title: hippocampus_phenytoin-Resistant_rep14

city: Braine-l'Alleud

first: Jonathan

last: van Eyll

address: UCB Pharma - Building S2C

department: NewMedicines

country: Belgium

institute: UCB Pharma

hyb_protocol: 750 ng of biotinylated cRNA was hubridized onto Illumina MouseRef-8 v2 (Illumina, Inc., San Diego, CA, USA). Hybridization and washing were performed according to Illumina Manual Direct Hybridization Assay Guide.

scan_protocol: Scanning was performed using Illumina's iScan (). Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 Gene expression software with default settings (no background substraction and no normalization).

data_processing: QC and normalization of microarray data were performed using “Lumi” package in R- Bioconductor. Briefly, samples that passed QC were Log2-transformed and normalized by quantiles between chips. Only QC passed samples are provided in this dataset.

source_name: Male NMRI mouse hippocampus from resistant to phenytoin

label_protocol: Biotinylated (Biotin-16-UTP) cRNA was prepared using the Illumina TotalPrep RNA Amplification kit (Ambion, Inc., Austin, TX, USA) according to manufacturer's protocol with an input of 200 ng of total RNA

extract_protocol: Snap frozen hippocampi (n=15/group) from selected mice were homogenized in RLT buffer (Qiagen, 74134) using precellys® system in CK14 tubes following manufacturer’s instructions. Total RNA was obtained from mouse hippocampi using RNeasy Plus Mini Kit (Qiagen, 74134) following manufacturer’s instructions. RNA concentration was measured with a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: Mice were phenotyped for their response to phénytoin (PHT) using a 6Hz stimulation protocol. Mice were divided in 2 groups of interest, PHT responders and PHT non-responders.

value: NMRI

tag: gender

value: Male

value: Hippocampus

value: Adult - 12 weeks


title: Crypt_FVR_high_rep1

status: Public on Sep 11 2020

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from crypt cells with high expression of FVR

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G

data_processing: Expression console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including median polish and sketch-quantile normalisation). The 18 samples have been normalized together but RMA data provided for only 6 samples.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Crypt cells with high expression of FVR, pool derived from 2 animals

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: No growth

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: Small intestinal crypts were isolated from FltpZV/+ mice. Single cells were pepared and FAC-sorted according to the GFP level.

tag: tissue

value: small intestinal crypts

tag: strain

tag: age

value: 4 months

tag: genotype

value: FltpZV/+


title: Control at 5 days, rep 3 [CT_5D_REP3_ATGTCA]

type: SRA

city: Institute

first: Sridhar

middle: A

last: Malkaram

state: West Virginia

address: Barron Drive

department: Mathematics and Computer Sciences

country: USA

institute: West Virginia State University

library_source: transcriptomic

data_processing:
The fastq read files were quality checked using using fastqc ver. 0.11.5 and 3-prime end trimmed for the Illumina TruSeq adapters and low quality bases (phred score < 20) using trimgalore ver. 0.4.4. The reads were then aligned to the Chicken genome (ensemblgenomes Gallus gallus ver. 5.0.88) using Hisat2 ver. 2.0.5 and bowtie2 ver. 2.3.2.
The aligned reads from each sample were then assembled using stringtie ver. 1.3.3b and the ensembl gene annotation file for Gallus gallus genome version 5.0.88. A second stringtie run was used to create merged assembly combining the individual sample assemblies.
Finally stringtie was again run using the merged assembly as the reference annotation.
A table of gene expression abundances for each sample was prepared using custom perl scripts. Differential expression analysis was done using the DESeq2 package in R ver 3.3.1.
The time,  nicotine treatment, and the time:nicotine interaction variables were included in the DESeq2's model. Differential expression comparisons were made for the effect of time, effect of nicotine and the interaction effect of nicotine and time. Genes with a multiple testing adjusted p-value cutoff of < 0.05 were considered as significant.
Genome_build: ensemblgenomes Gallus gallus ver. 5.0.88
Supplementary_files_format_and_content: gene expression abundances for each sample (*.matrix); CSV format of Processed results for DESeq2 differential expression (*.all.csv).

organism: Gallus gallus

source_name: Control at 5 days_spinal cord

growth_protocol: Two cohorts of 24 fertile specific pathogen-free eggs of the domestic chicken were obtained from Charles River Laboratories (Catskill, New York, USA). Eggs were randomly assigned to treatment and control cohorts.

extract_protocol:
At the time point of sacrifice (5 or 7 days), egg shells were chipped off and the animals’ viability and proper development was verified. The verification of viability was based on observation of a heartbeat. Appropriate development and lack of gross abnormalities in animals were also verified (Hamburger and Hamilton 1951).  Embryos (randomly selected 4 biological replicates for each treatment and time point) were harvested in RNAse- free conditions and dissected in cold DEPC-treated PBS. The section between the mid portion of the neck and posterior border of the anterior limb was cut out. A part of this section containing spinal cord was dissected using fine scissors, tweezers, and glass needles and then placed into a 1.5 ml tube filled with ice-cold DEPC-treated PBS. The samples were homogenized in TRI Reagent® or Trizol®(Sigma) and RNA extraction was completed using Ambion® PureLink® RNA Mini Kit (all reagents were obtained from Sigma-Aldrich (St. Louis, Missouri, USA)).  All RNA samples were stored at -80 °C before being shipped to Marshall University Genomics and Bioinformatics Core (GABC) where the expression analysis was conducted.
The RNA samples were sequenced (2 x 50 Paired End sequencing, 25 million reads per library) at  Marshall University, WV, genomics core facility
Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,   AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,

treatment_protocol: Nicotine (nicotine hydrogen bitartrate calculated as free base) and vehicle chemicals (sodium bitartrate monohydrate) were obtained from Sigma-Aldrich (St. Louis, Missouri, USA).  Nicotine doses of 30 ng/ml and corresponding doses of vehicle control were calculated according to the weight of the egg. The injections were delivered from the blunt pole of the egg before incubation as described previously (Dalgic, Armagan et al. 2009). The drugs were dissolved in Chicken Ringer's solution and sterilized before injection using .22µm Millex® syringe filter units (Sigma-Aldrich, St. Louis, Missouri, USA).

tag: breed

value: Domestic chicken

tag: genotype/variation

value: wild type

tag: treated with

value: Spinal cord section


title: Crypt_FVR_low_rep1

description: Gene expression data from crypt cells with low expression of FVR

hyb_protocol: According to the Affymetrix expression protocol

source_name: Crypt cells with low expression of FVR, pool derived from 2 animals


title: hippocampus_phenytoin-Responder_rep13

source_name: Male NMRI mouse hippocampus from responder to phenytoin


title: Crypt_FVR_high_rep2


title: Control at 5 days, rep 2 [CT_5D_REP2_AGTTCC]

value: vehicle chemicals (sodium bitartrate monohydrate)


title: Crypt_FVR_neg_rep2

description: Gene expression data from crypt cells not expressing FVR

source_name: Crypt cells not expressing FVR, pool derived from 2 animals


title: Crypt_FVR_low_rep2


title: Control at 5 days, rep 1 [CT_5D_REP1_AGTCAA]


title: hippocampus_phenytoin-Resistant_rep15


title: NCoRw-418

city: Davis

first: Michael

middle: L

last: Goodson

state: CA

address: One Shields Ave

institute: University of California Davis

data_processing:
Base calling was done using Illumina Casava
Aligned to GRCM38 (mm10) genome using Salmon
Normalized read counts per gene were extracted from the Salmon quantification file using the R packages TXI and DESeq2
Differential gene expression for specific comparisons (constrasts) were calculated using DESeq2
Genome_build: GRCM38 (mm10)

source_name: Liver

growth_protocol: Adult male mice fed either a low (10% kcal) or a high (60% kcal) fat diet for 17 weeks.

extract_protocol:
Qiagen RNEasy
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: male

value: liver

value: 25 weeks

tag: diet

value: HFD

value: DKO


title: NCoRw-426

value: WT


title: NCoRw-430

value: LFD


title: NCoRw-421


title: NCoRw-417


title: hippocampus_phenytoin-Responder_rep15

value: NMRI

value: Male


title: hippocampus_phenytoin-Responder_rep14

value: Hippocampus

value: Adult - 12 weeks


title: Nicotine-treated at 5 days, rep 4 [NI_5D_REP4_CTTGTA]

source_name: Nicotine at 5 days_spinal cord

value: Nicotine (nicotine hydrogen bitartrate)


title: Crypt_FVR_neg_rep1

value: small intestinal crypts

value: 4 months

value: FltpZV/+


title: hippocampus_phenytoin-Resistant_rep13


title: hippocampus_phenytoin-Responder_rep12


title: mTmG_42_rep4

description: Gene expression data from Flattop expressing intestinal crypt cells

hyb_protocol: According to the Affymetrix expression protocol including minor modifications as suggested in the Encore Biotin protocol

data_processing: RMA normalized using R/Bioconductor package oligo (version 1.38.0)

extract_protocol: miRNeasy Micro Kit (Qiagen)

treatment_protocol: As described in the paper. Briefly, single cells were pepared and FACS-sorted

value: mixed C57BL/6J, CD1, 129/SvJ

value: 3-6 months

value: FltpT2AiCre crossed with Gt(ROSA)26mTmG


title: hippocampus_phenytoin-Resistant_rep12


title: NCoRw-416

value: male

value: liver


title: mTmG_08_rep2

source_name: Flattop expressing intestinal crypt cells


title: mTmG_04_rep1


title: hippocampus_phenytoin-Resistant_rep11


title: Nicotine-treated at 5 days, rep 3 [NI_5D_REP3_GGCTAC]

value: Domestic chicken

value: wild type

value: Spinal cord section


title: NCoRw-409

value: 25 weeks

value: LFD

value: DKO


title: mTmG_38_rep3


title: NCoRw-406


title: NCoRw-407


title: small intestinal crypt cells, FVF enrichment, 50:50 mix with live crypt cells [CD3 ]

city: Garching

first: Maren

last: Büttner

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

data_processing:
The 10X Genomics core computational software Cellranger v.2.1 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment. (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
For QC, filtering, normalization, and doublet exclusion the scanpy python package v.1.3.1, anndata v0.6.1 and scrublet v.0.1 were used.
Genome_build: mm10
Supplementary_files_format_and_content: anndata (annotated data matrix) object saved in h5ad-file format. The file contains the preprocessed, normalized and annotated count data of all experiments.
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.

