title: 6-10B + H-exo

city: Guangzhou

first: Fei

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen university

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 ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

source_name: NPC cells

growth_protocol: NPC cells were treated with or without H-exo and cultured in 10%FBS RPMI medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: NPC cells were treated with or without H-exo for 48h.

tag: development stage

value: Nasopharyngeal epithelial cancer cells

value: H-exo

value: Nasopharynx


title: S26 + H-exo

status: Public on May 02 2020

type: SRA

last: Li

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment

tag: tissue


title: Liver_Fast food diet + EGFRi_2 months

type: RNA

city: Pittsburgh

first: George

middle: K

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

country: USA

institute: University of Pittsburgh

description:
C57BL6/J male mice
Gene expression data at 2 months in fast food diet-fed mice treated with EGFR inhibitor (Canertinib) for entire 2 months period

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Mus musculus

source_name: Fast food diet-fed and EGFRi-treated mice liver tissue at 2 months

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: For the two months study, 6-8 weeks old male C57BL6/J mice were fed ad libitum (i) chow diet, (ii) fast-food diet [western diet - high saturated fats (21% by weight; 42% kcal from fat), high cholesterol (0.2%) and high carbohydrates (sucrose: 34% by weight)  in diet  (TD.88137, Teklad) - along with high-fructose-glucose solution (d-glucose: 18.9g/L  and d-fructose: 23.1g/L) in drinking water] or (iii) Canertinib (a highly potent and selective EGFR inhibitor/ EGFRi) added in the same fast-food diet for 2-months. Canertinib was administered to mice in diet for estimated dose of 80 mg/kg/day. For the five months study, 6-8 weeks old male C57BL6/J mice were fed ad libitum (i) chow diet, (ii) and (iii) fast-food diet for 5-months. Group (ii) and (iii) were administered vehicle (PBS) and Canertinib (80mg/kg; i.p.), respectively, 5 days/week for the last 5-weeks of 5-months period.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For the two months study, Canertinib (a highly potent and selective EGFR inhibitor/ EGFRi) was added in the fast-food diet for entire 2-months period. For the five months study, Canertinib (80mg/kg; i.p.) was administered 5 days/week for the last 5-weeks of 5-months period.

tag: strain

tag: gender

value: male


title: 6-10B NC


title: RNA_Dwil_wing

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

data_processing:
Reads with residual adapter sequences were discarded (FastX cliper version 0.012 option -M15)
Reads were mapped against their own-species genome by  TOPHAT v2.0 (default parameters)
Gene expression counts were computed by HTSeq (str=no) with the following genome annotations (D.melanogaster 5.46, D.simulans 1.4, D.yakuba 1.3, D.ananassae 1.3, D.pseudoobscura 2.30, D.willistoni 1.3, D.mojavensis 1.3 and D.virilis 1.2)
Genome_build: Drosophila melanogaster FB5, D.pseudoobscura FB2 and the rest of species, D.simulans, D.yakuba, D.ananassae, D.willistoni, D.mojavensis and D.virilis FB1
Supplementary_files_format_and_content: RNAseq samples:Gene counts in original species annotation and normalized data across species and tissues in D.melanogaster gene annotation.

organism: Drosophila willistoni

source_name: wing imaginal disc

growth_protocol: All flies were raised at 25 degrees Celsius on standard fly food

extract_protocol:
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were generated for sequencing using standard Illumina TruSeq protocols

treatment_protocol: Wandering 3rd instar larvae were dissected in PBS to extract the tissues of interest

tag: developmental time point

value: third instar wandering larvae

value: wing imaginal disc

tag: genotype

value: Dwil\wild-type

tag: stock


title: RNA_Dvir_EA

organism: Drosophila virilis

source_name: eye-antennal imaginal disc

value: eye-antennal imaginal disc

value: Dvir\wild-type


title: Liver_Fast food diet_2 months

description:
C57BL6/J male mice
Gene expression data at 2 months in fast food diet-fed mice

source_name: Fast food diet-fed mice liver tissue at 2 months


title: Liver_Fast food diet + EGFRi_5 months

description:
C57BL6/J male mice
Gene expression data at 5 months in fast food diet-fed mice treated with EGFR inhibitor (Canertinib) for last five weeks of 5 months period

source_name: Fast food diet-fed and EGFRi-treated mice liver tissue at 5 months


title: THF IFNAR-/- mock rep1

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St. West

department: Department of Pathology

country: Canada

institute: McMaster University

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to the GRCh38/hg38 reference version using HISAT.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
For the preprocessed CSV file - we have used the filterByExpr function in the edgeR package (all default parameters).
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file contains a matrix containing normalized data from all samples.

source_name: fibroblast

growth_protocol: THF cells were cultured in DMEM containing 10% fetal bovine serum in 150cm flasks at 37C 5% CO2 and re-plated every 3-4 days

extract_protocol:
THF cells were pelleted and RNA harvested and purified using an Invitrogen PureLink RNA Mini Kit.
Libraries were generated using an Illumina TruSeq Stranded RNA kit

treatment_protocol: THF cells were seeded to 6-well plates 24 hours before infection for 1 hour in minimal serum-free DMEM containing 0.02 pfu/cell HCMV, 8e-5 HAU/cell SeV, or media alone inactivated with 800uJ/cm^2. Infection media was replaced with complete media and THF cells incubated at 37C for 6 hours.

value: IFNAR-/-

tag: infection

value: fibroblast


title: RNA_Dwil_EA


title: RNA_Dwil_brain

source_name: brain

value: brain


title: input DNA

city: Qingdao

first: Qing

last: Kong

state: Shandong

address: Yushan Road 5

department: Food Science and Engineering

institute: Ocean University of China

library_source: genomic

data_processing:
ChIP-sequencing was accomplished on the Illumina HiSeq 2500 with the ChIP-seq libraries.
Reads were trimmed and cleaned of Illumina adaptors using  Trimmomatic and aligned to the A. flavus NRRL3357 genome using bowtie2-2.1.0. The genome  and annotations of A. flavus NRRL3357 were downloaded from NCBI (The National Center for  Biotechnology Information). Reads that aligned concordantly were used for peak calling.
The   resulting bam files were used as an input for peak calling by Model-based Analysis for ChIP  Sequencing (MACS2) version 2.0.10.20131216. Peak calling was done with the ChIP-seq samples  and input control samples using a False Discovery Rate (FDR) cutoff of 0.05.
The topGO R package was used for functional enrichment and gene ontology (GO) analysis as described previously. The p-value cutoff was set at 0.05 for GO analyses.
The online motif finding program Multiple EM for Motif Elicitation (MEME, Version 5.1.1) was used to predict AfAflR-binding motifs within  ChIP-seq peaks. The sequences of the 200 bp centered on each of the peaks were uploaded into  MEME.
Genome_build: JCBI-AFL1-V2.0
Supplementary_files_format_and_content: wig files were generated using the Samtools.

molecule: genomic DNA

organism: Aspergillus flavus

source_name: chromosome

growth_protocol: A. flavus NRRL3357 was grown in 200 mL (1 × 10e6 spores/mL) of potato  dextrose broth (PDB) in 500 mL shaking flasks at 28 °C for 24 h. Three replicate cultures were  prepared. The cultures were centrifuged and transferred to a cross-linking solution for ChIP  experiments.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: The cross-linking, DNA sonication, and chromatin immunoprecipitation were  performed according to the protocols of Chung et al. Briefly, the chromatin was extracted and  sonicated (Branson sonifier, Danbury, CT, USA) at half-maximal power over ten 10-sec pulses with  chilling on ice for 2 min after each pulse. An aliquot of the chromatin solution (1/10 of the total  volume) was used as input DNA to determine the DNA fragment sizes. The average sizes of the  resultant DNA fragments were ~0.2–1.5 kb. The remaining chromatin solution was divided into two  parts: one was incubated with the addition of 10 μl of the antibodies (anti-AfAflR), and the other was  incubated without antibodies (mock). Immunoprecipitated DNA was used for sequencing. Millipore  Chromatin Immunoprecipitation Assay Kit (17-295, EMD Millipore Corporation, Temecula, CA,  USA) was used in ChIP experiments.

tag: medium

value: PDB

tag: incubation

value: 28℃ for 24 h

tag: chip antibody


title: S26 NC


title: MCT treatment for 4 week (MCTW4) rep3

city: Fuzhou

first: Genfa

last: Xiao

state: Fujian

address: chazhong road 20

institute: First Affiliated Hospital of Fujian Medical University

data_processing:
The quality of generated reads was assessed by FastQC software.
The low quality reads and adapter sequences were removed by Skewer software.
The alignment of clean reads to rat reference genome was performed using STAR software .
The transcripts were assembled by using the StringTie software.
The values of transcript expression in each sample were determined by HTSeq software throuth calculation of fragments per kilobase of transcript per million fragments mapped (FPKM).
Genome_build: Rn6
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Rattus norvegicus

source_name: lung tissue

growth_protocol: Sprague-Dawley rats, male and female rats, 200-250g, were raised and housed in the animal room and received food and water ad libitum.

extract_protocol:
Rat lungs were isolated and frozen in liquid nitrogen and then stored at -80°C after sacrifice.Total RNA was isolated from 50 mg lung tissues using 1 mL Trizol reagent following manufacturer’s instructions. RNA integrity and quality were assessed by gel electrophoresis and its concentration and purity were determined by the Thermo Scientific NanoDropTM instruments. Total RNA with high quality was used for cDNA library preparation.
Library preparation and RNA-seq were performed on an Illumina HiSeq 2000 platform by Genenergy Biotechnology (Shanghai) Co., Ltd.

treatment_protocol: PAH model in rats was induced by a single intraperitoneal injection of 40 mg/kg MCT. A total of 17 rats were used in this study, 12 rats were randomly assigned into 4 groups and treated with MCT (n = 3, each group). 5 remaining rats served as control and treated with saline.. Control and MCT-treated rats were sacrificed at week 0, 1, 2, 3 and 4.

value: Sprague-Dawley

value: lung

value: monocrotaline (MCT)

tag: sacrifice time

value: sacrificed at week 4 after MCT treatment


title: KK-S10

city: Chicago

first: Erica

last: Davis

state: IL

address: 225 E Chicago Avenue

department: Advanced Center for Translational and Genetic Medicine (ACT-GeM)

institute: Ann & Robert H Lurie Children's Hospital of Chicago

data_processing:
RNA-seq data were processed using the TrimGalore toolkit (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of reads. Only reads that were 20 nt or longer after trimming were kept for further analysis. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA-seq alignment tool and retained for subsequent analysis if they mapped to a single genomic location. Gene counts were compiled using the HTSeq tool (http://www-huber.embl.de/users/anders/HTSeq/), and only genes that had ≥10 reads in any given library were used in subsequent analyses.
Normalization and differential expression were carried out using the DESeq2 Bioconductor package with the R statistical programming environment (www.r-project.org). False discovery rate was calculated to control for multiple hypothesis testing.
Gene set enrichment analysis was performed to identify gene ontology terms associated with altered gene expression for each comparison.
Alternative splicing was characterized using the rMATS algorithm, which employs the STAR alignment tool along with the Zv10r87 version of the zebrafish genome and transcriptome.
DAVID pathway analysis was run on significant genes (FDR <= 5%) on each of the five alternative splicing event categories as well as the union set of all five lists.
Genome_build: Zv10r87 version of the zebrafish genome and transcriptome
Supplementary_files_format_and_content: The processesd files are in Excel sheet format. The differential expression file include differential expression values (Log2Fold change) along with statistical significance. The rMATs file contain alternative splicing events analysis across wild type and fam50a KO mutants

organism: Danio rerio

growth_protocol: Embryos were obtained from natural matings of adult fam50a heterozygous KO mutants zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media (0.3 g/L NaCl, 75 mg/L CaSO4, 37.5 mg/L NaHC03, 0.003% methylene blue) at 28°C until 2 dpf.

