title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C11_AD006

status: Public on Nov 24 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: MOp

tag: target

value: SSp

tag: gender

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C11_AD010

value: ACA

value: TH

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C11_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C11_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C11_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C11_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C10_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C10_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C10_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B9_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B9_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C12_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B8_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B8_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B8_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B8_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B7_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B7_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C10_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B6_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B5_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B4_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B4_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B4_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B3_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B4_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B3_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_C10_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B3_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B3_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B3_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B7_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B2_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B6_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B6_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B7_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B5_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B2_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B2_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B1_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B2_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B2_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B1_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B1_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B1_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B12_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B12_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B11_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B10_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B10_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B11_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B11_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B10_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B11_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A8_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A7_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A8_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_B10_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A6_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A7_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A5_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A7_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A6_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A4_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A4_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A7_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A4_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A3_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A3_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A2_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A6_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A2_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A1_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A1_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A2_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A1_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A12_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A12_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A11_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A11_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A11_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A11_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A11_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A10_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A10_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A10_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H9_AD012

value: PTLp

value: Pons


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H8_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H9_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H9_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H9_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H9_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H8_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H9_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H7_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H7_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H7_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H7_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H7_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H7_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H7_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H6_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H6_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H6_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H6_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_A10_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H6_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H5_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H5_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H5_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H5_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H4_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H4_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H4_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H4_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H4_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H3_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H4_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H3_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H3_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H3_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H2_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H2_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H4_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H2_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H2_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H1_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H1_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H1_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H2_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H1_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H1_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H1_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H12_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H1_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H12_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H12_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H12_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H11_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H2_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H12_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H3_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H12_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H11_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G9_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H10_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H10_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G9_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G9_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H10_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G9_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G9_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H10_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H10_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H10_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H11_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H11_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G9_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G9_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G7_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G8_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G6_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G6_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G9_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G8_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G6_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G5_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G5_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G5_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G5_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G2_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G2_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G2_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G1_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G1_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G12_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G1_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_H8_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G12_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G12_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G2_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G1_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G12_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G11_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G5_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G3_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G11_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G10_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G11_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G11_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G10_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G12_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G10_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G1_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G1_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G10_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F8_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F8_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F9_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F8_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F9_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G10_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F9_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F7_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F7_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F8_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F7_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F7_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F7_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F7_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F9_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_G10_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F8_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F6_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F5_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F5_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F5_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F5_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F4_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F3_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F3_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F4_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F2_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F5_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F2_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F3_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F4_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F4_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F4_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F6_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F2_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F3_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F4_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F2_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F1_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F2_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F6_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F1_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F1_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F1_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F1_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F1_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F2_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F1_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F12_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F12_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F12_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F12_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F11_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F11_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F10_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F12_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F10_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E9_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F10_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F11_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F11_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F11_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F10_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F11_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_F5_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E9_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E9_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E9_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E9_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E9_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E9_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E8_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E9_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E8_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E8_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E8_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E7_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E6_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E5_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E6_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E6_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E5_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E6_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E5_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E5_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E3_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E8_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E4_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E5_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E3_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E5_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E3_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E3_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E3_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E2_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E3_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E2_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E12_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E1_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E1_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E1_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E2_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E2_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E1_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E1_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E12_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E12_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E1_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E12_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E2_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E12_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E11_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E11_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E11_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E1_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E11_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E10_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E10_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E12_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E10_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E10_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E10_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D8_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D7_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E11_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D7_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D7_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D7_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D6_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D7_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E11_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D8_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_E11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D6_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D6_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D8_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D7_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D6_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D5_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D5_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D6_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D4_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D5_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D5_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D5_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D5_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D4_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D4_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D4_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D3_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D3_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D3_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D4_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D2_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D4_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D4_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D2_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D3_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D2_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D3_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D5_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D1_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D1_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D2_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D12_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D12_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D1_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D11_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D1_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D12_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D1_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D10_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D12_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D11_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C9_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D10_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D1_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C9_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D10_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D11_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D10_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D10_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D10_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D11_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C9_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C8_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C8_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C8_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C9_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C9_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C8_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D11_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C8_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C7_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C7_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C7_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C6_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C7_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C6_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C5_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C6_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C7_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C4_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C4_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C5_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C4_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C5_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C5_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C5_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C4_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C4_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_D12_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C4_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C3_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C6_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C3_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C5_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C3_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C3_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C3_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C1_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C2_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C2_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C2_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C12_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C12_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C2_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C12_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C12_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C12_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C11_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C12_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C12_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C11_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C2_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C11_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C1_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C12_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C10_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C10_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B9_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C10_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B9_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C10_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C11_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C11_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C10_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B9_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B8_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B9_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B9_AD001


title: ecoli_ccl34b.1_pos_3

city: HK

first: Zilong

last: WEN

address: Academic Bld., HKUST, Clearwater Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description: processed data_counts.csv

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCz11.94 (danRer11) zebrafish reference genome using STAR.
Aligned reads were converted to counts for each gene using featureCounts.
Quality control, filtering of lowly expressed genes, normalization, transformation, and differentially expressed gene (DE genes) analysis was done using the pipeline of the DESeq2 package.
Genome_build: danRer11 (GRCz11)
Supplementary_files_format_and_content: processed_data_counts.csv: Comma-delimited file containing all 28 samples and read counts.

