title: AML Day 5 mTORC1 High 3


title: siLemD2_6_BIC

status: Public on Nov 29 2020

type: SRA

city: Innsbruck

first: Galina

last: Apostolova

state: Tyrol

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck

library_source: transcriptomic

data_processing:
Reads were aligned to mm10 using RNA STAR (default parameters)
Reads were counted using featureCounts
Batch correction by removal of unvanted variation (RUVseq)
Differentail analysis with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing gene counts

molecule: total RNA

organism: Mus musculus

source_name: cortex

growth_protocol: Corical tissue was dissected from P0-P1 mice, dissociated with papain and titurated. Dissociated cortical neurons were plated in serum-containing attachment medium (MEM, 10% horse serum) on plates previously coated with poly-L-ornithine (Sigma) and laminin (Thermo Fisher Scientific). After pre-culturing for 2 h, MEM was exchanged with Neurobasal A medium, supplemented with B27 (Thermo Fisher Scientific), Glutamax (Thermo Fisher Scientific), and penicillin/streptomycin (Thermo Fisher Scientific). Neurons were cultured for 14 days at 5% CO2 and 37°C. Glial cell proliferation was inhibited by adding 5 µM cytosine arabinoside (Sigma) to the culture medium at DIV3.

extract_protocol:
RNA was isolated from primary cortical neurons using PureLink™ RNA Micro Scale Kit (Thermo Fisher Scientific).
Libraries were made according to Illumina mRNA select standard protocols

treatment_protocol: Cortical neurons were treated on DIV14 with NBQX (10 µM) for 4h or stimulated (after silencing with NBQX) with bicuculline (50 µM) for 1 h.

tag: strain

tag: tissue

value: Primary cortical cultures

tag: age

tag: genotype

value: wild type


title: siLemD2_5_BIC


title: AML Day 5 mTORC1 Low 3

city: Boston

first: Toshihiko

last: Oki

state: MA

address: 185 Cambridge Street

department: Center for Regenerative Medicine

country: USA

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
Library strategy: DNA sequencing
Illumina software used to basecalling.
The data was analyzed with the Python program provided by Addgene for alignment.
Supplementary_files_format_and_content: Tab-deliniated files include raw counts for each barcde for each sample.
Supplementary_files_format_and_content: The matrix file with raw counts for every barcode and every sample.

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
Two million FM4-Venus cells were subjected to lentiviral infection of the Clontracer library plasmid with DsRed selection marker (Addgene (Cambridge, MA, USA)) with MOI < 10%. They were incubated for 3 days and sorted with FACS AriaII (BD). One million sorted cells were obtained. The sorted cells were expanded up to 1 billion by culturing for 10 days. One million cells were transplanted into each of the four groups of the four mice.  Four hundred thousand mVenus-high or low AML cells were sorted from the mouse bone marrow by sacrificing the mice immediately before (day 0) or at either of the 3 different time after chemotherapy (day 5, 7, and 14).
Genomic DNA was extracted with the DNA/RNA mini kit (Qiagen) and sequencing libraries were constructed according to the protocol from Addgene.

tag: cell type

value: mouse AML cell line with MLL-AF9 (mFM4-mVenus)

tag: treatment

value: Day 5 of Chemothrapy (Ara-C and Doxo)


title: scramble_6_BIC


title: siLemD2_4_BIC


title: AML Day 5 mTORC1 High 2


title: A549-IVA-1H_moi1_rep1

city: Los Alamos

first: Sofiya

middle: N

last: Micheva-Viteva

state: New Mexico

address: Los Alamos National Lab

department: Bioscience

institute: Los Alamos National Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
With the PiReT application (https://github.com/mshakya/piret) we performed quality control on the RNA-seq data using FaQC v2.09. The reads that passed the QC were mapped using HISAT2 v2.1.0 against its graph FM index (GFM) human reference genome
Using htseq-count v0.11.1 we calculated the number of reads that mapped to coding sequences: Anders, S.;  Pyl, P. T.; Huber, Bioinformatics 2015, 31 (2), 166-169.
Applying count data, we calculated transcripts per kilobase per million (TPM) and found differentially expressed genes using R package DESeq2 v1.18.1.
Genome_build: human reference genome GRCh38
Supplementary_files_format_and_content: DESeq2 output

organism:
Homo sapiens
Influenza A virus (A/Port Chalmers/1/1973(H3N2))

source_name: Lung epithelial cells

growth_protocol: A549 carcinoma human alveolar epithelial cells were maintained in high-glucose DMEM (Gibco-Thermo Fisher, Grand Island, NY) supplemented with 10% (v/v) fetal bovine serum (Gibco-Thermo Fisher, Grand Island, NY).