extract_protocol:
We extracted total RNA from embryo heads with Trizol (ThermoFisher), according to manufacturer's instructions. N=20 embryos/pool. Samples were treated with DNase prior to RNAseq
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit following the manufacturer’s protocol. In brief, mRNA transcripts were first captured using magnetic oligo-dT beads, fragmented using heat and magnesium, and reverse transcribed using random priming. During the 2nd strand synthesis, the cDNA:RNA hybrid was converted into double-stranded cDNA (dscDNA) and dUTP incorporated into the 2nd cDNA strand. Illumina sequencing adapters were ligated to the dscDNA fragments and amplified to produce final RNA-seq libraries. Libraries were indexed and pooled in an equimolar ratio prior to 50 bp single end sequencing on the same lane of a HiSeq 4000 (Illumina). Sequence data were demultiplexed and Fastq files were generated using Bcl2Fastq conversion software (Illumina).

tag: sample type

tag: developmental stage

value: 2 day post-fertilization

value: fam50a KO


title: MCT treatment for 4 week (MCTW4) rep1


title: MCT treatment for 4 week (MCTW4) rep2


title: KK-S9


title: MCT treatment for 3 week (MCTW3) rep3

value: sacrificed at week 3 after MCT treatment


title: sRNA Root

city: Huntsville

first: Alex

last: Harkess

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Rt_Aspa
small RNA

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides.
Genome_build: Asparagus officinalis v1.1 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Aofficinalis_er)
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Asparagus officinalis

source_name: root

extract_protocol:
Trizol RNA
The small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by  Illumina sRNA TruSeq sample preparation kit followed by sequencing with Illumina's HiSeq 2500 instrument. The adapter sequences were removed, and the abundance of each distinct small RNA was determined."

value: root


title: KK-S8


title: sRNA Shoot

description:
St_Aspa
small RNA

source_name: shoot

value: shoot


title: KK-S7


title: sRNA Male Flower Early

description:
MFE_Aspa
small RNA

source_name: flower bud

value: Male

value: flower bud


title: KK-S6


title: MCT treatment for 3 week (MCTW3) rep1


title: sRNA Leaf

description:
Lf_Aspa
small RNA

source_name: leaf

value: leaf


title: KK-S5

value: wild type


title: MCT treatment for 3 week (MCTW3) rep2


title: KK-S4


title: MCT treatment for 2 week (MCTW2) rep3

value: sacrificed at week 2 after MCT treatment


title: sRNA Female Flower Mid

description:
FeFM_Aspa
small RNA

value: Female


title: sRNA Male Flower Mid

description:
MFM_Aspa
small RNA


title: KK-S3


title: AflR_ChIPSeq

value: PDB

value: AflR (multiclonal antibody of AfAflR was produced in rabbits by Abcam (Shanghai, China); goat anti-rabbit antibody (anti-AfAflR) purchased from Abmart (Shanghai, China))


title: sRNA Female Flower Early

description:
FeFE_Aspa
small RNA


title: MCT treatment for 2 week (MCTW2) rep2

value: Sprague-Dawley


title: MCT treatment for 2 week (MCTW2) rep1

value: lung


title: KK-S2


title: Liver_Chow_2 months

description:
C57BL6/J male mice
Gene expression data at 2 months in Chow-fed mice

source_name: Chow diet-fed mice liver tissue at 2 months

value: male


title: sRNA line 8B Male

description:
8B_Ms
small RNA

source_name: 6inch spear tip

value: 6inch spear tip


title: KK-S1

value: 2 day post-fertilization


title: MCT treatment for 1 week (MCTW1) rep2

value: monocrotaline (MCT)

value: sacrificed at week 1 after MCT treatment


title: sRNA line 8B Female

description:
8B_Fs
small RNA


title: MCT treatment for 1 week (MCTW1) rep1


title: sRNA line 8A Supermale

description:
8A_SMs
small RNA

value: Supermale


title: Control (CTW) rep5

value: saline

value: sacrificed at week 4


title: sRNA line 8B Supermale

description:
8B_SMs
small RNA


title: sRNA line 8A Male

description:
8A_Ms
small RNA

value: Male


title: MCT treatment for 1 week (MCTW1) rep3


title: 27HSC1

city: Tsukuba

first: Takashi

last: Fujikawa

state: Ibaraki

address: Fujimoto 2-1

department: Institute of Fruit Tree and Tea Sience

country: Japan

institute: National Agriculture and Food Research Organization

description: presented in Psa6_RNA-seq_CLC-output.xlsx and Psa6_RNA-seq_Ranalyzed-output.xlsx

data_processing:
Ion Torrent Server software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by CLC Genomics Workbench software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by CLC Genomics Workbench software and normalized.
Using R software with some packages, the gene expression values relative to the 27 °C HS medium were calculated to log2 values of fold change (log2FC) with FDR (false discovery rate) values.
Genome_build: Psa6 MAFF 212134 (accession no. MSBW00000000)
Supplementary_files_format_and_content: A tab-delimited text file include RPKM values and normalized values and the statistical data for each sample in "Psa6_RNA-seq_CLC-output.xlsx".  And a tab-delimited text file include relative values of gene expression relatively to the 27 °C HS medium in "Psa6_RNA-seq_Ranalyzed-output.xlsx".

organism: Pseudomonas syringae pv. actinidiae

source_name: culture on HSC medium at 27 °C

extract_protocol:
RNeasy Plant Mini Kit (Qiagen)
total RNA (rRNAs-depleted)
Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific Inc.) and Ion Xpress RNA-Seq barcode (Thermo Fisher Scientific Inc.).

value: HSC

tag: temperature

value: 27 °C


title: Control (CTW) rep3

value: sacrificed at week 2


title: 27HS3

source_name: culture on HS medium at 27 °C

value: HS


title: 27HSC2


title: 27HS1


title: Control (CTW) rep2

value: sacrificed at week 1


title: ATF4 O/E_rep3

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

description: replicate 3

data_processing:
Preprocessing of RNA-seq reads was performed using the FASTX toolkit. Adapters were clipped, poor quality reads were filtered out, and identical reads were collapsed.
Reads were then aligned to the human genome (build GRCh37/hg19) using Tophat2 with default settings.
Raw gene counts were obtained using htseq-count from the HTSeq library.
Differential gene expression analysis was performed using the R statistical package DESeq2.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Comma delimited text files with log fold change values as estimated by Deseq2.

source_name: ATF4 O/E_4wks

extract_protocol:
RNA was extracted with mirVana kit (Invitrogen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Libraries were generated from 1 μg of total RNA from three biological replicates of 4-week-old forebrain neurons using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB) following the manufacturer’s protocol.

value: iPSC-derived forebrain neurons

tag: age

value: ATF4 over-expression


title: RNA_Dyak_wing

organism: Drosophila yakuba

source_name: wing imaginal disc

value: third instar wandering larvae

value: wing imaginal disc

value: Dyak\wild-type


title: sRNA line 8A Female

description:
8A_Fs
small RNA

value: Female

value: 6inch spear tip


title: sRNA line 10 Female

description:
10_Fs
small RNA


title: RNA_Dyak_brain

value: brain


title: 27HS2


title: 18HSC3

source_name: culture on HSC medium at 18 °C

value: 18 °C


title: Control (CTW) rep1

value: Sprague-Dawley

value: lung

value: saline

value: sacrificed at week 0


title: 27HSC3

value: HSC

value: 27 °C


title: RNA_Dmel_CS_brain: Larval_brain_WT_cs

organism: Drosophila melanogaster

value: Canton S


title: RNA_Dyak_EA

source_name: eye-antennal imaginal disc

value: eye-antennal imaginal disc


title: ATF4 O/E_rep2

description: replicate 2

tag: cell type

value: iPSC-derived forebrain neurons


title: 18HSC2


title: 18HS3

source_name: culture on HS medium at 18 °C

value: HS


title: ATF4 O/E_rep1

description: replicate 1

value: ATF4 over-expression


title: RNA_Dmel_CS_wing: wing_imaginal_disc_WT_cs

value: third instar wandering larvae

value: wing imaginal disc


title: 3_HepaRG_Diff_day7

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background correction using negative control probes and quantile normalization using negative and positive control probes, was performed with the neqc function of the R/Bioconductor package limma.

source_name: HepaRG cells

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

growth_protocol: HepaRG cells (Biopredic) were cultured in William’s E medium (Gibco 12551-032) at 37°C and 5% CO2, and were regularly tested for mycoplasma contamination (MycoAlert detection kit, Lonza).

extract_protocol: Total RNA was isolated using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions. RNA quantity and quality were assessed with a ND-8000 spectrophotometer and bioanalyzer. 500 ng of total RNA was used for each Human HT-12 Expression BeadChips (Illumina).

treatment_protocol: Cells were plated and allowed to adhere before adding differentiation medium.

tag: treatment

value: differentiation

tag: Stage

value: day 7 differentiation


title: ctrl_rep3

description: replicate 3

value: control


title: 4_HepaRG_Diff_day7


title: 18HS2

tag: strain

value: 18 °C


title: G_HepaRG_prolif_BS_rep2

type: genomic

description: liver progenitor cell line

hyb_protocol: bisulfite and oxidative bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R/Bioconductor: normalization was performed with the swan function in the minfi package

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from liver cell lines using desalting protocol

treatment_protocol: Cells were plated and allowed to adhere before adding differentiation medium or differentiating medium + IFC-305.

