title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A4_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A1_AD008

status: Public on Nov 20 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: AUD

tag: target

value: Pons

tag: gender

value: male


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A1_AD010

value: female


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A2_AD004

value: VIS

value: ACA


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A1_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A1_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A1_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A2_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A6_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A3_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A2_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A12_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A1_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A12_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A2_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A11_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A11_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A12_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A10_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A10_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A11_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A11_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A11_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A10_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A12_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A12_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A12_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A11_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A11_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A10_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A12_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H9_AD008

value: SSp


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H9_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H9_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A10_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H9_AD006

value: MOp


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A10_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H9_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A11_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H9_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P3_180503_P4_A10_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H8_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H8_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H8_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H8_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H9_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H8_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H6_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H7_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H6_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H7_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H7_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H7_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H7_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H8_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H6_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H7_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H6_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H6_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H8_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H6_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H6_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H5_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H5_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H6_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H9_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H5_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H5_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H5_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H5_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H4_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H4_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H4_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H4_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H4_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H3_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H3_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H4_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H3_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H3_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H4_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H2_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H2_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H2_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H2_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H3_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H1_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H2_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H3_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H2_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H2_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H1_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H5_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H1_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H1_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H12_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H1_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H12_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H12_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H12_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H4_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H12_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H3_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H2_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H12_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H11_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H11_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H10_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H10_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H10_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G9_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G9_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G9_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H10_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G9_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H10_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G9_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G8_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H11_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G8_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H11_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G7_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G7_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G7_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G6_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G6_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H11_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H11_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H11_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G6_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G6_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G6_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_H10_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G9_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G6_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G6_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G6_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G5_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G5_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G5_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G5_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G7_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G8_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G5_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G4_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G7_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G4_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G5_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G4_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G4_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G4_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G4_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G3_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G4_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G3_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G3_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G3_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G3_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G3_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G4_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G5_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G2_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G2_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G2_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G1_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G2_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G1_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G1_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G1_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G2_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G1_AD004


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G1_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G12_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G12_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G12_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G12_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G12_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G11_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G11_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G2_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G1_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G12_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G11_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G11_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G11_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G11_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G11_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G2_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G10_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G10_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G1_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G11_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G12_AD008


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G10_AD007


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G10_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_G10_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F9_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F9_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F9_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F7_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F8_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F7_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F7_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F9_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F7_AD012


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F5_AD008


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F3_AD002


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F2_AD010


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F2_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F1_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F1_AD006


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F12_AD012


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F1_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F1_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F1_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F11_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F11_AD004


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_F11_AD008


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title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D7_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D9_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D7_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D7_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D7_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D6_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D6_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D6_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D6_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D6_AD002


title: yGV_7 RNA-seq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina Nextseq500 platform using the default RTA analysis software.
RNA-seq libraries were aligned to the GRCm38 mouse genome build using HiSat270 (v2.1.0) using options --dta --sp 1000,1000 --no-mixed --no-discordant.
Primary alignments were assigened to features of the mouse oocyte transcriptome (Veselovska et al., 2015) using Seqmonk (v1.44.0) with the options 'Generate Raw Counts' and 'merge transcript isoforms'
Genome_build: GRCm38

molecule: total RNA

source_name: germinal vesicle (GV) oocyte

extract_protocol:
Oocytes were released from the ovaries mechanically with a fine needle and cleaned in M2 medium (Sigma). Clean oocytes were washed twice in PBS, inspected to ensure complete removal of adherent granulosa cells, then individually lysed and flash-frozen in 5μl RLT Plus buffer (Qiagen) and stored at -80°C until further use.
DNA and RNA from individual oocytes were physically separated using the G&T protocol (Angermueller et al., 2016). Briefly, Smart-seq2 oligo-dTs (Picelli et al., 2013, 2014) were annealed to magnetic beads (MyOne C1, Life Technologies) and used to capture polyadenylated mRNA from individual oocyte lysates. The remaining lysate containing the DNA was transferred to a separate tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U μl−1 of RNAsin (Promega). The washing solutions were added to the DNA tube to maximise recovery. mRNA on the beads was immediately processed further for cDNA conversion by resuspending beads in 10 μl of reverse transcriptase mastermix (100 U SuperScript II (Invitrogen), 10 U RNAsin (Promega), 1 × Superscript II First-Strand Buffer, 2.5 mM DTT (Invitrogen), 1 M betaine (Sigma), 9 mM MgCl2 (Invitrogen), 1 μM Template-Switching Oligo (TSO, Exiqon (Picelli et al., 2013, 2014)), 1 mM dNTP mix (Roche)). The mRNA mixture was reverse transcribed by incubation for 60 min at 42 °C followed by 30 min at 50 °C and 10 min at 60 °C. The cDNA was amplified by PCR by adding 11 μl of 2 × KAPA HiFi HotStart ReadyMix and 1 μl ISPCR primer (2 μM; (Picelli et al., 2013, 2014)). Samples were incubated in a thermocycler at 98 °C for 3 min, followed by 18 cycles of 98 °C for 15 s, 67 °C for 20 s, 72 °C for 6 min and finally 72 °C for 5 min. The amplified product was purified using Ampure XP beads with a 1:1 ratio and eluted into 20 μl of water. In parallel, the lysate containing the DNA was purified using a 0.8:1 volumetric ratio of Ampure XP Beads (Beckman Coulter) and eluted into 10 μl of water to use for scBS-seq library preparation.
Libraries were prepared from 100 to 400 pg of cDNA using the Nextera XT Kit (Illumina), per the manufacturer’s instructions but with one-fifth volumes.

tag: developmental stage

value: germinal vesicle (GV)

tag: age group

value: young


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D5_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D5_AD010


title: liver-control-rep2

type: RNA

city: Manchester

first: Kate

last: Bloch

address: Alderley Park, Alderley Edge

institute: Manchester University

scan_protocol: The gene chips were washed and stained using the Affymetrix Fluidics Station 450 and scanned by means of an Affymetrix GeneArray scanner.

data_processing: Analysis and quality controls were done in R using: simpleaffy (Wilson and Miller, 2005), affycoretools (MacDonald, 2008), affyPLM (Bolstad et al., 2005), all BioConductor packages. The raw data from CEL files were read into the R environment using the package affy (Gautier et al., 2004). To identify the differentially expressed genes (DEGs) limma package (Ritchie, 2015) was used. Comparisons were made between control (corn oil) and TCE treated samples. Three rats were used per condition. Genes with adjusted P-value < 0.05 (FDR) were considered significant and discussed further.

label: biotin

organism: Rattus norvegicus

source_name: liver

growth_protocol: Wistar-derived rats where bred in the Life Science Support Unit at Liverpool John Moores University. The rats were housed in plastic cages in a room maintained at 20 °C ± 2 °C and a relative humidity of 50% ± 5% with a 12 h light-dark cycle starting at 04.00 h. Rats were allowed food (rat expanded diet), and water ad libitum.

