title: Cochlea SGNs Mouse 4

city: Boston

first: Gabriela

last: Pregernig

state: Massachusetts

address: 1325 Boylston Street, Suite 500

institute: Decibel Therapeutics

description: 3' polyA RNASeq reads

data_processing:
3' polyA RNA-Seq (10X Genomics, chemistry v2)
CellRanger 2.0.1 (reference genome: mm10)
The gene count matrices were loaded into Seurat (v1.4) using the CreateSeuratObject function. Parameters used were min.cells=10, min.genes=100 and normalization.method="LogNormalize". Cells containing >5% red blood cell transcripts were removed.
Dimensional reduction (PCA) and clustering were performed using Seurat.
Clusters of cells expressing known spiral ganglion neuron markers (such as Nefh) were selected. Cells identified as type I spiral ganglion neurons were further subclustered to identify type I neuronal subtypes.
Genome_build: mm10
Supplementary_files_format_and_content: SGNs_rawCounts.txt : UMI counts (as calculated using CellRanger pipeline) showing the expression levels for each gene (rows) in each single cell (columns). The column header provides the cell barcode and the sample/mouse of origin separated by '_'.
Supplementary_files_format_and_content: SGNs_normCounts.txt : normalized counts (after Seurat processing) showing the expression levels for each gene (rows) in each single cell (columns). The column header provides the cell barcode and the sample/mouse of origin separated by '_'.
Supplementary_files_format_and_content: SGNs_metadata.txt : Table containing cell metadata. Columns are Cell (cell barcode and sample of origin, as appears in count matrices), NeuronType (indicates Type I or Type II spiral ganglion neuron identity) and NeuronSubtype (indicates Type I spiral ganglion subtype).

source_name: WT mouse spiral ganglion cells

extract_protocol:
Temporal bones from 9 wko, male CBA/CaJ mice (n = 8 capsules from 4 mice) were isolated in ice-cold Leibovitz’s L-15 medium, and the overlying bone and lateral wall was extracted from apex to base, leaving just the modiolus.  The remaining structures consisted of the spiral ganglion, the spiral limbus, inner sulcus, and portions of the organ of Corti and outer sulcus.  Microdissected tissue from each mouse was pooled in a solution of Leibovitz containing 200 units/mL collagenase IV (Sigma) and 10 kunitz/ml DNase I (Stem Cell Technologies) and incubated for 30 min at 37 °C to digest extracellular matrix.  The collagenase IV solution was then replaced with EBSS containing 100 units of papain (Worthington Biochemical), 1.6 mM L-cysteine, 0.8 mM EDTA, 15 mM HEPES, and 10 kunitz/ml DNase I and incubated for an additional 30 min at 37 °C, triturating with a 1000 uL pipette every 10 min to generate a single cell suspension.  An equal volume of Leibovitz containing 20% ovomucoid protease inhibitor (Worthington Biochemical) was added, and the dissociated cells were passed through a 20 mm filter (pluriSelect) to remove large debris.  The cells were pelleted at 300g for 5 min, washed with PBS, and then pelleted and resuspended in PBS containing 0.1% BSA.  Finally, a 10 uL sample of the cell suspension was counted on a Luna Fl automated counter using a Live/Dead assay (Thermo Fisher Scientific).  Total time from euthanasia to single-cell capture was 2.5 h.
The cell suspension was diluted to a concentration of ~10,000 cells per uL and immediately captured, lysed, and primed for reverse transcription (RT) using the high throughput, droplet microfluidics Gemcode platform from 10X Genomics with v2 chemistry (Zheng et al., 2017). Each droplet on the Gemcode co-encapsulates a cell and a gel bead that is hybridized with oligo(dT) primers encoding a unique cell barcode and unique molecular identifiers (UMIs) in lysis buffer.  The capture process takes 5 min, after which the transcriptomes captured on gel beads are pooled and immediately reverse transcribed to cDNA. Since all cDNA is pooled and PCR amplified, cell barcodes and UMIs facilitate demultiplexing of the originating cell and mRNA transcript after sequencing.  RT, PCR amplification of cDNA, and preparation of a library from 3’ ends were conducted according to the manufacturer’s published protocol.  The library was sequenced on an Illumina NovaSeq 6000 at the Broad Institute using 2 x 100 bp paired-end reads.

value: CBA/CaJ

tag: age

value: 9 weeks

tag: genotype/variation

value: wild-type

tag: Sex

value: male

value: temporal bones


title: Cochlea SGNs Mouse 3

status: Public on Aug 13 2018

type: SRA

country: USA

description: 3' polyA RNASeq reads

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: German7

type: genomic

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description:
Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).
processed and raw data files:
Tambets_et_al_660k_Matrix_processed.txt; Tambets_et_al_660k_Matrix_signal_intensities.txt

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Germans

tag: region

value: Europe

value: blood


title: Cochlea SGNs Mouse 1

description: 3' polyA RNASeq reads


title: Fev-Cre;mTmG reporter

city: San Francisco

first: Jeremy

last: Reiter

state: California

address: 555 Mission Bay Boulevard South

institute: UCSF

description:
single cell RNA sequencing of E14.5 Fev-Cre;mTmG pancreas, aligned to mm10 genome with GFP and TdTomato added
Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v2.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v2.1 using default parameteres.
Genome_build: mm10 for all Swiss Webster. For Fev-Cre;Rosa26mTmG, eGFP and TdTomato sequences from the mTmG mouse line (Muzumdar MD. et. al., 2007) were added to the mm10 genome FASTA and annotations. The genome was prepared as according to 10X Genomics instructions for custom genome builds.
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: pancreatic cells

extract_protocol:
Pancreata were isolated from mouse embryos and dissociated in TrypLE Express at 37C with pipet trituration at 5-minute intervals during incubation. E12.5 pancreata were dissociated for 10 minutes, E14.5 pancreata for 15 minutes, and E17.5 pancreata for 30 minutes. Dissociations were neutralized with FACS buffer (10% FBS + 2mM EDTA in phenol-red free HBSS). Dissociated cells were passed through a 30um cell strainer and stained with Sytox live/dead stain (Thermo Fisher), along with protocol specific stains noted in the individual sample extract protocol descriptions. Stained cells were washed twice in FACS buffer and then processed through a BD FACS Aria II.
For E14.5 Fev-Cre;ROSA26mTmGpancreata, live GFP+ and Tdtomato+ cells were collected in separate tubes.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument with v2 kit and reagents.
droplet-based single cell RNA-Seq

value: pancreas

tag: developmental stage


title: Cochlea SGNs Mouse 2

description: 3' polyA RNASeq reads


title: HCC + LECT2_3

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® MTA1.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, Chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V20 was used for annotation.

label: biotin

source_name: HCC + LECT2

label_protocol: 400 pg of total RNA is reverse transcribed  following the Ovation PicoV2 kit (Nugen). Briefly, the resulting double stranded cDNA is used to produce sens target cDNA using SPIA amplification. This cDNA is fragmented and biotin labelled using EncoreBiotin module (Nugen)

extract_protocol: Total RNA from FACS sorted myeloid cells were extracted using Rneasy Micro Kit Plus (Qiagen) according to the manufacturer's instruction

value: liver tumor

tag: cell type

value: Monocytes

tag: genotype

value: + LECT2


title: control_0hr_rep2

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

country: United Kingdom

institute: GSK

hyb_protocol: Labelled cDNA was hybridized onto Mouse Genome 430 2.0  GeneChip oligonucleotide arrays (Affymetrix).

scan_protocol: Standard protocols

data_processing: Data were analysed in R/Bioconductor, normalised by RMA

label: Biotin

source_name: S. pneumoniae infected mice_control_0hr_whole lung

label_protocol: FL-Ovation cDNA Biotin Module V2 kit (NuGen).

growth_protocol: Standard laboratory conditions

extract_protocol: WT-Ovation Pico RNA Amplification System (NuGen).

treatment_protocol: intranasal

tag: strain C57BL/6Babr

tag: mouse status

value: S. pneumoniae infected mouse

tag: treated with

value: control

tag: time point

value: whole lung


title: control_0hr_rep5


title: HCC + LECT2_2


title: control_0hr_rep4


title: HCC -LECT2_3

source_name: HCC -LECT2

value: - LECT2


title: control_0hr_rep3


title: control_0hr_rep6


title: HCC -LECT2_1


title: Fev-Cre;mTmG no reporter

description:
single cell RNA sequencing of E14.5 Fev-Cre;mTmG pancreas, aligned to mm10 genome without GFP or TdTomato added
Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10


title: control_0hr_rep1

data_processing:
Data were analysed in R/Bioconductor, normalised by RMA
Data were analysed in R/Bioconductor, normalised by RMA


title: E17.5 2 SW

description:
single cell RNA sequencing of E17.5 swiss webster pancreas (technical replicate 2)
Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10

extract_protocol:
Pancreata were isolated from mouse embryos and dissociated in TrypLE Express at 37C with pipet trituration at 5-minute intervals during incubation. E12.5 pancreata were dissociated for 10 minutes, E14.5 pancreata for 15 minutes, and E17.5 pancreata for 30 minutes. Dissociations were neutralized with FACS buffer (10% FBS + 2mM EDTA in phenol-red free HBSS). Dissociated cells were passed through a 30um cell strainer and stained with Sytox live/dead stain (Thermo Fisher), along with protocol specific stains noted in the individual sample extract protocol descriptions. Stained cells were washed twice in FACS buffer and then processed through a BD FACS Aria II.
For Swiss Webster embryonic pancreatic dissociations, cells were also stained with the mesenchymal marker, CD140a. Stained cells were washed twice in FACS buffer and then processed through a BD FACS Aria II. To enrich for epithelial populations, live, CD140a- cells were collected from E12.5, E14.5, and E17.5 Swiss Webster pancreata.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument with v2 kit and reagents.
droplet-based single cell RNA-Seq

value: Swiss Webster


title: HCC + LECT2_1


title: TET2 shRNA-1: MDS-L cells with shTET2-Replicate1

city: Duarte

first: Sun

last: Jie

state: CA

address: 1500 East Duarte Road

institute: City of Hope

description: MDS-L cells transduced with lentiviral vector containing interference squence targeting TET2 replicate 1

hyb_protocol: 0.1 µg Cy5-labeled aRNA of the respective sample was fragmented and hybridized onto HlncOA 1.0 using Phalanx OneArray hybridization kit (Phalanx Biotech Group). Hybridization was performed for 17h, rotating at a speed of 10rpm at 65℃ in an Agilent hybridization oven (G2545A). After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 and 1 minute with 37℃Wash buffer 2.

