title: COLO320HSR_rep8_atac

city: Stanford

first: Howard

last: Chang

address: CCSR 2130, 269 Campus Drive

institute: Stanford University

description: Single cell multiome ATAC library

data_processing:
Processed with cellranger-arc pipeline, version 1.0.0
Genome_build: hg19
Supplementary_files_format_and_content: Fragment files (single cell ATAC)
Supplementary_files_format_and_content: mtx  (single cell RNA)

source_name: COLO320-HSR cells

growth_protocol: Cells were maintained in RPMI (Life Technologies, #11875-119) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol: 10X Genomics Single Cell Multiome ATAC + Gene Expression Kit


title: BMMCs, WT_UN_H3K4me1 rep2

status: Public on Nov 25 2020

type: SRA

city: Denver

first: Hua

last: Huang

state: CO

address: 1400 Jackson St

department: Biomedical Research

country: USA

institute: National Jewish Health

library_source: genomic

data_processing:
The adaptor sequences in raw reads (average 24.0 million reads, two biological replicates for each group) were trimmed using Trimmomatic (version 0.33) (Bolger et al., 2014) and the quality of trimmed sequence data was analyzed by FastQC (version 0.11.9).
The trimmed reads were aligned to the mm10 reference genome using Bowtie2 (version 2.3.5.1) (Langmead and Salzberg, 2012).
Peak calling was performed using MACS2 (version 2.1.2) with default parameters (Zhang et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: Tdf and bedgraph files for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: BMMCs

growth_protocol: Bone marrow-derived mast cells (BMMCs) were cultured from bone marrow cells of Balb/c mice in Iscove’s DMEM (10016CV, CorningTM cellgroTM, Manassas, VA) plus 10% FBS,100 units/mL penicillin, 100 ug/mL streptomycin, and 2 mM beta-mercaptoethanol in the presence of 20 ng/mL IL-3 for four weeks. Over 99% of BMMCs were mast cells as determined by FACS analysis (FcεRIa+ c-Kit+).

extract_protocol:
Briefly, 1x10e7 BMMCs that were not treated or treated with IgE receptor crosslinking were fixed in complete medium with 1% Formaldehyde (Thermo Scientific, 28908). The fixation was quenched by adding glycine and then washed with ice-cold PBS. The cells were resuspended in lysis buffer with protease inhibitor cocktail (Sigma, SRE0055-1BO) and sonicated using Covaris S220 Focused-ultrasonicator (Covaris, Woburn, MA). The lysate was pre-cleared by incubating with protein A agarose/salmon sperm DNA slurry (Millipore, Cat# 16-157) and the supernatant was incubated with the anti-H3K4me1 antibody (ab8895, Abcam, Cambridge, MA) or anti-H3K27ac antibody (ab4729, Abcam) at 4 °C overnight. Then, the samples were incubated with salmon sperm DNA/protein A beads at 4 °C for one hour. The beads were washed using low salt immune complex wash buffer, high salt immune complex wash buffer once, LiCl immune complex wash buffer once and TE buffer twice. The beads were eluted with elution buffer. The crosslinking of eluted immunocomplexes was reversed by incubating with NaCl and RNase A (Roche, Cat# 11119915001) at 65 °C overnight, followed by incubation with Tris pH 6.5, EDTA pH 8.0, and Proteinase K at 55 °C for one hour. Finally, the recovered DNA was cleaned up using a QIAGEN QIAquick PCR purification kit (Qiagen, Valencia, CA).
ChIP-seq library was prepared using TruSeq ChIP Library Preparation Kit (IP-202-1024, Illumina, San Diego, CA) according to the manufacturer’s instructions. Briefly, 10 ng of ChIPed DNA was converted into blunt-ended fragments. A single adenosine nucleotide was added to the 3’ ends of the blunt-ended fragments before indexing adaptors were ligated to the adenylated 3' ends. The ligated product was purified, size-selected and PCR amplified according to the manufacturer’s instructions. The quality and quantity of the DNA library were assessed on an Agilent Technologies 2100 Bioanalyzer. The paired-ended sequencing was performed on an Illumina NovaSEQ6000 platform.

treatment_protocol:
(Stimulation)  BMMCs were sensitized with 1 ug/mL IgE anti-2, 4, 6-Trinitrophenyl (TNP) antibody (100 ng/mL) (IGEL 2a, ATCC, Manassas, VA). Twenty-four hours later, the cells were challenged with 100 ng/mL TNP-BSA (T-5050-100, LGC Biosearch Technologies, Novato, CA) for 2 additional hours before the cells were collected for further analysis.
(Gata2 deletion)  BMMCs cultured from bone marrow cells of Gata2f/fRosaYfp/YfpTgCreErt2hemi mice or Gata2+/+RosaYfp/YfpTgCreErt2hemi mice were treated with 25 nM 4-hydroxytamoxifen (4-OHT; Calbiochem, Billerica, MA) for five days as described previously (Li et al., 2018; Li et al., 2015). The expression of FceR1a (PE-CY7–conjugated anti-FcεRIa (MAR-1), Biolegend, 134317) and c-Kit (allophycocyanin-CY7–conjugated anti–c-Kit (2B8), Biolegend, 105825) on mast cells were analyzed by Flow cytometry. The YFP+ cells were FACS-sorted and the deletion of the Gata2 gene was determined to be near 100%. The sorted cells were then used for the next-generation sequencing analysis.

tag: strain

value: Balb/cJ

tag: cell type

value: Bone-marrow derived mast cells

tag: chip antibody

value: H3K4me1, (Abcam, ab8895)

tag: genotype

value: wild type

tag: treatment


title: Chopp41: WT immature CD4SP thymocytes replicate 3

city: Bethesda

first: Remy

last: Bosselut

state: MD

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

library_source: transcriptomic

data_processing:
Basecalls performed with Illumina RTA 1.18.64
Demultiplexing with Bcl2fastq 2.17
Filtering with Trimmomatic 0.36
Alignment--STAR aligner 2.4.0 to mm10
Counts per million normalized BigWig files performed with DeepTools
Genome_build: mm10
Supplementary_files_format_and_content: Htseq count table, counts per million normalized bigwig

molecule: total RNA

source_name: Thymus

extract_protocol:
RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
Clontech  Ultra Low Input reagent (Takara) and Nextera XT DNA (Illumina), paired-end 2x150

value: Thpok fl/fl; ThpokGFP; Cd4-Cre negative

tag: flow markers

value: CD44low MHC-I-low CD8alow CD69+ ThpokGFP+ CD4+

tag: tissue

value: Thymus


title: COLO320HSR_rep8_gex

middle: Y

state: CA

department: Center for Personal Dynamic Regulomes

description: Single cell multiome gene expression library

molecule: polyA RNA

organism: Homo sapiens


title: hESC-RPE, s6_POS_Drug3

city: Dresden

first: Seba

last: Almedawar

address: Fetscherstrasse 105

country: Germany

institute: CRTD- TU Dresden

data_processing:
[basecalling] Basecalls were performed using Illumina bcl2fastq version 2.17.1.14.
[mapping]  Reads were aligned to the human genome assembly (hg38) using GSNAP (2017-08-15; parameters: --gunzip -A sam  --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-81.ss.hg38.iit) with known splice sites from Ensembl (v81) as support.
[gene counting]  Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.5.3; parameters: -a EnsemblGene-81.hg38.TR.gtf -s 2 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (bfx582.featureCounts.hg38.e81.txt.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'

source_name: Human embryonic stem cells-derived retinal pigment epithelium

growth_protocol: Cells were differentiated from human embryonic stem cells according to the paper: Zhu, Y. et al. (2013) ‘Three-Dimensional Neuroepithelial Culture from Human Embryonic Stem Cells and Its Use for Quantitative Conversion to Retinal Pigment Epithelium’, PLoS ONE, 8(1), p. e54552. doi: 10.1371/journal.pone.0054552.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit by lysing the cells inside the wells.
mRNA enrichment and  reverse-transcription into cDNA was done with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocol.

treatment_protocol: Cells were treated for 1 hour without POS at 37 degrees with 5% CO2 with the treatment without POS. POS were added and treatment was kept for three more hours. Cells were lysed and RNA was prepared for RNA seq.

tag: photoreceptor outer segment

value: Yes

value: MFGE8 0.625 µg/ml+Ramoplanin (10µM)

tag: experiment time

value: 1 hour incubation without POS+3 hours with POS


title: COLO320HSR_rep7_atac

description: Single cell multiome ATAC library


title: hESC-RPE, s5_POS_Drug2

value: Human embryonic stem cells-derived retinal pigment epithelium


title: Chopp2: Unsignaled DP thymocytes replicate 2

data_processing:
Basecalls performed with Illumina RTA 1.18.66.3
Demultiplexing with Bcl2fastq 2.17
Filtering with Trimmomatic 0.36
Alignment--STAR aligner 2.4.0 to mm10
Counts per million normalized BigWig files performed with DeepTools
Read counts with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Htseq count table, counts per million normalized bigwig

extract_protocol:
RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMART-seq Ultra Low Input RNA kit (Takara) and Nextera XT DNA (Illumina), paired-end 2x150

