title: CNS tumor

city: Rome

first: Sabina

last: Barresi

address: Viale San Paolo 15

institute: Ospedale Pediatrico Bambino Gesu

description: FFPE DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Platform using standard recommended Illumina setting

data_processing: Raw IDAT files were processed using R package ChAMP v.2.20

source_name: Tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: A was extracted according to MagPurix FFPE DNA Extraction Kit

value: male

tag: age (y)

value: brain


title: input_H3K9me2rep1_ChIP-Seq_O.sativa_2weeks

status: Public on Dec 02 2020

type: SRA

city: Beijing

first: Lei

last: Li

state: Beijing

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

country: China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: input H3K9me2rep1 ChIP-Seq O.sativa 2weeks

library_source: genomic

data_processing:
Typically 16-25 million read pairs for each library were obtained after removal of adaptor and low quality reads by flexbar2.5.
Clean reads were then mapped to genomes by Bowtie with default parameters (-v 0 –m 1). For repressive marks (H3K9me2 and H3K27me), we simply let Bowtie to randomly choose multi-hit positions when reads align to repeat-rich regions (-v 0 –M1 --best).
Since a single nucleosome often occupies about 147bp DNA, we linked mapped read pairs into single end reads for all ChIP libraries.
The resulting bed file was then used to call signal enrichment peaks by MACS2 and at the same time a genome wide signal density file was generated by genomeCoverageBed. The final peaks and density results were used for downstream qualitative and quantitative analysis.
We developed a pipeline to simultaneously visualize the comparative genomic features and the chromatin state.
Genome_build: We downloaded and used the rice genome version 6.1 from the MSU official ftp.  Four IOMAP (International Oryza Map Alignment Project) genomes, Oryza glaberrima, Oryza punctata, Oryza brachyantha RS2, Leersia perrieri and the sorgJGI2.0 were applied for bowtie mapping.

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: seedling stage plant

growth_protocol: green-house plant

extract_protocol:
Sixty-day fresh above-ground tissues were collected at the tillering stage for O. sativa vg. japonica, O. glaberrima, O. punctata, O. brachyantha, L. perrieri, and S. bicolor. Two-week fresh above-ground tissues at the seedling stage were also collected for O. sativa and O. brachyantha. ChIP experiments were performed as described in Gendrel et al. 2005 with minor modification. Briefly, 4g (for seedling stage) or 8g (for tillering stage) tissue were fine grounded in liquid nitrogen, followed by 3% formaldehyde fixation step. Nucleus were extracted and chromatin was sonicated into 300-500bp fragments in Bioruptor (Diagenode). Since each antibody has its own concentration and binding efficiency, we tested the optimal antibody volume for each antibodies. Typically we use 20ul antibody (1ug/ul) in a 350ul-400ul hybrid solution.
The final DNA precipitation was used for library construction with the NEB Next N6240 kit (New England BioLabs) and decoded by Hiseq 2000 (Ilumina) with pair end 90bp strategy.

tag: tissue

value: seedling shoot

tag: developmental stage

value: seedling stage 2 weeks after germination

tag: antibody

value: no antibody


title: H3K9me2rep2_ChIP-Seq_O.sativa_2weeks

description: H3K9me2rep2 ChIP-Seq O.sativa 2weeks

value: H3K9me2 (ab1220 Abcam)


title: H3K9me2rep1_ChIP-Seq_O.sativa_2weeks

description: H3K9me2rep1 ChIP-Seq O.sativa 2weeks


title: tet2/3DM 2dpf neutrophils rep 2

city: New York

first: Kelly

middle: Madigan

last: Banks

state: NY

address: 1300 York Ave, LC711

department: Surgery

country: USA

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
Tophat and Cufflinks
DESeq2 Differential Analysis in R
Supplementary_files_format_and_content: Normalized count file

molecule: total RNA

organism: Danio rerio

source_name: zebrafish embryos, neutrophils

extract_protocol:
Rneasy micro kit
TruSeq RNA Library Prep Kit v2 (Illumina)