scan_protocol: HlncOA 1.0arrays were scanned by Agilent Microarray Scanner( G2505C ) HD_1X color protocol （Dye channel: R ; Scan resolution : 2 um; Tiff: 20-bit; Red PMT gain: 100%; XDR: No）and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by R language (v3.4.0). The probes will filter out control probes and normalized by median scaling method between all samples. Pair-wise comparisons between samples were calculated by Bioconductor limma package and presented by log2 fold change and p-value.

source_name: MDS-L cells with shTET2

label_protocol: 0.5 µg of total RNA was reverse-transcribed and amplified using Onearray Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group). Indirect labeled the aa-UTP by NHS-Cy5 (AAT Bioquest ). Dye incorporation and aRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RPMI 1640 medium with 10% FBS and 1% penicillin-streptomycin in the presence of 30 ng/mL human recombinant human IL-3.

extract_protocol: Total RNA was extracted using Trizol Reagent (Thermo Fisher Scientific) following the manufacture`s instructions. RNA quality was assessed by spectrophotometry(NanoDrop, ND1000) and gel electrophoresis. To be considered as high-quality, the RNA had to have the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: MDS-L cells were transduced with SIRT1 shRNA, TET2 shRNA or control shRNA

tag: cell line

value: MDS-L


title: TET2 shRNA-2: MDS-L cells with shTET2-Replicate2

description: MDS-L cells transduced with lentiviral vector containing interference squence targeting TET2 replicate 2


title: poorly differentiated HCC_3

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

source_name: poorly differentiated HCC

label_protocol: 390 ng of total RNA is reverse transcribed  following the Gene chip® WT Plus kit (Affymetrix). Briefly, the resulting double stranded cDNA is used to produce single stranded RNA using T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled.

extract_protocol: Total RNA from frozen liver tissues were extracted using Rneasy Mini Kit (Qiagen) according to the manufacturer's instruction

value: Liver

tag: histology

value: poorly differentiated HCC


title: Erythroid Cells-adult-4

city: Khlong Nung

first: Pavita

last: Kaewprommal

state: Pathum Thani

department: NBT

country: Thailand

institute: NSTDA

hyb_protocol: Sample were hybridized to Affymetrix Human Gene 2.0 ST Array for 16 h at 45C with rotation at 60 rpm, washed and stained using the FS450_0002 fluidics protocol

scan_protocol: Affymetrix3000 7G scanner

data_processing: data were preprocessed using robust multi-array average (RMA) method

source_name: Adult cells, peripheral blood

label_protocol: Biotinylated fragmented cRNA was synthesized from 100 ng of each RNA using the AffymetrixGeneChip® WT PLUS Reagent kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Primary CD34 cells derived from fetal liver and adult healthy peripheral blood were cultured by using a two-phase liquid culture system.  Cells were cultured for 4 days in phase I medium which consisted of Modified Dulbecco’s Medium (IMDM) supplemented with 20% of Fetal Bovien Serum (FBS), 300 ng/mL holo-transferrin (holo-TF), 25 ng/mL interleukin-3, 50 ng/mL human stem cell factor, and 2 units/mL human recombinant erythropoietin (EPO). After 4 days, cells were collected and reseeded in phase II medium which consisted of IMDM supplemented with 20% FBS, 300 ng/ml holo-TF, and 5 units/mL EPO. The culture was maintained under an atmosphere of 5% CO2 at 37 °C.

extract_protocol: Cells were stained for CD71 and GPA cell surface markers and FACS sorted for erythroid populations comprising of high CD71 and GPA expression (CD71high/GPA+ve) using BD FACSAria™ III cell sorter. Total RNA was isolated using the RNeasyPlus Micro kit (Qiagen)

value: Adult cell

value: Erythroid


title: TET2 shCtrl-2: MDS-L cells with shCtrl for TET2-Replicate2

description: MDS-L cells transduced with lentiviral vector containing interference control squence replicate 2

source_name: MDS-L cells with shCtrl for TET2


title: Erythroid Cells-adult-1


title: Erythroid Cells-adult-5


title: E17.5 1 SW

description:
single cell RNA sequencing of E17.5 swiss webster pancreas (technical replicate 1)
Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10


title: E14.5 SW

description:
single cell RNA sequencing of E14.5 swiss webster pancreas
Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10


title: Erythroid Cells-adult-2


title: poorly differentiated HCC_4


title: TET2 shCtrl-1: MDS-L cells with shCtrl for TET2-Replicate1

description: MDS-L cells transduced with lentiviral vector containing interference control squence replicate 1


title: E12.5 SW

description:
single cell RNA sequencing of E12.5 swiss webster pancreas
Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10


title: HCC -LECT2_2


title: Erythroid Cells-adult-3


title: Erythroid Cells-fetal-4

source_name: Fetal liver, aborted fetuses

value: Fetal liver


title: well differentiated HCC_4

source_name: well differentiated HCC

value: well differentiated HCC


title: Erythroid Cells-fetal-5


title: Erythroid Cells-fetal-2


title: SIRT1 shRNA-2: MDS-L cells with shSIRT1-Replicate2

description: MDS-L cells transduced with lentiviral vector containing interference squence targeting SIRT1 replicate 2

source_name: MDS-L cells with shSIRT1


title: well differentiated HCC_3


title: Erythroid Cells-fetal-1


title: poorly differentiated HCC_2


title: SIRT1 shCtrl-1: MDS-L cells with shCtrl for SIRT1-Replicate1

source_name: MDS-L cells with shCtrl for SIRT1


title: SIRT1 shRNA-1: MDS-L cells with shSIRT1-Replicate1

description: MDS-L cells transduced with lentiviral vector containing interference squence targeting SIRT1 replicate 1


title: well differentiated HCC_1


title: well differentiated HCC_2


title: SIRT1 shRNA-3: MDS-L cells with shSIRT1-Replicate3

description: MDS-L cells transduced with lentiviral vector containing interference squence targeting SIRT1 replicate 3


title: SIRT1 shCtrl-3: MDS-L cells with shCtrl for SIRT1-Replicate3

description: MDS-L cells transduced with lentiviral vector containing interference control squence replicate 3


title: SIRT1 shCtrl-2: MDS-L cells with shCtrl for SIRT1-Replicate2


title: poorly differentiated HCC_1


title: Erythroid Cells-fetal-3


title: Tmp_RZ468_F85_AD6

status: Public on Aug 12 2018

city: Saarbruecken

first: Pavlo

last: Lutsik

country: Germany

institute: Saarland University

description: Fresh frozen human post-mortem brain tissue from temporal cortex.

hyb_protocol: standard as recommended by Illumina

scan_protocol: standard as recommended by Illumina

data_processing: The raw data was background corrected and scale-normalized in accordance with the manufacturer recommended procedures. Probes with a detection p-value < 0.01 were removed and all samples were merged. The normalized data was corrected for array batch effects using combat (sva package)

source_name: Temporal Cortex

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ DNA methylation Gold kit (Zymo Research) according to the manufacturer's standard protocol.

extract_protocol: Brain tissue from 100-600 mg of human post-mortem occipital cortex was used for extraction of intact nuclei. Nuclei were fixed and immuo-labled with antibodies against pan-neuronal marker NeuN and then FACS-separated into neuron- (NeuN-positive) and glia-enriched (NeuN-negative) fractions. DNA was isolated using the QIAamp DNA Micro Kit (Qiagen) according to the manufacturer's protocol and then checked for purity and degradation before analysis.

value: bulk

tag: diagnosis

value: AD

value: Temporal cortex

value: F


title: Tmp_RZ375_M80_AD5

tag: age

value: M


title: Tmp_RZ433_F75_AD6


title: Tmp_RZ339_M60_CTRL0

value: CTRL


title: Tmp_RZ296_M87_AD5


title: Tmp_RZ459_F79_AD5


title: Tmp_RZ323_M76_AD5


title: Tmp_RZ413_M70_AD6


title: Tmp_RZ369_F88_AD5


title: Tmp_RZ262_F78_AD6


title: Tmp_RZ160_M62_AD6


title: Tmp_RZ307_F78_AD6


title: Tmp_RZ181_F93_AD4


title: Tmp_RZ342_F83_CTRL2


title: Tmp_RZ155_F85_AD3


title: Tmp_RZ340_M54_CTRL0


title: Tmp_RZ149_F78_AD6


title: Tmp_RZ256_M87_AD5


title: Tmp_RZ244_F76_AD6


title: Tmp_RZ302_M83_AD5


title: Tmp_RZ163_F85_AD4


title: Tmp_RZ171_F73_AD6


title: Tmp_RZ162_F97_AD5


title: Tmp_RZ261_F88_AD6


title: Tmp_RZ147_F80_CTRL4


title: Tmp_RZ146_M46_CTRL0


title: nst1-1_nst3-1_stem_rep3

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes to produce the normalized signal value.

organism: Arabidopsis thaliana

source_name: nst1-1 nst3-1 Arabidopsis Col0 stem, 10 cm long

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Qick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown on soil in greenhouse at 23 Celsius degree in 16h/8h day/night cycle.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: None applied

value: nst1-1 nst3-1

value: stem


title: Tmp_RZ170_F93_AD5


title: Tmp_RZ148_F77_CTRL2


title: Tmp_RZ391_F80_AD5


title: Tmp_RZ145_F85_CTRL1


title: Tmp_RZ144_F68_AD6


title: Tmp_RZ140_M87_CTRL2


title: Tmp_RZ119_M75_AD6


title: Tmp_RZ143_M61_CTRL0


title: Tmp_RZ109_F89_AD4


title: Tmp_RZ092_M71_CTRL1


title: Tmp_RZ090_M53_CTRL1


title: Tmp_RZ133_M85_CTRL4


title: Tmp_RZ104_M59_CTRL2


title: Tmp_RZ089_M53_CTRL0


title: Tmp_RZ085_M63_CTRL1


title: Tmp_RZ098_F73_AD


title: Tmp_RZ079_F75_CTRL4


title: Tmp_RZ076_M18_CTRL0


title: Tmp_RZ084_M50_CTRL0


title: Tmp_RZ077_M57_CTRL1


title: Tmp_RZ068_F93_AD6


title: Tmp_RZ082_F46_CTRL1


title: Tmp_RZ051_M90_AD


title: Tmp_RZ081_F76_CTRL4


title: Tmp_RZ058_F77_CTRL2


title: Tmp_RZ052_F82_AD5


title: Tmp_RZ067_F67_AD6


title: Tmp_RZ070_M53_CTRL0


title: Tmp_RZ059_M75_CTRL2


title: Tmp_RZ055_M80_AD5


title: Tmp_RZ065_F65_AD6


title: Tmp_RZ099_F55_CTRL0


title: Tmp_RZ057_F88_CTRL2


title: Tmp_RZ069_M74_AD6


title: Ftl_RZ459_F79_AD5

description: Fresh frozen human post-mortem brain tissue from frontal cortex.

