title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E12_AD001

status: Public on Nov 19 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: ACA

tag: target

value: SSp

tag: gender

value: male


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E1_AD012

value: AI

value: female


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E11_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E11_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E10_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D9_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D8_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E11_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D9_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D8_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D8_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E10_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D7_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D7_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D7_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E10_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D5_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D6_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D5_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D5_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D4_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D3_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D3_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D4_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D3_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D3_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D3_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D4_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D4_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D3_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D3_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D2_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D2_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D2_AD006


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D1_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D1_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D12_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G10_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D12_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D11_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D11_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D11_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D11_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D10_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C9_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C8_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C8_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C8_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C7_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C8_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_D10_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C6_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C5_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C5_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C9_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C5_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C3_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C3_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C3_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C3_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C3_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C2_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C2_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C2_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C1_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C12_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C1_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C1_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C1_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C12_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C3_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C11_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C3_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C10_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C11_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C11_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C10_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C10_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B9_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C11_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C12_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_C1_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B9_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B9_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B8_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B7_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B7_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B8_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B7_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B6_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B5_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B6_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B5_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B5_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B8_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B3_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B3_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B3_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B3_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B3_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B3_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B3_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B2_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B3_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B2_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B1_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B4_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B1_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B2_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B4_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B1_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B1_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B12_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B12_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B12_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B11_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B12_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B11_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B10_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B10_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A9_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_B10_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A8_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A8_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A9_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A7_AD004


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A7_AD007


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A8_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A5_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A5_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A4_AD007


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A5_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A4_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A3_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A3_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A3_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A4_AD010


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A2_AD002


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A1_AD008


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A1_AD002


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A12_AD001


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A11_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A11_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A11_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A10_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H9_AD006

value: VIS


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H9_AD007

value: Pons


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A12_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A10_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A1_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H8_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H9_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H9_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_A10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H8_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H7_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H8_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H6_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H4_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H9_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H4_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H4_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H7_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H3_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H3_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H3_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H3_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H3_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H3_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H3_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H1_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H1_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H12_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H1_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H12_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H11_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H10_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H11_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H10_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H2_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G9_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H12_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_H10_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G9_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G9_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G8_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G8_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G7_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G7_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G6_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G6_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G5_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G5_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G5_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G3_AD010


title: sth1 mutant with Dox Rep3

city: Mumbai

first: Santanu

last: Ghosh

state: Maharashtra

address: Lab 303, BSBE Dept, IIT Bombay, Powai

department: Biosciences and Bioengineering

country: India

institute: IIT Bombay

library_source: transcriptomic

data_processing:
Raw fastq files were analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics. In this study, RNAsik pipeline (Tsyganov et al. 2018) was run with STAR aligner option (Dobin et al. 2013) and reads were quantified with featureCounts (Liao et al., 2014). The reference genome (FASTA) and annotation (GFF) files were downloaded from  http://www.candidagenome.org database.
Degust (Powell, 2015) web tool was used to perform differential expression analysis on the raw counts to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots. In this study, limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell, 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalization and trimmed mean of M values (TMM) normalization (Robinson and Oshlack 2010) for RNA composition normalization.
Genome_build: C. albicans SC5314 reference genome assembly 22

molecule: total RNA

organism: Candida albicans

source_name: Mutant strain

growth_protocol: Overnight cultures were adjusted to an initial OD of 0.05 in YPD and grown for 2 hours before adding 20 µg/ml doxycycline. Depletion was performed for 7 hours. Cell were harvested by centrifugation, washed once with PBS, frozen and stored at -80°C.

extract_protocol:
Total RNA was extracted from frozen cell pellets using hot phenol method and assessed for integrity on 2100 Bioanalyzer (Agilent).
Four micrograms of RNA were used to prepare poly-A RNA-Seq libraries using Illumina TruSeq Stranded mRNA Sample prep protocol

tag: background

value: SN148 RPS10/RPS10::CIp10-URA3

tag: genotype

tag: treatment

value: 20 ug/ml dox


title: sth1 mutant without Dox Rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G3_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G4_AD010


title: sth1 mutant with Dox Rep2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G3_AD007


title: sth1 mutant without Dox Rep3


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G3_AD012


title: sth1 mutant without Dox Rep2


title: Control with Dox Rep3

source_name: Control strain

growth_protocol: Overnight cultures were adjusted to an initial OD of 0.05 in YPD and grown for 2 hours. Equivalent volume of vehicle control (50% ethanol) was added and growth continued for 7 hours. Cell were harvested by centrifugation, washed once with PBS, frozen and stored at -80°C.


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G3_AD002


title: sth1 mutant with Dox Rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G4_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G3_AD001


title: Control with Dox Rep2


title: Control with Dox Rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G7_AD001


title: Control without Dox Rep3


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G2_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G2_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G3_AD008


title: Control without Dox Rep2


title: Control without Dox Rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G2_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G2_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G2_AD001


title: DRG_WT_01_Rep2

city: Marseille Cedex 9

first: Michaël

last: Pierrelée

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: Aix-Marseille University, CNRS, IBDM

description: injection of 20µL carrageenan 1% into the left hind paw and sampling 1 day after

data_processing:
Adapter trimming, Cutadapt, v2.10, -j 16 -m 1 -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTT -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -a GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGACGGTGATCTCGTA -A AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTT -A AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -A GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGACGGTGATCTCGTA
Read aligment, STAR, v2.7.5a
Read counts, featureCounts, v2.0.1 ,-O -p -T 16 -F GTF -t exon
Genome_build: UCSC mm10
Supplementary_files_format_and_content: mouse_DRG_WT_timecourse_counts.txt: comma-separated table of raw counts generated by featureCounts

source_name: dorsal root ganglion

extract_protocol:
Mice were deeply anesthetized with a mix of ketamine/xylazine and transcardially perfused with 5-10 mL RNA Later (Qiagen). L3 to L5 dorsal root ganglions were rapidly dissected and RNA was extracted by using RNeasy Micro Kit (Qiagen), according to manufacturer's instructions. For quality control, RNAs were loaded on a RNA NanoChip (Agilent) and processed with 2100 Bioanalyzer system (Agilent technology).
DRG RNAs were extracted in experimental duplicates from 2-3 mice each. RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina). All libraries were validated for concentration and fragment size using Agilent DNA1000 chips. Sequencing was performed on a HiSeq 2000 (Illumina) and base calling performed using RTA (Illumina).

tag: cell type

value: DRG neurons

value: dorsal root ganglion

tag: time

value: day 1 (after injection)


title: DRG_WT_03_Rep2

description: injection of 20µL carrageenan 1% into the left hind paw and sampling 3 days after

value: day 3 (after injection)


title: DRG_WT_03_Rep1


title: DRG_WT_30_Rep2

description: injection of 20µL carrageenan 1% into the left hind paw and sampling 30 days after

value: day 30 (after injection)


