title: ATAC_Chr1467-2162-19neg

first: Richard

last: Koche

state: New York

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of 0 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: sorted Cd19- proB cells

growth_protocol: Setd2f/f mice were bred to Mx1, Vav1, Cd19, Mb1, Cd2-cre mice to homozygosity. At 6-8 weeks of age, mice were sacrificed and bone marrow from femurs, tibias, hips, and spines were isolated. BM was then RBC lysed and stained with B220-biotin (BD pharmingen) and subsequently stained with Anti-biotin microbeads (Miltenyi) and applied on a LS column. Subsequent staining for cellular antigens was conducted. For VDJ recombination product assessment, RNA-Seq, ChIP-Seq, ChIP-PCR, qPCR proB and preB cells were isolated as follows: cells were then stained and sorted by FACS (BD-Aria) for B220+Cd43+IgM-Cd25- Cd19- proB cells

extract_protocol:
Lysis Buffer 10mM Tris·Cl, pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% (v/v) Igepal CA-630 (Buenrostro et al., 2015 protocol)
ATAC-seq was performed as previously described (Buenrostro et al. 2013 Nature Methods). For each sample, cell nuclei were prepared from 50,000 cells, and incubated with 2.5 uL transposase (Illumina) in a 50 uL reaction for 30 min at 37°C. Following purification of transposase fragmented DNA, the library was amplified by PCR and subjected to high-throughput sequencing using Illumina HiSeq 2500 platform.

value: Cd19- proB cells

value: Setd2 KO


title: Bergeron bud 800 rep3

status: Public on Mar 23 2020

type: SRA

city: Knoxville

first: Margaret

last: Staton

email: mestato@gmail.com, mstaton1@utk.edu

state: Tennessee

address: 2505 EJ Chapman Blvd, 370 PBB

country: USA

institute: University of Tennessee

library_source: transcriptomic

data_processing:
Adaptors and low-quality reads were trimmed by skewer for each library
Trimmed reads were aligned to Prunus persica v1 and Prunus persica v2 by STAR-2.5.3a
Gene counts were quantified by HTSeq-count
Gene counts of Prupe.1G531100 to Prupe.1G531700 (Pp01:43417246...43480648) in the Purnus persica v2 were replaced by ppa018667m, ppb017585m, ppa010758m, ppa011123m, ppa010822m, and ppa010714m in Prunus persica v1
Genome_build: Prunus persica v2 and Prunus persica v1
Supplementary_files_format_and_content: comma-delimited files with gene counts for apricot and peach

molecule: total RNA

organism: Prunus armeniaca

source_name: floral bud

growth_protocol: Apricot trees were grown in France. Peach trees were grown in South Carolina, USA

extract_protocol:
Total RNA from apricot bud tissue were extracted using NuceloSpin RNA XS Isolation kit (Macherey-Nagel, France). Total RNA from peach tissue were extracted using ??? Kit
Library construction was followed the illumina TruSeq RNA Library Prep Kit

tag: tissue

value: floral bud

tag: Stage

tag: cultivar name

value: Bergeron

tag: cultivar number


title: MP_4

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

data_processing:
Fastq files obtained from Beckman Coulter Genomics
Mapping was performed by Beckman Coulter Genomics on the human genome reference sequence GRCh38, using Tophat version 2.0.10 in conjunction with Bowtie version 1.0.0. Tophat was provided with a transcriptome reference generated from the Ensembl annotation of GRCh38. HTSeq was used to obtain a read count for all genes of the GRCh38 ENSEMBL annotation.
The average gene expression value in each population, given as Fragments Per Kilobase of transcript per Million map read (FPKM), was obtained using Cufflinks.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with FPKM

organism: Homo sapiens

source_name: Endothelial cell (EC) differentiation from human embryonic stem cells (hESC)

growth_protocol: A previously published protocol method was employed to generate endothelial cells from H9 human embryonic stem cells (Boulberdaa et al, 2016 Mol Ther). Briefly, hESCs, were dissociated into single cells using Tryple Select (Life Technologies). 1 × 10^4 cells were seeded into a 5% Pluronic F-127 (Sigma-Aldrich) coated 96- well round bottom microplates to generate embryoid bodies (EBs). The plates were centrifuged at 300 g for 3 minutes. Cells were cultured in Stemline II Hematopoietic expansion medium with the addition of 5 ng/mL Activin A (Peprotech), 10 µmol/L Y-27632 (Millipore), 10 ng/mL vascular endothelial growth factor (VEGF) (Peprotech), and 10 ng/mL bone morphogenetic protein 4 (BMP4) R and D Systems, Minneapolis. After 2 days, the EBs were supplemented Stemline II Hematopoietic expansion medium containing 10 ng/mL VEGF, 70 ng/mL Wnt3A, 140 ng/mL BMP4 and 35 ng/mL Activin A. On day 3, EBs were transferred to 0.1% gelatine-coated 6 well culture dishes (Sigma-Aldrich) and resuspended in endothelial growth medium-2 (EGM-2) (Lonza). The media was supplemented with 50 ng/ml of VEGF and the accompanying bullet kit, minus the VEGF and FBS supplement.  Cells were maintained until day 7, when they were harvested.

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen)
Ribosomal-depleted stranded libraries were prepared by Beckman Coulter Genomics and sequenced with an Illumina HiSeq (paired end 2 x 100bp).

treatment_protocol: Cell populations were dissociated by enzymatic digestion. Harvested cells were washed in PBS and incubated with specific antibodies (BD Bioscience). FACS sorting was performed using anti-human CD326, anti human-CD56, anti human-CD31, and anti human-CD144 by  FACSAria I or Aria III cell sorter (BD Biosciences). Sorted cell populations were taken forward for RNA extraction.

tag: cell type

value: day 3 mesoderm population (CD326lowCD56+ purified from embryoid bodies)

tag: replicate

value: replicate 4


title: MP_3

value: replicate 3


title: non-EC_2

value: the day 7 remaining population

value: replicate 2


title: Bergeron bud 400 rep3


title: MP_2


title: A323 bud  600 chill hours rep3

organism: Prunus persica


title: A318 bud  600 chill hours rep4


title: ATAC_Chr1461-6009-19neg

city: New York

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: genotype


title: A323 bud  600 chill hours rep1


title: Bergeron bud 100 rep3


title: MP_1

value: replicate 1


title: hESC_4

value: human embryonic stem cells


title: Bergeron bud 0 rep3

value: 0 CH


title: A318 bud  600 chill hours rep3


title: A323 bud  600 chill hours rep4


title: ATAC_Chr1470-2163-19neg

value: Setd2 WT


title: A318 bud  600 chill hours rep2


title: hESC_3


title: Bergeron petal visible rep2

value: petal visible


title: hESC_2


title: ATAC_Chr1464-6013-19neg


title: A318 bud  600 chill hours rep1


title: A209 bud  600 chill hours rep4


title: hESC_1


title: Bergeron bud 800 rep2


title: Bergeron bud 400 rep2


title: Bergeron sepal visble rep2

value: sepal visible


title: Bergeron bud 100 rep2


title: A209 bud  600 chill hours rep3


title: A209 bud  600 chill hours rep1


title: Bergeron bud 0 rep2


title: Bergeron petal visible rep3


title: A209 bud  600 chill hours rep2


title: A340 bud  100 chill hours rep4


title: Bergeron petal visible rep1


title: A340 bud  100 chill hours rep3


title: L2.72

type: RNA

city: Los Angeles

first: Stella

last: Tommasi

state: California

address: 1450 Biggy St

institute: University of Southern California

hyb_protocol: cDNA synthesis, fragmentation and hybridization were performed according to the manufacturer's instructions (Affymetrix)

scan_protocol: Scanning was performed according to the manufacturer's instructions (Affymetrix)

data_processing: Analysis was performed using the affymetrix Expression Console software (Affymetrix)

label: biotin

source_name: SHS 4M + 1M RECOVERY

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was isolated from liver tissues of SHS-treated and controls, using the Rneasy Mini Kit (Qiagen)

tag: strain

tag: Sex

value: MALE


title: Bergeron sepal visble rep1


title: L2.73


title: A340 bud  100 chill hours rep2


title: L2.71


title: TRP3 LX-2-sup DMOG 3

city: Zürich

first: Konstantin

last: Dirscherl

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

description:
P202_12_TRP3_LX-2_Sup_DMOG-3
TRP3 passage 15 incubated in supernatant of LX-2 DMOG 3

hyb_protocol: 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S human arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450

scan_protocol: the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de). Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software.
After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.

source_name: TRP3 after 24 hour incubation with supernatants of DMOG-treated LX-2

label_protocol: Sample preparation for microarray hybridization was performed using the Affymetrix GeneChip WT PLUS Reagent Kit according to the Manifacturers Instructions.

growth_protocol: LX-2 human hepatic stellate cells were cultured in MCDB131 medium with 10% Fetal Clone II Serum, 10 mmol/l GlutaMAX, 1 µg/ml hydrocortisone, penicillin/streptomycin as described, 250 µg/ml adenosine 3´,5´-cyclic monophosphate and 50 µg/ml endothelial cell growth supplement from bovine tissue. TRP3 liver sinusoidal endothelial cells were cultured in supernatants of LX-2 for 24 hours.

extract_protocol: Total RNA was extracted from cultured LX-2 and TRP3 according to the manufacturer’s instructions using the RNeasy Mini Kit

treatment_protocol: DMOG 1mM was added to the culture medium of LX-2. TRP3 were incubated with supernatants of LX-2 treated with 1mM DMOG for 24 hours or of control LX-2.

tag: cell line

value: human immortalized liver sinusoidal endothelial  cell line

tag: passage

value: passage 15

tag: treatment

value: incubated in supernatant of LX-2 DMOG


title: Bergeron bud 800 rep1

value: floral bud


title: L2.70


title: Bergeron bud 400 rep1

value: Bergeron


title: TRP3 LX-2-sup DMOG 1

description:
P202_10_TRP3_LX-2_Sup_DMOG-1
TRP3 passage 10 incubated in supernatant of LX-2 DMOG 1

value: passage 10


title: TRP3 LX-2-sup control 3

description:
P202_09_TRP3_LX-2_Sup_Ctrl-3
TRP3 passage 15 incubated in supernatant of LX-2 control 3

source_name: TRP3 after 24 hour incubation with supernatants of control LX-2


title: L2.69

source_name: SHS 4M


title: L2.66


title: L2.67


title: TRP3 LX-2-sup control 2

description:
P202_08_TRP3_LX-2_Sup_Ctrl-2
TRP3 passage 13 incubated in supernatant of LX-2 control 2

value: passage 13


title: L2.4

source_name: CONTROL


title: A323 bud  100 chill hours rep4


title: Bergeron bud 100 rep1


title: A340 bud  100 chill hours rep1


title: L2.68


title: HOC313 siControl_m6A_IP_replicate2

city: Sendai

first: Fan-Yan

last: Wei

address: Seiryo-machi 4-1

country: Japan

institute: Tohoku University

description: m6A antibody IP

data_processing:
Base-calling was performed using Illumina protocols
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome using HISAT2
Aligned reads were counted using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each gene

source_name: HOC318 cells

growth_protocol: DMEM with 10%FBS

extract_protocol:
Total RNA was isolated using Trizol. mRNA were purified using Oligo-dT beads.
mRNA was fragmentated and subjected to sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with siRNA against FTO.

