title: FN025.0: Genomic DNA from sperm of nut-fed individual FN025 (baseline)

description: Purified sperm sample

source_name: Semen sample 13


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B12_ad006

status: Public on Sep 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:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 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
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 Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: LSX

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B12_ad008


title: FN030.0: Genomic DNA from sperm of nut-fed individual FN030 (baseline)

type: genomic

city: Salt Lake City

first: Albert

last: Salas-Huetos

state: UT

address: 675S Arapeen Dr

department: Andrology

institute: University of Utah

description: Purified sperm sample

hyb_protocol: A total of 500ng of extracted DNA was bisulfite converted with EZ-96 DNA Methylation-Gold kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s recommendations specifically for use with Illumina array platforms. The converted DNA was then hybridized to Infinium® MethylationEPIC BeadChip microarrays (Illumina) array and analyzed according to Illumina protocols at the University of Utah Genomics Core Facility.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data from microarrays were processed by using the minfi Bioconductor package (minfi; package at http://www.bioconductor.org) and Useq bioinformatics software package (https://sourceforge.net/projects/useq/).

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Semen sample 17

label_protocol: Standard Illumina protocols.

extract_protocol: Genomic DNA was extracted from purified sperm samples using QIAamp DNA Mini kit according to manufacturer protocol.

treatment_protocol: Prior to DNA isolation, a somatic cell lysis methodology was performed by incubation sperm samples with somatic cell lysis buffer, which contained both 0.1% SDS and 0.5% Triton X-100 (in Milli-Q® water), on ice.

tag: gender

value: Male

tag: sample type

value: Sperm

tag: baseline or final intervention

value: Baseline


title: Molt16 DMSO Rep3 RNA-seq

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

library_source: transcriptomic

data_processing:
RNA sequencing reads were aligned to GRCh38 using STAR (version 2.4.2a)42 and quantified on Gencode v24.
Normalization of counts was done using DESeq2.
Genome_build: hg38

molecule: total RNA

source_name: T-ALL cell line MOLT-16

growth_protocol: Cell lines were cultured in RPMI-1640 medium supplemented with 10 or 20% fetal calf serum, 100 U/ml penicillin, 100 µg/ml streptomycin, and 2 mM L-glutamine at 37°C with 5% CO2.

extract_protocol:
RNA extraction was performed using the miRNeasy Mini Kit (Qiagen).
RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen)

treatment_protocol: Cell lines were treated with 1μM Decitabine or DMSO control for 48h

tag: cell line

tag: treatment

value: DMSO

tag: tissue

value: T-ALL cell line


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B12_ad010


title: FN022.3: Genomic DNA from sperm of control individual FN022 (final)

description: Purified sperm sample

source_name: Semen sample 12

value: Final


title: TALL1 DMSO Rep2 RNA-seq

source_name: T-ALL cell line TALL-1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B12_ad012


title: TALL1 DMSO Rep1 RNA-seq


title: Mlp124518-1

city: Trois-Rivières

first: KarenCristine

last: GonçalvesdosSantos

state: QC

address: 3351 boulevard des Forges

department: Chemistry, biochemistry and physics

country: Canada

institute: Université du Québec à Trois-Rivières

data_processing:
Trimmomatic (PE, phred33, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25)
HISAT2 alignment to TAIR10
Read count TAIR10 - R package GenomicFeatures for "makeTxDbFromBiomart" and R package GenomicAligments for "summarizeOverlaps", options "features=tx, mode=Union, singleEnd=F, ignore.strand=FALSE, fragments=T"
Genome_build: TAIR10
HISAT2 alignment to CEs-GFP
Read count Ces-GFP - R package GenomicFeatures for "makeTxDbFromBiomart" and R package GenomicAligments for "summarizeOverlaps", options "features=tx, mode=IntersectionStrict, singleEnd=F, ignore.strand=FALSE, fragments=T"

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Aerial tissue of transgenic Arabidopsis

growth_protocol: plants grown in growth-chamber (22C, 16h of light) in soil for 14 days

extract_protocol:
Genaid Total RNA mini kit Plant
NeoPrep/TruSeq Illumina

tag: genotype/variation

value: Aerial tissue


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B12_ad007


title: Molt16 DAC Rep1 RNA-seq

value: Decitabine


title: FN025.3: Genomic DNA from sperm of nut-fed individual FN025 (final)

description: Purified sperm sample

source_name: Semen sample 14


title: Mlp124499-3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B11_ad010


title: TALL1 DAC Rep3 RNA-seq


title: Mlp124499-2


title: FN021.3: Genomic DNA from sperm of control individual FN021 (final)

description: Purified sperm sample

source_name: Semen sample 10


title: Loucy DAC Rep1 RNA-seq

source_name: T-ALL cell line Loucy

value: Loucy


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B11_ad012


title: TALL1 DAC Rep2 RNA-seq


title: FN010.3: Genomic DNA from sperm of nut-fed individual FN010 (final)

description: Purified sperm sample

source_name: Semen sample 8


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B11_ad006


title: TALL1 DMSO Rep3 RNA-seq


title: TALL1 DAC Rep1 RNA-seq


title: Mlp124518-3


title: Mlp124499-1


title: FN021.0: Genomic DNA from sperm of control individual FN021 (baseline)

description: Purified sperm sample

source_name: Semen sample 9


title: PEER DMSO Rep2 RNA-seq

source_name: T-ALL cell line PEER

value: PEER


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B11_ad007


title: FN010.0: Genomic DNA from sperm of nut-fed individual FN010 (baseline)

description: Purified sperm sample

source_name: Semen sample 7


title: Mlp124497-2


title: FN006.0: Genomic DNA from sperm of nut-fed individual FN006 (baseline)

description: Purified sperm sample

source_name: Semen sample 5


title: Mlp124497-1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B11_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B11_ad004


title: Mlp124466-3


title: PEER DMSO Rep3 RNA-seq


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B10_ad008


title: PEER DAC Rep3 RNA-seq


title: FN006.3: Genomic DNA from sperm of nut-fed individual FN006 (final)

description: Purified sperm sample

source_name: Semen sample 6


title: Mlp124466-2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B10_ad012


title: Mlp124518-2


title: FN022.0: Genomic DNA from sperm of control individual FN022 (baseline)

description: Purified sperm sample

source_name: Semen sample 11


title: FN116.0: Genomic DNA from sperm of nut-fed individual FN116 (baseline)

description: Purified sperm sample

source_name: Semen sample 47


title: Mlp124357-3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B10_ad010

source_name: C57BL/6J Male P56 Mouse Brain


title: PEER DMSO Rep1 RNA-seq


title: FN004.3: Genomic DNA from sperm of nut-fed individual FN004 (final)

description: Purified sperm sample

source_name: Semen sample 4


title: Mlp124497-3


title: Mlp124357-2


title: Spleen-PDX T-ALL2 Decitabine Rep3 RNA-seq

source_name: T-ALL blasts from PDX spleen

treatment_protocol: Mice were randomized in 2 groups of 3 and treated for 5 days with vehicle-only or Decitabine (0.5 mg/kg bodyweight). At day 7, animals were sacrificed, and tumor cells collected from the spleen.

