title: 293T-EMX1-APODel-PD_rep1

description:
replicate 1
Detect-seq EMX1 APODerep1 in HEK293T cells

value: embryonic kidney derived epithelial cells

value: Wild Type


title: Sham scRNA rep 1

status: Public on Apr 08 2021

type: SRA

city: San Francisco

first: Pawel

last: Przytycki

state: California

address: 1650 Owens Street

department: GIDB

country: USA

institute: Gladstone Institutes

library_source: transcriptomic

data_processing:
cellranger (version 3.0.2) mkfastq with default parameters to demultiplex raw base calls
cellranger (version 3.0.2) count with default parameters for alignment, filtering, barcode counting, UMI counting, and cell calling. See https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms/overview for details
Genome_build: Mm10
Supplementary_files_format_and_content: We provide barcodes.tsv files, matrix.mtx files and features.tsv files (for single cell RNA seq) or peaks.bed files (for single cell ATAC seq) generated by the 10x Genomics cellranger command. We provide BigWig files for PROseq and 4C. We provide bed files and bigWig files for ChIPseq. We provide excel files for differential expression analysis with Reads Per Kilobase of exon per Megabase of library size (RPKM) for every gene.

molecule: polyA RNA

organism: Mus musculus

source_name: Heart tissue (non-cardiomyocyte cells)

extract_protocol:
Briefly, after proper anesthesia level was reached, thoracotomy was performed, and mouse heart was isolated. The isolated heart was cannulated and perfused with perfusion buffer (120.4 mM NaCl, 14.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 10 mM Na-HEPES, 4.6 mM NaHCO3, 30 mM taurine, 10 mM 2,3-butanedione monoxime, and 5.5 mM glucose, pH 7.0) in a Langendorff perfusion system (Radnoti 120108EZ) for 5-10 minutes at 37 °C. The cannulated heart was then digested by digestion buffer (perfusion buffer with 300 units/mL collagenase II (Worthington Biochemical) and 50 μM CaCl2) for about 10 min at 37 °C. At the end of digestion, the atria and great vessels were removed and the ventricular tissue was transferred to and gently teased into small pieces in stop buffer (perfusion buffer with 10% fetal bovine serum) at 37 °C. After gently pipetting, cell suspension was passed through a 250uM strainer in a falcon tube and then at 30xg for 3 minutes at room temperature (RT). Then, the supernatant - containing most of the non-cardiomyocytes (CMs) - was divided from the pellet (containing the CM fraction). The non-CM fraction was centrifuged again at 30xg for 3 minutes at RT and the supernatant kept. The supernatant was then filtered with a cell strainer (70um) and finally centrifuged at 400xg for 3 minutes at RT for eliminating debris. The non-CM pellet was finally resuspended in 1mL cold PBS 0.5% BSA. 30k cells were counted with trypan blue using a hemocytometer and then used for subsequent 10X Genomics Chromium single cell RNAseq preparation. For single cell ATAC, 500k isolated and purified non-CMs were resuspended in 100uL lysis buffer (Tris-HCl 10mM pH 7.4, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, P40 0.1%, Digitonin 0.01%, BSA 1% in Nuclease-free water), pipetted 10 times and kept on ice for 5 minutes. Nuclei were then washed 1mL 1X PBS with 1% BSA and then centrifuged at for 5 minutes at 4C. The nuclei pellet was resuspended in 1mL 1X PBS with 1% BSA and filtered with a 10uM strainer (pluriSelect #43-50010-00). Nuclei were then counted with DAPI using a hemocytometer and finally 30k non-CM nuclei used for subsequent 10X Genomics Chromium single cell ATACseq preparation. The CM-fraction was, after the first centrifugation, centrifugated again at 30xg for 3 minutes at RT in stopping buffer and the supernatant was discarded. The CM pellet was finally centrifuged at 400xg for 3 minutes in stopping buffer at RT and after discarding the supernatant, the cell pellet was lysed in Qiazol (miRNeasy kit - Qiagen) for subsequent RNA extraction.
Single-cell droplet libraries from the non-CM cell suspension (2x Sham, 2x TAC-Veh, 2x TAC-JQ1 and 2x TAC-JQ1 withdrawn) were generated in the 10X Genomics Chromium controller according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagent Kit v.2 User Guide. Additional components used for library preparation include the Chromium Single Cell 3′ Library and Gel Bead Kit v.2 (PN-120237) and the Chromium Single Cell 3′ Chip kit v.2 (PN-120236). Libraries were prepared according to the manufacturer’s instructions using the Chromium Single Cell 3′ Library and Gel Bead Kit v.2 (PN-120237) and Chromium i7 Multiplex Kit (PN-120262). Final libraries were sequenced on the NextSeq 500 (Illumina) for a quality control run and then on the NovaSeq (Illumina) for deeper sequencing. All the 8 samples were pooled and sequenced in one single lane. Sequencing parameters were selected according to the Chromium Single Cell v.2 specifications. All libraries were sequenced to a mean read depth of at least 50,000 total aligned reads per cell. Raw sequencing reads were processed using the Cell Ranger v.2.2.0 pipeline from 10X Genomics. In brief, reads were demultiplexed, aligned to the mouse mm10 genome and UMI counts were quantified per gene per cell to generate a gene-barcode matrix. Data from the 8 samples were aggregated and normalized to the same sequencing depth, resulting in a combined gene-barcode matrix of all samples.

tag: heart surgery

value: Sham

tag: treatment

value: Vehicle

tag: type of experiment

value: Single cell RNA seq

tag: cell type

value: Heart tissue (non-cardiomyocyte cells)


title: 10d_Female_Input_2

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

institute: Florida State University

data_processing:
RNA-seq reads were aligned using STAR (v. 2.7.2a) to the D. melanogaster dm6 UCSC genome assembly. Aligned reads were sorted using the sort function in SAMtools (v.1.2).
Exon-level count tables were generated with FeatureCounts on the meta-feature level excluding multimapping as follows: -s 0 -O -t exon -g exon_id.
Expression was then quantified for each exon using Reads Per Million Mapped Reads (RPM/CPM) in EdgeR using cpm function.
Genome_build: UCSC dm6 (BDGP Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Processed data files for exon counts are in the .CSV format and contain following columns: exon id, chromosome , exon start, exon end, strand, exon length, gene_id, number of reads in exon region.
Supplementary_files_format_and_content: Supplementary file contains Reads Per Million (RPM) for all exons listed in first column and all samples in data set in subsequent columns.

organism: Drosophila melanogaster

source_name: total RNA input

growth_protocol: Flies were reared on standard cornmeal food at 25°C on a 12 12-h light/12-h dark cycle.

extract_protocol:
Translated mRNA purification was performed as described in Newell et al. 2016 with the following modifications: the 40µl of lysate supernatant (input) and TRAP (IP) fractions were placed into/resuspended in RA1 lysis buffer (Machery-Nagel Nucleospin RNA) for total RNA isolation according to manufacturer’s protocol.
The isolated total RNA from for TRAP and input libraries underwent poly(A)+ selection using the NEBNext Poly(A) mRNA isolation module. TRAP and input libraries were prepared with the NEBNext Ultra RNA library Prep Kit for Illumina.

treatment_protocol: Approximately 1000 10-12 day post eclosion sex-sorted flies were collected for fru P1 TRAP experiments, (n=4). Flies were collected and sex sorted 0-48hrs post-eclosion for appropriate aging to 10-12 days and snap frozen in liquid nitrogen between ZT1 and ZT2. All frozen animals were stored at -80°C until they were processed for downstream experiments.

tag: tissue

value: Whole head

tag: developmental stage

value: 10-12day Adult

tag: Sex

value: Female


title: 10d_Female_TRAP_3

source_name: RNA from fru P1-expressing neurons


title: 293T-EMX1-All-PD_rep2

city: Beijing

first: Howard

last: MENG

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

description:
replicate 2
Detect-seq EMX1 All Prep2 in HEK293T cells

library_source: genomic

data_processing:
Library strategy: Detect-seq
Detect-seq raw FASTQ files are remove Illumina sequencing adapters with cutadapt software (version 1.18). Working command and key parameters are: cutadapt --times 1 -e 0.1 -O 3 --quality-cutoff 25 -m 50. After adapter removal, FASTQ files are mapped to the reference genome (hg38) with Bismark(version 0.22.3) aligner without special settings. Then the unmapped and low MAPQ (MAPQ < 20) FASTQ reads are re-mapped by BWA MEM (version 0.7.17) with default behavior. The Bismark-generated BAM and BWA-generated BAM are merged, then sorted by reference coordinate with samtools sort command (version 1.9). Sored BAM files are removed duplications by Picard MarkDuplicates (version 2.0.1) with default settings. Considering of CBE usually generate indel byproducts, BAM files are needed to be re-aligned with GATK RealignerTargetCreator and IndelRealigner (version 3.8.1) with default settings, and SNP know sites are download from NCBI dbSNP.
After Detect-seq mapping steps, several computation and analysis steps should perform to achieve final Detect-seq off-targets. While making it an easy-achieve analysis pipeline, we offer Detect-seq tools on GitHub (https://github.com/menghaowei/Detect-seq), which contains several useful Python scripts. And those tools can help to perform Detect-seq analysis like off-targets finding, sgRNA alignment, and result visualization.
Genome_build: hg38
Supplementary_files_format_and_content: The bed files are the final off-target results generated by the Detect-seq protocol

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: The HEK293T and MCF7 is separately cultivated in DMEM and MEM with 10% FBS and 1% PS at 37°C cultivator with 5% CO2. The subculture of cells was performed every 2–3 days and only passage 3-10 were used for experiments. All the cells were routinely tested for Mycoplasma contamination with TransDetect PCR Mycoplasma Detection Kit (TRANSGEN BIOTECH, FM311-01).

