title: H1

city: Quechee

first: Michael

middle: J

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

data_processing:
10X Genomics Cell Ranger sample processing. Cell counts were generated using the 10X Genomics Cell Ranger v3.1.0 pipeline against the GRCh38 reference genome (10X genome version 3.0.0; Ensembl release 93, July 2018; http://jul2018.archive.ensembl.org). The filtered count matrices generated by Cell Ranger were used as input. The Chromium R package v0.1.5 (https://chromium.acidgenomics.com) was used to perform additional cell quality control analysis and filtering prior to clustering. Similar to the approach used for the SureCell samples, UMIs per cell, genes per cell, and mitochondrial ratio cutoffs were applied to remove additional low quality cells from analysis.
Bio-Rad SureCell sample processing. Cell counts were generated with the bcbio-nextgen Python toolkit v1.1.1a0-06f3c2a9 (https://bcbio-nextgen.readthedocs.io). Reads were assigned per cell via the cellular barcodes, and per gene via the UMIs, using the umis toolkit v1.0.0 [@Svensson2017-hp]. Reads were quasi-mapped to the Ensembl GRCh38 transcriptome (Release 90, August 2017; https://aug2017.archive.ensembl.org) using Rapmap v0.5.0 [@Srivastava2016-tm]. Only cells containing at least 1,000 reads were analyzed. The bcbioSingleCell R package v0.4.12 (https://bioinformatics.sph.harvard.edu/bcbioSingleCell) was used to perform cell quality control analysis and filtering prior to clustering. The distributions of reads per cell, UMIs per cell, genes per cell, and mitochondrial ratio per cell were used to remove low quality cells from analysis.
Clustering analysis. Clustering analysis was performed with the Seurat R package v3.1.5. [@Satija2015-rr]. Counts were log normalized and scaled per cell to account for variations in sequencing depth. Linear dimensional reduction was performed using PCA on the most variable genes detected; these are determined via binned z-scores based on the average expression and dispersion for each gene (Satija et al., 2015). Non-linear dimensional reduction was performed using t-SNE [@Maaten2008-qy] and UMAP [@McInnes2018-aa, @Becht2018-jn]. We defined cell cluster specific marker genes using the Findmarkers function in Seurat across all samples using a Wilcoxon rank sum test. Differential expression analysis was performed using the edgeR package  v3.30.3 [@Robinson2010-eu]. Plots were generated using the acidplots v0.2.29 (https://acidplots.acidgenomics.com/) and pointillism v0.4.11 (https://pointillism.acidgenomics.com/) R packages.
Genome_build: SureCell: Homo sapiens GRCh38 (Ensembl release 90);  Chromium: Homo sapiens GRCh38 (10X genome version 3.0.0; Ensembl release 93)
Supplementary_files_format_and_content: Matrix Market Exchange Format (sparse matrix)

source_name: stromal vascular cells

extract_protocol:
Adipose tissue was minced into 3 mm pieces and subjected to collagenase digestion for 50 min at 37°C with continuous rotation. Collagenase buffer consisted of 1X PBS containing calcium and magnesium, 2% bovine serum albumin (BSA; MP Bio, USA), 0.2 mg/mL DNase I (Sigma Aldrich, USA), and 1mg/mL collagenase II (Invitrogen, USA). Following digestion, cells were incubated with 0.01 M EDTA for an additional 10 min then filtered through a 100 µM cell strainer (Fisherbrand, USA) and centrifuged at 1500 rpm for 5 min. The pellet was resuspended in 1X RBC Lysis Buffer (Invitrogen, USA) as per manufacturer’s instruction. The samples were centrifuged as above, and the final pellet was converted to a single-cell suspension and frozen for later analysis such that all samples could be run at the same time. The cell-freezing protocol for scRNAseq was developed in conjunction with Bio-Rad Genomics. Briefly, the cell pellet was thoroughly mixed by pipetting up and down 10 times. Cells were counted a total of 4 times for each cell preparation to ensure accuracy of total cell count and viability. Aliquots of 5*10^6 cells/ml were prepared in chilled cryopreservation medium (DMEM + 20% FBS + 10% DMSO) and placed in a 4°C pre-chilled CoolCell FTS30 and placed in a -80C freezer for at least 4 hrs. After 4 hrs the cryovials were transferred to liquid nitrogen for long-term storage.
CrF vs. H-MAT. Single-cell libraries of the dissociated SVCs were prepared using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X Genomics) and the Chromium Chip B Single Cell Kit protocols, aiming for recovery of 1200 cells for each sample. Briefly, cells were individually partitioned and encapsulated into subnanoliter oil droplets in the Chromium Controller instrument for cell lysis and barcoded reverse transcription of mRNA, followed by amplification, shearing and Illumina library construction. Single-cell-barcoded cDNA libraries were sequenced on the Illumina NextSeq platform.    CrF vs. CD MAT and UC MAT. Dissociated SVCs were first diluted to 2500 cells/uL in PBS with 0.1% BSA. Cells were individually partitioned and co-encapsulated with barcodes into subnanoliter oil droplets using the ddSEQ single-cell isolator (Bio-Rad, USA) as per manufacturer’s instructions in the Illumina Bio-Rad SureCell WTA 3' Library Prep Kit. Following cell isolation, the droplets were transferred to a 96-well PCR plate for cell lysis, barcoding, reverse transcription using a thermal cycler. The droplet emulsion was then disrupted for generation of second strand cDNA, followed by fragmentation, tagging and amplification of cDNA. Single-cell-barcoded cDNA libraries were sequenced on the Illumina NextSeq platform at an average read depth of 175,000 reads/sample.

value: stromal vascular cells

tag: technology

value: 10X Genomics Chromium

value: Cell Ranger

tag: condition

value: Non-IBD control

value: healthy


title: Dengue Infection_Day5 follow-up [Sample_20260_F]

status: Public on Aug 25 2020

type: SRA

city: Faridabad

first: Abhay

middle: Deep

last: Pandey

address: 3rd Milestone, Faridabad-Gurgaon Expressway

department: Virology

country: India

institute: Regional Centre for Biotechnology

library_source: transcriptomic

data_processing:
Inbuilt Illumina Casava 1.8.2 software used for basecalling.
QC of sequenced reads were done by FASTQC.
Adapter cutting were done by cutadapt.
Using mirdeep2 and edgeR packages, we have detected differentially expressed  microRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Normalised count values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Dengue Infection_Day5 follow-up_plasma

extract_protocol:
MicroRNA were isolated from 150 µl of plasma according to the miRNeasy RNA isolation protocol (Qiagen). Quality of isolated small RNA was checked using small RNA chips in 2100 Bioanalyzer (Agilent) for each sample and quantitation was performed in Qubit Fluorometer using micro RNA assay kit (Invitrogen). Small RNA sequencing library preparation was performed using Illumina® TruSeq® Small RNA Library Prep Kit according to the manufacturer’s instructions. Four nanogram of small RNA per sample was used for library preparation.
RNA-seq library preparation was performed using TruSeq® RNA library Prep Kit v2 (Illumina).

