title: A008-E-015, snRNAseq

description: 10x Genomics


title: mouse-27-PBS-CA1

status: Public on Apr 28 2022

type: SRA

city: Winnipeg

first: Jessy

middle: Andrew

last: Slota

state: Manitoba

address: 1015 Arlington St.

department: One Health Division

country: Canada

institute: National Microbiology Laboratory; Public Health Agency of Canada

library_source: transcriptomic

data_processing:
raw sequecing reads were trimmed using trimmomatic (sliding window trimming quality > 20, drop reads average quality < 25 and drop reads length < 20)
rRNA reads were removed using Bowtie2 by writing unaligned reads to fastq files
reads were mapped to the mm10 reference genome with HISAT2 with default parameters
raw read counts were counted for each transcript using FeatureCounts with default parameters
Assembly: mm10
Supplementary files format and content: Raw read counts are provided in CSV format for each sample

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was isolated from microdissected CA1 or thalamus tissues using the RNAqueous–Micro Kit (Life Technologies Inc.)
Sequencing libraries were prepared from total RNA using the Smart-Seq v4 Ultra Low Input RNA Kit (TakaraBio)

treatment_protocol: Mice were intraperitoneally inoculated with either 2% RML scrapie brain homogenate (RML) or non-infectious brain homogenate (Mock)

tag: tissue

tag: genotype

tag: treatment

value: Mock

tag: days post_infection


title: Restricted hematopoietic progenitor 1 (HPC-1) 7

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

country: Germany

institute: Medical Faculty TU Dresden

description:
raw_counts+metadata.csv
counts_filtered.csv
counts_filtered_normalized_log.csv
cell_metadata_filtered.csv

data_processing:
Alignment of the samples with GSNAP (version 2018–07-04) to the mm10 reference, and using Ensembl 87 for the support of splicesite detection
featureCounts (version1.6.2) was used to assign the reads to genes with the help of Ensembl 87 annotation
Genome_build: mm10

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Whole bone marrow cells were isolated by crushing long bones with mortar and pestle using PBS/2% FCS/2 mM EDTA and filtered through a 100 µm mesh. After erythrocyte lysis in hypotonic NH4Cl-buffer, cells were filtered through a 40 µm mesh. Hematopoietic lineage+ cells were removed with the lineage cell depletion kit (Miltenyi Biotec). Cells were incubated with antibodies in PBS / 2% FCS for 30 min, washed twice with PBS / 2% FCS. Single BM HSPC cells were sorted on an BD ARIA II SORP flow cytometer. Single hematopoietic stem and progenitor cells were index-sorted into 384 well plates containing 0.5 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. After thawing, 0.5 µl of a primer mix were added (5 mM dNTP (Invitrogen), 0.5 µM dT-primer (C6 aminolinkerAAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), 1 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription (RT) was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG), 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 µM UP-primer (AAGCAGTGGTATCAACGCAGAGT) under following cycling conditions: initial denaturation at 98°C for 3 min, 23 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA was eluted in 12 µl nuclease free water and the concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium).
For library preparation up to 700 pg cDNA was desiccated and rehydrated in 1 µl Tagmentation mix (1x TruePrep Tagment Buffer L, 0.1 µl TruePrep Tagment Enzyme V50; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme) and tagmented at 55°C for 5 min. Subsequently, Illumina indices are added during PCR (72°C 3 min, 98°C 30 sec, 13 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina 50 bp paired-end sequencing on a Novaseq6000 aiming at an average sequencing depth of 0.5 mio reads per cell.

tag: col1a1 genotype

tag: rosa26 genotype

value: rtTA/rtTA

tag: doxycyclin induction

value: induced


title: Restricted hematopoietic progenitor 1 (HPC-1) 8


title: HUVEC cells, P3, siCTRL 10hr TNF, Biol Rep 3

city: New Haven

first: Joseph Wayne

middle: Montano

last: Fowler

state: CT

address: 10 Amistad St.

department: Pharmacology

country: USA

institute: Yale University

data_processing:
Reads aligned to hg19 build of human genome with STAR
Quantified to hr19 RefSeq annotation model through Partek E/M
Genes were normalized as counts per million
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes cpm values for each Sample

organism: Homo sapiens

source_name: HUVEC

growth_protocol: HUVECs were obtained from the Yale School of Medicine, Vascular Biology and Therapeutics Core facility. Cells were cultured in EGM-2 media (Lonza) with 10% fetal bovine serum (FBS), penicillin/streptomycin and glutamine (2.8 mM) in a 37°C incubator with 5% CO2 supply

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated from control cells using TrueSeq Small RNA Library preparation (Illumina)

treatment_protocol: HUVEC were treated with 20nM of indicated siRNA for 10 hours and refed with fresh media. 48hrs later, HUVEC were treated with 10ng/mL TNF for indicated time.

tag: cell line

value: HUVEC

tag: cell type

value: Primary Endothlelial Cell

value: CTRL

value: 10ng/mL TNF, 10hr


title: HUVEC cells, P3, siRELA 0hr TNF, Biol Rep 1

value: RELA Knockdown

value: Vehicle


title: mouse-38-PBS-CA1


title: A002-C-121, Replicate1, snRNAseq

city: Stanford

first: Winston

last: Becker

state: CA

address: 1291 Welch Road, B259 Beckman Center

department: Genetics

institute: Stanford University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, alignment, and gene counting were done using Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The expression matricies produced from Cell Ranger are included as processed data.
Assembly: hg38
Supplementary files format and content: Expression matricies divided into matrix, barcode, and feature files.

source_name: Colon

extract_protocol:
The isolation of nuclei was accomplished using the OmniATAC protocol (Corces*, Granja* et al. Science 362, 2018). Dissociation of nuclei was carried out entirely on wet ice. 40-60mg of flash-frozen tissue was placed into 2ml dounce tissue grinders containing 1ml HB (Lysis) Buffer (1.0341x HB Stable solution, 1M DTT, 500 mM Spermidine, 150mM Spermine, 10% NP40, cOmplete Protease Inhibitor, Ribolock), gently triturated, then allowed to thaw for 5 minutes in the solution. After 5 minutes, tissue was dounced 10 times with pestle A and 20 times with pestle B, or until there was no resistance from either pestle. Sample was filtered through a 40um cell strainer (Falcon; 352340) and resulting homogenate transferred to a pre-chilled 2ml LoBind tube. Samples were spun in a 4°C fixed angle centrifuge for 5 minutes at 350 RCF to pellet nuclei. After spinning, all but 50ul of supernatant was removed. 350ul HB was added to the nuclei pellet for a total volume of 400ul. Nuclei were gently resuspended with a wide bore pipet. One volume of 50% Iodixanol (60% OptiPrep [Sigma Aldrich; D1556], Diluent Buffer [2M KCl, 1M MgCl2, 0.75M Tricine-KOH pH 7.8], Water) was added and gently triturated. Next, 600ul of 30% Iodixanol was carefully layered under the 25% mixture. Finally, 600ul of 40% Iodixanol was layered under the 30% mixture. Sample was then spun in a 4°C swinging bucket centrifuge for 20 min at 3,000 RCF. Upon completion of the spin, a band of nuclei was visible. Supernatant was aspirated down to within 200-300ul of the nuclei band. The nuclei band was then collected at 200ul and transferred to a fresh 1.5ml tube. Sample was diluted with one volume (200ul) Resuspension Buffer (1x PBS, 1% BSA, 0.2u/uL Ribolock). Nuclei concentration was determined using the Countess II FL Automated Cell Counter (ThermoFisher; AMQAF1000). In addition to isolating nuclei with the omni-ATAC dounce method, we used the Singulator from S2 Genomics to isolate nuclei for 4 samples (2 normal and 2 polyp) from patient A002. The same buffers (lysis, wash, resuspension) were used for both the manual omni-ATAC dounce and S2 Singulator methods. HB buffer was prepared following the OmniATAC protocol, with the addition of 15ul Ribolock per 1mL HB buffer to help maintain RNA integrity. Approximately 50-70mg tissue in small chunks were placed into the Nuclei Isolation Cartridge. We ran the Extended Nuclei Isolation Singulator program which includes disruption, 5 minute incubation, disruption, filtration (150um and 40um filters) and buffer rinse of the cartridge. Following dissociation, nuclei were spun at 300g for 5 minutes. Supernatant was removed and nuclei were resuspended in Resuspension Buffer (noted above). Nuclei were counted using the Countess Automated Cell Counter (ThermoFisher). The total dissociation time for 4 samples was approximately 1 hour, as one sample can be run at a time on the S2 Singulator.
snRNA-seq targeting 9,000 cells per sample was performed using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, 1000121) and Chromium Next GEM Chip G Single Cell Kit (10x Genomics, 1000120).

value: Colon

tag: disease stage

value: Unaffected

tag: familial adenomatous_polyposis

value: Y

tag: Sex

value: F


title: Restricted hematopoietic progenitor 1 (HPC-1) 6


title: mouse-26-PBS-CA1


title: HUVEC cells, P3, siRELA 0hr TNF, Biol Rep 2


title: Restricted hematopoietic progenitor 1 (HPC-1) 5


title: mouse-26-PBS-TH

source_name: thalamus

value: thalamus


title: Restricted hematopoietic progenitor 1 (HPC-1) 11


title: mouse-24-PBS-TH


title: Restricted hematopoietic progenitor 1 (HPC-1) 10


title: Restricted hematopoietic progenitor 1 (HPC-1) 4


title: HUVEC cells, P3, siCTRL 10hr TNF, Biol Rep 1


title: mouse-37-PBS-TH


title: HUVEC cells, P3, siCTRL 10hr TNF, Biol Rep 2


title: Restricted hematopoietic progenitor 1 (HPC-1) 9


title: mouse-24-PBS-CA1


title: A002-C-116, snRNAseq

description: 10x Genomics

value: Polyp


title: A002-C-205, snRNAseq

description: 10x Genomics


title: HUVEC cells, P3, siCTRL 4hr TNF, Biol Rep 3

value: 10ng/mL TNF, 4hr


title: A002-C-114, snRNAseq

description: 10x Genomics


title: A002-C-203, snRNAseq

description: 10x Genomics


title: A002-C-106, snRNAseq

description: 10x Genomics


title: HUVEC cells, P3, siCTRL 4hr TNF, Biol Rep 2


title: Restricted hematopoietic progenitor 1 (HPC-1) 2


title: mouse-195-RML-CA1

value: RML


title: A002-C-021, snRNAseq

description: 10x Genomics


title: mouse-22-PBS-CA1

value: Mock


title: A002-C-024, snRNAseq

description: 10x Genomics


title: E34 Hematopoietic Stem Cell (E34 HSC) 16

value: rtTA/rtTA


title: Restricted hematopoietic progenitor 1 (HPC-1) 1

value: induced


title: mouse-186-RML-TH


title: A002-C-016, snRNAseq

description: 10x Genomics


title: A002-C-121, Replicate2, snRNAseq

description: 10x Genomics


title: HUVEC cells, P3, siCTRL 4hr TNF, Biol Rep 1

value: HUVEC


title: E34 Hematopoietic Stem Cell (E34 HSC) 15


title: HUVEC cells, P3, siCTRL 0hr TNF, Biol Rep 2

value: Primary Endothlelial Cell


title: HUVEC cells, P3, siCTRL 0hr TNF, Biol Rep 1

value: CTRL


title: mouse-22-PBS-TH


title: mouse-186-RML-CA1


title: A002-C-010, Replicate2, snRNAseq

description: 10x Genomics


title: A002-C-010, Replicate1, snRNAseq

description: 10x Genomics


title: Restricted hematopoietic progenitor 1 (HPC-1) 3


title: SNU1033_24h_133_100nM  [SNU_9]

city: San Diego

first: Peter

last: Olson

state: California

address: 3545 Cray Court

institute: Mirati Therapeutics

data_processing:
QC was performed by FastQCv0.11.8. Mouse read contamination was removed using Xenome 1.0.1-r
RNA-seq reads were trimmed and low-quality reads were removed using Trimgalore v0.6.3_dev
trimmed fastq sequences were aligned to the human reference genome GRCh38 using STAR aligner v2.7.1a
raw counts were normalized to total number of reads by calculateing log2CPM and lowly expressed genes (average log2CPM<-2) were eliminated before differential gene expression analysis
Assembly: GRCh38
Supplementary files format and content: read_counts

source_name: in-vitro cell line

growth_protocol: All cell lines were maintained in vendor recommended grwoth media + 10% FBS with 5% CO2. Cell lines were passaged ~ twice/week and maintained in log growth phase prior to implant into mice or drug treatment.

extract_protocol:
Followed manufacturer protocol for RNA extraction using Qiagen RNeasy kit for both cell lysates and tumor fragments and sent to Genewiz, LLC for RNA library preparation and sequencing. Extracted RNA samples were quantified using Qubit  2.0 fluorometer and RNA integrity was checked using Agilent TapeStation 4200.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina  following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with  Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second  strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at  3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library  enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation  (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen,  Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on 1 flowcell lane. After clustering, the flowcell was loaded on the  Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples  were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were  conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina  HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One  mismatch was allowed for index sequence identification.

treatment_protocol: In vitro: cell were treated with either DMSO or MRTX1133 at the dose level indicated and incubated for 3 and 24hrs. Post incubation cells were washed once, and scraped in RNALater, with storage at -20 until extraction. In vivo: cell lines were implanted into nude mice, and treated as described. Tumors were harvest post treatment and stored in RNALater at -20 until extraction.