value: HOC318 cells

tag: genotype/variation

value: siControl


title: A323 bud  100 chill hours rep2


title: TRP3 LX-2-sup DMOG 2

description:
P202_11_TRP3_LX-2_Sup_DMOG-2
TRP3 passage 13 incubated in supernatant of LX-2 DMOG 2


title: L2.3


title: TRP3 LX-2-sup control 1

description:
P202_07_TRP3_LX-2_Sup_Ctrl-l
TRP3 passage 10 incubated in supernatant of LX-2 control 1


title: HOC313 siFTO_IgG_IP

description: Control IgG IP

source_name: HOC317 cells

value: HOC317 cells

value: FTO-knockdown


title: L2.1


title: Palsteyn petal visible rep2

value: Palsteyn


title: HOC313 siFTO_m6A_IP

description: m6A antibody IP

source_name: HOC316 cells

value: HOC316 cells


title: Palsteyn sepal visble rep2


title: Bergeron bud 0 rep1

value: 0 CH


title: HOC313 siControl_IgG_IP

description: Control IgG IP

source_name: HOC315 cells

value: HOC315 cells


title: A209 bud  100 chill hours rep3


title: Palsteyn flower 800 rep2

source_name: flower

value: flower


title: A209 bud  100 chill hours rep4


title: LX-2 DMOG 1

description:
P202_04_LX-2_DMOG-1
LX-2 passage 12 after treatment with 1 mM DMOG for 24 hours

source_name: LX-2 after treatment with 1mM DMOG for 24 hours treatment

value: human immortalized hepatic stellate cell line

value: passage 12


title: HOC313 siControl_m6A_IP_replicate1

description: m6A antibody IP

source_name: HOC314 cells

value: HOC314 cells


title: LX-2 DMOG 3

description:
P202_06_LX-2_DMOG-3
LX-2 passage 24 after treatment with 1 mM DMOG for 24 hours

value: passage 24


title: A209 bud  100 chill hours rep2

value: floral bud


title: HOC313 siFTO RNAseq 3

source_name: HOC313 cells

value: HOC313 cells


title: Palsteyn bud 400 rep2


title: A209 bud  100 chill hours rep1


title: LX-2 DMOG 2

description:
P202_05_LX-2_DMOG-2
LX-2 passage 16 after treatment with 1 mM DMOG for 24 hours

value: passage 16


title: LX-2 control 3

description:
P202_03_LX-2_Ctrl-3
LX-2 passage 24 without stimulation

source_name: LX-2 without treatment

value: without stimulation


title: Palsteyn bud 100 rep2


title: A323 bud  100 chill hours rep1


title: L2.2

value: MALE


title: A318 bud  100 chill hours rep4


title: LX-2 control 1

description:
P202_01_LX-2_Ctrl-1
LX-2 passage 12 without stimulation


title: HOC313 siFTO RNAseq 2


title: HOC313 siFTO RNAseq 1


title: Palsteyn bud 0 rep2


title: A318 bud  100 chill hours rep3


title: LX-2 control 2

description:
P202_02_LX-2_Ctrl-2
LX-2 passage 16 without stimulation


title: HOC313 siControl RNAseq 3

value: siControl


title: Palsteyn petal visible rep1

value: petal visible


title: A318 bud  100 chill hours rep2


title: Palsteyn sepal visble rep1

value: sepal visible


title: A318 bud  0 chill hours rep1


title: HOC313 siControl RNAseq 2


title: nasal mucosa_ NaB+AR group_ treated with both OVA and NaB_rep3

city: Xi’an

first: jie

middle: wang

last: wang

state: shanxi

address: 17 Changle Western Road

department: Department of Otolaryngology-Head and Neck Surgery

country: China

institute: Xijing Hospita,Air Force Military Medical University

description:
Gene expression in mice nasal mucosa with treated with both OVA and NaB
B18

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x180k array slides.

data_processing: The scanned images were analyzed with Feature Extraction(v10.7) (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.The array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software v13 (Agilent).

source_name: nasal mucosa, NaB+AR group, treated with both OVA and NaB,rep3

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reactions ; the procedure has been improved using the CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China) to produce higher yields of labeled cDNA.Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

growth_protocol: Mice were raised in a pathogen-free environment under a 12-h light/12-h dark cycle at 22 °C with free access to food and water.

extract_protocol: Total RNA,was extracted from the nasal mucosa using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA purity and concentration were determined based on optical density (OD)260/280 readings with a spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: Mice began to feed after weaning at 3 weeks of age. The NaB+AR group received feed containing NaB (Sigma-Aldrich, St. Louis, MO, USA) mixed into their feed (Air Force Military Medical University) at 30 g/kg. Each mouse in this group ate an average of 5 g of feed per day, which contained 0.15 g NaB. The other two groups were given normal feed throughout the study period. At 7 weeks of age, mice in both the AR and NaB+AR groups received intraperitoneal injections of mixed OVA solution (20 mg) and aluminum (2 mg) in phosphate-buffered solution (PBS, 0.5 mL) on days 1, 3, 6, and 8, whereas control mice received injections of aluminum (2 mg) in PBS (0.5 mL) with the same schedule. Mice in the AR and NaB+AR groups were also treated with OVA challenge (10%, 20 μl) through intranasal instillation once daily from days 15 to 24. Mice in the control group were treated with PBS (20 μl) through intranasal instillation once daily during the same period.

value: nasal mucosa

tag: gender

value: male


title: A340 bud  0 chill hours rep4

source_name: floral bud

value: 0 CH


title: nasal mucosa_ NaB+AR group_ treated with both OVA and NaB_rep2

description:
Gene expression in mice nasal mucosa with treated with both OVA and NaB
B17

source_name: nasal mucosa, NaB+AR group, treated with both OVA and NaB,rep2


title: HOC313 siControl RNAseq 1


title: Palsteyn flower 800 rep1

value: Palsteyn


title: Palsteyn bud 100 rep1


title: RSE3: the (p)ppGpp0 mutant

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)
Sequenced reads were trimmed for adaptor sequence, then mapped to Erwinia amylovora CFBP1430  whole genome using bowtie v0.12.7 with parameters -t --sam -v 2 -B 1 -3 20 --best
The number of reads mapped to CDS of Erwinia amylovora CFBP1430  were counted using bedtools 2.17.0
Normalization and statistical analysis were carried out using the R package DESeq2 as described in Love et al. Genome biology, 2014.
Genome_build: bowtieNC_013961
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample ('p' in file name denotes plasmid abundance measurements; no 'p' in file name denotes genomic abundance measurements)

organism: Erwinia amylovora

source_name: bacterial cells

growth_protocol: Overnight cultures of wild-type and mutant strains grown in LB were harvested and washed twice with hrp-inducing minimal media.

extract_protocol:
Bacterial cells were harvested, and RNA was isolated using Qiagen RNeasy bacteria Mini kit
The stranded RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'

treatment_protocol: Bacterial cells of WT and (p)ppGpp mutant were adjusted to 2 x 10^8 cfu/ml in 5 mL of hrp-inducing minimal media and incubated 3hr at 18 °C.

value: delta-relA/spoT


title: RSE2: the (p)ppGpp0 mutant


title: Palsteyn bud 0 rep1


title: A340 bud  0 chill hours rep3


title: A340 bud  0 chill hours rep2


title: A318 bud  0 chill hours rep3


title: nasal mucosa_ NaB+AR group_ treated with both OVA and NaB_rep1

description:
Gene expression in mice nasal mucosa with treated with both OVA and NaB
B16

source_name: nasal mucosa, NaB+AR group, treated with both OVA and NaB,rep1


title: nasal mucosa_AR group_ treated with ovalbumin_rep3

description:
Gene expression in mice nasal mucosa with treated with ovalbumin
B15

source_name: nasal mucosa,AR group,treated with ovalbumin,rep3


title: nasal mucosa_AR group_ treated with ovalbumin_rep2

description:
Gene expression in mice nasal mucosa with treated with ovalbumin
B14

source_name: nasal mucosa,AR group,treated with ovalbumin_rep2


title: Palsteyn bud 400 rep1


title: A340 bud  0 chill hours rep1


title: Bakour sepal visible rep3

value: Bakour


title: EBV+FK506_8 [IonXpress_075]

city: Zurich

first: Christian

last: Münz

department: Institute of Experimental Immunology

institute: University Of Zurich

data_processing:
Sequencing reads were mapped to Homo sapiens (human) genome assembly GRCh37, and initial analysis, quality control, and normalization of mapped reads as RPM (reads per million mapped reads) was performed by the ampliSeqRNA plug-in on the Ion Torrent server.
All subsequent statistical analysis of the transcriptome data was performed using the R environment for statistical computing (R version 3.4.1 (2017-06-30)) with Bioconductor (Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015;12(2):115-21) and dedicated packages.
To avoid technical artifacts the data were filtered such that genes for which the average over all samples was less than 1 were removed.
Identification and correction for spurious batch effects of unknown origin was performed via application of surrogate variable analysis (Leek JT, and Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007;3(9):1724-35.)
Differential expression was modeled using mixed-effect linear regression with empirical Bayes variance estimation, as implemented in the limma package (3.34.3) (Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, and Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.)
Mapping of the transcripts to HGNC symbols and ENTREZID’s was performed using the org.Hs.eg.db package version 3.5.0.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (RPM) for each sample

source_name: CD19+ splenocytes isolated from humanized NSG mice 5 wks post EBV-infection and following 2 wks of FK506 injections every other day

growth_protocol: Newborn HLA-A2 transgenic NOD/LtSz-scid IL2Rgnull (NSG-A2) mice mice (up to five days old) were irradiated with 1 Gy. Five to seven hours after irradiation, mice were injected intrahepatically with 1-4×105 CD34+ human hematopoietic progenitor cells (HPCs) derived from human fetal liver (HFL) tissue. Individual mouse cohorts were reconstituted with cells derived from three different HFL donors (A-C). Reconstitution of human immune system components in mice was analyzed in the week before the start of the experiments by flow cytometry.

extract_protocol:
Single cell suspensions of huNSG-A2-derived splenocytes were subjected to lysis of erythrocytes by ACK lysing buffer (Life Technologies) followed by magnetoc cell sorting of B cells using CD19 microbeads (Miltenyi Biotech). Total RNA of CD19+ cells was isolated using the RNeasy Mini Kit (QIAGEN) and traces of genomic DNA were removed by on-column DNase digestion (Qiagen). Purified RNA was stored at −20°C.
RNA quality was assessed further by an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit. All RIN numbers were ≥ 9.5. RNA was quantified by NanoDrop 1000 spectrophotometry. Reverse transcription of 10 ng total RNA, amplification of targets by ultra-high multiplex PCR, and sequencing library construction was performed using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific; #A26325) and Ion Xpress barcodes. Unamplified libraries were quantified by qPCR and equal amounts were combined for sequencing (6 µl of 100 pM total libraries). Templating of Ion Sphere Particles by emulsion PCR was conducted using the Ion 540 Kit (Thermo Fisher Scientific #A27753) and an OT2 instrument. Sequencing using an Ion 540 semiconductor chip was carried out on the Ion S5 System (Thermo Fisher Scientific).
The Ion AmpliSeq Transcriptome Human Gene Expression Kit uses primers targeting 18,574 mRNAs and 2,228 non-coding RNAs (ncRNAs) for a total of 20,802 transcripts. 10 ng total RNA per sample were processed, and IonXpress barcodes were used for library building.