value: T-ALL blasts from PDX spleen

tag: pdx

value: PDX T-ALL2


title: PEER DAC Rep2 RNA-seq


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B10_ad004


title: Mlp124357-1


title: FN112.3: Genomic DNA from sperm of nut-fed individual FN112 (final)

description: Purified sperm sample

source_name: Semen sample 46


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B10_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B10_ad002


title: Spleen-PDX T-ALL2 Decitabine Rep1 RNA-seq


title: Spleen-PDX T-ALL2 Decitabine Rep2 RNA-seq


title: PEER DAC Rep1 RNA-seq


title: Mlp124266-3


title: FN003.0: Genomic DNA from sperm of control individual FN003 (baseline)

description: Purified sperm sample

source_name: Semen sample 1


title: FN112.0: Genomic DNA from sperm of nut-fed individual FN112 (baseline)

description: Purified sperm sample

source_name: Semen sample 45


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B1_ad006


title: FN003.3: Genomic DNA from sperm of control individual FN003 (final)

description: Purified sperm sample

source_name: Semen sample 2


title: Mlp124266-2

source_name: Aerial tissue of transgenic Arabidopsis


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B1_ad012


title: Spleen-PDX T-ALL2 DMSO Rep2 RNA-seq


title: Spleen-PDX T-ALL2 DMSO Rep3 RNA-seq


title: Mlp124266-1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B1_ad010


title: Spleen-PDX T-ALL2 DMSO Rep1 RNA-seq


title: Mlp124256-3


title: FN105.0: Genomic DNA from sperm of nut-fed individual FN105 (baseline)

description: Purified sperm sample

source_name: Semen sample 43


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B1_ad008


title: Mlp124256-2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B1_ad007


title: Spleen-PDX T-ALL1 Decitabine Rep2 RNA-seq

value: PDX T-ALL1


title: Mlp124256-1


title: FN095.0: Genomic DNA from sperm of nut-fed individual FN095 (baseline)

description: Purified sperm sample

source_name: Semen sample 41


title: Spleen-PDX T-ALL1 Decitabine Rep1 RNA-seq


title: FN092.3: Genomic DNA from sperm of nut-fed individual FN092 (final)

description: Purified sperm sample

source_name: Semen sample 40


title: Spleen-PDX T-ALL1 DMSO Rep3 RNA-seq


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B1_ad004


title: Mlp123531-2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B1_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A9_ad008


title: Spleen-PDX T-ALL1 DMSO Rep2 RNA-seq


title: FN079.3: Genomic DNA from sperm of nut-fed individual FN079 (final)

description: Purified sperm sample

source_name: Semen sample 38


title: Mlp123531-3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A9_ad002


title: Spleen-PDX T-ALL1 DMSO Rep1 RNA-seq


title: FN105.3: Genomic DNA from sperm of nut-fed individual FN105 (final)

description: Purified sperm sample

source_name: Semen sample 44


title: FN077.3: Genomic DNA from sperm of nut-fed individual FN077 (final)

description: Purified sperm sample

source_name: Semen sample 36


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A9_ad010


title: Mlp123227-3


title: Input T_ALL6 ChIPmentation

data_processing:
Library strategy: ChIPmentation
Reads were trimmed by Trimmomatic and aligned to the reference genome hg38 with Bowtie2.
Peaks were called with MACS2 with the respective input control for each donor pool. Options for MACS2 were set to --extsize 73 –nomodel –broad
A matrix containing all significant peaks was made as reference for counting reads from BAM files using the function summarizeOverlaps from the R package GenomicAlignments.
Normalization of counts was done using DESeq2
Genome_build: hg38

source_name: PDX derived T-ALL blasts

extract_protocol:
50-100 000 CD45+ sorted, fixed cells were lysed in lysis buffer complemented with 20mM NaBU HDAC inhibitor and sheared on the Bioruptor Pico (Diagenode). Sheared chromatin was magnetically immunoprecipitated and tagmentated using the Auto ChIPmentation Kit for Histones (Diagenode).
Libraries were constructed with the Auto ChIPmentation Kit for histones (Diagenode). Libraries were sequenced with the Nextseq500 (SR75, High Output).

value: PDX derived T-ALL blasts

tag: cosme subgroup

tag: antibody


title: Mlp124466-1


title: Mlp123227-2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A9_ad012


title: Input T_ALL5 ChIPmentation


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A9_ad007


title: FN075.3: Genomic DNA from sperm of nut-fed individual FN075 (final)

description: Purified sperm sample

source_name: Semen sample 34


title: Input T_ALL4 ChIPmentation


title: FN092.0: Genomic DNA from sperm of nut-fed individual FN092 (baseline)

description: Purified sperm sample

source_name: Semen sample 39


title: FN075.0: Genomic DNA from sperm of nut-fed individual FN075 (baseline)

description: Purified sperm sample

source_name: Semen sample 33


title: Mlp123218-3


title: FN073.0: Genomic DNA from sperm of nut-fed individual FN073 (baseline)

description: Purified sperm sample

source_name: Semen sample 31


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A9_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: Input T_ALL3 ChIPmentation


title: Mlp123531-1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A8_ad006


title: Mlp123227-1


title: Mlp123218-2


title: Mlp123218-1


title: Input T_ALL1 ChIPmentation


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A8_ad012


title: Mlp106078-3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A8_ad010


title: FN052.3: Genomic DNA from sperm of nut-fed individual FN052 (final)

description: Purified sperm sample

source_name: Semen sample 30


title: H3K27me3 T_ALL6 ChIPmentation


title: Spleen-PDX T-ALL1 Decitabine Rep3 RNA-seq

source_name: T-ALL blasts from PDX spleen


title: H3K27me3 T_ALL5 ChIPmentation


title: FN052.0: Genomic DNA from sperm of nut-fed individual FN052 (baseline)

description: Purified sperm sample

source_name: Semen sample 29


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A8_ad008


title: FN042.3: Genomic DNA from sperm of nut-fed individual FN042 (final)

description: Purified sperm sample

source_name: Semen sample 24


title: Mlp106078-1

source_name: Aerial tissue of transgenic Arabidopsis


title: FN044.3: Genomic DNA from sperm of nut-fed individual FN044 (final)

description: Purified sperm sample

source_name: Semen sample 26


title: H3K27me3 T_ALL4 ChIPmentation


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A8_ad007


title: Mlp102036-3


title: FN047.0: Genomic DNA from sperm of nut-fed individual FN047 (baseline)

description: Purified sperm sample

source_name: Semen sample 27


title: FN077.0: Genomic DNA from sperm of nut-fed individual FN077 (baseline)

description: Purified sperm sample

source_name: Semen sample 35


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A8_ad004


title: Input T_ALL2 ChIPmentation


title: FN044.0: Genomic DNA from sperm of nut-fed individual FN044 (baseline)

description: Purified sperm sample

source_name: Semen sample 25


title: H3K27me3 T_ALL3 ChIPmentation


title: Mlp102036-2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A8_ad002


title: H3K27me3 T_ALL2 ChIPmentation


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A7_ad006


title: Mlp102036-1


title: H3K27me3 T_ALL1 ChIPmentation


title: Mlp72983-3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A7_ad012


title: MDM-72H-M2

city: Seoul

first: Suji

last: Kim

state: Gwanak-gu

address: 1, Gwanak-ro

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
canFam3
tab-delimited text files include read count values for each Sample
Genome_build: canFam3
Supplementary_files_format_and_content: abundance measurement

organism: Canis lupus familiaris

source_name: MDMs stimulated with M. intracellulare

extract_protocol:
total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: breed

value: beagle

value: whole blood

tag: cell type

value: monocyte-derived macrophages


title: FN042.0: Genomic DNA from sperm of nut-fed individual FN042 (baseline)

description: Purified sperm sample

source_name: Semen sample 23

value: Male


title: MDM-72H-M1


title: Mlp72983-2


title: Mlp72983-1


title: Mlp106078-2


title: FN039.0: Genomic DNA from sperm of nut-fed individual FN039 (baseline)

description: Purified sperm sample

source_name: Semen sample 21

value: Sperm


title: MDM-72H-C3

source_name: Control MDMs


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A7_ad007

value: LSX

value: male


title: MDM-72H-C2


title: Mlp37347-3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A7_ad004


title: Mlp37347-2


title: MDM-24H-M2


title: FN032.0: Genomic DNA from sperm of nut-fed individual FN032 (baseline)

description: Purified sperm sample

source_name: Semen sample 17

value: Baseline


title: FN027.3: Genomic DNA from sperm of nut-fed individual FN027 (final)

description: Purified sperm sample

source_name: Semen sample 16

value: Final


title: FN037.0: Genomic DNA from sperm of nut-fed individual FN037 (baseline)

description: Purified sperm sample

source_name: Semen sample 19


title: Mlp37347-1

value: Aerial tissue


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A7_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: MDM-24H-M1


title: Control-3

value: Control


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A6_ad006


title: MDM-24H-C2


title: FN032.3: Genomic DNA from sperm of nut-fed individual FN032 (final)

