title: TGTTTGT

city: St. Louis

first: Vipul

last: Sharma

state: Missouri

address: Campus Box 8234, 600 S. Euclid

department: Surgery

institute: Washington University in St.Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Fetal heart tissue

growth_protocol: Pregant dams were used for the experiment

extract_protocol:
Fetuses were cryosectioned and laser microdissection was used to get the heart tissue. This heart tissue was used to extract RNA.
Clontech SMARTer Ultra-Low RNA kit

treatment_protocol: Pregant dams were divided into two groups - control and infected with CVB3 at E9. All fetuses were collected at E14.

tag: developmental stage

value: infected

value: left ventricle


title: TCCCAGC

status: Public on Sep 05 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: treatment

value: control

tag: tissue

value: interventricular septum


title: TTTAACT

value: right ventricle


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B3_ad002

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

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

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: SSp

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B12_ad007


title: PAG_109 Noninfective stage miRNA Year1 Sample

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
Poor quality reads/bases or technical sequences such as adapters are removed from the paired end reads using Trimmomatic v0.32
Trimmed reads were further processed with the FASTX Toolkit v0.0.14 to filter out reads with tail quality < 15 nucleotides and retain reads of 16-25 nucleotides length for downstream analyses.
High-quality reads were subject to small RNAs annotation and quantification using the online tool OASIS and miRbase v21
miRNAs expressed at a minimum count of 10 reads in at least 50% of the samples per experimental condition were retained
Genome_build: hg38

organism: Homo sapiens

source_name: Blood

extract_protocol:
Tempus Spin RNA Isolation Kit
Truseq small rna library prep kit (Illumina) and KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems), respectively. Small RNA

tag: visit

value: Noninfective stage


title: TCAACTG


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B12_ad002


title: PAG_102 Post treatment miRNA Year1 Sample

value: Post treatment


title: TACATGG


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B12_ad001


title: PAG_102 Malaria Symptomatic stage miRNA Year1 Sample

value: Malaria Symptomatic stage


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B11_ad012


title: GTCGATA


title: PAG_102 Malaria non-symptomatic stage miRNA Year1 Sample

value: Malaria non-symptomatic stage


title: PAG_104 Malaria Symptomatic stage miRNA Year1 Sample


title: GGGTCAA


title: GGTCCTC


title: PAG_102 Noninfective stage miRNA Year1 Sample


title: GTACGGC


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B12_ad006


title: GCTTAGA


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B11_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B11_ad004


title: PAG_104 Noninfective stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B11_ad007


title: PAG_093 Noninfective stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B11_ad001


title: TACAGAC


title: GCAACGC


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B11_ad008


title: PAG_085 Malaria non-symptomatic stage miRNA Year1 Sample


title: CGGTGGC


title: PAG_075 Malaria non-symptomatic stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B10_ad008


title: CTCCCGA


title: GCCGTTT


title: CCGGACC


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B10_ad010


title: CAATATC


title: PAG_074 Malaria non-symptomatic stage miRNA Year1 Sample


title: PAG_056 Post treatment miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B11_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B10_ad007


title: PAG_093 Post treatment miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B11_ad002


title: ATGACAG


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B10_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B10_ad004


title: PAG_056 Malaria Symptomatic stage miRNA Year1 Sample


title: AGATACT


title: PAG_093 Malaria Symptomatic stage miRNA Year1 Sample


title: PAG_056 Malaria non-symptomatic stage miRNA Year1 Sample


title: ACCCACT


title: PAG_056 Noninfective stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B10_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B10_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B1_ad001


title: PAG_023 Malaria Symptomatic stage miRNA Year1 Sample


title: JpB.skin.32

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

description:
sample name in processed data file:
XMB_109.E_M9mo_S_sham_GW_2018-05-24_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

data_processing:
Illumina Hi-Seq 2000 was used to sequence all samples
raw reads were trimmed and filtered using a custom Perl script,The reads were truncated based on similarity to library adaptor sequences. Then, low-scoring sections of each read were removed, preserving the longest remaining fragment
Filtered reads are mapped to the Xiphophorus genome using Tophat2
Gene expression were quantified using featureCount
Genome_build: Xiphophorus maculatus GCF_002775205.1
Supplementary_files_format_and_content: Format: .xls; Content: gene expression profiles

organism: Xiphophorus maculatus

source_name: skin

growth_protocol: Animal: Animal use was approved by the Texas State University Institutional Animal Care and Use Review Board (IACUC protocol #2015107711). Fish utilized in this study were maintained in accordance with the applicable OLAW guidelines governing animal experimentation in the USA, and international legislation regulations governing animal experimentation.   Xiphophorus utilized in this study were bred and maintained in the Xiphophorus Genetic Stock Center (http://www.xiphophorus.txstate.edu). Xiphophorus maculatus (X. maculatus) JpA and JpB strains used for genome re-sequencing were at their 116th and 109th generation of inbreeding, respectively.

extract_protocol:
For RNA isolation, fish were anesthetized in an ice bath and upon loss of gill movement were sacrificed by cranial resection. Skin and liver tissues were dissected directly into TRI reagent (Sigma Inc., St Louis, MO, USA) and flash frozen in an ethanol dry ice bath. For JpA, skin samples and liver samples were collected; For JpB, skin samples, and liver samples  were collected for RNA isolation and sequencing library preparation. RNA isolation was performed following the Qiagen RNeasy RNA isolation protocol (Qiagen, Valencia, CA, USA). Tissue samples harvested from fish were first homogenized using a hand-held homogenizer in a 1.5 mL microcentrifuge tube while the sample remained frozen in TRI Reagent (Sigma Inc., St Louis, MO, USA). After homogenization, 300 μL of fresh 4°C TRI Reagent was added to the samples followed by room temperature incubation for 5 min. Chloroform extraction was performed by adding 120 μL chloroform and shaken for 15 s. Samples were centrifuged (16,100 rcf for 5 min at 4°C) for phase partitioning. The aqueous layer was transferred to a new 1.5 mL microcentrifuge tube and a second chloroform extraction performed (300 μL TRI Reagent, 60 μL chloroform). After extraction, nucleic acids in the aqueous phase were precipitated with 500 μL 70% EtOH in diethylpyrocarbonate (DEPC) treated water. The sample was then transferred to a Qiagen RNeasy mini spin column and on-column DNase treatment was performed for 15 min at 25°C. RNA samples were then washed and eluted in 100 μL RNase free water. RNA concentration was measured with a Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY, USA). To further assess the RNA quality, an RNA integrity (RIN) score was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All samples processed for RNA sequencing had a RIN score above 8.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: 9 month old


title: JpB.liver.3

description:
sample name in processed data file:
XMB_109.D_M9mo_L_sham_GW_2018-05-24_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

source_name: liver

value: liver


title: JpB.liver.4

description:
sample name in processed data file:
XMB_109.E_M9mo_L_sham_GW_2018-05-24_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG_023 Post treatment miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B1_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B1_ad010


title: JpB.liver.2

description:
sample name in processed data file:
XMB_109.C_M9mo_L_0min_GW_2018-05-24_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B1_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B1_ad004


title: PAG_023 Noninfective stage miRNA Year1 Sample


title: JpB.skin.30

description:
sample name in processed data file:
XMB_109.B_M9mo_S_0min_GW_2018-05-24_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG_023 Malaria non-symptomatic stage miRNA Year1 Sample


title: PAG_009 Post treatment miRNA Year1 Sample


title: JpB.skin.29

description:
sample name in processed data file:
XMB_106F.mc_M11mo_S_0pt_GW_2016-03-09_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: 11 month old