treatment_protocol: 13 to 19 weeks after engraftment, huNSG-A2 mice were injected with 105 RIU of EBV (B95-8) or 100µl PBS intraperitoneally. Animals were treated with 10mg/kg body weight of FK506 (Prograph injectable solution, Astellas) diluted 1:3 in PBS subcutaneously every second day starting at day 22 p.i. or left untreated.

tag: human fetal liver donor

value: C

tag: infection group

value: EBV (EBV+)

tag: treatment group

tag: cohort# - animal#

value: B cells

tag: cell subtype

value: CD19+ splenocytes

tag: macroscopic tumor

value: positive


title: Bakour petal visible rep3

tag: tissue

value: floral bud

tag: Stage

tag: cultivar name

tag: cultivar number


title: EBV+FK506_7 [IonXpress_074]

tag: cell type


title: Ea2: WT

tag: strain

tag: genotype

value: wild-type


title: nasal mucosa_AR group_ treated with ovalbumin_rep1

description:
Gene expression in mice nasal mucosa with treated with ovalbumin
B13

source_name: nasal mucosa,AR group,treated with ovalbumin_rep1


title: Bakour flower 800 rep3

value: flower


title: A209 bud  0 chill hours rep1


title: Ea3: WT


title: A209 bud  0 chill hours rep3


title: RSE1: the (p)ppGpp0 mutant


title: nasal mucosa_control group_ no treatment_rep2

description:
Gene expression in mice nasal mucosa with no treat
B11

source_name: nasal mucosa,control group,no treatment,rep2


title: EBV+FK506_6 [IonXpress_072]


title: nasal mucosa_control group_ no treatment_rep1

description:
Gene expression in mice nasal mucosa with no treat
B10

source_name: nasal mucosa,control group, no treatment,rep1


title: nasal mucosa_control group_ no treatment_rep3

description:
Gene expression in mice nasal mucosa with no treat
B12

source_name: nasal mucosa,control group,no treatment_rep3


title: EBV+FK506_5 [IonXpress_068]


title: Bakour bud 400 rep3


title: Ea1: WT


title: EBV+FK506_4 [IonXpress_067]


title: Bakour bud 100 rep3


title: A209 bud  0 chill hours rep2


title: EBV+FK506_3 [IonXpress_038]

value: B

value: negative


title: Bakour petal visible rep2

value: petal visible


title: A209 bud  0 chill hours rep4


title: EBV+FK506_2 [IonXpress_037]


title: A323 bud  0 chill hours rep3


title: NBPAT63

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

description: SAMPLE 63

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: Data was quantile normalized using R statistical programming language and 'preprocessCore' library

source_name: Neuroblastoma

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturers protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

extract_protocol: Total  RNA was extracted with Magnetic Beads Total Nucleic Acid Isolation Kit for FFPE (Sileks, Russia) according to manufacturer instruction. RNA was quantified using Nanodrop.

tag: tumor localisation

value: retroperitoneal region

tag: patient id

value: patient #63


title: Bakour sepal visible rep2

value: sepal visible


title: NBPAT62

description: SAMPLE 62

value: right adrenal gland

value: patient #62


title: A323 bud  0 chill hours rep1

value: 0 CH


title: Bakour flower 800 rep2

source_name: flower

value: Bakour


title: A323 bud  0 chill hours rep4


title: EBV+FK506_1 [IonXpress_007]

value: C

value: EBV (EBV+)


title: A318 bud  0 chill hours rep2


title: Bakour bud 0 rep2


title: EBV_7 [IonXpress_076]

source_name: CD19+ splenocytes isolated from humanized NSG mice 5 wks post EBV-infection

value: Mock (FK506–)

value: B cells

value: CD19+ splenocytes


title: EBV_6 [IonXpress_073]


title: Bakour bud 400 rep2

value: floral bud


title: A323 bud  0 chill hours rep2


title: Bakour petal visible rep1


title: Bakour bud 100 rep2


title: LB-5 Rep2 [LB-5-2]

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence   then used Trinity (Grabherr et al, 2011) to assemble the reads into transcriptome within para:min_kmer_cov:2 ,after that, we mapped reads  to transcriptome using bowtie2 with default parameters.
Reads Count were stated for each sample, and Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced(FPKM) were calculated for each unigene .
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: FPKM

organism: Lycium barbarum

source_name: L. barbarum_fruit develoment stage 5

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

value: wild type

tag: age

value: fruit develoment stage 5

value: Fruit


title: NBPAT61

description: SAMPLE 61

value: left adrenal gland

value: patient #61


title: NBPAT59

description: SAMPLE 59

value: retroperitoneal region

value: patient #59


title: Bakour sepal visible rep1

value: sepal visible


title: NBPAT60

description: SAMPLE 60

value: adrenal gland

value: patient #60


title: EBV_4 [IonXpress_036]

value: B

value: negative


title: EBV_3 [IonXpress_035]

value: EBV (EBV+)


title: NBPAT58

description: SAMPLE 58

value: retroperitoneal region, right

value: patient #58


title: LB-5 Rep1 [LB-5-1]


title: EBV_2 [IonXpress_034]

value: Mock (FK506–)

value: B cells

value: CD19+ splenocytes


title: Bakour flower 800 rep1

value: flower

value: Bakour


title: LB-4 Rep3 [LB-4-3]

source_name: L. barbarum_fruit develoment stage 4

value: wild type

value: fruit develoment stage 4

value: Fruit


title: EBV_5 [IonXpress_066]

value: C

value: positive


title: LB-5 Rep3 [LB-5-3]

value: fruit develoment stage 5


title: NBPAT56

description: SAMPLE 56

value: adrenal gland

value: patient #56


title: EBV_1 [IonXpress_033]

value: B

value: negative


title: RSB3: the (p)ppGpp0 mutant

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)
Sequenced reads were trimmed for adaptor sequence, then mapped to PstDC3000 and PssB728a  whole genome using bowtie v0.12.7 with parameters -t --sam -v 2 -B 1 -3 20 --best
The number of reads mapped to CDS of PstDC3000 and PssB728a were counted using bedtools 2.17.0
Normalization and statistical analysis were carried out using the R package DESeq2 as described in Love et al. Genome biology, 2014.
Genome_build: bowtieNC_013961
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample ('p' in file name denotes plasmid abundance measurements; no 'p' in file name denotes genomic abundance measurements)

organism: Pseudomonas syringae

growth_protocol: Overnight cultures of wild-type and mutant strains grown in KB were harvested and washed twice with hrp-inducing minimal media.

treatment_protocol: Bacterial cells were adjusted to 2 x 10^8 cfu/ml in 5 mL of hrp-inducing minimal media and incubated for 3 h at 18 °C.

value: delta-relA/spoT


title: LB-4 Rep1 [LB-4-1]


title: RSB2: the (p)ppGpp0 mutant


title: LB-4 Rep2 [LB-4-2]


title: FK506_6 [IonXpress_059]

source_name: CD19+ splenocytes isolated from humanized NSG mice 5 wks post mock-infection and following 2 wks of FK506 injections every other day

value: A

value: Mock (EBV–)


title: RSB1: the (p)ppGpp0 mutant


title: NBPAT55

description: SAMPLE 55

value: patient #55


title: LB-3 Rep3 [LB-3-3]

source_name: L. barbarum_fruit develoment stage 3

value: fruit develoment stage 3


title: FK506_5 [IonXpress_058]

value: B cells

value: CD19+ splenocytes


title: NBPAT64

description: SAMPLE 64

value: retroperitoneal region, right

value: patient #64


title: NBPAT57

description: SAMPLE 57

value: left adrenal gland

value: patient #57


title: LB-3 Rep2 [LB-3-2]

value: wild type

value: Fruit


title: NBPAT54

description: SAMPLE 54

value: retroperitoneal region, left (lymph node)

value: patient #54


title: NBPAT52

description: SAMPLE 52

value: patient #52


title: NBPAT53

description: SAMPLE 53

value: posterior mediastinum, right

value: patient #53


title: B73: WT_B728a

value: wild-type


title: FK506_3 [IonXpress_006]

value: B

value: Mock (EBV–)

value: negative


title: FK506_4 [IonXpress_057]

value: A

value: B cells


title: B72: WT_B728a


title: NBPAT51

description: SAMPLE 51

value: retroperitoneal region, right

value: patient #51


title: LB-3 Rep1 [LB-3-1]

value: fruit develoment stage 3


title: NBPAT49

description: SAMPLE 49

value: patient #49


title: B71: WT_B728a


title: FK506_2 [IonXpress_005]

value: CD19+ splenocytes


title: LB-2 Rep3 [LB-2-3]

source_name: L. barbarum_fruit develoment stage 2

value: wild type

value: fruit develoment stage 2

value: Fruit


title: FK506_1 [IonXpress_004]


title: FRS3: the (p)ppGpp0 mutant

source_name: bacterial cells

value: delta-relA/spoT/fpRel


title: FRS2: the (p)ppGpp0 mutant


title: LB-2 Rep2 [LB-2-2]


title: LB-2 Rep1 [LB-2-1]


title: Mock_4 [IonXpress_042]

source_name: CD19+ splenocytes isolated from humanized NSG mice 5 wks post mock-infection

value: Mock (FK506–)


title: NBPAT48

description: SAMPLE 48

value: right adrenal gland

value: patient #48


title: FRS1: the (p)ppGpp0 mutant


title: Mock_3 [IonXpress_040]

value: B


title: DC3: WT_DC3000

value: wild-type


title: LB-1 Rep3 [LB-1-3]

source_name: L. barbarum_fruit develoment stage 1

value: fruit develoment stage 1


title: LB-1 Rep1 [LB-1-1]


title: Mock_1 [IonXpress_002]

value: A

value: Mock (EBV–)

value: negative


title: NBPAT50

description: SAMPLE 50

value: retroperitoneal region

value: patient #50


title: NBPAT46

description: SAMPLE 46

value: retroperitoneal region, left

value: patient #46


title: DC1: WT_DC3000


title: Mock_2 [IonXpress_003]

value: B cells

value: CD19+ splenocytes


title: DC2: WT_DC3000


title: NBPAT45

description: SAMPLE 45

value: lymph node

value: patient #45


title: Mock_5 [IonXpress_060]

value: Mock (FK506–)


title: NBPAT43

description: SAMPLE 43

value: posterior mediastinum, right

value: patient #43


title: NBPAT44

description: SAMPLE 44

value: left adrenal gland

value: patient #44


title: LB-1 Rep2 [LB-1-2]

value: wild type

value: fruit develoment stage 1

value: Fruit


title: NBPAT47

description: SAMPLE 47

value: patient #47


title: NBPAT42

description: SAMPLE 42

value: peritoneal cavity

value: patient #42


title: CC595_eCCA

status: Public on Mar 22 2020

city: Barcelona

first: Robert

last: Montal

address: Rosselló 153

country: Spain

institute: IDIBAPS

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with GenePattern (Broad Institute) using Expression file creator module and the RMA algorithm.