description: Purified sperm sample

source_name: Semen sample 18


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A6_ad012


title: MDM-24H-C1


title: FN004.0: Genomic DNA from sperm of nut-fed individual FN004 (baseline)

description: Purified sperm sample

source_name: Semen sample 3


title: FN116.3: Genomic DNA from sperm of nut-fed individual FN116 (final)

description: Purified sperm sample

source_name: Semen sample 48


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A7_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A7_ad008


title: Control-2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A6_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A6_ad007


title: MDM-6H-C2


title: MDM-6H-M2


title: mel1_prophase_I_degradome_rep2

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

data_processing:
sRNA-seq:Low quality reads were removed and 3' adapter sequences were trimmed using cutadapt2.7. Clean sRNA reads in sizes of 18–30 nt were mapped to the rice reference genome (MSU v7) using bowtie, allowing no mismatches. 21-nt and 24-nt PHAS loci were identified and characterized by PhaseTank and Unitas as previously described using all 21-nt and 24-nt genome-matched reads from spikelets and male germ cells. The overlapped results between these two programs are considered as our final annotated phasiRNA loci.For annotation of phasiRNA loci that were not previously identified, only those loci with higher phase score than lowest score of previous PHAS catalog(phase score=10) were considered as the newly identified loci.For examining the dependence of phasiRNA accumulation on MEL1 or OsRDR6, the read counts of each phasiRNA from three biological replicates of wild-type and mutant plants were compared using edegR.  PhasiRNAs with a ≥ 2-fold reduction in the mutant and an FDR ≤ 0.05 were considered to be dependent on OsRDR6 or MEL1.
RNA-seq:Low quality reads were removed and adapters were trimmed using Trimmomatic (v0.36). Clean RNA reads were then mapped to the reference genome (MSU v7) with default parameters using TopHat v2.1.1. The expression level of each gene was normalized to Fragments Per Kilobase of transcript per Million mapped reads (FPKM). Differential gene expression analysis was performed using Cuffdiff. Genes with a ≥ 1.5-fold change and an FDR ≤ 0.05 were identified as differentially expressed genes.
Degradome：All of annotated phasiRNAs were aligned to rice cDNA sequences downloaded from rice genome database (MSU v7) using psRobot_tar(-ts 3.5 –fp 2 –tp 17). Genes (include TEs) that pair with phasiRNAs with mispair scores ≤ 3.5 were selected as an initial pool of phasiRNA targets.Mispaired score was calculated by psRobot as the following rules: 1) Mismatches, gaps or bulges are evaluated with a penalty of +1 2); G:U pairs are evaluated a penalty of +0.5; 3) Half penalty scores will be evaluated outside the defined essential sequence region(2-17).Cleavage products of predicted phasiRNA targets were then searched in degradome libraries using psRobot_deg. We characterized our predicted phasiRNA targets to five categories(Category 0-Category 4) base on degradome tags distribution of 10th and 11thcleavage sites as previous described38 Only predicted phasiRNA target filled with category 0 and category 1 were considered phasiRNA targets in this study for further analysis. When a gene has ≥ 4 degradome tags between the 10th and 11th nucleotides from the 5'ends of the aligned phasiRNAs and these degradome tags accounted for ≥ 10% of the total degradome tags along this gene locus, the gene was defined as a target of the aligned phasiRNA.
Genome_build: MSU v7
Supplementary_files_format_and_content: For RNA-Seq processed dataset，our provided file is the expression matrix of genes . The expression level of lncRNAs are estimated  as FPKM. For sRNA-seq /degradome processed datasets, our provided files contain genome match small RNA sequences and their counts.

organism: Oryza sativa

growth_protocol: Rice seeds of Nipponbare (japonica), Zhongxian 3037 (indica), Huanghuazhan (indica) as well as rdr6-2 and mel1-4 were sterilized with 5% NaClO containing 0.05% Tween-20 for 45 min. The seeds were then germinated and grown in either a paddy field in Changping District, Beijing, China (116.42°, 40.10°) from May to October or in a greenhouse with 40% humidity and daily cycles of 14?h of light at 32?°C and 10?h of dark at 26?°C. Tillers at a proper stage were harvested for collection of spikelets and male germ cells.

extract_protocol:
Libraries for degradome sequencing were constructed based on the PARE method  with considerable modifications that allow use of low-input RNAs. In detail, 5’ RNA adaptor was first heated at 75 °C for 3 min and then immediately chilled on ice for 2 min. For 5’ RNA adapter ligation, total RNA (3 μL) was added to a solution composed of 1 μL of T4 RNA ligase buffer, 1 μL of 10 mM ATP, 0.5 μL of RNasin, 0.5 μL of 10 μM treated RNA adaptor, 3 μL of PEG8000 (50% v/v), and 1 μL of T4 RNA ligase 1 and incubated at room temperature for 1 h. Then 1 μL of 10 mM dNTP and 0.5 μL of 10 μM reverse transcription primer Oligo(dT)VN  were added. After incubating at 75°C for 5 min and chilling on ice for 2 min, 5 μL of first strand RT buffer, 5 μL of 5 M betaine (Sigma, 61962), 1.25 μL of 0.1 M DTT, 0.9 μL of 1/6 M MgCl2, 0.5 μL of Ribonuclease inhibitor (Promega, N2511), and 1 μL of SuperScriptIII reverse transcriptase (Invitrogen, 18080-085) were added for reverse transcription. The condition for reverse transcription was 44°C for 1 h followed by 15 cycle of 50°C for 2 min and 44°C for 2 min. After reverse transcription, the products were purified with 2 × AMPure XP beads (v/v). Then the products (20 μL) were pre-amplified using GXL DNA polymerase (Takara, R050A) with 5’ biotin-labelled forward primer F1 and reverse primer R1 in a solution composed of 10 μL of 5 × GXL buffer, 4 μL of 2.5 mM dNTP, 1.5 μL of 10 μM F-primer, 1.5 μL of 10 μM R-primer, 2 μL of GXL DNA polymerase, 11 μL of ddH2O. The PCR was performed at 98°C for 2 min followed by 20 cycle of 98°C for 10 s, 60°C for 15 s, 68°C for 3 min and then 68°C for 5 min. After PCR, 1 μL of Exonuclease I (NEB, M0293L) and 5.7 μL of 10 × Exonuclease I buffer were added to the sample and the mixture was incubated at 37°C for 1 h. Then 19 μL of 4 × binding buffer (40 mM Tris-HCl, pH 8.0, 2 mM EDTA, 4 M NaCl) was added and the mixture was incubated with DynabeadsMyOne Streptavidin C1 beads (Invitrogen, 65001) at room temperature for 30 min with rotation. The beads were washed once with 1 × TWB buffer (10 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20 v/v) and 3 times with 1 × EBT buffer (10 mM Tris-HCl, pH 8.0, 0.02% Triton X-100 v/v) and then digested with MmeI (NEB, R0637L) in a solution composed of 3 μL of 10 × NEB buffer 2, 3 μL of 0.5 mM SAM, 2 μL of Mme I and 22 μL of ddH2O at 37°C for 2 h with rotation. The beads were washed once with 1 × TWB buffer and 3 times with 1 × EBT buffer. The DNA products bound to the beads were ligated to 3’ DNA adaptor in a solution composed of 3 μL of 2 × quick ligase reaction buffer, 1 μL of 10 mM adaptor, 1 μL of quick ligase (NEB, M2200L) and 25 μL of ddH2O at room temperature for 30 min with rotation. The 3’ DNA adapter was prepared by annealing of two DNA oligos in 1 × annealing buffer (10 mM Tris-HCl pH 7.5, 0.1 mM EDTA, 50 mM NaCl). The beads were washed once with 1 × TWB buffer and 3 times with 1 × EBT buffer and resuspended in 30 μL of 0.05% Triton X-100. The samples were incubated at 80°C for 30 min with rotation to elute the DNA products. Then the DNA products were subjected to final PCR amplification using GXL DNA polymerase and primers F2 and R2. PCR was performed at 98°C for 2 min followed by 22 cycle of 98°C for 10 s, 60°C for 15 s, 68°C for 20 s and then 68°Cfor 5 min. The final products were resolved on a PAGE gel and ~140-bp bands were excised and purified for sequencing on an Illumina HiSeqX-Ten platform.
Total RNA was extracted using TRIzol (Takara, 9109). MgCl2 (final concentration: 0.2 M) was added to prevent loss of sRNAs with low GC content. The extracted RNA was stored at -80°Cin LoBind tubes (Eppendorf, 022431021).