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G1_AD010


title: DRG_WT_01_Rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G1_AD007


title: ChIP_V5_WT_E2

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences using trimgalore
Reads were aligned to mouse assembly hg38 using bowtie2 (v2.2.2) with default parameters.
Read count tables were created using featureCounts v1.6.0.
To create density files, the signal was normalised using the scalefactors from DESeq2 converted to BigWig using BEDTools.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files containing read densities normalized using DESeq2

organism: Homo sapiens

growth_protocol: Cells were seeded in full media; the following day media was changed to either estrogen depleted media (for DMSO and E2 groups) or same DMEM/F12 50/50 full media (for FM); cells were incubated for 72h; the day of cell harvesting media was refreshed

extract_protocol:
Cells were crosslinked in adherent conditions, crosslinked cells were lysed to obtain nuclear extracts, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (prod. no: E6240L)

treatment_protocol: DMSO and E2 conditions were subjected to DMSO or E2 treatment for 1h

tag: cell line

value: breast cancer cell line

tag: overexpression

tag: antibody

value: Anti-V5, Abcam ab9116, Lot GR3224488-6

value: E2 1h Induction


title: Input_V5_F266L_E2


title: Input_V5_WT_E2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G1_AD002

value: brain


title: ChIP_V5_F266L_E2


title: DRG_WT_00_Rep2

value: day 0 (before injection)


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G1_AD001

value: SSp

value: male


title: ChIP_V5_WT_DMSO

value: DMSO control


title: ChIP_V5_F266L_DMSO


title: ATAC_FoxA_wt_KI_rep2

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences using trimgalore
Reads were aligned to mouse assembly hg38 using bowtie2 (v2.2.2) with default parameters.
Read count tables were created using featureCounts v1.6.0.
To create density files, the signal was normalised using the scalefactors from DESeq2 converted to BigWig using BEDTools.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files containing read densities normalized using DESeq2

extract_protocol:
Cells were deattached with accutase, spinned down, counted and 100K cells were used to perform Omni-ATAC protocol
Amplification with barcode employing NEBNext Q5 Hot Start HiFi PCR Master Mix (prod. no: M0543L)

value: wild type


title: DRG_WT_00_Rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G1_AD012

value: VIS

value: Pons

value: female


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G12_AD012


title: DRG_WT_30_Rep1

value: DRG neurons


title: ATAC_FoxA_wt_KI_rep1


title: ATAC_FoxA_SY242CS_KI_rep2

value: FOXA1 mutant (SY242CS) knockin


title: Input_V5_WT_DMSO


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G12_AD010


title: ATAC_FoxA_SY242CS_KI_rep1


title: Input_V5_F266L_DMSO


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G12_AD004


title: HT22-R-ctrl-LR_4

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

description: long-RNA

data_processing:
Quality of the sequenced reads was estimated using FASTQC from the Babraham Institute (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimming of adapter sequences was performed using cutadapt-1.18 (DOI: http://dx.doi.org/10.14806/ej.17.1.200) with standard Illumina adaptor sequences
Mapping small RNA-seq reads to UCSC mm10 using bwa-0.7.17 (PMID: 19451168) single end mode, with aln option and default parameters. Mapping long RNA-seq reads to ensembl GRCm38 primary assembly using hisat2-2.1.0 (PMID: 31375807) single end mode, with parameters: --dta -k 1.
Conversion of bam files to genomic coordinates was done using bedtools-2.26.0 (PMID: 20110278). For small RNA-seq, in house python scripts were implemented to construct an accumulation model around a hypothetical common Transcription Start Site (TSS) for all B2 elements. For long RNA-seq, FPKM and TPM for genes were generated using StringTie-1.3.4d (PMID: 25690850), with annotation: ensembl GRCm38 patch 94 gff3 file.
Genome_build: mm10
Supplementary_files_format_and_content: B2_count files for short-RNA-seq reads: 5' end read count per position across the B2 loci metagene, constructed by aligning to the start position all B2 loci identified by RepeatMasker (mm1a,mm1t, mm2 repeat names). CSV file inlcudes two columns with column one representing the position from the metagene start and column two representing the counts of the 5' ends of each read mapping to these B2 RNAs. Gene_abund files for long-RNA-seq reads, tab delimited text files contain FPKM and TPM values for genes calculated by stringtie.

source_name: HT-22 cells

growth_protocol: The HT-22 hippocampal cell line was grown as a monolayer up to 70% confluency in DMEM, 1% pen/strep, 10%Calf Serum (heat inactivated)

extract_protocol:
Trizol RNA extraction: 1mL trizol added to pelleted cells, dissolved 5min. 200uL chloroform added to trizol treated cells, incubate 2min. Centrifuged at 12 000xg 4C. Aqueous layer treated with 500uL isopropanol, incubate -20C 1hour, centrifuged at 12 000xg 10min 4C, pellet washed with 75% ethanol and centrifuged at 7 500xg 5min 4C. Pellet dried 1min, resuspended in 30uL pure H2O
Libraries prepared as described before (Zovoilis et al, Cell 2016) and in the manuscript that accompanies the current submission. Enrichemnt of short RNAs was done using a  modified protocol for the MiRvana size selection kit. Short-RNA-seq library performed using NEBNext Multiplex Small Library Prep E7560S and a customized bead cleaning approach to get rid of very small fragments (miRNAs) and adapter dimers. Long-RNA-seq library performed after fragmentation and ribosomal RNA depletion with NEBNext rRNA depletion kit using  NEBNext Ultra RNA Library Prep Kit for Illumina (E7530)

treatment_protocol: 200,000 HT22 cells treated with anti-HSF1 LNA (150nM) or scramble (50uM) LNA for 24h, following treatment with 30uM (final concentration) of amyloid beta peptides (42/ 1-42 aa) or a control peptide with an inverted amino acid sequence (R/ reverse 42-1) dissolved in DMSO. Cells grown in 6 well plated (1mL growth media).

value: Hippocampal cell line

tag: passages


title: HT22-R-anti-HSF1-LR_1

description: long-RNA


title: DC_ST01

city: Oviedo

first: Patricia

last: Martínez-Botía

state: Asturias

address: Avda/ Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del principado de Asturias

data_processing:
Samples were prepped with the Illumina TruSeq Stranded mRNA Library Prep Kit.
Resulting DNA libraries were sequenced according to the Illumina TruSeq Rapid v2 protocol. Reads were generated of 50 base-pairs length.
Adapter sequences were trimmed off and the trimmed reads were mapped against the reference using HiSat2 (version 2.1.0).
Gene expression values were called with htseq-count (version 0.11.2).
Genes with at least 30 counts pero million reads in at least one group (min.count = 30) were kept for analysis in edgeR (version 3.26.8), and were considered significantly differentially expressed when adjusted (FDR) P-values < 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: .txt format files from raw read counts for all genes and samples (non-filtered)

source_name: Dendritic cells

growth_protocol: moDCs were isolated from the PBMC fraction of the blood from healthy donors. 0.5x106 monocytes mL-1 were cultured for 7 days in RPMI-1640 supplemented with 10% FCS, 1% Penicillin and Streptomycin (all from Life Technologies, Carlsbad, CA, USA), 10 ng mL-1 GM-CSF and 10 ng mL-1 IL-4 (both Peprotech, Rocky Hill, NJ, USA).