label: Biotin

source_name: extrahepatic cholangiocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Samples collected after surgical resection and FFPE

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

treatment_protocol: Not applicable. Archived tissue was obtained at our Insitution upon patient's consent

value: extrahepatic cholangiocarcinoma

tag: center

value: Lausanne


title: CC597_eCCA


title: CC602_BD

source_name: non-tumor bile duct

value: non-tumor bile duct


title: CC603_eCCA


title: CC585_eCCA


title: CC591_eCCA


title: CC587_eCCA


title: CC589_eCCA


title: CC599_eCCA


title: CC601_eCCA


title: CC581_eCCA


title: CC593_eCCA


title: CC559_eCCA


title: CC577_eCCA


title: CC555_eCCA


title: CC583_eCCA


title: CC565_eCCA


title: CC569_eCCA


title: CC567_eCCA


title: CC563_eCCA


title: CC547_eCCA


title: CC545_eCCA


title: CC579_eCCA


title: CC571_eCCA


title: CC561_eCCA


title: CC573_eCCA


title: CC553_eCCA


title: CC557_eCCA


title: CC570_BD


title: CC549_eCCA


title: CC543_eCCA


title: CC541_eCCA


title: CC539_eCCA


title: CC537_eCCA


title: pdm3 RNAi rep3 [Pdm3 RNAi_3_ATGTCA]

city: Philadelphia

first: Matthew

last: Kayser

state: PA

address: 415 Curie Boulevard, CRB 320

department: Psychiatry

institute: University of Pennsylvania

data_processing:
Sequenced reads were mapped to the Drosophila melanogaster genome assembly dm6 using STAR v2.7.0f(Dobin et al., 2013)
STAR was run with the default parameters with the following exceptions: --outFilterMultimapNmax 1 and --twopassMode Basic. The aligned reads were assigned to genes and counted using featureCounts (v1.6.4) run with default options on the dmel-all-r6.27 version of the Drosophila melanogaster annotation.
Differential gene expression was performed on the gene count data in R v3.4.2 using DEseq2 v1.22.2(Love et al., 2014). The annotated genes exhibiting an adjusted-P value < 0.05 and |log2FC|>1.0 were considered differentially expressed compared to control.
Genome_build: dm6
Supplementary_files_format_and_content: read counts; DESeq analysis results

organism: Drosophila melanogaster

source_name: pdm3 RNAi_pupal brain

extract_protocol:
40 brains per sample at the mid-pupal stage were dissected in cold AHL (108 mM NaCl, 5 mM KCl, 2 mM CaCl2, 8.2 mM MgCl2, 4 mM NaHCO3, 1 mM NaH2PO4-H2O, 5mM trehalose, 10 mM sucrose, 5 mM HEPES). Four biological replicates (each with 40 brains) were dissected per genotype. Brains were transferred to 1ml of Trizol and incubated for 5 min at room temperature (RT). 0.2 ml of chloroform was added and samples were inverted. Samples were incubated 2-3 min at RT, then centrifuged at 12000g for 15 min at 4oC. Genomic DNA was removed using a gDNA eliminator column (RNeasy Plus Micro Kit, Qiagen). RNA was then extracted using the RNeasy MinElute Cleanup Kit (Qiagen).
Sequence libraries for each sample were synthesized using the NEBNext Ultra II Directional RNA kit following supplier recommendations and were sequenced on Illumina HiSeq-4000 sequencer as single-reads of 100 base reads following Illumina’s instructions. The quality of the data was analyzed using fastqc v0.11.8 and multiqc v1.0.dev0.

value: 6d post-egg lay at 25c

tag: genotype/variation

value: Elav-GAL4 > UAS pdm3 RNAi

value: pupal brain


title: pdm3 RNAi rep2 [Pdm3 RNAi_2_AGTTCC]


title: pdm3 RNAi rep4 [Pdm3 RNAi_4_CCGTCC]


title: pdm3 RNAi rep1 [Pdm3 RNAi_1_AGTCAA]


title: CC531_eCCA


title: Dolastatin 15; solvent control for 24H sample 1

city: Gainesville

first: Tongjun

last: Gu

state: FL

address: 2033 Mowry Road

department: ICBR

institute: The University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCh38 using star/2.5.2b
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using rsem/1.2.28
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HCT116 cells were cultured in DMEM medium with 10% FBS and maintained at 5% CO2. Treatmenst were carried out in 6-well assay plates and RNA extracted using a Qiagen kit following protocol for cells.

extract_protocol:
16 hours and 24 hours post drug treatment RNA was extracted using a qiagen kit following the manufacturers protocol for cells.
RNA concentration was determined on Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). Total RNA with 28S/18S > 1 and RNA integrity number (RIN) ≥ 7 are used for RNAseq library construction.   RNAseq library were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Basically, 1000ng of total RNA was used for mRNA isolation using NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490 ). Then followed by RNA library construction with NEBNext Ultra II Directional Lib Prep  (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. 12 barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT. Finally, 12 individual libraries were pooled with equimolar and sequenced by Illumina HiSeq 3000 2X100 cycles run for total of 2 runs (Illumina Inc., CA, U.S.)    RNA library construction was performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression & Genotyping Core, University of Florida (UF).    HiSeq 3000 sequencing run was performed at the Interdisciplinary Center for Biotechnology Research (ICBR) NextGen DNA Sequencing core, University of Florida (UF).

treatment_protocol: Cells were seeded in DMEM with 5% FBS medium at a density of 400K/well and allowed to attach overnight. Dolastatin sample stocks were prepared in DMSO (Sigma) and cells treated at the appropriate concentrations in duplicate along with solvent controls. DMSO concentration is cells were maintained at 0.25%.

tag: cell line

tag: treatment

value: control


title: Dolastatin 15; 100 nM treatment at 24H sample 2

value: Dolastatin 15


title: CC523_eCCA

value: VH


title: CC533_eCCA


title: CC525_eCCA


title: control rep4 [Control_4_CTTGTA]

source_name: control_pupal brain

value: Elav-GAL4 / +


title: CC527_eCCA


title: Dolastatin 15; 100 nM treatment at 16H sample 2


title: control rep2 [Control_2_TAGCTT]


title: control rep1 [Control_1_GATCAG]


title: Dolastatin 15; 20 nM treatment at 24H sample 1


title: Dolastatin 15; solvent control for 16H sample 1


title: Dolastatin 15; solvent control for 16H sample 2


title: Dolastatin 15; 20 nM treatment at 24H sample 2


title: CC521_eCCA


title: Dolastatin 15; solvent control for 24H sample 2


title: Dolastatin 15; 100 nM treatment at 16H sample 1


title: Dolastatin 15; 20 nM treatment at 16H sample 2


title: CC535_eCCA


title: CC519_eCCA


title: CC529_eCCA


title: control rep3 [Control_3_GGCTAC]


title: Dolastatin 15; 100 nM treatment at 24H sample 1


title: miR-146a KO mouse 1

city: Freiburg

first: Severin

last: Dicks

address: Breisacherstr. 153

department: Institute of Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Freiburg Medical Center

data_processing:
bcl2fastq 2.20.0.422 illumina; basecalling and demultiplexing
cellranger count 3.1.0 10x genomics; generate single cell feature counts
Genome_build: mm10 from version 3.0.0 10x genomics
Supplementary_files_format_and_content: non normalized filtered countmatrix h5 format

molecule: polyA RNA

source_name: mice treated with anti-PD-1 therapy

extract_protocol:
Pan T cells were isolated from murine spleens using magnetic activated cell sorting.
scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10× Genomics) according to the manufacturer’s instructions (one sample per GEM well).
scRNA-seq

treatment_protocol: Mice were treated intraperitoneally with anti-PD-1 antibody twice a week for three weeks.To induce irAEs, mice were additionally treated intraperitoneally with low-dose LPS once a week. The experiment was ended and cells extracted on day 22 after the first treatment.

value: spleen

value: splenic T cells

value: miR-146a knockout


title: WT mouse 2

value: wildtype


title: WT mouse 1


title: Dolastatin 15; 20 nM treatment at 16H sample 1


title: miR-146a KO mouse 2


title: CC495_eCCA

value: Clinic


title: CC515_eCCA


title: CC484_BD


title: CC489_eCCA


title: CC478_BD


title: CC491_eCCA


title: CC486_BD


title: CC499_eCCA


title: CC485_eCCA


title: CC490_BD


title: CC477_eCCA


title: CC500_BD


title: CC507_eCCA


title: CC517_eCCA


title: CC502_BD


title: CC505_eCCA


title: CC466_BD


title: CC483_eCCA


title: CC481_eCCA


title: CC492_BD


title: CC475_eCCA


title: CC509_eCCA


title: CC469_eCCA


title: CC503_eCCA


title: CC501_eCCA


title: CC513_eCCA


title: CC465_eCCA


title: CC473_eCCA


title: CC482_BD


title: CC457_eCCA


title: CC455_eCCA


title: CC462_BD


title: CC451_eCCA


title: CC445_eCCA


title: CC454_BD


title: CC461_eCCA


title: CC443_eCCA


title: CC456_BD


title: CC436_BD


title: CC435_eCCA


title: CC433_eCCA


title: CC459_eCCA


title: CC449_eCCA


title: CC444_BD


title: CC438_BD


title: CC442_BD


title: CC453_eCCA


title: CC425_eCCA


title: CC429_eCCA


title: CC437_eCCA


title: CC423_eCCA


title: CC441_eCCA


title: CC422_BD


title: CC421_eCCA


title: CC430_BD


title: CC431_eCCA


title: CC424_BD


title: HUVECs, CTRL2

city: Beijing

first: Jiayi

last: Chen

address: 27 Tai-Ping Road

institute: National Center of Biomedical Analysis

data_processing:
Clean data were obtained by Trimmomatic.
Bowtie2 and eXpress were used to calculate the FPKMs (Fragments Per kb Per Million Reads) of known genes.
Differentially expressed genes were identified using the DESeq R package functions estimateSizeFactors and nbinomTest.
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample

source_name: HUVEC cells under histamine treatment

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HUVECs

value: shNT


title: HUVECs, HA2


title: HUVECs, CTRL1


title: HUVECs, HA1


title: RA-FLS_TNF_HF_24_hr [MY014]

city: Boston

first: John

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

data_processing:
Alignment and soft-trimming, STAR aligner version 2.4.1d, with options: --runThreadN 6 --outFilterMultimapNmax 10 --outSAMstrandField intronMotif
Feature counting with featureCounts, version 1.4.4, from the SUBREAD package with options: -s 0
Differential expression with limma voom  (limma package, version 3.22.1)
Genome_build: hg19
Supplementary_files_format_and_content: rawcounts.tsv - tab delimited file with EnsemblIDs and raw feature counts; normalizedcounts.tsv - tab delimited file with HGNC gene symbol IDs and limma voom normalized feature counts

growth_protocol: Grown in DMEM 10% FCS, starved overnight in 0.2% FBS

extract_protocol:
Trizol  extraction, followed by preparation according to Truseq instructions
Poly-A enriched libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit, sequenced using a single-end approach with 100 bp reads at a total sequencing depth of 30 million reads on an Illumina 4000 instrument

treatment_protocol: Primary RA-FLS were left in serum-reduced media (0.2% FBS) for 24 hours, pre-treated for 16 hrs with 300 nM HF or vehicle, and then treated for 8 or 24 hours with 10 ng/ml TNF  or vehicle.