value: embryos

tag: genotype

tag: cell type

value: neutrophils


title: tet2/3DM 2dpf neutrophils rep 1


title: tet3-/- 2dpf neutrophils rep 3


title: tet2/3DM 2dpf neutrophils rep 3


title: O_sativa_60d_RNASEQ

data_processing:
For data analysis, raw reads were filtered for adaptor and low quality reads by flexbar2.5.
Clean reads were mapped by Tophat2 package with default parameters.
Resulting BAM files were calculated by Cufflinks for gene expression FPKM  in each species
Genome_build: We downloaded and used the rice genome version 6.1 from the MSU official ftp.  Four IOMAP (International Oryza Map Alignment Project) genomes, Oryza glaberrima, Oryza punctata, Oryza brachyantha RS2, Leersia perrieri and the sorgJGI2.0 were applied for bowtie mapping.

source_name: 60d after germination plant

growth_protocol: plants are grown in greenhouse

extract_protocol:
In brief, total RNA was extracted using TRIzol buffer with 4g fresh tissue from the same plant which was used for ChIP experiment. Then RNA quality was validated by Agilent Bioanalyzer and samples with good quality were purified by RNA Purification Beads and submitted to BGI (shenzhen) for RNASEQ library construction
RNASEQ library was constructed with TruSeq RNA Sample Prep Kit (Illumina) according to the standard protocol. Six RNASEQ libraries were adjusted and sequenced in the same lane with proper barcodes with pair end 90bp strategy.

value: aerial tissue

value: tillering stage 60d after germination


title: tet2-/- 2dpf neutrophils rep 3


title: tet3-/- 2dpf neutrophils rep 2


title: tet2-/- 2dpf neutrophils rep 2


title: tet2-/- 2dpf neutrophils rep 1


title: input_H3K27me_ChIP-Seq_O.sativa_2weeks

description: input H3K27me ChIP-Seq O.sativa 2weeks


title: wildtype 1.5dpf neutrophils rep 3

value: wildtype


title: wildtype 1.5dpf neutrophils rep 2


title: wildtype 1.5dpf neutrophils rep 1


title: input_H3K9me2_ChIP-Seq_O.glaberrima_60d

description: input H3K9me2 ChIP-Seq O.glaberrima 60d

organism: Oryza glaberrima

source_name: tillering stage plant


title: Sample_123611_18h3

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
FastQC (v0.11.3) was used to ensure the quality of data
Align reads to the dm6 reference genome including mRNAs  with HISAT2 (version 2.1.0) and default parameters
Stringtie (version 1.3.4) to quantify expression at the gene and isoform level
DESeq2 (version 1.20.0) for differential expression testing
Normalization and differential expression are performed with DESeq2 using a negative binomial generalized linear model
Data are pre-filtered to remove genes with 0 counts in all samples
Genome_build: dm6
Supplementary_files_format_and_content: The raw counts produced in tab-delimited text format

organism: Drosophila melanogaster

source_name: brat mutant brains following 18 hours of Insb overexpression

growth_protocol: brat mutant larvae were cultured at 25 degree for 5 days to enrich type II neurolbast in brain.

extract_protocol:
Larval brains were dissected, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Rneasy Mini Kit (QIAGEN; Cat# 74104) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Insb transgene is induced by culturing larvae at 33 degree.

tag: genotype/variation

tag: timepoint

tag: phenotype

value: second wave of differentiation

value: neural stem cells


title: wildtype 2dpf neutrophils rep 3


title: H3_H3K9me2rep2_ChIP-Seq_O.sativa_2weeks

description: H3 H3K9me2rep2 ChIP-Seq O.sativa 2weeks

value: H3 ab1791 (Abcam)


title: wildtype 2dpf neutrophils rep 1


title: wildtype 2dpf neutrophils rep 2


title: H3K9me2_ChIP-Seq_O.glaberrima_60d

description: H3K9me2 ChIP-Seq O.glaberrima 60d


title: WT_40gen_vs_240gen_R2

type: RNA

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

hyb_protocol: Labeled probes were hybridized to microarrays in 8x15k format, made by Agilent (Design ID: 016322) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.

scan_protocol: After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).

data_processing: GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized Log2 Ratio data from technical replicates (dye swap) were averaged.

organism: Saccharomyces cerevisiae W303

source_name: cells from continuous culture

label_protocol: Samples of total RNA (5μg) were labeled with QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.

