title: WT-PBS

type: RNA

city: Columbus

first: Tsonwin

last: Hai

state: OH

address: 1060 Carmack Rd.

department: Biological Chemistry and Pharmacology

institute: Ohio State University

description: Gene expression data from WT-PBS lung monocytes/macrophages.

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on Clariom S mouse array.

scan_protocol: Arrays were scanned using the GeneChip 3000 instrument system.

data_processing: The data were analyzed with Transcriptone Analysis Console 4.0 using Affymetrix/Applied Biosystems default analysis settings and global scaling as normalization method.

label: biotin

source_name: WT FVB mouse treated with PBS and injected with MVT-1 breast cancer cells 4 days later.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix/Applied Biosystems protocol from 100 ng total RNA (GeneChip WT PLUS Reagent Kit User Guide, Applied Biosystems, 2020).

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

treatment_protocol: WT/Atf3 KO FVB/n mice were treated with PBS/cyclophosphamide. Four days later, 1x10^6 MVT-1 breast cancer cells were IV injected through tail vein. Lungs were collected 3 d later. Lung monocytes/macrophages isolated by FACS.

value: lung macrophage/monocyte

tag: age

value: 8-12 weeks

value: WT

value: FVB


title: H2A.X WT Rep1 - D6

status: Public on Aug 03 2021

type: SRA

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

country: USA

institute: University of Rochester

library_source: transcriptomic

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRCh39/hg38 + Gencode 31
Supplementary_files_format_and_content: raw gene counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were grown in expansion media and the cells were allowed to mature in differentiation media. Cells were taken at D0 and D6 of differentiation.

extract_protocol: The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome.

tag: cell line

tag: differentiation day

tag: genotype

value: H2A.X WT


title: pfap2-g5_trun_3D7_T_rep1_RNA-seq

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

country: China

institute: Tongji University

description: WT_vs_pfap2-g5_trun_3D7_rep1_FPKM_sense_and_antisense_RNA.xlsx

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 75 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0)  with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1)  with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above. Then FPKM of each gene was calculated in R.

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in medium containing 0.5% Albumax II with O type fresh red blood cells, and a gas phase with 5% O2, 5 % CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from parasites with a combination of TRIzol (Invitrogen) treatment and using a Direct-zol RNA Kit (Zymo Research) as manufacturer’s instructions.
Library preparation for strand-specific RNA-seq was carried out by poly(A) selection with the KAPA mRNA Capture Beads (KAPA), and fragmented to about 300–400 nucleotides (nt) in length, then all subsequent steps were performed according to a KAPA Stranded mRNA-Seq Kit Illumina platform (KK8421).

treatment_protocol: Parasite lines were  synchronized twice in two continuous intraerythrocytic cycles by 5% sorbitol solution followed by a percoll treatment in the cycle to obtain asexual ring (10-15 hpi), trophozoite (25-30 hpi), schizont (40-45 hpi) at continuous timepoints.  At the same time, the highly synchronized ring-stage parasites were set up at 2% parasitemia (4% haematocrit) to perform gametocytogenesis assay . After re-invasion, 50 mM N-acetyl-D-glucosamine was added into the cultures to kill the asexual replicating forms after sexual commitment. The growth of the parasites was monitored by making Giemsa smears every day until mature gametocytes were observed in the culture by Giemsa staining of thin blood smears. Parasites were harvested at day 2, 4, 6, 8, 10  during the process of gametocyte induction.

tag: development stage

value: Trophozoite

tag: strain

value: Pf 3D7

tag: host

value: Homo sapiens


title: pfap2-g5_trun_3D7_T_rep2_RNA-seq

description: WT_vs_pfap2-g5_trun_3D7_rep2_FPKM_sense_and_antisense_RNA.xlsx


title: PfAP2-G_GFP_WT_T_rep1_TF_ChIP-seq

library_source: genomic

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3)  with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8) .
MACS2 (v2.1.1) was used to perform peak calling with the p-value cutoff of 0.01.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611.

molecule: genomic DNA

extract_protocol:
Synchronized PfAP2-G5-GFP::WT, PfAP2-G-GFP::WT, PfAP2-G-GFP::pfap2-g5_trun parasites at different stages were harvested and cross-linked immediately with 1% paraformaldehyde (Sigma) by rotating for 10 min at 37 ℃, then quenched with 0.125 M glycine for 5 min. The culture was resuspended with 1 x PBS and parasites were released from iRBC with 0.15% saponin for 10- 15 min on ice. The washed nuclei were isolated by incubation with 2 ml of Lysis Buffer (10 mM HEPES pH 7.9, 10 mM KCl, 0.1 mM EDTA pH8.0, 0.1mM EGTA pH8.0, 1mM DTT, 0.25% NP40, 1 x protease inhibitors cocktail) for 30 min on ice, and followed by dounce homogenization for 100 strokes. Afterwards the nuclei were resuspended in 200 μl of SDS Lysis Buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH8.0) for sonication to generate 200–500 bp fragments in length. The sonicated chromatin was diluted ten-fold with dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 150 mM NaCl, 1 x protease inhibitors cocktail) and precleared with Protein A/G magnetic beads (Pierce) for two hours. The precleared chromatin supernatant was incubated with 1 μg rabbit anti-GFP (Abcam, ab290) or rabbit IgG (Abcam) as control and Protein A/G magnetic beads at 4 ℃ overnight with a small volume of non-immunoprecipitated input material kept separately. After extensive washes, protein-DNA complexes were eluted with Elution Buffer (1% SDS, 0.1 M NaHCO3). Crosslinking was reversed by incubating overnight at 45°C and DNA was treated with RNase A at 37°C for 30 min and Proteinase K at 45°C for two hours. ChIP-DNA was extracted using MinElute PCR purification kit (Qiagen, 28006).
ChIP-DNA was end-repaired (Epicentre No.ER81050), adding protruding 3’ A base (NEB No.M0212L), adapter ligation(NEB No.M2200L), size selection and amplification of libraries(KAPA Biosystems, KB2500) with a PCR program: 1 min at 98 ℃, 12 cycles of 10 s at 98 ℃, 1 min at 65 ℃; finally extended 5 min at 65 ℃.

treatment_protocol: PfAP2-G5-GFP::WT, PfAP2-G-GFP::WT, PfAP2-G-GFP::pfap2-g5_trun parasite lines were  synchronized twice in two continuous intraerythrocytic cycles by 5% sorbitol solution to harvest  trophozoite stage parasites. PfAP2-G5-GFP::WT line was synchronized twice with 5% sorbitol solution followed by a percoll treatment in the cycle before the cultures were set up for gametocytogenesis assay. Then the highly synchronized ring-stage parasites were set up at 2% parasitemia (4% haematocrit). After re-invasion, 50 mM N-acetyl-D-glucosamine was added into the cultures to kill the asexual replicating forms after sexual commitment to harvest G0-G1 stage parasites.

value: Trophozoite (30-40hpi)

tag: chip antibody

value: GFP, abcam, ab290

value: wild type


title: HDAC1_shPAX9_2

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: cells transduced with PAX9 shRNA #2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
ChIP-seq ATAC-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 and STAR version 2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
ATAC-seq reads were aligned to UCSC hg19 using BWA version 0.7.12. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: cells were maintained with DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. For ATAC-seq, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience). 50K to 100K nuclei were then centrifuge (pre-chilled) at 500 g for 10 min. Supernatant was then removed and the nuclei were resuspended in 50 uL of tagmentated DNA by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer shaking at 1,000 rpm, and then cleaned up by the MiniElute reaction clean up kit (Qiagen).
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
ATAC-seq: Tagmentated DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 50M PE reads (25M in each direction) per sample.

treatment_protocol: Cells were treated with either DMSO or HDAC1/2 inhibitor MERCK60 or EZH2 inhibitior GSK126 for 24 to 96 hours.

tag: cell type

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

value: anti-HDAC1 (activemotif 40967)


title: PfAP2-G5_GFP_WT_D5_rep2_TF_ChIP-seq

value: Pf NF54


title: H2A.X KO Rep2 - D6

value: H2A.X KO


title: HDAC1_shNONT

description: cells transduced with non-targeting shRNA


title: WT_3D7_S_rep1_RNA-seq

value: Schizont


title: WT_3D7_T_rep2_RNA-seq


title: HDAC2_shNONT

value: anti-HDAC2 (abcam ab7029)


title: KO-CTX

description: Gene expression data from KO-CTX lung monocytes/macrophages.

organism: Mus musculus

source_name: KO FVB mouse treated with CTX and injected with MVT-1 breast cancer cells 4 days later.

value: lung macrophage/monocyte

value: 8-12 weeks

value: Atf3 KO


title: Sample 1_IPMN_ZX-2

city: Beijing

first: Han

last: Li

address: Gongti Road

department: HBP

institute: Beijing Chaoyang hosipital

description: one sample from intraductal papillary mucinous neoplasm

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Intraductal papillary mucinous neoplasm

extract_protocol:
Three specimens were stored in GEXSCOPETM tissue preservation solution (Nanjing, Singleron), washed with Hanks Balanced Salt Solution three times, and minced into 1-2mm fragments with a sterile surgical scalpel. Then, we digested tissue pieces with 2ml GEXSCOPETM solution at 37℃ for 15min, in a 15ml centrifuge tube, with sustained agitation. Tissue slurry was passed through a 40μm sterile cell strainer, and the single-cell suspension was centrifuged at 1,000 RPM for 5 minutes. After discarding the supernatant, we resuspended the sediment in 1ml PBS (HyClone) and added 2 mL GEXSCOPETM red blood cell lysis buffer (Nanjing, Singleron) incubating 10 minutes at 25°C, to remove the red blood cells. The solution was then centrifuged at 500 × g for 5 min and suspended in PBS. Finally, we stained single cells with trypan blue (Sigma) and evaluated their viability microscopically.
We adjusted the concentration of single-cell suspensions to 1×105 cells/mL in PBS (HyClone) and loaded them onto microfluidic devices. Next, we applied GEXSCOPETM Single-Cell RNA Library Kit (Singleron Biotechnologies) to construct scRNA-seq libraries. We diluted individual libraries to 4nM and pooled them for sequencing on Illumina HiSeq X with 150 bp paired-end reads.

tag: tissue type

value: Intraductal papillary mucinous neoplasm

value: 74 years

tag: gender

value: Male

tag: cell number


title: KO-PBS

description: Gene expression data from KO-PBS lung monocytes/macrophages.

source_name: KO FVB mouse treated with PBS and injected with MVT-1 breast cancer cells 4 days later.

value: FVB


title: WT_3D7_R_rep2_RNA-seq

value: Ring

value: Pf 3D7

value: Homo sapiens


title: pfap2-g5_trun_3D7_S_rep2_RNA-seq


title: HDAC1_shPAX9_1

description: cells transduced with PAX9 shRNA #1

value: small cell lung cancer

value: wild type


title: WT-CTX

description: Gene expression data from WT-CTX lung monocytes/macrophages.

source_name: WT FVB mouse treated with CTX and injected with MVT-1 breast cancer cells 4 days later.