value: rheumatoid arthritis fibroblast like synoviocytes (RA-FLS)

tag: time (hrs)


title: RA-FLS_TNF_24_hr [MY013]

value: TNF


title: CC419_eCCA

value: extrahepatic cholangiocarcinoma


title: CC420_BD

value: non-tumor bile duct


title: CC415_eCCA


title: CC417_eCCA


title: CC413_eCCA


title: CC411_eCCA


title: CC377_eCCA

value: Mayo


title: CC389_eCCA


title: CC401_eCCA


title: CC387_eCCA


title: CC383_eCCA


title: CC407_eCCA


title: CC403_eCCA


title: RA-FLS_TNF_HF_8_hr [MY012]


title: CC375_eCCA


title: CC391_eCCA


title: CC385_eCCA


title: Malignant mesothelioma 8

type: genomic

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

hyb_protocol: The labeled DNA was hybridized with Agilent SurePrint G3 Rat CGH 4x180k microarray at 65°C for 24 hours according to the manufacturer's protocol (Version 7.1).

scan_protocol: The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).

organism: Rattus norvegicus

source_name: F1 hybrid rat non-neoplastic kidney

label_protocol: The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 7.1).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

treatment_protocol: F1 hybrid rats were injected with tremolite (5 mg) twice at 6th and 7th weeks. From 10th to 21st weeks, rats were treated with either saline or nitrilotriacetate (80 mg/kg body weight) once a week for 12 weeks. The rats were euthanized when they show the signs of MM developments.

value: non-neoplastic kidney

value: F1 hybrid (Brown-Norway X Fischer344)

tag: Sex

value: male

value: Malignant mesothelioma

value: Tremolite 10 mg


title: RA-FLS_TNF_8_hr [MY011]


title: CC379_eCCA


title: RA-FLS_HF_24_hr [MY010]

value: HF


title: CC412_BD


title: CC373_eCCA


title: Malignant mesothelioma 7


title: Malignant mesothelioma 6


title: Malignant mesothelioma 5


title: CC369_eCCA


title: CC367_eCCA


title: RA-FLS_HF_8hr [MY009]


title: CC393_eCCA


title: CC365_eCCA


title: RA-FLS_untreated [MY008]

value: untreated


title: Malignant mesothelioma 4

value: female


title: CC363_eCCA


title: CC361_eCCA


title: CC371_eCCA


title: RA-FLS_TNF_24_hr [MY006]


title: Malignant mesothelioma 2


title: Malignant mesothelioma 3


title: Flag_Input_1

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1: AGATCGGAAGAGC; end2: AGATCGGAAGAGC) trimmed with fastx_clipper
Reads were mapped using tophat2 -N 4. Uniq mapped reads were remained.
To assess m6A level of each genes, reads only unambiguously aligned were preserved to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million). Furthermore, the m6A regions (statistically significant m6A peaks) were identified by comparing the read abundance between m6A and input samples using MACS (version 1.4.1). The command line don’t require shifting of the enriched reads, since RIP- Seq libraries come from single-stranded RNA, whereas the bimodal property observed in ChIP-seq for double-stranded DNA. The following parameters were used: -nomodel -shiftsize=1. The remaining parameters were set to system defaults.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each sample

source_name: Hela cells

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (FBS) (Hyclone) and 1% penicillin/streptomycin (Hyclone) at 37℃ in a humidified incubator with 5% CO2.

extract_protocol: mRNAs were extracted using GenElute™ mRNA Miniprep Kit ( sigma, MRN10) and were fragmented into 100nt length by using RNA Fragmentation buffer (0.1M Tris-HCL PH 7.0, 0.1M ZnCl2). 7ug Fragmented mRNAs were incubated for 2h at 4°C with 12.5ug of anti-m6A antibody (source: sysy, cat# 202003, lot# 1362523) in IP buffer (0.05M Tris-HCL pH 7.4, 0.375M NaCl, 0.5% Igepal CA-630). The mixture was then subjected to immunoprecipitation by incubation with Pierce™ ChIP-grade Protein A/G Magnetic Beads (Thermo, 26162) at 4°C for 2h. After sufficient washing, bound RNA was eluted from the beads with Elution buffer (1×IP buffer, 7mM m6A, RNase inhibitor), and ethanol precipitated. The eluted RNA was resuspended in H2O and used to generate the cDNA library according to RNA-Seq Library Preparation Kit for Transcriptome Discovery–Illumina Compatible, which was then sequenced using the HiSeq 2000 system (Illumina) according to the manufacturer’s instructions.

value: HeLa

value: Hela cells transfected with only pCMV-Tag.2B-flag vector not containing FTO gene wide type Hela cells, control


title: FTO_Input_1

value: Hela cells transfected with pCMV-Tag.2B-flag vector containing FTO gene wide type Hela cells, FTO overexpression


title: Flag_meRIP_1


title: FTO_meRIP_1


title: RA-FLS_TNF_HF_24_hr [MY007]


title: RA-FLS_TNF_8_hr [MY004]


title: Flag

data_processing:
Library strategy: CLIP-seq
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACT) trimmed with fastx_clipper
Reads were mapped using tophat2 -N 2. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
Reads with overlap region on the locus of genome were clustered. The read number (N), read length and observed max depth were then counted for each cluster. For each gene, a same number of reads with coincident lengths were generated using computational simulation. The outputting reads were further randomly placed to same genes to generate max peak height from overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (p value ＜ 0.01) were selected, while the FTO peaks that have an overlap with control peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files include FTO binding peaks for each sample

extract_protocol: Dissociated cells are UV crosslinked on ice for 400 mJ/cm2, leading to formation of a covalent bond between protein and RNA. After lysis, the ligated RNA product was treated with RQ I to prevent DNA contamination and partially digested with MNase. Protein–RNA complex is puriﬁed by immunoprecipitation by incubating with DynaBeads protein G conjugated with anti-FTO antibody (source: MBL, cat# RN121PW, lot# 1254635), IgG (source: Millipore, cat# 12-370, lot# 3256125 ) or anti-Flag antibody (sigma, cat# F7425, lot# 2323211) at 4 °C for 2 hours. RNA is dephosphorylated at 3’ end and phosphorylated at 5’ end. The protein–RNA complex is separated by 4-12% NuPAGE Bis-Tris gel and the region of the membrane 30 kDa above the protein size is excised. Protein is digested by proteinase K and isolated RNA was used to prepare sequencing library using Balancer sm/miRNA Library Preparation Kit according to the manufacturer’s instructions. The Kit provides one-day single tube procedure that starts with total RNA, goes through adapter ligation, RT, PCR and gel purification, then generates a library ready for Illumina machines. The cDNA libraries were subsequently quantified and sequenced on the Illumina Nextseq platform. Image processing and base-calling were performed by Illumina Pipeline.


title: CC357_eCCA


title: CC355_eCCA


title: CC351_eCCA


title: CC347_eCCA


title: CC349_eCCA


title: RA-FLS_HF_24_hr [MY003]


title: CC359_eCCA


title: CC341_eCCA


title: Malignant mesothelioma 1


title: RA-FLS_untreated [MY001]


title: RA-FLS_TNF_HF_8_hr [MY005]


title: FTO_Flag

value: Hela cells transfected with pCMV-Tag.2B-flag vector containing FTO gene wide type Hela cells, FTO overexprssion


title: rep2_FTO

value: wild type Hela cells


title: rep2_IgG


title: RA-FLS_HF_8hr [MY002]

value: rheumatoid arthritis fibroblast like synoviocytes (RA-FLS)


title: CC339_eCCA

value: extrahepatic cholangiocarcinoma


title: CC345_eCCA


title: GCN2 KD TNF HFol [Mm024]

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.17) for converting BCL to fastq format coupled with adapter trimming
Map the reads to a reference genomeusing STAR(2.5.2b) and featureCounts(v1.5.0-p3)
Test for differentially expressed genes under various conditions using DEseq.
Genome_build: Human: NCBI/build37.2
Supplementary_files_format_and_content: rawcounts.tsv - un-normalized counts from feature counts, genes (by HGNC symbol) in rows, samples in columns

source_name: GCN2 KD TNF HFol

extract_protocol:
Trizol  extraction, followed by preparation according to Truseq instructions
Poly A enriched TruSeq mRNA library Prep  kit

treatment_protocol: Treated +/- 250 nM HFol (24 hours prior to harvest) +/- 10 ng/ml TNF (8 hours prior to harvest)

value: K4 fibroblast like synoviocytes (FLS)

value: GCN2 knockdown


title: CC335_eCCA

value: Mayo


title: CC323_eCCA


title: CC333_eCCA


title: rep1_IgG


title: GCN2 KD TNF HFol [Mm023]


title: CC317_eCCA


title: rep1_FTO


title: CC337_eCCA


title: CC311_eCCA


title: CC299_eCCA


title: GCN2 KD TNF [Mm022]

source_name: GCN2 KD TNF

value: TNF


title: ATAC-seq from mouse ESC with stably integrated Zprom::GFP reporter, sorted for presence of GFP

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
Basecalls performed using CASAVA.
Reads were aligned with bowtie 2.2.4 using default settings.
Genome coverage was calculated with genomeCoverageBed -bg -scale, with scaling factor 10^-6*total aligned reads.
Genome coverage file was converted to bigwig with bedGraphToBigWig (Kent tools).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bw: BigWig of normalized ChIP read density: reads per base per million.

source_name: E14 mouse ESC with stably integrated Zscan4c promoter reporter driving expression of GFP

growth_protocol: E14Tg2a (E14) male mouse ESC were maintained as previously described (Buecker et al., 2014) on 7.5μg/ml poly-l-ornithine (Sigma) and 5μg/ml laminine (Life Technologies) coated tissue culture dishes, in a serum-free N2B27-based DMEM/F12 medium supplemented with 5mg/ml BSA Albumax II, sodium pyruvate, L-glutamine, N2 Neuroplex, B27 without retinoic acid, non-essential amino acids, Beta-mercaptoethanol, penicillin/streptomycin, 0.8μM MEK inhibitor (PD0325901, Selleck Chemicals) and 3.3μM GSK3β inhibitor (CHIR99021, Selleck Chemicals).

extract_protocol:
50,000 nuclei were lysed and transposed with the Nextera DNA library preparation kit.
Libraries were generated using the Nextera DNA Library Preparation Kit (Illumina).

treatment_protocol: GFP positive 2C-like cells were collected by FACS.

