title: pCREB5

city: Jinan

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

description: This sample is of LNCaP transfected with PcDNA3-1 plasmid with CREB5 gene sequence.

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifμgation.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Ageilent DNA Microarray Scanner and uploaded into Agilent Feature Extraction (v11.0.0.1), and Cy3 label intensities determined.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the Agilent GeneSpring GX software package, version 12.1 .

label_protocol: cDNA samples were amplified, Cy3-labeled with Agilent Quick Amp labeling kit following manufacturer’s protocol.

growth_protocol: Cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: LNCaP cells transfected with plasmid are referred as PcDNA3-1 and pCREB5.

tag: cell type

value: prostate cancer cell line LNCaP

value: CREB5 overexpression


title: TNBS_Propy_20uM_Myeloid TAGCGCTC_TCGCATAA

status: Public on Oct 10 2022

type: SRA

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

country: USA

institute: Dana Farber Cancer Institute

description:
TNBS_Propy_20uM_Myeloid
Control and 20 uM of Propyzamide
Myeloid cells from TNBS-induced Zebrafish treated by 20 uM of Propyzamide

library_source: transcriptomic

data_processing:
The sample is aligned to GRCz38 transcriptome and quantified using Kallisto
Genome_build: GRCz38
Supplementary_files_format_and_content: gzipped abundance.tsv output from Kallisto

molecule: total RNA

organism: Danio rerio

extract_protocol:
N/A
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

tag: strain

value: AB

tag: Sex

tag: age


title: 99_4_DCA_FROZ

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

data_processing:
FASTQ files uploaded to PartekFlow (Partek build version 9.0.20.0202, St. OLouis, MO)
Reads mapped to mm10 using Star 2.6
Quantitation (Partek expectation maximization) to mm10 - RefSeq Transcripts 92
Raw gene counts were offset by a 0.0001 count, filtered to remove any gene feature with geometric mean across all samples <1, counts per million mapped reads (CPM) normalized and log2 transformed
Significant differentially expressed genes (DEGs) were identified using Partek Gene Specific Analysis (GSA) fit to multiple models (negative binomial, normal and log-normal). The lowest corrected Akaike Information Criterion (AIC) was used to select the gene model fit. Significant DEGs were defined as genes with false discovery rate (FDR) adjusted p-value <0.05 (Benjamini and Hochberg 1995) and absolute fold change > 2.
Genome_build: MM10
Supplementary_files_format_and_content: tab deliminated files with filtered, counts per million mapped reads normalized, and log2 transformed counts for all genes

organism: Mus musculus

source_name: frozen liver (mixed lobes)

growth_protocol: Studies were conducted in 4 week-old male B6C3F1 mice maintained under standard housing conditions at the U.S. Environmental Protection Agency (US EPA) AAALAC-accredited animal facility (Research Triangle Park, NC). Animal care and procedures were conducted under protocols approved by the Institutional Animal Care and Use Committee of the USEPA.

extract_protocol:
RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome.
Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500  platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads.
Targeted RNA-seq

treatment_protocol: Dichloroacetic acid (CAS 79-43-6, Aldrich) was administered in the drinking water at doses of 0, 1.0, 2.0, and 3.5 g/L (as described in DeAngelo et al. 1991) for six days. Drinkin water consumption along with measured DCA dose-levels were converted to mg per kg bodyweight per day (mg/kg-d) as 0, 198, 313, and 427 mg DCA/kg-d

tag: tissue

value: liver

value: 4 weeks

value: male

tag: treatment

value: dichloroacetic acid (DCA)

tag: dose

value: 427 mg/kg-d


title: 98_4_DCA_FROZ


title: PREMIERE8

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

description:
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Seurat_07302021.h5Seurat
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Counts_07302021.RDS
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_07302021.txt
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_Field_Descriptions.txt

data_processing:
Basecalls were performed using NovaSeq Control Software v1.7.0
Sample demultiplexing, barcode processing, and gene expression quantifications were performed with the 10X Cell Ranger v3 pipeline using the GRCh38 (hg38) reference genome
A cutoff of < 50% mitochondrial reads per cell was applied
Ambient mRNA contamination was corrected using SoupX (v1.5.0)
Cell barcodes having greater than 500 and less than 5000 genes detected were kept for downstream analyses
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Seurat object in h5Seurat format, raw RNA counts provided in RDS format, sample metadata table in txt format, and metadata field descriptions in txt format

molecule: polyA RNA

organism: Homo sapiens

source_name: Kidney

extract_protocol:
Single cells were isolated from frozen tissues according to the following protocol: dx.doi.org/10.17504/protocols.io.7dthi6n
10X single cell RNA sequencing was performed according to dx.doi.org/10.17504/protocols.io.7dthi6n using the 10X Chromium Single-Cell 3’ Reagent Kit v3

tag: patient

tag: condition

value: Acute Kidney Injury (AKI)

value: Kidney

tag: tissue source

value: Biopsy

tag: project

value: KPMP

tag: raw data location

tag: assay

value: 10X scRNA-seq


title: 97_4_DCA_FROZ


title: mutant-009c

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description:
number of genes expressed: 2606
innerEar.gene.expression.tables.FPKM.txt.gz

data_processing:
The fastq read-pairs were aligned to mouse reference genome (mm10) using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to mouse gene model by GENCODE (v19) using Cufflinks and HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for all genes

extract_protocol:
RNA extraction from dissociated cells was done according to Smartseq2 protocol (Picelli et al., 2014)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: inner ear

value: Endolymphatic sac

tag: genotype

value: Sox9Y440X/+ endolymphatic sacs


title: PcDNA3-1

type: RNA

first: Jing

country: China

description: This sample is of LNCaP transfected with empty plasmid PcDNA3-1 .

value: control


title: PREMIERE7


title: TNBS_Propy_20uM_Myeloid ATGCGCAG_TCGCATAA


title: WT-009

description:
number of genes expressed: 5594
innerEar.gene.expression.tables.FPKM.txt.gz

value: Wild-type


title: TNBS_Propy_20uM_Myeloid TACGCTGC_TCGCATAA


title: PREMIERE6


title: mutant-008c

description:
number of genes expressed: 3839
innerEar.gene.expression.tables.FPKM.txt.gz


title: 78_3_DCA_FROZ

value: 313 mg/kg-d


title: 77_3_DCA_FROZ


title: PREMIERE5


title: TNBS_Control_0uM_Myeloid CGGAGCCT_TCGCATAA

description:
TNBS_Control_0uM_Myeloid
Control and Control
Myeloid cells from TNBS-induced Zebrafish

value: AB


title: 76_3_DCA_FROZ

value: liver


title: PREMIERE4


title: TNBS_Control_0uM_Myeloid GGAGCTAC_TCGCATAA


title: PREMIERE3


title: WT-007

description:
number of genes expressed: 5346
innerEar.gene.expression.tables.FPKM.txt.gz


title: 75_3_DCA_FROZ

value: 4 weeks


title: mutant-006c

description:
number of genes expressed: 4139
innerEar.gene.expression.tables.FPKM.txt.gz


title: TNBS_Control_0uM_Myeloid ACTCGCTA_TCGCATAA


title: PREMIERE2


title: WT-006

description:
number of genes expressed: 2989
innerEar.gene.expression.tables.FPKM.txt.gz


title: TNBS_Propy_1uM_Lymph TCGACGTC_TAAGGCTC

description:
TNBS_Propy_1uM_Lymph
Control and 4 uM of Propyzamide
Lymphoid cells from TNBS-induced Zebrafish treated by 4 uM of Propyzamide


title: 54_2_DCA_FROZ

value: male

value: 198 mg/kg-d


title: 73_3_DCA_FROZ

value: dichloroacetic acid (DCA)


title: mutant-005c

description:
number of genes expressed: 4134
innerEar.gene.expression.tables.FPKM.txt.gz


title: Puck_200906_18

data_processing:
Demultiplexing, genome alignment and spatial matching was performed using Slide-seq tools github.com/MacoskoLab/slideseq-tools/releases/tag/0.1
Giotto (version 1.0.3) was used for data handling and RCTD (version 1.2.0) for the cell type deconvolution
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Giotto objects in RDS format containing bead location and count matrices and cell type weights after deconvolution; raw counts digital gene expression (DGE) matrix (.txt.gz) and a bead barcode locations file (.csv)

source_name: Kidney Cortex

extract_protocol:
Tissue pucks were prepared according to the step-by-step protocol: dx.doi.org/10.17504/protocols.io.bpgzmjx6
Sequencing libraries were prepared according to the step-by-step protocol: dx.doi.org/10.17504/protocols.io.bpgzmjx6

value: Reference

value: Kidney Cortex

value: Nephrectomy

value: HuBMAP

tag: raw data id


title: TNBS_Propy_1uM_Lymph TGCAGCTA_TAAGGCTC


title: mutant-004c

description:
number of genes expressed: 4232
innerEar.gene.expression.tables.FPKM.txt.gz


title: Puck_200906_10


title: TNBS_Propy_1uM_Lymph CGATCAGT_TAAGGCTC


title: WT-004

description:
number of genes expressed: 2100
innerEar.gene.expression.tables.FPKM.txt.gz


title: 53_2_DCA_FROZ


title: TNBS_Propy_1uM_Lymph CCTAAGAC_TAAGGCTC


title: 52_2_DCA_FROZ


title: Puck_200903_26


title: 51_2_DCA_FROZ


title: WT-008

description:
number of genes expressed: 6331
innerEar.gene.expression.tables.FPKM.txt.gz


title: TNBS_Control_0uM_Myeloid GCGTAGTA_TCGCATAA


title: mutant-003c

description:
number of genes expressed: 5310
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-002c

description:
number of genes expressed: 457
innerEar.gene.expression.tables.FPKM.txt.gz


title: TNBS_Propy_20uM_Lymph TAGCGCTC_TAAGGCTC

description:
TNBS_Propy_20uM_Lymph
Control and 20 uM of Propyzamide
Lymphoid cells from TNBS-induced Zebrafish treated by 20 uM of Propyzamide


title: TNBS_Propy_20uM_Lymph ACTGAGCG_TAAGGCTC


title: 74_3_DCA_FROZ


title: Puck_200903_07


title: 50_2_DCA_FROZ


title: WT-002

description:
number of genes expressed: 4072
innerEar.gene.expression.tables.FPKM.txt.gz


title: Puck_200903_25


title: TNBS_Propy_20uM_Lymph ATGCGCAG_TAAGGCTC


title: PREMIERE1

description:
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Seurat_07302021.h5Seurat
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Counts_07302021.RDS
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_07302021.txt
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_Field_Descriptions.txt

value: Acute Kidney Injury (AKI)

value: Kidney

value: Biopsy

value: KPMP

value: 10X scRNA-seq


title: mutant-001c

description:
number of genes expressed: 3070
innerEar.gene.expression.tables.FPKM.txt.gz

