title: IFN alpha+LPS-stimulated Dendritic Cells (8h/4h) [mm_DC_IFNA8h_LPS4h_RS252]

value: 8h, 1000U/ml, murine IFN alpha; 4h, 10ng/ml, LPS


title: H&S3_2

status: Public on Jun 04 2019

type: SRA

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiaotong University School of Medicine

library_source: transcriptomic

data_processing:
Sequencing reads from each sample were mapped to the mouse or human reference genomes (mm10 or hg38 version) by using TopHat v2.1.1
Sequencing counts at the gene level were obtained using HTSeq v 0.9.1.
R (version 3.4.0) package DESeq2 was then used to normalize gene counts and identify differential expressed genes between different conditions.
Genome_build: hg38 (human)
Supplementary_files_format_and_content: tab-delimited text files include normalized gene counts values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: hESC derived progenitor cells

growth_protocol: Human ESCs were broken up into colonies and suspended in hESCM for 4 days to form EBs. EBs were then switched to the NIM to guide the cells toward the NE fate for 2 days. During the period, SB431542 (2 µM, Stemgent) and LDN193189 (200 nM, Stemgent), inhibitors to block TGF-β and BMP signaling, were added to the EBs from Days 0 to 6. At Days 6-17, cell aggregates were adherently cultured and neuroectoderm cells were formed. For ventralization, a combination of SHH (250 ng/mL, R&D Systems) and the smoothened activator purmorphamine (0.3μM, Stemgent) were added to the neuroectoderm cells from day 10 to day 17. For Caudalization,  retinoic acid 1:10000 were added to the neuroectoderm cells from day 10 to day 17

extract_protocol:
MGE cells were collected, or MGE was removed from embryo. RNA was harvested using Trizol reagent. NEBNext Ultra RNA library Prep Kit for Illumina (E7530) was used with 500 ng of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using the manufacturer’s protocol

treatment_protocol: As to virus groups, ZIKA virus were added into the NIM medium from day 17, keep 3 and 6 days

tag: cell line

tag: cell type

value: hESC-derived neuron progenitor cells

tag: Stage

value: Day 17 after differentiation

tag: time point

value: 3 dpi

tag: agent


title: FVz3_1

value: ZIKV


title: IFN gamma+LPS-stimulated Dendritic Cells (8h/4h) [mm_DC_IFNG8h_LPS4h_RS260]

city: Poznań

first: Anna

last: Piaszyk-Borychowska

address: ul. Umultowska 89

department: Department of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

data_processing:
Alignment with TopHat v2.0.7 using default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: N/A

organism: Mus musculus

source_name: bone marrow

growth_protocol: VSMC were cultured in DMEM complete medium supplemented with 10% FBS, 1:100 L-glutamine and 1:100 antibiotic/antimycotic solution. On the day before treatment, complete medium was exchanged onto 2% FBS containing starving medium. Differentiated BMDM and DC were immediately placed in serum free medium or 2% FBS containing RMPI1640 supplemented with 1:100 antibiotic/antimycotic solution and 50μM β-ME, respectively, for 24 hours.

extract_protocol:
Total RNA from primary VSMC, BMDM and DC was isolated with GeneMATRIX Universal RNA Purification Kit (EURx) according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.

treatment_protocol: VSMC, BMDM and DC were left unstimulated or treated with single stimulus as follows: 1000U/ml of IFN alpha or 10ng/ml of IFN gamma for 8 hours; 10ng/ml (BMDM and DC)/1μg/ml (VSMC) of LPS for 4 hours. To further study the effect of IFNs pretreatment on LPS signaling, the cells were first treated with IFN alpha/IFN gamma for 8 hours followed by LPS stimulation for another 4 hours, as abovementioned.

tag: strain/background

tag: genotype/variation

value: Wild type

value: Bone Marrow-Derived Dendritic Cells

tag: stimulation

value: 8h, 10ng/ml, murine IFN gamma; 4h, 10ng/ml, LPS


title: IFN alpha-stimulated Dendritic Cells (8h) [mm_DC_IFNA8h_RS257]

value: 8h, 1000U/ml, murine IFN alpha


title: H&Sz3_1


title: IFN alpha+LPS-stimulated Dendritic Cells (8h/4h) [mm_DC_IFNA8h_LPS4h_RS234]


title: IFN gamma-stimulated Dendritic Cells (8h) [mm_DC_IFNG8h_RS229]

value: 8h, 10ng/ml, murine IFN gamma


title: FVz3_2


title: IFN alpha-stimulated Dendritic Cells (8h) [mm_DC_IFNA8h_RS248]


title: FV3_1


title: IFN alpha+LPS-stimulated Dendritic Cells (8h/4h) [mm_DC_IFNA8h_LPS4h_RS243]


title: IFN alpha-stimulated Dendritic Cells (8h) [mm_DC_IFNA8h_RS239]


title: H&S3_1


title: IFN alpha-stimulated Dendritic Cells (8h) [mm_DC_IFNA8h_RS230]


title: FDz3_1


title: unstimulated Dendritic Cells [mm_DC_control_RS263]


title: H&Sz3_2


title: unstimulated Dendritic Cells [mm_DC_control_RS255]


title: FD3_2


title: FD3_1


title: FVz6_2

value: 6 dpi


title: unstimulated Dendritic Cells [mm_DC_control_RS246]


title: FV6_2


title: FVz6_1


title: unstimulated Dendritic Cells [mm_DC_control_RS245]


title: unstimulated Dendritic Cells [mm_DC_control_RS237]


title: H&Sz6_2


title: H&Sz6_1


title: FDz6_2


title: H&S6_2


title: unstimulated Dendritic Cells [mm_DC_control_RS228]

value: Bone Marrow-Derived Macrophages


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS214]

value: 4h, 10ng/ml, LPS


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS226]


title: FV6_1


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS210]


title: H&S6_1


title: FD6_2


title: FDz6_1


title: FD6_1


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS206]


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS218]


title: unstimulated Dendritic Cells [mm_DC_control_RS254]


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS198]


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS202]


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS194]


title: IFN gamma+LPS-stimulated Bone Marrow-Derived Macrophages (8h/4h) [mm_BMDM_IFNG8h_LPS4h_RS199]


title: unstimulated Dendritic Cells [mm_DC_control_RS236]


title: LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS222]


title: IFN gamma-stimulated Bone Marrow-Derived Macrophages (8h) [mm_BMDM_IFNG8h_RS197]


title: IFN gamma-stimulated Bone Marrow-Derived Macrophages (8h) [mm_BMDM_IFNG8h_RS193]


title: IFN alpha+LPS-stimulated Bone Marrow-Derived Macrophages (8h/4h) [mm_BMDM_IFNA8h_LPS4h_RS219]


title: IFN alpha+LPS-stimulated Bone Marrow-Derived Macrophages (8h/4h) [mm_BMDM_IFNA8h_LPS4h_RS223]


title: IFN alpha+LPS-stimulated Bone Marrow-Derived Macrophages (8h/4h) [mm_BMDM_IFNA8h_LPS4h_RS227]


title: IFN alpha-stimulated Bone Marrow-Derived Macrophages (8h) [mm_BMDM_IFNA8h_RS221]


title: IFN alpha-stimulated Bone Marrow-Derived Macrophages (8h) [mm_BMDM_IFNA8h_RS217]


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS224]


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS220]


title: IFN alpha-stimulated Bone Marrow-Derived Macrophages (8h) [mm_BMDM_IFNA8h_RS225]


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS216]


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS208]


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS204]


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS200]


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS196]


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_RS294]

source_name: aorta

value: Vascular Smooth Muscle Cells

value: 4h, 1ug/ml, LPS


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS212]


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_RS282]


title: unstimulated Bone Marrow-Derived Macrophages [mm_BMDM_control_RS192]


title: IFN gamma-stimulated Bone Marrow-Derived Macrophages (8h) [mm_BMDM_IFNG8h_RS201]


title: IFN gamma+LPS-stimulated Bone Marrow-Derived Macrophages (8h/4h) [mm_BMDM_IFNG8h_LPS4h_RS195]


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_RS274]


title: IFN gamma+LPS-stimulated Bone Marrow-Derived Macrophages (8h/4h) [mm_BMDM_IFNG8h_LPS4h_RS203]


title: sRNA_GM12891

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

data_processing:
Basecalls were performed using CASAVA v1.8.4
Sequenced reads were trimmmed using trim_galore v0.3.3
Sequenced reads were aligned to Homo sapiens (hg38) reference genome+decoy+EBV using STAR v2.5.2b with following parameters: --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1
Reads were filtered for 5' soft clipping with samtools v1.2 : samtools view -h $BAM | awk '{S=0; split($6,C,/[0-9]*/); n=split($6,L,/[NMSID]/);  if (and($2,0x10)>0 && C[n]=="S") {S=L[n-1]} else if (and($2,0x10)==0 && C[2]=="S") {S=L[1]}; if (S<=1) print }' | samtools view -Sb - > ${BAM%.bam}filtered.bam
Counts within miRBase v21 mature miRNAs were generated by featureCounts from subread v. 1.5.0-p1
Genome_build: GENCODE hg38 + decoy + EBV
Supplementary_files_format_and_content: table of raw miRNA counts for each sample; a bed file containing the discovered eQTL-miRNA

growth_protocol: Lymphoblastoid cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.

extract_protocol:
2 million cells were harvested during the exponential growth phase. Pelleted by centrifuging 3000g for 10min at 4C. Supernatant was discarded and 700ul of Triazol was add, mixed by vortexing and then kept frozen at -80C until extraction via Qiagen miRNAeasy mini kit
Libraries were constructed using NEBNext Small RNA Library Prep Kit with size selection via Pippin Prep

value: EBV-transformed lymphoblastoid cell line

tag: number of cells


title: sRNA_GM12892


title: sRNA_GM12893


title: sRNA_GM12890


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_RS270]


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_RS266]


title: IFN gamma+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNG8h_LPS4h_RS275]

value: 8h, 10ng/ml, murine IFN gamma; 4h, 1ug/ml, LPS


title: sRNA_GM12888


title: IFN gamma+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNG8h_LPS4h_RS271]


title: IFN gamma+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNG8h_LPS4h_RS267]


title: IFN gamma-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNG8h_RS273]


title: sRNA_GM12887


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_RS290]


title: sRNA_GM12883


title: IFN gamma-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNG8h_RS265]


title: sRNA_GM12885


title: IFN alpha+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNA8h_LPS4h_RS283]

value: 8h, 1000U/ml, murine IFN alpha; 4h, 1ug/ml, LPS


title: IFN gamma-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNG8h_RS269]


title: IFN alpha+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNA8h_LPS4h_RS279]