molecule: polyA RNA

organism: Danio rerio

source_name: brain

extract_protocol:
Whole brains were dissected and collected into 1ml ice-cold PBS, and homogenized with 27G needles. Cells were spun down (800g 4°C for 5 min) and resuspended with 0.25% Trypsin-EDTA, then incubated at 30 °C for 20-30 mins. After termination of the reaction with 10 μM CaCl2 and 10% FBS, samples were centrifuged and washed with ice-cold 1% BSA/PBS buffer, and finally pushed through a Falcon® 40 µm Cell Strainer to obtain single-cell suspensions. ccl34b.1+mpeg1+ and ccl34b.1- mpeg1+ microglia (100 cells for each sample) were directly sorted into lysis buffer (0.2% Triton X-100 solution) in a FACS Aria IIIu sorter based on the eGFP and DsRedx fluorescence.
The Smart-seq2 protocol was used for whole transcriptome amplification and library preparation. Cell lysates were hybridized together with oligo-dT primer and dNTP at 72 °C for 3 min, then added with reverse transcription mix containing SuperScript™ II Reverse Transcriptase and a template-switching oligo. After reverse transcription, first-strand reaction products were PCR amplified using KAPA HiFi HotStart ReadyMix with 24 PCR cycles and purified using Ampure XP beads with a magnetic stand. cDNA quality was assessed using an Agilent Fragment Analyzer System. Sequencing libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina® following the instructions (0.5 ng cDNA input). After tagmentation, samples were amplified with TruePrep Index Kit V2 for Illumina® (12 cycles) and purified with Ampure XP beads. Library quality was assessed using Agilent Fragment Analyzer System.

tag: genotype/variation

value: 6 months

tag: cell type

value: microglia

tag: gate

tag: treatment

value: E. coli injected


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B8_AD001


title: ecoli_ccl34b.1_neg_2

description: processed data_counts.csv


title: ecoli_ccl34b.1_neg_1

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B7_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C10_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B7_AD006


title: ecoli_ccl34b.1_neg_3

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B7_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_C10_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B7_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B7_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B6_AD008


title: pbs_ccl34b.1_neg_3

description: processed data_counts.csv

value: PBS injected


title: ecoli_ccl34b.1_pos_1

description: processed data_counts.csv


title: ecoli_ccl34b.1_pos_2

description: processed data_counts.csv


title: pbs_ccl34b.1_neg_4

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B7_AD002


title: pbs_ccl34b.1_pos_4

description: processed data_counts.csv


title: pbs_ccl34b.1_neg_2

description: processed data_counts.csv


title: pbs_ccl34b.1_pos_3

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B6_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B5_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B5_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B5_AD010


title: pbs_ccl34b.1_neg_1

description: processed data_counts.csv


title: ctrl_ccl34b.1_pos_2

description: processed data_counts.csv


title: pbs_ccl34b.1_pos_1

description: processed data_counts.csv


title: ctrl_ccl34b.1_pos_1

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B5_AD007


title: ctrl_ccl34b.1_neg_2

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B5_AD006


title: ctrl_ccl34b.1_neg_1

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B5_AD001


title: pbs_ccl34b.1_pos_2

description: processed data_counts.csv


title: Monocytes from mouse ko 9

city: Pieve Emanuele

first: sarah

middle: natalia

last: mapelli

state: Milan

address: Via Rita Levi Montalcini 4

department: Experimental Immunopathology

country: Italy

institute: Humanitas research

description:
DEG_monocytes_wt_vs_C3_ko.txt
Lib_EMA-30_S30_R1_001
s2_M9

data_processing:
fastq files were generated running bcl2fastq v2.19.0.316
Reads were aligned with STAR 2.7.2b on GRCm38 genome
Reads were quantified with STAR 2.7.2b based on Mus_musculus.GRCm38.98.gtf with the option --quantMode GeneCounts
Raw counts were normalized with DESeq2 rlog funtion with the option blind = TRUE
Differential expression was performed with DESeq2 after removing genes whose counts sum across samples was lowere than 2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files including rlog normalized counts and differential expression results

molecule: total RNA

source_name: monocytes

extract_protocol:
Tumors were collected 21 days after tumor cell injection and washed once with physiologic solution. Single-cell suspension were obtained by mechanical and enzymatic dissociation in 0.1 mg/ml Type IV Collagenase for 1h at +37°C. RNA was purified from FACS sorted MN/MCA1 tumor-infiltrating monocytes (CD45+, CD11b+, Ly6G-, CD11c-, F4/80-, Ly6C+) and macrophages (CD45+, CD11b+, Ly6G-, CD11c-, Ly6C-, F4/80+) with the Single Cell RNA Purification Kit.
Libraries for mRNA sequencing were prepared starting from 5 ng totRNA for each sample by using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara), this allows to add defined PCR adapters directly to both  ends of the first-strand cDNA.

value: mouse sarcoma MN/MCA1 tumor

value: Monocytes

tag: genotype


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B4_AD012


title: Macrophages from mouse ko 8

description:
DEG_macrophages_wt_vs_C3_ko.txt
Lib_EMA-25_S25_R1_001
s1_M8

source_name: macrophages

value: Macrophages


title: Monocytes from mouse ko 8

description:
DEG_monocytes_wt_vs_C3_ko.txt
Lib_EMA-26_S26_R1_001
s2_M8


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B4_AD001


title: Macrophages from mouse ko 9

description:
DEG_macrophages_wt_vs_C3_ko.txt
Lib_EMA-29_S29_R1_001
s1_M9


title: Monocytes from mouse ko 7

description:
DEG_monocytes_wt_vs_C3_ko.txt
Lib_EMA-22_S22_R1_001
s2_M7


title: Macrophages from mouse ko 7

description:
DEG_macrophages_wt_vs_C3_ko.txt
Lib_EMA-21_S21_R1_001
s1_M7


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B3_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B4_AD004


title: Macrophages from mouse ko 6

description:
DEG_macrophages_wt_vs_C3_ko.txt
Lib_EMA-17_S17_R1_001
s1_M6


title: Monocytes from mouse ko 6

description:
DEG_monocytes_wt_vs_C3_ko.txt
Lib_EMA-18_S18_R1_001
s2_M6


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B3_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B3_AD006


title: Macrophages from mouse wt 2

description:
DEG_macrophages_wt_vs_C3_ko.txt
Lib_EMA-05_S5_R1_001
s1_M2

value: wild type


title: Macrophages from mouse wt 4

description:
DEG_macrophages_wt_vs_C3_ko.txt
Lib_EMA-13_S13_R1_001
s1_M4


title: Monocytes from mouse wt 4

description:
DEG_monocytes_wt_vs_C3_ko.txt
Lib_EMA-14_S14_R1_001
s2_M4


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B3_AD007

value: brain


title: Monocytes from mouse wt 2

description:
DEG_monocytes_wt_vs_C3_ko.txt
Lib_EMA-06_S6_R1_001
s2_M2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B4_AD006


