Smarter smRNA-Seq kit (Takara). All the libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 150 bp.

value: AB strain

value: 2 hpf

value: whole embryo


title: RIP-INPUT 2hpf rep2


title: RIP-BS_3hpf

data_processing:
library strategy: RNA-RIP-BisSeq
Reads were aligned to the zv9 genome assembly using meRanTK v1.2.0
m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed.
MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed.
Genome_build: zv9
Supplementary_files_format_and_content: Ybx1-binding m5C sites in one biological replicates.

source_name: Zebrafish embryo

extract_protocol:
Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-BisSeq library construction.
Thus purified mRNA was used for RNA-BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 (Dhfr mRNA serves as methylation conversion control) was fragmented to ~100-nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent (Ambion), then stopped by 10× RNA stop solution (Ambion), and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution (pH 5.1), which is a 100:1 mixture of 40% sodium bisulfite (Sigma) and 600 µM hydroquinone (Sigma) and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns (PALL Corporation) with centrifugation. After washed with nuclease-free water and centrifuged for five times, the RNA was finally disolved in 75 μl nuclease-free water and then desulfonated by incubation with an equal volume of 1 M Tris-HCl (pH 9.0) at 75 °C for 1 h. After ethanol precipitation, the RNA was resuspended in 11 µl of RNase-free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase (Invitrogen) and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

value: 3 hpf

tag: rip antibody

value: polyclonal anti-Ybx1 antibody


title: RIP-BS_0hpf

value: 0 hpf


title: Res_Kelly_shBORIS_1


title: Res_Kelly_JQ1_2

source_name: JQ1 treated TAE resistant Kelly cells


title: Res_Kelly_shLUC_1


title: Cerebella_NoCreControl_2

description:
no cre Gska+-, GskBff 2
Whole cerebella from 1 replicate


title: Bcl11b-KO_Treg_Foxp3_rep2

description:
Foxp3 ChIP DNA
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_Bcl11b-KO-Treg-Foxp3-specific.bed
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_common.bed
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_WT-Treg-Foxp3-specific.bed


title: Cerebella_NoCreControl_1

description:
no cre Gska+-, GskBff 1
Whole cerebella from 1 replicate


title: par_Kelly_DMSO_2

source_name: Kelly cells

value: sensitive

value: DMSO


title: RIP-INPUT 0hpf rep2

source_name: RIP-INPUT 0hpf


title: Cerebella_MCreControl_2

description:
M1Cre Gska+-, GskBff 2
Whole cerebella from 1 replicate

value: cerebellum


title: par_Kelly_DMSO_1


title: Bcl11b-KO_Treg_Input_rep2

description: Input DNA


title: Res_Kelly_JQ1_1

value: resistant


title: Cerebella_MCreControl_1

description:
M1Cre Gska+-, GskBff 1
Whole cerebella from 1 replicate


title: Bcl11b-KO_Treg_Foxp3_rep1


title: Cerebella_GSK-3DKO_5

description:
cg1724 P1 #8 Gsk DKO
Whole cerebella from 1 replicate

source_name: Whole cerebella, Gsk-3 deleted CGNPs

value: GSK-3 DKO


title: RIP 2hpf rep1

source_name: RIP 2hpf

value: rabbit polyclonal anti-Ybx1 antibody


title: Res_Kelly_TAE_1

value: Neuroblastoma Kelly cells


title: Het_WT_Treg_rep4

data_processing:
The quality of sequenced reads (50 bp; paired-end) was measured using FastQC , and low quality portions of the sequenced reads were trimmed using Trim Galore (version 0.4.2; with Cutadapt (version 1.12).
The trimmed reads were mapped to the mouse genome (reference assembly mm10) using STAR (version 2.5.1)
The abundances of reference genes were estimated using Cuffnorm (version 2.2.1)
Differentially expressed genes (DEGs) between conditions were identified using Cuffdiff (version 2.2.1) with a false discovery rate (FDR)-adjusted p-value cutoff of 0.05
The fragments per kilobase of transcript per million mapped reads (FPKM) values were used to compare gene’s expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: Text file (normalized expression level by means of FPKM)

source_name: Bcl11b sufficient Treg cells

growth_protocol: Single cell supension were prepared from drainig lymphnodes and spleen. Respective cell population were sorted using BD Moflo-XDP cell sorter at >97% purity .

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Qiagen -74004). Integrity and concentration of purified RNA was checked using Agilent RNA 6000 Nano Kit (5067-1511) in Agilent Bioanalyzer and Nanodrop respectively.
Library was prepared from total RNA using TruSeq Stranded Total RNA kit (Illumina- RS-122-2001) following manufacturer's protocols. Briefly, cDNA was made from Total RNA followed by Adenylation, barcoded adaptor-ligation and PCR amplification (15 cycles). Libraries were size selected for 200-300-bp fragments using Agencourt AMPure XP beads (A63880) and size distribution was confirmed using Agilent High Sensitivity DNA Kit (5067-4626)  in Agilent Bioanalyzer. Equivalent amounts of barcoded libraries were pooled and sequenced using HiSeq 2500 or MiSeq (Illumina) instruments.

value: Sorted CD4+YFP+ cells

value: Bcl11b f/+ Foxp3-YFP-Cre/+


title: RIP 2hpf rep2


title: RIP 0hpf rep2

source_name: RIP 0hpf


title: RIP-INPUT 0hpf rep1


title: ribo-WT_4hpf_rep2

data_processing:
Reads were aligned to the zv9 genome assembly using TopHat v2.1.1
The number of reads mapped to each Ensemble gene was counted using the HTSeq v0.6.0
Genome_build: zv9
Supplementary_files_format_and_content: Reads count for each gene in wild type sample

extract_protocol:
Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-Seq library construction.
The RNA was subjected to ribosomal RNA depletion with Ribo-Zero rRNA Removal Kit (Illumina) followed by library construction using NEB Next® Ultra™ RNA library Prep Kit (NEB).

value: 4 hpf


title: RIP 0hpf rep1


title: Het_KO_Treg_rep3

value: Bcl11b f/f Foxp3-YFP-Cre/+


title: Het_WT_Treg_rep3


title: ribo-WT_4hpf_rep1

value: AB strain


title: ribo-amanitin_6hpf_rep2

value: 6 hpf

value: 0.2 ng of Pol II inhibition α-amanitin


title: Het_KO_Treg_rep4


title: ribo-amanitin_6hpf_rep1

value: whole embryo


title: ribo-amanitin_4hpf_rep2


title: NKTR-2-T12

city: Los Angeles

last: Tsoi

state: CA

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

data_processing:
Reads were mapped using HISAT2 version 2.0.4 and aligned to the Mus musculus genome NCBI build GRCm38.
Reads were quantified HTSeq version 0.6.12 and normalized to fragments per kilobase of exon per million fragments mapped (FPKM) expression values.
Genome_build: Mus musculus genome NCBI build GRCm38
Supplementary_files_format_and_content: Matrix of gene expression measurements in FPKM

source_name: B16F10 tumors_ACT+NKTR

extract_protocol:
RNeasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: host strain

tag: implanted with

value: B16F10 syngeneic murine melanoma cell line

value: B16F10 tumors

value: adoptive cell transfer (ACT) of pmel-1 T cells with NKTR-214

tag: time point

value: day 12 after treatment


title: ribo-amanitin_4hpf_rep1


title: NKTR-3-T12


title: NKTR-1-T12


title: Cerebella_GSK-3DKO_1

description:
Gsk 1 DKO
Whole cerebella from 1 replicate

value: cerebellum


title: Cerebella_GSK-3DKO_3

description:
Gsk 3 DKO
Whole cerebella from 1 replicate


title: XJQ: sinus rhythm (control)

first: Lei

last: Zhao

state: Beijing

address: Gongti Nanlu No.8

institute: Beijing Chaoyang Hospital

data_processing:
Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8) used for basecalling
Sequence quality was examined using the FastQC software
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software
The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown.
The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT to assess the coding potential of those sequences. Use rMATS to detect alternative splicing events and plots.
Genome_build: GRCh37
Supplementary_files_format_and_content: excel files for the FPKM of transcript and gene in samples

source_name: epicardial adipose tissue

extract_protocol:
Total RNA was extracted from freshly frozen epicardial adipose tissue using a QIAGEN miRNAeasy Mini Kits (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Isolated total RNA was subjected to ribosomal RNA deletion using a Ribo-Zero Magnetic Kit (EpiCentre, Madison, WI), randomly fragmented and then used to construct RNA sequencing library using KAPA Stranded RNA-Seq Library Prep Kit for Illumina.
The RNA fragments were primed with random hexametric primers to synthesize the first cDNA strand, and the second cDNA strand was incorporated with dUTP instead of dTTP. The resulting cDNA were amplified in situ using TruSeq SR Cluster Kit v3-cBot-HS. The strand-specific libraries were qualified on the Agilent 2100 Bioanalyzer and subsequently sequenced on the Illimina HiSeq 4000 platform.

value: epicardial adipose tissue

tag: diagnosis

value: sinus rhythm (control)


title: ZYQ: persistent non-valvular atrial fibrillation (AF)


title: XXX: persistent non-valvular atrial fibrillation (AF)


title: Cerebella_GSK-3DKO_4

description:
Gsk 4 DKO
Whole cerebella from 1 replicate

value: GSK-3 DKO


title: Cerebella_GSK-3DKO_2

description:
Gsk 2 DKO
Whole cerebella from 1 replicate


title: hichip_Kelly_Sens_SMC1_rep3_50l

description:
Res_vs_Sens_functional_loops_info.IGV.bed
Res_vs_Sens_functional_loops_info.txt

data_processing:
Library strategy: HiChIP
Reads were first trimmed to a uniform length of 50 bp using trimmomatic.
Trimmed reads were processed using the HiC-Pro pipeline with default settings for the human genome (build hg19, GRCh37.75) and corresponding MboI cut sites
Loops were directly called from the HiC-Pro output using hichipper, with parameter ‘peaks = combined, all’, and subsequently diffloop with default settings
Only loops that were detected in all 3 biological replicates of a sample (sensitive, resistant, shGFP or shBORIS) with a minimum of 5 paired-end tags (PETs) in total and an FDR  0.01 were retained for further analysis
To call differential loops between samples, the quickAssocVoom function was used and significantly different loops were either considered reinforced (mango.FDR < 0.01 and log2FC > 1) or lost (mango.FDR < 0.01 and log2FC < -1).
Genome_build: hg19
Supplementary_files_format_and_content: Text files and corresponding bedpe files with information about loops, anchors and differential looping.

