title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G2_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G2_ad008

status: Public on Dec 02 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

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.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: SSp

tag: target

value: MOp

tag: gender

value: female


title: NT_1 (S13)

city: Rehovot

first: Jung-Seok

last: Kim

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Putative open chromatin regions (peaks) were called using HOMER (Heinz et al., 2010) (using parameters compatible with IDR analysis: –L 0 –C 0 –fdr 0.9). The irreproducible discovery rate (IDR) was computed for each peak using the Homer peak score for each replicate experiment ; peaks with IDR > 0.05 were filtered away.
Genome_build: mm9
Supplementary_files_format_and_content: alignment files
Supplementary_files_format_and_content: peaks files

source_name: Mouse brain

extract_protocol:
Brain homogenization and microglia enrichment
20,000–50,000 cells were used for ATACseq (Buenrostro et al., 2013) applying described changes (Lara-Astiaso et al., 2014). Briefly, nuclei were obtained by lysing the cells and nuclei were pelleted by centrifugation for 20 min at 500 g, 4 °C using a swing rotor. Supernatant was discarded and nuclei were re-suspended in 25 μl reaction buffer. The reaction was incubated at 37 °C for 1 hr. DNA was released from chromatin by adding 5 μl of cleanup buffer, followed by an incubation for 30 min at 40 °C. Tagmentated DNA was isolated using 2× volumes of SPRI beads and eluted in 21 μl. For library amplification, two sequential PCRs (nine cycles, followed by an additional six cycles) were performed in order to enrich small tagmentated DNA fragments. We used the indexing primers as described (Buenrostro et al., 2013) and KAPA HiFi HotStart ready mix. After the first PCR, the libraries were size-selected using double SPRI bead selection. Then the second PCR was performed with the same conditions in order to obtain the final library. DNA concentration was measured with a Qubit fluorometer,  and library sizes were determined using TapeStation. Libraries where sequenced on the Illumina NextSeq 500, obtaining an average of 20 million reads per sample.

treatment_protocol: 2.5mg/kg LPS injection

value: Brain

tag: cell type

value: Microglia

tag: treatment

value: Steady state

tag: genotype


title: atac_emf1_1

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Quality trimming and adapters removal were performed using Trimmomatic
PCR duplicates were discarded from the mapped reads using Picard
Reads mapped to the blacklisted genomic regions were eliminated using samtools
Read mapping to the reference genome was performed using bowtie with parameters -v 2 --best --strata -m 1 (http://bowtie-bio.sourceforge.net/index.shtml)
Peak calling was performed using MACS2 with default parameters (https://github.com/taoliu/MACS)
BigWIG files with CPM normalized signal were generated using the deepTools utility bamCoverage with a bin size of 10 (https://deeptools.readthedocs.io/en/latest/)
Subsequent data analysis and visualization was performed using the R bioconductor packages ChIPpeakAnno, ChIPSeeker, limma and ClusterProfiler.
Genome_build: tair10
Supplementary_files_format_and_content: signal in bigWIG format

organism: Arabidopsis thaliana

extract_protocol:
Nuclei was extracted from 10-day-old whole seedlings. Next, 30,000 nuclei were counted and resuspended in 50 μL transposition reaction mix using the TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme, TD501). Reactions were incubated for 30 min at 37°C before isolation DNA using the VAHTSTM DNA Clean Beads (Vazyme, N411)
Libraries were prepared by PCR amplification using two index (i5 and i7) Illumina barcodes (Vazyme, TD202) with 13 cycles. Libraries were purified with a VAHTSTM DNA Clean Beads.

tag: ecotype

value: seedlings


title: N2, repeat 1

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

description:
Sample_N2_1
processed data file: featureCounts.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to the C. elegans genome (WBcel235) using STAR (version 2.5.3a) with the following parameter (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
featureCounts (subread-1.5.2) was used to count the features after the alignment.
Bioconductor packages edgeR (version 3.10.0 ) was used for differential gene expression analysis.
Genome_build: WBcel235 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6/)
Supplementary_files_format_and_content: featureCounts.txt: Tab-delimited text file includes the raw count values from featureCounts for each sample.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: L4 Worms

growth_protocol: Grew on OP50 20c to L4 stage.

extract_protocol:
Chloroform Ethanol extraction.
Illumina Index in adapters: TruSeq.
MultiPLEX single End.

treatment_protocol: None.

tag: strain/background

tag: genotype/variation

value: WT

value: Whole body

tag: developmental stage


title: atac_clfswn_2

value: clfswn


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G2_ad007

value: male


title: NT_4 (S4)


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G2_ad004

value: ACA

value: VISp


title: NT_3 (S3)


title: atac_clfswn_1


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G2_ad001


title: atac_bmi1abc_2


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G1_ad012


title: N2, repeat 3

description:
Sample_N2_3
processed data file: featureCounts.txt


title: NT_2 (S2)


title: NT_1 (S1)


title: emf1_3

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using E.Z.N.A.® Plant RNA Kit (Omega, R6827-01)
Libraries were prepared using 1 μg of total RNA with the VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Vazyme, NR603) according to the manufacturer’s instructions.


title: N2, repeat 2

description:
Sample_N2_2
processed data file: featureCounts.txt


title: ATFS-1 (null), repeat 1

description:
Sample_null_1
processed data file: featureCounts.txt

value: atfs-1 (null)


title: atac_emf1_2


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G1_ad010


title: E11.5 TrkC neurons - ATAC rep2

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

institute: The Weizmann Institute

data_processing:
Adapter trimming and filtration of low quality reads using cutadapt 1.18
reads were aligned to the genome using bowtie2 v2.3.5.1
peak calling for the H3K27Ac samples were performed with MACS2 using the default parameters and the WCE samples as controls.
For the ATACseq samples, only properly paired reads with insert size <120bp were selected for downstram analysis
ATACseq peaks were called with macs2 using the parameters -f BAMPE --SPMR -B --nomodel
A list of consensus peaks from every experiment was generated using bedtools, demending an overlap of at least 50% between replicates
Genome_build: mm10

source_name: TrkC neurons of DRG

extract_protocol:
DRG were dissected from E11.5 embryos and dissociated with Trypsin B/Collagenase H.  Cells were PFA fixed and GFP positive cells were FACS isolated and frozen.  50,000 thawed cells were lyzed and sonicated followed by ATAC or anti H3K27ac ab mediated histone-DNA complexes isolation.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for no more than 15 cycles and library fragments up to ~600 bp (insert plus adaptor and PCR primer sequences) were SPRI (x0.55) purified. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

value: dorsal root ganglia (DRG)

value: TrkC proprioceptive neurons

tag: organism

value: Mus musculus

value: Runx3-BAC-GFP-CB6 transgenic mice


title: E11.5 TrkC neurons - input DNA 2

tag: antibodies


title: emf1_1


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G1_ad007

value: brain

value: SSp

value: MOp


title: E11.5 TrkC neurons - ATAC rep1


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G1_ad008

value: female


title: emf1_2


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G1_ad004


title: atac_bmi1abc_1


title: ring1ab_3


title: Whole animal anterior to gills_KD_30DPF_REP3

type: RNA

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

country: United Kingdom

institute: University of Manchester

hyb_protocol: RGT KIT,HYB WASH STAIN for Affymetrix Zebgene 1.0st

scan_protocol: Arrays were  scanned on an Affymetrix GeneChip  scanner and assessed for quality against internal and hybridization controls.

data_processing:
Gene level expression was determined and processing and normalization of gene expression data were performed using a Robust Multi-array Average background correction with quantile normalization. Analysis performed in Qlucore Omics Explorer.
Log2 normalised and scaled (mean of 0, standard deviation of1) RMA values from Qlucore Omics Explorer. Gene level summary of array data.

label: biotin

organism: Danio rerio

source_name: Whole animal anterior to gills 30DPF

label_protocol: GeneChip WT PLUS Reagent Kit for Affymetrix Zebgene 1.0st

growth_protocol: AB zebrafish were maintained under standard conditions (≈28 °C; 14 h light/10 h dark cycle; stocking density < 5 fish per litre) within the Biological Services Unit of The University of Manchester. Embryos were collected and raised in egg water (Instant Ocean salt 60 µg/mL) up to 5 days post-fertilisation (dpf) and transferred to the main aquarium system. Young fry were fed powdered food and rotifers, while older fry and adults were fed powdered food and brine shrimp (ZM Fish Food and Equipment, Winchester, UK). All regulated procedures received ethical approval from the Institution’s ethical review board and were performed under a Home Office Licence (PPL P005EFE9F9 to HAS).