value: inner ear

value: Endolymphatic sac

value: Sox9Y440X/+ endolymphatic sacs


title: TNBS_Propy_20uM_Lymph TACGCTGC_TAAGGCTC

value: AB


title: Puck_200903_06


title: Puck_200903_05


title: WT-001

description:
number of genes expressed: 4795
innerEar.gene.expression.tables.FPKM.txt.gz

value: Wild-type


title: 7_1_control_FROZ

value: liver

value: 4 weeks

value: male

value: 0 mg/kg-d


title: Puck_200903_03

value: Reference

value: Kidney Cortex


title: TNBS_Control_0uM_Lymph CGGAGCCT_TAAGGCTC

description:
TNBS_Control_0uM_Lymph
Control and Control
Lymphoid cells from TNBS-induced Zebrafish


title: TNBS_Control_0uM_Lymph GCGTAGTA_TAAGGCTC


title: RTCB-KO-6W-3

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description: RTCB.FPKM.normbyERCC.txt

data_processing:
RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Expression level  was further normalized with the ERCC spike-in.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: Fully-grown GV oocyte

extract_protocol:
Oocytes were collected from indicated genotypes (10 oocytes per sample) after PMSG treatment for 44-48h. Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

value: oocyte

tag: developmental stage

value: Fully-grown GV

tag: genotype/variation

value: Rtcb knock-out


title: Puck_200903_02

value: Nephrectomy

value: HuBMAP


title: 6_1_control_FROZ

tag: strain

value: dichloroacetic acid (DCA)


title: 49_2_DCA_FROZ

tag: Sex

value: 198 mg/kg-d


title: 5_1_control_FROZ

tag: age


title: BUKMAP_20200211H_SNARE2-AC

description:
SNARE2 ATAC-Seq
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Seurat_08042021.rda
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-AC_Peak-Counts_08042021.RDS
BUKMAP.fragments.sort.tsv.gz
BUKMAP.fragments.sort.tsv.gz.tbi
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Metadata_08042021.txt
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Metadata_Field_Descriptions.txt

library_source: genomic

data_processing:
Library strategy: SNARE-Seq2
Basecalls were performed using NovaSeq Control Software v1.6.0
SNARE-Seq2 data was processed using the snarePip pipeline (github.com/huqiwen0313/snarePip)
For RNA processing, AC contaminating reads were removed using cutadapt (version 3.1)
For RNA processing, cell barcodes were extracted using dropEst (version 0.8.6)
For RNA processing, STAR (v2.5.2b) was used to align tagged reads to the genome (GRCh38)
For AC processing, snaptools (version v1.2.3) and minimap (version 2-2.20) were used for alignment to the genome (GRCh38).
For RNA processing, mitochondrial transcripts (MT-*) were removed
Doublets that were identified by both DoubletDetection (v3.0) and Scrublet (github.com/swolock/scrublet, version 0.2.2) using SNARE2-RNA data were removed
For RNA processing, cell barcodes for each sample were retained with the following criteria: having DropEst cell score greater than 0.9; having greater than 200 UMI detected; having greater than 200 and less than 7500 genes detected
For RNA processing, a gene UMI ratio filter (gene.vs.molecule.cell.filter) was applied using Pagoda2 (github.com/hms-dbmi/pagoda2)
Peak calling was performed using the Signac (v1.1.1, default parameters) and MACS (v3.0.0a6, github.com/macs3-project/MACS) separately for clusters, subclass.l1 and subclass.l3 level annotations. Peak regions were then combined and used to generate a peak count matrix
For AC processing, cell barcodes for each sample that had already passed quality filtering from RNA data were further retained with the following criteria: having tss enrichment greater than 0.15; having at least 1000 read fragments and at least 500 UMI; having fragments overlapping the promoter region ratio of greater than 0.15. Samples were only retained if they exhibited greater than 500 dual omic cells after quality filtering.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Seurat object in R Data format, tabulated ATAC-seq captured fragments for each cell in BED-like format, raw RNA counts provided in RDS format, peak counts provided in RDS format, sample metadata table in txt format, and metadata field descriptions in txt format

molecule: genomic DNA

extract_protocol:
Nuclei were isolated from cryosectioned tissues according to the following protocol: dx.doi.org/10.17504/protocols.io.ufketkw with the exception that 4',6-diamidino-2-phenylindole (DAPI) was excluded from the nuclear extraction buffer and only used to stain a subset of nuclei used for counting
SNARE-Seq2, as outlined (Nature Protocols, DOI:10.1038/s41596-021-00507-3), was performed according to the following protocol: dx.doi.org/10.17504/protocols.io.be5gjg3w
Dual RNA-Seq and ATAC-Seq

tag: tissue

value: Deceased Donor


title: RTCB-KO-6W-2

description: RTCB.FPKM.normbyERCC.txt


title: TNBS_Control_0uM_Lymph GGAGCTAC_TAAGGCTC


title: RTCB-KO-6W-1

description: RTCB.FPKM.normbyERCC.txt


title: Puck_200903_01


title: 4_1_control_FROZ

tag: treatment


title: WT-6W-3

description: RTCB.FPKM.normbyERCC.txt

value: WT


title: TNBS_Control_0uM_Lymph ACTCGCTA_TAAGGCTC

value: AB


title: 8_1_control_FROZ

tag: dose


title: BUKMAP_20200211H_SNARE2-R

description:
SNARE2 RNA-Seq
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Seurat_08042021.rda
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA_Counts_08042021.RDS
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Metadata_08042021.txt
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Metadata_Field_Descriptions.txt

tag: patient


title: Naive_Propy_1uM_Myeloid TGCAGCTA_ATAGCCTT

description:
Naive_Propy_1uM_Myeloid
Control and 4 uM of Propyzamide
Myeloid cells from Naive Zebrafish treated by 4 uM of Propyzamide


title: 3_1_control_FROZ


title: POOL NORMAL 3

city: Botucatu

first: Ana

middle: Laura

last: Seneda

state: São Paulo

address: Prof. Mário Rubens Guimarães Montenegro, Avenue - UNESP - Campus de Botucatu

department: Surgery and Orthopedics

country: Brazil

institute: São Paulo State University (UNESP), Faculty of Medicine

description:
Control
microRNA
pool of 3 individuals: one female, two male
Individual ages: 67, 62, 52

data_processing: The software used was ExpressionSuite Software, V 1.1, from Thermo Fisher. We used normal globalization and two genes as control: RNU44-001094 and RNU48-001006.

label: Taqman

source_name: Lung FFPE tissue

extract_protocol: Total RNA was isolated using the RecoverAll Total Nucleic Acid Isolation (Thermo Fisher Scientific, Waltham, MA, USA) according to Goswami RS, Atenafu EG, Xuan Y, Waldron L, Reis PP, Sun T, et al. MicroRNA signature obtained from the comparison of aggressive with indolent non-Hodgkin lymphomas: potential prognostic value in mantle-cell lymphoma. J Clin Oncol [Internet]. 2013;31(23):2903–11.

treatment_protocol: Samples obtained from FFPE tissue blocks  were needle microdissected using the stereomicroscope Leica EZ4 (Leica Microsystems, Wetzlar, Germany) before RNA extraction, in order to isolate the target tumor or normal cell populations.

value: Histological Normal Lung Tissue

tag: gender

value: mixed

value: average age of 60

tag: tobacco use

value: not provided

tag: Stage

tag: tnm classification

tag: tumor size

tag: nodal status

tag: distant metastasis


title: WT-6W-2

description: RTCB.FPKM.normbyERCC.txt


title: BUKMAP_20200211G_SNARE2-AC

source_name: Kidney Medulla

tag: condition

value: Kidney Medulla

tag: tissue source

tag: project

tag: raw data location

tag: raw data id

tag: assay


title: POOL NORMAL 2

description:
Control
microRNA
pool of 3 individuals: one female, two male
Individual ages: 59, 53, 58

tag: tissue

tag: age

value: average age of 56


title: Naive_Propy_1uM_Myeloid CGATCAGT_ATAGCCTT

tag: strain

tag: Sex


title: BUKMAP_20200211G_SNARE2-R

tag: patient

value: Reference


title: POOL NORMAL 1

description:
Control
microRNA
pool of 3 individuals: all male
Individual ages: 73, 52, 66

tag: gender

value: Male

value: average age of 63

tag: tobacco use


title: Naive_Propy_1uM_Myeloid TCGACGTC_ATAGCCTT


title: WT-6W-1

description: RTCB.FPKM.normbyERCC.txt

value: oocyte

tag: developmental stage

value: Fully-grown GV

tag: genotype/variation


title: T13: blood_treated_13

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Applied Biological Chemistry Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

hyb_protocol: Biotin-labeled RNA 21.5µL were hybridized for 16hr at 48C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed using the Transcriptome Analysis Console (Affymetrix), and the RMA+DABG method.

label: biotin

source_name: blood extracted from treated stroke patient

label_protocol: Biotin-labeled RNA was synthesized from 900ng total RNA according to the manufacture's protocol.

extract_protocol: Total RNA was extracted from the blood sample using TRIzol LS Reagent(Thermo Fisher Scientific) , according to the manufacture's protocol.

treatment_protocol: The T-group treated with tissue plasminogen activator

tag: gendar

value: male

value: 39 years old

tag: disease

value: After treatment


title: BUKMAP_20200211F_SNARE2-AC

tag: condition

value: Kidney Cortex

value: Deceased Donor

value: HuBMAP


title: METASTASIS

description:
Test
microRNA

value: Lymph Node Metastasis

value: Female

value: No

tag: Stage

tag: tnm classification

tag: tumor size

tag: nodal status

value: Lymph node metastasis

tag: distant metastasis


title: T11: blood_treated_11

value: 78 years old


title: Naive_Propy_20uM_Myeloid ACTGAGCG_ATAGCCTT

description:
Naive_Propy_20uM_Myeloid
Control and 20 uM of Propyzamide
Myeloid cells from Naive Zebrafish treated by 20 uM of Propyzamide

value: AB


title: BUKMAP_20200211F_SNARE2-R

value: Reference

tag: tissue

tag: tissue source

tag: project

tag: raw data location

tag: raw data id

tag: assay


title: T5: blood_treated_5

tag: age

value: 84 years old


title: TUMOR 1A

description:
Test
microRNA

value: Typical Lung Carcinoid Tumor

tag: gender

tag: tobacco use

value: IIB

value: Yes


title: BUKMAP_20200211E_SNARE2-AC

tag: patient

value: Kidney Medulla


title: T4: blood_treated_4

tag: gendar

value: female

value: 79 years old

tag: disease


title: BUKMAP_20200211E_SNARE2-R

tag: condition


title: Naive_Propy_1uM_Myeloid CCTAAGAC_ATAGCCTT

tag: strain

tag: Sex


title: Naive_Propy_20uM_Myeloid ATGCGCAG_ATAGCCTT


title: Naive_Propy_20uM_Myeloid TACGCTGC_ATAGCCTT


title: TUMOR 1B

description:
Test
microRNA

tag: Stage

tag: tnm classification

tag: tumor size

tag: nodal status


title: BUKMAP_20200211D_SNARE2-AC

tag: tissue

value: Kidney Cortex

tag: tissue source

value: Nephrectomy

tag: project


title: BUKMAP_20200211D_SNARE2-R

value: HuBMAP

tag: raw data location

tag: raw data id

tag: assay


title: T1: blood_treated_1

value: male

tag: age

value: 73 years old

value: After treatment


title: Human Pseudo-islets, shTSPAN7, rep3

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Reads were splice-aligned to a human genome (GRCh38) using GSNAP
FeatureCounts was used to assign reads to exons thus eventually getting counts per gene.
Assembly: hg38
Supplementary files format and content: comma-separated file (csv) includes count values for each Sample

source_name: Pseudo-islet

growth_protocol: Human pseudo-islets were used. Donor organs were obtained with written consent and research ethics approval at the University of Alberta, and human islets were isolated as previous described (doi: 10.17504/protocols.io.x3mfqk6). Islets were dispersed into a single-cell suspension using trypsin (TryLE Express, Gibco) and transduced with Ad-ShTSPAN7 or Ad-Scramble before forming human pseudo-islets using centrifugal-forced-aggregation as previously described (doi: 10.1007/s00125-018-4672-5).