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, C57BL/6 recipient

tag: surface markers

value: CD44low CD69- ThpokGFP- Runx3RFP- CD8a+ CD4+


title: BMMCs, WT_UN_H3K4me1 rep1


title: Chopp40: Thpok KO re-directed CD8SP thymocytes replicate 3

value: Thpok fl/fl; ThpokGFP; Cd4-Cre positive

value: CD44low CD4low CD69+ CD8a+ ThpokGFP+


title: hESC-RPE, s4_POS_Drug1


title: Chopp39: Thpok KO immature CD4SP thymocytes replicate 3


title: COLO320HSR_rep7_gex


title: hESC-RPE, s3_control3

value: No

value: MFGE8 0.625 µg/ml

value: 4 hours incubation


title: BMMCs, Gata2_KO_ST_ATAC-seq rep1

data_processing:
Raw sequencing reads (average 118.2 million reads, 2 biological replicates for each group) were adaptor trimmed by Trimmomatic 0.33 and the quality of sequenced data was analyzed by FastQC.
The trimmed reads were aligned to the mm10 reference genome using Bowtie2 with -very-sensitive and -x 2000 parameters.
The read alignments were filtered using SAMtools (version 1.7) to remove mitochondrial genome and PCR duplicates.
Peaks were identified by MACS2 with the q-value cut-off of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Tdf and bedgraph files for each sample

extract_protocol:
Briefly, 50,000 BMMCs that were either untreated or treated with IgE receptor crosslinking were spin down and washed with cold PBS once. Then the cells were resuspended in 50 uL cold ATAC-RSB-lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin) and incubated for 3 minutes. The lysis buffer was immediately washed out with 1 mL ATAC-RSB buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% Tween-20). The cell pellet was resuspended in 50 ul transposition mixture (25 uL 2X TD buffer, 2.5 uL transposase (Illumina, FC-121-1030), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O) and incubated at 37 C for 30 minutes. The reaction was stopped by adding 2.5 uL of 0.5M EDTA pH 8 and transposed DNA was purified using Qiagen MiniElute PCR purification kit (Qiagen).
Purified DNA was amplified using the following condition: 72℃ for 5 min, 98 ℃ for 30 s, and 7 cycles: 98 ℃ for 10 s, 63 ℃ for 30 s, 72 ℃ for 1 min. The amplified libraries were cleaned up, size-selected, and the quality and quantity of libraries were assessed on an Agilent Technologies 2100 Bioanalyzer.
Omni-ATAC-seq

value: Bone-marrow derived mast cells

value: IgE anti_TNP and TNP-BSA


title: Chopp38: WT immature CD8SP thymocytes replicate 2

value: CD44low CD4low CD69+ CD8a+


title: hESC-RPE, s2_control2


title: Chopp42: WT immature CD8SP thymocytes replicate 3

value: Thpok fl/fl; ThpokGFP; Cd4-Cre negative


title: COLO320HSR_rep6_atac

description: Single cell multiome ATAC library


title: COLO320HSR_rep6_gex


title: BMMCs, Gata2_KO_UN_ATAC-seq rep2


title: Chopp37: WT immature CD4SP thymocytes replicate 2

value: CD44low MHC-I-low CD8alow CD69+ ThpokGFP+ CD4+


title: Chopp36: Thpok KO re-directed CD8SP thymocytes replicate 2

value: Thymus


title: BMMCs, Gata2_WT_ST_ATAC-seq rep2

value: wild type


title: hESC-RPE, s1_control1


title: COLO320HSR_rep5_atac

description: Single cell multiome ATAC library


title: COLO320HSR_rep4_atac

description: Single cell multiome ATAC library


title: COLO320HSR_rep5_gex


title: Chopp35: Thpok KO immature CD4SP thymocytes replicate 2


title: BMMCs, Gata2_KO_UN_ATAC-seq rep1


title: Hypoxia1

city: Göttingen

first: Hannelore

last: Ehrenreich

address: Hermann Rein Straße 3

department: Clinical Neuroscience

institute: Max Planck Institute of Experimental Medicine

description: Hypoxia

data_processing:
CellRanger v2.2.0 software was used to align sequence reads to the customized mouse mm10 reference genome to which the ODD and tdTomato sequences were added.
Genome_build: customized mm10 (tdTomato + ODD sequences added)
Supplementary_files_format_and_content: Butt_et_al_hypoxia_counts.csv file contains the final set of UMI counts of cells and genes included in the analyses after quality control (Seurat v2.3.0) and doublet removal (manual+DoubletFinder (McGinnis et al, 2019)). Butt_et_al_hypoxia_metadata.csv contains all relevant cell metadata, including UMI and feature counts per cell, initial and final cellular identity, sample ID and experimental group. Butt_et_al_hypoxia_Seurat.RDS is the final processed Seurat (v3; Stuart et al, 2019) object after QC, integration, clustering, annotation and doublet removal (manual+DoubletFinder (McGinnis et al, 2019)).

source_name: Hippocampus

extract_protocol:
CAG-CreERT2-ODD::R26R-tdTomato mice, 4 weeks old, received tamoxifen (100mg/kg/d) daily for 5 consecutive days before being exposed to either inspiratory hypoxia (6%O2) or normoxia (21%O2) for 6h each. Mice were handled identically and sacrificed on day 5 immediately after the last hypoxia/normoxia session. Hippocampi were dissected in Earle’s Balanced Salt Solution (EBSS1) and later digested with a working solution of Papain/DNaseI prepared in EBSS1, according to manufacturer’s instructions (Worthington Biochemical Corp). All steps were carried out on ice except the Papain/DNaseI dissociation. The samples were then incubated at 37°C for 40min with constant shaking in water bath and switched to 5%CO2 every 10min. Papain/DNaseI was removed and samples were further diluted in 5ml EBSS2. Dissociated tissues were manually triturated (avoid air bubbles), followed by centrifugation at 900rpm for 10min at 4°C. Supernatant was discarded and the cell pellet gently resuspended in 200µl of EBSS2 until a smooth and creamy suspension was obtained. Dissociated cells were washed frequently with DMEM/F12 (Sigma) without phenol-red containing 3% fetal bovine serum (FBS; Life Technologies) and centrifuged at 900rpm for 10min at 4°C. Cell pellet was resuspended in 1ml of DMEM/F12 and filtered through a 70µm strainer cap (Corning) smoothly to harvest a clear cell suspension. Cell viability and yield was calculated by mixing an equal volume of acridine orange and propidium iodide and checked at the cell counter (Nexcelom Bioscience, MA, USA). Cell suspension (1ml) was diluted with 3ml PBS containing 0.04% BSA and centrifuged. Supernatant was removed and cell pellet resuspended in 400µl PBS containing 0.04% BSA. Cells were fixed by adding 1.6ml methanol dropwise and kept at -20°C for 30min and stored at -80°C for further use.
The Methanol fixed cell suspensions were stored at -80°C for less than 7 days before processing. For each sample, approximately 1.5 million cells were taken for rehydration and downstream scRNA-seq experiment. Cells were first placed on ice and equilibrated to 4°C. After equilibration, cells were washed 2 times by 1ml pre-chilled rehydration buffer (1.0% BSA, 0.5U/µl RNAse inhibitor in 1x Dulbecco's Phosphate-Buffered Saline, DPBS). Centrifugation was done at 3000rcf for 10min at 4°C. Finally, cells were resuspended in pre-chilled 1xDPBS with 0.04% BSA and 0.5U/µl RNase inhibitor to achieve a concentration of 1,000 cells/µl. Rehydrated cells were immediately used for the scRNA-seq using the 10X genomics chromium single-cell gene expression platform. Around 35,000 cells from each sample were loaded on 1 well of 10X Single Cell A chip, where each single-cell was lysed and its transcriptome combined with a single barcoded gel bead in an oil droplet. Barcode cDNA libraries were then prepared using Chromium Single Cell 3’ Library and Gel-beads kit v2 according to the manufacturer’s instructions. Library quality was checked using Agilent High Sensitivity DNA chip on Agilent 2100 Bioanalyzer. High quality libraries were sequenced on Illumina HiSeq 4000 sequencer with an average depth of 200,000 reads per cell.

treatment_protocol: P28 male mice, 5xHypoxia (6% O2, 6h/day) or 5xNormoxia (21% O2, 6h/day), sacrificed immediately afterwards

tag: age


title: Chopp34: Thpok KO re-directed CD8SP thymocytes replicate 1


title: COLO320HSR_rep4_gex


title: BMMCs, Gata2_WT_UN_ATAC-seq rep2


title: Chopp33: Thpok KO immature CD4SP thymocytes replicate 1


title: COLO320HSR_rep3_atac

description: Single cell multiome ATAC library


title: Chopp32: WT immature CD8SP thymocytes replicate 1


title: BMMCs, Gata2_WT_UN_ATAC-seq rep1


title: 9_F33L: MCA_tMCAO_nonoccluded_3hrs

type: RNA

city: Calgary

first: Simona

middle: Denise

last: Frederiksen

state: Alberta

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

description: gene expression data from experimental stroke MCAs

hyb_protocol: 16h at 45 degrees celsius in an Affymetrix Gene Chip Hybridization 645 oven.

scan_protocol: Affymetrix GeneChip scanner 3000 7G.