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A9_ad012


title: JpB.skin.31

description:
sample name in processed data file:
XMB_109.C_M9mo_S_0min_GW_2018-05-24_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG_009 Noninfective stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B1_ad002


title: PAG_009 Malaria Symptomatic stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B1_ad008


title: JpB.liver.1

description:
sample name in processed data file:
XMB_109.A_M9mo_L_0min_GW_2018-05-24_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG_036 Malaria non-symptomatic stage miRNA Year1 Sample


title: JpB.skin.27

description:
sample name in processed data file:
XMB_106F.ma_M11mo_S_0pt_GW_2016-03-09_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A9_ad001


title: PAG_008 Malaria Symptomatic stage miRNA Year1 Sample


title: JpB.skin.26

description:
sample name in processed data file:
XMB_106F.a_M11mo_S_0pt_GW_2016-03-09_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG_008 Noninfective stage miRNA Year1 Sample


title: PAG178 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A9_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A9_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A9_ad010


title: JpB.skin.25

description:
sample name in processed data file:
XMB_105f.c_M10mo_S_0min_BC_2015-01-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: 10 month old


title: PAG_008 Post treatment miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A9_ad004


title: PAG174 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG158 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.24

description:
sample name in processed data file:
XMB_105B.bb_M9mo_S_0min_BC_2015-01-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: JpB.skin.23

description:
sample name in processed data file:
XMB_105b.a_M10mo_S_0min_BC_2015-01-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG163 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A8_ad012


title: JpB.skin.22

description:
sample name in processed data file:
XMB_105b.ac_M12mo_S_0pt_BC_2015-06-03_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: 12 month old


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A8_ad001


title: PAG153 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.19

description:
sample name in processed data file:
XMB_105b.ab_M12mo_S_0pt_BC_2015-04-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A8_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A9_ad008


title: PAG151 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.21

description:
sample name in processed data file:
XMB_105b.ac_M12mo_S_0pt_BC_2015-04-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG155 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.18

description:
sample name in processed data file:
XMB_105b.ab_M12mo_S_0min_BC_2015-06-03_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A8_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A8_ad004


title: PAG145 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.15

description:
sample name in processed data file:
XMB_104f.b_M9mo_S_UV-0KJ_SP_2014-04-14_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A8_ad002


title: JpB.skin.16

description:
sample name in processed data file:
XMB_104f.b_M9mo_S_UV-0KJ_SP_2014-07-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG144 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG143 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.13

description:
sample name in processed data file:
XMB_104d.m_M10mo_S_0min_SP_2014-05-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A8_ad008


title: PAG137 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A7_ad001


title: JpB.skin.12

description:
sample name in processed data file:
XMB_104d.D_M10mo_S_0min_SP_2014-05-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG132 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.11

description:
sample name in processed data file:
XMB_104d.C_M10mo_S_0min_SP_2014-05-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG136 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A7_ad006


title: JpB.skin.9

description:
sample name in processed data file:
XMB_104d.ao_M12mo_S_CO-0min_SP_2014-07-31_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: JpB.skin.10

description:
sample name in processed data file:
XMB_104d.ap_M12mo_S_CO-0min_SP_2014-07-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A7_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A8_ad010


title: PAG_095 Malaria non-symptomatic stage miRNA Year1 Sample


title: PAG124 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.17

description:
sample name in processed data file:
XMB_105B.aa_M9mo_S_0min_BC_2015-01-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A7_ad010


title: PAG146 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.14

description:
sample name in processed data file:
XMB_104d.n_M10mo_S_0min_SP_2014-05-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A6_ad012


title: PAG121 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.8

description:
sample name in processed data file:
XMB_104d.ao_M12mo_S_CO-0min_SP_2014-07-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A6_ad001


title: PAG120 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A6_ad007


title: JpB.skin.5

description:
sample name in processed data file:
XMB_104d.a_M9mo_S_UV-0KJ_SP_2014-07-30b_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: JpB.skin.4

description:
sample name in processed data file:
XMB_104d.a_M9mo_S_UV-0KJ_SP_2014-04-14_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A6_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A6_ad002


title: PAG115 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.3

description:
sample name in processed data file:
XMB_104d.a_M9mo_S_UV-0KJ_SP_2014-03-24B_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG111 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG102 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG100 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: Jpa.liver.4

description:
sample name in processed data file:
XMA.z-r_M20mo_L_0min_GW_2016-10-14_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: 20 month old


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A5_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A6_ad008


title: Jpa.skin.25

description:
sample name in processed data file:
XMA.z_M20mo_S_Sham_GW_2016-10-05_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A5_ad006


title: PAG099 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A5_ad010


title: JpB.skin.6

description:
sample name in processed data file:
XMB_104d.a_M9mo_S_UV-0KJ_SP_2014-07-30_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: Jpa.skin.24

description:
sample name in processed data file:
XMA.z_M20mo_S_0pt_GW_2016-10-05_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG094 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A5_ad002


title: HumanMono_RNA_803.2_16hr

city: Lebanon

first: Evelien

last: Schaafsma

state: New Hampshire

address: One Medical Drive

institute: Dartmouth

description: Human monocytes treated with anti-VISTA (10 mg/ml) for 16 hours.

data_processing:
RNA-seq and scATAC-seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: The quality of the runs was confirmed using the FastQC software. Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and mapped to GRCm38 whole genome using STAR v2.6.1 with parameters  --quantMode. The count data were transformed to log2-transformed transcripts per million (TPM) for downstream analyses and heatmap displays.
scATAC-seq: The CellRanger ATAC v1.1.0 pipeline as used for initial processing. Raw base call (BCL) files were demultiplexed into FASTQ files using “mkfastq”. Reads were aligned to the mouse mm10 reference genome using “count”. Peak count matrices were aggregated into one file using the “aggr” function.
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample. Matrix tables with raw read counts for every peak and cell.

source_name: Human monocytes

growth_protocol:
Ficoll-Paque (GE Healthcare) was used to isolate PBMCs from healthy volunteers by differential centrifugation. The RPMI 1640 medium (Sigma113 Aldrich) was supplemented with 10 mM L-glutamine and 10 mM pyruvate (Life Technologies). Monocytes were obtained by depletion of CD3, CD19 and CD56 positive cells from PBMCs obtained upon Ficoll isolation of a buffycoat. CD3 MicroBeads (130-050- 101), CD19 MicroBeads (130-050- 301) and CD56 (130-050-401) were purchased from Miltenyi Biotec and used according to the manufacturer protocol. For RNA-seq analysis of the monocytes, additional CD14 positive cells selection was performed on the CD3-, CD19- and CD56- population using CD14 MicroBeads (130- 050-201) from Miltenyi Biotec.
See sample information

extract_protocol:
RNA-seq: RNA was extracted using the Kapa Hyperprep with RiboErase kit, according to the manufacturer’s instructions. scATAC-seq: Nuclei from BMDMs were isolated following the 10X Genomics protocol.
RNA-seq and scATAC-seq: RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: See sample information

tag: cell type

value: Monoctyes

value: anti-VISTA (803)


title: PAG117 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: Jpa.skin.23

description:
sample name in processed data file:
XMA.x_M20mo_S_Sham_GW_2016-10-05_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A5_ad008


title: JpB.skin.1

description:
sample name in processed data file:
XMB_101C.a_M_S_UVB-Sham-0kJ_EA_2012-01-31_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG080 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: HumanMono_RNA_803.3_8hr

description: Human monocytes treated with anti-VISTA (10 mg/ml) for 8 hours.


title: Jpa.liver.2

description:
sample name in processed data file:
XMA.x_M20mo_L_0min_GW_2016-10-14_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A4_ad001


title: Jpa.skin.22

description:
sample name in processed data file:
XMA.x_M20mo_S_0pt_GW_2016-10-05_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: HumanMono_RNA_803.1_16hr


title: PAG072 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG076 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A4_ad007


title: PAG069 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: Jpa.skin.21

description:
sample name in processed data file:
XMA.w_M24mo_S_8AM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: 24 month old


title: HumanMono_RNA_803.1_8hr


title: Jpa.liver.3

description:
sample name in processed data file:
XMA.z_M20mo_L_0min_GW_2016-10-14_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: HumanMono_RNA_803.3_16hr