extract_protocol: Total RNA, Qiagen Rneasy

treatment_protocol: In accordance with current guidelines for morpholino use in zebrafish,  the use of morpholino-modified antisense oligonucleotides to knockdown (KD) grb10a was validated in several ways. Morpholinos targeting two distinct sites should yield a similar phenotype, which should display a dose-response effect and be rescuable by RNA co-injection, and a suitable control morpholino with no phenotypic effect should be used to account for microinjection technique. dpf or four (e4i4) were designed by and obtained from Gene Tools, LLC (Philomath, OR, USA) along with a standard control (SC) oligonucleotide targeting human β-globin. Concentrations of ingredients were consistent with standard practice. Phenol red and nCerulean (nuclear-targeting blue fluorescent protein) mRNA were included in each solution to allow monitoring of successful injection. A P-97 Flaming/Brown Micropipette Puller (Sutter Instruments, Novato, CA, USA) was used to generate microinjection needles from 1 mm OD glass capillaries, which were backloaded with 2 μl of injection solution and mounted on a needle holder held in a micromanipulator attached to a PLI-100A Picoliter Injector (Warner Instruments, Hamden, CT, USA). Embryos were injected once, as per established method, into the yolk directly below the cell mass. Embryos were injected before the four-cell stage and were screened for fluorescence at 48 hours post fertilisation (hpf) to ensure constitutive and even uptake of the injection material. Non-uniformly or weakly-fluorescent embryos were removed.

value: AB

value: all tissue anterior to gills

value: KD

tag: time


title: E11.5 TrkC neurons - input DNA 1


title: ring1ab_2

value: seedlings


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G1_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G1_ad001


title: ring1ab_1


title: E11.5 TrkC neurons - H3K27Ac rep2


title: E11.5 TrkC neurons - H3K27Ac rep1


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G12_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G12_ad007


title: clfswn_3


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G12_ad006


title: Whole animal anterior to gills_SC_30DPF_REP2

value: SC


title: Whole animal anterior to gills_KD_30DPF_REP2


title: clfswn_2


title: Whole animal anterior to gills_SC_30DPF_REP1


title: Whole animal anterior to gills_KD_30DPF_REP1


title: clfswn_1


title: Whole animal anterior to gills_KD_20DPF_REP3

source_name: Whole animal anterior to gills 20DPF


title: Vis9A

city: Ithaca

first: David

middle: William

last: McKellar

state: NY

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using spaceranger v1.0 pipeline
Gene expression data was processed with Seurat v3.2.1
Initial data filtering (minium genes to be expressed in an included spot = 500)
Filtering by number of UMIs in included cells (minimum 1000)
Log-normalization of expression data
Spot composition calculated using the R package TED, v1.0
Genome_build: mm10
Supplementary_files_format_and_content: tar.gzped, market exchange format (MEF) for raw, filtered, and scrubbed (SoupX) transcript count matrices; .csv files of single-cell metadata information.
Vis9A_raw_feature_bc_matrix.tar.gz:  raw transcript counts for all cell barcodes (cellranger)
Vis9A_filtered_feature_bc_matrix.tar.gz:  filtered transcript counts (cellranger)
Vis9A_Stitched_Image_0.tif:  stitched H&E image of sample
V19T19-051-D1_Vis9A.json:  filter for spots beneath the tissue slice (Loop Browser)
Vis9A_meta.csv:  Metadata for each spot, including predicted cell type content (BayesPrism)

source_name: Tibialis anterior muscle

extract_protocol:
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v3 kit) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tibialis anterior muscle

value: 5 months

tag: Sex

value: F

value: Notexin injury (Day 7)


title: Vis5A

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using spaceranger v1.0 pipeline
Gene expression data was processed with Seurat v3.2.1
Initial data filtering (minium genes to be expressed in an included spot = 500)
Filtering by number of UMIs in included cells (minimum 1000)
Log-normalization of expression data
Spot composition calculated using the R package TED, v1.0
Genome_build: mm10
Supplementary_files_format_and_content: tar.gzped, market exchange format (MEF) for raw, filtered, and scrubbed (SoupX) transcript count matrices; .csv files of single-cell metadata information.
Vis5A_raw_feature_bc_matrix.tar.gz:  raw transcript counts for all cell barcodes (cellranger)
Vis5A_filtered_feature_bc_matrix.tar.gz:  filtered transcript counts (cellranger)
Vis5A_Stitched_Image_0.tif:  stitched H&E image of sample
V19T19-051-B1_Vis5A.json:  filter for spots beneath the tissue slice (Loop Browser)
Vis5A_meta.csv:  Metadata for each spot, including predicted cell type content (BayesPrism)

value: Notexin injury (Day 2)


title: Whole animal anterior to gills_SC_20DPF_REP2

tag: strain


title: Whole animal anterior to gills_SC_20DPF_REP3


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G12_ad004

tag: age

value: ACA

value: VISp

value: male


title: Vis7B

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using spaceranger v1.0 pipeline
Gene expression data was processed with Seurat v3.2.1
Initial data filtering (minium genes to be expressed in an included spot = 500)
Filtering by number of UMIs in included cells (minimum 1000)
Log-normalization of expression data
Spot composition calculated using the R package TED, v1.0
Genome_build: mm10
Supplementary_files_format_and_content: tar.gzped, market exchange format (MEF) for raw, filtered, and scrubbed (SoupX) transcript count matrices; .csv files of single-cell metadata information.
Vis7B_raw_feature_bc_matrix.tar.gz:  raw transcript counts for all cell barcodes (cellranger)
Vis7B_filtered_feature_bc_matrix.tar.gz:  filtered transcript counts (cellranger)
Vis7B_Stitched_Image_0.tif:  stitched H&E image of sample
V19T19-051-C1_Vis7B.json:  filter for spots beneath the tissue slice (Loop Browser)
Vis7B_meta.csv:  Metadata for each spot, including predicted cell type content (BayesPrism)

tag: tissue

value: Notexin injury (Day 5)


title: Whole animal anterior to gills_KD_20DPF_REP2


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G12_ad002

value: brain

tag: source


title: col0_3

value: wt


title: col0_2


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G12_ad001

tag: target


title: Input_shINTS8_DLD1_rep1_ChIPSeq

city: Shanghai

first: Xuan

last: Cao

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences

data_processing:
CHIP-Seq reads were aligned to the human genome (UCSC hg19) by using alignment software Bowtie (1.1.1) (Langmeadet al., 2009) with the following options: -S –m 1 –k 1.
Only unique reads mapping to a single genomic location were kept. Duplicate reads were removed by using in house script.
We calculated the ChIP-seq signal as reads per million mapped reads (RPM) based on sequence depth. We counted the number of spike-in reads by aligning to the mouse genome(mm10) with bowtie. We normalized ChIP-seq signal by multiplying the RPM  by the spike-in factor a=  which  is the count of reads (in millions) mapped to mouse genome(David A. Orlando(2014)). Density genome track were generated by using bedtools genomecov program to conver bam files to bigwig files (Quinlan, 2014)
Peaks were called using macs (1.3.7.1) (Zhang, 2008)with the following parameters: --nomodel –nolambda and the peaks with 10*log10 (pvalue) > 100 were kept.
Genome_build: hg19

organism: Homo sapiens

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
Lysates were clarified from sonicated cells and INTAC-DNA complexes were isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: One replicate was shRNA-containing lentivirus treated for 4 days.

tag: cell line

value: colorectal adenocarcinoma cell line

tag: chip antibody

value: Input

tag: shRNA treatment


title: Liver of TG2 at ZT14

city: Ube, Yamaguchi

first: Yasuharu

last: Ohta

address: 1-1-1, Minami Kogushi

department: Endocrinology, Metabolism, Hematological Science and Therapeutics

country: Japan

institute: Yamaguchi University Scool of Medicine

data_processing:
FASTQ files produced by Illimina NEXTSeq were imported to CLC Genomics Workbench software (ver.9.01).
Reads with more than 2 ambiguous nucleotides and reads with quality scores less  than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.8.01).
The trimmed reads were mapped to the mouse reference genome mm10 using CLC Genomics Workbench software (ver.9.01) with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.9.01).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each Sample.

source_name: Liver of TG at ZT14

growth_protocol: Chow: normal diet and randomly fed, temprature: 22℃±1℃, Light-dark cycle: 12-hour light and 12-hour dark (lights on at AM8 and lights off at PM8)

extract_protocol:
Livers were removed, and total RNA was isolated using RNeasy mini kit (Invitrogen). Polyadenylated mRNA was separated from 850 ng of total RNA using GeneReadPure mRNA kit (NEB). Sepqrated polyadenylated mRNA was subjected to construction of sequencing libraries using NEBNext Ultra RNA LibraryPrep kit for Illumina (NEB).
Libraries were prepared for sequencing using protocols of NEBNext Ultra RNA LibraryPrep kit for Illumina (NEB).