source_name: Frontal Cortex

value: Frontal cortex


title: Tmp_RZ063_M73_AD6


title: Ftl_RZ391_F80_AD5


title: Ftl_RZ369_F88_AD5


title: Tmp_RZ016_M83_AD6


title: Ftl_RZ339_M60_CTRL0


title: Ftl_RZ307_F78_AD6


title: Ftl_RZ323_M76_AD5


title: Ftl_RZ342_F83_CTRL2


title: Ftl_RZ302_M83_AD5


title: Ftl_RZ433_F75_AD6


title: Ftl_RZ149_F78_AD6


title: Ftl_RZ340_M54_CTRL0


title: Ftl_RZ262_F78_AD6


title: Ftl_RZ163_F85_AD4


title: Ftl_RZ413_M70_AD6


title: Ftl_RZ244_F76_AD6


title: Ftl_RZ256_M87_AD5


title: Ftl_RZ261_F88_AD6


title: Ftl_RZ162_F97_AD5


title: Ftl_RZ147_F80_CTRL4


title: Ftl_RZ375_M80_AD5


title: Ftl_RZ296_M87_AD5


title: Ftl_RZ160_M62_AD6


title: Ftl_RZ155_F85_AD3


title: Ftl_RZ171_F73_AD6


title: Ftl_RZ145_F85_CTRL1


title: Ftl_RZ144_F68_AD6


title: Tmp_RZ121_M83_AD6


title: Ftl_RZ146_M46_CTRL0


title: Ftl_RZ148_F77_CTRL2


title: Ftl_RZ143_M61_CTRL0


title: Ftl_RZ122_F82_AD6


title: Ftl_RZ133_M85_CTRL4


title: Ftl_RZ121_M83_AD6


title: Tmp_RZ021_M81_AD


title: Ftl_RZ099_F55_CTRL0


title: Ftl_RZ082_F46_CTRL1


title: Ftl_RZ092_M71_CTRL1


title: Ftl_RZ109_F89_AD4


title: Ftl_RZ085_M63_CTRL1


title: Ftl_RZ104_M59_CTRL2


title: Ftl_RZ119_M75_AD6


title: Ftl_RZ098_F73_AD


title: Ftl_RZ084_M50_CTRL0


title: Ftl_RZ070_M53_CTRL0


title: Ftl_RZ089_M53_CTRL0


title: Ftl_RZ067_F67_AD6


title: Ftl_RZ069_M74_AD6


title: Ftl_RZ090_M53_CTRL1


title: Ftl_RZ076_M18_CTRL0


title: Ftl_RZ081_F76_CTRL4


title: Ftl_RZ079_F75_CTRL4


title: Ftl_RZ068_F93_AD6


title: Ftl_RZ058_F77_CTRL2


title: Ftl_RZ059_M75_CTRL2


title: Ftl_RZ065_F65_AD6


title: Ftl_RZ052_F82_AD5


title: Ftl_RZ063_M73_AD6


title: Ftl_RZ051_M90_AD


title: Ftl_RZ055_M80_AD5


title: MUN.2015.016.AD.F.73.Neuron

description: Fresh frozen human post-mortem brain tissue from occipital cortex separated into neuron- and glia-specific fractions.

source_name: Occipital Cortex

value: Neuron

value: Occipital cortex


title: MUN.2015.015.AD.M.85.Neuron


title: Ftl_RZ021_M81_AD


title: Tmp_RZ122_F82_AD6


title: Ftl_RZ057_F88_CTRL2


title: Ftl_RZ181_F93_AD4


title: MUN.2015.013.AD.F.93.Neuron


title: MUN.2015.012.AD.F.78.Neuron


title: Ftl_RZ170_F93_AD5


title: MUN.2015.014.AD.M.70.Neuron


title: MUN.2015.011.CTRL.F.63.Glia

value: Glia


title: MUN.2015.014.AD.M.70.Glia


title: MUN.2015.013.AD.F.93.Glia


title: MUN.2015.016.AD.F.73.Glia


title: Ftl_RZ077_M57_CTRL1


title: MUN.2015.008.CTRL.M.85.Neuron


title: MUN.2015.012.AD.F.78.Glia


title: MUN.2015.015.AD.M.85.Glia


title: MUN.2015.009.CTRL.F.85.Glia


title: MUN.2015.007.CTRL.M.63.Neuron


title: MUN.2014.006.CTRL.M.75.Neuron


title: MUN.2014.005.CTRL.M.71.Neuron


title: MUN.2015.007.CTRL.M.63.Glia


title: MUN.2014.003.AD.M.76.Glia


title: MUN.2014.006.CTRL.M.75.Glia


title: MUN.2014.003.AD.M.76.Neuron


title: MUN.2015.009.CTRL.F.85.Neuron


title: MUN.2014.005.CTRL.M.71.Glia


title: MUN.2014.004.AD.F.75.Glia


title: MUN.2015.008.CTRL.M.85.Glia


title: MUN.2014.002.CTRL.F.77.Glia


title: MUN.2014.004.AD.F.75.Neuron


title: MUN.2014.002.CTRL.F.77.Neuron


title: Dnr19_M_71_CTRL_Neuron


title: Dnr19_M_71_CTRL_Glia


title: Dnr20_M_75_CTRL_Neuron


title: Dnr16_F_88_CTRL_Glia


title: Dnr16_F_88_CTRL_Neuron


title: Dnr18_M_87_CTRL_Neuron


title: Dnr17_M_19_CTRL_Neuron


title: Dnr20_M_75_CTRL_Glia


title: MUN.2015.011.CTRL.F.63.Neuron


title: Dnr14_F_77_CTRL_Neuron


title: Dnr18_M_87_CTRL_Glia


title: Dnr17_M_19_CTRL_Glia


title: Dnr14_F_77_CTRL_Glia


title: Dnr15_F_83_CTRL_Glia


title: mPGES-1 KO Ly6C-low

city: Sagamihara

first: Nobuyuki

last: Nishizawa

address: 1-15-1 Kitasato Minami-ku

department: Surgery

institute: Kitasato University school of midicine

description: RMA expression value derived from Expression Console software; gene-level analysis

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multiarray Average (RMA) using Affymetrix default analysis settings.

source_name: Livers from mPGES-1 knock out mice

label_protocol: Biotinylated ssDNA were prepared using Affymetrix GeneChip WT Pico Reagent Kit according to the standard Affymetrix protocol from 5 ng total RNA.

extract_protocol: RNA was isolated with the TRIzol, according to the manufacturer’s instructions.

value: Hepatic macrophages

value: Liver tissue

tag: genotype/variation

value: mPGES-1 knock out


title: mPGES-1 KO Ly6C-hi


title: Ftl_RZ140_M87_CTRL2

tag: Sex


title: WT Ly6C-low

source_name: Livers from wild type mice

tag: strain

value: wild type


title: Dnr10_F_88_AD_Neuron


title: WT Ly6C-hi

tag: tissue


title: Dnr13_F_77_CTRL_Glia


title: Dnr10_F_88_AD_Glia


title: Dnr11_F_81_AD_Glia


title: Dnr11_F_81_AD_Neuron


title: HO-20-43R

status: Public on Aug 11 2018

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

organism: Saccharomyces cerevisiae

source_name: cell culture of strain HO-20-43R

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: JSC25 cells were grown in 7 mL YPD overnight to reach an OD600 of 0.2. Yeast cells (5×107) were collected by centrifugation and arrested in G1 in 1 mL YPD containing 2.5 μg α-factor at 30 degree. After two hours, H2O2 was added into the cell culture. Cell culture was incubated at 30 degree for another hour. Yeast cells were then washed twice to remove α-factor and H2O2 before plating. Yeast  cells were cultured at  30 degree for 3 days and sectored colonies were selected for chromosome IV SNP-specific microarrays.

tag: ploidy

value: diploid strain

source_name: cell culture of JSC24

value: control strain JSC24


title: HO-20-42W

source_name: cell culture of strain HO-20-42W


title: Dnr06_M_18_CTRL_Neuron


title: Dnr13_F_77_CTRL_Neuron


title: Dnr12_F_77_AD_Glia

value: AD


title: Dnr12_F_77_AD_Neuron


title: Dnr15_F_83_CTRL_Neuron


title: Dnr06_M_18_CTRL_Glia


title: Dnr03_F_75_AD_Neuron


title: HO-20-19W

source_name: cell culture of strain HO-20-19W


title: Dnr05_M_94_AD_Neuron


title: Dnr02_M_76_AD_Glia


title: HO-20-41R

source_name: cell culture of strain HO-20-41R


title: Dnr04_F_85_AD_Neuron


title: Dnr01_F_78_AD_Glia


title: HO-20-18W

source_name: cell culture of strain HO-20-18W


title: Dnr03_F_75_AD_Glia


title: Dnr02_M_76_AD_Neuron


title: NTM_M3

city: Fuyang

first: Yong

last: Liu

address: Qinghe West Road

institute: Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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 normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8 whole genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Nuclear transfer morula

extract_protocol:
The in vivo embryos were produced by superovulating C57BL/6 female mice and mating with DBA2 male mouse. The NTC embryos were manufactured by cumulus cell nuclear transfer and sequential embryos in an in vitro culture. The NTM embryos were manufactured by MEF cell nuclear transfer and sequential embryos in an in vitro culture. Each type of embryo was collected at 6 pronuclear stages, i.e., the 2-cell, 4-cell, 8-cell, morula and blastocyst stages. Each embryo was transferred to lysate buffer in a PCR tube and immediately stored in a -80℃ refrigerator. Embryos were collected from each stage in at least three independent experiments
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample group

value: Nuclear transfer embryos reconstructed with mouse embryonic fibroblast cell nuclei