value: BS

value: prolif


title: 2_HepaRG_Prolif_day0

value: day 0 progenitors


title: 18HSC1


title: RNA_Dmel_RAL-208_wing: wing_imaginal_disc_WT_RAL-208

tag: tissue


title: sRNA line 10 Male

description:
10_Ms
small RNA

value: Male

value: 6inch spear tip


title: RNA_Dmel_RAL-208_brain: Larval_brain_WT_RAL-208

source_name: brain

tag: developmental time point

value: brain


title: RNA_Dmel_RAL-208_EA: RNA_seq_eye-antennal_imaginal_disc_wild-type [RAL-208]

tag: genotype


title: ctrl_rep2

description: replicate 2


title: 18HS1


title: D_HepaRG_IFC_BS_rep2

description: liver progenitor cell line

value: IFC


title: 1_HepaRG_Prolif_day0


title: E_HepaRG_IFC_BS_rep3

description: liver progenitor cell line


title: H_HepaRG_prolif_BS2_rep2

description: liver progenitor cell line


title: A_HepaRG_week1_BS_rep1

description: liver progenitor cell line


title: intron dCas9 ChIP-seq

status: Public on May 01 2020

city: Paris

first: Sebastian

last: Baumgarten

address: 25, Rue du Dr. Roux

department: Parasites and Insect Vectors

institute: Institut Pasteur

data_processing:
For dCas9 ChIP-seq and dCas-RIP-seq, sequencing reads were aligned to the P. falciparum genome using bwa ‘mem’ allowing only unique read mappings (option ‘-c 1’). Optical duplicates and alignments with a quality score < 20 were removed using samtools’ ‘rmdup’ and ‘view’, respectively
For dCas9 ChIP-seq bedGraph coverage plots, deeptool’s 'bamCompare' was used to normalize the read coverage per genome position (option ‘--bs 1’) in the respective input and ChIP samples to the total number of mapped reads in each library (option ‘--normalizeUsingRPKM’). Normalized input coverage per bin was subtracted from the IP values (option ‘--ratio subtract’)
For dCas9 RIP-seq bedGraph coverage plots, deeptool’s 'bamCompare' was used to normalize the read coverage per genome position (option ‘--bs 1’) in the respective anti-HA and anti-IgG samples to the total number of mapped reads in each library (option ‘--normalizeUsingRPKM’). Normalized anti-IgG coverage per bin was subtracted from the anti-HA values (option ‘--ratio subtract’)
Genome_build: Plasmodium falciparum v28 (plasmoDB.org)
Supplementary_files_format_and_content: dCas9 ChIP-seq and dCas9 RIP-seq bedGraph files contain input normalized IP enrichments (IP minus input for dCas9 ChIP-seq and anti-HA minus anti-IgG for dCas9 RIP) at single nucleotide resolution.

organism: Plasmodium falciparum

source_name: cell culture

extract_protocol:
Synchronized parasites (14 hpi ± 3 hours) were cross-linked by adding formaldehyde (ThermoScientific Pierce 28908) to the culture (final concentration 1%) and incubating with gentle agitation for 10 minutes at room temperature.  Cross-linking was quenched with glycine (final concentration 0.125 M) for five minutes at room temperature.  Cross-linked iRBCs were washed with cold PBS, lysed in 0.15% saponin for 5-10 minutes, and washed twice with cold PBS.  2 x 108 cross-linked parasites were resuspended in 2 mL of lysis buffer [10 mM HEPES pH 8, 10 mM KCl, 0.1 mM EDTA pH 8, complete protease inhibitors (Roche 11836170001) (PI)] and incubated at 4°C for 30 minutes.  IGEPAL CA-630 was added to a final concentration of 0.25% and cells were lysed in a dounce homogenizer.  Extracts were centrifuged for 10 minutes at 13,500 g at 4°C and the supernatant was removed.  The pellet was resuspended in 300 mL SDS lysis buffer [50 mM Tris-HCl pH 8, 10 mM EDTA pH 8, 1% SDS, PI] and transferred to 1.5 mL sonication tubes from Diagenode.  The sample was sonicated for 12 minutes total (24 cycles of 30 sec on, 30 sec off) in a Diagenode Pico Bioruptor at 4°C, the target DNA fragment size being 1-2 kb.  Extracts were centrifuged for 10 minutes at 13,500 g at 4°C and 120 μL of supernatant was diluted 1:10 in ChIP dilution buffer [16.7 mM Tris-HCl pH 8, 150 mM NaCl, 1.2 mM EDTA pH 8, 1% Triton X-100, 0.01% SDS, PI].  170 μL of elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA pH 8, 1% SDS) were added to 30 μL of supernatant and kept as “Input”.  25 μL of Protein G Dynabeads (Invitrogen 10004D) conjugated to one μg of anti-HA antibody (Abcam ab9110) were added to the diluted chromatin sample and incubated overnight with rotation at 4°C.  Beads were collected on a magnet and washed at 4°C with 1 mL for five minutes with rotation of the following buffers, sequentially: low salt wash buffer [20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton X-100, 0.1% SDS, PI], high salt wash buffer [20 mM Tris-HCl pH 8, 500 mM NaCl, 2 mM EDTA pH 8, 1% Triton X-100, 0.1% SDS, PI], LiCl was buffer [10 mM Tris-HCl pH 8, 250 mM NaCl, 1 mM EDTA pH 8, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, PI], and TE wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8).  DNA was eluted from the beads with 205 μL of elution buffer for 30 min at 65°C with agitation.  Beads were separated from the eluate and 200 μL were kept as the “ChIP” sample.  Input and ChIP samples were de-cross-linked for ~10 hr at 65°C.  200 μL of TE buffer were added to each sample.  RNaseA was added (final concentration of 0.2 ug/mL) and samples were incubated at 37°C for two hours.  Proteinase K was added (final concentration of 0.2 ug/mL) and samples were incubated at 55°C for two hours.  DNA was purified with phenol:chloroform:isoamyl alcohol
Libraries were prepared with the Diagenode MicroPlex library preparation kit (C05010014) following the manufacturer's instructions.

value: 14 hpi

tag: antibody


title: ctrl_rep1

description: replicate 1

value: iPSC-derived forebrain neurons


title: promoter dCas9 ChIP-seq


title: H_HepaRG_prolif_BS2_rep1

description: liver progenitor cell line


title: F_HepaRG_prolif_oxBS_rep1

description: liver progenitor cell line

value: oxBS


title: Recombinant human thrombomodulin treated mouse 3 30 hours after LPS administration

city: Gifu

first: Hideshi

last: Okada

address: 1-1 Yanagido

department: Emergency and Disaster Medicine

institute: Gifu University Graduate School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: rhTIM treated mouse_30 hours after LPS administration

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Ten week-old male C57BL6 mice were obtained from Chubu Kagaku Shizai Co. Ltd. (Nagoya, Japan).

extract_protocol: Total RNA was extracted using a RNeasy kit (Qiagen, TX, USA) according to the manufacturer’s protocol. cDNAs were synthesized using a SuperScript III First-Strand Synthesis Kit (Life Technologies, Inc., MD, USA).

treatment_protocol: Following 16-h starvation, mice were intraperitoneally injected with LPS (20 mg/kg; MilliporeSigma, Burlington, MA), and in some assays, with saline or recombinant human thrombomodulin (rhTM; Asahi Kasei Pharma Corporation, Tokyo, Japan) at 3 and 24 h post-LPS injection.

tag: Sex

value: male

value: 10 weeks old

value: Recombinant human thrombomodulin at 3 and 24 h post-LPS injection

tag: harvest time point

value: 30hr after LPS injection

value: lung


title: Control (CTW) rep4

source_name: lung tissue

value: Sprague-Dawley

value: saline

value: sacrificed at week 3


title: promoter dCas9 RIP-seq

extract_protocol:
Synchronized parasites (14 hpi ± 3 hours) were cross-linked by adding formaldehyde (ThermoScientific Pierce 28908) to the culture (final concentration 1%) and incubating with gentle agitation for 10 minutes at room temperature.  Cross-linking was quenched with glycine (final concentration 0.125 M) for five minutes at room temperature.  Cross-linked iRBCs were washed with cold PBS, lysed in 0.15% saponin for 5-10 minutes, and washed twice with cold PBS.  2 x 108 cross-linked parasites were resuspended in 2 mL of lysis buffer [10 mM HEPES pH 8, 10 mM KCl, 0.1 mM EDTA pH 8, complete protease inhibitors (Roche 11836170001) (PI)] and incubated at 4°C for 30 minutes.  IGEPAL CA-630 was added to a final concentration of 0.25% and cells were lysed in a dounce homogenizer.  Extracts were centrifuged for 10 minutes at 13,500 g at 4°C and the supernatant was removed.  The pellet was resuspended in 300 mL SDS lysis buffer [50 mM Tris-HCl pH 8, 10 mM EDTA pH 8, 1% SDS, PI] and transferred to 1.5 mL sonication tubes from Diagenode.  The sample was sonicated for 12 minutes total (24 cycles of 30 sec on, 30 sec off) in a Diagenode Pico Bioruptor at 4°C, the target DNA fragment size being 1-2 kb.  Extracts were centrifuged for 10 minutes at 13,500 g at 4°C and 120 μL of supernatant was diluted 1:10 in ChIP dilution buffer [16.7 mM Tris-HCl pH 8, 150 mM NaCl, 1.2 mM EDTA pH 8, 1% Triton X-100, 0.01% SDS, PI].  25 μL of Protein G Dynabeads (Invitrogen 10004D) conjugated to one μg of anti-HA antibody (Abcam ab9110) were added to the diluted chromatin sample and incubated overnight with rotation at 4°C.  Beads were collected on a magnet and washed at 4°C with 1 mL for five minutes with rotation of the following buffers, sequentially: low salt wash buffer [20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton X-100, 0.1% SDS, PI], high salt wash buffer [20 mM Tris-HCl pH 8, 500 mM NaCl, 2 mM EDTA pH 8, 1% Triton X-100, 0.1% SDS, PI], LiCl was buffer [10 mM Tris-HCl pH 8, 250 mM NaCl, 1 mM EDTA pH 8, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, PI], and TE wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8). For RNA isolation from ChIP-seq material, RNase inhibitor (RNasin from Promega) was added to all lysis and wash buffers.  An IgG control (1μg/25μL of beads, Diagenode C15410206) was included.  Samples were reverse-crosslinked at 70°C for 30 min.  One μL of DNase Turbo (ThermoFisher Scientific) was added and samples were incubated at 37°C for 20 min.  600 μL Trizol LS was mixed with the sample, followed by 160 μL chloroform.  Samples were then purified with the RNeasy MinElute Cleanup Kit (Qiagen)
RNA libraries were prepared with the TruSeq stranded mRNA library prep kit (Illumina) without mRNA selection, ribosomal RNA depletion, or fragmentation.