data_processing: Expression Console Software (v1.1.2)

label: biotin allonamide triphosphate

organism: Rattus norvegicus

source_name: MCA, non-occluded, after tMCAO, 3 hrs

label_protocol: Biotin Allonamide Triphosphate-labelled, labelling reaction at 37 degrees celsius

growth_protocol: Environmental enriched cages with a 12-hour light/dark cycle (lights on 7am-7pm), climate- and humidity-controlled environment and with free access to food and water. Animals were subjected to an acclimatization period. Female rats in the high estrogen phase, proestrus, were not included.

extract_protocol: Nucleospin miRNA isolation kit (Machery-Nagel, Düren, Germany), following the manufactures instructions for extraction of total RNA.

treatment_protocol: MCA occlusion using the intraluminal filament technique, anesthesia induced by 3.5% isoflurane in N2O:O2 (70:30) and maintained by continuous inhalation of 2.5% isoflurane in N2O:O2 (70:30), allowed to recover with free access to food and water for 3 hours, euthanized with carbon dioxide and decapitation.

value: Wistar

value: middle cerebral artery

tag: Sex

value: female

tag: weight

value: approx. 250 gram

tag: model

value: tMCAO

tag: group

value: non-occluded MCA


title: COLO320HSR_rep3_gex


title: Chopp31: WT immature CD4SP thymocytes replicate 1


title: Enterococcus faecium -TEX [ID-005246]

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

department: Institute for Molecular Infection Biology

institute: Universität Würzburg

description: dRNA-seq

data_processing:
Illumina reads in FASTQ format were trimmed using Cutadapt version 1.12 with the options –m 1 –q 20 to trim 3’ bases with a Phred quality score of less than 20.
Mapping was performed with the READemption pipeline (Förstner et al., 2014) version 0.4.3 using the subcommands “create”, “align” and “coverage”. The “align” command was run with the options -c -r -q -g.
Coverage plots (wig files) were produced by READemption.
Genome_build: E. faecium AUS0004 assembly ASM25094v1
Supplementary_files_format_and_content: Normalized and non-normalized wig files.

organism: Enterococcus faecium Aus0004

source_name: Liquid culture at OD600 2.0

growth_protocol: E. faecalis V583 or E. faecium AUS0004 were grown overnight at 37°C on M17 agar plates (Oxoid or Sigma-Aldrich) supplemented with 0.5% glucose. For liquid cultures, single colonies were inoculated into a 25 mL glass tube containing 8.3 mL M17 medium supplemented with 0.5% glucose, in order to keep the final proportions of one third of media to two thirds of oxygen. Cultures were grown overnight at 37°C without agitation. Overnight cultures were back-diluted 1:100 into fresh M17 supplemented with 0.5% glucose and grown at 37°C without agitation to late logarithmic/early stationary phase (optical density (OD)600 of 2.0).

extract_protocol:
Frozen bacterial cultures were thawed on ice, centrifuged, and cell pellets were resuspended in a lysis solution of 600 µl of 10 mg/ml lysozyme in Tris-EDTA (TE) buffer (pH 8.0) and 60 µl of 10% (w/v) sodium dodecyl sulphate (SDS). Bacterial cells were lysed by placing the samples for 10-12 minutes at 64°C in a water bath. Total RNA was extracted from the lysates using the hot phenol method (Blomberg 1990).
cDNA library construction and sequencing of dRNA-seq samples was performed by Vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/). First, total RNA samples were examined by capillary electrophoresis on a Shimadzu MultiNA microchip electrophoresis system to check RNA quality. Total RNA samples were then fragmented by ultrasound (4 pulses of 30 sec at 4°C) and treated with T4 Polynucleotide Kinase (NEB). Each sample was then divided into two halves and one half was subjected to Terminator exonuclease treatment (+TEX) while the other half remained untreated (-TEX). For cDNA synthesis, the +TEX and -TEX RNA samples were poly(A)-tailed using poly(A) polymerase. Next, RNA 5’ Polyphosphatase (Epicentre) was used to remove the 5’PPP structures. Subsequently, an RNA adapter was ligated to the 5’-monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to around 10-20 ng/µl using a high fidelity DNA polymerase. PCR cycles (12-15 rounds) were performed, with barcode sequences in the 5’ sequencing adapter. The primers for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and were analyzed by capillary electrophoresis. cDNA samples were pooled for sequencing. The library pool was fractionated in the range of 200-600 bp via a differential clean-up with the Agencourt AMPure kit, and an aliquot of the size-fractionated cDNA pool was analyzed by capillary electrophoresis. The cDNA pool was single end sequenced on an Illumina NextSeq 500 system using 1x75 bp read length.

tag: strain/background

tag: rna treatment

value: -TEX


title: COLO320HSR_rep2_atac

description: Single cell multiome ATAC library


title: Enterococcus faecium +TEX [ID-005280]

description:
dRNA-seq
TEX-treated total RNA.

value: +TEX


title: Dex-differentiated CAD  rep3

city: Payathai

first: Witchuda

last: Saengsawang

state: Bangkok

address: 272 Rama 6 Ave.

department: Physiology

country: Thailand

institute: Mahidol University

description: Sample 6_DEX3

data_processing:
Base calling was performed using NextSeq Control Software version 4.0 and checked quality with FASTQC V0.11.9
Raw fastq data was preprocessed using Trim-galore program V0.6.4 with auto adater detection in paired-end mode.
The filtered sequencing reads was mapped to Mouse reference genome GRCm38.p6 using HISAT2 (V2.2.0) program with default parameter
Mapped reads were cout usng feature count (with defuat parameter) software of Subread package release 1.6.4
Differential exprssion analysis was conducted using DESeq2 software
Genome_build: Mouse reference genome GRCm38.p6
Supplementary_files_format_and_content: Gene counts and differential exprssed genes list

source_name: CAD cell line (RRID:CVCL_0199)

growth_protocol: CAD cells (ECACC, RRID:CVCL_0199) were cultured as recommended in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12; DMEM/F12 (catalog number 12500062, Gibco, USA) supplemented with 8% fetal bovine serum (FBS) (catalog number 10270106, Hyclone, USA,); 1% antibiotic-antimycotic 100X (catalog number 2185242, Gibco, USA). The cells were maintained in a humidified incubator at 37 °C with 5% CO2 and 95% air (v/v). The passages of cells directed for this study were less than 10.

extract_protocol:
Total RNAs were extracted from undifferentiated CAD cells (Pro 1-3) and Dex-differentiated cells (5 days, Dex 1-3) using the TRIzol reagent (reference number 15596026, lot number 262308, Ambion, Life technologies Corporation, USA), according to the manufacturer’s instructions. Three independent samples were collected from both experimental groups. RNA concentration and purification were preliminary examined using a NanodropTM 2000 spectrophotometer (Thermo Fisher Scientific, USA).
Quality of the submitted total RNAs were evaluated using a Bioanalyzer (Agilent, USA). All mRNA libraries were constructed using 500 ng of input total RNA, as outlined by the QIAseq Standard mRNA Select kit (Qiagen, USA). QIAseq Beads were used to separate the cDNA from the reaction mix. Subsequently, indexing adapters were ligated to the cDNA, and the cDNA libraries were enriched using 12 cycles, as recommended by the Qiagen CleanStart library amplification protocol. Library quality assurance was conducted using a Bioanalyzer and fluorometer (DeNovix, USA). Next, a library size as recommended by Illumina for this type of library was observed to demonstrate a successful library preparation. Finally, all libraries were combined equally at 10 nM and further diluted to 1.8 pM. The sequencing step was performed on NextSeq with a 75 base-pair end read length.

treatment_protocol: For Dex-mediated differentiation, the cells were incubated with 100 µM of Dex (catalog number D4902, Sigma-Aldrich, USA) dissolved in DMEM/F12 supplemented with 1% FBS. The cultured media were replenished every 48 h.

tag: strain

value: C57BL/6 x DBA/2

value: Male

tag: transformant

value: NCBI_TaxID; 1891767; Simian virus 40 (SV40)

tag: cell line

value: CNS cell line CAD

value: Dexamethasone


title: Enterococcus faecium -TEX [ID-005245]

description: dRNA-seq


title: Dex-differentiated CAD  rep2

description: Sample 5_DEX2


title: RE1 KO_mut4_LV

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: CRISPR deletion regulatory element (RE1) in Nppa-Nppb locus

data_processing:
RNA-seq: reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al., 2013).
RNA-seq: Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Nppa-b-SE-RNA-seq-counts.xlsx (Excel file with raw and normalized (DESeq2) count data per gene & differential expression analysis).

source_name: HOM

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.

extract_protocol:
Total RNA was isolated from left ventricular tissue of RE1-deficient mice and wildtype littermates using Tri Reagent (Sigma Aldrich) according to the manufacturer’s protocol (Sigma Aldrich) and further purified using Nucleospin RNA Clean-up Kit with DnaseI treatment (Macherey-Nagel)
cDNA was prepared with the Truseq Stranded Total RNA Library Preparation Kit (Illumina, Part# 15031048 Rev. E). Total RNA (900 ng) was purified and sheared into small fragments followed by cDNA synthesis and ligation of the adapter. The quality and size distribution of the cDNA library templates were validated with Agilent DNA 1000 on 2100 Bioanalyzer (Agilent Technologies). cDNA samples were pooled per lane of paired-end 125 bp sequencing on an Illumina HiSeq 2500 instrument.