tag: subject status/time point

value: Day 5 Followup

tag: tissue

value: Plasma


title: fetal liver Eto2 mut-2

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

country: USA

institute: NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 and mm10  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.22.1
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample

organism: Mus musculus

source_name: Fetal livers

growth_protocol: Human K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum.  Control C57BL/6J and Eto2 KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (human K562 cells) and PicoPure RNA isolation kit (fetal liver cells)
RNA sequencing libraries were generating from 1 ug (K562 cells and total fetal liver cells) or 10 ng (FACS sorted fetal liver cells) of RNA using Illumina TruSeq  mRNA Library Preparation kit following manufacturer’s protocol.

tag: strain

value: Fetal livers

tag: age

value: embryonic day 14.5

tag: genotype


title: D1

molecule: polyA RNA

tag: cell type


title: Dengue Infection_Day5 follow-up [Sample_20654_F]


title: fetal liver Eto2 mut-1


title: A16

value: Crohn's disease

value: inflamed


title: PBMC CD3+ T-cells CFS 200256300057_R05C02

type: genomic

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

description: PBMC CD3+ T-cells CFS

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PBMC CD3+ T-cells

label_protocol: Standard Illumina Protocol

extract_protocol: CD3+ T-cells were isolated from PBMC samples using flurescently labelled antibodies and a FACSAria flow cytometer. Genomic DNA was extracted by MasterPure Complete DNA and RNA Purification Kit (Epicentre)

tag: sample group

value: CFS


title: RNA-seq ASZ_AP1_inh_rep2

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

data_processing:
Tophat used for alignment.
Homer is used to calculate raw counts and FPKM values
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: ASZ001 murine BCC cell line

growth_protocol: ASZ001 cells were cultured in 154CF medium (Life Technologies) supplemented with 2% chelated FBS and 0.05 mM CaCl2.

extract_protocol:
RNA isolated using the QIAGEN RNeasy Mini Kit according to the manufacturer's protocol.
The RNA-seq libraries were constructed by TruSeq Stranded mRNA Library Prep kit (Illumina) per manufacturer's protocol and sequenced using the Illumina Hiseq2000 platform.

treatment_protocol: Experiments were carried out using low serum conditions with 154CF medium containing 0.2% chelated FBS and 0.05 mM CaCl2 for 24 hours.

tag: treatment


title: fetal liver wt-6


title: PBMC CD3+ T-cells CFS 200256300061_R01C01

description: PBMC CD3+ T-cells CFS


title: Dengue Severe [Sample_C9]

source_name: Dengue Severe_plasma

value: Dengue Severe


title: PBMC CD3+ T-cells CFS 200256300057_R06C02

description: PBMC CD3+ T-cells CFS


title: A04


title: fetal liver wt-5


title: PBMC CD3+ T-cells CFS 200256300061_R03C01

description: PBMC CD3+ T-cells CFS


title: Dengue Severe [Sample_C8]


title: fetal liver wt-4


title: PBMC CD3+ T-cells CFS 200256300057_R04C02

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300057_R01C02

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300057_R03C02

description: PBMC CD3+ T-cells CFS


title: fetal liver wt-2


title: UC4H

value: Bio-Rad SureCell

value: bcbio

value: Ulcerative colitis


title: fetal liver wt-1


title: PBMC CD3+ T-cells Ctrl 200256300061_R04C02

description: PBMC CD3+ T-cells Ctrl

value: control


title: fetal liver Eto2 mut-6


title: UC4I

value: stromal vascular cells


title: PBMC CD3+ T-cells CFS 200256300057_R06C01

description: PBMC CD3+ T-cells CFS


title: CD11I


title: Dengue Severe [Sample_C4]


title: FACS-sorted fetal liver wt-2-S3-m


title: CD11H


title: Dengue Severe [Sample_20654]


title: Dengue Severe [Sample_C3]


title: FACS-sorted fetal liver wt-2-S4/S5


title: CD5I


title: PBMC CD3+ T-cells CFS 200256300057_R02C02

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300057_R03C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300057_R04C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300057_R05C01

description: PBMC CD3+ T-cells CFS


title: Dengue Severe [Sample_C5]


title: FACS-sorted fetal liver wt-2-S2


title: Dengue Severe [Sample_C7]


title: UC6H


title: PBMC CD3+ T-cells CFS 200256300057_R02C01

description: PBMC CD3+ T-cells CFS


title: Dengue Severe [Sample_C15]


title: FACS-sorted fetal liver wt-2-S1


title: CD3I


title: PBMC CD3+ T-cells Ctrl 200256300052_R06C02

description: PBMC CD3+ T-cells Ctrl


title: fetal liver wt-3


title: Dengue Severe [Sample_C14]


title: FACS-sorted fetal liver wt-2-S0 med


title: CD3H


title: Dengue Severe [Sample_C13]


title: PBMC CD3+ T-cells CFS 200256300057_R01C01

description: PBMC CD3+ T-cells CFS


title: FACS-sorted fetal liver wt-2-S0 low


title: Dengue Severe [Sample_C2]


title: FACS-sorted fetal liver wt-2-S3-C


title: UC6I


title: PBMC CD3+ T-cells Ctrl 200256300052_R03C02

description: PBMC CD3+ T-cells Ctrl


title: Dengue Severe [Sample_C11]


title: PBMC CD3+ T-cells Ctrl 200256300052_R04C02

description: PBMC CD3+ T-cells Ctrl


title: FACS-sorted fetal liver wt-1-S4/S5


title: SCLII_WT

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

data_processing:
Library strategy: PAR-CLIP-seq
Standard Illumina base-calling (NextSeq)
Adapter trimming using cutadapt
PARalyzer pipeline (PMID: 21851591), with default parameters and the GRCh37 human genome, via the ‘bpipe’ tool (PMID: 22500002) for running and managing bioinformatics pipelines
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel files showing mapping summaries

source_name: skin cells

growth_protocol: Standard cell culture techniques

extract_protocol:
AGO2 PAR-CLIP asdesribed in PMID 22926237 except using a native Ago2 antibody (#ab57113, Abcam Cambridge, CB4 OFW, UK)
NextFlex or in-house small RNA library preparation (as described in PMID 22926237)

treatment_protocol: Incubation with 4-thiouridine prior to UV-crosslinking

value: SCLII epidermal cell line

tag: transfection

tag: library preparation

value: NEXTFLEX Small RNA-Seq Kit

tag: 3' adapter sequence

value: NNNNTGGAATTCTCGGGTGCCAAGG


title: HaCaT_197

value: HaCaT keratinocyte cell line

value: In-house

value: NNNNTCATCTGGAATTCTCGGGTGCCAAGG


title: FACS-sorted fetal liver wt-1-S3-m

value: Fetal livers


title: FACS-sorted fetal liver wt-1-S2

value: embryonic day 14.5


title: PBMC CD3+ T-cells Ctrl 200256300052_R05C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells Ctrl 200256300052_R01C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells Ctrl 200256300052_R02C02

description: PBMC CD3+ T-cells Ctrl


title: Dengue Severe [Sample_C1]

value: Plasma


title: FACS-sorted fetal liver wt-1-S1


title: PBMC CD3+ T-cells CFS 200256300052_R04C01

description: PBMC CD3+ T-cells CFS


title: Dengue Warning Sign [Sample_B8]