growth_protocol: Resistant Kelly cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in the presence of the ALK inhibitor TAE684 at 1µM, in order to obtain 10 million cells to be prepared for each sample.

extract_protocol:
HiChIP libraries were generated as follows: nuclei isolation, in situ Hi-C contact generation, ChIP, DNA isolation and biotin capture of Hi-C contacts.
On bead Tn5 libraries were generated,  PCR-amplified, purified, and size-selected before performing sequencing.

treatment_protocol: Cells were infected for 24 h with viral particles containing either the shBORIS or the shGFP (control) construct in the presence of polybrene (8 µg/ml), and then selected with puromycin for 48h before performing HiChIP.

value: Neuroblastoma Kelly cells

value: sensitive

value: DMSO


title: hichip_Kelly_Sens_SMC1_rep2_50l


title: ribo-amanitin_2hpf_rep2

value: 2 hpf


title: hichip_Kelly_Sens_SMC1_rep1_50l


title: hichip_Kelly_Res_SMC1_shGFP_rep3

description:
shBORIS_vs_shGFP_functional_loops_info.IGV.bed
shBORIS_vs_shGFP_functional_loops_info.txt

value: resistant

value: shGFP


title: IL2-3-T12

source_name: B16F10 tumors_ACT+IL2

value: adoptive cell transfer (ACT) of pmel-1 T cells with IL-2


title: THY: persistent non-valvular atrial fibrillation (AF)


title: ribo-amanitin_2hpf_rep1

value: AB strain

value: 0.2 ng of Pol II inhibition α-amanitin


title: IL2-2-T12

value: B16F10 syngeneic murine melanoma cell line


title: SYL: sinus rhythm (control)


title: hichip_Kelly_Res_SMC1_shGFP_rep2


title: MOpabpc1a 6hpf rep2

description: MOpabpc1a 6hpf rep2

data_processing:
Reads were aligned to the zv9 genome assembly using TopHat v2.1.1
The number of reads mapped to each Ensemble gene was counted using the HTSeq v0.6.0
Genome_build: zv9
Supplementary_files_format_and_content: Reads count for each gene in wild type, ybx1 MO and pabpc1a MO sample

source_name: MOpabpc1a 6hpf

extract_protocol:
Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-Seq library construction.
Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

value: AB

tag: genotype/variation

value: pabpc1a MO

value: 6 hpf

value: whole embryo


title: IL2-1-T12

value: B16F10 tumors

value: day 12 after treatment


title: hichip_Kelly_Res_SMC1_shGFP_rep1


title: MOpabpc1a 6hpf rep1

description: MOpabpc1a 6hpf rep1


title: hichip_Kelly_Res_SMC1_shBORIS_rep3

value: shBORIS


title: MOpabpc1a 4hpf rep2

description: MOpabpc1a 4hpf rep2

source_name: MOpabpc1a 4hpf

value: 4 hpf


title: SHY: persistent non-valvular atrial fibrillation (AF)

value: epicardial adipose tissue


title: hichip_Kelly_Res_SMC1_shBORIS_rep2

value: Neuroblastoma Kelly cells


title: QP: persistent non-valvular atrial fibrillation (AF)


title: Logcere-3 logarithmic phase replicate 3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Samples are normalized to 2nM concentrations and then multiplexed 4 samples per lane. Then they have been denatured at a concentration of 1nM using 0.1N NaOH, 5’at room temperature to be finally diluted at 9pM. Each sample is loaded on the flowcell at 9pM. Sequencing of the 24 samples was performed on the HiSeq 2500 sequencer (Illumina) in 65 bases single-end mode.
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -s 1 )
Count data were analyzed using R version 3.3.1 and the Bioconductor package DESeq2 version 1.12.3 The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed without applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between D0, D8AE, D8ANA and Log. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure  and genes with an adjusted p-value lower than 0.01 were considered differentially expressed.
Genome_build: Cryptococcus neoformans var. grubii H99 from Broad Institute
Supplementary_files_format_and_content: Matrix of count from featureCounts

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Cryptococcus neoformans H99 strain stored in 20% glycerol at -80°C was cultured on Sabouraud agar plate at room temperature (step 1). After 2 to 5 days of culture, 10^7 cells were suspended in 10 mL of YPD in a T25cm3 flask and cultured for 22 hours at 30 °C, 150 rpm with lateral shaking until stationary phase (final concentration=2×10^8/mL) (step 2). 3×10^7 cells of this first culture was suspended in 10mL YPD (second culture) under the same conditions until stationary phase (Step 3). Then, flasks were incubated in hypoxia generated using a GENbag® anaer (Biomérieux) atmosphere generator in a dedicated plastic bag for 8 days in the dark at 30°C. A control sample always performed in parallel is incubated under the same conditions but in normoxia (Step 4). Logarithmic phase for Cryptococcus neoformans or Saccharomyces cerevisiae were grown during 17h in YPD.

extract_protocol:
The RNA protocol extraction used was adapted from (Moyrand et al., Eukaryotic Cell, 2008). Briefly, the samples were lyophilized overnight. RNAs were extracted following a protocol divided in 3 parts: i) an extraction step was performed in Trizol reagent (Invitrogen), ii) a second step by adding Chloroform (Invitrogen) iii) the last step was an overnight Isopropanol precipitation at -20°C.
We used 1 μg of total RNA to purify polyadenylated mRNAs and to build an RNA library, using TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-9004DOC) as recommended by the manufacturer. Directional library are checked for concentration and quality on DNA chips with the Bioanalyser Agilent. More precise and accurate quantification is performed with sensitive fluorescent-based quantitation assays ("Quant-It" assays kit and QuBit fluorometer, Invitrogen).


title: hichip_Kelly_Res_SMC1_shBORIS_rep1

source_name: TAE resistant Kelly cells


title: MOpabpc1a 4hpf rep1

description: MOpabpc1a 4hpf rep1


title: LJ: sinus rhythm (control)

value: sinus rhythm (control)


title: SSF: sinus rhythm (control)


title: Logcere-1 logarithmic phase replicate 1


title: D8ANAcere-3 logarithmic phase replicate 3


title: iCLIP 4hpf rep2

description: iCLIP 4hpf rep2

data_processing:
RIP-seq and iCLIP-seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10, respectively.
RIP-seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. iCLIP: To identify the Ybx1 targets’ locus, the mode of truncation calling was performed. For each truncation position, the coverages of unique tag (k) and truncations (m) were determined by CIMS.pl program (CLIP Tool Kit, CTK). The sites were annotated by applying BEDTools’ intersectBed.
Genome_build: zv9
Supplementary_files_format_and_content: Ybx1 binding sites in two biological replicates.

extract_protocol:
RIP-seq: Briefly, 500 zebrafish embryos at shield stage (4 hpf) were resuspended with 2 ml lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 0.4 U/μl RNasin) by rotating at 4°C for 30 min and centrifuged at 15,000 g for 15 min. The supernatant was collected and pre-cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre-cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti-Ybx1 antibody (prepared by AbMax, China) and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. After washing with1 ml ice-cold NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 0.4U/µl RNasin) for eight times and once with 1ml ice-cold 1× PK buffer (100 mM Tris-HCl pH 7.4, 50 mM NaCl, 10 mM EDTA , 0.2% SDS), the beads was treated in 200 ul PK buffer containing 20 ul proteinase K (Roche, 0311582001) for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 (pH4.3~4.7) and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase (Invitrogen, AM2238).  iCLIP-seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 (Stratalinker 2400, Stratagene), lysed and subjected to mild fragmentation. Crosslinked RNA-protein complexes were immunoprecipated using polyclonal Ybx1 antibody (Abmax) and protein A dynabeads.
RNA was extracted and subjected to library construction using Smarter smRNA-Seq kit (Takara). All the libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 150 bp.