tag: strain background

value: transgenic mice (TG) with liver-specific E4BP4 overexpression

value: 8 week old

value: Liver


title: col0_1

tag: ecotype

tag: genotype

value: seedlings


title: input_col0

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using bowtie with parameters -v 2 --best --strata -m 1 (http://bowtie-bio.sourceforge.net/index.shtml)
Peak calling was performed using MACS2 with default parameters (https://github.com/taoliu/MACS)
BigWIG files with CPM normalized signal were generated using the deepTools utility bamCoverage with a bin size of 10 (https://deeptools.readthedocs.io/en/latest/)
Subsequent data analysis and visualization was performed using the R bioconductor packages ChIPpeakAnno, ChIPSeeker, limma and ClusterProfiler.
Genome_build: tair10
Supplementary_files_format_and_content: signal in bigWIG format

extract_protocol:
Chromatin was extracted from 10-day-old whole seedlings. Anti-H2Aub (Cell Signaling Technology, 8240S) and anti-H3K27me3 (Millipore, 07-449) antibodies were used for chromatin immunoprecipitation.
Libraries were prepared with end repair, A-tailing and ligation of Illumina-compatible adapters using the Ovation® Ultralow Library Systems (NuGEN). The ligated product was amplified with 14 cycles of PCR. DNA of a size range between 200 and 600 bp was purified from an agarose gel. Amplification was confirmed by testing an aliquot of the library before and after amplification by qPCR.


title: Liver of TG1 at ZT14

tag: genotype/variation


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G11_ad012

value: SSp

value: MOp

tag: gender

value: female


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G11_ad010


title: Liver of WT3 at ZT14

source_name: Liver of WT at ZT14

value: wild type


title: Whole animal anterior to gills_KD_20DPF_REP1

value: AB

value: all tissue anterior to gills

tag: treatment

value: KD


title: Whole animal anterior to gills_KD_15DPF_REP3

source_name: Whole animal anterior to gills 15DPF


title: Liver of TG3 at ZT14

value: male


title: Liver of WT2 at ZT14


title: h3k27me3_lhp1_2

value: Anti-H3K27me3 (Millipore, 07-449)


title: Whole animal anterior to gills_KD_15DPF_REP1


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G11_ad008

value: brain


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G11_ad007


title: Whole animal anterior to gills_SC_30DPF_REP3

value: SC


title: Liver of WT1 at ZT14


title: h3k27me3_lhp1_1


title: h3k27me3_ring1ab_2


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G11_ad006

value: ACA

value: VISp


title: Liver of TG3 at ZT2

source_name: Liver of TG at ZT2

value: transgenic mice (TG) with liver-specific E4BP4 overexpression


title: Whole animal anterior to gills_SC_15DPF_REP2


title: h3k27me3_ring1ab_1


title: Liver of TG2 at ZT2

value: 8 week old


title: Liver of TG1 at ZT2

value: Liver


title: h3k27me3_emf1_1

value: seedlings


title: MA-X3-2

city: Atlanta

first: Ken

last: Moberg

state: Georgia

address: 615 Michael Street

department: Cell Biology

institute: Emory University School of Medicine

data_processing:
Multiple data processing steps, detailed below, were conducted on the Galaxy web platform, specifically using the public server at usegalaxy.org.
Concatentaion of reads from across all 4 NextSeq500 flow cell lanes was performed using the “Concatenate datasets tail-to-head (cat)” tool (Galaxy Version 0.1.0).
Reads were mapped to the BDGP6 release of the Drosophila melanogaster genome (downloaded from release 92 of the Ensembl database) using RNA STAR, Galaxy Version 2.5.2b-0 and default parameters with the following exceptions: read type—paired, reference genome—from history (using the previously refereenced Ensembl FASTA and GTF), and length of genomic sequence around annotated junctions—74.
Mapped reads were assigned to exons/genes and tallied using featureCounts, Galaxy Version 1.6.0.3 and default parameters with the following exceptions: gene annotation file—history (using the Ensembl GTF above), count fragments instead of reads—enabled, GFF gene identifier—gene_name, and strand specificity—Stranded(reverse).
Read count normalization and differential expression analysis was conducted for all 12 samples at once using DESeq2, Galaxy Version 2.11.40.1 and default parameters with the following exceptions: factors—4 levels, each a group of three biological replicates, output normalized counts table—true, output all levels vs all levels—true.
Genome_build: BDGP Release 6 (downloaded from release 92 of the Ensembl database)
Supplementary_files_format_and_content: The DESeq2-normalized counts file ("Galaxy309…") is a tab-delimited text file containing a matrix of NORMALIZED READ COUNTS for all 12 samples generated by DESeq2. DESeq2 normalization accounts for library size and composition, enabling accurate comparison of relative RNA abundance for a given gene between samples. FPKM and similar methods do not account for library composition. Critically, DESeq2-normalized counts should not be directly compared between different genes—instead, genes should be compared by comparing relative fold changes (e.g. the fold change for gene X between wild type and mutant females vs. the fold change for gene Y between wild type and mutant females). The inclusion of "Parametric" in the file name refers to the "fit type" setting used when running DESeq2.
Supplementary_files_format_and_content: The "Differential Expression Results…" file is a tab-delimited text file containing the output of our DESeq2 DIFFERENTIAL EXPRESSION ANALYSIS. Differential expression data (e.g. fold changes, adjusted p values) are reported for each gene and across 4 pairwise comparisons—female Nab2 null vs. female wild type (FE-X3_vs_FE-P4), male Nab2 null vs. male wild type (MA-X3_vs_MA-P4), female wild type vs. male wild type (FE-P4_vs_MA-P4), and female Nab2 null vs. male Nab2 null (FE-X3_vs_MA-X3). Data are reported for all 17,737 genes in the Drosophila melanogaster genome used for read mapping/tallying (i.e BDGP Release 6 as downloaded from release 92 of the Ensembl database).
Supplementary_files_format_and_content: All "…featureCounts…" files are .tabular files that contain, for a single sample, unedited, non-normalized RAW COUNTS per gene as assigned by featureCounts analysis of the appropriate .bam read mapping/alignment file produced by STAR. These files are may be opened by text editors and Microsoft Excel.

organism: Drosophila melanogaster

source_name: Heads

extract_protocol:
Heads were collected on dry ice, lysed in TRIzol (ThermoFisher), phase-separated with chloroform, and further purified through an RNeasy Mini Kit (QIAGEN).
rRNA was depleted using a Ribo-Zero Gold Kit (Illumina) and cDNA libraries were prepared using a KAPA Stranded RNA-Seq Kit (Roche). Quality control steps included initial Qubit quantification along with RNA fragment size assessment on an Agilent 2100 Bioanalzyer before and after rRNA depletion. The cDNA libraries were then sequenced for 150 cycles on a NextSeq 500 High Output Flow Cell (Illumina) set to generate paired-end, 75 base-pair (bp) reads.

tag: genotype (shorthand)

value: Nab2 null

value: decapitated heads, collected on dry ice

tag: input amount

value: 60 heads

value: newly-eclosed adults


title: MA-X3-1

tag: Sex


title: MA-P4-3

value: wild type


title: Liver of WT3 at ZT2

source_name: Liver of WT at ZT2


title: Whole animal anterior to gills_KD_10DPF_REP2

source_name: Whole animal anterior to gills 10DPF

tag: strain

value: AB

value: all tissue anterior to gills

tag: time


title: MA-P4-1

value: male

tag: tissue

tag: age


title: h3k27me3_col0_1

value: wt

value: Anti-H3K27me3 (Millipore, 07-449)


title: h2aub_ring1ab_1

value: Anti-H2Aub (Cell Signaling Technology, 8240S)


title: Whole animal anterior to gills_KD_10DPF_REP3

value: KD


title: Liver of WT1 at ZT2


title: MA-P4-2


title: Whole animal anterior to gills_SC_15DPF_REP3

value: SC


title: h2aub_ring1ab_2


title: Whole animal anterior to gills_SC_10DPF_REP3


title: Whole animal anterior to gills_KD_10DPF_REP1


title: Whole animal anterior to gills_SC_10DPF_REP1


title: Whole animal anterior to gills_KD_5DPF_REP2

source_name: Whole animal anterior to gills 5DPF


title: Whole animal anterior to gills_SC_15DPF_REP1


title: Whole animal anterior to gills_SC_10DPF_REP2


title: h3k27me3_col0_2


title: Liver of WT2 at ZT2


title: P8 Lhx6-GFP scRNA-Seq

city: Baltimore

first: Dong Won

middle: Thomas

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description: scRNA-Seq 10x v3