tag: developemental stage

value: Nuclear transfer morula


title: NTM_M2


title: HO-20-17W

source_name: cell culture of strain HO-20-17W


title: Dnr05_M_94_AD_Glia

tag: cell type

value: M


title: HO-20-16W

source_name: cell culture of strain HO-20-16W


title: HO-20-43W

source_name: cell culture of strain HO-20-43W


title: HO-0.5-20W

source_name: cell culture of strain HO-0.5-20W


title: HO-0.5-14W

source_name: cell culture of strain HO-0.5-14W


title: HO-0.5-18R

source_name: cell culture of strain HO-0.5-18R


title: HO-0.5-13R

source_name: cell culture of strain HO-0.5-13R


title: HO-20-19R

source_name: cell culture of strain HO-20-19R


title: HO-20-17R

source_name: cell culture of strain HO-20-17R


title: HO-0.5-13W

source_name: cell culture of strain HO-0.5-13W


title: HO-0.5-20R

source_name: cell culture of strain HO-0.5-20R


title: HO-0.5-16W

source_name: cell culture of strain HO-0.5-16W

source_name: cell culture of JSC24


title: HO-0.5-17R

source_name: cell culture of strain HO-0.5-17R


title: HO-0.5-14R

source_name: cell culture of strain HO-0.5-14R


title: HO-0.5-19R

source_name: cell culture of strain HO-0.5-19R


title: HO-0.5-15R

source_name: cell culture of strain HO-0.5-15R


title: HO-20-18R

source_name: cell culture of strain HO-20-18R


title: HO-20-16R

source_name: cell culture of strain HO-20-16R


title: HO-0.5-18W

source_name: cell culture of strain HO-0.5-18W


title: HO-0.5-16R

source_name: cell culture of strain HO-0.5-16R


title: HO-0.5-15W

source_name: cell culture of strain HO-0.5-15W


title: HO-20-41W

source_name: cell culture of strain HO-20-41W


title: HO-20-42R

source_name: cell culture of strain HO-20-42R


title: Dnr04_F_85_AD_Glia

source_name: Occipital Cortex

value: F


title: NTM_M1

source_name: Nuclear transfer morula


title: HO-0.5-19W

source_name: cell culture of strain HO-0.5-19W


title: Dnr01_F_78_AD_Neuron


title: NTM_B1

source_name: Nuclear transfer blastula

value: Nuclear transfer blastula


title: NTM_82

source_name: Nuclear transfer 8-cell embryo

value: Nuclear transfer 8-cell embryo


title: NTM_B2


title: NTM_83


title: NTM_43

source_name: Nuclear transfer 4-cell embryo

value: Nuclear transfer 4-cell embryo


title: NTM_81


title: NTM_42


title: NTM_41


title: NTM_11

source_name: Nuclear transfer 1-cell embryo

value: Nuclear transfer 1-cell embryo


title: NTM_21

source_name: Nuclear transfer 2-cell embryo

value: Nuclear transfer 2-cell embryo


title: NTM_22


title: NTM_12


title: NTM_13


title: NTM_23


title: NTC_M3


title: NTC_M2


title: HO-0.5-17W

source_name: cell culture of strain HO-0.5-17W

source_name: cell culture of JSC24


title: NTM_B3


title: NTC_B2


title: NTC_B1


title: NTC_B3


title: NTC_43


title: NTC_83


title: NTC_81


title: NTC_82


title: NTC_41


title: NTC_42


title: NTC_23


title: NTC_22


title: FUSE_37B: FUSE of cells treated with DMS at 37°C (replicate B)

city: Berlin

first: Dmitriy

last: Ignatov

address: Charitéplatz 1

institute: Max Planck Unit for the Science of Pathogens

description: cDNA prepared according to FUSE protocol

data_processing:
Library strategy: FUSE
Basecalls performed using CASAVA version 1.8
The sequencing reads aligned to Listeria monocytogenes EGD-e genome (NC_003210.1) with Bowtie 2 aligner using the --end-to-end --very-sensitive mode
Genome regions corresponding to non-coding RNAs, 5’ UTRs and the first 30 nucleotides of coding sequences were selected for further analysis. For each nucleotide position of these regions, coverage was calculated as the number of reads mapped at that position, and mismatch rate was calculated as the ratio between the number of mismatches and coverage at that position. To account for variability in DMS treatment conditions, the mismatch rates of adenines and cytosines were separately divided by the average mismatch rates of these nucleotides in the respective sample. The resulting values got the name ‘DMS values’.
Genome_build: NC_003210.1
Supplementary_files_format_and_content: The analysis was performed for genome positions corresponding to A and C nucleotides located in the following regions of the genome:    1) The 5' UTRs of mRNAs and the first 30 nucleotides of the coding sequences ("five_prime_utr").  2) Signal recognition particle RNA ("SRP_RNA").  3) RNase P RNA ("RNase_P_RNA").  4) Small RNAs ("small_regulatory_ncRNA").  5) Antisense RNAs ("antisense_RNA").  6) Regulatory regions located in the 5'UTRs, including riboswitches, T-boxes, attenuators etc. ("transcription_regulatory_region").    For each of these nucleotides the following information is presented:    Position_genome - coordinate of the nucleotide in L. monocytogenes EGD-e genome (NCBI Reference Sequence: NC_003210.1).  Position_TSS - coordinate of the nucleotide relative to the transcription start site of the respective RNA.  Position_start_codon - if the nucleotide belongs to 5'UTR, this field denotes coordinate relative to the first nucleotide of the start-codon. Otherwise, the field is set to "NA".  Strand - genome strand encoding the nucleotide.  Feature - the locus to which the nucleotide corresponds. If the nucleotide corresponds to several loci, all of them are written.  Type - the type of locus the nucleotide corresponds.  Nucleotide - adenine or cytosine.  cvg_XXX - number of reads mapped to the nucleotide in library XXX.  mis_XXX - number of mismatches at the nucleotide in library XXX.  dms_XXX - DMS value calculated for the nucleotide in library XXX.

organism: Listeria monocytogenes EGD-e

source_name: Bacterial cells grown in culture

growth_protocol: Bacteria were grown in BHI media at 37°C to OD=1.0. 3ml of the culture was moved to 15 ml tube in the 37°C thermostat and incubated for 3 minutes prior to DMS treatment.

extract_protocol:
10 ml of bacterial culture was mixed with 5 ml of 1:20 phenol:ethanol solution and centrifuged at 7000 g for 10 minutes. The pellet was resuspended in the Disruption solution (10% glucose, 12.5 mM Tris-HCl pH 7.6, and 5 mM EDTA) and immediately transferred to 2 ml screw-capped tubes with roughly 0.4 g glass beads and 500 μl of acid phenol (pH 4.5). The bacteria were disrupted using a mini bead beater (Biospec products) for 30 s. After centrifugation (5 min, 12000 g) RNA was recovered by addition of 1 ml of TRI Reagen Solution (Thermo Fisher) and 100 μl of chloroform, followed by centrifugation. Samples were thereafter subjected to two additional chloroform extractions. The aqueous phase was precipitated by adding isopropanol (0.7×) and incubation at −20°C for 20 min. For collection of the pellet, the RNA samples were centrifuged for 25 min. The pellet was washed with 80% ethanol and dissolved in 50 μl of RNase-free water.
After modification with DMS, RNA was treated with DNase I (Roche) and purified on RNeasy MinElute columns (Qiagen). RNA was treated with RNA 5’-Polyphosphatase (Epicentre) and once again purified on the columns. RNA was depleted of ribosomal fraction with Ribo-Zero rRNA Removal Kit (Illumina), and purified on RNeasy columns. RNA solution was concentrated on SpeedVac Concentrator (ThermoFisher Scientific) to 4.5 µl, mixed with 1 µl of 15 µM PAGE-purified 5’RA ribooligonucleotid (UCCCUACACGACGCUCUUCCGAUCU), heated for 3 min at 65°C and cooled on ice. The ligation reaction was assembled with T4 RNA Ligase 1 (NEB) and 10% DMSO, and proceeded for 2 hours at room temperature. RNA was ethanol precipitated, dissolved in 9 µl of mQ water and fragmented with RNA Fragmentation Reagents (Thermo Fisher Scientific) for 3.5 min at 70°C. Following the fragmentation, RNA was run on 6% denaturing polyacrylamide gel, and fragments ranging in size from 125 to 400 nucleotides were isolated from the gel. RNA fragments were dephosphorylated with T4 Polynucleotide Kinase (Thermo Fisher Scientific) in the dephosphorylation buffer (100 mM MES pH6.0, 10 mM MgCl2) and purified on RNeasy columns according to the modified protocol (100 µL of RNA solution was mixed with 350 µL RLT buffer and 550 µL 96% ethanol). The modified protocol preserves fragments shorter than 200 nucleotides and is used at the steps following RNA fragmentation. 3’DA adapter (5phos/AGATCGGAAGAGCACACGTCTGAACTCCAG/3ddC) was adenylated with 5' DNA Adenylation Kit (NEB). RNA solution was concentrated to 4.5 µL and mixed with 1 µl of 15 µM adenyl-3’DA. Ligation reaction with T4 RNA Ligase 2, truncated (NEB) and 25% PEG8000 was allowed to proceed for 2 hours at room temperature. RNA was ethanol precipitated, dissolved in 20 µL of mQ water and treated with 1.6x vol:vol AMPure XP beads (Beckman Coulter) to remove not ligated adaptors. cDNA was synthesized with TGIRTIII enzyme (InGex): RNA solution was concentrated to 4.5 µl, mixed with 1 µl of 1 µM RT primer and heated for 2 min at 80°C. The primer was annealed for 5 minutes at room temperature, and the reverse transcription reaction was assembled in RT buffer (50 mM Tris-HCl pH8.3, 75 mM KCl, 3 mM MgCl2) with 1 mM dNTPs mix, 5 mM DTT and 100U of TGIRTIII enzyme. The reverse transcription proceeded for 2 hours at 57°C. After that 1 µl of 5N NaOH was added to the reaction and the reverse transcriptase was inactivated by heating at 95°C for 3 min. The first strands of cDNA were ethanol precipitated, dissolved in mQ water and cDNA libraries were amplified by 2 rounds of PCR. The first 12 cycles of PCR were performed with primers LibAmp_F (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTC) and LibAmp_RPI_R (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCT), which introduced sequences identical to Illumina TruSeq adapters (Oligonucleotide sequences © 2018 Illumina, Inc. All rights reserved) to cDNA. The product of the first PCR reaction was purified with 1x vol:vol AMPure XP beads and used as matrix for the second 6-8 cycles PCR reaction with primers Enrich_F (AATGATACGGCGACCACCGAGATC) and Enrich_R (CAAGCAGAAGACGGCATACGAGAT). The product of the second PCR reaction was sequentially purified with RNeasy PCR Purification Kit (Qiagen) and 1x vol:vol AMPure XP beads.