value: Zebrafish embryo


title: hichip_Kelly_Res_SMC1_rep3_50l

value: resistant


title: D8ANAcere-2 logarithmic phase replicate 2


title: iCLIP 4hpf rep1

description: iCLIP 4hpf rep1


title: D8ANAcere-1 logarithmic phase replicate 1


title: BYP: sinus rhythm (control)


title: RIP 4hpf rep2

description: RIP 4hpf rep2


title: hichip_Kelly_Res_SMC1_rep2_50l


title: hichip_Kelly_Res_SMC1_rep1_50l


title: siBRCA2_input

city: Palo Alto

first: Michael

last: Snyder

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

description:
input chromatin
B2_input.bw

data_processing:
Paired-end 100 bp reads were trimmed with cutadapt version 1.8.1 with flags –u -50 –U -50 –a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -O 5 -m 30 -q 15.
Bowtie (Langmead et al., 2009) version 1.1.1 was used to align trimmed reads to hg19 with flags -q --phred33-quals -X 2000 -m 1 --fr -p 8 -S --chunkmbs 400, followed by samtools sort command.
Duplicates were marked with Picard-tools version 1.92, then samtools view with flags –b –f 1 -F12 –L were used to filter mitochondrial mapping reads with a bed file containing all chromosomes except chrM.
For ChIP-seq, SPP/phantom (Kharchenko et al., 2008; Landt et al., 2012) was run to obtain the fragment length with maximum strand cross-correlation.
MACS2 (Zhang et al., 2008) broadpeak function was then performed with flags -q 0.01 --nomodel –shiftsize=1/2 fragment length obtained from SPP.
The program align2rawsignal (Kundaje) was used to create genome-wide signal coverage tracks with normalization to account for depth of sequencing and read mappability with flags kernel (k)=epanechnikov, fragment length (l)=150 (ATAC-seq) or (l)=1/2 fragment length from SPP for ChIP-seq, smoothing window (w)=150, normFlag(n)=5, mapFilter (f)=0.
Diffbind was then used with input controls to define differential peaks between BRCA2 ChIP and input, using summits=250 parameter.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig of ChIP-seq tracks

source_name: hTert-HME1 cells

growth_protocol: hTert-HME1 cells were grown in Mammary Epithelial Growth Medium (Lonza) and harvested at log-phase growth

extract_protocol:
Log-phase growth cells were crosslinked in 1% formaldehyde at a density of 5x10^5 cells per milliliter for 10 minutes at room temperature, then quenched with 125 mM glycine for 5 minutes, washed in PBS and snap frozen.  Cells were then thawed and nuclei isolated by triton-X permeabilization followed by washing in a low detergent buffer.  Then RIPA was added and sonication was performed by Branson (3 pulses of 30 seconds each with power output 4 W), followed by 14 cycles of sonication on the Bioruptor Pico.  Chromatin extracts were then cleared by centrifugation and immunoprecipitation was performed with antibodies and protein A/G agarose beads overnight.  The next day the beads were extensively washed with RIPA, then PBS, then resuspended in TE with 1% SDS and crosslinks were reversed overnight at 65 degrees Celcius.  The next day RNase A treatment and proteinase K treatment were performed, followed by recovery of DNA with the Qiaquick spin columns.
High throughput sequencing libraries were then constructed by A tailing, adapter ligation and 10-15 cycles of PCR followed by library purification, removal of PCR primer-dimers and high-throughput sequencing by HiSeq 4000.

treatment_protocol: siRNA was transfected with RNAiMAX and then cells were passaged 4 times (12 days)

tag: cell  line

tag: chip antibody

value: none (input)


title: Logcere-2 logarithmic phase replicate 2


title: D8AEcere-3 logarithmic phase replicate 3


title: Kelly_shLUC2_1

description: shLUC-results.csv

data_processing:
Raw paired-end tags (PETs) were trimmed of the bridge linker sequence using cutadapt version 1.8 using the following options: -n 3 -O 3 -m 15 -a forward=ACGCGATATCTTATCTGACT -a reverse=AGTCAGATAAGATATCGCGT
Trimmed reads were individually mapped using bowtie 1 to the hg19 reference genome with the following options: -n 1 -m 1. Reads were re-paired post-alignment by read name.
Peaks were called on mapped reads using macs v1.4 using the following options: -g hs -p 1e-9 --nolambda --nomodel --shiftsize=100
The contact map for each cell type was generated by identifying all peaks linked by at least 1 PET such that the ends of each PET were in different peaks.
Each contact was assigned a probability of being an interaction using a semi-Bayesian mixture model strategy described in Debruyne et al. High-confidence interactions were called by taking all contacts with a posterior probability of at least 0.9.
Genome_build: hg19
Supplementary_files_format_and_content: BEDPE file (.csv) containing all observed contacts in the corresponding ChIA-PET data with the last three columns as PET count, Hypergeometric p-value and Bayes probability.

growth_protocol: Resistant Kelly cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in the presence of the ALK inhibitor TAE684 at 1µM, in order to obtain 20 million cells to be prepared for each sample.

extract_protocol:
ChIA-PET libraries were generated in three stages: ChIP, proximity ligation of ChIP-DNA fragments and tagmentation of the ligated products. Obtained fragments were then purified, PCR-amplified and size-selected before performing sequencing.
Libraries were prepared using the Nextera DNA Library Prep Kit from Illumina (FC-121-1031), according to the manufacturer’s protocol.

treatment_protocol: Cells were infected for 24 h with viral particles containing either the shBORIS or the shLUC (control) construct in the presence of polybrene (8 µg/ml), and then selected with puromycin for 48h before performing Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET).

value: shLUC


title: LSQ: persistent non-valvular atrial fibrillation (AF)


title: D8AEcere-2 logarithmic phase replicate 2


title: siControl_input

description:
input chromatin
con_input.bw

value: siControl


title: MO 4hpf m5C rep1

description: MO 4hpf rep1

data_processing:
Reads were aligned to the zv9 and hg19 genome assembly using meRanTK v1.2.0
m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed.
Genome_build: zv9 and hg19
Supplementary_files_format_and_content: m5C sites in two biological replicates.

extract_protocol:
Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-BisSeq library construction.
Thus purified mRNA was used for RNA-BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 (Dhfr mRNA serves as methylation conversion control) was fragmented to ~100-nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent (Ambion), then stopped by 10× RNA stop solution (Ambion), and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution (pH 5.1), which is a 100:1 mixture of 40% sodium bisulfite (Sigma) and 600 µM hydroquinone (Sigma) and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns (PALL Corporation) with centrifugation. After washed with nuclease-free water and centrifuged for five times, the RNA was finally disolved in 75 μl nuclease-free water and then desulfonated by incubation with an equal volume of 1 M Tris-HCl (pH 9.0) at 75 °C for 1 h. After ethanol precipitation, the RNA was resuspended in 11 µl of RNase-free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase (Invitrogen) and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.
RNA-BisSeq

value: AB strain

tag: age


title: Kelly_shLUC1_1

description: shLUC-results.csv


title: D8AEcere-1 logarithmic phase replicate 1


title: Kelly_shBORIS2_1

description: shBORIS-results.csv


title: WT 6hpf m5C rep2

description: WT 6hpf rep2


title: Kelly_shBORIS1_1

description: shBORIS-results.csv


title: WT 6hpf m5C rep1

description: WT 6hpf rep1


title: WT 4hpf m5C rep2

description: WT 4hpf rep2


title: siBRCA2_2

description:
histone H4 lysine 12 acetylation
B2_H4k12ac.bw

tag: genotype

value: anti-H4K12 ac


title: siBRCA2_1


title: siControl_2

description:
histone H4 lysine 12 acetylation
con_H4k12ac.bw


title: siBRCA2-2_EGF_B

description: sample name found in the normMatrix file header: BRCA2_EGF_B

data_processing:
Alignment with tophat version 2.0.11 using gencode hg19 GTF gencode.v19.annotation.gtf
Reads counted with summarizeOverlaps function from GenomicAlignments R package (Bioconductor)
DESeq2 workflow was followed: DESeqDataSet was used to make a dds object using the design formula: ~media + siRNA_type
data was rlog transformed
This resulted in the 20160508normMatrix.csv file
Genome_build: hg19
Supplementary_files_format_and_content: supplementary file: 20160508normMatrix.csv has normalized, transformed read counts for each ensemble gene per sample

source_name: hTert-HME1 cell line

growth_protocol: Mammary Epithelial Growth Medium (Lonza) at 37degC with 5% CO2

extract_protocol:
AllPrep (Qiagen) followed by mRNA purification with mRNA Direct (Dynabeads, Ambion)
Script-seq v2 (Illumina)

treatment_protocol: siRNA transfection with RNAiMAX (Invitrogen)

tag: sirna

tag: media

value: -EGF

tag: passages

tag: biological replicate

value: B


title: siControl_1


title: D0cere-2 logarithmic phase replicate 2

tag: strain


title: D0cere-1 logarithmic phase replicate 1


title: siBRCA2-2_EGF_A

description: sample name found in the normMatrix file header: BRCA2_EGF_A

tag: cell line

value: A


title: RIP 4hpf rep1

description: RIP 4hpf rep1

source_name: Zebrafish embryo

tag: cell type

tag: tissue

value: whole embryo


title: MO 4hpf m5C rep2

description: MO 4hpf rep2


title: input 2

extract_protocol:
Log-phase growth cells were crosslinked in 1% formaldehyde at a density of 5x105 cells per milliliter for 10 minutes at room temperature, then quenched with 125 mM glycine for 5 minutes, washed in PBS and snap frozen.  Cells were then thawed and nuclei isolated by triton-X permeabilization followed by washing in a low detergent buffer.  Then RIPA was added and sonication was performed by Branson (3 pulses of 30 seconds each with power output 4 W), followed by 14 cycles of sonication on the Bioruptor Pico.  Chromatin extracts were then cleared by centrifugation and immunoprecipitation was performed with antibodies and protein A/G agarose beads overnight.  The next day the beads were extensively washed with RIPA, then PBS, then resuspended in TE with 1% SDS and crosslinks were reversed overnight at 65 degrees Celcius.  The next day RNase A treatment and proteinase K treatment were performed, followed by recovery of DNA with the Qiaquick spin columns.
High throughput sequencing libraries were then constructed by A tailing, adapter ligation and 10-15 cycles of PCR followed by library purification, removal of PCR primer-dimers and high-throughput sequencing by HiSeq 4000.

