title: Heart_tissue_normal_rep1

city: Zhengzhou

first: Lin

last: Liu

address: 7 Weiwu Road, Jinshui District

institute: Henan Provincial People’s Hospital

description:
circRNA
Gene expression of heart tissue samples of normal children

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 (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Heart tissue, normal, replicate 1

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: 5 TOF children with no other intracardiac and extracardiac malformations and 5 normal fetuses.

value: Heart Tissue

tag: gender

value: 25 weeks

tag: disease state

value: normal


title: Heart_tissue_normal_rep3

status: Public on Mar 01 2023

type: RNA

country: China

molecule: total RNA

organism: Homo sapiens

source_name: Heart tissue, normal, replicate 3

tag: tissue

value: Male

tag: age

value: 26 weeks


title: LTC_Caco2_MonoCal_Cont.rep2

type: SRA

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

description: mRNA-seq (polyA+) data from CaCO2 cells without treatments of free fatty acids, replicate 2

library_source: transcriptomic

data_processing:
The seuqence data was mapped to the genome sequence with minimap2 ver. 2.22.
Assembly: GRCh38.fa
Supplementary files format and content: Expression values of Ensemble GRCh38.98 gene models were counted with bam files.

molecule: polyA RNA

source_name: Caco-2  Cell Line

growth_protocol: CaCO2 and HepG2 cells were maintained a microfluidic device with Dulbecco’s modified Eagle medium, supplemented with 10%(v/v) fetal bovine serum, 1%(v/v) non-essential amino acids and 1%(v/v) penicillin/streptomycin in a humidified incubator at 37°C with 5%(v/v) CO2.

extract_protocol:
Total RNA was extracted from differentiated primary myoblasts using the RNeasy mini kit (QIAGEN).
PCR-cDNA Barcoding Kit ( Oxford NANOPORE Technologies )

treatment_protocol: Free fatty acids (total 1 mM of palmitic acid and oleic acid with 1:2 molecular ratio) in Dulbecco’s modified Eagle medium supplemented with 1% BSA-fatty acid free, 1% P/S, and 1 mM nonessential amino acids and subjected to sample preparation after 1 day.

tag: condition

value: No treatments with free fatty acid

tag: derived tissue

value: Human intestine

tag: cell line


title: Heart_tissue_normal_rep2

source_name: Heart tissue, normal, replicate 2


title: WT 2

city: Bethesda

first: Marian

last: Young

state: MD

address: Building 30, Room 5A509

country: USA

institute: NIH

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v5.0.0 using default settings.
Genome_build: mm10-2020-A (10X Genomics)
Supplementary_files_format_and_content: CellRanger v5.0.0 standard output gene count matrices.

organism: Mus musculus

source_name: bone cells

extract_protocol: scRNA-Seq


title: Bgn KO 1


title: LTC_Caco2_MonoCal_Cont.rep1

description: mRNA-seq (polyA+) data from CaCO2 cells without treatments of free fatty acids, replicate 1


title: LTC_Caco2_CoCal_FA.rep1

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells with treatments of free fatty acids (1 mM), replicate 1

value: Co-cultured with HepG2 cells. Treatments with free fatty acid (1 mM)


title: Heart_tissue_patient_rep5

description:
circRNA
Gene expression of tissue samples of the right ventricular outflow tract of  TOF children with no other intracardiac and extracardiac malformations

source_name: Heart tissue, patient, replicate 5

value: Female

value: 17 months

value: Tetralogy of Fallot


title: WT 1


title: LTC_Caco2_CoCal_Cont.rep2

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells without treatments of free fatty acids, replicate 2

value: Co-cultured with HepG2 cells. No treatments with free fatty acid


title: Heart_tissue_patient_rep1

source_name: Heart tissue, patient, replicate 1

value: 6 months


title: Heart_tissue_normal_rep4

source_name: Heart tissue, normal, replicate 4

value: 28 weeks


title: LTC_Caco2_CoCal_Cont.rep1

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells without treatments of free fatty acids, replicate 1


title: Heart_tissue_patient_rep3

source_name: Heart tissue, patient, replicate 3

value: 9 months


title: Heart_tissue_patient_rep4

source_name: Heart tissue, patient, replicate 4

value: 22 months


title: LTC_Caco2_CoCal_FA.rep2

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells with treatments of free fatty acids (1 mM), replicate 2


title: Heart_tissue_patient_rep2

source_name: Heart tissue, patient, replicate 2

value: 13 months


title: Neg g rep2_HUDEP-2 cells

city: Philadelphia

first: KUNHUA

last: QIN

email: qink@chop.edu, kunhua.qin@gmail.com

state: PA

address: 3615 Civic Center Blvd, 315H

institute: Children's Hospital of Philadelphia

data_processing:
Sequencing reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/)
Assembly: hg38
Supplementary files format and content: TSV files include RPKM and expected count values for each Sample

growth_protocol: cells were grown in StemSpanTM serum-free medium (SFEM) supplemented with 50 ng/ml human stem cell factor (hSCF), 10 µM dexamethasone, 1 µg/ml doxycycline, 3 IU/ml erythropoietin, and 1% pen-strep

extract_protocol:
RNA was prepared from 0.5-2 million HUDEP2 cells (day 6 or 7 of differentiation) or primary progenies of CD34+ HSPCs (day 8 or 13 of culture) using RNeasy® Mini Kit following the manufacturer's instruction
Libraries were prepared using TruSeq Stranded Total RNA kit following the manufacturer's instruction

treatment_protocol: For induction of erythroid differentiation, HUDEP2 cells were grown in IMDM supplemented with 50 ng/ml hSCF, 3 IU/ml erythropoietin, 2.5% fetal bovine serum, 250 µg/ml holo-transferrin, 10 ng/ml heparin, 10 µg/ml insulin, 1 µg/ml doxycycline, and 1% pen-step for the first 3 days then followed by another 3 or 4 days of culture with fresh media of the same recipe without hSCF

tag: cell type

value: adult erythroid cells

tag: genotype

value: Cas12a neg sgRNA transduction

tag: treatment

value: Erythorid differentiation

tag: time

value: Day 6 Diff


title: Neg2_CD34+ cells, Donor #3909

source_name: CD34+ HSPCs, Donor #3909

value: CD34+ HSPCs, Donor #3909

value: Cas9 Neg1 RNP

value: Day 8 Diff


title: BMI g1_CD34+ cells, Donor #3909

value: Cas9 BMI1 g#1 RNP


title: EZH2 g rep1_HUDEP-2 cells

value: Cas12a EZH2 gRNA transduction


title: BMI g3_CD34+ cells, Donor #3911

source_name: CD34+ HSPCs, Donor #3911

value: CD34+ HSPCs, Donor #3911

value: Cas9 BMI1 g#3 RNP


title: BMI g3_CD34+ cells, Donor #3917

source_name: CD34+ HSPCs, Donor #3917

value: CD34+ HSPCs, Donor #3917


title: Neg2_CD34+ cells, Donor #3911


title: EZH2 g rep2_HUDEP-2 cells


title: Neg g rep1_HUDEP-2 cells


title: Neg g (rep2 2/15)_HUDEP-2 cells

value: Cas12a neg gRNA transduction

value: Day 7 Diff


title: BMI g1_CD34+ cells, Donor #3917


title: BMI g1_CD34+ cells, Donor #3911


title: CBX2-4-8 g ( rep2 2/15)_HUDEP-2 cells

value: Cas12a CBX2-4-8 g#1 transduction


title: BMI g3_CD34+ cells, Donor #3909


title: Neg g (rep1 2/11)_HUDEP-2 cells


title: BMI1 g1 rep2_HUDEP-2 cells

value: Cas9 BMI1 #1 sgRNA infection


title: Neg2 rep2_HUDEP-2 cells

value: Cas9 Neg2 sgRNA infection


title: CBX2-4-8 g (rep1 2/11)_HUDEP-2 cells

value: adult erythroid cells


title: BMI1 g2 rep2_HUDEP-2 cells

value: Cas9 BMI1 #2 sgRNA infection


title: BMI1 g1 rep1_HUDEP-2 cells

value: Erythorid differentiation


title: BMI1 g2 rep1_HUDEP-2 cells

value: Day 6 Diff


title: CUTRUN_6e_HUDEP2_H3K4me3_Cas12a BMI gRNA #1 transduction_rep2

library_source: genomic

data_processing:
Sequencing data were analyzed by CUT&RUNTools 2.0
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
Cells were directly used in CUT&RUN or fixed with 1% formaldehyde for 10 minutes in ChIP-seq
Sequencing libraries were generated using NEB kits (E7645 and E6440S)

value: Human erythroblasts

tag: differeniation stage

value: undifferentiated

value: Cas12a BMI gRNA #1

tag: chip antibody

value: H3K4me3(Cell signaling #9751S)


title: Neg2 rep1_HUDEP-2 cells


title: CUTRUN_6b_HUDEP2_H3K27me3_Cas12a BMI gRNA #1 transduction_rep2

value: H3K27me3(Cell signaling #9733S)


title: CUTRUN_6c_HUDEP2_H3K27me3_Cas12a CBX2-4-8 gRNA #1 transduction_rep2

value: Cas12a CBX2-4-8 gRNA #1


title: CUTRUN_6d_HUDEP2_H3K4me3_Cas12a Neg gRNA transduction_rep2

value: Cas12a Neg gRNA #1


title: CUTRUN_6f_HUDEP2_H3K4me3_Cas12a CBX2-4-8 gRNA #1 transduction_rep2


title: CUTRUN_4314_HUDEP2_H3K4me3_Cas12a CBX2-4-8 gRNA #1 transduction_rep1

value: H3K4me3(Cell signaling_#9751S)


title: CUTRUN_4311_HUDEP2_H3K27me3_Cas12a BMI gRNA #1 transduction_rep1

value: H3K27me3(Cell signaling_#9733S)


title: CUTRUN_4325_Primary Erythroblasts derived from Adult perpheral blood CD34+ donor #3917_CBX7_no treatment

value: Day 9

value: CBX7(Abcam #ab21873)


title: ChIPseq_4439_Primary Erythroblasts derived from Adult perpheral blood CD34+ donor #3917_CBX4_no treatment

data_processing:
Sequencing data were analyzed by CUT&RUNTools 2.0
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigWig

value: Day 11

value: CBX4(Proteintech #18544-1-AP)


title: CUTRUN_4309_HUDEP2_H3K27me3_Cas12a Neg gRNA transduction_rep1


title: CUTRUN_3458_Primary Erythroblasts derived from Cord blood CD34+_H3K27ac_no treatment


title: CUTRUN_5g_Primary Erythroblasts derived from Adult perpheral blood CD34+ donor #3917_EZH2_no treatment

value: EZH2(The Bonasio Lab)


title: CUTRUN_4310_HUDEP2_H3K4me3_Cas12a Neg gRNA transduction_rep1


title: CUTRUN_4313_HUDEP2_H3K27me3_Cas12a CBX2-4-8 gRNA #1 transduction_rep1


title: CUTRUN_3426_Primary Erythroblasts derived from Adult peripheral blood CD34+_H3K27ac_no treatment


title: CUTRUN_3442_Primary Erythroblasts derived from Fetal liver CD34+_H3K27ac_no treatment


title: CUTRUN_3434_Primary Erythroblasts derived from Fetal liver CD34+_H3K27ac_no treatment


title: CUTRUN_3450_Primary Erythroblasts derived from Cord blood CD34+_H3K27ac_no treatment


title: CUTRUN_4324_Primary Erythroblasts derived from Adult perpheral blood CD34+ donor #3917_CBX2_no treatment

value: CBX2(Cell signaling #18687S)