tag: genotype

value: Wild-type

tag: dms treatment

value: 90 µl of DMS(3% v:v)  was added and the culture was incubated at 37°C for 3 minutes pipetting every 10 seconds with the pipette volume set to 500 µl.


title: FUSE_37A: FUSE of cells treated with DMS at 37°C (replicate A)


title: FUSE_lhrA: FUSE of lhrA-mut mutant cells treated with DMS at 37°C

value: lhrA-mut mutant


title: FUSE_37shift: FUSE of cells grown 26°C and treated with DMS at 37°C

growth_protocol: Bacteria were grown in BHI media at 26°C to OD=1.0. 3ml of the culture was moved to 15 ml tube at the 37°C thermostat and incubated for 3 minutes prior to DMS treatment.


title: FUSE_hfq: FUSE of Δhfq mutant cells treated with DMS at 37°C

value: {delta}hfq mutant


title: FUSE_prfA: FUSE of prfA* mutant cells treated with DMS at 37°C

value: prfA* mutant


title: NTC_12


title: FUSE_26: FUSE of cells treated with DMS at 26°C

growth_protocol: Bacteria were grown in BHI media at 26°C to OD=1.0. 3ml of the culture was moved to 15 ml tube at the 26°C thermostat and incubated for 3 minutes prior to DMS treatment.

value: 150 µl of DMS (5% v:v) was added and the culture was incubated at 26°C for 3 minutes pipetting every 10 seconds with the pipette volume set to 500 µl.


title: Structure-seq: Structure-seq of cells treated with DMS at 37°C

description: cDNA prepared according to Structure-seq protocol

extract_protocol:
10 ml of bacterial culture was mixed with 5 ml of 1:20 phenol:ethanol solution and centrifuged at 7000 g for 10 minutes. The pellet was resuspended in the Disruption solution (10% glucose, 12.5 mM Tris-HCl pH 7.6, and 5 mM EDTA) and immediately transferred to 2 ml screw-capped tubes with roughly 0.4 g glass beads and 500 μl of acid phenol (pH 4.5). The bacteria were disrupted using a mini bead beater (Biospec products) for 30 s. After centrifugation (5 min, 12000 g) RNA was recovered by addition of 1 ml of TRI Reagen Solution (Thermo Fisher) and 100 μl of chloroform, followed by centrifugation. Samples were thereafter subjected to two additional chloroform extractions. The aqueous phase was precipitated by adding isopropanol (0.7×) and incubation at −20°C for 20 min. For collection of the pellet, the RNA samples were centrifuged for 25 min. The pellet was washed with 80% ethanol and dissolved in 50 μl of RNase-free water.
RNA was depleted of ribosomal fraction with Ribo-Zero rRNA Removal Kit (Illumina), and purified on RNeasy columns. RNA was fragmented with RNA Fragmentation Reagents (Thermo Fisher Scientific) for 3.5 min at 70°C, and purified on RNeasy columns according to the modified protocol (100 µL of RNA solution was mixed with 350 µL RLT buffer and 550 µL 96% ethanol). RNA fragments were dephosphorylated with Shrimp Alkaline Phosphatase (NEB), purified on RNeasy columns according to the modified protocol, 5’ phosphorylated with T4 Polynucleotide Kinase (NEB), and once again purified on the columns according to the modified protocol. RNA solution was concentrated to 4.5 µl, mixed with 1 µl of 15 µM PAGE purified 5’RA ribooligonucleotid (UCCCUACACGACGCUCUUCCGAUCU), heated for 3 min at 65°C and cooled on ice. The ligation reaction was assembled with T4 RNA Ligase (NEB) and 10% DMSO, and proceeded for 2 hours at room temperature. RNA was ethanol precipitated, run on 6% denaturing polyacrylamide gel, and fragments ranging in size from 100 to 400 nucleotides were isolated from the gel. Adenylated 3’-DA adapter (5phos/AGATCGGAAGAGCACACGTCTGAACTCCAG/3ddC) was ligated to the RNA fragments with T4 RNA Ligase 2, truncated (NEB) in the presence of 25% PEG8000 for 2 hours at room temperature. RNA was treated with 1.6x vol:vol AMPure XP beads (Beckman Coulter) to remove not ligated adaptors.  cDNA was synthesized with TGIRTIII enzyme (InGex): RNA solution was concentrated to 4.5 µl, mixed with 1 µl of 1 µM RT primer and heated for 2 min at 80°C. The primer was annealed for 5 minutes at room temperature, and the reverse transcription reaction was assembled in RT buffer (50 mM Tris-HCl pH8.3, 75 mM KCl, 3 mM MgCl2) with 1 mM dNTPs mix, 5 mM DTT and 100U of TGIRTIII enzyme. The reverse transcription proceeded for 2 hours at 57°C. After that 1 µl of 5N NaOH was added to the reaction and the reverse transcriptase was inactivated by heating at 95°C for 3 min. The first strands of cDNA were ethanol precipitated, dissolved in mQ water and cDNA libraries were amplified by 2 rounds of PCR. The first 12 cycles of PCR were performed with primers LibAmp_F (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTC) and LibAmp_RPI_R (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCT), which introduced sequences identical to Illumina TruSeq adapters (Oligonucleotide sequences © 2018 Illumina, Inc. All rights reserved) to cDNA. The product of the first PCR reaction was purified with 1x vol:vol AMPure XP beads and used as matrix for the second 6-8 cycles PCR reaction with primers Enrich_F (AATGATACGGCGACCACCGAGATC) and Enrich_R (CAAGCAGAAGACGGCATACGAGAT). The product of the second PCR reaction was sequentially purified with RNeasy PCR Purification Kit (Qiagen) and 1x vol:vol AMPure XP beads.


title: NTC_13


title: NTC_11


title: NTC_21


title: FUSE_invitro: FUSE of RNA treated with DMS in vitro at 37°C

growth_protocol: Bacteria were grown in BHI media at 37°C to OD=1.0

value: 9 µl of DMS (3% v:v) was added and the solution was incubated for 3 minutes at 37°C pipetting every 10 seconds with the pipette volume set to 50 µl.


title: FUSE_K: FUSE of DMS untreated sample

value: No DMS treatment, 90 µl of mQ (3% v:v) was added and the culture was incubated at 37°C for 3 minutes pipetting every 10 seconds with the pipette volume set to 500 µl.


title: NTC_M1


title: MEF_3

source_name: mouse embryonic fibroblast cells

value: mouse embryonic fibroblast cells


title: MEF_2


title: Invivo_M2

source_name: Invivo morula

value: in vivo fertilized embryos

value: Invivo morula


title: Invivo_M3


title: MEF_1


title: 4mpf_3TD_37

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Trimming using trim_galore using default parameters
Mapping using HISAT2 with default parameters
Counts per gene generated using htseq-count with default parameters
Genome_build: Zebrafish GRCz10

organism: Danio rerio

source_name: beta-cells

extract_protocol:
FACS
SMART-Seq v4

tag: feeding

value: Three-times-a-day-feeding


title: 4mpf_3TD_35


title: 4mpf_3TD_34


title: 4mpf_3TD_38


title: 4mpf_3TD_40


title: 4mpf_3TD_39


title: 4mpf_3TD_33


title: Invivo_B3

source_name: Invivo blastula

value: Invivo blastula


title: Invivo_B1


title: 4mpf_3TD_30


title: 4mpf_3TD_32


title: Invivo_81

source_name: Invivo 8-cell embryo

value: Invivo 8-cell embryo


title: Invivo_42

source_name: Invivo 4-cell embryo

value: Invivo 4-cell embryo


title: Invivo_82


title: Invivo_43


title: Invivo_B2


title: 4mpf_3TD_27


title: 4mpf_3TD_25


title: 4mpf_3TD_26


title: 4mpf_3TD_29


title: Invivo_41


title: 4mpf_3TD_36


title: Invivo_83


title: 4mpf_3TD_24


title: Invivo_23

source_name: Invivo 2-cell embryo

value: Invivo 2-cell embryo


title: Invivo_22


title: 4mpf_3TD_23


title: Invivo_M1


title: 4mpf_3TD_20


title: Invivo_13

source_name: Invivo 1-cell embryo

value: Invivo 1-cell embryo


title: 4mpf_3TD_31


title: Invivo_21


title: 4mpf_3TD_28


title: 4mpf_3TD_22


title: 4mpf_3TD_21


title: Invivo_12


title: 4mpf_3TD_19


title: Invivo_11


title: 4mpf_3TD_17


title: CC_3

source_name: cumulus cells

value: cumulus cells


title: CC_1


title: 4mpf_3TD_18


title: 4mpf_3TD_16


title: 4mpf_3TD_15


title: 4mpf_3TD_14


title: 4mpf_3TD_12


title: 4mpf_3TD_11


title: 4mpf_3TD_9


title: 4mpf_3TD_7


title: 4mpf_3TD_6


title: CC_2


title: 4mpf_3TD_13


title: 4mpf_3TD_3


title: 4mpf_3TD_4


title: 4mpf_3TD_2


title: 4mpf_3TD_1


title: PT084_P121_H04_S376

first: Simona

last: Cristea

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

data_processing:
Fastq files were quantified to transcript per million (TPM) expression values with RSEM with default parameters
Low quality cells were filtered as follows: 4 median absolute deviations (MADs) below the median for any of the three metrics concering: i) library size; ii) number of expressed genes; iii) total amount of mRNA
Unexpressed genes were removed as follows: a gene was considered unexpressed if log2(TPM+1) < 0.1 in at least 95% of cells separately for each patient
Data was normalized following a three-step combination approach: i) Transform the TPM values into relative counts with the Census algorithm (Qiu et al, 2017); ii) Normalize the Census counts with the deconvolution strategy implemented in scran (Lun et al 2016); iii) Remove additional sources of variation with RUVSeq (Risso et al, 2014)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files representing: TPM values (tpm_rsem.txt); counts (counts_rsem.txt); normalized data as described above (norm_data.txt)

source_name: breast

extract_protocol:
Fresly collected human tumor samples were mechanically and enzymatically digested using tumor dissociation kit (Miltenyi Biotec). Single cells were sorted by flow cytometry, lysed and snap frozen on dry ice immediately.
RNA libraries were prepared using Smart-seq2 protocol (Picelli et al., 2014)