extract_protocol:
With Trizol, followed by a standard RNA isolation protocol
Samples were prepped with the Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: At day 7, half of the cells were stimulated with 500 ng mL-1 LPS (Santa Cruz Biotechnology, Dallas, TX, USA) and the cells were harvested at day 10.

value: Steady state

value: Monocyte-derived dendritic cells

value: Blood PBMCs


title: DC_LPS02

value: LPS


title: 22Rv1 cells, OE Rep2

city: Detroit

first: Jian

last: Wang

state: MI

address: 6135 Woodward Ave

department: Pathology

institute: Wayne State University School of Medicine

data_processing:
Data were demutiplexed using Illumina's CASAVA 1.8.2 software
After quality was assessed using FastQC, reads were aligned to the human reference genome using STAR before tabulation using htseq-count.
RNA-seq data were analyzed using the R/Bioconductor package edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include expression values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 22Rv1 cells, OE

extract_protocol:
RNA was harvested using Trizol reagent.
Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Cat#015.96) was used to prepare the sequencing library.

value: prostate cancer cell

value: overexpressing ABHD5


title: DC_LPS01


title: HT22-R-anti-HSF1-LR_2

description: long-RNA


title: HT22-R-anti-HSF1-LR_3

description: long-RNA


title: 22Rv1 cells, OE Rep3


title: HT22-R-ctrl-LR_2

description: long-RNA


title: 22Rv1 cells, OE Rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G11_AD008

value: brain


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G12_AD001

value: SSp


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G11_AD010


title: HT22-R-ctrl-LR_3

description: long-RNA


title: 22Rv1 cells, Control Rep2

source_name: 22Rv1 cells, Control

value: control


title: HT22-42-anti-HSF1-LR_3

description: long-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G11_AD007

value: male


title: 22Rv1 cells, Control Rep1


title: HT22-R-ctrl-LR_1

description: long-RNA


title: 22Rv1 cells, Control Rep3


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G11_AD006


title: M06_scRNAseq

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

country: United Kingdom

institute: University of Surrey

description: scRNAseq

data_processing: Cell Ranger workflow using GRCh38-3.0.0

source_name: Monocytes

extract_protocol:
10X 5’ v1.0 Chemistry
10X Illumina library prep

treatment_protocol: Ficoll-Paque PBMC isolation. Cells sorted by FACS into 4 populations using CD14/CD16 quadrants, with prior CSF1R selection.

tag: subject


title: M34_scRNAseq

description: scRNAseq


title: M33_scRNAseq

description: scRNAseq


title: HT22-42-anti-HSF1-LR_2

description: long-RNA


title: WTNS_FM_Input_Rep2 ChIP-Seq

source_name: Full media

value: breast cancer

tag: chip antibody

value: none (input)


title: WTNS_E2_Input_Rep2 ChIP-Seq

source_name: E2 1h Induction


title: DC_ST02


title: WTNS_DMSO_Input_Rep2 ChIP-Seq

source_name: DMSO control


title: HT22-42-anti-HSF1-LR_1

description: long-RNA

tag: strain


title: SY242CS_FM_Input_Rep2 ChIP-Seq


title: SY242CS_DMSO_Input_Rep2 ChIP-Seq


title: SY242CS_E2_Input_Rep2 ChIP-Seq


title: S250F_FM_Input_Rep2 ChIP-Seq


title: HT22-42-ctrl-LR_4

description: long-RNA


title: HT22-42-ctrl-LR_3

description: long-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G11_AD001

tag: age

value: VIS


title: S250F_DMSO_Input_Rep2 ChIP-Seq


title: H247Y_FM_Input_Rep2 ChIP-Seq


title: HT22-42-ctrl-LR_1

description: long-RNA

tag: tissue


title: HT22-42-ctrl-LR_2

description: long-RNA


title: HT22-R-anti-HSF1-sR_3

description: long-RNA


title: F266L_E2_Input_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G10_AD004

tag: source


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G10_AD007

tag: target

value: Pons


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G11_AD004

tag: gender


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G10_AD006

value: female


title: HT22-R-anti-HSF1-sR_2

description: short-RNA


title: H247Y_DMSO_Input_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G10_AD002


title: F266L_FM_Input_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G10_AD012


title: HT22-R-anti-HSF1-sR_1

description: short-RNA


title: HT22-R-ctrl-sR_4

description: short-RNA


title: S250F_E2_Input_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_G10_AD001


title: EV_E2_Input_Rep2 ChIP-Seq


title: WTNS_E2_Input_Rep1 ChIP-Seq


title: EV_DMSO_Input_Rep2 ChIP-Seq


title: EV_FM_Input_Rep2 ChIP-Seq


title: H247Y_E2_Input_Rep2 ChIP-Seq


title: WTNS_FM_Input_Rep1 ChIP-Seq


title: SY242CS_FM_Input_Rep1 ChIP-Seq


title: WTNS_DMSO_Input_Rep1 ChIP-Seq


title: SY242CS_E2_Input_Rep1 ChIP-Seq


title: HT22-R-ctrl-sR_3

description: short-RNA


title: HT22-R-ctrl-sR_2

description: short-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F9_AD010


title: F266L_DMSO_Input_Rep2 ChIP-Seq


title: S250F_FM_Input_Rep1 ChIP-Seq


title: SY242CS_DMSO_Input_Rep1 ChIP-Seq


title: S250F_DMSO_Input_Rep1 ChIP-Seq


title: H247Y_FM_Input_Rep1 ChIP-Seq


title: S250F_E2_Input_Rep1 ChIP-Seq


title: HT22-42-anti-HSF1-sR_3

description: short-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F9_AD007


title: HT22-R-ctrl-sR_1

description: short-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F9_AD006


title: H247Y_E2_Input_Rep1 ChIP-Seq


title: HT22-42-anti-HSF1-sR_2

description: short-RNA


title: F266L_FM_Input_Rep1 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F9_AD004


title: HT22-42-anti-HSF1-sR_1

description: short-RNA


title: H247Y_DMSO_Input_Rep1 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F9_AD002


title: F266L_DMSO_Input_Rep1 ChIP-Seq


title: HT22-42-ctrl-sR_4

description: short-RNA


title: EV_FM_Input_Rep1 ChIP-Seq


title: EV_E2_Input_Rep1 ChIP-Seq


title: HT22-42-ctrl-sR_3

description: short-RNA


title: EV_DMSO_Input_Rep1 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F8_AD012


title: HT22-42-ctrl-sR_2

description: short-RNA


title: F266L_E2_Input_Rep1 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F9_AD008