extract_protocol:
Human pseudo-islets were preserved in Trizol before their total RNA was extracted using Quick-RNA MicroPrep kit (R1050 Zymo Research).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: Transduced with adenoviruses expressing shRNA for silencing of human TSPAN7 (Ad-ShTSPAN7, SKU# shADV-226651) or scrambled shRNA control (Ad-Scramble, SKU# 1122) together with eGFP under a CMV promoter, purchased from Vector Biolabs.

tag: cell type

value: Pseudo-islet

tag: derived from

value: pancreatic islet

tag: treatment


title: Human Pseudo-islets, shTSPAN7, rep1


title: T2: blood_treated_2

tag: gendar

value: 82 years old

tag: disease


title: Naive_Control_0uM_Myeloid CGGAGCCT_ATAGCCTT

description:
Naive_Control_0uM_Myeloid
Control and Control
Myeloid cells from Naive Zebrafish

tag: strain

value: AB

tag: Sex


title: Naive_Control_0uM_Myeloid GCGTAGTA_ATAGCCTT


title: BUKMAP_20200211C_SNARE2-AC

tag: patient

tag: condition

value: Reference


title: Human Pseudo-islets, shTSPAN7, rep2


title: Naive_Control_0uM_Myeloid GGAGCTAC_ATAGCCTT


title: P27: blood_patient_27

source_name: blood extracted from stroke patient

value: 70 years old

value: Cerebral infarction symptoms


title: Human Pseudo-islets, shControl, rep3

value: shControl


title: BUKMAP_20200211C_SNARE2-R

value: Kidney Medulla


title: P25: blood_patient_25

value: female

value: 90 years old


title: Human Pseudo-islets, shControl, rep2


title: Naive_Control_0uM_Myeloid ACTCGCTA_ATAGCCTT


title: BUKMAP_20200211B_SNARE2-AC

value: Kidney Cortex


title: Human Pseudo-islets, shControl, rep1


title: Naive_Propy_20uM_Myeloid TAGCGCTC_ATAGCCTT


title: T3: blood_treated_3

value: 74 years old


title: BUKMAP_20200211B_SNARE2-R

value: Nephrectomy

value: HuBMAP


title: P23: blood_patient_23

value: male

value: 49 years old


title: BUKMAP_20200211A_SNARE2-AC


title: RNA-seq, Drosophila adults

city: Thibodaux

first: Himanshu

middle: Shekhar

last: Raje

state: Louisiana

address: 906 East First Street

department: Biological Sciences

institute: Nicholls State University

data_processing:
Raw sequence reads were mapped against Drosophila melanogaster genome assembly dm6 at Mr. DNA labs, Shallowater, Texas, USA.
Assembly: dm6
Supplementary files format and content: the number of raw sequence reads mapping with individual listed genes in Drosophila adults.

organism: Drosophila melanogaster

source_name: adults

growth_protocol: Oregon-R (WT) Drosophila melanogaster were grown at room temperature (22-24 degree Celsius) on a standard fly medium.

extract_protocol:
Total RNA was isolated from Drosophila adults using Quick RNA MiniPrep kit (Zymo Research). 1 microgram of total RNA was used for cDNA synthesis using Maxima H minus reverse transcriptase master mix (ThermoFisher).
The single stranded cDNA was converted into double stranded cDNA by linear amplification using REPLI-g Midi kit (Qiagen). The linear amplified cDNA was cleaned using DNEasy PowerClean Pro Cleanup Kit (Qiagen). 50 ng cDNA was used to prepare the library using Illumina DNA Prep, (M) Tagmentation library preparation kit (Illumina) following the manufacturer's user guide.

treatment_protocol: Oregon-R (WT) Drosophila melanogaster were allowed to age naturally until their eclosion into the adult life stage.

value: adults

value: Oregon-R

tag: genotype

value: WT

value: Aging


title: P22: blood_patient_22


title: BUKMAP_20200211A_SNARE2-R

value: Reference

tag: tissue


title: Naive_Propy_1uM_Lymph CGATCAGT_CTTAATAG

description:
Naive_Propy_1uM_Lymph
Control and 4 uM of Propyzamide
Lymphoid cells from Naive Zebrafish treated by 4 uM of Propyzamide

value: AB


title: Naive_Propy_1uM_Lymph CCTAAGAC_CTTAATAG


title: BUKMAP_20190822E_SNARE2-R

tag: tissue source


title: P20: blood_patient_20

value: 50 years old

value: Cerebral infarction symptoms


title: BUKMAP_20190822E_SNARE2-AC

value: Kidney Medulla

tag: project


title: P18: blood_patient_18

value: 71 years old


title: Naive_Propy_20uM_Lymph ACTGAGCG_CTTAATAG

description:
Naive_Propy_20uM_Lymph
Control and 20 uM of Propyzamide
Lymphoid cells from Naive Zebrafish treated by 20 uM of Propyzamide


title: Naive_Propy_20uM_Lymph TAGCGCTC_CTTAATAG


title: Naive_Propy_1uM_Lymph TCGACGTC_CTTAATAG


title: Naive_Propy_20uM_Lymph ATGCGCAG_CTTAATAG


title: P24: blood_patient_24

value: 83 years old


title: P16: blood_patient_16

value: 78 years old


title: P14: blood_patient_14

value: 57 years old


title: Naive_Propy_1uM_Lymph TGCAGCTA_CTTAATAG


title: Naive_Propy_20uM_Lymph TACGCTGC_CTTAATAG


title: BUKMAP_20190822C_SNARE2-AC

value: Deceased Donor

tag: raw data location


title: P13: blood_patient_13

value: 39 years old


title: BUKMAP_20190822C_SNARE2-R

value: HuBMAP

tag: raw data id


title: Naive_Control_0uM_Lymph CGGAGCCT_CTTAATAG

description:
Naive_Control_0uM_Lymph
Control and Control
Lymphoid cells from Naive Zebrafish


title: P12: blood_patient_12

value: female

value: 86 years old


title: P17: blood_patient_17

value: male

value: 28 years old


title: BUKMAP_20190822B_SNARE2-AC

tag: assay


title: Naive_Control_0uM_Lymph GCGTAGTA_CTTAATAG

tag: age


title: P11: blood_patient_11


title: BUKMAP_20190822B_SNARE2-R


title: BUKMAP_20190822D_SNARE2-AC

value: Kidney Cortex

value: Nephrectomy


title: Naive_Control_0uM_Lymph GGAGCTAC_CTTAATAG

value: AB


title: P10: blood_patient_10

value: 81 years old


title: Naive_Control_0uM_Lymph ACTCGCTA_CTTAATAG


title: P9: blood_patient_9

value: 77 years old

value: Cerebral infarction symptoms


title: BUKMAP_20190822A_SNARE2-AC

value: Reference

value: Kidney Medulla


title: BUKMAP_20190822A_SNARE2-R


title: P8: blood_patient_8

value: 63 years old


title: P7: blood_patient_7

value: 65 years old


title: si-NMDAR+H/R sample-3b

city: Changchun

first: Qiwei

last: Yang

state: Jilin

address: Ziqiang Street No.218

institute: Jilin University

data_processing:
Illunima Casava 1.8
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: The mouse hippocampal neuron HT22 cells were cultured in DMEM high-glucose medium containing 10% FBS and 1% penicillin-streptomycin double antibody. Cells were incubated at 37°C in a humidified environment containing 5% carbon dioxide and 95% air. The medium was changed every 2-3 days, and when the cell density reached about 80%, the passage was carried out according to 1:3-1:4.

extract_protocol:
Total RNA was extracted using a Tirzol Reagent following the manual.
The RNA was then broken into short fragments of 250-300 bp using RNase R enzyme, the fragmented RNA was used as a template, and random oligonucleotides were used as primers to synthesize the first strand of cDNA. Subsequently, the RNA strand was degraded by RNase H, and the second strand of cDNA was synthesized from dNTPs under the DNA polymerase I system. The purified double-stranded cDNA was end-repaired, A-tailed, and ligated with sequencing adapters. AMPure XP beads were used to screen cDNAs of about 350-400 bp. The second strand of U-containing cDNA was degraded by USER enzyme, and finally PCR amplification was performed to obtain cDNA libraries.

treatment_protocol: H/R stimulation: the cells were cultured under hypoxic conditions of 1% oxygen, 5% carbon dioxide, and 94% nitrogen, other culture conditions remained unchanged. Normal conditions were resumed after 2 hours. Knockdown of NMDAR: HT22 cells were seeded in a 6-well plate. When the cell density reached 70%, Lipofectamine 2000 was used for transfection according to the instructions. Two μg siRNA was used for each well of the experimental group, and an equal volume of PBS was used for the control group. The medium was changed to conventional medium 6 hours after transfection.

tag: cell line

tag: cell type

value: mouse hippocampal neuron

value: NMDAR knockdown

value: hypoxia/reoxygenation


title: hiPSC-EC2, MEHP, 72Hr, Sup

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

description:
SG4 (Sup)
Supernatant
Cy5 = Immunoprecipitated, Cy3 = Supernatant

hyb_protocol: 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 1 out of 6 samples were retained. When comparing two samples without replicates (see Comparison example3), the statistical significance (p-value) for such comparison is not available. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. The default thresholds are |FC| ≥1.5 and p-values ≤0.05.
The “m6A quantity” was calculated for the m6A methylation amount of each transcript based on the IP (Cy5-labelled) normalized intensities.

source_name: iPSC-EC

label_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10x Blocking Agent and 1 μL of 25x Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2x Hybridization buffer.

extract_protocol: Cells were lysed in Trizol, and total RNA extracts were isolated for sequencing.

treatment_protocol: Cells were treated with 120µM MEHP (Wako Chemicals) for 72 hours. MEHP was dissolved in DMSO, and the concentration of DMSO was maintained at 0.1% for MEHP treatment and control.