value: Embryonic stem cells (ESC)

value: Stably integrated Zscan4c promoter reporter driving expression of GFP

tag: cell population

value: GFP positive (2C-like cells)


title: GCN2 KD Hfol [Mm020]

source_name: GCN2 KD Hfol

value: Hfol


title: GCN2 KD TNF [Mm021]


title: CC285_eCCA

tag: tissue

value: MS


title: CC301_eCCA


title: CC277_eCCA


title: CC271_eCCA


title: CC275_eCCA


title: CC266_BD

value: non-tumor bile duct


title: CC265_eCCA


title: GCN2 KD untreated [Mm018]

source_name: GCN2 KD untreated

value: untreated


title: GCN2 KD untreated [Mm017]


title: RNAseq from sorted GFP-pos subpopulation of ESC with Zscan4c promoter reporter driving expression of GFP-Zscan4c fusion

description:
RNAseq_Zscan_PlusGFP
Poly-A enriched mRNA

data_processing:
Basecalls performed using CASAVA.
Reads were aligned with hisat2 2.1.0 using default settings.
TPMs were obtained with StringTie 1.3.5 using GRCm38.84 gene models.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *csv: Comma-separated text files include TPM (transcripts per million).

source_name: E14 mouse ESC with stably integrated Zscan4c promoter reporter driving expression of GFP-Zscan4c fusion

growth_protocol: E14Tg2a male mouse ESC were maintained as previously described (Buecker et al., 2014) on 7.5μg/ml poly-l-ornithine (Sigma) and 5μg/ml laminine (Life Technologies) coated tissue culture dishes, in a serum-free N2B27-based DMEM/F12 medium supplemented with 5mg/ml BSA Albumax II, sodium pyruvate, L-glutamine, N2 Neuroplex, B27 without retinoic acid, non-essential amino acids, Beta-mercaptoethanol, penicillin/streptomycin, 0.8μM MEK inhibitor (PD0325901, Selleck Chemicals) and 3.3μM GSK3β inhibitor (CHIR99021, Selleck Chemicals).

extract_protocol:
Total RNA was extracted with TRIZOL and mRNA was purified using Oligo-dT Dynabeads mRNA purification kit (Invitrogen). mRNA was fragmented using 10X Fragmentation reagent (Thermo Fisher Scientific) and subjected to first strand synthesis with random hexamers and Superscript II (Invitrogen), and second strand synthesis with RNaseH (Invitrogen) and E. coli DNA polymerase I (NEB).
Sequencing libraries were prepared starting from ~30ng polyA enriched cDNA with NEBNext Multiplex Oligos for Illumina kit.

treatment_protocol: GFP positive 2C-like cells and GFP negative pluripotent cells were collected by FACS from each reporter line.

value: Stably integrated Zscan4c promoter reporter driving expression of GFP-Zscan4c fusion


title: CC262_BD


title: CC267_eCCA


title: CC263_eCCA


title: Input control in 2C-like (GFP+) cells from Zprom::GFP-Zscan4 mouse ESC reporter line

description:
GFP-Zscan_Input
We profiled direct targets of Zscan4 in 2C-like cells by performing ChIP-seq using a GFP antibody in 2C-like cells (GFP positive population) from the Zprom::GFP-Zscan4 reporter line, and from the Zprom::GFP line as control.
Genome-wide binding analysis showed that Zscan4 specifically recognizes a subset of (CA)n microsatellite repeat sequences in 2C-like cells.

source_name: E14 mouse ESC with Zscan4c promoter reporter driving expression of GFP-Zscan4c fusion

extract_protocol:
Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody. After reverse-crosslinking, input and ChIP DNA were purified by phenol:chloroform extraction.
Sequencing libraries were prepared starting from ~30ng of input or ChIP DNA with NEBNext Multiplex Oligos for Illumina kit.

treatment_protocol: Cells were detached and crosslinked in media containing 1% formaldehyde for 10 minutes and then quenched with 0.125M glycine for 5 minutes. Crosslinked cells were collected by centrifugation, washed with PBS, strained through a 35µm cell strainer and subjected to two rounds of FACS sorting to enrich for GFP positive or negative cells as required. Cells were lysed and sonicated with a bioruptor sonicator (Diagenode).

value: GFP+ (2C-like cells)

tag: chip antibody


title: GFP ChIP in 2C-like (GFP+) cells from Zprom::GFP mouse ESC reporter line

description:
GFP_GFP_ChIP
We profiled direct targets of Zscan4 in 2C-like cells by performing ChIP-seq using a GFP antibody in 2C-like cells (GFP positive population) from the Zprom::GFP-Zscan4 reporter line, and from the Zprom::GFP line as control.
Genome-wide binding analysis showed that Zscan4 specifically recognizes a subset of (CA)n microsatellite repeat sequences in 2C-like cells.

source_name: E14 mouse ESC with Zscan4c promoter reporter driving expression of GFP

value: GFP (ab290, Abcam)


title: CC264_BD


title: CC416_BD

value: Clinic


title: CC261_eCCA


title: CC260_BD


title: RNAseq from sorted GFP-neg subpopulation of ESC with Zscan4c promoter reporter driving expression of GFP-Zscan4c fusion

description:
RNAseq_Zscan_NoGFP
Poly-A enriched mRNA

value: GFP negative (pluripotent cells)


title: CC259_eCCA

value: extrahepatic cholangiocarcinoma


title: RNAseq from sorted GFP-pos subpopulation of ESC with Zscan4c promoter reporter driving expression of GFP

description:
RNAseq_Con_PlusGFP
Poly-A enriched mRNA


title: CC257_eCCA


title: CC258_BD


title: CC255_eCCA


title: CC256_BD


title: wt tnf [Mm006]

source_name: wt tnf

value: K4 fibroblast like synoviocytes (FLS)

value: wildtype


title: wt tnf hfol [Mm007]

source_name: wt tnf hfol


title: wt tnf hfol [Mm008]


title: wt tnf [Mm005]


title: wt Hfol [Mm004]

source_name: wt Hfol


title: CC251_eCCA

source_name: extrahepatic cholangiocarcinoma


title: CC247_eCCA


title: CC252_BD

source_name: non-tumor bile duct


title: wt Hfol [Mm003]


title: CC248_BD


title: RNA-seq_ApcKO-2

city: Montpellier

first: Philippe

last: Jay

address: 141 rue de la Cardonille

country: France

institute: CNRS-Inserm-University

data_processing:
Sequenced reads were trimmed,  masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome reference genome or reference transcriptome using Bowtie generating genome / transcriptome alignments. TopHat identifies the potential exon-exon splice junctions of the initial alignment.
Cufflinks identified and quantified the transcripts from the preprocessed RNA-Seq alignment- assembly. After this, Cuffmerge merged the identified transcript pieces to full length transcripts and annotated the transcripts based on the given annotations.
Operating on the RNA-Seq alignments and Cufflinks processing, Cuffdiff tracked the mapped reads and determined the fragment per kilobase per million mapped reads (FPKM) for each transcript in all the samples. Primary transcripts and gene FPKMs were then computed by adding up the FPKMs of each primary transcript group or gene group, to determine the differential expression levels at transcript and gene level including a measure of significance between samples / conditions
Genome_build: mm10 / GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Lgr5+-GFP+ cells

extract_protocol:
Lgr5-GFP+ cells were FACS-sorted in RLT+ buffer for further gDNA/RNA extraction performed with Allprep mini Kit (Qiagen) at day 15.
Random primed cDNA library

treatment_protocol: Mice injected once with tamoxifen followed by 5 consecutive days of tamoxifen-containing diet.

value: intestinal epithelium

value: Lgr5+-GFP+ intestinal stem cells

value: ApcFlox/Flox ; Lgr5-CreERT2-ires-eGFP


title: RNA-seq_ApcKO-4


title: RNA-seq_ApcKO-3


title: wt untreated [Mm002]

source_name: wt untreated


title: wt untreated [Mm001]


title: RNA-seq_ApcKO-1


title: RNA-seq_ApcHET-4

value: ApcFlox/+ ; Lgr5-CreERT2-ires-eGFP


title: RNA-seq_ApcHET-3


title: CC242_BD


title: RNA-seq_ApcHET-2


title: 24hrA_H3K9me1ChIPSeq

city: Madison

first: Spencer

last: Haws

state: WI

address: 330 N. Orchard St.

institute: University of Wisconsin-Madison

data_processing:
ChIP-Seq reads were aligned using bowtie2-2.1.0 with the following settings: -q -S -a -p 1 -x hg19.
SAM files were converted to BAM files, sorted and indexed using samtools 1.5.
Broad peaks were called using MACS2-2.1.1.20160309 with the following settings: --broad -g hs -p 0.0001.
Genome_build: hg19
Supplementary_files_format_and_content: H3K9me1 and H3K9me3 called peak excel files containing peak calling parameters, chromosome number, peak starting and ending base pair, length, pileup, -log10 p-value, and -log10 q-value.

source_name: HCT116 cells

growth_protocol: HCT116 cells grown in RPMI-1640 (Gibco) +10% FBS (Gibco).

extract_protocol:
Lysates were clarified from sonicated whole-cells and histone-DNA complexes were isolated with either a H3K9me1 or H3K9me3 antibody.
Libraries were prepared by the University of Wisconsin-Madison Biotechnology Center using an Illumina TruSeq DNA Nano kit.

treatment_protocol: Cellls were washed 2x with PBS pH 7.4 and cultured in methionine free RPMI-1640 (Gibco) + 10% FBS (Gibco) for 24 hours.

value: HCT116 cells

value: colorectal carcinoma

tag: passages

value: H3K9me1 (Abcam, Rb mAb Cat#176880


title: 0hrB_H3K9me1_ChIPSeq


title: 24hrB_H3K9me1_ChIPSeq


title: RNA-seq_ApcHET-1


title: CC245_eCCA

value: MS


title: CC239_eCCA


title: CC230_BD

value: non-tumor bile duct


title: CC241_eCCA


title: CC233_eCCA


title: CC240_BD


title: RNA-seq_ApcWT-4

value: Apc+/+ ; Lgr5-CreERT2-ires-eGFP


title: CC237_eCCA


title: CC246_BD


title: CC227_eCCA


title: CC223_eCCA


title: CC221_eCCA


title: CC234_BD


title: CC217_eCCA


title: CC225_eCCA


title: CC219_eCCA


title: CC229_eCCA


title: CC213_eCCA


title: CC215_eCCA


title: RNA-seq_ApcWT-3


title: 24hrB_H3K9me3_ChIPSeq

data_processing:
ChIP-Seq reads were aligned using bowtie2-2.1.0 with the following settings: -q -S -a -p 1 -x hg19.
SAM files were converted to BAM files, sorted and indexed using samtools 1.5.
Broad peaks were called using default settings of MACS2-2.1.1.20160309.
Genome_build: hg29
Supplementary_files_format_and_content: peak files containing peak calling parameters, chromosome number, peak starting and ending base pair, length, pileup, -log10 p-value, and -log10 q-value.

extract_protocol:
Lysates were clarified from sonicated whole-cells and histone-DNA complexes were isolated with H3K9me3 antibody.
Libraries were prepared by the University of Wisconsin-Madison Biotechnology Center using an Illumina TruSeq DNA Nano kit.