title: Monocytes from mouse wt 3

description:
DEG_monocytes_wt_vs_C3_ko.txt
Lib_EMA-10_S10_R1_001
s2_M3


title: Monocytes from mouse wt 1

description:
DEG_monocytes_wt_vs_C3_ko.txt
Lib_EMA-02_S2_R1_001
s2_M1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B4_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B2_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B6_AD007


title: Macrophages from mouse wt 1

description:
DEG_macrophages_wt_vs_C3_ko.txt
Lib_EMA-01_S1_R1_001
s1_M1


title: S15: Fat1+/-, EtOH, replicate 5

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Basecalls performed using Illumina FASTQ Generation v1.0.0 (Illumina Workflow v1.37.0; bcl2fastq)
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1). The FastQC results indicate sequence trimming was not necessary for the samples.
The sequences were directly aligned to the Mus musculus (mouse) reference genome assembly (mm10) using star v020201, generating alignment files in bam format.
In addition to alignment to the mouse genome, the FAT-1 gene used in the treatment groups was from C. elegans. The original reads were aligned to the C. elegans genome (ce10). A small fraction of the reads (less than 1%) mapped to C. elegans, as expected.
Differentially expressed genes were identified for four comparisons: WT EtOH vs WT PF, Fat EtoH vs Fat PF, Fat PF vs WT PF, and Fat EtOH vs WT EtOH Fat PF  using the tuxedo suite of programs including cufflinks-cuffdiff2 (version 2.2.1).
Genome_build: mm10

source_name: ileum

extract_protocol:
Total RNA was isolated using Trizol, DNase digested, and then cleaned-up using the GeneJet system from ThermoFisher.
Poly A purification and RNA fragmentation were performed on 600ng total RNA. Superscript II was used to generate cDNA and then RNA template was removed. Second strand synthesis was performed with incorporation of dUTP to ensure stranded libraries, and ds cDNA was purified with AMPure XP beads. 3’ ends were adenylated, indexing adapters were ligated onto the ends, and libraries once again purified with AMPure beads. 15 cycles of PCR were used to enrich DNA fragments, followed by two AMPure bead clean-up steps. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer. Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems.

treatment_protocol: Males were placed onto an all liquid diet with gradually increasing amounts of ethanol as follows:  no ethanol for 2 days, 1% (v/v) for 2 days, 2% for 2 days, 4% for 1 week, 5% for 1 week, and 6% for 3 weeks.

tag: Sex

value: ileum


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B2_AD001


title: S14: Fat1+/-, EtOH, replicate 4


title: S13: Fat1+/-, EtOH, replicate 3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B1_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B1_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B1_AD006


title: Macrophages from mouse wt 3

description:
DEG_macrophages_wt_vs_C3_ko.txt
Lib_EMA-09_S9_R1_001
s1_M3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B3_AD004


title: S11: Fat1+/-, EtOH, replicate 2


title: S16: Wild-type, EtOH, replicate 3

value: Wild-type


title: S9: Fat1+/-, EtOH, replicate 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B1_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B1_AD001


title: S12: Wild-type, EtOH, replicate 2


title: S10: Wild-type, EtOH, replicate 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B12_AD008


title: S7: Fat1+/-, pair-fed replicate 4


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B12_AD010

value: female


title: S6: Fat1+/-, pair-fed replicate 3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B12_AD007


title: S5: Fat1+/-, pair-fed replicate 2


title: S8: Wild-type, pair-fed replicate 4


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B12_AD004


title: S3: Fat1+/-, pair-fed replicate 1


title: S4: Wild-type, pair-fed replicate 3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B11_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B1_AD004


title: S2: Wild-type, pair-fed replicate 2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B12_AD001


title: S1: Wild-type, pair-fed replicate 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B11_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B10_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B11_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B11_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B10_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B10_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B10_AD002


title: NPC_SC_1811_Tumor_TCR

city: Guangzhou

first: Jin-Xin

last: Bei

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina-implemented software bcl2fastq (version v2.19.0.316) was used for basecalling.
cDNA sequencing reads were aligned to the human reference genome (hg38) and EBV reference sequence (Akata; https://github.com/flemingtonlab/public/tree/master/annotation). The digital gene expression matrix was built using STAR algorithm in CellRanger (“count” option; version 3.0.1; 10x Genomics).
TCR reads were aligned to human reference VDJ dataset (http://cf.10Xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0.tar.gz) using CellRanger (“vdj” option; version 3.0.1; 10x Genomics).
Genome_build: hg38 and Akata
Supplementary_files_format_and_content: Each sample was represented by comma-separated text files including raw counts of each gene for each cell. TCR information were respectively represented by comma-separated text files including 20 samples.

organism: Homo sapiens

extract_protocol:
Viable single cells were prepared from the PBMC and tumor of 10 nasopharyngeal carcinoma patients.
The concentration of single cell suspension was determined using a Cellometer Auto 2000 instrument (Cellometer) and adjusted to 1,000 cells/μl. Approximately 14,000 cells were loaded into a CHROMIUM instrument (10x Genomics, CA, USA) according to the standard protocol of the Chromium single cell V(D)J kit (v1) in order to capture 5,000 ~ 10,000 cells per channel. In brief, mRNA transcripts from each sample were ligated with barcoded indexes at 5'-end and reverse transcribed into cDNA, using GemCode technology (10x Genomics, USA). cDNA libraries including the enriched fragments spanning the full-length V(D)J segments of T cell receptors (TCR), and 5'-end fragments for gene expression were separately constructed, which were subsequently subjected for high-throughput sequencing.