source_name: Dengue Warning Sign_plasma

value: Dengue Warning Sign


title: Dengue Severe [Sample_C12]


title: FACS-sorted fetal liver wt-1-S0 med


title: Dengue Warning Sign [Sample_B7]


title: Dengue Warning Sign [Sample_B9]


title: HTR_HaCaT

value: control RNA


title: PBMC CD3+ T-cells CFS 200256300052_R06C01

description: PBMC CD3+ T-cells CFS

value: CFS


title: Dengue Warning Sign [sample_B6]


title: WT_HaCaT


title: FACS-sorted fetal liver wt-1-S3-C


title: SCLII_199


title: PBMC CD3+ T-cells CFS 200256300052_R03C01

description: PBMC CD3+ T-cells CFS


title: Dengue Severe [Sample_C6]

value: Dengue Severe


title: Dengue Warning Sign [Sample_B5]


title: FACS-sorted fetal liver Eto2 mut-2-S3-m


title: PLZFneg_iLN2

city: Dublin

first: Lydia

last: Lynch

address: Trinity Biomedical Sciences Institute 152-160 Pearse St

country: Ireland

institute: Trinity College Dublin

data_processing:
Reads were mapped to the mouse genome (mm10) using HISAT (0.1.6-beta release).
Bam files were sorted and indexed by SAMtools (1.2 release).
Merged transcriptome (constructed from all samples that went through sequencing, only the samples described in the paper are deposited here) was used as a reference annotation for quantification, normalization and differential expression analysis.
Quantification and normalization were performed using CuffLinks (1.2 release), according to the Tuxedo pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet containing TMM-normalized gene expression values for each sample.

source_name: γδ T cells

growth_protocol: Male mice were fed ad libitum and sacrificed between 16-22 weeks of age.

extract_protocol:
PLZF+ and PLZF- γδ T cells were sorted  from the spleen, inguinal lymph nodes, lungs and adipose tissue of PLZF-GFP mice using a FACSAria Fusion into 5µl of TCL buffer into a 96 well plate.
RNA libraries were prepared for sequencing using Illumina SMARTseq2 protocol

tag: gender

value: Male

value: Inguinal Lymph Nodes

value: 16-22 weeks

value: PLZF- {gamma}{delta} T cell subsets


title: PLZFneg_iLN1


title: PBMC CD3+ T-cells CFS 200256300052_R05C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300052_R02C01

description: PBMC CD3+ T-cells CFS


title: PLZFpos_iLN3

value: PLZF+ {gamma}{delta} T cell subsets


title: PBMC CD3+ T-cells CFS 200256300052_R01C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells Ctrl 200090280071_R06C02

description: PBMC CD3+ T-cells Ctrl

value: control


title: Dengue Warning Sign [Sample_B4]


title: Dengue Warning Sign [Sample_B3]


title: HaCaT_WT

value: NNNNTCACTTGGAATTCTCGGGTGCCAAGG


title: PLZFpos_iLN2


title: FACS-sorted fetal liver Eto2 mut-2-S2


title: FACS-sorted fetal liver Eto2 mut-2-S1


title: Dengue Warning Sign [Sample_B2]


title: PLZFneg_lung3

value: Lung


title: Dengue Warning Sign [sample_B15]


title: FACS-sorted fetal liver Eto2 mut-2-S0 med


title: PBMC CD3+ T-cells Ctrl 200090280071_R03C02

description: PBMC CD3+ T-cells Ctrl


title: PLZFpos_iLN1


title: FACS-sorted fetal liver wt-1-S0 low


title: Dengue Warning Sign [Sample_B14]


title: FACS-sorted fetal liver Eto2 mut-2-S0 low


title: PLZFneg_lung2


title: Dengue Warning Sign [Sample_B13]


title: PBMC CD3+ T-cells Ctrl 200090280071_R02C02

description: PBMC CD3+ T-cells Ctrl


title: PLZFneg_lung1


title: Dengue Severe [sample_C10]


title: PBMC CD3+ T-cells CFS 200090280071_R06C01

description: PBMC CD3+ T-cells CFS


title: FACS-sorted fetal liver Eto2 mut-1-S3-m


title: PBMC CD3+ T-cells Ctrl 200090280071_R01C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells Ctrl 200090280071_R04C02

description: PBMC CD3+ T-cells Ctrl


title: Dengue Warning Sign [Sample_B12]


title: FACS-sorted etal liver Eto2 mut-2-S3-C


title: PLZFpos_lung3


title: NsiR3_t8_2

type: RNA

city: Freiburg im Breisgau

first: Manuel

last: Brenes-Álvarez

address: Schänzlestraße 1

department: Genetics and Experimental Bioinformatics

country: Germany

institute: University of Freiburg

description: Gene expression after 8 hours of nitrogen depletion

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: PCC7120 ΔNsiR3_t8

label_protocol: DNAse-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in: Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: Liquid culture in BG110 medium supplemented with 6 mM ammonium chloride under standard illumination at 30 centigrades.

extract_protocol: RNA was prepared using a hot phenol-based protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Removal of combined nitrogen by filtration for cells growing in the presence of ammonium.

tag: genotype/variation

value: nitrogen deprivation for 8h


title: CD5H

value: stromal vascular cells

value: Bio-Rad SureCell

value: bcbio

value: Crohn's disease

value: healthy


title: Dengue Warning Sign [Sample_B11]

value: Dengue Warning Sign

value: Plasma


title: PBMC CD3+ T-cells Ctrl 200090280071_R05C02

description: PBMC CD3+ T-cells Ctrl


title: FACS-sorted fetal liver Eto2 mut-1-S4/S5

value: Fetal livers

value: embryonic day 14.5


title: 197_HaCaT

value: HaCaT keratinocyte cell line

value: NEXTFLEX Small RNA-Seq Kit

value: NNNNTGGAATTCTCGGGTGCCAAGG


title: PLZFneg_iLN3

value: Male

value: Inguinal Lymph Nodes

value: 16-22 weeks

value: PLZF- {gamma}{delta} T cell subsets


title: PLZFpos_lung2

value: Lung

value: PLZF+ {gamma}{delta} T cell subsets


title: NsiR3_t8_1

value: nitrogen deprivation for 8h


title: NsiR3_t0_2

description: Gene expression in medium with ammonium as nitrogen source

source_name: PCC7120 ΔNsiR3_t0

value: nitrogen deprivation for 0h


title: Dengue Infection_day0 [Sample_20736]

source_name: Dengue Infection_day0_plasma

value: day 0


title: FACS-sorted fetal liver Eto2 mut-1-S1


title: NsiR3_t0_1


title: Dengue Infection_day0 [Sample_20688]


title: PBMC CD3+ T-cells CFS 200090280071_R05C01

description: PBMC CD3+ T-cells CFS

value: CFS


title: PBMC CD3+ T-cells CFS 200090280071_R03C01

description: PBMC CD3+ T-cells CFS


title: FACS-sorted fetal liver Eto2 mut-2-S4/S5


title: PLZFneg_spleen3

value: Spleen


title: Dengue Warning Sign [sample_B10]

value: Dengue Warning Sign

value: Plasma


title: PLZFneg_spleen2


title: Monocytes cult 3

city: RTP

first: Rick

middle: David

last: Fannin

state: NC

address: 111 Tw Alexander Dr, MD D204

department: NIEHS/NIH

institute: Mr.