value: FVB

value: 8-12 weeks

value: Left ventricle


title: RE1 KO_mut2_LV


title: COLO320HSR_rep1_atac

description: Single cell multiome ATAC library

tag: cell type


title: Enterococcus faecium +TEX [ID-005279]

description:
dRNA-seq
TEX-treated total RNA.


title: COLO320HSR_rep1_gex


title: RE1 KO_mut1_LV


title: Undifferentiated/proliferative CAD rep2

description: Sample 2_PRO2

tag: treatment

value: control


title: COLO320DM_rep8_atac

description: Single cell multiome ATAC library

source_name: COLO320-DM cells


title: Enterococcus faecium +TEX [ID-005278]

description:
dRNA-seq
TEX-treated total RNA.


title: WT4_LV (RE1 KO control)

source_name: WT


title: Enterococcus faecalis -TEX [ID-005243]

description: dRNA-seq

data_processing:
Illumina reads in FASTQ format were trimmed using Cutadapt version 1.12 with the options –m 1 –q 20 to trim 3’ bases with a Phred quality score of less than 20.
Mapping was performed with the READemption pipeline (Förstner et al., 2014) version 0.4.3 using the subcommands “create”, “align” and “coverage”. The “align” command was run with the options -c -r -q -g.
Coverage plots (wig files) were produced by READemption.
Genome_build: E. faecalis V583 assembly ASM778v1
Supplementary_files_format_and_content: Normalized and non-normalized wig files.

organism: Enterococcus faecalis V583


title: COLO320DM_rep8_gex


title: Undifferentiated/proliferative CAD rep1

description: Sample 1_PRO1


title: WT3_LV (RE1 KO control)


title: Dex-differentiated CAD  rep1

description: Sample 4_DEX1


title: Enterococcus faecalis +TEX [ID-005277]

description:
dRNA-seq
TEX-treated total RNA.


title: WT2_LV (RE1 KO control)


title: Chopp71: MHCII_deficient_replicate2

data_processing:
Basecalls performed with Illumina RTA 2.4.6
Demultiplexing with Bcl2fastq 2.17
10x data for scATAC samples are run through cellranger ATAC (v1.0) software to produce the fastqfiles
The fastq files are processed through cellranger, including alignment, identification of cut sites, and peak calling.
Genome_build: mm10
Supplementary_files_format_and_content: raw_peak_bc_matrix.h5: Raw peak barcode matrix
Supplementary_files_format_and_content: fragments.tsv: Fragment file
Supplementary_files_format_and_content: fragments.tsv.gz.tbi: Fragment file index
Supplementary_files_format_and_content: singlecell.csv: Metadata

extract_protocol:
Nuclei were isolated following the recommended protocol from 10X Genomics. Transposition and scATACseq capture was performed with the 10X Chromium Single Cell ATAC Solution (v1.0) , following the manufacturer's recommended protocol
Libraries were run on a NextSeq500, Parameters:50bp (Read1), 8bp (Index1), 16bp (Index2), 50bp (Read2), Indexing 2 samples (SCAF1016_II, SI-NA-G5; SCAF1017_B, SI-NA-G6)

value: IAB-/-

tag: flow markers

value: Thymus


title: COLO320DM_rep7_atac

description: Single cell multiome ATAC library


title: Undifferentiated/proliferative CAD rep3

description: Sample 3_PRO3


title: Enterococcus faecalis -TEX [ID-005242]

description: dRNA-seq


title: Chopp70: B2m_deficient_replicate2

tag: tissue


title: Enterococcus faecium -TEX [ID-005244]

description: dRNA-seq


title: COLO320DM_rep7_gex


title: BMMCs, WT_ST_H3K4me1 rep1

value: Balb/cJ

value: Bone-marrow derived mast cells

tag: chip antibody

value: H3K4me1, (Abcam, ab8895)

tag: genotype

value: wild type

value: IgE anti_TNP and TNP-BSA


title: WT1_LV (RE1 KO control)


title: Enterococcus faecalis +TEX [ID-005276]

description:
dRNA-seq
TEX-treated total RNA.

value: +TEX


title: COLO320DM_rep6_atac

description: Single cell multiome ATAC library


title: Chopp69: MHCII_deficient_replicate1


title: WT_rep2

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
The RNA-Seq alignment and quantification pipeline is available at https://github.com/ren-lab/rnaseq-pipeline. Briefly, reads were aligned to mm10 (GRCm38) and GENCODE GTF version M25 with rnaSTAR77.
PCR duplicates were removed using Picard. Raw reads for each gene were quantified using featureCounts. RPKM values were calculated for each gene
Particularly, we created two extra chromosomes for the two tagged Sox2 alleles. Reads uniquely mapped to egfp and mCherry sequences were counted using samtools. Expression level of Sox2 gene from CAST and 129 allele was calculated by RPKM values of the egfp and mCherry gene, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: embryonic stem cells

growth_protocol: Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.

extract_protocol:
Total RNA from cells was extracted using the TRIzol Plus RNA purification kit (Thermo Fisher Scientific, Catlog: 12183555).
RNA-Seq libraries were prepared from 4 µg total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit Set A (RS-122-2101; Illumina) or Set B (RS-122-2102; Illumina). RNA-seq libraries were sequenced on illumine Next-seq 550 and Hi-seq4000 platforms (75-bp paired ends).

value: F123 ESC

value: F1 hybrid (castaneus X 129/SvJae)

value: Wild-type


title: Enterococcus faecalis -TEX [ID-005241]

description: dRNA-seq

value: -TEX


title: WT_rep1


title: Chopp68: B2m_deficient_replicate1


title: COLO320DM_rep6_gex


title: Enterococcus faecalis +TEX [ID-005275]

description:
dRNA-seq
TEX-treated total RNA.


title: ΔZF9-11_Syn1-6_Rad21_rep2

data_processing:
Inserted sequence was add to the mm10 genome. And a customized mm10 genome was indexed by bowtie2-build
ChIP-seq sequencing data was trimmed and aligned to mm10 by bowtie2. Unmapped, multimapped and PCR duplicates were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Signal tracks were generated by bamCoverage with parameters "--normalizeUsingRPKM -bs 50 --smoothLength 150" (deepTools)

extract_protocol: Crosslinked cells were processed by Covaris truChIP Chromatin Shearing kit and chromatin were sonicated to 300-500bp by Covaris M220. ChIP DNA and Input DNA were constucted into illumina Tru-seq libraries as previously described (Jian Yan et al., 2013), followed by size selection for 300-500bp.

value: F1 hybrid (castaneus x S129/SvJae)

value: Syn1-6-insertion, CTCF <delta>ZF9-11


title: Rbs1HTP_wt_2

city: Warsaw

first: Tomasz

middle: Wojciech

last: Turowski

address: Pawinskiego 5a

department: Laboratory of Transcription Mechanisms

country: Poland

institute: Insitute of Biochemistry and Biophysics PAS

description:
NNNCACTAGC_Rbs1HTP_wt_2
RNA covalently attached to Rbs1

data_processing:
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were kept. Barcode is always first segment of each name: NNNAGAGC_BY4741_1.fastq   NNNCACTAGC_Rbs1HTP_wt_2.fastq  NNNGTGAGC_Rbs1HTP_wt_1.fastq
Collapsing reads: To remove PCR duplicates, reads were collapsed usinf fastx_collapser, part of FASTX Toolkit 0.0.14
Debarcoding: The 5' barcodes were removed using pyBarcodeFilter.py v3.0 script from pyCRAC package.
Filtering reads: Reads were trimmed using flexbar v3.4.0 to remove the 3 -linker sequence (TGGAATTCTCGGGTGCCAAGGC) and were additionaly filtered and only 3'linker-containing reads were included to further analyses.  Reads alignment: Reads were aligned to the Saccharomyces cerevisiae genome sequence (Ensembl release EF4.74) by novoalign version 2.07.00.
Reads alignment: Reads were aligned to the Saccharomyces cerevisiae genome sequence (Ensembl release EF4.74) by novoalign version 2.07.00.
Additional processing: novoalign SAM reads were modified using custom made script to keep only the 5' or 3' ends of reads. SAM files were converted to BAM format using samtools v1.9 and BigWig files were generated using bamCoverage v3.1.3.
Genome_build: sacCer3, EF4.74
Supplementary_files_format_and_content: Genomic coordinates of the 3' ends of mapped reads in BigWig format