extract_protocol:
At indicated time points post initiation of infection cells were washed with cold phosphate buffered saline (PBS) and lysed in the well with 350 µL 1% beta-mercaptoethanol supplemented RLT buffer from the RNeasy Plus Mini kit (QIAGEN, Maryland). Total RNA was isolated according to the manufacturer’s protocol including on-column removal of gDNA. After elution total RNA was treated with Turbo DNA-free Kit (AM1907, Thermo Fisher Scientific) for complete elimination of gDNA. RNA quality was determined by both direct observation of rRNA on 1% denaturing agarose gel and by Agilent bioanalyzer scan. For the preparation of Illumina libraries 5µg total RNA per sample were processed with the TruSeq Stranded Total RNA Ribo-Zero H/M/R kit (RS-122-2201, Illumina). Following rRNA removal polyA-mRNA species were separated from the non-polyA RNA pool with the polyA Spin mRNA Isolation Kit (S1560S, NEB). The two RNA sample pools were further quantified by Qubit (Invitrogen) and 15 ng were subjected to size fragmentation followed by cDNA synthesis and the addition of a terminal tagged oligonucleotide.
Tagged cDNA was purified with Agencourt AMpure XP beads and amplified with 15 cycles of PCR. Fragment length distributin of all libraries was analyzed on a BioAnalyzer high-sensitivity LabChip. Diluted libraries (5 pmol) were multiplex sequenced on the Illumina MiSeq (2- by 250-bp paired-end run, 3 to 4 million reads/sample).

treatment_protocol: The virus work was performed in compliance with CDC guidelines for biosafety level 2 agents. Virus stocks (harvested from MDCK producer cells in serum free media) were treated with 20 µg/mL TPCK trypsin for 10 min at 37◦C to activate cleavage of viral HA glycoprotein to HA1 and HA2, followed by dilution in high glucose DMEM supplemented with 10% Fetal clone III serum (10%DMEM) to neutralize the trypsin. For this infection method, A549 cells were plated 18h prior to infection in 10%-DMEM at 1x106 per well in 6-well format dishes.  Pre-activated virus stock was adjusted to the required MOI in 10% DMEM and was layered on target cells. After 2 hours of incubation of A549 cells with mock infected media or 250 µL virus containing 10%DMEM at 37◦C the media was topped with fresh 10%DMEM to a total volume of 2ml and cells were incubated at 37◦C prior to harvest.

tag: cell line

value: Influenza A/Port Chalmers/1/73 (H3N2) infected at MOI1

tag: treatment time

value: 1 hour post infection [hpi]


title: A549-IVA-1H_moi5_rep2

value: Influenza A/Port Chalmers/1/73 (H3N2) infected at MOI5


title: siLemd2_2_NBQX


title: scramble_5_BIC


title: siLemd2_1_NBQX


title: A549-IVA-1H_moi5_rep1


title: AML Day 5 mTORC1 Low 1


title: AML Day 5 mTORC1 Low 2


title: scramble_4_BIC


title: cKO7 NBQX


title: AML Day 0 mTORC1 Low 4

value: Berfore treatment


title: cKO7 BIC


title: siLemd2_3_NBQX


title: A549-IVA-3H_moi5_rep1

value: 3 hour post infection [hpi]


title: scramble_2_NBQX


title: mouse AML cells with chemotherapy mouse 4

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using STAR.
Count per million (cpm) were calculated using a protocol from Robinson MD, McCarthy DJ and Smyth GK (2010) and edgeR package. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalizedtby the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Mouse AML cells were sorted and collected from harvested mouse bone marrow with cell sorter based on expression of CD45.1 and iRFP. The sorted cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent and Qiagen DNA/RNA microkit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse AML cell line with MLL-AF9 (FM4-mVenus)