extract_protocol: Total RNA was isolated from a small (50 mg) portion of the renal-cortex and liver of corn oil (control) or TCE treated rats. Trizol reagent was used for RNA isolation. Total RNA was purified using the RNeasy Total RNA Mini Kit (Qiagen) according to manufacturer's instructions. RNA was checked for purity and integrity using Agilent 2001 Bioanalyzer (Agilent Technologies GmbH, Germany) before processing. Transcriptomics data was generated using GeneChip Rat Genome 230 2.0 Arrays. cDNA was prepared using the Affymetrix IVT express kit (Affymetrix, Santa Clara). cDNA synthesis and labelling was performed according to the manufacturer's procedures. Subsequent labelling of the samples was conducted by synthesis of Biotin-labelled complementary RNA (cRNA) using the GeneChip IVT labelling kit (Affymetrix). Purified cRNA was quantified using a spectrophotometer, and unfragmented samples were checked on the Bioanalyzer. Subsequently, cRNA samples were fragmented for target preparation according to the Affymetrix manual and checked on the Bioanalyzer. Samples were stored at −20 °C until ready to perform hybridization. cRNA targets were hybridized on high-density oligonucleotide gene chips GeneChip Rat Genome 230 2.0 Arrays according to the Affymetrix Eukaryotic Target Hybridization manual. The gene chips were washed and stained using the Affymetrix Fluidics Station 450 and Genechip Operating Software and scanned by means of an Affymetrix GeneArray scanner.

treatment_protocol: 3 rats were dosed orally for 3 days with TCE in corn oil at 16mg/kg/day at 5ml/kg. 3 control rats received corn oil alone.

value: liver

value: F-344 (Wistar-derived)

tag: Sex


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D6_AD001


title: kidney-control-rep3

hyb_protocol: cRNA targets were hybridized on high-density oligonucleotide gene chips GeneChip Rat Genome 230 2.0 Arrays according to the Affymetrix Eukaryotic Target Hybridization manual.

source_name: kidney

label_protocol: Subsequent labelling of the samples was conducted by synthesis of Biotin-labelled complementary RNA (cRNA) using the GeneChip IVT labelling kit (Affymetrix).

value: kidney


title: kidney-control-rep2


title: yGV_7A RNA-seq


title: liver-control-rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D5_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D5_AD012


title: liver-control-rep3


title: liver-case-rep1


title: kidney-case-rep3


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D5_AD001


title: yGV_5 RNA-seq


title: yGV_6 RNA-seq


title: kidney-control-rep1


title: kidney-case-rep2


title: liver-case-rep2


title: kidney-case-rep1


title: yGV_3 RNA-seq


title: yGV_4 RNA-seq


title: yGV_4A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D5_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D5_AD002


title: liver-case-rep3


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D4_AD012


title: yGV_5A RNA-seq


title: yGV_3A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D4_AD010


title: yGV_39 RNA-seq


title: yGV_38 RNA-seq


title: yGV_6A RNA-seq


title: yGV_39A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D4_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D4_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D4_AD006


title: yGV_38A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D4_AD004


title: yGV_37A RNA-seq


title: yGV_37 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D3_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D3_AD008


title: yGV_35A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D3_AD007


title: yGV_35 RNA-seq


title: yGV_34 RNA-seq


title: yGV_33 RNA-seq


title: yGV_2 RNA-seq


title: yGV_33A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D3_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D3_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D3_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D4_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D2_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D2_AD012


title: yGV_2A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D2_AD008


title: yGV_24A RNA-seq


title: yGV_23 RNA-seq


title: yGV_36A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D2_AD007


title: yGV_21 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D2_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D3_AD004


title: yGV_34A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D1_AD012


title: yGV_21A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D2_AD001


title: yGV_20 RNA-seq


title: yGV_1 RNA-seq


title: yGV_20A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D1_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D1_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D1_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D1_AD002


title: yGV_24 RNA-seq


title: yGV_1A RNA-seq


title: yGV_22 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D2_AD006


title: yGV_19A RNA-seq


title: yGV_19 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D2_AD004


title: yGV_22A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D1_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D12_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D12_AD008


title: yGV_18A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D12_AD010


title: yGV_17 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D12_AD007


title: yGV_18 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D1_AD010


title: oGV_9 RNA-seq

value: old


title: yGV_17A RNA-seq


title: oGV_9A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D12_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D12_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D12_AD004


title: oGV_48 RNA-seq


title: oGV_48A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D11_AD012


title: oGV_47 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D11_AD010


title: oGV_47A RNA-seq


title: oGV_46A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D11_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D11_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D11_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D11_AD004


title: oGV_44 RNA-seq


title: oGV_45A RNA-seq


title: oGV_45 RNA-seq


title: oGV_44A RNA-seq


title: oGV_43A RNA-seq


title: oGV_43 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D11_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D10_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D10_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D10_AD008


title: oGV_42 RNA-seq


title: oGV_42A RNA-seq


title: oGV_41 RNA-seq


title: oGV_41A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D10_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D10_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D10_AD006


title: oGV_31 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C9_AD012


title: oGV_31A RNA-seq


title: oGV_46 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C9_AD010


title: oGV_30A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D11_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C9_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C9_AD007


title: oGV_28 RNA-seq


title: oGV_29A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_D10_AD004


title: oGV_29 RNA-seq


title: oGV_28A RNA-seq


title: oGV_26 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C9_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C9_AD006


title: oGV_27 RNA-seq


title: oGV_27A RNA-seq


title: oGV_26A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C9_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C8_AD007


title: oGV_25 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C8_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C8_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C9_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C8_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C8_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C8_AD004


title: oGV_25A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C8_AD002


title: oGV_16A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C8_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C7_AD012


title: oGV_15 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C7_AD008


title: oGV_14 RNA-seq


title: oGV_15A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C7_AD006


title: oGV_13A RNA-seq


title: oGV_13 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C7_AD002


title: oGV_30 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C7_AD001


title: oGV_11A RNA-seq


title: oGV_12A RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C6_AD010


title: oGV_16 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C6_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C6_AD004


title: oGV_10A RNA-seq


title: oGV_11 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C5_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C6_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C6_AD002


title: oGV_10 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C5_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C5_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C7_AD007


title: yGV_7 [BiSulfite-seq]

data_processing:
Libraries were sequenced on the Illumina Nextseq500 platform using the default RTA analysis software.
Alignment was performed in single-end non-directional mode followed by deduplication (deduplicate_bismark) and methylation calling (bismark_methylation_extractor) using Bismark (v0.18.2). The methylation calls for both Read 1 and Read 2 were then merged afterwards using a Python script.
Libraries having a mapping efficiency <10%, fewer than 500,000 CpGs covered, or greater than 50% methylated CpGs were discarded
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