tag: genotype

value: mel1-4 (HHZ background)

tag: Stage

value: meiocyte (prophase I)

tag: molecule subtype

value: poly (A)+ RNAs


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A6_ad008

tag: brain region

tag: Sex

tag: age


title: H3K4me3 from UC Davis FAANG chicken spleen rep B

first: Colin

last: Kern

address: 9500 Gilman Dr

institute: UC San Diego

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with BWA mem 0.7.17 to the galGal6, Sscrofa11.2, and ARS-UCD1.2 genomes
Alignments were filtered with Samtools 1.10 using arguments -F 1804 -q 30
Duplicates were removed with Picard toolkit 2.18.17
Genome_build: galGal6,susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: bed file, peak calls using Macs 2.1.1 -q 0.01

organism: Gallus gallus

source_name: Spleen

extract_protocol:
ChIP-seq experiments were performed on frozen tissue using the iDeal ChIP-seq kit for Histones (Diagenode Cat.#C01010059, Denville, NJ) according to the manufacturer’s protocol except for the following changes. 20-30 mg of frozen tissue was powdered using liquid nitrogen in pre-chilled mortar. Cross-linking was performed with 1% formaldehyde which was diluted from 16% methanol-free formaldehyde (Thermo Scientific, Cat.#28906, Waltham, MA) for 8 minutes and quenched with glycine for 10 minutes. Nuclei were harvested by centrifugation at 2000g for 5 minutes and resuspended in iS1 buffer for incubation on ice for 30 minutes. Chromatin was sheared using the Covaris E220 between 6-12 minutes depending on the tissue. For immunoprecipitation experiments, about 1000 ng of sheared chromatin (estimated from DNA extraction) was used as input after which the kit protocol was followed with 1 μg (histone modifications) or 1.5 μg (CTCF) of antibody. The following antibodies used were from Diagenode: H3K4me3 (in kit), H3K27me3 (#C15410069), H3K27ac (#C15410174), H3K4me1 (#C15410037), and CTCF (#15410210). An input (no antibody) was performed for each sample.
NEBNext Ultra DNA library prep kit for Illumina libraries (New England Biolabs #E7645L, Ipswich, MA) was used for library construction, selecting for 150-200 bp (H3K4me3, H3K27ac, CTCF) or 200-400 bp (H3K27me3, H3K4me1) insert fragment sizes using Ampure beads (Beckman Coulter #A63881). Libraries were sequenced on Illumina’s HiSeq 4000 with single-end 50 bp reads.

tag: chip antibody

value: spleen


title: H3K4me3 from UC Davis FAANG chicken spleen rep A


title: Control-1

source_name: Aerial tissue of transgenic Arabidopsis


title: FN020.3: Genomic DNA from sperm of nut-fed individual FN020 (final)

description: Purified sperm sample

source_name: Semen sample 14

tag: gender

tag: sample type

tag: baseline or final intervention


title: mel1_prophase_I_degradome_rep1


title: FN027.0: Genomic DNA from sperm of nut-fed individual FN027 (baseline)

description: Purified sperm sample

source_name: Semen sample 15


title: mel1_prophase_I_degradome_rep3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A6_ad004

tag: strain


title: H3K4me3 from UC Davis FAANG chicken skeletal muscle rep B

source_name: Muscle

tag: tissue

value: skeletal muscle


title: FN018.0: Genomic DNA from sperm of nut-fed individual FN018 (baseline)

description: Purified sperm sample

source_name: Semen sample 11


title: HHZ_prophase_I_degradome_rep3

value: Huanghuazhan


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A6_ad002


title: FN016.3: Genomic DNA from sperm of nut-fed individual FN016 (final)

description: Purified sperm sample

source_name: Semen sample 10


title: MDM-6H-M1

source_name: MDMs stimulated with M. intracellulare

value: beagle


title: MDM-0H-M3

value: whole blood


title: H3K4me3 from UC Davis FAANG chicken skeletal muscle rep A


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A5_ad006


title: FN020.0: Genomic DNA from sperm of nut-fed individual FN020 (baseline)

description: Purified sperm sample

source_name: Semen sample 13


title: FN095.3: Genomic DNA from sperm of nut-fed individual FN095 (final)

description: Purified sperm sample

source_name: Semen sample 42


title: MDM-0H-M2

value: monocyte-derived macrophages


title: HHZ_prophase_I_degradome_rep2


title: FN037.3: Genomic DNA from sperm of nut-fed individual FN037 (final)

description: Purified sperm sample

source_name: Semen sample 20

value: Male


title: HHZ_prophase_I_degradome_rep1


title: H3K4me3 from UC Davis FAANG chicken lung rep B

source_name: Lung

value: lung


title: FN079.0: Genomic DNA from sperm of nut-fed individual FN079 (baseline)

description: Purified sperm sample

source_name: Semen sample 37

value: Sperm


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A5_ad012

source_name: C57BL/6J Male P56 Mouse Brain

value: LSX

value: male


title: H3K4me3 from UC Davis FAANG chicken lung rep A


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A5_ad010


title: 3037_prophase_I_degradome_rep3


title: FN047.3: Genomic DNA from sperm of nut-fed individual FN047 (final)

description: Purified sperm sample

source_name: Semen sample 28

value: Final


title: MDM-0H-C1

source_name: Control MDMs


title: H3K4me3 from UC Davis FAANG chicken liver rep B

source_name: Liver

value: liver


title: MDM-6H-C1


title: 3037_prophase_I_degradome_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A5_ad008


title: H3K4me3 from UC Davis FAANG chicken liver rep A


title: 3037_prophase_I_degradome_rep1


title: RP4_WT_S3 scRNA-seq

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

data_processing:
Library strategy: scRNA-seq
Cell Ranger Version3.0.2
Seurat V3.2
Genome_build: mm10
Supplementary_files_format_and_content: Robject with identified cell clusters

extract_protocol:
10X GEM generation
Single Cell 3' v3

tag: disease state

value: WT

value: mouse embryo cranial region


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A5_ad007


title: RP9_KO_S2 scRNA-seq

source_name: E9.5 KO

value: NTD


title: H3K4me3 from UC Davis FAANG chicken hypothalamus rep B

source_name: Hypothalamus

value: hypothalamus


title: rdr6_prophase_I_degradome_rep3

value: osrdr6-2 (3037 background)

value: meiocyte (prophase I)

value: poly (A)+ RNAs


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A5_ad004


title: RP8_WT_S1 scRNA-seq

source_name: E9.5 WT


title: H3K4me3 from UC Davis FAANG chicken hypothalamus rep A


title: FN018.3: Genomic DNA from sperm of nut-fed individual FN018 (final)

description: Purified sperm sample

source_name: Semen sample 12


title: H3K4me3 from UC Davis FAANG chicken cerebral cortex rep B

source_name: Cortex

value: cerebral cortex


title: FN011.3: Genomic DNA from sperm of nut-fed individual FN011 (final)

description: Purified sperm sample

source_name: Semen sample 6


title: rdr6_prophase_I_degradome_rep1


title: FN039.3: Genomic DNA from sperm of nut-fed individual FN039 (final)

description: Purified sperm sample

source_name: Semen sample 22


title: MDM-0H-C2

value: beagle

value: whole blood


title: H3K4me3 from UC Davis FAANG chicken cerebral cortex rep A


title: rdr6_prophase_I_degradome_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A4_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A4_ad004


title: H3K4me3 from UC Davis FAANG chicken cerebellum rep B

source_name: Cerebellum

value: cerebellum


title: H3K4me3 from UC Davis FAANG chicken cerebellum rep A


title: tetrad_degradome_rep2

value: Nipponbare

value: meiocyte (tetrad)