extract_protocol:
Genomic DNA was freshly extracted using CWBIO universal genomic DNA kit (CWbiotech, CW2298M) and stored in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) at -80 °C.
Extracted genomic DNA was fragmented into ~300 bp through Covaris Focused-ultrasonicator™ Instrument (ME220), followed by a purification using DNA Clean & Concentrator-5 (Vistech, DC2005). ~5 ug DNA fragments and 10 pg spike-in model sequences were subjected to end repair with NEBNext End Repair Module (NEB, E6050), and 1 μl E. coli ligase (NEB, M0205) was added to repair nicks in DNA. Then hydroxylamine protection of endogenous 5fC was performed in 100 mM MES buffer (pH 5.0), 10 mM O-ethylhydroxylamine (EtONH2, Aldrich, 274992) at 37 °C for 6 h. The product underwent 5fC protection was diluted 2.5 times and purified with DNA Clean & Concentrator-5. Next, dA-tailing procedure was carried out using NEBNext dA-Tailing Module (NEB, E6053) followed by a DNA purification with 1.8 × AMPure XP beads.   DNA damage that may interfere the subsequent labeling step was repaired in a mixture of 2 μl endonuclease IV (Endo IV, NEB, M0304), 1 μl Bst full-length polymerase (NEB, M0328), 2 μl Taq ligase (NEB, M0208), 1 μl NAD+ (NEB, B9007), 1 μl dNTP (2.5 mM each) in NEBuffer 3 for 1 h at 37 °C and 1 h at 45 °C. DNA was purified and subjected to in vitro BER labeling reaction containing a mixture of 1 μl UDG (NEB, M0280), 1.5 μl Endo IV, 0.8 μl Bst full-length polymerase, 1.7 μl Taq ligase, 1 μl NAD+, 200 nM biotin-dUTP, 800 nM d5fCTP, 200 nM dATP and 200 nM dGTP in NEBuffer 3 for 40 min at 37 °C. The DNA was incubated with 75 mM of malononitrile in 10 mM Tris-HCl (pH 7.0) at 37°C for 20 h in an enclosed thermomixer (Eppendorf, 850 rpm), away from light. The reaction product was then purified with 1.8 × AMPure XP beads.  Labeled fragments were enriched by streptavidin C1 beads (Invitrogen) following the manufacturer's instruction. Y adaptor (see Supplementary Note 1) was ligated (NEBNext Quick Ligation Module, E6056) to double-stranded DNA on streptavidin C1 beads so that free adaptor can be removed by three-times washing of 1×B&W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20). After washing once with 1× SSC buffer (pH 7.0), beads with biotinylated DNA strands were resuspended in freshly prepared 0.15 M NaOH and incubated at room temperature for 10 min, followed by a sequential washing of 1× SSC buffer (7.0) and 1× TE buffer (pH 7.5) for once. The DNA was eluted from C1 beads using deionized water after heating at 95 °C for 3 min.   Eluted DNA was finally subjected to library amplification with indexed primers (NEB). To obtain sufficient DNA template, 2 rounds of amplification were first performed by using MightyAmp DNA polymerase (Takara), which was proved to read through regions containing biotin-dU and d5fC-malononitrile sites more easily. The PCR product was recovered via DNA Clean & Concentrator-5 and then PCR amplified for ~12 cycles using NEBNext® Q5® Hot Start HiFi PCR Master Mix (NEB, M0543). The constructed libraries were checked using the Agilent 2100 bioanalyzer. Sequencing was performed by Illumina Hiseq X Ten.

treatment_protocol: 6.4 × 106 of HEK293T cells or 2.5 × 106 of MCF-7 cells were seeded into 6-well culture plates (Corning) for 16 h growth. Adherent cells were transfected with 4 μg BE and 2720 ng sgRNA plasmids per well using lipofectamine LTX following the manufacturer’s protocol. Cells were then collected after 72 h of transfection.

tag: cell line

value: HEK293T cells

tag: genotype


title: TAC JQ1 scRNA rep 2

value: TAC


title: TAC JQ1 scRNA rep 1


title: 10d_Female_TRAP_2


title: 293T-EMX1-All-PD_rep1

description:
replicate 1
Detect-seq EMX1 All Prep1 in HEK293T cells


title: HF-2927_ChIP-free-chia-pet

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

description: ChIAPET

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categaries: PET reads, single tag reads and no-linker reads. Tags identified (>=18bp) and reads without linkers were mapped to hg19 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped,multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categaries were merged. CPU furhter clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5,-20 -3 5,480 -t 16 -O).
Illumina RTA-1.18 software used for basecalling
Genome_build: hg19

source_name: Glioblastoma neurosphere cell suspensions

growth_protocol: Tumor specimens were dissociated and cultured as neurospheres in DMEM/F12 medium (11330-032, Gibco) supplemented with N-2 supplement (17502-048, Gibco) and growth factors (EGF and FGF-basic). Cells with passages between 15 and 26 were used for experiments.

extract_protocol:
10 million cells were dual-crosslinked with 1.5mM EGS (21565, Thermo Fisher) for 45 min followed by 1% formaldehyde (F8775, Sigma) for 20 min at room temperature and then quenched with 0.125 M Glycine (G8898, Sigma) for 10 min. The crosslinked cells were washed with PBS twice and lysed in 100 ul 0.55% SDS with incubation at room temperature, 62°C and 37°C sequentially for 10 min each, which was followed by 37°C for 30 min with addition of 25 ul 25% Triton-X 100 to quench SDS and 37°C overnight with addition of 50 ul AluI (R0137L, NEB), 50 μl 10 × CutSmart buffer and 275 μl H2O to fragmentize the chromatin. The pelleted digested nuclei were resuspended in 500 ul A-tailing solution containing 50 μl 10 × CutSmart buffer, 10 μl BSA (B9000S, NEB), 10 μl 10 mM dATP (N0440S, NEB), 10 μl Klenow (3’- 5’ exo-) (M0202L, NEB), and 420 μl H2O  with 1 hr incubation at room temperature and then subjected to proximity ligation by adding 200 μl 5 × ligation buffer (B6058S, NEB), 6 μl biotinylated bridge linker (200 ng/ul), 10 μl T4 DNA ligase (M0202L, NEB) and 284 μl H2O and incubating at 16°C overnight. The ligated chromatins were then sheared by sonication and decrosslinked.
The decrosslinked DNA were tagmented using the Nextera DNA Sample Preparation Kit (Illumina). The linker ligated ChIA-PET constructs were selected using streptavidin magnetic beads. The magnetic beads were blocked with sheared gDNA prior to the selection. The streptavidin selected constructs were amplified with PCR and purified.

tag: source

value: Glioblastoma

tag: ip antibody


title: Kmt2d_CHO25

city: Easton

first: Ezra

last: Lencer

state: PA

address: 746 High Street

department: Department of Biology

institute: Lafayette College

data_processing:
Alignment to human genome (hg38) using STAR aligner (v2.7.3a) and computing counts using quant mode.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data are raw per-gene counts from STAR quant mode in tab-delimited format

molecule: total RNA

source_name: Human lymphoblastoid cell line from KMT2D  patient

growth_protocol: Standard

extract_protocol:
Zymo Research Direct-zol RNA MiniPrep Ki
Nugen mRNA Kit

treatment_protocol: KMT2d and KDM6A patient derived cell lines

value: Human lymphoblastoid cell line

value: KMT2D Mutation


title: TAC scRNA rep 2


title: 10d_Female_Input_4


title: 10d_Female_Input_5


title: TAC scRNA rep 1


title: TAC JQ1 withdrawn scATAC rep 2

data_processing:
cellranger-atac (version 1.0.0) mkfastq with default paramaters to demultiplex raw base calls
cellranger-atac (version 1.0.0) count with default parameters for alignment, filtering, barcode counting, UMI counting, peak calling, and cell calling. See https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/algorithms/overview for details
Genome_build: Mm10
Supplementary_files_format_and_content: We provide barcodes.tsv files, matrix.mtx files and features.tsv files (for single cell RNA seq) or peaks.bed files (for single cell ATAC seq) generated by the 10x Genomics cellranger command. We provide BigWig files for PROseq and 4C. We provide bed files and bigWig files for ChIPseq. We provide excel files for differential expression analysis with Reads Per Kilobase of exon per Megabase of library size (RPKM) for every gene.

extract_protocol:
Briefly, after proper anesthesia level was reached, thoracotomy was performed, and mouse heart was isolated. The isolated heart was cannulated and perfused with perfusion buffer (120.4 mM NaCl, 14.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 10 mM Na-HEPES, 4.6 mM NaHCO3, 30 mM taurine, 10 mM 2,3-butanedione monoxime, and 5.5 mM glucose, pH 7.0) in a Langendorff perfusion system (Radnoti 120108EZ) for 5-10 minutes at 37 °C. The cannulated heart was then digested by digestion buffer (perfusion buffer with 300 units/mL collagenase II (Worthington Biochemical) and 50 μM CaCl2) for about 10 min at 37 °C. At the end of digestion, the atria and great vessels were removed and the ventricular tissue was transferred to and gently teased into small pieces in stop buffer (perfusion buffer with 10% fetal bovine serum) at 37 °C. After gently pipetting, cell suspension was passed through a 250uM strainer in a falcon tube and then at 30xg for 3 minutes at room temperature (RT). Then, the supernatant - containing most of the non-cardiomyocytes (CMs) - was divided from the pellet (containing the CM fraction). The non-CM fraction was centrifuged again at 30xg for 3 minutes at RT and the supernatant kept. The supernatant was then filtered with a cell strainer (70um) and finally centrifuged at 400xg for 3 minutes at RT for eliminating debris. The non-CM pellet was finally resuspended in 1mL cold PBS 0.5% BSA. 30k cells were counted with trypan blue using a hemocytometer and then used for subsequent 10X Genomics Chromium single cell RNAseq preparation. For single cell ATAC, 500k isolated and purified non-CMs were resuspended in 100uL lysis buffer (Tris-HCl 10mM pH 7.4, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, P40 0.1%, Digitonin 0.01%, BSA 1% in Nuclease-free water), pipetted 10 times and kept on ice for 5 minutes. Nuclei were then washed 1mL 1X PBS with 1% BSA and then centrifuged at for 5 minutes at 4C. The nuclei pellet was resuspended in 1mL 1X PBS with 1% BSA and filtered with a 10uM strainer (pluriSelect #43-50010-00). Nuclei were then counted with DAPI using a hemocytometer and finally 30k non-CM nuclei used for subsequent 10X Genomics Chromium single cell ATACseq preparation. The CM-fraction was, after the first centrifugation, centrifugated again at 30xg for 3 minutes at RT in stopping buffer and the supernatant was discarded. The CM pellet was finally centrifuged at 400xg for 3 minutes in stopping buffer at RT and after discarding the supernatant, the cell pellet was lysed in Qiazol (miRNeasy kit - Qiagen) for subsequent RNA extraction.
After successful nuclei isolation, nuclei were then processed according to the 10X Genomics Single Cell ATAC kit v1.0 (PN-1000110) by first incubating with Tn5 Transposase for 1 hour, followed by GEM generation and barcode amplification using the 10X Genomics Chromium controller according to the manufacturer’s instructions. Additional components used for library preparation include the Chromium Chip E Single Cell ATAC kit (PN-1000082) and Chromium i7 Multiplex Kit N, Set A primers (PN-1000084). Final libraries were sequenced on the NextSeq 500 (Illumina) for a quality control run and then on the NovaSeq (Illumina) for deeper sequencing. All the 8 samples (2x Sham, 2x TAC-Veh, 2x TAC-JQ1 and 2x TAC-JQ1 withdrawn) were pooled and sequenced in one NovaSeq single lane. Sequencing parameters were selected according to the Chromium Single Cell ATAC v1.0 specifications.