extract_protocol:
Oocytes were released from the ovaries mechanically with a fine needle and cleaned in M2 medium (Sigma). Clean oocytes were washed twice in PBS, inspected to ensure complete removal of adherent granulosa cells, then individually lysed and flash-frozen in 5μl RLT Plus buffer (Qiagen) and stored at -80°C until further use.
DNA and RNA from individual oocytes were physically separated using the G&T protocol (Angermueller et al., 2016). Briefly, Smart-seq2 oligo-dTs (Picelli et al., 2013, 2014) were annealed to magnetic beads (MyOne C1, Life Technologies) and used to capture polyadenylated mRNA from individual oocyte lysates. The remaining lysate containing the DNA was transferred to a separate tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U μl−1 of RNAsin (Promega). The washing solutions were added to the DNA tube to maximise recovery. mRNA on the beads was immediately processed further for cDNA conversion by resuspending beads in 10 μl of reverse transcriptase mastermix (100 U SuperScript II (Invitrogen), 10 U RNAsin (Promega), 1 × Superscript II First-Strand Buffer, 2.5 mM DTT (Invitrogen), 1 M betaine (Sigma), 9 mM MgCl2 (Invitrogen), 1 μM Template-Switching Oligo (TSO, Exiqon (Picelli et al., 2013, 2014)), 1 mM dNTP mix (Roche)). The mRNA mixture was reverse transcribed by incubation for 60 min at 42 °C followed by 30 min at 50 °C and 10 min at 60 °C. The cDNA was amplified by PCR by adding 11 μl of 2 × KAPA HiFi HotStart ReadyMix and 1 μl ISPCR primer (2 μM; (Picelli et al., 2013, 2014)). Samples were incubated in a thermocycler at 98 °C for 3 min, followed by 18 cycles of 98 °C for 15 s, 67 °C for 20 s, 72 °C for 6 min and finally 72 °C for 5 min. The amplified product was purified using Ampure XP beads with a 1:1 ratio and eluted into 20 μl of water. In parallel, the lysate containing the DNA was purified using a 0.8:1 volumetric ratio of Ampure XP Beads (Beckman Coulter) and eluted into 10 μl of water to use for scBS-seq library preparation.
Single-cell BS-seq (scBS-seq) libraries were prepared as previously described (Smallwood et al., 2014), with minor changes. DNA purified from single cells was bisulphite converted using the EZ Methylation Direct kit (Zymo) according to the manufacturer’s instructions, but using half volumes. Five rounds of first-strand synthesis were carried out, starting by eluting bisulphite-converted DNA into 40 μl of first-strand synthesis mastermix (1 × Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4μM 6NF oligo (IDT)). The mixture was heated to 65 °C for 2 min and cooled on ice. 50U of Klenow exo- (Enzymatics) was added and the mixture incubated on a thermocycler at 37 °C for 30 min after slowly ramping from 4 °C. First-strand synthesis was repeated 4 more times with the addition of 2.5 μl of reaction mixture (1× blue buffer, 0.25 mM dNTPs, 10 mM 6NF oligo and 25U Klenow exo‑). In the final round, samples were incubated for 90 min at 37 °C. Exonuclease digestion was carried out by adding 20U of exonuclease I (NEB) to the reactions, diluting with water to a total volume of 100 μl, followed by incubation at 37 °C for 1 hour. Samples were purified with AMPure XP beads using a 0.75:1 ratio. Beads were resuspended in 50 μl second-strand master mix (1× Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4 μM 6NF oligo (IDT). Reactions were heated for 98 °C for 1 min, cooled on ice, before adding 50U of Klenow exo- (Enzymatics). The mixture was incubated on a thermocycler at 37 °C for 90 min after slowly ramping from 4 °C. Samples were purified using a 0.75:1 ratio of AMPure XP beads and libraries were amplified in 50 μl of PCR mastermix (1× KAPA HiFi Readymix, 0.2 μM PE1.0 primer, 0.2 μM iTAG index primer) using the following protocol: 2 min at 95 °C, 14 cycles of 80 sec at 94 °C, 30 sec at 65 °C, 30 sec at 72 °C and final extension for 3 min at 72 °C. Finally, scBS-seq libraries were purified using a 0.7:1 volumetric ratio of AMPure XP beads and eluted in 15 µl EB buffer before pooling and sequencing.


title: yGV_6 [BiSulfite-seq]


title: oGV_14A RNA-seq


title: yGV_5 [BiSulfite-seq]


title: oGV_12 RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C5_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C5_AD004


title: yGV_4 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C6_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C5_AD002


title: yGV_39A [BiSulfite-seq]


title: yGV_3 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C5_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C4_AD012


title: yGV_37 [BiSulfite-seq]


title: yGV_38A [BiSulfite-seq]


title: yGV_38 [BiSulfite-seq]


title: yGV_36 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C4_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C4_AD008


title: yGV_36A [BiSulfite-seq]


title: yGV_37A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C4_AD007


title: yGV_35 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C4_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C4_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C3_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C3_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C3_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C3_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C3_AD006


title: yGV_39 [BiSulfite-seq]


title: yGV_34 [BiSulfite-seq]


title: yGV_35A [BiSulfite-seq]


title: yGV_33 [BiSulfite-seq]


title: yGV_34A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C3_AD004


title: yGV_33A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C3_AD002


title: yGV_2 [BiSulfite-seq]


title: yGV_2A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C3_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C2_AD010


title: yGV_24A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C2_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C2_AD008


title: yGV_23 [BiSulfite-seq]


title: yGV_24 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C2_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C2_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C2_AD007


title: yGV_22A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C2_AD002


title: yGV_21 [BiSulfite-seq]


title: yGV_23A [BiSulfite-seq]


title: yGV_22 [BiSulfite-seq]


title: yGV_21A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C2_AD001


title: yGV_20 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C1_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C1_AD008


title: yGV_20A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C1_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C1_AD002


title: yGV_1A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C1_AD007


title: yGV_1 [BiSulfite-seq]


title: yGV_19 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C1_AD001


title: yGV_19A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C12_AD012


title: yGV_18 [BiSulfite-seq]


title: yGV_17 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C12_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C12_AD008


title: yGV_17A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C12_AD004


title: oGV_9 [BiSulfite-seq]


title: Tg Vehicle-4

city: Houston

first: Hui

last: Zheng

state: TX

address: 1 Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

data_processing: Data were analyzed using nSolver 4.0 and the Advanced Analysis 2.0 plugin. Fold-change expression and p-values were calculated by linear regression analysis using negative binomial or log-linear models.

label: Biotin & color-coded tag

source_name: Mouse hippocampus

label_protocol: For Nanostring nCounter panel analysis, RNA was isolated and 770 transcripts were quantified with the Nanostring nCounter multiplexed target platform using the Mouse Neuroinflammation panel (https://www.nanostring.com). nCounts of mRNA transcripts were normalized using the geometric means of 10 housekeeping genes (Csnk2a2, Ccdc127, Xpnpep1, Lars, Supt7l, Tada2b, Aars, Mto1, Tbp, and Fam104a)

growth_protocol: 5xFAD and littermate control male mice were mainted in notmal housing as per IACUC gideline. .