molecule: polyA RNA

source_name: small intestine

extract_protocol: Small intestines were removed, washed with cold PBS and villi were scraped off with a glass slide. The remaining tissue was cut into 2-cm pieces, washed several times with cold PBS and incubated in 2 mM EDTA/PBS for 35 min at 4 °C. Subsequently, crypts were harvested by rigorous shaking and filtered through a 70-µm mesh to remove villous fragments. For single cell suspension, isolated crypts were incubated with TrypLE (Life technologies, #12605) for 5 min on ice and then 5 min at 37 °C and treated with 10 µg/ml DNase in crypt complete medium (DMEM/F-12 containing 10 % FCS) for 5 min at 37 °C.

value: small intestine

value: Foxa2 FVF/FVF


title: small intestinal crypt cells, FVF enrichment, 50:50 mix with live crypt cells [CD2]


title: NCoRw-405


title: Nicotine-treated at 7 days, rep 1 [NI_7D_REP1_ATCACG]

source_name: Nicotine at 7 days_spinal cord

value: Nicotine (nicotine hydrogen bitartrate)


title: Lgr5_GFPhigh_45_rep5

description: Gene expression data from intestinal stem cells expressing high levels of Lgr5 and GFP

source_name: Intestinal stem cells expressing high levels of Lgr5 and GFP


title: NCoRd-512

value: OKO


title: Lgr5_GFPhigh_46_rep6


title: Nicotine-treated at 5 days, rep 2 [NI_5D_REP2_TAGCTT]


title: small intestinal crypt cells, FVF enrichment, 50:50 mix with live crypt cells [CD1]


title: hippocampus_phenytoin-Resistant_rep10

value: NMRI

value: Male

value: Hippocampus

value: Adult - 12 weeks


title: NCoRd-513

value: HFD


title: Lgr5_GFPhigh_44_rep4

value: 3-6 months


title: small intestinal crypt cells, FVR enrichment, 10:90 mix with whole crypt cells [Mutant_4_FVR]

value: C57BL/6, Balbc

value: Celsr1crsh/+; FltpZV/ZV,


title: NCoRd-509

value: male

value: liver


title: hippocampus_phenytoin-Responder_rep10


title: hippocampus_phenytoin-Responder_rep9


title: hippocampus_phenytoin-Resistant_rep9


title: Lgr5_GFPhigh_03_rep3


title: small intestinal crypt cells, FVR enrichment, 10:90 mix with whole crypt cells [Mutant_3_FVR]


title: Lgr5_GFPhigh_01_rep1


title: hippocampus_phenytoin-Responder_rep8


title: mN82R

city: Aarhus C

first: Thomas

middle: B

last: Hansen

state: State...

address: C.F. Moellers Alle 3, build 1130

country: Denmark

institute: MBG, Aarhus University

data_processing:
circRNA prediction was conducted using find_circ, ciri2 (v2.0.6) and circExplorer2 (v2.3) using default settings
Genome_build: mm10
Supplementary_files_format_and_content: Merged raw counts provided by ciri2, find_circ or circexplorer2

source_name: neurons_RNAseR treated

growth_protocol: E14 mESCs were grown on 0.1% gelatin coated plates in 2i medium36 containing: DMEM/F12 (Gibco, 31331) and Neurobasal (Gibco, 12348) 1:1, N2 supplement (Gibco, 17502048), B27 supplement (Gibco, 17504044),  1X glutaMax (Gibco, 35050061), 1X penicilin/streptomycin (Gibco, 15140122), 1 mM sodium pyruvate (Gibco, 11360070), 50 nM 2-mercaptoethanol (Gibco, 31350010), nonessential amino acids (Gibco, 11140076), LIF, 3 μM GSK3 inhibitor (CHIR-99021) and 1 μM MEK inhibitor (PD0325901). They were differentiated into neurons as previously described.

extract_protocol:
20 µg TriZOL purified RNA from each sample was depleted of rRNA using a Ribo-Zero rRNA Magnetic Kit (Epicentre) including the optional RiboGuard RNase inhibitor according to manufacturer’s protocol. The concentration was normalised so that each sample contained the same amount of RNA. To 1/3 of the sample 1/10 of the recommended amount of spike-in (ERCC RNA spike-in mix, Ambion) was added, ethanol precipitated, and resuspended in ‘Elute, fragment, finish mix’ (Illumina). The remaining 2/3 of the sample was ethanol precipitated and resuspended in 15 µl nuclease free water. The sample was heated to 70˚C for 1 min and incubated on ice for 2 min. 5 µl RNase R mixture (Epicentre) was added to the sample before incubation at 37˚C for 30 min. RNase R was removed by phenol/chloroform extraction. The RNA was resuspended in ‘Elute, fragment, finish mix’ (Illumina).
Sequencing libraries were prepared using Truseq stranded RNA LT kit (Illumina) from both Ribo-Zero and Ribo-Zero/RNase R samples, by fragmentation, 1st and 2nd strand cDNA synthesis, 3’-end adenylation, ligation of adaptors, and enrichment of DNA fragments using the manufacturer’s protocol
The samples were sequenced using the Illumina Illumina HiSeq 2500 platform with 100 bp paired-end reads (AROS Applied Biotechnology)

tag: cell type

value: differentiated glutamatergic neurons

tag: treatment

value: RNAseR treated

tag: ribo-depletion

value: Ribo-Zero


title: mN82

value: Untreated


title: Lgr5_GFPhigh_02_rep2


title: hippocampus_phenytoin-Resistant_rep8


title: hippocampus_phenytoin-Resistant_rep7


title: mN81R


title: small intestinal crypt cells [Mutant_1]

value: small intestine


title: mNPC2R

source_name: mNPC_RNAseR treated

value: Neural progenitor cells


title: NCoRd-505

value: 25 weeks

value: LFD

value: OKO


title: mNPC2


title: small intestinal crypt cells [Mutant_2]


title: mN81


title: small intestinal crypt cells, FVR enrichment, 90:10 mix with whole crypt cells [Control_7_FVR]

value: FltpZV/+


title: hippocampus_phenytoin-Responder_rep11

value: NMRI

value: Male

value: Hippocampus

value: Adult - 12 weeks


title: hippocampus_phenytoin-Responder_rep6


title: small intestinal crypt cells, FVR enrichment, 50:50 mix with whole crypt cells [Control_5_FVR]

value: C57BL/6, Balbc


title: hippocampus_phenytoin-Responder_rep7


title: NCoRd-504

value: male


title: NCoRd-507

value: liver

value: HFD


title: mNPC1R

value: RNAseR treated


title: hippocampus_phenytoin-Resistant_rep6


title: hippocampus_phenytoin-Resistant_rep5


title: hippocampus_phenytoin-Responder_rep4


title: mESC2R

source_name: mESC_RNAseR treated

value: Embryonic Stem Cells

value: Ribo-Zero


title: mNPC1

value: Untreated


title: hippocampus_phenytoin-Resistant_rep4


title: C57BL-6N-326

value: WT


title: hippocampus_phenytoin-Responder_rep5


title: small intestinal crypt cells, FVR enrichment, 10:90 mix with whole crypt cells [Control_4_FVR]

value: small intestine


title: C57BL-6N-324

value: 25 weeks


title: mESC2


title: small intestinal crypt cells [Control_1]

value: wildtype


title: small intestinal crypt cells, FVR enrichment, 10:90 mix with whole crypt cells [Control_3_FVR]

value: FltpZV/+


title: small intestinal crypt cells [Control_2]


title: mESC1R


title: s36_BMMs_cKO_neg

city: Baltimore

first: Vivek

last: Thumbigere Math

state: MD

address: 650 W Baltimore Street

department: Periodontics

institute: Universityof Maryland

data_processing:
Convert from BCL and demultiplex using Casava 1.8.4 or bcl2fastq 2.17.1
Sorted cells: Map to mm10 using HISAT2
Sorted cells: calculate normalized counts using DESeq2
Sorted cells: ANOVA comparisons done using DESeq2
Sorted Cells: PCA plots were generated using R statistical analysis software
Normalized BigWig files using deepTools bamCoverage
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and 34 samples as 2 samples (outliers) were excluded from the analysis.

source_name: cultured BMMs

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

treatment_protocol: FACS sorted BMMs from Irf8 cWT and Irf8 cKO mice were cultured in the presence of 20 ng/ml MCSF and 40 ng/mL RANKL for 4 days to generate terminally differentiated osteoclasts.

value: Bone Marrow Derived Monocytes

value: BMMs


title: C57BL-6N-323


title: hippocampus_phenytoin-Responder_rep3

value: NMRI

value: Male

value: Hippocampus


title: mESC1


title: C57BL-6N-325

value: male


title: s35_BMMs_cKO_neg


title: hippocampus_phenytoin-Resistant_rep2

value: Adult - 12 weeks


title: s33_BMMs_cKO_int


title: hippocampus_phenytoin-Responder_rep2


title: hippocampus_phenytoin-Resistant_rep3


title: s31_BMMs_cKO_int


title: HCN4FEA 3

city: Hannover

first: Christian

last: Wahl-Schott

address: Carl-Neuberg-Str. 1

department: Institute for Neurophysiology

institute: Hannover Medical School

description: dissected SAN tissue

hyb_protocol: Fragmented and labeled cDNA was hybridized onto murine MouseGene1.1-ST Gene Chips

scan_protocol: Staining of biotinylated cDNA and scanning of arrays were performed according to the manufacturer's recommendations

data_processing:
Raw CEL-files were imported into Expression Console 1.0. RMA (Affymetrix, USA) and used for array normalization and signal calculation. Normalized signal values were imported into Partek Genomics Suite 6.5.
The probe sets were used to calculate differentially expressed transcripts using Welch's t-test with a p-value cut-off of 0.05 and a Fold-change of 1.5.