title: FN016.0: Genomic DNA from sperm of nut-fed individual FN016 (baseline)

description: Purified sperm sample

source_name: Semen sample 9

value: Male

value: Sperm

value: Baseline


title: microspore_degradome_rep3

value: microspore


title: tetrad_degradome_rep3


title: H3K4me3 from UC Davis FAANG chicken adipose rep A

source_name: Adipose

value: adipose


title: H3K4me3 from UC Davis FAANG chicken adipose rep B


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A4_ad002

value: LSX

value: male


title: tetrad_degradome_rep1


title: FN008.0: Genomic DNA from sperm of nut-fed individual FN008 (baseline)

description: Purified sperm sample

source_name: Semen sample 3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A4_ad010


title: microspore_degradome_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A5_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A3_ad006


title: FN013.0: Genomic DNA from sperm of nut-fed individual FN013 (baseline)

description: Purified sperm sample

source_name: Semen sample 7


title: FN013.3: Genomic DNA from sperm of nut-fed individual FN013 (final)

description: Purified sperm sample

source_name: Semen sample 8

value: Final


title: microspore_degradome_rep1


title: H3K4me1 from UC Davis FAANG chicken spleen rep A

source_name: Spleen

value: spleen


title: prophase_I_degradome_rep3_run2

extract_protocol:
Libraries for mRNA-seq were constructed using the Smart2-seq method40. Briefly, total RNA was used for reverse transcription and cDNA second strand synthesis using SuperScript II reverse transcriptase (Invitrogen,18064-14) and template-switching oligos. After PCR preamplification and purification with AMPure XP beads (Beckman, A63880), the products were subjected to fragmentation and adaptor ligation using TruePrepTM DNA Library Prep Kit (Vazyme, TD503). PCR amplification was then performed with index-containing primers and 300–800-bp products were purified with AMPure XP beads. Libraries were pair-end sequenced on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).
Total RNA was extracted using TRIzol (Takara, 9109). MgCl2 (final concentration: 0.2 M) was added to prevent loss of sRNAs with low GC content. The extracted RNA was stored at -80°Cin LoBind tubes (Eppendorf, 022431021).

value: meiocyte (prophase I)


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A3_ad012

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A3_ad010


title: H3K4me1 from UC Davis FAANG chicken skeletal muscle rep B

source_name: Muscle

value: skeletal muscle


title: FN011.0: Genomic DNA from sperm of nut-fed individual FN011 (baseline)

description: Purified sperm sample

source_name: Semen sample 5


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A3_ad007


title: prophase_I_degradome_rep3_run1

value: poly (A)+ RNAs


title: H3K4me1 from UC Davis FAANG chicken skeletal muscle rep A


title: prophase_I_degradome_rep2_run1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A2_ad006


title: H3K4me1 from UC Davis FAANG chicken lung rep A

source_name: Lung

value: lung


title: FN073.3: Genomic DNA from sperm of nut-fed individual FN073 (final)

description: Purified sperm sample

source_name: Semen sample 32


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A3_ad002


title: prophase_I_degradome_rep2_run2


title: prophase_I_degradome_rep1


title: H3K4me1 from UC Davis FAANG chicken liver rep B

source_name: Liver

value: liver


title: rdr6_prophase_I_RNA_rep3

description: processed data file: genes.fpkm_table.xlsx.gz


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A2_ad012


title: FN008.3: Genomic DNA from sperm of nut-fed individual FN008 (final)

description: Purified sperm sample

source_name: Semen sample 4


title: H3K4me1 from UC Davis FAANG chicken liver rep A


title: rdr6_prophase_I_RNA_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A2_ad010


title: H3K4me1 from UC Davis FAANG chicken hypothalamus rep B

source_name: Hypothalamus

value: hypothalamus


title: mel1_prophase_I_RNA_rep3

value: mel1-4 (HHZ background)


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A2_ad004


title: rdr6_prophase_I_RNA_rep1


title: H3K4me1 from UC Davis FAANG chicken hypothalamus rep A


title: FN002.3: Genomic DNA from sperm of nut-fed individual FN002 (final)

description: Purified sperm sample

source_name: Semen sample 2


title: H3K4me1 from UC Davis FAANG chicken cerebral cortex rep A

source_name: Cortex

value: cerebral cortex


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A12_ad004


title: mel1_prophase_I_RNA_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A12_ad002


title: FN002.0: Genomic DNA from sperm of nut-fed individual FN002 (baseline)

description: Purified sperm sample

source_name: Semen sample 1

value: Male


title: HHZ_prophase_I_RNA_rep3

value: Huanghuazhan


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A12_ad012


title: mel1_prophase_I_RNA_rep1


title: H3K4me1 from UC Davis FAANG chicken cerebellum rep A

source_name: Cerebellum

value: cerebellum


title: H3K4me1 from UC Davis FAANG chicken cerebellum rep B


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A12_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A12_ad010


title: H3K4me1 from UC Davis FAANG chicken cerebral cortex rep B


title: HHZ_prophase_I_RNA_rep1


title: H3K4me1 from UC Davis FAANG chicken adipose rep A

source_name: Adipose


title: H3K4me1 from UC Davis FAANG chicken adipose rep B


title: H3K27me3 from UC Davis FAANG chicken spleen rep B

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with BWA mem 0.7.17 to the galGal6, Sscrofa11.2, and ARS-UCD1.2 genomes
Alignments were filtered with Samtools 1.10 using arguments -F 1804 -q 30
Duplicates were removed with Picard toolkit 2.18.17
Genome_build: galGal6,susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: bed file, peak calls using Macs 2.1.1 -q 0.05 --broad


title: 3037_prophase_I_RNA_rep3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A2_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A11_ad012


title: 3037_prophase_I_RNA_rep1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A11_ad007


title: H3K27me3 from UC Davis FAANG chicken spleen rep A


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A11_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A11_ad008


title: CD2-Lmo2 TG T-ALL Rep 4 RRBS

data_processing:
Reads were trimmed using TrimGalore (v0.4.5) with –rrbs and –non-directional and aligned with Bismark (v0.20.0) on GRCm38.
RRBS data was analyzed using RnBeads.mm10 in R (versions >3.4). β values were obtained after filtering and normalization using the default preprocessing pipeline.
Genome_build: GRCm38

extract_protocol:
DNA was isolated from full thymus using the QiaAMP DNA Mini kit (Qiagen).
RRBS was done using MSPI digest.

value: Spleen

tag: time point

value: T-ALL


title: 3037_prophase_I_RNA_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A11_ad010

value: LSX


title: CD2-Lmo2 TG T-ALL Rep 3 RRBS


title: mel1_prophase_I_sRNA_rep3

extract_protocol:
Libraries for sRNA-seq were constructed as previously described (Yang et al, 2016) with minor modifications. Briefly, 3'adaptor, DNA oligonucleotide with 5'adenylation, was obtained using 5′ DNA Adenylation Kit (NEB, E2601L). Total RNA was ligated to 3 adaptor using T4 RNA ligase 2, truncated KQ (NEB, M0373L). Following annealing with reverse transcription primer, RNA was ligated to 5'RNA adaptor using T4 RNA ligase 1 (NEB, M0204L). After reverse transcription and PCR amplification, 135–160-bp products were gel-purified. Libraries were pair-end sequenced on an Illumina HiSeqX-Ten platform.
Total RNA was extracted using TRIzol (Takara, 9109). MgCl2 (final concentration: 0.2 M) was added to prevent loss of sRNAs with low GC content. The extracted RNA was stored at -80°Cin LoBind tubes (Eppendorf, 022431021).