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A4_ad010


title: Jpa.skin.20

description:
sample name in processed data file:
XMA.v_M24mo_S_8AM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG064 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG083 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A4_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A4_ad004


title: HumanMono_RNA_803.3_4hr

description: Human monocytes treated with anti-VISTA (10 mg/ml) for 4 hours.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A4_ad012


title: Jpa.skin.18

description:
sample name in processed data file:
XMA.s_M24mo_S_2AM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG061 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: HumanMono_RNA_803.2_8hr


title: Jpa.skin.17

description:
sample name in processed data file:
XMA.r_M24mo_S_8PM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG053 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: Jpa.skin.16

description:
sample name in processed data file:
XMA.p_M24mo_S_8PM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A4_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A4_ad002


title: HumanMono_RNA_803.1_4hr


title: PAG052 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: HumanMono_RNA_IgG.3_16hr

description: Human monocytes treated with IgG (10 mg/ml) for 16 hours.

value: Control IgG


title: PAG050 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A3_ad008

value: SSp


title: HumanMono_RNA_IgG.2_16hr


title: PAG049 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: Jpa.skin.14

description:
sample name in processed data file:
XMA.n_M20mo_S_Sham_GW_2016-10-05_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: male


title: HumanMono_RNA_IgG.1_16hr


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A3_ad007


title: Jpa.skin.15

description:
sample name in processed data file:
XMA.o_M24mo_S_2PM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: HumanMono_RNA_IgG.3_8hr

description: Human monocytes treated with IgG (10 mg/ml) for 8 hours.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A3_ad004


title: HumanMono_RNA_803.2_4hr


title: PAG054 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpA.liver.1

description:
sample name in processed data file:
XMA.n_M20mo_L_Sham_GW_2016-10-14_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: Jpa.skin.19

description:
sample name in processed data file:
XMA.u_M24mo_S_2AM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG044 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpA.skin.13

description:
sample name in processed data file:
XMA.m_M24mo_S_2PM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A3_ad006


title: HumanMono_RNA_IgG.2_8hr


title: PAG037 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG034 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: HumanMono_RNA_IgG.3_4hr

description: Human monocytes treated with IgG (10 mg/ml) for 4 hours.


title: JpA.skin.12

description:
sample name in processed data file:
XMA.ak_M24mo_S_11PM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG031 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpA.skin.11

description:
sample name in processed data file:
XMA.aj_M24mo_S_11PM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A2_ad001


title: HumanMono_RNA_IgG.1_8hr


title: JpA.skin.10

description:
sample name in processed data file:
XMA.ah_M24mo_S_5PM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A2_ad010


title: PAG030 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A2_ad007


title: PAG029 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: HumanMono_RNA_IgG.1_4hr


title: HumanMono_RNA_IgG.2_4hr


title: PAG025 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpA.skin.9

description:
sample name in processed data file:
XMA.ag_M24mo_S_5PM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A2_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A2_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A2_ad008


title: PAG021 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpA.skin.8

description:
sample name in processed data file:
XMA.ae_M24mo_S_11AM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: LNCaP 4hr induced rep1

city: Chicago

first: Sebastian

last: Pott

state: IL

address: 920 E 58th St

institute: The University of Chicago

data_processing:
Sequences from each experiment were aligned to the genome using BWA (Li et al., 2008) for the GRCh37 (hg19) assembly.
DNase-seq genome-wide cleavage counts of 5’ positions were obtained using bedtools with parameters: genomecov -5 -strand -bg, then converted the BedGraph files to bigWig format using bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files of DNase-seq genome-wide cleavage counts for the forward or reverse strand.

source_name: LNCaP prostate cancer cells

extract_protocol:
See http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase
Libraries were sequenced on the Illumina HiSeq 2000 platform.

treatment_protocol: Cells were grown in RPMI-1640 medium with 10% charcoal:dextran stripped medium for 60 hours, then stimulated with androgen (R1881, methyltrienolone) for 45 minutes or 4 hours,  or vehicle (ethanol).

value: LNCaP

value: treated with R1881

tag: time point

value: 4 hours


title: LNCaP 45min induced rep2

value: 45 minutes


title: LNCaP 4hr induced rep2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A2_ad012


title: JpA.skin.7

description:
sample name in processed data file:
XMA.ad_M24mo_S_11AM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: skin


title: JpA.skin.6

description:
sample name in processed data file:
XMA.ac_M24mo_S_5AM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: JpA.skin.5

description:
sample name in processed data file:
XMA.ab_M24mo_S_5AM_GW_2016-10-13_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG020 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication

value: Malaria Symptomatic stage


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A12_ad010


title: JpB.skin.28

description:
sample name in processed data file:
XMB_106F.mb_M11mo_S_0pt_GW_2016-03-09_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: LNCaP uninduced rep2

value: untreated


title: LNCaP 45min induced rep1


title: JpA.skin.4

description:
sample name in processed data file:
XMA.d_M13mo_S_SHAM_GW_2018-01-08_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: 13 month old


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A12_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A12_ad007


title: PAG018 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: LNCaP uninduced rep1


title: PAG016 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpA.skin.3

description:
sample name in processed data file:
XMA.c_M13mo_S_SHAM_GW_2018-01-08_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A12_ad006


title: PAG_097 Malaria non-symptomatic stage miRNA Year1 Sample

value: Malaria non-symptomatic stage


title: JpA.skin.2

description:
sample name in processed data file:
XMA.b_M13mo_S_0min_GW_2018-01-08_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A12_ad004


title: JpA.skin.1

description:
sample name in processed data file:
XMA.a_M13mo_S_0min_GW_2018-01-08_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG006 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG008 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: HGPS169 H3K27me3 input

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

data_processing:
Reads were aligned to the hg38-noalt reference human genome available in the bcbio-nextgen pipeline, using bwa aln (version 0.7.12) with options -n 2 -k 2 and saved the results in sam format with bwa samse.
The sam files were converted to bam and name sorted with samtools (version 1.3.1). We marked PCR duplicates using the biobambam2 toolset (version 2.0.54). We discarded reads mapping to non-autosomal chromosomes, PCR duplicates, qcfail, multimapping and unmapped reads with samtools.
We calculated the genome wide IP - input signal for all samples, using the SPP package (version 1.15.4). We imported bam files into the R (version 3.3.1) statistical environment, and selected informative reads with the get.binding.characteristics and select.informative.tags functions, removed anomalous positions with extremely high number of reads using the remove.local.tag.anomalies function, and calculated the differential signal, smoothed by a Gaussian kernel, using the get.smoothed.tag.density function with the default bandwidth and tag.shift parameters.
We called H3K27me3 ChIP-seq peaks with the get.broad.enrichment.clusters function of SPP on the preprocessed data with window.size = 2000 and z.thr = 3, tag.shift = ((cross correlation peak position) / 2) parameters.
We used the Enriched Domain Detector (EDD) tool to select significantly enriched SAMMY-seq domains by comparing less accessible fractions to more accessible ones (S3 vs S2, S4 vs S3 and S4 vs S2 comparisons) in each sample, with the following options: --gap-penalty 25 --bin-size 250 --write-log-ratios --write-bin-scores and also excluding blacklisted genomic regions containing telomeric, centromeric, and certain heterochromatic regions. We also changed the required_fraction_of_informative_bins parameter to 0.98.
Genome_build: hg38-noalt
Supplementary_files_format_and_content: bed: H3K27me3 peak coordinates or SAMMY-seq enriched domain coordinates for a specific sample. bigWig: genome wide IP - input signal for a specific sample, smoothed by a Gaussian kernel.