hyb_protocol: Reporter and Capture probes were added according to the manufacturer’s directions (nanostring.com) to 50 ng of total RNA in a final volume of 15ul followed by hybridization for at least 14 hours at 65oC

scan_protocol: After sample processing according to manufacturer’s instructions on the nCounter Prep Station Model 5S, sample cartridges were scanned on an nCounter Digital Analyzer Model 5S, using 555 Fields of Vision (FOV) and the .rlf file 'Ns_Mm_Myeloid_v2'.

data_processing: Data  were adjusted utilizing the manufacturer’s positive and negative experimental control probes, as well as 2 HK genes (Sap130 and Sdha).  All samples passed nSolver’s initial QA/QC controls. Compiled raw and data adjusted with positive/negative controls and the HK genes were exported as .csv files. nSolver adjusted data were then imported into Partek_v7.0 for further analysis

source_name: Mus musculus

extract_protocol: RNA was isolated from cells using Trizol, Dnase treated with Dnase I and further purified using Qiagen Rneasy mini kits. RNA concentration and purity was determined using a Qubit and Nanodrop.

treatment_protocol: C57BL/6 mice were inhaled house dust extract (10 micrograms) together with ovalbumin (100 micrograms). Sixteen hours later, lungs were excised, and Ly-6C+CD11b+, Ly-6C– CD11b+, and CD103+ cDCs (CD11c+ I-A+ CD45+ CD88– Siglec-F– F4/80– Live/Dead–) and monocytes (CD45+ F4/80+ CD88– Siglec-F– I-A– Live/Dead–) were purified by flow cytometric sorting. Purified lung cDCs and monocytes (2×105 cells/200 μL/well) were cultured for 2 days in complete RPMI1640 medium containing 10% fetal bovine serum. Total RNA (50 ng of each ) was isolated from freshly isolated or cultured cells, and mRNA expression was examined using the NanoString platform utilizing the Mouse Myeloid Innate Immunity Panel v2.

tag: Sex

value: male

value: Monoctes


title: FACS-sorted fetal liver Eto2 mut-1-S2

value: Fetal livers

value: embryonic day 14.5


title: PLZFpos_lung1

value: Male


title: PLZFneg_spleen1


title: Dengue Infection_day0 [sample_20476]


title: PBMC CD3+ T-cells CFS 200090280071_R01C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200090280071_R02C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200090280071_R04C01

description: PBMC CD3+ T-cells CFS


title: FACS-sorted fetal liver Eto2 mut-1-S3-C


title: Monocytes cult 2


title: Dengue Infection_day0 [Sample_20655]


title: Monocytes cult 1


title: PLZFpos_spleen3


title: Dengue Infection_day0 [Sample_20464]


title: Ly6C+ CD11b cult 3

value: Ly-6C+ CD11b+ cDCs


title: Ly6C+ CD11b cult 2


title: PLZFpos_spleen2

value: 16-22 weeks


title: FACS-sorted fetal liver Eto2 mut-1-S0 low


title: Dengue Infection_day0 [Sample_20260]


title: HHSteC-Cy80-2

city: Osaka

first: Le

middle: Thi Thanh

last: Thuy

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan

department: Department of Hepatology

country: Japan

institute: Osaka City University, Graduate School of Medicine

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated using FastQC v0.11.7
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed
Trimmed reads are mapped to reference genome with HISAT2 version 2.1.0, splice-aware aligner
Transcript is assembled by StringTie version 1.3.4d with aligned reads
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM value or the RPKM is used as a normalization value.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing
In case of known gene annotation, functional annotation and gene-set enrichment analysis are performed using GO and KEGG database on differentially expressed genes
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Cell line

growth_protocol: HHSteCs were cultured in complete Stellate Cell Medium (SteCM) consisted of 2% fetal bovine serum (FBS), 1% stellate cell growth supplement (S) and 1% penicillin-streptomycin (P/S) in a humidified atmosphere containing 95% air and 5% CO2. HHSteCs were passaged when sub-confluent and were used between passages 3 - 10 for the experiments

extract_protocol:
1 μg of total RNA was subjected to library synthesis using TruSeq Stranded mRNA LT Sample Prep Kit. The resulting mRNA was fragmented, reverse transcribed using random primers into cDNA, and ligated adapters onto both ends of the cDNA fragments. After amplifying fragments using PCR, select fragments with insert sizes between 200-400 bp. For paired-end sequencing, both ends of the cDNA is sequenced by the read length
TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: HHSteCs were plated into 12-well plate at 1 × 10^5 cells/well, in the final volume of 1 ml complete SteCM. On the following day, the medium was replaced with the fresh 0.2% FBS/SteCM without the supplement to activate HSCs. After 24 hours, rhCYGB were added and incubated for 48 hours.

tag: cell line

value: HHSteCs

value: Human hepatic stellate cells

value: treated with rhCYGB (80 microg/ml) for 48 hours


title: Ly6C+ CD11b cult 1


title: Dengue Infection_day0 [sample_20185]


title: PLZFneg_adipose3

value: Epididymal adipose

value: PLZF- {gamma}{delta} T cell subsets


title: CD11b Ly6C– cult 3


title: HHSteC-Cont-3

value: untreated


title: PLZFpos_spleen1

value: PLZF+ {gamma}{delta} T cell subsets


title: PLZFneg_adipose2


title: HHSteC-Cont-2


title: PBMC CD3+ T-cells CFS 200090280070_R06C01

description: PBMC CD3+ T-cells CFS

value: CFS


title: Dengue Infection_day0 [Sample_20139]

value: day 0


title: CD11b Ly6C– cult 2


title: Dengue Infection_day0 [sample_20035]

value: Plasma


title: HHSteC-Cont-1


title: HHSteC-Cy80-3


title: Patient 13_D0

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

data_processing:
The quality of raw data was checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The  reads were mapped into the human genome (Ensembl GRCh38.p10) using Bowtie 2
HTSeq-counts  were used to count aligned reads
Clustering and differential expression were analyzed using DESeq2 package
Genome_build: Ensembl GRCh38.p10
Supplementary_files_format_and_content: counts, fold-change

source_name: vivax malaria patient_D0

growth_protocol: At Day 1 (diagnosis visit) and Day 42 (convalescence visit), 4 mL of bone marrow aspirates from iliac crest were obtained.

extract_protocol:
CD71+ cells were resuspended in 200 µL of Trizol® reagent and total RNA extracted according to the manufacturers´ instructions
Sample processing for library preparation and sequencing were performed at the CRG genomics facility, Barcelona

treatment_protocol: Magnetic isolation of erythroblasts and young reticulocytes (CD71+ cells) was done with LS columns.

tag: subject status

value: Plasmodium vivax patient

value: bone marrow

value: affinity purified CD71+ cells

tag: time point

value: during the acute attack


title: Stagte 6 ES-Islet [ESSt6]