value: Endothelial Cell

tag: treatment

value: MEHP

tag: antibody


title: hiPSC-EC3, MEHP, 72Hr, Sup

description:
SG6 (Sup)
Supernatant
Cy5 = Immunoprecipitated, Cy3 = Supernatant


title: BUKMAP_20190529G_SNARE2-R

value: Deceased Donor

value: HuBMAP


title: si-NMDAR+H/R sample-3a


title: hiPSC-EC1, MEHP, 72Hr, Sup

description:
SG2 (Sup)
Supernatant
Cy5 = Immunoprecipitated, Cy3 = Supernatant


title: hiPSC-EC3, DMSO, 72Hr, Sup

description:
SG5 (Sup)
Supernatant
Cy5 = Immunoprecipitated, Cy3 = Supernatant

value: Untreated


title: BUKMAP_20190529F_SNARE2-AC

value: Kidney Cortex


title: P6: blood_patient_6

tag: gendar

value: male

value: 50 years old

tag: disease


title: hiPSC-EC3, MEHP, 72Hr, IP

description:
SG6 (IP)
Immunoprecipitated
m6a IP RNA
Cy5 = Immunoprecipitated, Cy3 = Supernatant

value: anti-m6A rabbit polyclonal antibody (Synaptic Systems)


title: hiPSC-EC2, MEHP, 72Hr, IP

description:
SG4 (IP)
Immunoprecipitated
m6a IP RNA
Cy5 = Immunoprecipitated, Cy3 = Supernatant


title: hiPSC-EC2, DMSO, 72Hr, Sup

description:
SG3 (Sup)
Supernatant
Cy5 = Immunoprecipitated, Cy3 = Supernatant


title: hiPSC-EC1, DMSO, 72Hr, Sup

description:
SG1 (Sup)
Supernatant
Cy5 = Immunoprecipitated, Cy3 = Supernatant


title: P5: blood_patient_5

value: 84 years old

value: Cerebral infarction symptoms


title: si-NMDAR+H/R sample-2


title: BUKMAP_20190529F_SNARE2-R

description:
SNARE2 RNA-Seq
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Seurat_08042021.rda
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA_Counts_08042021.RDS
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Metadata_08042021.txt
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Metadata_Field_Descriptions.txt

value: Reference


title: P4: blood_patient_4

value: female

value: 79 years old


title: BUKMAP_20190529G_SNARE2-AC

description:
SNARE2 ATAC-Seq
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Seurat_08042021.rda
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-AC_Peak-Counts_08042021.RDS
BUKMAP.fragments.sort.tsv.gz
BUKMAP.fragments.sort.tsv.gz.tbi
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Metadata_08042021.txt
Kidney_Healthy-Injury_Cell_Atlas_SNARE2-RNA-AC_Metadata_Field_Descriptions.txt


title: si-NMDAR+H/R sample-1

value: mouse hippocampal neuron


title: P2: blood_patient_2

value: 82 years old


title: P3: blood_patient_3

value: 74years old


title: hiPSC-EC2, DMSO, 72Hr, IP

description:
SG3 (IP)
Immunoprecipitated
m6a IP RNA
Cy5 = Immunoprecipitated, Cy3 = Supernatant

value: Endothelial Cell


title: BUKMAP_20190529E_SNARE2-R

value: Kidney Medulla


title: si-NMDAR sample-3

value: NMDAR knockdown


title: si-NMDAR sample-2


title: hiPSC-EC3, DMSO, 72Hr, IP

description:
SG5 (IP)
Immunoprecipitated
m6a IP RNA
Cy5 = Immunoprecipitated, Cy3 = Supernatant


title: hiPSC-EC1, DMSO, 72Hr, IP

description:
SG1 (IP)
Immunoprecipitated
m6a IP RNA
Cy5 = Immunoprecipitated, Cy3 = Supernatant


title: S4R: sham-4

city: Shijiazhuang

first: Wen

last: Cao

state: China

address: 215 Hepingxi Road Shijiazhuang, Hebei,China

institute: Second Hospital of Hebei Medical University

description: sham, corresponding right cortex, sample 4

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

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

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

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: brain tissue

tag: gender


title: BUKMAP_20190822D_SNARE2-R

tag: patient

value: Nephrectomy

value: HuBMAP


title: hiPSC-EC1, MEHP, 72Hr, IP

description:
SG2 (IP)
Immunoprecipitated
m6a IP RNA
Cy5 = Immunoprecipitated, Cy3 = Supernatant

value: MEHP


title: S1R: sham-1

description: sham, corresponding right cortex, sample 1

value: male


title: M4R: dMCAO-4

description: dMCAO, right peri-infarct cortex, sample 4


title: S3R: sham-3

description: sham, corresponding right cortex, sample 3


title: BUKMAP_20190529D_SNARE2-AC

tag: condition

value: Deceased Donor


title: S2R: sham-2

description: sham, corresponding right cortex, sample 2


title: M3R: dMCAO-3

description: dMCAO, right peri-infarct cortex, sample 3


title: si-NMDAR sample-1

tag: genotype


title: P1: blood_patient_1

value: 73 years old


title: C27: blood_control_27

source_name: blood extracted from not stroke patient

value: 72 years old

value: Not cerebral infarction symptoms


title: M2R: dMCAO-2

description: dMCAO, right peri-infarct cortex, sample 2

tag: tissue


title: C25: blood_control_25

value: female

value: 89 years old


title: NRVC-NM-rep3

city: Shanghai

first: Mengying

last: Feng

address: no. 67 Chifeng road, Yangpu district

department: School of Life Sciences and Technology

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 or mm10 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S
Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the edgeR (v3.20.9).
Genome_build: rn6 or hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Neoatal Rat Ventricular Cardiomyocytes

growth_protocol: Neonatal rat’s hearts were harvested from 1-day old SD rats. Next, the ventricles were separated and cut into pieces (1–3 mm2), then they were dissociated in 0.25% trypsin (Gibco, 15090046) at 4 °C overnight. Then the tissue was transferred to 0.1% collagenase type Ⅱ (Worthington, LS004176) to further digest at 37°C at 145 rpm, and the supernatant was collected into DMEM medium containing 10% FBS every 5 min. The digestion procedure was repeated 3-4 times. When the tissue was completely digested, the supernatant was centrifuged at 1500 rpm for 6 min. Then, the cells were plated in DMEM medium which containing 10% FBS, 100 unit/ml penicillin and 100 mg/ml streptomycin at 15 cm dishes at an atmosphere of 5% CO2 at 37℃ for 90 min, to remove cells that are easier attached the dishes than cardiomyocytes. Finally, the culture supernatant was collected, plated in the plates which were coated with collagen and then incubated 24 h in an atmosphere of 5% CO2 at 37 ℃ with the same medium. After 24 h, the medium was changed to cardiomyocyte medium: DMEM: F12 (1:1) medium containing 0.25% FBS, 3 mM sodium pyruvate, 0.1 mM Vitamin C and 2 mM L-Glu. hPSC-CMs were produced from ZSSY001 (Nuwacell) by regulating Wnt signaling pathway. hPSCs were grown on Matrigel (Corning, 354277) in Essential 8 TM Medium (Gibco, A15169-01, A15171-01). Cardiac differentiation was performed using dense monolayers of hPSCs treated with 6µM CHIR-99021 (Sellect, S1263) for 48 h and 5μM IWP-2 (Sellect, S7065) for 2 days in RPMI 1640 (Gibco, 11875-093)/B-27 minus insulin Medium (Gibco, A18956-01) previously described protocol . Spontaneously beating hPSC-CMs appeared after 7 days. Then the containing medium was replaced with RPMI 1640/B-27 Medium (Gibco, A17504-044). Metabolism selection was performed using Cardiomyocyte Selection Medium (ScienCell, 5911, 5962) for high purity cardiomyocytes.

extract_protocol:
The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NRVCs and hPSC-CMs were treated with NM for 12h.

value: cardiomyocytes

tag: agent

value: Nimodipine


title: NRVC-NM-rep1


title: C24: blood_control_24

value: 85 years old


title: BUKMAP_20190529E_SNARE2-AC

value: Reference

tag: tissue source

tag: project


title: BUKMAP_20190529D_SNARE2-R

value: Kidney Medulla

tag: raw data location

tag: raw data id


title: si-NC sample-2

value: mouse hippocampal neuron

value: WT


title: si-NC sample-3


title: si-NC sample-1b


title: NRVC-NM-rep2


title: Si_C101

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

description: adult human bone marrow mesenchymal stem cells

data_processing:
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
use FastQC performs basic statistics on the quality of the raw reads.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
Fragment size estimation For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 predicted method with default parameters(Model-based analysis of ChIP-Seq (MACS), Genome Biol).
Peak detection After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Genome_build: Homo_sapiens_Ensemble_94.fa
Supplementary_files_format_and_content: bw

source_name: Immunoprecipitated chromatin of  NFATC1 RNAi AhBMSCs

extract_protocol:
Genomic DNA degradation and contamination was was monitored on agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA).  DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
RNA samples were fragmented into **-nucleotide-long fragments by RNA fragmentation buffer (10 mM Tris-HCl [pH 7.0], 10 mM ZnCl2). Fragmented RNA was incubated for 2 hr at 4C with 0.5 mg/ml antim6A polyclonal antibody in IP buffer (150 mM NaCl, 0.1% Igepal CA-630, 10 mM Tris-HCl [pH 7.4]) supplemented with RNasin Plus RNase inhibitor (Promega). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: age

value: adult

value: bone marrow stem cells

tag: transfection

value: NFATC1 RNAi


title: NRVC-Ctrl-rep3

tag: cell type


title: si-NC sample-1a

tag: cell line

tag: treatment


title: C23: blood_control_23

tag: gendar

value: male

value: 46 years old


title: Si_C102

source_name: Immunoprecipitated chromatin of  NFATC1  RNAi AhBMSCs

tag: antibody


title: Si_C103


title: NRVC-Ctrl-rep2


title: C22: blood_control_22

value: 66 years old

tag: disease


title: Meirav_DMEM_2

city: Rehovot

first: Ruth

last: Scherz-Shouval

state: Rehovot

address: Herzl 234

country: Israel

institute: Weizmann institute of science

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab delimited files include raw counts values for each sample

source_name: Immortalized pancreatic stellate cells

growth_protocol: 20,000 PSCs were seeded in matrigel GFR and cultured in frowth media (DMEM 10% FBS).

extract_protocol:
The cells were released from the matrigel by wash and lysed using
A variation of MARS-seq was used as described (Jaitin et al., 2014), developed for single-cell RNA-seq to produce expression libraries.
RNA sequencing 3' end

treatment_protocol: After four days of culturing with growth media, the media was replaced to KPC organoid-shBRCA2 or KPC organoid-shControl conditioned medium, or to PSC own conditioned medium as control for four days.  The cells were then harvested and RNA was purified for RNA-sequencing.

