title: WT31 uninduced 4 RNA-seq


title: 24-KO-K01: miR-34a KO 3

status: Public on Mar 08 2021

type: SRA

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

description: primary chondrocytes

library_source: transcriptomic

data_processing:
Conversion of .bcl to .fastq files was performed for each sample using Illumina’s bcl2fastq2 conversion tool (v2.19.1.403)
Initial quality assessment of each sample revealed that the reads were of high quality (>Q30). Cutadapt (v1.18) software was used to maintain minimum read length of 25 bp post trimming of adapters (very few reads being contaminated=3%) as well as trimming of N’s.
Splice-aware alignment of reads using a Hierarchical Graph FM index (HGFM) method was performed using HISAT2 software (v2.1.0) with parameters (--rna-strandness FR –dta) against mouse reference genome (mm10).
To assemble the aligned reads into transcripts, StringTie software (v1.3.5) was used with parameters (--rf assuming it was a stranded library fr-firststrand).
To obtain the abundance of each of these transcripts based only on the known reference genome and transcriptome, StringTie was run again using different parameters (-e -B -G referencetranscripts.gtf) to generate output of Ballgown software compatible table files.
A script was provided by StringTie software named ‘prepDE.py’, which retrieves raw counts for genes and transcripts separately based on the table files, was used for Differential Expression Analysis (DEA).
For DEA, retain genes with at least 10 CPM in 2 samples and apply TMM normalization on remaining genes.
Assigned WT and KO groups and estimated dispersion.
Applied the exact test with trended dispersion in edgeR.
Retained genes with Benjamini-Hochberg adjusted FDR<0.05
Genome_build: mm10
Supplementary_files_format_and_content: 1 combined tab-delimited text file includes raw count values for each Sample ...

molecule: total RNA

organism: Mus musculus

source_name: articular cartilage

growth_protocol: Cells were grown in 6-well plates in complete DMEM medium supplemented with 10% FBS and 1%Pen-Strep until confluent (approx. 1 week)

extract_protocol:
Articular cartilage was scraped from tibial plateau and femoral condyle surfaces in the knee joint as well as hip. Cartilage was incubated in 3mg/ml collagenase overnight at 37 degrees celsius in an incubator and filtered in a 70µm sterile filter. Filtrate was centrifuged and pellet was resuspended in complete medium. Cells were counted and plated. Primary chondrocytes were used for RNA extraction using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocol (TruSeq Stranded Total RNA, Cat # 20020596).

treatment_protocol: No treatment

tag: tissue

value: articular cartilage

tag: strain

tag: genotype

tag: model nomenclature

value: Mir34atm1.2 Mrl

tag: age

value: 5 weeks


title: 1520-L

status: Public on Feb 02 2021

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

country: USA

institute: Northwestern University Feinberg School of Medicine

description:
Single Read
50bases

data_processing:
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed, including 4N before pulldown sequence and 2N after
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Counts were normalized to 1 million reads per sample, and reads with fewer than 6 normalized counts summed across all samples were discarded
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with normalized read counts for each sample comparison of interest, along with cell viability and blast-based annotations

organism: Homo sapiens

source_name: Ovarian cancer patient

extract_protocol:
Tumor pieces or cells were lyzed and proteins were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Tumor pieces from ovarian cancer patients (either primry tumor (P) or recurrent tumor ('R))

tag: cancer tissue

value: Primary tumor from ovarian cancer patient  - Pt sensitive

value: Ovaries


title: 1061-I

description:
Single Read
50bases

value: Primary tumor from ovarian cancer patient  - Pt sensitive (intermediate)


title: 86-S

description:
Single Read
50bases

value: Primary tumor from ovarian cancer patient  - Pt resistant


title: 1536-L

description:
Single Read
50bases


title: 1012-I

description:
Single Read
50bases


title: R5+siMxy-2; 1nM; 24h_total smRNA

description:
Single Read
50bases

data_processing:
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Counts were normalized to 1 million reads per sample, and reads with fewer than 6 normalized counts summed across all samples were discarded
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with normalized read counts for each sample comparison of interest, along with cell viability and blast-based annotations

source_name: Lab of Ken Nephew (Indiana University)

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Cells were transfected with 1 nM of siRNA and 24 hrs after transfection RNA was extracted.

tag: cell line

value: A2780 cells subjected to 5 cycles of cisplatin treatment as described (PMID:9041185).