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilized by in-vivo UV crosslinking

tag: expressing


title: Chopp56: B2m_deficient_replicate2

data_processing:
Basecalls performed with Illumina RTA 2.4.6
Demultiplexing with Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger (v2.2) software to produce the fastqfiles
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: mm10
Supplementary_files_format_and_content: h5

extract_protocol:
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics)
Libraries were pooled and sequenced with paired-end reads of 26x98bp or 26x57bp on a NextSeq500 sequencer (Illumina)


title: Chopp55: MHCII_deficient_replicate1


title: COLO320DM_rep4_atac

description: Single cell multiome ATAC library

data_processing:
Processed with cellranger-arc pipeline, version 1.0.0
Genome_build: hg19
Supplementary_files_format_and_content: Fragment files (single cell ATAC)
Supplementary_files_format_and_content: mtx  (single cell RNA)


title: COLO320DM_rep5_gex


title: RE1 KO_mut3_LV

value: FVB

tag: age

value: 8-12 weeks


title: Rbs1HTP_wt_1

description:
NNNGTGAGC_Rbs1HTP_wt_1
RNA covalently attached to Rbs1


title: ΔZF9-11_Syn1-6_CTCF_rep2


title: BMMCs, WT_ST_RNA rep3

data_processing:
The raw reads were analyzed and quality checked by FastQC.
The reads were aligned to the mm10 reference genome (GRCm38) using the Spliced Transcripts Alignment to a Reference (STAR, version 2.4.0.1) software (Dobin et al., 2013).
The aligned reads were assembled into reference transcripts using Cufflinks (version 2.2.1). The differential gene expression between the resting and stimulated samples was analyzed using Cuffdiff (Trapnell et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample .

extract_protocol:
To prepare RNA samples for RNA-seq, total RNA from 1x106 BMMCs that were not treated or treated with IgE receptor crosslinking were isolated using RNeasy mini kit (Qiagen), which was treated with DNase I according to manufacturer’s instructions. The quality of RNA was analyzed by using Agilent Technologies 2100 Bioanalyzer.
RNA-seq library was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770S, New England Biolabs, Ipswich, MA). Briefly, polyA mRNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). The isolated mRNA was fragmented, reverse transcribed into cDNA, end-repaired, and adaptor-ligated. The ligated samples were USER enzyme digested and PCR amplified and purified using AMPure-XP beads (Beckman Coulter Life Sciences, A63881, Indianapolis, IN). The quality and quantity of RNA libraries were assessed on an Agilent Technologies 2100 Bioanalyzer.


title: Chopp54: B2m_deficient_replicate1


title: COLO320DM_rep4_gex

extract_protocol: 10X Genomics Single Cell Multiome ATAC + Gene Expression Kit


title: BY4741_1

description:
NNNAGAGC_BY4741_1
negative control

value: Rbs1 with no tag (control)


title: ΔZF9-11_Syn1-6_CTCF_rep1


title: Chopp78: ThpokWT_replicate2

data_processing:
Basecalls performed with Illumina RTA 2.4.6
Demultiplexing with Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger (v3.1.0) software to produce the fastq files.
The fastq files are processed through the cellranger count to get differential expression counts.
Genome_build: mm10
Supplementary_files_format_and_content: h5 files

extract_protocol:
Single Cell 5' Reagent Kits v1.1 per the manufacturer instructions (10X genomics)
Libraries were pooled and sequenced with paired-end reads of 26x98bp or 26x57bp on a NextSeq500 sequencer (Illumina)

value: Thpok fl/fl; ThpokGFP; Cd4-Cre positive

value: Mixture of ThpokGFP+ and CD69- DP


title: ΔZF9-11_Syn1-6_Rad21_rep1


title: COLO320DM_rep5_atac

description: Single cell multiome ATAC library


title: COLO320DM_rep3_atac

description: Single cell multiome ATAC library


title: BMMCs, Gata2_WT_ST_ATAC-seq rep1


title: Chopp57: MHCII_deficient_replicate3

value: IAB-/-

value: Thymus


title: COLO320DM_rep3_gex


title: nBd_Syn1-6_swap_Rad21_rep1


title: Chopp76: ThpokWT_replicate1


title: ssz1∆_rep2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description:
ssz2
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)

data_processing:
Library strategy: 5PSeq
Base-calling was done during processing of sequencing data with the Illumina pipeline casava v1.8.2.
For each read we trimmed the first 8 nt (UMI, unique molecular identifier) and aligned the rest to S. cerevisiae genome (version R64-1-1) using Novoalign V3.02.05 (http://www.novocraft.com) with default settings. Reads with the same 5’mapping site and UMI were considered PCR duplicates and omitted from the analysis.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads for positive and negative strand.

growth_protocol: Saccharomyces cerevisiae grown in YPGal at 30°C.

extract_protocol:
RNA was extracted from yeast cells using the hot phenol procedure. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
5PSeq methods was performed as previously described (PMID: 26820793). 100µg of total RNA was used as input. In brief, an RNA oligo (rP5_RND) containing an Illumina adaptor and unique molecular identifiers (UMI) was ligated to the intermediates of mRNA co-translation degradation (5’P). Partially polyadenylated molecules were enriched using Dynabeads oligo(dT)25 and used for the generation of Illumina-compatible libraries. Libraries were PCR amplified (18 cycles). Ampure beads size selected libraries with an average length of 346 nt were sent for sequencing.

treatment_protocol: Cells were shifted for 16h to selective SD media.

value: ssz1::HIS3MX6 rpl3::kanMX4 [pLCGTA-RPL3] [YCplac22-RPL3]

tag: parental strain


title: COLO320DM_rep2_atac

description: Single cell multiome ATAC library


title: Syn1-6_swap_Rad21_rep2


title: Chopp75: ThpokKO_replicate1

value: Thpok fl/fl; ThpokGFP; Cd4-Cre negative

value: Mixture of ThpokGFP+, CD8SP, and CD69- DP


title: ssz1∆_rep1

description:
ssz1
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)


title: rpl3[W255C]ssz1∆_rep2

description:
rplssz2
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)

value: ssz1::HIS3MX6 rpl3::kanMX4 [pLCGTA-RPL3] [YCplac22-rpl3-W255C]


title: Syn1-6_swap_Rad21_rep1

value: F123 ESC


title: rpl3[W255C]zuo1∆_rep2

description:
rplzuo2
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)

value: zuo1::HIS3MX6 rpl3::kanMX4 [pLCGTA-RPL3] [YCplac22-rpl3-W255C]


title: RNA_seq-B6xC3H-B_cell-DS38895

city: New York

first: Matthew

middle: T

last: Maurano

state: NY

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU School of Medicine

data_processing:
Trimmed to remove low-quality sequence or adapter contamination using the trimmomatic tool (Parameters: TOPHRED33 ILLUMINACLIP: TruSeq3-PE2.fa:2:5:5:1:true MAXINFO:27:0.95 TRAILING:20 MINLEN:27')
Reads were mapped with Burrows-Wheeler Aligner to the mouse reference assembly and the strain-specific genome (Parameters: bwa aln -n 0.04 -l 32 -t 2 -Y)
Alignments were post-processed with a custom Python script using pysam to retain only properly-paired or single-end reads mapping  uniquely to the autosomes and chrX with a mapping quality of at least 20. Paired end reads were required to have an inferred template length of less than 500 bp.
Duplicate reads were flagged on a per-library basis using Samblaster
Mapped tags were converted to BED format using awk and bedops
DNase I hypersensitive sites were identified using hotspot2
RNA-seq eads were mapped to the mm10 reference and strain-specific genomes in parallel using STAR
Transcript counts were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: bed.gz file containing DHS hotspots
Supplementary_files_format_and_content: bigWig files indicate DHS density
Supplementary_files_format_and_content: tsv file containing count data for Gencode M10 transcripts
Supplementary_files_format_and_content: bigWig indicating RNA-seq read denisty

source_name: B cell

extract_protocol:
Whole liver (all lobes), both kidneys and all lobes of the lungs were rapidly dissected from sacrificed mice. Tissues were minced in 2 mm square pieces and resuspended in 5 mL of homogenization buffer per tissue. Nuclei were released using 5-10 strokes in a Dounce homogenizer with a loose-fitting type-A pestle and the resulting homogenate was filtered through a 120µm filter. Marrow was obtained from femurs of 8 week old female mice. B cells were isolated using an AutoMACS (Miltenyi Biotech) to deplete CD43 and Mac-1/CD11b markers. Nuclei were extracted by resuspending cells in buffer A supplemented with 0.015% detergent (IGEPAL-CA630) (Sigma) and incubating for 5-10 minutes on ice.
Fresh nuclei were digested with DNase I for 3 minutes. Fragments <250 bp were recovered by sucrose ultracentrifugation, end-repaired and ligated with adapters compatible with the Illumina sequencing platform. Libraries were amplified using minimal PCR cycles based on a trial qPCR amplification. Total RNA was isolated using the mirVana miRNA Isolation Kit with phenol (AM1560). Spike-in controls were mixed in (Ambion-ERCC Mix, Cat no. 4456740) and Illumina sequencing libraries were made using the RNA TruSeq Stranded total RNA (Illumina).

value: B cell


title: nBd_Syn1-6_swap_Rad21_rep2


title: rpl3[W255C]zuo1∆_rep1

description:
rplzuo1
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)


title: COLO320DM_rep1_gex


title: RNA_seq-B6xSPRET-Liver-DS37600

source_name: Liver

value: Liver


title: Chopp77: ThpokKO_replicate2


title: nBd_Syn1-6_scramble_Rad21_rep1

value: F1 hybrid (castaneus x S129/SvJae)


title: zuo1∆_rep2

description:
zuo2
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)

value: zuo1::HIS3MX6 rpl3::kanMX4 [pLCGTA-RPL3] [YCplac22-RPL3]


title: RNA_seq-B6xSPRET-Kidney-DS37587

source_name: Kidney

value: Kidney


title: Chopp12: MHC-I signaled CD4+CD8int thymocytes replicate 1

data_processing:
Basecalls performed with Illumina RTA 1.18.66.3
Demultiplexing with Bcl2fastq 2.17
Filtering with Trimmomatic 0.36
Alignment--STAR aligner 2.4.0 to mm10
Counts per million normalized BigWig files performed with DeepTools
Read counts with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Htseq count table, counts per million normalized bigwig

extract_protocol:
RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMART-seq Ultra Low Input RNA kit (Takara) and Nextera XT DNA (Illumina), paired-end 2x150