value: PSC own CM


title: Si_inp3

source_name: Input chromatin of NFATC1 RNAi AhBMSCs


title: NRVC-Ctrl-rep1


title: C20: blood_control_20

value: 55 years old

value: Not cerebral infarction symptoms


title: Si_inp2


title: Mixed Cell Culture, Rep2, deeper sequencing

first: Emma

last: West

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
S436E
Barcodes for each cell population are: TATGGA = HEK cells; GTTAGG = 3T3 cells

data_processing:
Assembly: hg38, mm39
Extracted Light-Seq DNA barcodes (corresponding to different cell populations) using UMI-tools 1.1.1
Aligned to genome with STAR aligner 2.7.9a
Used featureCounts (subread) 2.0.1 to assign mapped reads to genes
Deduplicated reads based on UMIs + mapped gene pairs (samtools 1.9, 1.12)
Supplementary files format and content: CSV file containing Light-Seq read counts per gene. Rows are genes, columns are replicates for each cell population

organism:
Homo sapiens
Mus musculus

extract_protocol:
Light-Seq
Nextera tagmentation

value: mixed culture

tag: genome build


title: C18: blood_control_18

value: 73 years old


title: Meirav_NT3

value: KPC organoid shControl CM


title: Si_inp1


title: Mixed Cell Culture, Rep3

description:
436F
Barcodes for each cell population are: TATGGA = HEK cells; GTTAGG = 3T3 cells


title: NC_C103

source_name: Immunoprecipitated chromatin of  SCR tranfected AhBMSCs

value: SCR


title: C16: blood_control_16

value: 75 years old


title: Meirav_NT2


title: C17: blood_control_17

value: 26 years old


title: Mixed Cell Culture, Rep1

description:
436D
Barcodes for each cell population are: TATGGA = HEK cells; GTTAGG = 3T3 cells


title: Mixed Cell Culture, Rep2

description:
436E
Barcodes for each cell population are: TATGGA = HEK cells; GTTAGG = 3T3 cells


title: M1R: dMCAO-1

description: dMCAO, right peri-infarct cortex, sample 1

value: brain tissue

tag: gender


title: NC_C102


title: Meirav_BRCA_3

value: KPC organoid shBRCA CM


title: C13: blood_control_13

value: 40 years old


title: Meirav_BRCA_1


title: NC_inp3

source_name: Input chromatin of SCR tranfected AhBMSCs

value: adult

value: bone marrow stem cells


title: C12: blood_control_12

value: female

value: 90 years old


title: SCC13 shCTR ChIP H3K27ac

city: Charlestown

first: Sandro

last: Goruppi

state: Massachusetts

address: 13th Street

department: CBRC

institute: MGH-Partners Healthcare

description: SCC13 infected with plko shCTR lentivirus, selected for three days with puromycin and expanded for 10 days

data_processing:
Construction of libraries from ChIPs samples, QCs, processing and analysis of the data was performed by Novogene Co Ltd.
The initial image data produced by High-throughput sequencing Illumina platform was converted to sequenced reads by CASAVA Base Calling
The procedure for data trimming is in the following:(1) Discard the reads with low quality (proportion of low quality bases larger than 50%); (2) Discard the reads with N ratio (unsure base) larger than 15%;(3) Discard the reads with adaptor at the 5’-end;(4) Discard the reads without adaptor and inserted fragment at the 3’-end;(5) Trim the adapter sequence at the 3’-end;(6) Discard the reads whose length are less than 18nt after trimming.
The mapping of the reads to the reference genome hg38 was performed using BWA  software
Duplicates were labeled using SAMBLAST and mapping quality value was calculated with MAPQ
The peak callingusing was made using MACS2 software (and to calculate the number of peaks, the peak width and its distribution, and find the peak related genes)
Genome_build: hg38
Supplementary_files_format_and_content: wig files

source_name: Squamous carcinoma cells expressing shCTR

growth_protocol: SCC13 cells were routinely grown in DMEM 10%FBS. For gene silencing cells were infected o/n with either plkoshCTR- or plkoshULK3- expressing lentiviruses, selected for 3 days with 1µg/ml of Puromycin (GIBCO) and then expanded for 10 days

extract_protocol:
Lysates were clarified from sonicated nuclei and ULK3- or histone- DNA complexes were isolated with specific antibodies.  ChIP was performed by using Simple ChIP sonication kit (plus) from Cell Signaling #76155
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit, at Novagene. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

treatment_protocol: Cells were harvested 48 hours after seeding.

tag: rrid and silencing construct

value: RRID:CVCL_4029 + plKO (SHC016)

tag: ChIP

value: Anti H3K27ac Antibody

tag: cat #

value: Abcam # 4729


title: SCC13 shULK3 ChIP H3K27ac

description: SCC13 infected with plko shULK3 lentivirus, selected for three days with puromycin and expanded for 10 days

source_name: Squamous carcinoma cells expressing shULK3

value: RRID:CVCL_4029 + plKO TRC00037419


title: Meirav_DMEM_1

value: PSC own CM


title: SCC13 shULK3 cells input


title: C11: blood_control_11

value: male

value: 76 years old

value: Not cerebral infarction symptoms


title: NC_inp2

value: SCR


title: NC_inp1


title: FK506_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index ofthe reference genome was builtusing Hisat2 v2.0.5 andpaired-endcleanreadswerealignedtothereferencegenomeusingHisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Homo_sapiens_Ensemble_94.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: FK508 treated AhBMSCs

extract_protocol:
total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

tag: agent


title: C10: blood_control_10

value: 82 years old


title: SCC13 shCTR cells input


title: Gil_CC_15

source_name: KPC cells shControl

extract_protocol:
Live cells were FACS sorted into 40 ml of lysis binding buffer (Thermo-Fisher scientific), and mRNA was isolated using Dynabeads oligo (dT)  (Thermo-Fisher scientific).
A variation of MARS-seq was used as described (Jaitin et al., 2014), developed for single-cell RNA-seq to produce expression libraries.
RNA sequencing 3' end

value: Non-targeting shRNA control


title: Gil_CC_14


title: Meirav_NT1

value: KPC organoid shControl CM


title: SCC13 cells ChIP ULK3Ab

description: SCC13 cells

source_name: Squamous carcinoma cells

value: Anti ULK3 mAb Antibody


title: FK506_2

source_name: FK507 treated AhBMSCs

value: adult


title: C14: blood_control_14

value: 61 years old


title: C9: blood_control_9

value: female

value: 78 years old


title: NC_C101

value: bone marrow stem cells


title: C7: blood_control_7


title: Gil_CC_13


title: DMSO_3

source_name: DMSO treated AhBMSCs

value: DMSO


title: FK506_1

source_name: FK506 treated AhBMSCs


title: SCC13 cells input DNA

description: SCC13 cells


title: C6: blood_control_6

value: 51 years old


title: Meirav_BRCA_2

value: KPC organoid shBRCA CM


title: Gil_CC_11

source_name: KPC cells shBrca2

value: shRNA knock down of Brca2


title: C4: blood_control_4

source_name: blood extracted from not stroke patient

value: 80 years old


title: C5: blood_control_5

value: male

value: 83 years old


title: Gil_CC_10


title: DMSO_1


title: DMSO_2


title: C3: blood_control_3

value: 79 years old

value: Not cerebral infarction symptoms


title: siC1_3

source_name: NFATC3 siRNA tranfected AhBMSCs

value: NFATC3 siRNA


title: BRCA_3

source_name: Cancer associated fibroblasts from KPC tumor

extract_protocol:
CD45-/CD31-/EpCAM-/PDPN+ cells were FACS-sorted into 40 ul of lysis/binding buffer (Thermo-Fisher scientific) and mRNA was isolated using Dynabeads oligo (dT) (Thermo-Fisher scientific).
A variation of MARS-seq was used as described (Jaitin et al., 2014), developed for single-cell RNA-seq to produce expression libraries.
RNA sequencing 3' end

tag: strain

tag: brca2 status of kpc cells

value: shRNA knock down of BRCA2


title: hiPSC-EC2, MEHP, 72Hr

data_processing:
Raw Fastq files were uploaded to the cloud based analysis suite, BioJupies, and analyzed using the default parameters.
Supplementary files format and content: RNA-seq_MEHP_raw_readcounts.txt: Raw read counts in processed data file are listed in a tab-delimited .txt file.

source_name: iPSC-EC

extract_protocol:
Cells were lysed in Trizol, and total RNA extracts were isolated and submitted for sequencing.
Prepared according to manufacturer's specifications.

value: iPSC-EC

value: Endothelial Cell

value: MEHP

tag: time

value: 72 hours


title: BRCA_2


title: siC1_2

source_name: NFATC2 siRNA tranfected AhBMSCs

tag: age

value: adult

value: NFATC2 siRNA


title: hiPSC-EC3, DMSO, 72Hr

value: DMSO


title: C1: blood_control_1

value: 74 years old


title: NC_3

source_name: SCR tranfected AhBMSCs

tag: transfection

value: SCR

value: bone marrow stem cells


title: hiPSC-EC2, DMSO, 72Hr

tag: cell type


title: NT_4

value: Non-targeting shRNA control


title: Gil_CC_12

value: shRNA knock down of Brca2


title: siC1_1

source_name: NFATC1 siRNA tranfected AhBMSCs

value: NFATC1 siRNA


title: BRCA_1


title: hiPSC-EC1, MEHP, 72Hr

tag: cell line


title: hiPSC-EC1, DMSO, 72Hr

tag: treatment


title: NC_1


title: NT_2


title: BRCA_4


title: hiPSC-EC3, MEHP, 72Hr


title: NC_2


title: RSLA1.

city: Trivandrum

first: Rakesh

middle: S

last: Laishram

state: Kerala

address: Thycaud P O, Poojappura

department: Cardiovascular and Diabetes Biology Group

institute: Rajiv Gandhi Centre for Biotechnology(RGCB)

data_processing:
The raw data generated was checked for the quality with FastQC1 and pre-processed for removing adapter sequences and low quality bases using Genotypic's proprietary script. It was then aligned using Tophat-2.0.133  to E. coli (K-12)
Transcript assembly was done using Cufflinks-2.2.14 which assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Using cuffmerge, cufflinks assemblies were combined followed by differntial gene expression analysis using "Cuffdiff"  to obtain the significant changes in transcript expression.
Uniprot knowledge base was used to annotate the genes for Gene Ontology (GO). Differential gene expression studies were carried out between PABPN1 expressed group versus wild type MG1655 samples.
Assembly: Differentially expressed genes were further annotated for the protein name and Gene Ontology and heat map generated as a representation of the expression values (as colours).
Supplementary files format and content: Matrix table with log fold change