growth_protocol: Continuous cultures of W303 Saccharomyces cerevisiae strain were conducted in chemostat at a dilution rate of 0.17–0.18 volumes per hour, and the culture was continued for 240 generations at a constant temperature of 30 °C. Cell samples were collected after 40 genrations and after 240 generations. Cells were sedimented by centrifugation, flash-frozen in LN2 and kept at –80oC.

extract_protocol: Total RNA was prepared from deeply frozen yeast cell pellet samples using the hot acidic phenol procedure.

tag: strain

tag: growth period

value: 40 generations

tag: tag

value: 240 generations


title: Sample_123610_18h2

value: brat mutant brains following 18 hours of Insb overexpression


title: Sample_123605_0h3

source_name: brat mutant brain without Insb overexpression (0-hr)

value: Fully packed with neuroblasts


title: Sample_123608_9h3

source_name: brat mutant brains following 9 hours of Insb overexpression

value: initial differentiation


title: Sample_123607_9h2

value: brat mutant brains following 9 hours of Insb overexpression


title: Sample_123606_9h1


title: tet3-/- 2dpf neutrophils rep 1


title: Sample_123604_0h2

value: brat mutant brain without Insb overexpression (0-hr)


title: Sample_123603_0h1


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F9_ad008

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

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

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: age

value: brain

tag: source

value: SSp

tag: target

value: MOp

tag: gender

value: female


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G10_ad002

value: ACA

value: VISp


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G10_ad010

value: male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F9_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G11_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G11_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G10_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F8_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F9_ad007


title: Sample_123609_18h1

value: second wave of differentiation


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F9_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F9_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F8_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F7_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F8_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F8_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F8_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F7_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F7_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F7_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F7_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F7_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F5_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F6_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F4_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F6_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F4_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F6_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F7_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F5_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F5_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F4_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F4_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F5_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F3_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F5_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F3_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F5_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F5_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F3_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F3_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F4_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F3_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F5_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F3_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F2_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F6_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F2_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F2_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F1_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F1_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F4_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F1_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F12_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F12_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F12_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F12_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F12_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F2_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F12_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F11_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F11_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F10_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F11_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F10_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F11_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F1_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E9_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E9_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E9_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E9_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F11_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F11_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E8_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E8_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E8_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E8_ad001


title: BM mononuclear cells of C7

first: yuan

middle: jiu

last: yun

address: Beijing xizhimen station

institute: Company

hyb_protocol: Following labeling, cDNA was hybridized on a Clariom  D Assay(human, Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip Scanner 3000 7G

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

label: biotin

organism: Homo sapiens

source_name: BM mononuclear cells from normal donor

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

extract_protocol: 0.5mL mononuclear cells of blood marrow samples were placed into 1.5ml EP tubes containing Trizol lysate and total RNA was extracted using the RNeasy Mini Kit according to the manufacturer's instruction.

treatment_protocol: BM mononuclear cells of multiple myeloma patients and normal donors were immediately stored in liquid nitrogen or stored in the -80 ℃ refrigerator after 2 hours

tag: subject status

value: normal donor

tag: tissue/cell type

value: BM mononuclear cells


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F10_ad002

tag: tissue


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_F1_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E7_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E7_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E7_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E6_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E7_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E9_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E6_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E6_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E6_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E6_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E5_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E6_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E6_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E3_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E4_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E4_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E4_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E3_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E3_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E4_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E3_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E3_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E2_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E2_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E2_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E1_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E7_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E3_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E1_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E3_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E1_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E12_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E12_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E3_ad001


title: Spo_L_M_negative_rep1

city: Vilnius

first: Elena

last: Serviene

address: Akademijos 2

country: Lithuania

institute: Nature Research Centre

data_processing:
Obtained reads were processed using CLC Genomics Workbench v. 12.0 (CLC Inc., Aarhus, Denmark) (http://www.clcbio.com). Raw reads were trimmed for sequencing adapters, ambiguous nucleotides (ambiguities 1), low quality sequences (limit = 0.01) and sequences less than 50 nt in length. Filtered reads were mapped to the S. paradoxus CBS432 reference genome (NCBI reference sequence: https://yjx1217.github.io/Yeast_PacBio_2016/data/, 5531 genes in total) using the following alignment scores: mismatch cost 2; minimum length fraction 0.9; minimum identity within the mapped sequence 0.99; maximum number of best-scoring hits for a read 30.
The expression values for each transcript were calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using CLC Genomic workbench v 12.0
Supplementary_files_format_and_content: Fold change