source_name: HCN4FEA, SAN

label_protocol: RNA was processed for Affymetrix Gene Chips using Affymetrix whole transcript sense target labeling kit (Affymetrix, USA)

growth_protocol: SAN tissue dissected from adult mice

extract_protocol: RNA was isolated using RNeasy Micro Kit (Qiagen, Netherlands) and quality of RNA specimen was checked on an Agilent BioAnalyzer 2100 (Agilent Technologies, Germany)

value: sinoatrial node (SAN)


title: s34_BMMs_cKO_neg


title: s29_BMMs_cKO_high


title: hippocampus_phenytoin-Resistant_rep1

source_name: Male NMRI mouse hippocampus from resistant to phenytoin


title: ME21

city: San Diego

first: Tariq

last: Rana

address: 9500 Gilman Dr

department: Paediatrics

institute: UCSD

data_processing:
demultiplexing based on illumina indexing sequences
Filtering and alignment to GRCh38.p11 were performed using the 10x Genomics Cell Ranger 2.0.0 pipeline following standard parameters
Genome_build: GRCh38.p11
Supplementary_files_format_and_content: .mtx sparse matrix for gene expresson and .tsv files for single cell barcodes and gene names

organism: Homo sapiens

source_name: hESC derived cerebral organoid

growth_protocol: cerebral organoids were generated using the intrinsic approach developed by Lancaster et al. Briefly, embyroid bodies were generated from h9 human embyronic stem cells were using microwell plates or hanging drop method and differentiated into neural and glial lineages with retinoic acid, insulin, B27 and N2 in suspension culture within spinner flasks.

extract_protocol:
RNAs were extracted from single cells using the 10x Genomics Chromium controller to generate gel bead emulsions.
scRNA-seq libraries were generated following the 10x Genomics V2 scRNA-seq protocol.

treatment_protocol: Cerebral organoids were treated with 5uM methamphetamine for 7 days before being analyzed by scRNA-seq.

value: hESC derived cerebral organoid

value: 5uM Methamphetamine


title: ME20


title: s30_BMMs_cKO_high


title: hippocampus_phenytoin-Responder_rep1


title: s28_BMMs_cKO_high


title: s32_BMMs_cKO_int


title: WT 3

description: dissected SAN tissue

source_name: wild-type, SAN

value: wild-type


title: ME19


title: WT 2

description: dissected SAN tissue


title: HCN4FEA 2

description: dissected SAN tissue


title: NI JAX #3_AB2496

city: Bethesda

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description:
_3998687038_G
PolyA RNA

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using HiScan-SQ.

data_processing: Raw data filtered to include only probes detected in at least two arrays, using the detection_pvalue parameter output from GenomeStudio, cutoff is 0.1. Each array normalized using quantile normalization of bead_average intensity, performed using JMP/Genomics software.

source_name: spleen

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays.

growth_protocol: Inbred female C57BL/6 mice, aged 6–8 weeks, were purchased from Charles River Laboratory (CRL) or Jackson laboratory (JAX). March1 Knockout line was derived from C57BL/6 mice sourced from CRL.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer or TapeStation.

treatment_protocol: An inoculum containing 10×10^6 iRBC suspended in 100 ml of phosphate-buffered saline, pH 7.4, from donor mice was injected intravenously into each experimental C57BL/6 mouse to initiate infection. Naive mice receiving an equivalent number of uninfected RBCs served as a negative control group. Three or four mice as a group were infected with each parasite, and parasitemia were monitored by microscopic examination of Giemsa-stained thin tail blood smears.

tag: host strain/background

tag: host genotype

tag: host vendor

value: JAX

tag: parasite strain

value: Naive

tag: day post infection

value: Spleen

value: Female

tag: rna sample id


title: NI CRL #3_AB2500

description:
_3998687038_H
PolyA RNA

value: WT

value: CRL

tag: tissue

tag: gender


title: WT 1

description: dissected SAN tissue

tag: genotype


title: s27_OCs_WT_neg

value: Bone Marrow Derived Monocytes

value: Mature OCs


title: YM March1 KO D4 #2_AB2547

description:
_3998687038_F
PolyA RNA

value: [CRL originally]

value: YM


title: HCN4FEA 1

description: dissected SAN tissue


title: s26_OCs_WT_neg


title: s25_OCs_WT_neg


title: YM JAX D4 #2_AB2539

description:
_3998687038_D
PolyA RNA


title: YM March1 KO D1 #2_AB2536

description:
_3998687038_C
PolyA RNA


title: M1


title: NT6

value: mock treated


title: 18_flu: Flu rep 3

city: Fort Collins

state: CO

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing: FASTQ files were subjected to quality control analysis using the Rqc Bioconductor package in R. Reads were mapped using the STAR algorithm. The annotation database for alignment was built using GenomicFeatures Bioconductor package in R utilizing the UCSC genome browser files (TXDb object) for the mouse mm10 genome. RNA-seq files were aligned to the mouse genome with the GenomeFeatures Bioconductor R package. Aligned reads were filtered based on read counts; genes with reads <2 was discarded from analysis. After filtering, 20,776 genes were analysis ready and analyzed using DESeq2 package in R. Multiple comparison adjustments were made using the Benjamini-Hochberg procedure to control the false discovery rate (FDR) method.

source_name: Thymus

extract_protocol:
RNA was extracted from two to three individual placentae from each litter and from pooled fetal thymuses from sham- and influenza-inoculated female (E3.5, E7.5 and E12.5) groups using TRIzol reagent (Ambion, Carlsbad, CA). RNA samples were further purified using Qiagen MiniElute columns according to the manufacturer’s instructions (Qiagen, USA).  The RNA quantity and quality for RT-qPCR were assessed using a Nanodrop ND-1000 spectrophotometer (Thermoscientific). RNA concentrations for all samples had 260/280 ratios >2.03.
RNA extracted from an individual placenta from each of 3 litters (E7.5 and E12.5) from Experiment 1 were selected at random for RNA sequencing (RNA seq) and analysis (provided by Ted Shade, University of Colorado Cancer Center-Genomics and Microarray Core, Aurora, CO.) in addition, RNA extracted from 3 control and 3 influenza-inoculated E7.5 litters pooled fetal thymuses were submitted for RNA seq. The quantity of RNA was determined using TECAN.  The quality and integrity of the RNA samples was assessed using Agilent Tape Station 2200 or 4200 prior to library prep: RNA sequencing and data analysis were performed. Briefly, messenger RNA (mRNA) was purified, disrupted and a double-stranded cDNA library was synthesized using the TruSight mRNA kit (Illumina San Diego, CA). The cDNA library was sequenced using an Illumina HiSeq2500 platform and the quality of single-end (SE) reads using Real-Time Analysis (RTA) v2.7.3.

treatment_protocol: Pregnant females were inoculated with PBS or influenza A virus on days E7.5 or E12.5.  On E18.5, females were anesthetized with 100 ug/kg ketamine + 10 ug/kg xylazine administered by intraperitoneal route and placental and thymus tissues were collected. Transcriptome analysis was completed on E18.5 placenta infected with PBS or flu on E7.5 and E12.5 and on E18.5 thyums infected with PBS or flu on E7.5

tag: strain

value: Thymus

tag: tissue embryonic day

tag: embryonic day of flu infection


title: March1 KO-D4-3_AB2283

description:
_3998687029_F
PolyA RNA


title: 17_flu: Flu rep2


title: YM CRL D4 #2_AB2543

description:
_3998687038_E
PolyA RNA


title: 15_ctrl: Control rep 3


title: s23_OCs_WT_int


title: NT5


title: s22_OCs_WT_int


title: YM CRL D1 #2_AB2532

description:
_3998687038_B
PolyA RNA


title: NT4


title: 16_flu: Flu rep 1


title: s21_OCs_WT_high


title: NT3


title: 14_ctrl: Control rep 2


title: YM JAX D1 #2_AB2528

description:
_3998687038_A
PolyA RNA


title: March1 KO-D1-3_AB2280

description:
_3998687029_E
PolyA RNA


title: s20_OCs_WT_high


title: 13_ctrl: Control rep 1


title: March1 KO-3_AB2277

description:
_3998687029_D
PolyA RNA


title: NT2_1


title: 12_flu: Flu rep 3

source_name: Placenta

value: Placenta


title: 11_flu: Flu rep2


title: WT-D4-3_AB2274

description:
_3998687029_C
PolyA RNA


title: s24_OCs_WT_int


title: s18_BMMs_WT_neg

value: BMMs


title: NT1_2

value: hESC derived cerebral organoid


title: s19_OCs_WT_high


title: NT1_1


title: 10_flu: Flu rep 1


title: WT-3_AB2268

description:
_3998687029_A
PolyA RNA


title: March1 KO-D4-2_AB2282

description:
_3998687011_F
PolyA RNA


title: March1 KO-D1-2_AB2279

description:
_3998687011_E
PolyA RNA


title: WT-D1-3_AB2271

description:
_3998687029_B
PolyA RNA


title: s16_BMMs_WT_neg


title: March1 KO-2_AB2276

description:
_3998687011_D
PolyA RNA


title: NT2_2


title: 9_ctrl: Control rep 3


title: KO_SAT

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

data_processing:
processed with 10X standardard cellranger (3.1.0) pipeline reference (cellranger-mm10-3.0.0) using STAR aligner (version 2.6)
Genome_build: cellranger-mm10-3.0.0
Supplementary_files_format_and_content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: white adipose tissue