value: Ara-C and Doxo


title: mouse AML cells with chemotherapy mouse 5


title: AML Day 0 mTORC1 High 4


title: scramble_1_NBQX


title: cKO4 BIC


title: AML Day 0 mTORC1 High 3


title: mouse AML cells with chemotherapy mouse 2


title: cKO4 NBQX


title: Flx4 BIC


title: cKO6 BIC


title: cKO6 NBQX


title: AML Day 0 mTORC1 Low 3


title: AML Day 5 mTORC1 High 1


title: mouse AML cells with chemotherapy mouse 1


title: Flx6 BIC


title: mouse AML cells without chemotherapy mouse 7

value: vehicle


title: Flx7 BIC


title: scramble_3_NBQX


title: cKO5 NBQX


title: AML Day 0 mTORC1 High 1


title: mouse AML cells with chemotherapy mouse 3


title: mouse AML cells without chemotherapy mouse 5


title: Flx4 NBQX


title: mouse AML cells without chemotherapy mouse 6


title: AML Day 0 mTORC1 High 2


title: cKO3 NBQX


title: AML Day 0 mTORC1 Low 2


title: AML Day 0 mTORC1 Low 1


title: mouse AML cells without chemotherapy mouse 4


title: cKO3 BIC


title: Flx5 BIC


title: Flx3 NBQX


title: mouse AML cells without chemotherapy mouse 2


title: Flx3 BIC


title: atx1-II input DNA

city: Chongqing

first: Xianqiang

last: Wang

address: Tiansheng Road

country: China

institute: Southwest University

data_processing:
ChIP-seq reads were aligned to Arabidopsis thaliana genome (TAIR 10) using BWA with default parameters and only uniquely mapped reads were kept.
Then MACS2 (version 2.1.0) peak calling software was used to identify regions of IP enrichment over background.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig

organism: Arabidopsis thaliana

source_name: inflorescence stems

growth_protocol: Arabidopsis were grown under long day (16h light, 8h dark, 22℃)

extract_protocol:
Histone-DNA complexes were isolated with H3K4me3 antibody
The ChIP-seq library was constructed by Novogene Corporation (Beijing, China).

value: inflorescence stems

tag: chip antibody

tag: stem region

value: II


title: A549-MOCK-12H_rep3

organism: Homo sapiens

value: untreated control, time matched for infected cells

value: 12 hours


title: mouse AML cells without chemotherapy mouse 3


title: cKO2 NBQX


title: ChIP-seq of H3K4me3 in atx1-II

value: H3K4me3 (Millipore, 04-745)


title: WT-II input DNA

value: WT


title: A549-MOCK-12H_rep2


title: WT-I input DNA

value: I


title: A549-MOCK-12H_rep1


title: cKO2 BIC

value: Primary cortical cultures


title: A549-MOCK-8H_rep3

value: 8 hours


title: cKO5 BIC


title: Flx5 NBQX


title: ChIP-seq of H3K4me3 in WT-II


title: ChIP-seq of H3K4me3 in WT-I


title: Flx2 NBQX


title: mTORC1 low AML cells mouse 4

extract_protocol:
mouse mTORC1 high and low AML cells were sorted and collected from harvested mouse bone marrow with cell sorter based on mVenus intensity. The sorted cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent and Qiagen DNA/RNA microkit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mtorc1 level

value: low

value: AML cell line with MLL-AF9 (FM4-mvenus)

value: untreated


title: Flx2 BIC


title: mTORC1 high AML cells mouse 4

value: high


title: A549-MOCK-8H_rep2


title: cKO1 BIC


title: mTORC1 low AML cells mouse 1


title: A549-MOCK-4H_rep2

value: 4 hours


title: mTORC1 low AML cells mouse 2


title: A549-MOCK-4H_rep1


title: cKO1 NBQX


title: mouse AML cells without chemotherapy mouse 1

value: mouse AML cell line with MLL-AF9 (FM4-mVenus)


title: mTORC1 low AML cells mouse 3


title: RNA-seq in atx1-II

data_processing:
The RNA sequencing reads were filtered using trimmomatic and aligned to Arabidopsis genome (TAIR10) using HISAT and Bowtie2
Gene expression was defined by RSEM and estimated by FPKM
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
Total RNA was extracted from stems using Biospin Plant Total RNA Extraction Kit (Bioflux, China).
The transcriptome library was constructed by Beijing Genomics Institute (Shenzhen, China)


title: RNA-seq in WT-I


title: RNA-seq in WT-III

value: III


title: Flx1 BIC


title: competition_amplicons_pilot_A

status: Public on Nov 28 2020

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

description: UMI collapsed barcode for each strain wer tallied and demultiplexed for PCR1 and PCR2 indices.

data_processing:
Base calls performed using Casava version 1.7.
UMIs collapsed barcode counts for each strain in each condition (demultiplexed from PCR indices in the read) were counted using custom Matlab scripts. See Data S6 from paper for details on amplicon.
genome build: N/A
Library strategy: PCR amplicons with cell barcodes, UMIs, and multiplexing indices.