organism: Saccharomyces paradoxus

source_name: yeast cells

extract_protocol:
The total RNA was isolated using GeneJET RNA Purification Kit (Thermo Fisher), according to the Yeast Total RNA Purification Protocol
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E11_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E1_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E5_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E11_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E12_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E1_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E5_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E12_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E12_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E11_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E11_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D9_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D9_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E10_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E1_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E10_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E10_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D8_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D8_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D9_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D9_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D9_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D7_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D8_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D9_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D8_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D7_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D9_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D6_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D6_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_E12_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D6_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D8_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D8_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D7_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D6_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D5_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D5_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D5_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D7_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D6_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D3_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D5_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D5_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D3_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D5_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D5_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D5_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D4_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D4_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D2_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D2_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D4_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D1_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D4_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D3_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D3_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D3_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D3_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D1_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D1_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D12_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D2_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D2_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D2_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D1_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D3_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D1_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D11_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D12_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D2_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D12_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D12_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D12_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D11_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D11_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D11_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D11_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D10_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D10_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D10_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C9_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C9_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_D11_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C9_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C9_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C8_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C7_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C8_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C7_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C8_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C7_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C7_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C7_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C9_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C6_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C6_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C6_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C5_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C6_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C6_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C5_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C5_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C7_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C5_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C4_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C4_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C5_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C6_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C5_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C4_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C4_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C4_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C3_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C3_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C3_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C3_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C3_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C3_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C2_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C2_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C2_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C12_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C2_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C12_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C12_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C12_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C11_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C12_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C11_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C11_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C11_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C11_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C2_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C10_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C10_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C11_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B9_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B9_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C2_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_C10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B9_ad004


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B5_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B5_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B5_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B8_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B5_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B5_ad002


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B7_ad004


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B4_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B3_ad008


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A4_ad007


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A5_ad010


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A7_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A2_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A2_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A1_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A2_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A1_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A12_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A1_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A12_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A1_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A12_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A12_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A12_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A12_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A10_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H9_ad012

value: AI


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H9_ad004

value: AUD


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A1_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A1_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H8_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_A6_ad012


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H4_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H4_ad008


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_B6_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H3_ad007


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H3_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H3_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H7_ad008


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H2_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H2_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H3_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H1_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H1_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H1_ad008


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H12_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H12_ad002


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title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H11_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H11_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H11_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H11_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H10_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H10_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H10_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H10_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H10_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G9_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H10_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G9_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G9_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G9_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G9_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G9_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G8_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H11_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G8_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G8_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G8_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G8_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H11_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G8_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H11_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G7_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G7_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_H10_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G7_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G7_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G7_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G6_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G7_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G6_ad007


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G6_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G6_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G6_ad006


title: M-SCT KO-input

city: Wuxi

first: Li

last: Yan

institute: Jiangnan University

data_processing:
Base calling were performed using Off-Line Basecaller software (OLB V1.8)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse genome (UCSC mm10) using Bowtie2 software
Aligned reads were used for peak calling, LncRNA, mRNA and small ncRNA associated MeDIP enriched regions (peaks) with statistically significant were identified for each sample, using a q-value threshold of 10-4 by MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: The signal profiles inUCSC binary wig file format were generated from MeDIP-seq data

source_name: inguinal WAT

extract_protocol:
Genomic DNA was sonicated to 200-800bp fragments, 1μg of fragmented sample was ligated to Illumina's genomic adapters
Fragmented sample was ligated to Illumina's genomic adapters with Genomic DNA Sample Kit (#FC-102-1002,Illumina),following the manufacturer's instructions