tag: subject/sample id

tag: disease

value: nasopharyngeal carcinoma (NPC)

value: Nasopharynx


title: NPC_SC_1810_PBMC_TCR

value: Peripheral blood


title: NPC_SC_1815_PBMC_TCR


title: NPC_SC_1813_Tumor_TCR


title: NPC_SC_1811_PBMC_TCR


title: NPC_SC_1816_PBMC_TCR


title: NPC_SC_1816_Tumor_TCR


title: NPC_SC_1813_PBMC_TCR


title: NPC_SC_1808_Tumor_TCR


title: NPC_SC_1808_PBMC_TCR


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A9_AD007

value: PTLp

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A9_AD010

value: Pons


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B11_AD004

value: TH


title: NPC_SC_1807_Tumor_TCR


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A9_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A9_AD008


title: NPC_SC_1810_Tumor_TCR


title: NPC_SC_1815_Tumor_TCR


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A9_AD002


title: NPC_SC_1807_PBMC_TCR


title: NPC_SC_1806_Tumor_TCR


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A8_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A9_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A8_AD006


title: NPC_SC_1805_Tumor_TCR


title: NPC_SC_1806_PBMC_TCR


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A8_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A7_AD001


title: NPC_SC_1802_Tumor_TCR


title: NPC_SC_1802_PBMC_TCR


title: NPC_SC_1816_Tumor_cDNA


title: NPC_SC_1805_PBMC_TCR


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A6_AD008


title: NPC_SC_1813_PBMC_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_B4_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A5_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A6_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A6_AD006


title: NPC_SC_1815_PBMC_cDNA


title: NPC_SC_1811_PBMC_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A5_AD008


title: NPC_SC_1815_Tumor_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A5_AD010


title: NPC_SC_1811_Tumor_cDNA


title: NPC_SC_1816_PBMC_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A5_AD002


title: NPC_SC_1808_Tumor_cDNA


title: NPC_SC_1813_Tumor_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A4_AD012


title: NPC_SC_1810_Tumor_cDNA


title: NPC_SC_1810_PBMC_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A4_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A4_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A4_AD006


title: NPC_SC_1807_Tumor_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A4_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A4_AD001


title: NPC_SC_1806_Tumor_cDNA


title: NPC_SC_1805_PBMC_cDNA


title: NPC_SC_1805_Tumor_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A3_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A3_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A3_AD008


title: NPC_SC_1806_PBMC_cDNA


title: NPC_SC_1802_PBMC_cDNA


title: ccl34b.1_neg_5

description: processed data_counts.csv

value: 4 months

value: microglia


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A3_AD007


title: NPC_SC_1802_Tumor_cDNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A3_AD002


title: ccl34b.1_neg_4

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A3_AD004


title: NPC_SC_1807_PBMC_cDNA


title: NPC_SC_1808_PBMC_cDNA


title: ccl34b.1_neg_2

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A3_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A4_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A2_AD001


title: ccl34b.1_pos_5

description: processed data_counts.csv


title: ccl34b.1_neg_1

description: processed data_counts.csv


title: ccl34b.1_pos_4

description: processed data_counts.csv


title: ccl34b.1_pos_2

description: processed data_counts.csv


title: ccl34b.1_neg_3

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A1_AD010


title: ccl34b.1_pos_1

description: processed data_counts.csv


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A1_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A1_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A1_AD004


title: D. mauritiana x D. simulans cross, late stage 5 embryo, replicate 3, XX genotype

city: Davis

first: Susan

middle: E.

last: Lott

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

description:
mauxsim_st5_F_3
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt

data_processing:
Adapter sequences trimmed using Cutadapt (v. 1.7.1).
Reads aligned to genomes using Tophat2 (v. 2.0.13).
Variants to identify allele-specific reads called using GATK haplotype caller.
Allele-specific reads counted using custom Python and R scripts (available with publication).
Counts normalized to upper quantile for total number of counts mapped per individual to a genome.
Genome_build: D. simulans (version r2.02); D. sechellia (version r1.3); D. mauritiana M17 assembly (Nolte et al., 2013; see Methods in publication).
Supplementary_files_format_and_content: *.txt: Allele-specific counts, mapping each hybrid individual to both parental genomes.

organism: Drosophila mauritiana x Drosophila simulans

source_name: late stage 5 embryo

growth_protocol: Cornmeal media, 25 degrees, population-controlled, eggs collected from mothers 4-14 days old.

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Standard Illumina mRNA-Seq library prep protocols, using Illumina TruSeq kits.

treatment_protocol: Crosses between species as specified, to produce hybrid maternal transcriptomes for stage 2 embryos and hybrid zygotic transcriptomes for late stage 5 embryos.

value: embryo

tag: generation

value: F1 hybrid embryo

tag: embryonic stage

value: late stage 5

tag: embryo sex

value: XX genotype

tag: replicate number


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A1_AD002

tag: strain

tag: age

value: brain


title: D. mauritiana x D. simulans cross, late stage 5 embryo, replicate 5, XY genotype

description:
mauxsim_st5_M_5
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt

tag: tissue

value: XY genotype


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A1_AD001

tag: source

tag: target


title: D. mauritiana x D. simulans cross, late stage 5 embryo, replicate 1, XX genotype

description:
mauxsim_st5_F_1
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: D. mauritiana x D. simulans cross, late stage 5 embryo, replicate 6, XY genotype

description:
mauxsim_st5_M_6
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A12_AD008

tag: gender


title: D. mauritiana x D. simulans cross, late stage 5 embryo, replicate 2, XX genotype

description:
mauxsim_st5_F_2
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A12_AD012


title: D. mauritiana x D. simulans F1 backcross, stage 2 embryo, replicate 3

description:
mauxsim_st2_3
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt

source_name: stage 2 embryo

value: F2 hybrid embryo

value: stage 2

value: unknown


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A12_AD010

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A12_AD002


title: ccl34b.1_pos_3

description: processed data_counts.csv

tag: genotype/variation

tag: cell type


title: D. simulans x D. mauritiana cross, late stage 5 embryo, replicate 6, XX genotype

description:
simxmau_st5_F_6
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt

organism: Drosophila simulans x Drosophila mauritiana


title: D. mauritiana x D. simulans F1 backcross, stage 2 embryo, replicate 1

description:
mauxsim_st2_1
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: D. mauritiana x D. simulans F1 backcross, stage 2 embryo, replicate 2

description:
mauxsim_st2_2
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A12_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A11_AD007