title: CUTRUN_4326_Primary Erythroblasts derived from Adult perpheral blood CD34+ donor #3917_CBX8_no treatment

value: CBX8(Cell signaling #14696S)


title: CUTRUN_3419_Primary Erythroblasts derived from Adult peripheral blood CD34+_H3K27ac_no treatment


title: CUTRUN_3452_Primary Erythroblasts derived from Cord blood CD34+_H3K27me3_no treatment


title: CUTRUN_3444_Primary Erythroblasts derived from Cord blood CD34+_H3K27me3_no treatment


title: CUTRUN_3436_Primary Erythroblasts derived from Fetal liver CD34+_H3K27me3_no treatment


title: CUTRUN_3414_Primary Erythroblasts derived from Adult peripheral blood CD34+_H3K27me3_no treatment


title: CUTRUN_6a_HUDEP2_H3K27me3_Cas12a Neg gRNA transduction_rep2


title: CUTRUN_3421_Primary Erythroblasts derived from Adult peripheral blood CD34+_H3K27me3_no treatment


title: CUTRUN_4312_HUDEP2_H3K4me3_Cas12a BMI gRNA #1 transduction_rep1


title: Neg2_CD34+ cells, Donor #3917

value: CD34+ HSPCs, Donor #3917

value: adult erythroid cells

value: Cas9 Neg1 RNP

value: Erythorid differentiation

value: Day 8 Diff


title: CUTRUN_4323_Primary Erythroblasts derived from Adult perpheral blood CD34+ donor #3917_RING1b_no treatment

value: Human erythroblasts

value: RING1b(Cell signaling #5694S)


title: CUTRUN_3428_Primary Erythroblasts derived from Fetal liver CD34+_H3K27me3_no treatment

value: H3K27me3(Cell signaling #9733S)


title: CUTRUN_4012_HUDEP2_H2AK119ub1_Cas12a BMI gRNA transduction rep2

value: undifferentiated

value: Cas12a BMI gRNA rep2

value: H2AK119ub1(Cell signaling_#8240S)


title: CUTRUN_4008_HUDEP2_H2AK119ub1_Cas12a Neg gRNA transduction rep2

value: Cas12a Neg gRNA rep2


title: CUTRUN_4009_HUDEP2_H3K27me3_Cas12a BMI gRNA transduction rep1

value: Cas12a BMI gRNA rep1

value: H3K27me3(Cell signaling_#9733S)


title: CUTRUN_4006_HUDEP2_H2AK119ub1_Cas12a Neg gRNA transduction rep1

value: Cas12a Neg gRNA rep1


title: CUTRUN_3938_Primary Erythroblasts derived from Adult perpheral blood CD34+ donor #3905_BMI1_no treatment

value: Day 10

value: BMI1(Cell signaling_#5856S)


title: CUTRUN_4034_HUDEP2_BMI1_Cas9 BMI gRNA #1 transduction

value: Cas9 BMI gRNA #1


title: CUTRUN_4007_HUDEP2_H3K27me3_Cas12a Neg gRNA transduction rep2


title: CUTRUN_4083_HUDEP2_BMI1_neg gRNA transduction

value: Cas9 neg gRNA


title: Col36, P21, V

city: Toronto

first: Amro

last: Zayed

state: Ontario

address: 4700 Keele Street

department: Biology

country: Canada

institute: York University

data_processing:
The reads were trimmed using Trimmomatic, removing adapters and low-quality bases, filtering out reads less than 50 base pairs
Reads were then aligned and indexed against the Apis mellifera genome (Amel_4.5) using STAR
Alignment quality was assessed using MultiQC
HtSeq was used to count the aligned reads in R
Differential Expression analysis was carried out using EdgeR (66).
Assembly: Apis mellifera genome (Amel_4.5)
Supplementary files format and content: .txt, transcipt name and count

organism: Apis mellifera

source_name: Ventriculus

growth_protocol: Newly emerged honey bee workers were marked with non-toxic paint and returned to their original colony. At 7 days of age, they were collected from the colony and placed into a 33oC incubator in individual Petri dishes with air holes and 50% sucrose solution.

extract_protocol:
Frozen bees were placed in 1 ml of chilled RNAlater (Invitrogen) and thawed over ice.  We performed dissections of the brain, Malpighian tubules, and ventriculus and kept them at -80oC until RNA could be extracted.  RNA extractions were completed using the miRNeasy Mini kit (Qiagen).  Briefly, we added 700 µl of Qiazol lysis reagent to the tissues and homogenized the solution using a pipette.  The protocol provided by the manufacturer was then followed in order to extract the RNA. We added 140 µl of chloroform to the mixture and shook the tubes before allowing them to sit at room temperature for 5 minutes.  We then spun the mixture at 12 000 g for 15 minutes, and 1.5 volumes of 100% ethanol was added to the upper phase.  Once a precipitate had formed, we ran the mixture through an RNeasy spin column.  700 µl of buffer RWT was then added, and once again run through the column, after which 500 µl of buffer RPE was run through the column twice before drying the membrane. Then, 30 µl of RNA-free water was run through the column. RNA quality and quantity were assessed using a NanoDrop ND-1000 UV-Vis. The ventriculus, brains, and Malpighian tubules of 5 individual bees from each patriline were pooled separately based on their organ (e,g., all the brains of a patriline were pooled together). To ensure equal representation for each bee, we added 300 ng of RNA to each pool (1500 ng/5 bees).
Illumina Stranded Total RNA Prep

treatment_protocol: On the day after collection from the hive, the bees were starved for 2 hours, after which they were given a pre-weighed small feeder with 20 µL of 4.27ppb of clothianidin in 50% sucrose solution for 4 hours, at which point the small feeder was removed, weighed, and replaced with a large feeder of 50% w/v sugar solution. These bees were then placed into the incubator for 24 hours after the removal of the small feeder. All of the bees were frozen at -80oC at that point

value: Ventriculus

value: Clothianidin 4.27ppb


title: Col36, P21, B

source_name: Brain

value: Brain


title: Col36, P24, B


title: Col36, P11, MT

source_name: Malpighian tubules

value: Malpighian tubules


title: Col36, P11, V


title: Col36, P21, MT


title: Col36, P11, B


title: Col36, P1, MT


title: CUTRUN_4011_HUDEP2_H3K27me3_Cas12a BMI gRNA transduction rep2

value: Human erythroblasts


title: Col36, P1, V


title: Col36, P1, B


title: Col36, P7, V


title: Col36, P8, V


title: Col36, P24, V


title: Col36, P8, MT


title: Col36, P8, B


title: Col36, P24, MT


title: CUTRUN_4010_HUDEP2_H2AK119ub1_Cas12a BMI gRNA transduction rep1


title: CUTRUN_4005_HUDEP2_H3K27me3_Cas12a Neg gRNA transduction rep1


title: Col36, P7, MT


title: Col36, P7, B


title: Pep30, HEK293T WT, mid-low mCherry-to-EGFP ratio, biological replicate

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street, P&S 10-401

institute: Columbia University

data_processing:
Reads were aligned to a custom index for the Pep30 library generated with the command bowtie-build in bowtie version 1.2.3 and the option -v 3 --best (best alignment with up to 3 mismatches). The counts of each Pep30 sequence were extracted from the alignment with the bash command cut -f 3 | sort | uniq -c.
Pep13: unique 40-nt read sequences were counted directly from fastq files. Sequences do not end with T were removed (encoded by the vector)
Assembly: Custom
Supplementary files format and content: Pep30lib-GFP-high-vs-low.txt: tab-delimited. Columns are: ID, DNA sequence, GFP_high read count, GFP_low read count, Peptide
Supplementary files format and content: Pep30lib-GFP-mCherry-ratio.txt (both replicates): space-delimited. Columns are: ID Seq Peptide KO_high KO_midhigh KO_midlow KO_low WT_high WT_midhigh WT_midlow WT_low
Supplementary files format and content: Pep13.txt: tab-delimited. Columns are: DNA sequence, peptide sequence (stop codon decoded as *), peptide length, followed by read counts in libraries of DNA, RNA, GFP-high, and GFP-low
Library strategy: DNA amplicon sequencing

growth_protocol: HEK293T cells used in this study were purchased from ATCC, from which the BAG6 KO cells were derived using CRISPR/Cas9. Cells were cultured in DMEM with 4.5 g/L D-Glucose supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin was added except when producing lentivirus. Low passage number cells were used and maintained under 90% visual confluency. Cells were maintained at 5% CO2 and 37 °C. HEK293T cells used in this study were confirmed to be negative for Mycoplasma Contamination and routinely tested using the MycoAlertTM Mycoplasma Detection Kit (Lonza, LT07-418).

extract_protocol:
Genomic DNA was isolated from the cell populations using QIAGEN QIAamp DNA mini kit or Machery Nagel Nucleospin Tissue kit. For Pep13, genomic DNA from unsorted input cells was also extracted. In addition, RNA was also isolated using Trizol for Pep13 cells.
Genomic DNA was eluted in 50 uL of elution buffer. Libraries were then amplified using PCR with custom Illumina adapters, using Q5 high-fidelity PCR mix with 1000 ng input gDNA per sample. Libraries were amplified for a total of 24-27 cycles. After amplification, libraries were cleanup up using SPRISelect beads at a ratio of 0.7x. Purified library size was confirmed via gel and libraries were quantified using the KAPA qPCR Illumina library quantification kit. Libraries were subsequently pooled in a ratio based on the number of total cells collected from each sample. Pep13 RNA was reverse transcribed into cDNA and then preped using the same protocol described above.

treatment_protocol: Sorting based on EGFP alone in HEK293T cells: cells were transduced with Pep30 lentivirus at low MOI, grown for 6 days, then FACS sort top and bottom 20% GFP cells. Sorting based on mCherry/EGFP ratio of WT and BAG6 KO cells: HEK293T as well as a clonal BAG6 knockout cell line were reverse transduced with the Pep30 library such that less than 30% of cells were transduced (thus are most likely a single integration per cell). The virus-containing media was removed after 24 hours and fresh media with 10% FBS and 1% PenStrep was added to the plates. After another 24 hours, transduced cells were purified based on their expression of mCherry. The transduced populations were returned to culture and allowed to grow out for an additional 6 days, with passaging as necessary to maintain confluence below 80%. After 6 days, both populations were sorted into 4 bins based on the ratio of EGFP/mCherry expression (High, mid-high, mid-low, and low) using a FACSAria cell sorter. The same mCherry/EGFP ratio gates were used for both WT and BAG6 KO cells. Sorted cells were spun down at 500 RCF for 5 minutes, washed once with 1000 uL PBS, spun down again, then frozen at -20 as a cell pellet.

value: Human embryonic kidney

value: wild-type


title: Pep30, HEK293T BAG6 KO, mid-low mCherry-to-EGFP ratio, biological replicate

value: BAG6 KO


title: Pep30, HEK293T BAG6 KO, low mCherry-to-EGFP ratio, biological replicate


title: Pep30, HEK293T BAG6 KO, high mCherry-to-EGFP ratio, biological replicate


title: Pep30, HEK293T WT, mid-high mCherry-to-EGFP ratio, biological replicate


title: Pep30, HEK293T WT, high mCherry-to-EGFP ratio, biological replicate


title: Pep30, HEK293T WT, low mCherry-to-EGFP ratio, biological replicate


title: PA14 delta-amrZ delta-16550 cells, biol rep 2

city: Stillwater

first: Matthew

last: Cabeen

state: Oklahoma

address: 307 Life Science East

department: Microbiology and Molecular Genetics

institute: Oklahoma State University

data_processing:
Sequence reads were processed and trimmed using FastQC and Cutadapt
Sequence reads were aligned to genome using Bowtie 2.
Differential gene expression analysis was processed using EdgeR.
All software was set using default parameters.
Assembly: NC_008463
Supplementary files format and content: Excel file includes gene list with max group means, log2 and raw fold changes, P values and false discovery rate (FDR) P-values

organism: Pseudomonas aeruginosa

source_name: whole cells

growth_protocol: P. aeruginosa strains as noted were grown for 3 d on M6301-1% agar at 25C in a standard microbiological incubator

extract_protocol:
Total RNA was extracted using the NEB Monarch total RNA extraction kit according to the manufacturer's protocol for gram-negative bacteria. Ribosomal RNA was removed using the Ribo-Zero kit.
Libraries were constructed using the NEB directional kit according to the manufacturer's protocol.