value: anti-HA


title: B_HepaRG_week1_BS_rep2

description: liver progenitor cell line

value: BS


title: Recombinant human thrombomodulin treated mouse 1 30 hours after LPS administration


title: Saline treated mouse 1 30 hours after LPS injected

source_name: Saline treated mouse_30 hours after LPS injected

value: Saline at 3 and 24 h post-LPS injection


title: C_HepaRG_IFC_BS_rep1

description: liver progenitor cell line


title: F_HepaRG_prolif_BS_rep1

description: liver progenitor cell line

value: prolif


title: control dCas9 RIP-seq

value: anti-IgG


title: RNA_Dmel_CS_EA:  RNA_seq_eye-antennal_imaginal_disc_wild-type [CantonS]

value: third instar wandering larvae

value: eye-antennal imaginal disc

value: Canton S

tag: stock


title: zfATACldtP36R1

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

department: Ophthalmology

institute: Johns Hopkins University

data_processing:
Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR
Raw counts of genes were further used to calculate FPKM (Fragments Per Kilobase Of Exon Per Million) and identify differentially expressed genes through EdgeR
After removing adaptors using cutadapt (58), 50bp paired-end ATAC-Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters
We filtered reads from chromosome M and Y, and included high mapping-quality reads (MAPQ score > 10) through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program.
ATAC-Seq peak regions were called using MACS2 with parameters --nomodel --shift -100 --extsize 200. The blacklisted regions in mouse were excluded from peak regions (https://www.encodeproject.org/annotations/ENCSR636HFF/).
We counted the raw fragments for each peak region using HTSeq.
Genome_build: GRCm38/mm10 and GRCz10/danRer10
Supplementary_files_format_and_content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome, start, stop, name, length of peak region, strand, integer score for display, fold-change, -log10(pvalue), -log10(qvalue), relative summit position to peak start.

source_name: Retina

growth_protocol: To induce Cre recombination, GLASTCreERT2; Sun1-sGFP mice at ~2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for 2 consecutive days at 1mg/dose. Nfialox/lox; Nfiblox/lox, and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1-sGFP mice. To generate MG-specific loss of function mutants of NFIa/b/x genes, 3 week-old GLASTCreERT2; NFIa/bxlox/lox;Sun1-sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate-controlled pathogen free facility on a 14 h-10 h light/dark cycle (07:00 lights on – 19:00 lights off). The adult zebrafish used in these studies were 6 to 12 months old (3-5cm in length). Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.

extract_protocol:
RNA was extracted from both GFP-positive and GFP-negative cell fractions using miRNAeasy Mini Kit (#217004, Qiagen). Ribosomal RNA was depleted, and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo-ZeroTM Gold (# 15032619, Illumina). For tagmentation, cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler (Illumnia Nextera DNA library prep kit, #FC1211030). DNA was cleaned up using MinElute PCR purification kit (#28006, Qiagen) and eluted in 10UL of EB buffer.
Flow-sorted RNA samples were sent to the Deep Sequencing and Microarray Core (Johns Hopkins University) for library preparation and sequencing. Around 8-10 libraries were pooled and sequenced for paired-end 75 cycles using the NextSeq 500 system with ~400-500 million reads per run, resulting in ~45-55 million reads per library. Sorted cells (~50k-75k) from GFP-positive samples were used for ATAC library preparation. Completed ATAC-Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired-end 75 cycles using the NextSeq 500 system with ~400-500 million reads per run.

treatment_protocol: For NMDA damage, adult mice, either CD1 or GLASTCreERT2; Sun1-sGFP mice at ~2 months of age, were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt-ended needle. Mice were sacrificed, and retinas were collected at indicated timepoints. For light damage, the mice were reared in cyclic 12-hour low light/12-hour dark conditions at the University of Florida animal housing facility. Prior to light damage, mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter (Thermo Fisher Scientific Inc., Waltham, MA) and set to 2000 lux. To induce death of rods and cones, adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days, then transferred to clear polycarbonate tanks placed between four fluorescent bulbs (20,000 lux) and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2-phenoxyethanol in system water. To induce amacrine and ganglion cell death, we injected N-methyl-D-aspartic acid (NMDA) (Sigma-Aldrich; St. Louis, MO) intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2-phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2-phenoxyethanol in system water.

value: Retina

value: Tg[gfap:EGFP]nt11, albino

tag: condition

value: Light damage

tag: cell population of facs sorting

value: GFP+

tag: time

tag: replicate

value: Replicate 1


title: control dCas9 ChIP-seq

tag: developmental stage

value: 14 hpi


title: zfATACldtP36R2

value: Replicate 2


title: G_HepaRG_prolif_oxBS_rep2

description: liver progenitor cell line

value: oxBS


title: zfRNAnmdahN36R2

value: Tg[gfap:GFP]mi2001, AB

value: NMDA treatment

value: GFP-


title: zfRNAnmdahN36R1


title: zfATACldtP10R2


title: C_HepaRG_IFC_oxBS_rep1

description: liver progenitor cell line

value: IFC


title: Saline treated mouse 2 30 hours after LPS injected

value: male

tag: age

value: 10 weeks old

value: Saline at 3 and 24 h post-LPS injection

value: 30hr after LPS injection

value: lung


title: zfATACldtP20R1

value: Retina


title: zfATACldtP04R2

value: Tg[gfap:EGFP]nt11, albino


title: zfATACldtP10R1

value: Light damage


title: zfRNAnmdahN20R2


title: zfATACldtP00R2

value: GFP+

value: Adult


title: zfATACnmdahP36R2


title: zfRNAnmdahN20R1

value: Replicate 1


title: zfATACldtP04R1


title: zfRNAnmdahP36R2

value: Replicate 2


title: E_HepaRG_IFC_oxBS_rep3

description: liver progenitor cell line

value: oxBS


title: B_HepaRG_week1_oxBS_rep2

description: liver progenitor cell line


title: D_HepaRG_IFC_oxBS_rep2

description: liver progenitor cell line


title: zfRNAnmdaN36R2

value: Tg[gfap:GFP]mi2001, AB


title: zfRNAnmdahP20R1

value: NMDA treatment


title: zfATACadAbP00R1

value: Control


title: zfRNAnmdaN20R2

value: GFP-


title: zfATACnmdahP20R2


title: zfATACnmdahP36R1


title: zfRNAnmdahP20R2


title: zfRNAnmdaN20R1


title: zfATACnmdahP20R1


title: zfRNAnmdaN10R2


title: zfRNAnmdaP36R2


title: zfRNAnmdaP36R1


title: zfRNAnmdaN04R2


title: zfRNAnmdahP36R1


title: zfRNAnmdaN36R1


title: zfRNAnmdaP20R2R2


title: zfATACldtP20R2


title: zfRNAnmdaN10R1


title: zfRNAnmdaP04R2


title: zfRNAnmdaP04R1


title: zfRNAnmdaP20R2R1


title: zfRNAnmdaP10R2


title: zfRNAldtN36R1


title: zfRNAnmdaP20R1


title: zfRNAnmdaN04R1


title: zfRNAldtN20R2


title: zfRNAldtN10R2


title: zfRNAldtN20R1


title: zfRNAldtN36R2


title: zfRNAnmdaP10R1


title: zfRNAldtN04R2


title: zfRNAldtN10R1R1


title: Saline treated mouse 3 30 hours after LPS injected

value: male


title: A_HepaRG_week1_oxBS_rep1

description: liver progenitor cell line


title: zfRNAldtP20R3


title: zfRNAldtP36R1R2


title: zfRNAldtN10R1R2


title: zfRNAldtP04R2R2


title: zfRNAldtP10R3R1


title: zfRNAldtP04R2R1


title: zfRNAldtP10R3R2


title: zfRNAldtP20R1R2


title: zfRNAldtP10R1R2


title: zfRNAldtP04R1R2


title: zfRNAldtN04R1R2


title: zfRNAldtP04R1R1


title: zfATACnmdahP10R1


title: zfRNAadtP00R1


title: zfRNAadtN00R2


title: zfRNAadtP00R2


title: zfRNAldN36R2


title: zfRNAldtP36R2R2


title: Recombinant human thrombomodulin treated mouse 2 30 hours after LPS administration

value: 10 weeks old

value: Recombinant human thrombomodulin at 3 and 24 h post-LPS injection


title: zfRNAldN36R1


title: zfATACnmdahP04R1


title: zfATACnmdahP04R2


title: zfATACldtP00R1


title: zfRNAldN00R2


title: zfRNAldN00R1


title: zfRNAldP36R1


title: zfRNAldP36R2


title: zfRNAadtN00R1


title: pleg1c replicate 3 [pleg1c_3]

city: Hangzhou

first: Yanna

last: Dang

email: yannadang@126.com, yannadang@zju.edu.cn

state: Zhejiang

address: 866 Yuhangtang Rd

department: College of Animal Sciences

institute: Zhejiang University

description:
pleg1c_3
processed data file: proc_data.txt

data_processing:
Reads were trimmed to remove the bases with low quality and adapter sequences.
The trimmed reads were assigned directly to transcripts and counted with Salmon software.
Gene expression level was quantified and normalized by Salmon.
Differentially expressed genes between control and pleg1 overexpression group were selected by DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: proc_data.txt: Tab-delimited text file includes normalized counts by DESeq2 for each sample.

source_name: human liver carcinoma

growth_protocol: HepG2 cells were purchased from the American Type Culture Collection (ATCC) and cultured in DMEM (Hyclone) with 10% fetal bovine serum (Hyclone).

extract_protocol:
Total RNA was isolated using MiniBEST Universal RNA extraction kit (Takara).
mRNAs were separated with oligo(dT)25 beads from total RNA. mRNA was fragmented and reverse transcribed. The cDNA library was subjected to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

treatment_protocol: Transfection reactions were performed when 1 × 10e6 cells reached 80% confluency in 6-well plates with 3 micrograms of endotoxin-free plasmids (Endofree Mini Plasmid Kit II, Tiangen) using lipofectamine 3000 (Thermo Fisher) according to the guidelines. For each plasmid, transfections were carried out in triplicate.

tag: cell line

tag: overexpression


title: pleg1c replicate 2 [pleg1c_2]

description:
pleg1c_2
processed data file: proc_data.txt


title: pleg1c replicate 1 [pleg1c_1]

description:
pleg1c_1
processed data file: proc_data.txt


title: zfRNAldP00R1


title: zfRNAldP00R2


title: control replicate 3 [ctrl2_3]

description:
ctrl2_3
processed data file: proc_data.txt


title: pleg1a replicate 1 [1a-1]

description:
1a-1
processed data file: proc_data.txt


title: pleg1b replicate 2 [1b-2]

description:
1b-2
processed data file: proc_data.txt


title: control replicate 1 [ctrl2_1]

description:
ctrl2_1
processed data file: proc_data.txt


title: pleg1a replicate 3 [1a-3]

description:
1a-3
processed data file: proc_data.txt


title: pleg1b replicate 3 [1b-3]

description:
1b-3
processed data file: proc_data.txt


title: pleg1b replicate 1 [1b-1]

description:
1b-1
processed data file: proc_data.txt


title: control replicate 3 [ctrl1_3]

description:
ctrl1_3
processed data file: proc_data.txt


title: zfATACadAbP00R2


title: HeLa_M_phase_plus_Aphidicolin_negative_control

first: Fang

last: Ji

address: Zijingang campus of Zhejiang University, No.866 of Yuhangtang Road

data_processing:
Library strategy: MiDA-seq
Raw reads of MiDASeq were trimmed using Trim Galore with default settings and mapped to the human genomes (hg38) by Bowtie2 both for the experimental group and the negative control group.
We used SAMtools to remove PCR duplicates and transformed clean reads to BigWig format using deepTools2.
Through visualization with IGV, we manually picked out potential MiDAS regions based on the height of the peaks. These regions were then divided into 100 kb-width bins. The read coverage was quantified by using reads per kilobase (RPK) for each bin, which was calculated using bedtools and R. To eliminate the background noise, the read coverage of an experimental group was divided by that of the negative control group to get the MiDASeq signal fold change (FC) for each bin.
The threshold for defining positive genomic bins was first restrained in an approximate range by referring to the FC at most frequently expressed landmark CFSs such as FRA3B, FRA16D and FRA7J, and then determined manually by visual inspection across the whole genome using IGV.
Then, the adjacent positive bins (within 100 kb) were merged using bedtools and defined as MDSs.
Genome_build: hg38
Supplementary_files_format_and_content: Bed files containing the MiDAS sites;  Bw files containing depth information of sequencing data.