value: JQ1 withdrawn

value: Single cell ATAC seq


title: Ctrl2_Ct2

source_name: Human lymphoblastoid cell line

value: Control


title: Sham scRNA rep 2


title: Kdm6_Cho34

source_name: Human lymphoblastoid cell line from KDM6 patient

value: KDM6A Mutation


title: 48hrAPF_Female_TRAP_5

data_processing:
RNA-seq reads were aligned using STAR (v. 2.7.2a) to the D. melanogaster dm6 UCSC genome assembly (BDGP release 6). Aligned reads were sorted using the sort function in SAMtools (v.1.2).
Exon-level count tables were generated with FeatureCounts on the meta-feature level excluding multimapping with appropriate strandedness of libraries indicated reads as follows: -s 2 -O -t exon -g exon_id.
Expression was then quantified for each exon using Reads Per Million Mapped Reads (RPM/CPM) in EdgeR using cpm function.
Genome_build: UCSC dm6 (BDGP Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Processed data files for exon counts are in the .CSV format and contain following columns: exon id, chromosome , exon start, exon end, strand, exon length, gene_id, number of reads in exon region.
Supplementary_files_format_and_content: Supplementary file contains Reads Per Million (RPM) for all exons listed in first column and all samples in data set in subsequent columns.

growth_protocol: Pupae were sex-sorted at white pre-pupal stage and aged to 48hr after Puparium formation (APF) on Bromophenol blue agar plates at 25˚C on a 12 hour light and 12 hour dark cycle.

extract_protocol:
Translated mRNA purification was performed as described in Newell et al. 2016 with the following modifications: the 40µl of lysate supernatant (input) and TRAP (IP) fractions were placed into/resuspended in RA1 lysis buffer (Machery-Nagel Nucleospin RNA) for total RNA isolation according to manufacturer’s protocol.
The isolated total RNA from for TRAP and Input libraries underwent poly(A)+ selection using the NEBNext Poly(A) mRNA isolation module. TRAP and input libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Approximately 1000 48hr after pupal formation (APF, +/- 1hr) sex-sorted flies were collected for fru P1 TRAP experiments, (n=4-5). Flies were collected and sex sorted at the white prepupal stage for appropriate aging to 48hr APF and snap frozen in liquid nitrogen between ZT1 and ZT2. All frozen animals were stored at -80°C until they were processed for downstream experiments.

value: Whole pupae

value: 48hr APF


title: 48hrAPF_Female_TRAP_4


title: 10d_Male_TRAP_1

value: Male


title: 293T-Empty-PD_rep1

description:
replicate 1
Detect-seq Empty PD rep1 in HEK293T cells

value: embryonic kidney derived epithelial cells

value: Wild Type

value: Empty-PD


title: TAC scATAC rep 2

value: Vehicle

value: Heart tissue (non-cardiomyocyte cells)


title: Kmt2d_RNA25


title: 10d_Male_TRAP_5

value: Whole head

value: 10-12day Adult


title: 10d_Male_TRAP_4


title: TAC JQ1 withdrawn scATAC rep 1

value: TAC


title: TAC JQ1 scATAC rep 2


title: Ctrl1_Ct1

value: Human lymphoblastoid cell line


title: 10d_Male_TRAP_2


title: TAC scATAC rep 1


title: 48hrAPF_Female_TRAP_3

value: Female


title: 10d_Male_Input_3


title: TAC JQ1 scATAC rep 1


title: 10d_Male_Input_2


title: 48hrAPF_Female_TRAP_2


title: Sham scATAC rep 2

value: Sham


title: 10d_Male_Input_4


title: SDALL11

city: Davis

first: Mariana

last: Guedes Weber

address: 451 Health Sciences Dr.

institute: UC Davis

data_processing:
base calling performed with RTA 2.7.7 (UC Davis Genome Core)
de-multiplexing performed with bcl2fastq2  (UC Davis Genome Core)
md5sum checked using bash script and fastQC v0.11.9 to assess raw data quality
Trimmomatic v0.36 with parameters to remove bases lower than Q20 (sliding window=4), adapters and reads < 50 bp removed
STAR v2.7.3a performed read alignment and counts
R v3.6.1 and EdgeR v3.28.1 used for read normalization (CPM) and differential expression analysis (at least 1 read in a minimum of 3 samples to be included for DE)
Genome_build: Mmul_10

organism: Macaca mulatta

source_name: Ileum

extract_protocol:
Ileum tissue were obtained from rhesus macaque at necropsy time point (70 days post-intection), and total RNA was harvested using  Qiagen RNeasy Mini Kit.
Barcoded sequencing libraries were prepared using the QuantSeq FWD kit  for multiplexed sequencing according to manufacturer recommendations using UDI-adapter and UMI Second-Strand Synthesis modules (Lexogen). 3'Tag RNA-Seq

value: Ileum

tag: cell types included

value: epithelial, lymphphatic, adipose and muscular

tag: collection timepoint

value: 0 days

value: SIV-neg

tag: rin score


title: SDALL14


title: SDALL13


title: 48hrAPF_Female_Input_2

value: Whole pupae

value: 48hr APF


title: SDALL15


title: 48hrAPF_Female_Input_4


title: 48hrAPF_Female_Input_5


title: 48hrAPF_Female_Input_3


title: Sham scATAC rep 1

value: Single cell ATAC seq


title: 10d_Male_Input_1

value: Male


title: SDALL10

value: 70 days

value: SIV-pos and MSC-treated


title: 48hrAPF_Male_TRAP_6


title: SDALL12


title: 48hrAPF_Male_TRAP_3


title: SDALL07


title: Sun1_1

city: Shanghai

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Read mapping as well as filtering and iterative correction were performed using scripts derived from those at https://bitbucket.org/mirnylab/hiclib.
Heatmap generation, calculation of expected interaction frequency and comparison of chromosome ends interactions between genotypes were performed on combined interaction matrices using scripts at https://github.com/dekkerlab/cworld-dekker
Genome_build: mm10
Supplementary_files_format_and_content: cool

source_name: spermatocytes

extract_protocol: In situ Hi-C was performed on two independently prepared biological replicates using a previously published protocol (doi:10.1016/j.cell.2014.11.021)

tag: strain

value: Sun1 W151R

value: pachytene-like spermatocytes


title: 48hrAPF_Male_TRAP_2


title: SDALL09


title: 48hrAPF_Male_TRAP_1


title: Sun1_2


title: SDALL06


title: 48hrAPF_Male_Input_6


title: SDALL05

value: SIV-pos


title: SDALL04


title: 48hrAPF_Male_Input_5


title: 48hrAPF_Male_TRAP_5


title: SDALL08


title: SDALL02


title: 48hrAPF_Male_Input_2


title: AML8

type: RNA

city: Essen

first: Yi-Yang

last: Chen

state: NW

address: Hufelandstraße 55

country: Germany

institute: University Hospital Essen

hyb_protocol: Fragmentation and hybridization of the biotin-labeled samples to the gene chip, washing and staining were performed according to the manufacturer's recommendations

scan_protocol: Arrays were finally scanned in a GeneChip® 3000 scanner with G7 update

data_processing: Array images were processed using the Robust Multi-array Average (RMA) algorithm implemented in Partek® Genomics Suite® (PartekGS) software.

label: biotin

source_name: Mesenchymal stem and progenitor cells from first diagnosed AML patient

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

extract_protocol: After bone marrow aspiration, samples received Ficoll-Hypaque density gradient centrifugation followed by digestion and stained with fluorochrome conjugated antibodies. Cells were freshly isolated by FACS-ARIA III, total RNA were collected and extracted with Qiagen Rneasy kit

tag: individual

value: first diagnosed acute myeloid leukemia patient

value: Bone marrow

value: mesenchymal stem and progenitor cells


title: Control3

source_name: Mesenchymal stem and progenitor cells from non-leukemic donor

value: non-leukemic donor


title: AML7


title: D439_ILF3 sh1

first: Aderem

last: Lab

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Gene expression of human monocyte-derived DCs after 5 days post-transduction of ILF3 sh1 shRNA in the presence of virus-like particles packaging Vpx

hyb_protocol: 600ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 8x60K Microarrays using the Agilent hybridization chambers. The hybridization was allowed to run for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by compressed air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area  61mmx21.6mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid:039494_D_F_20120628. Probe sequences were mapped against the Ensembl transcript database (ensembl.org, GRCh37.74). Only sequences that matched with at most 5 mismatches and were best matches were retained. Sequences that mapped to more than one gene were removed for a  total of 37,623 unique probe sequences. Probe-specific logarithmically transformed expression was quantile-normalized. Duplicate probe sequences were averaged.

source_name: monocyte-derived dendritic cells treated with ILF3 sh1 shRNA and Vpx, donor: D439

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100-200ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 2x10^5 CD14+ magnetically-isolated monocytes were incubated in RPMI containing 10% heat-inactivated fetal bovine serum, 50 U/mL penicillin, 50 μg/mL streptomycin, 10 mM HEPES, 2-Mercaptoethanol, and 2 mM L-glutamine, in the presence of recombinant human GM-CSF at 10 ng/mL and IL-4 at 50 ng/mL. Virus-like particules containing VPX were provided in trans to allow for transduction with either control, ILF3 shRNA 1, or ILF3 shRNA 2 lentivirus. (10uL). Cells were fed the next day with half volume of IL-4/GM-CSF. Cells taken for RNA isolation on Day 5 post-transduction.

extract_protocol: ~2x10^5 MDDCs transduced with control, ILF3 sh1, or ILF3 sh2 shRNA lentivirus were isolated in Trizol on day 5 post-transduction.