value: whole cells

value: delta-amrZ delta-16550


title: PA14 delta-amrZ cells, biol rep 3

value: delta-amrZ


title: Pep30, HEK293T BAG6 KO, mid-high mCherry-to-EGFP ratio, biological replicate


title: PA14 delta-amrZ delta-16550 cells, biol rep 1


title: PA14 delta-amrZ delta-16550 cells, biol rep 4


title: PA14 delta-amrZ cells, biol rep 4


title: Luminal labelled mouse 1

city: Lebanon

first: Diwakar

last: Pattabiraman

state: New Hampshire

address: 1 Medical Center Drive

department: Molecular systems biology

institute: Geisel School of Medicine at Dartmouth

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed to create individual FASTQ files using Cell Ranger (v.6.0.1) mkfastq (10X Genomics)
Cell Ranger count was used to map sequence reads to the reference genome (mm10-2020-A) and construct a matrix of raw read counts
Expression data were processed for downstream analysis using R-package Seurat v.4.0.3
Doublets were identified and removed using the simulation-based approach implemented by function scDblFinder from R-package scDblFinder, with the doublet rate argument (dbr) set based on the number of recovered cells from each experiment
Cells with ≤ 500 UMIs or ≤ 200 detected features were removed from further analyses
Outlier cells based of proportion of reads mapping to mitochonrial features were identified using function isOutlier from R-package scater v.1.18.6, and excluded from downstream analysis
Assembly: mm10-2020-A
Supplementary files format and content: raw gene expression counts are provided for each sample in the matrix.mtx.gz file (in Market exchange format for sparse matrices). These files contain cell associated barcodes provided by the 'filtered' output from the CellRanger software
Supplementary files format and content: barcode and feature tsv files provide column names (cells) and gene names rows, respectively, for the associated gene expression matrix file (matrix.mtx.gz)
Supplementary files format and content: raw_counts.mtx.zip provides raw counts for all samples aggregated into a single expression matrix (In Market exchange format). Note that only cells included in downstream analyses are included, therefore raw_counts.mtx.zip represents a subset of the cells present in K8_Tumor_397B_matrix.mtx.gz & K8_Tumor_440B_matrix.mtx.gz
Supplementary files format and content: gene_names.txt provides row names for raw_counts.mtx.zip
Supplementary files format and content: cell_IDs.txt provides column names for raw_counts.mtx.zip
Supplementary files format and content: cell_annotations.txt provides annotation data for individual cells, including assigned clusters
Supplementary files format and content: cell_anotation_dictionary.xlsx provides description for variables in cell_annotations.txt

source_name: Mouse MMTV-PyMT tumor

growth_protocol: Animals were maintained under approved IACUC protocols

extract_protocol:
Tumors were harvested once tumor volume reached 1.5cm3. Tumors were digested in Collagenase and hyaluronidase in DMEM for 2 hours, and strained through 70um and 40um filters
Chromium Single Cell 3’ v3.1 kit (10x Genomics)
RNA-seq, paired-end (read 1: 28bp, read 2: 90bp)

treatment_protocol: Mice were treated with 150mg/kg Tamoxifen dissolved in corn oil for 3 days at 5 weeks and 3 days at 6 weeks, for a total of 6 days

value: Mammary epithelial carcinoma

value: Primary tumor cell


title: PA14 delta-amrZ delta-16550 cells, biol rep 3


title: PA14 delta-amrZ cells, biol rep 1


title: WT NB 1


title: PA14 cells, biol rep 3


title: PA14 cells, biol rep 2


title: PA14 cells, biol rep 1


title: Heart_tissue_normal_rep4

description:
miRNA
Gene expression of heart tissue samples of normal children

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: Heart Tissue

value: Female

value: 28 weeks

value: normal


title: Heart_tissue_normal_rep2

value: Male

value: 26 weeks


title: Heart_tissue_normal_rep3

source_name: Heart tissue, normal, replicate 3


title: Heart_tissue_normal_rep1

source_name: Heart tissue, normal, replicate 1

value: 25 weeks


title: Heart_tissue_patient_rep5

description:
miRNA
Gene expression of tissue samples of the right ventricular outflow tract of  TOF children with no other intracardiac and extracardiac malformations

value: 17 months

value: Tetralogy of Fallot


title: Heart_tissue_patient_rep3

value: 9 months


title: Heart_tissue_patient_rep4

value: 22 months


title: Heart_tissue_patient_rep2

value: 13 months


title: Heart_tissue_patient_rep1

value: 6 months


title: PA14 delta-amrZ cells, biol rep 2

value: whole cells


title: 48 hpf dnajc21 mutant rep2

city: Ottawa

first: Sergey

last: Prykhozhij

state: ON

address: Room 318/319 | CAREG, 20 Marie-Curie Private

institute: CHEO Research Institute/University of Ottawa

data_processing:
Reads were trimmed to remove Illumina adaptors.
Reads were aligned to DanRer11 reference genome using STAR, for example: STAR --runThreadN 8 --genomeDir /media/sf_shared/star_index_v43  --outFileNamePrefix 48h_casper_1 --readFilesIn /media/sf_shared/00_fastq/48h_casper_1.fastq
Perform second-pass transcriptome-aware alignment, for example: STAR --runThreadN 8 --genomeDir /media/sf_shared/star_index_v43 --quantMode TranscriptomeSAM  --sjdbFileChrStartEnd  48h_casper_1SJ.out.tab --outFileNamePrefix 48h_casper_1_2nd_pass_ --readFilesIn /media/sf_shared/00_fastq/48h_casper_1.fastq
Genes and transcripts were quantified using a custom zebrafish annotation from the Lawson lab: https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/
RSEM gene and transcript quantification was performed on the second-pass STAR alignments, for example: rsem-calculate-expression --num-threads 8 --alignments 48h_casper_1_2nd_pass_Aligned.toTranscriptome.out.bam /media/sf_shared/rsem_index/rsem_v43 48h_casper_1_2nd_pass_
Differential analysis was performed using DESeq2.
Assembly: danRer11
Supplementary files format and content: data frame with gene-level count estimates

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Zebrafish experiments and husbandry follows standard protocols in accordance with the standards of the University of Ottawa Animal Care Committee (approval number: CHEOe-3193). Zebrafish embryos were maintained at 28.5 °C during development and as adults. Embryos were grown in egg water (1x E3 prepared from 60x E3 stock).

extract_protocol:
Each total RNA sample was extracted from 30-50 zebrafish embryos by homogenizing them in 500 µL Trizol reagent (Thermo Fisher Scientific, 15596026) using 1 mL syringe and 22G needle. Lysates were centrifuged at 12,000 g at 4ºC for 5 minutes and the supernatant was transferred to Phasemaker Tubes (Thermo Fisher Scientific, A33248) and RNA was purified according to the Phasemaker Tubes protocol manual.
Total RNA samples were measured and analyzed for integrity on Agilent Tape Station. Samples with RNA integration number ≥8 were selected for library preparation. Poly-A enrichment was performed from 2 µg of total RNA to enrich for mRNA (Dyna beads mRNA direct micro Kit). poly-A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module (RNA Seq V2 kit, Life Technologies). The size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape assay and 50 ng of fragmented polyA-enriched RNA was used to prepare whole transcriptome library (RNA seq V2). Yield and size distribution of the library was analyzed on Agilent Tape Station using D1000 screen tape. The library was sequenced on the NextSeq 550 instrument (Illumina).

value: Whole embryo

value: dnajc21 mutant homozygous


title: GCSC-AD-03

city: Shenzhen

first: Jixian

last: Xiong

state: Guangdong

address: Xueyuan Ave 1066

institute: Shenzhen University

data_processing:
Real time Analysis (RTA): HiSeq 4000 - RTA v2.7.7, Application Version: HD 3.4.0.38
Base-calling: bcl2fastq v2.17.1.14
Alignment: Reads in gzipped fastq format were aligned using  STAR version-2.4.2a with default parameters to the Rat genome Rnor_6.0, Ensembl release 81.
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 81 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: edgeR (1.10.1) package in R was used to perform TMM (trimmed mean of M values) and CPM (count per million) normalization for the the gene expression
Assembly: hg19

source_name: gastric cancer

extract_protocol:
GCSCs were cultured with or without serum media for 6 days, RNA was extracted using TRIzol, and total RNA was polyA enriched.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gastric adenocarcinoma

value: patient-derived gastric cancer stem cell

tag: group

value: AD

value: Cultured with serum-containing media to induce differentiation


title: GCSC-SP-03

value: SP

value: Cultured with EGF and FGF to induce sphere formation


title: GCSC-SP-01


title: GCSC-SP-02


title: GCSC-AD-01


title: 48 hpf dnajc21 mutant rep1


title: BM mononuclear cells, relapsed patients with CML without drug treatment, rep5

city: Guiyang

first: Yunsheng

last: Ran

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

description:
WZQ
BM mononuclear cells derived from the relapsed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Assembly: GRCh_38
Supplementary files format and content: all.counts.txt: Tab-delimited text file contains counts for each sample.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Bone marrow mononuclear cells

value: WT

tag: phenotype

value: TKI-resistant

value: Without drug treatment


title: BM mononuclear cells, relapsed patients with CML without drug treatment, rep6

description:
ZXJ
BM mononuclear cells derived from the relapsed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, relapsed patients with CML without drug treatment, rep4

description:
TB
BM mononuclear cells derived from the relapsed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: 48 hpf wildtype rep3

value: wildtype


title: BM mononuclear cells, newly diagnosed patients with CML without drug treatment, rep7

description:
ZQ
BM mononuclear cells derived from the newly diagnosed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.

value: TKI-sensitive


title: 48 hpf dnajc21 mutant rep3


title: 48 hpf wildtype rep1


title: GCSC-AD-02


title: BM mononuclear cells, relapsed patients with CML without drug treatment, rep7

description:
ZF
BM mononuclear cells derived from the relapsed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, relapsed patients with CML without drug treatment, rep2

description:
PDT
BM mononuclear cells derived from the relapsed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, relapsed patients with CML without drug treatment, rep3

description:
PZQ
BM mononuclear cells derived from the relapsed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, newly diagnosed patients with CML without drug treatment, rep6

description:
LXL
BM mononuclear cells derived from the newly diagnosed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, newly diagnosed patients with CML without drug treatment, rep5

description:
LTH
BM mononuclear cells derived from the newly diagnosed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, newly diagnosed patients with CML without drug treatment, rep4

description:
LKZ
BM mononuclear cells derived from the newly diagnosed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, newly diagnosed patients with CML without drug treatment, rep1

description:
HWZ
BM mononuclear cells derived from the newly diagnosed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, newly diagnosed patients with CML without drug treatment, rep3

description:
LLY
BM mononuclear cells derived from the newly diagnosed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: BM mononuclear cells, newly diagnosed patients with CML without drug treatment, rep2

description:
HXY
BM mononuclear cells derived from the newly diagnosed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: 48 hpf wildtype rep2


title: ChIPSeq_Rad21_mE2

city: Shanghai

first: yonghu

last: wu

address: 800# Dongchuan Road

institute: Shanghai JiaoTong University

description: mouse enhancer element HS5-1BL inserted into human Pcdha cluster.

data_processing:
Sequenced reads were trimmed for adaptor sequence and  then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1).
Peaks were called using MACS program (version 1.4.2).
Genome_build: hg19
Supplementary_files_format_and_content: bed files: enrichments for every peak called by MACS.