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: Overnight cultures started from fresh colonies were pooled and diluted to OD600 = 0.01. At OD600 =0.1, the pool were diluted to OD600 = 0.0001 in 25 mL pre-warmed medium. The culture was kept in a 125 mL flask at 37C with aeration (200 rpm) until OD600 reached 0.3.

extract_protocol:
8 mL of culture (from the pool of barcoded strains in competition) was collected at OD600=0.1 and mixed with 0.8 mL of 10:1 ethanol/phenol stop solution by rapid inversion. Cells were pelleted at 3000 rcf at 4∘C for 10 min and the supernatant decanted. The cell pellets were stored at -80∘C until DNA extraction. To extract genomic DNA (gDNA), we used the Promega Wizard gDNA extraction kit, following the manufacturer’s protocol (scaling reagents volumes by 1/3×).
Amplicons were generated by two rounds of nested PCRs to append UMIs, multiplexing indices, and sequencing adapters.

value: strains GLB115, GLB452, GLB434, GLB435, see Data S1 in paper for strain details

tag: growth medium

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with 10 uM IPTG, 0.035% wv xylose.


title: RNA-seq in WT-II

value: inflorescence stems

value: II


title: competition_amplicons_pilot_B

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with 10 uM IPTG.


title: Flx1 NBQX


title: competition_amplicons_pilot_D

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with 500 uM IPTG, 0.5% w/v xylose.


title: A549-MOCK-8H_rep1

value: untreated control, time matched for infected cells


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D4_ad006

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

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

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

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

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

value: brain

tag: source

value: PTLp

tag: target

value: VISp

tag: gender

value: female


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D4_ad007

value: RSP

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D5_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D4_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D5_ad010


title: mTORC1 high AML cells mouse 3

value: high

value: AML cell line with MLL-AF9 (FM4-mvenus)

value: untreated


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D3_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D5_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D4_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D4_ad010


title: competition_amplicons_pilot_C

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with 25 uM IPTG.


title: mTORC1 high AML cells mouse 1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D3_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D2_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D3_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D2_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D1_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D1_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D3_ad001


title: A549-MOCK-4H_rep3

value: 4 hours


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D2_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D3_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D4_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D3_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D12_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D12_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D12_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D12_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D1_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D12_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D11_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D2_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D11_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D11_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D11_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D11_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D1_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D11_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D11_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D11_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D12_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D10_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D10_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D10_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D10_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D12_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D5_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_C9_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_C9_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_C9_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_C8_ad012


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A2_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A2_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A2_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A1_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A5_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A2_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A2_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A4_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A1_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A1_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A1_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A1_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A1_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A12_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A12_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A12_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A12_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A10_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A3_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A2_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A12_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A12_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A10_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A10_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A10_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A10_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A10_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H9_ad006

value: VIS

value: SC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H9_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A10_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H8_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H8_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H9_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A3_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H7_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H7_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H7_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A12_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H6_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H6_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_A10_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H3_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H5_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H6_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H3_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H4_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H4_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H3_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H2_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H4_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H2_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H1_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H11_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H10_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G9_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H5_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H12_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H10_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G9_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G9_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G8_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G8_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H3_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G8_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G7_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G6_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_H1_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G6_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G3_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G3_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G5_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G6_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G7_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G5_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G7_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G2_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G12_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G1_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G1_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G4_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G4_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G11_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G10_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G10_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G4_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F9_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F9_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G2_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F8_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F8_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G10_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F7_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F6_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F7_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F6_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F7_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F9_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_G11_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F5_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F5_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F4_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F4_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F4_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F5_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F3_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F3_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F3_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F8_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F2_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F3_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F2_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F2_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F6_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E8_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F4_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E9_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E9_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E8_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F10_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F11_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F12_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F10_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F10_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_F12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E7_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E8_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E5_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E6_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E6_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E7_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E9_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E5_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E5_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E5_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E4_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E4_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E3_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E4_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E4_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E3_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E3_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E7_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E2_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E3_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E2_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E12_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E11_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E1_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E11_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D9_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E10_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E10_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D8_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D7_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D6_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D8_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E10_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D9_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D6_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D8_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D7_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D5_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E1_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D5_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E2_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D4_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D5_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E11_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D4_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D5_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D4_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D3_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D7_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D1_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D2_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D3_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D2_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D3_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D11_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D11_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D4_ad006