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, I-AB deficient recipient

tag: surface markers

value: CD44low CD69+ ThpokGFP- Runx3RFP- CD8aint CD4+


title: Syn1-6_scramble_Rad21_rep2


title: Syn1-6_scramble_Rad21_rep1


title: MMC70_RAP_rep1

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

data_processing:
Demultiplexing of reads from superpools into separate pools was performed with bcl2fastq.
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
RNA peak calling performed using ExomePeak R package
Genome_build: hg19
Supplementary_files_format_and_content: list of significantly enriched RNA peaks present in both RAP replicates

source_name: primary melanoma cell line MMC70

extract_protocol:
The cells were lysed in lysis buffer containing 1%SDS, 50 mM Tris-HCl, 1mM EDTA, 1mM DTT , 1mM PMSF, sonicated and hybridized to TINCR antisense probes for 4 h at 37C
RNAseqV2Trueseq Library Prep Kit (Illumina). The libraries were prepared in two biological replicates for each condition (odd and even antisense probes)

treatment_protocol: The cells were crosslinked with 1% gluthgaraldehyde for 10 min at RT

value: primary melanoma cell line

tag: passage

tag: melanoma mutation

value: BRAFWT

tag: molecule subtype

value: RNA antisense pulldown even probes


title: nBd_Syn1-6_scramble_Rad21_rep2


title: Chopp53: ThpokCtrlChip

data_processing:
Alignment--bowtie2 (v2.3.4) --end-to-end --sensitive --no-unal
Filtering with samtools (v1.6) -q 20
Sorting and indexing with samtools
Convert to bed with bedtools (v2.29.2)
Remove blacklisted regions with bedtools
Convert bamfile to counts per million normalized bigwig with Deeptools (v3.3.0)
Peak calling with Macs2 (v2.2.4) --nomodel --nolambda --extsize 300 -q 0.9 --keep-dup-all
Genome_build: mm10
Supplementary_files_format_and_content: Counts per million normalized bigwig file

extract_protocol:
CD4SP thymocytes were sorted and fixed in 1% formaldehyde. Cells were sonicated, lysates clarified, and protein-DNA complexes immunoprecipitated.
Libraries were prepared and sequenced following standard Illumina protocols

value: Thpok+/+ Rosa26BirA+

value: CD44low CD25- CD4+ CD8a-

value: Thymus


title: rpl3[W255C]_rep1

description:
rpl1
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)


title: zuo1∆_rep1

description:
zuo1
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)


title: rpl3[W255C]ssz1∆_rep1

description:
rplssz1
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)


title: MMC70_RAP_input

value: RNA antsisense pulldown input


title: WM902B_RAP_rep2

source_name: primary melanoma cell line WM902B

value: RNA antisense pulldown odd probes


title: WM902B_RAP_rep1


title: rpl3[W255C]_rep2

description:
rpl2
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)


title: RNA_seq-B6xPWK-Kidney-DS37491


title: WM902B_RAP_input


title: COLO320DM_rep2_gex


title: COLO320DM_rep1_atac

description: Single cell multiome ATAC library


title: RNA_seq-B6xSPRET-Lung-DS37580

source_name: Lung

value: Lung


title: RNA_seq-B6xPWK-Liver-DS37504


title: Chopp52: ThpokChIP_replicate3

value: ThpokBio/+ Rosa26BirA+


title: MMC70_RAP_rep2


title: Chopp50: ThpokChIP_replicate1


title: RNA_seq-B6xPWK-Lung-DS37484


title: RPL3_rep2

description:
wt2
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)


title: Night sample - Replicate 3

status: Public on Nov 24 2020

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

data_processing:
Sequencing was performed using SOLiD 3 sequencer according to the manufacturer’s instructions. 3 samples were sequenced for each condition and each sequencing generated 30 to 55 million reads
Reads mapping and transcriptome index building were performed with Bowtie (v1.2.3) using -C option. Colorspace reads were mapped to S. pistillata gene models as single-end alignments.
Differential expression analysis was performed using DESeq2 R package
Genome_build: S.pistillata gene models (available at http://spis.reefgenomics.org/download/Spis.genome.annotation.CDS.longest.fa.gz)
Supplementary_files_format_and_content: tab-delimited text file includes Raw counts for each sample

organism: Stylophora pistillata

source_name: coral branch apex tissue

growth_protocol: Colonies were supplied with water from the Mediterranean Sea (exchange rate 2% per hour) under controlled conditions, including a semi-open circuit, a temperature of 25°C, salinity of 38, irradiance of 175 µmol photons m-2 s-1 on a 12:12 photoperiod. Corals were fed daily with frozen rotifers and twice a week with artemia nauplii. Microcolonies were propagated by cutting terminal portions of branches (6–10 mm in length) from three syngenic parent colonies, hung by nylon thread with a specific label in a dedicated aquarium under similar conditions, and left for 10 days for recovery prior to experiments

extract_protocol:
Total RNA was extracted with Trizol Reagent (Invitrogen). Frozen coral samples were ground into powder in a cryogrinder (Freezer/Mill 6770, Spex Sample Prep) and dissolved in 20 mL Trizol Reagent. Samples were vortexed and incubated at room temperature (RT) for 5 min. Three centrifugations (10 min, 15,000 × g, 4°C) were performed to remove the skeleton. We added 4 mL chloroform to the last supernatant. Centrifugation (15 min, 12,000 × g, 4°C) was performed to separate the two phases (aqueous and phenol-chloroform). RNA remained exclusively in the aqueous phase. The aqueous phase was subjected to another chloroform extraction (v/v). We added 10 mL isopropanol to the second aqueous phase, which was vigorously shaken and incubated for 10 min at RT. Centrifugation (15 min, 12,000 × g, 4°C) was performed to pellet the RNA. The pellet was resuspended in 5 mL 70% ethanol, vortexed vigorously, centrifuged for 5 min at 7,500 × g and 4°C, dried for about 10 min at RT, and then resuspended in 100–200 μL RNase-free water
The concentration and quality of total RNA were assessed with a Bioanalyser and RNA 6000 nano kit. mRNA was prepared with the MicroPoly(A) purist kit (AM1919; Applied Biosystems)

treatment_protocol: AJ/Day (or AN/Night) samples were flash frozen 1 hour before the end of the light (or dark) phase of their photoperiod (, respectively).

tag: photoperiod

value: dark phase

value: coral branch apex tissue


title: RPL3_rep1

description:
wt1
polyA RNA
parental strain: W303-1B (MATα ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1)


title: Night sample - Replicate 2


title: Day sample - Replicate 1

value: light phase


title: Night sample - Replicate 1


title: Day sample - Replicate 3


title: RNA_seq-B6xPWK-B_cell-DS36866

tag: strain

value: B cell


title: Chopp51: ThpokChIP_replicate2

source_name: Thymus


title: nBd_Syn1-6_scramble_CTCF_rep2

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)


title: hESC-RPE, s9_Drug3

data_processing:
[basecalling] Basecalls were performed using Illumina bcl2fastq version 2.17.1.14.
[mapping]  Reads were aligned to the human genome assembly (hg38) using GSNAP (2017-08-15; parameters: --gunzip -A sam  --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-81.ss.hg38.iit) with known splice sites from Ensembl (v81) as support.
[gene counting]  Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.5.3; parameters: -a EnsemblGene-81.hg38.TR.gtf -s 2 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (bfx582.featureCounts.hg38.e81.txt.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'

source_name: Human embryonic stem cells-derived retinal pigment epithelium

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit by lysing the cells inside the wells.
mRNA enrichment and  reverse-transcription into cDNA was done with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocol.

tag: photoreceptor outer segment

value: No

value: MFGE8 0.625 µg/ml+Ramoplanin (10µM)

tag: experiment time

value: 4 hours incubation


title: Chopp17: Semi-Mature CD4SP thymocytes replicate 1

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, b2m deficient recipient

value: CD44low MHC-I-+ CD8alow CD69+ ThpokGFP+ CD4+


title: Pfu RNA repl. 2

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were identified by a 4 nucleotide barcode which was removed
Cutadapt v1.2 was used to remove the 3’ adaptor and discard reads shorter than 15 nucleotides.
The trimmed reads were mapped to a selection of non-coding RNAs of P.furiosus using the Bowtie 2 aligner v 2.1.0 with default settings
Genome_build: ASM730v1
Supplementary_files_format_and_content: RiboMethseq data. Read-end counts and scores for 2´ribose methylation

organism: Pyrococcus furiosus

source_name: Cell culture

growth_protocol: Pyrococcus furiosus cells were grown in 1/2 SME medium (pH 6.5) supplemented with 0.1 % yeast extract, 0.1 % peptone and 0.1 % starch. The gas phase was N2 /CO2 (80:20) and the incubation temperature was 95 °C. The culture was grown for 30 h to a final cell density 3 x 107 cells/mL.