value: 15–30-nt sRNAs


title: H3K27me3 from UC Davis FAANG chicken skeletal muscle rep A


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A10_ad008

value: male


title: H3K4me1 from UC Davis FAANG chicken spleen rep B

value: spleen


title: HHZ_prophase_I_RNA_rep2

value: meiocyte (prophase I)


title: CD2-Lmo2 TG T-ALL Rep 2 RRBS


title: H3K27me3 from UC Davis FAANG chicken lung rep B


title: mel1_prophase_I_sRNA_rep1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A10_ad004


title: CD2-Lmo2 TG T-ALL Rep 1 RRBS


title: CD2-Lmo2 TG 24w Rep 4 RRBS

source_name: Thymus

value: Thymus

value: 24 weeks


title: HHZ_prophase_I_sRNA_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A10_ad002


title: H3K27me3 from UC Davis FAANG chicken liver rep B


title: H3K27me3 from UC Davis FAANG chicken lung rep A

value: lung


title: HHZ_prophase_I_sRNA_rep3


title: H3K27me3 from UC Davis FAANG chicken liver rep A

value: liver


title: H3K27me3 from UC Davis FAANG chicken skeletal muscle rep B

value: skeletal muscle


title: HHZ_prophase_I_sRNA_rep1


title: H3K27me3 from UC Davis FAANG chicken hypothalamus rep B

value: hypothalamus


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A10_ad010


title: rdr6_prophase_I_sRNA_rep3

value: osrdr6-2 (3037 background)


title: CD2-Lmo2 TG 24w Rep 2 RRBS


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A4_ad008


title: mel1_prophase_I_sRNA_rep2

value: mel1-4 (HHZ background)


title: CD2-Lmo2 TG 24w Rep 1 RRBS


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A10_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A10_ad006


title: CD2-Lmo2 TG 16w Rep 4 RRBS

value: 16 weeks


title: rdr6_prophase_I_sRNA_rep2


title: CD2-Lmo2 TG 16w Rep 3 RRBS


title: H3K27me3 from UC Davis FAANG chicken cerebral cortex rep B

value: cerebral cortex


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A1_ad007


title: H3K27me3 from UC Davis FAANG chicken cerebral cortex rep A


title: CD2-Lmo2 TG 24w Rep 3 RRBS


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A10_ad012


title: 3037_prophase_I_sRNA_rep3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A1_ad008


title: CD2-Lmo2 TG 16w Rep 2 RRBS


title: 3037_prophase_I_sRNA_rep2


title: H3K27me3 from UC Davis FAANG chicken hypothalamus rep A


title: CD2-Lmo2 TG 16w Rep 1 RRBS


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A1_ad012


title: 3037_prophase_I_sRNA_rep1


title: H3K27me3 from UC Davis FAANG chicken cerebellum rep A

value: cerebellum


title: rdr6_prophase_I_sRNA_rep1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A1_ad010


title: CD2-Lmo2 TG 8w Rep 4 RRBS

value: 8 weeks


title: CD2-Lmo2 TG 8w Rep 3 RRBS


title: tetrad_sRNA_rep2

value: Nipponbare

value: meiocyte (tetrad)


title: H3K27me3 from UC Davis FAANG chicken adipose rep A

value: adipose


title: H3K27ac from UC Davis FAANG chicken spleen rep B

value: spleen


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A1_ad002

value: LSX

value: male


title: CD2-Lmo2 TG 8w Rep 2 RRBS

value: Thymus


title: CD2-Lmo2 TG 8w Rep 1 RRBS


title: tetrad_sRNA_rep1

value: 15–30-nt sRNAs


title: ATAC-seq from UC Davis FAANG cattle spleen rep M22

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the -atac argument
Reads were aligned with BWA mem 0.7.17 to the Sscrofa11.2 and ARS-UCD1.2 genomes
Alignments were filtered with Samtools 1.10 using arguments -F 1804 -q 30
Duplicates were removed with Picard toolkit 2.18.17
Genome_build: susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: bed file, peak calls using Macs 2.1.1 -q 0.05 --broad

organism: Bos taurus

extract_protocol:
Cryopreserved nuclei prepared from fresh tissue were slowly thawed on ice, centrifuged for 5 minutes at 500 rcf, and resuspended in cold PBS. Nuclei were then washed once with cold ATAC-seq cell lysis buffer and resuspended with cold PBS for counting on a hemocytometer. Approximately 200K cryopreserved nuclei were centrifuged, supernatant aspirated, then treated with 50μl transposition mix (25μl TD buffer,2.5 μl TDE1, 22.5 μl ddH2O) for 1 hour at 37°C and 300 rpm. DNA was purified using the MinElute PCR purification kit (Qiagen, #28004, Germantown, MD) and diluted with 10μl EB buffer. DNA was amplified with primers whose detailed descriptions are found in Buenrostro et al. (2013).
Libraries were purified using the MinElute PCR purification kit and run on Agilent Bioanalyzer (Agilent, Santa Clara, CA) for quality traces. Size-selection on libraries for 150-250bp fragments was performed on PippinHT system (Sage Science, Beverly, MA). Libraries were sequenced on Illumina’s NextSeq with PE 40bp reads.


title: H3K27me3 from UC Davis FAANG chicken cerebellum rep B


title: CD2-Lmo2 WT 24w Rep 4 RRBS

value: 24 weeks

value: WT


title: H3K27ac from UC Davis FAANG chicken skeletal muscle rep B

value: skeletal muscle


title: ATAC-seq from UC Davis FAANG cattle spleen rep M08


title: H3K27me3 from UC Davis FAANG chicken adipose rep B


title: ATAC-seq from UC Davis FAANG cattle skeletal muscle rep M22


title: CD2-Lmo2 WT 24w Rep 3 RRBS


title: premeiosis_spikelet_sRNA_rep2

value: premeiotic spikelet


title: H3K27ac from UC Davis FAANG chicken skeletal muscle rep A


title: tetrad_sRNA_rep3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_A1_ad004


title: ATAC-seq from UC Davis FAANG cattle skeletal muscle rep M08


title: premeiosis_spikelet_sRNA_rep1


title: H3K27ac from UC Davis FAANG chicken lung rep B

value: lung


title: CD2-Lmo2 WT 24w Rep 1 RRBS


title: H3K27ac from UC Davis FAANG chicken lung rep A


title: ATAC-seq from UC Davis FAANG cattle lung rep M08


title: premeiosis_spikelet_sRNA_rep3


title: H3K27ac from UC Davis FAANG chicken liver rep A

value: liver


title: microspore_sRNA_rep3

value: microspore


title: microspore_sRNA_rep2


title: ATAC-seq from UC Davis FAANG cattle liver rep M22


title: ATAC-seq from UC Davis FAANG cattle liver rep M08


title: CD2-Lmo2 WT 16w Rep 3 RRBS

value: 16 weeks


title: meiosis_spikelet_sRNA_rep3

value: meiotic spikelet


title: H3K27ac from UC Davis FAANG chicken liver rep B


title: ATAC-seq from UC Davis FAANG cattle lung rep M22


title: microspore_sRNA_rep1

value: Nipponbare


title: CD2-Lmo2 WT 16w Rep 2 RRBS


title: H3K27ac from UC Davis FAANG chicken hypothalamus rep B

value: hypothalamus


title: CD2-Lmo2 WT 24w Rep 2 RRBS


title: CD2-Lmo2 WT 16w Rep 1 RRBS


title: H3K27ac from UC Davis FAANG chicken hypothalamus rep A


title: meiosis_spikelet_sRNA_rep2


title: ATAC-seq from UC Davis FAANG cattle hypothalamus rep M08


title: CD2-Lmo2 WT 8w Rep 4 RRBS

value: 8 weeks


title: ATAC-seq from UC Davis FAANG cattle hypothalamus rep M22


title: meiosis_spikelet_sRNA_rep1


title: ATAC-seq from UC Davis FAANG cattle cerebral cortex rep M22

value: cerebral cortex


title: H3K27ac from UC Davis FAANG chicken cerebral cortex rep B


title: ATAC-seq from UC Davis FAANG cattle cerebral cortex rep M08


title: ATAC-seq from UC Davis FAANG cattle cerebellum rep M22

value: cerebellum


title: CD2-Lmo2 WT 8w Rep 2 RRBS


title: H3K27ac from UC Davis FAANG chicken spleen rep A

value: spleen


title: prophase_I_sRNA_rep2

value: meiocyte (prophase I)