tag: age

value: 45Y (at sampling)

value: female

tag: disease

value: Colorectal adenocarcinoma

tag: biological replicate

value: Biological replicate 3


title: E34 Hematopoietic Stem Cell (E34 HSC) 12


title: E34 Hematopoietic Stem Cell (E34 HSC) 13


title: SNU1033_24h_133_100nM  [SNU_8]

value: Colon

value: Biological replicate 2


title: A001-C-223, snRNAseq

description: 10x Genomics

value: Unaffected

value: Y

value: M


title: mouse-185-RML-TH

value: thalamus


title: E34 Hematopoietic Stem Cell (E34 HSC) 11


title: SNU1033_24h_133_100nM  [SNU_7]

value: Biological replicate 1


title: E34 Hematopoietic Stem Cell (E34 HSC) 10


title: mouse-167-RML-TH

value: RML


title: mouse-195-RML-TH


title: SNU1033_24h_DMSO  [SNU_6]

value: DMSO 24h


title: HUVEC cells, P3, siCTRL 0hr TNF, Biol Rep 3

value: Vehicle


title: A001-C-203, snRNAseq

description: 10x Genomics

value: Polyp


title: A001-C-207, snRNAseq

description: 10x Genomics


title: mouse-166-RML-TH


title: A001-C-202, snRNAseq

description: 10x Genomics


title: E34 Hematopoietic Stem Cell (E34 HSC) 9

value: rtTA/rtTA

value: induced


title: SNU1033_24h_DMSO  [SNU_5]

value: 45Y (at sampling)


title: SNU1033_24h_DMSO  [SNU_4]

value: female


title: E34 Hematopoietic Stem Cell (E34 HSC) 8


title: E34 Hematopoietic Stem Cell (E34 HSC) 14


title: mouse-166-RML-CA1


title: A001-C-108, snRNAseq

description: 10x Genomics


title: A001-C-124, snRNAseq

description: 10x Genomics


title: mouse-165-RML-TH


title: A001-C-104, snRNAseq

description: 10x Genomics


title: SNU1033_3h_133_100nM  [SNU_3]

value: Colorectal adenocarcinoma


title: A001-C-119, snRNAseq

description: 10x Genomics


title: mouse-138-RML-CA1


title: mouse-138-RML-TH


title: E34 Hematopoietic Stem Cell (E34 HSC) 6


title: SNU1033_3h_133_100nM  [SNU_1]


title: E34 Hematopoietic Stem Cell (E34 HSC) 3


title: mouse-167-RML-CA1


title: mouse-135-RML-TH


title: E34 Hematopoietic Stem Cell (E34 HSC) 5


title: E34 Hematopoietic Stem Cell (E34 HSC) 4


title: A001-C-023, snRNAseq

description: 10x Genomics


title: mouse-165-RML-CA1


title: LS180_24h_133_100nM  [LS_9]

value: 58Y (at sampling)

value: Colon adenocarcinoma

value: Biological replicate 3


title: E34 Hematopoietic Stem Cell (E34 HSC) 1


title: mouse-134-RML-TH


title: A001-C-014, snRNAseq

description: 10x Genomics

value: Colon


title: LS180_24h_133_100nM  [LS_8]

value: Biological replicate 2


title: mouse-135-RML-CA1


title: A001-C-007, snRNAseq

description: 10x Genomics

value: CRC

value: Y

value: M


title: Hematopoietic stem cell (HSC) 31


title: mouse-122-RML-CA1

value: RML


title: mouse-121-RML-TH

value: thalamus


title: Hematopoietic stem cell (HSC) 29


title: B004-A-204, Dounce, scATACseq

description: 10x genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcode processing, alignment, and fragments file generation was performed using Cell Ranger ATAC v1.2.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: hg38
Supplementary files format and content: Fragments files and tabix index of fragments files

molecule: genomic DNA

extract_protocol:
The isolation of nuclei was accomplished using the OmniATAC protocol (Corces*, Granja* et al. Science 362, 2018). Dissociation of nuclei was carried out entirely on wet ice. 40-60mg of flash-frozen tissue was placed into 2ml dounce tissue grinders containing 1ml HB (Lysis) Buffer (1.0341x HB Stable solution, 1M DTT, 500 mM Spermidine, 150mM Spermine, 10% NP40, cOmplete Protease Inhibitor, Ribolock), gently triturated, then allowed to thaw for 5 minutes in the solution. After 5 minutes, tissue was dounced 10 times with pestle A and 20 times with pestle B, or until there was no resistance from either pestle. Sample was filtered through a 40um cell strainer (Falcon; 352340) and resulting homogenate transferred to a pre-chilled 2ml LoBind tube. Samples were spun in a 4°C fixed angle centrifuge for 5 minutes at 350 RCF to pellet nuclei. After spinning, all but 50ul of supernatant was removed. 350ul HB was added to the nuclei pellet for a total volume of 400ul. Nuclei were gently resuspended with a wide bore pipet. One volume of 50% Iodixanol (60% OptiPrep [Sigma Aldrich; D1556], Diluent Buffer [2M KCl, 1M MgCl2, 0.75M Tricine-KOH pH 7.8], Water) was added and gently triturated. Next, 600ul of 30% Iodixanol was carefully layered under the 25% mixture. Finally, 600ul of 40% Iodixanol was layered under the 30% mixture. Sample was then spun in a 4°C swinging bucket centrifuge for 20 min at 3,000 RCF. Upon completion of the spin, a band of nuclei was visible. Supernatant was aspirated down to within 200-300ul of the nuclei band. The nuclei band was then collected at 200ul and transferred to a fresh 1.5ml tube. Sample was diluted with one volume (200ul) Resuspension Buffer (1x PBS, 1% BSA, 0.2u/uL Ribolock). Nuclei concentration was determined using the Countess II FL Automated Cell Counter (ThermoFisher; AMQAF1000). In addition to isolating nuclei with the omni-ATAC dounce method, we used the Singulator from S2 Genomics to isolate nuclei for 4 samples (2 normal and 2 polyp) from patient A002. The same buffers (lysis, wash, resuspension) were used for both the manual omni-ATAC dounce and S2 Singulator methods. HB buffer was prepared following the OmniATAC protocol, with the addition of 15ul Ribolock per 1mL HB buffer to help maintain RNA integrity. Approximately 50-70mg tissue in small chunks were placed into the Nuclei Isolation Cartridge. We ran the Extended Nuclei Isolation Singulator program which includes disruption, 5 minute incubation, disruption, filtration (150um and 40um filters) and buffer rinse of the cartridge. Following dissociation, nuclei were spun at 300g for 5 minutes. Supernatant was removed and nuclei were resuspended in Resuspension Buffer (noted above). Nuclei were counted using the Countess Automated Cell Counter (ThermoFisher). The total dissociation time for 4 samples was approximately 1 hour, as one sample can be run at a time on the S2 Singulator.
scATAC-seq targeting 9,000 cells per sample was performed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10x Genomics, 1000175) and Chromium Next GEM Chip H (10x Genomics, 1000161).

tag: disease state

value: Normal

value: N


title: LS180_24h_DMSO  [LS_6]

value: DMSO 24h


title: Hematopoietic stem cell (HSC) 28

value: rtTA/rtTA

value: induced


title: Hematopoietic stem cell (HSC) 32


title: SNU1033_3h_133_100nM  [SNU_2]

value: 45Y (at sampling)

value: female


title: B004-A-008, Dounce, scATACseq

description: 10x genomics


title: LS180_24h_DMSO  [LS_5]

value: 58Y (at sampling)


title: LS180_24h_DMSO  [LS_4]

value: Colon adenocarcinoma

value: Biological replicate 1


title: Hematopoietic stem cell (HSC) 30


title: mouse-121-RML-CA1


title: B004-A-004, Replicate1, Dounce, scATACseq

description: 10x genomics

value: Colon


title: Hematopoietic stem cell (HSC) 27


title: LS180_3h_133_100nM  [LS_1]


title: B001-A-301, Dounce, scATACseq

description: 10x genomics

value: F


title: F091, Dounce, scATACseq

description: 10x genomics

value: Polyp


title: ASPC1_24h_133_100nM  [ASPC1_9]

value: Pancreas

value: 62Y (at sampling)

value: Pancreatic adenocarcinoma

value: Biological replicate 3


title: mouse-185-RML-CA1

value: RML


title: Hematopoietic stem cell (HSC) 26


title: mouse-118-RML-TH

value: thalamus


title: B004-A-004, Replicate2, Dounce, scATACseq

description: 10x genomics

value: Normal

value: N

value: M


title: Hematopoietic stem cell (HSC) 25

value: rtTA/rtTA

value: induced


title: F034, Dounce, scATACseq

description: 10x genomics

value: Y


title: mouse-134-RML-CA1


title: mouse-120-RML-CA1


title: F072B, Dounce, scATACseq

description: 10x genomics


title: ASPC1_24h_133_100nM  [ASPC1_8]

value: female

value: Biological replicate 2


title: ASPC1_24h_133_100nM  [ASPC1_7]

value: Biological replicate 1


title: hash2_w_o_control [control_3b]

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

institute: University of Würzburg

data_processing:
Raw RNA-Seq reads were trimmed, filtered and mapped to the UPEC genome. Small RNAs (sRNAs) were additionally added to the UPEC annotation file using a series of bash commands. Briefly, sRNA sequences of Escherichia coli str. K-12 substr. MG1655 were aligned to the UPEC genome using BLASTN (v2.9.0), and the alignment match with the lowest E-value was added as sRNA to the UPEC annotation. All added sRNAs had more than 89% identical matches and the largest number of mismatches was 4
Then, BBduk was used to trim nucleobases with Phred quality scores below 10 and to remove adapter sequences.
Next, Reads were mapped against the UPEC genome using BBMap (v38.84)
resulting alignments were assigned to both coding sequences and sRNAs using the featureCounts methods of the Subread (2.0.1) package.
Genome_build: Escherichia coli 536
Supplementary_files_format_and_content: counttable.tsv

organism: Escherichia coli 536

source_name: UPEC with water

growth_protocol: The strain was streaked on Luria-Bertani plates and cultured in non-cation adjusted Mueller-Hinton Broth, with aeration at 37°C and 220 rpm shaking.

extract_protocol:
Total RNA was purified from bacterial pellets using the miRNeasy Mini kit (Qiagen) according to the protocol #3 described in Popella et al. (REF). Briefly, cells were resuspended in 0.5 mg/mL lysozyme (Roth) in TE buffer (pH 8.0) and incubated for 5 min. Afterwards, RLT buffer supplemented with β-mercaptoethanol, and ethanol were added according to the manufacturer’s instructions. After sample loading, column wash-steps were performed according to the manual. RNA concentration was measured with a NanoDrop spectrophotometer.
Briefly, samples were treated with DNase (XXX) and quality was checked on a bioanalyzer (RNA chip XXX). Then, RNA was subjected to cDNA library preparation using the Corall kit (Lexogen) and including the depletion of ribosomal RNA (RiboCop-META kit, Lexogen) according to the manufacturer’s instructions. Afterwards, library samples were pooled in equimolar amounts and quality was verified using a bioanalyzer (DNA chip XXX). The cDNA pools were sequenced using the NextSeq 500 system (HighOutput flow cell, 400 M, 1x 75 cycle single-end; Illumina).

treatment_protocol: Bacterial overnight cultures were diluted 1:100 in fresh MHB and grown to an OD600 of 0.5. Subsequently, obtained cultures were again diluted 1:100 in fresh MHB to adjust a cell concentration of approximately 106 cfu/mL. After transferring 1.9 mL of the bacterial solution into 5 mL low-binding tubes (LABsolute), 100 µL of 20x PPNA stock solutions were added to reach a final concentration of 5 µM for all KFF-conjugated PNAs. In parallel, an equal amount of cells was treated with the respective volume of sterile nuclease-free water, which was used as solvent for the test compounds, and served as negative control. After incubating the samples for 15 min at 37 °C, RNAprotect Bacteria (Qiagen) was added according to the manufacturer’s instructions. Following a 10-min incubation, cells were pelleted at 4 °C and 21,100 xg for 20 min. The supernatant was discarded and pellets were either directly used or stored at – 20 °C (< 1 day) for subsequent bacterial RNA isolation.

tag: strain

tag: condition

value: UPEC with water

value: Water-treated


title: F007, Dounce, scATACseq

description: 10x genomics

tag: tissue

value: Colon

value: Polyp


title: LS180_3h_133_100nM  [LS_3]

value: 58Y (at sampling)

value: Colon adenocarcinoma

tag: treatment


title: E34 Hematopoietic Stem Cell (E34 HSC) 7


title: E34 Hematopoietic Stem Cell (E34 HSC) 2


title: mouse-118-RML-CA1

tag: genotype

value: RML

tag: days post_infection


title: CRC-4-8456, Dounce, scATACseq

description: 10x genomics

value: CRC


title: Hematopoietic stem cell (HSC) 23

tag: col1a1 genotype

tag: rosa26 genotype


title: mouse-120-RML-TH

value: thalamus


title: ASPC1_24h_DMSO  [ASPC1_6]

tag: cell line

value: Pancreas

value: 62Y (at sampling)

value: Pancreatic adenocarcinoma

value: Biological replicate 3

value: DMSO 24h


title: CRC-3-11773, Dounce, scATACseq

description: 10x genomics

value: N

value: F


title: Hematopoietic stem cell (HSC) 21

value: rtTA/rtTA

tag: doxycyclin induction

value: induced


title: hash1_w_o_control [control_3a]

value: UPEC with water

value: Water-treated


title: hash1_Jvpna93 [ispH_3a]

source_name: UPEC with ispH PNA

value: UPEC with ispH PNA

value: 15 min exposure to 5 uM PNA


title: Hematopoietic stem cell (HSC) 20


title: hash2_Jvpna93 [ispH_3b]


title: A022-C-002, Dounce, scATACseq

description: 10x genomics

value: Colon

value: Polyp

value: M


title: Hematopoietic stem cell (HSC) 19


title: LS180_24h_133_100nM  [LS_7]

tag: cell type

value: 58Y (at sampling)

value: female

value: Colon adenocarcinoma

value: Biological replicate 1


title: A018-C-020, Dounce, scATACseq

description: 10x genomics

tag: familial adenomatous_polyposis

value: Y


title: ASPC1_3h_133_100nM  [ASPC1_1]

value: Pancreas

value: 62Y (at sampling)

tag: Sex

value: Pancreatic adenocarcinoma


title: Hematopoietic stem cell (HSC) 24

value: rtTA/rtTA


title: L2100423_2_JVpna48 [rpsH_2]

source_name: UPEC with rpsH PNA

value: UPEC with rpsH PNA


title: LS180_3h_133_100nM  [LS_2]

tag: age

value: Biological replicate 2


title: CRC-2-15564, Dounce, scATACseq

description: 10x genomics

value: CRC

value: N


title: ASPC1_24h_DMSO  [ASPC1_4]

tag: disease

value: DMSO 24h


title: ASPC1_24h_DMSO  [ASPC1_5]

tag: biological replicate


title: CRC-1-8810, Dounce, scATACseq

description: 10x genomics

value: Colon

tag: disease state


title: Hematopoietic stem cell (HSC) 22

value: induced


title: AGS_24h_133_100nM  [AGS_9]

value: AGS

value: Stomach

value: 54Y (at sampling)