title: D. simulans x D. mauritiana cross, late stage 5 embryo, replicate 5, XY genotype

description:
simxmau_st5_M_5
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: D. mauritiana x D. simulans cross, late stage 5 embryo, replicate 4, XY genotype

description:
mauxsim_st5_M_4
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A10_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A10_AD008


title: D. simulans x D. mauritiana cross, late stage 5 embryo, replicate 3, XX genotype

description:
simxmau_st5_F_3
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: D. simulans x D. mauritiana cross, late stage 5 embryo, replicate 4, XX genotype

description:
simxmau_st5_F_4
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: D. simulans x D. mauritiana cross, late stage 5 embryo, replicate 1, XX genotype

description:
simxmau_st5_F_1
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A10_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A10_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A10_AD004


title: D. simulans x D. mauritiana F1 backcross, stage 2 embryo, replicate 2

description:
simxmau_st2_2
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A10_AD001


title: D. simulans x D. sechellia cross, late stage 5 embryo, replicate 5, XX genotype

description:
simxsec_st5_F_5
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt

organism: Drosophila simulans x Drosophila sechellia


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H9_AD012

value: ACA


title: D. simulans x D. sechellia cross, late stage 5 embryo, replicate 4, XY genotype

description:
simxsec_st5_M_4
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: D. simulans x D. sechellia cross, late stage 5 embryo, replicate 6, XX genotype

description:
simxsec_st5_F_6
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P3_180726_P4_A10_AD002

value: PTLp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H9_AD008

value: male


title: D. simulans x D. sechellia cross, late stage 5 embryo, replicate 3, XY genotype

description:
simxsec_st5_M_3
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: D. simulans x D. sechellia cross, late stage 5 embryo, replicate 1, XY genotype

description:
simxsec_st5_M_1
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: D. simulans x D. sechellia F1 backcross, stage 2 embryo, replicate 3

description:
simxsec_st2_3
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H9_AD004

value: SSp


title: D. simulans x D. mauritiana cross, late stage 5 embryo, replicate 2, XY genotype

description:
simxmau_st5_M_2
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: D. simulans x D. mauritiana F1 backcross, stage 2 embryo, replicate 3

description:
simxmau_st2_3
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: D. simulans x D. sechellia cross, late stage 5 embryo, replicate 2, XX genotype

description:
simxsec_st5_F_2
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H9_AD010


title: D. simulans x D. sechellia F1 backcross, stage 2 embryo, replicate 1

description:
simxsec_st2_1
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: D. simulans x D. mauritiana F1 backcross, stage 2 embryo, replicate 1

description:
simxmau_st2_1
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H8_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H8_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H9_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H9_AD007


title: hct116_t7_chip_rep_2

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: HCT116 cells T7 chip rep 2

data_processing:
ChIP-seq read quality was analysed using FASTQC (v0.11.4), with low quality reads and adaptors removed using trim-galore with default settings (v0.4.1). Reads were aligned to the combined hg38 and dm6 genome using bowtie 2 (v2.3.1, with settings: -N 1 -L 20 -- no-unal). Additional settings were used during alignment to remove discordant reads: --no-mixed --no-discordant -X 1000. Multi-mapping reads excluded using SAMtools (v1.6, with settings: -bq 10). PCR duplicates excluded using SAMBAMBA (v0.5.9).
Tracks for data visualisation were generated using Deeptools (v3.2.0). Counts per million normalised tracks were generated using the bamCoverage function (settings: --normalizeUsing CPM) with the default bin size of 50bp. The mean of replicate tracks was calculated using the bigwigCompare function (settings: --operation mean). The estimated fragment length of 150bp was used.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files derived as described above.

source_name: Human cell line

growth_protocol: HCT116  were a gift from B. Vogelstein (Rhee et al 2002 PMID: 11932749). T7 DNMT3B cells were generated using CRISPR to knock a triple T7 tag into the N-terminus of DNMT3B in HCT116 cells. Cells were cultured in McCoy’s 5A medium (Gibco) supplemented with 10% fetal calf serum (Life technologies) and penicillin-streptomycin antibiotics at 140 and 400 µg/ml respectively.

extract_protocol:
1x107 cells were harvested, washed and crosslinked with 1% methanol-free formaldehyde in PBS for 8 min at room temperature. Crosslinked cells were lysed for 10 min on ice in 50 l of lysis buffer (50mM Tris-HCl pH8, 150mM NaCl, 1mM EDTA, 1% SDS) freshly supplemented with proteinase inhibitor (Sigma-Aldrich). IP dilution buffer (20 mM Tris-HCl pH8, 150 mM NaCl, 1 mM EDTA, 0.1% Triton X-100) freshly supplemented with proteinase inhibitor, DTT and PMSF was added to the samples to reach a final volume of 500ul. As prolonged sonication caused T7-DNMT3B degradation, chromatin was fragmented using Benzonase as recommended by Pchelintsev et al. 2016 (PMID: 26821228). Briefly, samples were sonicated on ice with Soniprep 150 twice for 30 sec to break up nuclei. Then 200U of Benzonase Nuclease (Sigma) and MgCl2 (final concentration 2.5 mM) were added and samples were incubated on ice for 15 min. The reaction was blocked by adding 10ul of 0.5M EDTA pH 8. 20ug of Spike-in chromatin (ActiveMotif 53083) was added to each sample prior to sonication. IP dilution buffer (20 mM Tris-HCl pH8, 150 mM NaCl, 1 mM EDTA, 0.1% Triton X-100) freshly supplemented with proteinase inhibitor, DTT and PMSF was added to the samples to reach a final volume of 500ul. Following centrifugation for 30 min at 14,000 rpm at 4 oC, supernatants were collected and supplemented with Triton X-100 (final concentration 1%) and 5% input aliquots were retained for later use. Protein A dynabeads (Invitrogen) previously coupled with T7-Tag antibody (D9E1X, Cell Signalling) in blocking solution (1xPBS, 0.5% BSA) were added and the samples incubated overnight under rotation at 4 oC. 2ul of spike-in antibody per sample (ActiveMotif 61686) was also added in a ratio 1:5 versus the T7-antibody. Beads were then washed for 10 min at 4 oC with the following buffers: IP dilution buffer 1% Triton X-100 (20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), buffer A (50 mM Hepes pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B (20 mM Tris pH 8, 1mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), TE buffer (1 mM EDTA pH 8, 10 mM Tris pH 8). Chromatin was eluted by incubating the beads in extraction buffer (0.1M NaHCO3, 1% SDS) for 15 min at 37oC. To reverse the cross-linking Tris-HCl pH 6.8 and NaCl were added to final concentrations of 130 mM and 300mM respectively. IP samples were then incubated at 65 oC overnight. Samples were then incubated at 37 oC for 1h after addition of 2ul of RNase Cocktail Enzyme Mix (Ambion). Then 40 ug of Proteinase K (Roche) were added, followed by 2h incubation at 55oC. Input material was similarly de-crosslinked. Samples were purified with the MinElute PCR purification kit (QIAGEN).
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645) according to the manufacturer instructions. Barcoded adapters (NEBNext® Multiplex Oligos for Illumina® Index Primers Set 1, E7335) were used. Libraries were sequenced using the NextSeq 500/550 high-output version 2.5 kit (75bp paired end reads). Libraries were combined into equimolar pools to run within individual flow cells. Sequencing was performed by the Edinburgh Clinical Research Facility.