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). HEK-293T Cells were cultured in DMEM medium (Hyclone),supplemented with 10% (v/v) FBS (Gibco)and 1× penicillin-streptomycin (Gibco).Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the DNA Sample Kit (#E7645).

value: human endometrial adenocarcinoma

tag: antibody

value: Rad21 (Abcam, ab992)


title: ChIPSeq_Rad21_HEC1B_WT

description: wildtype


title: ChIPSeq_Rad21_mE1

description: mouse enhancer element HS5-1 inserted into human Pcdha cluster.


title: ChIPSeq_CTCF_mE2_CBSmut

description: CBSs mutated mouse enhancer element HS5-1BL inserted into human Pcdha cluster.

value: CTCF (Millipore, 07-729)


title: ChIPSeq_CTCF_mE2


title: ChIPSeq_H3K27ac_293T_WT

description: wildtype

value: human emborynic kidney

value: H3K27ac (Abcam, ab4729 )


title: ChIPSeq_CTCF_293T_WT

description: wildtype


title: RNA_293T_WT_rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, then aligned to the reference human genome (GRCh38/hg38) using the HISAT2 program (version 2.0.4).
The Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) value was calculated using the Cufflinks program (version 2.1.1).
Genome_build: hg38
Supplementary_files_format_and_content: csv files: the FPKM values for each RNA-seq sample

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). HEK-293T (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
Total RNAs were extracted using TRIZOL regent and mRNA was purified from total RNA using the NEBNext poly(A) mRNA magnetic isolation module.
RNA-Seq libraries were generated by  NEBNext® Ultra™ II RNA Library Prep Kit for Illumina(NEB #E7775)

value: human embryonic kidney


title: RNA_293T_WT_rep1


title: RNA_mE2_CBSmut_rep1


title: RNA_mE2_CBSmut_rep2


title: RNA_mE2_rep2


title: ChIPSeq_CTCF_HEC1B_WT

description: wildtype


title: RNA_mE1_CBSmut_rep1


title: RNA_mE2_rep1


title: RNA_ac1rep_rep1

value: ac1 repeat


title: RNA_mE1_rep2


title: ChIPSeq_H3K27ac_HEC1B_WT

description: wildtype


title: BM mononuclear cells, relapsed patients with CML without drug treatment, rep1

description:
LQY
BM mononuclear cells derived from the relapsed patients with CML without tyrosine kinase inhibitor (TKI) treatment were collected for RNA-seq.


title: RNA_mE1_rep1


title: RNA_ac1rep_rep2


title: RNA_HEC1B_WT_rep1


title: RNA_HEC1B_WT_rep2


title: RNA_mE1_CBSmut_rep2


title: ChIPSeq_CTCF_mE1_CBSmut

description: CBSs mutated mouse enhancer element HS5-1 inserted into human Pcdha cluster.


title: 4C_insert_mE2_rep2

description: insertion site viewpoint

data_processing:
Library strategy: 4C-seq
Sequenced reads were trimmed for adaptor sequence and the bait sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1).
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files: the reads per million (RPM) value in 4C-seq experiments.

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). HEK-293T cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
After cross-linking with 2% formaldehyde, cells were lysed and then digested with DpnII and ligated with T4 DNA ligase.
4C libraries were generated by PCR.

tag: restriction enzyme

value: DpnII


title: 4C_insert_mE2_CBSmut_rep2

description: insertion site viewpoint


title: 4C_insert_mE2_CBSmut_rep1

description: insertion site viewpoint


title: ChIPSeq_CTCF_mE1


title: 4C_insert_mE1_CBSmut_rep2

description: insertion site viewpoint


title: 4C_insert_mE2_rep1

description: insertion site viewpoint


title: 4C_insert_mE1_CBSmut_rep1

description: insertion site viewpoint


title: 4C_insert_mE1_rep2

description: insertion site viewpoint


title: 4C_insert_mE1_rep1

description: insertion site viewpoint


title: 4C_insert_HEC1B_WT_rep2

description: insertion site viewpoint


title: 4C_insert_HEC1B_WT_rep1

description: insertion site viewpoint


title: 4C_HS51_mE2_CBSmut_rep2

description: enhancer HS5-1 viewpoint


title: 4C_HS51_mE2_CBSmut_rep1

description: enhancer HS5-1 viewpoint


title: 4C_HS51_mE2_rep2

description: enhancer HS5-1 viewpoint


title: 4C_HS51_mE2_rep1

description: enhancer HS5-1 viewpoint


title: 4C_HS51_mE1_CBSmut_rep1

description: enhancer HS5-1 viewpoint


title: 4C_HS51_mE1_CBSmut_rep2

description: enhancer HS5-1 viewpoint


title: 4C_HS51_mE1_rep2

description: enhancer HS5-1 viewpoint


title: 4C_HS51_HEC1B_WT_rep1

description: enhancer HS5-1 viewpoint


title: 4C_HS51_ac1rep_rep1

description: enhancer HS5-1 viewpoint


title: 4C_HS51_mE1_rep1

description: enhancer HS5-1 viewpoint


title: 4C_HS51_ac1rep_rep2

description: enhancer HS5-1 viewpoint


title: 4C_AC1in_ac1rep_rep2

description: Pcdhac1 downstream viewpoint


title: 4C_AC1in_ac1rep_rep1

description: Pcdhac1 downstream viewpoint


title: 4C_HS51_293T_WT_rep1

description: enhancer HS5-1 viewpoint


title: 4C_AC1in_HEC1B_WT_rep2

description: Pcdhac1 downstream viewpoint


title: 4C_AC1in_HEC1B_WT_rep1

description: Pcdhac1 downstream viewpoint


title: 4C_a12_mE2_CBSmut_rep1

description: Pcdha12 viewpoint


title: 4C_a12_mE2_rep2

description: Pcdha12 viewpoint


title: 4C_a12_mE2_rep1

description: Pcdha12 viewpoint


title: 4C_a12_mE1_CBSmut_rep2

description: Pcdha12 viewpoint


title: 4C_a12_mE1_CBSmut_rep1

description: Pcdha12 viewpoint


title: 4C_a12_HEC1B_WT_rep2

description: Pcdha12 viewpoint


title: 4C_a12_HEC1B_WT_rep1

description: Pcdha12 viewpoint


title: 4C_a6_mE2_CBSmut_rep2

description: Pcdha6 viewpoint


title: 4C_a12_mE1_rep1

description: Pcdha12 viewpoint


title: 4C_HS51_HEC1B_WT_rep2

description: enhancer HS5-1 viewpoint


title: 4C_a6_mE1_CBSmut_rep2

description: Pcdha6 viewpoint


title: 4C_a12_mE1_rep2

description: Pcdha12 viewpoint


title: 4C_a6_mE1_CBSmut_rep1

description: Pcdha6 viewpoint


title: 4C_a6_mE1_rep2

description: Pcdha6 viewpoint


title: 4C_a6_HEC1B_WT_rep1

description: Pcdha6 viewpoint


title: 4C_a6_HEC1B_WT_rep2

description: Pcdha6 viewpoint


title: 4C_a12_mE2_CBSmut_rep2

description: Pcdha12 viewpoint


title: 4C_a6_mE1_rep1

description: Pcdha6 viewpoint


title: mES_Nanopore_dRNAseq_WT

city: Guangzhou

first: Zhendong

last: Zhong

address: Xingangxi Roda 135#

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
After default live basecalling in MinKNOW (v20.06.9), reads that passed the quality threshold (7) were base-called again with newer versions of Guppy (v5.0.7) with default parameters. Reads that passes the quality threshold (7) for the second time were kept. Then m6A sites detected by 10 ONT tools (Tombo (v1.5.1), MINES, Nanom6A (v2.0), m6Anet (v1.0), Nanocompore (v1.0.0), Xpore (v2.0), DiffErr (v0.2), DRUMMER, ELIGOS (v2.0.1) and Epinano (v1.2.0)) with their respective default parameters but limited in the RRACH motif.
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: bed; m6A sites detected by 10 ONT tools.

source_name: mouse 129 embryonic stem cells

growth_protocol: Wild type (WT) of mouse 129 embryonic stem cells (mESCs) and Mettl3 knockout (KO) mESCs were provided by Dr. Jiekai Chen (Guangzhou Institutes of Biomedicine and Health, CAS).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, 15596026) and the mRNA was purified using Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, 61006). mRNA was treated by TURBO DNase (Thermo Fisher, AM2238) at 37 ℃ for 30 min and purified by ethanol precipitation or RNA Clean & Concentrator-5 kit (Zymo Research, R1015) to remove genomic DNA.
Nanopore direct RNA sequencing libraries were prepared using about 800ng ployA RNA following the SQK-RNA002 kit protocol (version: DRS_9080_v2_revK_14Aug2019). RNA Sequencing on the MinION platform was performed on the FLO-MIN106 flow cell, and raw data was generated by MinKNOW (v20.06.9).

value: mESC

tag: sample type

value: WT cellular mRNA

tag: sequence type

value: Nanopore direct RNA sequencing


title: ChIPSeq_H3K27ac_mE1

data_processing:
Sequenced reads were trimmed for adaptor sequence and  then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1).
Peaks were called using program (version 1.4.2).
Genome_build: hg19
Supplementary_files_format_and_content: bed files: enrichments for every peak called by MACS.

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). Human K562 cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.


title: 4C_a6_mE2_CBSmut_rep1

description: Pcdha6 viewpoint


title: Menadione (10uM) treatment_24 hours_Rep3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: miRNA expression 24 hours post Menadion (10uM) treatment

hyb_protocol: The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking solution (Agilent Technologies, Part Number: 5190-0456) and Hi-RPM Hybridization Buffer (Agilent Technologies, Part Number: 5190-0456) and incubated at 100oC for 5 minutes followed by snap chill on ice for 5 minutes.  The samples were hybridized on the Human miRNA 8x60K Arrays. The hybridization was carried out at 55°C for 20 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes.

scan_protocol: The microarray slide was scanned on a G2600D scanner (Agilent Technologies)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 90th percentile shift miRNA based.

source_name: SW-620 Colorectal Cancer cellls

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Part Number: 5190-0456).The total RNA sample was diluted to 100ng/ul in nuclease free water. About 200ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master mix (Agilent Technologies, Part Number: 5190-0456) by incubating at 37oC for 30 minutes. The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide (DMSO) and heating at 100 oC for 10 minutes and transferred to ice-water bath. The Ligation master mix (Agilent Technologies, Part Number: 5190-0456) containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16oC for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus, Catalog Number 5305000) at 45oC for 2 hour.

extract_protocol: Cells were collected and Trizol-method was used for RNA extraction.