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

description: Mapped to Human Genome

data_processing:
Data was generated and processed by McDonnell Genome Institute (MGI) at Washington University
Singe Cell RNA sequencing files were processed by Cell Ranger 3.0.2
Genome_build: h_sapien Ensembl_R76
Supplementary_files_format_and_content: Single cell RNA sequencing data presented as matrix files.

source_name: Stagte 6 ES-Islet

growth_protocol: Stem cells were grown and differentiated in SC-Islets as described (Hogrebe et al., Nature Biotechnolony 2020)

extract_protocol:
Transplanted cells were extracted use Miltenyi Mouse Cell Depletion Kit
Library construction for single cell was constructed using 10X Chromium Protocol.

treatment_protocol: SC-Islets were transplanted into the kidney capsul of diabetic mice.

tag: cell type source

value: Stem Cell Derived Islets

value: ES-Derived Islet

tag: Stage

value: In Vitro

tag: kit used

value: Gel Bead Kit v3 (10X Genomics)


title: PLZFneg_adipose1

tag: strain

value: Male

tag: tissue

tag: age

value: 16-22 weeks


title: PLZFpos_adipose2

value: Epididymal adipose

tag: cell type


title: Patient 13_D42

source_name: vivax malaria patient_D42

value: 42 days after drug cure treatment


title: CD11b Ly6C– cult 1

value: male

value: Ly-6C+ CD11b+ cDCs


title: Patient 5_D42


title: CD103 cult 3


title: CD103 cult 2


title: HHSteC-Cy80-1

value: HHSteCs

value: Human hepatic stellate cells

tag: treatment

value: treated with rhCYGB (80 microg/ml) for 48 hours


title: PLZFpos_adipose3

value: PLZF+ {gamma}{delta} T cell subsets


title: PLZFpos_adipose1


title: Transplanted IPS-Islet 2 [IPS2txp]

description: Mapped to Human Genome

source_name: Transplanted IPS-Islet

value: IPS-Derived Islet

value: Transplanted


title: Patient 5_D0

value: Plasmodium vivax patient

value: bone marrow

value: affinity purified CD71+ cells

value: during the acute attack


title: Monocytes fresh 3

value: Monoctes


title: Patient 1_D42


title: input_pSmad3-ChIPseq_rep2

library_source: genomic

data_processing:
bowtie used for alignment.
peaks called using MACS
Genome_build: mm9

extract_protocol:
50 million cells per replicate were cross-linked with 1% formaldehyde for 10 min, then lysed in modified RIPA buffer. Cellular extracts were sonicated using a Covaris B208 ultrasonicator to produce chromatin fragments 100–400 bp in length. Cleared extract was incubated with 10 μg of antibody against phosphoSmad2/3 (abcam ab52903) or nonspecific rabbit IgG control antibody (Cell Signaling) overnight and precipitated using magnetic Protein A Dynabeads (Invitrogen). Beads were washed with ChIP wash buffer and protein–DNA complexes were eluted with 1% SDS, 50 mM NaCOH3, then cross-links were reversed by incubation with 0.2M NaCl at 67 °C overnight. DNA was isolated using Qiagen MinElute columns following the manufacturer's instructions, and used for ChIP-seq library prep.
ChIP–seq libraries were generated using the standard protocol for the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs)

tag: chip antibody


title: Monocytes fresh 2


title: Patient 1_D0


title: input_pSmad3-ChIPseq_rep1


title: Transplanted ES-Islet 3 [ES3txp]

description: Mapped to Human Genome

source_name: Transplanted ES-Islet

value: Stem Cell Derived Islets

value: ES-Derived Islet

value: Gel Bead Kit v3 (10X Genomics)


title: T5224_pSmad3-ChIPseq_rep2

value: 20 uM T-5224 (SelleckChem) 24 hours

value: phospho-Smad2/3 (abcam 52903)


title: Ly6C+ CD11b fresh 3

value: male

value: conventional dendritic cells


title: Transplanted ES-Islet 1 [ES1txp]

description: Mapped to Human Genome


title: A549 RB1 knockout replicate 2

city: Macau

first: Joong

middle: Sup

last: Shim

address: Avenida da Universidade, Taipa

department: Faculty of Health Science

country: Macau

institute: University of Macau

description: Transcriptome profiling for A549 RB1 wild-type vs knockout cell lines.xlsx

data_processing:
The base-calling and alignment were processed by Tophat, the FASTQ data was aligned to GRCh38/hg38 for alignment.
The generation of normlized abundance measurements was performed by cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file was in xlsx format.

source_name: cancer cells

growth_protocol: The cells were cultured with RPMI-1640 medium supplemented with 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol:
The total RNA was extracted by RNAeasy plus mini kit. Then, the mRNA and cDNA were captured from by NEBNext® Ultra™ Directional RNA Library Prep Kit. Finally, the cDNA was transferred to Illumina 2500 sequencer for RNA sequencing.
The mRNA and cDNA were captured from by NEBNext® Ultra™ Directional RNA Library Prep Kit.

treatment_protocol: There's no treatment for the cell lines.

tag: passages

value: knock out


title: Transplanted ES-Islet 2 [ES2txp]

description: Mapped to Human Genome


title: Monocytes fresh 1


title: CD103 cult 1

value: Ly-6C+ CD11b+ cDCs


title: T5224_pSmad3-ChIPseq_rep1


title: TGFB_pSmad3-ChIPseq_rep2

value: 5 ng/ml TGFB3 (Peprotech) 2 hours


title: A549 RB1 knockout replicate 1


title: A549 RB1 wild-type replicate 2

value: wild type


title: single cell RNA seq of human epididymis epithelial tissue [AXH014]

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

data_processing:
CellRanger 1.1
hg19 genome v1.0
Supplementary_files_format_and_content: 10X genomics CellRanger output: UMI count expression values for each gene (rows) in each cell (columns)

source_name: scRNA-seq of HEE tissue

extract_protocol:
A total of 2500–3000 cells were used for scRNA-seq using the 10X Genomics Chromium system.
Chromium Single Cell 3ʹ Library kit

treatment_protocol: Connective tissue and fat were removed from epididymis tissue within ~ 2 hr of surgery and the tissue separated into efferent ducts, caput and corpus according to anatomical features.   Caput tissue was cut into 1-2mm pieces and digested with collagenase (2 mg/mL collagenase + 150 µg/mL DNAse I, both from Worthington Biochemical Corp.) at 37oC for 2 hr with constant shaking. Digesting tissue was then agitated by pipetting, allowed to settle for 4 min and the supernatant collected and stored on ice as cell suspension 1. Fresh collagenase solution was then added to the tissue, which was digested for a further 2 hr with shaking at 37C, with subsequent agitation and settling as before. The supernatant (cell suspension 2) was then pooled with cell suspension 1 and tissue debris removed by passage through a 100 µm cell strainer (Pluristrainer). Following centrifugation (300×g) of the cells they were washed once in PBS and then digested with Accutase (STEMCELL Technologies) for 20-30 min. At this point cells were resuspended by gentle pipetting and examined by phase-contrast microscopy and if cell clumps were still present the Accutase digestion was repeated by adding fresh Accutase after centrifugation. Once single cell digestion was complete the cell pellet was lysed with ammonium chloride solution (310 mM NH4Cl, 23.8 mM NaHCO3 and 0.2 mM EDTA) for 3 min followed by adding 2.5× volume of PBS + 2% fetal bovine serum (FBS) and centrifuged at 300×g for 5 min to remove red blood cells. Epithelial cells collected were washed twice in Hank's Balanced Salt Solution (HBBS) + 2% FBS with centrifugation at (200×g), then resuspended in HBBS and passed through Flowmi cell strainers (40 µm, Bel-Art) to prepare single cells. Cells were counted and then used for single cell RNA-sequencing (scRNA-seq).