title: WTNS_FM_si_Foxa1_Rep2 ChIP-Seq


title: WTNS_E2_si_Foxa1_Rep2 ChIP-Seq


title: HT22-42-ctrl-sR_1

description: short-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F8_AD007


title: WTNS_E2_si_Foxa1_Rep1 ChIP-Seq


title: WTNS_DMSO_si_Foxa1_Rep2 ChIP-Seq


title: Ctrl-12m-LR_3

description: long-RNA

source_name: Hippocampus L+R

value: Hippocampus


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F8_AD008


title: WTNS_DMSO_si_Foxa1_Rep1 ChIP-Seq


title: SY242CS_FM_si_Foxa1_Rep2 ChIP-Seq


title: Ctrl-12m-LR_2

description: long-RNA


title: SY242CS_FM_si_Foxa1_Rep1 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F9_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F8_AD006


title: SY242CS_E2_si_Foxa1_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F7_AD008


title: WTNS_FM_si_Foxa1_Rep1 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F7_AD007


title: Ctrl-12m-LR_1

description: long-RNA


title: Ctrl-6m-LR_2

description: long-RNA


title: Untreated

city: Melbourne

first: Stephanie

last: Neville

state: Victoria

address: 792 Elizabeth Street

department: Microbiology and Immunology

country: Australia

institute: The University of Melbourne

data_processing:
Reads were aligned to the S. pneumoniae D39 genome (NC_008533) using BOWTIE2 version 2.2.6
Counts for each gene were determined using SAMtools version 1.3 and BEDtools version 2.24.0
Differential gene expression was determined using R (DESeq Library) version 3.2.2
Genome_build: NC_008533 reference sequence was used for alignment
Supplementary_files_format_and_content:
countsD39WT_Untreated.txt - Raw counts of sequencing reads for all genes as .txt file
counts30Cd.txt -  Raw counts of sequencing reads for all genes as .txt file
D39_WT_Unt_vs_D39_WT_30Cd_Analysis.csv - Output from DESeq (normalized counts) as .csv file.  Column baseMeanA represents untreated, column baseMeanB represents cadmium-treated.

organism: Streptococcus pneumoniae

source_name: Bacteria

growth_protocol: S. pneumoniae taken from overnight growth on horse blood agar and inoculated into C+Y media at a starting OD600= 0.05. Culture were grown to OD600= 0.3 at 37 C + 5% CO2 prior to RNA extraction

extract_protocol:
RNA was extracted using Qiagen RNeasy kit. DNA was depleted using Qiagen RNase-free Dnase. RNA integrity was determined using an Agilent Bioanalyzer.
Performed by Australian Genome Research Facility. RNA was prepared using standard Illuminia Sequening protocols with Ultra Directional RNA kit (New England Biolabs)  to generate barcoded libraries.

treatment_protocol: Untreated samples were grown in C+Y + 1 µM manganese, cadmium treated samples were grown in C+Y + 1 µM manganese + 30 µM cadmium


title: 30 µM cadmium treated

value: cadmium


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F7_AD006


title: SY242CS_DMSO_si_Foxa1_Rep1 ChIP-Seq


title: SY242CS_DMSO_si_Foxa1_Rep2 ChIP-Seq


title: S250F_FM_si_Foxa1_Rep2 ChIP-Seq


title: Ctrl-6m-LR_1

description: long-RNA


title: S250F_E2_si_Foxa1_Rep2 ChIP-Seq


title: S250F_E2_si_Foxa1_Rep1 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F6_AD010


title: APP-12m-LR_3

description: long-RNA

value: APP NL-G-F


title: Ctrl-3m-LR_1

description: long-RNA


title: S250F_FM_si_Foxa1_Rep1 ChIP-Seq


title: SY242CS_E2_si_Foxa1_Rep1 ChIP-Seq


title: S250F_DMSO_si_Foxa1_Rep2 ChIP-Seq


title: Ctrl-6m-LR_3

description: long-RNA


title: APP-12m-LR_2

description: long-RNA


title: S250F_DMSO_si_Foxa1_Rep1 ChIP-Seq


title: APP-12m-LR_1

description: long-RNA


title: APP-6m-LR_3

description: long-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F6_AD006


title: Ctrl-3m-LR_2

description: long-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F6_AD004


title: H247Y_FM_si_Foxa1_Rep1 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F7_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F6_AD002


title: APP-6m-LR_2

description: long-RNA


title: H247Y_FM_si_Foxa1_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F5_AD012


title: H247Y_E2_si_Foxa1_Rep1 ChIP-Seq


title: H247Y_E2_si_Foxa1_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F5_AD008


title: H247Y_DMSO_si_Foxa1_Rep2 ChIP-Seq


title: APP-3m-LR_3

description: long-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F5_AD007


title: APP-3m-LR_2

description: long-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F6_AD001


title: Before_Basal_sample_9

type: RNA

city: Tampa

first: Hemang

middle: Mahendrakumar

last: Parikh

state: FL

address: 3650 Spectrum Blvd.

department: Health Informatics Institute

institute: University of South Florida

description: Gene expression before bed rest

hyb_protocol: Targets were hybridized to the one-color Cyanine-3 (Cy3, green) Agilent Whole Human Genome Oligo Microarray (G4112F (Feature Number version)) which contains 44,000 60-mer oligonucleotide probes representing 41,000 unique genes and transcripts. Probe labeling and hybridization were performed according to manufacturer’s recommendation

scan_protocol: Images were analyzed using the Agilent Feature Extraction Software (version 9.5)

data_processing: The median intensities of each spot on the array were calculated using the GenePix Pro software (version 6). We performed quantile-based normalization between arrays without background subtraction using linear models for microarray data (limma) package in R

source_name: Before bed rest

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions

extract_protocol: RNA was extracted using Tri reagent (Sigma-Aldrich, St. Louis, MO) followed by RNeasy Midi kit (Qiagen, Düsseldorf, Germany). The RNA was further concentrated by RNeasy MiniElute (Qiagen, Düsseldorf, Germany) and SpeedVac (DNA 120 SpeedVac, Thermo Savant, Waltham, MA)

treatment_protocol: Muscle biopsies were taken from the right vastus lateralis muscle under local anesthesia (Lidocaine 1%), using a 6 mm Bergström needle (Stille AB, Sweden). Biopsies were immediately stored in RNAlater (Ambion, Austin, TX) and after overnight incubation at 4 C snap frozen at -80 C until further processing. The double staining method was used for capillary staining. Myofibrillar ATPase histochemistry was performed by preincubation at pH 4.4, 4.6, and 10.3 to identify muscle fiber types. Computer image analysis was performed using BioPix IQ 2.0.16 software (BioPix AB, Sweden)

value: Vastus lateralis muscle

value: Male


title: Before_Basal_sample_5

description: Gene expression before bed rest


title: Before_Basal_sample_8

description: Gene expression before bed rest


title: Before_Basal_sample_6

description: Gene expression before bed rest


title: Before_Basal_sample_7

description: Gene expression before bed rest


title: Before_Basal_sample_3

description: Gene expression before bed rest


title: H247Y_DMSO_si_Foxa1_Rep1 ChIP-Seq


title: Before_Basal_sample_4

description: Gene expression before bed rest


title: FH_positive_sample_18

description: Gene expression data before exercise

hyb_protocol: Hybridization to the Affymetrix Custom Array NuGO-Hs1a520180 GeneChip (http://www.nugo.org) were performed according to the manufacturer’s recommendation