value: Human colorectal cancer cell line


title: Menadione (10uM) treatment_24 hours_Rep1


title: 4C_a6_mE2_rep1

description: Pcdha6 viewpoint


title: Plumbagin (10uM) treatment_24 hours_Rep2

description: miRNA expression 24 hours post Plumbagin (10uM) treatment


title: Dog4_abTcells_Transcriptome

city: Davis

first: Stefan

middle: Matthias

last: Keller

state: California

address: One Shields Avenue

department: Pathology, Immunology, Microbiology

institute: University of California, Davis

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software version cellranger 5.0.1
Assembly: CanFam 3.1 annotation genebuild updated 2019-06, GenBank assembly accession: GCA_000002285
Supplementary files format and content: Raw data: 1) Transcriptome: bam files; 2) VDJ: bam files
Supplementary files format and content: Processed data: 1) Transcriptome: CellRanger output files (barcodes, features, matrix files); 2) VDJ: CellRanger output files (airr format)

organism: Canis lupus familiaris

source_name: peripheral T cells, TCRab+

extract_protocol:
Venous blood was taken from 4 healthy experimental Beagle dogs (one female, three male, age: 5 – 9 years) into heparinized vacutainer tubes (The study was authorized by the Animal Care and Usage Committee of the Saxony State Office (Landesdirektion Sachsen) in Leipzig, Germany; approval number: A 28/18). PBMC were isolated by density gradient centrifugation and stained with the fixable viability dye eFluor 780 (Thermo Fisher Scientific, Carlsbad, USA) according to the manufacturer’s protocol to discriminate dead from viable cells. In a second step, they were incubated with a mixture of heat-inactivated normal serum derived from dog and rat (each 15% in PBS) to block unspecific binding of Fc receptors. Then, cells were incubated with anti-canine TCRαβ (clone CA15.8G7) hybridoma supernatant, for 15 min in the dark on ice. A PerCP/Cy5.5-conjugated goat-anti-mouse IgG secondary antibody (Biolegend, San Diego, USA) was used for detection. After exclusion of dead cells and doublets, TCRαβ+ T cells from the lymphocyte gate were sorted using the BD FACSAriaTM III flow cytometer (Becton Dickinson, Heidelberg, Germany) with a purity >99% (Re-analysis using the FlowJoTM10 software (Treestar Inc., Ashland, OR, USA). Isolated TCRαβ+ T cells were cryopreserved (FCS, 10% DMSO) and shipped to the Institute of Pathology, Microbiology & Immunology of the UC Davis. There, the cellularity (1.1-1.4 x 106 cells/ml) and viability (78-90%) of TCRαβ+ T cells was confirmed.
Transcriptome and V(D)J libraries were prepared at the UC Davis Genome Center. Briefly, ~10,000 TCRαβ+ T cells per lane were loaded on a Chromium Single Cell Controller (10× Genomics). Captured cells were lysed, and the released RNAs were barcoded through reverse transcription in individual gel beads in emulsion (GEMs). Starting mRNA molecules were indexed using Unique Molecular Identifier (UMI). Following emulsion breakage, barcoded cDNA was amplified and libraries were constructed using the Chromium Next GEM Single Cell 5' Kit v2. The canine T cell receptor alpha (TRA) and T cell receptor beta (TRB) genes were amplified using the Chromium Single Cell V(D)J Enrichment Kit according to the manufacturer’s instructions but with primers adapted for the canine genes. Libraries were sequenced using the Illumina NovaSeq S4 platform using 150 paired-end reads to a target read depth of 30,000 reads per cell.

tag: breed

value: Beagle

tag: name

value: Zappa

tag: Sex

value: male

value: peripheral T cells, TCRab+

value: healthy


title: Dog4_abTcells_VDJ

tag: age


title: ChIPSeq_H3K27ac_mE1_mut

value: human endometrial adenocarcinoma


title: ChIPSeq_H3K27ac_mE2


title: Control_Rep_2

description: miRNA expression 24 hours post vehicle treatment


title: Control_Rep_1


title: mES_Nanopore_dRNAseq_KO

value: Mettl3 KO cellular mRNA


title: Dog3_abTcells_VDJ

value: Toto


title: Dog2_abTcells_VDJ

value: Theo


title: Dog3_abTcells_Transcriptome


title: Dog2_abTcells_Transcriptome


title: Wt3RestingPDH

city: Utrecht

first: Enric

last: Mocholi Gimeno

state: Utrecht

address: Heidelberglaan 100

department: CMM

country: Netherlands

institute: UMC Utrecht

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Mice (WT) Resting 3

growth_protocol: RPMI, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: Total RNA was extracted using the RNAeasy kit (Qiagen).Sample preparation was performed using TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and samples were sequenced 75bp single-end on Illumina NextSeq500 (Utrecht DNA sequencing facility).

tag: tissue

value: CD4 T cells

value: Wt

value: Nothing


title: Wt2RestingPDH

source_name: Mice (WT) Resting 2


title: Wt1RestingPDH

source_name: Mice (WT) Resting 1


title: Dog1_abTcells_VDJ

value: Irma

value: female

tag: cell type


title: Wt3ActivPDH

source_name: Mice (WT) Activated 3

tag: genotype


title: Ko1RestingPDH

source_name: Mice (Pdha1fl/fl CD4CreERT2) Resting 1

value: Pdha1fl/fl CD4CreERT2

tag: treatment


title: Wt2ActivPDH

source_name: Mice (WT) Activated 2


title: Ko2RestingPDH

source_name: Mice (Pdha1fl/fl CD4CreERT2) Resting 2


title: Ko3RestingPDH

source_name: Mice (Pdha1fl/fl CD4CreERT2) Resting 3


title: Wt1ActivPDH

source_name: Mice (WT) Activated 1


title: Plumbagin (10uM) treatment_24 hours_Rep1


title: Menadione (10uM) treatment_24 hours_Rep2


title: Ko3ActivPDH

source_name: Mice (Pdha1fl/fl CD4CreERT2) Activated 3


title: Control_Rep_3


title: Ko2ActivPDH

source_name: Mice (Pdha1fl/fl CD4CreERT2) Activated 2


title: Ko1ActivPDH

source_name: Mice (Pdha1fl/fl CD4CreERT2) Activated 1


title: Dog1_abTcells_Transcriptome


title: Wt3RestingACLY


title: Wt2RestingACLY


title: Ko2RestingACLY

source_name: Mice (CD4-Cre Aclyfl/fl) Resting 2

value: CD4-Cre Aclyfl/f


title: Ko1RestingACLY

source_name: Mice (CD4-Cre Aclyfl/fl) Resting 1


title: Wt2ActivACLY


title: Wt1RestingACLY


title: Wt3ActivACLY


title: Wt1ActivACLY


title: Ko3ActivACLY

source_name: Mice (CD4-Cre Aclyfl/fl) Activated 3


title: Ko1ActivACLY

source_name: Mice (CD4-Cre Aclyfl/fl) Activated 1


title: GH astrocyte, replicate 1, scRNAseq

city: Houston

first: Yi-Ting

last: Cheng

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
10x Genomics
YC165

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: RDS file

source_name: hippocampus

extract_protocol:
Tissues were dissociated by using MACS neural tissu dissociatation, and the cleaned up by MACS red blood cell revomal kit, debris removal kit, and dead cell removal kit. Then we used FACS to isolate GFP-positive astrocytes.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: astrocytes

value: hippocampus

tag: strain

value: 8 weeks old


title: SH astrocyte, replicate 1, scRNAseq

description:
10x Genomics
YC166


title: Cx-6-10, 6-months old, cortex

city: Sherbrooke

first: Benoit

last: Laurent

address: 3201 Jean Mignault

institute: University of Sherbrooke

data_processing:
Quality control of RNA-seq data was performed using FastQC (version 0.11.8) with default parameters.
Trimming of the reads was achieved using TrimGalore (version 0.6.4) with default parameters except for: --illumina --max_n 5 --clip_R1 3 --three_prime_clip_R1 3.
Reads were mapped to the mouse genome (GRCm38, GENCODE vM23, primary assembly) with STAR (version 2.7.3a). STAR was used with default parameters except for: --outFilterMultimapMmax 10 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outSAMprimaryFlag AllBestScore --outFilterMismatchNmax 5.
The evaluation of gene expression (CPM and TPM) was done using FeatureCounts from the SubRead package (version 2.0.0). FeatureCounts was used with default parameters except for: -M --fraction -Q 15 --fracOverlap 0.25 --largestOverlap --minOverlap 15. Exons were set as features (-t exon) and grouped by gene (-g gene_id).
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include raw counts and TPM values for each sample

source_name: Cortex

growth_protocol: C57BL/6J mice received a standard diet i.e., NIH-31 modified open formula mouse/ rat sterilized diet and were kept on a 12:12 day light cycle at 22-23°C with access to a small house and tissues for nesting.

extract_protocol:
Cortex powder was first homogenized in 500µL of cold TRIzol and then 500µL of chloroform:isoamyl alcohol 24:1 (Sigma Aldrich) were added. Samples were vortexed for 20 seconds and incubated 2 min at room temperature. The samples were then centrifuged at 10,000g for 18 min at 4°C. The aqueous phase, that contains RNAs, was transferred in a new Eppendorf tube. An equal volume of ethanol 100% was added and the mixture was then loaded into a Zymo-Spin™ IIICG Column from the Quick-RNA™ Miniprep Kit. Further steps were conducted according to the manufacturer’s protocol. The RNA concentration in ng/µL was determined using a Nanodrop system (Thermo Fisher Sscientific).
Library preparation was initiated with 10ng of total RNA.
RNA-seq libraries were prepared using NEBNext® single cell/low input RNA library preparation Kit (New England Biolabs).

treatment_protocol: Mice were placed under anesthesia (isoflurane) and then a cervical dislocation was performed. Each frozen sample of cortex was crushed and powdered using the BioSqueezer Snap Freeze Press system (Biospec),

value: Cortex

value: 6 months

value: male

value: WT

value: isoflurane for anesthesia


title: Ko2ActivACLY

source_name: Mice (CD4-Cre Aclyfl/fl) Activated 2


title: Cx-24-4, 24-months old, cortex

value: 24 months


title: Cx-6-11, 6-months old, cortex


title: Cx-24-5, 24-months old, cortex


title: Cx-6-17, 6-months old, cortex


title: rep2_Luc_0hr

city: Durham

first: Anna Mae

last: Diehl

address: 905 S LaSalle St

institute: Duke University

description:
10x Genomics
heps_Cre+Luc_0hr_9207.rds

data_processing:
Cell Ranger from 10X Genomics was used for initial data processing. Cell-by-gene expression
matrices were generated with valid cell barcodes. Low quality cells with high
mitochondrial contents (>= 60%) and possible doublets were excluded.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files and rds files

source_name: liver

extract_protocol:
Freshly isolated hepatocytes were washed and re-suspended in 0.04% UltraPure BSA and counted using the automated cell counter.
GEM generation, post GEM-RT cleanup, cDNA amplification and library construction were performed following 10X Genomics Single Cell 3’ v2 chemistry.
Libraries were sequenced on Illumina NovaSeq PE150. 500 million paired-end reads were obtained for each sample as recommended.

value: hepatocytes

value: liver

value: 12-14 weeks old


title: rep2_Cre_0hr

description:
10x Genomics
heps_Cre+Luc_0hr_9207.rds


title: Cx-24-2, 24-months old, cortex


title: rep1_batch01_Cre_0hr

description:
10x Genomics
heps_Cre+Luc_0hr_9207.rds


title: rep1_batch01_Luc_0hr

description:
10x Genomics
heps_Cre+Luc_0hr_9207.rds


title: Ko3RestingACLY

source_name: Mice (CD4-Cre Aclyfl/fl) Resting 3

value: CD4 T cells

value: Nothing


title: Ana_S1

city: Ithaca

first: Tudorita

last: Tumbar

address: 526 Campus Rd

department: Molecular biology and genetics

institute: Cornell University

description: tdTomato+ cells were FACS sorted from back skin of PD32 (anagen) tdTomato;Cdh5-CreERT2;Krt14-H2BGFP mice, barcoded single-cell 3′ cDNA libraries were generated using Chromium Single Cell 3′ gel bead and library Kit v3 (10x Genomics) and sequenced using an Illumina NextSeq-500.