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: All bacterial strains were grown at 37°C in nutrient rich, Luria Bertani broth until OD600 = 0.6

extract_protocol:
Bacterial cells were grown in 37°C, harvested at OD600 of ~0.6 and total RNA was isolated by trizol method. 4 μg of QC passed total RNA was used for ribo-depletion using RiboMinus Bacterial Kit (Invitrogen). Further, 100 ng of Qubit quantified ribo-depleted RNA was taken for Transcriptome library preparation according to Sure Select Strand-Specific RNA Library Prep Kit protocol outlined in “SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing” (Illumina).
Briefly, the RNA was fragmented for 4 minutes at 94oC in the presence of divalent cations and first strand cDNA was synthesised. The single stranded cDNA was cleaned up using High Prep (Magbio, Cat # AC-60050). Strand specificity was maintained by the addition of actinomycin D. Second strand cDNA was synthesised and end repaired using Second Strand Synthesis using End Repair mix. The cDNA was cleaned up using High Prep (Magbio, Cat # AC-60050). Adapters were ligated to the cDNA molecules after addition of “A” base. High Prep cleanup was performed post ligation. The library was indexed and enriched for adapter ligated fragments using 10 cycles of PCR. The prepared library was quantified using Qubit and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent). 150 (75X 2) bp Paired End Sequencing was carried out on Illumina platform to generate 20-25 million PE Reads per sample.

tag: genotype


title: NT_1


title: L-3

status: Public on Oct 09 2022

city: Xuzhou

first: Hui

last: Li

state: Jiangsu

address: No.209, Tongshan Road, Huangshan Street

department: School of Life Sciences

institute: Xuzhou Medical University

data_processing:
The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library.
Library was validating on the Agilent Technologies 2100 bioanalyzer.
The library was amplified with phi29 to make DNA nanoball (DNB) which have more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS)
Assembly: Reference Genome Version: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include read_count values for each Sample

source_name: hippocampus

growth_protocol: Mice were allowed ad libitum access to food and water and were maintained at 25 ± 2 °C with a 12-h light/12-h dark cycle.

extract_protocol:
Use Agilent 2100 Bioanalyzer to test sample integrity and concentration, and NanoDrop to Inorganic ions orpolycarbonate contamination. This step aimed to provide a reference for library construction and later analysis.
BGISEQ-500 Small RNA Sample Library Construction

treatment_protocol: All of the mice, except for those in the saline group, were intraperitoneally injected with a single dose of 1 mg/kg LPS. Subsequently, mice were treated with GAS (100 mg/kg) 1h after LPS stimulation.

tag: tissue

value: hippocampus

value: received an equal volume of 0.12% saline and intraperitoneally injected with a single dose of 1 mg/kg LPS


title: G-2

value: treated with GAS(100 mg/kg) 1h after LPS stimulation


title: G-1


title: L-2


title: C2: blood_control_2

extract_protocol: Total RNA was extracted from the blood sample using TRIzol LS Reagent(Thermo Fisher Scientific) , according to the manufacture's protocol.

tag: gendar

value: male

value: 80 years old

tag: disease

value: Not cerebral infarction symptoms


title: G-3


title: L-1


title: S-3

value: received an equal volume of 0.9% saline


title: S-1


title: siNap1l5.PE_2

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
BGI used BGISEQ platform for RNA-Seq
The raw data include low quality, contamination of joints, and high levels of unknown base n reads, which need to be removed before analysis to ensure the reliability of the results
The clean reads were align to the reference genome sequnence using HISAT
The clean reads were align to the reference genome sequnence using Bowtie2
Genome_build: NCBI, Rattus_norvegicus , GCF_000001895.5_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 raw gene counts for every gene and every sample

source_name: Neonatal rat ventricular myocytes (NRVMs)

growth_protocol: NRVMs were maintained in DMEM supplemented with 1% Insulin-Transferrin-Selenium (ITS-G, BD Biosciences, CA, USA), 100 U/mL penicillin and 100 μg/ml streptomycin.

extract_protocol:
RNA of NRVMs extracted according to the manufacturer's instructions using Trizol reagent.
RNA libraries were prepared for sequencing according to manufacturer's instructions of Beijing Genomics Institution (BGI)

treatment_protocol: NRVMs were first transfected with siNap1l5 or siNeg, then treated with PE for 36h after 12h.

value: Sprague-Dawley (SD) Rat

value: treated with PE for 36 hours


title: siNap1l5.PE_1


title: siNap1l5.PE_3


title: S-2


title: siNap1l5_3

value: untreated


title: siNap1l5_2


title: siNeg.PEtreated_3

value: siNeg


title: siNeg.PEtreated_1


title: siNeg_untreated_3


title: siNap1l5_1


title: RSLC1.

value: K-12 MG1655-pcnB null mutation


title: siNeg.PEtreated_2


title: siNeg_untreated_2


title: siNeg_untreated_1


title: 2Multiple-library

city: Stanford

first: Xinbo

state: CA

address: 279 Campus Drive

department: MCP

institute: Stanford University

description: pMHC

data_processing:
Merge paired-end data files
Extract round 5 selection data with barcode
convert file from Fasta to pfam format
filter the sequence with pre-mature stop codon
Count unique stats for individual sequence
Assembly: N/A
Supplementary files format and content: pfam/Amino acid sequence from round 5 selection
Supplementary files format and content: csv/Counts of individual peptide

organism: Saccharomyces cerevisiae

source_name: EBY 100

extract_protocol:
DNA of 5X10^7 yeast from selections were isolated by miniprep (Zymoprep II kit, Zymo Research).
Library construction is described in previous publication (Gee, M.H. et al. Cell 2018)

value: EBY 100


title: 4Multiple-library

description: pMHC


title: 3Multiple-library

description: pMHC


title: KT, scRNAseq

city: Palo Alto

first: Kristy

last: Red-Horse

address: 265 Campus Drive

department: Department of Biology and Institute for Stem Cell Biology and Regenerative Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
BmxCreERT2;RosatdTomato/tdTomato;Cxcr4flox/+ males were crossed to ;Cxcr4flox/flox females, which were dosed with tamoxifen at E9.5. E17.5 embryos from two litters were harvested in cold, sterile 1X PBS. Three BmxCreERT2;RosatdTomato/tdTomato;Cxcr4flox/+ (heterozygous, controls) and five BmxCreERT2;RosatdTomato/tdTomato;Cxcr4flox/+ (mutants) embryos were identified by genomic PCR using Cre; Cxcr4flox and tdTomato primers. Hearts were isolated and dissected to remove the atria,  pulmonary and aortic valves. Hearts were then dissociated in a 600 μl mix consisting of 500 U/ml collagenase IV (Worthington #LS004186), 1.2 U/ml dispase (Worthington #LS02100), 32 U/ml DNase I (Worthington #LS002007), and sterile DPBS with Mg2+ and Ca2+ at 37 degrees for 45 min and resuspended by pipetting every 5 min. Once digestion was complete, 5 ml of a cold 5% FBS in 1X PBS mixture was added and the suspension was filtered through a 40 µm strainer. After further rinsing the strainer with 5 ml of 5% FBS/PBS, the cell suspension was centrifuged at 400 g at 4°C for 5 min. The cells were washed and resuspended once more in 1 ml 5% FBS/PBS. The following antibodies were added at the concentration of 1:50 and incubated on ice for 45 min: APC/Cy7 Cd45 (Biolegend #103116), APC Pecam1 (Biolegend #102410), APC/Cy7 Ter-119 (Biolegend #116223). DAPI (1.1 μM) was added to the cells immediately before FACS. Once stained, the cells were sorted on a Sony MA900 cell sortrer into 1.5 ml tubes. The gates were set up to sort cells with low DAPI, low Cd45 (hematopoietic cells), low Ter119 (erythroid cells), high Pecam1 (endothelial marker), and either high or low PE-Texas Red (tdTomato positive or negative). Compensation controls were set up for each single channel (PE-Texas Red, APC, APC/Cy7) before sorting the final cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics) and and sequencing was performed on two lanes of a Illumina NovaSeq 6000 SP flow cell.

value: Endothelial cells

value: heart

value: Cxcr4fl/fl (The Jackson Laboratory, B6.129P2-Cxcr4tm2Yzo/J, Stock# 008767


title: BMDM-K-2 (7K-Cho)

city: Nanjing

first: Shiqun

address: 22 Hankou Road

institute: Nanjing university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Mus_musculus (GRCm39)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: BMDMs

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Bone marrow cells were obtained from C57 mice and futher differentiated into BMDMs in vitro. BMDMs were treated with vehicle, DOX, or 7K-Cho for 6h. Cells were harvested and stored at -80°C.

tag: strain background

value: BMDMs


title: BMDM-K-3 (7K-Cho)


title: Multiple-library

description: pMHC


title: HT, scRNAseq

description: 10x Genomics


title: BMDM-D-3 (DOX)

value: doxycycline


title: Min6, Input

first: shao

middle: yi

last: xue

address: LongMian street

institute: Nanjing Medical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.  Frist at all, we use FastQC performs basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below:   (1) Remove low-quality reads: The reads that mean quality value less than 20 were removed.  (2) Remove the reads that contain more than 15 percent N bases.  (3) Remove adapters. Remove the reads that alignment with the adapter sequence.  (4) Drop reads blow the 18 bases long after trimming.  (5) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last,we use FastQC performs basic statistics on the quality of the clean reads
the UCSC mm10 genome were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. the fragment size was estimated with MACS2 predicted method with default parameters(Model-based analysis of ChIP-Seq (MACS). MACS scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) peak finding algorithm to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
MEME and DREME were used to detect the sequence motif, which determined to detect long and short consensus sequence. After motif detection, Tomtom software was performed to annotate the motifs, which based on the sequence similarity.  PeakAnnotator was used to identify the nearest TSS of every peak and the distance distribution between peaks and TSS was shown. Peak related genes can be confirmed by PeakAnnotator. GO enrichment analysis was implemented by the GOseq R package. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by peak related genes. KOBAS software was used to test the statistical enrichment of peak related genes in KEGG pathways.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: The Min6 cells were cultured in DMEM medium containing 25mM D- glucose, 15％ FBS, 10mM HEPES, 1mM sodium pyruvate, 100 U/mL penicillin, 100 μg/mL streptomycin and 50μmol/Lβ- mercaptoethanol, and incubated in a cell incubator at 37℃ with 95% air and 5% CO2.

extract_protocol:
Chromatin was crosslinked by 1% formaldehyde for 10 min at RT, and cross-linking was terminated by using 0.125 mol/l glycine. Cells were collected after two washings with iced PBS in a lysis buffer (1% SDS, 10 mmol/l EDTA, 50 mmol/l Tris-HCl, pH 8.1, 1 mmol/l phenylmethylsulfonyl fluoride, 2 × 106 cells/200 μl) and then sonicated on ice.
ChIP-seq was carried out at Novogene (Beijing, China). The purity of DNA from Ets-1 ChIP was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA). The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Before transfection, the cell state was observed, and at least 2x107 cells were used for each experiment. Control virus (Ad-GFP) and Ets-1 overexpression adenovirus (Ad-Ets-1) were transfected into Min6 cells in 10cm dish for 24h, respectively.