value: WT


title: HDAC2_shPAX9_1

description: cells transduced with PAX9 shRNA #1

value: Low passages (6-10)


title: Sample 2_PASC_ZX-3

description: one sample from pancreatic adenosquamous carcinoma

source_name: Pancreatic adenosquamous carcinoma

value: Pancreatic adenosquamous carcinoma

value: 59 years


title: HDAC2_shPAX9_2

description: cells transduced with PAX9 shRNA #2

value: anti-HDAC2 (abcam ab7029)


title: H3K27Ac_shPAX9_1

value: anti-H3K27Ac (CST #8173)

tag: treatment

value: cells transduced with PAX9 shRNA #1

value: PAX9 depletion


title: H3K27Ac_shNONT

value: cells transduced with non-targeting shRNA

value: control


title: H3K27Ac_shPAX9_2

value: cells transduced with PAX9 shRNA #2


title: pfap2-g5_trun_3D7_S_rep1_RNA-seq

value: Schizont


title: WT_3D7_T_rep1_RNA-seq

value: Trophozoite


title: WT_3D7_S_rep2_RNA-seq

value: Pf 3D7


title: H3K27me3_NCI_H1963

value: normal cells


title: pfap2-g5_trun_3D7_R_rep2_RNA-seq

value: Ring

value: Homo sapiens


title: pfap2-g4_trun_NF54_D8_rep1_RNA-seq

description: WT_vs_pfap2-g4_trun_NF54_rep1_FPKM_sense_and_antisense_RNA.xlsx

value: Pf NF54


title: PAX9_Rep2

value: small cell lung cancer

value: Low passages (6-10)

value: anti-PAX9 (CST #12847)


title: pfap2-g5_trun_3D7_R_rep1_RNA-seq


title: MTA2_H1963

value: anti-MTA2 (abcam ab8106)


title: Sample 3_normal pancreas_ZX-4

description: one sample from normal pancreas

source_name: normal pancreas sample

value: normal pancreas sample

value: 50 years

value: Male


title: pfap2-g4_trun_NF54_D10_rep2_RNA-seq

description: WT_vs_pfap2-g4_trun_NF54_rep2_FPKM_sense_and_antisense_RNA.xlsx


title: mature_mTEC_WT2

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

description:
RNA from 1 individual mouse
mature_mtec_transcripts.counts.gz

data_processing:
Basecalling was performed using Albacore (v2.3.1) and reads were trimmed using Porechop (v0.2.3)
Fastqs from 3 replicates were merged and mapped using Minimap2 (-ax splice, v2.14-r883)
Counts were quantified using featureCounts (-L option, v1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: [*mtec_transcripts.counts.txt]  tab-delimited files including transcript counts from the combined mature and immature samples

source_name: mature mTEC

extract_protocol:
Thymi were dissected from mice, enriched for CD45- cells (AutoMACS) and 10,000 cells sorted by FACS (CD80-CD86- immature versus CD80+CD86+ mature mTEC). RNA was extracted using QUIAGEN RNeasy micro plus kit.
Libraries were prepared using the cDNA-PCR kit (SQK-PCS108) from Oxford Nanopore Technologies.

value: 4-6 weeks

tag: Sex

value: female

value: wildtype

tag: tissue

value: thymus

value: mature medullary thymic epithelial cells (mTEC)

tag: facs phenotype

value: CD45- EpCAM+  Ly51- UEA+  CD80+ CD86+


title: pfap2-g4_trun_NF54_D10_rep1_RNA-seq


title: immature_mTEC_WT3

description:
RNA from 1 individual mouse
immature_mtec_transcripts.counts.gz

source_name: immature mTEC

tag: age

value: immature medullary thymic epithelial cells (mTEC)

value: CD45- EpCAM+  Ly51- UEA+  CD80- CD86-


title: immature_mTEC_WT1

description:
RNA of 3 mice was pooled
immature_mtec_transcripts.counts.gz


title: WT_3D7_R_rep1_RNA-seq

value: Ring

value: Pf 3D7

value: wild type

value: Homo sapiens


title: pfap2-g4_trun_NF54_D8_rep2_RNA-seq

value: Pf NF54


title: pfap2-g4_trun_NF54_D6_rep1_RNA-seq


title: pfap2-g4_trun_NF54_T_rep2_RNA-seq

value: Trophozoite


title: mature_mTEC_WT3


title: pfap2-g4_trun_NF54_T_rep1_RNA-seq


title: pfap2-g4_trun_NF54_D6_rep2_RNA-seq


title: pfap2-g4_trun_NF54_D4_rep1_RNA-seq


title: mature_mTEC_WT1

description:
RNA of 3 mice was pooled
mature_mtec_transcripts.counts.gz


title: immature_mTEC_WT2


title: H3K4me3_NCI_H1963

tag: cell line

value: small cell lung cancer

value: Low passages (6-10)

value: anti-H3K4me3 (CST #9751)

value: normal cells

value: control


title: Mouse retina P8 (scATAC-seq)

city: Baltimore

first: Seth

last: Blackshaw

state: Maryland

address: 733 N. Broadway Avenue

institute: Johns Hopkins University

data_processing:
The Cell Ranger (Zheng et al., 2017) ATAC pipeline was used to process the raw sequencing data for mapping, de-duplication and identification of Tn5 cut sites.
We generated the cell-by-peaks matrix for each sample using the same method as described in Satpathy, A. T. et al .First, we constructed 2.5-kb tiled windows across the mm10 genome using the local script.  Next, a cell-by-window sparse matrix was computed by counting the Tn5 insertion overlaps for each cell, and this matrix was then binarized and inputted to Signac package (0.2.5) to create a Seurat object using ‘CreateSeuratObject.’  Second, we normalized the cell-by-window matrix by TF-IDF methods using ‘RunTFIDF’ and ran a singular value decomposition (SVD) on the TF-IDF normalized matrix with ‘RunSVD.'  We retained the 2nd to 30th dimensions, and identified clusters using SNN graph clustering with 'FindClusters' with a resolution of 0.3.  Third, to identify high-quality peaks for each cluster in each sample, we called peaks for each cluster by MACS2 with the command: '-shift -75 --extsize 150 --nomodel --callsummits --nolambda --keep-dup all -q 0.05'.  The peak summits were then extended to 250 bp on either side to a final width of 500 bp and then filtered by the mm10 v2 blacklist regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10blacklist.v2.bed.gz). The top 50,000 peaks for each cluster in each sample were kept, converted to Granges, and merged into a union peak set with the function ‘reduce’ in the GenomicRanges package.
The ArchR package(Granja et al., 2020) was used to process the fragment files.  We calculated the TSS enrichment, unique fragments and nucleosome banding for each cell with the function ‘createArrowFiles’’. Then we kept the high-quality cells with the following criteria: 1) The number of unique nuclear fragments > 1000.  2) TSS enrichment score > 10.  3) nucleosome banding score < 4. We next identified potential doublets with the function ‘addDoubletScores’, and removed doublets using ‘filterDoublets’’ with the following parameters: cutEnrich = 2, cutScore = -Inf, and filterRatio =2. Finally, we filtered the fragment files according to the cells we retained. These cleaned fragment files were used for all downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell annotation txt files

source_name: Mouse retina P8

extract_protocol:
Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.Trypan blue staining.
ScATAC-seq was performed using the 10x Genomic single cell ATAC reagent v1.1 kit following the manufacturer’s instruction. Briefly, dissociated cells were centrifuged at 300xg for 5 min at 4oC. Cell pellet was resuspended in 100 μl of Lysis buffer, mixed 10x by pipetting and incubated on ice for 3 min. Wash buffer (1 ml) was added to the lysed cells, and cell nuclei were centrifuged at 500xg for 5 min at 40C. Nuclei pellet was re-suspended in 250 μl of 1x Nuclei buffer. Cell nuclei were then counted using Trypan blue. Re-suspended cell nuclei (10-15k) were used for transposition and loaded into the 10x Genomics Chromium Single Cell system. Libraries were amplified with 10 PCR cycles and were sequenced on Illumina NextSeq or NovaSeq with ~200 million reads per library. Sequencing data was processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) using default parameters.

treatment_protocol: CD1 mice were purchased from Charles River Laboratories.  All experimental procedures were pre-approved by the Institutional Animal Care and Use Committee (IACUC) of the Johns Hopkins University School of Medicine. Mouse embryos or pups at different timepoints of retinal development (E11, E12, E14, E16, E18, P0, P2, P5, P8, P11 and P14) were used for this study.

tag: time point


title: PAX9_Rep1

value: anti-PAX9 (CST #12847)

tag: genotype


title: pfap2-g4_trun_NF54_D2_rep2_RNA-seq

tag: development stage


title: Mouse retina P2 (scATAC-seq)

source_name: Mouse retina P2


title: pfap2-g4_trun_NF54_D2_rep1_RNA-seq

tag: strain


title: Mouse retina P14 (scATAC-seq)

source_name: Mouse retina P14


title: Mouse retina P0 (scATAC-seq)

source_name: Mouse retina P0


title: WT_NF54_D10_rep1_RNA-seq (control for pfap2-g4_trun)

tag: host


title: WT_NF54_D8_rep2_RNA-seq (control for pfap2-g4_trun)


title: pfap2-g4_trun_NF54_D4_rep2_RNA-seq


title: WT_NF54_D8_rep1_RNA-seq (control for pfap2-g4_trun)


title: Mouse retina E18 (scATAC-seq)

source_name: Mouse retina E18


title: Mouse retina P11 (scATAC-seq)

source_name: Mouse retina P11


title: WT_NF54_D6_rep1_RNA-seq (control for pfap2-g4_trun)


title: Mouse retina E16 (scATAC-seq)

source_name: Mouse retina E16


title: Mouse retina E12 (scATAC-seq)

source_name: Mouse retina E12


title: WT_NF54_D10_rep2_RNA-seq (control for pfap2-g4_trun)


title: WT_NF54_D4_rep1_RNA-seq (control for pfap2-g4_trun)


title: Mouse retina P5 (scATAC-seq)

source_name: Mouse retina P5


title: WT_NF54_D2_rep1_RNA-seq (control for pfap2-g4_trun)


title: pfap2-g4_trun_NF54_R_rep1_RNA-seq


title: Treated 1

city: East Lansing

first: Timothy

last: Zacharewski

state: MI

address: 603 Wilson Rd., BCH Building RM#212

department: Biochemistry and Molecular Biology

institute: Michigan State University

description:
source_ontology: http://purl.obolibrary.org/obo/UBERON_0002107
organism_ontology: http://purl.obolibrary.org/obo/NCBITaxon_10090
sex_ontology: http://purl.obolibrary.org/obo/PATO_0000384
days
age_unit_ontology: http://purl.obolibrary.org/obo/UO_0000033
temperature_unit_ontology: http://purl.obolibrary.org/obo/UO_0000195
humidity_unit_ontology: http://purl.obolibrary.org/obo/UO_0000187
toxic_substance_ontology: http://purl.obolibrary.org/obo/CHEBI_28119
vehicle_substance_ontology: http://purl.obolibrary.org/obo/FOODON_03304152
dose_unit_ontology: http://purl.obolibrary.org/obo/NCIT_C67396
dose_unit_ontology: http://purl.obolibrary.org/obo/XCO_0000581
Mice gavaged once and livers collected 2 hours following exposure. Five livers were pooled.