source_name: HeLa cell

growth_protocol: U2OS and HeLa Cells were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (Gibco). HBE cells were grown in RPMI Medium Modified (HyClone) with 10% fetal bovine serum (Gibco). All media were supplemented with 1% penicillin-streptomycin (Invitrogen). Cells were grown at 37˚C under 5% CO2.

extract_protocol:
Cells were lysed in the Lysis buffer (50mM Tris-HCl, pH 8.0, 1% SDS, 20mg/ml RNase A, 20mg/ml protease K) in a 37˚C water bath for over 6h. The DNA was extracted using the phenol/chloroform method and sonicated to an average size of 300-400 bp using a Bioruptor (Diagenode).
DNA library was constructed with KAPA Hyper Prep Kit (KK8502). Briefly, 3ul of Enzyme Mix and 7ul of corresponding buffer were added to beads adsorbed with biotin-DNA. End repair and an A-tailing reaction were performed in a thermocycler according to the manufacturer’s protocol. Adaptor stock was diluted to 300nM and adaptor ligation was accomplished at 20˚C for 0.5h. The beads were washed with a double volume of the TE buffer (10 mM Tris-HCl, pH 8, and 1 mM EDTA) at least three times to remove unligated adaptor and adaptor-dimer molecules. Each library amplification reaction contained KAPA HiFi HotStart ReadyMix and the Primer Mix (10X) and was carried out using amplification for 15 cycles. Reactions were cleaned up using AMPure XP (Beckman Coulter, A63880).

treatment_protocol: For M phase, cells were grown to 20-30% confluence before being treated with 2mM thymidine (Sigma, T9250). Following aphidicolin (Sigma, A0781, 0.3µM) and RO3306 (Selleck, S7747, 7µM) treatments, cells were washed three times with PBS (pre-warmed to 37˚C) within 5 min, and then released into warm media with or without (as the negative control group) 20uM EdU for incubation for another 30 min. Afterwards, mitotic cells were then manually collected by mitotic shake-off. For S phase, cells were treated with or without aphidicolin (Sigma, A0781, 0.3µM) for 18h and EdU for the last 0.5h (no EdU treatment as the negative control) and sorted by flow cytometry depending on DNA content.

value: Cervix

value: HeLa


title: U2OS_M_phase_plus_Aphidicolin_replicate_2

source_name: Osteosarcoma cell

value: Bone


title: U2OS_M_phase_plus_Aphidicolin_replicate_1


title: U2OS_M_phase_plus_Aphidicolin_negative_control_1


title: U2OS_M_phase_minus_Aphidicolin


title: U2OS_S_phase_plus_Aphidicolin


title: HeLa_M_phase_plus_Aphidicolin


title: HBE_M_phase_plus_Aphidicolin

source_name: Human bronchial epithelial cell

value: Bronchus

value: HBE


title: U2OS_S_phase_minus_Aphidicolin


title: U2OS_M_phase_plus_Aphidicolin_replicate_3


title: HBE_M_phase_plus_Aphidicolin_negative_control


title: U2OS_S_phase_plus_Aphidicolin_negative_control


title: U2OS_M_phase_plus_Aphidicolin_negative_control_2


title: pleg1a replicate 2 [1a-2]

description:
1a-2
processed data file: proc_data.txt


title: control replicate 2 [ctrl2_2]

description:
ctrl2_2
processed data file: proc_data.txt


title: control replicate 2 [ctrl1_2]

description:
ctrl1_2
processed data file: proc_data.txt


title: control replicate 1 [ctrl1_1]

description:
ctrl1_1
processed data file: proc_data.txt


title: mRNA-seq-Control SW620_2

city: Kunming

first: Hongjin

last: Wu

state: China / Yunnan

address: Xichang Road#295

institute: The NHC Key Laboratory of Drug Addiction Medicine

data_processing:
We aligned the sequencing reads to a human genome reference (hg19) using TopHat version 2.0.13.
The resulting read alignments were assembled through Cufflinks version 1.1, and it created a novel transcript using Cufflinks reference annotation-based transcript (RABT) algorithm.
The transcripts combined with Cuffcompare were used to calculate relative abundances of each transcript through Cuffdiff.
Gene expression levels were determined by measuring the sum of fragments per kilobase of exon model per million mapped reads (FPKM) values of its exons.
Genome_build: hg19
Supplementary_files_format_and_content: excel file with gene expression with FPKM

source_name: colorectal cancer cells

growth_protocol: All cells were cultured in RPM1640 medium supplemented with 10% fetal calf serum and 2 mM L-glutamine. Flag-GAP43 plasmids and Control plasmids were stable-trasfected into SW620 cancer cells.

extract_protocol:
~4×10^6 cells were havested and total RNA were extracted with RNeasy Mini Kit (Qiagen, Valencia, CA).
The mRNA was purified and fragmented from total RNA (2 μg) using poly-T oligo-attached magnetic beads with two rounds of purification. Cleaved RNA fragments primed with random hexamers were reverse transcribed into first-strand cDNA using reverse transcriptase and random primers. The RNA template was removed and synthesized a replacement strand to generate double-strand cDNA. End repair, A-tailing, adaptor ligation, cDNA template purification and enrichment of the purified cDNA templates using PCR were then performed.
Constructed libraries were 150 bp paired-end sequenced by an Illumina X10 sequencer, following manufacturer’s instructions.

tag: passages

tag: treatment


title: mRNA-seq-GAP43 SW620_2

value: Overexpressed GAP43


title: mRNA-seq-GAP43 SW620_1


title: mRNA-seq-Control SW620_1


title: siGLIS2.1-5FU-H3K4me3

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to mouse reference genome (hg19) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files; Scores represent the RPM value.

source_name: Colorectal cancer cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND604).

tag: cell type

tag: chip antibody

value: H3K4me3 (Millipore 04-745)


title: siGLIS2.2-5FU-H3K4me3


title: Nutlin3a-p53-SC-rep1

value: Colorectal cancer cells

value: p53 (Santa Cruz sc-126)


title: zfATACnmdahP10R2

tag: tissue

value: Retina

tag: genotype

value: GFP+

value: Replicate 2


title: siGLIS2.2-DMSO-H3K4me3

value: DMSO


title: siGLIS2.2-DMSO-Input

description: Input for siGLIS2.2-DMSO-H3K27ac, siGLIS2.2-DMSO-H3K4me1 and siGLIS2.2-DMSO-H3K4me3


title: siCtrl-DMSO-H3K4me1


title: siGLIS2.2-5FU-H3K27ac

value: H3K27ac (Abcam ab4729)


title: siGLIS2.1-DMSO-H3K4me1


title: siCtrl-DMSO-Input

description: Input for siCtrl-DMSO-H3K27ac, siCtrl-DMSO-H3K4me1 and siCtrl-DMSO-H3K4me3


title: siGLIS2.2-5FU-Input

description: Input for siGLIS2.2-5FU-H3K27ac, siGLIS2.2-5FU-H3K4me1 and siGLIS2.2-5FU-H3K4me3


title: siGLIS2.1-DMSO-H3K27ac


title: siGLIS2.1-DMSO-Input

description: Input for siGLIS2.1-DMSO-H3K27ac, siGLIS2.1-DMSO-H3K4me1 and siGLIS2.1-DMSO-H3K4me3


title: siGLIS2.2-5FU-H3K4me1


title: siCtrl-DMSO-H3K27ac


title: siGLIS2.1-5FU-Input

description: Input for siGLIS2.1-5FU-H3K27ac, siGLIS2.1-5FU-H3K4me1 and siGLIS2.1-5FU-H3K4me3


title: siCtrl-5FU-H3K4me1


title: siCtrl-5FU-H3K27ac


title: siGLIS2.1-5FU-H3K4me1


title: siGLIS2.2-DMSO-H3K27ac


title: siCtrl-5FU-p53


title: siGLIS2.2-5FU-p53


title: siGLIS2.1-5FU-p53-Input

description: Input for siGLIS2.1-5FU-p53


title: siCtrl-DMSO-p53


title: siGLIS2.1-DMSO-p53


title: siGLIS2.2-5FU-p53-Input

description: Input for siGLIS2.2-5FU-p53


title: siGLIS2.1-DMSO-H3K4me3


title: siCtrl-DMSO-H3K4me3


title: siCtrl-5FU-Input

description: Input for siCtrl-5FU-H3K27ac, siCtrl-5FU-H3K4me1 and siCtrl-5FU-H3K4me3


title: siGLIS2.2-DMSO-p53


title: siCtrl-5FU-p53-Input

description: Input for siCtrl-5FU-p53


title: siGLIS2.1-DMSO-p53-Input

description: Input for siGLIS2.1-DMSO-p53


title: siGLIS2.2-DMSO-p53-Input

description: Input for siGLIS2.2-DMSO-p53


title: 5FU-GLIS2

value: Dynabeads MyOne streptavidin C1 (Thermo-Fisher 65001)


title: DMSO-GLIS2


title: siGLIS2.1-5FU-p53


title: Nutlin3a-p53-SC-rep2


title: siCtrl-DMSO-p53-Input

description: Input for siCtrl-DMSO-p53


title: 5FU-p53-SC-rep2


title: Nutlin3a-p300

value: p300 (Santa Cruz sc-585x)


title: Input-2-rep2

description: Input for DMSO-p53-SC-rep2, 5FU-p53-SC-rep2 and Nutlin3a-p53-SC-rep2


title: DMSO-p53-CST


title: 5FU-p53-CST


title: Input-1

description: Input for DMSO-p53-CST, 5FU-p53-CST, Nutlin3a-p53-CST, DMSO-H3K27ac, 5FU-H3K27ac, Nutlin3a-H3K27ac, DMSO-p300, 5FU-p300 and Nutlin3a-p300


title: siGLIS2.2-5FU

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat  v2.1.1 with default  parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

extract_protocol:
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

value: 5-FU + siGLIS2-2


title: DMSO-GLIS2-Input

description: Input for DMSO-GLIS2


title: DMSO-p53-SC-rep2


title: 5FU-GLIS2-Input

description: Input for 5FU-GLIS2


title: Input-2-rep1

description: Input for DMSO-p53-SC-rep1, 5FU-p53-SC-rep1 and Nutlin3a-p53-SC-rep1