value: donor D439

value: monocyte-derived dendritic cells

value: ILF3 sh1 shRNA

value: Vpx


title: D439_ILF3 sh2

description: Gene expression of human monocyte-derived DCs after 5 days post-transduction of ILF3 sh2 shRNA in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells treated with ILF3 sh2 shRNA and Vpx, donor: D439

value: ILF3 sh2 shRNA


title: SDALL01

value: Ileum

value: epithelial, lymphphatic, adipose and muscular


title: D438_ILF3 sh2

source_name: monocyte-derived dendritic cells treated with ILF3 sh2 shRNA and Vpx, donor: D438

value: donor D438


title: 48hrAPF_Male_Input_3

value: Whole pupae

value: 48hr APF

value: Male


title: Control2


title: AML6


title: 48hrAPF_Male_Input_1


title: Control1


title: D438_ILF3 sh1

source_name: monocyte-derived dendritic cells treated with ILF3 sh1 shRNA and Vpx, donor: D438


title: SDALL03

value: 70 days


title: AML4


title: D439_Control

description: Gene expression of human monocyte-derived DCs after 5 days post-transduction of control shRNA in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells treated with control shRNA and Vpx, donor: D439

value: control shRNA


title: AML5

value: first diagnosed acute myeloid leukemia patient


title: D436_ILF3 sh2

source_name: monocyte-derived dendritic cells treated with ILF3 sh2 shRNA and Vpx, donor: D436

value: donor D436


title: D436_Control

source_name: monocyte-derived dendritic cells treated with control shRNA and Vpx, donor: D436


title: AML3

value: Bone marrow

value: mesenchymal stem and progenitor cells


title: AML2


title: D438_Control

source_name: monocyte-derived dendritic cells treated with control shRNA and Vpx, donor: D438


title: D436_ILF3 sh1

source_name: monocyte-derived dendritic cells treated with ILF3 sh1 shRNA and Vpx, donor: D436


title: Y389_YPD_Rep1_Gen10

status: Public on Apr 07 2021

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

description: Moby Sample 88

data_processing:
library strategy:Bar-Seq
Read counts generated using a script to identify samples from fastq files that are associated with each 10bp index tag
Supplementary_files_format_and_content: Text file with read counts for each sample

organism: Saccharomyces cerevisiae

growth_protocol: Frozen glycerol stocks were thawed and cells added to 100 mL of liquid YPD with G418 (200 mg/L) at a starting OD600 of 0.05. The remaining cells from the frozen stocks were pelleted by centrifugation and represented the starting pool of the plasmid library (generation 0) for each strain.  After precisely five generations (OD600 ~1.6), each pooled culture was diluted to an OD600 of 0.05 in fresh YPD containing G418 to maintain cells in log phase. At 10 generations we pelleted 10 mL of each culture and stored at -80C until plasmid DNA extraction

extract_protocol:
Plasmids were isolated from cell pellets using the Qiagen Spin MiniPrep Kit.
Libraries were constructed using PCR where plasmid barcodes were amplified with multiplex primers containing Illumina adapters and unique 10bp index tags to allow for sample identification after sequencing.

treatment_protocol: Cell pellets were pretreated with 1ul Zymolyase for 1 hour at 30C prior to plasmid isolation