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_RS278]


title: sRNA_GM12880


title: sRNA_GM12882


title: sRNA_GM12881


title: IFN alpha-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNA8h_RS277]


title: sRNA_GM12879


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_RS292]


title: IFN alpha-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNA8h_RS281]


title: sRNA_GM12889


title: ATAC_GM128793_rep2

library_source: genomic

data_processing:
Basecalls were performed using CASAVA v1.8.4
Sequenced reads were trimmmed using trim_galore v0.3.3
Sequenced reads were aligned to Homo sapiens (hg38) reference genome+decoy+EBV using Burrows-Wheeler Aligner (BWA-MEM v0.7.13)
Reads were filtered for unique alignments and deduplicated using picard-tools v1.92 and samtools v0.1.19
Reads were shifted using bedtools2 v2.24.0
Peaks were called for each replicate using MACS2 v.2.1.0
Peaks with an Irreproducible discovery rate (IDR) of < 0.05 were retained and filtered by consensus blacklisted regions as well as mitchondria homologous regions.
Peaks and summits were called using MACS2 v.2.1.0 on the combined reads from all of replicate 1 and of replicate 2 separately; and subsequently processed as above to create master peak and summit lists
Genome_build: GENCODE hg38 + decoy + EBV
Supplementary_files_format_and_content: bed file containing the IDR<0.05, filtered peaks [5th column contains the scaled IDR value; min(int(log2(-125IDR), 1000)] for each cell line; master summit and peak filtered files from all cell lines; the regions of homology to simulated mitocondrial reads; normalized counts for ATAC signal within summits; a bed file containing the discovered caQTL-summits

molecule: genomic DNA

growth_protocol: Lymphoblatoid cell lines were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.

extract_protocol:
50,000 cells  were harvested during the exponential growth phase. The cells were spun at 500 g for 5 minutes at 4˚C and then washed using 50 μL of cold 1X PBS. Samples were then centrifuged at 500 g for 5 minutes. Cells were lysed in cold lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and immediately spun at 500 g for 5 minutes at 4˚C.
The pellet was then resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL transposase and 22.5 μL nuclease-free water; Illumina Nextera). Following a 30-minute incubation at 37˚C, the samples were purified using the Zymo DNA Clean and Concentrator purification kit. Following the purification, the libraries were amplified with the following PCR conditions: 72°C for 5 minutes; 98°C for 30 seconds; and a total of 10 cycles of 98°C for 10 seconds; 63°C for 30 seconds; 1 minute for 72°C. Subsequently, the libraries were purified using Agencourt AMpure XP beads; large fragments were filtered by using 0.6x (of PCR mixture volume) magnetic bead volume and taking the supernatant. Primer-dimer and short fragments were removed by collecting bead-associated DNA in a 1:1 (bead solution volume:mixture volume) mix.


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_RS284]


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_RS288]


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_RS280]


title: sRNA_GM12884


title: sRNA_GM12877


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_RS276]


title: ATAC_GM128792_rep2


title: sRNA_GM12878


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_RS268]


title: sRNA_GM12886


title: ATAC_GM128793_rep1


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_RS264]


title: ATAC_GM128792_rep1


title: ATAC_GM128790_rep2


title: IFN gamma+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNG8h_LPS4h_STAT1_B]

data_processing:
Sequence reads were aligned to the mouse mm10 (GRCm38) genome assembly using the Burrows-Wheeler alignment (BWA) tool (v0.7.10), and bam files were created by SAMTools (v0.1.19). Following converting mapped reads (bam files) by makeTagDirectory (HOMER v4.2 Hypergeometric Optimization of Motif EnRichment) to become accessible by the further HOMER tools, genome coverage (bedgraph) files were created by makeUCSCfile.pl (HOMER) and converted to tiled data files (tdfs) by IGVtools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.bedgraph.tdf

growth_protocol: VSMC were cultured in DMEM complete medium supplemented with 10% FBS, 1:100 L-glutamine and 1:100 antibiotic/antimycotic solution. On the day before treatment, complete medium was exchanged onto 2% FBS containing starving medium.

extract_protocol:
ChIP was carried out as previously described (Siersbaek et al. 2012), with minor modifications.
Indexed ChIP DNA libraries were prepared following the TruSeq™ ChIP Library Preparation kit (Illumina, Inc.) protocol.

treatment_protocol: VSMC were left unstimulated or treated with single stimulus as follows: 1000U/ml of IFN alpha or 10ng/ml of IFN gamma for 8 hours and 1μg/ml of LPS for 4 hours. To further study the effect of IFNs pretreatment on LPS signaling, the cells were first treated with IFN alpha/IFN gamma for 8 hours followed by LPS stimulation for another 4 hours, as abovementioned.

tag: chip antibody

value: STAT1 (Cell Signaling Technology, cat# 14994, lot #4)


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_STAT1_B]


title: ATAC_GM128791_rep2


title: IFN gamma+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNG8h_LPS4h_STAT1_A]


title: ATAC_GM128790_rep1


title: ATAC_GM128791_rep1


title: IFN gamma-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNG8h_STAT1_B]


title: ATAC_GM128789_rep2


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_STAT1_A]


title: scSeq1

city: Tel Aviv

first: Yoav

last: Gothilf

address: Sherman Building, room 405

country: Israel

institute: Tel Aviv University

description: 10x Chromium V2 libraries

data_processing:
Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
R1 contains the barcode at bp 1-16 and UMI at bp 17-26.
R2 contains the biological sequence.
A reference genome was prepared from GRCz10, Ensembl release 91 annotations, and exogenous transgenes following 10x Genomics' instructions for custom genome builds (cellranger mkref).
FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper (cellranger mkfastq).
Finally, reads were aligned, UMIs processed, and transcripts counted to generate gene/barcode matrices, which were filtered to eliminate non-cellular barcodes (cellranger count).
Genome_build: GRCz10
Supplementary_files_format_and_content: Filtered gene/barcode matrices containing UMI counts with gene names (rows) and cell barcodes (columns) stored as TSV files.

molecule: polyA RNA

organism: Danio rerio

source_name: pineal glands

extract_protocol:
Pineal glands were dissected and enzymatically dissociated (Papain Dissociation System, Worthington Biochemical) to produce isolated cells. This single-cell suspension was then loaded onto a commercially available droplet-based 10x Chromium system (10x genomics).
Libraries were constructed using 10x Genomics' Single Cell 3’ Reagent Kit v2 according to the manufacturer's instructions (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry).

tag: tissue

value: pineal glands

tag: transgenic background

tag: age

value: 6-12 months


title: ATAC_GM128789_rep1


title: IFN gamma-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNG8h_STAT1_A]


title: ATAC_GM128788_rep2


title: scSeq2

description: 10x Chromium V2 libraries


title: IFN alpha+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNA8h_LPS4h_STAT1_A]


title: ATAC_GM128788_rep1


title: IFN alpha+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNA8h_LPS4h_STAT1_B]


title: ATAC_GM128787_rep2


title: ATAC_GM128787_rep1


title: ATAC_GM128786_rep2


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_STAT1_B]


title: IFN alpha-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNA8h_STAT1_A]


title: Huh-7-24h-1

type: RNA

city: Fuzhou

first: Guo

last: Zheng

state: Fujian

address: No.1 Xuefu North Road

department: Department of Bioinformatics

institute: Fujian Medical University

description:
Huh-7_treatment1
Gene expression data from Huh-7 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 24 hours

hyb_protocol: Following fragmentation, 12 ug of cRNA 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: Arrays were scanned with Affymetrix Genechip™ Scanner 30007G.

data_processing: The data were analyzed with Bioconductor using the RMA normalization method.

label: biotin

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip™ 3' IVT PLUS Reagent Kit User Manual, 2017, Affymetrix).

growth_protocol: The gastric adenocarcinoma cell line HGC-27 and colorectal adenocarcinoma cell line HCT-8 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 medium (Hyclone, Logan, UT, USA.). The human hepatocellular carcinoma cell lines HepG2 and Huh-7 were cultured in Dulbecco’s modified Eagle's medium (DMEM) (Hyclone, Logan, UT, USA.).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.


title: ATAC_GM128786_rep1


title: Huh-7-24h-2

description:
Huh-7_treatment2
Gene expression data from Huh-7 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 24 hours


title: Huh-7-24h-3

description:
Huh-7_treatment3
Gene expression data from Huh-7 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 24 hours


title: Huh-7-0h-3

description:
Huh-7_control3
Gene expression data from Huh-7 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 0 hours


title: Huh-7-0h-2

description:
Huh-7_control2
Gene expression data from Huh-7 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 0 hours


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_STAT1_A]


title: HepG2-0h-3

description:
HepG2_control3
Gene expression data from HepG2 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 0 hours


title: ATAC_GM128785_rep2


title: IFN alpha-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNA8h_STAT1_B]


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_p65_B]

value: NFKB p65 (Cell Signaling Technology, cat# 6956, lot# 7)


title: HepG2-24h-3

description:
HepG2_treatment3
Gene expression data from HepG2 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 24 hours


title: HepG2-24h-2

description:
HepG2_treatment2
Gene expression data from HepG2 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 24 hours


title: HepG2-24h-1

description:
HepG2_treatment1
Gene expression data from HepG2 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 24 hours


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_p65_A]

value: Wild type


title: IFN gamma+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNG8h_LPS4h_p65_B]


title: HepG2-0h-2

description:
HepG2_control2
Gene expression data from HepG2 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 0 hours


title: Huh-7-0h-1

description:
Huh-7_control1
Gene expression data from Huh-7 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 0 hours


title: ATAC_GM128784_rep2


title: HCT-8-24h-3

description:
HCT-8_treatment3
Gene expression data from HCT-8 human colorectal carcinoma (CRC) wild type cells treated with melatonin for 24 hours


title: HCT-8-24h-1

description:
HCT-8_treatment1
Gene expression data from HCT-8 human colorectal carcinoma (CRC) wild type cells treated with melatonin for 24 hours


title: HCT-8-0h-2

description:
HCT-8_control2
Gene expression data from HCT-8 human colorectal carcinoma (CRC) wild type cells treated with melatonin for 0 hours


title: IFN gamma+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNG8h_LPS4h_p65_A]


title: HCT-8-24h-2

description:
HCT-8_treatment2
Gene expression data from HCT-8 human colorectal carcinoma (CRC) wild type cells treated with melatonin for 24 hours


title: ATAC_GM128784_rep1


title: HGC-27-24h-3

description:
HGC-27_treatment3
Gene expression data from HGC-27 human gastric carcinoma (GC) wild type cells treated with melatonin for 24 hours


title: HCT-8-0h-1

description:
HCT-8_control1
Gene expression data from HCT-8 human colorectal carcinoma (CRC) wild type cells treated with melatonin for 0 hours


title: HCT-8-0h-3

description:
HCT-8_control3
Gene expression data from HCT-8 human colorectal carcinoma (CRC) wild type cells treated with melatonin for 0 hours


title: ATAC_GM128783_rep2


title: IFN gamma-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNG8h_p65_B]


title: ATAC_GM128785_rep1


title: ATAC_GM128783_rep1


title: IFN gamma-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNG8h_p65_A]


title: ATAC_GM128782_rep2


title: HGC-27-24h-1

description:
HGC-27_treatment1
Gene expression data from HGC-27 human gastric carcinoma (GC) wild type cells treated with melatonin for 24 hours


title: ATAC_GM128782_rep1


title: IFN alpha+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNA8h_LPS4h_p65_A]


title: HGC-27-0h-2

description:
HGC-27_control2
Gene expression data from HGC-27 human gastric carcinoma (GC) wild type cells treated with melatonin for 0 hours


title: IFN alpha-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNA8h_p65_B]


title: OM-QUE1-brown-fat

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to mm10 genome using hisat2 software.
Reads were counted by Htsseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: low-dose quercetin_brown adipose tissue (BAT)

extract_protocol:
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: All animal experiments were performed according to protocols approved by the Chinese Academy of Science Institutional Animal Care and Use Committee. Wild-type C57BL/6J mice were maintained separately in a pathogen-free facility at 23–24 °C under a 12-hour light, 12-hour dark regimen with free access to normal chow and water. Cages and bedding were changed weekly. For Que treatment, quercetin (0.125 mg/kg) was administered via oral gavage with 100 µL of 10% PEG400 in PBS. For the lifespan study, 14-month-old male mice were treated with Que or vehicle (10% PEG400 in PBS) every week until death. Quercetin hydrate (Que, TCI, P0042) was used in this study. All other reagents were purchased from Sigma.