value: Gastric cancer

value: Biological replicate 3


title: Hematopoietic stem cell (HSC) 17


title: ASPC1_3h_133_100nM  [ASPC1_3]

value: female


title: L2100425_2_JVpna50 [csrA_2]

source_name: UPEC with csrA PNA

tag: strain

value: UPEC with csrA PNA

value: 15 min exposure to 5 uM PNA


title: ASPC1_3h_133_100nM  [ASPC1_2]

value: Pancreas

value: 62Y (at sampling)

value: Pancreatic adenocarcinoma


title: A015-C-206, Dounce, scATACseq

description: 10x genomics

value: Unaffected

value: Y

value: F


title: Hematopoietic stem cell (HSC) 18

value: rtTA/rtTA


title: L2100418_2_JVpna43 [pyrH_2]

source_name: UPEC with pyrH PNA

tag: condition

value: UPEC with pyrH PNA


title: A018-C-013, Dounce, scATACseq

description: 10x genomics

tag: tissue

value: Colon

value: Polyp

value: M


title: A015-C-204, Dounce, scATACseq

description: 10x genomics


title: L2100422_2_JVpna47 [nusG_2]

source_name: UPEC with nusG PNA

value: UPEC with nusG PNA

tag: treatment


title: AGS_24h_133_100nM  [AGS_8]

value: AGS

value: Stomach

value: 54Y (at sampling)

value: Gastric cancer

value: Biological replicate 2


title: Megakaryocyte Progenitor (MkP) 31

value: induced


title: L2100419_2_JVpna44 [yidC_2]

source_name: UPEC with ydiC PNA

value: UPEC with ydiC PNA

value: 15 min exposure to 5 uM PNA


title: A015-C-208, Dounce, scATACseq

description: 10x genomics

value: Unaffected


title: L2100424_2_JVpna49 [rplS_2]

source_name: UPEC with rplS PNA

value: UPEC with rplS PNA


title: AGS_24h_DMSO  [AGS_5]

value: female

value: DMSO 24h


title: AGS_24h_133_100nM  [AGS_7]

value: Biological replicate 1


title: L2100417_2_JVpna42 [rpoD_2]

source_name: UPEC with rpoD PNA

value: UPEC with rpoD PNA


title: Megakaryocyte Progenitor (MkP) 29

value: rtTA/rtTA


title: AGS_24h_DMSO  [AGS_6]

value: Biological replicate 3


title: A015-C-109, Dounce, scATACseq

description: 10x genomics

value: Colon

value: Y

value: F


title: Megakaryocyte Progenitor (MkP) 30


title: Megakaryocyte Progenitor (MkP) 28


title: Megakaryocyte Progenitor (MkP) 26


title: L2100416_2_JVpna41 [ftsZ_2]

source_name: UPEC with ftsZ PNA

value: UPEC with ftsZ PNA


title: AGS_24h_DMSO  [AGS_4]

value: AGS

value: Stomach

value: 54Y (at sampling)

value: Gastric cancer


title: Megakaryocyte Progenitor (MkP) 27

value: induced


title: A015-C-202, Dounce, scATACseq

description: 10x genomics

value: Polyp


title: AGS_3h_133_100nM  [AGS_3]


title: L2100415_2_JVpna40 [dnaB_2]

source_name: UPEC with dnaB PNA

value: UPEC with dnaB PNA

value: 15 min exposure to 5 uM PNA


title: L2100413_2_JVpna21 [acpP_2]

source_name: UPEC with acpP PNA

value: UPEC with acpP PNA


title: Megakaryocyte Progenitor (MkP) 25

source_name: bone marrow


title: A015-C-203, Dounce, scATACseq

description: 10x genomics


title: L2100412_2_JVpna22 [acpP-scr_2]

source_name: UPEC with scrambled PNA

value: UPEC with scrambled PNA


title: A015-C-106, Dounce, scATACseq

description: 10x genomics

source_name: Colon


title: AGS_3h_133_100nM  [AGS_2]

value: female

value: Biological replicate 2


title: L2100411_2_w_o_control [control_2]

value: UPEC with water

value: Water-treated


title: L2100410_1_JVpna50 [csrA_1]

value: UPEC with csrA PNA


title: AGS_3h_133_100nM  [AGS_1]

value: Biological replicate 1


title: A015-C-104, Dounce, scATACseq

description: 10x genomics

value: Colon

value: Y

value: F


title: Megakaryocyte Progenitor (MkP) 24

value: rtTA/rtTA


title: A015-C-102, Dounce, scATACseq

description: 10x genomics


title: Megakaryocyte Progenitor (MkP) 23


title: A427_24h_133_100nM  [A427_9]

value: Lung

value: 52Y (at sampling)

value: male

value: NSCLC adenocarcinoma

value: Biological replicate 3


title: A015-C-010, Dounce, scATACseq

description: 10x genomics

value: Unaffected


title: A427_24h_133_100nM  [A427_8]


title: Megakaryocyte Progenitor (MkP) 22

value: induced


title: L2100409_1_JVpna49 [rplS_1]

value: UPEC with rplS PNA

value: 15 min exposure to 5 uM PNA


title: A427_24h_133_100nM  [A427_7]


title: A015-C-008, Dounce, scATACseq

description: 10x genomics


title: Megakaryocyte Progenitor (MkP) 21


title: A015-C-006, Dounce, scATACseq

description: 10x genomics

value: Polyp


title: L2100408_1_JVpna48 [rpsH_1]

value: UPEC with rpsH PNA


title: Megakaryocyte Progenitor (MkP) 20


title: A427_24h_DMSO  [A427_6]

value: DMSO 24h


title: L2100407_1_JVpna47 [nusG_1]

value: UPEC with nusG PNA


title: A015-C-002, Dounce, scATACseq

description: 10x genomics

value: Colon


title: A427_24h_DMSO  [A427_5]

value: Biological replicate 2


title: A427_24h_DMSO  [A427_4]

value: Biological replicate 1


title: Megakaryocyte Progenitor (MkP) 19

value: rtTA/rtTA


title: A015-C-005, Dounce, scATACseq

description: 10x genomics

value: Y

value: F


title: Megakaryocyte Progenitor (MkP) 18


title: A015-C-001, Dounce, scATACseq

description: 10x genomics

value: CRC


title: A427_3h_133_100nM  [A427_3]

value: Lung

value: 52Y (at sampling)

value: male

value: NSCLC adenocarcinoma


title: Megakaryocyte Progenitor (MkP) 17

value: induced


title: L2100403_1_JVpna43 [pyrH_1]

value: UPEC with pyrH PNA

value: 15 min exposure to 5 uM PNA


title: L2100402_1_JVpna42 [rpoD_1]

value: UPEC with rpoD PNA


title: L2100404_1_JVpna44 [yidC_1]

value: UPEC with ydiC PNA


title: A014-C-201, Dounce, scATACseq

description: 10x genomics

value: Unaffected


title: A427_3h_133_100nM  [A427_2]


title: Megakaryocyte Progenitor (MkP) 16


title: A427_3h_133_100nM  [A427_1]


title: Hematopoietic stem cell (HSC) 16


title: A014-C-114, Dounce, scATACseq

description: 10x genomics

value: Colon


title: L2100400_1_JVpna40 [dnaB_1]

value: UPEC with dnaB PNA


title: A014-C-111, Dounce, scATACseq

description: 10x genomics


title: LS180_24_MRTX1133_30mg_kg_QD_cetuximab_QD [L_4_6]

source_name: xenograft

value: 58Y (at sampling)

value: female

value: Colon adenocarcinoma

value: Biological replicate 3

value: MRTX1133 30mg/kg QD 24h


title: L2100398_1_JVpna21 [acpP_1]

value: UPEC with acpP PNA


title: Hematopoietic stem cell (HSC) 15

value: rtTA/rtTA


title: A014-C-108, Dounce, scATACseq

description: 10x genomics

value: Polyp

value: Y

value: F


title: LS180_24_MRTX1133_30mg_kg_QD_cetuximab_QD [L_4_5]

value: Biological replicate 2


title: Hematopoietic stem cell (HSC) 14

value: induced


title: LS180_24_MRTX1133_30mg_kg_QD_cetuximab_QD [L_4_4]

value: Biological replicate 1


title: Hematopoietic stem cell (HSC) 13


title: L2100397_1_JVpna22 [acpP-scr_1]

value: UPEC with scrambled PNA

value: 15 min exposure to 5 uM PNA


title: L2100396_1_w_o_control [control_1]

value: UPEC with water

value: Water-treated


title: A014-C-101, Dounce, scATACseq

description: 10x genomics

value: Colon


title: A014-C-054, Dounce, scATACseq

description: 10x genomics

value: Unaffected


title: 3_w_o_control [control_3]


title: A014-C-052, Dounce, scATACseq

description: 10x genomics


title: LS180_6_MRTX1133_30mg_kg_QD_cetuximab_QD [L_4_1]

value: 58Y (at sampling)

value: female

value: Colon adenocarcinoma

value: MRTX1133 30mg/kg QD 6h


title: A014-C-043, Dounce, scATACseq

description: 10x genomics


title: 3_JVpna50 [csrA_3]

value: UPEC with csrA PNA


title: Hematopoietic stem cell (HSC) 11

value: rtTA/rtTA


title: 3_JVpna93 [ispH_3]

value: UPEC with ispH PNA


title: Hematopoietic stem cell (HSC) 10


title: A014-C-040, Dounce, scATACseq

description: 10x genomics

value: Polyp

value: Y

value: F


title: Hematopoietic stem cell (HSC) 9

value: induced


title: 3_JVpna49 [rplS_3]

value: UPEC with rplS PNA


title: A014-C-013, Dounce, scATACseq

description: 10x genomics


title: LS180_24_MRTX1133_30mg_kg_QD [L_2_5]

value: Biological replicate 2

value: MRTX1133 30mg/kg QD 24h


title: LS180_24_MRTX1133_30mg_kg_QD [L_2_4]

value: Biological replicate 1


title: 3_JVpna48 [rpsH_3]

value: UPEC with rpsH PNA

value: 15 min exposure to 5 uM PNA


title: Hematopoietic stem cell (HSC) 8


title: A014-C-008, Dounce, scATACseq

description: 10x genomics

value: Colon


title: L2100401_1_JVpna41 [ftsZ_1]

value: UPEC with ftsZ PNA


title: Hematopoietic stem cell (HSC) 7


title: 3_JVpna44 [yidC_3]

value: UPEC with ydiC PNA


title: LS180_6_MRTX1133_30mg_kg_QD [L_2_3]

value: 58Y (at sampling)

value: female

value: Colon adenocarcinoma

value: Biological replicate 3

value: MRTX1133 30mg/kg QD 6h


title: LS180_6_MRTX1133_30mg_kg_QD [L_2_2]


title: Hematopoietic stem cell (HSC) 6

value: rtTA/rtTA


title: A014-C-001, Dounce, scATACseq

description: 10x genomics

value: Polyp

value: Y

value: F


title: A014-C-002, Dounce, scATACseq

description: 10x genomics


title: Hematopoietic stem cell (HSC) 5

value: induced


title: 3_JVpna43 [pyrH_3]

value: UPEC with pyrH PNA


title: LS180_6_MRTX1133_30mg_kg_QD_cetuximab_QD [L_4_3]


title: Hematopoietic stem cell (HSC) 12


title: LS180_6_MRTX1133_30mg_kg_QD [L_2_1]

value: Biological replicate 1


title: Hematopoietic stem cell (HSC) 4


title: LS180_6_MRTX1133_30mg_kg_QD_cetuximab_QD [L_4_2]

value: Biological replicate 2


title: LS180_24_Vehicle [L_1_3]

value: Vehicle


title: Hematopoietic stem cell (HSC) 3


title: A010-C-023, Dounce, scATACseq

description: 10x genomics

value: Colon

value: M


title: A010-C-018, Dounce, scATACseq

description: 10x genomics


title: 3_JVpna41 [ftsZ_3]

value: UPEC with ftsZ PNA

value: 15 min exposure to 5 uM PNA


title: LS180_24_MRTX1133_30mg_kg_QD [L_2_6]

value: 58Y (at sampling)

value: female

value: MRTX1133 30mg/kg QD 24h


title: Hematopoietic stem cell (HSC) 1


title: LS180_24_Vehicle [L_1_1]

value: Colon adenocarcinoma


title: 3_JVpna40 [dnaB_3]

value: UPEC with dnaB PNA


title: 3_JVpna22 [acpP-scr_3]

value: UPEC with scrambled PNA


title: A008-C-008, Dounce, scATACseq

description: 10x genomics

value: Polyp

value: Y


title: HPAC_12_MRTX1133_30mg_kg_QD [H_4_8]

value: HPAC

value: Pancreas

value: 64Y (at sampling)

value: Pancreatic adenocarcinoma

value: MRTX1133 30mg/kg QD 12h


title: Hematopoietic stem cell (HSC) 2

value: rtTA/rtTA

value: induced


title: lineage- kit+ CD150+ cell 7


title: HPAC_12_MRTX1133_30mg_kg_QD [H_4_9]

value: Biological replicate 3


title: A002-C-205, Dounce, scATACseq

description: 10x genomics

value: Colon

value: F


title: 3_JVpna21 [acpP_3]

value: UPEC with acpP PNA

value: 15 min exposure to 5 uM PNA


title: 3_JVpna47 [nusG_3]

value: UPEC with nusG PNA


title: Primary Hepatocytes Sorafenib 24 hours replicate 3

type: RNA

city: Sevilla

first: Patricia

last: de la Cruz-Ojeda

address: Avda. Manuel Siurot s/n

country: Spain

institute: Institute of Biomedicine of Seville

hyb_protocol: miRNAs were profiled by qRT-PCR using the TaqMan® OpenArray® Human miRNA Panel (Ref. 4470187, Life Technologies, Carlsbad, USA), following manufacturer instructions

data_processing: Expression levels were calculated using the relative threshold cycle (Crt) method. Crt values were normalized using the global mean strategy. Relative miRNA expression levels between control and experimental groups were calculated by using the ∆∆Crt method (15). Fold change values were calculated as 2-∆∆rt. Thermo Fisher Could was used to analyze data

source_name: Hepatocellular carcinoma (HCC)

label_protocol: Extracts were not labelled

growth_protocol: Cells were cultured in minimal essential medium (MEM) with Earle's balanced salts with L-glutamine suplemented with 10% fetal bovine serum, 1% sodium pyruvate, 1% non-essential amino acids and penicillin-streptomycin solution; cells were grown in culture flasks at 37 ºC in a humidified incubator with 5% CO2. Cells were plated at 100.000 cells/cm2

extract_protocol: Total RNA was extracted using a miRNeasy mini kit according to the manufacturer’s instructions(QIAGEN, Germany).