value: iWAT

value: SCTf/+, vil1-Cre-/-

tag: genotype of the mother

value: vSCT KO


title: M-SCT KO3


title: M-SCT floxed-input

value: SCT-floxed


title: M-SCT KO1


title: M-SCT floxed3


title: M-SCT floxed2


title: scRNA-seq - VEHICLE

city: Melbourne

first: Emily

middle: Jane

last: Lelliott

state: VIC

address: 305 Grattan Street

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Cellranger (version 3.0): for producing fastq files, alignment and counting to mm10 with default parameters
Seurat (version 3): for quality control, visualisation and analyses. If not specified default parameters were used
Data were filtered with the following parameters  min.transcripts = 400,  min.cells = 5,  high.mito.thresh = 0.08,  high.umi.thresh = 10000
Data were normalised using Seurat SCTransform
Data were integrated sample-wise using Seurat IntegrateData with 30 principal component
Dimensionality reduction was performed with Seurat
TCR count matrix was analysed using tidyverse
Genome_build: mm10
Supplementary_files_format_and_content: R objects (rds and rda)

molecule: polyA RNA

source_name: Tumor-infiltrating CD45.2+ immune cells

growth_protocol: YOVAL1.1 cells were grown subcutaneously in C57BL/6 mice until tumors reached ~100mm^3

extract_protocol:
Tumors were harvested, processed and FAC sorted for CD45.2+ immune cells followed by droplet encapsulation for single cell sequencing using 10xGenomics platform
Libraries were prepared using 10x Genomics Single Cell V(D)J kit as per the manufacturer’s instructions. T-cell receptor (TCR) libraries were prepared using the 10x Chromium Single Cell V(D)J. Enrichment Kit.

treatment_protocol: Mice were treated with triple (dabrafenib/trametinib/palbociclib) or corresponding vehicles for 7 days, administered daily by oral gavage

tag: mouse strain

tag: tumor type

value: YOVAL1.1 subcut

tag: treatment

value: Vehicle - 1 week


title: scRNA-seq - TRIPLE

value: Triple (dabrafenib, trametinib, palbociclib) - 1 week


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H9_ad002

value: brain

value: PTLp

value: MOp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H8_ad006

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H9_ad001

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H9_ad008

value: VIS


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H8_ad010


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P5_190607_P6_G7_ad004

value: VISp


title: M-SCT floxed1

tag: genotype


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H7_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H7_ad008


title: M-SCT KO2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H8_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H6_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H6_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H7_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H7_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H8_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H6_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H5_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H5_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H5_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H5_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H5_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H5_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H8_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H4_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H4_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H2_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H3_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H3_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H3_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H3_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H1_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H4_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H1_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H1_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H4_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H2_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H2_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H12_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H12_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H1_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H11_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H11_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H11_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H11_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H10_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H10_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H10_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G9_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G8_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G9_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G8_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G8_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G6_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G6_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G6_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G6_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G5_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_H10_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G5_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G5_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G4_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G3_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G3_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G4_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G6_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G7_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G4_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G3_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G3_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G3_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G2_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G2_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G2_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G8_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G7_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G2_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G1_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G3_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G12_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G12_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G11_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G11_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G10_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G11_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G10_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G11_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G10_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G10_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G10_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F9_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F9_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F8_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F9_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F8_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F8_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F8_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F6_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F8_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F7_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F7_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F6_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_G1_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F7_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F6_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F6_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F6_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F5_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F6_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F5_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F5_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F4_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F4_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F4_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F3_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F3_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F3_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F3_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F3_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F1_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F1_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F2_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F2_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F2_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F1_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F5_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F12_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F12_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F12_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F1_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F12_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F1_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F12_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F11_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F11_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F10_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F11_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F10_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F10_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E9_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E8_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E8_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E9_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E9_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E8_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F11_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E7_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E7_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E6_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E7_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E6_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E6_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E6_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E6_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E6_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_F10_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E6_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E5_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E5_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E8_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E8_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E4_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E5_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E4_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E4_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E5_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E3_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E3_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E3_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E3_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E2_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E2_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E5_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E2_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E1_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E5_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E12_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E1_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E12_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E12_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E4_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E12_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E11_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E11_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E11_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E11_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E10_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E2_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E1_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E12_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D8_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D8_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D7_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D8_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D9_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D8_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D8_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D8_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D7_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D9_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D7_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E10_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D7_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_E10_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D7_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D6_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D6_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D5_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D5_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D5_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D5_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D4_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D3_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D4_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D3_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D3_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D3_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D3_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D2_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D1_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D2_ad012


title: X1D30-1

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

data_processing:
Illumina HiSeq TM 2500 by Gene Denovo Biotechnology Co
To get clean tags,sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
All of the clean tags were aligned with small RNAs in GeneBank database (Release 209.0) and Rfam database  (Release11.0) to identify and remove rRNA,scRNA,snoRNA,snRNA and tRNA.Then aligned with Genome to remove introns and repeat sequences.
Identification of exist miRNA,known miRNA and novel miRNA with miRbase database (Release 2).
Differentially expressed miRNA (DE miRNA) analysis and target gene prediction
Supplementary_files_format_and_content: tab-delimited text files include miRNA expression  for each Sample.