tag: strain

tag: treatment

value: low-dose quercetin (0.125 mg/kg body weight) treatment

value: brown adipose tissue (BAT)


title: HGC-27-24h-2

description:
HGC-27_treatment2
Gene expression data from HGC-27 human gastric carcinoma (GC) wild type cells treated with melatonin for 24 hours


title: GBM cell-shARL4C biological  rep2

city: Chong qing

first: qian

last: chen

address: Gaotanyan street， shapingba

institute: Southwest hospital

description: Gene expression data from one patient with primary GBM

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

scan_protocol: eneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: GBM cell were trancfcted with shARL4C

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: cells were cultured in 37 ℃  in a humidified incubator with 5% CO2

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ，Life technologies, Carlsbad, CA, 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).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Human primay GBM cell was transfected with control or eGFP-Sh-ARL4C lentivirus

value: primary gliobalstoma cell


title: OM-PEG2-brown-fat

source_name: vehicle_brown adipose tissue (BAT)

value: vehicle (10% PEG400 in PBS) treatment


title: OM-PEG3-brown-fat


title: GBM cell-vector biological rep2

source_name: GBM cell were trancfcted with vector


title: ATAC_GM128781_rep1


title: OM-PEG1-brown-fat


title: GBM cell-vector biological rep3


title: HGC-27-0h-3

description:
HGC-27_control3
Gene expression data from HGC-27 human gastric carcinoma (GC) wild type cells treated with melatonin for 0 hours


title: HGC-27-0h-1

description:
HGC-27_control1
Gene expression data from HGC-27 human gastric carcinoma (GC) wild type cells treated with melatonin for 0 hours


title: OM-QUE2-white-fat

source_name: low-dose quercetin_white adipose tissue (WAT)

value: white adipose tissue (WAT)


title: IFN alpha-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNA8h_p65_A]

value: 8h, 1000U/ml, murine IFN alpha


title: ATAC_GM128780_rep2


title: GBM cell-shARL4C biological  rep3


title: GBM cell-shARL4C biological rep1


title: GBM cell-vector  biological rep1


title: OM-QUE1-white-fat


title: IFN alpha+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNA8h_LPS4h_p65_B]


title: OM-QUE2-brown-fat


title: OM-QUE3-brown-fat


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_p65_B]


title: OM-PEG3-white-fat

source_name: vehicle_white adipose tissue (WAT)


title: ATAC_GM128781_rep2


title: OM-PEG2-white-fat


title: ATAC_GM12879_rep2


title: OM-QUE3-muscle

source_name: low-dose quercetin_skeletal muscles (SKM)

value: skeletal muscles (SKM)


title: ATAC_GM128780_rep1


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_p65_A]

value: Vascular Smooth Muscle Cells


title: OM-QUE3-white-fat


title: IFN gamma+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNG8h_LPS4h_INPUT]


title: OM-PEG1-white-fat


title: LPS-stimulated Vascular Smooth Muscle Cells (4h) [mm_VSMC_LPS4h_INPUT]

value: 4h, 1ug/ml, LPS


title: OM-QUE2-muscle


title: OM-QUE1-muscle


title: ATAC_GM12879_rep1

value: EBV-transformed lymphoblastoid cell line


title: OM-PEG2-muscle

source_name: vehicle_skeletal muscles (SKM)


title: ATAC_GM12878_rep1


title: OM-PEG3-muscle


title: IFN alpha+LPS-stimulated Vascular Smooth Muscle Cells (8h/4h) [mm_VSMC_IFNA8h_LPS4h_INPUT]


title: OM-PEG1-muscle


title: IFN gamma-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNG8h_INPUT]

value: 8h, 10ng/ml, murine IFN gamma


title: ATAC_GM12878_rep2


title: SC_OE_2

city: Suzhou

first: Zongbing

last: Hao

address: 199 Ren-ai Road

institute: Soochow University

description: 6_months_cortex_and_spinal_cord_raw_counts

data_processing:
FASTQ files were trimmed with Trimmomatic (v0.30) to remove quality of bases lower than 20
clean data were aligned to reference genome (Ensembl, mm10) via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) was used to estimate gene and isoform expression levels from the pair-end clean data
Genome_build: mm10
Supplementary_files_format_and_content: xls format files include raw counts of sequencing reads for each sample

source_name: spinal cord

extract_protocol:
The cerebellum, cortex and spinal cord of control and heterozygous mice were removed, flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent. The library for next-generation sequencing was constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genetic background

tag: strain id

tag: genotype

value: GFP-PR28 heterozygote

value: spinal cord

value: 6 months


title: IFN alpha-stimulated Vascular Smooth Muscle Cells (8h) [mm_VSMC_IFNA8h_INPUT]

tag: cell type


title: SC_OE_3


title: ATAC_GM12877_rep2

tag: cell line


title: SC_WT_3

value: WT


title: ATAC_GM12877_rep1


title: SC_WT_2


title: unstimulated Vascular Smooth Muscle Cells [mm_VSMC_control_INPUT]


title: dirRNA_GM12893

data_processing:
Basecalls were performed using CASAVA v1.8.4
Sequenced reads were trimmmed using trim_galore v0.3.3
Sequenced reads were aligned to Homo sapiens (hg38) reference genome+decoy+EBV using STAR v2.5.2b using ENCODE parameters (see manual) for QC
Sequence reads were also aligned to GENCODE v24 protein coding, long noncoding RNAs, EBV genes using Kallisto v0.42.5 followed by quantification with Sleuth v. 0.30.0
Genome_build: GENCODE v24 hg38 + decoy + EBV
Supplementary_files_format_and_content: table of sleuth generated TPMs aggregated by gene for each sample; a table containing the discovered eQTL-genes

extract_protocol:
2 million cells were harvested during the exponential growth phase. Pelleted by centrifuging 3000g for 10min at 4C. Supernatant was discarded and 700ul of Triazol was add, mixed by vortexing and then kept frozen at -80C until extraction via Qiagen miRNAeasy mini kit
Libraries were constructed by removing rRNA and generating strand senstive reads with a KAPA Stranded RNA-Seq Kit with RiboErase (HMR) kit


title: Ctx_OE_3

source_name: cortex

value: cortex


title: Ctx_OE_1


title: Ctx_OE_2


title: SC_WT_1


title: dirRNA_GM12892


title: Ctx_WT_3


title: dirRNA_GM12891


title: input DNA Rep2

city: Toronto

first: Tae-Hee

last: Kim

state: Ontario

address: 686 Bay Street. Room 16.9709

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Adaptor sequences were trimmed using Trimmomatic 0.36 with adaptor sequence file TruSeq3-PE-2.fa
Reads were aligned to the mm9 reference genome using default parameters of BWA MEM
Aligned reads were filtered using bamtools to exclude unmappped reads, mapping quality < 5, and not proper pairs.
ENCODE blacklist regions in mm9 were filtered out using bedtools
Peaks were called using MACS2 with q = 0.05. --broad option was used for histone marks
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage tool from DeepTools

source_name: E17.5 intestine

extract_protocol:
E17.5 intestines were dissected, cut into small pieces, and crosslinked in solution A (1% formaldehyde, 50mM Hepes-KOH, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA) for 20 minutes at room temperature. 1/20 volume of 2.5 M glycine was added to quench formaldehyde. Tissues were rinsed in ice-cold PBS and dounced in Wheaton tissue grinder. Cell suspensions were passed through a 100μm cell strainer to remove connective tissues, then centrifuged at 4 °C at 2500 × rcf for 3 min, followed by a wash in PBS. Gli2, H27K27ac, or H3K36me3 antibodies were incubated with pre-blocked magnetic beads in 250μL total volume for 8 hours at 4 °C, then washed and resuspended in 100μL 0.5% BSA (w/v) solution. Cell pellets were lysed by sequentially resuspending and centrifuging in LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), and LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA). Pellet was resuspended in LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine) and sonicated into 200-400bp fragments. Sonicated lysates were diluted with LB3. After saving 50μL for input control, they were split into tubes containing 10% v/v Triton X-100 with Gli2, H3K27ac, or H3K36me3 antibody, and incubated overnight. Beads were washed 6 times in RIPA buffer (50 mM Hepes-KOH, pH 7.5; 500 mM LiCl; 1mM EDTA; 1% NP-40 or Igepal CA-630; 0.7% Na-Deoxycholate), and once in TBS (20 mM Tris-HCl, pH 7.6; 150 mM NaCl). Protein-DNA complexes were eluted and crosslink reversed with 200 μL of elution buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS). The 50μL input lysate was also included in this step. Eluted DNA was diluted with 200 μL of TE, and treated with RNaseA for 30 min at 37°C, and subsequently with proteinase K for 2 hours at 55°C. Phenol:chloroform:isoamyl alcohol was used to extract DNA.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit.

value: intestine

value: Sufu;Spop double knockout


title: Ctx_WT_1


title: H3K36me3_ChIPSeq Rep2

data_processing:
Adaptor sequences were trimmed using Trimmomatic 0.36 with adaptor sequence file TruSeq3-PE-2.fa
Reads were aligned to the mm9 reference genome using default parameters of BWA MEM
Aligned reads were filtered using bamtools to exclude unmappped reads, mapping quality < 5, and not proper pairs.
ENCODE blacklist regions in mm9 were filtered out using bedtools
Peaks were called using MACS2 with q = 0.05. --broad option was used for histone marks
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage tool from DeepTools
Supplementary_files_format_and_content: Peaks from individual replicates were merged using "cat" shell command. "mergeBed" tool from BedTools was used to remove duplicate peaks and generate the final BED file specifiying the genomic position of the peaks.