treatment_protocol: Sorafenib was added at the concentration of 10 µM at 24 h hours after transfection, and lysates were obtained after 6 and 24 hours after treatment. Control cells were treated in parallel with dimethyl sulfoxide (DMSO), vehicle in wich Sorafenib was dissolved.

value: Primary Human Hepatocytes

value: Hepatocellular carcinoma (HCC)

value: Sorafenib 10 uM 24h


title: lineage- kit+ CD150+ cell 5


title: A002-C-212, Dounce, scATACseq

description: 10x genomics

value: Unaffected

value: Y


title: HPAC_12_MRTX1133_30mg_kg_QD [H_4_7]

value: HPAC

value: Pancreas

value: female

value: Biological replicate 1


title: lineage- kit+ CD150+ cell 6

value: rtTA/rtTA


title: A002-C-203, Dounce, scATACseq

description: 10x genomics

value: Polyp


title: Primary Hepatocytes Sorafenib 24 hours replicate 2

scan_protocol: miRNAs were profiled by qRT-PCR using the TaqMan® OpenArray® Human miRNA Panel (Ref. 4470187, Life Technologies, Carlsbad, USA), following manufacturer instructions


title: HPAC_6_MRTX1133_30mg_kg_QD [H_4_6]

value: 64Y (at sampling)

value: Pancreatic adenocarcinoma

value: Biological replicate 3

value: MRTX1133 30mg/kg QD 6h


title: lineage- kit+ CD150+ cell 4

value: induced


title: 3_JVpna42 [rpoD_3]

value: UPEC with rpoD PNA

value: 15 min exposure to 5 uM PNA


title: HPAC_6_MRTX1133_30mg_kg_QD [H_4_5]

value: Biological replicate 2


title: lineage- kit+ CD150+ cell 3


title: Primary Hepatocytes control 24 hours replicate 3

value: Primary Human Hepatocytes

value: Hepatocellular carcinoma (HCC)

value: Control (DMSO) 24h


title: A002-C-202, Dounce, scATACseq

description: 10x genomics

value: Colon

value: Y

value: F


title: A008-C-015, Dounce, scATACseq

description: 10x genomics


title: LS180_24_Vehicle [L_1_2]

value: 58Y (at sampling)

value: female

value: Colon adenocarcinoma

value: Vehicle


title: HPAC_6_MRTX1133_30mg_kg_QD [H_4_4]

value: HPAC

value: Pancreas

value: 64Y (at sampling)

value: Pancreatic adenocarcinoma

value: Biological replicate 1


title: Primary Hepatocytes control 24 hours replicate 2


title: lineage- kit+ CD150+ cell 2

value: rtTA/rtTA

value: induced


title: A002-C-121, S2, scATACseq

description: 10x genomics

value: Unaffected


title: HepG2 cells Sorafenib 24 hours replicate 3

value: Hepatocellular carcinoma (HCC)

value: Sorafenib 10 uM 24h


title: lineage- kit+ CD150+ cell 1


title: lineage- kit+ CD41- CD150- cell 8


title: A002-C-116, S2, scATACseq

description: 10x genomics

value: Colon

value: Polyp


title: HepG2 cells Sorafenib 24 hours replicate 2


title: HPAC_24_MRTX1133_30mg_kg_QD [H_4_1]

value: Biological replicate 3

value: MRTX1133 30mg/kg QD 24h


title: A002-C-204, Dounce, scATACseq

description: 10x genomics

value: Y

value: F


title: A002-C-116, Dounce, scATACseq

description: 10x genomics


title: HepG2 cells Sorafenib 24 hours replicate 1


title: lineage- kit+ CD41- CD150- cell 6


title: A002-C-114, Dounce, scATACseq

description: 10x genomics


title: HepG2 cells control 24 hours replicate 3

value: Control (DMSO) 24h


title: HPAC_24_MRTX1133_30mg_kg_QD [H_4_11]

value: HPAC

value: female


title: lineage- kit+ CD41- CD150- cell 5


title: A002-C-106, Dounce, scATACseq

description: 10x genomics


title: Primary Hepatocytes Sorafenib 24 hours replicate 1

value: Primary Human Hepatocytes


title: HPAC_1_MRTX1133_30mg_kg_QD [H_4_10]

value: Pancreas

value: 64Y (at sampling)

value: Pancreatic adenocarcinoma

value: MRTX1133 30mg/kg QD 1h


title: HepG2 cells control 24 hours replicate 2


title: lineage- kit+ CD41- CD150- cell 4

value: rtTA/rtTA

value: induced


title: A002-C-201, Dounce, scATACseq

description: 10x genomics


title: HPAC_24_Vehicle [H_1_6]

value: Vehicle


title: lineage- kit+ CD41- CD150- cell 3


title: HepG2 cells control 24 hours replicate 1

value: Hepatocellular carcinoma (HCC)


title: A002-C-025, Dounce, scATACseq

description: 10x genomics

value: Colon

value: Unaffected


title: Primary Hepatocytes control 24 hours replicate 1


title: HepG2 cells Sorafenib 6 hours replicate 3

value: Sorafenib 10 uM 6h


title: A002-C-121, Dounce, scATACseq

description: 10x genomics

value: Y


title: HPAC_1_MRTX1133_30mg_kg_QD [H_4_3]

value: Biological replicate 2


title: A002-C-024, Dounce, scATACseq

description: 10x genomics

value: F


title: HPAC_24_Vehicle [H_1_4]

value: HPAC

value: Biological replicate 1


title: HepG2 cells Sorafenib 6 hours replicate 2


title: HPAC_1_MRTX1133_30mg_kg_QD [H_4_2]

value: female


title: lineage- kit+ CD41- CD150- cell 7


title: lineage- kit+ CD41- CD150- cell 1


title: HPAC_24_MRTX1133_30mg_kg_QD [H_4_12]

value: Pancreas

value: MRTX1133 30mg/kg QD 24h


title: HPAC_1_Vehicle [H_1_2]

value: 64Y (at sampling)

value: Pancreatic adenocarcinoma


title: HPAC_1_Vehicle [H_1_3]

value: Biological replicate 3


title: HepG2 cells Sorafenib 6 hours replicate 1


title: Multipotent Progenitor (MPP) 15

value: rtTA/rtTA

value: induced


title: A002-C-016, Dounce, scATACseq

description: 10x genomics

value: Polyp


title: HepG2 cells control 6 hours replicate 3

value: Hepatocellular carcinoma (HCC)

value: Control (DMSO) 6h


title: Multipotent Progenitor (MPP) 14


title: A002-C-010, S2, scATACseq

description: 10x genomics

value: Colon


title: HepG2 cells control 6 hours replicate 2


title: HPAC_1_Vehicle [H_1_1]

value: Vehicle


title: Multipotent Progenitor (MPP) 13


title: A002-C-010, Replicate2, Dounce, scATACseq

description: 10x genomics

value: Y


title: Multipotent Progenitor (MPP) 12


title: A002-C-025, S2, scATACseq

description: 10x genomics

value: Unaffected

value: F


title: HPAC_24_Vehicle [H_1_5]

value: HPAC

value: Biological replicate 2


title: HepG2 cells control 6 hours replicate 1


title: A002-C-010, Replicate1, Dounce, scATACseq

description: 10x genomics


title: AsPC1_24_MRTX1133_30mg_kg_BID_x_7_days_Cetuximab_Q3D [A_6_5]

value: Pancreas

value: 62Y (at sampling)

value: female

value: MRTX1133 30mg/kg BID 24hr x 7 days Cetuximab Q3D


title: lineage- kit+ CD41- CD150- cell 2


title: Multipotent Progenitor (MPP) 11


title: Mpyr-13-4_RNA-Rep1-156

city: ROSCOFF

first: Olivier

last: GODFROY

address: Place Georges Teissier CS90074

department: Station Biologique de Roscoff

country: France

institute: CNRS

description:
Corresponding replicate: Rep2-157
featureCounts_Mpyr-13-4-Wtmale-Wtfemale.tab
deseq_Mpyr134_vs_WT_male.csv
deseq_WT_female_vs_Mpyr134.csv
Mac13-4--156_R1-R1/Mac13-4-156-accepted_hits.bam

data_processing:
Illumina base calling
Data quality was assessed using the FastQC (Wingett et al. 2018). Reads were trimmed and filtered using Trimmomatic (Bolger et al. 2014) with average quality > 28, a quality threshold of 24 (base calling) and a minimal size of 60 bp.
Filtered reads were mapped to the M. pyrifera genome (Lipinska et al. 2019a) using TopHat2 (Kim et al. 2013) with the Bowtie2 aligner (Langmead and Salzberg 2012).
The mapped sequencing data were then processed with FeatureCounts (Liao et al. 2014) to obtain counts for sequencing reads mapped to exons and counts by gene. Transcript abundances, measured as transcript per million (TPM).
Differential expression analysis was performed with the DESeq2 package (Love et al. 2014) (Bioconductor) using an adjusted P-value cut-off of 0.05 and a minimal fold-change of 2.
Genome_build: M. pyrifera genome (Lipinska et al. 2019, Genome Biol. 20:35)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtract from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or broadPeak (bed12) format.

organism: Macrocystis pyrifera

growth_protocol: Cultures were grown in 140 mm round Petri dishes in natural sea water with 0.01% Provasoli enrichment at 13°C with a 14h/10h day/night cycle and 20 (µmol photons).m-2.s-1 irradiance of red light.

extract_protocol:
For each sample, total RNA was extracted from 2 independent bulks of app. 1000 male individuals and 2 bulks of 1000 female individuals (two biological replicates for each sex) using the Qiagen Mini kit (http://www.qiagen.com) as previously described (Lipinska, Cormier, et al. 2015; Arun et al. 2019). RNA from wild-type male and female and variant Mpyr-13-4 line pools was extracted using the protocol described by (Apt et al. 1995).
For each replicate, the RNA was quantified and cDNA was synthesized using an oligo-dT primer. The cDNA was fragmented, cloned, and sequenced by Fasteris (CH-1228 Plan-les-Ouates, Switzerland) using an Illumina Hi-seq 2000 set to generate 150-bp single-end reads.

treatment_protocol: No treatment

value: Female

value: whole organism

tag: Stage

value: immature gametophyte

tag: phenotype

value: partial sex reversal

value: 1 mg Colchicine (12-16 weeks)

tag: sample code


title: Mpyr-13-4_RNA-Rep2-157

description:
Corresponding replicate: Rep1-156
featureCounts_Mpyr-13-4-Wtmale-Wtfemale.tab
deseq_Mpyr134_vs_WT_male.csv
deseq_WT_female_vs_Mpyr134.csv
Mac13-4--157_R1-R1/Mac13-4-157-accepted_hits.bam


title: AsPC1_24_MRTX1133_30mg_kg_BID_x_7_days_Cetuximab_Q3D [A_6_4]

value: Pancreatic adenocarcinoma

value: Biological replicate 1


title: A001-C-218, Dounce, scATACseq

description: 10x genomics

value: Colon

value: Polyp

value: M


title: A002-C-021, Dounce, scATACseq

description: 10x genomics

value: Y

value: F


title: A001-C-223, Dounce, scATACseq

description: 10x genomics

value: Unaffected


title: AsPC1_6_MRTX1133_30mg_kg_BID_x_7_days_Cetuximab_Q3D [A_6_3]

value: Pancreas

value: Biological replicate 3

value: MRTX1133 30mg/kg BID 6hr x 7 days Cetuximab Q3D


title: Multipotent Progenitor (MPP) 9

tag: col1a1 genotype

tag: rosa26 genotype

value: rtTA/rtTA

value: induced


title: A001-C-207, Dounce, scATACseq

description: 10x genomics


title: Mpyr-cur6-Wtmale-RNA-Rep1-170

description:
Corresponding replicate: Rep2-171
featureCounts_Mpyr-13-4-Wtmale-Wtfemale.tab
deseq_WT_female_vs_WT_male.csv
deseq_Mpyr134_vs_WT_male.csv
Mac-cur6--170_R1-R1/Mac-cur6-170-accepted_hits.bam

source_name: WT-male

value: Male

value: whole organism

value: WT

value: no treatment


title: AsPC1_6_MRTX1133_30mg_kg_BID_x_7_days_Cetuximab_Q3D [A_6_1]

tag: cell line

value: 62Y (at sampling)

value: female

value: Pancreatic adenocarcinoma


title: AsPC1_6_MRTX1133_30mg_kg_BID_x_7_days_Cetuximab_Q3D [A_6_2]

tag: cell type

value: Biological replicate 2


title: Mpyr-cur6-Wtmale-RNA-Rep2-171

description:
Corresponding replicate: Rep1-170
featureCounts_Mpyr-13-4-Wtmale-Wtfemale.tab
deseq_WT_female_vs_WT_male.csv
deseq_Mpyr134_vs_WT_male.csv
Mac-cur6--171_R1-R1/Mac-cur6-171-accepted_hits.bam

value: immature gametophyte


title: A001-C-203, Dounce, scATACseq

description: 10x genomics

value: Colon

value: Polyp

tag: familial adenomatous_polyposis

value: Y

value: M


title: Multipotent Progenitor (MPP) 7

tag: doxycyclin induction


title: A001-C-202, Dounce, scATACseq

description: 10x genomics

tag: Sex


title: AsPC1_24_MRTX1133_30mg_kg_BID_x_7_days [A_5_6]

value: Pancreas

tag: age

tag: disease

value: Biological replicate 3

value: MRTX1133 30mg/kg BID 24hr x 7 days


title: Mpyr-cur4-Wtfemale_RNA-Rep2-172

description:
Corresponding replicate: Rep1-152
featureCounts_Mpyr-13-4-Wtmale-Wtfemale.tab
deseq_WT_female_vs_WT_male.csv
deseq_WT_female_vs_Mpyr134.csv
Mac-F4--172_R1-R1/Mac-f4-172-accepted_hits.bam

source_name: WT-female

value: Female


title: Multipotent Progenitor (MPP) 6

value: rtTA/rtTA

value: induced


title: A001-C-124, Replicate2, Dounce, scATACseq

description: 10x genomics

tag: disease state

value: Unaffected


title: AsPC1_24_MRTX1133_30mg_kg_BID_x_7_days_Cetuximab_Q3D [A_6_6]

tag: biological replicate

value: MRTX1133 30mg/kg BID 24hr x 7 days Cetuximab Q3D


title: Multipotent Progenitor (MPP) 5


title: AsPC1_24_MRTX1133_30mg_kg_BID_x_7_days [A_5_5]

value: 62Y (at sampling)


title: Multipotent Progenitor (MPP) 10


title: Pg_5

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

library_source: genomic

data_processing:
Fastq files were downloaded from Illumina's BaseSpace for analysis.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1) for each sequencing sample.
The majority of the trailing G's were removed at the ends of the sequences as well as the transposon sequence GAAGACCGGGGACTTATCATCCAACCTGTTA.
Trimmed reads were then aligned to the P. gingivalis genome ATCC 33277 (accession AP009380.1) using STAR aligner.
For the analysis using DESeq2, raw counts were obtained from the STAR aligned bam format files using HTSeq version 0.10.0
Genome_build: AP009380.1
Supplementary_files_format_and_content: tab-delimited text files with raw counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Porphyromonas gingivalis

source_name: Mouse abscess

growth_protocol: A saturating transposon library using a Mariner-based transoposon was created by transposon mutagenesis in P. gingivalis.