extract_protocol:
Cells were prepared according to 10x Genomics® Single Cell Protocols Cell Preparation Guide, followed by MACS Dead Cell Removal Kit 130-090-101 and RBC removal
single-cell transcritpome caputred by 10X 3' Reagent Kiits (v3)
After running on 10X Chromium Single Cell Controller, gel beads-in-emulsion (GEMs) were generated. The barcoded and full-length cDNAs were produced after incubation of the GEMs and amplified via PCR.
Library was qualified by Agilent Bioanalyzer 2100 and quantified by real-time PCR on QuantStudio3. Sequenced was done with Illumina NextSeq 550 System using High Output Kit v2.5 (50,000 reads per cell).
R1 (barcode and UMI), R2 (3' cDNA reads), I1 (index files)

value: Pdgfrb-Cre; TERT fl/fl

value: inguinal adipose tissue

value: Stromal/vascular


title: WT-D4-2_AB2273

description:
_3998687011_C
PolyA RNA


title: 8_ctrl: Control rep 2


title: s15_BMMs_WT_int


title: 7_ctrl: Control rep 1


title: A_SAT

value: Pdgfra-Cre; TERT fl/fl


title: PBS_SAT

value: TERT +/+


title: 6_flu: Flu rep 3


title: s13_BMMs_WT_int


title: WT-D1-2_AB2270

description:
_3998687011_B
PolyA RNA

value: Spleen

value: Female


title: s17_BMMs_WT_neg

value: WT


title: 5_flu: Flu rep2


title: s12_BMMs_WT_high

value: Bone Marrow Derived Monocytes


title: Control LA biological replicate 7

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description: Cardiomyoyte-specific nuclear RNA

data_processing:
RNA-Seq reads were trimmed by cutadapt first, then trimmed read were aligned against human genome (GENCODE human V23) using STAR v2.4.2a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread: featureCount (5) with human GENCODE gene annotation.
All gene-level transcript counts were then imported into the R/Bioconductor package EdgeR, and the trimmed mean of M-values (TMM) normalization method was used to adjust for differences in library size

source_name: Heart

extract_protocol:
Human heart tissue was flash frozen using liquid nitrogen. RNA was extracted from PCM1+ cardiomyocytes nuclei using Zymo Direct-zol RNA MicroPrep kit(Cat# 11-330M) and submitted to the Genome Technology Access Center (GTAC) at Washington University School of Medicine (St. Louis, MO) for RNA sequencing.
Indexed RNA libraries were prepared from 10 ng of RNA from each sample with the Sigma Seqplex RNA amplification Kit (Sigma, Cat# SEQR). cDNA libraries were PCR-amplified in the presence of indexing adapters and pooled for RNA-sequencing. To minimize batch effects, library preparations for samples from each individual heart were performed simultaneously. Single-end 1 × 50 sequencing was performed at the on an Illumina HiSeq 2500 sequencer.

value: Heart left atrium


title: 4_flu: Flu rep 1


title: Control RA biological replicate 6

description: Cardiomyoyte-specific nuclear RNA

value: Heart right atrium


title: s11_BMMs_WT_high


title: WT-2_AB2267

description:
_3998687011_A
PolyA RNA

value: CRL

value: Naive


title: small intestinal crypt cells [Control_6]

value: small intestine

value: C57BL/6, Balbc

value: FltpZV/+


title: 3-ctrl: Control rep 3

value: Placenta


title: C57BL-6N-327

source_name: Liver

tag: Sex

value: male

value: liver

tag: age

value: 25 weeks

value: LFD


title: Control LA biological replicate 6

description: Cardiomyoyte-specific nuclear RNA


title: s10_BMMs_WT_high

tag: cell type

value: BMMs


title: March1 KO-D1-1_AB2278

description:
_3998687006_E
PolyA RNA

value: [CRL originally]

value: Spleen


title: 2_ctrl: Control rep 2


title: Control RA biological replicate 7

description: Cardiomyoyte-specific nuclear RNA


title: Control RA biological replicate 5

description: Cardiomyoyte-specific nuclear RNA


title: Control LA biological replicate 5

description: Cardiomyoyte-specific nuclear RNA


title: s09_OCs_cKO_neg

value: Mature OCs


title: 1_ctrl: Control rep 1


title: March1 KO-D4-1_AB2281

description:
_3998687006_F
PolyA RNA

value: Female


title: WT-D4-1_AB2272

description:
_3998687006_C
PolyA RNA

value: WT


title: March1 KO-1_AB2275

description:
_3998687006_D
PolyA RNA


title: Control RA biological replicate 4

description: Cardiomyoyte-specific nuclear RNA

value: Heart right atrium


title: s14_BMMs_WT_int

value: Bone Marrow Derived Monocytes


title: s06_OCs_cKO_int


title: Control LA biological replicate 4

description: Cardiomyoyte-specific nuclear RNA

value: Heart left atrium


title: NCoRd-508

tag: diet

value: HFD

value: OKO


title: N67C March1 KO D4 #2_AB2525

description:
_3998624068_H
PolyA RNA


title: WT-D1-1_AB2269

description:
_3998687006_B
PolyA RNA

value: CRL


title: s05_OCs_cKO_int


title: Control RA biological replicate 3

description: Cardiomyoyte-specific nuclear RNA


title: s07_OCs_cKO_neg


title: s04_OCs_cKO_int


title: s08_OCs_cKO_neg


title: Macrophage sample (MFK9)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Macrophage sample (MFK9)

data_processing:
Raw data files in FASTQ format was analyzed with Partek Flow v7
FASTQ files were trimmed with Quality Score method
Torrent Suite Software v 5.2 was used for basecalling, alignment, and mapping validated reads to HG19 transcriptome and AmpliSeq specific bed files.
Mapped reads were quantificed to  uisng Partek E/M method
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: read counts RNA-seq

source_name: Macrophage

growth_protocol: Human Kupffer were isolated following the protocol previously described in Perea et al, Hepatology. 2017 Sep;66(3):953-968. doi: 10.1002/hep.29215. Epub 2017 Jul 18.

extract_protocol: Proton RNA-seq libraries were prepared for sequencing using standard ribosomal RNA depletion method for Proton RNA-seq.

value: Macrophage

tag: disease state

value: Control


title: Control RA biological replicate 2

description: Cardiomyoyte-specific nuclear RNA


title: s03_OCs_cKO_high


title: Control LA biological replicate 3

description: Cardiomyoyte-specific nuclear RNA


title: s02_OCs_cKO_high


title: Macrophage sample (MFK8)

description: Macrophage sample (MFK8)

value: Cirrhosis


title: Control LA biological replicate 2

description: Cardiomyoyte-specific nuclear RNA


title: Macrophage sample (MFK18)

description: Macrophage sample (MFK18)


title: Liver_4h fasted_rep4

city: Philadelphia

first: Daniel

last: Rader

address: 3400 Civic Center Blvd

institute: University of Pennsyvania

description: Biological replicate 4 of 4.

hyb_protocol: Labelled samples were hybridized using Agilent hybridization chamber and oven as recommended by the manufacturer(Parameters: Chamber type = OTHER: Agilent chamber, Quantity of label target used = 825, Mass unit = Nano gram, time = 17, Tiny time unit = hours, Volume = 100, Volume unit = Micro litre, temperature = 65).

scan_protocol: GE2_1010_Sep10 protocol with Agilent Technologies Scanner G2505C according to manufacturer's specification.

data_processing: The data were normalized by the Loess method using the limma (Linear Models for Microarray Data) package in R. Statistical analysis of the microarray data was performed using the significance of microarrays (SAM) package.

source_name: 4 hour fasted livers-WT4

label_protocol: Five-hundred nanograms of total RNA of each sample were amplified and labeled using the Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Mice were maintained on chow diet

extract_protocol: Total RNA was extracted with TRIzol reagent (Ambion) according to the manufacturer's instructions.

treatment_protocol: Livers were harvested from 4 hour fasted mice and snap frozen for storage before further processing for RNA.

value: Male

value: liver

source_name: 4 hour fasted livers-KO4

value: IlrunKO


title: Liver_4h fasted_rep3

description: Biological replicate 3 of 4.

source_name: 4 hour fasted livers-WT3

source_name: 4 hour fasted livers-KO3


title: Control RA biological replicate 1

description: Cardiomyoyte-specific nuclear RNA


title: Control LA biological replicate 1

description: Cardiomyoyte-specific nuclear RNA


title: Liver_4h fasted_rep2

description: Biological replicate 2 of 4.

source_name: 4 hour fasted livers-KO2

source_name: 4 hour fasted livers-WT2


title: YM CRL D4 #4_AB2545

description:
_3998624067_G
PolyA RNA

tag: host strain/background

value: YM


title: YM JAX D4 #4_AB2541

description:
_3998624067_F
PolyA RNA

tag: host genotype

value: JAX

value: Spleen


title: Liver_4h fasted_rep1

description: Biological replicate 1 of 4.

source_name: 4 hour fasted livers-KO1

source_name: 4 hour fasted livers-WT1


title: YM JAX D1 #4_AB2530

description:
_3998624067_D
PolyA RNA

tag: host vendor

value: Female


title: Macrophage sample (MFK15)

description: Macrophage sample (MFK15)


title: Irf8_cKO_OCs_3

first: Stephen

middle: R

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Convert from BCL and demultiplex using Casava 1.8.4 or bcl2fastq 2.17.1
Unsorted cells: Map to mm9 using Tophat 2.1.0
Unsorted cells: calculate RPKM using Partek GS 6.6
Unsorted cells: ANOVA comparisons on Log2 RPKM (with 0.1 offse) using Partek GS 6.6
Unsorted Cells: PCA plots of RPKM values using Partek GS 6.6
Normalized BigWig files using deepTools bamCoverage
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Excel ANOVA table
Supplementary_files_format_and_content: Excel RPKM table

source_name: cultured BMM

treatment_protocol: BMMs from Irf8 cWT, Irf8 cKO, Irf8 gWT, and Irf8 gKO mice were cultured in the presence of 20 ng/ml MCSF and 40 ng/mL RANKL for 6 days to generate terminally differentiated osteoclasts.