value: wt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H8_AD004


title: hct116_t7_dnmt3b_t7_input_rep_2

description: HCT116 cells with T7 tagged DNMT3B input rep 2

value: T7 tagged DNMT3B


title: hct116_t7_input_rep_2

description: HCT116 cells input rep 2


title: hct116_t7_dnmt3b_t7_chip_rep_2

description: HCT116 cells with T7 tagged DNMT3B T7 chip rep 2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H7_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H8_AD001


title: D. simulans x D. sechellia F1 backcross, stage 2 embryo, replicate 2

description:
simxsec_st2_2
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H8_AD010


title: hct116_t7_chip_rep_1

description: HCT116 cells T7 chip rep 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H9_AD002


title: hct116_t7_input_rep_1

description: HCT116 cells input rep 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H7_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H7_AD010


title: hct116_t7_dnmt3b_t7_chip_rep_1

description: HCT116 cells with T7 tagged DNMT3B T7 chip rep 1


title: hct116_dko_k36me3_chip_rep_2

description: HCT116 lacking DNMT1 and DNMT3B k36me3 chip rep 2

data_processing:
ChIP-seq read quality was analysed using FASTQC (v0.11.4), with low quality reads and adaptors removed using trim-galore with default settings (v0.4.1). Reads were aligned to the combined hg38 and dm6 genome using bowtie 2 (v2.3.1, with settings: -N 1 -L 20 -- no-unal). Multi-mapping reads excluded using SAMtools (v1.6, with settings: -bq 10). PCR duplicates excluded using SAMBAMBA (v0.5.9).
Tracks for data visualisation were generated using Deeptools (v3.2.0). Counts per million normalised tracks were generated using the bamCoverage function (settings: --normalizeUsing CPM) with the default bin size of 50bp. The mean of replicate tracks was calculated using the bigwigCompare function (settings: --operation mean). The estimated fragment length of 150bp was used.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files derived as described above.

growth_protocol: HCT116  and DKO cells were gifts from B. Vogelstein (Rhee et al 2002 PMID: 11932749). Cells were cultured in McCoy’s 5A medium (Gibco) supplemented with 10% fetal calf serum (Life technologies) and penicillin-streptomycin antibiotics at 140 and 400 µg/ml respectively.

extract_protocol:
0.5x107 cells were harvested and crosslinked with 1% methanol-free formaldehyde in PBS for 5 min at room temperature. Crosslinked Drosophila S2 cells were spiked into samples before sonication at a ratio of 20:1 human to Drosophila cells. Following nuclei rupture by sonication on ice with Soniprep 150, chromatin was fragmented using Bioruptor Plus sonicator (Diagenode) for 40 cycle (30 s on/30 s off on high setting at 4oC). Crosslinked cells were lysed for 10 min on ice in 50ul of lysis buffer (50mM Tris-HCl pH8, 150mM NaCl, 1mM EDTA, 1% SDS) freshly supplemented with proteinase inhibitor (Sigma-Aldrich). IP dilution buffer (20 mM Tris-HCl pH8, 150 mM NaCl, 1 mM EDTA, 0.1% Triton X-100) freshly supplemented with proteinase inhibitor, DTT and PMSF was added to the samples to reach a final volume of 500ul. Following centrifugation for 30 min at 14,000 rpm at 4 oC, supernatants were collected and supplemented with Triton X-100 (final concentration 1%) and 5% input aliquots were retained for later use. Protein A dynabeads (Invitrogen) previously coupled with H3K36me3 antibody (ab9050, Abcam) in blocking solution (1xPBS, 0.5% BSA) were added and the samples incubated overnight under rotation at 4 oC. Beads were then washed for 10 min at 4 oC with the following buffers: IP dilution buffer 1% Triton X-100 (20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), buffer A (50 mM Hepes pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B (20 mM Tris pH 8, 1mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), TE buffer (1 mM EDTA pH 8, 10 mM Tris pH 8). Chromatin was eluted by incubating the beads in extraction buffer (0.1M NaHCO3, 1% SDS) for 15 min at 37oC. To reverse the cross-linking Tris-HCl pH 6.8 and NaCl were added to final concentrations of 130 mM and 300mM respectively. IP samples were then incubated at 65 oC overnight. Samples were then incubated at 37 oC for 1h after addition of 2ul of RNase Cocktail Enzyme Mix (Ambion). Then 40 ug of Proteinase K (Roche) were added, followed by 2h incubation at 55oC. Input material was similarly de-crosslinked. Samples were purified with the MinElute PCR purification kit (QIAGEN).
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645) according to the manufacturer instructions. Barcoded adapters (NEBNext® Multiplex Oligos for Illumina® Index Primers Set 1, E7335) were used. Adapter-ligated DNA was size selected for an insert size of 150 bp using AMPure XP beads.  Libraries were sequenced using the NextSeq 500/550 high-output version 2.5 kit (75bp single end reads). Libraries were combined into equimolar pools to run within individual flow cells. Sequencing was performed by the Edinburgh Clinical Research Facility.