extract_protocol:
Genomic DNA was also isolated from the bacteria recovered from abscesses as well as from the input P. gingivalis library. DNA was shearded targeting 200-600 bp sing a Covaris sonicator. The sheared DNA was purified using a Qiagen PCR cleanup kit to remove te buffer. The DNA was used for C-tailing with Tdt and a mixture of dCTP and ddCTP optimized to give about 18 C residues. This reaction was cleaned up using a column and the product was used for PCR with a primer that binds inside the transposon near to the insertion site and a second poly G primer. The resulting PCR products (200-700 bp) contained the amplified DNA at the transposon insertion site and were then gel purified.
Library was constructed using a Nextera XT Kit (FC-121-1012).

treatment_protocol: BALB/cJ mice were inoculated subcutaneously with either the library alone or in conjunction with either Streptococcus gordonii, or Fusobacterium necleatum. Bacteria were recovered and the transposon library was grown in vitro and passaged twice.

tag: treatment group

value: Pg Only


title: AsPC1_6_MRTX1133_30mg_kg_BID_x_7_days [A_5_3]

value: female

value: Pancreatic adenocarcinoma

value: MRTX1133 30mg/kg BID 6hr x 7 days


title: A001-C-123, Dounce, scATACseq

description: 10x genomics

tag: tissue

value: Colon


title: Multipotent Progenitor (MPP) 2


title: A001-C-124, Replicate1, Dounce, scATACseq

description: 10x genomics


title: Pg_3


title: AsPC1_6_MRTX1133_30mg_kg_BID_x_7_days [A_5_2]

value: Biological replicate 2

tag: treatment


title: AsPC1_6_MRTX1133_30mg_kg_BID_x_7_days [A_5_1]

value: Biological replicate 1


title: A001-C-119, Dounce, scATACseq

description: 10x genomics

value: Polyp

value: Y

value: M


title: Multipotent Progenitor (MPP) 4


title: Multipotent Progenitor (MPP) 3


title: AsPC1_24_MRTX1133_30mg_kg_BID_x_7_days [A_5_4]

value: Pancreas

value: MRTX1133 30mg/kg BID 24hr x 7 days


title: Multipotent Progenitor (MPP) 8

value: rtTA/rtTA


title: Pg_4


title: AsPC1_24_MRTX1133_30mg_kg_BID_cetuximab [A_4_5]

value: MRTX1133 30mg/kg BID + Cetuximab 24hr


title: A001-C-108, Dounce, scATACseq

description: 10x genomics


title: A001-C-104, Replicate2, Dounce, scATACseq

description: 10x genomics


title: Pg_2


title: Pg_1


title: Megakaryocyte Progenitor (MkP) 14

value: induced


title: AsPC1_24_MRTX1133_30mg_kg_BID_cetuximab [A_4_6]

value: Biological replicate 3


title: Fn_5

value: Pg + Fn


title: Megakaryocyte Progenitor (MkP) 15


title: AsPC1_24_MRTX1133_30mg_kg_BID_cetuximab [A_4_4]

value: 62Y (at sampling)


title: Mpyr-cur4-Wtfemale_RNA-Rep1-152

description:
Corresponding replicate: Rep2-172
featureCounts_Mpyr-13-4-Wtmale-Wtfemale.tab
deseq_WT_female_vs_WT_male.csv
deseq_WT_female_vs_Mpyr134.csv
Mac-F4--152_R1-R1/Mac-f4-152-accepted_hits.bam

tag: strain

value: Female

value: whole organism

tag: Stage

value: immature gametophyte

value: WT

value: no treatment


title: A001-C-104, Replicate1, Dounce, scATACseq

description: 10x genomics

value: Colon


title: Fn_4


title: AsPC1_6_MRTX1133_30mg_kg_BID_cetuximab [A_4_3]

value: female

value: Pancreatic adenocarcinoma

value: MRTX1133 30mg/kg BID + Cetuximab 6hr


title: A001-C-023, Replicate2, Dounce, scATACseq

description: 10x genomics

value: Unaffected

value: Y

value: M


title: A001-C-023, Replicate1, Dounce, scATACseq

description: 10x genomics


title: Megakaryocyte Progenitor (MkP) 12

value: rtTA/rtTA


title: AsPC1_6_MRTX1133_30mg_kg_BID_cetuximab [A_4_2]

value: Pancreas

value: Biological replicate 2


title: Fn_3

value: Pg + Fn


title: Megakaryocyte Progenitor (MkP) 13

value: induced


title: A001-C-014, Dounce, scATACseq

description: 10x genomics

value: Polyp


title: Fn_2


title: A001-C-007, Dounce, scATACseq

description: 10x genomics

value: CRC


title: Multipotent Progenitor (MPP) 1


title: Megakaryocyte Progenitor (MkP) 10


title: AsPC1_6_MRTX1133_30mg_kg_BID_cetuximab [A_4_1]

value: 62Y (at sampling)

value: Biological replicate 1


title: Megakaryocyte Progenitor (MkP) 11


title: Fn_1


title: Sg_5

value: Pg + Sg


title: A001-C-002, Dounce, scATACseq

description: 10x genomics

value: Colon


title: AsPC1_24_MRTX1133_30mg_kg_BID [A_2_6]

value: female

value: Biological replicate 3

value: MRTX1133 30mg/kg BID 24hr


title: Megakaryocyte Progenitor (MkP) 9


title: Perilesional skin RNA expression compared with uninvolved skin control 1

city: Klong Luang

first: Onjira

last: Jumlongpim

state: Pathumthanii

address: Chulabhorn international college of medicine, 99 Moo 18

department: Dermatology

country: Thailand

institute: Chulabhorn International College of Medicine, Thammasat University

data_processing:
The NGS was carried out using NovaSeq 6000 S4 Reagent Kit on the NovaSeq 6000 System according to the user guide (Illumina Inc., San Diego, CA, USA) with 100 bp paired-end reads.
Trimmed reads were mapped to referent genome with HISAT2, splice-aware aligner
The transcripts were assembled by StringTie with aligned reads
The Fragments Per Kilobase of Transcript Per Million Mapped Reads (FPKM) value was used as a normalization value.
the read counts to statically analyze the differentially expressed genes (DEGs) using the edgeR Bioconductor statistical library version 3.13 on RStudio
Supplementary_files_format_and_content: The table shows the transcripts with their read count and FPKM  (xlsx file)

source_name: Uninvoled skin

extract_protocol:
Total RNAs were extracted from each skin biopsy of the volunteers (PR skin, n = 3; UN skin, n = 2) using TRIzol Reagent (Ambion, Austin, Tx, USA) according to the manufacturer’s instruction. The next-generation sequencing (NGS) was carried out by a commercial company (Macrogen, Seoul, Korea). Briefly, RNA quality was qualified by an Agilent 2100 bioanalyzer (RIN>7).
Libraries for these sequencing were constructed using SMARTer Universal Low Input RNA Kit, TruSeq RNA Sample Prep Kit v2 (pair-end). The cDNAs were checked for the quantity and quality by the bioanalyzer.

tag: tissue donor

value: Untreated patient with moderate to severe sporiasis vulgaris

value: Whole skin biopsy, punch

tag: biopsy position

value: Normal phenotypic skin, 10 cm away from lesional skin

tag: group

value: Control


title: Megakaryocyte Progenitor (MkP) 8

tag: col1a1 genotype

tag: rosa26 genotype

value: rtTA/rtTA


title: AsPC1_24_MRTX1133_30mg_kg_BID [A_2_4]

tag: cell line

tag: cell type

value: Pancreas

value: Pancreatic adenocarcinoma


title: Perilesional skin RNA expression compared with uninvolved skin test 3

source_name: Perilesional skin

value: Edge of lesion

value: test


title: Megakaryocyte Progenitor (MkP) 7

tag: doxycyclin induction

value: induced


title: Sg_2


title: AsPC1_6_MRTX1133_30mg_kg_BID [A_2_3]

tag: age

value: 62Y (at sampling)

tag: Sex

value: MRTX1133 30mg/kg BID 6hr


title: Sg_4

value: Pg + Sg


title: Megakaryocyte Progenitor (MkP) 6


title: AsPC1_6_MRTX1133_30mg_kg_BID [A_2_2]

tag: disease

value: Biological replicate 2


title: Megakaryocyte Progenitor (MkP) 5


title: Perilesional skin RNA expression compared with uninvolved skin test 2

value: Untreated patinet with modertate to severe sporiasis vulgaris


title: Sg_1


title: Input_5

source_name: Culture

value: Input Pool


title: Megakaryocyte Progenitor (MkP) 4


title: Perilesional skin RNA expression compared with uninvolved skin test 1


title: control pateints/ group II (with history of two or more successful deliveries)

city: New Delhi

first: Ankita

last: Ray

state: Delhi

address: Safdarjung hospital campus

country: India

institute: ICMR-National Institute of Pathology

description: control

data_processing:
The normalization and all the data analysis were performed manually by delta Ct method
For the normalization, C.elegans miR-39_1 was used as housekeeping gene
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_ref)
All calculations were performed manually using 2^-deltaCt method

label: SYBR Green

source_name: non-heparanized blood

label_protocol: RT- PCR assay was performed on total RNA isolated from serum. Total RNA was reverse transcribed to cDNA using miR script II reverse transcriptase kit (Qiagen). Reaction conditions were performed as follows: annealing temperature of 56°C and 59°C for SOD1 and SOD2 respectively for 40 cycles

extract_protocol: Total RNA was extracted with Trizol method

tag: gendr

value: female

value: serum


title: AsPC1_6_MRTX1133_30mg_kg_BID [A_2_1]

tag: biological replicate

value: Biological replicate 1


title: Input_3

tag: treatment group


title: non-infected patients group Ib (recurrent spontaneous aborters)

description: Test

tag: tissue


title: Input_4


title: Megakaryocyte Progenitor (MkP) 3


title: Megakaryocyte Progenitor (MkP) 2


title: AsPC1_24_Vehicle [A_1_3]

value: Biological replicate 3

tag: treatment

value: Vehicle


title: Sg_3


title: Input_2


title: AsPC1_24_Vehicle [A_1_2]


title: AsPC1_24_MRTX1133_30mg_kg_BID [A_2_5]

value: MRTX1133 30mg/kg BID 24hr


title: Chlamydia trachomatis- infected patients/group Ia (recurrent spontaneous aborters)

description: Test

label_protocol: RT- PCR assay was performed on total RNA isolated from serum. Total RNA was reverse transcribed to cDNA using miR script II reverse transcriptase kit (Qiagen). Reaction conditions were performed as follows: denaturation at 94°C for 15 sec,  annealing temperature of 55°C for 30 sec and extension for 30 sec at 70°C for 40 cycles.


title: Perilesional skin RNA expression compared with uninvolved skin control 2

value: Untreated patient with moderate to severe sporiasis vulgaris

value: Whole skin biopsy, punch

value: Normal phenotypic skin,10 cm away from lesional skin

value: Control


title: Megakaryocyte Progenitor (MkP) 1

value: rtTA/rtTA

value: induced


title: Input_1


title: AsPC1_24_Vehicle [A_1_1]

value: Pancreas

value: 62Y (at sampling)

value: Pancreatic adenocarcinoma


title: Bone marrow 3

status: Public on Apr 27 2022

city: TLALNEPANTLA

first: LAURA

last: CASTAÑEDA-PARTIDA

state: ESTADO DE MÉXICO

address: AV. DE LOS BARRIOS 1

department: BIOLOGY

country: Mexico

institute: FES IZTACALA, UNAM

description: Gene expression data from flow-sorted CD10+/CD19+ pre B lymphoblasts from bone marrow (BM) sample of B-ALL patient before remission induction therapy

hyb_protocol: The labeled cDNA product  was  heated to 95°C and hybridized to the HuGene-1_0-st-v1 microarray (Affymetrix) for 17h at 45°C. Samples were washed with low and high stringency buffers and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip Scanner 3000 7G (Affymetrix) was used to collect fluorescent signals signal and quality data of the scanned arrays.

data_processing: The  Expression Console software (Affymetrix) was used to obtain intensity.

label: biotin

source_name: B-ALL pediatric patient (ID 11) before remission induction therapy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol:
11 pediatric patients (< 16 years old) newly diagnosed with pre-B ALL by morphology and immunophenotyping of cells from peripheral blood (PB) samples or bone marrow (BM) aspirates.
Three to five milliliters of PB or BM from the newly diagnosed B-ALL patients were collected using Vacutainer tubes containing EDTA (BD) before remission induction therapy.

extract_protocol: Total RNA was extracted by Trizol reagent and resuspended in RNase free water (Invitrogen) according to the manufacturer´s instructions. Samples with an A260/280 ratio ≥1.8 were selected and stored at −70°C until use.