tag: strain/isolate

tag: genetic lineage

value: Mosaic

tag: media

value: YPD

tag: generation

tag: index tag

value: CGCACAATTG

tag: molecule subtype

value: plasmid DNA


title: NCYC3290_YPD_Rep1_Gen0

description: Moby Sample 76

value: West African

value: CATAGGTGTC


title: Y389_YPD_Rep3_Gen0

description: Moby Sample 87

value: GAAGCCATCT


title: DBVPG1373_YPD_Rep1_Gen0

description: Moby Sample 79

value: Wine/European

value: CAGTCAGATC


title: Y389_YPD_Rep2_Gen10

description: Moby Sample 89

value: AGTCATCAGG


title: YJM1389_YPD_Rep1_Gen0

description: Moby Sample 82

value: ATAGACGTCC


title: YJM1389_YPD_Rep3_Gen0

description: Moby Sample 84

value: ATCGAGTCGA


title: YJM1389_YPD_Rep2_Gen0

description: Moby Sample 83

value: ACTCAAGTCG


title: DBVPG1373_YPD_Rep3_Gen0

description: Moby Sample 81

value: AGCTGGACTA


title: DBVPG1373_YPD_Rep2_Gen0

description: Moby Sample 80

value: TTCCGGAACA


title: NCYC3290_YPD_Rep3_Gen0

description: Moby Sample 78

value: AATCGGTCGT


title: YPS163_YPD_Rep2_Gen0

description: Moby Sample 74

value: North American

value: AGAATGGCCT


title: Y12_YPD_Rep3_Gen0

description: Moby Sample 72

value: Asian/Sake

value: YPD

value: ACCAGGTACT


title: Y389_YPD_Rep2_Gen0

description: Moby Sample 86

value: Mosaic

value: CAGTGAATCC

value: plasmid DNA


title: NCYC3290_YPD_Rep2_Gen0

description: Moby Sample 77

value: West African

value: ATAAGCTGCC


title: YPS163_YPD_Rep3_Gen0

description: Moby Sample 75

value: CGACGTTAGT


title: YPS163_YPD_Rep1_Gen0

description: Moby Sample 73

value: GGCTACTAAC


title: Y12_YPD_Rep2_Gen0

description: Moby Sample 71

value: ATGGTCACAG


title: AML1

value: first diagnosed acute myeloid leukemia patient

tag: tissue

value: Bone marrow

tag: cell type

value: mesenchymal stem and progenitor cells


title: YJM978_YPD_Rep1_Gen0

description: Moby Sample 67

value: Wine/European

value: TGAATCCGCA


title: YJM978_YPD_Rep3_Gen0

description: Moby Sample 69

value: ATCAGTGAGC


title: YPS606_YPD_Rep3_Gen0

description: Moby Sample 66

value: North American

value: CCGATCAGTT


title: Y12_YPD_Rep1_Gen0

description: Moby Sample 70

value: Asian/Sake

value: YPD

value: CATCGGTGAA


title: Y2209_YPD_Rep3_Gen0

description: Moby Sample 63

value: Mosaic

value: ACACGTATGC

value: plasmid DNA


title: Y2209_YPD_Rep2_Gen0

description: Moby Sample 62

value: CATAGTCTGG


title: YPS606_YPD_Rep1_Gen0

description: Moby Sample 64

value: GCTATAGCGA


title: YJM1592_YPD_Rep2_Gen0

description: Moby Sample 59

value: CACAAGGTTG


title: Y389_YPD_Rep3_Gen10

description: Moby Sample 90

value: CACATGTCGA


title: YPS606_YPD_Rep3_Gen10

description: Moby Sample 54

value: TGTCTCGAGA


title: YPS128_YPD_Rep3_Gen0

description: Moby Sample 57

value: TAACAGCGCT


title: YJM1592_YPD_Rep3_Gen0

description: Moby Sample 60

value: CTCAAGGTGT


title: YPS128_YPD_Rep2_Gen0

description: Moby Sample 56

value: CTGTGGAACA


title: YPS606_YPD_Rep2_Gen10

description: Moby Sample 53

value: CAGTTCACGT


title: YPS606_YPD_Rep1_Gen10

description: Moby Sample 52

value: North American

value: TTGCATGAGC


title: YPS128_YPD_Rep3_Gen10

description: Moby Sample 51

value: AGCTAAGTGC


title: YPS128_YPD_Rep2_Gen10

description: Moby Sample 50

value: YPD

value: GGAATCCACT


title: YJM1592_YPD_Rep3_Gen10

description: Moby Sample 48

value: Asian/Sake

value: GATGCCTTGA


title: YJM1592_YPD_Rep2_Gen10

description: Moby Sample 47

value: TCAGCATGAG

value: plasmid DNA


title: YJM1389_YPD_Rep3_Gen10

description: Moby Sample 45

value: GTATCGAACC


title: YJM1592_YPD_Rep1_Gen10

description: Moby Sample 46

value: AACCGATTGC


title: YJM1389_YPD_Rep1_Gen10

description: Moby Sample 43

value: GTACATCCGA


title: Y2209_YPD_Rep1_Gen0

description: Moby Sample 61

value: Mosaic

value: TCAGCAGGTA


title: NCYC3290_YPD_Rep3_Gen10

description: Moby Sample 39

value: West African

value: CGTATCATGG


title: DBVPG1373_YPD_Rep2_Gen10

description: Moby Sample 41

value: Wine/European

value: TAACTGGCAC


title: DBVPG1373_YPD_Rep3_Gen10

description: Moby Sample 42

value: CATTGGAACG


title: NCYC3290_YPD_Rep1_Gen10

description: Moby Sample 37

value: CTTAAGAGCG


title: NCYC3290_YPD_Rep2_Gen10

description: Moby Sample 38

value: YPD

value: ATGGCATGCA


title: YPS128_YPD_Rep1_Gen0

description: Moby Sample 55

value: North American

value: AGGAATCTCC


title: YJM978_YPD_Rep3_Gen10

description: Moby Sample 30

value: AGAGCGTTCT


title: YJM978_YPD_Rep2_Gen10

description: Moby Sample 29

value: TGCTGAATGC

value: plasmid DNA


title: Y2209_YPD_Rep3_Gen10

description: Moby Sample 27

value: TAATGGCTGC


title: YPS128_YPD_Rep1_Gen10

description: Moby Sample 49

value: TATCGGAAGC


title: DBVPG1373_YPD_Rep1_Gen10

description: Moby Sample 40

value: CCGTCGATTA


title: YJM1273_YPD_Rep3_Gen0

description: Moby Sample 23

value: GGTAACGTAC


title: YJM1273_YPD_Rep2_Gen10

description: Moby Sample 22

value: TCGCGATTCA


title: YPS163_YPD_Rep3_Gen10

description: Moby Sample 36

value: ATTAGGACCG


title: Y2209_YPD_Rep1_Gen10

description: Moby Sample 25

value: Mosaic

value: AGTATGCACC


title: YJM1273_YPD_Rep2_Gen0

description: Moby Sample 21

value: CTGCAAGTTC


title: YJM1389_YPD_Rep2_Gen10

description: Moby Sample 44

value: Asian/Sake

value: ACTGACGAGT


title: YPS163_YPD_Rep1_Gen10

description: Moby Sample 34

value: YPD

value: CGGTACAACT


title: Y12_YPD_Rep1_Gen10

description: Moby Sample 31

value: TGCGAGCATT


title: Y7568_YPD_Rep3_Gen10

description: Moby Sample 18

value: CGATAACGCT


title: YJM1273_YPD_Rep1_Gen0

description: Moby Sample 19

value: North American

value: TACCGGAATG


title: YJM978_YPD_Rep1_Gen10

description: Moby Sample 28

value: Wine/European

value: CATCTGGTAG

value: plasmid DNA


title: Y2209_YPD_Rep2_Gen10

description: Moby Sample 26

value: GCTAGCAGTA


title: Y12_YPD_Rep3_Gen10

description: Moby Sample 33

value: TAAGATCCGG


title: Y7568_YPD_Rep3_Gen0

description: Moby Sample 17

value: AGGTACCTAC


title: Y12_YPD_Rep2_Gen10

description: Moby Sample 32

value: GTACGGCATT


title: Y7568_YPD_Rep2_Gen0

description: Moby Sample 15

value: Mosaic

value: ATACCTCGGA


title: Y7568_YPD_Rep1_Gen10

description: Moby Sample 14

value: GCGGATTAAC


title: YJM1273_YPD_Rep3_Gen10

description: Moby Sample 24

value: AAGACCTGTG


title: Y7568_YPD_Rep1_Gen0

description: Moby Sample 13

value: YPD

value: AGCGTATGTC


title: BY4743_YPD_Rep2_Gen0

description: Moby Sample 9

value: Laboratory

value: ATTGCCGGAA


title: BC187_YPD_Rep3_Gen10

description: Moby Sample 6

value: ACGCGGATTA


title: BY4743_YPD_Rep3_Gen10

description: Moby Sample 12

value: GTCAAGCACT


title: YJM1273_YPD_Rep1_Gen10

description: Moby Sample 20

value: North American

value: TAGGACCAGT


title: BY4743_YPD_Rep3_Gen0

description: Moby Sample 11

value: TACGCTGCAT

value: plasmid DNA


title: BY4743_YPD_Rep2_Gen10

description: Moby Sample 10

value: GACATGCTAG


title: YPS606 Rep3

data_processing:
Reads trimmed w/ Trimmomatic-0.30
Read alignment done w/ BWA mem Version: 0.7.12-r1039
Read sorting and indexing w/ Samtools 1.2 (htslib 1.2.1)
Gene counts generated w/ HTSeq version 0.6.0
Genome_build: SGD S288C R64-1-1
Supplementary_files_format_and_content: HTSeq count tables w/ gene counts for each sample

growth_protocol: All strains were grown in YPD for at least 3 generations to an OD600 ~0.5

extract_protocol:
RNA was extracted with hot phenol protocol; RNA was rRNA-depleted with Illumina's Ribo-Zero (Yeast) rRNA Removal Kit
cDNA library was prepared with Illumina's TruSeq Total RNA Stranded Kit


title: YPS606 Rep2


title: BY4743_YPD_Rep1_Gen10

description: Moby Sample 8

value: CGGTAGACTA


title: YPS163 Rep2


title: BY4743_YPD_Rep1_Gen0

description: Moby Sample 7

value: GCTTACGGAA


title: YPS163 Rep1


title: YPS128 Rep3


title: YJM1592_YPD_Rep1_Gen0

description: Moby Sample 58

value: Asian/Sake

value: CACCGATTAG


title: BC187_YPD_Rep3_Gen0

description: Moby Sample 5

value: Wine/European

value: AATGAGCCGT


title: BC187_YPD_Rep2_Gen10

description: Moby Sample 4

value: YPD

value: GATTAGCCTC


title: BC187_YPD_Rep2_Gen0

description: Moby Sample 3

value: ATCCTAGCAG


title: BC187_YPD_Rep1_Gen10

description: Moby Sample 2

value: TACAGTTGCG


title: YJM1592 Rep2


title: BC187_YPD_Rep1_Gen0

description: Moby Sample 1

value: AATAGGCGCT


title: Y7568_YPD_Rep2_Gen10

description: Moby Sample 16

value: Mosaic

value: GGTAGACATC


title: YPS606 Rep1

value: North American


title: YJM1273 Rep2


title: YJM1592 Rep3


title: YPS128 Rep1


title: YJM1389 Rep1


title: YPS128 Rep2


title: YJM1592 Rep1


title: Y7568 Rep1


title: Y2209 Rep3


title: YJM1389 Rep2


title: YJM1273 Rep3


title: YPS163 Rep3


title: YJM1273 Rep1


title: Y7568 Rep3


title: YJM978 Rep3


title: Y12 Rep2


title: Y12 Rep1


title: NCYC3290 Rep2

value: West African


title: YPS163_YPD_Rep2_Gen10

description: Moby Sample 35

value: ATTGGTCCGA

value: plasmid DNA


title: DBVPG1373 Rep3


title: Y7568 Rep2


title: YJM978 Rep1


title: Y389 Rep3


title: DBVPG1373 Rep1


title: Y2209 Rep1


title: Y389 Rep2


title: Y12 Rep3


title: YJM1389 Rep3


title: BY4743 Rep3

value: Laboratory


title: NCYC3290 Rep3


title: YJM978 Rep2


title: NCYC3290 Rep1


title: BC187 Rep3


title: Y2209 Rep2


title: Y389 Rep1


title: BC187 Rep1


title: BC187 Rep2


title: BY4743 Rep2


title: BY4743 Rep1


title: Y389_YPD_Rep1_Gen0

description: Moby Sample 85

value: ACCAGTAGTC


title: DBVPG1373 Rep2


title: Rmd9_PARCLIP

city: Goettingen

first: Katharina

middle: Bettina

last: Hofmann

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

description: Protocol: PAR-CLIP

data_processing:
library strategy: PAR-CLIP
Adapter sequences are trimmed and a quality filter discards reads containing unidentified nucleotides (N), Phred scores below 20, or reads shorter than 20
High-quality reads are aligned to S. cerevisiae genome (sacCer3, version 64.2.1) using Bowtie (v1.2). Reads are mapped uniquely with a maximum of one tolerated mismatch
Mockinbird is used for statistical evaluation of binding sites. A p-value threshold of 0.005 was set as well as the minimum coverage of 2 per site.
Genome_build: S. cerevisiae genome (sacCer3, version 64.1.1)
Supplementary_files_format_and_content: tab delimited text files containing verified cross-link sites (p-value<0.005), their genomic locations, p-values and occupancies

source_name: Yeast cell extract

growth_protocol: 4tU-labeled yeast cells (BY4741) expressing C-terminally TAP-tagged protein were UV-irradiated with an energy dose of 12 J/cm2 at 365 nm.

extract_protocol:
The cells were lysed by bead beating and IP was performed with rabbit IgG-conjugated protein G magnetic Dynabeads (Invitrogen). The cross-linked RNA was partially digested with RNase T1 (Thermo Scientific) and the IP was controlled by performing a western blot analysis of a part of the sample using the Peroxidase Anti-Peroxidase (PAP; Sigma) antibody. Following adapter ligation, RNA was recovered by digestion with proteinase K (New England Biolabs) and a subsequent acidic phenol/chloroform extraction.
Reverse transcription was performed with SuperScript III RTase (Invitrogen) and was followed by PCR amplification using the NEXTflex barcode primer kit (Bio Scientific). The generated cDNA was purified, size selected, and quantified using TapeStation (Agilent Technologies). The resulting samples were then PCR-amplified and sequenced on an Illumina HiSeq 2500 system.

treatment_protocol: 1 mM 4tU for 4 h.

tag: strain background

tag: genotype/variation

value: crosslinked RNA


title: YPS606_YPD_Rep2_Gen0

description: Moby Sample 65

value: TTGTCGAACG


title: YJM978_YPD_Rep2_Gen0

description: Moby Sample 68

value: Wine/European

value: ATGCCATGAG


title: 58-80-batch_2-IL17E_100_ng_ml

city: Ballerup

first: Maxim

middle: Alexandre Xavier

last: Tollenaere

address: Industriparken 55

department: Advanced Biologics

country: Denmark

institute: LEO Pharma

hyb_protocol: Hybridizations was performed with the GeneChip™ Hybridization Control Kit according to the manufacturer's instructions.

scan_protocol: Scanning has been performed according to the GeneTitan manufacturer's instructions.

data_processing: The normalization and summarization was carried out in R, using RMA (Affy) and robust quantile normalization (preprocessCore)

source_name: abdominal skin

label_protocol: The extracts were labeled with GeneChip™ WT Terminal Labeling Kit according to the manufacturer's instructions.

extract_protocol: RNA was extracted from ex vivo cultured human skin biopsies using the mirVana kit (Life Technologies) according to the manufacturer’s instructions and Precellys® 24 bead-based homogenizer (Precellys® Bertin Technologies, France) for the mechanical lysing of the tissue.

tag: batch

tag: treatment


title: 53-74-batch_2-IL17E_10_ng_ml


title: 51-71-batch_1-IL17E_10_ng_ml


title: 59-81-batch_2-IL17E_100_ng_ml


title: 56-78-batch_1-IL17E_100_ng_ml


title: 52-73-batch_2-IL17E_10_ng_ml


title: 50-70-batch_4-IL17C_100_ng_ml


title: 55-77-batch_4-IL17E_10_ng_ml


title: 57-79-batch_1-IL17E_100_ng_ml


title: 47-65-batch_1-IL17C_100_ng_ml


title: 45-63-batch_4-IL17C_10_ng_ml


title: 43-61-batch_3-IL17C_10_ng_ml


title: 44-62-batch_3-IL17C_10_ng_ml


title: 40-56-batch_4-IL17F_100_ng_ml


title: 41-58-batch_1-IL17C_10_ng_ml


title: 48-66-batch_2-IL17C_100_ng_ml


title: 60-82-batch_3-IL17E_100_ng_ml


title: 46-64-batch_1-IL17C_100_ng_ml


title: 54-75-batch_3-IL17E_10_ng_ml


title: 49-67-batch_2-IL17C_100_ng_ml


title: 35-48-batch_3-IL17F_10_ng_ml


title: 42-60-batch_2-IL17C_10_ng_ml


title: 38-53-batch_2-IL17F_100_ng_ml


title: 39-55-batch_3-IL17F_100_ng_ml


title: 36-51-batch_1-IL17F_100_ng_ml


title: 37-52-batch_2-IL17F_100_ng_ml


title: 33-46-batch_2-IL17F_10_ng_ml


title: 30-42-batch_4-IL17AF_100_ng_ml


title: 25-35-batch_4-IL17AF_10_ng_ml


title: 29-41-batch_3-IL17AF_100_ng_ml


title: 22-31-batch_2-IL17AF_10_ng_ml


title: 31-43-batch_1-IL17F_10_ng_ml


title: 26-37-batch_1-IL17AF_100_ng_ml


title: 23-32-batch_2-IL17AF_10_ng_ml


title: 27-38-batch_2-IL17AF_100_ng_ml


title: 32-44-batch_1-IL17F_10_ng_ml


title: 28-39-batch_2-IL17AF_100_ng_ml


title: 20-28-batch_4-IL17A_100_ng_ml


title: 19-25-batch_2-IL17A_100_ng_ml


title: 24-33-batch_3-IL17AF_10_ng_ml


title: 14-20-batch_3-IL17A_10_ng_ml


title: 21-30-batch_1-IL17AF_10_ng_ml


title: 16-22-batch_1-IL17A_100_ng_ml


title: 18-24-batch_2-IL17A_100_ng_ml


title: 17-23-batch_1-IL17A_100_ng_ml


title: 15-21-batch_4-IL17A_10_ng_ml


title: 34-47-batch_3-IL17F_10_ng_ml


title: 13-19-batch_3-IL17A_10_ng_ml


title: 11-16-batch_1-IL17A_10_ng_ml


title: 10-14-batch_4-IL17A_1_ng_ml


title: 08-11-batch_2-IL17A_1_ng_ml


title: 201118840090_R01C01 Sample930

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: hapten-labeled dideoxynucleotides