value: human epididymis epithelial (HEE) tissue


title: Ly6C+ CD11b fresh 2


title: Transplanted IPS-Islet 1 [IPS1txp]

description: Mapped to Human Genome

value: IPS-Derived Islet

value: Transplanted


title: A549 RB1 wild-type replicate 1


title: Ly6C+ CD11b fresh 1


title: single cell RNA seq of human epididymis epithelial tissue [AXH009]


title: single cell RNA seq of human epididymis epithelial tissue [AXH012]


title: dnTCF4 3

city: Prague

first: Petr

last: Danek

address: Videnska 1083

department: Laboratory of Hemato-oncology

country: Czech Republic

institute: Institute of Molecular Genetics of the CAS

description:
dn3
processed data file: Danek_GEO_RPKM.csv

data_processing:
Fastq files were aligned to mm10 version of mouse reference genome GRCm38 using STAR.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm.
Expression data normalization and differential gene expression were performed using DEseq2 in R.
After summarizing the reads, RPKM was calculated with edgeR extracting the gene length from the Gencode GTF version M16.
Genome_build: mm10 version of GRCm38 reference genome.
Supplementary_files_format_and_content: Danek_GEO_RPKM.csv: Comma-separated file (csv) containing RPKM values.

source_name: ST-HSC

extract_protocol:
BM cells were extracted by grinding long bones, pelvis, and spine and ST-HSC were sorted on Influx instrument (BD Biosciences, San Jose, CA, USA) into Tri Reagent RT (Molecular Research Center, Cincinnati, OH, USA. RNA was extracted using RNeasy MinElute Cleanup Kit (Qiagen, Venlo, Netherlands).
cDNA was synthesized from 20 ng of extracted RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio Inc., Mountain View, CA, USA). Sequencing libraries were constructed using Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA, USA) following manufacturer’s instructions.

value: Primary Lin- ckit+ CD48+ CD150- cells

tag: background strain

tag: genotype


title: CD11b Ly6C– fresh 3


title: dnTCF4 2

description:
dn2
processed data file: Danek_GEO_RPKM.csv


title: CD11b Ly6C– fresh 2


title: CD11b Ly6C– fresh 1


title: WT 1

description:
wt1
processed data file: Danek_GEO_RPKM.csv


title: WT 2

description:
wt2
processed data file: Danek_GEO_RPKM.csv


title: WT 3

description:
wt3
processed data file: Danek_GEO_RPKM.csv


title: CD103 fresh 3


title: CD103 fresh 2


title: CD103 fresh 1


title: HeLa_hypoxia_6h_meRIP-seq

city: Guangzhou

first: Yan-Jie

last: Wang

address: 107, West Yanjiang Road

country: China

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
Sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR (version 020201)
For meRIP-seq data, exomePeak software (version 3.10) was used for m6A peak calling, and m6A peaks were annotated by Homer (version 4.9)
Genome_build: hg19
Supplementary_files_format_and_content: bw and FPKM data for RNA-seq samples

source_name: Cervical cancer cells

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1 × penicillin-streptomycin (Beyotime) and maintained in a 5% CO2 and 95% air incubator [20% (vol/vol) O2]. For hypoxia exposure, cells were placed in a modular incubator chamber (MART) filled with a hypoxic gas mixture containing 1% O2, 5% CO2, and 94% N2 for various time periods.

extract_protocol: For meRIP-seq, the libraries were constructed by Truseq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions and quantified by BioAnalyzer High Sensitivity DNA chip, and then deeply sequenced on the Illumina HiSeq X10 to generate 150-bp paired-end reads. For RNA-seq library, mRNA enrichment, cDNA synthesis, adaptor addition, circularization, PCR amplification and library examination were performed on the BGIseq 500 at Beijing Genome Institute (BGI; Shenzhen, China)

treatment_protocol:
Total RNA from the indicated samples was extracted using TRIZol reagent (Invitrogen Life Technologies) according to the manufacturer’s instruction. All samples were treated with DNase I to avoid genomic DNA contaminations.
poly(A)+ RNA was isolated from total RNA using Oligotex mRNA Kits and subsequently fragmented into around 150 nt fragments using the RNA fragmentation buffer (20 mM Tris-HCl, pH 7.4, 20 mM ZnCl2) at 94 ℃ for 40 s. The reaction was then stopped with 0.05 M EDTA. For m6A-IP, 2 μg fragmented RNA was incubated with 3 μg anti-m6A antibody (Abcam) in immunoprecipitation buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% Igepal CA-630) supplemented with RNase inhibitor for 2 h at 4 ℃. Then the above mixture was incubated with 20 μl protein A/G beads (Thermo Fisher Scientific, #88803) for additional 2 h at 4 ℃ on a rotating wheel. After washing 5 times with immunoprecipitation buffer, bound RNA was extracted by proteinase K digestion, phenol-chloroform extraction followed by standard ethanol precipitation.

value: HeLa

value: Cervical cancer cells

tag: merip antibody

value: N6-methyladenosine (Abcam, ab151230)


title: TGFB_pSmad3-ChIPseq_rep1

source_name: ASZ001 murine BCC cell line


title: 3: control in OGD condition

city: Chongqing

first: Zhong

last: Jianjun

address: NO.1 Youyi Road, Yuzhong District, Chongqing

department: Neurosurgery Department

institute: The first Affiliated Hospital of Chongqing Medical University

description: Sample 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2 with parameters read-mismatches=2，read-gap-length=2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: HT22 cells

growth_protocol: HT22 cells were cultured in Dulbecco’s Modified Eagle’s Medium.

extract_protocol:
Total RNA was harvested from HT22 cells and RNA integrity was assessed and judged by A260/A280. Then the total RNA was fragmented into ~200 base pair (bp) units. RNA fragments were used to generate double-stranded cDNA, and then single strand of cDNA labeled by deoxy-UTP, which was enriched by PCR for 12 cycles.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Firstly, adenovirus was diluted to 2×10*6 pfu/mL with culture medium to infect HT22 cells 2 h after seeding. Secondly, a special culture medium without glucose was used to induce oxygen/glucose-deprivation (OGD) conditions (which lasted for 6 h), and all O2 was replaced with N2.