value: 24hr after methionine/SAM depletion

value: H3K9me3 (Abcam, Rb mAb Cat#8898)


title: 24hrB_input DNA


title: RNA-seq_ApcWT-1


title: 0hrA_H3K9me1_ChIPSeq


title: CC203_eCCA


title: CC207_eCCA


title: 24hrA_H3K9me3_ChIPSeq


title: 24hrA_input DNA


title: Flag_Input_2

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1: AGATCGGAAGAGC; end2: AGATCGGAAGAGC) trimmed with fastx_clipper
Reads were mapped using tophat2 -N 4. Uniq mapped reads were remained.
To assess m6A level of each genes, reads only unambiguously aligned were preserved to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million). To identify the m6A regions (statistically significant m6A peaks), we called m6A peaks from MeRIP-seq data by running ABLIRC pipeline. Briefly, reads after removing PCR duplicates were clustered for at least 1bp overlap, and the max depth for each cluster was determined. For each gene, we calculate the P value by randomly scattering the same number of faux reads as real reads across a faux transcript that was the same effective length as the real transcript for 500 iterations. All the observed peaks with heights higher than those of random max peaks (P value ＜ 0.01) were selected, while the m6A IP peaks that had an overlap with input control peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include m6a peak information for each sample

source_name: HeLa cells

extract_protocol:
mRNAs were extracted using GenElute™ mRNA Miniprep Kit (source: sigma, cat# MRN10) and were fragmented into 100nt length by using RNA Fragmentation buffer (0.1M Tris-HCL PH 7.0, 0.1M ZnCl2).
7ug Fragmented mRNAs were incubated for 2h at 4°C with 12.5ug of anti-m6A antibody (sysy, 202003) in IP buffer (0.05M Tris-HCL pH 7.4, 0.375M NaCl, 0.5% Igepal CA-630). The mixture was then subjected to immunoprecipitation by incubation with Pierce™ ChIP-grade Protein A/G Magnetic Beads (Thermo, 26162) at 4°C for 2h. After sufficient washing, bound RNA was eluted from the beads with Elution buffer (1×IP buffer, 7mM m6A, RNase inhibitor), and ethanol precipitated. The eluted RNA was resuspended in H2O and used to generate the cDNA library according to RNA-Seq Library Preparation Kit for Transcriptome Discovery–Illumina Compatible, which was then sequenced using the HiSeq 2000 system (Illumina) according to the manufacturer’s instructions.

value: HeLa

value: Hela cells transfected with only pCMV-Tag.2B-flag vector not containing FTO gene, control


title: 0hrB_H3K9me3_ChIPSeq

value: control


title: RNA-seq_ApcWT-2


title: FTO_Input_2

value: Hela cells transfected with pCMV-Tag.2B-flag vector containing FTO gene, FTO overexprssion


title: 0hrB_input DNA


title: Flag_meRIP_2


title: 0hrA_H3K9me3_ChIPSeq


title: 0hrA_input DNA


title: CC211_eCCA

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

value: extrahepatic cholangiocarcinoma


title: RGCs, Myh9/10 dKO 3

city: Tampa

first: Xuewei

last: Wang

address: 4001 E Fletcher Ave, ALZ 339

department: Molecular Medicine

institute: University of South Florida

description: Myh9/10 double knockout

data_processing:
Sequenced reads were mapped to mouse genome GRCm38 using STAR aligner (v2.7.0d) with parameters  -runThreadN 6 -outSAMtype BAM SortedByCoordinate -outSAMattributes Standard -quantMode GeneCounts
Low expression genes with less than 50 counts in total from all samples were excluded
DESeq2 (v1.22.2) was used to obtain differentially expressed genes with the threhold (adjusted p value < 0.05, log2 fold change >1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited txt file containing gene counts for all samples

source_name: Retinal ganglion cells

extract_protocol:
Total RNA of FACS-purified RGCs was isolated using the PicoPure RNA isolation kit (Thermo Fisher Scientific) following the manufacturer’s manual.
RNA libraries were prepared using the TruSeq stranded total RNA kit (Illumina) following the manufacturer’s recommended procedure.

treatment_protocol: Myh9/10 double-floxed mice were intravitreally injected with AAV2-GFP or AAV2-Cre 2 weeks before sacrifice. Each replicate in each condition had 3 retinas from 3 different mice.

value: Retina

value: Retinal ganglion cells (RGCs)

value: Myh9/10 double-floxed


title: CC201_eCCA

data_processing: The data were analyzed with GenePattern (Broad Institute) using Expression file creator module and the RMA algorithm.


title: CC205_eCCA


title: Malignant mesothelioma 19

hyb_protocol: The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 65°C for 24 hours according to the manufacturer's protocol (Version 7.1).

source_name: C57BL/6 non-neoplastic kidney

treatment_protocol: The mice received intraperitoneal injection of crocidolite 1.5 mg twice at 6 and 7-week-old. After injection of crocidolite 3 mg, the mice were observed for 600-700 days. When mice show the signs of MM development, mice were euthanized and examined macroscopically and microscopically.

value: Crocidolite


title: Malignant mesothelioma 20


title: Malignant mesothelioma 15


title: FTO_meRIP_2


title: CC197_eCCA


title: RGCs, Myh9/10 dKO 2

description: Myh9/10 double knockout


title: RGCs, Myh9/10 dKO 1

description: Myh9/10 double knockout


title: CC195_eCCA


title: nonOIR replicate 7

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Quality control with FastQC, Galaxy Version 0.72
Reads were mapped to mm10 with RNA STAR Galaxy Version 2.6.0b-1 (Gene annotation file: Gencode M20, gencodegenes.org)
Reads were counted using featureCounts Galaxy Version 1.6.2 (Gene annotation file: Gencode M20, gencodegenes.org)
Differential gene expression was analyzed using DESeq2 Galaxy Version 2.11.40.2
Genome_build: mm10
Supplementary_files_format_and_content: data.csv, comma seperated values, ENSEMBL ID, Symbol, Description, statistical parameters, normalized counts (DESeq2), raw counts (feature counts)

extract_protocol:
Total RNA was extracted from cells stabilized in RNAprotect buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting, the RNAprotect buffer was replaced by RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 750 pg total-RNA. Double stranded cDNA was amplified by LD PCR (12 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on an HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in .bcl files, which were converted into .fastq.gz files with the bcl2fastq v2.18 software. RNA extraction, library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de).

treatment_protocol: To induce nuclear CreER recombinase activity, young Cx3cr1CreERT2:Rosa26-tdTomato mice were given a subcutaneous injection of 5 µl of 21 mg/ml tamoxifen dissolved in corn oil (C8267, Sigma-Aldrich) at postnatal day (p) 1.

value: Post natal day 17

tag: oir/nonoir

value: nonOIR


title: CC193_eCCA


title: nonOIR replicate 6

tag: cell type


title: Malignant mesothelioma 18


title: nonOIR replicate 8

tag: strain


title: Malignant mesothelioma 14

tag: genotype

value: MutyhKO


title: CC199_eCCA

value: MS


title: CC191_eCCA


title: CC190_BD

value: non-tumor bile duct


title: RGCs, WT3

description: wild type


title: GFP ChIP in 2C-like (GFP+) cells from Zprom::GFP-Zscan4 mouse ESC reporter line

description:
GFP-Zscan_GFP_ChIP
We profiled direct targets of Zscan4 in 2C-like cells by performing ChIP-seq using a GFP antibody in 2C-like cells (GFP positive population) from the Zprom::GFP-Zscan4 reporter line, and from the Zprom::GFP line as control.
Genome-wide binding analysis showed that Zscan4 specifically recognizes a subset of (CA)n microsatellite repeat sequences in 2C-like cells.

value: Embryonic stem cells (ESC)

value: Zscan4c promoter reporter driving expression of GFP-Zscan4c fusion

value: GFP+ (2C-like cells)

value: GFP (ab290, Abcam)


title: CC189_eCCA


title: Malignant mesothelioma 17


title: Malignant mesothelioma 16


title: CC187_eCCA


title: GCN2 KD Hfol [Mm019]

value: K4 fibroblast like synoviocytes (FLS)

value: GCN2 knockdown

value: Hfol


title: nonOIR replicate 5


title: RGCs, WT2

description: wild type


title: Malignant mesothelioma 13


title: Malignant mesothelioma 12


title: nonOIR replicate 3


title: nonOIR replicate 4


title: Zscan4 ChIP in 2C-like (GFP+) cells from Zprom::GFP mouse ESC reporter line

description:
PlusGFP_Zscan4_ChIP
We profiled genomic occupancy of endogenous Zscan4 in 2C-like cells by performing ChIP-seq using a Zscan4 antibody in the GFP positive population (and control GFP negative population) isolated from the Zprom::GFP line.
Genome-wide binding analysis showed that Zscan4 specifically recognizes a subset of (CA)n microsatellite repeat sequences in 2C-like cells.

treatment_protocol: Cells were detached and crosslinked in media containing 1% formaldehyde for 10 minutes and then quenched with 0.125M glycine for 5 minutes. Crosslinked cells were collected by centrifugation, washed with PBS, strained through a 35µm cell strainer and subjected to two rounds of FACS sorting to enrich for GFP positive or negative cells as required. Cells were lysed and sonicated with a Covaris sonicator.

value: Zscan4c promoter reporter driving expression of GFP

value: Zscan4 (AB4340, Millipore)


title: CC181_eCCA

value: extrahepatic cholangiocarcinoma


title: Input control (Zscan4 ChIP) in 2C-like (GFP+) cells from Zprom::GFP mouse ESC reporter line

description:
PlusGFP_input
We profiled genomic occupancy of endogenous Zscan4 in 2C-like cells by performing ChIP-seq using a Zscan4 antibody in the GFP positive population (and control GFP negative population) isolated from the Zprom::GFP line.
Genome-wide binding analysis showed that Zscan4 specifically recognizes a subset of (CA)n microsatellite repeat sequences in 2C-like cells.


title: nonOIR replicate 1


title: nonOIR replicate 2


title: Input control (GFP ChIP) in 2C-like (GFP+) cells from Zprom::GFP mouse ESC reporter line

description:
GFP_Input
We profiled direct targets of Zscan4 in 2C-like cells by performing ChIP-seq using a GFP antibody in 2C-like cells (GFP positive population) from the Zprom::GFP-Zscan4 reporter line, and from the Zprom::GFP line as control.
Genome-wide binding analysis showed that Zscan4 specifically recognizes a subset of (CA)n microsatellite repeat sequences in 2C-like cells.


title: OIR replicate 8

value: OIR


title: Zscan4 ChIP in pluripotent (GFP-) cells from Zprom::GFP mouse ESC reporter line

description:
NoGFP_Zscan4_ChIP
We profiled genomic occupancy of endogenous Zscan4 in 2C-like cells by performing ChIP-seq using a Zscan4 antibody in the GFP positive population (and control GFP negative population) isolated from the Zprom::GFP line.
Genome-wide binding analysis showed that Zscan4 specifically recognizes a subset of (CA)n microsatellite repeat sequences in 2C-like cells.