value: hTert-HME1 cell line

tag: index for hiseq

value: TGACCA

tag: antibody

value: input chromatin


title: WT 3hpf m5C rep2

description: WT 3hpf rep2

value: 3 hpf


title: NTGF rep2

city: Baoding

first: KE

last: XU

state: Hebei

institute: Hebei agricultural university

data_processing:
Sequencing libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, San Diego, CA, USA)
Raw reads in FASTQ format were processed via Perl scripts.
The PCR products were purified (AMPure XP system, Beckman Coulter, Brea, CA, UAS), and library quality was assessed using an Agilent Bioanalyzer 2100 system (Agilent, Palo Alto, CA, USA).
Genome_build: (IWGSC RefSeq v1.0) (http://www.wheatgenome.org/)
Supplementary_files_format_and_content: txt  files include readcount  for each Sample

organism: Triticum aestivum

source_name: unacclimation and freezing: NTGF

extract_protocol:
Samples were removed, stored at −80°C for RNA extraction.Total RNA from crown samples was isolated using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: SEEDING

tag: treatment

tag: treatment time

tag: treatment group

value: unacclimation/freezing


title: NTGF rep3


title: sscon1_comp_B

description: sample name found in the normMatrix file header: CON_Comp_B

value: +EGF (complete)


title: input 1

value: CAGATC


title: NTGF rep1


title: BRCA2_ChIP_2

value: CGATGT


title: WT 3hpf m5C rep1

description: WT 3hpf rep1

value: Zebrafish embryo


title: WT 2hpf m5C rep2

description: WT 2hpf rep2

value: 2 hpf


title: LTAF rep3

source_name: acclimation and freezing: LTAF

value: cold acclimation/freezing


title: BRCA2_ChIP_1

value: GATCAG


title: siB2-2_comp_P4

description: sample name found in the normMatrix file header: BRCA2_P4


title: WT 2hpf m5C rep1

description: WT 2hpf rep1

value: AB strain


title: LTAF rep2


title: WT 0hpf m5C rep2

description: WT 0hpf rep2

value: 0 hpf


title: WT 4hpf m5C rep1

description: WT 4hpf rep1

value: 4 hpf


title: Fully_resistant

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: hg19
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

molecule: polyA RNA

source_name: TAE fully resistant Kelly cells

growth_protocol: Cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, in the presence of DMSO (sensitive) or TAE684 at a concentration of 500nM (intermediate resistanct) or 1µM (fully resistant).

extract_protocol:
After reaching approximately 70% confluence, cells were trypsinized, washed twice with 1X PBS, resuspended into single cells at a concentration of 10^6 per ml in 1X PBS with 0.4%BSA for 10X genomics processing.
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

tag: tae response

value: fully resistant

value: Kelly cells


title: Intermediate_resistant

source_name: TAE intermediate resistant Kelly cells

value: intermediate resistant


title: sscon1_comp_P4

description: sample name found in the normMatrix file header: CON_P4

value: A


title: Kelly-SMC1

data_processing:
Library strategy: ChIA-PET
Raw paired-end tags (PETs) were trimmed of the bridge linker sequence using cutadapt version 1.8 using the following options: -n 3 -O 3 -m 15 -a forward=ACGCGATATCTTATCTGACT -a reverse=AGTCAGATAAGATATCGCGT
Trimmed reads were individually mapped using bowtie 1 to the hg19 reference genome with the following options: -n 1 -m 1. Reads were re-paired post-alignment by read name.
Peaks were called on mapped reads using macs v1.4 using the following options: -g hs -p 1e-9 --nolambda --nomodel --shiftsize=100
The contact map for each cell type was generated by identifying all peaks linked by at least 1 PET such that the ends of each PET were in different peaks.
Each contact was assigned a probability of being an interaction using a semi-Bayesian mixture model strategy described in Debruyne et al. High-confidence interactions were called by taking all contacts with a posterior probability of at least 0.9.
Genome_build: hg19
Supplementary_files_format_and_content: BEDPE file containing all observed contacts in the corresponding ChIA-PET data with either their interaction probability score or PET count

source_name: Kelly cells

growth_protocol: Sensitive and resistant Kelly cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, in order to obtain 20 million cells to be prepared for each sample.

treatment_protocol: Cells were incubated for 48 h in the presence of DMSO (sensitive),or the ALK inhibitor TAE684 at 1µM (resistant) before performing Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET).

tag: cell origin

value: Neuroblastoma Kelly cells

value: sensitive


title: LTAF rep1

value: SEEDING


title: MO 6hpf rep2

description: MO 6hpf rep2

tag: age

value: 6 hpf

value: whole embryo


title: NTG rep3

source_name: unacclimation: NTG

value: unacclimation


title: Kelly-Res-SMC1

value: resistant


title: Sensitive


title: d12_m_307: male embryo on Day12

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

data_processing:
The obtained sequence reads (Fastq files) were analyzed with a locally installed version of Galaxy
The resulting read count table was used for statistical analysis in EdgeR to identify differentially expressed genes
Genome_build: Sscrofa 11.1

organism: Sus scrofa

source_name: male embryo on Day12

extract_protocol:
AllPrep DNA/RNA Micro Kit
Illumina TruSeq Stranded mRNA library construction

treatment_protocol: Four gilts were slaughtered each on Days 8, 10, and 12 post insemination, respectively. The respective gilts were randomly assigned to the date of slaughtering. The embryos were flushed from the uterus using 10 mL of phosphate-buffered saline (PBS, pH 7.4) per horn, and then were transferred into a petri-dish containing PBS for morphological observation. All embryos were then individually shock-frozen in liquid nitrogen immediately and stored at –80 °C for further DNA and RNA analyses.

tag: gender

value: male

value: embryo


title: NTG rep2


title: sscon1_comp_A

description: sample name found in the normMatrix file header: CON_Comp_A

tag: sirna

tag: media

value: +EGF (complete)


title: MO 4hpf rep2

description: MO 4hpf rep2

value: AB strain

value: Zebrafish embryo


title: NTG rep1


title: d12_m_276: male embryo on Day12


title: C3.C.3

data_processing:
Adapter trimming with Trim Galore version 0.4.1 with default setting in paired end mode
Alignment with bsmap version 2.89
Picard-tools version 1.92 MarkDuplicates to remove duplicates
Moabs version 1.3.0 used to calculate per CpG methylation values
mean CpG methylation signal over target capture regions was computed (methylated = 1, unmethylated = 0).
Genome_build: hg19
Supplementary_files_format_and_content: Bed file has CpG methyl calls (read counts) for every CpG in target capture regions with calculated ratio and breakdown for minus and plus strands, and local context

extract_protocol:
AllPrep (Qiagen)
Agilent SureSelectXT Methyl-seq kit

tag: passages

tag: biological replicate


title: LTA rep2

source_name: cold acclimation: LTA

value: cold acclimation


title: MO 4hpf rep1

description: MO 4hpf rep1

tag: strain

value: 4 hpf


title: MO 3hpf rep2

description: MO 3hpf rep2

tag: cell type

value: 3 hpf


title: d12_m_249: male embryo on Day12

tag: tissue


title: LTA rep1


title: d12_m_275: male embryo on Day12


title: C1.C.3

tag: cell line


title: WT 0hpf m5C rep1

description: WT 0hpf rep1

value: 0 hpf


title: d12_f_299: female embryo on Day12

source_name: female embryo on Day12

value: female


title: MO 3hpf rep1

description: MO 3hpf rep1


title: ago18b::mum RNA-Seq

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq (v2.16.0.10) was used to convert bcl files to fastq files.
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor and removing low quality bases (less than 20), too short reads (less than 16nt) were also dropped. FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the reference genome by tophat2 (Kim et al., 2013) for mRNA-Seq and RIP-Seq. Aligned reads with more than one genome location were discarded due to their ambiguous location. Uniquely localized reads were used to do the following analysis.
For RNA-seq and RIP-Seq analysis, the gene expression level was calculated by using RPKM method (reads per kilobase transcriptome per million mapped reads).
The differentially expressed gene (DEG) of a given transcript in zmago18b mutants (MU) and W22-ref (WT) was computed with edgeR.
Genome_build: Zma B73 AGPv2
Supplementary_files_format_and_content: Tab separated Microsoft Excel files report abundance measurements

organism: Zea mays

growth_protocol: A total of 195 and 358 from the same BC2F2 progeny were grown at Sanya (18°N, 109°E) in 2014 winter and Wuhan (30°N, 114°E) in 2015 spring of China, respectively. Homologous individuals at ZmAGO18b were selfed to develop the zmago18b::Mu lines and corresponding controls (W22-ref), respectively.

extract_protocol:
Two pools of more than 10 cm tassels were from homozygous zmago18b mutants and wild-type sibling plants. Freshly dissected tassel tissue was dissected and immediately frozen in liquid nitrogen. Total RNA was extracted from pools of tassel tissue using Trizol (Life Technologies, Invitrogen, Carlsbad, CA, USA) and treated with RQ1 DNase (promega) to remove DNA.
For each sample, 10μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen, USA) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95 oC followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and applied to Illumina NextSeq 500 system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).

treatment_protocol: Choose mitosis or meiosis tassels from developing maize at 10-15 days before tasseling were fixed in Cano fixed liquid (95% ethanol: glacial acetic acid = 3:1) and stored in 70% ethanol, and used Green Nucleic Acid Stain(Invitrogen, Carlsbad, CA, USA) to determinate the chromosomal dynamic change in mother cells of microspore. Fluorescent detective at 504 nm excitation and 523 nm emission. The anther dehiscence were observed at pollinating period, and pollen fertility was measured with potassium iodide solution staining (I2-KI solution, 1g iodinde and 2g potassium iodide in 300ml distilled water, 10 times dilution).