organism: Apis mellifera ligustica

source_name: brain tissue

extract_protocol:
Brain tissue were collected,and total RNA was extracted by Trizol reagent kit (Invitrogen, Carlsbad, CA,USA). Sequenced using Illumina HiSeq TM 2500 by Gene Denovo Biotechnology Co.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D1_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D12_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D12_ad012


title: X1D30-2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D12_ad002


title: X1D20-3


title: X1D20-2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D11_ad008


title: X1D30-3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D2_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D11_ad010


title: X1D20-1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D11_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D11_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D11_ad007


title: X1D10-3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D11_ad004


title: X1D10-2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D11_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D2_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D10_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D12_ad001


title: X1D10-1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D10_ad010


title: CK-3


title: CK-2


title: 37c_1m_rep1 chromatin, cell 4

city: San Francisco

first: Colin

last: McNally

address: 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

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

source_name: K562 cells

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

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

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

tag: mnase digestion temperature

tag: mnase digestion duration

value: 1 min

tag: ecogii methylation

value: EcoGII Methylated


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D10_ad001

tag: strain


title: 4c_10m_rep2 chromatin, cell 4

value: 10 min


title: 4c_10m_rep1 chromatin, cell 4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C9_ad007


title: 4c_10m_rep1 chromatin, cell 3


title: 4c_10m_rep2 chromatin, cell 3


title: 4c_60m_rep1 chromatin, cell 3

value: 60 min


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D10_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C8_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C9_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C9_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C9_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C9_ad008


title: 37c_1m_rep1 chromatin, cell 3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C8_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C7_ad007


title: k562 negative control rep 2

value: Unmethylated


title: k562 positive control rep 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C7_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C7_ad002


title: k562 negative control rep 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_D10_ad007


title: 4c_60m_rep1 chromatin, cell 4


title: k562 chromatin rep 1, cell 2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C6_ad008


title: k562 chromatin rep 2, cell 1


title: k562 chromatin rep 1, cell 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C6_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C6_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C5_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C6_ad004


title: k562 positive control rep 2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C5_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C5_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C5_ad007


title: RPE1 BRCA1_KO sgALC1_1

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

data_processing:
Raw reads were mapped to the human (hg38) genome using Lexogen  Quantseq 2.3.1 FWD platform with low quality reads removed. Raw reads were mapped  into hg38 genome using STAR Aligner with modified ENCODE settings. Gene raw read  count files were generated with HTSeq-count.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene read counts for each sample

source_name: RPE1 BRCA1_KO sgALC1

growth_protocol:
DLD1 BRCA2-/- were and cultured in RPMI 1640 with GlutaMAX media and supplemented with 10% FBS and 1x penicillin-streptomycin (P/S).
hTERT-RPE1 p53-/-BRCA-/- Cas9 cells were cultured in DMEM media with 10% FBS and 1x P/S. ells Cells were maintained at 3% oxygen.

extract_protocol:
Cells were lysed in TRIzol (Invitrogen) and RNA was isolated using Direct-zolTM RNA Miniprep  Plus kit (ZYMO).
RNA-seq libraries were  prepared with QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) by  using 2 μg of total RNA as input and 11 cycles for PCR amplification.

treatment_protocol: BRCA1 mutant hTERT-RPE1 cells and BRCA2 mutant DLD1 cells were infected with either sgNegative or two different sgRNAs targeting ALC1 in a lentiviral format and 1~5 million cells were harvested at the 4th population doubling time after peak the day of peak GFP/ Tinitial.