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C5_ad004


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C5_ad001


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C4_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C7_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_D12_ad004


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C3_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C3_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C1_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C11_ad006


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B8_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B6_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B7_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B9_ad001


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B5_ad006


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B6_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B4_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B4_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B3_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B3_ad002


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B2_ad002


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B1_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B5_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B1_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A8_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B10_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A8_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B11_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B11_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B11_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A8_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A9_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A9_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B10_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_B3_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A6_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_C10_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A6_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A7_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A7_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A5_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A6_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A5_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A4_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A4_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A5_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A3_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A2_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A7_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A12_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A11_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A1_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A11_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A12_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A12_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H9_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A10_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A1_ad001


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A11_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H9_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H9_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A10_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A5_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A10_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H9_ad004


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A2_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H9_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H8_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H8_ad007


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title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A1_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H8_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H8_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_A2_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H7_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H6_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H9_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H7_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H7_ad007


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title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H6_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H6_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H6_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H4_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H8_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H4_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H4_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H5_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H4_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H4_ad002


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title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H10_ad007


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title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G9_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G9_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H12_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G7_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G8_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_H10_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G8_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G8_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G8_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G7_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G8_ad007


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title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G6_ad010


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title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G7_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G6_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G5_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G5_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G7_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G5_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G4_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G7_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G4_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G4_ad007


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title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_G4_ad002


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title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E11_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E10_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E10_ad010


title: t15_MCCM_REP2

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

description: total RNA with depletion of rRNA

data_processing:
The quality of cDNA reads was analyzed using FastQC (version 0.11.2). Paired-end reads were aligned to the LUZ19 and P. aeruginosa PAO1 reference genomes (NC_010326.1 and NC_002516.2) using Bowtie 2. Next, the aligned reads were assigned to gene features using featureCounts. Reads that mapped to rRNA (60-80%,) were removed in silico.
Subsequently, counts were first normalized by gene length and then by the number of non-ribosomal reads in each sample to obtain RPKM values. Samples variance was analyzed using Principal Component Analysis (PCA) in R and outliers were excluded for further analysis, namely samples from assay MCCM_3 were discharged for further analysis being considered samples from two independent assays in MCCM and samples from three independent assays for LB medium for further analysis.
Differential gene expression analysis was performed using negative binomial distribution test from DESeq Bioconductor package in R. ANOVA test was performed to identify the most significantly up- or down-regulated genes. The p-values were adjusted using the “BH” method, which is the standard method built into the DEseq package) and are referred to as “padj”.
Genome_build: NC_002516.2
Genome_build: NC_010326.1
Supplementary_files_format_and_content: csv file containing RPKM values for all LUZ19 and PA01 genes in every sample
Supplementary_files_format_and_content: xlsx containing differential expression analysis of PA01 genes between different media (MCCM vs LB) without phage infection (0m)
Supplementary_files_format_and_content: xlsx containing differential expression analysis of LUZ19 and PA01 genes between timepoints in each medium

organism:
Pseudomonas aeruginosa PAO1
Pseudomonas phage LUZ19

source_name: early exponential 15 min infected with phage

growth_protocol: P. aeruginosa PAO1 overnight cultures were diluted 1:100 in 25 mL of either fresh LB or MCCM medium and grown to the early-exponential phase (OD600nm = 0.3, corresponding to approximately 2×108 CFU/mL). At this point, the number of colony forming units of the culture (CFU/mL) were counted by plating serial dilutions in LB plates (21) and a sample of 4.5 mL of culture was taken simultaneously (t=0 min). This sample was immediately mixed with 1:10 vol of an ice-cold stop solution (1:10 buffered phenol, 9:10 absolute EtOH) and kept on ice to stabilize RNA.