data_processing:
Single-cell RNA-Sequencing: hree libraries were sequenced on Illumina NextSeq 500 with ~200 million reads per library. Sequenced files were processed through the CellRanger pipeline (v3.1.0, 10x Genomics) using mm10 genome. Seurat V3  (Stuart et al., 2019)  was used to perform downstream analysis following the standard pipeline described previously (Bell et al., 2020), analyzing cells that express high Lhx6 transcript. Louvain algorithm was used to generate different clusters, and spatial information of individual clusters at E12.5 and E15.5 were identified by referring to our previous hypothalamus scRNA-Seq database HyDD (D. W. Kim et al., 2019), as well as our previous knowledge of anatomical locations of transcription factors  (Shimogori et al., 2010). For P8 scRNA-Seq, region-specific transcription factors that are expressed were compared to E12.5 and E15.5 scRNA-Seq gene lists, as well as matching the identified gene lists to the Allen Brain Atlas ISH data (Lein et al., 2007). Previously published scRNA-Seq from E13.5 medial ganglionic eminence (MGE) (Mayer et al., 2018) was processed as described above, and key markers that label individual clusters were compared to E12.5 Lhx6-expressing hypothalamic cells.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM-generated counts (bulk RNA-seq samples),  count matrix/barcode/genes (scRNA-seq samples),  individual peak files (ATAC-seq samples)

source_name: P8 Lhx6-GFP scRNA-Seq

extract_protocol: Single-cell RNA-Sequencing: Time-mated E12.5, E15.5 and P8 Lhx6-GFP mice were collected, and dissection and dissociated were performed as described previously (D. W. Kim et al., 2019). Between 6 and 10 embryos/pups from 2 different litters were collected. Following dissociation, GFP+ cells were flow-sorted using Aria IIu Sorter (BD). Between 20,000 and 25,000 cells were flow-sorted for E12 and E15, 2,000 cells were flow-sorted for P8. Flow-sorted cells were used for the 10x Genomics Chromium Single Cell System (10x Genomics, CA, USA) using V3.0 chemistry per manufacturer’s instruction.

value: Hypothalamus

value: pooled male and female

tag: flow-sorting

value: GFP+


title: MA-X3-3


title: Whole animal anterior to gills_KD_15DPF_REP2


title: E12.5 Lhx6-GFP scRNA-Seq

description: scRNA-Seq 10x v3

source_name: E12.5 Lhx6-GFP scRNA-Seq


title: E15.5 Lhx6-GFP scRNA-Seq

description: scRNA-Seq 10x v3

source_name: E15.5 Lhx6-GFP scRNA-Seq


title: h2aub_emf1_2

value: seedlings


title: FE-X3-3

value: female

value: Nab2 null


title: FE-X3-2

value: decapitated heads, collected on dry ice

value: 60 heads


title: h2aub_emf1_1


title: Lhx6-CreER;Ai9-2

description:
bulk RNA-Seq
Replicate 2

data_processing:
Lhx6 pulse-chase sample sequencingLhx6 pulse-chase sample sequencing: Libraries were sequenced with Illumina NextSeq500, paired-end read of 75 bp, 50 million reads per library. Illumina adapters of sequenced libraries were trimmed using Cutadapt (v1.18)/TrimGalore (v0.5.0) (Martin, 2011) with default parameters, library qualities were assessed using FastQC (v0.11.7)/MultiQC (Ewels et al., 2016). Libraries were then aligned to mm10 using STAR (v2.54b) (Dobin et al., 2013) with --twopassMode Basic, and RSEM (v1.3.0) was used for quantification (Li and Dewey, 2011) with rsem-calculate-expression (--forward-prob 0.5). Expected counts value from RSEM was used to perform differential expression using edgeR (v3.24.3) (Robinson et al., 2010) using default parameters except calcNormFactors (method = “TMM”).  Lhx6CreER/+;Ai9 or Lhx6CreER/+;Lhx6lox/+;Baxlox/lox;Ai9 enriched genes (fold change > 2 consistent gene value across replicates), were used with EnrichR (Kuleshov et al., 2016). Lhx6lox/+;Baxlox/lox;Ai9 enriched genes were compared to Mouse Cells and Tissues (MESA) dataset available ascot.cs.jhu.edu (Ling et al., 2020), relying in robustness of expression (NAUC >20) and specificity, as many of enriched genes were not commonly expressed in the developing brain. We reasoned that the enriched genes in Lhx6CreER/+;Ai9.compare to Lhx6CreER/+;Lhx6lox/+;Baxlox/lox;Ai9 would be either a result of an absence of Lhx6 and/or Bax. Furthermore, since tdTomato expression is detected in blood vessels due to weak Lhx6 expression in endothelial cells during development (Liu et al., 2017), we wanted to enrich expression from Lhx6+ cells of the hypothalamus. P8 Lhx6-GFP, in which GFP expression is absent in endothelial cells, were used to generate bulk RNA-Sequencing (bulk RNA-Seq) from the cortex and hypothalamus (method described below). Hypothalamus-enriched genes from P8 Lhx6-GFP bulk RNA-Seq data was used to enrich genes that are highly expressed in the hypothalamus Lhx6 cells. After enrichment, the gene lists were compared to single-cell RNA-Sequencing (scRNA-Seq) data from P8 Lhx6-GFP hypothalamus using the method described below to further cross-check specificity of expression and remove any possible contamination that may occurred during flow-sorting from bulk RNA-Seq. EnrichR was used to identify gene pathways, and pathways that are involved with neuronal survival across literature were selected.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM-generated counts (bulk RNA-seq samples),  count matrix/barcode/genes (scRNA-seq samples),  individual peak files (ATAC-seq samples)

extract_protocol: Lhx6 pulse-chase sample sequencing: Lhx6CreER/+;Ai9 and Lhx6CreER/+;Lhx6lox/+;Baxlox/lox;Ai9 P1 pups were treated with 4-OHT, and collected at P10. Between 4 and 6 pups from 2 different litters were pooled per sample without regard to the sex, and papain-based enzymatic dissociation was performed on the dissected hypothalamus as previously described (D. W. Kim et al., 2019). Dissociated cells were flow-sorted for tdTomato signal, and between 25,000 and 30,000 cells were collected directly into TRIzolTM LS reagent. RNA was extracted using Direct-zol RNA kits (Zymo Research) and RNA-Sequencing libraries were made using stranded Total RNASeq library prep. 2 libraries were made for Lhx6CreER/+;Ai9 and 3 libraries were made for Lhx6CreER/+;Lhx6lox/+;Baxlox/lox;Ai9. Libraries were sequenced with Illumina NextSeq500, paired-end read of 75 bp, 50 million reads per library. Illumina adapters of sequenced libraries were trimmed using Cutadapt (v1.18)/TrimGalore (v0.5.0) (Martin, 2011) with default parameters, library qualities were assessed using FastQC (v0.11.7)/MultiQC (Ewels et al., 2016).

value: tdTomato+


title: Whole animal anterior to gills_KD_5DPF_REP1

value: AB


title: h3k27me3_emf1_2


title: h2aub_col0_2


title: FE-X3-1

value: newly-eclosed adults


title: Whole animal anterior to gills_SC_20DPF_REP1

value: all tissue anterior to gills


title: h2aub_col0_1

value: wt


title: In vitro positive control - Sequel I

city: San Francisco

first: Colin

last: McNally

address: 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration. Histone octamers (Luger et al., 1999) were assembled onto purified DNA via salt gradient dialysis.

data_processing:
Library strategy: SAMOSA
Demultiplexing BAM files using Lima
Generating circular concensus sequences (CCS) using ccs
Aligning CCS to hg38 using pbmm2 (in vivo samples only)
Aligning subreads to nonanucleosomal molecule reference (in vitro samples only)
Extracting IPD measurements from subreads, summarizing them by base, and then predicting methylation status using extractIPD.py (https://github.com/RamaniLab/SAMOSA)
Supplementary_files_format_and_content: In vitro samples: A numpy matrix where each column is a base pair in the DNA molecule and each row is a sequenced molecule. The values are the probability that that base in that molecule is methylated, if the base is A/T. In vivo samples: A dictionary containing the methylation probabilities for each base in each molecule in numpy arrays, and a separate pandas dataframe containing information about each molecule, including the ZMW hole numbers used to index the dictionary.

organism: unidentified plasmid

source_name: 2.2kb DNA molecule with 9 Widom 601 repeats

growth_protocol: K562 cells were grown in RPMI 1640 (Gibco) supplemented with 10% Fetal Bovine Serum (Gemini, Lot#A98G00K) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Chromatin was purified with 10uL RNaseA at RT for 10 minutes (in vivo samples only), 10uL Proteinase K (20mg/mL) and 10uL 10% SDS at 65°C for a minimum of 2 hours up to overnight). DNA was extracted with Phenol-Chloroform and ethanol precipitatation.
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit.
PacBio SMRTbell® library preparation

treatment_protocol:
1.5ug of chromatin was methylated with 2.5uL of the non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 6.25mM (NEB) after 15 minutes.
Isolated K562 nuclei were digested with Micrococcal Nuclease (Sigma) at 1U per 50e6 nuclei at varying conditions (see characteristics above). MNase-digested nuclei were treated with 300ug/mL of Lysolethicin (L-α-Lysophosphatidylcholine from bovine brain, Sigma) for nuclear lysis and liberation of chromatin fibres.