source_name: HGPS169 H3K27me3 input

growth_protocol: Primary fibroblast cell lines were cultured in DMEM High glucose with glutamax supplemented with 15% FBS and 1% Pen/Strep.

extract_protocol:
Cells were cross-linked with 1% HCHO for 12 minutes at room temperature, lysed and chromatin sheared using Covaris M220 focused-ultrasonicator. IP were performed overnight on a wheel at 4° with 2 micrograms of H3K27me3 antibody (07-449, Millipore). The following day, antibody-chromatin immunocomplexes were loaded onto Dynal G magnetic beads (Invitrogen 10004D); the bound complexes were washed once in Low Salt Solution (0,1% SDS, 2mM EDTA, 1% Triton X-100, 20mM Tris pH 8, 150 mM NaCl), once in High Salt Solution (0,1% SDS, 2mM EDTA, 1% Triton X-100, 20mM Tris pH 8, 500 mM NaCl), once again in Low Salt Solution and once in Tris/EDTA 50 mM NaCl. Crosslinking was reversed at 65°C overnight in Elution Buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS). DNA purified by standard phenol/chloroform extraction, precipitated and resuspended in 30 μl of 10 mM Tris pH 8. ChIP efficiency was tested by qPCR reactions, performed in triplicate (precipitated DNA samples as well as input DNA) using QuantiTect SYBR Green master mix (Qiagen) on a StepOnePlus™ Real-Time PCR System (Applied Biosystems). Relative enrichment was calculated as ChIP / Input ratio.
Libraries for sequencing were created using NEBNext Ultra II DNA Library Prep Kit (NEB), then qualitatively and quantitatively checked using Agilent High Sensitivity DNA Kit (Agilent Technologies, 5067-4627) on a Bioanalyzer 2100 (Agilent Technologies). Libraries with distinct adapter indexes were multiplexed and, after cluster generation on FlowCell, were sequenced for 50bp in the single read mode on a HiSeq 2000 sequencer (Illumina).

value: patient derived skin fibroblast

tag: passage

tag: chip antibody


title: HGPS188 H3K27me3 input

source_name: HGPS188 H3K27me3 input


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A12_ad002


title: JpB.liver.6

description:
sample name in processed data file:
XMA.B_M13mo_L_sham_GW_2018-02-23_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: liver


title: HGPS167 H3K27me3 input

source_name: HGPS167 H3K27me3 input


title: PAG002 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: PAG019 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: HGPS188 H3K27me3 ChIP-seq

source_name: HGPS188 H3K27me3 ChIP-seq

value: 07-449, Millipore


title: JpB.liver.5

description:
sample name in processed data file:
XMA.A_M13mo_L_sham_GW_2018-02-23_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.


title: PAG001 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: JpB.skin.33

description:
sample name in processed data file:
XMB_109.F_M9mo_S_sham_GW_2018-05-24_pe1.r.fastq
Note: the time included  in sample names (5AM, 11AM, etc) refer to the time of sacrifice. "0min" and "SHAM" are the designation for control experiment.No treatments were given to these samples.

value: 9 month old


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A11_ad012


title: HCMV-infected HELF cells

city: Shenyang

first: Jingui

last: Deng

state: Liaoning

address: No.36 Sanhao Street, Heping District

department: Virus Laboratory

country: China

institute: the Affiliated Shengjing Hospital, China Medical University

data_processing:
RNA-seq raw reads were first filtered by Seqtk (https://github.com/lh3/seqtk) to remove the reads below standards (reads are shorted than 25nt, the ribosome RNA reads and reads containing adaptor sequence)
Clean reads were mapped to reference genomes (GRCH37/hg19). FASTQ reads that aligned contiguously and full length to the genomes by BWA-MEM were discarded
20‐nt from both ends of the unmapped reads were extracted and aligned independently to find unique anchor positions within spliced exons by CIRI. Anchors that aligned in the reversed orientation (head‐to‐tail) indicated circRNA splicing (circRNA candidate)
annotate the functional element of circRNA using ANNOVAR database
Junction reads for each circRNA candidate were normalized to  SRPBM to compute the circRNA expression . Fold-change was calculated according to SRPBM. The differences in expression of circRNAs between mock-infection and HCMV infection cultures were analyzed with edgeR. The obtained p-value was subjected to multiple hypothesis test correction and q-value (adjusted p-value) was achieved by controlling the false discovery rate. Differential expression of circ-RNAs was filtered by the standards of >2 (or<-2) fold-change and q-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: excel files include SRPBM values for each Sample

source_name: human embryonic lung fibroblasts

growth_protocol: HELF cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100units/ml penicillin and 100units/ml streptomycin.

extract_protocol:
HCMV infected HELF cells were collected at 72 hours post-infection (hpi). Mock-infected cells were harvested as control. Total RNAs were extracted using TRIzol Reagent (ThermoFisher) according to the manufactures’ instruction. Then, both of the two group RNAs were subjected rRNA depletion using using Ribo-Zero rRNA Removal Kits (Epicentre) and linear RNA removal using RNase R treatment  (Epicentre) according to the manufactures’ instruction.
The rRNA-depleted and RNase R treated RNA were fragmented randomly and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HELF cells were infected with HCMV clinical strain HAN, which was isolated from a urine sample of a 5-month-old infant hospitalized in Shengjing Hospital of China Medical University,  at a multiplicity of infection (MOI) of 3.

value: embryonic lung

value: fibroblasts

tag: passages

tag: infection

value: HCMV-infected

tag: time

value: 72 hours post infection


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A11_ad007

value: SSp

value: male


title: mock-infected HELF cells

value: mock-infected


title: HGPS167 H3K27me3 ChIP-seq

source_name: HGPS167 H3K27me3 ChIP-seq


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A11_ad010


title: HGPS169 H3K27me3 ChIP-seq

source_name: HGPS169 H3K27me3 ChIP-seq


title: HGPS167 SAMMY-seq S3, late passage replicate 2

description: processed data (*S4vsS3) files are linked to the S4 sample records

data_processing:
Reads were aligned to the hg38-noalt reference human genome available in the bcbio-nextgen pipeline, using bwa aln (version 0.7.12) with options -n 2 -k 2 and saved the results in sam format with bwa samse.
The sam files were converted to bam and name sorted with samtools (version 1.3.1). We marked PCR duplicates using the biobambam2 toolset (version 2.0.54). We discarded reads mapping to non-autosomal chromosomes, PCR duplicates, qcfail, multimapping and unmapped reads with samtools.
We calculated the genome wide IP - input signal for all samples, using the SPP package (version 1.15.4). We imported bam files into the R (version 3.3.1) statistical environment, and selected informative reads with the get.binding.characteristics and select.informative.tags functions, removed anomalous positions with extremely high number of reads using the remove.local.tag.anomalies function, and calculated the differential signal, smoothed by a Gaussian kernel, using the get.smoothed.tag.density function with the default bandwidth and tag.shift = 0 parameters.
We used the Enriched Domain Detector (EDD) tool to select significantly enriched SAMMY-seq domains by comparing less accessible fractions to more accessible ones (S3 vs S2, S4 vs S3 and S4 vs S2 comparisons) in each sample, with the following options: --gap-penalty 45 --bin-size 200 --write-log-ratios --write-bin-scores and also excluding blacklisted genomic regions containing telomeric, centromeric, and certain heterochromatic regions62. We also changed the required_fraction_of_informative_bins parameter to 0.98.
Genome_build: hg38-noalt
Supplementary_files_format_and_content: bed: SAMMY-seq enriched domain coordinates for a specific sample. bigWig: genome wide IP - input signal for a specific sample, smoothed by a Gaussian kernel.