value: infected with control adenovirus

tag: condition

value: in oxygen-glucose-deprived condition


title: HeLa_hypoxia_12h_meRIP-seq

tag: cell line


title: 4: AK046375 knockdown in OGD condition

description: Sample 4

value: infected with adenovirus to knockdown AK046375


title: 1: control in normal condition

description: Sample 1

value: in normal condition


title: HeLa_hypoxia_24h_meRIP-seq


title: 2: AK046375 knockdown in normal condition

description: Sample 2


title: HeLa_normoxia_meRIP-seq


title: dnTCF4 1

description:
dn1
processed data file: Danek_GEO_RPKM.csv


title: 222_US

status: Public on Aug 24 2020

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

description:
small RNA
pooled RNA from symptomatic leaves

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC Program and CLC Genomic Workbench 11
Trimming of raw reads was performed using the CLC Genomic Workbench 11
Removing redundant reads using the CLC Genomic Workbench 11
Supplementary_files_format_and_content: trimmed redundant list, each read with its number of counts

organism: Panicum miliaceum

source_name: leaf

extract_protocol:
phenol-chloroform extraction method
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

value: leaf

tag: plant source

value: samples derived from symptomatic plant


title: 221_BA


title: Iso_seq_10_oocyte_3

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: applying single cell method to 10 merged oocytes

data_processing:
Illumina Casava1.7 software used for basecalling.
5' and 3' sequences were extracted from paired-end sequences using Perl, Python and shell script
5' and 3' sequences were aligned  to mm10, using STAR (2.6.1a), with with parameters (--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.6 --outFilterMatchNminOverLread 0.6).
Peaks were called with CAGEr (v 1.24.0) .
For smart-seq2 data, sequenced reads were trimmed for adaptor sequence using cutapapt (v 1.18) and aligned to mm10 using STAR  with with parameters as described above.
For Iso-seq data, sequence data were processed using the SMRTlink5.0 software. Circular consensus sequence (CCS) was generated from subread BAM files, parameters: min_length 200, max_drop_fraction 0.8, no_polish TRUE, min_zscore -9999, min_passes 1, min_predicted_accuracy 0.8, max_length 18000. CCS.BAM files were  classified into full length and non-full length reads using pbclassify.py script, ignore polyA false, minSeq Length 200. Non-full length and full-length fasta files produced were then fed into the cluster step, which does isoform-level clustering(ICE), followed by final Arrow polishing, hq_quiver_min_accuracy 0.99, bin_by_primer false, bin_size_kb 1, qv_trim_5p 100, qv_trim_3p 30.
Additional nucleotide errors in consensus reads were corrected using the Illumina RNA seq data with the software LoRDEC.
consensus reads were aligned to reference Genome using GMAP with parameters --no-chimeras --cross-species --expand-offsets 1 –B 5 –K 50000 –f samse –n 1 against reference genome.
Gene structure analysis was performed using TAPIS pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: [scRCAT-seq] tc*.txt reports the region and the normalized RPM values of each peak.
Supplementary_files_format_and_content: [Iso-seq] *gtf reports the isoform information which were detected by Iso-seq.

source_name: oocyte

extract_protocol:
DRG, oocytes, hESC, HEK293T, ARPE, mESC, hESC_drived_organoid were dissected and dissociated into single cells. hESC, HEK293T, ARPE, mESC, hESC_drived_organoid were dissected respectively and mixed together.
The scRCAT-seq library was prepared according to the scRCAT-seq protocol.
The smart-seq2 library was prepared according to the smart-seq2 protocol.
The Iso-Seq library was prepared according to the Isoform Sequencing protocol.

value: oocyte


title: Iso_seq_10_oocyte_2


title: CAF10

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Samples were hybridized to Agilent human genome CGH+SNP Microarrays (Agilent Technologies)

scan_protocol: Scanning with an Agilent G2505C Microarray Scanner (Agilent Technologies)

data_processing: Image and data processing were performed using Feature Extraction software version 12 (Agilent Technologies) and Agilent Genomic Workbench version 7 (Agilent Technologies). Aberrant regions were detected using ADM-2 algorithm with threshold set to 6. To avoid false positive calls the minimum number of consecutive probes for amplifications/deletions was set to 3, together with a minimum average absolute Log Ratio ≥ 0.25.

source_name: Cancer Associated Fibroblast (CAF)

label_protocol: CAF samples were labeled with Cy5 and  reference genome (Promega) was labeled with Cy3

extract_protocol: Total DNA was isolated from CAFs using a DNeasy blood and tissue kit (Qiagen).

tag: strain id

value: strain 10

tag: source gender

value: Female

value: Cancer Associated Fibroblast (CAF)

tag: passage

value: 2nd passage after tumor dissociation

source_name: reference genome

tag: sample type

value: pooled reference genome (Promega)

tag: gender


title: Iso_seq_10_oocyte_1

tag: strain

tag: tissue


title: Iso_seq_single_oocyte_2

description: applying single cell method to oocyte


title: Iso_seq_single_oocyte_3

description: applying single cell method to oocyte


title: fun30 rep3

city: Shanghai

first: Yan

last: Zhu

address: 2005, Songhu Road

department: Biochemistry

institute: Fudan University, School of life sciences

description: Gene expression in fun30 mutant

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 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried 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) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: fun30 mutant, 12-day-old seedling, rep3

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.

growth_protocol: Standard Arabidopsis growth condition

extract_protocol: RNA was extracted from seedlings by using the TRIzol kit according to standard procedures (Invitrogen). Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: without additional treatment

value: 12-day-old seedling

value: fun30 mutant


title: Iso_seq_single_oocyte_1

description: applying single cell method to oocyte


title: fun30 rep2

description: Gene expression in fun30 mutant

source_name: fun30 mutant, 12-day-old seedling, rep2


title: Iso_seq_single_DRG_2

description: applying single cell method to DRG neuron

source_name: Dorsal root ganglion neuron

value: Dorsal root ganglion neuron


title: fun30 rep1

description: Gene expression in fun30 mutant

source_name: fun30 mutant, 12-day-old seedling, rep1


title: WT rep1

description: Gene expression in WT

source_name: WT, 12-day-old seedling, rep1

value: WT


title: WT rep2

description: Gene expression in WT

source_name: WT, 12-day-old seedling, rep2


title: CAF9

value: strain 9

value: Male

tag: cell type


title: CAF8

value: strain 8


title: 22-RR_22-279622369

city: Gainesville

first: Kyulim

last: Lee

address: 1395 Center Drive

institute: University Florida

description: repeat 3 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Genome_build: CP013651.1
Supplementary_files_format_and_content: Counts obtained from step 6: htseq-count, listed along side each open reading frame

organism: Streptococcus sp. A12

source_name: Whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in BHI medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.4)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

tag: treatment

value: grown in BHI to OD600 nm = 0.4

value: pcfR mutant A12 strain


title: Iso_seq_single_DRG_1


title: 2-WT_2-279627369

description: repeat 2 of 3

value: A12 wild-type


title: 14-HK_14-279620371

description: repeat 2 of 3

value: pcfK mutant A12 strain


title: 20-RR_20-279623370

description: repeat 1 of 3


title: 1-WT_1-279620366

description: repeat 1 of 3


title: 3-WT_3-279590199

description: repeat 3 of 3


title: 1_rep3 [p3138_o6708/15]

city: Zurich

first: Weihong

last: Qi

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETHZ

data_processing:
Raw reads were trimmed and filtered using fastp version version 0.20.0
Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
Trancript level normalized counts were generated using kllisto version 0.44.0
Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)