value: lacking DNMT1 and DNMT3B


title: hct116_t7_dnmt3b_t7_input_rep_1

description: HCT116 cells with T7 tagged DNMT3B input rep 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H7_AD006


title: hct116_dko_k36me3_input_rep_2

description: HCT116 lacking DNMT1 and DNMT3B input rep 2


title: hct116_k36me3_chip_rep_2

description: HCT116 cells k36me3 chip rep 2


title: hct116_k36me3_input_rep_2

description: HCT116 cells input rep 2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H7_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H6_AD007


title: hct116_k36me3_chip_rep_1

description: HCT116 cells k36me3 chip rep 1


title: hct116_dko_k36me3_input_rep_1

description: HCT116 lacking DNMT1 and DNMT3B input rep 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H6_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H6_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H5_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H6_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H7_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H5_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H5_AD007


title: Krogan_Huh7-5_OC43_A_S7_L003

city: New York

first: John

last: Poirier

address: 550 1st Ave

institute: NYU Langone Health

data_processing:
Trimming performed with cutadapt 2.10
Counts table generated by MaGECK 0.5.9.4
Genome_build: Krogan
Supplementary_files_format_and_content: raw counts table

source_name: Huh-7.5 cells

extract_protocol:
Ammonium acetate salt precipitation
Nextera
CRISPR

tag: cell line

value: Huh-7.5 cells

tag: treatment

tag: temperature

tag: replicate

value: A

tag: lane


title: Krogan_Huh7-5_OC43_C_S9_L004

value: C


title: Krogan_Huh7-5_OC43_A_S7_L004


title: Krogan_Huh7-5_OC43_B_S8_L003

value: B


title: Krogan_Huh7-5_OC43_B_S8_L004


title: Krogan_Huh7-5_OC43_C_S9_L003


title: Krogan_Huh7-5_OC43_C_S9_L002


title: hct116_k36me3_input_rep_1

description: HCT116 cells input rep 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H5_AD002

value: brain


title: Krogan_Huh7-5_OC43_C_S9_L001


title: Krogan_Huh7-5_OC43_B_S8_L002


title: hct116_dko_k36me3_chip_rep_1

description: HCT116 lacking DNMT1 and DNMT3B k36me3 chip rep 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H5_AD004


title: Krogan_Huh7-5_OC43_A_S7_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H4_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H4_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H5_AD006


title: Krogan_Huh7-5_Day_0_S11_L004

value: baseline


title: Krogan_Huh7-5_OC43_B_S8_L001


title: Krogan_Huh7-5_Day_0_S11_L003


title: Krogan_Huh7-5_Day_0_S11_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H4_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H4_AD006


title: Krogan_Huh7-5_Day_0_S11_L001


title: Krogan_Huh7-5_37C_SARS-CoV-2_C_S41_L003


title: Krogan_Huh7-5_37C_SARS-CoV-2_C_S41_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H4_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H3_AD010


title: Krogan_Huh7-5_37C_SARS-CoV-2_C_S41_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H3_AD012


title: Krogan_Huh7-5_OC43_A_S7_L002


title: Krogan_Huh7-5_37C_SARS-CoV-2_C_S41_L002


title: Krogan_Huh7-5_37C_SARS-CoV-2_B_S40_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H3_AD007


title: Krogan_Huh7-5_37C_SARS-CoV-2_B_S40_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H4_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H5_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H3_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H3_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H4_AD008


title: Krogan_Huh7-5_37C_SARS-CoV-2_B_S40_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H3_AD001


title: Krogan_Huh7-5_37C_SARS-CoV-2_B_S40_L001


title: Krogan_Huh7-5_37C_SARS-CoV-2_A_S39_L004


title: Krogan_Huh7-5_37C_SARS-CoV-2_A_S39_L003


title: Krogan_Huh7-5_37C_SARS-CoV-2_A_S39_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H2_AD012


title: Krogan_Huh7-5_37C_SARS-CoV-2_A_S39_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H2_AD008


title: Krogan_Huh7-5_37C_Mock_C_S35_L003

value: mock


title: Krogan_Huh7-5_37C_Mock_C_S35_L004


title: Krogan_Huh7-5_37C_Mock_C_S35_L001


title: Krogan_Huh7-5_37C_Mock_C_S35_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H3_AD006


title: Krogan_Huh7-5_37C_Mock_B_S34_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H2_AD006


title: Krogan_Huh7-5_37C_Mock_B_S34_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H2_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H1_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H2_AD002


title: Krogan_Huh7-5_37C_Mock_B_S34_L003


title: Krogan_Huh7-5_37C_Mock_A_S33_L004


title: Krogan_Huh7-5_37C_Mock_B_S34_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H2_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H1_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H1_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H1_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H1_AD004


title: Krogan_Huh7-5_37C_Mock_A_S33_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H12_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H1_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H1_AD006


title: Krogan_Huh7-5_37C_Mock_A_S33_L003


title: Krogan_Huh7-5_37C_229E_C_S14_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H2_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H12_AD008


title: Krogan_Huh7-5_37C_Mock_A_S33_L001


title: Krogan_Huh7-5_37C_229E_C_S14_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H12_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H12_AD004


title: Krogan_Huh7-5_37C_229E_B_S13_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H11_AD007


title: Krogan_Huh7-5_37C_229E_A_S12_L004


title: Krogan_Huh7-5_37C_229E_A_S12_L002


title: Krogan_Huh7-5_37C_229E_C_S14_L001


title: Krogan_Huh7-5_37C_229E_A_S12_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H11_AD012


title: Krogan_Huh7-5_37C_229E_B_S13_L001


title: Krogan_Huh7-5_37C_229E_B_S13_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H12_AD001


title: Krogan_Huh7-5_37C_229E_B_S13_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H12_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H10_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H11_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H11_AD002