data_processing:
The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-2020-A) using the 10X Genomics Cell Ranger pipeline (v6.0.1)
The raw scRNA-seq data was processed using Cell Ranger from the 10X platform to generate an expression matrix that was further analyzed in R using the Seurat package version 4.0
Principle Component Analysis (PCA) was performed on the gene expression matrix using the least number of principal components (PCs) that could be used to explain the majority of the variance in the data
The PCA embeddings were used by Harmony to integrated the datasets. Unsupervised shared nearest neighbor (SNN) clustering was done on the Harmony integrated Seurat object
Assembly: mm10-2020-A
Supplementary files format and content: feature.tsv, barcode.tsv and matrix.mtx files for each sample

source_name: Mouse back skin

extract_protocol:
The VE-cadherin+ cells were labeled with tdTomato by injecting tamoxifen (200 μg/g) at postnatal day (PD)17, and dorsal skin was collected at PD20, PD25 and PD32. The dorsal skin was digested in collagenase and Dispase mixture as previously described (Chovatiya et al., 2021). The dead cells were removed by LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (ThermoFisher). FACS Aria (BD Biosciences) was used for the cell sorting.
Single-cell 3′ cDNA libraries were generated using Chromium Single Cell 3′ gel bead and library Kit v3.
Libraries were generated following the manufacturer’s protocols (10x Genomics).

value: Skin

value: Post natal day 32

value: wild type

tag: cell line

value: VE-cadherin+ lineages


title: Ana_S2


title: Alk1KO_S2

description: tdTomato+ cells were FACS sorted from back skin of PD25 (telogen) Alk1 flox/flox;tdTomato;Cdh5-CreERT2 mice, barcoded single-cell 3′ cDNA libraries were generated using Chromium Single Cell 3′ gel bead and library Kit v3 (10x Genomics) and sequenced using an Illumina NextSeq-500.

value: Post natal day 25


title: Alk1KO_S1


title: Telo_S1

description: tdTomato+ cells were FACS sorted from back skin of PD20 (telogen) tdTomato;Cdh5-CreERT2;Krt14-H2BGFP mice, barcoded single-cell 3′ cDNA libraries were generated using Chromium Single Cell 3′ gel bead and library Kit v3 (10x Genomics) and sequenced using an Illumina NextSeq-500.

value: Post natal day 20


title: PGE2#1

city: Cold Spring Harbor

first: Aybuke

last: Alici

address: 1 Bungtown Rd.

institute: Cold Spring Harbor Laboratory

data_processing:
The Cellranger pipeline (v4.0.0 10X Genomics) was used to align FASTQs to the mouse reference genome (gex-mm10-2020-A, 10X Genomics)
Digital gene-cell counts matrices were produced with default parameters
Assembly: mm10-2.1.0
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format

source_name: Intestinal Organoids

growth_protocol: Mouse intestinal organoids were generated from isolated mouse crypts and seeded into Matrigel using the media supplemented with in Advence DMEM (Gibco) media, recombinant murine EGF 40 ng/ml (PeproTech), recombinant murine Noggin 50 ng/ml (PeproTech), R-spondin 62.5 ng/ml (R&D Systems), N-acetyl-L-cysteine 1 uM (Sigma-Aldrich), CHIR-99021 5 uM (Tocris), Y-27632 20 ng/ml (Tocris), B27 1X (Gibco), N2 1X (Gibco)

extract_protocol:
Organoids were dissociated into single cell suspensions at 37C using TrypLE, and passed through a 100 um FlowMi cell strainer.  Cells were stained with DAPI and sorted on a Sony SH800S sorter. DAPI-negative viable cells were sorted into a chilled microcentrifuge tube containing PBS. Viability was confirmed to be >75% using a Countess FL II cell counter (Life Technologies #AMQAF1000) before proceeding to single cell library preparation.
Single cell libraries were prepared using a 10X Genomics Chromium Controller (cat Chromium Next GEM Single Cell 3' Gene Expression kit (cat #1000268) according to the manufacturer's instructions.  Cell suspensions were adjusted to target a yield of 8,000 cells per sample. Single cell 3' digital gene expression with cell barcodes and unique molecular identifiers (UMIs).

treatment_protocol: Intestinal organoids were treated with Vehicle, AA 25 uM and PGE2 50 nM for 3 days.

value: Mouse intestinal organoids

tag: agent

value: 6,16-dimethyl PGE2)


title: Telo_S2


title: AA#1

value: arachidonic acid


title: AA#2


title: Veh#2

value: vehicle


title: ARD#1

data_processing:
The Cellranger pipeline (v4.0.0 10X Genomics) was used to align FASTQs to the mouse reference genome (gex-mm10-2020-A, 10X Genomics)
Digital gene-cell counts matrices were produced with default parameters
Assembly: mm10-2020-A
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format

source_name: Intestinal crypts

growth_protocol: Mouse intestinal crypts were isolated from Control or ARD mice.

treatment_protocol: Mice were fed with control and AR- diets for 4 months

value: Mouse intestinal crypts

value: ARD


title: Veh#1


title: ARD#2


title: Cont#2

value: Control


title: ChIP_pDC_Irf8

city: Aachen

first: Zhijian

last: Li

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen University

data_processing:
Sequenced reads were trimmed for adapter sequences using Trim Galore with -q 30 --trim1 --paired .
Reads mapped to mm9 whole genome by Bowtie2 with -X 2000 --no-mixed –no-discordant
Duplicates were remove. Reads were filtered for alignment quality of Q > 30 and were required to be properly paired
Reads mapping to chromosome Y, mitochondria and unassembled "random" contigs were removed from all downstream analysis
Peaks were called using MACS2 with -g mm --keep-dup all --call-summits –nomodel
Assembly: mm9
Supplementary files format and content: TDF

source_name: Plasmacytoid dendritic cells

extract_protocol: Omni-ATAC-seq was performed according to  with minor modifications. Prior to transposition dead cells were removed by centrifugation (800 rpm, 4 min, 4°C). The transposition reaction was with 7.5 μL Tagment DNA Enzyme 1 (TDE1) for 60 ‘min at 37°C. Pre-amplification was with NEBNext Ultra II Q5 Master Mix and Nextera PCR Primers (5 cycles). Quantitative PCR amplification was with NEBNext Ultra II Q5 Master Mix, Nextera PCR Primer and SYBR Gold to determine the number of additional cycles. PCR amplification of additional cycles was as for pre-amplification. PCR fragments were purified with Qiagen MinElute PCR Purification Kit and library concentration and quality were determined by Agilent High Sensitive DNA Kit and TapeStation, respectively. ATACseq libraries were sequenced on the Illumina NextSeq 500 Platform with 75 bps paired-end reads in duplicates.RNA-Seq libraries were prepared and subjected to strand-specific RNA-seq on the Illumina platform according to the manufacturer's protocols.

value: Plasmacytoid dendritic cells


title: Cont#1


title: RNA_pDC


title: RNA_cDC1

source_name: Classical dendritic cell

value: Classical dendritic cell


title: QKO_EpiLC_4C_Tbx3

city: Dublin

first: Cheng

last: Wang

address: College Green

department: Genetics

country: Ireland

institute: Smurfit Institute of Genetics, Trinity College Dublin

data_processing:
library strategy: 4C-seq
4C-seq reads quality was confirmed by fastqc, then processed with pipe4C pipeline.
For UCSC genome browser visualization, bigwigs were generated by pipe4C pipeline.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Epiblast-like cells (EpiLC)

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatinized culture dishes in GMEM (Sigma) supplemented with 20% FBS (Gibco), 100U/mL Penicillin-Streptomycin (Gibco), 50 μM β-mercaptoethanol (Sigma), 1:100 GlutaMax, 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 1:500 homemade leukaemia inhibitory factor (LIF), and 2i components; 3 μM GSK inhibitor CHIRON99021 (Cayman) and 1 μM MEK inhibitor PD0325901 (Cayman).The ESCs were spited and changed medium every 2 days.For EpiLC differentiation experiments, the dishes were coated with 16 μl/ml fibronectin for 2~3 hours. 2 million ESCs were washed three times with PBS and seeded on the fibronectin coated dished in NDiff227 medium (Takara) supplemented with 20 ng/ml Activin A (Peprotech), 12 ng/ml bFGF (Gibco) and 1% Knockout Serum Replacement (KSR, Thermo) for 2 days. The EpiLC culture medium were changed daily.

extract_protocol:
Circularized chromosome conformation capture (4C) assays were performed using a modified published approach(van de Werken et al., 2012; Wang et al., 2019). Briefly, 10 million detached ESCs or EpiLCs were fixed with 1% final formaldehyde for 10 minutes, and quenched with final 0.125 M glycine. The cells were lysed in the 30 ml lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 0.5% NP-40, 1% Triton, 5 mM EDTA, and  proteinase inhibitors: 2 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1mM PMSF ) with rotation at 4 °C for 45  minutes. Isolated nuclei were then fully digested by restricted enzyme DpnII overnight digestion followed by overnight ligation with 50 U T4 DNA ligase at cool room temperature (18~20  °C) . Ligated circular DNA were purified after de-crosslinking incubation with proteinase K at 65 °C for overnight, followed by further incubation with Rnase A at 37  °C for 1 hour . The purified  DNA was further digested with restricted enzyme NlaIII and then ligated again and purified. The 4C libraries were amplified with the viewpoint-specific primers with inverse PCR using Roche Expand Long Template PCR System. For each viewpoint, at least 8 PCR reaction products were pooled to enhance the library complexity. The 4C PCR products were purified using Qiagen Quick PCR purification Kit. Tbx3 promoter viewpoint primers are AAGGGAAGAAGCTGCAGATC (Reading primer) and TGAAGGGAGCCCCACATG.
4C-seq library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol.

treatment_protocol: No treatment/stimulations for this project.

value: PHF1, MTF2, PHF19, JARID2 KO EpiLC

tag: restrict enzyme

value: DpnII-NlaIII


title: WT_EpiLC_4C_Tbx3

value: WT EpiLC


title: RNA_MPP

source_name: Multi-potent progenitor cell

value: Multi-potent progenitor cell


title: ATAC_cDC2_1


title: ATAC_cDC2_2


title: PCGF2_4_KO_EpiLC_4C_Tbx3

value: PCGF2, PCGF4 KO EpiLC


title: RNA_cDC2


title: ATAC_MPP_3


title: ATAC_CDP_1

source_name: Dendritic cell progenitor

value: Dendritic cell progenitor


title: ATAC_CDP_2


title: ATAC_MPP_2


title: ATAC_MPP_1


title: 8_AD_hippocampus.2

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

data_processing:
RNA-Seq reads were mapped to the mouse GRCm38.p4 genome with STAR [42] (version 2.4.2.a).
Reads were assigned to genes with featureCounts (version 1.4.6-p5) using the following parameters: -t exon -g gene_id, and with Genecode grcm38.p4-vM6 gtf reference.
The differential expression analysis was carried out with DESeq2 (version 1.12.4) using default parameters
Assembly: GRCm38.p4
Supplementary files format and content: XLS file with raw gene counts

growth_protocol: Animal care was in accordance with the directive 2010/63/EU. The MDC has signed the Basel Declaration in 2012 and observes an internal animal welfare directive. Experimental procedures were approved by the local animal welfare authority in Berlin, Germany under license number TVV G0073/17. Mice were group-housed in cages with wooden bedding, environmental enrichment and ad libitum food and water supply.