source_name: Whole Blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: DNA was extracted using a phenol/chloroform method

tag: phenotype

value: Control

tag: Sex

value: Female

tag: age


title: 201118840090_R05C01 Sample932

value: Male


title: 12-17-batch_2-IL17A_10_ng_ml


title: 06-8-batch_1-IL17A_1_ng_ml


title: 201118840090_R02C01 Sample931


title: 201118840089_R04C01 Sample927


title: 201118840089_R01C01 Sample925


title: 200970100058_R08C01 Sample922

value: Case


title: 05-7-batch_4-untreated

value: untreated


title: 02-3-batch_2-untreated


title: 09-12-batch_3-IL17A_1_ng_ml


title: 201118840090_R06C01 Sample933


title: 200970100058_R05C01 Sample919


title: 07-9-batch_1-IL17A_1_ng_ml


title: 201118840089_R07C01 Sample928


title: 201118840089_R02C01 Sample926


title: 200970100059_R02C01 Sample924


title: 200970100059_R01C01 Sample923


title: 201118840110_R01C01 Sample934


title: 01-2-batch_1-untreated


title: 03-4-batch_2-untreated


title: 200970100058_R07C01 Sample921


title: 200970100058_R06C01 Sample920


title: 200970100034_R01C01 Sample910


title: 200970100034_R02C01 Sample911


title: 200970100017_R07C01 Sample908


title: 200970100034_R03C01 Sample912


title: 200970100058_R04C01 Sample918


title: 200970100034_R05C01 Sample913


title: 200970100017_R05C01 Sample906


title: 200970100017_R06C01 Sample907


title: 200970100009_R08C01 Sample903


title: 200970100009_R05C01 Sample901


title: 200970100009_R04C01 Sample900


title: 200970100058_R01C01 Sample917


title: 201118840089_R08C01 Sample929


title: 200970100034_R06C01 Sample914


title: 200970100017_R08C01 Sample909


title: 200970100009_R07C01 Sample902


title: 200970100034_R07C01 Sample915


title: 200970100017_R01C01 Sample904


title: 200970100017_R03C01 Sample905


title: 200970100009_R02C01 Sample898


title: 04-6-batch_3-untreated


title: 200970100009_R01C01 Sample897


title: 200970100009_R03C01 Sample899


title: 200970100006_R08C01 Sample896


title: 201118840084_R08C01 Sample891


title: 200970100006_R02C01 Sample892


title: 200970100006_R07C01 Sample895


title: 200970100034_R08C01 Sample916


title: 201118840084_R01C01 Sample887


title: 201118840084_R05C01 Sample888


title: 201118840080_R07C01 Sample885


title: 201118840084_R07C01 Sample890


title: 201118840080_R08C01 Sample886


title: 201118840080_R04C01 Sample883


title: 200970100006_R06C01 Sample894


title: 200970100006_R03C01 Sample893


title: 201118840084_R06C01 Sample889


title: 201118840080_R03C01 Sample882


title: 201118840080_R02C01 Sample881


title: 201118840080_R06C01 Sample884


title: 201118840079_R06C01 Sample879


title: 201118840079_R08C01 Sample880


title: 201118840079_R05C01 Sample878


title: 201118840079_R03C01 Sample876


title: 201118840079_R04C01 Sample877


title: 201118840075_R08C01 Sample874


title: 201118840079_R01C01 Sample875


title: 201118840075_R06C01 Sample872


title: 201118840075_R07C01 Sample873


title: 201118840075_R04C01 Sample871


title: 201118840075_R03C01 Sample870


title: 1,25 NP 8

city: Rochester

first: Sanjay

last: Misra

state: MN

address: 200 First Street SW

department: Radiology

institute: Mayo Clinic

description: Treatment

data_processing:
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.
BAM files were imported into the RNA-Seq pipeline of mm10. Exclusions included a minimum RPKM value of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: The average RPKMs of each group (KI-A or KI-V) were calculated and KI-A/KI-V was considered as fold change.  The genes that were >1.5 or <0.75 were considered as differentially expressed genes and the genes that were <1.5 or > 0. 75 were excluded. A simple t-test was performed to determine the P value and P<0.05 was considered as significant different compared to KI-V and the genes that were >0.05 were excluded.

organism: Sus scrofa

source_name: Vein

extract_protocol:
Extraction protocol 0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: Chronic Kidney disease created to a human CX3CR1 knock-in mouse as described in methods. 28days later an arteriovenous fistula was clreated by ligation of carotid artery and jugular vein. Mice were injected human CX3CR1 (30 mg/kg) antibody (KI+AB) or equal volume of vehicle control (KI-V) intraperitonially for two times per week. 7 days after AVF creation, animals were euthanized and the outflow veins of AVFs were harvested.

value: 1,25 NP PLGA+Hydrogel


title: 1,25 NP 7

description: Treatment


title: 201118840075_R02C01 Sample869


title: 201118840067_R08C01 Sample868


title: 1,25 NP 6

description: Treatment


title: 201118840067_R06C01 Sample866


title: 201118840067_R07C01 Sample867


title: 1,25 NP 4

description: Treatment


title: 201118840067_R04C01 Sample865


title: 1,25 NP 3

description: Treatment


title: 1,25 NP 2

description: Treatment


title: 201118840067_R02C01 Sample863


title: 201118840067_R03C01 Sample864


title: Control 4

description: Vehicle

value: PLGA+Hydrogel


title: 201118840067_R01C01 Sample862


title: Control 5

description: Vehicle


title: 1,25 NP 1

description: Treatment


title: 201118840063_R08C01 Sample861


title: 201118840063_R04C01 Sample858


title: Control 2

description: Vehicle


title: Control 1

description: Vehicle


title: 201118840063_R06C01 Sample860


title: Control 3

description: Vehicle


title: 201118840063_R02C01 Sample856


title: 201118840063_R03C01 Sample857


title: Zhongke 1878_Mock_96h

first: Xianrui

last: Guo

address: No.1 West Beichen Road,Chaoyang District, Beijing

institute: Institute of Genetics and Developmental Biology

data_processing:
Sequenced reads were trimmed using Trimmomatic (version: 0.36).
The sequenced transcripts were aligned with Chinese Spring reference genome (IWGSC v1.0) using GMAP (-min-trimmed-coverage 0.9 min-identity 0.85).
The sequenced reads were mapped to the unmapped transcripts using hisat2 (version: 2.0.0).
The expression level was measured using Stringtie (version:1.3.3b).
Genome_build: Wheat Chinese Spring IWGSC RefSeq v1.0 genome assembly
Supplementary_files_format_and_content: Excel, fasta

organism: Thinopyrum elongatum

source_name: wheat-Th. elongatum translocation line

growth_protocol: The wheat-Th. elongatum translocation line Zhongke 1878 were planted in field for RNA-Seq experiment.

extract_protocol:
Total RNA was extracted using TRIzol reagent.
The cDNA libraries were constructed following standard protocols and sequenced by Berry Genomics Co. Ltd, China.

treatment_protocol: Approximately 20 μL of F. graminearum fungal suspension (1×10^6 conidia/ml) or mung bean soup was injected into the central spikelet at early flowering stage. The inoculated spikes were covered with a plastic bag for 2 d to keep moist for fungal infection.

tag: line

value: Zhongke 1878

value: Spikes

value: inoculation with mung bean soup

tag: time point


title: 201118840063_R01C01 Sample855


title: Zhongke 1878_Fg_48h

value: inoculation with Fusarium graminearum


title: 201118840059_R07C01 Sample854


title: Zhongke 1878_Mock_48h


title: 1,25 NP 5

description: Treatment


title: 201118840059_R06C01 Sample853


title: Zhongke 1878_Fg_24h


title: Zhongke 1878_Mock_24h


title: 201118840059_R05C01 Sample852


title: 201118840059_R04C01 Sample851


title: 201118840059_R02C01 Sample849


title: 201118840059_R03C01 Sample850


title: Zhongke 1878_Fg_12h


title: Zhongke 1878_Mock_12h


title: 201118840059_R01C01 Sample848


title: Macrophages LPS + MIC-1 Treated Rep 3

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

institute: Rutgers, the State University of New Jersey

description:
Rep 3
MIC-1 (80mg/kg) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before an LPS intraperitoneal injection
Macrophages LPS + MIC-1 Treated
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Macrophages_AntiInflammatory_LPSvsLPS_10uM_MIC.txt

data_processing:
Alignment: RNA-seq: Kallisto v0.45.0.
RNA-seq Transcript Import: tximport 1.8.0
DESeq2 1.20.0
Genome_build: RefSeq mm9
Supplementary_files_format_and_content: RNA-Seq: FPKM table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments and Results table outputted by DESeq2 that extracts Log2FC values, p values, adjusted p values, baseMean values, and test statistic values.