extract_protocol:
Total RNA was extracted from cell pellets using the Purelink RNA Mini Kit (Invitrogen), according to the manufacturer’s instructions.. Subsequently, each sample was treated with TURBO DNAse (Invitrogen) at 37°C to remove genomic DNA (gDNA) and then co-precipitated overnight at -20°C with 1:10 (v/v) NaOAc and 2.5 vol of absolute EtOH.   Precipitated RNA samples were centrifuged (16,000 g, 4 °C, 1h) and pellets were washed twice with 70% (v/v) EtOH. The air-dried RNA pellets were dissolved in 60 µl of DNAse and RNAse free water (Invitrogen). Total RNA concentration and purity were measured on a Nanodrop 2000 Spectrophotometer (Thermo Scientific, MA, USA) and on a Qubit 4 Fluorometer (ThermoFisher Scientific). In addition, the absence of gDNA contamination was confirmed by PCR using specific primers for both phage LUZ19 (Forward: 5’-ccgacaagatcgtccgcatgc-3’, Reverse: 5’-ggctgaagctacgcttggcc-3’) and its host (Forward: 5’-cggtcggaatctctacgcacc-3’, Reverse: 5’-cgacgccaacaacgccacg-3’). To assess RNA integrity, samples were analyzed on a Bioanalyzer (Agilent, Santa Clara, California, US) with a RNA 6000 Nano Kit (Agilent) according to manufacturer’s instructions. Samples with good RNA integrity (RNA integrity number (RIN) > 8) were treated with RiboMinus™ Transcriptome Isolation Kit (bacteria) (Invitrogen) to deplete ribosomal RNA (rRNA), according to the manufacturer’s instructions.
Depleted rRNA samples were precipitated and washed as mentioned previously and resuspended in 18-19 µL of Fragment Prime Finish mix from TruSeq Stranded mRNA Library Prep (Illumina). Successful rRNA depletion was verified on a Bioanalyzer and the final concentrations were determined using the Qubit 4 Fluorometer (Invitrogen).rRNA-depleted samples were processed immediately, according to TruSeq Stranded mRNA Library Prep recommendations. In the end, cDNA libraries were evaluated on a Bioanalyzer (Agilent) to confirm average fragments between the range of 200-300 bp and final concentrations were measured on a Qubit. The libraries’ normalization and pooling were performed according to MiniSeq System Denature and Dilute Libraries Guide: protocol A from Illumina. For each run, a library of three samples with equimolar amounts was combined with PhiX control (spike-in of 0.5-2%) and paired end sequenced (2×75 bp) on an in-house Illumina Miniseq sequencer.

treatment_protocol: At t=5 (early infection), t=10 (middle infection) and t=15 (late infection) minutes post-infection, 4.5 mL of culture was mixed with chilled stop solution and placed on ice. Immediately after, all collected samples were frozen at -80°C to block RNA transcription and degradation until sample processing.  Biologically independent infection experiments, showing a CFU reduction of at least 95% within 5 min post-infection (only 5% bacterial culture survival to LUZ19 infection) were considered as synchronized infection. Triplicate samples from synchronized infections were used for total RNA extraction.

tag: medium

value: MCCM

tag: Stage

value: early exponential

value: 15 min with phage

tag: phage moi

tag: bacteria strain


title: t15_MCCM_REP3

description: total RNA with depletion of rRNA


title: t10_MCCM_REP3

description: total RNA with depletion of rRNA

source_name: early exponential 10 min infected with phage

value: 10 min with phage


title: t10_MCCM_REP1

description: total RNA with depletion of rRNA


title: t10_MCCM_REP2

description: total RNA with depletion of rRNA


title: t5_MCCM_REP3

description: total RNA with depletion of rRNA

source_name: early exponential 5 min infected with phage

value: 5 min with phage


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E10_ad004

tag: strain

tag: age

tag: tissue

value: brain


title: t5_MCCM_REP2

description: total RNA with depletion of rRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E10_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E10_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E10_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D9_ad012

value: PTLp


title: t5_MCCM_REP1

description: total RNA with depletion of rRNA


title: t15_MCCM_REP1

description: total RNA with depletion of rRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D9_ad010

value: female


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D9_ad006

value: RSP


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D9_ad007

value: male


title: t15_LB_REP1

description: total RNA with depletion of rRNA

value: LB


title: t10_LB_REP3

description: total RNA with depletion of rRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D9_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D9_ad008