title: H3K27ac from UC Davis FAANG chicken cerebral cortex rep A


title: CD2-Lmo2 WT 16w Rep 4 RRBS

value: Thymus


title: CD2-Lmo2 WT 8w Rep 1 RRBS


title: prophase_I_sRNA_rep1

value: 15–30-nt sRNAs


title: embryo_sRNA_rep3

value: embryo


title: H3K4me1 from UC Davis FAANG chicken lung rep B


title: Pten KO T-ALL Rep 3 RRBS

value: T-ALL

value: Lck-Cretg/+ Ptenfl/fl


title: ATAC-seq from UC Davis FAANG cattle adipose rep M08

value: adipose


title: embryo_sRNA_rep2


title: prophase_I_sRNA_rep3


title: CD2-Lmo2 WT 8w Rep 3 RRBS

value: WT


title: H3K27ac from UC Davis FAANG chicken adipose rep A


title: embryo_sRNA_rep1


title: CTCF from UC Davis FAANG chicken spleen rep B


title: RNA-seq from UC Davis FAANG cattle spleen rep M22

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with STAR 2.5.4a to the galGal6, Sscrofa11.2, and ARS-UCD1.2 genomes with the arguments --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20
Alignments were filtered with Samtools 1.10 using argument -q 30
Gene counts were obtained with htseq-count 0.11.1 using the Ensembl 99 annotations with arguments -r pos --stranded=reverse
Genome_build: galGal6,susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: 2-column tsv, Ensembl gene ID and raw read count

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. DNase I (Ambion, Austin, TX) digestion was carried out after RNA isolation and the RNA concentration and purity were determined by measuring absorbance at 260 nm and A260/A280 ratio using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA samples were stored at − 80 °C until further use. Total RNA (1 μg) was subjected to two rounds of hybridization to oligo (dT) beads (Invitrogen, Carlsbad, CA) to enrich poly-adenylated transcripts.
Stranded RNA-seq libraries were prepared using the TruSeq RNA Illumina protocol, and libraries were sequenced on an Illumina HiSeq-3000 using 100 bp PE


title: H3K27ac from UC Davis FAANG chicken cerebellum rep B


title: RNA-seq from UC Davis FAANG cattle spleen rep M08


title: Pten KO T-ALL Rep 2 RRBS


title: RNA-seq from UC Davis FAANG pig spleen rep P350

organism: Sus scrofa


title: Pten KO T-ALL Rep 1 RRBS


title: CTCF from UC Davis FAANG chicken spleen rep A


title: Pten KO T-ALL Rep 4 RRBS


title: H3K27ac from UC Davis FAANG chicken adipose rep B


title: H3K27ac from UC Davis FAANG chicken cerebellum rep A


title: ATAC-seq from UC Davis FAANG cattle adipose rep M22


title: RNA-seq from UC Davis FAANG cattle skeletal muscle rep M22

value: skeletal muscle


title: RNA-seq from UC Davis FAANG pig spleen rep P348


title: Pten KO 8w Rep 4 RRBS


title: RNA-seq from UC Davis FAANG cattle skeletal muscle rep M08


title: Pten KO 8w Rep 3 RRBS


title: RNA-seq from UC Davis FAANG pig skeletal muscle rep P350


title: CTCF from UC Davis FAANG chicken skeletal muscle rep A


title: CTCF from UC Davis FAANG chicken skeletal muscle rep B


title: RNA-seq from UC Davis FAANG pig skeletal muscle rep P348


title: RNA-seq from UC Davis FAANG cattle lung rep M22

value: lung


title: Pten KO 8w Rep 2 RRBS


title: CTCF from UC Davis FAANG chicken lung rep B


title: RNA-seq from UC Davis FAANG pig lung rep P350


title: Pten KO 8w Rep 1 RRBS


title: RNA-seq from UC Davis FAANG cattle lung rep M08


title: CTCF from UC Davis FAANG chicken lung rep A


title: Pten WT 8w Rep 4 RRBS


title: RNA-seq from UC Davis FAANG cattle liver rep M22

value: liver


title: RNA-seq from UC Davis FAANG pig liver rep P350


title: CTCF from UC Davis FAANG chicken liver rep B


title: RNA-seq from UC Davis FAANG cattle liver rep M08


title: CTCF from UC Davis FAANG chicken liver rep A


title: RNA-seq from UC Davis FAANG pig liver rep P348


title: RNA-seq from UC Davis FAANG cattle hypothalamus rep M22


title: Pten WT 8w Rep 2 RRBS


title: Pten WT 8w Rep 3 RRBS


title: RNA-seq from UC Davis FAANG pig hypothalamus rep P350


title: RNA-seq from UC Davis FAANG cattle hypothalamus rep M08


title: CTCF from UC Davis FAANG chicken hypothalamus rep B


title: RNA-seq from UC Davis FAANG cattle cerebral cortex rep M08


title: CTCF from UC Davis FAANG chicken cerebral cortex rep B


title: CTCF from UC Davis FAANG chicken hypothalamus rep A


title: RNA-seq from UC Davis FAANG pig cerebral cortex rep P350


title: CTCF from UC Davis FAANG chicken cerebral cortex rep A


title: RNA-seq from UC Davis FAANG pig hypothalamus rep P348


title: Pten WT 8w Rep 1 RRBS


title: RNA-seq from UC Davis FAANG pig cerebral cortex rep P348


title: RNA-seq from UC Davis FAANG cattle cerebellum rep M22


title: RNA-seq from UC Davis FAANG cattle cerebral cortex rep M22


title: CTCF from UC Davis FAANG chicken cerebellum rep B


title: RNA-seq from UC Davis FAANG pig cerebellum rep P350


title: RNA-seq from UC Davis FAANG pig lung rep P348


title: RNA-seq from UC Davis FAANG cattle cerebellum rep M08


title: RNA-seq from UC Davis FAANG cattle adipose rep M22


title: RNA-seq from UC Davis FAANG pig cerebellum rep P348


title: CTCF from UC Davis FAANG chicken adipose rep B


title: RNA-seq from UC Davis FAANG pig adipose rep P350


title: CTCF from UC Davis FAANG chicken adipose rep A


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G9_ad004

status: Public on Sep 23 2020

value: SSp

value: male


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G8_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G9_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G8_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G8_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G7_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G8_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G7_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G8_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G7_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G7_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G8_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G7_ad006


title: CTCF from UC Davis FAANG chicken cerebellum rep A


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G7_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G7_ad002


title: RNA-seq from UC Davis FAANG pig adipose rep P348


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G7_ad008


title: RNA-seq from UC Davis FAANG cattle adipose rep M08


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G6_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G6_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G6_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G6_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G6_ad007


title: control2

type: RNA

city: Hangzhou

first: Harrison

last: Bai

state: Zhejiang

address: Tianmu Road 148#

institute: Zhejiang University

hyb_protocol: Standard the Agilent protocol.

scan_protocol: the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring (version13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data.
the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

growth_protocol: colitis-associated colon cancer model is established using AOM-DSS in C57 mice

extract_protocol: total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

treatment_protocol: CAC mice are treated with PBS (Control) and Rgnanomedicine (Test) via oral administration.

value: Colitis-associated colon cancer

value: colon tumor

tag: treatment

value: PBS (Control)


title: test3

value: Rgnanomedicine (Test)


title: control1


title: test1


title: control3


title: test2


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G6_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G6_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G6_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G5_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G5_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G5_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G5_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G5_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G3_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G4_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G4_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G4_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G5_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G5_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G3_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G4_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G4_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G3_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G3_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G4_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G3_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G3_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G3_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G5_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G2_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G2_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G2_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G2_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G2_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G2_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G2_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G12_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G12_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G12_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G12_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G12_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G12_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G12_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G11_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G11_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G1_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G11_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G10_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G10_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G10_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G1_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F9_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G10_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F9_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F9_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G1_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F8_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G12_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F8_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G11_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G11_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F8_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G1_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F9_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G1_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G2_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F8_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F9_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G1_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F9_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G1_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F8_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F8_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F7_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F7_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F7_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F7_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F8_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F7_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F6_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F7_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F6_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F6_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F6_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F5_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F6_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F4_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F5_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F5_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F5_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F4_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F4_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F6_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F4_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F5_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F6_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F5_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F5_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F4_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F4_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F7_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F4_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F6_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F4_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F3_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F3_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F3_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F3_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F2_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F2_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F3_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F2_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F3_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F2_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F2_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F12_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F2_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F12_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F12_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F12_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F11_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F12_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F12_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F11_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F11_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F11_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F11_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F11_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F10_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F10_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F10_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F10_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F3_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F11_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F10_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F2_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F12_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F10_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F1_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F10_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F10_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F1_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F1_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F1_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F1_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F1_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E9_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E9_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E9_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E9_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E9_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E9_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E7_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E8_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E8_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E9_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E7_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E8_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E8_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E7_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E7_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E7_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E7_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F1_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E7_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E8_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E6_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E6_ad010