scan_protocol: Images were analyzed using the GeneChip Operating System (GCOS; Affymetrix) software

data_processing: We used ENTREZ custom chip definition files (http://brainarray.mbni.med.umich.edu) to regroup the individual probes into consistent probesets and remap to the correct sets of genes for Affymetrix Custom Array NuGO-Hs1a520180 array which resulted in a total of 16,313 genes. We used the GC-content robust multi-array average (GC-RMA) method with additional background adjustment using sequence information to estimate probe affinity for nonspecific binding, quantile-based normalization, and summarization based on a multi-array model fit using the median polish algorithm

label: biotin

source_name: Before exercise

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

tag: family history of type 2 diabetes

value: Yes


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F5_AD004


title: F266L_FM_si_Foxa1_Rep2 ChIP-Seq


title: Before_basal_sample_2

description: Gene expression before bed rest


title: F266L_FM_si_Foxa1_Rep1 ChIP-Seq


title: APP-3m-LR_1

description: long-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F5_AD001


title: Ctrl-12m-sR_3

description: short-RNA


title: F266L_E2_si_Foxa1_Rep2 ChIP-Seq


title: Ctrl-12m-sR_2

description: short-RNA


title: Ctrl-12m-sR_1

description: short-RNA


title: F266L_E2_si_Foxa1_Rep1 ChIP-Seq


title: APP-6m-LR_1

description: long-RNA


title: FH_positive_sample_15

description: Gene expression data before exercise


title: FH_positive_sample_16

description: Gene expression data before exercise


title: FH_positive_sample_17

description: Gene expression data before exercise


title: FH_positive_sample_14

description: Gene expression data before exercise


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F4_AD012


title: Before_Basal_sample_1

description: Gene expression before bed rest


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F4_AD008


title: F266L_DMSO_si_Foxa1_Rep1 ChIP-Seq


title: Ctrl-6m-sR_2

description: short-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F4_AD006


title: Ctrl-6m-sR_1

description: short-RNA


title: FH_positive_sample_13

description: Gene expression data before exercise


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F4_AD002


title: Ctrl-3m-sR_2

description: short-RNA


title: Ctrl-3m-sR_1

description: short-RNA


title: EV_FM_si_Foxa1_Rep1 ChIP-Seq


title: EV_E2_si_Foxa1_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F4_AD010


title: APP-12m-sR_3

description: short-RNA


title: EV_E2_si_Foxa1_Rep1 ChIP-Seq


title: FH_positive_sample_12

description: Gene expression data before exercise


title: FH_positive_sample_9

description: Gene expression data before exercise


title: APP-12m-sR_2

description: short-RNA


title: Ctrl-6m-sR_3

description: short-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F3_AD012


title: FH_positive_sample_11

description: Gene expression data before exercise


title: FH_positive_sample_10

description: Gene expression data before exercise


title: F266L_DMSO_si_Foxa1_Rep2 ChIP-Seq


title: EV_FM_si_Foxa1_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F3_AD010


title: EV_DMSO_si_Foxa1_Rep2 ChIP-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F3_AD008


title: EV_DMSO_si_Foxa1_Rep1 ChIP-Seq


title: APP-12m-sR_1

description: short-RNA


title: FH_positive_sample_7

description: Gene expression data before exercise


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F3_AD007


title: FH_positive_sample_6

description: Gene expression data before exercise


title: APP-6m-sR_3

description: short-RNA


title: FH_positive_sample_8

description: Gene expression data before exercise


title: APP-6m-sR_2

description: short-RNA


title: WTNS_FM_Rep1 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F3_AD006


title: APP-6m-sR_1

description: short-RNA


title: FH_positive_sample_5

description: Gene expression data before exercise


title: FH_positive_sample_4

description: Gene expression data before exercise


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F2_AD012


title: WTNS_E2_Rep2 ATAC-Seq


title: WTNS_E2_Rep1 ATAC-Seq


title: APP-3m-sR_3

description: short-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F2_AD006


title: WTNS_DMSO_Rep2 ATAC-Seq


title: WTNS_FM_Rep2 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F2_AD008


title: FH_positive_sample_3

description: Gene expression data before exercise


title: APP-3m-sR_1

description: short-RNA


title: APP-3m-sR_2

description: short-RNA


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F2_AD007


title: SY242CS_FM_Rep2 ATAC-Seq


title: SY242CS_FM_Rep1 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F2_AD004


title: WTNS_DMSO_Rep1 ATAC-Seq


title: FH_positive_sample_1

description: Gene expression data before exercise


title: FH_negative_sample_18

description: Gene expression data before exercise

value: No


title: ChIP_input_ret

city: San Joan d'Alacant

first: Eloísa

last: Herrera

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias Alicante

institute: CSIC-UMH

description:
processed data file:
ChIP_input_ret.tdf

data_processing:
All sequenced datasets adapters were trimmed using cutadapt v1.18 (Martin, 2011) and aligned to mm10. Only reads with mapq > 30. Data was processed with the extensive use of custom scripts, and Samtools (v1.9) (Li et al., 2009), bedtools v2.26.0 (Quinlan and Hall, 2010). RNA-seq data: Reads were aligned with STAR (v2.5.0c) (Dobin et al., 2013). To retrieve differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2015). ChIPseq data: Reads were aligned using bowtie2 (v2.2.9) (Langmead and Salzberg, 2012). Peak calling for Zic2 ChIP-seq was run using MACS2 (v2.1) (Zhang et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: tdf files from whole genome alignments normalized to RPM (read per million sequenced reads).

source_name: retina

growth_protocol: Mice were kept in a timed pregnancy breeding colony at the Instituto de Neurociencias (IN). The animal protocols were approved by the IN Animal Care and Use Committee and met European and Spanish regulations.

extract_protocol: Whole retinas or spinal cords were dissected from embryos at E16, chopped, crosslinked with 1.1% PFA at room temperature for 20 minutes and quenched with glycine. Then, chromatin was sheared by biorruptor sonication. 10  micrograms of Chromatin were used for each IP. Diluted chromatin was incubated overnight at 4ºC with the specific antibody against mouse Zic2 at 1/500 (Millipore, AB15392) or IgG isotype control pre-immune serum at 1/500 (Abcam, ab27478). Immunoprecipitated chromatin was treated with RNAse and Protein Kinase and purified using Quiaquick PCR purification Kit (Quiagen, ID:28104). Inputs, control IgG and anti-zic2 ChIP samples were sent for library preparation and NGS service to Fasteris SA (Switzerland).