tag: mnase digestion temperature

tag: mnase digestion duration

tag: ecogii methylation

value: EcoGII Methylated


title: FE-P4-2

value: wild type


title: FE-P4-3


title: Lhx6-CreER;Ai9-1

description:
bulk RNA-Seq
Replicate 1


title: Bax;Lhx6-CreER/lox;Ai9-3

description:
bulk RNA-Seq
Replicate 3


title: atac_col0_1


title: Whole animal anterior to gills_KD_5DPF_REP3

value: KD


title: In vitro chromatin - Sequel I


title: FE-P4-1


title: Bax;Lhx6-CreER/lox;Ai9-2

description:
bulk RNA-Seq
Replicate 2


title: Whole animal anterior to gills_SC_5DPF_REP3

value: SC


title: Bax;Lhx6-CreER/lox;Ai9-1

description:
bulk RNA-Seq
Replicate 1

value: Hypothalamus


title: M3_ctrl_5d

status: Public on Dec 01 2020

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
fastqc, version 0.11.5
trimmomatic, version  0.36, "PE ILLUMINACLIP:adapters.fasta:2:30:10 HEADCROP:13 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36"
hisat2, version 2.0.4,
kallisto, version 0.43, 10000 bootstraps
Genome_build: Potato DM 4.04 (http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml), P. infestans ASM14294v1 (https://protists.ensembl.org/Phytophthora_infestans/Info/Index)
Supplementary_files_format_and_content: tsv, kallisto count

organism: Solanum tuberosum

source_name: Solanum tuberosum inoculated with H2O

growth_protocol: Potato plants cv. Sarpo Mira were grown in-vitro at 22°C with a 16-h photoperiod on Murashige-Skoog (MS) medium (Duchefa Biochemie B.V., Amsterdam, Netherlands), supplemented with 2% (w/v) sucrose and 0.3% (w/v) gelrite (Duchefa). After 3 weeks plants were transferred to pots with soil in a growth chamber with the same light and temperature regime. Plants were grown for 4 weeks post transfer to soil from in-vitro conditions before inoculation. Mycelia was grown for 7 days in liquid pea broth.

extract_protocol:
RNeasy plant mini kit (Qiagen; Limburg, Netherlands)
Illumina TruSeq stranded Total RNA Library preparation kit. Libraries were prepared by the SciLife sequencing platform (Stockholm, Sweden) under their in-house conditions and sequenced by using Illumina HiSeq 2500

treatment_protocol: 5x104 spores/ml water of each P. infestans strain was used for potato leaf inoculations.

value: Leaves

tag: inoculum

tag: days past inoculation

tag: potato cultivar

value: Sarpo Mira


title: Whole animal anterior to gills_SC_5DPF_REP2


title: LP_XGPAC1_rep1

city: Amherst

first: Ezgi

last: Ozcan

state: MASSACHUSETTS

address: 424 Chenoweth Lab, 102 Holdsworth Way

institute: University of Massachusetts Amherst

data_processing:
Sequenced reads were trimmed for adaptor sequence using trimmomatic, and masked for low-complexity or low-quality sequence, cleaned for 16S rRNA contamination using bbduk then mapped to L. plantarum WCFS1 whole genome using bowtie2 v2.3.4.3 with parameters -p 8
Aligned reads were then name sorted using Samtools (v1.4.1) and total and specific gene counts were obtained by overlapping to a specific genomic locus(i.e. locus tag) with genomic feature and annotation (GFF) using HTSeq (v0.10.0) with parameters --stranded=reverse --nonunique=all --mode=union --order=name .
Raw gene counts were subject to DEseq2 and log2 fold changes obtained for one condition relative to other
Genome_build: Lactobacillus plantarum WCFS1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Normalized differential expression as log2 fold change from DeSeq2

organism: Lactiplantibacillus plantarum

source_name: bacteria from human oral cavity

growth_protocol: Lactobacillus plantarum were routinely propagated in De Man Rogosa Sharp medium supplemented with 0.05 % (m/v) L-cysteine hydrochloride at 37°C under anaerobic conditions. Cells then transferred into 3 ml of modified MRS medium (no carbohydrate source). Carbohydrate source is replaced with either 1% w/v xyloglucans, human milk oligosaccharides, fructoligosaccharides, and glucose as the control. Two PAC fractions were added as 1 mg/ml and cells were grown till mid-log phase under same conditions.

extract_protocol:
Cells were suspended in lysis buffer in Lysing Matrix E beadbeating tubes to disrupt cell walls with a FastPrep 56624 bead beater. Bead beating was performed twice at 5.5 m/s for 30 seconds with a 1 min incubation on ice. The Ambion RNAqeous protocol was followed and terminated with total RNA elution into 50 μl of EB solution. Then, total RNA were treated for DNA removal. DNA-free extracts were subjected to ribosomal RNA depletion via the Ribo-Zero Magnetic Kit for bacteria and cleaned up with RNeasy MinElute Cleanup Kit. Purified mRNA was used asseses for quality and used for RNA-seq library preparation.
mRNA enriched library preparation was performed with the NEBNext Ultra II Directional kit

treatment_protocol: glucose, xyloglucans isolated from cranberries with or without two cranberry proanthocyanidin (PAC) extracts, human milk oligosaccharides with or without PACs, fructooligosaccharides with or without PACs, glucose and two extract of PACs alone

value: ATCC BAA-793

value: XG and PAC fraction 1


title: LP_XGPAC1_rep2


title: LP_XGPAC2_rep1

value: XG and PAC fraction 2


title: LP_XG_rep1

value: cranberry xyloglucans (XG)


title: LP_HMOPAC2_rep2

value: HMO and PAC fraction 2


title: M2_ctrl_5d


title: LP_HMOPAC2_rep1


title: LP_HMOPAC1_rep2

value: HMO and PAC fraction 1


title: atac_col0_2

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Quality trimming and adapters removal were performed using Trimmomatic
PCR duplicates were discarded from the mapped reads using Picard
Reads mapped to the blacklisted genomic regions were eliminated using samtools
Read mapping to the reference genome was performed using bowtie with parameters -v 2 --best --strata -m 1 (http://bowtie-bio.sourceforge.net/index.shtml)
Peak calling was performed using MACS2 with default parameters (https://github.com/taoliu/MACS)
BigWIG files with CPM normalized signal were generated using the deepTools utility bamCoverage with a bin size of 10 (https://deeptools.readthedocs.io/en/latest/)
Subsequent data analysis and visualization was performed using the R bioconductor packages ChIPpeakAnno, ChIPSeeker, limma and ClusterProfiler.
Genome_build: tair10
Supplementary_files_format_and_content: signal in bigWIG format

tag: ecotype

tag: genotype

value: seedlings


title: In vitro negative control - Sequel I

value: Unmethylated


title: LP_HMOPAC1_rep1

tag: treatment


title: LP_HMO_rep2

value: pooled human milk oligosaccharides (HMO)


title: M1_ctrl_5d


title: LP_XGPAC2_rep2


title: LP_HMO_rep1


title: Whole animal anterior to gills_SC_5DPF_REP1

value: AB

value: all tissue anterior to gills


title: LP_FOSPAC1_rep2

value: fructooligosaccharides and PAC fraction 1


title: LP_FOSPAC1_rep1


title: LP_FOSPAC2_rep2

value: fructooligosaccharides and PAC fraction 2


title: LP_FOSPAC2_rep1


title: LP_PAC2_rep2

value: Proanthocyanidin(PAC) fraction 2


title: LP_PAC2_rep1


title: LP_GLC_rep1

value: glucose


title: LP_PAC1_rep1

value: Proanthocyanidin(PAC) fraction 1


title: LP_PAC1_rep2


title: LP_XG_rep2


title: LP_GLC_rep2


title: DAP-MpoMYCx

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

description:
Sample 26
Protein-DNA interaction

data_processing:
Library strategy: DAP-seq
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Genome_build: Arabidopsis TAIR10 genome (Ensemble Release 42)
Genome_build: Solanum lycopersicum SL4.0 assembly, ITAG4.0 annotation
Genome_build: Marchantia polymnorpha MpTak1v5 version
Supplementary_files_format_and_content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4

organism: Marchantia polymorpha

source_name: 21-d-old gemmalings

growth_protocol: 10 days-old seedlings grown in MS medium

extract_protocol:
Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.