title: t10_LB_REP2

description: total RNA with depletion of rRNA


title: t15_LB_REP2

description: total RNA with depletion of rRNA


title: t15_LB_REP3

description: total RNA with depletion of rRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D8_ad004


title: 6-month-old male group

city: Guangzhou

first: Yugu

last: Li

address: Wushan street

institute: South China Agricultural University

data_processing:
Firstly, cutadapt-1.9 (cutadapt.readthedocs.io/en/stable/) was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used hisat2-2.0.4 (ccb.jhu.edu/software/hisat2/)to map reads to the genome of Homo sapiens, Ensembl v96 (command line: hisat2 -1 R1.fastq.gz -2 R2.fastq.gz -S mapped.sam). The mapped reads of each sample were assembled using stringtie-1.3.4 (ccb.jhu.edu/software/stringtie/) with default parameters (command line: stringtie -p 2 -G genome.gtf -o output.gtf -l mapped.bam). Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using gffcompare (github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kb)]).
LncRNA identification:First of all, transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC0.9-r2 (cpc2.cbi.pku.edu.cn/) with default parameters(cpc2 -i novel.fa -o cpc2.out) and CNCI2.0 (wwww.bioinfo.org/software/cnci) with default parameters (CNCI.py -f novel.fa -o CNCI.result -p 1 -m ve -g novel.gtf -d genome.fa) to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed and remained transcripts were considered as lncRNAs.
Different expression analysis of mRNAs and lncRNAs:StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM. The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >= 1 or log2 (fold change) <= -1 and with statistical significance p value < 0.05 by R package edgeR (bioconductor.org/packages/release/bioc/html/edgeR.html/) .
Target gene prediction and functional analysis of lncRNAs:To explore the function of lncRNAs, we predicted the cis-target genes of lncRNAs. lncRNAs may play a cis role acting on neighboring target genes. In this study, coding genes in 100,000 upstream and downstream were selected by python script. Then, we showed functional analysis of the target genes for lncRNAs with GO and KEGG enrichment analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Thymus

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). After the enriched circRNAs were fragmented into small pieces using divalent cations under high temperature. After removing ribosomal RNAs, the left RNAs were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs.The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: BALB/c

value: thymus


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E12_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D8_ad002


title: t5_LB_REP3

description: total RNA with depletion of rRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D8_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D8_ad008


title: t5_LB_REP2

description: total RNA with depletion of rRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D7_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D8_ad001


title: 6-month-old female group


title: 1-month-old male group


title: t5_LB_REP1

description: total RNA with depletion of rRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D7_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D7_ad007


title: a-100ul-1-input-combined_DNA

city: Beijing

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

data_processing:
bcl2fastq2 v.2.17.1.14 software was used for generating fastq files.
We removed low-quality reads including those with ≥ 5% unidentified nucleotides, > 5 nt aligned to the adapter, and with > 50% of bases with phred quality < 19. Then,for RNA-seq data, high-quality reads of four non-strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4); for ChIPSeq data,high-quality reads of four non-strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Bowtie2.
For RNASeq, mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Stringtie (v.1.3.3);for ChIPSeq, we remove PCR duplicate used samtools.
For RNASeq,, reads counts of sequence files were obtained using featureCounts(v.1.6.4); For ChIPSeq, we used MACS2 to call peaks.
For RNASeq, Differentially expressed genes of samples were obtained using DESeq2; for ChipSeq, ChipSeeker was used for annotating peaks.
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: For RNASeq, Comma-delimited text files include FPKM values for each sample. For ChIPSeq, we provided bigWig file for every sample.

organism: Sus scrofa

source_name: Pig iPS

growth_protocol: LCDMV culture system maitain pig iPS selfrenew and growth.

extract_protocol:
The suspended cells were collected for RNA extraction according to the RNA extrac kit, leaving behind the attached cells (primarily consisting of feeders). Total RNA samples (2 µg each) were suspended in 15 µL RNAase-free ddH2O, packed in dry ice, and submitted to Anoroad Gene Technology Corporation (Beijing, China) for RNA sequencing.
Approximately 2 µg total RNA (each sample) and the Oligo(dT) magnetic head were used for generating RNA-Seq cDNA libraries, and then, RNA -seq was conducted following the manufacturer's standard procedures.