extract_protocol:
RNA was extracted by re-suspending 0.5 g of pelleted cells in 2.5 mL TMN buffer (50 mM Tris-Cl, pH 7.5, 10 mM MgCl2, 100 mM NH4Cl) Cells were run twice through a French press, followed by addition of 4 mL of TRIzol (Life Technologies). After 5 min incubation at room temperature, 0.8 mL chloroform was added. The samples were centrifuged at 12,000X g for 5 min and the aqueous phase transferred to a new tube for extraction with phenol/chloroform. Total RNA was then precipitated by ethanol precipitation.
RNA was degraded by alkaline into short fragments and the 20-40 nt fraction purified from gels. Then, adaptors were ligated to the library fragments using a modified Arabidopsis tRNA ligase. Finally, the library was sequenced on the Ion Proton sequencing platform.
Other. Ribomethseq

tag: sample type

value: cells


title: Pfu RNA repl. 1


title: B5

city: Storrs

first: Jose

middle: E

last: Manautou

state: Connecticut

address: 69 N Eagleville Rd, Room 517

department: Pharmaceutical Sciences

institute: University of Connecticut

data_processing:
Sequencing Reads Filtering was peroformed using SOAPnuke; version:v1.5.2; parameters: -l 15 -q 0.5 -n 0.1
Gene expresssion analysis was performed using Bowtie2 : Version: v2.2.5; Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 - X1000--no-mixed--no-discordant -p1-k200
Differetial gene expression analysis was performed using  DEGseq: Parameters:FoldChange>=2 and Adjusted P value<=0.001;  PossionDis: Parameters: Fold Change >= 2.00 and FDR <= 0.001
Data presented as FPKM
Genome_build: mm9
Supplementary_files_format_and_content: excel file

source_name: White adipose tissue (epididymal fat)

extract_protocol:
White adipose tissue (epididyma fat) were collected from mice, flash frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent
RNA was purified using the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification,the RNA is fragmented into small pieces using divalent cations under elevated temperature.The cleaved RNA fragments are copied into first strand cDNA using reverset ranscriptase and random primers.This is followed by second strand cDNA synthesis using DNA PolymeraseI and RNaseH. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter.The products are then purifiedand enriched with PCR amplificat ion.We then quant ified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNAcircle), which gave the final library.DNA nanoballs(DNBs)were generated with the ssDNAcircle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100bp were read through on the BGISEQ-500platform for the following data analysis study.For this step, the BGISEQ-500 platform combines the DNAnanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

value: White adipose tissue (epididymal fat)

value: 16 weeks age old

value: Mrp4 KO (Mrp4-/-)


title: BMMCs, Gata2_KO_ST_ATAC-seq rep2

data_processing:
Raw sequencing reads (average 118.2 million reads, 2 biological replicates for each group) were adaptor trimmed by Trimmomatic 0.33 and the quality of sequenced data was analyzed by FastQC.
The trimmed reads were aligned to the mm10 reference genome using Bowtie2 with -very-sensitive and -x 2000 parameters.
The read alignments were filtered using SAMtools (version 1.7) to remove mitochondrial genome and PCR duplicates.
Peaks were identified by MACS2 with the q-value cut-off of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Tdf and bedgraph files for each sample

source_name: BMMCs

extract_protocol:
Briefly, 50,000 BMMCs that were either untreated or treated with IgE receptor crosslinking were spin down and washed with cold PBS once. Then the cells were resuspended in 50 uL cold ATAC-RSB-lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin) and incubated for 3 minutes. The lysis buffer was immediately washed out with 1 mL ATAC-RSB buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% Tween-20). The cell pellet was resuspended in 50 ul transposition mixture (25 uL 2X TD buffer, 2.5 uL transposase (Illumina, FC-121-1030), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O) and incubated at 37 C for 30 minutes. The reaction was stopped by adding 2.5 uL of 0.5M EDTA pH 8 and transposed DNA was purified using Qiagen MiniElute PCR purification kit (Qiagen).
Purified DNA was amplified using the following condition: 72℃ for 5 min, 98 ℃ for 30 s, and 7 cycles: 98 ℃ for 10 s, 63 ℃ for 30 s, 72 ℃ for 1 min. The amplified libraries were cleaned up, size-selected, and the quality and quantity of libraries were assessed on an Agilent Technologies 2100 Bioanalyzer.
Omni-ATAC-seq

tag: cell type

value: Bone-marrow derived mast cells

tag: treatment

value: IgE anti_TNP and TNP-BSA


title: B2

tag: tissue


title: A3

value: wild type


title: A4


title: B1


title: A1


title: A2


title: B4


title: Day sample - Replicate 2

value: coral branch apex tissue


title: YP3

city: Stanford

first: Paras

middle: Singh

last: Minhas

state: California

address: 1201 Welch Road

department: Neurology & Neurological Sciences

institute: Stanford University

description: NanoString nCounter Mouse RNA Expression Assay

hyb_protocol: 65 degrees C for 16h

scan_protocol: Cartridges were scanned at 280 fields of view (FOV)

data_processing:
Raw data counts were normalized using the genometric mean of both postivie control probes (technical variability) and housekeeping gene probes (assay input variability).
Normalized data was uploaded to the interactive analysis platform Rosalind (https://rosalind.onramp.bio/) with a HyperScale architecture developed by OnRamp Bioinfromatiocs, inc. (San Diego, CA). The limma R library1 was used to calculate fold changes and p-values and perform optional covariate correction.

label: biotin

source_name: Peritoneal Macrophages

label_protocol: See manufacturer's website (www.nanostring.com)

extract_protocol: Qiagen Rneasy Mini Kit on peritoneal mouse macrophages

treatment_protocol: PF044 (2.5mg/kg/d) for 6 weeks by oral gavage in young and aged mice

tag: agent


title: YP1


title: YV1


title: AP2


title: YP2


title: AV2


title: AV3


title: YV3


title: YV2


title: AP3


title: rmr12-3 rep3

city: COLUMBUS

first: Natalie

middle: Christine

last: Deans

state: OH

address: 318 W. 12th Ave, 500 Aronoff

department: Molecular Genetics

institute: The Ohio State University

description:
rmr12-3_rep3
small RNA
cluster_characteristics.csv
cluster_counts.csv

data_processing:
Quality filtering: bbduk (ktrim=r k=18 mink=11 hdist=1 tp=4 ftl=4 minlen=18 maxlength=30)
Alignment of mate 1 (sense reads) to the genome and cluster calling: ShortStack with options (--mismatches 0 --mmap n --nohp --pad 75 --mincov 91). Minimum depth represents 0.5 reads per million clean reads (18-30nt).
Genome_build: B73_Refgen_v4
Supplementary_files_format_and_content: csv files with ShortStack results including position and characteristics for each cluster called and counts for each cluster per library.

organism: Zea mays

source_name: Aerial seedling

growth_protocol: Seedlings were grown in a soil flat in a growth chamber with 15hr light (25oC 300-450 µmol m-2 s-1 light intensity) 9hr dark (22oC) to day-8.

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions.
Small RNAs were enriched and libraries were prepared for sequencing using the BIOO Scientific NEXTFLEX Small RNA-Seq kit V3.

tag: strain/background

tag: genotype/variation

value: Aerial seedling


title: AV1

tag: age


title: AP1


title: rmr12-3 rep2

description:
rmr12-3_rep2
small RNA
cluster_characteristics.csv
cluster_counts.csv


title: Non-mutant rep2

description:
Rmr12_rep2
small RNA
cluster_characteristics.csv
cluster_counts.csv


title: rmr12-3 rep1

description:
rmr12-3_rep1
small RNA
cluster_characteristics.csv
cluster_counts.csv


title: Non-mutant rep1

description:
Rmr12_rep1
small RNA
cluster_characteristics.csv
cluster_counts.csv


title: BCPAP_siEPB41L4A_rep3

city: Columbus

first: Albert

last: de la Chapelle

address: 460 W. 12th Avenue

institute: The Ohio State University Wexner Medical Center

hyb_protocol: Samples were hybridized using herring sperm DNA, acetylated BSA (50 mg/mL). Eukaryotic Hybridization Controls (Affymetrix) were heated at 65°C for 5 minutes, 99°C for 5 minutes, 45°C for 5 minutes, centrifuged at maximum speed for 5 minutes, then hybridized 16 hours at 45°C at 60 rpm. Fluidics washing is protocol FS450_0001.

scan_protocol: The arrays were scanned with the Affymetrix Genen Chip Scannner 3000 7G system using Affymetrix GeneChip Command Console (AGCC) software.

data_processing: Signal intensities were processed by RMA method using Affymetrix Expression Console software

label: Biotin

source_name: BCPAP cells treated with EPB41L4A siRNA for 72 hours

label_protocol: 5.5 ug of single-stranded cDNA were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: BCPAP cells were seeded in 6-well plate and grown to 75% confluence at the time of transfection.