source_name: HGPS167 SAMMY-seq S3, late passage

extract_protocol: 4 million fibroblasts were washed in PBS 1X, and extracted in cytoskeleton buffer (CSK: 10 mM PIPES pH 6,8; 100 mM NaCl; 1 mM EGTA; 300 mM Sucrose; 3 mM MgCl2; 1X protease Inhibitors by Roche Diagnostics; 1 mM PMSF) supplemented with 1 mM DTT and 0,5% Triton X-100. After 5 min at 4°C the cytoskeletal structure was separated from soluble proteins by centrifugation at 3000 rpm for 3 min, and the supernatant was labeled as S1 fraction. The pellets were washed with an additional volume of cytoskeleton buffer. Chromatin was solubilized by DNA digestion with 25U of RNase–free DNase (Invitrogen) in CSK buffer for 30 min at 37°C. To stop digestion, ammonium sulphate was added in CSK buffer to a final concentration of 250 mM and, after 5 min at 4°C samples were pelleted at 5000 rpm for 3 min at 4°C and the supernatant was labeled as S2 fraction. After a wash in CSK buffer, the pellet was further extracted with 2M NaCl in CSK buffer for 5 min at 4°C, centrifuged at 5000 rpm 3 min at 4°C and the supernatant was labeled as S3 fraction. This treatment removed the majority of histones from chromatin. After 2 washing in NaCl 2M CSK, the pellets were solubilized in 8M urea buffer to remove any remaining protein component by applying highly denaturing conditions. This remaining fraction was labeled as S4.

tag: fraction


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A11_ad008


title: HGPS167 SAMMY-seq S4, late passage replicate 2

source_name: HGPS167 SAMMY-seq S4, late passage


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A12_ad001


title: PAG141 Malaria Symptomatic stage miRNA Year2 Sample

description: Replication


title: HGPS167 SAMMY-seq S3, late passage replicate 1


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A11_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A11_ad002


title: HGPS167 SAMMY-seq S2, late passage replicate 2

description: processed data (*S4vsS2) files are linked to the S4 sample records

source_name: HGPS167 SAMMY-seq S2, late passage


title: HGPS167 SAMMY-seq S4, late passage replicate 1


title: HGPS188 S2 fraction

data_processing:
library strategy: Sequential Analysis of MacroMolecules accessibilitY (SAMMY-seq)
Reads were aligned to the hg38-noalt reference human genome available in the bcbio-nextgen pipeline, using bwa aln (version 0.7.12) with options -n 2 -k 2 and saved the results in sam format with bwa samse.
The sam files were converted to bam and name sorted with samtools (version 1.3.1). We marked PCR duplicates using the biobambam2 toolset (version 2.0.54). We discarded reads mapping to non-autosomal chromosomes, PCR duplicates, qcfail, multimapping and unmapped reads with samtools.
We calculated the genome wide IP - input signal for all samples, using the SPP package (version 1.15.4). We imported bam files into the R (version 3.3.1) statistical environment, and selected informative reads with the get.binding.characteristics and select.informative.tags functions, removed anomalous positions with extremely high number of reads using the remove.local.tag.anomalies function, and calculated the differential signal, smoothed by a Gaussian kernel, using the get.smoothed.tag.density function with the default bandwidth and tag.shift = 0 parameters.
We used the Enriched Domain Detector (EDD) tool to select significantly enriched SAMMY-seq domains by comparing less accessible fractions to more accessible ones (S3 vs S2, S4 vs S3 and S4 vs S2 comparisons) in each sample, with the following options: --gap-penalty 25 --bin-size 50 --write-log-ratios --write-bin-scores and also excluding blacklisted genomic regions containing telomeric, centromeric, and certain heterochromatic regions62. We also changed the required_fraction_of_informative_bins parameter to 0.98.
Genome_build: hg38-noalt
Supplementary_files_format_and_content: bed: SAMMY-seq enriched domain coordinates for a specific sample. bigWig: genome wide IP - input signal for a specific sample, smoothed by a Gaussian kernel.

source_name: Hutchinson-Gilford progeria syndrome (HGPS) skin fibroblasts

extract_protocol:
4 million fibroblasts were washed in PBS 1X, and extracted in cytoskeleton buffer (CSK: 10 mM PIPES pH 6,8; 100 mM NaCl; 1 mM EGTA; 300 mM Sucrose; 3 mM MgCl2; 1X protease Inhibitors by Roche Diagnostics; 1 mM PMSF) supplemented with 1 mM DTT and 0,5% Triton X-100. After 5 min at 4°C the cytoskeletal structure was separated from soluble proteins by centrifugation at 3000 rpm for 3 min, and the supernatant was labeled as S1 fraction. The pellets were washed with an additional volume of cytoskeleton buffer. Chromatin was solubilized by DNA digestion with 25U of RNase–free DNase (Invitrogen) in CSK buffer for 30 min at 37°C. To stop digestion, ammonium sulphate was added in CSK buffer to a final concentration of 250 mM and, after 5 min at 4°C samples were pelleted at 5000 rpm for 3 min at 4°C and the supernatant was labeled as S2 fraction. After a wash in CSK buffer, the pellet was further extracted with 2M NaCl in CSK buffer for 5 min at 4°C, centrifuged at 5000 rpm 3 min at 4°C and the supernatant was labeled as S3 fraction. This treatment removed the majority of histones from chromatin. After 2 washing in NaCl 2M CSK, the pellets were solubilized in 8M urea buffer to remove any remaining protein component by applying highly denaturing conditions. This remaining fraction was labeled as S4.
For DNA fractionation, we took an aliquot corresponding to 30% of volume of S2, S3, S4 fractions and added TE buffer to reach a final volume of 300μL. After incubation with RNAse A (Roche) (90 minutes at 37°) and Proteinase K (Sigma) (150 minutes at 55°), DNA was extracted from beads by standard phenol/chloroform extraction, precipitated and resuspended in 25μl milliQ H2O. After Nanodrop (260/280 = 1,7-1,9; 260/230 ≥ 2) and Qubit HS DNA quantification, we added H2O to a final volume of 105μL. Then samples were transferred to 96 well plates and sonicated 4 times with Bioruptor sonicator (10 minutes 30 seconds ON - 30 seconds OFF, High Power). The DNA profiles were finally checked by capillary electrophoresis (Agilent 2100 Bioanalyzer). Finally, DNA libraries were prepared by using NuGEN Ovation Ultralow Library Prep System kit and then sequenced using an Illumina HiSeq 2500 instrument according to manufacturer’s instructions (Illumina).


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A10_ad010

source_name: C57BL/6J Male P56 Mouse Brain


title: HGPS188 S3 fraction


title: CTRL004 SAMMY-seq S4, late passage replicate 2

source_name: CTRL004 SAMMY-seq S4, late passage


title: HGPS169 S4 fraction


title: HGPS169 S3 fraction


title: HGPS169 S2 fraction


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A10_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A10_ad006


title: CTRL004 SAMMY-seq S2, late passage replicate 2

source_name: CTRL004 SAMMY-seq S2, late passage


title: HGPS188 S4 fraction


title: HGPS169 input

data_processing:
We trimmed reads, using Trimmomatic61 (version 0.32) in single end mode.
Reads were aligned to the hg38-noalt reference human genome available in the bcbio-nextgen pipeline, using bwa aln (version 0.7.12) with options -n 2 -k 2 and saved the results in sam format with bwa samse.
The sam files were converted to bam and name sorted with samtools (version 1.3.1). We marked PCR duplicates using the biobambam2 toolset (version 2.0.54). We discarded reads mapping to non-autosomal chromosomes, PCR duplicates, qcfail, multimapping and unmapped reads with samtools.
We calculated the genome wide IP - input signal for all samples, using the SPP package (version 1.15.4). We imported bam files into the R (version 3.3.1) statistical environment, and selected informative reads with the get.binding.characteristics and select.informative.tags functions, removed anomalous positions with extremely high number of reads using the remove.local.tag.anomalies function, and calculated the differential signal, smoothed by a Gaussian kernel, using the get.smoothed.tag.density function with the default bandwidth and tag.shift parameters.
We used the Enriched Domain Detector (EDD) tool to call H3K9me3 peaks, with the following options: --fdr 0.1 –gap-penalty 10 –bin-size 100 –write-log-ratios –write-bin-scores and also excluding blacklisted genomic regions containing telomeric, centromeric, and certain heterochromatic regions. We also changed the required_fraction_of_informative_bins parameter to 0.98.
Genome_build: hg38-noalt
Supplementary_files_format_and_content: bed: H3K9me3 peak coordinates for a specific sample. bigWig: genome wide IP - input signal for a specific sample, smoothed by a Gaussian kernel.