extract_protocol:
The brain tissue was homogenized in TRIzol® Reagent (Ambion) using a Precellys homogenizer (Bertin Instruments) and extracted according to the TRIzol® Reagent protocol, with an additional phenol/chloroform purification step and the final isopropanol precipitation. For the total RNA sequencing we used 1,000 ng of total RNA; rRNA was depleted using a RNase H-based protocol. We mixed total RNA with 1 μg of a DNA oligonucleotide pool comprising a 50-nt long oligonucleotide mix covering the reverse complement of the entire length of each human rRNA (28S rRNA, 18S rRNA, 16S rRNA, 5.8S rRNA, 5S rRNA, 12S rRNA), incubated with 1U of RNase H (Hybridase Thermostable RNase H, Epicentre), purified using RNA Cleanup XP beads (Agencourt), DNase treated using TURBO DNase rigorous treatment protocol (Thermo Fisher Scientific), and purified again with RNA Cleanup XP beads.
We fragmented the rRNA-depleted RNA samples and processed them into strand-specific cDNA libraries using TruSeq Stranded Total LT Sample Prep Kit (Illumina) and then sequenced them on NextSeq 500, High Output Kit, 1 x 150 cycles.

tag: mouse id


title: 8_AD_hippocampus.1


title: 8_AD_hippocampus


title: 8_AD_cortex

source_name: cortex


title: 8_WT_hippocampus.2

value: WT


title: ChIP_cDC_Irf8

tag: antibody


title: WT_ESC_4C_Tbx3

source_name: Mouse Embryonic stem cells (Healy et al 2019)

value: Mouse Embryonic stem cells (ESC)


title: 8_WT_cortex.1


title: ATAC_CDP_3


title: 8_WT_hippocampus.1


title: 8_WT_cortex


title: 5_AD_hippocampus.2


title: 5_AD_hippocampus


title: 5_AD_cortex


title: 5_WT_hippocampus.2


title: 5_AD_cortex.1


title: 5_WT_cortex.2


title: 5_AD_cortex.2


title: 5_WT_cortex.1


title: 5_WT_hippocampus.1


title: 5_WT_cortex


title: 5_WT_hippocampus


title: 2_AD_hippocampus.2


title: 8_AD_cortex.1


title: 2_AD_hippocampus


title: 2_AD_hippocampus.1


title: 8_WT_cortex.2


title: 2_AD_cortex


title: 2_AD_cortex.1


title: 8_WT_hippocampus


title: 2_WT_cortex.1


title: 2_WT_hippocampus.2


title: 2_WT_cortex.2


title: 2_WT_hippocampus


title: 5_AD_hippocampus.1


title: 2_WT_hippocampus.1


title: 2_WT_cortex


title: intestinal organoids, AA_D6#4

data_processing:
RNA-seq reads were implemented to trimming (cutadapt), mapping (STAR), and expression quantification (quantMode GeneCount), respectively.
Reads were mapped to Homo sapiens GRCh38.p6 (release M24)
Differential gene expression analyses were performed using DESeq2 ref. Lowly-expressed genes were filtered out from the differential expression analysis input matrix.
Limma (v3.46) was used to adjust for sequencing batch effects, prior to rlog normalization of the size-factor normalized read counts.
Genome_build: GRCh38.P6
Supplementary_files_format_and_content: tab-separated values version of raw counts of sequencing reads for all samples

source_name: intestinal organoids, AA_D6

extract_protocol:
Intestinal organoids rescued from matrigel using cell recovery solution, RNA was harvested using Trizol Reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Intestinal organoids were treated with vehicle, AA 25 µM and PGE2 50 nM for 1 Day, 3 Day and 6 Day

value: intestinal organoids

value: AA

tag: time


title: intestinal organoids, AA_D6#3


title: intestinal organoids, AA_D6#2


title: intestinal organoids, Veh_D6#2

source_name: intestinal organoids, Veh_D6

value: Vehicle


title: intestinal organoids, AA_D6#1


title: intestinal organoids, Veh_D6#1


title: intestinal organoids, Veh_D6#4


title: intestinal organoids, PGE2_D3#3

source_name: intestinal organoids, PGE2_D3


title: intestinal organoids, PGE2_D3#2


title: intestinal organoids, AA_D3#2

source_name: intestinal organoids, AA_D3


title: intestinal organoids, Veh_D3#3

source_name: intestinal organoids, Veh_D3


title: intestinal organoids, AA_D3#3


title: intestinal organoids, Veh_D3#2


title: intestinal organoids, Veh_D3#1


title: intestinal organoids, AA_D3#1


title: RNA_CDP


title: intestinal organoids, PGE2_D1#3

source_name: intestinal organoids, PGE2_D1


title: intestinal organoids, PGE2_D1#1


title: intestinal organoids, AA_D1#2

source_name: intestinal organoids, AA_D1


title: intestinal organoids, AA_D1#3


title: intestinal organoids, Veh_D1#3

source_name: intestinal organoids, Veh_D1


title: intestinal organoids, PGE2_D1#2


title: intestinal organoids, Veh_D1#2


title: intestinal organoids, PGE2_D3#1


title: intestinal organoids, Veh_D6#3


title: scATAC-seq analysis of Msi2-MycT58A Mouse Pancreas Pre-cancer cells

city: La Jolla

first: Michael

last: Hamilton

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

data_processing:
Cell Range ATAC v2.0.0
Signac v1.1.1 was used for secondary analysis
Genome_build: mm10
Supplementary_files_format_and_content: h5

source_name: Mouse Pancreas Pre-cancer Cells

extract_protocol:
Cells were isolated per 10x Genomics manufacture instructions.
Libraries were constructed per 10x Genomics manufacture instructions.
scATAC-seq

treatment_protocol: In vivo tamoxifen induction of 8 week old Msi2-CreER MycT58A mice.  Pre-cancer pancreas cells isolated 5 weeks post tamoxifen induction.  ASCP tumor cells isolated of orthotopic transplant from primary ASCP tumor from Msi2CreER-MycT58A mouse.

tag: condition

value: Pre-cancer

tag: donor strain

tag: recipient strain

value: Not applicable


title: Ezra_seq_MEF

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

data_processing:
Library strategy: Ezra-seq
The adaptor AAAAAAAAAAAA was trimmed by Cutadapt. The reads with length <15 nt were not included.
The trimmed reads were aligned to human or mouse transcriptome, using STAR with default parameters. The uniquely mapped reads were used for analysis.
Genome_build: GRCm38/GRCh38
Supplementary_files_format_and_content: The processed files are read count  on mRNAs. The first column is the ENSEMBL transcript ID. The second column is the read count on mRNA.

source_name: Mouse embryonic fibroblasts

growth_protocol: HEK293-Kb or MEF cells are maintained in Dulbecco’s Modification of Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
A total of 4 plates (10-cm) HEK293-Kb cells grown to 80% confluency were changed with fresh medium to remove the dead cells 2 h before harvesting.Cells were washed by cold PBS and lysed in the polysome lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 100 μg/mL cycloheximide with 2 % Triton X-100). The lysates were cleared by centrifugation at 14,000 rpm for 10 min at 4 °C. 15-45 % (wt/vol) sucrose density gradients were freshly prepared in a SW41 ultracentrifuge tube using a Gradient Master. 500 μL of cytosolic extracts were loaded onto sucrose gradients followed by ultracentrifugation for 2 h 30 min at 32,000 rpm 4 °C in a SW41 rotor. Polysome profiles were recorded at A254 using the Brandel Gradient Fractionation System and an ISCO UA-6 UV/Vis detector. An aliquot of ribosome fractions representing monosome or polysome were collected followed by digestion with E. coli RNase I (750 U per 100 A260 units) by incubation at 4 °C for 1 h. Total RNA was extracted using Trizol LS reagent. Purified RNAs were used for cDNA library construction.
The ribosome-protected mRNA fragments were separated on a 15% polyacrylamide TBE-urea gel and visualized using SYBR Gold. Selected regions in the gel corresponding to 25–35 nt were excised. RNA fragments were dissolved by soaking overnight in 400 μL RNA elution buffer (300mM NaOAc, pH 5.2, 1mM EDTA, 0.1 U mL−1 SUPERase_In). The gel debris was removed using a Spin-X column, followed by ethanol precipitation. Purified RNA fragments were resuspended in nuclease-free water and quantified using Qubit 2.0 Fluorometer. A fraction of RNAs (10~200 ng) were used for cDNA library construction. In brief, 10 μL RNAs were mixed thoroughly with 1 μL T4 PNK (10 U), 1 μL purified TS2126 and 1 μL PAP1 enzyme in 7 μL Ezra buffer). The mixture was incubated at 37°C for 30 min followed by 65°C for 20 min. After ethanol precipitation at - 20°C for 30 min, the dissolved RNA pellet was mixed with 0.5 μM 5’ end adaptor followed by ligation for 90 min at 22 °C in a 10 μL reaction mixture (1 × T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated KQ). The ligated RNA sample was mixed with 1 μl 0.5 mM dNTP and 1 μl 0.5 μM RT primer and incubated at 65 °C for 3 min, followed by incubation on ice for 1 min. The reaction mix was then added with 9 μl cDNA synthesis mix (5 × first strand buffer, 0.1 M DTT and 750 μg/μl m-MLV-mut5) followed by incubation at 50°C for 30 min. The synthesized cDNAs were mixed with 10 μL rRNA depletion oligo mix tagged with biotin (1 μL 25 μM oligo mix and 3 μL 20 × SSC buffer) and heated at 94°C for 30 s followed by slowly cooling down (3 °C/min) to 37 °C. 30 μL pre-washed streptavidin magnetic beads was added to each sample and stay at room temperature for 10 min. After placing on magnet stand for 1 min, the supernatant was transferred to a new tube and precipitated by ethanol. rRNA depleted cDNAs were amplified by PCR using barcoded sequencing primers. The PCR contains 1 × HF buffer, 0.2 mM dNTP, 0.5 μM oligonucleotide primers, and 0.5 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel. Expected DNA at 180 bp was excised and recovered from DNA gel elution. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts  of barcoded samples were pooled into sequencing lanes, which were sequenced using NextSeq 500.

value: Mouse embryonic fibroblasts


title: Ezra_seq_mouse_heart

source_name: Mouse heart

value: Mouse heart


title: intestinal organoids, Veh_D1#1


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors [ASCP4]

state: United States

data_processing:
kallisto pseudoaligner v0.44.0
sleuth v0.30.0 for differential expression analysis and gene count quantification
Differentially expressed genes filtered on FDR<%5 and beta<1
Genome_build: mm10
Supplementary_files_format_and_content: xls, differential expression analysis and calculated absolute expression values

source_name: Epcam+ Mouse Pancreas Tumors Cells

extract_protocol:
Total RNA was isolated using the RNeasy Micro Plus kit (QIAGEN).
RNA libraries were generated using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). Libraries were pooled and single end sequenced (1x75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina).

treatment_protocol: In vivo tamoxifen induction of 8 week old Msi2-CreER MycT58A mice.  Pancreas tumors isolated and sorted for Epcam+ tumor cells 12 weeks following tamoxifen induction.

value: ASCP


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors [GFP1]

source_name: Msi2-GFP sorted cells from Normal Mouse Pancreas

value: Normal Pancreas


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors [GFP2]


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors [ASCP2]


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors [ASCP1]