value: C57/DBA F1

value: retina

value: male and female


title: FH_negative_sample_20

description: Gene expression data before exercise


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F2_AD002

source_name: C57BL/6J P56 Mouse Brain

value: brain

value: SSp


title: ChIP_zic2_sc

description:
processed data file:
ChIP_zic2_sc.tdf

source_name: spinal cords

value: spinal cords

value: anti-Zic2  (Millipore, AB15392)


title: SY242CS_E2_Rep2 ATAC-Seq

value: breast cancer


title: ChIP_input_sc

description:
processed data file:
ChIP_input_sc.tdf

value: none (input)


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F2_AD001

value: VIS

value: male


title: FH_negative_sample_19

description: Gene expression data before exercise


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F1_AD012

value: Pons

value: female


title: FH_negative_sample_17

description: Gene expression data before exercise

value: Vastus lateralis muscle


title: SY242CS_E2_Rep1 ATAC-Seq


title: TRQ-STA3, biological replicate3

city: Beijing

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Gene expression data from TRQ-treated PAO1 grown till stationary phase

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper software
To identify DEGs (differential expression genes) between two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. The method edgeR was used for differential expression analysis
Genome_build: Pseudomonas aeruginosa PAO1

organism: Pseudomonas aeruginosa

source_name: Stationary phase bacterial culture of PAO1 treated by TRQ

growth_protocol: Bacterial cells were grown for 6 (EXP) and 12 (STA) hr to reach exponential phase at 37C.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5 μg of total RNA. Briefly, rRNA was removed by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200~300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.

treatment_protocol: Bacterial cells were collected and kept on ice to extract RNA.

value: TRQ-treated PAO1 strain in lB medium

tag: growth phase

value: Stationary phase


title: FH_positive_sample_2

description: Gene expression data before exercise

value: Yes

value: Male


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F1_AD010


title: SY242CS_DMSO_Rep2 ATAC-Seq


title: ChIP_zic2_ret

description:
processed data file:
ChIP_zic2_ret.tdf

value: C57/DBA F1

value: retina


title: TRQ-STA2, biological replicate2

tag: treatment


title: SY242CS_DMSO_Rep1 ATAC-Seq

tag: cell type


title: FH_negative_sample_15

description: Gene expression data before exercise

value: No


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F1_AD004

value: brain

value: SSp


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F1_AD002


title: PAO1-STA3, biological replicate3

description: Gene expression data from PAO1 grown till stationary phase

source_name: Stationary phase bacterial culture of PAO1

value: PAO1 strain in liquid LB medium


title: TRQ-STA1, biological replicate1


title: FH_negative_sample_14

description: Gene expression data before exercise


title: S250F_FM_Rep2 ATAC-Seq

value: breast cancer


title: S250F_FM_Rep1 ATAC-Seq


title: PAO1-STA2, biological replicate2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F1_AD001


title: S250F_E2_Rep2 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F12_AD012


title: PAO1-STA1, biological replicate1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F12_AD008


title: S250F_E2_Rep1 ATAC-Seq


title: S250F_DMSO_Rep2 ATAC-Seq


title: FH_negative_sample_16

description: Gene expression data before exercise


title: FH_negative_sample_13

description: Gene expression data before exercise


title: FH_negative_sample_10

description: Gene expression data before exercise


title: TRQ-EXP2, biological replicate2

description: Gene expression data from TRQ-treated PAO1 grown till exponential phase

source_name: Exponential phase bacterial culture of PAO1 treated by TRQ

value: Exponential phase


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F12_AD007

value: VIS


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F12_AD006


title: FH_negative_sample_11

description: Gene expression data before exercise


title: S250F_DMSO_Rep1 ATAC-Seq


title: FH_negative_sample_12

description: Gene expression data before exercise


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F12_AD004

value: male


title: PAO1-EXP3, biological replicate3

description: Gene expression data from PAO1 grown till exponential phase

source_name: Exponential phase bacterial culture of PAO1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F12_AD001


title: FH_negative_sample_8

description: Gene expression data before exercise


title: H247Y_FM_Rep1 ATAC-Seq


title: PAO1-EXP2, biological replicate2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F11_AD012

value: Pons


title: H247Y_E2_Rep2 ATAC-Seq


title: FH_negative_sample_9

description: Gene expression data before exercise


title: PAO1-EXP1, biological replicate1


title: H247Y_E2_Rep1 ATAC-Seq


title: H247Y_DMSO_Rep2 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F11_AD007


title: TRQ-EXP1, biological replicate1


title: FH_negative_sample_7

description: Gene expression data before exercise


title: H247Y_FM_Rep2 ATAC-Seq


title: F266L_FM_Rep2 ATAC-Seq


title: FH_negative_sample_3

description: Gene expression data before exercise


title: FH_negative_sample_4

description: Gene expression data before exercise


title: FH_negative_sample_5

description: Gene expression data before exercise


title: FH_negative_sample_6

description: Gene expression data before exercise


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F11_AD006

value: female


title: lung, IR3

first: Kun

last: Xiao

address: 28 Fuxing Road, Haidian District

institute: CHINESE PLA GENERAL HOSPITAL

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
Genome_build: Rattus norvegicus_Ensemble_93
Supplementary_files_format_and_content: Readcount_TPM.txt (hairpin.fa and hairpin.pos list the sequence and position of novel mirRNAs)

organism: Rattus norvegicus

source_name: lung

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.RNA was isolated using TRIZOL.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0  Flurometer (Life Technologies, CA, USA).RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg total RNA per sample was used as input material for the  small RNA library. Sequencing libraries were generated using NEBNext®  Multiplex Small RNA Library Prep Set for Illumina®  (NEB, USA.) following  manufacturer’s recommendations and index codes were added to attribute  sequences to each sample.

value: lung

value: Sprague-Dawley

value: lung ischemia-reperfusion


title: lung, IR2


title: lung, IR1


title: FH_negative_sample_2

description: Gene expression data before exercise

value: Vastus lateralis muscle


title: FH_negative_sample_1

description: Gene expression data before exercise

value: Male


title: lung, NC3

value: control


title: 5hMeDIP_inputRJ2

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

institute: CNRS

description:
17144FL-08-03-03_S139_L005
Control of 5hMeDIP-seq for the RJ2 mouse

data_processing:
Base-calling was performed  using CASAVA
All reads were trimmed to 50bp before processing because fragment length in both experiment are short (mean around 100bp). Sequencing up to 150bp was linked to facility organization.
Using trimmomatic, adapters were then removed and reads with sequencing quality lower than 28 were discarded.
Reads were aligned to the mm10 genome using Bowtie2 (for 5hMeDIP-seq, with only R1 reads) or BWA and its modified algorithm proposed in Khil et al., 2012  (for DMC1 ChIP-SSDS).
Reads that were unmapped or duplicated were filtered out in each experiment.
DMC1 ChIP-SSDS peaks were called using MACS2.
IDR method was used to deal with replicates for DMC1 peaks. Final peaksets were built from merged replicates, according to the IDR method.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig were built from merged replicates after alignment step for DMC1 ChIP-SSDS and 5hMeDIP-seq experiments. Input from B6 was subtracted for 5hMeDIP of B6, Spo11KO and HellscKO mice; input from RJ2 was subtracted for 5hMeDIP of RJ2.