extract_protocol:
Cells were cross-linked with 1% HCHO for 12 minutes at room temperature, lysed and chromatin sheared using Branson Digital Sonifier. IP were performed overnight on a wheel at 4° with 2.4 micrograms of H3K9me3 antibody (ab8898, Abcam). The following day, antibody-chromatin immunocomplexes were loaded onto Dynal G magnetic beads (Invitrogen 10004D); the bound complexes were washed once in Low Salt Solution (0,1% SDS, 2mM EDTA, 1% Triton X-100, 20mM Tris pH 8, 150 mM NaCl), once in High Salt Solution (0,1% SDS, 2mM EDTA, 1% Triton X-100, 20mM Tris pH 8, 500 mM NaCl), once again in Low Salt Solution and once in Tris/EDTA 50 mM NaCl. Crosslinking was reversed at 65°C overnight in Elution Buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and DNA extracted from beads by standard phenol/chloroform extraction, precipitated and resuspended in 30 μl of 10 mM Tris pH 8. ChIP efficiency was tested by qPCR reactions, performed in triplicate (precipitated DNA samples as well as input DNA) using QuantiTect SYBR Green master mix (Qiagen) on a StepOnePlus™ Real-Time PCR System (Applied Biosystems). Relative enrichment was calculated as ChIP / Input ratio. Libraries for sequencing were created using the automation instrument Biomek FX (Beckman Coulter), then qualitatively and quantitatively checked using Agilent High Sensitivity DNA Kit (Agilent Technologies, 5067-4627) on a Bioanalyzer 2100 (Agilent Technologies).
Libraries with distinct adapter indexes were multiplexed and, after cluster generation on FlowCell, were sequenced for 50bp in the single read mode on a HiSeq 2000 sequencer at the IEO Genomic Unit in Milan.


title: HGPS167 S3 fraction


title: HGPS167 S4 fraction


title: HGPS167 input


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A11_ad004


title: HGPS167 SAMMY-seq S2, late passage replicate 1


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A10_ad004


title: CTRL013 input

source_name: normal control fibroblasts


title: CTRL004 SAMMY-seq S4, late passage replicate 1


title: CTRL004 SAMMY-seq S3, late passage replicate 1

source_name: CTRL004 SAMMY-seq S3, late passage


title: CTRL013 S4 fraction


title: CTRL013 S3 fraction


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A10_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A10_ad001


title: HGPS188 input


title: CTRL004 SAMMY-seq S2, late passage replicate 1


title: CTRL013 S2 fraction


title: HGPS167 S2 fraction


title: HGPS188 H3K9me3 ChIP-seq

value: H3K9me3, Abcam, ab8898


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A1_ad012


title: CTRL004 SAMMY-seq S3, late passage replicate 2


title: CTRL004 S4 fraction 10K rep2

source_name: CTRL004 S4 fraction 10K

extract_protocol:
250 thousand, 50 thousand or 10 thousand fibroblasts were washed in PBS 1X, and extracted in cytoskeleton buffer (CSK: 10 mM PIPES pH 6,8; 100 mM NaCl; 1 mM EGTA; 300 mM Sucrose; 3 mM MgCl2; 1X protease Inhibitors by Roche Diagnostics; 1 mM PMSF) supplemented with 1 mM DTT and 0,5% Triton X-100. After 5 min at 4°C the cytoskeletal structure was separated from soluble proteins by centrifugation at 845 g for 3 min, and the supernatant was labeled as S1 fraction. The pellets were washed with an additional volume of cytoskeleton buffer. Chromatin was solubilized by DNA digestion with 8U of RNase–free DNase (Invitrogen) in CSK buffer for 60 min at 37°C. To stop digestion, ammonium sulphate was added in CSK buffer to a final concentration of 250 mM and, after 5 min at 4°C samples were pelleted at 2350 g for 3 min at 4°C and the supernatant was labeled as S2 fraction. After a wash in CSK buffer, the pellet was further extracted with 2M NaCl in CSK buffer for 5 min at 4°C, centrifuged at 2350 g 3 min at 4°C and the supernatant was labeled as S3 fraction. This treatment removed the majority of histones from chromatin. After 2 washings in NaCl 2M CSK, the pellets were solubilized in 8M urea buffer to remove any remaining protein component by applying highly denaturing conditions. This remaining fraction was labeled as S4.
We added to each fraction TE buffer to reach a final volume of 200μL. After incubation with RNAse cocktail (Ambion) (90 minutes at 37°) and Proteinase K (Thermo Scientific) (150 minutes at 55°), DNA was extracted by standard phenol/chloroform extraction, precipitated and resuspended in 16μl of nuclease-free water. Then S3 and S4 samples were transferred to microTUBE-15 AFA Beads Screw-Cap (Covaris) and sonicated with Covaris M220 focused-ultrasonicator (water bath 20°C, peak power 30.0, duty factor 20.0, cycles/burst 50, duration 150 seconds). S2 samples were further purified using PCR DNA Purification Kit (Qiagen) and suspend in 30μL of nuclease-free water and they were not sonicated. All the samples were quantified using Qubit HS DNA kit (Life Technologies) and library prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) using Unique Dual Index NEBNext Multiplex Oligos for Illumina (NEB). Library were quantified using Qubit HS DNA kit (Life Technologies) and profiles were checked by capillary electrophoresis on a Agilent 2100 Bioanalyzer. Finally, DNA libraries were sequenced using an Illumina NovaSeq 6000 instrument according to manufacturer’s instructions.


title: CTRL004 S3 fraction 10K rep2

source_name: CTRL004 S3 fraction 10K


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A10_ad007


title: CTRL004 input


title: HGPS169 H3K9me3 ChIP-seq


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A1_ad001


title: HGPS167 H3K9me3 ChIP-seq


title: CTRL004 S2 fraction 10K rep2

source_name: CTRL004 S2 fraction 10K


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A1_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A1_ad010


title: CTRL004 H3K9me3 ChIP-seq


title: HGPS188 RNA-seq

data_processing:
Transcript level quantification was done with Kallisto (version 0.43.0) to estimate transcript level read counts and TPM (Transcripts Per Million) values. The GENCODE v27 annotation was used to build the transcriptome index. Kallisto was run with the --bias option to perform sequence based bias correction on each sample.
Genome_build: GENCODE v27
Supplementary_files_format_and_content: tsv: length, effective length, estimated read count and TPM for transcripts from the GENCODE v27 annotation.

extract_protocol:
cDNA libraries were prepared from total RNA, extracted with Trizol.
We constructed libraries by using Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero GOLD. cDNA fragments of ~300 bp were purified from each library and were sequenced for 125bp, using an Illumina HiSeq 2500 instrument according to manufacturer’s instructions (Illumina).