title: siGLIS2.1-5FU

value: 5-FU + siGLIS2-1


title: DMSO-p53-SC-rep1


title: siGLIS2.1-DMSO

value: DMSO + siGLIS2-1


title: siGLIS2.2-DMSO

value: DMSO + siGLIS2-2


title: Nutlin3a-rep2


title: siCtrl-DMSO

value: DMSO + siCtrl


title: Nutlin3a-rep1


title: Nutlin3a-H3K27ac


title: 5FU-p300


title: DMSO-H3K27ac


title: Nutlin3a-p53-CST


title: 5FU-H3K27ac


title: DMSO-p300


title: 5FU-rep1


title: 5FU-rep2


title: DMSO-rep1


title: DMSO-rep2


title: siCtrl-5FU-H3K4me3


title: HO107

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description:
DNA methylation
human_MethValues_allSamples_crossSpecies.txt

data_processing:
Illumina specific adapter sequences and low quality sequences were removed from raw sequencing data using Trimmomatic50. Reads were aligned to a bisulfite converted human (hg19) or canine (canfam3.1) genome using WALT51. Duplicate sequences were removed from alignment data using MethPipe52 duplicate-remover and bisulfite conversion rates were estimated for each sample using bsrate. All samples had conversion efficiencies > 99%. Sequencing depths for each sample were such that an average of 88.3% and 81.3% of targeted CpGs were sequenced at a 10X depth or higher. MethPipe methcounts was used to calculate methylation levels and read coverage at individual CpGs in each sample. A custom perl script was used to isolate CpGs with a read depth of 10 or greater and MethPipe roimethstats was used to summarize methylation levels in 500 bp windows, generated by BEDtools53 windowBed, along the capture targets in each genome.  CpG methylation levels were expressed as a value between 0 and 1.
USCS utility liftOver with the appropriate genome wide alignment file was used to convert the canine genomic coordinates for each 500bp window from CanFam3.1 to hg19. and the human genomic coordinates for each 500bp window to GRCh38. Converting both sets of coordinates to GRCh38 resulted in the highest number of 500bp windows being conserved between the two species. Genomic regions were considered homologs if the converted GRCh38 coordinates were within 1,000bp of each other as calculated by BEDtools closest.
Genome_build: hg19, canfam3.1

source_name: primary osteosarcoma

extract_protocol: Tumor tissues were removed from -86℃ and sectioned to avoid areas of necrosis. Thirty mg of tissue were placed in 80 µL of phosphate buffered saline (PBS) solution and pulverized in a tissue homogenizer. Isolation of genomic DNA was done according to the manufacturer’s protocol using the QIAamp DNA Mini Kit from Qiagen.Illumina library preparation, bisulfited converted and bead capture was performed as specified in the Roch SeqCap Epi protocol outlined in Li et al (doi: 10.1093/nar/gkv244)

value: osteosarcoma


title: HO111B


title: HO106


title: HO105


title: HO004


title: HO110B


title: HO003


title: HO062


title: HO063


title: HO025


title: HO034


title: HO101


title: HO028


title: HO041


title: 5FU-p53-SC-rep1


title: HO040


title: HO031


title: siCtrl-5FU

value: 5-FU + siCtrl


title: HO036


title: HO104


title: HO108


title: 0529A_U

city: Beijing

first: Wei

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

data_processing:
Basecalls performed using bcl2fastq software
raw data fastqc
sequencing data filtering and statistics using fastp software
clean data fastqc
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: FPKM

source_name: colorectal adenomas organoid

extract_protocol:
Cultured human adenoma organoids were transferred into Buffer RLT in (RNeasy Micro kit, Qiagen) and RNA isolated according to the manufacturer’s instruction.
2~3 μg of total RNA were enriched by using Ribo-Zero Magnetic Kit (Epicentre), and sequencing libraries were prepared using the NEBNext Ultra RNA library prep kit (NEB).


title: siGLIS2.1-5FU-H3K27ac


title: 0529A_S


title: HO030


title: LCL1_Brusatol_rep1

city: Shenzhen

first: Yonggang

last: Pei

state: GD

address: 1088 Xueyuan Avenue

department: School of Public Health and Emergency Management

institute: Southern University of Science and Technology

data_processing:
The raw RNA-seq reads were performed quality check (FastQC, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), cut the adapters (Trim Galore, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped with hg38 genome (HISAT2). Differently expressed transcripts were defined with Cuffdiff tools and visualized in R software (https://www.r-project.org/).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files

source_name: Lymphoblastoid cell line

extract_protocol:
Total RNAs from untreated or treated LCL1 cells were extracted with Trizol (Invitrogen, Inc., Carlsbad, CA).
The cDNA library was prepared with the commercial Illumina library preparation kits (TruSeq Stranded RNA LT Kit, TruSeq Stranded RNA LT Ribo-Zero H/M/R Kit) according to the manufacturer's protocols, and sequenced with an Illumina HiSeq2000 instrument at the Washington University Genome Sequencing Center.

value: EBV-transformed lymphoblastoid cell line

tag: agent

value: Brusatol


title: HO032


title: LCL1_Brusatol_rep2


title: RRBS_R2shp53-WNT1_SA_replicate2

city: montpellier

first: stanislas

middle: P

last: du manoir

address: 280 rue des apothicaires

institute: IRCM

data_processing:
We cleaned sequencing reads with Trim Galore v0.2.1 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired.
We aligned reads to the human genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1.
We extracted methylation percent values with methratio.py from BSMAP v2.74 using the parameters -z -u -g.
We filtered CGs to have a minimum sequencing depth of 8X.
Genome_build: hg19
Supplementary_files_format_and_content: We provide igv files containing methylation scores for all CGs with at least 8X sequencing depth.

source_name: Human Mammary Epithelial Cells (HMECs) transduced and selected in Soft Agar

extract_protocol:
DNA was isolated using the QIAmp DNA Mini kit (Qiagen).
We prepared RRBS libraries as previously described (Auclair G et al, 2014). Briefly, genomic DNA was digested for 5 h with MspI (Thermo Scientific) followed by end-repair, A- tailing (with Klenow fragment, Thermo Scientific) and ligation to paired-end methylated adapters (with T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. We purified fragments between 150 and 400 bp by electrophoresis and performed two rounds of bisulfite conversion with the EpiTect kit (Qiagen). Final RRBS libraries were generated with PfUTurbo Cx hotstart DNA polymerase (Agilent) and indexed PE Illumina primers with 12-15 cycles of PCR. The libraries were purified with AMPure magnetic beads (Beckman Coulter).

tag: gender

value: female

value: primary human mammary epithelial cells (HMECs)

tag: transduced with


title: siGLIS2.2-DMSO-H3K4me1


title: HO033


title: RRBS_R2shp53-WNT1_SA_replicate1


title: RG087

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

data_processing:
Raw data were aligned to hg19/mm10 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Genome_build: hg19 for human samples, mm10 for mouse
Supplementary_files_format_and_content: Raw junction counts for each sample as output by STAR
Supplementary_files_format_and_content: column 1:  chromosome
Supplementary_files_format_and_content: column 2:  first base of the intron (1-based)
Supplementary_files_format_and_content: column 3:  last base of the intron (1-based)
Supplementary_files_format_and_content: column 4:  strand (0:  undefined, 1:  +, 2:  -)
Supplementary_files_format_and_content: column 5:  intron  motif:  0:  non-canonical;  1:  GT/AG,  2:  CT/AC,  3:  GC/AG,  4:  CT/GC,  5: AT/AC, 6:  GT/AT
Supplementary_files_format_and_content: column 6:  0:  unannotated, 1:  annotated (only if splice junctions database is used)
Supplementary_files_format_and_content: column 7:  number of uniquely mapping reads crossing the junction
Supplementary_files_format_and_content: column 8:  number of multi-mapping reads crossing the junction
Supplementary_files_format_and_content: column 9:  maximum spliced alignment overhang

molecule: polyA RNA

source_name: Primary CLL cells

growth_protocol: primary CLL cells were thawed in Iscove's Modified Dulbecco's Medium (Life Technologies) supplemented with 20% fetal bovine serum (FBS) (Sigma-Aldrich), penicillin (100 U/ml) and streptomycin (100 μg/ml) and immediately harvested.

extract_protocol:
Total RNA was extracted from primary CLL cases with the RNeasy Mini Kit (QIAGEN) with on column DNAse treatment and poly-A pull-down was performed to enrich mRNAs from total RNA.  RNA-Seq libraries were prepared using the Illumina TruSeq RNA prep kit and sequenced using the Illumina HiSeq2500 instrument.
RNA TruSeqv2 PE100 60M (2x100bp) for primary CLL cells


title: RRBS_R2shp53-RASV12_SA_replicate2


title: LCL1_Control_rep2


title: HO039


title: RG082

value: wild type


title: RRBS_R2shp53-WNT1_Late_replicate2

source_name: Human Mammary Epithelial Cells (HMECs) transduced


title: RRBS_R2shp53-RASV12_SA_replicate1


title: RG034


title: RG084


title: RRBS_R2shp53-RASV12_Late_replicate1


title: RRBS_R2shp53-RASV12_Late_replicate2


title: RRBS_R2shp53-CCNE1_SA_replicate2


title: HO042


title: RRBS_R2shp53-CCNE1_SA_replicate1


title: RRBS_R2shp53-CCNE1_Late_replicate2


title: RRBS_R2shp53-CCNE1_Late_replicate1


title: RRBS_R2shP53_Late_replicate2


title: LCL1_Control_rep1


title: RRBS_R2shP53_Late_replicate1


title: RRBS_R2shP53_Early_replicate2


title: RRBS_R2shP53_Early_replicate1


title: RRBS_R2_replicate2

source_name: Human Mammary Epithelial Cells (HMECs)


title: B_11H160_GPR56plusCD34plus

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were masked for sequencing adapters and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

growth_protocol: Viable cells from patients or harvested from NSG mice after engraftment were frozen in DMSO. For sorting experiments cells were thawed and treated as described below.