value: Mature OCs

tag: time point

value: day 6


title: Heart Failure only RA biological replicate 3

description: Cardiomyoyte-specific nuclear RNA

value: Heart right atrium


title: YM CRL D1 #4_AB2534

description:
_3998624067_E
PolyA RNA

value: WT

tag: parasite strain

tag: day post infection


title: NI CRL #2_AB2499

description:
_3998624068_A
PolyA RNA

value: Naive

tag: tissue

tag: rna sample id


title: Macrophage sample (MFK14)

description: Macrophage sample (MFK14)


title: Irf8_cKO_OCs_2

value: Bone Marrow Derived Monocytes

tag: genotype


title: N67C March1 KO D1 #2_AB2514

description:
_3998624068_E
PolyA RNA

value: [CRL originally]

tag: gender


title: Irf8_cKO_OCs_1

tag: strain


title: N67C JAX D4 #2_AB2517

description:
_3998624068_F
PolyA RNA


title: Heart Failure only LA biological replicate 3

description: Cardiomyoyte-specific nuclear RNA

value: Heart left atrium


title: N67C CRL D1 #4_AB2512

description:
_3998624067_A
PolyA RNA

value: CRL


title: N67C JAX D4 #4_AB2519

description:
_3998624067_B
PolyA RNA


title: Heart Failure only RA biological replicate 2

description: Cardiomyoyte-specific nuclear RNA


title: Irf8_cKO_PreOCs_2

value: PreOCs

value: day 3


title: Heart Failure only LA biological replicate 2

description: Cardiomyoyte-specific nuclear RNA


title: Macrophage sample (MFK11)

description: Macrophage sample (MFK11)

value: Macrophage

value: Control


title: N67C JAX D1 #4_AB2508

description:
_3998624058_H
PolyA RNA


title: Heart Failure only RA biological replicate 1

description: Cardiomyoyte-specific nuclear RNA


title: Liver tissue sample (MFK8)

description: Liver tissue sample (MFK8)

source_name: Liver tissue

value: Liver tissue

value: Cirrhosis


title: NI JAX #4_AB2497

description:
_3998624058_F
PolyA RNA

source_name: spleen

value: JAX

value: Spleen


title: Liver tissue sample (MFK9)

description: Liver tissue sample (MFK9)


title: Irf8_cKO_PreOCs_1


title: Irf8_cKO_BMMs_3

value: BMMs

value: day 0


title: fetal_liver_tissue_human_whole_tissue

city: Madison

first: Srikumar

last: Sengupta

state: WI

address: 330 N Orchard St

department: Regenerative Biology

institute: Morgridge Institute for Research

description:
Human_fetal_liver_whole_tissue_RNA
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
Sequencing reads were mapped to chimera transcriptome using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: hg19
Supplementary_files_format_and_content: collated rsem output into tab files, expected counts (ec) and transcripts per million (TPMs)

growth_protocol: MEFs were cultured to passage 1 (p1) to passage 3 (p3) in growth medium (1X DMEM, 10X heat inactivated fetal bovine serum (FBS), 1X nonessential amino acids) and irradiated with a dose of 80Gy using a Mark I 137Cs irradiator (from J. L. Shepherd and Associates).

extract_protocol:
Total RNA from cells were isolated with RNeasy Plus kit (QIAGEN).
Sequencing libraries were prepared following the LM-seq protocol (Hou et al., 2015).
Sequenced on Illumina HiSeq 2500 and HiSeq 3000  at a depth of 48 samples per lane.

treatment_protocol: Irradiated MEFs were seeded onto 0.1% gelatin coated plates at a concentration of 1.8 × 10e5 cells/mL to be used for culturing SHPCs. SHPC medium was E6 based (Chen et al., 2011) and contained Dexamethasone (1 μM), epidermal growth factor (100 ng/ml), Oncostatin M (10 μg/ml), 20% FBS, insulin (2 μl/ml), Nicotinamide (100 mM), Y27632 (10 μM), A-083 (0.5 μM), CHIR99021 (3 μM), and N2 and B27 (both at 1X).

tag: passage

tag: donor


title: Macrophage sample (MFK13)

description: Macrophage sample (MFK13)


title: Irf8_cKO_BMMs_2


title: Irf8_cKO_PreOCs_3


title: s01_OCs_cKO_high

source_name: cultured BMMs

value: Mature OCs


title: af13_298ra: AF RA biological replicate 5

description: run_2874_s_1_withindex_sequence.txt_ATCGAGC

value: Heart:right atrium

value: Atrial Fibrillation

tag: molecule subtype

value: Cardiomyoyte-specific nuclear RNA


title: Irf8_cKO_BMMs_1

value: Bone Marrow Derived Monocytes

tag: cell type


title: YM March1 KO D4 #3_AB2548

description:
_3998624058_E
PolyA RNA

value: [CRL originally]

value: YM

value: Female


title: Liver tissue sample (MFK16)

description: Liver tissue sample (MFK16)


title: Irf8_cWT_OCs_3

value: day 6


title: YM JAX D4 #3_AB2540

description:
_3998624058_C
PolyA RNA

value: WT


title: Heart Failure only LA biological replicate 1

description: Cardiomyoyte-specific nuclear RNA

value: Heart left atrium


title: YM CRL D4 #3_AB2544

description:
_3998624058_D
PolyA RNA

value: CRL


title: YM March1 KO D1 #3_AB2537

description:
_3998624058_B
PolyA RNA


title: YM CRL D1 #3_AB2533

description:
_3998624058_A
PolyA RNA


title: af13_129ra: AF RA biological replicate 3

description: run_2874_s_1_withindex_sequence.txt_ATGACAG


title: Liver tissue sample (MFK14)

description: Liver tissue sample (MFK14)

value: Liver tissue

value: Control


title: af13_111ra: AF RA biological replicate 2

description: run_2874_s_1_withindex_sequence.txt_GCTTAGA


title: NI CRL #4_AB2501

description:
_3998624058_G
PolyA RNA

value: Naive

value: Spleen


title: Irf8_cWT_PreOCs_3

value: PreOCs

value: day 3


title: N67C CRL D4 #4_AB2523

description:
_3998624067_C
PolyA RNA


title: Liver tissue sample (MFK12)

description: Liver tissue sample (MFK12)


title: Irf8_cWT_OCs_1

value: Mature OCs


title: Liver tissue sample (MFK13)

description: Liver tissue sample (MFK13)


title: Liver tissue sample (MFK15)

description: Liver tissue sample (MFK15)

value: Cirrhosis


title: Irf8_cWT_PreOCs_2


title: Liver tissue sample (MFK11)

description: Liver tissue sample (MFK11)


title: h90lv-2n: Control LV, 2n ploidy, biological replicate 3

description: run_2785_s_1_withindex_sequence.txt_GGAGTCC

value: Heart:left ventricle

value: No Atrial Fibrillation

value: Cardiomyoyte-specific nuclear RNA


title: af11_106ra_1: AF RA biological replicate 1

description: run_2874_s_1_withindex_sequence.txt_TGAGGTT

value: Heart:right atrium

value: Atrial Fibrillation


title: Irf8_cWT_OCs_2

value: Bone Marrow Derived Monocytes

value: day 6


title: h90lv-4n: Control LV, 4n ploidy, biological replicate 3

description: run_2785_s_1_withindex_sequence.txt_TGGCATA


title: Irf8_cWT_PreOCs_1


title: af13_289ra: AF RA biological replicate 4

description: run_2874_s_1_withindex_sequence.txt_CACCTCC


title: NI JAX #2_AB2495

description:
_3998624057_H
PolyA RNA

value: WT

value: JAX

value: Female


title: h88lv-2n-2: Control LV, 2n ploidy, biological replicate 2

description: run_2785_s_1_withindex_sequence.txt_GTAAAAA


title: YM JAX D4 #1_AB2538

description:
_3998624057_E
PolyA RNA

value: YM


title: YM March1 KO D4 #1_AB2546

description:
_3998624057_G
PolyA RNA

value: [CRL originally]


title: Irf8_cWT_BMMs_3

value: BMMs

value: day 0


title: YM March1 KO D1 #1_AB2535

description:
_3998624057_D
PolyA RNA

value: Spleen


title: Irf8_cWT_BMMs_2


title: NL1_B2_D12

city: Seongbuk-gu

first: Gyu-Bum

last: Yeon

state: Seoul

address: 145, Anam-ro

department: Department of Biodtechnology

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw FASTQ files were trimmed for adapters using BBDuk, aligned to the ENSEMBL GRCh38 genome build by using STAR (2.7.2a) with parameter --runThreadN 12 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 31000000000 --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 20 -alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD
Normalized abundance measurements was conducted with DESeq2 (1.27.12)
Genome_build: ENSEMBL GRCh38
Supplementary_files_format_and_content: raw counts, normalized abundance measurements

source_name: Neural progenitor cells, NfiB overexpression for 12 days

extract_protocol:
The total RNAs were extracted using TRIzol® (Thermo Fisher Scientific) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using QuantSeq 3' mRNA-Seq Library Prep Kit FWD
RNA-seq (QunatSeq)

treatment_protocol: hPSC-NPCs of a passage number less than 5 were plated at 3 × 10e4 cells/cm2 on a Matrigel-coated 6-well plate. Subsequently, the cells were infected with viruses and 1 μg/ml polybrene (Millipore Sigma) (MOI: 1.0). The viral infection was accompanied by centrifugation (1000 g for 1 h at room temperature (RT)), while the cells adhered to the plate to improve the transduction efficiency (O'Doherty, Swiggard, & Malim, 2000). After 18 h of incubation, the virus-containing medium was replaced with a fresh NPC medium containing 10 ng/ml ciliary neurotrophic factor (CNTF), 10 ng/ml BMP4 (Peprotech), and 2.5 μg/ml doxycycline (Millipore Sigma) to induce NFIB expression. The day doxycycline was added was designated as day 0 (Figure 1A). On day 2, the NPC medium was replaced with a commercial astrocyte medium (ScienCell, Carlsbad, CA, USA) and this medium was used until day 14 of differentiation.