source_name: Macrophages

extract_protocol:
C57BL/6 mice were purchased from Charles River Laboratories (Malvern, PA) and acclimated for one week at 22 ± 2°C on a light/dark cycle of 12 h. Animals were housed two per cage and allowed access to food and water ad libitum. Experiments were performed using the approved protocol by the Rutgers University Institutional Animal Care and Use Committee. All in vivo experiments were standardized to MIC-1 (based on 38.9% w/w MIC-1 in MSE). C57BL/6 mice divided into three groups of 6 animals randomly as follows: Group a: Vehicle Control group injected with saline; Group b: LPS (10 mg/kg); treated group c: MIC-1 (80mg/kg) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before an LPS intraperitoneal injection and then sacrificed at 16 hours for tissue and blood collection.
RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

tag: genotype

value: wild type

tag: strain


title: Macrophages LPS + MIC-1 Treated Rep 2

description:
Rep 2
MIC-1 (80mg/kg) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before an LPS intraperitoneal injection
Macrophages LPS + MIC-1 Treated
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Macrophages_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: Macrophages LPS + MIC-1 Treated Rep 1

description:
Rep 1
MIC-1 (80mg/kg) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before an LPS intraperitoneal injection
Macrophages LPS + MIC-1 Treated
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Macrophages_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: 201118840058_R06C01 Sample846


title: 201118840058_R05C01 Sample845


title: Macrophages LPS Treated Rep 3

description:
Rep 3
LPS treated (10 mg/kg)
Macrophages LPS Treated
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS.txt
Results_Macrophages_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: Zhongke 1878_Fg_96h


title: 201118840058_R03C01 Sample844


title: Macrophages LPS Treated Rep 1

description:
Rep 1
LPS treated (10 mg/kg)
Macrophages LPS Treated
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS.txt
Results_Macrophages_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: 201118840058_R02C01 Sample843


title: Macrophages LPS Treated Rep 2

description:
Rep 2
LPS treated (10 mg/kg)
Macrophages LPS Treated
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS.txt
Results_Macrophages_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: 201118840058_R01C01 Sample842


title: 200970150059_R08C01 Sample841


title: Macrophages Control Rep 1

description:
Rep 1
none
Macrophages Control
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS.txt


title: 200970150059_R07C01 Sample840


title: Macrophages Control Rep 2

description:
Rep 2
none
Macrophages Control
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS.txt


title: 201118840063_R05C01 Sample859


title: Liver LPS + MIC-1 Treated Rep 3

description:
Rep 3
MIC-1 (80mg/kg) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before an LPS intraperitoneal injection
Liver LPS + MIC-1 Treated
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Liver_AntiInflammatory_LPSvsLPS_10uM_MIC.txt

source_name: Liver


title: 200970150059_R05C01 Sample839


title: 200970150059_R04C01 Sample838


title: Macrophages Control Rep 3

description:
Rep 3
none
Macrophages Control
Processed data files:
FPKM_Macrophages.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Macrophages_AntiInflammatory_ControlvsLPS.txt


title: Liver LPS + MIC-1 Treated Rep 1

description:
Rep 1
MIC-1 (80mg/kg) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before an LPS intraperitoneal injection
Liver LPS + MIC-1 Treated
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Liver_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: 201118840058_R07C01 Sample847


title: Liver LPS Treated Rep 3

description:
Rep 3
LPS treated (10 mg/kg)
Liver LPS Treated
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS.txt
Results_Liver_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: 200970150059_R03C01 Sample837


title: 200970150059_R01C01 Sample835


title: 200970150020_R08C01 Sample834


title: Liver LPS Treated Rep 2

description:
Rep 2
LPS treated (10 mg/kg)
Liver LPS Treated
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS.txt
Results_Liver_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: 200970150020_R07C01 Sample833


title: Liver LPS Treated Rep 1

description:
Rep 1
LPS treated (10 mg/kg)
Liver LPS Treated
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS.txt
Results_Liver_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: 200970150020_R06C01 Sample832


title: Liver Control Rep 3

description:
Rep 3
none
Liver Control
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Liver_AntiInflammatory_ControlvsLPS.txt


title: Liver Control Rep 2

description:
Rep 2
none
Liver Control
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Liver_AntiInflammatory_ControlvsLPS.txt


title: 200970150020_R05C01 Sample831


title: Liver Control Rep 1

description:
Rep 1
none
Liver Control
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Liver_AntiInflammatory_ControlvsLPS.txt


title: 200970150020_R04C01 Sample830


title: Zhongke 1878_full_96h


title: 200970150020_R03C01 Sample829


title: 200970150020_R02C01 Sample828


title: Liver LPS + MIC-1 Treated Rep 2

description:
Rep 2
MIC-1 (80mg/kg) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before an LPS intraperitoneal injection
Liver LPS + MIC-1 Treated
Processed data files:
FPKM_Liver.txt
Results_Liver_AntiInflammatory_ControlvsLPS_10uM_MIC.txt
Results_Liver_AntiInflammatory_LPSvsLPS_10uM_MIC.txt


title: sn C57BL/6J Aged 4V rep1

city: Cambridge

first: Rebecca

middle: H

last: Herbst

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute of MIT and Harvard

description:
single-nucleus RNA-seq
sn_Aged_HCP_1

data_processing:
Cellranger software (1.1.0 for V1 10X chemistry, and 1.2.0 for V2 10X chemistry)
Genome_build: mm10
Supplementary_files_format_and_content: Unique molecular identifiers (UMI) counts table (mtx file), with separate file for cell barcodes and genes. Exported for single-cell and single-nucleus RNA-seq data separatel.

source_name: sn C57BL/6J Aged 4V_choroid plexus

extract_protocol:
For embryonic single cell sequencing, whole cells were isolated by treatment of lateral, third and fourth ventricle choroid plexus tissue with Collagenase II (Gibco), TyrpLE (Life Technologies) and trituation. Healthy cells were then FACS sorted using LIVE/DEAD stainig kit (ThermoFisher).
For nuclei isolation from each ventricle across all ages, we first minced the tissue in CST Lysis buffer. Nuclear suspension diluted with ST buffer and samples were filtered and collected by centrifuation followed by filtration before loading.

value: 20 months post natal

value: choroid plexus

tag: ventricle


title: sn C57BL/6J Aged 4V rep2

description:
single-nucleus RNA-seq
sn_Aged_HCP_2


title: 200970150017_R08C01 Sample827


title: 200970150017_R07C01 Sample826


title: sn C57BL/6J Aged 3V rep3

description:
single-nucleus RNA-seq
sn_Aged_DCP_3

source_name: sn C57BL/6J Aged 3V_choroid plexus


title: sn C57BL/6J Aged 3V rep2

description:
single-nucleus RNA-seq
sn_Aged_DCP_2


title: 200970150017_R05C01 Sample825


title: sn C57BL/6J Aged 3V rep1

description:
single-nucleus RNA-seq
sn_Aged_DCP_1


title: 200970150059_R02C01 Sample836


title: 200970150017_R03C01 Sample823


title: 200970150017_R04C01 Sample824


title: sn C57BL/6J Aged LV rep3

description:
single-nucleus RNA-seq
sn_Aged_TCP_3

source_name: sn C57BL/6J Aged LV_choroid plexus

value: LV


title: 200970150017_R02C01 Sample822


title: sn C57BL/6J Adut 4V rep1

description:
single-nucleus RNA-seq
sn_Adult_HCP_1

source_name: sn C57BL/6J Adut 4V_choroid plexus

value: 4 months post natal


title: 200970150008_R03C01 Sample819


title: sn C57BL/6J Aged LV rep2

description:
single-nucleus RNA-seq
sn_Aged_TCP_2


title: 200970150008_R07C01 Sample821


title: sn C57BL/6J Aged LV rep1

description:
single-nucleus RNA-seq
sn_Aged_TCP_1


title: sn C57BL/6J Aged 4V rep3

description:
single-nucleus RNA-seq
sn_Aged_HCP_3


title: sn C57BL/6J Adut 4V rep2

description:
single-nucleus RNA-seq
sn_Adult_HCP_2


title: 200970150008_R04C01 Sample820


title: sn C57BL/6J Adut LV rep2

description:
single-nucleus RNA-seq
sn_Adult_TCP_2

source_name: sn C57BL/6J Adut LV_choroid plexus


title: sn C57BL/6J Adut 3V rep1

description:
single-nucleus RNA-seq
sn_Adult_DCP_1

source_name: sn C57BL/6J Adut 3V_choroid plexus


title: sn C57BL/6J Embryo 3V rep1

description:
single-nucleus RNA-seq
sn_Embryo_DCP_1

source_name: sn C57BL/6J Embryo 3V_choroid plexus


title: 200992310016_R05C01 Sample815


title: sn C57BL/6J Adut LV rep1

description:
single-nucleus RNA-seq
sn_Adult_TCP_1


title: 200992310016_R04C01 Sample814


title: 200992310016_R07C01 Sample816


title: 200992310016_R03C01 Sample813


title: sn C57BL/6J Embryo 4V rep1

description:
single-nucleus RNA-seq
sn_Embryo_HCP_1

source_name: sn C57BL/6J Embryo 4V_choroid plexus


title: sn C57BL/6J Embryo LV rep1

description:
single-nucleus RNA-seq
sn_Embryo_TCP_1

source_name: sn C57BL/6J Embryo LV_choroid plexus


title: sc CD-1 Embryo 4V rep3

description:
single-cell RNA-seq
sc_Embryo_HCP_3

source_name: sc CD-1 Embryo 4V_choroid plexus


title: 200992310016_R08C01 Sample817


title: 200992310016_R02C01 Sample812


title: 200992310016_R01C01 Sample811


title: 200992310003_R08C01 Sample810


title: sc CD-1 Embryo 3V rep3

description:
single-cell RNA-seq
sc_Embryo_DCP_3

source_name: sc CD-1 Embryo 3V_choroid plexus


title: sc CD-1 Embryo 3V rep2

description:
single-cell RNA-seq
sc_Embryo_DCP_2


title: sc CD-1 Embryo 4V rep1

description:
single-cell RNA-seq
sc_Embryo_HCP_1


title: sc CD-1 Embryo 4V rep2

description:
single-cell RNA-seq
sc_Embryo_HCP_2


title: sc CD-1 Embryo 3V rep1

description:
single-cell RNA-seq
sc_Embryo_DCP_1


title: 200970150008_R01C01 Sample818


title: sc CD-1 Embryo LV rep3

description:
single-cell RNA-seq
sc_Embryo_TCP_3

source_name: sc CD-1 Embryo LV_choroid plexus


title: 200992310003_R05C01 Sample807

source_name: Whole Blood


title: 200992310003_R02C01 Sample805


title: CD8_3-3_ctl RNA-seq

city: Guangzhou

first: Qiaoqi

last: Sui

address: Dongfeng East Road 651

institute: Sun Yat-sen University Cancer Center

description: CD8+ T cells from Patient2 treated with mock

data_processing:
The purified l library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA) and then diluted to 10 pM for cluster generation in situ on the pair-end flow cell followed by sequencing (2×150 bp) on Illumina HiSeq3000.
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. HISAT2 was used to align the clean reads to the human reference genome hg19 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model. Differential expression was assessed by DE sequencing read counts as input.
The Benjamini–Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of adjusted p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including all samples were submitted. The RPKM data for individual genes of each sample was shown, supplemented with gene type, position, strand, length as well as the description.