tag: protein

value: MpoMYCx

tag: gene id

tag: protein expression

value: E.coli expressed


title: Input MpoDNA

description:
Sample 27
Input MpoDNA sample 26

value: Input MpoDNA sample 26

value: Input DNA


title: D7_ctrl_2

city: beijing

first: liang

middle: sheng

last: xian

address: shuangqing road

institute: chinese academy of science

data_processing:
Reads were filtered and then mapped to the reference genome sequence (UCSC hg38) with HISAT
Sequences were aligned to reference genes with Bowtie2 tool
The gene expression level was determined by the RSEM software
Genome_build: UCSC hg38
Supplementary_files_format_and_content: FPKMs

source_name: Hepatoblasts

growth_protocol: Undifferentiated H9 cells were maintained on vitronectin-coated tissue culture dishes in mTeSR1 medium.A previously reported hepatocyte-like cell differentiation protocol was performed to induce H9 cells into hepatocyte cells (Mathapati, et al., 2016)

extract_protocol:
Total RNA was extracted with the Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 0.1% DMSO as control, or 30 nM T3/T4.

tag: developmental stage

value: day 7

value: liver

tag: derived cell line

tag: cell type

value: Hepatoblasts

value: ctrl


title: D7_ctrl_1

tag: tissue


title: D7_T3_1


title: D7_T3_2


title: NTK_9279_36H_Liver [9279_36h_Liver_ACACTAAG-ATCCATAT]

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

institute: University of Illinois at Urbana-Champaign

data_processing:
The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).
The quality of the resulting fastq files was evaluated with the FastQC software (v. 0.11.6)
Single-end reads were first filtered using Trimmomatic (v 0.33) with a minimum quality score of 28  leading and trailing with a minimum length of 30 bp long and subsequently checked using FastQC (v 0.11.6). No reads were filtered as all had scores greater than 28.
Reads were then mapped to the Bos taurus UMD 3.1.1 reference genome using default settings of STAR (v 2.6.0)
Uniquely aligned reads were quantified using Feature Counts in the Subread package (v 1.5.2) based on the Refseq gene annotation.
Genome_build: Bos taurus UMD 3.1.1
Supplementary_files_format_and_content: Feature Count output file in text format (generated by the Feature Count function of the subread package). Column consist in Geneid, Chr, Start, End, Strand, Length, Count

organism: Bos taurus

extract_protocol:
After collection samples were snap frozen in liquid nitrogen, and stored at -80C until extraction. Tissue was weighted (~ 0.05 g), immediately placed in QIAzol Lysis Reagent (Qiagen, Hilden, Germany) (1  mL) and homogenized using a Mini-Beadbeater-24 (Biospec Products Inc., Bartlesville, OK) with two 30 s cycles, and 1 min incubation on ice in between the cycles. Samples were then centrifuged for 10 min at 12,000 × g and 4 °C, and the supernatant was transferred to a separate tube and mixed with chloroform (0.2 mL). After centrifugation for 15 min at 12,000 × g and 4 °C, the aqueous phase was transferred to a new tube, mixed with 100% ethanol (0.75 mL), and total RNA was cleaned using miRNeasy mini kit columns (Qiagen, Hilden, Germany) following manufacturer’s protocols. During purification, genomic DNA was removed using the RNase-Free DNase Set (Qiagen, Hilden, Germany). Quantity was determined using a Qubit Fluorometer (Invitrogen, Carlsbad, CA), while integrity was assessed via a Fragment Analyzer™ (Agilent Technologies, Santa Clara, CA). All samples had an RQN score greater than 7.0. RNA samples were stored at −80 °C until analysis.
After quality control, samples were handed to the DNA Service Lab of the University of Illinois Roy J. Carver Biotechnology Center for library preparation and sequencing. RNAseq libraries were constructed with the TruSeq Stranded mRNA Sample Prep kit (Illumina, San Diego, CA). The final libraries were quantitated with a Qubit Fluorometer (Invitrogen, Carlsbad, CA) and the average library fragment length was determined on a Fragment Analyzer™ (Agilent Technologies, Santa Clara, CA). The libraries were diluted to 10 nM and further quantitated by qPCR on a CFX Connect Real-Time qPCR system (Biorad, Hercules, CA) for accurate pooling of the barcoded libraries and maximization of number of clusters in the flowcell.

tag: breed

value: Holstein

value: NTK

tag: time

value: Liver


title: CON_9247_36H_Liver [9247_36h_Liver_TGGCCGGT-TAGAGCGC]

value: CON


title: D19_T3_2

source_name: Hepatocytes

value: day 19

value: Hepatocytes


title: D19_T3_1


title: D7_T4_1


title: D19_ctrl_1


title: D19_T4_2


title: D19_ctrl_2


title: NTK_9279_30D_Liver [9279_30day_Liver_AACTGTAG-ACGCCGCA]


title: D19_T4_1


title: CON_9247_30D_Liver [9247_30day_Liver_CGCTATGT-TCCGACAC]


title: CON_9238_36H_Liver [9238_36h_Liver_TGCGGCGT-CCTCGGTA]


title: NTK_9227_30D_Liver [9227_30day_Liver_AGTACTCC-AACCTGTT]


title: NTK_9227_36H_Liver [9227_36h_Liver_CATAATAC-TTCTAACG]


title: D7_T4_2


title: CON_9238_30D_Liver [9238_30day_Liver_GACGTCTT-GGTTCACC]


title: CON_9035_36H_Liver [9035_36h_Liver_GATCTATC-ATGAGGCT]


title: CON_9035_30D_Liver [9035_30day_Liver_TGCGAGAC-CATTGTTG]


title: CON_8923_36H_Liver [8923_36h_Liver_CCTTCACC-GACGCTCC]


title: CON_8909_30D_Liver [8909_30day_Liver_AGGTTATA-CAGTTCCG]


title: NTK_8788_30D_Liver [8788_30day_Liver_TATCGCAC-CTTAGTGT]


title: CON_8909_36H_Liver [8909_36h_Liver_CCATTCGA-GTTGTCCG]


title: Overexpression-2

city: changzhou

first: jiang

last: wei

address: juqian street

institute: Soochow University

hyb_protocol: Following fragmentation, chips  were hybridized for 16 hr, 60rpm at 45℃ on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChIP Scanner 3000

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Cultured cell lines (Caco-2)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: Colon carcinoma

value: apoM

tag: cell line


title: NTK_8788_36H_Liver [8788_36h_Liver_CAATTAAC-CGAGATAT]


title: CON_8923_30D_Liver [8923_30day_Liver_ACAGGCGC-CTCTGCCT]


title: NTK_9014_36H_Liver [9014_36h_Liver_TTCCTGTT-AGTATCTT]


title: CON_844_30D_Liver [844_30day_Liver_GGTCACGA-GTATTATG]


title: Overexpression-1


title: CON_8_30D_Liver [8_30day_Liver_TCATCCTT-AGCGAGCT]


title: CON_609_30D_Liver [609_30day_Liver_TCTGTTGG-TCGAATGG]


title: NTK_89_30D_Liver [89_30day_Liver_CTCACCAA-CTAGGCAA]


title: CON_609_36H_Liver [609_36h_Liver_GTCTACAC-GCCAAGGT]


title: Overexpression-3


title: NC-3

value: NC


title: Hep3B cell line knockout endogenous SOX4 via CRISPR/cas9

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: Gene expression data from Hep3B SOX4-/- cells

hyb_protocol: Standard Affymetrix/Applied Biosystems protocol

data_processing: Normalize with SST-RMA by Applied Biosystems Transcriptome Analysis Console (TAC) v4.0

source_name: hepatocellular carcinoma cell line

growth_protocol: Hep3B cell was maintained in Eagle's Minimum Essential Medium with 10% Fetal bovine serum,  2 mM L-glutamine, Earle's BSS adjusted to contain 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids, and 1.0 mM sodium pyruvate. Hep3B SOX4-/- cells was maintained as the same medium as Hep3B cells with supplement of Puromycin (1ug/ml).

extract_protocol: RNA extraction was purified via TRIzol reagent (Thermo Fisher Scientific, Inc., Waltham, MA, USA) following the manufacturer's recommendation. The contaminated DNA was removed via in-column DNase 1 treatment via RNA Minelute column (Qiagen). The RNA quality was determined via Agilent bioanalyzer.

treatment_protocol: The cells density reached to 80% confluence, both cells were washed three times of PBS, and then added 1ml TRIzol to the plate to extract total RNAs.