value: Mouse insulinoma cells


title: MA2 Fab selection pHLA-A2 yeast library round5

description: Synthetic DNA/peptide library

value: Yeast


title: BMDM-C-2 (CTRL)

value: vehicle


title: BMDM-C-3 (CTRL)


title: BMDM-C-1 (CTRL)


title: BMDM-D-2 (DOX)


title: 8F-MP-P4-C3-H9_S1245

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

description: Biological replicate 3

data_processing:
Sequence reads from each lane were obtained and mapped together to the mouse genome (GENCODE release M23 (GRCm38.p6)) using STAR (version 2.5.2a). ERCC spike-ins were added to the mouse genome as artificial chromosomes.
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts, using Salmon (version 0.14.1) and Tximport (version 1.12.3).
Assembly: GENCODE release M23 (GRCm38.p6)
Supplementary files format and content: comma separated value text files contain either TPMs or raw counts for all samples

source_name: mouse back skin

extract_protocol:
Single squamous cell cancer cells were FACS purified, and collected into 96-well plates containing lysis buffer and snap frozen in liquid nitrogen. Plates were stored at -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Reverse transcription reaction and whole transcriptome amplification were performed according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and the tagmentation reaction was performed by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequenced on an Illumina NovaSeq SP with 50 cycles paired-end mode (2 lanes).

tag: tumor stage

value: SCC

value: FVB/N

tag: mouse age

tag: mouse sex

value: Female

tag: lentivirus injected at e9.5

value: SBE-mCherry PGK-rtTA3

tag: sorting scheme

tag: read alignment program

tag: read quantification program

value: Tximport (v 1.12.3)


title: Min6, AdGFP--Ets1 IP (CST)

tag: chip antibody


title: 8F-MP-P4-C3-H8_S1244

description: Biological replicate 3

tag: strain


title: 8F-MP-P4-C3-H1_S1237

description: Biological replicate 3


title: 8F-MP-P4-C3-H5_S1241

description: Biological replicate 3


title: BMDM-K-1 (7K-Cho)

tag: cell type


title: 8F-MP-P4-C3-H6_S1242

description: Biological replicate 3


title: 8F-MP-P4-C3-H7_S1243

description: Biological replicate 3


title: 8F-MP-P4-C3-H2_S1238

description: Biological replicate 3


title: 8F-MP-P4-C3-H12_S1248

description: Biological replicate 3


title: 8F-MP-P4-C3-H11_S1247

description: Biological replicate 3


title: Min6, AdEts1--Ets1 IP (CST)

tag: cell line


title: 8F-MP-P4-C3-H10_S1246

description: Biological replicate 3


title: BMDM-D-1 (DOX)