extract_protocol: Following treatment, total RNA was extracted from cells or human or mouse brain tissues using RNeasy Mini kit (Qiagen, 74106).

treatment_protocol: 5xFAD mice were treated with TPPU (3 mg/kg) in drinking water for 2.5 months starting at 2 months of age. TPPU was dissolved in 1% polyethylene glycol 400. The vehicle received only 1% polyethylene glycol 400.

value: Hippocampus

tag: genotype/variation

value: Tg (5xFAD)

tag: treatment

value: vehicle


title: Tg Vehicle-3


title: oGV_9A [BiSulfite-seq]


title: Tg-TPPU-4

value: TPPU (3 mg/kg)


title: Tg-TPPU-1


title: Tg-TPPU-3


title: Tg-TPPU-2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C12_AD002

value: brain


title: Tg Vehicle-1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C11_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C12_AD010


title: yGV_18A [BiSulfite-seq]


title: oGV_48A [BiSulfite-seq]


title: oGV_47 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C11_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C12_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C11_AD008

value: male


title: oGV_47A [BiSulfite-seq]


title: N-Tg Vehicle-2

value: Non-transgenic (N-tg)


title: N-Tg Vehicle-4


title: N-Tg Vehicle-1


title: Tg Vehicle-2


title: SZ11_02_2_EB081_KO_aNK_S2

first: Santiago

last: Zelenay

state: UK

address: Alderley Park

institute: CRUK Manchester Institute

data_processing:
Raw sequencing data (bcl-files) were converted to fastq files with Illumina bcl2fastq tool, integrated into the CellRanger (10X Genomics) suite (version 2.1.1).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix starting from raw data.
Genome_build: Pre-build mouse genome (version mm10-1.2.0) was used as genome reference.
Supplementary_files_format_and_content: normalized counts, tab delimited text

source_name: Tumor

growth_protocol: Tumor cells in this study were grown under strandard conditions (RPMI 10%FBS, at 37C, 5%CO2)

extract_protocol:
Sixteen thousand soted CD45+ cells were loaded into a channel of a Chromium Chip B (10X Genomics, PN-1000073) and GEMs were generated on the Chromium Controller (10X Genomics, GCG-SR-1).
Indexed sequencing libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v3 (10X Genomics, PN-1000075, PN-120262) according to manufacturer’s instructions, with 11 cycles of cDNA amplification and 14 cycles of sample index PCR.

treatment_protocol: Mice in this study were untreated or in case of Sample 2 they received a cocktail of NK cell depleting antibodies (anti-NK1.1 clone PK136 200µg+antiASIALO GM1 30µg/mouse on day 0 and day2 from tumor cell injection)

value: Melanoma day4

value: 8 weeks old host

value: wildtype tumor cells


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C11_AD007

value: SSp

value: ACA


title: SZ8_12_12_Mac_KO3_S12

data_processing:
Basecalling was performed using Illumina bcl2fastq2 Conversion Software v2.16
Single-end sequencing reads were first trimmed using bbduk to remove the first 12 bases. Regions of length 20 or above with average quality of less than 10 were trimmed from the end of each read. Finally, trailing polyG and polyA were removed from the reads using cut adapt.
Trimmed reads were aligned to reference genome mm10 and assigned to features in the mm10 gene annotation using the STAR program.
Read Counts were read into R and processed using the edgeR package features were filtered to remove features with no counts
Library Sizes were normalised using the TMM normalisation in the edgeR package to produce normalised counts per million reads
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Comma separated text files

source_name: TAMs

growth_protocol: Tumor cell in this study were grown in vitro under strandard conditions (RPMI 10%FBS, at 37C, 5%CO2)

extract_protocol:
Tumor associated macrophages were FACS sorted. Purity of TAMs was >99% as determined by FACS. TAMs were stained (CD45-BV650, F4/80-PECy7, CD11b-BV785, Ly6C-FITC) and sorted on a FACSAria III cell sorter (BD Bioscience). RNA was prepared using standard Qiagen protocol.
Libraries were prepared with 800pg of total RNA using Lexogen QuantSeq 3′-mRNAseq Library Prep Kit (FWD, Cat. No. 015)

value: tumor associated macrophages (TAMs)

value: mice injected with Ptgs1/Ptgs2 deficient tumor cells


title: SZ11_01_1_EB081_KO_CTR_S1


title: N-Tg Vehicle-3


title: SZ8_11_11_Mac_KO2_S11


title: oGV_48 [BiSulfite-seq]

value: germinal vesicle (GV)


title: SZ8_10_10_Mac_KO1_S10


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C11_AD006

value: MOp

value: female


title: oGV_46A [BiSulfite-seq]

value: old


title: SZ8_08_8_Mac_WT2_S8

value: mice injected with wildtype tumor cells


title: oGV_46 [BiSulfite-seq]


title: Cisplatin elicited LLC exosomes_2

city: Zhengzhou

first: Yan

last: Yan

address: Jianshe Road

country: China

institute: The First Affiliated Hospital of Zhengzhou University

description: miRNA expression in cisplatin elicited LLC exosomes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis.

source_name: cell supernatant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: LLC cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, HyClone) supplemented with 10% fetal bovine serum (FBS, PAN Biotech), 100 IU/ml penicillin and 100 μg/ml streptomycin (Gibco) at 37 °C in a 5% CO2 incubator.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity(RIN) was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: 80% confluent cells were rinsed with phosphate-buffered saline (PBS) and then cultured in FBS-free DMEM with 5uM cisplatin. After 24h, the culture medium was collected for exosomes isolation.

tag: cell type

value: Lewis lung carcinoma (LLC) cell line

tag: sample source

value: cell culture supernatant

tag: rna population

value: exosome


title: Cisplatin elicited LLC exosomes_1


title: SZ3_12_12_EB046_KO3_aNK_S11

extract_protocol:
RNA was preaperd from bulk tumors isolated on day 4 using Direct-ZOL kit (Zymo research) #R071 following manufacturer's instructions
Libraries were prepared with 500ng of total RNA using Lexogen QuantSeq 3′-mRNAseq Library Prep Kit (FWD, Cat. No. 015)

treatment_protocol: Mice in this study were untreated or in case of Samples 8, 9 and 10 they received a cocktail of NK cell depleting antibodies (anti-NK1.1 clone PK136 200µg+antiASIALO GM1 30µg/mouse on day 0 and day2 from tumor cell injection)

value: 8 weeks old, NK cell-depleted host

value: Ptgs1/Ptgs2 deficient tumor cells


title: SZ8_07_7_Mac_WT1_S7


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C11_AD001

value: brain

value: male


title: oGV_45 [BiSulfite-seq]


title: SZ3_11_11_EB046_KO2_aNK_S10

value: Melanoma day4


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C10_AD012

value: SSp


title: SZ3_10_10_EB046_KO1_aNK_S9


title: SZ3_07_7_EB042_KO3_CTR_S6

value: 8 weeks old host


title: SZ3_06_6_EB046_KO2_CTR_S5


title: SZ3_03_3_EB046_WT3_CTR_S2

value: wildtype tumor cells


title: oGV_44A [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C10_AD010

value: ACA


title: SZ8_09_9_Mac_WT3_S9

value: tumor associated macrophages (TAMs)