extract_protocol: RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 40 uM siEPB41L4A or siNS were transfected into BCPAP cells using 7.5 ul Lipofectamine RNAiMAX (Thermo Fisher Scientific). Cells were harvest after 72 hours of treatment.

tag: cell line

value: BCPAP


title: BCPAP_siEPB41L4A_rep2


title: CM-D2-Mock_2

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced with 50bp single end reads on an Illumina HiSeq3000.
The reads were mapped with STAR 2.5.3a to the human genome (hg38) for the cultured human cell libraries or mouse genome (mm10) for the mouse cell libraries.
The counts for each gene were obtained using --quantMode GeneCounts in STAR commands, and the other parameters during alignment were set to default.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample

source_name: human in vitro hpsc derived cardiomyocyte

growth_protocol: All animal studies were approved by the Animal Research Committee, University of California, Los Angeles. Male C57Bl/6 mice (000664, Jackson Labs) (14-17 weeks) were housed in groups and fed standard chow diets. AAV9-CMV-hACE2 (AAV- 200183, Vector Biolabs) or control AAV9-CMV-eGFP viruses were purchased from Vector Biolabs. Animals were injected intravenously with 100-μl injection containing 2x1012 genomic copies of AAV-CMV-hACE2 or control (AAV-CMV-eGFP). Animals were housed in BSL-3 facility for the duration of the experiment (n=5/cage). Cage food weight and individual mouse body weight were recorded daily after SARS-CoV- 2 virus infection.

extract_protocol:
All samples were stored in RNA later stabilization solution and subsequently total RNA was extracted using RNA mini Kit (7326830, BioRad). cDNA was synthesized by using iScript cDNA Synthesis Kit (1708890, BioRad) and qPCR performed.
For RNA-sequencing, libraries were prepared by the Technology Center for Genomics & Bioinformatics at UCLA using Illumina TruSeq Stranded Total RNA Sample Prep kit and sequenced with 50bp single end reads on an Illumina HiSeq3000.

treatment_protocol: SARS-CoV-2, isolate USA-WA1/2020, was got from the Biodefense and Emerging Infections (BEI) Resources of the National Institute of Allergy and Infectious Diseases (NIAID). SARS-CoV-2 was passaged once in Vero-E6 cells (ATCC) and viral stocks were aliquoted and stored at -80 C. Virus titer was determined by plaque assay using Vero E6 Cells. 200μL of SARS-CoV2 (0.5 x 106 PFU/mL) was injected intraperitoneally.

value: mock


title: COLO320HSR_rep2_gex

first: Howard

last: Chang

address: CCSR 2130, 269 Campus Drive

description: Single cell multiome gene expression library

data_processing:
Processed with cellranger-arc pipeline, version 1.0.0
Genome_build: hg19
Supplementary_files_format_and_content: Fragment files (single cell ATAC)
Supplementary_files_format_and_content: mtx  (single cell RNA)

source_name: COLO320-HSR cells


title: CM-D2-Mock_1

value: human in vitro hpsc derived cardiomyocyte


title: CM-D2-cov2_3


title: BCPAP_siEPB41L4A_rep1


title: BCPAP_siEPB41L4A_rep4


title: CM-D2-cov2_2


title: CM-D1-Mock_3


title: quercetin-treated oocytes 3

city: JINAN

first: Yongzhi

last: Cao

address: NO. 44 Wenhuaxi Road

country: China

institute: Shandong University

description:
Quercetin3
SMART-Seq
T3
gene_expression.txt

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8.
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000 --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generated and normalized using Cufflink version 2.0.2.Linux_x86_64; the normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed using DEGseq function package in R program version 2.10.0.
Genome_build: GRCm38.91 mm10
Supplementary_files_format_and_content: gene_expression.txt: Tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample.

source_name: ovary

extract_protocol:
Smart-seq ® HT Kit was used to build the database of samples. In the experiment, the standard operating procedure manual provided by the Kit manufacturer was strictly followed, and the total RNA of samples was extracted.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: Samples included groups collected with or without 10 μM quercetin treatment.

value: Kunming (KM)

value: MII stage oocytes

tag: Sex

value: female

value: 9-10 months

value: quercetin


title: CM-D1-cov2_1


title: control oocytes 3

description:
Control3
SMART-Seq
C3
gene_expression.txt

value: control


title: control oocytes 2

description:
Control2
SMART-Seq
C2
gene_expression.txt


title: CM-D1-Mock_1


title: REP-HepG2_01

city: Wako

first: Luc

last: Gailhouste

state: Saitama

address: 408 Main Research Building, 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

hyb_protocol: Agilent one-color gene expression hyb/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The raw data were processed using Agilent’s Feature Extraction Software version 10.7.3.1 to analyze the array and calculate the intensities of the measured spots.

source_name: Epigenetically reprogrammed HepG2 cells, 5-AZA (2.5µM) 10 days

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol. Cyanine-3 (Cy3)

growth_protocol: Human HepG2 cells were from the American Type Culture Collection and maintained in DMEM (Gibco) supplemented with penicillin (50 IU/mL; Gibco), streptomycin (50 µg/mL; Gibco), and 10 % fetal bovine serum (FBS; Thermo Scientific).

extract_protocol: Total RNA was purified using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA samples were quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and the integrity of the RNA was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: For gene expression assessment, total RNA was collected from HepG2 cells after 10 days of treatment. The demethylating agent 5-azacytidine (5-AZA; PubChem CID: 9444) was from Sigma (#A2385). The compound was dissolved in phosphate-buffered saline as a 10 mM stock, filtered (0.22 µM), and stored at -20°C. The cells were treated with 5-AZA at a concentration of 2.5 µM. The drug and medium were replaced daily.

value: hepatocellular carcinoma

value: after epigenetic reprogramming


title: quercetin-treated oocytes 2

description:
Quercetin2
SMART-Seq
T2
gene_expression.txt


title: CM-D1-cov2_2


title: CM-D2-cov2_1


title: HepG2_01

source_name: HepG2 cells, negative control


title: CM-D1-Mock_2


title: CM-D2-Mock_3


title: quercetin-treated oocytes 1

description:
Quercetin1
SMART-Seq
T1
gene_expression.txt


title: CM-D1-cov2_3


title: control oocytes 1

description:
Control1
SMART-Seq
C1
gene_expression.txt


title: NG2 glia-1

city: Shanghai

first: Xiaoqi

last: Hong

address: 280 South Chongqing Road, Huangpu District, Shanghai, China, 200025

department: Discipline of Neuroscience and Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The Cell Ranger software pipeline (version 3.0.0) provided by 10xGenomic was used to demultiplex cellular barcodes, map reads to the mm10 reference assembly (v1.2.0, 10x Genomics), and generate gene UMI (unique molecular identifier) counts versus cells barcode matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: NG2 glia from hippocampus

extract_protocol:
NG2 glia with GFP fluorescent labeling from Pdgfra-creERTM; mGFP mouse brain was sorted and suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume bovine serum albumin (BSA). Then the cells were added to each channel, and the target cell will be recovered. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. The cDNA was generated by reverse transcription and amplified.
Chromium Single Cell 3ʹ Reagent Kits v3  was used  for the construction of sequencing libraries according to the manufacture’s introduction.

tag: strain background

value: Pdgfra-creERTM; Rosa26-mGFP

value: Brain


title: REP-HepG2_02


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G10_AD004

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT 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 INTACT
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 P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

value: brain

tag: source

value: MOp

tag: target

value: SSp

tag: gender


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F9_AD008

tag: strain

value: ACA

value: TH


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F9_AD001


title: HepG2_02


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F8_AD010

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F8_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F7_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F8_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F6_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F7_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F5_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F6_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F6_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F5_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F5_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F7_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F5_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F5_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F5_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F4_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F4_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F4_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F4_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F4_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F5_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F3_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F3_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F3_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F2_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F2_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F2_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F2_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F1_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F12_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F1_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F12_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F11_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F11_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F11_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F11_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F10_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F10_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F2_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F11_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F10_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F10_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E8_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E8_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E8_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E8_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E8_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E7_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_F3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E7_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E9_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E6_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E6_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E5_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E5_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E6_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E5_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E4_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E4_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E5_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E4_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E4_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E4_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E3_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E3_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E3_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E3_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E3_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E2_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E2_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E2_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E2_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E1_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E1_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E2_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E1_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E4_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E12_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E12_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E1_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E11_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E11_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E11_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E11_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E11_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E10_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E10_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E10_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D9_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D8_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E11_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E12_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D8_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D8_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D7_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D7_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D8_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_E10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D6_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D7_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D6_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D6_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D7_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D6_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D5_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D6_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D5_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D5_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D5_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D4_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D4_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D4_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D4_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D5_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D5_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D4_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D3_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D3_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D3_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D3_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D2_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D2_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D2_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D1_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D3_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D1_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D1_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D2_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D12_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D11_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D10_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D10_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C9_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D1_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C8_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_D10_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C8_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C7_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C9_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C7_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C7_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C6_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C8_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C6_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C6_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C5_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C6_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C4_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C5_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C4_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C4_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C3_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C5_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C3_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C3_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C3_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C2_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C2_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C2_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C2_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C4_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C1_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C1_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C4_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C12_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C1_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C12_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C12_AD001