extract_protocol:
For DMC1-SSDS experiment : Cell suspension was prepared by filtering homogenized tissue, then lysed. Lysates were sonicated and chromatin complexes were isolated with appropriate antibody. For 5hMeDIP-seq : genomic DNA was extracted by phenol/chloroform extraction  from a population of  ~95% pure leptotene/zygotene (L/Z) spermatocytes, obtained from synchronized FAC-sorted testes.
For DMC1 experiment, standard library construction was performed with the Illumina Trueseq protocol (Illumina, IP-202-9001DOC) with an additional step of kinetic enrichment as described in Khil et al. 2012. For 5hMeDIP-seq, Illumina adaptors were added to sonicated gDNA with NEB Next Ultra library preparation kit (NEB7370S), without the final PCR step. hMeDIP was then performed with Active Motif hMeDIP kit (AM, 55010) according to the manufacturers’ manual. Enriched fragments were then amplified by PCR, as recommended by the NEB Next Ultra library preparation kit.
Single Stranded DNA Sequencing (SSDS) method described in Khil et al. 2012 for DMC1 ChIPseq ; 5hMeDIP for 5hMeDIP-seq experiment

tag: strain background

tag: genotype/variation

tag: age/time point

value: 8 days post-injection

tag: tissue/cells

value: L/Z

tag: protocol

value: input


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F11_AD001

value: brain

value: SSp


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F11_AD010


title: 5hMeDIP_inputB6

description:
17144FL-06-03-02_S488_L008
Control of 5hMeDIP-seq for the B6 mouse

value: wild type


title: F266L_FM_Rep1 ATAC-Seq

tag: cell line

value: breast cancer


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F10_AD012

value: VIS


title: F266L_E2_Rep2 ATAC-Seq


title: lung, NC2


title: lung, NC1


title: H247Y_DMSO_Rep1 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F11_AD008

value: male


title: F266L_E2_Rep1 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F10_AD010

value: Pons


title: F266L_DMSO_Rep2 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F10_AD008


title: 5hMeDIP_Spo11KO_1

description:
17144FL-08-01-03_S133_L003
5hMeDIP-seq of the Spo11-/- mouse, replicate 1


title: M69_Sperm_Atrazine_ChIP

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each ChIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DHRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups as well as disease and non-disease groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DHRs. The DHR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DHR.
CpG density and other information was then calculated for the DHR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. F1- F3 generation control and atrazine lineages were housed in the same room and racks with lighting, food and water. All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 6252).

extract_protocol:
For each sample, the epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm.  The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in NIM buffer and stored at -80ºC for further processing.   An appropriate amount of rat sperm suspension was used for ChIP analysis. Rat sperm samples were sonicated and then pretreated with 50 µl 1M DTT in each sample tube. Samples were then incubated for 2h at RT on rotation. 123 mg of NEM dissolved in 1 mL of milliQ water in a 56ºC incubator. 120 µL of NEM added to each sample and then incubated for 30 min at RT on rotation. Chromatin prepared with  400 µl "Buffer 1 Stock" (see cited ChIP protocol), 102 mg sucrose and 0.5 µl 1M DTT. Samples then centrifuged at  2,500 rpm 5 min at RT. Supernatant discarded. Sperm resuspended in 1 ml 1X PBS and centrifuged at 2,500 rpm 5 min at RT. Supernatant discarded. Sperm resuspended in 130 µl of “Complete Buffer” (“Buffer 1 stock” + detergents) and placed in 130 µl Covaris tubes. Incubate 20 minutes on ice. Covaris program set to to the desired program: Chromatin shearing 10 min, Peak power: 75.0, Duty factor: 10.0, Cycles/Burst: 200. Program run for each tube. Samples removed from Covaris tube and placed it in 1.5 ml tube and centrifuged at 12,500 rpm 10 min at RT. Supernatant then collected and protease inhibitor cocktail ((20X) by dissolving 1 tablet in 500 µl MilliQ H2O) is added (11 µl of this solution per sample). Samples run on aa 1.5 % agarose gel to check bands size before resuming the IP protocol. Each sample had 3 µl of antibody (Ab anti-histone H3, CT, pan, clone A3S Millipore cat #05-928) added and were placed at 4ºC on rotation O/N. Samples then washed with magnetic beads (ChIP grade protein magnetic beads, Cell Signal, at 4ºC). 40 µl of beads for each sample were washed: placed on DynaMag-2 for two minutes and supernatant removed without disturbing the beads. Resuspended with 1 ml of 1X IP buffer, then repeat wash process once. Supernatant removed and resuspended in 350 µl of 1x IP. 40 µl of beads added to each sample and placed on rotation at 4ºC for 3 h. Tubes were then washed on DynaMag with 1X IP 3-4 times. With the final wash, beads resuspended in 300 µl “MeDIP digestion buffer." 3 µl of Proteinase K 20 mg/ml added to each tube and placed on rotation at 56ºC, 4 h (or O/N). Samples centrifuged quickly, then supernatant placed in new 1.5 ml tubes. 300 µl of phenol/chloroform/isoamyalcohol added to each tube and Centrifuged at 12,500 rpm 10 min at RT. The aqueous phase was placed in a new 1.5 ml tube and 2 µl of Glycoblue, one tenth vol of 3 M sodium acetate (NaOAc) and 2 vol of ethanol were added to each sample. Samples then precipitated O/N at 20ºC (O/N precipitation necessary for better yields). Tubes centrifuged at 12,500 rpm 30 min at 4ºC. Supernatant removed and 500 µl of 70% EtOH added. Centrifuged at 12,500 rpm 10 min at 4ºC. Supernatant removed and samples air dried 5-10 min. Pellets resuspended in 25 µl milliQ H2O. DNA concentration measured in Qubit with brDNA kit.
ChIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra DNA Library following the manufacturer’s protocol  and indexing each sample individually with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Outbred Sprague Dawley gestating female rats (F0 generation) were administered an intraperitoneal dose of 25 mg/kg body weight of atrazine (4% of rat oral LD50 [41] and 50% of NOAEL). These doses were administered at 90 days of age, during embryonic days 8-14 (E8-E14) of fetal gonadal sex determination. The F1 generation offspring was directly exposed as a fetus and F2 generation grand-offspring exposed as the germline in the F1 generation. These were each bred at 90 days of age within the lineage. The F3 generation great-grand-offspring is required to establish the transgenerational inheritance generation of ancestral exposure. A control lineage was established that used F0 gestating rats exposed to the vehicle control dimethyl sulfoxide (DMSO).