tag: cell line

tag: cell type

value: hTERT-immortalized retinal pigment epithelial cell line

value: This is a near-diploid human cell line

tag: genotype/variation

value: RPE1 BRCA1_KO sgALC1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C4_ad006

tag: age

tag: source

tag: target


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C4_ad002

tag: gender


title: RPE1 BRCA1_KO sgNeg_sgNeg ctrl_rep1

source_name: RPE1 BRCA1_KO sgNeg_sgNeg ctrl

value: RPE1 BRCA1_KO sgNeg_sgNeg ctrl


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C4_ad004

tag: tissue


title: DLD1 BRCA2_KO sgALC1_2

source_name: DLD1 BRCA2_KO sgALC1

value: Human colorectal adenocarcinoma cell line; epithelial

value: This is a pseudodiploid human cell line with the modal chromosome number of 46, occurring in 86% of cells. The rate of polyploidy was high at 17.1%. The karyotype of the line was 46,XY,-2,+dir dup(2)(p13-p23). The Y chromosome was slightly longer than N22 and had a large segment of heterochromatic, fluorescent distal q arms.

value: DLD1 BRCA2_KO sgALC1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C4_ad001

value: brain

value: PTLp

value: MOp


title: DLD1 BRCA2_KO sgNeg ctrl

source_name: DLD1 BRCA2_KO sgNeg ctrl

value: DLD1 BRCA2_KO sgNeg ctrl


title: k562 chromatin rep 2, cell 2


title: DLD1 BRCA2_KO sgALC1_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C3_ad007

value: VIS

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C3_ad008

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C3_ad002


title: panicle_siRNA_O.sativa

description: small RNA of panicle

data_processing:
Clean read pairs  were obtained after removal of adaptor and low quality reads by flexbar2.5.
Single end reads were preprocessed and mapped to genome by Bowtie.
Signal density was calculated by genomeCoverageBed.
Genome_build: rice tigr 6
Supplementary_files_format_and_content: small RNA single base density, bgizpped four columns bedgraph file

organism: Oryza sativa

source_name: panicle tissue

extract_protocol:
18-30bp small RNA was selected from total RNA extraction by PAGE
Sequence library was constructed with TruSeq Small RNA Sample Pre Kit (Illumina) by standard protocol.

value: panicle

tag: developmental stage

value: reproductive stage


title: CK-1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C2_ad012


title: RPE1 BRCA1_KO sgALC1_2


title: RPE1 BRCA1_KO sgNeg_sgNeg ctrl_rep2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C1_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C2_ad007


title: RNA_BrafSmarcb1_Veh_BS53965

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: thyroid tumor cell line

growth_protocol: To generate mouse tumor cell lines, tumors were dissected, minced in PBS, and resuspended in 10 mL of digestion medium (minimum essential media containing 112 U/mL type I collagenase (Worthington catalog # CLS-1), 1.2 U/mL dispase (Gibco catalog # 17105-041), penicillin (50 U/mL), and streptomycin (50 mg/mL). Cells were incubated at 37oC for 60 minutes with vigorous shaking, after which cells were spun down and resuspended in Coon’s modified F12 medium with penicillin/streptomycin/L-glutamine (P/S/G; Gemini; #400-110) and 0.5% bovine brain extract and plated into CellBind plates (Corning Inc., Lowell, MA, USA) for two weeks, and then switched to Coon’s modified F12 medium with P/S/G containing 5% FBS for routine culturing and maintenance.

extract_protocol:
RNA was isolated by TRIzol extraction
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

treatment_protocol: Thyroid tumor cell lines were treated with 300 nM CKI for 8 days in the presence of bovine TSH or vehicle (40% Trappsol, Cyclo Therapeutics, Alachua, FL).

value: thyroid tumor cell line

value: Braf(V600E) + Smarcb1 KO

value: Vehicle


title: RNA_Braf_Veh_B48051


title: RNA_Braf_Veh_B47275


title: RNA_Braf_Veh_B52482


title: RNA_WT_72248

value: wildtype


title: RNA_WT_72246


title: RNA_BrafSmarcb1_Veh_BS53958


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C1_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C12_ad010


title: RNA_BrafSmarcb1_Veh_BS53736


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C12_ad002


title: RNA_BrafSmarcb1_CKI_BS53965


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C12_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C11_ad008


title: RNA_WT_72252