value: SOX4 KO


title: Hep3B cell line

description: Gene expression data from Hep3B parental cells

scan_protocol: Standard Affymetrix/Applied Biosystems protocol

source_name: hepatocellular cell line

value: wildtype


title: NC-2


title: NC-1


title: NTK_9014_30D_Liver [9014_30day_Liver_CTGCTTCC-GATAGATC]


title: CON_844_36H_Liver [844_36h_Liver_GTGTCGGA-GCTTGCGC]


title: NTK_8950_36H_Liver [8950_36h_Liver_GCCACAGG-CATGCCAT]


title: CON_8_36H_Liver [8_36h_Liver_ATTGTGAA-TGCATTGC]


title: NTK_8950_30D_Liver [8950_30day_Liver_GAACCGCG-TGACCTTA]


title: NTK_89_36H_Liver [89_36h_Liver_ACTCGTGT-ATTGGAAC]


title: NTK_1416_36H_Liver [1416_36h_Liver_TAAGGTCA-TGTCGTAG]


title: NTK_1416_30D_Liver [1416_30day_Liver_GTGAATAT-TCTCATTC]


title: NTK_123_36H_Liver [123_36h_Liver_CGGAACTG-CACTACGA]


title: NTK_123_30D_Liver [123_30day_Liver_CATAGAGT-TGCCACCA]


title: NTK_9279_30D_Mammary [9279_30D_R_CTCACCAA-CTAGGCAA]

source_name: NTK_30D_Mammary gland

value: Mammary gland


title: NTK_9279_36H_Mammary [9279_36_R_ACTCGTGT-ATTGGAAC]

source_name: NTK_36H_Mammary gland


title: CON_9247_36H_Mammary [9247_36_R_ACAGGCGC-CTCTGCCT]

source_name: CON_36H_Mammary gland


title: CON_9247_30D_Mammary [9247_30D_R_TCGATATC-ACACGAGT]

source_name: CON_30D_Mammary gland


title: CON_9238_30D_Mammary [9238_30D_R_AACTGTAG-ACGCCGCA]


title: NTK_9227_36H_Mammary [9227_36_R_GTGTCGGA-GCTTGCGC]


title: NTK_9014_36H_Mammary [9014_36_R_CAATTAAC-CGAGATAT]


title: CON_9035_30D_Mammary [9035_30D_R_GGTCACGA-GTATTATG]


title: NTK_9227_30D_Mammary [9227_30D_R_GTGAATAT-TCTCATTC]


title: CON_9035_36H_Mammary [9035_36_R_TTCCTGTT-AGTATCTT]


title: NTK_8950_30D_Mammary [8950_30D_R_CGCTATGT-TCCGACAC]


title: CON_8923_36H_Mammary [8923_36_R_CCTTCACC-GACGCTCC]


title: NTK_9014_30D_Mammary [9014_30D_R_TATCGCAC-CTTAGTGT]


title: CON_8923_30D_Mammary [8923_30D_R_CTGCTTCC-GATAGATC]


title: CON_8909_36H_Mammary [8909_36_R_ATTGTGAA-TGCATTGC]


title: CON_8909_30D_Mammary [8909_30D_R_GAACCGCG-TGACCTTA]


title: NTK_89_36H_Mammary [89_36_R_GACGTCTT-GGTTCACC]


title: NTK_89_30D_Mammary [89_30D_R_ACGCACCT-GGTGAAGG]


title: CON_8_30D_Mammary [8_30D_R_GTATGTTC-AACAGGAA]


title: NTK_1416_36H_Mammary [1416_36H_R_CTAGCGCT-GTGTAGAC]


title: NTK_8788_30D_Mammary [8788_30D_R_CGTCTGCG-TTCACAAT]


title: CON_844_30D_Mammary [844_30D_R_TCTGTTGG-TCGAATGG]


title: CON_609_30D_Mammary [609_30D_R_TACTCATA-CCTGTGGC]


title: CON_609_36H_Mammary [609_36_R_TGCGAGAC-CATTGTTG]


title: CON_9238_36H_Mammary [9238_36_R_ACACTAAG-ATCCATAT]


title: NTK_123_36H_Mammary [123_36_R_GCCACAGG-CATGCCAT]


title: NTK_123_30D_Mammary [123_30D_R_TCATCCTT-AGCGAGCT]


title: M2_Nl_Mycelia

organism: Phytophthora infestans

source_name: Phytophthora infestans mycelia (NL11388)

value: Mycelia


title: E. invadens, encyst 72hr [IP-1_encyst72_35]

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

data_processing:
Basecalling was performed using Illumina Sequencing Data Analysis software
Adaptor sequences were removed from each read
Duplicate sequences were removed
Unique reads were filtered by removing all reads that mapped to genomic  tRNA, rDNA, LINES and SINES
Filtered reads were mapped to the genome using bowtie with the parameters: -v 1 --all
Genome_build: E. histoyiitca HM-1:IMSS  version 1.3 (http://amoebadb.org);E. invadens IP-1 version 1.3 (http://amoebadb.org)
Supplementary_files_format_and_content: txt files are bowtie output

organism: Entamoeba invadens

source_name: E. invadens trophozoites

growth_protocol: E. histolytica trohozoites were grown in TYI at 37°C; E. invadens was grown in standard axenic culture conditions (LYI @ 25°C); E. histolytica overexpressing cell lines are kept at 6μg/ml G418.

extract_protocol:
Parasites were harvested by chilling on ice, spun down, and washed 1x in cold PBS. RNA was isolated using Trizol (Invitrogen) following the manufacturer's protocol.
We used the NEBNext multiplex small RNA library prep set for Illumina (NEB#E7300S) and followed the manufacturer’s protocol with the following modifications: total RNA (25-50 µg) was first fractioned for the size 15-30nt RNA or 30-45nt RNA using 12% polyacrylamide urea gel. The size-selected RNA was then treated with tobacco acid pyrophosphatase [TAP] to convert 5’ poly-P to 5’ single-P (Epicentre) or RppH (NEB). The RNA sample was then fed into the pipeline as described in the manufacturer's protocol. Once the cDNA was made, the barcode primers were incorporated into each sample using PCR with kit’s provided barcoded primer; typically we used 8-12 PCR cycles to get a clear final PCR product band. The final PCR product was quantified using Nanodrop, and samples were pooled and shipped to the collaborator for Illumina sequencing. The platform MiSeq (Illumina) was used, the number
Sequencing of E. histolytica small RNAs for size-selected (30-45nt)  total RNA of E. histolytica trophozoites; from size-selected (30-45nt)  total RNAs of development of E. invadens; from IP-ed RNAs of EhAgo proteins and mutant.

treatment_protocol: The cell lysates for transfected cells: parasites were harvested by chilling on ice, spun down, and washed 1x in cold PBS and lysed by lysis buffer contains 20 mM Tris-HCl (pH 7.5), 1 mM MgCl2, 10% (v/v) glycerol and 50 mM NaCl, IGEPAL CA-630 (equivalent of NP-40) at 0.5% (v/v) plus 1mM NaF, 1mM DTT, 1mM PMSF and HALT EDTA free protease inhibitors (100x stock diluted to 2x)(Thermo Scientific) and RNase inhibitor (1 unit/ml).

tag: strain/genotype

tag: development stages

value: Encystation was induced by incubation in 47% low glucose media (LG)

value: size-selected at 30-45nt, cloned use TAP

tag: isolation method

value: RNA isolated by Trizol

tag: molecule subtype

value: small RNA


title: NTK_8950_36H_Mammary [8950_36_R_TGGCCGGT-TAGAGCGC]

value: Holstein


title: E. invadens Basal growth [IP-1_35]

value: trophozoites


title: NTK_8788_36H_Mammary [8788_36_R_CATAGAGT-TGCCACCA]

value: NTK


title: M2_88069_Mycelia

source_name: Phytophthora infestans mycelia (88069)


title: 39L

city: London

first: Magdalena

last: Zak

address: 332 Grays Inn Road

institute: UCL Ear Institute

data_processing:
Run data were demultiplexed and converted into fastq files using Illumina’s bcl2fastq Conversion Software v2.19
Kallisto package was used to map reads to a chicken reference genome (Gallus_gallus-5.0) and to quantifying abundances of transcripts using default settings
Genome_build: Gallus_gallus-5.0

organism: Gallus gallus

source_name: otocyst

extract_protocol:
Total RNA was extracted from each individual otocysts using the RNAqueous™-Micro Total RNA Isolation Kit (Ambion) according to the manufacturers protocol. The quality of isolated RNA was tested using Agilent 2200 Tapestation and only samples with RIN of at least 9 were used for library
Libraries were made using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech): cDNA was generated using the SMART (Switching Mechanism at 5' End of RNA Template) technology during 10 cycles of PCR. cDNA integrity and quantity was checked on the Agilent Bioanalyser using the High Sensitivity DNA kit, and 200pg of cDNA was then converted to sequencing library using the Nextera XT DNA protocol (Illumina
Samples were sequenced 43bp paired-end read and high output - 400 million reads per run on NextSeq 500 instrument (Illumina)

treatment_protocol: Both left and right otocyst were dissected from chicken embryos aged E2.5, cleaned from surrounding mesenchyme and individually incubated free floating in IWR-1-enriched (300µM, right otocyst) or control (DMSO, left otocyst) media for 24h.