tag: cell line

value: NL1 (hiPSC)

value: NfiB overexpression

tag: time

value: 12 days


title: h89lv-2n-2: Control LV, 2n ploidy, biological replicate 1

description: run_2785_s_1_withindex_sequence.txt_AATTCAT

value: Heart:left ventricle

tag: disease state

value: No Atrial Fibrillation


title: NL1_B2_D10

source_name: Neural progenitor cells, NfiB overexpression for 10 days

value: 10 days


title: h88lv-4n-2: Control LV, 4n ploidy, biological replicate 2

description: run_2785_s_1_withindex_sequence.txt_CTGCAAT

source_name: Heart

value: Cardiomyoyte-specific nuclear RNA


title: Irf8_cWT_BMMs_1

value: Bone Marrow Derived Monocytes


title: NL1_B2_D14

source_name: Neural progenitor cells, NfiB overexpression for 14 days

value: 14 days


title: Liver tissue sample (MFK18)

description: Liver tissue sample (MFK18)

value: Liver tissue

value: Cirrhosis


title: YM CRL D4 #1_AB2542

description:
_3998624057_F
PolyA RNA

tag: host strain/background

tag: host genotype

value: WT

value: CRL

value: Female


title: NL1_B2_D8

source_name: Neural progenitor cells, NfiB overexpression for 8 days

value: 8 days


title: NL1_B2_D6

source_name: Neural progenitor cells, NfiB overexpression for 6 days

value: 6 days


title: DL_af13_55la: AF LA biological replicate 5

description: run_2874_s_2_withindex_sequence.txt_AGACTGA

value: Heart:left atrium

value: Atrial Fibrillation


title: N67C March1 KO D4 #1_AB2524

description:
_3998624057_A
PolyA RNA

tag: host vendor

value: [CRL originally]

value: Spleen


title: Irf8_gKO_OCs_2

value: Mature OCs

tag: time point

value: day 6


title: YM CRL D1 #1_AB2531

description:
_3998624057_C
PolyA RNA

tag: parasite strain

value: YM

tag: day post infection


title: Irf8_gKO_OCs_3

tag: tissue


title: h89lv-4n-2: Control LV, 4n ploidy, biological replicate 1

description: run_2785_s_1_withindex_sequence.txt_AGGCGAA

tag: genotype

value: Heart:left ventricle

value: No Atrial Fibrillation

value: Cardiomyoyte-specific nuclear RNA


title: NL1_B2_D4

source_name: Neural progenitor cells, NfiB overexpression for 4 days

value: NL1 (hiPSC)

value: NfiB overexpression

value: 4 days


title: Irf8_gKO_OCs_1

value: Bone Marrow Derived Monocytes


title: NL1_B2_D2

source_name: Neural progenitor cells, NfiB overexpression for 2 days

value: 2 days


title: Irf8_gKO_PreOCs_3

value: PreOCs

value: day 3


title: afla106: AF LA biological replicate 3

description: run_2738_s_2_withindex_sequence.txt_GGAGTCC

value: Heart:left atrium


title: YM JAX D1 #1_AB2527

description:
_3998624057_B
PolyA RNA

value: WT

value: JAX

tag: gender

value: Female

tag: rna sample id


title: Irf8_gKO_PreOCs_2

tag: strain


title: Irf8_gKO_PreOCs_1


title: NL1_B2_D0

source_name: Neural progenitor cells, Control

value: Control


title: afla271: AF LA biological replicate 2

description: run_2738_s_2_withindex_sequence.txt_TGGCATA

value: Atrial Fibrillation


title: afla275: AF LA biological replicate 1

description: run_2738_s_2_withindex_sequence.txt_GTAAAAA


title: NL1_B1_D12

value: 12 days


title: N67C March1 KO D4 #3_AB2526

description:
_3998624056_G
PolyA RNA

value: [CRL originally]

value: Spleen


title: Macrophage sample (MFK16)

description: Macrophage sample (MFK16)

source_name: Macrophage

value: Macrophage

value: Cirrhosis


title: NL1_B1_D14

value: NL1 (hiPSC)

value: NfiB overexpression

value: 14 days


title: DL_af13_129la: AF LA biological replicate 4

description: run_2874_s_2_withindex_sequence.txt_TACTCTA

value: Cardiomyoyte-specific nuclear RNA


title: CL_h83la_ctla83: Control LA biological replicate 5

description: run_2874_s_2_withindex_sequence.txt_GGCAGCG

value: No Atrial Fibrillation


title: Irf8_gKO_BMMs_2

value: Bone Marrow Derived Monocytes

value: BMMs

value: day 0


title: NL1_B1_D8

value: 8 days


title: h86la: Control LA biological replicate 3

description: run_2738_s_2_withindex_sequence.txt_AATTCAT

value: Heart:left atrium


title: N67C JAX D4 #3_AB2518

description:
_3998624056_E
PolyA RNA

value: WT

value: JAX

value: Female


title: YM JAX D1 #3_AB2529

description:
_3998624056_H
PolyA RNA

value: YM


title: Irf8_gWT_OCs_3

value: Mature OCs

value: day 6


title: N67C CRL D4 #3_AB2522

description:
_3998624056_F
PolyA RNA

value: CRL

value: Spleen


title: N67C March1 KO D1 #3_AB2515

description:
_3998624056_D
PolyA RNA

value: [CRL originally]


title: NI March1 KO #3_AB2504

description:
_3998624056_A
PolyA RNA

value: Naive


title: h87la: Control LA biological replicate 2

description: run_2738_s_2_withindex_sequence.txt_AGGCGAA

value: Cardiomyoyte-specific nuclear RNA


title: N67C CRL D1 #3_AB2511

description:
_3998624056_C
PolyA RNA


title: N67C JAX D1 #3_AB2507

description:
_3998624056_B
PolyA RNA


title: Irf8_gWT_OCs_2


title: NL1_B1_D4

value: NL1 (hiPSC)

value: NfiB overexpression

value: 4 days


title: Irf8_gWT_OCs_1

value: Bone Marrow Derived Monocytes


title: NL1_B1_D2

value: 2 days


title: CR_h87ra: Control RA biological replicate 4

description: run_2874_s_2_withindex_sequence.txt_TAACAAG

value: Heart:right atrium

value: No Atrial Fibrillation


title: h77rv: Control RV biological repliate 1

description: run_2515_s_2_withindex_sequence.txt_TACTCTA

value: Heart:right ventricle


title: ctla67: Control LA biological replicate 4

description: run_2738_s_2_withindex_sequence.txt_CTGCAAT

value: Heart:left atrium


title: NL1_B1_D10

value: 10 days


title: NL1_B1_D0

value: Control


title: Irf8_gWT_PreOCs_3

value: PreOCs

value: day 3


title: CR_h86ra: Control RA biological replicate 3

description: run_2874_s_2_withindex_sequence.txt_CCATCAT


title: week 10

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: Memory T-Cells 10 weeks (day 74) after Daratumumab treatment

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.2 was used to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-hg19-1.2.0 as reference and expected-cells number of 3000 for each sample; polymorphisms removed.
For immune profiling Cell Ranger Single Cell Software Suite 3.0.2 was used for demultiplexing, barcode processing and assembly of the TCR sequences, using the vdj command and refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcode information for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. Fasta: high-confidence contig sequences of immune receptors annotated with the corresponding cellular barcode and contig-id; csv: results from the signle cell immune profiling comprising including the receptor type, VDJ-Genes annotation, CDR3 nucleotide and amino acid sequense as well as the count for the corresponding cellular barcode and contig.

source_name: CD3+CD45RA+CCR7- and CD3+CD45RA-CCR7+ peripheral blood T-cells

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMCs) were isolated with density gradient seperation and CD3+ non-naive (not CD45+CCR7+)  T-Cells were sorted by FACS. At week 0, cells were additionally sorted according to their CD38 protein expression.These were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
The purified cDNA was amplified using 16 cycles of PCR and then used for both 5’ gene expression (GEX) and TCR library preparation. TCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human T cells. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX and TCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.) and Mid Output v2 Kits (300 cycles) for TCR libraries (read1: 150nt, read2: 150nt, index1: 8nt, index2: n.a., 20% PhiX spike-in).

treatment_protocol: SLE patient treated with the anti-CD38 antibody Daratumumab on days 0, 7, 14, 21.

value: peripheral blood

value: Memory T-Cells

tag: patient diagnosis

value: Systemic Lupus Erythematosus


title: N67C March1 KO D1 #1_AB2513

description:
_3998624055_F
PolyA RNA

value: [CRL originally]

value: Spleen

value: Female


title: NL1_B1_D6

value: NL1 (hiPSC)

value: NfiB overexpression

value: 6 days


title: Irf8_gWT_PreOCs_2

value: Bone Marrow Derived Monocytes


title: h77ra#1  : Control RA biological replicate 2

description:
run_2515_s_2_withindex_sequence.txt_GCTTAGA
run_2874_s_2_withindex_sequence.txt_CTTGGAA

value: Heart:right atrium

value: No Atrial Fibrillation

tag: molecule subtype

value: Cardiomyoyte-specific nuclear RNA


title: Irf8_gWT_PreOCs_1

tag: cell type


title: N67C JAX D1 #1_AB2505

description:
_3998624055_D
PolyA RNA

value: WT

value: JAX


title: week 6

description: Memory T-Cells 6 weeks (day 41) after Daratumumab treatment


title: Irf8_gWT_BMMs_3

value: BMMs

value: day 0


title: N67C CRL D4 #1_AB2520

description:
_3998624055_H
PolyA RNA

value: CRL


title: h77lv#2  : Control LV biological replicate 1, technical replicate 2

description: run_2515_s_2_withindex_sequence.txt_ATCGAGC

value: Heart:left ventricle


title: h77lv#1  : Control LV biological replicate 1, technical replicate 1

description: run_2515_s_2_withindex_sequence.txt_CACCTCC


title: CD38+ week 0

description: Baseline CD38+ Memory T-Cells

source_name: CD3+CD45RA+CCR7-CD38+ and CD3+CD45RA-CCR7+CD38+ peripheral blood T-cells