value: H3K36me3 (Abcam ab9050)


title: 12_5m_OE

source_name: cerebellum

value: cerebellum

value: 5 months


title: SC_OE_1


title: Ctx_WT_2


title: dirRNA_GM12890


title: H3K36me3_ChIPSeq Rep1


title: 8_5m_OE


title: 10_5m_OE


title: H3K27ac_ChIPSeq Rep2

value: H3K27ac (Millipore 05-1334)


title: dirRNA_GM12889


title: dirRNA_GM12888


title: 9_5m_WT


title: H3K27ac_ChIPSeq Rep1


title: 7_5m_WT


title: 6_2m_OE

value: 2 months


title: dirRNA_GM12887


title: 4_2m_OE


title: input DNA Rep1


title: 5_2m_WT


title: 3_2m_WT


title: Gli2_ChIPSeq Rep1

value: Gli2 (homemade)


title: dirRNA_GM12885


title: MT_intestine_RNASeq Rep2

data_processing:
fastq reads were aligned to the mm9 transcriptome using kallisto 0.42.2 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files containing transcript ID, transcript length, effective length, estimated counts, and abundance in TPM were generated using kallisto 0.42.2

extract_protocol:
Intestines of control and Sufu and Spop double knockout E17.5 embryos were removed, and their epithelial and mesenchymal tissues were separated using EDTA. The mesenchymal part was kept at -20°C prior to RNA extraction with RNeasy kit (Qiagen). The integrity of the samples was checked on Agilent Bioanalyzer, and the samples with a RIN>8.5 were used. 1 to 2µg of RNA were used to prepare the PolyA RNA library.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® kit.


title: dirRNA_GM12884


title: MT_intestine_RNASeq Rep1


title: 2_2m_OE


title: dirRNA_GM12883


title: 11_5m_WT


title: CT_intestine_RNASeq Rep2

value: wildtype


title: H3H113N-dCCs1-SC-lys_rep1

city: Los Angeles

first: Oscar

middle: Antonio

last: Campos

state: CA

address: 615 Charles Young Dr. South

department: Biological Chemistry

institute: University of California, Los Angeles

data_processing:
Sequence reads were aligned to the R64-1-1 S288C reference genome assembly (sacCer3) using Tophat 2.0.9. The “-g 1” parameter was used to limit the number of alignments for each read to one, the top-scoring alignment.
Gene expression values, in reads per kilobase per million mapped reads (RPKMs), for 6692 annotated open reading frames were calculated using SAMMate 2.7.4. (Xu et al., 2011). In calculating RPKM values, only reads that align to annotated exons were considered. Reads aligning to introns or intergenic regions were not counted in normalizing the read counts to the total number of mapped reads. Read counts and RPKM values for all 6692 ORFs can be found in GEOoscarcampos_All_ORFs_RPKMs_Jun2017.txt.
Many of the 6692 annotated ORFs have no attributed function, localization, mutant phenotypes or interactions and are often labeled as “dubious” or “putative” in the Saccharomyces Genome Database (SGD). Furthermore, these putative ORFs typically have low expression values. We removed 1648 such ORFs from further analysis, and used the remaining 5044 ORFs for comparisons between groups. RPKM values for 5044 ORFs can be found in GEOoscarcampos_5044_ORFs_RPKMs_Jun2017.txt.
Genome_build: R64-1-1 S288C reference genome assembly (sacCer3)
Supplementary_files_format_and_content: GEOoscarcampos_All_ORFs_RPKMs_Jun2017.txt contains read counts and RPKM values in tab-delimited format. Each pair of columns corresponds to different samples and each row is an ORF. The first 4 columns contain ORF information. GEOoscarcampos_5044_ORFs_RPKMs_Jun2017.txt contains only RPKM values in tab-delimited format. Each column corresponds to different samples and each row is an ORF. The first 5 columns contain ORF information.

organism: Saccharomyces cerevisiae

growth_protocol: Following an overnight growth, cells were diluted in the various listed media conditions and cell culture densities. Cells were then grown/incubated for the indicated amounts of time. Note that due to different growth rates, time in culture was often different between strains.

extract_protocol:
Total RNA was extracted by the hot acid-phenol method (Schmitt et al., 1990), and further purified by phenol-chloroform extraction. Following extraction and ethanol precipitation, total RNA was DNAse-treated with Turbo DNAse (ThermoFisher) according to the manufacturer's protocol.
polyA+ RNA libraries were prepared using either the KAPA Stranded mRNA-seq library prep kit or the Illumina TruSeq Stranded mRNA Library Kit for NeoPrep, as indicated. Libraries were prepared according to the manufacturer's protocols. Both library preparation procedures first isolate polyA+ mRNAs using oligo-dT beads. Isolated polyA+ RNAs are then chemically fragmented, and random primers are used in the first cDNA reverse transcription step. Note that while both kits prepare "first strand" cDNA libraries, the strand-specific information was not used for data analysis in our study. However, that information can be extracted from the FASTQ files. Average library insert sizes were ~170 bp. High throughput sequencing was performed on Illumina’s HiSeq 4000 system, with single-end 50 bp insert reads, and dedicated index reads.
Library prep: KAPA Stranded mRNA-seq library prep kit

tag: strain background

tag: media condition

value: SC-lys

tag: starting cell density

tag: amount of growth/incubation

value: 24 hrs

tag: growth phase

value: very slow

value: Budding yeast cells


title: CT_intestine_RNASeq Rep1

tag: genotype/variation


title: dCCs1-SC-lys_rep2


title: dCcs1-SC-lys-Cu

value: SC-lys + 75 µM CuSO4

value: exponential


title: H3H113N-dCcs1-SC-lys-Cu


title: H3H113N-dCCs1-SC-lys_rep2


title: dirRNA_GM12881

value: EBV-transformed lymphoblastoid cell line

tag: number of cells


title: Gli2_ChIPSeq Rep2

tag: tissue

tag: chip antibody


title: dCCs1-SC-lys_rep1


title: A375-EOS-CNT3

city: Raleigh

first: Tyler

last: Allen

state: North Carolina

address: 1001 William Moore Drive

institute: NC State University

data_processing:
Genewiz standard data processing protocol was used.
Genome_build: hg18
Supplementary_files_format_and_content: normalized counts

source_name: A375 cells stably expressing EosFP

growth_protocol: Standard growth protocol for A375 cells.

extract_protocol: Cell pool was provided to Genewiz who conducted all extraction, prep, and sequencing.

value: A375 cells stably expressing EosFP

value: Tumor

tag: immortal

value: yes

tag: derivation location

value: skin

tag: sample type

value: control cells


title: H3H113N-dCcs1-SC_rep2

extract_protocol:
Total RNA was extracted by the hot acid-phenol method (Schmitt et al., 1990), and further purified by phenol-chloroform extraction. Following extraction and ethanol precipitation, total RNA was DNAse-treated with Turbo DNAse (ThermoFisher) according to the manufacturer's protocol.
polyA+ RNA libraries were prepared using either the KAPA Stranded mRNA-seq library prep kit or the Illumina TruSeq Stranded mRNA Library Kit for NeoPrep, as indicated. Libraries were prepared according to the manufacturer's protocols. Both library preparation procedures first isolate polyA+ mRNAs using oligo-dT beads. Isolated polyA+ RNAs are then chemically fragmented, and random primers are used in the first cDNA reverse transcription step. Note that while both kits prepare "first strand" cDNA libraries, the strand-specific information was not used for data analysis in our study. However, that information can be extracted from the FASTQ files. Average library insert sizes were ~170 bp. High throughput sequencing was performed on Illumina’s HiSeq 4000 system, with single-end 50 bp insert reads, and dedicated index reads.
Library prep: Illumina TruSeq Stranded mRNA Library Kit for NeoPrep

value: SC

value: 5 population doublings


title: dirRNA_GM12886


title: dirRNA_GM12880


title: A375-EOS-CNT2


title: dCcs1-SC_rep2


title: H3H113N-dCcs1-SC_rep1


title: 1_2m_WT

tag: genetic background

value: WT

value: cerebellum

tag: age

value: 2 months


title: dCcs1-SC_rep1


title: dirRNA_GM12879


title: HepG2-0h-1

description:
HepG2_control1
Gene expression data from HepG2 human hepatocellular carcinoma (HCC) wild type cells treated with melatonin for 0 hours


title: H3H113N-SC_rep3


title: H3H113N-SC_rep2


title: H3H113N-SC_rep1


title: dirRNA_GM12882


title: A375-EOS-MET3

value: extravasating cells


title: dirRNA_GM12878


title: dirRNA_GM12877


title: WT-SC_rep1

source_name: WT-SC


title: A375-EOS-MET2


title: WT-SC_rep2


title: BM-Rep2

city: West Lafayette

first: Michael

middle: K.

last: Wendt

state: IN

address: 201 S. University Street

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 2500.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE 25 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GENCODE 25
Supplementary_files_format_and_content: Raw counts from edgeR

source_name: Mammary epithelial cells

growth_protocol: All cells were cultured in DMEM high glucose including 10% FBS and pen/strep. All cells expression firefly luciferase under blasticidin selection and Her2 under puromycin selection

extract_protocol: E.Z.N.A. Total RNA kit from Omega bio-tek. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To generate TGFB population, the parental cells were treated with TGF-beta (5ng/ml) every three days for 4 weeks. To generate LAPR cells the parental population was treated with 1 micromolar lapatinib every three days for 4 weeks. The TGFB population was engrafted onto the mammary fat pad and a metastsis was isolated from the tibia BM cell population was

tag: subtype

value: Her2 transformation model

tag: culture conditions

value: ex vivo

value: Her2 transformed HMLE cells

tag: group

value: BM


title: BM-Rep1

tag: cell line


title: H3H113N-dCtr1-YPD_rep2

tag: strain background

tag: media condition

value: YPD

value: 3-4 population doublings

value: exponential

tag: cell type

value: Budding yeast cells


title: H3H113N-dCtr1-YPD_rep1

tag: starting cell density

tag: amount of growth/incubation

tag: growth phase


title: dCtr1-YPD_rep2

tag: genotype/variation


title: RP2

city: Seoul

first: Minwoo

last: Park

address: 25, Seonyu-ro 13-gil, youngdeungpo-gu

department: Research & Development

country: South Korea

institute: ebiogen

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Muscle

growth_protocol: Each mice were s.c. injected with 1 × 10^6 Lewis lung carcinama cells in 100 μl of saline. Normal mice were s.c. injected with same volume of saline. After 2 weeks, when tumor was grown, tumor size was measured using a caliper. The mice were re-grouped to match tumor size among experimental groups.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Normal group and Control group were orally administered with 200 μl of distilled water. RP group was orally administered with 100 mg/kg of Paeonia lactiflora 30% ethanol extract suspended in 200 μl of distilled water, daily for 2 weeks.