data_processing:
MACS 2.1.0 was used for peak calling
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of ChIP-seq tags

source_name: Liver

extract_protocol:
ChIP-seq analysis of COUP-TFII (NR2F2) and HNF4α  following 2 hrs TCDD exposure was performed using the FactorPath services by Active Motif (Carlsbad, CA) on ~100mg frozen liver sections. Livers cut in small pieces were incubated in 1% formaldehyde for 15 min at room temperature. Cross-linking was halted by the addition of 0.125 M glycine and tissue was homogenized by Dounce homogenizer followed by shearing DNA by sonication to achieve an average length of 300 – 500 bp. A total of 30 μg of precleared sheared chromatin with protein A agarose beads was immunoprecipitated using 5 μL of rabbit anti-NR2F2 polyclonal IgG (sc-8987; Santa Cruz, Dallas, TX) or 20uL of rabbit anti-HNF4a polyclonal IgG (61213; Active Motif) overnight at 4°C. Chromatin was eluted from the beads with SDS buffer and cross-links reversed by incubation with RNase and Proteinase K followed by an overnight incubation at 65°C.
Libraries for sequencing were prepared by Active Motif and sequenced using NextSeq 500 (1 x 75bp).

treatment_protocol: Male C57BL/6 mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected 2 hours following treatment.

value: Liver

value: Male

value: degree fahrenheit

value: percent

value: Innovive disposable cage

tag: bedding

value: ALPHA-dri bedding

tag: water

value: Aquavive water

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: vendor

value: Accustandard

value: Sesame oil

value: TCDD

tag: dose

tag: dose unit

value: Microgram per Kilogram

value: oral gavage

tag: duration

tag: duration unit

value: hours

tag: replicate

tag: chip antibody

tag: antibody vendor

value: Active Motif


title: Untreated 2

tag: tissue

tag: Sex

tag: age

tag: treatment

value: Sesame Oil

value: Santa Cruz


title: WT_NF54_T_rep1_RNA-seq (control for pfap2-g4_trun)

tag: development stage

value: Trophozoite

value: Pf NF54

tag: genotype

value: wild type

value: Homo sapiens


title: Input

value: Liver

tag: strain

value: Male

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: ALPHA-dri bedding

value: Input


title: WT_NF54_R_rep2_RNA-seq (control for pfap2-g4_trun)

value: Ring

tag: host


title: ATAC_H1963

tag: cell line

tag: cell type

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

value: normal cells

value: control


title: pfap2-g4_trun_NF54_S_rep1_RNA-seq

value: Schizont


title: pfap2-g5_trun_NF54_D10_rep2_RNA-seq

description: WT_vs_pfap2-g5_trun_NF54_rep2_FPKM_sense_and_antisense_RNA.xlsx


title: pfap2-g4_trun_NF54_S_rep2_RNA-seq


title: WT_NF54_D6_rep2_RNA-seq (control for pfap2-g4_trun)


title: pfap2-g5_trun_NF54_D10_rep1_RNA-seq

description: WT_vs_pfap2-g5_trun_NF54_rep1_FPKM_sense_and_antisense_RNA.xlsx


title: WT_NF54_D4_rep2_RNA-seq (control for pfap2-g4_trun)


title: pfap2-g5_trun_NF54_D8_rep2_RNA-seq


title: Mouse retina E14 (scATAC-seq)

source_name: Mouse retina E14

tag: time point


title: pfap2-g5_trun_NF54_D8_rep1_RNA-seq


title: Treated 2

tag: bedding

tag: water

value: Aquavive water

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: vendor

value: Accustandard

value: Sesame oil

value: TCDD

tag: dose

tag: dose unit

value: Microgram per Kilogram

value: oral gavage

tag: duration

value: hours

value: Santa Cruz


title: pfap2-g4_trun_NF54_R_rep2_RNA-seq

value: Pf NF54

value: Homo sapiens


title: pfap2-g5_trun_NF54_D6_rep1_RNA-seq


title: WT_NF54_T_rep2_RNA-seq (control for pfap2-g4_trun)

value: Trophozoite

value: wild type


title: pfap2-g5_trun_NF54_D4_rep1_RNA-seq


title: pfap2-g5_trun_NF54_R_rep2_RNA-seq

value: Ring


title: WT_NF54_S_rep1_RNA-seq (control for pfap2-g4_trun)


title: pfap2-g5_trun_NF54_T_rep1_RNA-seq


title: pfap2-g5_trun_NF54_S_rep1_RNA-seq


title: pfap2-g5_trun_NF54_D6_rep2_RNA-seq


title: mouse_smallRNA_3688

city: Indianapolis

first: Shannon

last: Hawkins

state: Indiana

institute: Indiana University School of Medicine

data_processing:
Demultiplexing of the reads was performed with bcl2fastq version unknown pipeline
Adapters and low quality bases were trimmed using Trimmomatic (version 0.32) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:16. Custom perl scripts along with FASTX-Toolkit version 0.0.14 with the following parameters, “-l 17 -v -M 1 -i “, were used to look for partial adapters within the reads
PolyA reads were mapped against GRCm38 or GRCh38 using TopHat2 version 2.1.1 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100
PolyA read counts for each gene were created using HTSeq-Count from the HTSeq package version 0.6.1p1 and Gencode v24 as the annotation for human reads and Gencode M9 as the annotation for mouse
smallRNA reads were mapped against GRCm38 or GRCh38 and also miRbase version 21 as reference using miRDeep2 version 2.0.0.7 to identify and quantify known microRNA’s.
Genome_build: GRCh38
Genome_build: GRCm38
Genome_build: miRbase version 21
Supplementary_files_format_and_content: humanCounts.polyA.tsv - Gene counts for each sample in tab-delimited format
Supplementary_files_format_and_content: human_mirna.counts.tsv - miRNA counts for each sample in tab-delimited format
Supplementary_files_format_and_content: mouseCounts.polyA.tsv - Gene counts for each sample in tab-delimited format
Supplementary_files_format_and_content: mouse_mirna.counts.tsv - miRNA counts for each sample in tab-delimited format

source_name: Uterus

extract_protocol:
Total RNA was extracted from mouse uterus ( three mice per genotype) and ishikawa cells (duplicate per phenotype) using the mirVana miRNA isolation kit. RNA quality control was performed on an Agilent 2100 bioanalyzer
Poly-A RNA libraries were constructed using mRNA Stranded TruSeq protocol (Illumina, San Diego, CA). Small RNA library construction was performed using the TruSeq Small RNA kit (Illumina). Purified libraries were visualized and quantified using a TapeStation HSD1000 (Agilent, Santa Clara, CA).

value: C57BL/6J;129S5/Brd mixed

tag: tissue

value: Uterus

tag: Sex

value: female

value: dcKO


title: WT_NF54_D2_rep2_RNA-seq (control for pfap2-g4_trun)


title: mouse_smallRNA_3686


title: mouse_smallRNA_3682

value: Pten-Dicer het


title: mouse_smallRNA_2747


title: mouse_smallRNA_2717


title: pfap2-g5_trun_NF54_T_rep2_RNA-seq


title: Mouse retina E11 (scATAC-seq)

source_name: Mouse retina E11


title: Untreated 1

value: Liver

value: Male

tag: age

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: ALPHA-dri bedding

value: Aquavive water

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard

tag: treatment

value: Sesame Oil

tag: duration unit

tag: replicate

tag: chip antibody

tag: antibody vendor

value: Active Motif


title: WT_NF54_D4_rep2_RNA-seq (control for pfap2-g5_trun)

tag: development stage

tag: strain

value: Pf NF54

tag: genotype

value: wild type

tag: host

value: Homo sapiens


title: pfap2-g5_trun_NF54_D4_rep2_RNA-seq


title: WT_NF54_S_rep2_RNA-seq (control for pfap2-g4_trun)

value: Schizont


title: WT_NF54_D6_rep1_RNA-seq (control for pfap2-g5_trun)


title: WT_NF54_R_rep1_RNA-seq (control for pfap2-g4_trun)

value: Ring


title: WT_NF54_D2_rep1_RNA-seq (control for pfap2-g5_trun)


title: pfap2-g5_trun_NF54_D2_rep1_RNA-seq


title: WT_NF54_T_rep1_RNA-seq (control for pfap2-g5_trun)

value: Trophozoite


title: WT_NF54_D8_rep2_RNA-seq (control for pfap2-g5_trun)


title: pfap2-g5_trun_NF54_R_rep1_RNA-seq


title: pfap2-g5_trun_NF54_D2_rep2_RNA-seq


title: WT_NF54_D10_rep1_RNA-seq (control for pfap2-g5_trun)


title: WT_NF54_D6_rep2_RNA-seq (control for pfap2-g5_trun)


title: mouse_polyA_2717

value: C57BL/6J;129S5/Brd mixed

value: Uterus

value: female

value: Pten-Dicer het


title: WT_NF54_D4_rep1_RNA-seq (control for pfap2-g5_trun)


title: mouse_polyA_2747


title: mouse_polyA_3601

value: Pten cKO


title: WT_NF54_R_rep2_RNA-seq (control for pfap2-g5_trun)


title: mouse_smallRNA_3699

value: dcKO


title: WT_NF54_D2_rep2_RNA-seq (control for pfap2-g5_trun)


title: WT_NF54_D8_rep1_RNA-seq (control for pfap2-g5_trun)


title: mouse_smallRNA_3601


title: mouse_smallRNA_3591


title: mouse_polyA_3591


title: mouse_polyA_3698

value: Pgr +/+


title: mouse_smallRNA_3698


title: mouse_polyA_3697


title: WT_NF54_S_rep1_RNA-seq (control for pfap2-g5_trun)


title: mouse_smallRNA_2746


title: WT_NF54_S_rep2_RNA-seq (control for pfap2-g5_trun)


title: mouse_polyA_3688


title: mouse_polyA_3699


title: WT_NF54_T_rep2_RNA-seq (control for pfap2-g5_trun)


title: mouse_smallRNA_3697


title: mouse_polyA_3686


title: mouse_polyA_3682


title: WT_NF54_R_rep1_RNA-seq (control for pfap2-g5_trun)


title: Mafb-cKO rep1

city: Tsukuba

first: Toshiaki

last: Usui

state: Ibaraki

address: 1-1-1 Tennoudai

department: Nephrology

country: Japan

institute: University of Tsukuba

data_processing:
Illumina Basespace Onsite software
FASTQ files were imported to CLC Genomics Workbench (Version 7.5.1), mapped to mm10 mouse genome and quantified for annotated genes in ENSEMBLE database to obtain RPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file format include RPKM values for each Sample ...

source_name: Glomeruli

extract_protocol:
Total RNA was extracted byt Triazol (15596-026, Invitrogen). Concentration and purity of RNA were determined using Nanodrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six weeks old mice carrying loxP-flanked Mafb allele with NPHS2 Cre-ERT2 as well as control (Mafbflox/flox) mice were received 75 mg tamoxifen/kg body weight intraperitoneally once daily for 5 consecutive days. Eight weeks later glomeruli were isolated using a magnetic particle and the purity of the isolated glomeruli was confirmed by light microscopy. Total RNA were then extracted and stored immediately in -80 C.