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Sample Preparation (Illumina)

treatment_protocol: Sorting was performed on a BD Aria II sorter after staining with anti-human CD34 APC (BD 555824) and anti-human GPR56 PE (BioLegend 358204).

value: Heparinised blood

value: sorted for CD34posGPR56pos


title: C_11H160_GPR56minusCD34plus

value: sorted for CD34negGPR56pos


title: RRBS_R2_replicate1


title: RRBS_R2shp53-WNT1_Late_replicate1


title: 10H166-CD34minGPR56plus


title: 11H009-CD34plusGPR56plus


title: 11H009-CD34minGPR56plus


title: 11H009-CD34minGPR56min

value: sorted for CD34negGPR56neg


title: 10H166-CD34plusGPR56plus


title: 10H166-CD34minGPR56min


title: 09H043-CD34plusGPR56plus

value: Bone marrow


title: 09H083-CD34minGPR56min

value: Leukapheresis


title: 09H083-CD34plusGPR56plus


title: 09H043-CD34minGPR56plus


title: 09H043-CD34minGPR56min


title: 08H012-CD34plusGPR56plus


title: 05H163-CD34plusGPR56min

value: sorted for CD34posGPR56neg


title: 09H083-CD34minGPR56plus


title: 05H149-CD34plusGPR56min


title: R3_3T3_143_input_control

city: New York

first: James

last: Gregory

state: NY

address: 101 Ave of the Americas

institute: New York Genome Center

description: NIH3T3 monoculture

data_processing:
basecalls were performed using bcl2fastq
fastqs were trimeed with trimGalore
fastqs were aligned to an hg38/mm20/GFP/mCherry combined reference using STAR (v2.5.2)
reads were counted with Samtools or FeatureCounts
Genome_build: mm20/hg38
Supplementary_files_format_and_content: Gene count files were generated using featureCounts

growth_protocol: standard cell culture

extract_protocol:
RNA from standard extracts or immunoprecipitation with the indicated antibody
SMART-seq cDNA prep followed by Nextera DNA Flex

tag: target ip cell type

tag: ip antibody

tag: ip order


title: 11H160-CD34minGPR56min


title: 08H012-CD34plusGPR56min


title: 05H163-CD34plusGPR56plus


title: 05H163-CD34minGPR56min


title: 05H149-CD34plusGPR56plus


title: DMSO treated, day 1, replicate B [DM1B]

city: St. Louis

first: MALAY

last: HALDAR

state: MO

address: 7751 charing square lane

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr  at 45ºC to Human Gene 2.0 ST Arrays using the GeneChip Hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip 3000 7G scanner.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Expression values were analyzed after RMA quantile normalization using ArrayStar software (DNASTAR).

label: Biotin

source_name: Cultured human monocytes treated with DMSO

label_protocol: cDNA biotinylated by terminal transferase end labeling according to the standard Affymetrix WT Plus protocol starting with 250ng of RNA (GeneChip® WT PLUS Reagent Kit  Manual Target Preparation for GeneChip®Whole Transcript (WT) Expression Arrays, 2013, Affymetrix)

growth_protocol: Human monocytes were collected from normal donors at the human immunology core facility at the University of Pennsylvania. Collected cells were cultured with GM-CSF (50 nanograms per ml) and Interleukin 4 (50 nanograms per ml) to promote dendritic cell differentiation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: At the onset of culture, either retinoic acid (20 nanomolar) or DMSO (control) were added. RNA was extracted 24 hours later.

value: cultured human monocytes

value: DMSO (control)


title: DMSO treated, day 1, replicate 1 [DM1]

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45ºC to Mouse Gene 2.0 ST Arrays using the GeneChip Hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: Cultured Ly6c-high bone marrow monocytes treated with DMSO

label_protocol: cDNA biotinylated by terminal transferase end labeling according to the standard Affymetrix WT Plus protocol starting with 250ng of RNA (GeneChip® WT PLUS Reagent Kit Manual Target Preparation for GeneChip®Whole Transcript (WT) Expression Arrays, 2013, Affymetrix).

growth_protocol: Bone marrow was harvested from three mice and pooled. Monocytes were enriched by using the monocyte enrichment kit from Miltenyi and Ly6C-high monocytes were further isolated by FACsorting. Purified cells were cultured with GM-CSF (20 nanograms per ml) and Interleukin 4 (20 nanograms per ml) to promote dendritic cell differentiation.

treatment_protocol: At the onset of culture, either retinoic acid (100 nanomolar) or DMSO (control) were added. RNA was extracted 24 hours later.

value: cultured Ly6c-high bone marrow monocytes


title: DMSO treated, day 1, replicate A [DM1A]


title: All-trans retinoic acid treated, day 1, replicate 1 [RA1]

source_name: Cultured Ly6c-high bone marrow monocytes treated with retinoic acid

value: retinoic acid (100 nanomolar)


title: DMSO treated, day 1, replicate 2 [DM2]


title: All-trans retinoic acid treated, day 1, replicate A [AT1A]

source_name: Cultured human monocytes treated with retinoic acid

value: retinoic acid (20 nanomolar)


title: All-trans retinoic acid treated, day 1, replicate 2 [RA2]


title: All-trans retinoic acid treated, day 1, replicate B [AT1B]


title: eosinophils, mock infected, biological replicate 7

city: Memphis

first: Robert

last: Rooney

state: TN

address: 50 N. Dunlap, Room 366R, LeBonheur CFRC

department: Pediatrics

institute: University of Tennessee Health Science Center

description: Gene expression data from mouse bone marrow derived eosinophils, mock infected

hyb_protocol: Following fragmentation, 5.5ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the PLIER algorithm using Affymetrix Expression Console software v1.1.

organism: Mus musculus domesticus

source_name: bone marrow cultured in eosinophil growth media for 14 days

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and bioton-labeled using the Affymetrix® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Eosinophils were derived from female C57BL/6 bone marrow by culturing for 14 days in eosinophil growth media.

extract_protocol: RNA was extracted from mock or PR8-pulsed BMdEos using RNeasy Mini (Qiagen Inc., Germantown, MD, USA) with β-mercaptoethanol added to the RLT buffer, as directed by the manufacturer, and eluted into RNase-free water.

treatment_protocol: On day 14 of differentiation, BMdEos were pulsed for 1 h with MOI 0.1 PR8. Cells were washed in PBS and cultured for a further 23 h at a density of 1 million live cells/mL in media supplemented with 1 µg/mL TPCK-Trypsin and 5 ng/mL mouse GM-CSF. At six hours prior to harvest, 1 µg/ml GolgiPlug (BD Biosciences) was added to the cells to reduce the release of endogenous RNases.

tag: strain

value: eosinophils

value: Female

value: 6 weeks old

tag: influenza strain

value: Mock


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 7

description: Gene expression data from mouse bone marrow derived eosinophils, infected with influenza strain PR8 (MOI: 0.1)

tag: age

value: Mouse adapted influenza strain A/PR/8/1934 (PR8)


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 2


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 3


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 8


title: eosinophils, mock infected, biological replicate 8


title: Light (Day 6)

city: Busan

first: Hyun-Myung

last: Oh

state: South Korea

address: Yongdang Campus, Sinseonro 365 Namgu

department: Marine Bio-Cnvergence Science

country: South Korea

institute: Pukyong National University

data_processing:
Alignment: Sequence reads were obtained and mapped to the IMCC1322 genome (GenBank Acc. No. CP001751) using Burrows-Wheeler Aligner (BWA) (K-mer=32, mismatch=2); All reads mapping with two or fewer mismatches were retained.
Arithmetic: Filtered and aligned reads were counted using BEDTools (version 2.9) and summarized in BAM file formats.

organism: Candidatus Puniceispirillum marinum IMCC1322

source_name: Bacterial culture of strain IMCC1322

growth_protocol: Modified R2A broth prepared in sea water was used for culture medium. Strain IMCC1322 was inoculated in spinner flasks (~1000 ml) and was treated as dark, light, and diel under green LED.

extract_protocol: Cell lysates were obtained by direct addition of 2.5 ml Trizol Reagent (Invitrogen) on to the pellets from 300 ml cultures. After adding 0.5 ml BCP phase separation reagent (MRC) upper aqueous total RNA fractions were centrifuged in MaxTract Low Density tubes (Qiagen). RNA solution, RLT buffer, and ethanol (2:7:5) were mixed for Qiagen RNeasy Maxi Kit protocol. Purified and concentrated RNAs were quality-checked on a Bioanalyzer and total RNAs in 10-Î¼g aliquots were purified using MICROBExpressâ¢ Bacterial mRNA Enrichment Kit (Ambion). For each mRNA from 20 Î¼g of RNA was purified once again on a MICROBExpressâ¢ kit (Ambion) and was quality-checked as above-mentioned. MessageAmpâ¢ II-Bacteria RNA Amplification Kit (Ambion) was exploited to amplify mRNA into cRNA. Libraries were prepared according to proprietary reagents from Illumina's and instructions therein. The purified DNA was captured on an Illumina flow cell for cluster generation. Six libraries were sequenced on the Genome Analyzer following the manufacturer's protocols using 36 cycles.

treatment_protocol: [1] Dark culture [2] Light culture : 260 Î¼J/cm2 Green Light [3] Incubator for Diel cycle: 260 Î¼J/cm2 Green Light  for 14hr and Dark for 10hr.

tag: culture condition

value: Light/R2A medium

tag: cell stage

value: Stationary


title: eosinophils, mock infected, biological replicate 6


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 1


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 6


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 10


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 9


title: eosinophils, mock infected, biological replicate 4


title: eosinophils, mock infected, biological replicate 9


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 4


title: eosinophils, mock infected, biological replicate 3


title: eosinophils, mock infected, biological replicate 10


title: Dark (Day 6)

value: Dark/R2A medium


title: eosinophils, mock infected, biological replicate 5


title: eosinophils, mock infected, biological replicate 1


title: eosinophils, mock infected, biological replicate 2


title: eosinophils, PR8 infected at MOI: 0.1, biological replicate 5


title: Diel Cycle (Day 3)

value: Diel Cycle/R2A medium

value: Log


title: Light (Day 3)


title: MLE12-10% CSE-10 hours-3

city: Cleveland

first: Anna

last: Blumental Perry

state: OH

address: 10900 Euclid Ave.

institute: Case Western Reserve University

description:
small RNA enriched total RNA
miRNA expression in 10 hours 10% CSE

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55C on Agilent 8X15K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters.

source_name: MLE12 cells treated with 10% CSE for 10 hours

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

growth_protocol: MLE12 cells were cultured in RPMI complete media: RPMI1640 medium (Cellgro, Manassas, VA, USA) supplemented with 4% fetal bovine serum (FBS; Serum International, Laval, QC, Canada), insulin-transferrin-selenous acid (ITS) premix (BD Biosciences, San Jose, CA, USA), 10nM hydrocortisone (Sigma-Aldrich), 10nM -estradiol (Sigma-Aldrich), 10mM HEPES, 2mM glutamine (CellGro), 100 U/ml penicillin, and 100 g/ml streptomycin.

extract_protocol: miRNA extraction from cells was done using miRNeasy kit (Qiagen).

treatment_protocol: Research-grade 1R5F cigarettes (Kentucky Tobacco and Health Research Institute, Lexington, KY, USA) were used to prepare the CSE. CSE was made fresh for each experiment by bubbling the smoke from 1 cigarette through 5 ml of serum-free medium in a 15-ml conical tube and filtering it through a 0.22um filter to remove large particles and maintain sterility. This solution was designated as 100% CSE and diluted in culture medium to yield concentrations specified for each experiment.