tag: strain

tag: tissue

value: Gastrocnemius Muscle


title: LAPR-Rep2

value: In vitro

value: LAPR


title: dCtr1-YPD_rep1


title: RP1


title: WT-YPEG_rep2

source_name: WT-YPEG

value: YPEG


title: H3H113N-YPEG_rep1


title: H3H113N-YPEG_rep2


title: A375-EOS-MET1

value: A375 cells stably expressing EosFP

value: Tumor

tag: immortal

value: yes

tag: derivation location

value: skin


title: Control3


title: LAPR-Rep1


title: TGFB-Rep2

value: TGFB


title: Control2


title: WT-YPEG_rep1

value: WT


title: H3H113N-YPD_rep2


title: WT-SC_rep3

value: SC

value: 5 population doublings


title: Par-Rep2

value: Her2 transformation model

value: Her2 transformed HMLE cells

value: Parental cell line


title: Normal3


title: WT-YPD_rep2

source_name: WT-YPD

value: YPD

value: 3-4 population doublings

value: exponential


title: Stage 8 Otx1 ChIP-seq replicate 1

city: Irvine

first: Kitt

middle: D.

last: Paraiso

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

description: processed data file: otx1-IDR-optimal-peaks.bed

data_processing:
ChIP-seq peak calling and IDR: Reads were aligned to the X. tropicalis genome v9.0 (Hellsete et al., 2010; Xenbase FTP) using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called against stage 8 input DNA (Charney et al., 2017) using Macs v2.0.10 (Zhang et al., 2008) with the option –p 0.001 but otherwise default options . ENCODE based irreproducibility discovery rate (IDR) was performed using the following p-value thresholds for the following comparisons: 0.01 for original biological replicates, 0.02 for pseudoreplicates of each biological replicate and 0.0025 for pseudoreplicates generated from pooled reads of biological replicates (Li et al., 2011).
Genome_build: Xenopus tropicalis genome v 9.0

organism: Xenopus tropicalis

source_name: Xenopus tropicalis embryo

growth_protocol: Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8, 10 minutes after fertilization and are then ready for manipulation. Embryos were staged using the Nieukwoop-Faber developmental table.

extract_protocol:
The fixed embryos were homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then centrifuged at 14,000rpm for 10 minutes at 4°C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 100-500bp. The resulting samples were centrifuged at 14,000 rpm for 30 minutes at 4°C to remove insoluble cellular debris. The sheared chromatin was pre-cleared by incubating with 20 mL Protein G-coated Dynabeads (Invitrogen) for 2 hours at 4°C with rotation. Meanwhile, another 20 mL Protein G Dynabeads were incubated in a tube rotator in 1 mg/mL torula RNA and 0.5% BSA in 1x PBS for 30 minutes at 4°C to block non-specific binding. This second 20 mL Protein G Dynabeads were then pre-bound with 4 mg anti-otx1 antibody at 4°C for > 1 hour. The pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4°C on a tube rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65°C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
ChIP-seq libraries were generated using Nextflex ChIP-seq kit (Bioo Scientific), analyzed using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina instruments.

treatment_protocol: Embryos were cross-linked in 1% formaldehyde in 1/9x MMR at room temperature for 50 minutes with gentle rocking where each microcentrifuge tube contains 200 embryos with 1mL of the formaldehyde solution. Crosslinking reactions were neutralized by the removal of the formaldehyde solution and incubation with 1ml 125mM glycine solution for 10 minutes on ice. Embryos were then washed twice with 400mL of cold RIPA buffer (50 mM Tris-HCl pH7.4, 150mM NaCl, 1mM EDTA, 0.25% sodium deoxycholate, 1% NP40, 0.1% SDS, 0.5 mM DTT, and Roche cOmplete protease inhibitor cocktail). Embryos were flash-frozen in liquid nitrogen and stored at -80°C.

tag: developmental stage

value: Stage 8

value: Whole embryo


title: Control1

value: Gastrocnemius Muscle


title: Stage 8 Vegt ChIP-seq replicate 2

description: processed data file: vegt-IDR-optimal-peaks.bed

extract_protocol:
The fixed embryos were homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then centrifuged at 14,000rpm for 10 minutes at 4°C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 100-500bp. The resulting samples were centrifuged at 14,000 rpm for 30 minutes at 4°C to remove insoluble cellular debris. The sheared chromatin was pre-cleared by incubating with 20 mL Protein G-coated Dynabeads (Invitrogen) for 2 hours at 4°C with rotation. Meanwhile, another 20 mL Protein G Dynabeads were incubated in a tube rotator in 1 mg/mL torula RNA and 0.5% BSA in 1x PBS for 30 minutes at 4°C to block non-specific binding. This second 20 mL Protein G Dynabeads were then pre-bound with 2 mg anti-vegt antibody at 4°C for > 1 hour. The pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4°C on a tube rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65°C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
ChIP-seq libraries were generated using Nextflex ChIP-seq kit (Bioo Scientific), analyzed using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina instruments.


title: Par-Rep1

value: In vitro


title: WT-YPD_rep1

value: Budding yeast cells


title: Normal2


title: 8-cell whole embryos replicate 3

description:
processed data file: 8cell-animal-vegetal-RNAseq-readcounts.txt
processed data file: 8cell-animal-vegetal-RNAseq-TPM.txt

data_processing:
RNA-seq gene expression calling: Reads were aligned using RSEM v.1.2.12 (Li and Dewey 2011) and Bowtie v2.2.7 (Langmead and Salzberg 2012) to the Xenopus tropicalis genome version 9.0 (Hellsten et al., 2010; Xenbase FTP). Read counts and transcripts per million were extracted from RSEM results output.
Genome_build: Xenopus tropicalis genome v 9.0

extract_protocol:
Total RNA was extracted using the acid guanidinium thiocyanate method of Chomczynski and Sacchi (1987: Analytical Biochemistry 162:156-159). Final RNA pellets were resuspended in DEPC-treated water and then precipitated overnight at 4°C in 2.5M LiCl to remove contaminating genomic DNA.
RNA-seq libraries were generated using Smart-seq2 cDNA synthesis followed by tagmentation, quality-tested using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina sequencers.

treatment_protocol: 8-cell stage embryos from the same clutch were collected from which RNA was harvested

value: 8-cell Stage


title: Healthy Input

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

country: United Kingdom

institute: King's College London

description: No ChIP

data_processing:
Libraries were subject to 50bp single end read sequencing and reads aligned to Human genome hg19 using Bowtie2 (Galaxy v2.2.6).
Blacklist regions (including chrN, chrUn and chrM) were subtracted from each BAM file prior to downstream analysis using the intersect -v function in bedtools.
Healthy (n=3) and Asthma (n=4) BAM files were merged using samtools (Galaxy), Input BAMs subtracted (-bamCompare) and BigWig’s generated and normalized to reads per kilobase per million mapped reads (RPKM, -bamCoverage, deepTools).
Differentially enriched regions (DERs) between Asthma (n=4) and Healthy BECs (n=3) were identified across non-overlapping and consecutive 1kb windows genome-wide using MEDIPS v1.20.1
Peaks were called for merged Healthy, Asthma and individual volunteer BAM files using MACS2 (p<5e-4, Galaxy v2.1)
Typical and Super enhancers (SEs) were identified and annotated using Rank Ordering of Super Enhancers algorithm (ROSE_main.py, -t 2000 and ROSE_geneMapper.py, searchwindow=default respectively)
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files contain H3K27ac enrichment (RPKM) in merged Healthy and Asthma BECs, BED files contain location of DERs and BEC-SEs

source_name: Bronchial epithelial cells

growth_protocol: Bronchial brushings were obtained from volunteers by fibre-optic bronchoscopy and seeded into supplemented bronchial epithelial growth medium (BEBM, Lonza) in a T25 flask. At passage 2, cells were seeded onto 10mm culture dishes (Primaria, Corning) and cultured until 80% confluent.

extract_protocol:
BECs were treated with hypotonic solution and mild detergent followed by clarification through sucrose gradient to isolate nuclei. Nuclei were treated with micrococcal nuclease (10U) for 10 minutes at 37°C, re pelleted and supernant containing mononucleosomes stored at 4°C. Mononuclesomal fractions were incubated with 4μg of H3K27ac antibody (Abcam, Ab4729) and 25μL Protein G dynabeads (Life Technologies) in modified RIPA buffer over night at 4°C. Bound complexes were washed and eluted and ChIP DNA extracted using phenol:chloroform/ethanol precipitation.
Libraries were prepared using half total volume of eluted ChIP DNA and NEBNext® DNA Library Prep Master Mix Set and Multiplex Oligos for Illumina® (New England Biolabs). Library quality was assessed using Bioanalyzer 2100 High Sensitivity DNA Gels (Agilent).

value: Bronchial epithelial cells

tag: status

value: Healthy

tag: Sex

value: Mixed

tag: passage

tag: chip antibody


title: Normal1


title: 8-cell whole embryos replicate 1


title: Asthma Input

description: No ChIP

value: Asthma


title: 8-cell vegetal blastomeres replicate 3

treatment_protocol: vegetal blastomeres from the same clutch were dissected at 8-cell stage from which RNA was harvested

value: Vegetal blastomeres


title: 8-cell vegetal blastomeres replicate 2


title: 8-cell animal blastomeres replicate 3

treatment_protocol: animal blastomeres from the same clutch were dissected at 8-cell stage from which RNA was harvested

value: Animal blastomeres


title: 8-cell vegetal blastomeres replicate 1


title: H108

description: H3K27ac ChIP

value: Female

value: H3K27ac antibody (Abcam, Ab4729)


title: Sp1_deltaDBD

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

description: Read 1 (R1) - Cell barcode (position 1-16bp) and unique molucular identifier (position 17-26bp). Read 2 (R2) - Biological reads. Index file (I1) - I7 indexes

data_processing:
Illumina base call (BCL) files were de-multiplexed and converted to fastq format using the mkfastq function in CellRanger version 2.1.1
The data was then aligned to the mouse genome (mm10) and unique molecular identifiers (UMI) were counted using the count function in the CellRanger software.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 feature barcode matrix files generated using the CellRanger count software. This file contains the UMI counts for each detected gene in each sequenced cell.

extract_protocol:
Single cell suspensions of Sp1 wild-type and DNA binding domain mutant cell were sorted for Kit (KIT-APC; BD Pharmingen 553356), expression at day 2 of blast culture prior to loading 4000 single cells of each population on a Chromium Single Cell Instrument (10X Genomics).
Library generation for scRNA-seq was performed as a service by the Genomics Birmingham Sequencing Facility using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (10X Genomics). Libraries were subjected to paired end sequencing on an Illumina NextSeq 500 sequencer according to 10X Genomics recommended cycle parameters.