value: Mafb cKO

value: 14 weeks


title: Mafb-cKO rep2


title: Mafb-cKO rep3


title: mouse_smallRNA_3599


title: CTX_CD4_rep5

city: Goyang-si

first: Chungyong

last: Han

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

description: CTX/CD4-treated replication 5

data_processing:
Library strategy: TCR-seq
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
Adapter sequences were removed from raw data using Scythe (v0.994) and Sickle. Sequences were cleaned by excluding reads shorter than 36 base pairs.
The processed data were then aligned in MiXCR (https://mixcr.readthedocs.io).
Aligned TCRα/β sequences were extracted using VDJtools (https://vdjtools-doc.readthedocs.io).
All TCR reads were down-sampled to 10,000 reads per sample and used for computing TCR diversity.
Genome_build: mm10
Supplementary_files_format_and_content: Each tab-delimited text file includes the following information for TCR(α or β) clonotypes of each sample: read count, frequency, nucleotide/amino acid sequence of CDR3, Variable/Diversity/Joining segments, and the reference points for Variable/Diversity/Joining region (starts with conserved Cys residue and ends with conserved PheTrp).

source_name: Lymphoid cells

growth_protocol: On day 0, six- to eight-week-old C57BL/6 female mice were intradermally inoculated with B16F10 (2E+05). On day 3, pre-conditioning lymphodepletion was induced via intraperitoneal injection of 300 mg/kg cyclophosphamide. On day 5, Pmel-1 cells (2E+06) were isolated from the splenocytes of Thy1.1 Pmel-1 transgenic mice (Thy1a/Cy Tg(TcraTcrb)8Rest/J; expressing transgenic TCR specific for gp10025–33 and congenic Thy1.1 antigen) and injected into tumor-bearing mice. Starting on day 5, recombinant human IL-2 (10,000 IU) was intraperitoneally injected daily for 3 days.

extract_protocol:
On day 25, the lymph nodes and spleen were gently disrupted and filtered through a 40 μm nylon cell strainer to make single-cell suspensions. Cells were treated with RBC lysis buffer before use. After staining with anti-CD8 and anti-Thy1.1 fluorochrome-conjugated antibodies, Thy1.1-negative CD8-positive endogenous T cells were isolated by fluorescence-activated cell sorting. Total RNA of each sample was extracted using the RNeasy Plus mini kit (Qiagen).
To generate the TCR sequencing library, 100 ng RNA per sample was reverse transcribed and amplified using nested polymerase chain reaction with a SMARTer mouse TCR a/b profiling kit (Takara Bio). Illumina-specific adaptor sequences were incorporated during amplification. The TCR sequencing library was size-selected and purified using AMPure XP beads (Beckman Coulter).

treatment_protocol: Starting from day 10, anti-CD4 treatment group involved weekly intraperitoneal injections of 200 μg anti-mouse CD4 monoclonal antibody (clone: GK1.5) for 3 weeks.

tag: gender

value: Female

value: Six- to eight-week-old

value: Inguinal lymph nodes and spleen

value: CTX/CD4-treated replication 5


title: CTX_CD4_rep4

description: CTX/CD4-treated replication 4

value: CTX/CD4-treated replication 4


title: WT_NF54_D10_rep2_RNA-seq (control for pfap2-g5_trun)

value: Pf NF54

value: wild type

value: Homo sapiens


title: CTX_CD4_rep3

description: CTX/CD4-treated replication 3

value: CTX/CD4-treated replication 3


title: CTX_CD4_rep2

description: CTX/CD4-treated replication 2

value: CTX/CD4-treated replication 2


title: CTX_CD4_rep1

description: CTX/CD4-treated replication 1

value: CTX/CD4-treated replication 1


title: pfap2-g5_trun_NF54_S_rep2_RNA-seq

value: Schizont


title: U2-OS NSD3 knockdown cells C

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre, University of Toronto

description: CRISPR knockdown

hyb_protocol: The labeled cDNA was hybridized to Affymetrix GeneChip® Human Gene 2.0 ST

scan_protocol: The arrays were then scanned using Affymetrix GeneChip Scanner 3000 (Scanner 2).

data_processing: Microarray data are normalized and analyzed using ‘limma’ package in R

label: Biotin Allonamide Triphosphate

source_name: U2_sgNSD3 biological replicate 3

label_protocol: The cDNA labeled with Biotin Allonamide Triphosphate

growth_protocol: U2-OS contorl and NSD3 knockdown cells are cultured in Dulbecco's modified Eagle's medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) at 37C and 5% CO2.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufactures' instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: Cells are harvested at 80-90% confluency for RNA extraction.

tag: transfection

value: NSD3-targeting sgRNA


title: U2-OS NSD3 knockdown cells B

description: CRISPR knockdown

source_name: U2_sgNSD3 biological replicate 2


title: mouse_polyA_3599

value: C57BL/6J;129S5/Brd mixed

value: Uterus

value: female

value: Pten cKO


title: U2-OS control cells B

description: CRISPR control

source_name: U2_sgCtrl biological replicate 2

value: non-target sgRNA


title: TH_M-Li_DRD_11

city: PASADENA

first: Bryan

last: Yoo

state: California

address: 1200 E California Blvd, Mc 156-29

department: BBE

institute: California Institute of Technology

description: TH_colon_differentially_expressed_genes_volcano.txt

data_processing:
De-multiplexed sequencing reads were generated using Illumina BaseSpace.
UMI specific workflows that were developed and distributed by Lexogen were used to extract reads that are free from PCR artifacts (i.e., deduplication). First, the umi2index tool was used to add the 6 nucleotide UMI sequence to the identifier of each read and trims the UMI from the start of each read. This generates a new FASTQ file, which is then processed through trimming and alignment. Second, after the quality and polyA trimming by BBDuk (Website-https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) and alignment by HISAT2 (version 2.1.0) (Kim et al., 2015) , the mapped reads are collapsed according to the UMI sequence of each read.
Reads are collapsed if they have the same mapping coordinates (CIGAR string) and identical UMI sequences. Collapsing reads in this manner removes PCR duplicates.
Read counts were calculated using HTSeq (Anders et al., 2015) by supplementing Ensembl gene annotation (GRCm38.78).
Raw read counts were run through ShinySeq to obtain differentially expressed genes and downstream gene ontology analyses
Genome_build: GRCm38.78 - mm10
Supplementary_files_format_and_content: differentially expressed gene measurements in txt files

source_name: proximal large intestine

extract_protocol:
Mice were cervically dislocated and the GI tract was removed. 1cm of tissue above and below the cecum were dissected and cleaned to represent tissue from the distal SI and proximal colon, respectively. Tissue was homogenized in TRIzol (ThermoFisher Scientific, Waltham. MA- Cat. No. 15596018) solution using bead-based homogenizing methods, and total RNA was extracted using chloroform per manufacturer’s instructions.
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Greenland, NH) supplemented with UMI (unique molecular index) as per the manufacturer’s instructions.
quant-seq

treatment_protocol: C21 was administered intraperitoneally (i.p.), once daily for 10 consecutive days to all mice

tag: mouse line

value: Th-Cre

tag: aav cargo

value: DREADD and XFP

value: Male


title: CH27_off_pre

city: Philadelphia PA

first: Melanie

middle: A.

last: Ruffner

state: Pennsylvania

address: 3615 Civic Center Blvd, Abramson Research Center

department: Allergy & Immunology

institute: Children's Hospital of Philadelphia

description: Subject CH27; off milk; treated with None

data_processing:
Alignemnt to GRCh38 using STAR run in the 2-pass mode
Gene-level read counts were normalized using the Rlog method
Genes with total read counts less than 6 were removed from analysis
Reads mapping to the Y chromosome were not included in the analysis due to uneven distribution of sex in our cohort of patients.
Reads mapping to both strands of transcripts were counted to account for un-stranded libraries
Differential gene expression between treatment groups was tested using the rank products method on data normalized by Rlog
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-level read counts in tab-delimited text format

source_name: CD4+ cells from  blood

growth_protocol: Human primary peripheral blood CD4+ cells were isolated using magnetic beads (Invitrogen Dynabeads, Carlsbad, CA, USA)

extract_protocol:
Total CD4+ T-cell RNA was extracted (TRIzol reagent, Invitrogen, Carlsbad, CA, USA) and purified (RNeasy Mini Kit, Qiagen, Hilden, Germany).
cDNA was generated and libraries were made with Ovation Ultralow Library System V2 (NuGen, Redwood City, CA, USA) per the manufacturer's instructions.  Paired-end reads were generated using an Illumina HiSeq 4000 (Illumina, San Diego, CA, USA)

treatment_protocol: RNA was isolated immediately from freshly isolated CD4+ cells

tag: ID

value: male

tag: milk consumption

value: Off

tag: eos/hpf


title: CH23_milk_pre

description: Subject CH23; on milk; treated with None

tag: Sex

tag: age

value: On


title: TH_M-Li_DRD_8


title: Control rep1

value: Mafbflox/flox (Control)

value: 14 weeks


title: mouse_polyA_2746

tag: tissue

value: Pgr +/+


title: TH_F-Li_DRD_3

value: Female


title: CH21_milk_EPIT

description: Subject CH21; on milk; treated with EPIT

tag: treatment

value: EPIT


title: CH21_milk_pre

description: Subject CH21; on milk; treated with None


title: TH_F-Li_DRD_4


title: CH20_milk_EPIT

description: Subject CH20; on milk; treated with EPIT


title: Control rep3


title: U2-OS control cells A

description: CRISPR control

source_name: U2_sgCtrl biological replicate 1


title: TH_M-Li_cont_11

value: Control and XFP


title: CH14_off_pre

description: Subject CH14; off milk; treated with None


title: Control rep2


title: CH31_milk_placebo

description: Subject CH31; on milk; treated with Placebo

value: placebo


title: CH32_milk_EPIT

description: Subject CH32; on milk; treated with EPIT


title: CTX_rep3

description: CTX-treated replication 3

value: Six- to eight-week-old

value: Inguinal lymph nodes and spleen

value: CTX-treated replication 3


title: TH_M-Li_cont_9


title: U2-OS NSD3 knockdown cells A

description: CRISPR knockdown

source_name: U2_sgNSD3 biological replicate 1

value: NSD3-targeting sgRNA


title: U2-OS control cells C

description: CRISPR control

source_name: U2_sgCtrl biological replicate 3

value: non-target sgRNA


title: CH30_milk_EPIT

description: Subject CH30; on milk; treated with EPIT


title: TH_F-Li_DRD_5

value: Th-Cre

value: DREADD and XFP


title: CH23_off_pre

description: Subject CH23; off milk; treated with None

value: female


title: CH27_milk_EPIT

description: Subject CH27; on milk; treated with EPIT

value: male


title: TH_M-Li_DRD_12

value: Male


title: CTX_rep1

description: CTX-treated replication 1

value: CTX-treated replication 1


title: CH22_milk_placebo

description: Subject CH22; on milk; treated with Placebo

value: On


title: CTX_rep2

description: CTX-treated replication 2

value: CTX-treated replication 2


title: TH_M-Li_DRD_13


title: TH_F-Li_DRD_2

value: Female


title: TH_M-Li_DRD_9


title: TH_F-Li_cont_3


title: TH_M-Si_DRD_13

description: TH_SI_differentially_expressed_genes_volcano.txt

source_name: distal small intestine


title: TH_F-Li_DRD_1


title: TH_M-Si_DRD_12


title: CH08_milk_pre

description: Subject CH08; on milk; treated with None


title: CH22_milk_pre

description: Subject CH22; on milk; treated with None


title: TH_M-Si_DRD_11


title: TH_M-Li_cont_10


title: TH_M-Li_cont_8


title: CH10_milk_pre

description: Subject CH10; on milk; treated with None


title: CH19_milk_EPIT

description: Subject CH19; on milk; treated with EPIT

value: EPIT


title: TH_M-Si_cont_12

value: Control and XFP


title: CH14_milk_pre

description: Subject CH14; on milk; treated with None


title: CH14_milk_EPIT

description: Subject CH14; on milk; treated with EPIT


title: CH05_off_pre

description: Subject CH05; off milk; treated with None

value: Off


title: CH05_milk_pre

description: Subject CH05; on milk; treated with None


title: TH_F-Li_cont_4

description: TH_colon_differentially_expressed_genes_volcano.txt


title: CH10_off_pre

description: Subject CH10; off milk; treated with None


title: CH09_off_pre

description: Subject CH09; off milk; treated with None


title: CH09_milk_EPIT

description: Subject CH09; on milk; treated with EPIT


title: CH09_milk_pre

description: Subject CH09; on milk; treated with None


title: TH_F-Li_cont_5


title: NRF2 mutant rep 3

first: Sean

middle: Micheal

last: O'Cathail

state: State...