value: Lung epithelial immortalized cells, surfactant producing

tag: cell line

value: 10 hours 10% CSE


title: MLE12-10% CSE-10 hours-1

tag: treatment


title: MLE12-10% CSE-10 hours-2

tag: cell type


title: MLE12-10% CSE-2 hours-3

description:
small RNA enriched total RNA
miRNA expression in 2 hours 10% CSE

source_name: MLE12 cells treated with 10% CSE for 2 hours

value: 2 hours 10% CSE


title: MLE12-10% CSE-2 hours-2


title: MLE12-10% CSE-2 hours-1


title: MLE12-Untreated -3

description:
small RNA enriched total RNA
miRNA expression in untreated cells

source_name: MLE12 cells Untreated

value: untreated cells


title: MLE12-Untreated -1


title: Diel Cycle (Day 6)


title: MLE12-Untreated -2


title: Dark (Day 3)


title: 10x_9392

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6". Expression values were calculated by   RSEM v1.2.3 in paired-end mode using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted. For the subset of cells processed with 10X, we used CellRanger with the default parameters.
We examined as quality control the number of genes detected in each cell and conservatively excluded cells with fewer than 2,000 detected genes.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited files containing log2(TPM/10+1) values (TPM=transcript-per-million reads) of 9609 cells profiled by 10x droplet scRNA-seq (10x file) and of 1297 cell profiled by SmartSeq2 (SS2 file). All quantified 23,686 genes are included in the SS2 file and 11,548 genes detected in at least 10 cells are included in the 10x file. Header lines include Cell ID, patient ID, time point of sample acquisition, and the cells assignment into clusters and coordinates in a tSNE analysis (as shown in an associated manuscript).

source_name: Malignant ascites  single cell

extract_protocol:
RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 384 cells with unique barcodes were combined and sequenced using a NextSeq 500 sequencer (Illumina). For a subset of samples, single cells were processed through the 10X Chromium 3 Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, cells were added to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index.

treatment_protocol: Ascites fluid was drained by an interventional radiologist and transferred for further processing in closed vacuum bottles. De-identified patient information, including their ovarian cancer histology, stage, treatment history, and BRCA mutation status were collected. Immediately following drainage, malignant ascites was transported on ice, aliquoted into 50 mL conical tubes (BD Falcon) and spun for 5 min at 580 × g at 4°C. The supernatant was aspirated and the remaining pellet was resuspended with 5 mL of hypotonic lysis buffer ACK (Life technologies) and incubated on ice for 5 min. 20 ml of PBS was used to quench the lysis buffer. Cell suspensions were pooled and pipetted into a new 50 mL conical tube through a 100 µm mesh and spun for 5 min at 580 × g at 4°C. Hypotonic lysis was repeated until no visible red blood cell component was present, usually for a total of 2-3 times (for the plate-based approach). Following red blood cell lysis, the cell pellet was resuspended in PBS with 2% (v/v) FBS. These cells were then used for both plate-based and droplet-based scRNA-seq. For plate-based scRNA-seq, cells were labeled with the following fluorophore-conjugated flow-cytometry antibodies: live/dead stain with Calcein-AM (LifeTechnologies), 7-AAD (7-Aminoactinomycin D) (LifeTechnologies), CD45-FITC (LifeTechnologies), EpCAM-PE (Miltenyi Biotec) and CD24-PE/Cy7 (BioLegend). Cells were incubated for 30 min on ice in the dark. Cells were washed twice by resuspending with PBS with 2% (v/v) FBS and spun 5 min at 580 × g at 4°C. Flow-cytometry and sorting was performed on a BD Biosciences cell sorter (IIu or UV). Following doublet exclusion, Calceinhigh7AAD-CD45-EPCAM+CD24+ single cells were sorted into 96-well microtiter plates (on a plate chiller) that were prepared with 10uL cell lysis buffer (TCL + 1% β-mercaptoethanol). Following completion of cell sorting, plates were covered with aluminum lids, vortexed for 10 seconds, centrifuged for 2 min at 580 × g at 4°C and immediately placed on dry ice prior to storage at -80°C.

value: Malignant ascites  single cell

tag: patient id

tag: time point


title: 10x_9381


title: 10x_9388


title: 10x_9387


title: 10x_9398


title: 10x_9393


title: 10x_9394


title: 10x_9395


title: 10x_9397


title: 10x_9396


title: 10x_9385


title: 10x_9391


title: 10x_9390


title: 10x_9386


title: 10x_9389


title: 10x_9382


title: 10x_9384


title: 10x_9383


title: 10x_9378


title: 10x_9380


title: 10x_9377


title: 10x_9379


title: 10x_9376


title: 10x_9375


title: 10x_9374


title: 10x_9370


title: 10x_9371


title: 10x_9369


title: 10x_9368


title: 10x_9367


title: 10x_9365


title: 10x_9364


title: 10x_9361


title: 10x_9366


title: 10x_9360


title: 10x_9372


title: 10x_9373


title: 10x_9353


title: 10x_9351


title: 10x_9355


title: 10x_9357


title: 10x_9354


title: 10x_9356


title: 10x_9352


title: 10x_9362


title: 10x_9344


title: 10x_9349


title: 10x_9363


title: 10x_9345


title: 10x_9350


title: 10x_9342


title: 10x_9348


title: 10x_9347


title: 10x_9346


title: 10x_9343


title: 10x_9358


title: 10x_9359


title: 10x_9341


title: 10x_9340


title: 10x_9338


title: 10x_9335


title: 10x_9336


title: 10x_9334


title: 10x_9333


title: 10x_9332


title: 10x_9331


title: 10x_9327


title: 10x_9330


title: 10x_9329


title: 10x_9316


title: 10x_9326


title: 10x_9325


title: 10x_9322


title: 10x_9323


title: 10x_9320


title: 10x_9318


title: 10x_9324


title: 10x_9317


title: 10x_9321


title: 10x_9319


title: 10x_9313


title: 10x_9337


title: 10x_9339


title: 10x_9312


title: 10x_9311


title: 10x_9328


title: 10x_9310


title: 10x_9309


title: 10x_9314


title: 10x_9306


title: 10x_9305


title: 10x_9315


title: 10x_9308


title: 10x_9307


title: 10x_9304


title: 10x_9302


title: 10x_9301


title: 10x_9300


title: 10x_9299


title: 10x_9296


title: 10x_9298


title: 10x_9297


title: 10x_9295


title: 10x_9293


title: 10x_9294


title: 10x_9290


title: 10x_9289


title: 10x_9288


title: 10x_9287


title: 10x_9283


title: 10x_9291


title: 10x_9286


title: 10x_9284


title: 10x_9285


title: 10x_9282


title: 10x_9303


title: 10x_9281


title: 10x_9279


title: 10x_9280


title: 10x_9276


title: 10x_9275


title: 10x_9274


title: 10x_9278


title: 10x_9277


title: 10x_9273


title: 10x_9272


title: 10x_9271


title: 10x_9270


title: 10x_9267


title: 10x_9269


title: 10x_9266


title: 10x_9265


title: 10x_9264


title: 10x_9263


title: 10x_9259


title: 10x_9261


title: 10x_9257


title: 10x_9258


title: 10x_9251


title: 10x_9253


title: 10x_9292


title: 10x_9256


title: 10x_9249


title: 10x_9250


title: 10x_9262


title: 10x_9252


title: 10x_9248


title: 10x_9260


title: 10x_9245


title: 10x_9247


title: 10x_9246


title: 10x_9255


title: 10x_9243


title: 10x_9242


title: 10x_9268


title: 10x_9238


title: 10x_9240


title: 10x_9239


title: 10x_9237


title: 10x_9236


title: 10x_9254


title: 10x_9235


title: 10x_9233


title: 10x_9234


title: 10x_9244


title: 10x_9231


title: 10x_9232


title: 10x_9230


title: 10x_9229


title: 10x_9228


title: 10x_9226


title: 10x_9224


title: 10x_9223


title: 10x_9225


title: 10x_9227


title: 10x_9222


title: 10x_9220


title: 10x_9241


title: 10x_9221


title: 10x_9219


title: 10x_9218


title: 10x_9217


title: 10x_9216


title: 10x_9215


title: 10x_9214


title: 10x_9213


title: 10x_9210


title: 10x_9212


title: 10x_9209


title: 10x_9207


title: 10x_9208


title: 10x_9205


title: 10x_9206


title: 10x_9204


title: 10x_9201


title: 10x_9202


title: 10x_9200


title: 10x_9199


title: 10x_9198


title: 10x_9196


title: 10x_9192


title: 10x_9193


title: 10x_9190


title: 10x_9191


title: 10x_9195


title: 10x_9197


title: 10x_9187


title: 10x_9185


title: 10x_9194


title: 10x_9189


title: 10x_9184


title: 10x_9186


title: 10x_9181


title: 10x_9182


title: 10x_9211


title: 10x_9188


title: 10x_9178


title: 10x_9203


title: 10x_9179


title: 10x_9177


title: 10x_9176


title: 10x_9172


title: 10x_9175


title: 10x_9174


title: 10x_9168


title: 10x_9169


title: 10x_9171


title: 10x_9166


title: 10x_9162


title: 10x_9173


title: 10x_9170


title: 10x_9165


title: 10x_9183


title: 10x_9159


title: 10x_9158


title: 10x_9164


title: 10x_9155


title: 10x_9157


title: 10x_9156


title: 10x_9180


title: 10x_9154


title: 10x_9153


title: 10x_9160


title: 10x_9152


title: 10x_9151


title: 10x_9150


title: 10x_9149


title: 10x_9147


title: 10x_9148


title: 10x_9163


title: 10x_9161


title: 10x_9146


title: 10x_9144


title: 10x_9141


title: 10x_9140


title: 10x_9142


title: 10x_9139


title: 10x_9135


title: 10x_9167


title: 10x_9137


title: 10x_9143


title: 10x_9136


title: 10x_9134


title: 10x_9133


title: 10x_9128


title: 10x_9127


title: 10x_9129


title: 10x_9126


title: 10x_9125


title: 10x_9124


title: 10x_9122


title: 10x_9145


title: 10x_9118


title: 10x_9121


title: 10x_9120


title: 10x_9119


title: 10x_9117


title: 10x_9114


title: 10x_9138


title: 10x_9115


title: 10x_9130


title: 10x_9132


title: 10x_9112


title: 10x_9111


title: 10x_9113


title: 10x_9110


title: 10x_9109


title: 10x_9107


title: 10x_9105


title: 10x_9123


title: 10x_9106


title: 10x_9103


title: 10x_9102


title: 10x_9100


title: 10x_9104


title: 10x_9101


title: 10x_9099


title: 10x_9098


title: 10x_9097


title: 10x_9096


title: 10x_9095


title: 10x_9094


title: 10x_9092


title: 10x_9093


title: 10x_9091


title: 10x_9090


title: 10x_9089


title: 10x_9108


title: 10x_9087


title: 10x_9086


title: 10x_9085


title: 10x_9084


title: 10x_9088


title: 10x_9083


title: 10x_9080


title: 10x_9082


title: 10x_9079


title: 10x_9077


title: 10x_9081


title: 10x_9075


title: 10x_9076


title: 10x_9074


title: 10x_9078