treatment_protocol:
Immediately after, the samples were separated using Histopaque-1077 (Sigma Aldrich) and the mononuclear cells were carefully collected according to the manufacturer´s instructions.
Extracted mononuclear cells resuspended in isotonic phosphate-buffered saline solution (PBS) were stained with Pacific Blue (PB)-conjugated anti-CD45 (HI30), Phycoerythrin (PE)-conjugated anti-CD34 (561), Fluorescein isothiocyanate (FITC)-conjugated anti-CD10 (HI10a) and Allophycocyanin (APC)-conjugated anti-CD19 (HIB19) (Biolegend).  They were incubated for 30 minutes at 4 C and then analyzed and purified by fluorescence activated cell sorting (FACS) in a FACSAria II flow cytometer (BD Biosciences). Lymphocytes were identified by side scatter and forward scatter properties and CD45+CD10+ CD34+ CD19+ were selected to finally obtain CD10+/CD19+ pre-B lymphoblasts. The purity was 90-95% for all samples and they were centrifuged at 5,000 rpm for three minutes and washed with PBS before RNA isolation.

value: CD10+/CD19+ pre B lymphoblasts from BM

value: bone marrow

value: 168 months


title: Peripheral blood 7

description: Gene expression data from flow-sorted CD10+/CD19+ pre B lymphoblasts from peripheral blood (PB) sample of B-ALL patient before remission induction therapy

source_name: B-ALL pediatric patient (ID 7) before remission induction therapy **

value: CD10+/CD19+ pre B lymphoblasts from PB

value: peripheral blood

value: 64 months


title: Bone marrow 2

source_name: B-ALL pediatric patient (ID 10) before remission induction therapy

value: 156 months


title: Bone marrow 4


title: Peripheral blood 1

source_name: B-ALL pediatric patient (ID 1) before remission induction therapy

value: 123 months


title: Peripheral blood 6

source_name: B-ALL pediatric patient (ID 6) before remission induction therapy *

value: 187 months


title: Bone marrow 1


title: Young_3, Cell 223 of 384 [AS-443621-LR-48446]

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

data_processing:
Single-end raw reads were aligned to the reference genome using HISAT2
Gene counts were obtained using HTSeq using Mus_musculus.GRCm38.99.gtf
Data matrix count table from individual count files was generated using R and Bioconductor
Assembly: Mus_musculus build GRCm38.99
Supplementary files format and content: tab-delimited text of raw gene expression count matrix

source_name: Lgr5 high-ISCs

growth_protocol: Lgr5 high-ISCs were sorted in 384 well low bind plates (Eppendorf) containing 1.2 µl lysis buffer (0.1% triton (Sigma-Aldrich), 1U/μl RNase Inhibitor (Takara Bio), 2.5 µM polyT primer (Thermo Fisher Scientific), 2.5 mM dNTPs (Thermo Fisher Scientific)). After sorting the plates spun down and immediately frozen at -80 °C for further processes.

extract_protocol: SMARTER mRNA-Seq: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Lgr5 high-ISCs

tag: sample group

tag: genotype


title: Peripheral blood 4

source_name: B-ALL pediatric patient (ID 4) before remission induction therapy

value: 47 months


title: Peripheral blood 3

source_name: B-ALL pediatric patient (ID 3) before remission induction therapy

value: 60 months


title: Young_3, Cell 212 of 384 [AS-443599-LR-48446]


title: Young_3, Cell 215 of 384 [AS-443605-LR-48446]


title: Young_3, Cell 213 of 384 [AS-443601-LR-48446]


title: Young_3, Cell 216 of 384 [AS-443607-LR-48446]


title: Young_3, Cell 220 of 384 [AS-443615-LR-48446]


title: Young_3, Cell 221 of 384 [AS-443617-LR-48446]


title: Young_3, Cell 219 of 384 [AS-443613-LR-48446]


title: Young_3, Cell 225 of 384 [AS-443625-LR-48446]


title: Young_3, Cell 217 of 384 [AS-443609-LR-48446]


title: Peripheral blood 5

source_name: B-ALL pediatric patient (ID 5) before remission induction therapy

value: 84 months


title: Young_3, Cell 224 of 384 [AS-443623-LR-48446]


title: Young_3, Cell 211 of 384 [AS-443597-LR-48446]


title: Young_3, Cell 214 of 384 [AS-443603-LR-48446]


title: Young_3, Cell 222 of 384 [AS-443619-LR-48446]


title: Peripheral blood 8

source_name: B-ALL pediatric patient (ID 8) before remission induction therapy

value: 48 months


title: Young_3, Cell 210 of 384 [AS-443595-LR-48446]


title: Young_3, Cell 209 of 384 [AS-443593-LR-48446]


title: Peripheral blood 2

source_name: B-ALL pediatric patient (ID 2) before remission induction therapy


title: Peripheral blood 9

source_name: B-ALL pediatric patient (ID 9) before remission induction therapy

value: 132 months


title: Young_3, Cell 208 of 384 [AS-443591-LR-48446]


title: Young_3, Cell 207 of 384 [AS-443589-LR-48446]


title: Young_3, Cell 218 of 384 [AS-443611-LR-48446]


title: Young_3, Cell 206 of 384 [AS-443587-LR-48446]


title: Young_3, Cell 205 of 384 [AS-443585-LR-48446]


title: Young_3, Cell 204 of 384 [AS-443583-LR-48446]


title: Young_3, Cell 203 of 384 [AS-443581-LR-48446]


title: Young_3, Cell 202 of 384 [AS-443579-LR-48446]


title: Young_3, Cell 201 of 384 [AS-443577-LR-48446]


title: Young_3, Cell 198 of 384 [AS-443571-LR-48446]


title: Young_3, Cell 199 of 384 [AS-443573-LR-48446]


title: Young_3, Cell 195 of 384 [AS-443565-LR-48446]


title: Young_3, Cell 187 of 384 [AS-443549-LR-48446]


title: Young_3, Cell 197 of 384 [AS-443569-LR-48446]


title: Young_3, Cell 186 of 384 [AS-443547-LR-48446]


title: Young_3, Cell 194 of 384 [AS-443563-LR-48446]


title: Young_3, Cell 196 of 384 [AS-443567-LR-48446]


title: Young_3, Cell 190 of 384 [AS-443555-LR-48446]


title: Young_3, Cell 200 of 384 [AS-443575-LR-48446]


title: Young_3, Cell 193 of 384 [AS-443561-LR-48446]


title: Young_3, Cell 188 of 384 [AS-443551-LR-48446]


title: Young_3, Cell 192 of 384 [AS-443559-LR-48446]


title: Young_3, Cell 183 of 384 [AS-443541-LR-48446]


title: Young_3, Cell 189 of 384 [AS-443553-LR-48446]


title: Young_3, Cell 191 of 384 [AS-443557-LR-48446]


title: Young_3, Cell 184 of 384 [AS-443543-LR-48446]


title: Young_3, Cell 185 of 384 [AS-443545-LR-48446]


title: Young_3, Cell 182 of 384 [AS-443539-LR-48446]


title: Young_3, Cell 181 of 384 [AS-443537-LR-48446]


title: Young_3, Cell 180 of 384 [AS-443535-LR-48446]


title: Young_3, Cell 178 of 384 [AS-443531-LR-48446]


title: Young_3, Cell 179 of 384 [AS-443533-LR-48446]


title: Young_3, Cell 176 of 384 [AS-443527-LR-48446]


title: Young_3, Cell 175 of 384 [AS-443525-LR-48446]


title: Young_3, Cell 174 of 384 [AS-443523-LR-48446]


title: Young_3, Cell 177 of 384 [AS-443529-LR-48446]


title: Young_3, Cell 171 of 384 [AS-443517-LR-48446]


title: Young_3, Cell 170 of 384 [AS-443515-LR-48446]


title: Young_3, Cell 167 of 384 [AS-443509-LR-48446]


title: Young_3, Cell 169 of 384 [AS-443513-LR-48446]


title: Young_3, Cell 172 of 384 [AS-443519-LR-48446]


title: Young_3, Cell 164 of 384 [AS-443503-LR-48446]


title: Young_3, Cell 166 of 384 [AS-443507-LR-48446]


title: Young_3, Cell 165 of 384 [AS-443505-LR-48446]


title: Young_3, Cell 163 of 384 [AS-443501-LR-48446]


title: Young_3, Cell 162 of 384 [AS-443499-LR-48446]


title: Young_3, Cell 161 of 384 [AS-443497-LR-48446]


title: Young_3, Cell 160 of 384 [AS-443495-LR-48446]


title: Young_3, Cell 159 of 384 [AS-443493-LR-48446]


title: Young_3, Cell 158 of 384 [AS-443491-LR-48446]


title: Young_3, Cell 157 of 384 [AS-443489-LR-48446]


title: Young_3, Cell 149 of 384 [AS-443473-LR-48446]


title: Young_3, Cell 156 of 384 [AS-443487-LR-48446]


title: Young_3, Cell 155 of 384 [AS-443485-LR-48446]


title: Young_3, Cell 147 of 384 [AS-443469-LR-48446]


title: Young_3, Cell 151 of 384 [AS-443477-LR-48446]


title: Young_3, Cell 145 of 384 [AS-443465-LR-48446]


title: Young_3, Cell 144 of 384 [AS-443463-LR-48446]


title: Young_3, Cell 153 of 384 [AS-443481-LR-48446]


title: Young_3, Cell 173 of 384 [AS-443521-LR-48446]


title: Young_3, Cell 150 of 384 [AS-443475-LR-48446]


title: Young_3, Cell 154 of 384 [AS-443483-LR-48446]


title: Young_3, Cell 140 of 384 [AS-443455-LR-48446]


title: Young_3, Cell 152 of 384 [AS-443479-LR-48446]


title: Young_3, Cell 148 of 384 [AS-443471-LR-48446]


title: Young_3, Cell 135 of 384 [AS-443445-LR-48446]


title: Young_3, Cell 133 of 384 [AS-443441-LR-48446]


title: Young_3, Cell 136 of 384 [AS-443447-LR-48446]


title: Young_3, Cell 168 of 384 [AS-443511-LR-48446]


title: Young_3, Cell 129 of 384 [AS-443433-LR-48446]


title: Young_3, Cell 146 of 384 [AS-443467-LR-48446]


title: Young_3, Cell 139 of 384 [AS-443453-LR-48446]


title: Young_3, Cell 142 of 384 [AS-443459-LR-48446]


title: Young_3, Cell 141 of 384 [AS-443457-LR-48446]


title: Young_3, Cell 128 of 384 [AS-443431-LR-48446]


title: Young_3, Cell 138 of 384 [AS-443451-LR-48446]


title: Young_3, Cell 125 of 384 [AS-443425-LR-48446]


title: Young_3, Cell 122 of 384 [AS-443419-LR-48446]


title: Young_3, Cell 137 of 384 [AS-443449-LR-48446]


title: Young_3, Cell 124 of 384 [AS-443423-LR-48446]


title: Young_3, Cell 143 of 384 [AS-443461-LR-48446]


title: Young_3, Cell 120 of 384 [AS-443415-LR-48446]


title: Young_3, Cell 132 of 384 [AS-443439-LR-48446]


title: Young_3, Cell 134 of 384 [AS-443443-LR-48446]


title: Young_3, Cell 116 of 384 [AS-443407-LR-48446]


title: Young_3, Cell 117 of 384 [AS-443409-LR-48446]


title: Young_3, Cell 131 of 384 [AS-443437-LR-48446]


title: Young_3, Cell 130 of 384 [AS-443435-LR-48446]


title: Young_3, Cell 126 of 384 [AS-443427-LR-48446]


title: Young_3, Cell 109 of 384 [AS-443393-LR-48446]


title: Young_3, Cell 106 of 384 [AS-443387-LR-48446]


title: Young_3, Cell 123 of 384 [AS-443421-LR-48446]


title: Young_3, Cell 103 of 384 [AS-443381-LR-48446]


title: Young_3, Cell 119 of 384 [AS-443413-LR-48446]


title: Young_3, Cell 115 of 384 [AS-443405-LR-48446]


title: Young_3, Cell 107 of 384 [AS-443389-LR-48446]


title: Young_3, Cell 100 of 384 [AS-443375-LR-48446]


title: Young_3, Cell 118 of 384 [AS-443411-LR-48446]


title: Young_3, Cell 127 of 384 [AS-443429-LR-48446]


title: Young_3, Cell 111 of 384 [AS-443397-LR-48446]


title: Young_3, Cell 114 of 384 [AS-443403-LR-48446]


title: Young_3, Cell 99 of 384 [AS-443373-LR-48446]


title: Young_3, Cell 98 of 384 [AS-443371-LR-48446]


title: Young_3, Cell 108 of 384 [AS-443391-LR-48446]


title: Young_3, Cell 121 of 384 [AS-443417-LR-48446]


title: Young_3, Cell 105 of 384 [AS-443385-LR-48446]


title: Young_3, Cell 101 of 384 [AS-443377-LR-48446]


title: Young_3, Cell 104 of 384 [AS-443383-LR-48446]


title: Young_3, Cell 102 of 384 [AS-443379-LR-48446]


title: Young_3, Cell 112 of 384 [AS-443399-LR-48446]


title: Young_3, Cell 97 of 384 [AS-443369-LR-48446]


title: Young_3, Cell 92 of 384 [AS-443359-LR-48446]


title: Young_3, Cell 113 of 384 [AS-443401-LR-48446]


title: Young_3, Cell 94 of 384 [AS-443363-LR-48446]


title: Young_3, Cell 110 of 384 [AS-443395-LR-48446]


title: Young_3, Cell 96 of 384 [AS-443367-LR-48446]


title: Young_3, Cell 91 of 384 [AS-443357-LR-48446]


title: Young_3, Cell 87 of 384 [AS-443349-LR-48446]


title: Young_3, Cell 86 of 384 [AS-443347-LR-48446]


title: Young_3, Cell 84 of 384 [AS-443343-LR-48446]


title: Young_3, Cell 83 of 384 [AS-443341-LR-48446]


title: Young_3, Cell 90 of 384 [AS-443355-LR-48446]


title: Young_3, Cell 95 of 384 [AS-443365-LR-48446]


title: Young_3, Cell 88 of 384 [AS-443351-LR-48446]


title: Young_3, Cell 85 of 384 [AS-443345-LR-48446]


title: Young_3, Cell 81 of 384 [AS-443337-LR-48446]


title: Young_3, Cell 75 of 384 [AS-443325-LR-48446]


title: Young_3, Cell 82 of 384 [AS-443339-LR-48446]


title: Young_3, Cell 78 of 384 [AS-443331-LR-48446]


title: Young_3, Cell 79 of 384 [AS-443333-LR-48446]


title: Young_3, Cell 76 of 384 [AS-443327-LR-48446]


title: Young_3, Cell 80 of 384 [AS-443335-LR-48446]


title: Young_3, Cell 89 of 384 [AS-443353-LR-48446]