tag: treatment


title: 8F-MP-P4-C3-G9_S1233

description: Biological replicate 3

tag: genotype


title: 8F-MP-P4-C3-G7_S1231

description: Biological replicate 3


title: 8F-MP-P4-C3-G6_S1230

description: Biological replicate 3


title: 8F-MP-P4-C3-G5_S1229

description: Biological replicate 3


title: 8F-MP-P4-C3-G8_S1232

description: Biological replicate 3


title: 8F-MP-P4-C3-G4_S1228

description: Biological replicate 3


title: 8F-MP-P4-C3-G2_S1226

description: Biological replicate 3


title: 8F-MP-P4-C3-G1_S1225

description: Biological replicate 3


title: 8F-MP-P4-C3-G3_S1227

description: Biological replicate 3


title: 8F-MP-P4-C3-H4_S1240

description: Biological replicate 3


title: 8F-MP-P4-C3-G11_S1235

description: Biological replicate 3


title: 8F-MP-P4-C3-F8_S1220

description: Biological replicate 3


title: 8F-MP-P4-C3-F7_S1219

description: Biological replicate 3


title: 8F-MP-P4-C3-F6_S1218

description: Biological replicate 3


title: 8F-MP-P4-C3-F5_S1217

description: Biological replicate 3


title: 8F-MP-P4-C3-G12_S1236

description: Biological replicate 3


title: 8F-MP-P4-C3-F9_S1221

description: Biological replicate 3


title: 8F-MP-P4-C3-F2_S1214

description: Biological replicate 3


title: 8F-MP-P4-C3-F1_S1213

description: Biological replicate 3


title: 8F-MP-P4-C3-F12_S1224

description: Biological replicate 3


title: 8F-MP-P4-C3-F4_S1216

description: Biological replicate 3


title: 8F-MP-P4-C3-F3_S1215

description: Biological replicate 3


title: 8F-MP-P4-C3-F11_S1223

description: Biological replicate 3


title: 8F-MP-P4-C3-F10_S1222

description: Biological replicate 3


title: 8F-MP-P4-C3-E9_S1209

description: Biological replicate 3


title: 8F-MP-P4-C3-E8_S1208

description: Biological replicate 3


title: 8F-MP-P4-C3-E5_S1205

description: Biological replicate 3


title: 8F-MP-P4-C3-E7_S1207

description: Biological replicate 3


title: 8F-MP-P4-C3-E3_S1203

description: Biological replicate 3


title: 8F-MP-P4-C3-E4_S1204

description: Biological replicate 3


title: 8F-MP-P4-C3-E11_S1211

description: Biological replicate 3


title: 8F-MP-P4-C3-D9_S1197

description: Biological replicate 3


title: 8F-MP-P4-C3-E12_S1212

description: Biological replicate 3


title: 8F-MP-P4-C3-E2_S1202

description: Biological replicate 3


title: 8F-MP-P4-C3-E10_S1210

description: Biological replicate 3


title: 8F-MP-P4-C3-G10_S1234

description: Biological replicate 3


title: 8F-MP-P4-C3-D8_S1196

description: Biological replicate 3


title: 8F-MP-P4-C3-D7_S1195

description: Biological replicate 3


title: 8F-MP-P4-C3-D5_S1193

description: Biological replicate 3


title: 8F-MP-P4-C3-E1_S1201

description: Biological replicate 3


title: 8F-MP-P4-C3-D4_S1192

description: Biological replicate 3


title: 8F-MP-P4-C3-D2_S1190

description: Biological replicate 3


title: 8F-MP-P4-C3-D1_S1189

description: Biological replicate 3


title: 8F-MP-P4-C3-E6_S1206

description: Biological replicate 3


title: 8F-MP-P4-C3-D12_S1200

description: Biological replicate 3


title: 8F-MP-P4-C3-D11_S1199

description: Biological replicate 3


title: 8F-MP-P4-C3-D10_S1198

description: Biological replicate 3


title: 8F-MP-P4-C3-C7_S1183

description: Biological replicate 3


title: 8F-MP-P4-C3-C6_S1182

description: Biological replicate 3


title: 8F-MP-P4-C3-C9_S1185

description: Biological replicate 3


title: 8F-MP-P4-C3-C8_S1184

description: Biological replicate 3


title: 8F-MP-P4-C3-C4_S1180

description: Biological replicate 3


title: 8F-MP-P4-C3-C3_S1179

description: Biological replicate 3


title: 8F-MP-P4-C3-C2_S1178

description: Biological replicate 3


title: 8F-MP-P4-C3-C12_S1188

description: Biological replicate 3


title: 8F-MP-P4-C3-C10_S1186

description: Biological replicate 3


title: 8F-MP-P4-C3-B9_S1173

description: Biological replicate 3


title: 8F-MP-P4-C3-C1_S1177

description: Biological replicate 3


title: 8F-MP-P4-C3-D6_S1194

description: Biological replicate 3


title: 8F-MP-P4-C3-B7_S1171

description: Biological replicate 3


title: 8F-MP-P4-C3-B8_S1172

description: Biological replicate 3


title: 8F-MP-P4-C3-B5_S1169

description: Biological replicate 3


title: 8F-MP-P4-C3-B6_S1170

description: Biological replicate 3


title: 8F-MP-P4-C3-D3_S1191

description: Biological replicate 3


title: 8F-MP-P4-C3-B2_S1166

description: Biological replicate 3


title: 8F-MP-P4-C3-B1_S1165

description: Biological replicate 3


title: 8F-MP-P4-C3-B3_S1167

description: Biological replicate 3


title: 8F-MP-P4-C3-B12_S1176

description: Biological replicate 3


title: 8F-MP-P4-C3-C5_S1181

description: Biological replicate 3


title: 8F-MP-P4-C3-B10_S1174

description: Biological replicate 3


title: 8F-MP-P4-C3-A9_S1161

description: Biological replicate 3


title: 8F-MP-P4-C3-A7_S1159

description: Biological replicate 3


title: 8F-MP-P4-C3-B11_S1175

description: Biological replicate 3


title: 8F-MP-P4-C3-A8_S1160

description: Biological replicate 3


title: 8F-MP-P4-C3-A5_S1157

description: Biological replicate 3


title: 8F-MP-P4-C3-C11_S1187

description: Biological replicate 3


title: 8F-MP-P4-C3-A4_S1156

description: Biological replicate 3


title: 8F-MP-P4-C3-A2_S1154

description: Biological replicate 3


title: 8F-MP-P4-C3-A6_S1158

description: Biological replicate 3


title: 8F-MP-P4-C3-A3_S1155

description: Biological replicate 3


title: 8F-MP-P4-C3-A1_S1153

description: Biological replicate 3


title: 8F-MP-P3-E1-H7_S2011

description: Biological replicate 3


title: 8F-MP-P3-E1-H9_S2013

description: Biological replicate 3


title: 8F-MP-P4-C3-A11_S1163

description: Biological replicate 3


title: 8F-MP-P4-C3-B4_S1168

description: Biological replicate 3


title: 8F-MP-P4-C3-A12_S1164

description: Biological replicate 3


title: 8F-MP-P3-E1-H4_S2008

description: Biological replicate 3


title: 8F-MP-P3-E1-H8_S2012

description: Biological replicate 3


title: 8F-MP-P3-E1-H5_S2009

description: Biological replicate 3


title: 8F-MP-P3-E1-H2_S2006

description: Biological replicate 3


title: 8F-MP-P3-E1-H6_S2010

description: Biological replicate 3


title: 8F-MP-P3-E1-H3_S2007

description: Biological replicate 3


title: 8F-MP-P3-E1-H12_S2016

description: Biological replicate 3


title: 8F-MP-P3-E1-H1_S2005

description: Biological replicate 3


title: 8F-MP-P3-E1-H10_S2014

description: Biological replicate 3


title: 8F-MP-P3-E1-H11_S2015

description: Biological replicate 3


title: 8F-MP-P3-E1-G8_S2000

description: Biological replicate 3


title: 8F-MP-P3-E1-G9_S2001

description: Biological replicate 3


title: 8F-MP-P3-E1-G6_S1998

description: Biological replicate 3


title: 8F-MP-P3-E1-G7_S1999

description: Biological replicate 3


title: 8F-MP-P3-E1-G4_S1996

description: Biological replicate 3


title: 8F-MP-P3-E1-G3_S1995

description: Biological replicate 3


title: 8F-MP-P3-E1-G2_S1994

description: Biological replicate 3


title: 8F-MP-P3-E1-G12_S2004

description: Biological replicate 3


title: 8F-MP-P3-E1-G1_S1993

description: Biological replicate 3


title: 8F-MP-P4-C3-A10_S1162

description: Biological replicate 3


title: 8F-MP-P3-E1-G10_S2002

description: Biological replicate 3


title: 8F-MP-P3-E1-G11_S2003

description: Biological replicate 3


title: 8F-MP-P3-E1-F9_S1989

description: Biological replicate 3


title: 8F-MP-P3-E1-F5_S1985

description: Biological replicate 3


title: 8F-MP-P3-E1-F8_S1988

description: Biological replicate 3


title: 8F-MP-P3-E1-F4_S1984

description: Biological replicate 3


title: 8F-MP-P3-E1-F3_S1983

description: Biological replicate 3


title: 8F-MP-P3-E1-F7_S1987

description: Biological replicate 3


title: 8F-MP-P3-E1-F2_S1982

description: Biological replicate 3


title: 8F-MP-P3-E1-F12_S1992

description: Biological replicate 3


title: 8F-MP-P3-E1-E9_S1977

description: Biological replicate 3


title: 8F-MP-P3-E1-E8_S1976

description: Biological replicate 3


title: 8F-MP-P3-E1-E7_S1975

description: Biological replicate 3


title: 8F-MP-P3-E1-F10_S1990

description: Biological replicate 3


title: 8F-MP-P3-E1-E5_S1973

description: Biological replicate 3


title: 8F-MP-P3-E1-E4_S1972

description: Biological replicate 3


title: 8F-MP-P3-E1-F11_S1991

description: Biological replicate 3


title: 8F-MP-P3-E1-G5_S1997

description: Biological replicate 3


title: 8F-MP-P3-E1-E2_S1970

description: Biological replicate 3


title: 8F-MP-P3-E1-E11_S1979

description: Biological replicate 3


title: 8F-MP-P3-E1-E1_S1969

description: Biological replicate 3


title: 8F-MP-P3-E1-D9_S1965

description: Biological replicate 3


title: 8F-MP-P3-E1-F6_S1986

description: Biological replicate 3


title: 8F-MP-P3-E1-E10_S1978

description: Biological replicate 3


title: 8F-MP-P3-E1-D6_S1962

description: Biological replicate 3


title: 8F-MP-P3-E1-D8_S1964

description: Biological replicate 3


title: 8F-MP-P3-E1-D4_S1960

description: Biological replicate 3


title: 8F-MP-P3-E1-D3_S1959

description: Biological replicate 3


title: 8F-MP-P3-E1-D5_S1961

description: Biological replicate 3


title: 8F-MP-P3-E1-D2_S1958

description: Biological replicate 3


title: 8F-MP-P3-E1-D12_S1968

description: Biological replicate 3


title: 8F-MP-P3-E1-D11_S1967

description: Biological replicate 3


title: 8F-MP-P3-E1-D1_S1957

description: Biological replicate 3


title: 8F-MP-P3-E1-F1_S1981

description: Biological replicate 3


title: 8F-MP-P3-E1-C8_S1952

description: Biological replicate 3


title: 8F-MP-P3-E1-D10_S1966

description: Biological replicate 3


title: 8F-MP-P3-E1-E6_S1974

description: Biological replicate 3


title: 8F-MP-P3-E1-C4_S1948

description: Biological replicate 3


title: 8F-MP-P3-E1-C7_S1951

description: Biological replicate 3


title: 8F-MP-P3-E1-C6_S1950

description: Biological replicate 3


title: 8F-MP-P3-E1-C2_S1946

description: Biological replicate 3


title: 8F-MP-P3-E1-C1_S1945

description: Biological replicate 3


title: 8F-MP-P3-E1-E12_S1980

description: Biological replicate 3


title: 8F-MP-P4-C3-H3_S1239

description: Biological replicate 3


title: 8F-MP-P3-E1-E3_S1971

description: Biological replicate 3


title: 8F-MP-P3-E1-C5_S1949

description: Biological replicate 3


title: 8F-MP-P3-E1-C12_S1956

description: Biological replicate 3


title: 8F-MP-P3-E1-C11_S1955

description: Biological replicate 3


title: 8F-MP-P3-E1-D7_S1963

description: Biological replicate 3


title: 8F-MP-P3-E1-B8_S1940

description: Biological replicate 3


title: 8F-MP-P3-E1-B7_S1939

description: Biological replicate 3


title: 8F-MP-P3-E1-C10_S1954

description: Biological replicate 3


title: 8F-MP-P3-E1-B6_S1938

description: Biological replicate 3


title: 8F-MP-P3-E1-B9_S1941

description: Biological replicate 3


title: 8F-MP-P3-E1-B4_S1936

description: Biological replicate 3


title: 8F-MP-P3-E1-B5_S1937

description: Biological replicate 3


title: 8F-MP-P3-E1-C9_S1953

description: Biological replicate 3


title: 8F-MP-P3-E1-B2_S1934

description: Biological replicate 3


title: 8F-MP-P3-E1-B12_S1944

description: Biological replicate 3


title: 8F-MP-P3-E1-B10_S1942

description: Biological replicate 3


title: 8F-MP-P3-E1-B1_S1933

description: Biological replicate 3


title: 8F-MP-P3-E1-B11_S1943

description: Biological replicate 3


title: 8F-MP-P3-E1-A9_S1929

description: Biological replicate 3


title: 8F-MP-P3-E1-A8_S1928

description: Biological replicate 3


title: 8F-MP-P3-E1-C3_S1947

description: Biological replicate 3


title: 8F-MP-P3-E1-A6_S1926

description: Biological replicate 3


title: 8F-MP-P3-E1-A7_S1927

description: Biological replicate 3


title: 8F-MP-P3-E1-A2_S1922

description: Biological replicate 3


title: 8F-MP-P3-E1-A4_S1924

description: Biological replicate 3


title: 8F-MP-P3-E1-A1_S1921

description: Biological replicate 3


title: 8F-MP-P3-E1-A3_S1923

description: Biological replicate 3


title: 8F-MP-P3-E1-A12_S1932

description: Biological replicate 3


title: 8F-MP-P3-E1-A10_S1930

description: Biological replicate 3


title: 8F-MP-P2-E4-H8_S2300

description: Biological replicate 3


title: 8F-MP-P3-E1-A11_S1931

description: Biological replicate 3


title: 8F-MP-P2-E4-H7_S2299

description: Biological replicate 3


title: 8F-MP-P2-E4-H6_S2298

description: Biological replicate 3


title: 8F-MP-P2-E4-H5_S2297

description: Biological replicate 3


title: 8F-MP-P2-E4-H3_S2295

description: Biological replicate 3


title: 8F-MP-P3-E1-B3_S1935

description: Biological replicate 3


title: 8F-MP-P2-E4-H1_S2293

description: Biological replicate 3


title: 8F-MP-P2-E4-H4_S2296

description: Biological replicate 3


title: 8F-MP-P2-E4-H2_S2294

description: Biological replicate 3


title: 8F-MP-P2-E4-H12_S2304

description: Biological replicate 3


title: 8F-MP-P2-E4-H10_S2302

description: Biological replicate 3


title: 8F-MP-P2-E4-H11_S2303

description: Biological replicate 3


title: 8F-MP-P2-E4-G7_S2287

description: Biological replicate 3


title: 8F-MP-P3-E1-A5_S1925

description: Biological replicate 3


title: 8F-MP-P2-E4-G5_S2285

description: Biological replicate 3


title: 8F-MP-P2-E4-G4_S2284

description: Biological replicate 3


title: 8F-MP-P2-E4-G8_S2288

description: Biological replicate 3


title: 8F-MP-P2-E4-G9_S2289

description: Biological replicate 3


title: 8F-MP-P2-E4-G6_S2286

description: Biological replicate 3


title: 8F-MP-P2-E4-G3_S2283

description: Biological replicate 3


title: 8F-MP-P2-E4-G1_S2281

description: Biological replicate 3


title: 8F-MP-P2-E4-G2_S2282

description: Biological replicate 3


title: 8F-MP-P2-E4-G10_S2290

description: Biological replicate 3


title: 8F-MP-P2-E4-G11_S2291

description: Biological replicate 3


title: 8F-MP-P2-E4-F9_S2277

description: Biological replicate 3


title: 8F-MP-P2-E4-F5_S2273

description: Biological replicate 3


title: 8F-MP-P2-E4-F7_S2275

description: Biological replicate 3


title: 8F-MP-P2-E4-F8_S2276

description: Biological replicate 3


title: 8F-MP-P2-E4-F4_S2272

description: Biological replicate 3


title: 8F-MP-P2-E4-F3_S2271

description: Biological replicate 3


title: 8F-MP-P2-E4-F1_S2269

description: Biological replicate 3


title: 8F-MP-P2-E4-F2_S2270

description: Biological replicate 3


title: 8F-MP-P2-E4-F12_S2280

description: Biological replicate 3


title: 8F-MP-P2-E4-F11_S2279

description: Biological replicate 3


title: 8F-MP-P2-E4-E9_S2265

description: Biological replicate 3


title: 8F-MP-P2-E4-F10_S2278

description: Biological replicate 3


title: 8F-MP-P2-E4-E6_S2262

description: Biological replicate 3


title: 8F-MP-P2-E4-E8_S2264

description: Biological replicate 3


title: 8F-MP-P2-E4-E5_S2261

description: Biological replicate 3


title: 8F-MP-P2-E4-E7_S2263

description: Biological replicate 3


title: 8F-MP-P2-E4-E4_S2260

description: Biological replicate 3


title: 8F-MP-P2-E4-E1_S2257

description: Biological replicate 3


title: 8F-MP-P2-E4-E2_S2258

description: Biological replicate 3


title: 8F-MP-P2-E4-G12_S2292

description: Biological replicate 3


title: 8F-MP-P2-E4-E10_S2266

description: Biological replicate 3


title: 8F-MP-P2-E4-D9_S2253

description: Biological replicate 3


title: 8F-MP-P2-E4-E12_S2268

description: Biological replicate 3


title: 8F-MP-P2-E4-E11_S2267

description: Biological replicate 3


title: 8F-MP-P2-E4-D7_S2251

description: Biological replicate 3


title: 8F-MP-P2-E4-D8_S2252

description: Biological replicate 3


title: 8F-MP-P2-E4-F6_S2274

description: Biological replicate 3


title: 8F-MP-P2-E4-D5_S2249

description: Biological replicate 3


title: 8F-MP-P2-E4-D6_S2250

description: Biological replicate 3


title: 8F-MP-P2-E4-D4_S2248

description: Biological replicate 3


title: 8F-MP-P2-E4-D2_S2246

description: Biological replicate 3


title: 8F-MP-P2-E4-D3_S2247

description: Biological replicate 3


title: 8F-MP-P2-E4-D11_S2255

description: Biological replicate 3


title: 8F-MP-P2-E4-D10_S2254

description: Biological replicate 3


title: 8F-MP-P2-E4-C8_S2240

description: Biological replicate 3