value: breast

tag: breast cancer subtype

value: TNBC

tag: patient


title: PT039_P10_E10_S250


title: PT039_P10_G05_S269


title: PT039_P121_D06_S330


title: PT039_P10_F10_S262


title: PT039_P1_E12


title: PT039_P121_C07_S319


title: PT039_P10_E05_S245


title: PT039_P10_H10_S286


title: PT126_P7_H12_S192


title: PT039_P10_D07_S235


title: PT126_P7_H10_S190


title: 4mpf_3TD_10


title: PT039_P10_G12_S276


title: 4mpf_IF_55


title: 4mpf_3TD_8


title: 4mpf_3TD_5


title: PT039_P10_C01_S217


title: PT126_P7_H07_S187


title: 4mpf_IF_53


title: 4mpf_IF_52


title: 4mpf_IF_50


title: PT126_P7_H09_S189


title: PT126_P7_H06_S186


title: PT126_P7_H05_S185


title: 4mpf_IF_54


title: PT126_P7_H11_S191


title: PT126_P7_H04_S184


title: PT126_P7_H02_S182


title: 4mpf_IF_47


title: PT126_P7_G12_S180


title: 4mpf_IF_49


title: PT126_P7_H01_S181


title: 4mpf_IF_46


title: PT126_P7_G10_S178


title: PT126_P7_H03_S183


title: 4mpf_IF_44


title: PT126_P7_G09_S177


title: 4mpf_IF_42


title: 4mpf_IF_48


title: PT126_P7_G11_S179


title: PT126_P7_H08_S188


title: 4mpf_IF_41


title: PT126_P7_G08_S176


title: 4mpf_IF_43


title: 4mpf_IF_51


title: PT126_P7_G07_S175


title: 4mpf_IF_40


title: 4mpf_IF_39


title: 4mpf_IF_45


title: PT126_P7_G06_S174


title: PT126_P7_G04_S172


title: PT126_P7_G03_S171


title: 4mpf_IF_38


title: PT126_P7_G02_S170


title: 4mpf_IF_35


title: 4mpf_IF_36


title: PT126_P7_F10_S166


title: PT126_P7_F11_S167


title: 4mpf_IF_34


title: PT126_P7_F08_S164


title: PT126_P7_G01_S169


title: 4mpf_IF_33


title: PT126_P7_F06_S162


title: PT126_P7_F12_S168


title: 4mpf_IF_30


title: PT126_P7_F09_S165


title: 4mpf_IF_31


title: PT126_P7_F07_S163


title: 4mpf_IF_32


title: PT126_P7_F04_S160


title: 4mpf_IF_26


title: 4mpf_IF_27


title: PT126_P7_G05_S173


title: PT126_P7_F03_S159


title: 4mpf_IF_24


title: PT126_P7_F02_S158


title: 4mpf_IF_28


title: PT126_P7_F01_S157


title: PT126_P7_F05_S161


title: 4mpf_IF_25


title: 4mpf_IF_29


title: 4mpf_IF_21


title: 4mpf_IF_22


title: 4mpf_IF_20


title: 4mpf_IF_23


title: PT126_P7_E09_S153


title: PT126_P7_E10_S154


title: PT126_P7_E11_S155


title: 4mpf_IF_19


title: 4mpf_IF_16


title: 4mpf_IF_17


title: PT126_P7_E08_S152


title: 4mpf_IF_14


title: 4mpf_IF_15


title: 4mpf_IF_10


title: 4mpf_IF_13


title: PT126_P7_E06_S150


title: PT126_P7_E03_S147


title: PT126_P7_E02_S146


title: PT126_P7_E05_S149


title: PT126_P7_E01_S145


title: 4mpf_IF_11


title: 4mpf_IF_18


title: 4mpf_IF_9


title: PT126_P7_D12_S144


title: PT126_P7_E12_S156


title: PT126_P7_E04_S148


title: PT126_P7_D11_S143


title: 4mpf_IF_8


title: PT126_P7_E07_S151


title: PT126_P7_D10_S142


title: 4mpf_IF_7


title: PT126_P7_D09_S141


title: 4mpf_IF_6


title: PT126_P7_D08_S140


title: PT126_P7_D07_S139


title: PT126_P7_D05_S137


title: 4mpf_IF_3


title: 4mpf_IF_5


title: PT126_P7_D06_S138


title: 1mpf_H12

value: Normal


title: PT126_P7_D03_S135


title: PT126_P7_D04_S136


title: 4mpf_IF_1


title: 4mpf_IF_2


title: 4mpf_IF_4


title: PT126_P7_D02_S134


title: PT126_P7_D01_S133


title: 1mpf_F12


title: 1mpf_G12


title: 4mpf_IF_12


title: 1mpf_E12


title: 13mpf_D12


title: 13mpf_C12


title: PT126_P7_C11_S131


title: PT126_P7_C10_S130


title: PT126_P7_C12_S132


title: PT126_P7_C09_S129


title: PT126_P7_C08_S128


title: 13mpf_B12


title: 1mpf_H11


title: PT126_P7_C07_S127


title: 13mpf_A12


title: 1mpf_F11


title: PT126_P7_C06_S126


title: 1mpf_E11


title: 1mpf_G11


title: PT126_P7_C04_S124


title: PT126_P7_C05_S125


title: PT126_P7_C03_S123


title: PT126_P7_C02_S122


title: PT126_P7_B12_S120


title: 13mpf_C11


title: 13mpf_D11


title: 13mpf_B11


title: PT126_P7_C01_S121


title: PT126_P7_B11_S119


title: 1mpf_F10


title: 1mpf_E10


title: 1mpf_H10


title: PT126_P7_B09_S117


title: PT126_P7_B10_S118


title: 1mpf_G10


title: PT126_P7_B08_S116


title: PT126_P7_B07_S115


title: 13mpf_C10


title: 13mpf_D10


title: 13mpf_A10


title: 13mpf_B10


title: PT126_P7_B05_S113


title: 1mpf_H09


title: 1mpf_G09


title: PT126_P7_B04_S112


title: PT126_P7_B03_S111


title: 1mpf_F09


title: PT126_P7_B02_S110


title: PT126_P7_B01_S109


title: PT126_P7_A12_S108


title: 13mpf_C09


title: 1mpf_E09


title: 13mpf_D09


title: 13mpf_A09


title: PT126_P7_A11_S107


title: PT126_P7_A09_S105


title: PT126_P7_A07_S103


title: PT126_P7_A08_S104


title: 13mpf_B09


title: 1mpf_H08


title: PT126_P7_A10_S106


title: PT126_P7_B06_S114


title: PT126_P7_A04_S100


title: 1mpf_E08


title: 1mpf_G08


title: PT126_P7_A05_S101


title: 13mpf_D08


title: PT126_P7_A03_S99


title: 1mpf_F08


title: 13mpf_C08


title: 4mpf_IF_37


title: 13mpf_B08


title: PT126_P7_A01_S97


title: 1mpf_H07


title: PT126_P7_A02_S98


title: PT126_P3_E07_S55


title: 1mpf_G07


title: PT126_P7_A06_S102


title: PT126_P3_D03_S39


title: PT126_P3_B08_S20


title: 1mpf_F07


title: 13mpf_C07


title: PT126_P3_B03_S15


title: PT084_P8_G08_S272


title: 13mpf_B07


title: 13mpf_D07


title: PT084_P8_B09_S213


title: 1mpf_H06


title: 13mpf_A07


title: PT084_P8_G04_S268


title: PT084_P8_D09_S237


title: PT084_P8_A04_S196


title: 1mpf_G06


title: PT084_P8_A09_S201


title: 13mpf_A08


title: 1mpf_F06


title: PT084_P1_H12


title: 13mpf_D06


title: PT084_P1_H11


title: PT126_P3_E11_S59


title: 13mpf_B06


title: 13mpf_A06


title: PT084_P1_H10


title: PT084_P1_H09


title: PT084_P1_H08


title: 1mpf_G05


title: 1mpf_H05


title: PT084_P1_H07


title: 13mpf_D05


title: PT084_P1_H06


title: PT084_P1_H04


title: 1mpf_F05


title: PT084_P1_H05


title: 1mpf_H04


title: PT084_P1_H03


title: 13mpf_C05


title: 13mpf_C06


title: PT084_P1_H02


title: PT084_P1_H01


title: 1mpf_G04


title: 13mpf_B05


title: 13mpf_A05


title: 1mpf_F04


title: 13mpf_E04


title: PT084_P1_G12


title: PT084_P1_G10


title: 13mpf_C04


title: PT084_P1_G09


title: 13mpf_D04


title: PT084_P1_G11


title: 13mpf_A04


title: PT084_P1_G07


title: PT084_P1_G06


title: 1mpf_H03


title: 1mpf_G03


title: PT084_P1_G04


title: 13mpf_E03


title: PT084_P1_G03


title: PT084_P1_G02


title: 13mpf_C03


title: PT084_P1_G01


title: PT084_P1_F12


title: PT084_P1_F11


title: 13mpf_A03


title: 1mpf_H02


title: PT084_P1_F10


title: 13mpf_B03


title: PT084_P1_F07


title: 13mpf_E02


title: PT084_P1_F06


title: 1mpf_F02


title: PT084_P1_F09


title: PT084_P1_F08


title: PT084_P1_G05


title: 1mpf_G02


title: PT084_P1_G08


title: 1mpf_F03


title: 13mpf_C02


title: PT084_P1_F04


title: 13mpf_A02


title: 13mpf_D03


title: 1mpf_G01


title: PT084_P1_F02


title: PT084_P1_F03


title: PT084_P1_F01


title: 1mpf_F01


title: PT084_P1_E12


title: 13mpf_E01


title: 13mpf_D01


title: PT084_P1_E11


title: 13mpf_D02


title: PT084_P1_E10


title: 13mpf_B01


title: PT084_P1_E09


title: PT084_P1_E08


title: PT084_P1_F05


title: 13mpf_A01


title: 13mpf_B02


title: PT084_P1_E06


title: PT084_P11_C12_S324


title: PT084_P1_E07


title: PT084_P11_A10_S298


title: 1mpf_H01


title: PT084_P11_A03_S291


title: PT084_P11_A02_S290


title: 9mpf_89


title: 9mpf_87


title: 9mpf_86


title: 9mpf_90


title: 9mpf_92


title: 9mpf_91


title: 13mpf_C01


title: 9mpf_85


title: 9mpf_84


title: PT081_P5_G12_S180


title: PT081_P5_G10_S178


title: 9mpf_81


title: PT081_P5_G07_S175


title: PT081_P5_F07_S163


title: 9mpf_79


title: 9mpf_80


title: 9mpf_78


title: 9mpf_77


title: PT084_P11_A08_S296


title: 9mpf_88


title: PT081_P5_E07_S151


title: 9mpf_76


title: PT081_P5_D08_S140


title: 9mpf_75


title: PT081_P5_D06_S138


title: PT081_P5_H10_S190


title: 9mpf_83


title: 9mpf_73


title: PT081_P5_H12_S192


title: PT084_P11_A01_S289


title: PT081_P5_D04_S136


title: 9mpf_72