tag: developmental stage

value: 14 cm length

value: tassel


title: B2.C.10B

value: B


title: WT 6hpf rep2

description: WT 6hpf rep2

value: 6 hpf


title: d12_f_297: female embryo on Day12


title: B2.E.10B

value: -EGF


title: W22-ref RNA-Seq


title: WT 6hpf rep1

description: WT 6hpf rep1

value: whole embryo


title: MO 6hpf rep1

description: MO 6hpf rep1


title: B1.E.10B


title: LTA rep3

tag: cultivar

value: SEEDING


title: d12_f_271: female embryo on Day12


title: d12_m_286: male embryo on Day12

value: male


title: WT 4hpf rep2

description: WT 4hpf rep2


title: WT 4hpf rep1

description: WT 4hpf rep1


title: C3.C.10B


title: d12_f_245: female embryo on Day12

value: embryo


title: AGZ: sinus rhythm (control)

source_name: epicardial adipose tissue

value: epicardial adipose tissue

tag: diagnosis

value: sinus rhythm (control)


title: C1.C.10B

value: +EGF (complete)


title: WT 3hpf rep2

description: WT 3hpf rep2

value: AB strain

value: Zebrafish embryo


title: d10_m_453: male embryo on Day10

source_name: male embryo on Day10


title: WT 3hpf rep1

description: WT 3hpf rep1

value: 3 hpf


title: d10_m_435: male embryo on Day10


title: B2.E.10A

value: A


title: B2.C.10A


title: d10_m_333: male embryo on Day10


title: WT 2hpf rep1

description: WT 2hpf rep1

value: 2 hpf


title: C3.C.10A


title: d10_m_318: male embryo on Day10


title: WT 0hpf rep2

description: WT 0hpf rep2

value: 0 hpf


title: siFOXA1#1 Replicate 3

city: Hull

first: Mark

last: Wade

state: Humberside

address: Room 121, Hardy Building, University of Hull, Cottingham Road

country: United Kingdom

institute: University of Hull

description:
FOXA1 targetting siRNA transfected cells
Sample 9

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed using Illumina GenomeStudio Gene Expression Module. Data was quantile normalised using the GenomeStudio Gene Expression Module with background subtraction.

source_name: MCF-7 breast cancer cells

label_protocol: According to manufacturer (Illumina) specifications.

extract_protocol: RNA was extracted with TRIzol reagent (Ambion, Life Technologies) following manufacturers instructions. Quality control was performed with Agilent Bioanalyser.

value: Human breast adenocarcinoma cell line


title: d10_m_321: male embryo on Day10


title: siKDM3A#1 Replicate 3

description:
KDM3A targetting siRNA transfected cells
Sample 8


title: WT 0hpf rep1

description: WT 0hpf rep1


title: Log-3 logarithmic phase replicate 3

organism: Cryptococcus neoformans

source_name: Yeast


title: siSCR Replicate 3

description:
Control siRNA (siSCR) transfected cells
Sample 7


title: T4: RNAseq (paired-end sequencing)

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

data_processing:
Fastq quality was determined by FASTQC in Galaxy server
Adapter removal was done for Riboseq data using Clip (FastX-tool kit) in galaxy server
Riboseq reads were further trimmed using Trim in galaxy server
Riboseq data was aligned to ribosomal mouse RNA sequences (custom genome file) using bowtie 2 in galaxy server and only the reads that dd not align were used for further analysis.
Reads not aligned to mouse genome (mm10) using tophat in galaxy server.
htseq-count in galaxy server was used to count the reads per gene. GTF file from ensembl modified to match the ucsd genome was used for counting.
Genome_build: mm10 (mus musculus)
Supplementary_files_format_and_content: Tabular format with read counts per gene (created using htseq-count.

source_name: resting state T cells

growth_protocol: Cells were isolated using Miltenyi magnetic sorting kit and cultured for 2 hours in complete RPMI medium at 37ºC, 5% CO2

extract_protocol:
Total RNA was isolated from the cells, subjected to library preparation and sequencing in illumina platform.
TruSeq RNA Sample Preparation v2 Guide

tag: origin

value: Spleen

value: resting state T cells


title: Log-2 logarithmic phase replicate 2


title: T1: RNAseq (paired-end sequencing)


title: Log-1 logarithmic phase replicate 1


title: siFOXA1#1 Replicate 2

description:
FOXA1 targetting siRNA transfected cells
Sample 6


title: d10_f_336: female embryo on Day10

source_name: female embryo on Day10

value: female


title: d10_f_433: female embryo on Day10


title: siKDM3A#1 Replicate 2

description:
KDM3A targetting siRNA transfected cells
Sample 5


title: WT 2hpf rep2

description: WT 2hpf rep2

value: whole embryo


title: d10_f_454: female embryo on Day10


title: B3: RNAseq (paired-end sequencing)

source_name: resting state B cells

value: resting state B cells


title: d10_f_317: female embryo on Day10


title: siKDM3A#1 Replicate 1

description:
KDM3A targetting siRNA transfected cells
Sample 2


title: siSCR Replicate 2

description:
Control siRNA (siSCR) transfected cells
Sample 4


title: D8ANA-3 hypoxia 8 d replicate 3


title: B1: RNAseq (paired-end sequencing)


title: siSCR Replicate 1

description:
Control siRNA (siSCR) transfected cells
Sample 1


title: D8ANA-2 hypoxia 8 d replicate 2


title: d10_f_315: female embryo on Day10


title: D8ANA-1 hypoxia 8 d replicate 1


title: d08_m_136: male embryo on Day8

source_name: male embryo on Day8

value: male


title: d08_m_133: male embryo on Day8

value: embryo


title: D8AE-3 normoxia 8 d replicate 3


title: d08_m_121: male embryo on Day8


title: D8AE-2 normoxia 8 d replicate 2


title: d08_m_103: male embryo on Day8


title: siFOXA1#1 Replicate 1

description:
FOXA1 targetting siRNA transfected cells
Sample 3


title: D0cere-3 logarithmic phase replicate 3


title: d08_m_111: male embryo on Day8


title: D8AE-1 normoxia 8 d replicate 1


title: D0-2 Stationnary phase replicate 2


title: D0-1 Stationnary phase replicate 1


title: d08_f_129: female embryo on Day8

source_name: female embryo on Day8


title: d08_f_130: female embryo on Day8


title: d08_f_124: female embryo on Day8


title: W22-ref IgG mRNA

description: Gene binding abundance.xlsx

source_name: W22-ref IgG

extract_protocol:
Frozen tissue was pulverized in liquid nitrogen by Grinding and was lysed in ice-cold lysis buffer (50 mM Tris 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5% deoxycholate) with freshly added 1mM DTT, 200 U/mL RNase inhibitor (Takara) and protease inhibitor cocktail (Roche) for 30 min on ice. After centrifugation for 30 min at 12000 rpm at 4 oC, the supernatant was transferred to a new tube and used for immunoprecipitation. For immunoprecipitation, 300 μL lysate was incubated with 10 μg antibody or control IgG antibody overnight at 4 oC. The immunuprecipitates were further incubated with protein A Dynabeads for 2h at 4 oC. After applying to magnet and removing the supernatants, the beads were sequentially washed with lysis buffer, high-salt buffer (250 mM Tris 7.4, 750 mM NaCl, 10 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5 deoxycholate), and PNK buffer (50 mM Tris, 20 mM EGTA and 0.5% NP-40) for two times, respectively. The immunoprecipitates were eluted from the beads with elution buffer (50 nM Tris 8.0, 10 mM EDTA and 1% SDS) and the RNA was purified with Trizol reagent (Life Technologies, Invitrogen, Carlsbad, CA, USA).
Carry the recovered RNA through a standard cDNA library preparation protocol originally described for cloning of small regulatory RNAs. The first step, 3' adapter ligation, was carried out as described on a 20 μl scale using 10.5 μl of the recovered RNA. Use the sequencing adapter sets described. Depending on the amount of RNA recovered, 5'-adapter-3'-adapter products without inserts may be detected after amplification of the cDNA as additional PCR bands. In such cases, excise the longer PCR product of expected size from a 3% NuSieve low-melting point agarose gel, elute the PCR product from the gel pieces using the GelElute kit (Qiagen).

value: 6 cm length

value: tassel

tag: rip antibody

value: IgG (abmart, custom)


title: ago18b::mum IgG mRNA

description: Gene binding abundance.xlsx

source_name: ago18b::mum IgG


title: ago18b::mum AGO18b mRNA

description: Gene binding abundance.xlsx

source_name: ago18b::mum AGO18b

value: AGO18b (abmart, custom)


title: d08_f_105: female embryo on Day8


title: d08_f_109: female embryo on Day8


title: Replicate 3 - wt control

city: Davis

first: Celina

middle: E

last: Juliano

state: California

address: 149 Briggs Hall

department: MCB

institute: University of California Davis

data_processing:
Adapters (Truseq3) were trimmed and reads filtered using trimmomatic-0.33 (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). RSEM v1.2.31/bowtie v1.1.2 were used to estimate expression levels using a transcriptome reference (rsem-calculate-expression --forward-prob 0).
tab-delimited text file of isoform level raw expression estimates - Differential_Gene_Expression_Count_Matrix.txt
Genome_build: Hydra vulgaris AEP transcriptome (aepLRv2) (Transcriptome Shotgun Assembly project: GHHG01000000)

organism: Hydra vulgaris

source_name: whole animal

growth_protocol: Hydra were cultured according to standard protocol (Lenhoff, 1983)  at 18˚C.

extract_protocol:
Trizol (Invitrogen)
TruSeq stranded RNA (RS-122-2201)

treatment_protocol: Offspring (without transgene) from the hywi RNAi-1 transgenic line were collected 4 days post hatching. 10 animals were used in RNA extractions.

value: whole animal

value: AEP

tag: genotype/variation

value: wild type offspring, lacking RNAi transgene


title: W22-ref AGO18b mRNA

description: Gene binding abundance.xlsx

source_name: W22-ref AGO18b


title: Replicate 1 - wt control


title: Replicate 2 - wt control


title: adapted T56-1 diesel exhaust atm. 3

first: Pier-Luc

last: Tremblay

address: 122 Luoshi Road

department: School of Chemistry, Chemical Engineering and Life Science

institute: Wuhan University of Technology

data_processing:
Quality-scored basecalling was performed with the Illumina HiSeq Control software.
Sequenced reads wer mapped on the reference E. coli BW25113 genome with Bowtie 2.
Fragments Per kilobase of transcript per million mapped reads (FPKM) were calculated with RSEM.
FDR-adjusted p-value (q-value) were calculated with EdgeR
Genome_build: NZ_CP009273.1
Supplementary_files_format_and_content: tab-delimited text files including gene, annotation, raw count for each replicate, fpkm for each replicate,  FPKM mean,  log2 fold change, p-value and q-value.