value: Mouse embryonic stem cells - Day 2 of blast culture

value: Sp1 - DNA binding domain mutant

tag: chemistry

value: Single cell 3prime v2


title: 8-cell animal blastomeres replicate 2


title: A375-EOS-CNT1

tag: cell line

value: A375 cells stably expressing EosFP

value: Tumor

value: yes

value: skin

tag: sample type

value: control cells


title: H3H113N-YPD_rep1

tag: strain background

tag: media condition

value: YPD

value: 3-4 population doublings

value: exponential

tag: cell type

value: Budding yeast cells


title: H009

description: H3K27ac ChIP

value: Bronchial epithelial cells

value: Healthy

value: Male


title: D3.Tg

city: Adelaide

first: Justine

last: Smith

address: Bedford Park

country: Australia

institute: Flinders University

data_processing:
Paired-end FASTQ files were combined from lane-level files for all mock- and T. gondii-infected samples and aligned to the human hg19 reference genome and to the T. gondii reference sequence (ToxoDB release 36, http://toxodb.org/toxo/showXmlDataContent.do?name=XmlQuestions.News&tag=toxodb02_18_release) using the subread-align program. Uniquely mapped reads were assigned to human and T. gondii genes with the read summarization program featureCounts. Reversely stranded read counting was performed.
Genome_build: human hg19 reference genome and T. gondii reference sequence
Supplementary_files_format_and_content: Read_Counts_Small_RNA.xlsx, Read_Counts_Total_RNA.xlsx

source_name: Retinal pigment epithelial cell

growth_protocol: The ARPE-19 cell line was cultured in DMEM:F12 medium with heat-inactivated 10% fetal bovine serum (FBS) at 37 °C and 5% CO2 in air. Primary retinal pigment epithelial cells were isolated from human cadaveric donor eyes by collagenase IA/IV digestion, followed by mechanical collection. These cells were first cultured in DMEM:F12 medium with 1x Insulin-Transferrin-Selenium (ITS), 100 U/mL Penicillin-Streptomycin, 1 μg/mL amphotericin and 10% heat-inactivated FBS at 37 °C and 5% CO2 in air, and later with 50% reduction in ITS and FBS.

extract_protocol:
Total RNA was extracted from TRIzol Reagent-lysed cells, according to the manufacturer’s instructions, and stored at -80 °C ahead of use for RNA-seq. RNA concentration was determined by spectrophotometry on the Qubit 2.0 Fluorometer (Thermo Fisher Scientific-Invitrogen) for RNA-seq. RNA integrity was confirmed on the 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).
Total and small RNA were converted to cDNA libraries, using the TruSeq Stranded Total RNA Kit with Ribo-Zero Gold and the TruSeq Small RNA Library Prep Kit, respectively (both from Illumina, San Diego, CA), in accordance with the manufacturer’s instructions with one exception: for small RNA, cDNA purification was performed using Pippin Prep (Sage Science, Beverly, MA), as described by the manufacturer.
RNA samples were diluted to 1 pM ahead of sequencing on the Illumina NextSeq 500, which was performed for total RNA with the NextSeq 500/550 High Output Kit (Illumina, 150 cycles) run as paired-end 2 x 75 bp, and for small RNA with the NextSeq 500/550 High Output Kit (Illumina, 75 cycles) run as single-read 1 x 75 bp. The PhiX Control v3 library (Illumina) was used as a sequencing control.

treatment_protocol: Confluent monolayers of retinal pigment epithelial cells were infected with T. gondii tachyzoites at MOI of 5 in 6-well plates for RNA-Seq or in 12-well plates (3.8 cm2 diameter wells) for RT-qPCR. Cells and tachyzoites were incubated in culture-specific medium [For ARPE-19 cells: DMEM:F12 medium with 5% heat-inactivated FBS; For primary cells: DMEM:F12 medium with 0.5x ITS, 100 U/mL Penicillin-Streptomycin, 1 μg/mL amphotericin and 5% heat-inactivated FBS] at 37 °C and 5% CO2 in air. After 4 hours, the monolayers were washed 4-times with medium to remove extracellular tachyzoites, and the infected cultures were returned to incubation in fresh medium to a total of 24 hours.

tag: donor

value: Primary retinal pigment epithelial cell isolate

tag: infection

value: T. gondii-infected


title: 8-cell animal blastomeres replicate 1

value: 8-cell Stage

value: Animal blastomeres


title: H002

description: H3K27ac ChIP

value: Female

value: H3K27ac antibody (Abcam, Ab4729)


title: D2.Tg


title: N2_Zn

city: Wenjiang Chendu

first: Wendi

last: Shuai

state: Sichuan

address: Huimin Road

institute: Sichuan Agricultural University

description: 500μM Zn,8 mM Ca(NO3)2·4H2O,10 mM KNO3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include RPKM and read count values for each Sample. A FASTA file with transcript sequence is available on the series record.

organism: Triticum polonicum

source_name: 500μM Zn,8 mM Ca(NO3)2·4H2O,10 mM KNO3

extract_protocol:
Fresh roots frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The groups treated with two Ca/K solution and Cd/Zn solution before collected.The samples were collected after one week treatment. The roots samples were immediately frozen in liquid nitrogen and stored at -80°C.It’s three biological replicates per treatment for subsequent RNA extraction and analysis.

value: roots

tag: age

tag: cultivar

value: dwarf Polish wheat


title: N2

description: 8 mM Ca(NO3)2·4H2O,10 mM KNO3

source_name: 8 mM Ca(NO3)2·4H2O,10 mM KNO3

tag: tissue


title: N2_Cd

description: 80μM CdCl2,8 mM Ca(NO3)2·4H2O,10 mM KNO3


title: A003

description: H3K27ac ChIP

value: Asthma


title: N2_Cd_Zn

description: 80μM CdCl2,500μM ZnSO4,8 mM Ca(NO3)2·4H2O,10 mM KNO3


title: 8-cell whole embryos replicate 2

value: Whole embryo


title: D1.Tg


title: A110

description: H3K27ac ChIP


title: D3.Ctrl

value: Mock-infected


title: N0_Cd

description: 80μM CdCl2,4 mM Ca(NO3)2·4H2O，5 mM KNO3

source_name: 80μM CdCl2,4 mM Ca(NO3)2·4H2O，5 mM KNO3


title: D2.Ctrl


title: Sp1_WT

value: Mouse embryonic stem cells - Day 2 of blast culture

tag: genotype/variation

value: Sp1 - wild-type

value: Single cell 3prime v2


title: A156

description: H3K27ac ChIP

value: Bronchial epithelial cells


title: N0

description: 4 mM Ca(NO3)2·4H2O,5 mM KNO3

source_name: 4 mM Ca(NO3)2·4H2O,5 mM KNO3


title: DX_female_28674

type: genomic

first: Xuemei

last: Deng

state: N/A = Not Applicable

address: No.2, Yuan Ming Yuan West Road, Haidian District

department: Department of animal breeding and genetics

institute: China Agricultural University

description: Dongxiang blue-shelled chicken

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations,.

data_processing: The first-step quality control and genotype calling from the raw data in the form of CEL files were performed using Affymetrix Power Tools v1.16.0 (APT) software with the criterion of dish quality control (DQC) > 0.82 and call rate > 97%. The SNP genotype was calling using Axiom™ Analysis Suite.

label: RAL

organism: Gallus gallus

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Regular quarantine inspection of the experimental farm in China Agricultural University was conducted.

extract_protocol: The genomic DNA was extracted from blood samples using the avian blood DNA extraction kit (Tiangen Co., LTD., Beijing, China).. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

value: brachial veins

value: female

tag: breed

value: Dongxiang blue-shelled


title: DX_female_21811

description: Dongxiang blue-shelled chicken


title: A149

description: H3K27ac ChIP

tag: status

value: Male


title: 19.Tg

source_name: ARPE-19 retinal pigment epithelial cell

value: T. gondii-infected


title: D1.Ctrl

value: Primary retinal pigment epithelial cell isolate


title: DX_female_21886

description: Dongxiang blue-shelled chicken

tag: Sex


title: DX_female_21888

description: Dongxiang blue-shelled chicken


title: DX_female_21958

description: Dongxiang blue-shelled chicken


title: 19.Ctrl


title: N0_Zn

description: 500μM Zn,4 mM Ca(NO3)2·4H2O,5 mM KNO3

source_name: 500μM Zn,4 mM Ca(NO3)2·4H2O,5 mM KNO3


title: DX_female_22691

description: Dongxiang blue-shelled chicken


title: DX_female_21957

description: Dongxiang blue-shelled chicken


title: TGFB-Rep1

tag: subtype

value: Her2 transformation model

tag: culture conditions

value: In vitro

value: Her2 transformed HMLE cells

tag: group

value: TGFB


title: DX_female_2209

description: Dongxiang blue-shelled chicken


title: DX_female_22670

description: Dongxiang blue-shelled chicken


title: 24 glucose RNAseq

city: Stanford

first: Douglas

last: Vollrath

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
Raw data was de-multiplexed using bcl2fastq2 from Illumina with default parameters. Reads were aligned against the hg19 human reference genome with STAR (v2.4.2a) 80 using GENCODE v19 annotations 81 and otherwise default parameters. After alignment, duplicate reads were marked using Picard MarkDuplicates (v2.0.1) and reads marked as duplicates or with non-perfect mapping qualities were removed.
We used HTSeq v0.6.0 82 to count the number of reads overlapping each gene based on the GENCODE v19 annotation. We counted reads on the reverse strand (ideal for Illumina's TruSeq library), required a minimum alignment quality of 10, but otherwise used default parameters. We also quantified RPKM using RNA-SeQC v1.1.8 83 using hg19 reference genome and GENCODE v19 annotation with flags "-noDoC -strictMode" but otherwise default parameters. We quantified allele-specific expression using the createASVCF.sh script from RASQUAL 45 with default parameters. For splicing quantification, we used LeafCutter 59 to determine intron excision levels with default parameters. Briefly, we first converted bam files to splice junction counts (bam2junc.sh) and clustered introns based on sharing of splice donor or acceptor sites (leafcutter cluster.py). For each cluster, We required a minimum number of 30 reads, and a minimum fraction of 0.1% in support of each junction. We required each intron must not exceed 100 kbp.
Genome_build: hg19
Supplementary_files_format_and_content: txt: tab-delimited text files; fastq.gz: gzipped fastq files.

source_name: fetal retinal pigment epithelium

growth_protocol: Primary human fetal RPE (fRPE) lines were isolated by collecting and freezing non-adherent cells cultured in low calcium medium as described 22. When needed, fRPE cells were thawed and plated onto 6-well plates in medium as described 23 with 15% FBS. The next day, medium was changed to 5% FBS and the cells were allowed to recover for two additional days. Cells were then trypsinized in 0.25% Trypsin-EDTA (Life Technologies Corporation #25200056), resuspended in medium with 15% FBS and plated onto human extracellular matrix-coated (BD Biosciences #354237) Corning 12-well transwells (#3460, Corning Inc., Corning, NY) at 240K cells per transwell. The next day medium was changed to 5% FBS. Cells were cultured for at least 10 weeks to become differentiated (transepithelial resistance of > 200 Ω * cm2) and highly pigmented. Medium with 5% FBS was changed every 2-3 days. For the galactose and glucose specific culture conditions, differentiated fRPE cells were cultured for 24 hrs prior to RNA isolation in DMEM medium (#D5030, Sigma) with 1 mM sodium pyruvate (#S8636, Sigma), 4 mM L-glutamine (#25030-081, Life Technologies Corporation), 1% Penicillin-Streptomycin (#15140-122, Life Technologies Corporation), and either 10 mM D-(+)-glucose (#G7021, Sigma) or 10 mM D-(+)-galactose (G5388, Sigma) 28.