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E6_ad008


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E5_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E5_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E5_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E4_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E4_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E5_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E3_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_F1_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E3_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E3_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E3_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E3_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E3_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E2_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E2_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E2_ad002


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E6_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E6_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E5_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E5_ad002


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E2_ad006


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E12_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E12_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E4_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E12_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E12_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E12_ad006


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E11_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E11_ad001


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E10_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E11_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E10_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E10_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E10_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_E10_ad006


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E1_ad010


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_E1_ad006


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title: CEMBA181023_6B_3_CEMBA181023_6B_4_D3_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D3_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D5_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D3_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D5_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D2_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D2_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D2_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D2_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D12_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D2_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D12_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D2_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D4_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D12_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D4_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D12_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D12_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D12_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D11_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D11_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D11_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D11_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D11_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D11_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D11_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D10_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D10_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D10_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D10_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D11_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D10_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D10_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D10_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D1_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D10_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D1_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D1_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D1_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D1_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C9_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C9_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D12_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C9_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D1_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D1_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D1_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_D12_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C9_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C9_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C9_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C8_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C8_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C8_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C8_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C8_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C8_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C8_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C7_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C8_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C6_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C7_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C7_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C7_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C7_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C6_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C6_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C6_ad008


title: SisEndoMS catalytic and DNA binding mutant Rep-3

city: Jimo, Qingdao

first: Qihong

last: Huang

state: Shandong

address: 72 Binhai Road

department: Microbial Technology Institute

institute: Shandong University

data_processing: The alignment of clean reads to the reference genome of S. islandicus REY15A was done by aligning clean reads to the reference using Bowtie (ver. 2.2.3) software. The read numbers mapped to each gene was counted by HTSeq (ver. 0.6.1) and the subsequent data were assessed by Fragments Per Kilobase of transcript sequence per Million base pairs sequenced (FPKM) analysis for the quantification of gene expression levels in S. islandicus genome. Differential genome expression analysis was performed by DESeq R package (ver. 1.18.0). The adjusted P-value (0.005) and log2 (fold change) of 1 were set as threshold for significantly differential expression.

organism: Saccharolobus islandicus REY15A

source_name: EndoMS mutant overexpression strain

growth_protocol: The overexpressed strains of wild type SisEndoMS and catalytic and DNA binding deficient mutant SisEndoMS were cultured at 75 oC in MCV (basic salts, 0.2% Casamino acids, 1% Vitamin solution)

extract_protocol:
Total RNAs was extracted by Trizol (Austin, USA). The RNA sequencing of the samples was carried out by Novogene (Beijing, China). Around 3 μg of RNA per sample was used for generation of sequencing libraries by NEBNext Ultra Directional RNA library Prep Kit for Illumina (New England Biolabs (NEB), MA, US) and the quality of the library was analyzed on Agilent Bioanalyzer 2100 system. Sample clustering was made on a cBot cluster generation system by TruSeq PE cluster Kit (v3, cBot-HS, Illumina), and library preparations were sequenced on Illumina Hiseq platform followed by generation of pair-end reads. The alignment of clean reads to the reference genome of S. islandicus REY15A  was done by aligning clean reads to the reference using Bowtie (ver. 2.2.3) software. The read numbers mapped to each gene was counted by HTSeq (ver. 0.6.1) and the subsequent data were assessed by Fragments Per Kilobase of transcript sequence per Million base pairs sequenced (FPKM) analysis for the quantification of gene expression levels in S. islandicus genome
Around 3 μg of RNA per sample was used for generation of sequencing libraries by NEBNext Ultra Directional RNA library Prep Kit for Illumina (New England Biolabs (NEB), MA, US) and the quality of the library was analyzed on Agilent Bioanalyzer 2100 system. Sample clustering was made on a cBot cluster generation system by TruSeq PE cluster Kit (v3, cBot-HS, Illumina), and library preparations were sequenced on Illumina Hiseq platform followed by generation of pair-end reads.

treatment_protocol: For arabinose treatment, each strain was grown at early exponentail phase (A600=ca. 0.20) at which 0.2% arabinose was supplemented to MCV media. The incubation was then continued at 75 oC. Cell samples for RNA extraction were taken after 2 hours of arabinose induction.

value: Arabinose induction

value: EndoMS mutant overexpression strain


title: SisEndoMS (WT) Overexpression strain Rep-3

source_name: EndoMS overexpression strain

value: EndoMS overexpression strain


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C6_ad004


title: SisEndoMS catalytic and DNA binding mutant Rep-2


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C6_ad002


title: SisEndoMS (WT) Overexpression strain Rep-2


title: SisEndoMS catalytic and DNA binding mutant Rep-1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C5_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C5_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C5_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C5_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C5_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C7_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C6_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C7_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C5_ad004


title: SisEndoMS (WT) Overexpression strain Rep-1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C7_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C5_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C5_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C3_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C4_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C4_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C4_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C3_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C4_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C3_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C4_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C2_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C3_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C3_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C2_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C2_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C2_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C3_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C12_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C2_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C2_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C3_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C12_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C2_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C12_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C12_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C12_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C12_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C11_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C11_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C4_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C11_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C11_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C11_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C10_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C11_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C10_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C10_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C11_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B9_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B9_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C10_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B9_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C10_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C1_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B9_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B9_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C10_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C10_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C10_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B9_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C12_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B9_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B8_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B8_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B8_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B8_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B8_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B8_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_C11_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B7_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B8_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B9_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B7_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B7_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B7_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B7_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B6_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B6_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B6_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B6_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B6_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B5_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B5_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B6_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B5_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B5_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B5_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B4_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B7_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B5_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B4_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B4_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B3_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B4_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B4_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B4_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B3_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B7_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B3_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B3_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B6_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B5_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B3_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B2_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B3_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B2_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B12_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B12_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B12_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B2_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B2_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B2_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B12_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B2_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B12_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B11_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B11_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B12_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B12_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B11_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B11_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B10_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B11_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B11_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B10_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B11_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B10_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B2_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B10_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B10_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B10_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B1_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B1_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B1_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B1_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B10_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A9_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A9_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A9_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B1_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A9_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_B1_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A9_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A9_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A8_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A8_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A7_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A8_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A8_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A7_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A8_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A8_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A6_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A7_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A7_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A6_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A6_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A9_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A7_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A9_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A6_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A6_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A6_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A8_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A5_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A7_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A7_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A5_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A5_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A4_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A4_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A4_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A4_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A3_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A4_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A3_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A7_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A3_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A6_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A3_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A3_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A2_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A3_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A5_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A5_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A2_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A3_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A5_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A2_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A3_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A12_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A2_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A2_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A5_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A2_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A12_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A12_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A12_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A12_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A11_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A10_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A12_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A10_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A10_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A10_ad008


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A1_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A10_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A2_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A1_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A1_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A1_ad012


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A2_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A1_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A10_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H9_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A1_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H9_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A12_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H9_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H8_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H9_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H9_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H9_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H8_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H8_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H8_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H8_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H8_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H8_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H7_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H7_ad001


title: CEMBA181023_6B_3_CEMBA181023_6B_4_A1_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H7_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H7_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H7_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H6_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H6_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H6_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H6_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H6_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H7_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H6_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H6_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H5_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_H5_ad004


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