organism: Escherichia coli BW25113

source_name: Bacterial culture

growth_protocol: E. coli BW25113 and T56-1 were grown to mid-log in M9-glucose medium under three different atmospheres. For all tested conditions, both strains were grown in triplicate in 100 ml volume.

extract_protocol:
Total RNA was extracted from E. coli strains with the TRIzol reagent from Invitrogen.  rRNA was depleted with the Ribo-Zero- rRNA Removal Kits from Epicentre.
The library was constructed with the Illumina TruSeq RNA sample preparation kit.

value: Diesel exhaust atmosphere-adapted

tag: number of transfer

tag: growth medium

tag: growth atmosphere

value: Diesel exhaust (PM2.5:613 ug m-3)

tag: growth phase

value: mid-log


title: adapted T56-1 diesel exhaust atm. 2


title: adapted T56-1 diesel exhaust atm. 1


title: Replicate 2 - hywi knockdown

treatment_protocol: Offspring (with transgene) from the hywi RNAi-1 transgenic line were collected 4 days post hatching. 10 animals were used in RNA extractions.

value: transgenic line expressing hywi hairpin transgene in epithelial stem cells


title: D0-3 Stationnary phase replicate 3

extract_protocol:
The RNA protocol extraction used was adapted from (Moyrand et al., Eukaryotic Cell, 2008). Briefly, the samples were lyophilized overnight. RNAs were extracted following a protocol divided in 3 parts: i) an extraction step was performed in Trizol reagent (Invitrogen), ii) a second step by adding Chloroform (Invitrogen) iii) the last step was an overnight Isopropanol precipitation at -20°C.
We used 1 μg of total RNA to purify polyadenylated mRNAs and to build an RNA library, using TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-9004DOC) as recommended by the manufacturer. Directional library are checked for concentration and quality on DNA chips with the Bioanalyser Agilent. More precise and accurate quantification is performed with sensitive fluorescent-based quantitation assays ("Quant-It" assays kit and QuBit fluorometer, Invitrogen).


title: ago18b::mum AGO18b 2nd

description:
miRNA_expression_level_RIP-Seq.xlsx
PhasiRNA_expression_level_RIP-Seq.xlsx

data_processing:
Illumina bcl2fastq (v2.16.0.10) was used to convert bcl files to fastq files.
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor and removing low quality bases (less than 20), too short reads (less than 16nt) were also dropped. FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the reference genome by bowtie (Langmead et al., 2009).
For sRNA and RIP sequencing, TPM (transcripts per million mapped reads) was used to calculate the abundance of miRNAs.
We then aligned the RIP-seq and miRNA-seq reads to the 21nt and 24nt phasiRNA loci, respectively. We evaluated the abundance of each phasiRNA by counting the 21nt reads number for each 21nt phasiRNA and 24nt reads number for 24nt phasiRNAs, respectively. The RPKM value for each phasiRNA was also obtained.
Genome_build: Zma B73 AGPv2
Supplementary_files_format_and_content: Tab separated Microsoft Excel files


title: ago18b::mum AGO18b 1st


title: ago18b::mum IgG 1st


title: W22-ref IgG 2nd


title: wild type diesel exhaust atm. 3

value: wild type


title: colchicine - Hywi IP

description: piRNA

data_processing:
2 rounds of trimming were performed using cutadapt: 1) cutadapt -a TGGAATTCTCGGGTGCCAAGG --minimum-length 28 2) cutadapt -u 4 -u -4 . Reads were mapped the Hydra vulgaris AEP transcriptome using rsem/1.2.31. piRNAs mapping in an antisense orientation were allowed up to three mismatches using the following parameters: "--forward-prob 0 --bowtie-n 3”. piRNAs mapping in a sense orientation were not allowed any mismatches using the following parameters: “--forward-prob 1 --bowtie-n 0”.
tab-delimited text file of isoform level raw expression estimates - piRNA_Counts_Matrix.txt
Genome_build: Hydra vulgaris AEP transcriptome (aepLRv2) (Transcriptome Shotgun Assembly project: GHHG01000000)

source_name: whole animal - interstitial cell depleted

extract_protocol:
Trizol (Invitrogen)
NEXTflex Small RNA-Seq Kit v3 (PerkinElmer Cat# NOVA-5132-05),The manufacturer’s protocol was followed, with modifications to 3’ and 5’ adapter ligations: 3’ adapter ligation was performed at 16°C overnight and 5’ adapter ligation was performed at 20°C for two hours. Following adapter ligation, libraries were amplified for 18 cycles and were selected for a size of 108-180 base pairs using BluePippin (Sage Science).

treatment_protocol: Immunoprecipitation (IP) of piRNAs from whole animals was performed using 225 epithelialized Hydra that were treated with colchicine.

value: cnnos1::GFP transgenic line (Hermmrich et al. 2012)


title: wild type diesel exhaust atm. 2


title: colchicine - Hyli IP

description: piRNA

value: whole animal - interstitial cell depleted


title: colchicine - degradome

data_processing:
2 rounds of trimming were performed using cutadapt: 1) cutadapt -a TGGAATTCTCGGGTGCCAAGG --minimum-length 28 2) cutadapt -u 4 -u -4 . Reads were mapped the Hydra vulgaris AEP transcriptome using rsem/1.2.31. piRNAs mapping in an antisense orientation were allowed up to three mismatches using the following parameters: "--forward-prob 0 --bowtie-n 3”. Degradome reads were mapped without any allowed mismatches using the following parameters: “--forward-prob 1 --bowtie-n 0”.
tab-delimited text file of isoform level raw expression estimates - Degradome_Counts_Matrix.txt
Genome_build: Hydra vulgaris AEP transcriptome (aepLRv2) (Transcriptome Shotgun Assembly project: GHHG01000000)

extract_protocol:
Trizol (Invitrogen)
NEXTflex Small RNA-Seq Kit v3 (PerkinElmer Cat# NOVA-5132-05). Starting with 2 ������g of total RNA, poly(A) enrichment was performed to capture mRNAs, which was followed by 5’ adapter ligation. Ligation of the 5’ adaptor was done without first removing the 5’ m7G cap so that only cleaved mRNAs were available for ligation. The RNA was then chemically fragmented and 3’ adapters were ligated. For ligations, 25% of the standard adapter mass was used.

treatment_protocol: RNA was extracted from 20 epithelialized Hydra that were treated with colchicine.


title: W22-ref AGO18b 2nd


title: W22-ref AGO18b 1st


title: wild type urban polluted atm. 2

value: Urban polluted (PM2.5:230 ug m-3)


title: wildtype - Hywi IP

description: piRNA

treatment_protocol: Immunoprecipitation (IP) of piRNAs from whole animals was performed using 225 Hydra vulgaris AEP.


title: ago18b::mum IgG 2nd


title: wild type urban polluted atm. 1


title: W22-ref IgG 1st


title: ago18b::mum 1st

description:
small RNA
miRNA_expression_level_sRNA-Seq.xlsx
PhasiRNA_expression_level_sRNA-Seq.xlsx

extract_protocol:
Two pools of more than 10 cm tassels were from homozygous zmago18b mutants and wild-type sibling plants. Freshly dissected tassel tissue was dissected and immediately frozen in liquid nitrogen. Total RNA was extracted from pools of tassel tissue using Trizol (Life Technologies, Invitrogen, Carlsbad, CA, USA) and treated with RQ1 DNase (promega) to remove DNA.
About 3 μg of total RNA was used for small RNA cDNA library preparation with Balancer NGS Library Preparation Kit for small/microRNA (GnomeGen) following manufacture's instruction. Briefly, RNAs were ligated to 3' and 5' adaptor sequentially, reverse transcribed to cDNA and PCR amplified. Whole library was applied to 10% native PAGE gel electrophoresis and bands corresponding to microRNA insertion were cut and eluted. After ethanol precipitation and washing, the purified small RNA libraries were quantified with Qubit Fluorometer (Invitrogen, USA).


title: wildtype - Hyli IP

description: piRNA

extract_protocol:
Trizol (Invitrogen)
NEXTflex Small RNA-Seq Kit v3 (PerkinElmer Cat# NOVA-5132-05), The manufacturer’s protocol was followed, with modifications to 3’ and 5’ adapter ligations: 3’ adapter ligation was performed at 16°C overnight and 5’ adapter ligation was performed at 20°C for two hours. Following adapter ligation, libraries were amplified for 18 cycles and were selected for a size of 108-180 base pairs using BluePippin (Sage Science).


title: Replicate 3 - hywi knockdown


title: wildtype - degradome

extract_protocol:
Trizol (Invitrogen)
NEXTflex Small RNA-Seq Kit v3 (PerkinElmer Cat# NOVA-5132-05).Starting with 2 ������g of total RNA, poly(A) enrichment was performed to capture mRNAs, which was followed by 5’ adapter ligation. Ligation of the 5’ adaptor was done without first removing the 5’ m7G cap so that only cleaved mRNAs were available for ligation. The RNA was then chemically fragmented and 3’ adapters were ligated. For ligations, 25% of the standard adapter mass was used.