source_name: Hepa1-6_saKKH-CBE3 + RFP_48h

extract_protocol: TruSeq RNA stranded

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

value: mRNA transfection

tag: genotype/variation

value: saKKH-CBE3 + RFP


title: 13-HK_13-279626370

description: repeat 1 of 3

tag: genotype


title: 0_5_rep3 [p3138_o6708/16]


title: WT rep3

description: Gene expression in WT

source_name: WT, 12-day-old seedling, rep3


title: 21-RR_21-279592147

description: repeat 2 of 3


title: 0_rep3 [p3138_o6708/18]

value: RFP


title: Tg_Intestine

city: Houston

first: Yuan

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

description: scRNAseq

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger V3.0 mkfastq
cellranger V3.0 count
reads are mapped to mm10
UMI counts are summarized are gene expression levels
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each Sample

growth_protocol: Single cell suspensions are made from fresh mouse small intestine

extract_protocol:
RNAs are extracted from single cell suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)

value: Mdm2+/- Cag-CreERTg

tag: age

value: 60 days post-natal

value: Fresh small intestine


title: 0_25_rep3 [p3138_o6708/17]


title: FMTg_Intestine

description: scRNAseq

value: Mdm2FM/- Cag-CreERTg


title: 2_rep3 [p3138_o6708/14]


title: 15-HK_15-279591154

description: repeat 3 of 3


title: 0_rep2 [p3138_o6708/12]


title: 4_rep3 [p3138_o6708/13]


title: 0_25_rep2 [p3138_o6708/11]


title: 0_5_rep2 [p3138_o6708/10]


title: 1_rep2 [p3138_o6708/9]


title: 4_rep2 [p3138_o6708/7]


title: 0_rep1 [p3138_o6708/6]


title: 0_5_rep1 [p3138_o6708/4]


title: 0_25_rep1 [p3138_o6708/5]


title: 1_rep1 [p3138_o6708/3]


title: 2_rep1 [p3138_o6708/2]


title: 4_rep1 [p3138_o6708/1]


title: 2 m after AAV injection [p3138_5721/22]

description:
20190725.B-22
20191015.B-22

source_name: Pah-enu2_2 m after AAV injection

value: Liver

value: adeno-associated virus (AAV)


title: 2 m after AAV injection [p3138_5721/21]

description:
20190725.B-21
20191015.B-21


title: FACS-sorted fetal liver Eto2 mut-1-S0 med

city: bethesda

first: Xiang

last: Guo

address: 50 south drive, blg50

institute: NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 and mm10  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.22.1
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample

source_name: Fetal livers

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (human K562 cells) and PicoPure RNA isolation kit (fetal liver cells)
RNA sequencing libraries were generating from 1 ug (K562 cells and total fetal liver cells) or 10 ng (FACS sorted fetal liver cells) of RNA using Illumina TruSeq  mRNA Library Preparation kit following manufacturer’s protocol.

value: Fetal livers

value: embryonic day 14.5


title: 48 h  after LNP injection [p3138_5721/19]

description:
20190725.B-19
20191015.B-19

source_name: Pah-enu2_48 h  after LNP injection

value: lipid nanoparticle (LNP)


title: 48 h  after LNP injection [p3138_5721/16]

description:
20190725.B-16
20191015.B-16


title: 16 m after AAV injection [p3138_5721/15]

description:
20190725.B-15
20191015.B-15

source_name: Pah-enu2_16 m after AAV injection


title: 16 m after AAV injection [p3138_5721/14]

description:
20190725.B-14
20191015.B-14


title: 16 m after AAV injection, no sgRNA [p3138_5721/10]

description:
20190725.B-10
20191015.B-10

source_name: Pah-enu2_16 m after AAV injection, no sgRNA


title: 16 m after AAV injection, no sgRNA [p3138_5721/11]

description:
20190725.B-11
20191015.B-11


title: 16 m after AAV injection, no sgRNA [p3138_5721/9]

description:
20190725.B-9
20191015.B-9


title: 1 m after LNP injection [p3138_5721/8]

description:
20190725.B-8
20191015.B-8

source_name: Pah-enu2_1 m after LNP injection


title: 1 m after LNP injection [p3138_5721/7]

description:
20190725.B-7
20191015.B-7


title: 16 m after AAV injection [p3138_5721/12]

description:
20190725.B-12
20191015.B-12


title: 16 m after AAV injection [p3138_5721/13]

description:
20190725.B-13
20191015.B-13


title: 2_rep2 [p3138_o6708/8]


title: 1 m after LNP injection [p3138_5721/6]

description:
20190725.B-6
20191015.B-6


title: Untreated [p3138_5721/4]

description:
20190725.B-4
20191015.B-4

value: Untreated


title: 1 m after LNP injection [p3138_5721/5]

description:
20190725.B-5
20191015.B-5


title: Untreated [p3138_5721/3]

description:
20190725.B-3
20191015.B-3


title: Untreated [p3138_5721/1]

description:
20190725.B-1
20191015.B-1


title: Untreated [p3138_5721/2]

description:
20190725.B-2
20191015.B-2


title: succinate_colon [4171_11]

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods  (the filtering code available at: https://github.com/KenLauLab/scRNAseqQC).
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al. 2019 - BioRxiv) Biological read: read2 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

growth_protocol: primary cells

extract_protocol:
Mouse epithelial cell suspensions were obtained by EDTA extraction and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on Novaseq6000 with a 2x150 paired-end kit standard run

tag: strain background

value: wild type

value: succinate

value: colon

value: primary epithelial cells


title: succinate_terminal ileum [4171_2]

source_name: succinate_terminal ileum

value: terminal ileum


title: succinate_terminal ileum [4171_6]


title: 48 h  after LNP injection [p3138_5721/18]

description:
20190725.B-18
20191015.B-18


title: 48 h  after LNP injection [p3138_5721/17]

description:
20190725.B-17
20191015.B-17


title: water_colon [4171_10]

value: water


title: succinate_terminal ileum [4171_9]


title: 2 m after AAV injection [p3138_5721/20]

description:
20190725.B-20
20191015.B-20


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_1_CEMBA180320_3E_2_A3_AD004_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PIR

tag: Sex

value: male


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H9_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_1_CEMBA180320_3E_2_A3_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H9_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H9_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H9_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H9_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H8_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H8_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H8_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H9_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H9_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H9_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H8_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H8_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_1_CEMBA180320_3E_2_B7_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H7_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H8_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H8_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H8_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H7_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_1_CEMBA180320_3E_2_A11_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H7_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H5_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H5_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H5_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H7_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H5_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H5_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H5_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H5_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H4_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H5_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H4_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H4_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H4_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H3_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H4_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H4_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H7_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H3_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H7_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H7_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H3_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H4_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H2_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H3_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H4_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H2_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H3_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H3_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H3_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H2_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H2_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H1_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H2_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H2_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H1_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H2_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H1_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H1_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H1_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H1_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H12_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H1_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H12_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H11_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H10_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H1_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H10_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H12_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H11_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H10_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_G9_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_H10_AD012_indexed


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title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_D3_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_D3_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_D3_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_D3_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180320_3E_3_CEMBA180320_3E_4_D4_AD010_indexed