value: peripheral blood

value: Baseline CD38+ Memory T-Cells

value: Systemic Lupus Erythematosus


title: CD38- week 0

description: Baseline CD38- Memory T-Cells

source_name: CD3+CD45RA+CCR7-CD38- and CD3+CD45RA-CCR7+CD38- peripheral blood T-cells

value: Baseline CD38- Memory T-Cells


title: h77la  : Control LA biological replicate 1

description:
run_2515_s_2_withindex_sequence.txt_ATGACAG
run_2874_s_2_withindex_sequence.txt_CCGATTA

value: Heart:left atrium


title: Irf8_gWT_BMMs_1

source_name: cultured BMM


title: Irf8_gWT_BMMs_2


title: NI March1 KO #1_AB2502

description:
_3998624055_C
PolyA RNA

value: [CRL originally]

value: Naive

value: Spleen

value: Female


title: Macrophage sample (MFK12)

description: Macrophage sample (MFK12)

value: Macrophage

value: Control


title: h76ra  : Control RA biological replicate 1

description: run_2515_s_2_withindex_sequence.txt_TGAGGTT

value: Heart:right atrium

value: No Atrial Fibrillation

value: Cardiomyoyte-specific nuclear RNA


title: Irf8_gKO_BMMs_1

value: Bone Marrow Derived Monocytes

value: BMMs

value: day 0


title: GSC 83+vehicle

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

country: China

institute: Shanghai Jiao Tong University

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. 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. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: Glioma stem cells

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

treatment_protocol: ACT001 treatment

value: Glioma stem cells

tag: treatment

value: Non-treatment


title: N67C CRL D1 #1_AB2509

description:
_3998624055_E
PolyA RNA

source_name: spleen

value: WT

value: CRL


title: WT-1_AB2266

description:
_3998687006_A
PolyA RNA


title: GSC 83+10 μM ACT001

value: 10 μM ACT001 for 24 h


title: NI CRL #1_AB2498

description:
_3998624055_B
PolyA RNA


title: N67C JAX D4 #1_AB2516

description:
_3998624055_G
PolyA RNA

value: JAX


title: human embryonic stem cells [H9-p98]

city: Jeonju-si

first: Myung-Kwan

last: Han

state: Jeollabuk-do

address: Baeje-daero 567

department: Department of Microbiology

institute: Jeonbuk National University Medical School

data_processing:
cellranger (v3.1.0) and bcl2fastq (v2.20.0) software used for basecalling and demultiplexing for other samples.
Pre-processed reads were align to reference genome and generate feature-barcode matrix using cellranger (v3.1.0) count module with default setting
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: barcodes.tsv.gz; tsv format with cell barcode information
Supplementary_files_format_and_content: features.tsv.gz; tsv format with gene information
Supplementary_files_format_and_content: matrix.mtx.gz; Matrix table with raw gene counts for every gene and every cell

source_name: H9 human embryonic stem cells

growth_protocol: hMSC-p7, H9-p98 and H9-EB-p98 were cultured wit conventional culture medium. S9-p10 were cultured with a 1:1 ratio of Neurobasal and DMEM/F12 media (Gibco) containing the following reagents: 20 ng/ml human LIF (Life Technologies), 15 ng/ml bFGF (R&D), 3 μM CHIR99021 (Calbiochem), 1 μM PD0325901 (Calbiochem), 250 ng/ml noggin (Koma biotech), 10 μM SB431542 (Sigma), 25 μg/ml ascorbic acid (Sigma), 5 μg/ml insulin (Roch), 1% N2 (Life Technologies), 2% vitamin A free B27 (Life Technologies), 1 mM glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 0.1% penicillin-streptomycin, and 5 mg/ml bovine serum albumin (BSA) (Sigma)

extract_protocol:
The Dead Cell Removal kit was used to remove dead cells from cell samples following the manufacturer’s instructions. Use LUNA-FL™ Automated Fluorescence Cell Counter to Consult the 10x Genomics Single Cell Protocols Cell Preparation Guide.
Cell suspension was mixed with master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell 3′ Chip. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets.   cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: The cultured cells were dissociated with trysinization.

value: H9 human embryonic stem cells

tag: passage


title: Cell aggregates of S. Typhimurium UMR1 treated with 15 µM clarithromycin [6_S6]

city: Stockholm

first: Ute

last: Römling

address: Solnavägen 9

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

description:
6_S6
Treated

data_processing:
Bcl files produced by NexSeq 550 were converted to fastq and demultiplexed using the bcl2fastq v2.20.0.422 program
Fastq files were aligned to the Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (NC_016856.1) genome using STAR v2.5.2b
Reads were then counted in annotated genes using featureCounts v1.5.1
Genome_build: NC_016856.1
Supplementary_files_format_and_content: counted reads in annotated genes

source_name: Rdar Biofilm-Forming Bacteria

growth_protocol: Prior to the experiment, single colonies of bacteria were inoculated in 5 mL LB and grown overnight at 37 ˚C with shaking.  Subsequently, strains were inoculated to OD600 0.02 and grown in Luria broth (LB) without salt medium under microaerophilic conditions (flask with 60% medium filling level) with shaking at 150 rpm at 28 ºC for 16 h.

extract_protocol:
Cells were harvested by centrifugation and disrupted by lysis buffer (50 mM Tris HCL pH 8, 8 % sucrose, 0.5 % Triton, 20 mM EDTA, 4 mg/mL), 200 µL acidic phenol was added, and samples were then heated at 65 ºC for 15 min, while shaking. The sample was cooled on ice for 5 min and centrifuged at 13000 rpm. The aqueous phase was collected and extracted once with an acid phenol:chloroform mix, and twice with chloroform. Finally, RNA was precipitated with 3 volumes of 100 % ethanol and 0.3 M sodium acetate overnight at -80 ºC. Pellets were washed with 1 mL 70 % ethanol, and air-dried after the supernatant was removed. Pellet was dissolved in 100 µL DEPC-treated distilled water. After DNase (Ambion RiboPure-Yeast DNase) treatment, the RNA samples were analysed by denaturating gel electrophoresis to assess DNA contamination and integrity of the isolated RNA. If DNA contamination was still present, the RNA was repeatedly incubated with DNAse. The RNA concentration was measured by Nano drop and the quality of RNA preparation assessed by Agilent Bioanalyzer 2100. The DNA-free RNA was stored at -80 ºC until use.
RNA samples were sequenced on a Nextseq 550 with medium output flowcell 150 cycles (2x75 PE) after depletion from ribosomal RNAs by the RiboMinus Transcriptome Isolation Kit (Invitrogen).

value: ATCC14028 Nalr (strain UMR1)

value: 15 µM clarithromycin


title: Cell aggregates of S. Typhimurium UMR1 treated with 15 µM clarithromycin [5_S5]

description:
5_S5
Treated

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: Cell aggregates of S. Typhimurium UMR1 treated with 15 µM clarithromycin [4_S4]

description:
4_S4
Treated


title: human musculoskeletal stem cells [S9-p10]

value: ES-derived human musculoskeletal stem cells


title: Cell aggregates of S. Typhimurium UMR1 [2_S2]

description:
2_S2
Control

value: none (untreated)


title: human embryoid bodies [H9-EB-p98]


title: human mesenchymal stem cells [hMSC-p7]

source_name: human mesenchymal stem cells

value: human mesenchymal stem cells


title: Cell aggregates of S. Typhimurium UMR1 [1_S1]

description:
1_S1
Control


title: NI JAX #1_AB2494

description:
_3998624055_A
PolyA RNA

value: Naive

value: Spleen

value: Female


title: Control2_54M

city: Sapporo

first: Masaki

last: Ito

address: North 15 West 7

department: Neurosurgery

country: Japan

institute: Hokkaido University

hyb_protocol: Hybridization (16h x 45 degrees Celsius) was processed according to the standard Affymetrix protocol.

scan_protocol: The HG-U133 Set was scanned with the Affymetrix® GeneArray Scanner 3000 7G according to the standard Affymetrix protocol

data_processing: Data processing was performed with Affymetrix® Micorarray Suite software (MAS) 5.0 using the default Statistical Algorithm parameters

source_name: Healthy control male

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

growth_protocol: Peripheral blood mononuclear cells were isolated by gradient centrifugation with Ficoll-Paque, then iPS cell lines were established. VSMCs were differentiated from iPS-derived neural crest stem cells confirmed as α-SMA, MYH11, SM22-α, and calponin positive cells.

extract_protocol: Total RNA was extracted from VSMCs using an RNeasy plus mini kit (Qiagen)

treatment_protocol: Not applicable

tag: cell source

value: induced neural crest stem cell derived VSMC

tag: Sex

value: male

value: G/G

tag: disease state

value: healthy control


title: PNU rMC-1 12h [3]

status: Public on Sep 10 2020

city: Kalamazoo

first: Cindy

last: Linn

state: MI

address: 1903 W. Michigan Avenue

department: Biological Sciences

institute: Western Michigan University

data_processing:
Illumina HiSeq, 2x150bp configuration, single index, per lane with ~350M raw paired-end reads per lane
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Rattus norvegicus Rnor6.0 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between DMSO-supernatant treated vs PNU-supernatant treated groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with a p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: log2 fold changes in MG between DMSO-treated RPE-J supernatant and PNU-treated RPE-J supernatant; TPM expression comparison between MG treated with DMSO-treated RPE-J supernatant and MG treated with PNU-treated RPE-J supernatant

organism: Rattus norvegicus

source_name: Retinal Muller glia cells

growth_protocol: Retinal Müller glia cells derived from rats (rMC-1; 4-6 passages) were grown in Dulbecco’s modified Eagle’s medium containing 8% fetal bovine serum, 1% L-Glutamine, and 1% penicillin-streptomycin, using standard cell culture techniques and incubated at 37°C with 5% CO2. After 3 days, cells were switched to 33°C with 5% CO2 for co-culture with treated RPE-J cell lines for varying amounts of time.