address: Old Road Campus Research Building

department: Oncology

institute: CRUK/MRC Oxford Institute for Radiation Oncology

description:
E79K+ NRF2 mutation
Mut3

data_processing:
Poly adenylated enriched mRNA libraries were sequenced as a 12 sample multiplex on one lane. Approximately 20 million reads per sample were obtained.
Reads were aligned to human reference genome (GRCh37) using HISAT2
Duplicate reads removed using Picard 'MarkDulplicates' tool
Unique reads mapped to Ensembl-annotated genes were summarised using featureCounts
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Colorectal cancer cells

growth_protocol: All cells were incubated at 37°C in 5% CO2 and grown in DMEM supplemented with 10% foetal bovine serum and 1% penicillin streptomycin. All cells were tested regularly for absence of mycoplasma.

extract_protocol:
RNA from all cell lines was extracted using Qiagen Rneasy mini kit as per manufacturer's protocol and DNAse treated prior to PCR. Samples were analysed on Agilent tapestation for RNA integritiy. All samples had RIN >7.
RNA libraries were prepared for sequencing using standard Illumina protocols (1031/18_MPX_10nM)

treatment_protocol: 180,000 cells per well were forward transfected with Lipofectamine and indicated siRNA (final concentration 1.8uM) suspended in reduced serum medium.

tag: cell type

value: E79K+ mutant


title: TH_M-Si_cont_8


title: TH_M-Si_DRD_9


title: TH_F-Si_DRD_2


title: CH06_milk_pre

description: Subject CH06; on milk; treated with None


title: CH08_milk_placebo

description: Subject CH08; on milk; treated with Placebo

value: placebo


title: NRF2 mutant rep 1

description:
E79K+ NRF2 mutation
Mut1


title: ChAt_M-Li_DRD_8

description: CHAT_colon_differentially_expressed_genes_volcano.txt

value: ChAt-Cre


title: ChAt_M-Li_DRD_7


title: NRF2 wild type rep 1

description:
NRF2 WT
WT1

value: wild type


title: TH_F-Si_DRD_1

description: TH_SI_differentially_expressed_genes_volcano.txt


title: TH_M-Si_cont_10


title: NRF2 siRNA cont rep3

description:
siNT treated
NT_3


title: TH_M-Si_cont_9


title: CH06_milk_EPIT

description: Subject CH06; on milk; treated with EPIT


title: CH04_milk_EPIT

description: Subject CH04; on milk; treated with EPIT


title: CH04_milk_pre

description: Subject CH04; on milk; treated with None


title: NRF2 siRNA cont rep2

description:
siNT treated
NT_2


title: TH_M-Si_cont_11


title: ChAt_F-Li_DRD_4


title: ChAt_F-Li_DRD_3


title: NRF2 wild type rep 3

description:
NRF2 WT
WT3


title: TH_M-Li_cont_12


title: CH04_off_pre

description: Subject CH04; off milk; treated with None


title: ChAt_M-Li_DRD_10


title: NRF2 mutant rep 2

description:
E79K+ NRF2 mutation
Mut2


title: ChAt_F-Li_DRD_1


title: NRF2 wild type rep 2

description:
NRF2 WT
WT2


title: NRF2 siRNA rep 1

description:
siNRF2 treated
NRF2_1

tag: sirna


title: ChAt_M-Li_cont_7


title: ChAt_M-Li_cont_6


title: ChAt_F-Li_cont_5


title: NRF2 siRNA rep 3

description:
siNRF2 treated
NRF2_3


title: ChAt_F-Li_cont_4


title: ChAt_F-Li_cont_2


title: ChAt_M-Li_DRD_6


title: ChAt_M-Si_DRD_10

description: CHAT_SI_differentially_expressed_genes_volcano.txt


title: NRF2 siRNA rep 2

description:
siNRF2 treated
NRF2_2


title: ChAt_F-Li_DRD_5


title: ChAt_F-Si_DRD_5


title: ChAt_F-Li_DRD_2


title: NRF2 siRNA cont rep1

description:
siNT treated
NT_1


title: ChAt_M-Li_cont_9


title: ChAt_M-Si_DRD_9


title: shRgs16 rep4

city: Guangzhou

first: Yilie

last: Liao

address: Kaiyuan Street No.190

institute: Bioland Laboratory

data_processing:
fastx_toolkit (Version 0.0.14), Sickle, SeqPrep and fastp (Version 0.19.5) for quality control.
Bowtie2 (Version 2.2.9) for sequence alignment.
GATK (Version 3.8) and samtools (Version 1.9) for SNP/Indel analysis.
Genome_build: not provided
Supplementary_files_format_and_content: shLacZ_vs_shG0s2.deseq2.annot.txt: Tab-delimited text file includes raw counts of sequencing reads.
Supplementary_files_format_and_content: shLacZ_vs_shRgs16.deseq2.annot.txt: Tab-delimited text file includes raw counts of sequencing reads.
Supplementary_files_format_and_content: shG0s2-shRgs16_Merged_DESeq2_Table.xlsx: Excel file includes normalized abundance measurements.

growth_protocol: Wild-type C57BL/6J mice, 12/12h light on/off, ad libum fed.

extract_protocol:
Livers were removed, snap-frozen in liquid nitrogen, and RNA was extracted using Trizol reagent. RNA was treated with DNaseI and cleaned with Ribo-zero magnetic core kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were administrated with 0.1 OD adenovirus containing shRNA by tail vein injection, and sacrificed 12 days later at ZT12 after a 6 hours food-withdrawn during the day.

value: liver

value: 8 weeks


title: shG0s2 rep4


title: shRgs16 rep2


title: shG0s2 rep2


title: shRgs16 rep1


title: shLacZ rep3

value: shLacZ


title: shLacZ rep4


title: shRgs16 rep3


title: shLacZ rep1


title: ChAt_F-Si_DRD_4

value: DREADD and XFP


title: ChAt_M-Si_cont_6


title: VQFR28_4sU AID-Zzz3 clone 2

city: Illkirch CEDEX

first: Veronique

last: Fischer

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed using cutadapt 1.10 in order to remove adaptors and low-quality sequences and reads shorter than 40 bp were removed for further analysis. Remaining reads were mapped to M. musculus, D. melanogaster and S. rRNA sequences for Samples 1-12 or Mus musculus and S. pombe rRNA sequences for Samples 13-22 using bowtie 2.2.8 and reads mapping to rRNA sequences were removed for further analysis. For Samples 1-12, remaining reads were aligned to an hybrid genome composed of mm10, BDGP6 and sacCer3 assemblies of M. musculus, D. melanogaster and S. cerevisiae genome respectively with STAR 2.5.3a. For Samples 13-22, the hybrid genome was composed of mm10 and ASM294v2 assemblies of M. musculus and S. pombe genome respectively. Gene quantification was performed with htseq-count 0.6.1p1, using “union” mode and Ensembl 93 annotations for all organisms except for S. pombe where Ensembl Fungi 41 annotations were used. For 4sU-seq data, “type” option was set to “gene” in order to take also into account reads aligned onto introns. Differential gene expression analysis was performed using DESeq2 1.16.1 Bioconductor R package on M. musculus counts normalized with size factors computed by the median-of-ratios method proposed by Anders and Huber, on D. melanogaster counts for Samples 1-12 or on S. pombe counts for Samples 13-22 (using the following options: cooksCutoff=TRUE, independentFiltering=TRUE, alpha=0.05). P-values were adjusted for multiple testing using the Benjamini and Hochberg method.
Genome_build: mm10
Supplementary_files_format_and_content: alldata*txt: raw counts, norm. counts, DESeq2 results
Supplementary_files_format_and_content: spike*txt: raw counts of spike-in RNA

source_name: mouse ES E14 cells

growth_protocol: Mouse ES E14 cells were cultured on plates coated with 0.1% gelatine solution in 1x PBS using DMEM medium supplemented with 15% foetal calf serum ES-tested, 2 mM ʟ-glutamine, 0.1% β-mercaptoethanol, 100 UI/ml penicillin and 100 μg/ml streptomycin, 0.1 mM non-essential amino acids, 1500 U/ml leukaemia inhibitory factor, 3 μM CHIR99021 and 1 μM PD0325901. Cells were grown at 37°C with 5% CO2 levels. Drosophila Schneider S2 cells were grown in Schneider's Drosophila medium containing 10% FCS (heat inactivated) and 0.5% penicillin and streptomycin at 27°C. S. pombe cells were grown in autoclaved YES medium (yeast extract, adenine, histidine, uracil, leucine, lysine, 3% glucose) at 32°C. S. cerevisiae cells were grown in autoclaved YPD medium (yeast extract, bactopeptone, 2% glucose) at 30°C.

extract_protocol:
We purify newly transcribed RNA by adding 4sU (4-thiouridine), a metabolic analogue of uridine, to the cell culture medium for 15 minutes before collecting the cells. The cells readily take up 4sU and incorporate it into RNA transcribed during the time period of 15 minutes. This protocol is used to label newly transcribed RNA in both, mouse embryonic stem cells and Drosophila melanogaster S2 cells. 4tU was used to label newly synthesized RNA from S. pombe cells. We use Drosophila S2 cells  (VQFR1-12) or S. pombe cells (VQFR13-28) as a external spike-in for normalization. The incorporation of 4sU (with its specific thiol group) into newly transcribed RNA allows to separate the 4sU-containing RNA from the total RNA using biotinylation and Streptavidin-coated beads. To be able to judge the specificity of the 4sU purification, we also added 10X of unlabelled S. cerevisiae RNA prior to the purification of Samples 1-12. Also, the total RNA, used for the purification of the 4sU-containing RNA, was fragmented prior to purification (into on average ~700 bp fragments).
Total RNA-Seq libraries were generated from 1000 ng of total RNA or 14-40 ng of newly synthesized, 4sU-labelled RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. This step was not performed for the newly synthesized (4sU) RNA. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94°C for 2 minutes (for newly synthesized RNA, which is already prefragmented, fragmentation was reduced to 1 minute). Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 10 cycles; 5 min at 72°C). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: All cell lines were treated for 24 hours with auxin (IAA).