treatment_protocol: Before RNA extraction, feeder cells were removed in order to avoid sequencing artifacts. Dissociated pig PC-iPS cells were plated onto six-well plates and cultured for 1 hour.

tag: breed

value: domestic pig

tag: developmental stage

value: adult

tag: cell type

value: Induced pluripotent stem cells (iPSCs)

tag: genotype/variation

value: overexpressing IRF1-flag


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D8_ad012

value: SC


title: 3-month-old female group


title: a100ul-2input_DNA


title: 1-month-old female group


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D7_ad002


title: DNA-flag-2-combined_ChIPSeq

tag: chip antibody

value: anti-FLAG


title: t10_LB_REP1

description: total RNA with depletion of rRNA

value: early exponential

tag: treatment time


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D7_ad001


title: 3-month-old male group


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_E10_ad007


title: ribo_GLB372

description: Sequence reads were trimmed for adaptor sequences.

data_processing:
Base calls performed using Casava version 1.7.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The footprint reads with size between 15 to 44 nucleotides in length were mapped to the genome using the center-weighted approach: for each footprint read, the center residues that are at least 10 nucleotides away from either ends were given a weight of one over the length of the fragment (minus the 10 nucleotides on both ends) to generate the wig file, for footprint <21 nt long, the read count of 1 was added at the center of the footprint.
genome build: NC_000964.3
processed data files format and content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position.
Library strategy: Ribo-Seq (ribosome protected mRNA)

growth_protocol: Overnight cultures were diluted to OD600 0.0003 in 250 mL fresh media. The culture was kept in a 2.8 L flask at 37C with aeration (200 rpm) until OD600 reached between 0.15 to  0.3.

extract_protocol:
Extraction was performed as described in detail previously (Li et al., Cell 2014 and Lalanne et al, 2018). 250 mL of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 mL canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C.
Ribosome protected mRNA fragments were size selected via gel purification, dephosphorylated at the 3’ end and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

value: GLB372, see Data S1 in paper for strain details

tag: growth medium


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D6_ad010

tag: source


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D6_ad008

tag: target


title: a-irfl-flag_DNA_ChIPSeq


title: DW.8_RNA-seq

description: processed data file: sample_genes_counts.txt

value: overexpression of IRF-1


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D6_ad006

value: brain

tag: gender


title: rend_GLB372

data_processing:
Base calls performed using Casava version 1.7.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 2 -m 2. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peak shadows were not removed.
genome build: NC_000964.3
processed data files format and content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position.
Library strategy: Rend-Seq

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D7_ad010

value: PTLp


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D6_ad004


title: DW.6_RNA-seq


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D7_ad006

value: female


title: shFTO-rep2

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
Reads were aligned to the hg19 genome assembly using TopHat v2.1.1
For each sample, reads counts of all genes were computed using HTSeq v0.6.0.Differentially-expressed genes between src and shFTO were determined  using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: hg19
Supplementary_files_format_and_content: txt: files include reads count for each sample.

source_name: hepatocellular carcinoma_shFTO

extract_protocol:
Total RNA were isolated by Trizol reagent , digested with DNase and purified with RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Human hepatoma derived cell line

tag: shRNA

tag: passage


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D7_ad004

value: RSP

value: male


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D6_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D5_ad010


title: shFTO-rep1


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D5_ad012


title: DW.3_RNA-seq


title: DW.1_RNA-seq


title: src-rep1

source_name: hepatocellular carcinoma_src


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D5_ad006


title: src-rep2


title: Tumorsphere-A1471_COMBO-treated_24h

first: Alain

last: Pacis

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling
Reads were mapped to mouse genome version mm10 using Spliced Transcripts Alignment to a Reference (STAR).
Read counts for each sample are obtained using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
A1005, A1129, and A1471 tumourspheres treated with inhibitors (DMSO, Crizotinib, PD173074, or drug combination for 24h) were collected and total RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions. High RNA quality was verified using the Bioanalyzer RNA 6000 Nano assay (Agilent).
The samples were sequenced using a NextSeq500 sequencer (Illumina) by the Genomics Core Facility of the Institute of for Research in Immunology and Cancer, Université de Montréal.

value: breast tumour

tag: genotype

tag: treatment

value: Combo