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen) per manufacturer instructions. RNA sequencing was performed on all samples with an RNA integrity number (RIN) of 8.0 or higher and with at least 500 ng total RNA.
Stranded, poly-A+ selected RNA-seq libraries were generated using the Illumina TruSeq Stranded mRNA protocol. We performed 75 bp paired-end RNA sequencing on an Illumina NextSeq 500 on all RPE samples

value: fetal retinal pigment epithelium


title: 24 galactose RNAseq


title: DX_female_28684

description: Dongxiang blue-shelled chicken


title: DX_female_21984

description: Dongxiang blue-shelled chicken


title: N0_Cd_Zn

description: 80μM CdCl2,500μM ZnSO4,4 mM Ca(NO3)2·4H2O，5 mM KNO3

value: roots

value: dwarf Polish wheat


title: DX_female_2176

description: Dongxiang blue-shelled chicken


title: DX_female_21991

description: Dongxiang blue-shelled chicken


title: DX_female_21903

description: Dongxiang blue-shelled chicken


title: DX_female_21889

description: Dongxiang blue-shelled chicken


title: DX_female_22698

description: Dongxiang blue-shelled chicken


title: Organoid Wild_type_sample_4

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: Following fragmentation, cDNA was hybridized for 20 hr at 48C to Affymetrix Mouse Genome 2.1 ST plate arrays.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the affy package implemented in the R-statistical environment version 3.4.0. RMA was used to estimate log2 transformed expression values for each probe-set.

source_name: Organoid from colon sample from wild type mouse 12

label_protocol: 100 ng total RNA was reverse-transcribed, amplified and labeled, with Affymetrix Affy Plus Kits.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), and purified using Rneasy columns (Qiagen). Quality was checked with an Agilent 2100 Bioanalyzer.

tag: strain

value: mixed C57BL/6 and 129 background

tag: treatment

value: 70 mg/kg tamoxifen, on 2 consecutive days

value: Female


title: 23 galactose RNAseq


title: Organoid Wild_type_sample_1

source_name: Organoid from colon sample from wild type mouse 9


title: DX_female_2167

description: Dongxiang blue-shelled chicken


title: 22 galactose RNAseq


title: Organoid Wild_type_sample_2

source_name: Organoid from colon sample from wild type mouse 10


title: Organoid Wild_type_sample_3

source_name: Organoid from colon sample from wild type mouse 11


title: Organoid Apc_fl/fl_sample_1

source_name: Organoid from colon sample of tamoxifen treated CDX2P-CreERT2, Apc fl/fl mouse 6


title: Organoid Apc_fl/fl_sample_3

source_name: Organoid from colon sample of tamoxifen treated CDX2P-CreERT2, Apc fl/fl mouse 8


title: DX_female_22069

description: Dongxiang blue-shelled chicken


title: 21 galactose RNAseq


title: 22 glucose RNAseq


title: DX_female_22058

description: Dongxiang blue-shelled chicken


title: DX_female_21844

description: Dongxiang blue-shelled chicken


title: Organoid Apc_fl/fl_sample_2

source_name: Organoid from colon sample of tamoxifen treated CDX2P-CreERT2, Apc fl/fl mouse 7


title: DX_female_2149

description: Dongxiang blue-shelled chicken


title: DX_female_2148

description: Dongxiang blue-shelled chicken


title: Organoid AKP_270/fl_sample_3

source_name: Organoid from colon sample of tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 5


title: 21 glucose RNAseq


title: DX_female_21960

description: Dongxiang blue-shelled chicken


title: DX_female_735

description: Dongxiang blue-shelled chicken

label: DCL


title: Organoid AKP_270/fl_sample_2

source_name: Organoid from colon sample of tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 4


title: 20 galactose RNAseq


title: DX_female_21929

description: Dongxiang blue-shelled chicken


title: Organoid AKP_270/fl_sample_1

source_name: Organoid from colon sample of tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 3


title: 20 glucose RNAseq


title: 19 galactose RNAseq


title: Organoid AKP_fl/fl_sample_2

source_name: Organoid from colon sample of tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 fl/fl mouse 2


title: DX_female_21823

description: Dongxiang blue-shelled chicken


title: DX_female_725

description: Dongxiang blue-shelled chicken


title: DX_female_722

description: Dongxiang blue-shelled chicken


title: DX_female_718

description: Dongxiang blue-shelled chicken


title: 23 glucose RNAseq


title: Organoid AKP_fl/fl_sample_1

source_name: Organoid from colon sample of tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 fl/fl mouse 1


title: DX_female_712

description: Dongxiang blue-shelled chicken


title: 18 galactose RNAseq


title: 19 glucose RNAseq


title: Tissue Wild_type_normal_sample_3

hyb_protocol: Following fragmentation, cDNA was hybridized for 20 hr at 48C to Affymetrix Mouse Genome 2.1 ST strip arrays.

source_name: Normal colon sample from wild type mouse 15

label_protocol: 10 ng total RNA was reverse-transcribed, amplified and labeled, with GeneChip WT Pico Kits (Applied Biosystems).

extract_protocol: Total RNA was extracted using Arcturus PicoPure RNA Isolation Kits (Applied Biosystems). Quality was checked with an Agilent 2100 Bioanalyzer.


title: DX_female_708

description: Dongxiang blue-shelled chicken


title: DX_female_706

description: Dongxiang blue-shelled chicken


title: 18 glucose RNAseq


title: DX_female_2379

description: Dongxiang blue-shelled chicken

label: RCL


title: Tissue Wild_type_normal_sample_1

source_name: Normal colon sample from wild type mouse 13


title: DX_female_730

description: Dongxiang blue-shelled chicken


title: DX_female_733

description: Dongxiang blue-shelled chicken


title: Tissue Wild_type_normal_sample_2

source_name: Normal colon sample from wild type mouse 14


title: DX_female_704

description: Dongxiang blue-shelled chicken


title: DX_female_1960

description: Dongxiang blue-shelled chicken


title: DX_female_1958

description: Dongxiang blue-shelled chicken


title: DX_female_1959

description: Dongxiang blue-shelled chicken


title: 17 glucose RNAseq


title: DX_female_1950

description: Dongxiang blue-shelled chicken


title: DX_female_1954

description: Dongxiang blue-shelled chicken


title: 16 galactose RNAseq


title: DX_female_1948

description: Dongxiang blue-shelled chicken


title: DX_female_1947

description: Dongxiang blue-shelled chicken


title: Tissue AKP_270/fl_sample_5

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 11


title: 15 galactose RNAseq

source_name: fetal retinal pigment epithelium


title: Tissue AKP_270/fl_sample_3

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 9


title: 16 glucose RNAseq


title: DX_female_1944

description: Dongxiang blue-shelled chicken


title: Tissue AKP_270/fl_sample_4

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 10


title: DX_female_1942

description: Dongxiang blue-shelled chicken


title: Tissue AKP_270/fl_sample_6

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 12


title: DX_female_1946

description: Dongxiang blue-shelled chicken


title: 15 glucose RNAseq


title: DX_female_1937

description: Dongxiang blue-shelled chicken


title: 17 galactose RNAseq


title: DX_female_1935

description: Dongxiang blue-shelled chicken


title: 14 galactose RNAseq


title: DX_female_1957

description: Dongxiang blue-shelled chicken


title: 14 glucose RNAseq


title: DX_female_1932

description: Dongxiang blue-shelled chicken


title: DX_female_797

description: Dongxiang blue-shelled chicken


title: DX_female_2337

description: Dongxiang blue-shelled chicken


title: Tissue AKP_270/fl_sample_2

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 8


title: Tissue AKP_fl/fl_sample_6

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 fl/fl mouse 6


title: Tissue AKP_270/fl_sample_1

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 R270H/fl mouse 7


title: DX_female_794

description: Dongxiang blue-shelled chicken


title: DX_female_795

description: Dongxiang blue-shelled chicken


title: Tissue AKP_fl/fl_sample_4

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 fl/fl mouse 4


title: Tissue AKP_fl/fl_sample_3

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 fl/fl mouse 3


title: DX_female_790

description: Dongxiang blue-shelled chicken


title: DX_female_793

description: Dongxiang blue-shelled chicken


title: 12 galactose RNAseq


title: DX_female_789

description: Dongxiang blue-shelled chicken


title: DX_female_786

description: Dongxiang blue-shelled chicken


title: Hour16_mo_rep3

city: New Haven

first: Martina

last: Brueckner

state: CT

address: 789 Howard Ave

department: Pediatrics

institute: Yale University

data_processing:
Sequences mapped using Kallisto
Differential gene expression of each sample was determined using Sleuth
Genome_build: JGI 7.1
Supplementary_files_format_and_content: tab deliminated text files containing all sleuth output fields
Supplementary_files_format_and_content: est_counts      tpm

organism: Xenopus laevis

source_name: embryo

growth_protocol: in vivo

extract_protocol:
Qiagen RNAeasy mini kit
Poly-A selection

treatment_protocol: morhpolino injections

tag: developmental stage

value: RNF20 morpholino


title: 12 glucose RNAseq


title: DX_female_788

description: Dongxiang blue-shelled chicken

value: brachial veins


title: DX_female_781

description: Dongxiang blue-shelled chicken

value: female


title: 11 galactose RNAseq


title: Hour16_mo_rep2


title: Hour16_mo_rep1


title: Tissue AKP_fl/fl_sample_2

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 fl/fl mouse 2


title: 11 glucose RNAseq


title: DX_female_779

description: Dongxiang blue-shelled chicken

value: Dongxiang blue-shelled


title: DX_female_780

description: Dongxiang blue-shelled chicken


title: DX_female_773

description: Dongxiang blue-shelled chicken


title: Hour16_wt_rep2

value: wild type


title: DX_female_785

description: Dongxiang blue-shelled chicken


title: 10 galactose RNAseq


title: 13 galactose RNAseq


title: DX_female_771

description: Dongxiang blue-shelled chicken


title: Tissue AKP_fl/fl_sample_5

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 fl/fl mouse 5

value: Male


title: Tissue AKP_fl/fl_sample_1

source_name: Colon Adenocarcinoma from tamoxifen treated CDX2P-CreERT2, Apc fl/+, Kras LSL-G12D/+, Tpr53 fl/fl mouse 1