value: ES E14 cells

tag: molecule subtype

value: 4sU RNA (newly synthesized RNA)


title: ChAt_M-Si_cont_8

value: Male


title: ChAt_F-Si_DRD_1


title: ChAt_F-Si_cont_2


title: VQFR27_4sU AID-Zzz3 clone 1


title: shG0s2 rep3

source_name: Liver

tag: strain


title: ChAt_M-Si_cont_7


title: VQFR18_4sU Supt7l-/- clone 2

tag: genotype


title: VQFR26_4sU WT with Tir1/BirA o/e

value: WT


title: VQFR17_4sU Supt7l-/- clone 1


title: VQFR13_4sU WT


title: shLacZ rep2


title: VQFR16_4sU AID-Yeats2 clone 2


title: VQFR15_4sU AID-Yeats2 clone 1


title: PDAC_FFPE_59

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
Raw reads were assessed for quality using FastqQC and adapter sequences were identified and removed using Trimmomatic.
Remaining reads were aligned against the human genome (hg38) using STAR software with two-round alignment mode.
mRNAs and lncRNAs were annotated in GencodeV29 and quantified using featureCounts software.
Genome_build: hg38
Supplementary_files_format_and_content: The gene expression profiles were normalized by TPM value for each samples.

source_name: PDAC

extract_protocol:
The RNAstorm™ Kit (biotium, USA) was used to extracted and isolated total RNA fraction from FFPE Tissue Samples.
RNA libraries were prepared for sequencing using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian Kit.

tag: disease

value: pancreatic ductal adenocarcinoma


title: PDAC_FFPE_55


title: PDAC_FFPE_54


title: PDAC_FFPE_57


title: PDAC_FFPE_58


title: PDAC_FFPE_53


title: PDAC_FFPE_61


title: PDAC_FFPE_56


title: PDAC_FFPE_60


title: VQFR25_4sU WT


title: PDAC_FFPE_51


title: PDAC_FFPE_47


title: VQFR14_4sU WT with Tir1/BirA o/e


title: VQFR8_4sU WT with Tir1/BirA o/e


title: VQFR12_4sU AID-Tada3 clone 2


title: PDAC_FFPE_46


title: shG0s2 rep1


title: VQFR7_4sU WT


title: PDAC_FFPE_52


title: ChAt_F-Si_cont_4

value: Female


title: PDAC_FFPE_50


title: VQFR2_total WT with Tir1/BirA o/e

value: total RNA


title: VQFR11_4sU AID-Tada3 clone 1


title: PDAC_FFPE_49


title: VQFR1_total WT


title: PDAC_FFPE_48


title: PDAC_FFPE_44


title: H3K9ac ChIP-seq Supt7l KO

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter sequences were removed and low-quality ends were trimmed. Sequence alignment was performed using the mm10 assembly for Mus musculus genome or the BDGP6 assembly for D. melanogaster genome using Bowtie (version 1.0.0) (Langmead.2012) choosing the zero multi-mapping option. Blacklisted reads for the mouse genome were filtered out using the ENCODE mm10 blacklist v2. Read counts were normalized across samples by dividing by size factors calculated using the spike-in D. melanogaster reads as follows. Uniquely mapped D. melanogaster reads were divided by black list filtered uniquely mapped mouse reads and then multiplied by 100. Bigwig tracks were generated using Homer software (v4.11.1) and normalized by the D. melanogaster size factors.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig of signal normalized to Drosophila spike-in

source_name: H3K9ac ChIP DNA from mouse embryonic stem cells with Drosophila DNA as a spike in (ratio 1:50)

growth_protocol: Mouse ES E14 cells were cultured on plates coated with 0.1% gelatine solution in 1x PBS using DMEM medium supplemented with 15% foetal calf serum ES-tested, 2 mM ʟ-glutamine, 0.1% β-mercaptoethanol, 100 UI/ml penicillin and 100 μg/ml streptomycin, 0.1 mM non-essential amino acids, 1500 U/ml leukaemia inhibitory factor, 3 μM CHIR99021 and 1 μM PD0325901. Cells were grown at 37°C with 5% CO2 levels.

extract_protocol:
Mouse ES E14 and Drosophila S2 cells were washed with 1x PBS, fixed at room temperature with 1% paraformaldehyde in 1x PBS for 10 minutes. Fixation was stopped by adding glycine to a final concentration of 125mM for 10 minutes at room temperature. Cells were washed twice with ice-cold 1x PBS and collected by scrapping. Cells were centrifuged at 2000g for 5 minutes at 4°C and washed once with ice-cold 1x PBS. Cells were lysed in L1 buffer (50 mM Tris-HCl ph 8.0, 2 mM EDTA pH 8.0, 0.1% NP40, 10% glycerol, 5 mM sodium butyrate and protease inhibitory cocktail) and incubated on ice for 10 minutes before centrifugation at 2000g for 10 minutes at 4°C. Nuclei were resuspended in L2 buffer (0.5% SDS, 10 mM EDTA ph 8.0, 50 mM Tris-HCl pH 8.0, 5 mM sodium butyrate and protease inhibitory cocktail) and sonicated using a Covaris E210 sonicator to on average 300 bp fragments. Protein-A sepharose beads were washed twice with TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA) and blocked for three hours with 1ug/ul denatured yeast tRNA and 1,5% fish-skin gelatine. Beads were washed twice with TE buffer and stored at 4°C. For ChIP, 49 µg of mouse chromatin was spiked with 1 µg of fly chromatin. The chromatin mix was diluted with chromatin dilution buffer (0.01% SDS, 1.1% Triton-X 100, 1.2 mM EDTA, 167 mM NaCl, 16.7 mM Tris-HCl pH 8.0, 5 mM sodium butyrate and protease inhibitory cocktail) to a volume of 800 µl and incubated with 30 µl of blocked bead slurry for 1 hour at 4°C for preclearing. Two µg of anti-H3K9ac antibody (abcam, cat # ab4441) was added to precleared chromatin and incubated overnight at 4°C. 50 µl of bead slurry was added to samples and incubated for two hours at 4°C with overhead shaking. After centrifugation for 2 minutes at 1000g, beads were washed two times with Low salt washing buffer (0.1% SDS, 1% Triton-X 100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris HCl pH 8.0, 5 mM sodium butyrate and protease inhibitory cocktail) for 10 minutes, two times with High salt washing buffer (0.1% SDS, 1% Triton-X 100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris HCl pH 8.0, 5 mM sodium butyrate and protease inhibitory cocktail) for 10 minutes, two times with LiCl washing buffer (250 mM LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0, 5 mM sodium butyrate and protease inhibitory cocktail) for 10 minutes and two times with TE buffer for 10 minutes. Bound fragments were eluted using with freshly prepared elution buffer (1% SDS and 0.1 M sodium bicarbonate) at room temperature. Chromatin was reverse crosslinked by addition of 0.2M NaCl and 50 µg/ml RNase A. Samples were incubated at 37°C for one hour. 20 µg of Proteinase K, 60 mM Tris ph 7.9, 20 mM EDTA was added and samples were incubated at 65°C overnight in a thermomixer. DNA was isolated by Phenol-chloroform purification and resuspended in water.
For library preparation, ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat#A63882) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 7 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (Diagenode, Cat# C05010014), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5' ends were ligated to the 5' end of the genomic DNA, leaving a nick at the 3' end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3' ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads to remove unincorporated primers and other reagents. The libraries were sequenced on Illumina Hiseq 4000 sequencer as single-Read 50 base reads following Illumina’s instructions.

value: Supt7l KO

value: embryonic stem cells

tag: chip antibody


title: H3K9ac ChIP-seq AID-Tada3


title: PDAC_FFPE_45


title: H3K9ac ChIP-seq Tada2a KO + Tada2b KO

value: Tada2a KO + Tada2b KO


title: ATAC-seq Supt7l KO rep 3

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14.
Data analysis was performed using the Encode ATAC-seq pipeline v1.4.2. Adapter sequences were removed and low-quality ends were trimmed. Sequence alignment was performed into the mm10 assembly of Mus musculus genome using Bowtie2 (version 2.2.6) (Langmead and Salzberg, 2012) choosing the zero multi-mapping option. Mitochondrial reads were removed. Peak calling was performed using MACS2 v2.1.1.20160309 (Zhang et al., 2008). Finally, the optimal set of IDR peaks were used for the downstream analysis. Peaks from different conditions were merged to form a consensus peak set. The peaks were annotated using annotatePeaks.pl script in Homer program and with Ensembl 94 database. The read coverage for each sample was calculated with multicov function from bedtools program (v2.26.0) (Quinlan and Hall, 2012). Read counts have been normalized across samples with the median-of-ratios method proposed by Love et al. and implemented in the Bioconductor package DESeq2 version 1.16.1 (Love et al. 2014). Differential expression analysis of interest were performed using the DESeq2 package. A multi-factor design was used to control an observed batch effect between day1 (rep1,2) and day2 (rep3,4).
Genome_build: mm10
Supplementary_files_format_and_content: pooled bigwig of four replicates
Supplementary_files_format_and_content: ATACseq_idr_deseq2_batchday.xlsx: Excel of DESeq2 of peak calling

extract_protocol:
ATAC-seq was preformed using an adaptation of protocols described in (Buenrostro et al. 2016; King and Klose, 2017). In short, 100.000 cells were used per sample and centrifuged at 2000xg for 5 minutes at 4°C. Cells were washed with ice-cold 1x PBS and centrifuged at 2000xg for 5 minutes at 4°C. Nuclei were isolated using 50 μl Lysis buffer (10 mM Tris HCl ph 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and centrifuged immediately at 2000xg for 10 minutes at 4°C. Immediately after removing supernatant pellet was resuspended in 50 μl of TAPS-buffer (10 mM TAPS-NaOH pH 8.5, 5 mM MgCl2, 10% DMF) containing 25 nM adaptor-loaded, home-made Tn5E54K,L372P transposase (plasmids provided by Dr. Kim Remans, EMBL Heidelberg, Germany). The reaction was incubated for 1 hour at 37⁰C and was immediately purified using NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel, Cat# 740609.50). DNA was eluted into a volume of 15 μl and stored at -20°C prior to library preparation.
For library preparation, adaptors described in (Buenrostro et al. 2013; Buenrostro et al. 2015a) were used using Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific, Cat# ) with the following PCR program: 1 cycle of 5 minutes at 72°C for gap filling, 1 cycle of 30 seconds at 98°C for pre-denaturation, 14 amplification cycles with 10 seconds at 98°C for denaturation, 20 seconds at 72°C for primer annealing and extension and 5 minutes at 72°C for final extension. After purification using 1.5x SPRIselect beads (Beckman-Coulter, Villepinte, France, Cat# B23319), libraries were verified using capillary electrophoresis and subsequently sequenced with 2x 100 base pairs on a HiSeq4000 machine (Illumina).