title: oGV_45A [BiSulfite-seq]

value: germinal vesicle (GV)


title: oGV_43 [BiSulfite-seq]


title: SZ3_05_5_EB046_KO1_CTR_S4


title: SZ3_02_2_EB046_WT2_CTR_S1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C11_AD002

value: MOp


title: SZ3_01_1_EB046_WT1_CTR_S1


title: oGV_42 [BiSulfite-seq]

value: old


title: Py+Tg3+ 5534 mCh-

city: Philadelphia

first: Rumela

last: Chakrabarti

state: PA

address: 380 S University Ave

institute: University of Pennsylvania School of Veterinary Medicine

description:
5_S7
processed data: neg_optimal_sort.bed

data_processing:
Nextera DNA Library Prep kit was used from Illumina, Cat Fc 121-1030.
ATAC-Seq transposition assay and library preparation were made following the published protocols (PMIDs- 25559105, 30089273).
Fastq files were processed in genotype-specific replicate batches to find open chromatin regions using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_optimal_sort.bed: Optimized peak files for mCh_neg and mCh_pos replicate groups.

source_name: Mammary tumor cells

extract_protocol:
Tumors from PyMT; Dll1-mCherry mice were digested with collagenase/hyaluronidase using method obtained from Shackleton et al., 2006. Single cells were sorted for epithelial cell enriched mCherry+ and mCherry- tumor cells. Epithelial cell enriched population was obtained by sorting out and removing stromal cells with CD45, CD31 and ter119 antibodies. 20, 00 cells were used.
Library construction protocol was made using standard protocol from Illumina.

value: MMTV-PyMT tumor cells

tag: cell population


title: oGV_43A [BiSulfite-seq]


title: Py+Tg3+ 5796 mCh+

description:
8_S6
processed data: pos_optimal_sort.bed


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C10_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C10_AD004

value: female


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C10_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C10_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_C10_AD001


title: oGV_42A [BiSulfite-seq]


title: H9.WTc.3.3_RNA-seq

first: Susanne

last: Bornelöv

address: Tennis Court Road

department: WT-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

description: Total RNA-seq

data_processing:
Trim_galore! was used to remove Illumina adaters.
TopHat2 (v 2.1.0) was used to align the reads to the hg38 reference genome using Gencode v23 gene models.
Ribo-seq reads were firstly aligned to a set of known rRNA and tRNAs (selected from the UCSC RepeatMasker tracks), followed by alignment of all unmapped reads to the reference genome.
FeatureCounts (with Gencode v23 gene models) was used to count the number of reads per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing counts for each gene and sample

organism: Homo sapiens

source_name: human embryonic stem cells

growth_protocol: The human embryonic stem cell (hESC) line Hues9 (H9) was obtained from the Wicell Research Institute (Madison, WI) and maintained in Essential 8 media (Thermo Fisher Scientific) on hESC-Qualified Matrigel (Corning) coated plates. Media was refreshed daily and the cultures were dissociated in clumps every 4 days using 0.5mM EDTA in PBS. HEK293 (HEK) cells were obtained from ATCC and grown in DMEM Media (Thermo Fisher Scientific) supplemented with 1mM Glutamax (Thermo Fisher Scientific), 10% heat inactivated FBS (Thermo Fisher Scientific). All cells were grown at 37°C, 5 % CO2.

extract_protocol:
Total RNA extraction by non ionic detergent-based cell lysis was performed for both H9 and HEK293 cells.
Libraries for H9 WT and NSun6 KO cells (at least 4 replicates each) were performed as described before (Bornelov et al, 2019, Blanco et al. 2016). For the RNA seq samples, we used the NEB ultra-directional library prep kit (NEB). Ribosomal profiling samples were made into libraries using the Illumina Truseq small RNA kit (Illumina). HEK293 WT and NSun6 KO libraries (4 replicates each) were prepared using the Illumina TruSeq Ribo Profile kit; the Total RNA libraries were depleted of ribosomal RNAs using the Illumina Ribo-Zero rRNA removal kit.

tag: cell line

tag: genotype

value: Control (Wild-type Crispr control (random))

tag: batch


title: oGV_44 [BiSulfite-seq]

tag: strain


title: Py+Tg3+ 4593 mCh-

description:
3_S3
processed data: neg_optimal_sort.bed


title: oGV_41 [BiSulfite-seq]


title: SZ3_04_4_EB042_WT2_CTR_S3

tag: tissue

tag: age


title: oGV_41A [BiSulfite-seq]


title: Py+Tg3+ 4562 mCh+

description:
2_S2
processed data: pos_optimal_sort.bed


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B9_AD008

tag: source

tag: target


title: Py+Tg3+ 4562 mCh-

description:
1_S1
processed data: neg_optimal_sort.bed


title: oGV_31 [BiSulfite-seq]

tag: developmental stage


title: oGV_31A [BiSulfite-seq]

tag: age group


title: Py+Tg3+ 5534 mCh+

description:
6_S8
processed data: pos_optimal_sort.bed


title: H9.WTc.3.1_RNA-seq

description: Total RNA-seq


title: H9.WT.2.3_RNA-seq

description: Total RNA-seq

value: Control (Wild-type)


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B9_AD012

tag: gender


title: mCh+Rep2

data_processing:
fastq files were mapped to the mouse transcriptome (gencode version M20) using salmon
read counts were summarized to the gene level using tximport
Genome_build: GRCm38.p6
transcriptome build: Gencode M20
Supplementary_files_format_and_content: summarized counts per gene - not normalized for sequencing depth

extract_protocol:
Tumors from PyMT; Dll1-mCherry and PyMT; Dll1-GFP mice were digested with collagenase/hyaluronidase using method obtained from Shackleton et al, 2006. Single cells were sorted for epithelial cell enriched GFP/mCherry+  and GFP/mCherry- tumor cells. Epithelial cell enriched population was obtained by sorting out and removing stromal cells with CD45, CD31 and ter119 antibodies. RNA was harvested using Purelink RNA Mini Kit cat#12183018A with 500 ug of total RNA for the construction of sequencing libraries.
Illumina TruSeq Stranded Library Prep Kit

tag: reporter

value: mCh

tag: dll1 expression

tag: mouseid


title: H9.WT.2.2_RNA-seq

description: Total RNA-seq


title: oGV_30 [BiSulfite-seq]


title: oGV_30A [BiSulfite-seq]


title: mCh+Rep1


title: H9.WT.2.1_RNA-seq

description: Total RNA-seq


title: oGV_29 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B9_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B9_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B9_AD006


title: H9.WTc.3.2_RNA-seq

description: Total RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B9_AD001


title: oGV_29A [BiSulfite-seq]