extract_protocol:
Treated rMC-1 cells were removed from transwells with trypsin and collected. Cells were processed using Trizol reagent and Total RNA was collected using Direct-zol RNA mini-prep kit (Zymo).
RNA library preperation with polyA selection from GeneWiz

treatment_protocol: Rat derived retinal pigment epitheial cells (RPE-J) were treated with 100nM PNU-282987 or with DMSO (vehicle control) for 24 hours. RPE-J cells were extensivley washed to remove all traces of PNU-282987. Treated RPE-J cell cultures were co-cultured with rMC-1 cells via a transwell system for 8, 12, 24 or 48 hours.

tag: cell line

value: rMC-1 immortalized cell line

tag: strain background

value: Sprague-Dawley

value: Retinal Muller glia cells

value: PNU-282987 treated RPE-J supernatant for 12 hours


title: Control3_48M


title: PNU rMC-1 8h [2]

value: PNU-282987 treated RPE-J supernatant for 8 hours


title: GSC 83+5 μM ACT001

value: Glioma stem cells

value: 5 μM ACT001 for 24 h


title: Control (DMSO) rMC-1 48h [1-Resub]

value: DMSO


title: PNU rMC-1 24h [4-Resub]

value: PNU-282987 treated RPE-J supernatant for 24 hours


title: PNU rMC-1 48h [5-Resub]

value: PNU-282987 treated RPE-J supernatant for 48 hours


title: MMD3_36F

source_name: Moyamoya disease female

value: female

value: A/G

value: Moyamoya disease


title: 6419c5.ctrl.no4

city: New York

first: Jinyang

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
transcript quantification using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: transcript per million (TPM)

source_name: mouse pancreatic tumor cell

growth_protocol: Tumor cells were sorted from subcutaneously implanted tumors.

extract_protocol:
RNA extracted using Qiagen Rneasy micro Kit
Done by Novogene, a commercial company

treatment_protocol: With or without treatment of a combination immunotherapy, including gemcitabine, abraxane, CD40 agonist, PD-1 blockade, and CTLA-4 blockade

value: control

value: Sorted subcutaneous pancreatic tumor cells

tag: tumor stage

value: subcutaneous tumor


title: 6419c5.ctrl.no3


title: 6419c5.ctrl.no1


title: 6419c5.GAFCP.no1

value: GAFCP combination immunotherapy


title: 6419c5.ctrl.no2


title: 6419c5.GAFCP.no2


title: Control1_48M

value: induced neural crest stem cell derived VSMC

value: male

value: G/G

value: healthy control


title: 6694c2.Kdm3aKO2.no2

treatment_protocol: No treatment


title: MMD1_39M

source_name: Moyamoya disease male


title: 6694c2.Kdm3aKO2.no1


title: 6694c2.Kdm3aKO1.no3


title: 6694c2.Kdm3aKO1.no2


title: 6694c2.WT.no3

value: WT


title: Irf8_gKO_BMMs_3

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

value: Bone Marrow Derived Monocytes

value: BMMs

tag: time point

value: day 0


title: 6694c2.WT.no1

tag: tissue


title: 6419c5.Kdm3aKO2.no3

tag: genotype


title: 6419c5.Kdm3aKO1.no2


title: 6419c5.WT.no3


title: 6419c5.WT.no1


title: 6419c5.WT.no2


title: 6419c5.Kdm3aKO1.no1


title: 6419c5.Kdm3aKO1.no3


title: 6419c5.Kdm3aKO2.no2


title: 6694c2.Kdm3aKO2.no3


title: MMD2_48F


title: 6649c2 Smad4KO.no1

description: 6649c2 Smad4KO.no1


title: Cell aggregates of S. Typhimurium UMR1 [3_S3]

description:
3_S3
Control

value: ATCC14028 Nalr (strain UMR1)

value: none (untreated)


title: 6649c2 Klf5KO.no3

description: 6649c2 Klf5KO.no3


title: 6649c2 EgfrKO.no3

description: 6649c2 EgfrKO.no3

value: EgfrKO


title: 6649c2 Smad4KO.no2

description: 6649c2 Smad4KO.no2


title: 6649c2 Smad4KO.no3

description: 6649c2 Smad4KO.no3


title: 6649c2 Klf5KO.no1

description: 6649c2 Klf5KO.no1


title: 6649c2 WT.no2

description: 6649c2 WT.no2


title: 6649c2 EgfrKO.no2

description: 6649c2 EgfrKO.no2


title: 6649c2 WT.no3

description: 6649c2 WT.no3


title: 79w_cortex_rep2_wgbs

city: SAINT LOUIS

first: Daofeng

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

library_source: genomic

data_processing:
All libraries were sequenced on Illumina NovaSeq 6000 platform. Reads were adapter-trimmed with cutadapt.
RNA-seq reads were aligned to mm9 genome using STAR and read counts for each gene were obtained using HTSeq.
WGBS and TAB-seq reads were aligned to mm9 using bismark with standard parameters.
Genome_build: mm9

molecule: genomic DNA

extract_protocol:
RNA was collected using Trizol following manufacture's recommendation.  DNA was extracted with 5hmC TAB-Seq Kit.
WGBS and TAB-seq was generated using 5hmC TAB-Seq Kit (WiseGene, K001).  RNA-seq was generated using Universal Plus mRNA-Seq kit.

tag: age

value: 79 week

tag: gender

value: cortex


title: 79w_cortex_rep2_tabSeq

data_processing:
Library strategy: TAB-seq
All libraries were sequenced on Illumina NovaSeq 6000 platform. Reads were adapter-trimmed with cutadapt.
RNA-seq reads were aligned to mm9 genome using STAR and read counts for each gene were obtained using HTSeq.
WGBS and TAB-seq reads were aligned to mm9 using bismark with standard parameters.
Genome_build: mm9

tag: strain


title: 6649c2 Klf5KO.no2

description: 6649c2 Klf5KO.no2


title: 79w_cortex_rep1_wgbs


title: 6694c2.Kdm3aKO1.no1


title: 6649c2 WT.no1

description: 6649c2 WT.no1


title: 7w_cortex_rep2_tabSeq

value: 7 week


title: 6419c5.Kdm3aKO2.no1

value: Sorted subcutaneous pancreatic tumor cells


title: 79w_cortex_rep1_tabSeq


title: 7w_cortex_rep1_tabSeq


title: 7w_cortex_rep1_wgbs


title: 79w_cerebellum_rep2_wgbs

value: cerebellum


title: 79w_cerebellum_rep2_techRep2_tabSeq

description: technical replicate2 for TAB-seq


title: 7w_cortex_rep2_wgbs


title: 79w_cerebellum_rep2_techRep1_tabSeq

description: technical replicate1 for TAB-seq


title: 79w_cerebellum_rep1_techRep2_tabSeq

description: technical replicate2 for TAB-seq


title: 79w_cerebellum_rep1_rnaSeq


title: 79w_cerebellum_rep1_wgbs


title: 7w_cerebellum_rep2_techRep2_tabSeq

description: technical replicate2 for TAB-seq


title: 6649c2 EgfrKO.no1

description: 6649c2 EgfrKO.no1

value: subcutaneous tumor


title: 7w_cerebellum_rep2_techRep1_tabSeq

description: technical replicate1 for TAB-seq


title: 7w_cerebellum_rep2_rnaSeq


title: 79w_cerebellum_rep1_techRep1_tabSeq

description: technical replicate1 for TAB-seq


title: 7w_cerebellum_rep1_rnaSeq


title: 7w_cerebellum_rep1_techRep1_tabSeq

description: technical replicate1 for TAB-seq


title: 7w_cerebellum_rep1_techRep2_tabSeq

description: technical replicate2 for TAB-seq


title: 7w_cerebellum_rep1_wgbs


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H9_ad008

city: La Jolla

first: Joseph

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: LSX


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H9_ad007

value: male


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H8_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H9_ad004


title: 7w_cerebellum_rep2_wgbs


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H8_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H8_ad007


title: 79w_cerebellum_rep2_rnaSeq


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H7_ad008


title: 6694c2.WT.no2


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H7_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H6_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H5_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H6_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H5_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H6_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H5_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H5_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H6_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H5_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H4_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H6_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H4_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H4_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H4_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H3_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H3_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H4_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H4_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H3_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H3_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H8_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H2_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H7_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H2_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H3_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H2_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H2_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H2_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H11_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H2_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H11_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H11_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H1_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H1_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H3_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H10_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H1_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G8_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G9_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G9_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H1_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G8_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G8_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G9_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G7_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G8_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G8_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G7_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_H10_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G7_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G6_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G7_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G9_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G7_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G7_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G6_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G6_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G9_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G6_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G5_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G5_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G5_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G5_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G5_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G4_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G3_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G4_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G5_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G4_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G4_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G6_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G3_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G2_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G3_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G3_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G3_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G12_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G2_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G2_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G2_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G6_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G12_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G12_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G3_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G12_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G12_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G2_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G12_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G3_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G11_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G11_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G12_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G10_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G2_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G11_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G10_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G10_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G1_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G1_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G10_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G10_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F9_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G10_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G11_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F9_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G10_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G1_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G1_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F9_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F7_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F8_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G1_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G11_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F9_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F7_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G1_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F7_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F7_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F7_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F9_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F6_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F9_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_G11_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F9_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F6_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F6_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F6_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F6_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F5_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F5_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F5_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F5_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F7_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F5_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F4_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F5_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F4_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F4_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F4_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F3_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F3_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F3_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F3_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F3_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F4_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F2_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F2_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F2_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F2_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F5_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F2_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F12_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F12_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F12_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F12_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F12_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F12_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F12_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F4_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F11_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F2_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F11_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F11_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F11_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F11_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F10_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F11_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F10_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F10_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F10_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F1_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F2_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F1_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F1_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F1_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E9_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F10_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F10_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E9_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E9_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E8_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E9_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E7_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E8_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_F10_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E7_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E7_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E7_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E9_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E6_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_E7_ad010


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