tag: strain

value: White Leghorn

tag: age

value: embryonic day 2.5

value: DMSO

tag: duration of treatment


title: CON_8_36H_Mammary [8_36_R_AGTACTCC-AACCTGTT]

tag: treatment

value: CON


title: 40L


title: 35L


title: 40R

value: 300uM IWR-1


title: 39R


title: 35R


title: NTK_1416_30D_Mammary [1416_30D_R_AGGTTATA-CAGTTCCG]


title: Roots_EBL_Rep1

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

description:
PolyA RNA
processed data file: genes_RPKM_summary.txt

data_processing:
Base-calling and demultiplexing with Illumina CASAVA 1.8.
Adapter clipping and quality filtering with Trimmomatic 0.33.
Mapping with tophat-2.0.13; parameters: -N 3 --read-gap-length 3 --read-edit-dist 3 --b2-very-sensitive -i 5 -I 60000 --coverage-search --min-coverage-intron 5 --max-coverage-intron 60000 --min-segment-intron 5 --max-segment-intron 60000 --library-type fr-firststrand
Differential expression analysis using Cufflinks version 2.2.1 --multi-read-correct, --compatible-hits-norm, --dispersion-method per-condition and --library-norm-method quartile
Genome_build: RefGen ZmB73 Assembly AGPv4
Supplementary_files_format_and_content: genes_RPKM_summary.txt: Tab-delimited matrix with normalized RPKM values for all the samples.

organism: Zea mays

source_name: primary root

growth_protocol: Maize seeds were germinated on wet filter paper at 25°C in the dark; after three days, seedlings were moved to a controlled environmental chamber in 500 ml tanks containing a nutrient medium (Quaggiotti et al. 2003).

extract_protocol:
Total RNA was extracted using TRIzol reagent, followed by DNase treatment.
TruSeq Stranded RNA Library Prep Kit.

treatment_protocol: 48h of growth in nutrient solution supplemented with 1nM Epibrassinolide.

tag: inbred

value: 1nM EBL

value: Roots


title: Leaves_control_Rep3

source_name: seedling 1st leaf

value: Control

value: Leaves


title: CON_844_36H_Mammary [844_36_R_GTCTACAC-GCCAAGGT]

value: Mammary gland


title: E. invadens, excyst 8hr [IP-1_excyst8_35]

value: Excystation was induced by incubation in LG + 1% glucose 1mg/ml bile and 40mM sodium barcarbonate


title: Shoots_control_Rep3

source_name: seedling shoot (stem, apex and coleoptile)

value: Shoots


title: Shoots_control_Rep2


title: Leaves_control_Rep2


title: Leaves_control_Rep1


title: Shoots_control_Rep1


title: Roots_control_Rep2


title: Roots_control_Rep3


title: Leaves_EBL_Rep3


title: Leaves_EBL_Rep1


title: Roots_control_Rep1


title: Leaves_EBL_Rep2


title: Shoots_EBL_Rep2


title: Shoots_EBL_Rep3


title: M1_Nl_Mycelia

value: Mycelia


title: M1_88069_Mycelia


title: Bacteroides xylanisolvens D22 mucin O-linked glycans 3

city: Ann Arbor

first: Eric

last: Martens

state: MI

address: 1150 W. Medical Center Dr.

institute: University of Michigan

data_processing:
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in mucin O-linked glycans was compared to gene expression in glucose reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and normalized expression level >1%
Genome_build: NZ_ADCK00000000.1, NZ_ACRS00000000.1, NZ_ACGA00000000.2, Ga0011936
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample

organism: Bacteroides xylanisolvens

source_name: Bacterial Total RNA

growth_protocol: Strains were grown to mid-log on 5 mg/ml mucin O-linked glycans or glucose as a sole carbon source in vitro.

extract_protocol:
Qiagen RNeasy kit and rRNA depleted with Bacteria Ribo-Zero Kit (Epicentre/Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with two volumes of RNA Protect (Qiagen) of the original culture volume then frozen at -80C until RNA was extracted

tag: carbon source

value: mucin O-linked glycans


title: Bacteroides xylanisolvens D22 mucin O-linked glycans 1


title: Bacteroides xylanisolvens D22 glucose 3

value: glucose


title: Roots_EBL_Rep2


title: Bacteroides xylanisolvens D22 glucose 2


title: Bacteroides xylanisolvens D22 mucin O-linked glycans 2


title: EXP24h2

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

data_processing:
Mapping to the mouse mm10 transcriptome was performed using HISAT2, data were normalized according to Novogene’s standard practices
Quality was assessed and reads were filtered by removing reads that contained adapters, reads that contained N>0.1% (N represents base that could not be determined), and low-quality reads (quality value of over 50% of bases of the read ≤20)
Differential analysis was performed using DESeq2 v2 with a model based on the negative binomial distribution
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: myotubes

growth_protocol: Myoblasts were differentiated in high-glucose DMEM with 10% horse serum and 1% pen/strep until large myotubes were observed

extract_protocol:
EVs were isolated using a polymer-based method, and myotube RNA was extracted using the Zymo MiniPrep Kit
Myotube RNA was prepared as a 250-300 bp non strand-specific library using the NEBNext Ultra RNA Library Prep Kit (NEB) followed by pair-end sequencing using an Illumina NovaSeq 6000 s4 platform.

treatment_protocol: MPC EVs were incubated on myotubes for 12 and 24 h, and EVs from growth media were used as controls

value: myotubes

value: exposed to EVs from proliferating primary myogenic progenitor cells


title: EXP24h1


title: CON24h2

value: control


title: EXP12h2


title: CON24h1


title: EXP12h1


title: Roots_EBL_Rep3


title: CON12h1


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G5_ad010

city: La Jolla

first: Joseph

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

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.

value: brain

tag: source

value: AI

tag: target

value: VISp

tag: gender

value: female


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G5_ad012

tag: tissue


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G5_ad008

value: male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G5_ad006

value: AUD


title: CON12h2

tag: cell type


title: Shoots_EBL_Rep1

value: 1nM EBL


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G4_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G4_ad008


title: Bacteroides xylanisolvens D22 glucose 1


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G4_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G4_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G4_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G4_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G3_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G4_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G3_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G3_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G3_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G3_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G3_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G2_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G6_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G2_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G2_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G2_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G5_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G5_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G1_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G2_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G1_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G1_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G2_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G12_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G12_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G1_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G1_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G12_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G12_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G12_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G12_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G12_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G12_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G11_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G11_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G11_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G10_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G10_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G1_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G4_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G10_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F9_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F9_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F9_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F8_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F9_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F8_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F8_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F8_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G11_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F8_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F7_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F7_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F7_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G10_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F7_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F7_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F7_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F6_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F7_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F6_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F5_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F5_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F5_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F5_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F6_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F5_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F5_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F4_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F4_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F4_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F4_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F4_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F3_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F3_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F3_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F3_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F3_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F3_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F6_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F2_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F2_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F2_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F2_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F2_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F2_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F1_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F1_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F1_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F1_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F4_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F1_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F1_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F12_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F12_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F12_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F12_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F3_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F12_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F10_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F11_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F11_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F11_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F11_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F10_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F10_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F1_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F10_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F10_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E9_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_F12_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E9_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E9_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E9_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E8_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E9_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E8_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E8_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E8_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E8_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E8_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E9_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E7_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E7_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E7_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E7_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E7_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E7_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E7_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E6_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E6_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E6_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E6_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E5_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E6_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E5_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E5_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E5_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E5_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E5_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E5_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E4_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E4_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E4_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E7_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E4_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E4_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E5_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E4_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E4_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E3_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E3_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E3_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E3_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E6_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E3_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E3_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E2_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E2_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E2_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E2_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E2_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E1_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E12_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E1_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E12_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E1_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E1_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E12_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E12_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E12_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E12_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E11_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E11_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E11_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E11_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E11_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E10_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E10_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E10_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D9_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D9_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E1_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D9_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D9_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E10_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E12_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D9_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_E11_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D8_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D8_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D8_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D8_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D7_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D9_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D7_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D7_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D7_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D7_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D6_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D6_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D7_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D7_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D5_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D6_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D5_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D6_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D5_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D5_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D5_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D4_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D5_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D7_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D4_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D4_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D4_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D4_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D4_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D3_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D3_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D3_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D4_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D3_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D1_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D2_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D1_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D2_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D2_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D2_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D4_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D5_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D1_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D1_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D12_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_D1_ad004