title: H9.WT.1.4_RNA-seq

description: Total RNA-seq


title: H9.WT.1.3_RNA-seq

description: Total RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B9_AD007


title: GFP+Rep2

value: GFP


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B8_AD012

value: brain


title: oGV_28A [BiSulfite-seq]


title: H9.WT.1.1_RNA-seq

description: Total RNA-seq


title: oGV_28 [BiSulfite-seq]


title: mCh-Rep1


title: GFP-Rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B8_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B8_AD008

value: male


title: H9.KO4.2.3_RNA-seq

description: Total RNA-seq

value: Nsun6 knockout (Clone 4 nucleotide indel exon2)


title: GFP-Rep1


title: GFP+Rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B8_AD006


title: H9.KO4.2.2_RNA-seq

description: Total RNA-seq


title: H9.KO4.2.1_RNA-seq

description: Total RNA-seq


title: DM_HAC_2

city: Boston

first: Qi

last: Liu

state: MASSACHUSETTS

address: Boston, 02115.USA

institute: Boston Children's Hospital

description: ALKB+HAC-treated

data_processing:
Adapter sequences were trimmed and low quality sequences (Q20) were discarded using trim_galore. For tRNA chemical sequencing data, clean reads were mapped to the mature tRNA sequences downloaded from GtRNAdb using Bowtie with a maximum of two mismatches allowed. The alignments were then processed to record the read depth of each site on tRNAs using Bedtools. Based on tRNA mapping bam files and read depth information, cleavage score and cleavage score ratio between input and chemically-treated sample using the program cleavage_score.R (https://github.com/rnabioinfor/TRAC-Seq).
Genome_build: hg19

growth_protocol: MCF7 cells were cultured in DMEM high glucose medium supplemented with 10% fetal bovine serum, 2.05 mM L-glutamine, 100 units per ml each of penicillin and streptomycin in a humidified atmosphere with 5% CO2  at 37 oC

extract_protocol:
Total RNA samples were extracted with Trizol following the manufacturer's protocol. Ribosomal RNA was removed by using the RiboMinusTM Eukaryote Kit for RNA-seq (Thermo Fisher Scientific).
Libraries were prepared by using the NEBNext Multiplex Small RNA Library Prep Set for Illumina.

tag: cell type

value: wild type

tag: treatment


title: oGV_26 [BiSulfite-seq]


title: oGV_27A [BiSulfite-seq]


title: H9.KO3.3.3_RNA-seq

description: Total RNA-seq

value: Nsun6 knockout (Clone 3 nucleotide indel exon9)


title: oGV_26A [BiSulfite-seq]


title: HAC_2

description: HAC-treated

value: HAC


title: oGV_25 [BiSulfite-seq]


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B8_AD004

value: ACA


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B8_AD002


title: H9.WT.1.2_RNA-seq

description: Total RNA-seq


title: HAC_1

description: HAC-treated


title: CTRL_2

description: Control

value: CTRL


title: H9.KO2.2.3_RNA-seq

description: Total RNA-seq

value: Nsun6 knockout (Clone 2 nucleotide indel exon2)


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B8_AD001

value: MOp


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B7_AD010

value: SSp


title: CTRL_1

description: Control


title: oGV_16 [BiSulfite-seq]

value: germinal vesicle (GV)

value: old


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B8_AD007


title: H9.KO2.2.2_RNA-seq

description: Total RNA-seq


title: DM_HAC_1

description: ALKB+HAC-treated


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B7_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B7_AD007


title: H9.KO3.3.2_RNA-seq

description: Total RNA-seq


title: VAL_MUT2

city: Granada

first: Pedro

last: Medina Vico

state: Granada

address: Avenida de Fuente Nueva, s/n

department: Biochemistry and Molecular Biology I

country: Spain

institute: University of Granada

data_processing:
Reads were aligned to the human genome GRCh38.d1.vd1 (downloaded from https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files) using STAR (version 2.6.1b) in “two-pass mode”.  GENCODE v31 was used as an annotation reference for splice junctions.
The multi-sample BAM was split into single-sample BAMs.
Read counts per gene were obtained using htseq-count (v0.11.2) with the following options: “-m intersection-nonempty -f bam -t exon -i gene_id -r pos -s reverse”.
Further analyses were performed using R (version 3.6.1, Bioconductor version 3.9) and the packages ‘edgeR’, ‘DESeq2’ and ‘EnhancedVolcano’. Hierarchical clustering and principal component analysis were performed to confirm the similarities among replicates and conditions. DESeq2 with default parameters was used for the differential expression analysis, considering each cell line / treatment combination as a different condition.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files containing the output from htseq-count (total read counts per gene).

molecule: polyA RNA

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Concentration and quality of extracted RNA were measured using the Qubit 4 Fluorometer (Thermo Fisher Scientific, MA, USA) and the 2100 Bioanalyzer Instrument (Agilent Technologies, CA, USA).  Libraries from mRNA were prepared using 1 μg of RNA starting material and the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: RNA was isolated from FACS-sorted reporter positive OCI-LY1 and VAL cells transduced with SAR2(LTR)-BCL7A-IRES-ZsGreen1expressing wild-type BCL7A, ∆27-BCL7A or the empty vector. Cells were transduced for 3 consecutive cycles of infection at MOI=2 with both short and long isoforms of wild-type BCL7A and ∆27-BCL7A. Two biological replicates from independent transductions were collected 10 and 17 days after transduction for OCI-LY1 and VAL cell lines respectively.

value: VAL (RRID:CVCL_1819)

tag: disease/cell type

value: Diffuse large B-cell lymphoma

value: Splice site mutant BCL7A overexpression


title: oGV_16A [BiSulfite-seq]


title: VAL_MUT1

tag: cell line


title: H9.KO1.1.4_RNA-seq

description: Total RNA-seq

tag: genotype

value: Nsun6 knockout (Clone 1 nucleotide indel exon2)


title: VAL_WT2

value: Wild type BCL7A overexpression


title: oGV_14 [BiSulfite-seq]


title: H9.KO1.1.3_RNA-seq

description: Total RNA-seq

tag: batch


title: H9.KO3.3.1_RNA-seq

description: Total RNA-seq


title: oGV_13 [BiSulfite-seq]

tag: strain


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B7_AD006

tag: tissue

value: brain

value: female


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B7_AD004

tag: age


title: VAL_WT1


title: oGV_12 [BiSulfite-seq]


title: VAL_EV2

value: Empty vector


title: oGV_25A [BiSulfite-seq]


title: oGV_11 [BiSulfite-seq]


title: H9.KO1.1.2_RNA-seq

description: Total RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B7_AD001

tag: source

value: male


title: VAL_EV1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B6_AD012

tag: target


title: H9.KO1.1.1_RNA-seq

description: Total RNA-seq


title: H9.WTc.3.3_Ribo-seq

description: Ribosome profiling

data_processing:
Library strategy: Ribo-seq
Trim_galore! was used to remove Illumina adaters.
TopHat2 (v 2.1.0) was used to align the reads to the hg38 reference genome using Gencode v23 gene models.
Ribo-seq reads were firstly aligned to a set of known rRNA and tRNAs (selected from the UCSC RepeatMasker tracks), followed by alignment of all unmapped reads to the reference genome.
FeatureCounts (with Gencode v23 gene models) was used to count the number of reads per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing counts for each gene and sample

value: Control (Wild-type Crispr control (random))


title: Py+Tg3+ 5796 mCh-

description:
7_S5
processed data: neg_optimal_sort.bed

value: MMTV-PyMT tumor cells

tag: genotype/variation

tag: cell population


title: oGV_27 [BiSulfite-seq]

tag: developmental stage

tag: age group


title: H9.KO2.2.1_RNA-seq

description: Total RNA-seq


title: mCh-Rep2

tag: reporter

value: mCh

tag: dll1 expression


title: oGV_15 [BiSulfite-seq]


title: OCILY1_MUT2

value: OCI-Ly1 (RRID:CVCL_1879)