source_name: Lymphocyte

growth_protocol: DLD1 (Human colorectal cancer cells) were cultured at 37°C in complete media (RMPI1640 supplemented with 100 µg/ml streptomycin, 100 IU/ml penicillin, and 10% FBS). Human total T cells and CD8+ T were isolated from the PBMCs with human pan T cell isolation kit and CD8+ T cell isolation kit according to the manufacturer’s instruction (Miltenyi Biotec).Cells were cultured in Human ImmunoCult-XF T Cell Expansion medium (Stem Cell) with penicillin (100 U/ml) and streptomycin (100 µg/ml) at 37 °C, supplemented with 5% CO2. Cells were pre-stimulated with IL-2 (200U/ml, Peprotech) in the presence of anti-CD3 (Peprotech) and anti-CD28 (Peprotech) for 48 hours before experiment.

extract_protocol:
Cells were collected, and RNA was isolated and purified with the Trizol (Invitrogen).then RNA was isolated and purified with the Trizol (Invitrogen). RNA purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RIN above 7.0. Briefly, rRNAs were removed from Total RNA using EpicentreRibo-Zero rRNA Removal Kit (illumina, USA) and fragmented to approximately 200bp. Subsequently, the purified RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).(Vazyme, Nanjing, China) to enrich mRNA, and RNA library was performed by using VAHTS mRNA-seq v2 Library Prep Kit from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells  were cultured in the presence or absence of 300 ng/ml DKK1 for 24 hours

value: Peripheral blood

value: mock

value: CD8+ T cells derived from blood of Patient with dMMR colorectal cancer


title: 200992310001_R08C01 Sample803

value: Female


title: sc CD-1 Embryo LV rep1

description:
single-cell RNA-seq
sc_Embryo_TCP_1


title: 200992310001_R07C01 Sample802

value: Case

value: Male


title: 200992310001_R04C01 Sample800

value: Control


title: CD8_3-1_D RNA-seq

description: CD8+ T cells from Patient1 treated with DKK1

value: 300ng/ml DKK1


title: CD8_3-1_ctl RNA-seq

description: CD8+ T cells from Patient1 treated with mock


title: 200992310001_R06C01 Sample801


title: T2-3_D RNA-seq

description: T cells from Patient treated with DKK1-3

value: T cells derived from blood of Patient with dMMR colorectal cancer


title: 200992310001_R03C01 Sample799


title: 200992310001_R01C01 Sample797


title: T2-2_D RNA-seq

description: T cells from Patient treated with DKK1-2


title: 200992310001_R02C01 Sample798


title: T2-1_D RNA-seq

description: T cells from Patient treated with DKK1-1


title: T2-3_ctl RNA-seq

description: T cells from Patient treated with mock-3


title: 200992310003_R06C01 Sample808


title: 200992320054_R06C01 Sample794


title: T2-1_ctl RNA-seq

description: T cells from Patient treated with mock-1


title: T1-3_D RNA-seq

description: T cells from healthy donor treated with DKK1-3

value: T cells derived from healthy donor's blood


title: 200992310003_R04C01 Sample806


title: 200992320054_R07C01 Sample795


title: 200992320054_R05C01 Sample793


title: T2-2_ctl RNA-seq

description: T cells from Patient treated with mock-2


title: 200992310003_R07C01 Sample809


title: T1-1_D RNA-seq

description: T cells from healthy donor treated with DKK1-1


title: sc CD-1 Embryo LV rep2

description:
single-cell RNA-seq
sc_Embryo_TCP_2


title: 200992320054_R08C01 Sample796


title: CD8_3-3_D RNA-seq

description: CD8+ T cells from Patient2 treated with DKK1


title: 200992320054_R04C01 Sample792


title: 200992320054_R03C01 Sample791


title: T1-2_ctl RNA-seq

description: T cells from healthy donor treated with mock-2


title: 200992320054_R02C01 Sample790


title: 200992320054_R01C01 Sample789


title: T1-3_ctl RNA-seq

description: T cells from healthy donor treated with mock-3


title: T1-1_ctl RNA-seq

description: T cells from healthy donor treated with mock-1


title: D3 RNA-seq

description: DLD1 cells treated with DKK1-3

source_name: colorectal carcinoma

value: colorectal carcinoma

value: dMMR colorectal cancer cell


title: 200992320024_R07C01 Sample787


title: C3 RNA-seq

description: DLD1 cells treated with mock-3


title: D2 RNA-seq

description: DLD1 cells treated with DKK1-2


title: C2 RNA-seq

description: DLD1 cells treated with mock-2


title: 200992320024_R03C01 Sample783


title: 200992320024_R06C01 Sample786


title: 200992320024_R04C01 Sample784


title: 200992320024_R02C01 Sample782


title: T1-2_D RNA-seq

description: T cells from healthy donor treated with DKK1-2


title: 200992320024_R01C01 Sample781


title: C1 RNA-seq

description: DLD1 cells treated with mock-1


title: 200992320022_R08C01 Sample780


title: 200992320022_R07C01 Sample779


title: 200992320022_R05C01 Sample778


title: 200992320022_R04C01 Sample777


title: 200992320022_R02C01 Sample775


title: 200992320022_R03C01 Sample776


title: 200992320024_R08C01 Sample788


title: 200992320024_R05C01 Sample785


title: D1 RNA-seq

description: DLD1 cells treated with DKK1-1


title: 200992320007_R05C01 Sample770


title: 200992320007_R07C01 Sample772


title: 200992320007_R06C01 Sample771


title: 200992310003_R01C01 Sample804


title: 200992320007_R04C01 Sample769


title: 200992320007_R03C01 Sample768


title: 200992320007_R02C01 Sample767


title: 200992320007_R01C01 Sample766


title: 200992320022_R01C01 Sample774


title: 3999547161_R06C02 Sample800

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

tag: status

value: SCZ

tag: gender

value: F

tag: ageatbloodcollection


title: C4: Healthy colon, biological rep.4

city: Thycaud

first: Dr. Harikumar

middle: K

last: B

state: Kerala

address: Poojappura

department: Cancer Research Program

country: India

institute: Rajiv Gandhi centre for Biotechnology

description: miRNA expression from AOM treated colon

hyb_protocol: Samples were hybridised using Affymetrix hybridisation kit. Briefly, biotin labelled sample and hybridisation master mix were incubated at 99oC for 5 mins, then at 45oC for 5 mins. 130ul was injected into the array and both septa covered with tough spots. Loaded into hybridisation oven and incubated at 48oC, 60rpm for 16-18hrs

scan_protocol: The chips were then scanned with an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, California, United States).

data_processing: The Data generated from the scan was then analyzed using the Bioconductor packages (Oligo, limma)

label: Biotin

source_name: Colon, normal

label_protocol: Total RNA was used for the reaction, Poly(A) tailing was performed followed by biotin labelling of the RNA. This was done by  Flash Tag Biotin HSR labelling kit by Affymetrix

growth_protocol: Colon collected from mice treated with AOM+DSS, followed by Cardamonin simultaneously treated or after tumor development. Colon from normal, healthy mice were used as control.

extract_protocol: Colon dissected and rinsed in 1X PBS, followed by snap freezing in liquid nitrogen. This was ground in liquid nitrogen, and mirVana miRNA isolation kit was used for the subsequent steps.

treatment_protocol: Azoxymethane (AOM) was given a single (10mg/kg B.wt) intraperitonielly at day 0 and three bouts of 5% DSS at days 5-10, 25-30, 45-50. At day 140, the mice were sacrificed. Cardamonin was administered orally, at a dose of 10mg/kg, 5 times every week for simultaneous group. And treatment started at a dose of 10mg/kg, 5times every week from 16th week to 30th week for the ''after tumor formation''group.

tag: tissue

value: Colon

tag: treatment regime

value: Untreated


title: 3999547161_R06C01 Sample799


title: C6: Healthy colon, biological rep.6

description: miRNA expression from AOM treated colon


title: 200992320007_R08C01 Sample773


title: 3999547161_R05C02 Sample798

value: FEP

value: M


title: 200992290036_R08C01 Sample765


title: C3: Healthy colon, biological rep.3

description: miRNA expression form normal colon


title: C1: Healthy colon, biological rep.1

description: miRNA expression form normal colon


title: G3_5: Colon, AOM+DSS treated, Cardamonin treatment after 16 week, biol.rep.3

description: miRNA expression from AOM and cardamonin treated samples

source_name: Colon, AOM, Cardamonin after 16 week

value: Treated - Cardamonin after tumor formation


title: G2-9: Colon, AOM+DSS treated, Cardamonin simultaneous treatment, biol.rep.3

source_name: Colon, AOM, Cardamonin simultaneous

value: Treated - Cardamonin simultanoeus


title: G3_4: Colon, AOM+DSS treated, Cardamonin treatment after 16 week, biol.rep.2


title: G1-9: Colon, AOM+DSS treated, Vehicle control, biological rep.4

source_name: Colon, AOM treated

value: Treated - vehicle control


title: G2-5: Colon, AOM+DSS treated, Cardamonin simultaneous treatment, biol.rep.2


title: G1-1: Colon, AOM+DSS treated, Vehicle control, biological rep.1


title: G1-5: Colon, AOM+DSS treated, Vehicle control, biological rep.3


title: 200992290036_R06C01 Sample764

value: Case


title: 200992290036_R04C01 Sample762

value: Male


title: G3-3: Colon, AOM+DSS treated, Cardamonin treatment after 16 week, biol.rep.1


title: G2-2: Colon, AOM+DSS treated, Cardamonin simultaneous treatment, biol.rep.1


title: C5: Healthy colon, biological rep.5

description: miRNA expression from AOM treated colon


title: G1-3: Colon, AOM+DSS treated, Vehicle control, biological rep.2


title: 200992290036_R05C01 Sample763

value: Control

value: Female


title: 200992290036_R03C01 Sample761


title: C2: Healthy colon, biological rep.2

description: miRNA expression form normal colon


title: 200992290036_R02C01 Sample760


title: 3999547161_R02C01 Sample791


title: 3999547161_R03C01 Sample793


title: 200992290035_R07C01 Sample757


title: 200992290035_R06C01 Sample756


title: 200992290036_R01C01 Sample759


title: 200992290035_R08C01 Sample758


title: 3999547161_R02C02 Sample792


title: 3999547161_R01C02 Sample790

value: CON


title: 200992290035_R05C01 Sample755


title: 3999547156_R06C02 Sample788


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title: 3999547161_R01C01 Sample789


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