title: Krogan_Huh7-5_33C_SARS-CoV-2_C_S38_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H10_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H10_AD010


title: Krogan_Huh7-5_37C_229E_A_S12_L003


title: Krogan_Huh7-5_37C_229E_C_S14_L003


title: Krogan_Huh7-5_33C_SARS-CoV-2_B_S37_L004


title: Krogan_Huh7-5_33C_SARS-CoV-2_C_S38_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H10_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H10_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H10_AD004


title: Krogan_Huh7-5_33C_SARS-CoV-2_B_S37_L002


title: Krogan_Huh7-5_33C_SARS-CoV-2_C_S38_L004


title: Krogan_Huh7-5_33C_SARS-CoV-2_B_S37_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H10_AD002


title: Krogan_Huh7-5_33C_SARS-CoV-2_A_S36_L001


title: Krogan_Huh7-5_33C_SARS-CoV-2_A_S36_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_H9_AD006


title: Krogan_Huh7-5_33C_NL63_C_S6_L004


title: Krogan_Huh7-5_33C_SARS-CoV-2_B_S37_L003


title: Krogan_Huh7-5_33C_NL63_C_S6_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G9_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G9_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G8_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G8_AD008


title: Krogan_Huh7-5_33C_NL63_C_S6_L001


title: Krogan_Huh7-5_33C_NL63_C_S6_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G8_AD007


title: Krogan_Huh7-5_33C_SARS-CoV-2_A_S36_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G9_AD010


title: Krogan_Huh7-5_33C_SARS-CoV-2_A_S36_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G9_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G9_AD001


title: Krogan_Huh7-5_33C_SARS-CoV-2_C_S38_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G9_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G8_AD012


title: Krogan_Huh7-5_33C_NL63_B_S5_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G8_AD006


title: Krogan_Huh7-5_33C_NL63_B_S5_L001


title: Krogan_Huh7-5_33C_NL63_B_S5_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G8_AD002


title: Krogan_Huh7-5_33C_NL63_A_S4_L004


title: Krogan_Huh7-5_33C_NL63_B_S5_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G7_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G7_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G6_AD010


title: Krogan_Huh7-5_33C_Mock_B_S2_L003


title: Krogan_Huh7-5_33C_Mock_C_S3_L003


title: Krogan_Huh7-5_33C_Mock_C_S3_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G7_AD008


title: Krogan_Huh7-5_33C_NL63_A_S4_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G7_AD006


title: Krogan_Huh7-5_33C_NL63_A_S4_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G7_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G6_AD008


title: Krogan_Huh7-5_33C_Mock_B_S2_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G6_AD012


title: Krogan_Huh7-5_33C_Mock_C_S3_L004


title: Krogan_Huh7-5_33C_Mock_C_S3_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G6_AD006


title: Krogan_Huh7-5_33C_Mock_A_S1_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G6_AD004


title: Krogan_Huh7-5_33C_NL63_A_S4_L003


title: Krogan_Huh7-5_33C_Mock_A_S1_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G6_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G8_AD004


title: Krogan_Huh7-5_33C_Mock_A_S1_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G5_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G5_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G5_AD007


title: Brunello_Huh75_Mock_C_S3_L001

data_processing:
Trimming performed with cutadapt 2.10
Counts table generated by MaGECK 0.5.9.4
Genome_build: Brunello
Supplementary_files_format_and_content: raw counts table


title: Krogan_Huh7-5_33C_Mock_B_S2_L001


title: Brunello_Huh75_Mock_C_S3_L004


title: Krogan_Huh7-5_33C_Mock_B_S2_L002


title: Krogan_Huh7-5_33C_Mock_A_S1_L004


title: Brunello_Huh75_Mock_B_S2_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G5_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G6_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G3_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G3_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G3_AD012


title: Brunello_Huh75_Mock_C_S3_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G5_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G5_AD001


title: Brunello_Huh75_Mock_A_S1_L001


title: Brunello_Huh75_Mock_B_S2_L001


title: Brunello_Huh75_Mock_B_S2_L003


title: Brunello_Huh75_Mock_A_S1_L003


title: Brunello_Huh75_Mock_A_S1_L004


title: Brunello_Huh75_Day0_S21_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G3_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G2_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G2_AD006


title: Brunello_Huh75_Mock_A_S1_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G2_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G1_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G1_AD010


title: Brunello_Huh75_37C_SARS-CoV2-C_S19_L004


title: Brunello_Huh75_37C_SARS-CoV2_A_S17_L004


title: Brunello_Huh75_Mock_B_S2_L002


title: D. mauritiana, late stage 5, replicate 3

description:
mau_st5_3
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

organism: Drosophila mauritiana

value: embryo

tag: generation

value: Parental

value: late stage 5


title: Brunello_Huh75_Day0_S21_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G1_AD008

value: ACA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G1_AD007

value: PTLp


title: Brunello_Huh75_Day0_S21_L002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G2_AD002

value: male


title: Brunello_Huh75_37C_SARS-CoV2_A_S17_L001


title: D. mauritiana, late stage 5, replicate 2,

description:
mau_st5_2
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

tag: embryonic stage

value: unknown


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G1_AD002

value: SSp


title: Brunello_Huh75_37C_SARS-CoV2-C_S19_L002


title: Brunello_Huh75_37C_SARS-CoV2_A_S17_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G2_AD001


title: Brunello_Huh75_37C_SARS-CoV2_A_S17_L002


title: Brunello_Huh75_Day0_S21_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G1_AD001


title: Brunello_Huh75_37C_SARS-CoV2-C_S19_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G12_AD007


title: D. mauritiana, stage 2, replicate 2,

description:
mau_st2_2
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: stage 2

tag: embryo sex


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G1_AD006

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G12_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G1_AD004


title: D. mauritiana, stage 2, replicate 3

description:
mau_st2_3
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

tag: replicate number


title: Brunello_Huh75_37C_SARS-CoV2-B_S18_L003

value: Huh-7.5 cells


title: D. mauritiana, stage 2, replicate 1

description:
mau_st2_1
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: Brunello_Huh75_37C_SARS-CoV2-C_S19_L003