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B6_AD010

value: ACA

tag: gender


title: H9.WTc.3.2_Ribo-seq

description: Ribosome profiling


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B6_AD008

value: SSp


title: H9.WTc.3.1_Ribo-seq

description: Ribosome profiling


title: OCILY1_WT2

tag: treatment


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B7_AD002

value: MOp


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B6_AD007


title: RNAseq_WT_cortex_m6AIP_rep2

city: Atlanta

first: Andrew

last: Shafik

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_WT_called_peaks.xlsx

data_processing:
Reads were aligned to mouse genome (mm9) or human genome (hg38) using Bowtie v2.2.4. Mapping parameters were set to local, sensitive and non-deterministic mode.
m6A peaks were identified using MACS2 with parameters:  –nomodel,–extsize 150, -p 5e-2
High-confidence peaks found in both biological replicates were annotated by ChiPSeeker
Differential methylation (DM) in m6A-RIP-seq data was analyzed by MACS2 bdgdiff
BAM files were converted to tiled data files (TDF) for the Integrative Genomics Viewer (IGV) using igvtools.
The genome-wide coverage data were normalized by 1,000,000/total read count for visualization in IGV.
TPM values were calculated by TPMCalculator.
Genome_build: mm9/hg38
Supplementary_files_format_and_content: xls files containing coordinate, gene name information of called m6A peaks. This was achieved using MACS2 callpeak; the input serves as the background.

source_name: Cortex

extract_protocol:
Trizol was used to extract total RNA from all samples.
Total RNA was fragmented to ~100 bp using chemical fragmentation. The input libraries were generated from approximatley 50 ng of poly(A) + mRNA. For the m6A libraries, total RNA was immunoprecipated using m6A antibody. Libraries were then constructed using the Illumina Truseq RNA Library Preparation kit v2, according to the manufacturer's protcol. An Agilent 2100 BioAnalyzer and DNA1000 kit were used to determine the concentration and quality of the final amplified cDNA libraries.

value: 6 month

value: wild type

tag: m6a antibody

value: Synaptic systems m6A antibody 202003


title: RNAseq_WT_cortex_input_rep2


title: H9.WT.2.3_Ribo-seq

description: Ribosome profiling

tag: cell line

value: Control (Wild-type)


title: OCILY1_WT1

tag: disease/cell type

value: Diffuse large B-cell lymphoma


title: RNAseq_WT_cortex_input_rep1


title: OCILY1_EV2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B6_AD006


title: H9.WT.2.1_Ribo-seq

description: Ribosome profiling

tag: genotype

tag: batch


title: RNAseq_WT_cortex_m6AIP_rep1

tag: strain


title: oGV_10 [BiSulfite-seq]

value: germinal vesicle (GV)

value: old


title: OCILY1_EV1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B6_AD001

tag: age

tag: tissue

value: brain


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B6_AD002

tag: source

tag: target


title: RNAseq_FAD_cortex_m6AIP_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_FAD_called_peaks.xlsx


title: H9.WT.1.4_Ribo-seq

description: Ribosome profiling


title: RNAseq_FAD_cortex_input_rep2


title: H9.WT.1.3_Ribo-seq

description: Ribosome profiling


title: OCILY1_MUT1

value: Splice site mutant BCL7A overexpression


title: H9.WT.1.2_Ribo-seq

description: Ribosome profiling


title: RNAseq_FAD_cortex_input_rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B5_AD012

value: female


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B5_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B5_AD008

value: male


title: RNAseq_FAD_cortex_m6AIP_rep1


title: SKOV3 Exp rep1

city: Shanghai

first: Wan

address: 160 Pujian Road

department: Department of Obstetrics and Gynecology, Ren Ji hospital

institute: School of Medicine, Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: SKOV3 Exp

extract_protocol:
The RNA of SKOV3 cells was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: rhCCL20 dissolved in 5% trehalose

tag: treatment time (hr)


title: H9.KO4.2.3_Ribo-seq

description: Ribosome profiling

value: Nsun6 knockout (Clone 4 nucleotide indel exon2)


title: SKOV3 Exp rep2


title: SKOV3 Exp rep3


title: SKOV3 Ctrl rep3

source_name: SKOV3 Ctrl

value: 5% trehalose


title: H9.WT.2.2_Ribo-seq

description: Ribosome profiling


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B5_AD007

value: ACA


title: RNAseq_1yr_cerebellum_m6AIP_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_1yr_cerebellum_called_peaks.txt

source_name: Cerebellum

tag: developmental stage

value: 1 yr old


title: H9.WT.1.1_Ribo-seq

description: Ribosome profiling


title: SKOV3 Ctrl rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B5_AD006

value: MOp


title: H9.KO4.2.2_Ribo-seq

description: Ribosome profiling


title: RNAseq_1yr_cerebellum_input_rep1


title: H9.KO4.2.1_Ribo-seq

description: Ribosome profiling


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B5_AD004


title: SKOV3 Ctrl rep1


title: RNAseq_1yr_cerebellum_m6AIP_rep1


title: RNAseq_old_input_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_old_called_peaks.xlsx

value: 71 yrs

value: control


title: RNAseq_1yr_cortex_m6AIP_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_1yr_cortex_called_peaks.txt

value: wild type

value: Synaptic systems m6A antibody 202003


title: RNAseq_old_m6AIP_rep2

value: 69 yrs


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B5_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B5_AD002


title: H9.KO3.3.1_Ribo-seq

description: Ribosome profiling

value: Nsun6 knockout (Clone 3 nucleotide indel exon9)


title: H9.KO2.2.4_Ribo-seq

description: Ribosome profiling

value: Nsun6 knockout (Clone 2 nucleotide indel exon2)


title: oGV_10A [BiSulfite-seq]

value: germinal vesicle (GV)

tag: age group

value: old


title: RNAseq_old_input_rep1


title: RNAseq_2wk_hippocampus_input_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_2wk_hippocampus_called_peaks.txt