title: H3K9ac ChIP-seq AID-Yeats2


title: H3K9ac ChIP-seq WT


title: Input WT

source_name: Input DNA from wildtype mouse embryonic stem cells with Drosophila DNA as a spike in (ratio 1:50)

value: none (input)


title: ATAC-seq Supt7l KO rep 4


title: PDAC_FFPE_43


title: PDAC_FFPE_40


title: PDAC_FFPE_35


title: PDAC_FFPE_37


title: PDAC_FFPE_38


title: PDAC_FFPE_42


title: ATAC-seq AID-Zzz3 rep 4


title: ATAC-seq AID-Yeats2 rep 4


title: ATAC-seq AID-Yeats2 rep 3


title: ATAC-seq AID-Zzz3 rep 3


title: PDAC_FFPE_36


title: PDAC_FFPE_39


title: PDAC_FFPE_41


title: PDAC_FFPE_34


title: OTH 180 min

city: Seongnam

first: Soojin

last: Jang

state: Gyeonggi

address: 16, Daewangpangyo-ro 712

department: Discovery Biology

institute: Institut Pasteur Korea

data_processing:
The sequence data for the reference genome was restrieved from the NCBI database.
Quality-filtered reads were aligned to the reference-genome sequence using Bowtie2.
The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM).
The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database was used to cluster gene into functionally related groups.
The KEGG (Kyoto Encyclopedia of Genes and Genomes) database was used to analyze metabolic pathway.
Genome_build: Accession: PRJNA57945 ; Oragnism: Pseduomonas aeruginosa PAO1
Supplementary_files_format_and_content: xlsx file ; Gene name; FPKM ; edgeR p-value; Contig; eggNOG category ; Product; Read; feature_index

organism: Pseudomonas aeruginosa

source_name: Bacteria culture

growth_protocol: Bacterial growth in M9 glucose media at 37°C with agitation.

extract_protocol:
Total RNA was extracted using Rneasy Mini kit (Qiagen, USA) following protocols provided by the manufacturer. The isolated RNA was stored at -80°C until use.
The Ribo-Zero rRNA removal kit (Epicentre, USA) was used for ribosomal RNA depletion according to manufacturer instruction. Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA sample prep kit (Illuminam, USA) following the manufacturer's protocol.

treatment_protocol: Oxythiamine treatment for 30 and 180 minutes

value: oxythiamine 3 mM

tag: time

value: 180 minutes


title: ATAC-seq WT rep 4


title: ATAC-seq WT rep 3


title: PDAC_FFPE_32


title: ATAC-seq Supt7l KO rep 1


title: ATAC-seq Supt7l KO rep 2


title: control 30 min

value: oxythiamine 0 mM

value: 30 minutes


title: control 180 min


title: OTH 30 min


title: KO_IL_IFN3

city: Kraków

first: Joanna

last: Bereta

address: Gronostajowa 7

department: Cell Biochemistry

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

description:
biological replicate 3
KO_IL_IFN_3.IonXpressRNA_012

data_processing:
Basecalling, quality control, mapping and read counts on Ion Torrent Suite v. 5.12.1
Genome_build: mm10
Supplementary_files_format_and_content: CRISPR RNAseq file containing numbers of reads for all genes and differential gene expression analysis

growth_protocol: The cells were grown in DMEM + 5% FBS at standard conditions (37°C, 5% CO2, 95% humidity).

extract_protocol:
The cells were lysed in Fenozol; total RNA was isolated using Direct-Zol RNA Mini Kit. poly(A)+ RNA was isolated using Dynabead mRNA DIRECT Micro Purification Kit
libraries were prepared according to the manufacturer's protocol with the Ion Total RNA-Seq Kit v2 (ThermoFisher)

treatment_protocol: 6 h,  IL1b (10 ng/ml) and  IFNg (10 ng/ml) or left untreated

tag: cell line

value: colon adenocarcima

value: hr IL1b (10 ng/ml) and mr IFNg (10 ng/ml)


title: KO_IL_IFN2

description:
biological replicate 2
KO_IL_IFN_2.IonXpressRNA_008


title: PDAC_FFPE_33


title: PDAC_FFPE_31


title: KO_IL_IFN

description:
biological replicate 1
KO_IL_IFN.IonXpressRNA_004


title: ATAC-seq AID-Yeats2 rep 2

value: ES E14 cells


title: PDAC_FFPE_30


title: KO_K3

description:
biological replicate 3
KO_K_3.IonXpressRNA_010

value: non treated


title: ATAC-seq AID-Zzz3 rep 2


title: PDAC_FFPE_28


title: ATAC-seq AID-Yeats2 rep 1


title: PDAC_FFPE_29


title: WT_IL_IFN

description:
biological replicate 1
WT_IL_IFN.IonXpressRNA_003

value: control


title: KO_K2

description:
biological replicate 2
KO_K_2.IonXpressRNA_006


title: WT_IL_IFN3

description:
biological replicate 3
WT_IL_IFN_3.IonXpressRNA_011


title: KO_K

description:
biological replicate 1
KO_K.IonXpressRNA_002


title: ATAC-seq AID-Zzz3 rep 1


title: ATAC-seq WT rep 2

value: WT


title: WT_K3

description:
biological replicate 3
WT_K_3.IonXpressRNA_009


title: ATAC-seq WT rep 1


title: WT_K2

description:
biological replicate 2
WT_K_2.IonXpressRNA_005


title: PDAC_FFPE_25

value: pancreatic ductal adenocarcinoma


title: PDAC_FFPE_27


title: PDAC_FFPE_26


title: Liver-DSS2

city: Tianjin

first: Jiang

last: Miaomiao

address: Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, P. R. China

description: allSample.expr.txt

data_processing:
Data filtering steps: Clean reads with high quality can be obtained by the treatment of raw reads by data quality control (QC) and filter. The filtering conditions include:1) Remove the sequence that contains the connector;2) Sequences with more than 5% N base removed;3) Remove more than 50% of the sequences with base mass less than 10
alignment: Read alignment software as HISAT2 (version2-2.0.5),main parameter:--no-mixed -I 100 -X 500 --no-unal
Calculation method of gene expression: In RNA SEQ analysis, we can use HTseq to further map the reads of the alignment genome to the gene exon region, and then count the number of reads on each gene alignment to estimate the gene expression level.HTSeq(v0.6.1),main parameters： -s no -a 0 -t exon -m intersection-nonempty
Differential expression analysis: Our difference analysis software is mainly degseq. Screening conditions: folder≥ 2 and Q-value (or FDR) ≤ 0.01.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

extract_protocol:
After the total RNA extracted from the samples was treated with DNase I, the eukaryotic mRNA was enriched with Oligo(dT) magnetic beads. Then adding a breaking reagent to break the mRNA into short segments, using the broken mRNA as a template and synthesizing a strand of cDNA by using a random hexamers, then adding a buffer solution, dNTPs, and DNA polymerase I to synthesize the second strand of cDNA, and carrying out PCR amplification enrichment after size selection on the obtained segments after purification and recovery by a kit, repair of a sticky end, the addition of a base' A' at the 3' end and connecting a sequencing joint. The constructed library was qualified by Agilent 2100 Bioanalyzer and ABI Step One Plus Real-time PCR system and sequenced using Illumina sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: Wistar rat

tag: gender

value: male

value: DSS


title: Liver-DSS1

institute: Tianjin University of Traditional Chinese Medicine

description: allSample.expr.txt


title: Liver-model2

description: allSample.expr.txt

value: model


title: Liver-model3

description: allSample.expr.txt


title: Liver-control3

description: allSample.expr.txt


title: PDAC_FFPE_23

city: Shanghai


title: Untreated, biological rep 3, S

city: Athens

first: Evdokia

last: Karagouni

state: Attica

address: 127 Vas. Sofias Avenue

department: Department of Microbiology

country: Greece

institute: Hellenic Pasteur Institute

data_processing:
Quality check and pre-processing of raw sequencing reads were conducted using FastQC and Cutadapt respectively
Alignment of pre-processed sequencing reads to the GRCm38 reference genome was performed using the STAR aligner
Quantification of expression at the gene level was conducted using RSEM
Differential expression analysis and pathway enrichment analysis were conducted using EBSeq and hypeR package repsectively.
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM quantification results at the gene level

source_name: murine skin tissue

extract_protocol:
total RNA was extracted from mouse skin and bone tissues; polyA selection was conducted prior to sequencing
Illumina sequencing libraries were prepared then sequenced on a HiSeq 4000 platform (2 x 150bp)

value: skin

value: female

value: 10 weeks

value: Untreated


title: Untreated, biological rep 1, S


title: WT_K

description:
biological replicate 1
WT_K.IonXpressRNA_001


title: Untreated, biological rep 2, S


title: Liver-control1

description: allSample.expr.txt


title: Tconv_donor4

type: genomic

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

institute: University of British Columbia

hyb_protocol: Bisulfite-converted genomic DNA was amplified, fragmented, and hybridized to Illumina Infinium MethylationEPIC BeadChips per the standard Illumina protocol.

scan_protocol: BeadChips were imaged using iScan System (Illumina).

data_processing: Raw red and green intensity data (IDAT) were imported into the R statistical environment (v4.0.2) with RStudio (v1.3.1093), converted into methylated and unmethylated signals, normalized using noob and functional normalization by preprocessFunnorm in minfi (v1.34.0) and by BMIQ in wateRmelon (v1.32.0), and corrected for batch effects (BeadChip ID and position) using ComBat in sva (v3.36.0). Probes with a detection p-value > 0.01 or a bead count < 3 in at least one sample were discarded. Probes previously characterized to have low-quality genomic mapping, cross-reactive or polymorphic sequences, or type I probes targeting a common SNP that could cause a colour channel switch were discarded (https://zwdzwd.github.io/InfiniumAnnotation). Because the cohort contained a mix of males and females, probes targeting X/Y chromosomes were discarded.

label: Cy5 and Cy3

source_name: Peripheral blood flow-sorted conventional T cell

label_protocol: Standard Illumina protocol

growth_protocol: Cells were cultured at 37°C, 5% CO2 in X-VIVO 15 (Lonza) with 5% (v/v) human serum (WISENT), 1% (v/v) penicillin-streptomycin (Gibco), 2 mM GlutaMAX (Gibco), and 15.97 mg/L phenol red (Sigma-Aldrich). Media and IL-2 were replenished every 2-3 days.

extract_protocol: Genomic DNA was isolated with an AllPrep DNA/RNA Mini Kit (Qiagen) and bisulfite-converted with an EZ DNA Methylation Kit (Zymo Research) per the manufacturer's protocols.

treatment_protocol: Naive Tregs were flow-sorted (CD4+CD25hiCD127loCD45RA+) and preactivated with CD3/CD28/CD2 tetrameric antibody complexes (STEMCELL Technologies) for 5 days. Cells were CRISPR-edited by electroporation (Neon Transfection System; Invitrogen) with Cas9 or a FOXP3-targeting ribonucleoprotein, transduced with AAV6-HDR encoding sfGFP, and expanded 1:1 with 75Gy-irradiated artificial antigen-presenting cells expressing CD32, CD58, CD80 + OKT3 (0.1 μg/ml) + IL-2 (1000 IU/ml) for 7 days. Edited cells were sorted as sfGFP+ and expanded with artificial antigen-presenting cells as above for an additional 7 days. Cells were rested overnight with reduced IL-2 (100 IU/ml). In parallel, flow-sorted conventional T cells were preactivated and expanded as above except with 100U/ml IL-2, and without electroporation or CRISPR editing.