title: Young_3, Cell 93 of 384 [AS-443361-LR-48446]


title: Young_3, Cell 71 of 384 [AS-443317-LR-48446]


title: Young_3, Cell 70 of 384 [AS-443315-LR-48446]


title: Young_3, Cell 68 of 384 [AS-443311-LR-48446]


title: Young_3, Cell 73 of 384 [AS-443321-LR-48446]


title: Young_3, Cell 69 of 384 [AS-443313-LR-48446]


title: Young_3, Cell 67 of 384 [AS-443309-LR-48446]


title: Young_3, Cell 64 of 384 [AS-443303-LR-48446]


title: Young_3, Cell 65 of 384 [AS-443305-LR-48446]


title: Young_3, Cell 61 of 384 [AS-443297-LR-48446]


title: Young_3, Cell 62 of 384 [AS-443299-LR-48446]


title: Young_3, Cell 63 of 384 [AS-443301-LR-48446]


title: Young_3, Cell 60 of 384 [AS-443295-LR-48446]


title: Young_3, Cell 59 of 384 [AS-443293-LR-48446]


title: Young_3, Cell 57 of 384 [AS-443289-LR-48446]


title: Young_3, Cell 72 of 384 [AS-443319-LR-48446]


title: Young_3, Cell 74 of 384 [AS-443323-LR-48446]


title: Young_3, Cell 49 of 384 [AS-443273-LR-48446]


title: Young_3, Cell 52 of 384 [AS-443279-LR-48446]


title: Young_3, Cell 51 of 384 [AS-443277-LR-48446]


title: Young_3, Cell 48 of 384 [AS-443271-LR-48446]


title: Young_3, Cell 45 of 384 [AS-443265-LR-48446]


title: Young_3, Cell 55 of 384 [AS-443285-LR-48446]


title: Young_3, Cell 53 of 384 [AS-443281-LR-48446]


title: Young_3, Cell 46 of 384 [AS-443267-LR-48446]


title: Young_3, Cell 50 of 384 [AS-443275-LR-48446]


title: Young_3, Cell 44 of 384 [AS-443263-LR-48446]


title: Young_3, Cell 54 of 384 [AS-443283-LR-48446]


title: Young_3, Cell 40 of 384 [AS-443255-LR-48446]


title: Young_3, Cell 56 of 384 [AS-443287-LR-48446]


title: Young_3, Cell 39 of 384 [AS-443253-LR-48446]


title: Young_3, Cell 77 of 384 [AS-443329-LR-48446]


title: Young_3, Cell 42 of 384 [AS-443259-LR-48446]


title: Young_3, Cell 36 of 384 [AS-443247-LR-48446]


title: Young_3, Cell 33 of 384 [AS-443241-LR-48446]


title: Young_3, Cell 38 of 384 [AS-443251-LR-48446]


title: Young_3, Cell 35 of 384 [AS-443245-LR-48446]


title: Young_3, Cell 66 of 384 [AS-443307-LR-48446]


title: Young_3, Cell 32 of 384 [AS-443239-LR-48446]


title: Young_3, Cell 47 of 384 [AS-443269-LR-48446]


title: Young_3, Cell 58 of 384 [AS-443291-LR-48446]


title: Young_3, Cell 41 of 384 [AS-443257-LR-48446]


title: Young_3, Cell 30 of 384 [AS-443235-LR-48446]


title: Young_3, Cell 26 of 384 [AS-443227-LR-48446]


title: Young_3, Cell 27 of 384 [AS-443229-LR-48446]


title: Young_3, Cell 20 of 384 [AS-443215-LR-48446]


title: Young_3, Cell 23 of 384 [AS-443221-LR-48446]


title: Young_3, Cell 29 of 384 [AS-443233-LR-48446]


title: Young_3, Cell 21 of 384 [AS-443217-LR-48446]


title: Young_3, Cell 18 of 384 [AS-443211-LR-48446]


title: Young_3, Cell 22 of 384 [AS-443219-LR-48446]


title: Young_3, Cell 43 of 384 [AS-443261-LR-48446]


title: Young_3, Cell 16 of 384 [AS-443207-LR-48446]


title: Young_3, Cell 17 of 384 [AS-443209-LR-48446]


title: Young_3, Cell 14 of 384 [AS-443203-LR-48446]


title: Young_3, Cell 15 of 384 [AS-443205-LR-48446]


title: Young_3, Cell 19 of 384 [AS-443213-LR-48446]


title: Young_3, Cell 12 of 384 [AS-443199-LR-48446]


title: Young_3, Cell 37 of 384 [AS-443249-LR-48446]


title: Young_3, Cell 11 of 384 [AS-443197-LR-48446]


title: Young_3, Cell 10 of 384 [AS-443195-LR-48446]


title: Young_3, Cell 34 of 384 [AS-443243-LR-48446]


title: Young_3, Cell 8 of 384 [AS-443191-LR-48446]


title: Young_3, Cell 9 of 384 [AS-443193-LR-48446]


title: Young_3, Cell 6 of 384 [AS-443187-LR-48446]


title: Young_3, Cell 24 of 384 [AS-443223-LR-48446]


title: Young_3, Cell 25 of 384 [AS-443225-LR-48446]


title: Young_3, Cell 28 of 384 [AS-443231-LR-48446]


title: Young_3, Cell 31 of 384 [AS-443237-LR-48446]


title: Young_3, Cell 1 of 384 [AS-443177-LR-48446]


title: Young_3, Cell 7 of 384 [AS-443189-LR-48446]


title: Young_3, Cell 5 of 384 [AS-443185-LR-48446]


title: Young_3, Cell 4 of 384 [AS-443183-LR-48446]


title: Young_3, Cell 3 of 384 [AS-443181-LR-48446]


title: Young_2, Cell 380 of 384 [AS-441973-LR-48394]


title: Young_2, Cell 379 of 384 [AS-441971-LR-48394]


title: Young_2, Cell 378 of 384 [AS-441969-LR-48394]


title: Young_3, Cell 2 of 384 [AS-443179-LR-48446]


title: Young_2, Cell 372 of 384 [AS-441957-LR-48394]


title: Young_2, Cell 375 of 384 [AS-441963-LR-48394]


title: Young_2, Cell 382 of 384 [AS-441977-LR-48394]


title: Young_3, Cell 13 of 384 [AS-443201-LR-48446]


title: Young_2, Cell 366 of 384 [AS-441945-LR-48394]


title: Young_2, Cell 364 of 384 [AS-441941-LR-48394]


title: Young_2, Cell 384 of 384 [AS-441981-LR-48394]


title: Young_2, Cell 381 of 384 [AS-441975-LR-48394]


title: Young_2, Cell 363 of 384 [AS-441939-LR-48394]


title: Young_2, Cell 373 of 384 [AS-441959-LR-48394]


title: Young_2, Cell 374 of 384 [AS-441961-LR-48394]


title: Young_2, Cell 383 of 384 [AS-441979-LR-48394]


title: Young_2, Cell 371 of 384 [AS-441955-LR-48394]


title: Young_2, Cell 358 of 384 [AS-441929-LR-48394]


title: Young_2, Cell 370 of 384 [AS-441953-LR-48394]


title: Young_2, Cell 357 of 384 [AS-441927-LR-48394]


title: Young_2, Cell 369 of 384 [AS-441951-LR-48394]


title: Young_2, Cell 361 of 384 [AS-441935-LR-48394]


title: Young_2, Cell 360 of 384 [AS-441933-LR-48394]


title: Young_2, Cell 356 of 384 [AS-441925-LR-48394]


title: Young_2, Cell 355 of 384 [AS-441923-LR-48394]


title: Young_2, Cell 354 of 384 [AS-441921-LR-48394]


title: Young_2, Cell 368 of 384 [AS-441949-LR-48394]


title: Young_2, Cell 351 of 384 [AS-441915-LR-48394]


title: Young_2, Cell 365 of 384 [AS-441943-LR-48394]


title: Young_2, Cell 352 of 384 [AS-441917-LR-48394]


title: Young_2, Cell 350 of 384 [AS-441913-LR-48394]


title: Young_2, Cell 367 of 384 [AS-441947-LR-48394]


title: Young_2, Cell 359 of 384 [AS-441931-LR-48394]


title: Young_2, Cell 377 of 384 [AS-441967-LR-48394]


title: Young_2, Cell 376 of 384 [AS-441965-LR-48394]


title: Young_2, Cell 362 of 384 [AS-441937-LR-48394]


title: Young_2, Cell 348 of 384 [AS-441909-LR-48394]


title: Young_2, Cell 346 of 384 [AS-441905-LR-48394]


title: Young_2, Cell 347 of 384 [AS-441907-LR-48394]


title: Young_2, Cell 353 of 384 [AS-441919-LR-48394]


title: Young_2, Cell 344 of 384 [AS-441901-LR-48394]


title: Young_2, Cell 337 of 384 [AS-441887-LR-48394]


title: Young_2, Cell 336 of 384 [AS-441885-LR-48394]


title: Young_2, Cell 334 of 384 [AS-441881-LR-48394]


title: Young_2, Cell 349 of 384 [AS-441911-LR-48394]


title: Young_2, Cell 332 of 384 [AS-441877-LR-48394]


title: Young_2, Cell 345 of 384 [AS-441903-LR-48394]


title: Young_2, Cell 330 of 384 [AS-441873-LR-48394]


title: Young_2, Cell 340 of 384 [AS-441893-LR-48394]


title: Young_2, Cell 341 of 384 [AS-441895-LR-48394]


title: Young_2, Cell 324 of 384 [AS-441861-LR-48394]


title: Young_2, Cell 320 of 384 [AS-441853-LR-48394]


title: Young_2, Cell 326 of 384 [AS-441865-LR-48394]


title: Young_2, Cell 339 of 384 [AS-441891-LR-48394]


title: Young_2, Cell 343 of 384 [AS-441899-LR-48394]


title: Young_2, Cell 333 of 384 [AS-441879-LR-48394]


title: Young_2, Cell 318 of 384 [AS-441849-LR-48394]


title: Young_2, Cell 342 of 384 [AS-441897-LR-48394]


title: Young_2, Cell 317 of 384 [AS-441847-LR-48394]


title: Young_2, Cell 316 of 384 [AS-441845-LR-48394]


title: Young_2, Cell 335 of 384 [AS-441883-LR-48394]


title: Young_2, Cell 315 of 384 [AS-441843-LR-48394]


title: Young_2, Cell 331 of 384 [AS-441875-LR-48394]


title: Young_2, Cell 328 of 384 [AS-441869-LR-48394]


title: Young_2, Cell 312 of 384 [AS-441837-LR-48394]


title: Young_2, Cell 319 of 384 [AS-441851-LR-48394]


title: Young_2, Cell 329 of 384 [AS-441871-LR-48394]


title: Young_2, Cell 322 of 384 [AS-441857-LR-48394]


title: Young_2, Cell 323 of 384 [AS-441859-LR-48394]


title: Young_2, Cell 321 of 384 [AS-441855-LR-48394]


title: Young_2, Cell 325 of 384 [AS-441863-LR-48394]


title: Young_2, Cell 306 of 384 [AS-441825-LR-48394]


title: Young_2, Cell 305 of 384 [AS-441823-LR-48394]


title: Young_2, Cell 327 of 384 [AS-441867-LR-48394]


title: Young_2, Cell 311 of 384 [AS-441835-LR-48394]


title: Young_2, Cell 313 of 384 [AS-441839-LR-48394]


title: Young_2, Cell 299 of 384 [AS-441811-LR-48394]


title: Young_2, Cell 338 of 384 [AS-441889-LR-48394]


title: Young_2, Cell 297 of 384 [AS-441807-LR-48394]


title: Young_2, Cell 310 of 384 [AS-441833-LR-48394]


title: Young_2, Cell 309 of 384 [AS-441831-LR-48394]


title: Young_2, Cell 296 of 384 [AS-441805-LR-48394]


title: Young_2, Cell 294 of 384 [AS-441801-LR-48394]


title: Young_2, Cell 293 of 384 [AS-441799-LR-48394]


title: Young_2, Cell 304 of 384 [AS-441821-LR-48394]


title: Young_2, Cell 303 of 384 [AS-441819-LR-48394]


title: Young_2, Cell 291 of 384 [AS-441795-LR-48394]


title: Young_2, Cell 300 of 384 [AS-441813-LR-48394]


title: Young_2, Cell 307 of 384 [AS-441827-LR-48394]


title: Young_2, Cell 308 of 384 [AS-441829-LR-48394]


title: Young_2, Cell 301 of 384 [AS-441815-LR-48394]


title: Young_2, Cell 290 of 384 [AS-441793-LR-48394]


title: Young_2, Cell 289 of 384 [AS-441791-LR-48394]


title: Young_2, Cell 314 of 384 [AS-441841-LR-48394]


title: Young_2, Cell 288 of 384 [AS-441789-LR-48394]


title: Young_2, Cell 298 of 384 [AS-441809-LR-48394]


title: Young_2, Cell 285 of 384 [AS-441783-LR-48394]


title: Young_2, Cell 292 of 384 [AS-441797-LR-48394]


title: Young_2, Cell 287 of 384 [AS-441787-LR-48394]


title: Young_2, Cell 284 of 384 [AS-441781-LR-48394]


title: Young_2, Cell 283 of 384 [AS-441779-LR-48394]


title: Young_2, Cell 295 of 384 [AS-441803-LR-48394]


title: Young_2, Cell 282 of 384 [AS-441777-LR-48394]


title: Young_2, Cell 302 of 384 [AS-441817-LR-48394]


title: Young_2, Cell 281 of 384 [AS-441775-LR-48394]


title: Young_2, Cell 286 of 384 [AS-441785-LR-48394]


title: Young_2, Cell 280 of 384 [AS-441773-LR-48394]


title: Young_2, Cell 279 of 384 [AS-441771-LR-48394]


title: Young_2, Cell 278 of 384 [AS-441769-LR-48394]


title: Young_2, Cell 276 of 384 [AS-441765-LR-48394]


title: Young_2, Cell 277 of 384 [AS-441767-LR-48394]


title: Young_2, Cell 275 of 384 [AS-441763-LR-48394]


title: Young_2, Cell 274 of 384 [AS-441761-LR-48394]


title: Young_2, Cell 273 of 384 [AS-441759-LR-48394]


title: Young_2, Cell 270 of 384 [AS-441753-LR-48394]


title: Young_2, Cell 272 of 384 [AS-441757-LR-48394]