title: HGPS169 RNA-seq


title: CTRL004 S3 fraction 10K rep1


title: CTRL004 S4 fraction


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A1_ad006


title: CTRL004 S4 fraction 50K rep2

source_name: CTRL004 S4 fraction 50K


title: WT-6 [MM056]

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

description:
NA
Normalized_matrix.txt
Reads sequenced on both Illumina HiSeq 2500 and HiSeq 4000 instruments.

data_processing:
RNA-seq pipeline description: Columbia Genome Center standard pipeline
Libraries were sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm10) using STAR(2.5.2b) and featureCounts(v1.5.0-p3). We test for differentially expressed genes under various conditions using DESeq2. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm10
Supplementary_files_format_and_content: Excel file includes DESeq2 normalized values for each sample

source_name: prostate tissue

extract_protocol:
For RNA sequencing of lineage-marked cells, YFP-positive cells were directly sorted into lysis buffer. cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) with 12-16 cycles of PCR amplification, depending on the number of sorted cells. Amplified cDNA was verified using the Agilent 2100 Bioanalyzer. For RNA isolation from bulk wild-type prostates, 2-3 prostates from three-week males (n=6 pools) were collected using the MagMax96 for Microarrays Total RNA Isolation kit (Invitrogen).
Libraries were prepared by the Columbia Genome Center. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Libraries were prepared using the Illumina TruSeq RNA prep kit.

value: prostate

value: 3 weeks

tag: genotype

value: wildtype


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A1_ad004


title: CTRL004 S2 fraction


title: CTRL013 RNA-seq


title: CTRL004 S2 fraction 50K rep2

source_name: CTRL004 S2 fraction 50K


title: WT-5 [MM055]


title: HGPS167 RNA-seq


title: WT-3 [MM053]


title: CTRL004 S3 fraction 50K rep2

source_name: CTRL004 S3 fraction 50K


title: CTRL004 S2 fraction 10K rep1


title: YAPTAZDKd_HS_3

city: CHENGDU

first: Min

last: Luo

state: SICHUAN

address: NO.17, the third section of South Renmin Road

institute: SICHUAN UNIVERSITY

data_processing:
Description: 2×150 paired-end sequence reads
1. Illumina Novaseq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.36.
2. Read quality was checked and QC reads were obtained for each sample using Fastp to remove low-quality, adaptor-polluted and high content of unknown base (N) reads.
3. The Clean reads is mapped to the reference genome by HISAT2 to obtain the SAM file, which is then converted into BAM by samtools software.
4. The FPKM, counts, and TPM were calculated by quantitative analysis of transcripts by stringtie.
5. Differential expression Analysis of genes between samples or under different conditions were calculated by DESeq2.
Genome_build: Alignment was to the genome (GRCm38)
Supplementary_files_format_and_content: CSV files include Gene ID and RPKM values for each sample.

source_name: skin melanoma cell

growth_protocol: B16-OVA cells were plated and cultured in 6 well plate with 2 mL medium/well(10% FBS RPMI 1640 with 50 ug/ml penicillin/streptomycin )

extract_protocol:
Then Cells were harvested for RNA extraction using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
The resulting RNA was then used to prepare libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA).

treatment_protocol: B16-OVA cells were transfected with control siRNA or a pool of siRNAs against YAP and TAZ. 48h later, cells were subjected to heat shock at 45℃  for 1 h and then recovered at 37℃ for 6 h.

tag: cell line

value: mouse melanoma cell

tag: transfection

value: pool of siRNAs against YAP and TAZ

value: heat shock 45C


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A1_ad008


title: WT-4 [MM054]

tag: tissue


title: WT-2 [MM052]


title: CTRL004 S3 fraction

value: patient derived skin fibroblast


title: CTRL013 H3K9me3 ChIP-seq


title: CTRL004 S4 fraction 50K rep1


title: CTRL004 S4 fraction 10K rep1


title: CEMBA180430_8B_1_CEMBA180430_8B_2_A1_ad002

tag: brain region


title: CNTT13

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline
Reads were mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Rattus_norvegicus.Rnor_6.0.cdna.all.fa file
Estimated transcript abundances from Salmon were imported into R using the tximeta package and analyzed for differential gene expression with edgeR
Genome_build: Rattus_norvegicus.Rnor_6.0.cdna.all.fa
Supplementary_files_format_and_content: RNA.seq.counts.csv include the counts as estimated by Salmon

organism: Rattus norvegicus

source_name: peritoneal macrophages_CNT-T- treated  rat

extract_protocol:
RNA was isolated using RNeasy mini kit (Cat. # 74104) from Qiagen. RNA quantity was measured with Qubit™ RNA HS Assay Kit (Thermofisher); the RNA integrity and quality were assessed using an Agilent Bioanalyzer using the Agilent RNA 6000 Nano kit. All RNA used had an RNA Integrity Number between 9 and 10.
Libraries were prepared starting from 100 ng of total RNA using the Illumina® TruSeq® Stranded mRNA Sample Preparation Kits following the standard protocol.
Libraries were sequenced using an Illumina HiSeq1500 platform. Approximately 50 million paired-end reads (2x125bp) per sample were obtained.

treatment_protocol: Peritoneal macrophages from CNT-7 or CNT-T-treated rats sacrificed after 15 days, were separated and isolated using flow cytometry cell sorting (FACSAria III, BD Biosciences).

value: Wistar

value: 8 weeks old

tag: injected particles

value: MWCNT-CNT-T (tangled)

value: 15 days after injection

value: Peritoneal macrophages


title: YAPTAZDKd_HS_2

tag: treatment


title: CTRL004 S3 fraction 50K rep1


title: CNTT12

tag: strain

tag: age


title: YAPTAZDKd_HS_1

tag: cell type


title: CTRL004 S2 fraction 50K rep1


title: CNTT2

tag: time point


title: CK5-trace AR-deleted luminal [MM012]

description:
P2 tamoxifen, dissected at 4 weeks
Normalized_matrix.txt
Reads sequenced on both Illumina HiSeq 2500 and HiSeq 4000 instruments.

source_name: FACs sorted prostate luminal cells

value: 4 weeks

value: CK5-CreERT2/+; R26R-YFP/+; Arflox/Y


title: CTRL004 S4 fraction 250K rep2

source_name: CTRL004 S4 fraction 250K

tag: passage


title: CK5-trace AR-deleted luminal [MM011]


title: CTRL004 RNA-seq


title: CTRL004 S3 fraction 250K rep2

source_name: CTRL004 S3 fraction 250K


title: CK5-trace luminal [MM007]

value: CK5-CreERT2/+; R26R-YFP/+


title: CTRL004 S2 fraction 250K rep2

source_name: CTRL004 S2 fraction 250K


title: YAPTAZDKd_NT_3


title: CNTT1


title: YAPTAZDKd_NT_2


title: WT_HS_3

value: control siRNA


title: CNT75

source_name: peritoneal macrophages_CNT-7-treated  rat

value: MWCNT-XNRI-7 (CNT-7)


title: CNT710


title: CNT711


title: CK8-trace AR-deleted luminal [MM005]

value: prostate

value: CK8-CreERT2/+; R26R-YFP/+; Arflox/Y


title: CTRL004 S4 fraction 250K rep1


title: CK8-trace AR-deleted luminal [MM006]


title: CK5-trace luminal [MM009]


title: WT-1 [MM051]

value: 3 weeks

value: wildtype


title: CNT73


title: YAPTAZDKd_NT_1

value: mouse melanoma cell

value: pool of siRNAs against YAP and TAZ


title: CTRL004 S3 fraction 250K rep1

value: patient derived skin fibroblast


title: WT_NT_3


title: CK8-trace AR-deleted luminal [MM004]