tag: experiment

tag: donor

value: F

value: Conventional T Cell

tag: gene modification

tag: total days of expansion

tag: methylationepic beadchip id

tag: methylationepic beadchip position

tag: methylationepic technical replicate


title: nTreg_FOXP3-HDR-KO_donor5_techrep2

source_name: Peripheral blood flow-sorted naive Treg

tag: Sex

value: M

tag: age

tag: cell type

value: Naive Treg

value: CRISPR/HDR-mediated FOXP3 KO, GFP sort-purified


title: WT_IL_IFN2

description:
biological replicate 2
WT_IL_IFN_2.IonXpressRNA_007

value: colon adenocarcima

tag: treatment

value: hr IL1b (10 ng/ml) and mr IFNg (10 ng/ml)

value: control


title: H_LLRR_S

city: Ann Arbor

first: Martin

middle: G

last: Myers Jr

address: 1000 Wall St

institute: University of Michigan

data_processing:
quality filtering with fastp 0.21.0
mapping and read counting with STAR 2.7.7a
Genome_build: GRCm39 with Cre and EGFP:L10a added as artificial chromosomes
Supplementary_files_format_and_content: tab-separated value of counts per sample

source_name: dorsal vagal complex

growth_protocol: Calcr-Cre mice were maintained on ad libitum chow and were either crossed to a R26 Cre-dependent EGFP:L10a mouse line or injected with a Cre-dependent AAV expressing EGFP:L10a in the NTS

extract_protocol:
We employed anti-eGFP TRAP on hindbrain material from Calcr-eGFP-L10a mice. Recovered RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA).
Samples with RNA integrity numbers of 7.5 or greater were prepared using the Illumina TruSeq mRNA Sample Prep v2 kit (catalog nos. RS-122-2001 and RS-122-2002; San Diego, CA), where 0.1 to 3 μg of total RNA was converted to mRNA using polyA purification. The mRNA was fragmented via chemical fragmentation and copied into first-strand complementary DNA (cDNA) using reverse transcription and random primers. The 3′ ends of the cDNA were adenylated, and 6-nucleotide‒barcoded adapters were ligated. The products were purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and quantitative PCR using a Library Quantification Kit for Illumina Sequencing platforms (catalog no. KK4835; Kapa Biosystems, Wilmington, MA). They were clustered on the cBot (Illumina) and sequenced four samples per lane on a 52-cycle or 66-cycle single-end run on a HiSeq 2000 (Illumina) using version 2 reagents according to the manufacturer’s protocols.

tag: run

tag: fraction

value: Sup

tag: transgene

value: genomic


title: PDAC_FFPE_22

tag: disease

value: pancreatic ductal adenocarcinoma


title: CalcR_NTS_AAV_eGFP_L10_B

value: Bead

value: viral


title: Tconv_donor7


title: Liver-DSS3

description: allSample.expr.txt

tag: tissue

value: liver

tag: strain

value: Wistar rat

value: male

value: DSS


title: nTreg_FOXP3-HDR-KO_donor5_techrep1

tag: experiment


title: Liver-control2

description: allSample.expr.txt

tag: gender


title: S-PRT treated, biological rep 3, S

value: skin

value: female

value: 10 weeks

value: S-PRT


title: S-PRT treated, biological rep 4, S


title: Untreated, biological rep 4, S

value: Untreated


title: PDAC_FFPE_24


title: H_LLRR_B


title: PDAC_FFPE_21


title: PDAC_FFPE_19


title: CalcR_NTS_AAV_eGFP_L10_S


title: PDAC_FFPE_18


title: F-PRT treated, biological rep 4, S

value: F-PRT


title: Tconv_donor5

tag: donor

value: M

value: Conventional T Cell

tag: gene modification


title: S-PRT treated, biological rep 2, S


title: PDAC_FFPE_20


title: F-PRT treated, biological rep 3, S


title: Liver-model1

description: allSample.expr.txt

value: model


title: S-PRT treated, biological rep 1, S


title: Canine OS primary sample 8

description: canine OS matched sample8

hyb_protocol: After sample denaturation and pre-annealing with 5µl of Human Cot-1 DNA (Invitrogen, Carlsbad, CA), hybridization was performed at 65°C with shaking for 24 hours. After hybridization, slides were washed sequential

scan_protocol: Agilent G2565C DNA Scanner

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: Canine OS primary tumor

label_protocol: 750ng of test DNA and control DNA were double-digested and labeled by random priming (Agilent Technologies) for 2 hours using Cy5-dUTP for the test DNA and Cy3-dUTP (Agilent Technologies) for the control DNA. Labeled DNAs were incubated at 65°C for 10 minutes and then purified.

growth_protocol: Canine OS specimens were obtained from University of Guelph veterinarian clinics.

extract_protocol: Genomic DNA were extracted using phenol chloroform and treated with RNaseA (Invitrogen) for 1 hour at 37°C

tag: breed

value: Great Pyrenees

value: 5 yrs

value: MC

source_name: normal bone tissue


title: nTreg_FOXP3-HDR-KO_donor0

value: Naive Treg

value: CRISPR/HDR-mediated FOXP3 KO, GFP sort-purified

tag: total days of expansion

tag: methylationepic beadchip id

tag: methylationepic beadchip position


title: Canine OS matched lung metastasis sample 8

description: canine OS matched sample8

source_name: Canine OS lung metastasis tumor

tag: age


title: F-PRT treated, biological rep 2, S


title: PDAC_FFPE_15

value: pancreatic ductal adenocarcinoma


title: nTreg_Cas9_donor7

tag: Sex

tag: cell type

tag: methylationepic technical replicate


title: Canine OS matched lung metastasis sample 6

description: canine OS matched sample6

value: Bull Mastiff

value: 8 yrs


title: Canine OS matched lung metastasis sample 5

description: canine OS matched sample5

value: Greyhound

value: 6 yrs


title: 18M_1_input

city: Lanzhou

first: Xingdong

last: Wang

address: The west lake street

institute: CAAS

data_processing:
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software.
HISAT2 2.0.4 software was used to compare the reference genome of valid data after preprocessing.
The m6A-enriched peaks in each m6A immunoprecipitation sample were identified by MeTDiff peak calling software with the corresponding input sample serving as control.
MeTDiff was run with options (FRAGMENT_LENGTH-200, PEAK_CUTOFF_PVALUE =0.01, PEAK_CUTOFF_FDR =0.05) for peak detection.
Called peaks were annotated by intersection with gene architecture using ChlPseeker
Genome_build: LU_Bosgru_v3.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Bos grunniens

source_name: Yak testis

growth_protocol: The testis tissues of 6 healthy yaks were collected at the same location and divided into two groups: 3 of them were 1.5 years old (before sexual maturity: M), and the other 3 were 5 years old (after sexual maturity: Y).

extract_protocol:
The total RNA was isolated and purified using the TRIzol reagent . Bioanalyzer 2100 (Agilent, CA, USA) and NanoDrop 2000 (Thermo Scientific) with RIN number > 7.0 were used to evaluate the total RNA quality and quantity.
poly (A) mRNA fractions are broken using divalent cations at high temperatures (RNA solution at 94°C for exactly 5 minutes using a thermocycler). Then, the fragmentation of broken RNA were incubated with m6A-Dynabeads (Anti-m6A, Synaptic Systems, Cat. No 202003) in an m6A-binding buffer (50 mM Tris-HCl pH7.4, 150 mM NaCl2, 1%NP-40, 2 mM EDTA), Allow the fragmented RNA to bind to the m6A-Dynabeads. Then washing of m6A-Dynabeads, Elution of m6A-positive RNA. Extraction and Cleanup of the RIP, Collecting m6A “enriched RNA”. We have generally utilized 100 ng of RNA (100 ng of input and 100 ng of post m6A-IP positive fraction) for library construction utilizing Illumina TrueSeq Stranded mRNA. Afterwards, we implemented the paired-end sequencing on an Illumina HiSeq X10 system, using a suggested protocol from the manufacturer.
MeRIP-seq

treatment_protocol: The testicular tissue is immediately stored in liquid nitrogen for RNA isolation. Testicular samples of group M were obtained by castration; testicular samples of group Y were collected from slaughtered yaks within 1 hour.

tag: developmental stage

value: after sexual maturity testis

value: testis

tag: condition

value: input


title: Untreated, biological rep 3, B

source_name: murine bone tissue

value: bone

value: female

value: 10 weeks

tag: treatment

value: Untreated


title: PDAC_FFPE_12

tag: disease


title: PDAC_FFPE_16


title: 5Y_2_input

value: before sexual maturity testis

tag: tissue


title: Untreated, biological rep 2, B


title: Canine OS matched lung metastasis sample 7

description: canine OS matched sample7

value: Great Pyrenees

value: 7 yrs

value: FS


title: Canine OS primary sample 5

description: canine OS matched sample5

value: MC


title: Canine OS primary sample 7

description: canine OS matched sample7


title: PDAC_FFPE_17

value: pancreatic ductal adenocarcinoma


title: PDAC_FFPE_11


title: 18M_2_input


title: Untreated, biological rep 4, B


title: F-PRT treated, biological rep 1, S

value: skin

value: F-PRT


title: nTreg_FOXP3-HDR-KO_donor4

tag: experiment

value: F

value: Naive Treg

value: CRISPR/HDR-mediated FOXP3 KO, GFP sort-purified


title: PDAC_FFPE_13


title: Canine OS primary sample 6

description: canine OS matched sample6

value: Bull Mastiff

value: 8 yrs

tag: gender


title: 18M_3_input

value: after sexual maturity testis

value: testis

value: input


title: S-PRT treated, biological rep 4, B

value: bone

value: female

value: 10 weeks

value: S-PRT


title: PDAC_FFPE_09


title: nTreg_Cas9_donor0

tag: donor

value: M


title: S-PRT treated, biological rep 3, B


title: PDAC_FFPE_14


title: nTreg_FOXP3-HDR-KO_donor3

tag: gene modification


title: nTreg_FOXP3-HDR-KO_donor7


title: Tconv_donor3

value: Conventional T Cell


title: nTreg_Cas9_donor3


title: PDAC_FFPE_08

value: pancreatic ductal adenocarcinoma


title: nTreg_Cas9_donor5


title: 5Y_3_input

value: before sexual maturity testis


title: 5Y_1_input


title: 18M_1

value: IP


title: Canine OS primary sample 2

description: canine OS matched sample2

tag: breed

value: Mixed Breed (German Shepherd/Collie/X)

value: MC


title: Canine OS matched lung metastasis sample 1

description: canine OS matched sample1

value: Rottweiler

value: 7 yrs


title: Canine OS matched  lung metastasis sample 3

description: canine OS matched sample3

value: Mixed Breed (Labrador Retriever/X)

value: 10 yrs

value: FS


title: 5Y_3

value: testis


title: 18M_3

value: after sexual maturity testis


title: PDAC_FFPE_07


title: Untreated, biological rep 1, B

value: bone

value: female

value: Untreated


title: Canine OS matched lung metastasis sample 4

description: canine OS matched sample4

value: Rottweiler X (Canine Mixed Breed)

value: 9 yrs


title: Canine OS primary sample 3

description: canine OS matched sample3


title: PDAC_FFPE_10

value: pancreatic ductal adenocarcinoma


title: S-PRT treated, biological rep 1, B

value: 10 weeks

value: S-PRT


title: S-PRT treated, biological rep 2, B


title: PDAC_FFPE_05


title: PDAC_FFPE_06


title: Tconv_donor0

value: M

value: Conventional T Cell

tag: total days of expansion


title: Canine OS matched lung metastasis sample 2

description: canine OS matched sample2

value: Mixed Breed (German Shepherd/Collie/X)

value: 8 yrs

value: MC


title: PDAC_FFPE_03


title: Canine OS primary sample 4

description: canine OS matched sample4


title: PDAC_FFPE_02