title: Young_2, Cell 271 of 384 [AS-441755-LR-48394]


title: Young_2, Cell 268 of 384 [AS-441749-LR-48394]


title: Young_2, Cell 265 of 384 [AS-441743-LR-48394]


title: Young_2, Cell 264 of 384 [AS-441741-LR-48394]


title: Young_2, Cell 258 of 384 [AS-441729-LR-48394]


title: Young_2, Cell 259 of 384 [AS-441731-LR-48394]


title: Young_2, Cell 257 of 384 [AS-441727-LR-48394]


title: Young_2, Cell 262 of 384 [AS-441737-LR-48394]


title: Young_2, Cell 267 of 384 [AS-441747-LR-48394]


title: Young_2, Cell 254 of 384 [AS-441721-LR-48394]


title: Young_2, Cell 266 of 384 [AS-441745-LR-48394]


title: Young_2, Cell 253 of 384 [AS-441719-LR-48394]


title: Young_2, Cell 269 of 384 [AS-441751-LR-48394]


title: Young_2, Cell 251 of 384 [AS-441715-LR-48394]


title: Young_2, Cell 260 of 384 [AS-441733-LR-48394]


title: Young_2, Cell 250 of 384 [AS-441713-LR-48394]


title: Young_2, Cell 252 of 384 [AS-441717-LR-48394]


title: Young_2, Cell 263 of 384 [AS-441739-LR-48394]


title: Young_2, Cell 255 of 384 [AS-441723-LR-48394]


title: Young_2, Cell 249 of 384 [AS-441711-LR-48394]


title: Young_2, Cell 261 of 384 [AS-441735-LR-48394]


title: Young_2, Cell 248 of 384 [AS-441709-LR-48394]


title: Young_2, Cell 247 of 384 [AS-441707-LR-48394]


title: Young_2, Cell 246 of 384 [AS-441705-LR-48394]


title: Young_2, Cell 245 of 384 [AS-441703-LR-48394]


title: Young_2, Cell 244 of 384 [AS-441701-LR-48394]


title: Young_2, Cell 243 of 384 [AS-441699-LR-48394]


title: Young_2, Cell 256 of 384 [AS-441725-LR-48394]


title: Young_2, Cell 241 of 384 [AS-441695-LR-48394]


title: Young_2, Cell 240 of 384 [AS-441693-LR-48394]


title: Young_2, Cell 242 of 384 [AS-441697-LR-48394]


title: Young_2, Cell 239 of 384 [AS-441691-LR-48394]


title: Young_2, Cell 238 of 384 [AS-441689-LR-48394]


title: Young_2, Cell 237 of 384 [AS-441687-LR-48394]


title: Young_2, Cell 235 of 384 [AS-441683-LR-48394]


title: Young_2, Cell 236 of 384 [AS-441685-LR-48394]


title: Young_2, Cell 234 of 384 [AS-441681-LR-48394]


title: Young_2, Cell 228 of 384 [AS-441669-LR-48394]


title: Young_2, Cell 232 of 384 [AS-441677-LR-48394]


title: Young_2, Cell 229 of 384 [AS-441671-LR-48394]


title: Young_2, Cell 230 of 384 [AS-441673-LR-48394]


title: Young_2, Cell 226 of 384 [AS-441665-LR-48394]


title: Young_2, Cell 231 of 384 [AS-441675-LR-48394]


title: Young_2, Cell 219 of 384 [AS-441651-LR-48394]


title: Young_2, Cell 223 of 384 [AS-441659-LR-48394]


title: Young_2, Cell 225 of 384 [AS-441663-LR-48394]


title: Young_2, Cell 218 of 384 [AS-441649-LR-48394]


title: Young_2, Cell 215 of 384 [AS-441643-LR-48394]


title: Young_2, Cell 224 of 384 [AS-441661-LR-48394]


title: Young_2, Cell 221 of 384 [AS-441655-LR-48394]


title: Young_2, Cell 214 of 384 [AS-441641-LR-48394]


title: Young_2, Cell 217 of 384 [AS-441647-LR-48394]


title: Young_2, Cell 220 of 384 [AS-441653-LR-48394]


title: Young_2, Cell 216 of 384 [AS-441645-LR-48394]


title: Young_2, Cell 211 of 384 [AS-441635-LR-48394]


title: Young_2, Cell 212 of 384 [AS-441637-LR-48394]


title: Young_2, Cell 213 of 384 [AS-441639-LR-48394]


title: Young_2, Cell 210 of 384 [AS-441633-LR-48394]


title: Young_2, Cell 209 of 384 [AS-441631-LR-48394]


title: Young_2, Cell 206 of 384 [AS-441625-LR-48394]


title: Young_2, Cell 233 of 384 [AS-441679-LR-48394]


title: Young_2, Cell 208 of 384 [AS-441629-LR-48394]


title: Young_2, Cell 207 of 384 [AS-441627-LR-48394]


title: Young_2, Cell 205 of 384 [AS-441623-LR-48394]


title: Young_2, Cell 227 of 384 [AS-441667-LR-48394]


title: Young_2, Cell 203 of 384 [AS-441619-LR-48394]


title: Young_2, Cell 222 of 384 [AS-441657-LR-48394]


title: Young_2, Cell 204 of 384 [AS-441621-LR-48394]


title: Young_2, Cell 201 of 384 [AS-441615-LR-48394]


title: Young_2, Cell 199 of 384 [AS-441611-LR-48394]


title: Young_2, Cell 200 of 384 [AS-441613-LR-48394]


title: Young_2, Cell 198 of 384 [AS-441609-LR-48394]


title: Young_2, Cell 195 of 384 [AS-441603-LR-48394]


title: Young_2, Cell 194 of 384 [AS-441601-LR-48394]


title: Young_2, Cell 196 of 384 [AS-441605-LR-48394]


title: Young_2, Cell 202 of 384 [AS-441617-LR-48394]


title: Young_2, Cell 191 of 384 [AS-441210-LR-48372]


title: Young_2, Cell 189 of 384 [AS-441206-LR-48372]


title: Young_2, Cell 187 of 384 [AS-441202-LR-48372]


title: Young_2, Cell 193 of 384 [AS-441599-LR-48394]


title: Young_2, Cell 192 of 384 [AS-441212-LR-48372]


title: Young_2, Cell 184 of 384 [AS-441196-LR-48372]


title: Young_2, Cell 180 of 384 [AS-441188-LR-48372]


title: Young_2, Cell 186 of 384 [AS-441200-LR-48372]


title: Young_2, Cell 181 of 384 [AS-441190-LR-48372]


title: Young_2, Cell 178 of 384 [AS-441184-LR-48372]


title: Young_2, Cell 182 of 384 [AS-441192-LR-48372]


title: Young_2, Cell 177 of 384 [AS-441182-LR-48372]


title: Young_2, Cell 176 of 384 [AS-441180-LR-48372]


title: Young_2, Cell 179 of 384 [AS-441186-LR-48372]


title: Young_2, Cell 174 of 384 [AS-441176-LR-48372]


title: Young_2, Cell 175 of 384 [AS-441178-LR-48372]


title: Young_2, Cell 172 of 384 [AS-441172-LR-48372]


title: Young_2, Cell 197 of 384 [AS-441607-LR-48394]


title: Young_2, Cell 173 of 384 [AS-441174-LR-48372]


title: Young_2, Cell 171 of 384 [AS-441170-LR-48372]


title: Young_2, Cell 170 of 384 [AS-441168-LR-48372]


title: Young_2, Cell 165 of 384 [AS-441158-LR-48372]


title: Young_2, Cell 166 of 384 [AS-441160-LR-48372]


title: Young_2, Cell 169 of 384 [AS-441166-LR-48372]


title: Young_2, Cell 190 of 384 [AS-441208-LR-48372]


title: Young_2, Cell 164 of 384 [AS-441156-LR-48372]


title: Young_2, Cell 188 of 384 [AS-441204-LR-48372]


title: Young_2, Cell 162 of 384 [AS-441152-LR-48372]


title: Young_2, Cell 161 of 384 [AS-441150-LR-48372]


title: Young_2, Cell 160 of 384 [AS-441148-LR-48372]


title: Young_2, Cell 185 of 384 [AS-441198-LR-48372]


title: Young_2, Cell 159 of 384 [AS-441146-LR-48372]


title: Young_2, Cell 158 of 384 [AS-441144-LR-48372]


title: Young_2, Cell 157 of 384 [AS-441142-LR-48372]


title: Young_2, Cell 183 of 384 [AS-441194-LR-48372]


title: Young_2, Cell 155 of 384 [AS-441138-LR-48372]


title: Young_2, Cell 154 of 384 [AS-441136-LR-48372]


title: Young_2, Cell 153 of 384 [AS-441134-LR-48372]


title: Young_2, Cell 151 of 384 [AS-441130-LR-48372]


title: Young_2, Cell 150 of 384 [AS-441128-LR-48372]


title: Young_2, Cell 149 of 384 [AS-441126-LR-48372]


title: Young_2, Cell 148 of 384 [AS-441124-LR-48372]


title: Young_2, Cell 147 of 384 [AS-441122-LR-48372]


title: Young_2, Cell 140 of 384 [AS-441108-LR-48372]


title: Young_2, Cell 167 of 384 [AS-441162-LR-48372]


title: Young_2, Cell 141 of 384 [AS-441110-LR-48372]


title: Young_2, Cell 168 of 384 [AS-441164-LR-48372]


title: Young_2, Cell 142 of 384 [AS-441112-LR-48372]


title: Young_2, Cell 138 of 384 [AS-441104-LR-48372]


title: Young_2, Cell 139 of 384 [AS-441106-LR-48372]


title: Young_2, Cell 137 of 384 [AS-441102-LR-48372]


title: Young_2, Cell 135 of 384 [AS-441098-LR-48372]


title: Young_2, Cell 134 of 384 [AS-441096-LR-48372]


title: Young_2, Cell 136 of 384 [AS-441100-LR-48372]


title: Young_2, Cell 133 of 384 [AS-441094-LR-48372]


title: Young_2, Cell 156 of 384 [AS-441140-LR-48372]


title: Young_2, Cell 132 of 384 [AS-441092-LR-48372]


title: Young_2, Cell 129 of 384 [AS-441086-LR-48372]


title: Young_2, Cell 127 of 384 [AS-441082-LR-48372]


title: Young_2, Cell 128 of 384 [AS-441084-LR-48372]


title: Young_2, Cell 125 of 384 [AS-441078-LR-48372]


title: Young_2, Cell 130 of 384 [AS-441088-LR-48372]


title: Young_2, Cell 124 of 384 [AS-441076-LR-48372]


title: Young_2, Cell 144 of 384 [AS-441116-LR-48372]


title: Young_2, Cell 163 of 384 [AS-441154-LR-48372]


title: Young_2, Cell 146 of 384 [AS-441120-LR-48372]


title: Young_2, Cell 143 of 384 [AS-441114-LR-48372]


title: Young_2, Cell 122 of 384 [AS-441072-LR-48372]


title: Young_2, Cell 120 of 384 [AS-441068-LR-48372]


title: Young_2, Cell 123 of 384 [AS-441074-LR-48372]


title: Young_2, Cell 121 of 384 [AS-441070-LR-48372]


title: Young_2, Cell 118 of 384 [AS-441064-LR-48372]


title: Young_2, Cell 115 of 384 [AS-441058-LR-48372]


title: Young_2, Cell 116 of 384 [AS-441060-LR-48372]


title: Young_2, Cell 117 of 384 [AS-441062-LR-48372]


title: Young_2, Cell 114 of 384 [AS-441056-LR-48372]


title: Young_2, Cell 112 of 384 [AS-441052-LR-48372]


title: Young_2, Cell 110 of 384 [AS-441048-LR-48372]


title: Young_2, Cell 111 of 384 [AS-441050-LR-48372]


title: Young_2, Cell 109 of 384 [AS-441046-LR-48372]


title: Young_2, Cell 131 of 384 [AS-441090-LR-48372]


title: Young_2, Cell 152 of 384 [AS-441132-LR-48372]


title: Young_2, Cell 106 of 384 [AS-441040-LR-48372]


title: Young_2, Cell 107 of 384 [AS-441042-LR-48372]


title: Young_2, Cell 105 of 384 [AS-441038-LR-48372]


title: Young_2, Cell 108 of 384 [AS-441044-LR-48372]


title: Young_2, Cell 101 of 384 [AS-441030-LR-48372]


title: Young_2, Cell 100 of 384 [AS-441028-LR-48372]


title: Young_2, Cell 104 of 384 [AS-441036-LR-48372]


title: Young_2, Cell 96 of 384 [AS-441020-LR-48372]


title: Young_2, Cell 99 of 384 [AS-441026-LR-48372]


title: Young_2, Cell 95 of 384 [AS-441018-LR-48372]


title: Young_2, Cell 98 of 384 [AS-441024-LR-48372]


title: Young_2, Cell 126 of 384 [AS-441080-LR-48372]


title: Young_2, Cell 103 of 384 [AS-441034-LR-48372]


title: Young_2, Cell 94 of 384 [AS-441016-LR-48372]


title: Young_2, Cell 93 of 384 [AS-441014-LR-48372]


title: Young_2, Cell 119 of 384 [AS-441066-LR-48372]


title: Young_2, Cell 90 of 384 [AS-441008-LR-48372]


title: Young_2, Cell 91 of 384 [AS-441010-LR-48372]


title: Young_2, Cell 89 of 384 [AS-441006-LR-48372]


title: Young_2, Cell 86 of 384 [AS-441000-LR-48372]


title: Young_2, Cell 113 of 384 [AS-441054-LR-48372]


title: Young_2, Cell 88 of 384 [AS-441004-LR-48372]


title: Young_2, Cell 84 of 384 [AS-440996-LR-48372]


title: Young_2, Cell 92 of 384 [AS-441012-LR-48372]


title: Young_2, Cell 83 of 384 [AS-440994-LR-48372]


title: Young_2, Cell 81 of 384 [AS-440990-LR-48372]


title: Young_2, Cell 85 of 384 [AS-440998-LR-48372]


title: Young_2, Cell 79 of 384 [AS-440986-LR-48372]


title: Young_2, Cell 78 of 384 [AS-440984-LR-48372]


title: Young_2, Cell 77 of 384 [AS-440982-LR-48372]


title: Young_2, Cell 102 of 384 [AS-441032-LR-48372]


title: Young_2, Cell 75 of 384 [AS-440978-LR-48372]