title: WT_HS_1

value: heat shock 45C


title: CTRL004 S2 fraction 250K rep1


title: WT_NT_2


title: CK8-trace luminal [MM002]

value: CK8-CreERT2/+; R26R-YFP/+


title: MCMV-ie2-SIINFEKL_day_60_OT1_scRNA-seq

city: Munich

first: Jonas

last: Mir

address: Trogerstraße 30

department: Institut für medizinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: Technische Universität München

description: scRNAseq

data_processing:
Cell Ranger (version 2.1.0; 10x Genomics) was used for demultiplexing and alignment using default parameters
velocyto 27 (version 0.17.17) performed counting of spliced and unspliced RNA molecules to create loom file
Python software package SCANPY (version 1.4.4) was used for downstream analysis
cells filtered out that express < 200 genes, > 3% mitochondrial genes, are no T cells; genes filtered out that express < 20 spliced counts, <10 unspliced counts
Gene counts were per-cell normalized and (log+1)-transformed
R package scater 54 (version 1.12.2) was utilized to identify 830 highly variable genes
Genome_build: mouse reference genome GRCm38 release 84
Supplementary_files_format_and_content: Matrix table with raw gene counts (unfiltered and unnormalized) in csv format
Supplementary_files_format_and_content: Matrix table with normalized and filtered (see above) gene counts
Supplementary_files_format_and_content: unnormalized and unfiltered loom-file, containing information about spliced and unspliced mRNA counts

source_name: OT-1 T cells

extract_protocol:
Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x genomics)
Chromium Single Cell 3′ Library Construction Kit (10x genomics)

value: CD8 T cell (OT-1)

value: spleen


title: Control rep2

status: Public on Sep 04 2020

city: Pittsburgh

first: Oleg

middle: E

last: Akilov

state: PA

address: 200 Lothrop Street

department: Dermatology

institute: University of Pittsburgh

data_processing:
For paired-end sequencing on Illumina NovaSeq 6000 S4 (2x150bp), both ends of the cDNA were sequenced by the read length (20M read depth; 40M total reads), which were performed by Psomagen Inc (Rockwell, MD).
The quality control of the sequenced raw read were analyzed. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics were calculated.
In order to reduce biases in analysis, artifacts such as low-quality reads, adaptor sequence, contaminant DNA, or PCR duplicates were removed. Trimmed reads were mapped to reference genome with HISAT2.
Transcripts were assembled by StringTie with aligned reads. A fold change cutoff of log2 < _1.5 or > 0.5 and a P-value cutoff of P < 0.05 were adopted to select differentially expressed and significantly regulated gene sets.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM_data2.xlsx

source_name: MBL2 cell line

growth_protocol: MBL2 were cultured in RPMI-C

extract_protocol:
Total RNA was extracted using TRIzol reagent (ThermoFisher Scientific, Waltham, MA) method immediately after cells were treated with drugs. DNA contamination was eliminated using DNase.
Library construction was performed by TruSeq Stranded mRNA. Randomly fragment purified RNA were isolated for short read sequencing. Fragmented RNA were reverse transcribed into cDNA. Adapters were ligated onto both ends of the cDNA fragments. After amplifying fragments using PCR, the fragments with sizes between 200-400 bo were selected.

treatment_protocol: 7x10^4 cells per well in 96-well plates were incubated with a single dose of drugs in three replicates. Cells along with the drug of interest, were co-incubated at 37 оC for 24 h.

value: Moloney MuLV-induced T-cell lymphoma

value: untreated control


title: Romidespin rep2

value: romidespin


title: Romidespin rep1


title: Talazoparib rep1

value: talazoparib


title: Combination rep2

value: talazoparib+romidepsin


title: Combination rep1


title: Talazoparib rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H9_ad004

source_name: C57BL/6J Male P56 Mouse Brain

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.

value: SSp

tag: Sex

value: male


title: Control rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H9_ad001


title: WT_NT_1

value: control siRNA


title: 9898MKO

city: Cincinnati

first: Shailendra

last: Patel

state: OH

address: 231 Albet Sabin Way

department: Endorcrinology

institute: University of Cincinnati

data_processing:
Fastq files were trimmed to remove adapter and low quality sequences using Trimmomatic V 0.33
Trimmed reads were mapped to the mouse reference (mm10) using hisat2 V 2.0.5
After trimming the reads were quantified using Kallisto V 0.43.1, this gives us TPM and COUNTS
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM and COUNTS for all samples

source_name: liver

growth_protocol: Dhcr7 KO and control animals were group housed with 4 animals per cage in climate controled facilty with 12hr light/dark cycle, and allowed to feed ad libtum on standard rodent chow.

extract_protocol:
Livers were stored in RNA later at -80 degrees until RNA extraction according to manufacturer protocol with Qiagen RNeasy RNA extraction kit.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA protocol

treatment_protocol: No other treatment, only difference between groups is the genetics

value: Male

value: Dhcr7flx/flx, Alb-Cre+


title: 9893FKO

value: Female


title: 9902FCon

value: Dhcr7flx/flx, Cre-


title: 9897MKO


title: 9878MCon


title: 9895FCon


title: 9889MCon


title: 9896MKO


title: 9880FKO


title: 9886FKO


title: 9908FCon


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H8_ad002

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


title: 9884MCon


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H6_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H6_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H7_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H6_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H9_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H7_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H7_ad006


title: 8-10wk livers

type: RNA

city: Iowa City

first: Jesse

last: Riordan

state: IA

address: 375 Newton Road

institute: University of Iowa

hyb_protocol: Hybridization was performed using the Gene Expression Hybridization Kit (Agilent) according to manufacturer instructions.

scan_protocol: Scanned on GenePix 4000B.

data_processing: Microarray data was processed using the R/Bioconductor package limma. Background correction was performed using the normexp + offset method. The loess and scale methods were used for normalization within and between arrays, respectively.

source_name: Liver

label_protocol: Total RNA was labeled with Cy5 (A1cf_Tg) or Cy3 (wt) dye using the Quick Amp Gene Expression Labeling Kit (Agilent) according to manufacturer instructions.

extract_protocol: Total RNA was extracted using TRIzol and treated with DNAse.

value: 8-10 weeks

value: wild-type C57BL/6J


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H5_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H5_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H4_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H5_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H4_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H6_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H5_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H3_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H3_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H3_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H12_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H12_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H7_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H12_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H11_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H2_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H2_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H3_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H11_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H2_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H10_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H11_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H10_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H10_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H11_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H1_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H1_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H2_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H1_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H1_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G9_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G8_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G8_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G9_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G8_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G7_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G9_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G7_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G9_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G7_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G7_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G6_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G6_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G7_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_H10_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G6_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G9_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G5_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G7_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G6_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G7_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G5_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G5_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G5_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G6_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G6_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G4_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G4_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G4_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G8_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G4_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G4_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G3_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G3_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G3_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G2_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G2_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G2_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G4_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G3_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G2_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G2_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G2_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G5_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G12_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G12_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G4_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G12_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G12_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G12_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G11_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G3_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G11_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G11_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G12_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G10_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G11_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G10_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G10_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G1_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G1_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G10_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G3_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G1_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F9_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G1_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F9_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F9_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F9_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F9_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F9_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G2_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F8_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G12_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F9_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_G10_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F8_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F8_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F8_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F8_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F8_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F8_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F7_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F7_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F7_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F7_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F7_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F6_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F7_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F6_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F7_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F6_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F6_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F6_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F6_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F8_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F5_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F5_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F6_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F5_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F5_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F5_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F7_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F5_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F5_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F6_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F4_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F4_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F4_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F3_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F4_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F4_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F4_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F3_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F3_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F5_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F3_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F2_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F2_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F3_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F3_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F2_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F2_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F2_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F2_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F2_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F2_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F12_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F12_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F12_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F11_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_F12_ad007


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