title: PT081_P5_C12_S132


title: 9mpf_74


title: PT081_P5_E11_S155


title: 9mpf_70


title: 9mpf_71


title: PT081_P3_H10_S286


title: PT081_P5_A01_S97


title: PT081_P3_H12_S288


title: PT081_P3_H08_S284


title: 9mpf_68


title: 9mpf_67


title: 9mpf_82


title: PT081_P3_H06_S282


title: 9mpf_66


title: 9mpf_65


title: PT081_P3_G12_S276


title: PT081_P3_G11_S275


title: PT081_P3_H01_S277


title: PT081_P5_B07_S115


title: 9mpf_61


title: PT081_P3_G09_S273


title: 9mpf_62


title: PT081_P3_G10_S274


title: PT081_P3_G08_S272


title: 9mpf_60


title: 9mpf_59


title: 9mpf_69


title: PT081_P3_G07_S271


title: PT081_P3_G06_S270


title: 9mpf_58


title: PT081_P3_G05_S269


title: PT081_P3_G02_S266


title: 9mpf_57


title: PT081_P3_F07_S259


title: 9mpf_56


title: PT081_P3_F05_S257


title: PT081_P3_F10_S262


title: 9mpf_54


title: 9mpf_55


title: PT081_P3_F02_S254


title: 9mpf_53


title: 9mpf_52


title: PT081_P3_E10_S250


title: 9mpf_64


title: 9mpf_63


title: 9mpf_51


title: 9mpf_50


title: PT081_P3_E05_S245


title: PT081_P3_D09_S237


title: 9mpf_48


title: PT081_P3_E09_S249


title: 9mpf_47


title: PT081_P3_D12_S240


title: PT081_P3_D08_S236


title: 9mpf_46


title: PT081_P3_D07_S235


title: 9mpf_45


title: 9mpf_43


title: 9mpf_42


title: PT081_P3_C08_S224


title: PT081_P3_B10_S214


title: PT081_P3_B11_S215


title: 9mpf_44


title: PT081_P3_A10_S202


title: PT081_P3_B06_S210


title: PT081_P3_A09_S201


title: PT081_P3_A07_S199


title: 9mpf_38


title: 9mpf_39


title: 9mpf_40


title: PT081_P3_A06_S198


title: 9mpf_36


title: PT081_P3_A01_S193


title: 9mpf_37


title: PT081_P1_H09


title: PT081_P1_H05


title: 9mpf_35


title: PT081_P1_H02


title: 9mpf_33


title: 9mpf_49


title: 9mpf_32


title: PT081_P1_G12


title: 9mpf_31


title: PT081_P1_G09


title: 9mpf_34


title: PT081_P1_F10


title: 9mpf_41


title: PT081_P1_F09


title: 9mpf_29


title: PT081_P3_C07_S223


title: 9mpf_30


title: 9mpf_28


title: 9mpf_27


title: PT081_P1_D11


title: 9mpf_26


title: PT081_P1_E08


title: 9mpf_25


title: PT081_P1_B09


title: PT081_P1_C10


title: 9mpf_24


title: PT081_P1_A11


title: 9mpf_23


title: PT081_P1_A04


title: 9mpf_20


title: PT058_P1_H10


title: 9mpf_22


title: PT058_P1_G12


title: 9mpf_21


title: PT058_P1_H09


title: 9mpf_18


title: 9mpf_19


title: PT058_P1_G09


title: 9mpf_17


title: PT058_P1_G06


title: 9mpf_15


title: 9mpf_14


title: PT058_P1_F03


title: PT058_P1_D10


title: PT058_P1_D08


title: PT058_P1_F06


title: 9mpf_13


title: 9mpf_16


title: PT058_P1_F05


title: PT058_P1_D01


title: 9mpf_11


title: 9mpf_12


title: PT058_P1_C03


title: 9mpf_10


title: PT058_P1_B12


title: PT058_P1_B07


title: PT058_P1_B01


title: PT058_P1_B05


title: PT058_P1_A09


title: 9mpf_6


title: 9mpf_9


title: 9mpf_7


title: 9mpf_8


title: PT039_P1_H11


title: 9mpf_2


title: PT039_P1_H10


title: 9mpf_3


title: 9mpf_4


title: 9mpf_5


title: PT058_P1_A03


title: PT039_P1_H12


title: 9mpf_1


title: PT039_P1_H07


title: PT039_P1_H09


title: 45dpf_89


title: 45dpf_91


title: PT039_P1_H05


title: PT039_P1_H06


title: PT039_P1_H08


title: 45dpf_87


title: PT039_P1_H04


title: 45dpf_88


title: 45dpf_86


title: 45dpf_85


title: PT039_P1_H02


title: 45dpf_84


title: PT039_P1_H01


title: 45dpf_90


title: PT039_P1_G12


title: PT039_P1_G11


title: 45dpf_81


title: PT039_P1_G10


title: 45dpf_83


title: 45dpf_78


title: 45dpf_77


title: 45dpf_82


title: 45dpf_76


title: PT039_P1_G05


title: PT039_P1_G07


title: PT039_P1_G03


title: 45dpf_80


title: PT039_P1_G09


title: 45dpf_73


title: PT039_P1_G02


title: 45dpf_79


title: 45dpf_74


title: 45dpf_75


title: PT039_P1_G04


title: PT039_P1_G01


title: 45dpf_71


title: PT039_P1_F12


title: PT039_P1_G08


title: PT039_P1_F11


title: 45dpf_69


title: PT039_P1_G06


title: PT039_P1_H03


title: 45dpf_70


title: 45dpf_67


title: PT039_P11_H09_S93


title: PT039_P11_H05_S89


title: 45dpf_68


title: PT081_P5_E10_S154


title: PT039_P11_G11_S83


title: 45dpf_72


title: 45dpf_65


title: PT039_P11_G06_S78


title: 45dpf_63


title: PT039_P11_F08_S68


title: 45dpf_62


title: 45dpf_66


title: PT039_P11_E10_S58


title: PT039_P11_F09_S69


title: 45dpf_60


title: 45dpf_64


title: PT039_P11_E08_S56


title: PT039_P11_F04_S64


title: 45dpf_61


title: 45dpf_59


title: PT039_P11_E07_S55


title: PT039_P11_D11_S47


title: 45dpf_58


title: PT039_P11_H11_S95


title: 45dpf_57


title: 45dpf_56


title: PT039_P11_D06_S42


title: 45dpf_55


title: PT039_P11_C10_S34


title: 45dpf_54


title: PT039_P11_C02_S26


title: PT039_P11_C08_S32


title: 45dpf_52


title: PT039_P11_C04_S28


title: 45dpf_53


title: PT039_P11_C01_S25


title: PT039_P11_B01_S13


title: PT039_P11_A10_S10


title: PT039_P11_A08_S8


title: 45dpf_47


title: 45dpf_48


title: 45dpf_50


title: 45dpf_46


title: PT039_P11_B12_S24


title: 45dpf_45


title: PT089_P9_F10_S166


title: 45dpf_51


title: PT039_P11_A05_S5


title: 45dpf_44


title: PT089_P7_H12_S96


title: 45dpf_43


title: PT089_P7_H11_S95


title: 45dpf_42


title: PT089_P7_H09_S93


title: PT089_P7_H07_S91


title: 45dpf_49


title: 45dpf_40


title: 45dpf_38


title: 45dpf_39


title: 45dpf_37


title: PT089_P7_H06_S90


title: 45dpf_36


title: PT089_P7_H04_S88


title: PT089_P7_H03_S87


title: 45dpf_34


title: PT089_P7_H05_S89


title: PT089_P7_H02_S86


title: 45dpf_33


title: PT089_P7_F01_S61


title: PT089_P7_D04_S40


title: 45dpf_30


title: PT089_P3_H08_S380


title: 45dpf_41


title: 45dpf_29


title: PT089_P3_H07_S379


title: PT089_P7_H10_S94


title: PT089_P7_H08_S92


title: PT089_P3_H06_S378


title: 45dpf_28


title: PT089_P3_G11_S371


title: 45dpf_35


title: PT089_P3_F04_S352


title: 45dpf_27


title: 45dpf_25


title: PT089_P7_H01_S85


title: 45dpf_26


title: PT089_P3_D11_S335


title: PT089_P3_G01_S361


title: PT089_P3_E12_S348


title: 45dpf_23


title: 45dpf_32


title: 45dpf_31


title: 45dpf_21


title: 45dpf_22


title: PT089_P3_E03_S339


title: PT089_P3_C12_S324


title: 45dpf_18


title: 45dpf_17


title: PT089_P3_D06_S330


title: PT089_P9_F12_S168


title: PT089_P3_C09_S321


title: 45dpf_16


title: PT089_P3_C08_S320


title: 45dpf_24


title: PT089_P3_C07_S319


title: 45dpf_15


title: 45dpf_14


title: 45dpf_12


title: 45dpf_13


title: PT089_P3_D07_S331


title: 45dpf_11


title: PT089_P3_B07_S307


title: PT089_P3_C01_S313


title: 45dpf_10


title: PT089_P3_B11_S311


title: PT089_P3_B03_S303


title: PT089_P3_B04_S304


title: 45dpf_19


title: 45dpf_9


title: 45dpf_7


title: PT089_P3_C11_S323


title: PT089_P3_A11_S299


title: PT089_P3_A09_S297


title: 45dpf_4


title: PT089_P3_A07_S295


title: 45dpf_6


title: 45dpf_5


title: 45dpf_3


title: PT089_P3_A04_S292


title: PT089_P3_C06_S318


title: 45dpf_2


title: PT089_P3_A01_S289


title: PT089_P3_A12_S300


title: PT089_P1_B10


title: 45dpf_1


title: 4mpf_Batch2_54


title: 45dpf_8


title: PT039_P10_H12_S288


title: 4mpf_Batch2_51


title: PT089_P3_A10_S298


title: PT039_P10_H09_S285


title: 4mpf_Batch2_53


title: 4mpf_Batch2_50


title: PT039_P10_H08_S284


title: 4mpf_Batch2_49


title: PT089_P3_A02_S290


title: PT039_P10_H06_S282


title: PT039_P10_H05_S281


title: PT039_P10_H04_S280


title: 4mpf_Batch2_47


title: 4mpf_Batch2_46


title: 4mpf_Batch2_48


title: PT039_P10_H03_S279


title: 4mpf_Batch2_45


title: PT039_P10_H02_S278


title: 4mpf_Batch2_44


title: 4mpf_Batch2_55


title: PT039_P10_H01_S277


title: PT039_P10_H11_S287


title: 4mpf_Batch2_52


title: PT039_P10_G11_S275


title: PT039_P10_G10_S274


title: PT039_P10_H07_S283


title: PT039_P10_G07_S271


title: 4mpf_Batch2_43


title: 4mpf_Batch2_40


title: 4mpf_Batch2_38