value: Sprague Dawley

tag: Sex

value: Sperm

value: DMSO

tag: measurement

value: ChIP

tag: disease

tag: lineage

value: Atrazine


title: TRQ-EXP3, biological replicate3

tag: strain

value: TRQ-treated PAO1 strain in lB medium

value: Exponential phase


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F10_AD004

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

tag: age

tag: tissue

tag: source

tag: target


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F10_AD006

tag: gender

value: female


title: M68_Sperm_Atrazine_ChIP

value: Male

tag: treatment


title: M67_Sperm_Atrazine_ChIP


title: M66_Sperm_Atrazine_ChIP

value: lean


title: EV_FM_Rep2 ATAC-Seq

tag: cell type


title: EV_FM_Rep1 ATAC-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F10_AD002

value: brain


title: EV_E2_Rep2 ATAC-Seq


title: 5hMeDIP_Spo11KO_2

description:
17144FL-08-02-01_S134_L004
5hMeDIP-seq of the  Spo11-/-  mouse, replicate 2

tag: strain background

tag: genotype/variation

value: 8 days post-injection

value: L/Z


title: 5hMeDIP_B6_2

description:
17144FL-08-01-02_S132_L003
5hMeDIP-seq of the B6 mouse, replicate 2

value: wild type

tag: age/time point

tag: tissue/cells


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_F10_AD001

value: VIS

value: SSp


title: 5hMeDIP_RJ2_1

description:
17144FL-08-02-02_S135_L004
5hMeDIP-seq of the RJ2 mouse, replicate 1

tag: protocol


title: 5hMeDIP_B6_1

description:
17144FL-06-03-03_S489_L008
5hMeDIP-seq of the B6 mouse, replicate 1


title: M65_Sperm_Atrazine_ChIP

tag: Sex


title: EV_E2_Rep1 ATAC-Seq

tag: cell line

value: breast cancer


title: 5hMeDIP_HellscKO_2

description:
17144FL-08-03-01_S137_L005
5hMeDIP-seq of the HellscKO mouse, replicate 2


title: 5hMeDIP_HellscKO_1

description:
17144FL-08-02-03_S136_L004
5hMeDIP-seq of the HellscKO mouse, replicate 1


title: M64_Sperm_Atrazine_ChIP

value: Sprague Dawley

tag: measurement

tag: disease

value: kidney


title: M63_Sperm_Atrazine_ChIP

tag: strain

value: Sperm

value: DMSO

value: multiple (kidney, lean)

tag: lineage


title: EV_DMSO_Rep2 ATAC-Seq


title: 5hMeDIP_RJ2_2

description:
17144FL-08-03-02_S138_L005
5hMeDIP-seq of the RJ2 mouse, replicate 2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E9_AD010

tag: age

tag: tissue

value: Pons


title: F266L_DMSO_Rep1 ATAC-Seq


title: M62_Sperm_Atrazine_ChIP

value: ChIP

value: Atrazine


title: EV_DMSO_Rep1 ATAC-Seq


title: CHIP_DMC1_HellscKO_1

description:
17144FL-07-01_S1_L001
DMC1-SSDS of the HellscKO mouse, replicate 1

value: adult

value: whole-testis

tag: chip antibody

value: Santa Cruz, goat polyclonal anti-DMC1, C-20, lot #D2215


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E9_AD008

value: brain

tag: source

tag: target

tag: gender

value: male


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E9_AD007


title: CHIP_DMC1_HellscKO_2

description:
17144FL-07-02_S3_L002
DMC1-SSDS of the HellscKO mouse, replicate 2

source_name: Hellsfl/Δ;Stra8-iCre _testis


title: M61_Sperm_Atrazine_ChIP

value: Male

tag: treatment

value: multiple (prostate, lean)


title: CHIP_DMC1_Hellsctrl_2

description:
17144FL-07-04_S2_L001
DMC1-SSDS of the Hellsctrl mouse, replicate 2

tag: genotype/variation

value: Hellsfl/{delta}


title: M60_Sperm_Atrazine_ChIP


title: Bovine endometrium_7_Control

city: Aberystwyth

first: Ruth

middle: Elizabeth

last: Wonfor

state: Ceredigion

address: Penglais

department: IBERS

institute: Aberystwyth University

description: Sample 13

data_processing:
All raw paired-end data were imported into the open source platform Galaxy (version 17.01), hosted by IBERS, Aberystwyth University
Raw paired-end data were submitted to FastQC analysis (Galaxy version 0.69).
Raw paired-end data were trimmed and clipped using Trimmomatic (Galaxy Version 0.36.0)
Trimmed data were submitted to FastQC analysis (Galaxy version 0.69) to assess read quality post trimming
Trimmed data were then aligned to produce BAM files using Bowtie 2 (Galaxy version 2.2.6)
BAM files were assessed for read abundance for annotated genes using the featureCounts package (Galaxy version 1.4.6.p5)
Counts for the two sequencing runs of samples 9-14 were added together in Excel.
Bioconductor package deSeq2 (as part of the R software package (version 3.4.0)) was used to determine the differential expression of genes using the read abundance data
Genome_build: UMD 3.1 (Ensembl version 89)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and each sample

organism: Bos taurus

source_name: Endometrium

growth_protocol: Endometrial tissue explants were dissected from bovine uteri post slaughter. An 8mm biopsy punch was used and the endometrium dissected away from the myometrium with sterile scissors. Tissue was randomly sampled from the intercaruncular tissue in the first third of the uterine horn closest to the utero-tubular junction, ipsilateral of the ovary staged as being in the follicular stage of the oestrous cycle. Explants were cultured in 6 well plates (one per well) with 3 mL of RPMI 1640 media, supplemented with 50 IU/mL penicillin, 50 µg/mL streptomycin and 2.5 µg/mL amphotericin B. Explants were incubated in a sterile incubator at 37 oC and 5 % CO2 for a total 30 h.

extract_protocol:
Total RNA was extracted using the Norgen Total RNA purification plus kit following the manufacturer’s instructions, with the addition of the use of a bead beater with the lysis buffer to aid tissue disruption.
Total RNA was prepared for sequencing using the TruSeq v2 RNA-Seq kit, using the manufacturer’s protocol, up to the validate library step. Following the enrichment of cDNA fragments with adapters, the cDNA was quantified using a Qubit 2.0, dsDNA broad range assay. Each sample was diluted to 10 nM with 10 nM Tris HCl and 0.5 % Tween-20 in nuclease free water. Samples were pooled and subsequently diluted to 2 nM with elution buffer (Qiagen, Manchester, UK) and then to 1 nM with 0.1 M sodium hydroxide, before being held at room temperature for 5 minutes to denature the DNA. Following denaturation, the samples were diluted to 10 pM in hybridisation buffer and loaded onto a cBot to cluster cDNA onto two lanes of a V4 High output flow cell. Samples were paired-end sequenced on an Illumina HiSeq 2500 and base pairs per read were set to 126 bp. Samples 9-14 were sequenced twice due to low reads due to the sequencing process compared to samples 1-8

treatment_protocol: Immediately after extraction, explant tissue from each animal was cultured either in medium alone or with the addition of sPIF (100nM) for 24 hours. Medium was then changed and replaced with the fresh medium alone or containing sPIF (100nM) for a further 6h.

value: no treatment

value: Endometrial explant


title: Bovine endometrium_7_sPIF

description: Sample 14

value: Treated with sPIF for 30h