title: Hour16_wt_rep1


title: 10 glucose RNAseq


title: DX_female_769

description: Dongxiang blue-shelled chicken


title: 13 glucose RNAseq


title: Hour15_mo_rep3


title: DX_female_763

description: Dongxiang blue-shelled chicken


title: DX_female_759

description: Dongxiang blue-shelled chicken


title: 9 galactose RNAseq


title: DX_female_758

description: Dongxiang blue-shelled chicken


title: Hour15_mo_rep1


title: DX_female_765

description: Dongxiang blue-shelled chicken


title: Hour15_wt_rep2


title: DX_female_756

description: Dongxiang blue-shelled chicken


title: DX_female_753

description: Dongxiang blue-shelled chicken


title: DX_female_752

description: Dongxiang blue-shelled chicken


title: DX_female_754

description: Dongxiang blue-shelled chicken


title: 7 galactose RNAseq


title: DX_female_749

description: Dongxiang blue-shelled chicken


title: Hour15_wt_rep1


title: 8 galactose RNAseq


title: 9 glucose RNAseq


title: 8 glucose RNAseq


title: DX_female_750

description: Dongxiang blue-shelled chicken


title: DX_female_747

description: Dongxiang blue-shelled chicken


title: Hour14_mo_rep2


title: DX_female_739

description: Dongxiang blue-shelled chicken


title: 6 galactose RNAseq


title: Hour14_mo_rep1


title: Hour15_mo_rep2


title: 6 glucose RNAseq


title: DX_female_738

description: Dongxiang blue-shelled chicken


title: DX_female_709

description: Dongxiang blue-shelled chicken


title: DX_female_755

description: Dongxiang blue-shelled chicken


title: DX_female_713

description: Dongxiang blue-shelled chicken


title: DX_female_711

description: Dongxiang blue-shelled chicken


title: Hour14_wt_rep1


title: 5 glucose RNAseq


title: 5 galactose RNAseq


title: 7 glucose RNAseq


title: DX_female_720

description: Dongxiang blue-shelled chicken


title: DX_female_727

description: Dongxiang blue-shelled chicken


title: DX_female_726

description: Dongxiang blue-shelled chicken


title: DX_female_740

description: Dongxiang blue-shelled chicken


title: DX_female_761

description: Dongxiang blue-shelled chicken


title: Hour13_mo_rep2


title: Hour14_mo_rep3


title: DX_female_716

description: Dongxiang blue-shelled chicken


title: DX_female_715

description: Dongxiang blue-shelled chicken


title: 4 galactose RNAseq


title: Hour13_mo_rep3


title: DX_female_719

description: Dongxiang blue-shelled chicken


title: DX_female_723

description: Dongxiang blue-shelled chicken


title: Hour13_mo_rep1


title: 3 galactose RNAseq


title: Hour13_wt_rep2


title: DX_female_724

description: Dongxiang blue-shelled chicken


title: DX_female_728

description: Dongxiang blue-shelled chicken


title: Hour14_wt_rep2


title: DX_female_707

description: Dongxiang blue-shelled chicken


title: DX_female_703

description: Dongxiang blue-shelled chicken


title: Hour13_wt_rep1


title: 3 glucose RNAseq


title: DX_female_731

description: Dongxiang blue-shelled chicken


title: 4 glucose RNAseq


title: DX_female_734

description: Dongxiang blue-shelled chicken


title: Hour12_mo_rep3


title: DX_female_736

description: Dongxiang blue-shelled chicken


title: DX_female_729

description: Dongxiang blue-shelled chicken


title: 2 glucose RNAseq


title: Hour12_mo_rep2


title: DX_female_721

description: Dongxiang blue-shelled chicken


title: Hour12_mo_rep1


title: 1 galactose RNAseq


title: DX_female_764

description: Dongxiang blue-shelled chicken


title: 2 galactose RNAseq


title: 1 glucose RNAseq


title: DX_female_702

description: Dongxiang blue-shelled chicken


title: Hour12_wt_rep2


title: DX_female_760

description: Dongxiang blue-shelled chicken


title: DX_female_766

description: Dongxiang blue-shelled chicken


title: DX_female_757

description: Dongxiang blue-shelled chicken


title: DX_female_743

description: Dongxiang blue-shelled chicken


title: DX_female_762

description: Dongxiang blue-shelled chicken


title: RNA standard

city: Berlin

first: Ivano

last: Legnini

state: Germany

address: Robert-Rössle-Straße 10, Haus 87

department: BIMSB

country: Germany

institute: MDC

data_processing:
Library strategy: FLAM-seq
CCS reads were produced with the SMRT Link browser 5.0 (minimum full pass 3, minimum predicted accuracy 90)
Fastq files were analyzed according to the FLAM-seq analysis pipeline: reads were filtered for containing at least 10 As followed by 9 Gs (or the rev. comp.), then reoriented to start with the adapter sequence, the UMI, the G tail and the poly(A) tail. Poly(A) tails were detected and removed, the remaining reads were aligned to hg38 or C. elegans WB235 genome assemblies using STARLong (Dobin et al., 2013). Each aligned read was then assigned to gene models (Ensembl GRCh38.84 for human, WBcel235_82 for worm) with FeatureCounts (Liao et al., 2014).
Genome_build: H. sapiens: hg38, C. elegans: WB235
Supplementary_files_format_and_content: Processed data contain read name, gene to which read is assigned using FeatureCounts, unique molecular identifier sequence, tail length and tail sequence

organism: synthetic RNA

source_name: synthetic RNA

extract_protocol:
All samples were collected in Trizol and poly(A)+ RNA was extracted with the Truseq mRNA preparation kit (RS-122-21-2, Illumina).
Libraries were constructed according to the FLAM-seq protocol.

tag: sample type

value: synthetic RNA


title: C. elegans adult rep. 2

organism: Caenorhabditis elegans

source_name: C. elegans adult – egg laying

growth_protocol: Caenorhabditis elegans animals (wild-type N2 Bristol) were cultured on OP50 bacteria, synchronized by bleaching, seeded and grown at 20 °C

value: wt N2 Bristol


title: DX_female_748

city: Beijing

description: Dongxiang blue-shelled chicken


title: XWGBS_GM12892

city: Bronx

first: Andrew

last: Johnston

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

data_processing:
FASTQ reads were adapter asked using cutadapt v1.9.1 for bisulfite converted adapter sequences
Masked reads were aligned to hg38+decoy+EBV using bwa-meth v0.10 with default parameters
Aligned reads were marked for duplicates using Picard v2.4.1
A custom perl script was used to filter "fill-in" artifact be qc-fail flagging reads with 3 or more methylated CHH's outside the first 11 cycles
Methylation ratios were determined, by CpG, CHG, CHH context, using MethylDackel v0.1.13 with min baseQ >= 20, min mapQ >=20 and excluding the first 11bases of R1 and R2 alignments
Genome_build: GENCODE hg38 + decoy + EBV
Supplementary_files_format_and_content: Compressed methylKit files were generated which capture CpG CHG, CHH methylation and coverage (https://github.com/al2na/methylKit); meth_10_fil_no99.rds is a serliazed R object containing filtered CpG sites with >10 read depth

extract_protocol:
2 million cells were pelleted at 2000g for 10' and frozen at -80C until extraction of DNA. Pellets were thawed and resspended in 10mM Tris pH 8.0, 150 mM EDTA solution before the addition of SDS to a final concentration of 1%. Protein was digested overnight at 50C with 25 ug of Proteinase K, followed by an hour incubation at 37C with 5 ug of RNAse A. Extraction of genomic DNA was then achieved through two consecutive phenol:chloroform steps, selecting the aqeous phase. The DNA was then concentrated and purified via ethanol precipitation.
100 ng of genomic DNA was treated with Tn5 transposase for tagmentation, then tagged DNA was filled with methylated dCTP, dATP, dGTP, dTTP mixture. The filled DNA was bisulphite treated using EZ DNA methylation Gold kit (Zymo research). The bisulphite treated samples were amplified with custom and Illumina index adapters. The amplified products were size selected using AMPureXP beads.

tag: cell line

tag: cell type

value: EBV-transformed lymphoblastoid cell line

tag: number of cells


title: XWGBS_GM12890


title: DX_female_767

description: Dongxiang blue-shelled chicken


title: XWGBS_GM12891


title: DX_female_776

description: Dongxiang blue-shelled chicken


title: DX_female_777

description: Dongxiang blue-shelled chicken


title: DX_female_774

description: Dongxiang blue-shelled chicken


title: DX_female_782

description: Dongxiang blue-shelled chicken


title: XWGBS_GM12889


title: DX_female_775

description: Dongxiang blue-shelled chicken


title: XWGBS_GM12888


title: XWGBS_GM12893


title: C. elegans L4 rep. 2

source_name: C. elegans L4 stage


title: C. elegans adult rep. 1


title: Hour12_wt_rep1


title: DX_female_783

description: Dongxiang blue-shelled chicken


title: DX_female_791

description: Dongxiang blue-shelled chicken


title: DX_female_778

description: Dongxiang blue-shelled chicken


title: L3 larvae brain RNA-seq: male wild-type; replicate 2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_male_KOvsWT.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_wt_male_rep2

data_processing:
MAPCap reads were further demultiplexed using the barcodes present in R2 read. Barcodes and corresponding sample names are provided as MAPCap_embryo_barcodes.tsv and MAPCap_larvae_barcodes.tsv. No demultiplexing required for RNAseq
MAPCap: Paired-end FASTQ files were trimmed for adaptors using Trimmomatic 56 (v 0.3.7). Samples were de-multiplexed by icetea (v0.99, demultiplexFastq) using provided barcode information, and mapped to the dm6 genome using Rsubread 57 (v 1.22.3, mapping wrapper provided in icetea). For de-duplication, we consider all reads mapping to the same 5’-position and having the same random barcode as duplicates and only keep the first instance of each such alignment (using icetea - filterDuplicates). BigWigs were created using deepTools 58 (v3.0.2) bamCoverage and bamCompare, with the option `--offSet 1 --binSize 1`.
RNA-seq: data was processed using snakePipes RNA-seq pipeline 65 (v1.0.0 beta) using the options ` -m alignment,deepTools_qc --star_options  --limitBAMsortRAM 60000000000 --outBAMsortingBinsN 30 dm6`. snakePipes performed alignment using STAR 66 (v2.6.1a), counting of reads on Ensembl GTF (release 79) via featureCounts 67 (v1.6.1), and quality-checks via deepTools 58 (v3.1.2). The gene-level counts obtained from featureCounts were then used for differential expression analysis via DESeq2 68 (v1.20.0).
Pipeline for processing MAPCap data is available at: https://github.com/vivekbhr/cage_pipeline
Pipeline for processing RNAseq data is available at: https://github.com/maxplanck-ie/snakepipes
Genome_build: dm6
Supplementary_files_format_and_content: bw, featureCounts, DESeq2 output

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Fruit flies (Drosophila melanogaster) were reared on standard cornflour-molasses medium. at 25°C, 70% relative humidity and 12 hrs dark/12 hrs light cycle. mle9, cn, bw/CyO flies  (BDSC #5873) have been ordered from the Bloomington Drosophila Stock Center (BDSC) and rebalanced with the help of w; CyO, Act5C-GFP/If to generate the w; mle9, cn, bw/CyO, Act5C-GFP flies used in this study.

extract_protocol:
RNA from embryos was extracted using the Quick RNA Kit (Zymo Research). RNA from dissected brains of larvae was isolated using the DirectZol Kit (Zymo Research). RNA was eluted in 25 ul of RNase-free water.
See our manuscript for full protocol of MAPCap library construction
MAPCap: custom strategy explained in the manuscript. RNAseq: Illumina TRUseq

value: L3 larvae (3rd Instar)

tag: genotype

value: wild-type

value: male


title: XWGBS_GM12887