title: 4mpf_Batch2_39


title: 4mpf_Batch2_42


title: PT039_P10_G08_S272


title: PT039_P10_G04_S268


title: PT039_P10_G06_S270


title: 4mpf_Batch2_41


title: 45dpf_20


title: 4mpf_Batch2_37


title: 4mpf_Batch2_36


title: PT039_P10_G03_S267


title: 4mpf_Batch2_35


title: PT039_P10_G02_S266


title: 4mpf_Batch2_34


title: PT039_P10_G01_S265


title: 4mpf_Batch2_32


title: PT039_P10_F12_S264


title: PT039_P10_F11_S263


title: 4mpf_Batch2_31


title: PT039_P10_G09_S273


title: PT039_P10_F09_S261


title: PT039_P10_F08_S260


title: 4mpf_Batch2_30


title: PT039_P10_F07_S259


title: 4mpf_Batch2_28


title: 4mpf_Batch2_29


title: PT039_P10_F06_S258


title: 4mpf_Batch2_24


title: PT039_P10_F03_S255


title: PT039_P10_F02_S254


title: 4mpf_Batch2_25


title: 4mpf_Batch2_26


title: 4mpf_Batch2_23


title: PT039_P10_F04_S256


title: PT039_P10_F01_S253


title: 4mpf_Batch2_33


title: 4mpf_Batch2_22


title: PT039_P10_E12_S252


title: 4mpf_Batch2_27


title: 4mpf_Batch2_21


title: 4mpf_Batch2_20


title: PT039_P10_E08_S248


title: 4mpf_Batch2_19


title: PT039_P10_E11_S251


title: 4mpf_Batch2_18


title: PT039_P10_E07_S247


title: 4mpf_Batch2_17


title: PT039_P10_E06_S246


title: PT039_P10_E04_S244


title: 4mpf_Batch2_16


title: PT039_P10_F05_S257


title: PT039_P10_E02_S242


title: 4mpf_Batch2_11


title: PT039_P10_D11_S239


title: PT039_P10_D10_S238


title: 4mpf_Batch2_15


title: PT039_P10_E03_S243


title: 4mpf_Batch2_10


title: 4mpf_Batch2_14


title: PT039_P10_D09_S237


title: 4mpf_Batch2_13


title: PT039_P10_E01_S241


title: 4mpf_Batch2_9


title: PT039_P10_D12_S240


title: 4mpf_Batch2_12


title: 4mpf_Batch2_8


title: PT039_P10_E09_S249


title: PT039_P10_D08_S236


title: 4mpf_Batch2_7


title: 4mpf_Batch2_5


title: 4mpf_Batch2_6


title: PT039_P10_D04_S232


title: PT039_P10_D06_S234


title: PT039_P10_D05_S233


title: PT039_P10_D03_S231


title: 4mpf_Batch2_4


title: PT039_P10_D02_S230


title: 4mpf_Batch2_3


title: 4mpf_Batch2_2


title: PT039_P10_D01_S229


title: 4mpf_Batch2_1


title: 3mpf_C1_71


title: 3mpf_C1_69


title: 3mpf_C1_73


title: 3mpf_C1_72


title: 3mpf_C1_68


title: 3mpf_C1_66


title: 3mpf_C1_70


title: PT039_P10_C07_S223


title: PT039_P10_C08_S224


title: PT039_P10_C12_S228


title: PT039_P10_C03_S219


title: PT039_P10_C05_S221


title: PT039_P10_C09_S225


title: PT039_P10_C11_S227


title: PT039_P10_C10_S226


title: PT039_P10_C06_S222


title: PT039_P10_C04_S220


title: PT039_P10_B12_S216


title: PT039_P10_C02_S218


title: PT039_P10_B11_S215


title: 3mpf_C1_63


title: 3mpf_C1_61


title: PT039_P10_B10_S214


title: 3mpf_C1_62


title: PT039_P10_B08_S212


title: PT039_P10_B09_S213


title: 3mpf_C1_59


title: 3mpf_C1_60


title: PT039_P10_B07_S211


title: 3mpf_C1_57


title: PT039_P10_B06_S210


title: 3mpf_C1_58


title: 3mpf_C1_56


title: PT039_P10_B05_S209


title: PT039_P10_B04_S208


title: 3mpf_C1_54


title: 3mpf_C1_52


title: PT039_P10_B02_S206


title: 3mpf_C1_53


title: PT039_P10_B03_S207


title: PT039_P10_B01_S205


title: 3mpf_C1_51


title: PT039_P10_A11_S203


title: 3mpf_C1_50


title: 3mpf_C1_49


title: PT039_P10_A10_S202


title: 3mpf_C1_48


title: 3mpf_C1_47


title: PT039_P10_A09_S201


title: 3mpf_C1_46


title: 3mpf_C1_44


title: 3mpf_C1_45


title: 3mpf_C1_55


title: PT039_P10_A05_S197


title: PT039_P10_A06_S198


title: PT039_P10_A04_S196


title: 3mpf_C1_42


title: PT039_P10_A02_S194


title: PT039_P10_A07_S199


title: 3mpf_C1_41


title: PT039_P10_A12_S204


title: 3mpf_C1_39


title: PT039_P10_A01_S193


title: 3mpf_C1_40


title: PT039_P10_A03_S195


title: 3mpf_C1_38


title: PT084_P121_H12_S384


title: PT084_P121_H11_S383


title: PT084_P121_H09_S381


title: PT084_P121_H10_S382


title: PT039_P10_A08_S200


title: 3mpf_C1_37


title: 3mpf_C1_43


title: PT084_P121_H08_S380


title: 3mpf_C1_35


title: 3mpf_C1_34


title: PT084_P121_H07_S379


title: PT084_P121_H06_S378


title: 3mpf_C1_33


title: PT084_P121_H05_S377


title: 3mpf_C1_31


title: 3mpf_C1_32


title: PT084_P121_H03_S375


title: 3mpf_C1_29


title: PT084_P121_H02_S374


title: 3mpf_C1_28


title: 3mpf_C1_26


title: PT084_P121_H01_S373


title: 3mpf_C1_30


title: PT084_P121_G12_S372


title: PT084_P121_G10_S370


title: 3mpf_C1_27


title: PT084_P121_G11_S371


title: 3mpf_C1_36


title: 3mpf_C1_25


title: 3mpf_C1_24


title: PT084_P121_G09_S369


title: 3mpf_C1_23


title: PT084_P121_G05_S365


title: PT084_P121_G07_S367


title: 3mpf_C1_21


title: 3mpf_C1_22


title: 3mpf_C1_20


title: PT084_P121_G08_S368


title: PT084_P121_G04_S364


title: 3mpf_C1_19


title: 3mpf_C1_16


title: 3mpf_C1_17


title: 3mpf_C1_18


title: PT084_P121_G03_S363


title: PT084_P121_F11_S359


title: PT084_P121_F12_S360


title: 3mpf_C1_13


title: 3mpf_C1_12


title: 3mpf_C1_15


title: 3mpf_C1_14


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title: PT084_P121_G01_S361


title: 3mpf_C1_11


title: PT084_P121_F10_S358


title: PT084_P121_F09_S357


title: PT084_P121_G06_S366


title: 3mpf_C1_10


title: 3mpf_C1_9


title: 3mpf_C1_8


title: PT084_P121_F07_S355


title: PT084_P121_F04_S352


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title: PT084_P121_F03_S351


title: 3mpf_C1_5


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title: PT084_P121_F08_S356


title: 3mpf_C1_4


title: 3mpf_C1_3


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title: 3mpf_C1_2


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title: PT084_P121_F06_S354


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title: PT084_P121_E07_S343


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title: 12mpf_140


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title: PT084_P121_F02_S350


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title: PT084_P121_E12_S348


title: PT039_P121_E02_S338


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title: PT039_P121_E01_S337


title: PT084_P121_E08_S344


title: 3mpf_C1_67


title: 3mpf_C1_65


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title: PT039_P121_D09_S333


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title: PT039_P121_C12_S324


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title: PT039_P121_D02_S326


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title: PT039_P121_C11_S323


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title: PT039_P121_C05_S317


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title: 12mpf_122


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title: PT039_P121_C04_S316


title: PT039_P121_C02_S314


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title: 12mpf_115


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title: PT081_P1_E06


title: 14mpf_47


title: PT081_P1_E05


title: 14mpf_46


title: PT081_P1_E04


title: PT081_P1_E03


title: PT081_P1_E02


title: 14mpf_43


title: 14mpf_42


title: 14mpf_41


title: PT081_P1_E01


title: PT081_P1_D12


title: 14mpf_40


title: 14mpf_38


title: 14mpf_39


title: PT081_P1_D10


title: PT081_P1_E09


title: 14mpf_37


title: PT081_P1_D06


title: 14mpf_36


title: PT081_P1_D08


title: PT081_P1_D07


title: PT081_P1_D05


title: 14mpf_34


title: 14mpf_35


title: PT081_P1_D04


title: PT081_P1_D03


title: PT081_P1_D02


title: 14mpf_45


title: 14mpf_44


title: PT081_P1_D09


title: 14mpf_31


title: 14mpf_30


title: PT081_P1_C11


title: PT081_P1_C09


title: 14mpf_28


title: 14mpf_29


title: PT081_P1_C08


title: PT081_P1_C07


title: PT081_P1_C05


title: PT081_P1_C06


title: PT081_P1_C04


title: 14mpf_24


title: 14mpf_22


title: PT081_P1_C03


title: 14mpf_23


title: PT081_P1_C02


title: 14mpf_25


title: 14mpf_32


title: PT081_P1_C01


title: 14mpf_26


title: 14mpf_20


title: 14mpf_33