source_name: Hippocampus

value: 2 week old


title: H9.KO2.2.3_Ribo-seq

description: Ribosome profiling


title: RNAseq_old_m6AIP_rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B4_AD010

value: brain

value: SSp

value: female


title: RNAseq_2wk_hippocampus_m6AIP_rep2


title: RNAseq_young_m6AIP_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_young_called_peaks.xlsx

value: 12 yrs


title: RNAseq_1yr_cortex_m6AIP_rep1


title: RNAseq_1yr_cortex_input_rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B4_AD008

value: ACA

value: male


title: RNAseq_young_input_rep2

value: 14 yrs


title: RNAseq_2wk_hippocampus_input_rep1


title: RNAseq_young_input_rep1


title: H9.KO2.2.1_Ribo-seq

description: Ribosome profiling


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B4_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B4_AD006

value: MOp


title: H9.KO1.1.4_Ribo-seq

description: Ribosome profiling

value: Nsun6 knockout (Clone 1 nucleotide indel exon2)


title: H9.KO3.3.2_Ribo-seq

description: Ribosome profiling


title: RNAseq_young_m6AIP_rep1

value: control


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B4_AD004


title: H9.KO1.1.3_Ribo-seq

description: Ribosome profiling


title: RNAseq_2wk_hypothalamus_input_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_2wk_hypothalamus_called_peaks.txt

source_name: Hypothalmus

value: wild type


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B4_AD012


title: H9.KO1.1.2_Ribo-seq

description: Ribosome profiling


title: H9.KO2.2.2_Ribo-seq

description: Ribosome profiling


title: H9.KO1.1.1_Ribo-seq

description: Ribosome profiling


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B4_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B4_AD002


title: RNAseq_2wk_hypothalamus_input_rep1


title: RNAseq_2wk_hypothalamus_m6AIP_rep1

value: Synaptic systems m6A antibody 202003


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B3_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B3_AD010


title: RNAseq_2wk_hypothalamus_m6AIP_rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B3_AD008


title: HEK.WT.4.2_RNA-seq

description: Total RNA-seq

source_name: human embryonic kidney 293 cells

value: Control (Wild-type)


title: RNAseq_2wk_cerebellum_input_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_2wk_cerebellum_called_peaks.txt


title: HEK.WT.4.3_RNA-seq

description: Total RNA-seq


title: RNAseq_2wk_cerebellum_m6AIP_rep2


title: Mus musculus A-B

city: Chiyoda-ku

first: Kento

last: Mio

state: Tokyo

address: 12 Sanban-cho

department: Studies in Human Life Sciences

country: Japan

institute: Otsuma Womenʼs University

description: Gene expression data of adipocytes extracted from Mus musculus fed a barley diet.

hyb_protocol: cDNA were hybridized to the GeneArray Mouse 2.0ST Array. The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G (Thermo Fisher Scientific, Inc.) according to the manufacturer’s recommendations.

data_processing: Expression values were generated using Expression Console software, version 1.3 (Thermo Fisher Scientific, Inc.) with default robust multichip analysis parameters.

source_name: adipocytes in Mus musculus fed cellulose diet

label_protocol: The resultant single-strand cDNA was fragmented and labeled with biotin.

extract_protocol: Total RNA in each organs were extracted by using protocol of RNeasy Mini kit (Qiagen, Hilden, Germany).

value: adipocytes

tag: dietary fiber

value: barley


title: RNAseq_2wk_hippocampus_m6AIP_rep1


title: RNAseq_2wk_cerebellum_input_rep1


title: HEK.WT.4.1_RNA-seq

description: Total RNA-seq


title: OID_f1_Rep4

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.3.4.1 with parameters --sensitive-local -p 4 -q
miRNA and GtRNA GTF files were acquired from UCSC genome browser. Raw reads were generated from R package GenomicAlignment and GenomicFeatures.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix for DESeq2 normalized counts for each sample

source_name: mature sperm cells

growth_protocol: CO and OID-fed males (F0) and their male offspring (F1) were euthanized and their caudal epididymis dissected for sperm collection. The epididymis was collected, punctured, and transferred to tissue culture dish containing M2 media (M2 Medium-with HEPES, without penicillin and streptomycin, liquid, sterile-filtered, suitable for mouse embryo, SIGMA, product #M7167) where it was incubated for 1 hour at 37°C

extract_protocol:
Total RNA was isolated from sperm using Qiagen’s miRNeasy extraction kit, according to the manufacturer’s instructions.
Samples were barcoded, pooled, precipitated and separated  on a 15% polyacrylamide gel (PAGE). The gel was stained with SYBR® gold dye and the small non-coding RNA segment corresponding to transfer RNA fragments or tRFs (30-45 nucleotides) excised and purified using a cDNA library preparation method

treatment_protocol: Sperm samples were isolated and purified from somatic cells. Briefly, the samples were washed with PBS, and then incubated with SCLB (somatic cell lysis buffer, 0.1% SDS, 0.5% TX-100 in Diethylpyrocarbonate water) for 1 hour.  SCLB was rinsed off with 2 washes of PBS and the somatic cell-free purified spermatozoa sample pelleted and used for RNA extraction.

tag: diet

value: obesity-inducing diet

tag: generation


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B3_AD007

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

source_name: C57BL/6J P56 Mouse Brain

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

tag: gender


title: HEK.KO2.4.4_RNA-seq

description: Total RNA-seq

value: Nsun6 knockout (Clone 2 nucleotide indel)


title: RNAseq_2wk_cerebellum_m6AIP_rep1

value: 2 week old

tag: m6a antibody


title: HEK.WT.4.4_RNA-seq

description: Total RNA-seq

tag: cell line


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B3_AD004

value: brain


title: OID_f1_Rep3


title: HEK.KO2.4.3_RNA-seq

description: Total RNA-seq


title: RNAseq_2wk_cortex_input_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_2wk_cortex_called_peaks.txt


title: OID_f1_Rep2


title: HEK.KO2.4.2_RNA-seq

description: Total RNA-seq


title: OID_f1_Rep1


title: RNAseq_2wk_cortex_m6AIP_rep2


title: Mus musculus L-B

description: Gene expression data of liver extracted from Mus musculus fed a barley diet.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G (Thermo Fisher Scientific, Inc.) according to the manufacturer’s recommendations.

source_name: liver in Mus musculus fed barley diet

value: liver


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B3_AD002


title: Mus musculus L-C

description: Gene expression data of liver extracted from Mus musculus fed a cellulose diet.

source_name: liver in Mus musculus fed cellulose diet

value: cellulose


title: OID_f0_Rep4


title: RNAseq_2wk_cortex_input_rep1


title: HEK.KO2.4.1_RNA-seq

description: Total RNA-seq


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B3_AD001

value: ACA


title: RNAseq_2wk_cortex_m6AIP_rep1


title: HEK.KO1.4.4_RNA-seq

description: Total RNA-seq

value: Nsun6 knockout (Clone 1 nucleotide indel)


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B3_AD006

value: female