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors [ACC2]

value: ACC


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors [ACC1]


title: scATAC-seq analysis of Msi2-MycT58A Mouse Pancreas ASCP Tumor

source_name: Mouse Pancreas Tumors Cells

value: NSG


title: Control DNA, 100% methylated

city: Pasadena

first: Yitong

last: Ma

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Caltech

library_source: other

data_processing:
Trim Galore!
Bismark methylation extractor
Assembly: Reference plasmid map (submitted the plasmid maps to addgene (addgene.org/plasmids/articles/28233817/))
Supplementary files format and content: txt file of CpG methylation calls
Library strategy: EM-seq

molecule: other

organism: Escherichia coli

source_name: WT bacterial cell

growth_protocol: Standard CHO condition

extract_protocol:
DNeasy Blood & Tissue Kits, Qiagen
NEBNext Enzymatic Methyl-seq Conversion Module, NEB; Nextera XT Library Prep protocol, Illumina
Enzymatic Methyl-seq

treatment_protocol: doxycycline 1ug/ml

value: WT bacterial cell

value: M.SssI treated

tag: sample type

value: plasmid DNA (control run before integration into cells)


title: Control DNA, 50% methylated

value: 50% mix of M.SssI treated and control


title: Control DNA, not methylated

value: control


title: intestinal organoids, AA_D1#1


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors [ASCP3]


title: TRD_TRG, SI-IEL, WT, replicate 1

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

institute: FAU Erlangen

data_processing:
Merging of corresponding paired-end sequences was performed with IgRepertoire Constructor with default settings (Safonova et al. 2015). Read Quality was verified by FASTQC analysis. Since each cDNA molecule was uniquely labelled during library preparation, PCR amplification bias and sequencing errors were corrected by only considering unique FID and RID combinations for downstream analysis (Khan et al. 2016). Subsequently, reads were annotated to TRG and TRD V-, D- and J-segments with the Change-O wrapper (Gupta et al. 2015) for IgBLAST using the IMGT reference.
Supplementary files format and content: tab-separated value files produced with IgBLAST

source_name: SI-IEL

extract_protocol:
To retrieve single cell suspensions from spleen, freshly-isolated organs were injected with Collagenase D/DNAse I solution (2mg/ml and 1mg/ml) with a syringe followed by a 15-minute incubation at 37°C. The organs were transferred into GentleMACS C-Tube containing 3ml PBS and subjected to the pre-defined “37 SDK” program in the gentleMACS Octo Dissociator. Retrieved cell suspensions were filtered through a 70 𝜇m filter and cells were pelleted, washed with PBS and subjected to erythrocyte lysis. Small intestines were removed and cleaned of connective tissue, Peyer's patches and luminal content. Intraepithelial cells were isolated by incubating in an EDTA-containing buffer at 37 °C and subsequent vigorous shaking. γδ T cells from spleen and the small intestinal epithelium were identified as CD3+ γδTCR+ αβTCR- and subjected to flow cytometry sorting (Astrios II). Cells were directly sorted into lysis buffer and stored at -20 °C until RNA extraction and reverse transcription to cDNA.
To apply a molecular amplification fingerprinting (MAF) strategy individual transcripts were labelled during cDNA synthesis. Thus, primers binding to the constant segment of TRG and TRD chains were used which included a Reverse Identifier (RID) and Illumina Adapter sequences for cDNA synthesis. TRG and TRD reads were transcribed from RNA to cDNA. cDNA products were cleaned up in three consecutive rounds with SPRI beads (Ampure/Agencourt) and subjected to multiplex PCR. V-gene specific primers included Forward Identifiers (FID) for correcting amplification and sequencing bias as well as Illumina Adapter sequences. The PCR products from the multiplex DNA step were cleaned up with SPRI beads (Ampure/Agencourt). After clean-up of the PCR products, individual sample indices were added to the PCR amplicons using Illumina Nextera i5 and i7 primers. The cleaned cDNA was then used as template for sample indexing via adding unique sample indices (Illumina Nextera Kit). At each step, success and quality of the PCRs were verified using gel electrophoresis

value: SI-IEL

value: gamma delta T cells

value: Tcrd KI/-


title: TRD_TRG, SI-IEL, WT, replicate 3

value: Tcrd +/-


title: TRD_TRG, SI-IEL, WT, replicate 2


title: TRD_TRG, SI-IEL, KI, replicate 3


title: TRD_TRG, SI-IEL, KI, replicate 2


title: TRD_TRG, spleen, KI, replicate 2

source_name: Spleen

value: Spleen


title: TRD_TRG, spleen, KI, replicate 3


title: TRD_TRG, spleen, WT, replicate 2


title: TRD_TRG, spleen, WT, replicate 1


title: TRD_TRG, spleen, KI, replicate 1


title: WT_2i_72h oxbis

city: Saarbrücken

first: Jörn

last: Walter

state: Saarland

address: Campus A2.4

department: Genetics and Epigenetics

institute: Saarland University

data_processing:
(a) The hidden states i.e. the estimated distribution of C, 5mC and 5hmC. More precisely: uu (unmethylated on both DNA strands), um or mu (methylated only on upper or lower strand, respectively), uh or hu (hydroxylated on upper or lower and unmethylated on the other strand), mm (methylated on both DNA strands), hh (hydroxylated on both DNA strands), mh or hm (methylated on one and hydroxylated on the other strand) and toth (total frequency of all states that contain at least one 5hmC).
(b) The efficiencies i.e. the activity of Dnmts and Tets given as De_novo (de novo methylation efficiency for Dnmts), maint (maintenance methylation efficiency for Dnmts) or hydroxyl (hydroxylation efficiency of Tet enzymes).
(c) The standard deviations of the estimated Efficiencies given as De_novo_sd (standard deviation given of de novo methylation efficiency) maint_sd (standard deviation of maintenance efficiency), hydroxyl_sd (standard deviation of hydroxylation efficiency).
Column 1 - Chromosome: name of the chromosome e.g. 1 for chromosome 1
Column 10 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was only methylated on the lower strands i.e. C/5mC.
Column 11 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was unmethylated on both DNA strands i.e. C/C.
Column 2 - Position of the cytosine: e.g. 3003721
Column 3 - DNA Strand: Either C (upper strand) or G (lower strand). Indicates to which DNA strand the methylation has been mapped. This is only relevant for the non-hairpin information given in columns 4, 5 and 6.
Column 4 - Coverage: lists the coverage of the analyzed cytosine.
Column 5 - Methylation: lists how often an analyzed cytosine has been methylated
Column 6 - Unmethylated: lists how often an analyzed cytosine has been unmethylated
Column 7 - Sequence context: Gives the sequence context of the analyzed cytosine. Can be âCGâ for CpG, âGCâ for GpC or âothersâ for CpH.
Column 8 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was methylated on both DNA strands i.e. 5mC/5mC.
Column 9 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was only methylated on the upper strands i.e. 5mC/C.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: DSI file format: the abbreviation âdsiâ stands for âdouble strand informationâ. The dsi file is a tab separated text file without header and contains the sequencing results of the hairpin bisulfite sequencing experiment, visualizing the four different states of a given CpG position i.e. both dna strand are methylated - 5mC/5mC; DNA is only methylated at the upper strand - 5mC/C, DNA only methylated on the lower strand - C/5mC or both DNA strands are unmethylated at a given CpG - C/C. DSI files can be visualized using the Integrative Genomics Viewer (IGV) (http://software.broadinstitute.org/software/igv/). The file contains the following elven columns:

source_name: cell culture

growth_protocol: Embryonic stem cells were cultured as discribed in Ficz et al. 2013. Briefly, ES cells were cultured without feeders either in standard serum-containing media (DMEM 4,500 mg/l glucose, 4 mM L-glutamine, 110 mg/l sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 microg/ml streptomycin, 0.1 mM nonessential amino acids, 50 microM Î²-mercaptoethanol, and 103 U/ml LIF ESGRO) or under 2i culturing conditions (Ying et al., 2008) (serum-free N2B27 [Cat. DMEM/F12: GIBCO 21331; Neurobasal: GIBCO 21103; N2: Stem Cells SF-NS-01-005; B27: GIBCO 17504-044] supplemented with 103 U/ml LIF and Mek inhibitor PD0325901 [1 microM] and Gsk3Î² inhibitor CHIR99021 [3 microM]).

extract_protocol: Genomic DNA was prepared using QIAamp DNA Micro Kit or AllPrep DNA/RNA mini kit (QIAGEN).  1.2 μg DNA is divided equally into three 0.5ml reaction tubes and digested in a 20 μl reaction using 20 U of HaeIII (NEB), AluI (NEB) and 10 U HpyCH4V (NEB), respectively. The reactions are incubated overnight for a minimum of 12 h at 37 °C. Restriction enzymes are inactivated at 80 °C for 30 min. The reactions are pooled and subjected to a ligation step. During this process, hairpin linker and sequencing adapter are introduced to the opposed ends of each restriction fragment. For this, 200 mM biotin labeled hairpin linker and 100 mM sequencing adapter are added to the digested DNA, incubatedwith 1 mM ATP and 2000 U T4 DNA Ligase (NEB) for 16 h at 16 °C. The reaction is purified using AMPureXP beadsfollowed by enrichment for hairpin containing fragments with streptavidin beads. The library is then subjected to BS/oxBS work-flow of the TrueMethyl kit from CEGX according tomanufacturer’s instructions. Amplification of the library was done with HotStarTaq® polymerase (Qiagen) and sequencing was performed on an Illumina HiSeq 2500 platform in a 150 bp paired-end sequencing mode.

value: embryonic stem cell


title: TRD_TRG, spleen, WT, replicate 3


title: lung-cancer-3(Ca3) MeDIP-seq

city: 上海

first: Yani

last: Kang

address: 东川路800号

institute: Shanghai Jiaotong University

data_processing:
Low-quality reads were filtered using trimmomatic. Then clean reads were mapped to the reference genome (GRCh38) using bowite2.
The SAM files were sorted to BAM files using samtools, and duplicates were removed using picard.
We calculated the MeDIP-seq reads per gene using htseq.
The edgeR package was used for the differential methylation analysis, with p value < 0.01 considered to be differentially methylated significantly.
Assembly: hg38
Supplementary files format and content: Xlsx file includes matrix table with results of edgeR analysis between lung cancer samples and adjacent normal samples

source_name: lung

extract_protocol:
Genomic DNA from human lung tissue samples  were extracted using the Axygen gDNA Extraction kit (Axygen, CA, USA) according to the protocol described by the manufacturer.
MeDIP-seq library was constructed using the EpiQuik™ MeDIP Ultra Kit (Cat # P-1052; Epigentek,NY,USA) according to the protocol described by the manufacturer.

value: lung

tag: disease

value: lung cancer


title: lung-normal-1(Cap1) MeDIP-seq

value: normal


title: lung-cancer-2(Ca2) MeDIP-seq


title: lung-normal-2(Cap2) MeDIP-seq


title: lung-cancer-1(Ca1) MeDIP-seq


title: EphB4 Mutant_heart 2

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

description: eI6.CEL_EphB4 mutat

hyb_protocol: 10 µg of cRNA were hybridized for 16hr on  Affymetrix Mouse Genome 430 2.0 Array as recommended by manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing:
The data was analyzed with   Affy – an Bioconductor package (http://www.bioconductor.org).  Briefly, after background correction, data was normalized using RMA (Robust Multiarray Average). Probe level data was summarized to gene level data.
Differential expression between Wt and mutant mouse was calculated using a One-way ANOVA

label: biotin

source_name: EphB4 Mutant_heart

label_protocol: Starting from 10 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions

growth_protocol: mouse heart Samples

extract_protocol: RNA was extracted from mouse heart using  RNeasy mini kit (Qiagen Valenica, CA)

tag: genotype/variation

value: EphB4 Mutant

value: heart


title: EphB4 Mutant_heart 3

description: eM5.CEL_EpHB4 mutant

tag: tissue


title: EphB4 Mutant_heart 1

description: eI5.CEL_EphB4 mutant


title: WT_heart 1

value: wild type


title: WT_heart 3


title: TRD_TRG, SI-IEL, KI, replicate 1

tag: cell type