treatment_protocol: RNA was extracted from 20 WT Hydra vulgaris AEP


title: wild type standard laboratory atm. 3

value: Standard laboratory  (PM 2.5:17 ug m-3)


title: wild type standard laboratory atm. 2


title: W22-ref 2nd


title: MIX 2hpf m5C rep2

description: MIX 2hpf rep2

organism:
Danio rerio
Homo sapiens

source_name: Zebrafish embryo and HeLa cell

extract_protocol:
Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-BisSeq library construction.
Thus purified mRNA was used for RNA-BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 (Dhfr mRNA serves as methylation conversion control) was fragmented to ~100-nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent (Ambion), then stopped by 10× RNA stop solution (Ambion), and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution (pH 5.1), which is a 100:1 mixture of 40% sodium bisulfite (Sigma) and 600 µM hydroquinone (Sigma) and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns (PALL Corporation) with centrifugation. After washed with nuclease-free water and centrifuged for five times, the RNA was finally disolved in 75 μl nuclease-free water and then desulfonated by incubation with an equal volume of 1 M Tris-HCl (pH 9.0) at 75 °C for 1 h. After ethanol precipitation, the RNA was resuspended in 11 µl of RNase-free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase (Invitrogen) and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.
RNA-BisSeq

value: AB strain and HeLa cell

value: Zebrafish embryo and HeLa cell

tag: age

value: 2 hpf

value: whole embryo and HeLa cell


title: W22-ref 1st

value: 6 cm length

value: tassel


title: Replicate 1 - hywi knockdown

value: whole animal

value: AEP


title: MIX 2hpf m5C rep1

description: MIX 2hpf rep1


title: wild type standard laboratory atm. 1

value: Standard laboratory (PM 2.5:17 ug m-3)


title: wild type diesel exhaust atm. 1

value: Diesel exhaust (PM2.5:613 ug m-3)


title: wild type urban polluted atm. 3

value: mid-log


title: Bif1Bif4_tassel_GH2017_rep2

status: Public on Aug 06 2019

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

data_processing:
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence using trimmomatic, then mapped to ZmB73v3 whole genome using Tophat v2.1.1
Differentially expressed genes were identified using DESeq2 and ht-seq-count
Genome_build: ZmB73v3.31

source_name: 2-4mm maize B73 greenhouse-grown Bif1;Bif4 mutant tassels

extract_protocol:
samples were snap frozen in liquid nitrogen and total RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment
Stranded Illumina mRNA sequencing libraries were generated using TruSeq (Illumina)

treatment_protocol: 2-4mm maize B73 greenhouse-grown tassels (5 wt tassels per replicate; 10 Bif1Bif4 tassels per rep) were harvested.

tag: background

value: Bif1;Bif4 double heterozygous mutant

value: tassels


title: w303scc1_rep3

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

data_processing:
FastQC (Babraham Bioinformatics, Cambridge, UK) - Sequence quality and contamination check
Read mapping and counting with HiSAT2 in Galaxy platform for BAM files output
Differential expression analysis (pairwise) performed using Galaxy Cuffdiff program
Adjusted p-values calculated with Benjamini-Hochberg multiple testing adjustment (qvalue).
Genome_build: sacCer3
Supplementary_files_format_and_content: [bigwig]  peaks of aboundance

source_name: scc1-73 mutant replicate3

growth_protocol: Cells were synchronized in G1 with alpha factor (0.5 o 1.0 µg/ml) in minimal complete media (SC). Cells were then washed three times with prewarmed rich media (YPAD, 37ºC) and released in this media at 37ºC with 50µg/ml of pronase (eliminate remaining alpha factor) and 15µg/ml of Nocodazole (block cells at the G2/M transition) until all of them reached a G2/M state determined by flow cytometry, budding index and DAPI staining

extract_protocol:
RNA was extracted using a standard hot acid phenol extraction protocol (Kohrer et al 1991) and purified with an RNeasy Plus Mini kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols and TruSeq stranded mRNA library preparation kit (20020594, Illumina )from 100ng of total RNA

treatment_protocol: Samples for RNA were washed with cold water and stored at -80ºC until use

value: ws73-4B (W303 background)

tag: genotype

value: MATa leu2-3,112 ura3-1 ade2-1 can1-100 his3-11 RAD5 scc1-73 bar1<delta>::natMX4


title: w303scc1_rep2

source_name: scc1-73 mutant replicate2


title: wildtype_tassel_GH2017_rep2

source_name: 2-4mm maize B73 greenhouse-grown wildtype tassels

growth_protocol: 2-4mm maize B73 greenhouse-grown tassels

value: wildtype


title: wildtype_tassel_GH2017_rep1


title: w303_rep1

source_name: wild type replicate 1

value: YK402-2 (W303 background)

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11 RAD5 bar1<delta>::HISG


title: cachectic patient muscle 5

city: Charleston

first: Erin

last: Talbert

state: SC

address: 70 President Street

department: Pediatrics

institute: Medical University of South Carolina

description:
muscle from cachectic pancreatic cancer patient 5
ML5

data_processing:
Illumina HiSeq4000 were used for sequencing
Sequence reads were mapped to GRCh38 using HISAT v.2.0.5 with default parameters
Sequences from 2 lanes were combined for each sample.
Raw counts were calculated using featureCounts v1.4.5
Genome_build: ensembl GRCh38 v86
Supplementary_files_format_and_content: Excel Worksheet file includes voom counts values for each sample

source_name: rectus abdominus muscle

extract_protocol:
Total RNA was purified from snap-frozen muscle using Trizol reagent. 200 ng of rRNA-depleted RNA was used for the construction of the library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: cachectic


title: cachectic patient muscle 3

description:
muscle from cachectic pancreatic cancer patient 3
ML3


title: w303scc1_rep1

source_name: scc1-73 mutant replicate1

value: ws73-10B (W303 background)


title: w303_rep2

source_name: wild type replicate 2


title: cachectic patient muscle 2

description:
muscle from cachectic pancreatic cancer patient 2
ML2


title: ago18b::mum 2nd

tag: strain


title: control patient muscle 5

description:
muscle from non cancer control patient 5
MC5

value: control


title: control patient muscle 4

description:
muscle from non cancer control patient 4
MC4


title: control patient muscle 3

description:
muscle from non cancer control patient 3
MC3


title: Bif1Bif4_tassel_GH2017_rep3

tag: tissue


title: control patient muscle 2

description:
muscle from non cancer control patient 2
MC2


title: ICH11580_Bcell

city: Oxford

first: Sorcha

last: O'Byrne

state: Oxford

address: MRC MHU and WIMM, John Radcliffe Hospital

department: Department of Paediatrics

institute: University of Oxford

data_processing:
Fastq files were trimmed with TrimGalore! (v0.4.1)
PCR duplicates removed using Picard v1.83 tools.
fastq files were aligned using STAR v2.4.2a
read counts were counted using featureCounts in the Subread 1.4.5 package
Transcripts per million (TPM) calculated in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcript per million table in csv format

source_name: fetal bone marrow

extract_protocol:
For bulk RNA-Sequencing, the SMART-Seq2 protocol was followed. Briefly, 100 purified HSC or progenitor cells were sorted directly into lysis buffer containing 0.4% Triton X-100 (Sigma-Aldrich), RNase inhibitor (Clontech), 2.5 mM dNTPs (Thermo Fisher) and 2.5 μM oligo-dT30VN primer (Biomers.net). cDNA was generated using SuperScript II (Invitrogen), pre-amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) using 18 cycles of amplification. After PCR amplification, the cDNA libraries were purified with AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. Post-purification libraries were resuspended in EB buffer (Qiagen). The quality of cDNA traces was assessed by using a High Sensitivity DNA Kit in a Bioanalyzer instrument (Agilent Technologies).
Tagmentation and library preparation was performed using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer's instructions.

tag: biological sample id

tag: population

value: Bcell

tag: unique identifier


title: control patient muscle 1

description:
muscle from non cancer control patient 1
MC1


title: ICH11875_MPP

value: MPP


title: ICH11875_HSC

value: HSC


title: ICH11580_HSC


title: Bif1Bif4_tassel_GH2017_rep1


title: ICH12636_Bcell


title: ICH11875_ProB

value: ProB


title: wildtype_tassel_GH2017_rep3


title: ICH11875_PreProB

value: PreProB


title: cachectic patient muscle 4

description:
muscle from cachectic pancreatic cancer patient 4
ML4


title: ICH12636_ProB


title: ICH11875_LMPP

value: LMPP


title: ICH12636_LMPP


title: ICH11580_ELP

value: ELP


title: ICH11875_Bcell


title: ICH11580_LMPP


title: ICH12636_MPP


title: ICH11580_MPP


title: ICH12636_PreProB


title: ICH11580_PreProB


title: ICH12636_ELP


title: ICH11875_ELP


title: ICH11580_ProB


title: ICH12636_HSC


title: d12_f_289: female embryo on Day12

source_name: female embryo on Day12

extract_protocol:
AllPrep DNA/RNA Micro Kit
Illumina TruSeq Stranded mRNA library construction

tag: gender

value: female

value: embryo


title: HumanLiver, tumor tissue [s19T_NS]

city: Shanghai

first: Ji-Min

last: Zhu

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital of Fudan University

description: Microarray profile of lncRNA and mRNA in the tumor tissue of Hepatocellular carcinoma