value: GFP- (pluripotent cells)


title: RGCs, WT1

description: wild type

value: Retina

value: Retinal ganglion cells (RGCs)

value: Myh9/10 double-floxed


title: CC177_eCCA

value: MS


title: CC173_eCCA


title: CC169_eCCA


title: Input control in pluripotent (GFP-) cells from Zprom::GFP mouse ESC reporter line

description:
noGFP_input
We profiled genomic occupancy of endogenous Zscan4 in 2C-like cells by performing ChIP-seq using a Zscan4 antibody in the GFP positive population (and control GFP negative population) isolated from the Zprom::GFP line.
Genome-wide binding analysis showed that Zscan4 specifically recognizes a subset of (CA)n microsatellite repeat sequences in 2C-like cells.


title: OIR replicate 7

value: Post natal day 17


title: Malignant mesothelioma 10

value: Wild type

source_name: Wile type-2

value: Crocidolite


title: Malignant mesothelioma 7


title: SSRP1 ChIP in DMSO treated mouse ESC replicate 2

description:
E14_DMSO_SSRP1_rep1
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.

source_name: E14 mouse ESC

treatment_protocol: Cells were treated with DMSO or curaxin (CBL0137, Cayman Chemical) for 1 hour and immediately crosslinked in 1% formaldehyde for 10 minutes followed by quenching with 0.125M glycine for 5 minutes. Cells were lysed and sonicated with a bioruptor sonicator (Diagenode).

value: Embryonic stem cells (ESC)

value: DMSO

value: SSRP1 (609702,10D1, Biolegend)


title: CC167_eCCA


title: CC171_eCCA


title: OIR replicate 6


title: SSRP1 ChIP in DMSO treated mouse ESC replicate 1

description:
E14_DMSO_SRP1_rep2
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.


title: CC165_eCCA


title: Malignant mesothelioma 11

source_name: Wile type-3


title: Input control in DMSO treated mouse ESC replicate 2

description:
E14_DMSO_Input_rep2
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.


title: Malignant mesothelioma 8


title: Malignant mesothelioma 9

source_name: Wild type-1


title: OIR replicate 5


title: Input control in DMSO treated mouse ESC replicate 1

description:
E14_DMSO_Input_rep1
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.


title: OIR replicate 3


title: ardC-

city: Santander

first: Gabriel

last: Moncalian

address: Albert Einstein 22

department: Molecular Biology

institute: University of Cantabria

data_processing:
Raw reads in FASTQ format were quality analyzed with FastQC.
The alignment of reads against R388 (NCBI Accession number NC_028464.1), E. coli str. K-12 substr. MG1655 (U00096.3) and P. putida KT2440 (AE015451.2) sequences was done with Bowtie2 software.
Artemis program was used to visualize the alignment and do the RPKM (reads per kilobase and million mapped reads) calculations.
Genome_build: R388 (NCBI Accession number NC_028464.1), E. coli str. K-12 substr. MG1655 (U00096.3) and P. putida KT2440 (AE015451.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism:
Escherichia coli
Pseudomonas putida KT2440

source_name: P. putida KT2440  and E. coli BW27783-NxR (pLGM25 ardc-)

growth_protocol: Conjugation assays were performed by mixing E. coli BW27783-NxR (bearing pSU2007, pLGM25 or no plasmid) with P. putida KT2440 recipient cells. E. coli cells were grown overnight at 37C and P. putida at 30C.  Cells at OD600=0.6 were mixed in a 5: 1 donor: recipient ratio, washed on LB medium, resuspended in 30 µL of LB and deposited on a 0.22 μm pore size cellulose acetate filters (Sartorius Stedim) in LB-agar plates previously incubated at 37ºC.

extract_protocol:
Cells were lysed with lysozyme (Sigma) and proteinase K (Roche). Total RNA was extracted with RNeasy® Mini Kit (Qiagen) and treated with RNase-free DNase (Qiagen) in column for DNA removal. Ambion® TURBO DNA-free™ DNase Treatment was also applied for a better DNA removal. RNA integrity and quality were validated by the Agilent RNA ScreenTape assay. The RNA integrity number equivalent (RINe) was assured to be above 8 to use the isolated RNA in the RNA-seq experiment.
Transcriptome libraries were prepared by Macrogen (Seoul, Korea) with Ribo-Zero rRNA Removal Kit and TruSeq® Stranded mRNA sample preparation kit (Illumina). Libraries were sequenced by Macrogen on the Illumina HiSeq 4000 platform. The transcriptome libraries were paired-end sequenced with 100-bp reads.

treatment_protocol: After 30 min. harvested cells from the conjugation filter were treated with RNAprotect® Bacteria Reagent (Qiagen) and snap-frozen.

tag: e. coli strain

value: E. coli BW27783-NxR bearing pLGM25 (ardC-)

tag: plasmid


title: ardC+

source_name: P. putida KT2440  and E. coli BW27783-NxR (pSU2007 ardc+)

value: E. coli BW27783-NxR bearing pSU2007 (ardC+)

value: R388 derivative; KnR cassette insertion


title: OIR replicate 4

tag: age


title: SSRP1 ChIP in 2.5μM curaxin treated mouse ESC replicate 1

description:
E14_2_5uM_SSRP1_rep1
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.

value: 2.5uM Curaxin


title: OIR replicate 1


title: SSRP1 ChIP in 2.5μM curaxin treated mouse ESC replicate 2

description:
E14_2_5uM_SSRP1_rep2
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.


title: NP

source_name: P. putida KT2440  and E. coli BW27783-NxR

value: E. coli BW27783-NxR bearing no plasmid (NP),

value: no plasmid


title: OIR replicate 2

value: OIR


title: Input control in 2.5μM curaxin treated mouse ESC replicate 2

description:
E14_2_5uM_Input_rep2
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.


title: RRBS_APCLgr5-KO4

data_processing:
Sequenced reads were trimmed using Trim Galore v0.4.2 (parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired).
Reads were aligned to the mouse mm10 genome using BSMAP v2.74 (parameters -v 2 -w 100 -r 1 -x 400 -m 30 -n 1 -D C-CGG).
We extracted methylation percent values as the ratio of the number of Cs over the total number of Cs and Ts with methratio.py from BSMAP v2.74 (parameters -z -u -g).
We then filtered CGs to have a minimum sequencing depth of 8x using custom developped scripts in R v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: IGV files containing methylation scores for all CGs with at least 8x sequencing depth.

extract_protocol:
Lgr5-GFP+ cells were FACS-sorted in RLT+ buffer for further gDNA/RNA extraction performed with Allprep mini Kit (Qiagen) at day 15.
RRBS libraries were prepared as previously described (Auclair G. et al, Genome Biol. 15, 545, 2014). Briefly, we digested 100 ng of genomic DNA 5 hours with MspI (Thermo Scientific), followed by end-repair and A-tailing (Klenow fragment, Thermo Scientific) and ligation to methylated adapters (T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14 cycles of PCR.

value: intestinal epithelium

value: Lgr5+-GFP+ intestinal stem cells

value: ApcFlox/Flox ; Lgr5-CreERT2-ires-eGFP


title: Input control in 2.5μM curaxin treated mouse ESC replicate 1

description:
E14_2_5uM_Input_rep1
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.


title: RRBS_APCLgr5-KO3


title: CC163_eCCA

treatment_protocol: Not applicable. Archived tissue was obtained at our Insitution upon patient's consent

value: extrahepatic cholangiocarcinoma

tag: center

value: MS


title: tasA1_48h

city: Malaga

first: Jesus

last: Camara-Almiron

address: Calle Severo Ochoa, 34

institute: University of Malaga

description: Bacillus subtilis NCIB3610

data_processing:
Raw reads were pre-processed with SeqTrimNext, using the specific NGS technology configuration parameters.
Clean reads were aligned and annotated using the Bacillus subtilis subsp. subtilis str. 168 genome (NC_000964.3) as a reference with Bowtie2.
Uniquely localized reads were used to calculate the read number value for each gene by using Sam2counts.
Differentially expressed genes (DEGs) between WT and ΔtasA were analyzed using DEgenes Hunter that provides a combined P-value from edgeR and DEseq2 that allowed differentially expressed genes ranking.
Genome_build: ASM904v1
Supplementary_files_format_and_content: Tab-delimited text files include the raw counts per gene for each sample.
Supplementary_files_format_and_content: Excel files include Log2FC of the comparison of WT strain and TasA mutant strain, with combined p-values.

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: B. subtilis tasA mutant

extract_protocol:
Single colonies of B. subtilis NCIB 3610 WT and tasA mutant were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 2 µl were spotted on MSgg-agar plates. Cultures were grown for 24 and 48 h at 30°C. After 72 h of growth, colonies were recovered and stored at -80ºC. The collected cells were resuspended and homogenized by passing through a 25 5/8 G needle in BirnBoim A (20% sucrose, 10mM tris-HCl pH 8, 10mM EDTA and 50mM NaCl). Lysozyme (10 mg/ml) was added and incubated 30 min at 37ºC. After disruption, suspensions were centrifuged, and pellets were resuspended in Trizol reagent (Invitrogen). Total RNA extraction was performed as indicated by the manufacturer. Removal of DNA was carried out by in-column treatment with the rDNase included in the Nucleo-Spin RNA Plant (Macherey-Nagel) following instructions from the manufacturer. Integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and by gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NCIB 3610

value: Single tasA mutant

tag: medium

value: Biofilm-inducing solid medium (MSgg)

tag: time point


title: tasA2_48h

description: Bacillus subtilis NCIB3610


title: CC157_eCCA

value: JH


title: CC161_eCCA


title: CC159_eCCA


title: Malignant mesothelioma 4

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

value: Wild type

source_name: Wild type(Dmt1)-4

tag: treatment

value: Crocidolite


title: Malignant mesothelioma 2

source_name: Wild type(Dmt1)-2


title: SSRP1 ChIP in 10μM curaxin treated mouse ESC replicate 2

description:
E14_10uM_SSRP1_rep2
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.

tag: cell line

value: Embryonic stem cells (ESC)

value: 10uM Curaxin

value: SSRP1 (609702,10D1, Biolegend)


title: Malignant mesothelioma 1

source_name: Wild type(Dmt1)-1


title: Malignant mesothelioma 6


title: CC151_eCCA

source_name: extrahepatic cholangiocarcinoma


title: CC153_eCCA


title: CC149_eCCA


title: RRBS_APCLgr5-KO2

source_name: Lgr5+-GFP+ cells


title: CC147_eCCA


title: Malignant mesothelioma 5


title: Malignant mesothelioma 3

source_name: Wild type(Dmt1)-3


title: tasA2_24h

description: Bacillus subtilis NCIB3610


title: RRBS_APCLgr5-KO1


title: SSRP1 ChIP in 10μM curaxin treated mouse ESC replicate 1

description:
E14_10uM_SSRP1_rep1
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.


title: RRBS_APCLgr5-HT4

value: ApcFlox/+ ; Lgr5-CreERT2-ires-eGFP


title: Input control in 10μM curaxin treated mouse ESC replicate 1

description:
E14_10uM_Input_rep1
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.


title: 3610_WT2_48h

description: Bacillus subtilis NCIB3610

source_name: B. subtilis 3610 WT

value: WT


title: RRBS_APCLgr5-HT2


title: CC145_eCCA


title: 3610_WT1_48h

description: Bacillus subtilis NCIB3610