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: human liver cancer tissue

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVanaTM miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: 7 pairs of HCC and matched adjacent tumor-free tissues were collected during the surgery from HCC patients admitted to Zhongshan Hospital of Fudan University between 2008 and 2009 and All tissue samples were stored at -80℃ immediately after surgery

value: hepatocellular carcinoma tissue

value: Male


title: HumanLiver, tumor tissue [s11T_NS]

value: Female


title: RELA_KP093_WDH

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: Biotin

source_name: mouse tumor

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

value: brain tumor

tag: development stage

tag: construct

value: human C11orf95-RELA fusion


title: HumanLiver, tumor tissue [s6T_NS]


title: HumanLiver, tumor adjacent tissue [s13P_NS]

description: Microarray profile of lncRNA and mRNA in the adjacent tissue of Hepatocellular carcinoma

source_name: human liver cancer adjacent tissue

value: hepatocellular carcinoma matched adjacent tissue


title: HumanLiver, tumor tissue [s10T_NS]


title: RELA_KP075_WDH


title: Liver, INPUT_ZT22 (DNA input)

city: Lausanne

first: Nicolas

last: Guex

state: Vaud

address: Genopode, Dorigny Campus

department: CIG - Center for Integrative Genomics

institute: University of Lausanne

description: pool of 5 mice

data_processing:
Basecalls performed using CASAVA version 1.82
ChIP-seq 50/100 bases paired-ended reads were aligned to mouse genome Ensemble GRCm37 (mm9) by Elandv2e
Tags were filtered by the threshold of 5 mismatchs and ambiguous mapping
Only fragments with both ends uniquely mapped were retained
The mm9 genome was divided into 500 bases long consecutive, non-overlapping bins to calculate the ChIP signal. For each bin, each sample has its own value of tag density which is the AUC (area under the curve) created by the fragments pilled-up. Full fragment lengths were kept for all analysis. The bin values were scaled by the total tags for each sample and 30 pseudo-counts were added to stabilize the variance of low scores. The same quantifications were done for all the INPUT samples. All the values were then log2 converted.
The log2 scaled bin values of each ChIP sample and of the corresponding time INPUT sample were used to compute ratio-mean distribution. This distribution was sectioned into 200 step-wise proportions along the mean axis. Smoothing function lowess with smoother-span 0.2 was applied for only the negative-ratio bin population of each step-wise proportion. From the predicted distribution of smooth function, the mirrored bins were selected on the positive-ratio population. Distribution function was applied for this positive-ratio population with the  mean and standard deviation derived from smooth function. The p-values were adjusted for false discovery rate (Benjamini–Hochberg). All bins with adjusted p-value less than 0.05 were considered significant. Comparison was reapeated with shifted of half bin size (250 bases).
The bins significant in both sets (non-shifted and 250-shifted) were merged. Consecutive significant bins with maximum distance of 250 were merged into significant regions.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated from remaining tags and scaled by the total tag number for each sample

source_name: liver tissue

growth_protocol: C57/BL6 male 12-14-week-old mice were housed in the standard 12 hours light/12 hours dark (LD) cycle. For 7 days they had access to food only between ZT12 and ZT24 (Zeitgeber time; ZT0 is the time when lights are turned on, ZT12 as time the lights turned off), but free access to water

extract_protocol:
The nuclei isolation was performed as described in (Ripperger and Schibler, 2006), except that the ultracentrifugation was performed for 1h at 24,000 rpm (100,000g) at 1°C in a Beckmann SW28 rotor. The nuclei were lysed with 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM EDTA and 1% SDS. The sonication of the chromatin was performed with a Branson SLPe sonicator during 15 cycles of 10 sec at 50% amplitude. The sheared chromatin was then diluted 10x in 50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.5 mM PMSF, and protease inhibitor cocktail (Sigma, #P8340).The inputs were isolated and the immunoprecipitation performed with a homemade anti-RXR antibody, generously provided by C Rochette-Egly, overnight at 4°C on a rotating platform. Protein A-sepharose CL-4B beads (GE Healthcare, #17-0780-01) were added and the tubes were kept rotating for 2 h at 4°C. The beads were then washed 2x with 50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 0.5 mM PMSF, and protease inhibitor cocktail (Sigma, #P8340); 2x with 50 mM Hepes pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 0.5 mM PMSF, and protease inhibitor cocktail (Sigma, #P8340); 2x with 20 mM Tris pH 8, 1 mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 0.5 mM PMSF, and protease inhibitor cocktail (Sigma, #P8340); and 2x with 10 mM Tris pH 8 and 1 mM EDTA. The elution of the chromatin from the beads was done twice with 50 mM Tris pH 8, 1 mM EDTA, 1% SDS and 50 mM NaHCO3 for 10 min at 65°C. NaCl was added to 200 mM and the chromatin was decrosslinked at 65°C overnight. The samples were treated with 25 µg/ml of RNase A for 1 h at 37°C, then with 5 mM of EDTA and 50 µg/ml of proteinase K for 2 h at 42°C. The DNA was purified with the NucleoSpin® Gel and PCR Clean-up from Macherey-Nagel. Nuclei isolation method as described in Nature Genetics by (Ripperger and Schibler, 2006).
The DNA concentration was measured with the Qubit® Fluorometer (Invitrogen). The libraries were prepared starting from 2.1 ng to 4.2 ng of IP samples and 8 ng of inputs samples, using the Microplex Library Preparation Kit (Diagenode, #C05010010)

treatment_protocol: At 7 time points of 4 hours interval (ZT02, ZT06, ZT10, ZT14, ZT18, ZT22 and ZT26) 5 mice were anesthetized with isoflurane and sacrificed. Their liver tissues were collected, pooled and immediately homogenized in PBS containing 1% formaldehyde for immunoprecipitation. All animal care and handling were performed based on the State of Lausanne’s law for animal protection.

value: liver tissue

value: 12-14 week old

tag: diet

value: Normal chow diet

tag: time point

tag: chip antibody


title: Liver, INPUT_ZT18 (DNA input)

description: pool of 5 mice


title: Liver, INPUT_ZT26 (DNA input)

description: pool of 5 mice


title: HumanLiver, tumor adjacent tissue [s10P_NS]


title: YAP_KP015_WDH

source_name: brain tumors induced by electroporating a human YAP1-MAMLD1 fusion construct into cerebral ventricular zone cells of fetal mice at E13.5

tag: developmental stage

value: human YAP1-MAMLD1 fusion


title: RELA_KP079_WDH


title: YAP_KP014_WDH


title: YAP_KP017_WDH


title: HumanLiver, tumor adjacent tissue [s6P_NS]


title: RELA_KP094_WDH


title: RELA_KP095_WDH


title: YAP_KP011_WDH


title: YAP_KP013_WDH


title: Liver, INPUT_ZT14 (DNA input)

description: pool of 5 mice


title: HumanLiver, tumor adjacent tissue [s19P_NS]


title: Liver, INPUT_ZT10 (DNA input)

description: pool of 5 mice


title: HumanLiver, tumor adjacent tissue [s11P_NS]


title: HumanLiver, tumor adjacent tissue [s9P_NS]


title: HumanLiver, tumor tissue [s13T_NS]


title: HumanLiver, tumor tissue [s9T_NS]


title: Liver, INPUT_ZT06 (DNA input)

description: pool of 5 mice


title: Liver, INPUT_ZT02 (DNA input)

description: pool of 5 mice


title: HumanLiver, tumor tissue [s5T_NS]


title: Liver, RXR_ZT26 (ChIP-seq)

description: pool of 5 mice

value: pan-RXR antibody (homemade, generously provided by C Rochette-Egly)


title: Liver, RXR_ZT22 (ChIP-seq)

description: pool of 5 mice


title: HumanLiver, tumor adjacent tissue [s5P_NS]


title: Liver, RXR_ZT14 (ChIP-seq)

description: pool of 5 mice


title: cachectic patient muscle 1

description:
muscle from cachectic pancreatic cancer patient 1
ML1

value: cachectic


title: Liver, RXR_ZT06 (ChIP-seq)

description: pool of 5 mice


title: Liver, RXR_ZT02 (ChIP-seq)

description: pool of 5 mice


title: Liver, RXR_ZT18 (ChIP-seq)

description: pool of 5 mice


title: T-N2G_Input

city: Aoba-ku, Sendai

first: Fumiki

last: Katsuoka

state: Miyagi

address: 2-1 Seiryo-cho

country: Japan

institute: Tohoku University

data_processing:
Illumina bcl2fastq v2.16.0.10 was used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 v2.2.9.
Peaks were called using MACS2 version2.1.1.20160309.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS2.

growth_protocol: MEFs were cultured in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
The cells were fixed with 1% formaldehyde for 10 min at room temperature and subsequently quenched with 0.125-M glycine. ChIP was performed with anti-MafG antibody (PMID: 22965115). The antibody incubation were performed overnight at 4℃.
Purified ChIPed DNA and input DNA were used for preparing the sequencing libraries by a NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: MEFs were treated with 100µM Diethyl Maleate (DEM) or Vehcle for 4 hr.

tag: cell type

value: embryonic fibroblast

tag: genotype/variation


title: 3_T-N2G_Veh

data_processing:
Illumina bcl2fastq v2.16.0.10 was used for basecalling.
Reads were mapped against mouse (mm9) genome using the TopHat v2.0.8b.
Differential gene analaysis was performed using Cuffdiff v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genotype were generated using Cuffdiff.

extract_protocol:
Total RNA was prepared by using RNeasy Mini Kit (QIAGEN).
Isolation of poly(A)-tailed RNA and library construction were performed using SureSelect Strand Specific RNA Sample Prep Kit (Agilent Technologies).

treatment_protocol: MEFs were treated with 100µM Diethyl Maleate (DEM) or Vehcle for 12 hr.

tag: treatment

value: Vehcle for 12 hrs


title: Liver, RXR_ZT10 (ChIP-seq)

description: pool of 5 mice

tag: age


title: 3_T-N2G_DEM

value: 100µM Diethyl Maleate (DEM) for 12 hrs


title: T-N2G_Veh


title: 3_Mock_DEM


title: 3_Mock_Veh


title: 2_Mock_DEM


title: 2_Mock_Veh


title: 2_T-N2G_DEM


title: 1_T-N2G_DEM


title: 2_T-N2G_Veh


title: T-N2G_DEM

extract_protocol:
The cells were fixed with 1% formaldehyde for 10 min at room temperature and subsequently quenched with 0.125-M glycine. ChIP was performed with anti-MafG antibody (PMID: 22965115). The antibody incubation were pereformed overnight at 4℃.
Purified ChIPed DNA and input DNA were used for preparing the sequencing libraries by a NEBNext Ultra II DNA Library Prep Kit.

tag: antibody


title: 1_Mock_DEM


title: 1_T-N2G_Veh