tag: treatment/infection

value: Transfected with 1nM of siGGGGGC for 24hrs


title: R5+siMxy-1; 1nM; 24h_total smRNA

description:
Single Read
50bases


title: R5+si34a-1; 1nM; 24h_total smRNA

description:
Single Read
50bases

value: Transfected with 1nM of siGGCAGU for 24hrs


title: 894-S

description:
Single Read
50bases


title: R5+siNT1-1; 1nM; 24h_total smRNA

description:
Single Read
50bases

value: Transfected with 1nM of siNT1 for 24hrs


title: R5+siNT1-2; 1nM; 24h_total smRNA

description:
Single Read
50bases


title: A2780+siNT1-2; 1nM; 24h_total smRNA

description:
Single Read
50bases

source_name: Sigma catalogue no. 93112517

value: A2780 human  ovarian cancer cell line


title: A2780+si34a-1; 1nM; 24h_total smRNA

description:
Single Read
50bases


title: A2780+si34a-2; 1nM; 24h_total smRNA

description:
Single Read
50bases


title: A2780+siMxy-2; 1nM; 24h_total smRNA

description:
Single Read
50bases


title: 598R

description:
Single Read
50bases
PR-22

source_name: Primary tumor from ovarian cancer patient

extract_protocol:
Tumor pieces or cells were lyzed and proteins were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 magnetic beads and RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

value: Recurrence ovarian cancer


title: A2780+siNT1-1; 1nM; 24h_total smRNA

description:
Single Read
50bases


title: 1461R

description:
Single Read
50bases
PR-18


title: 598P

description:
Single Read
50bases
PR-21

value: Primary ovarian cancer


title: 504_121R

description:
Single Read
50bases
PR-20


title: 504_121P

description:
Single Read
50bases
PR-19


title: 290R2

description:
Single Read
50bases
PR-15


title: 200_220R

description:
Single Read
50bases
PR-12


title: 290R3

description:
Single Read
50bases
PR-16


title: 2068R

description:
Single Read
50bases
PR-10


title: 1461P

description:
Single Read
50bases
PR-17


title: 290R1

description:
Single Read
50bases
PR-14


title: 290P

description:
Single Read
50bases
PR-13


title: 200_220P

description:
Single Read
50bases
PR-11


title: 2068P

description:
Single Read
50bases
PR-9


title: R5+si34a-2; 1nM; 24h_total smRNA

description:
Single Read
50bases


title: 1441R

description:
Single Read
50bases
PR-6


title: 828R

description:
Single Read
50bases
PR-8


title: 828P

description:
Single Read
50bases
PR-7


title: 2490P

description:
Single Read
50bases
PR-3


title: 2490R

description:
Single Read
50bases
PR-4


title: A2780+siMxy-1; 1nM; 24h_total smRNA

description:
Single Read
50bases


title: R5+si34a-2; 1nM; 24h

data_processing:
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed, including 4N before pulldown sequence and 2N after
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Counts were normalized to 1 million reads per sample, and reads with fewer than 6 normalized counts summed across all samples were discarded
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with normalized read counts for each sample comparison of interest, along with log2FoldChange values, p-values and adjusted p-values.

extract_protocol:
Cellls were lyzed and proteins were subjected to pull down with a GW182 peptide bound to anti-FLAG Ab beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol. Two small RNA-SEQ sub-libraries were generated: one containing library fragments 140-150 bp in size and one containing library fragments 150-200 bp in size (both including the sequencing adator of about 130bp).
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Cells were transfected with a 1 nM of three different siRNAs and 24hrs after transfection lyzed.

tag: treatment


title: R5+siMxy-1; 1nM; 24h


title: R5+siNT1-2; 1nM; 24h


title: A2780+siMxy-1; 1nM; 24h


title: R5+siNT1-1; 1nM; 24h


title: A2780+siMxy-2; 1nM; 24h


title: A2780+si34a-2; 1nM; 24h


title: 2065P

description:
Single Read
50bases
PR-1


title: A2780+si34a-1; 1nM; 24h


title: R5+si34a-1; 1nM; 24h


title: A2780+siNT1-2; 1nM; 24h


title: 796 carboplatin treated (3 injections+2wk recovery)

data_processing:
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed, including 4N before pulldown sequence and 2N after
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Counts were normalized to 1 million reads per sample, and reads with fewer than 6 normalized counts summed across all samples were discarded
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
raw counts were calculated by HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with normalized read counts for each sample comparison of interest, along with cell viability and blast-based annotations

source_name: OVCAR-5 cells, Millipor Sigma SCC259

growth_protocol: 2 million OVCAR5 cells were injected ip into nude mice.

extract_protocol:
Tumors were homogenized and proteins were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Mice were treated i.p. with either PBS or 25 mg/kg carboplatin between 3 and 5 injections over up to 5 weeks

value: OVCAR5 human  ovarian cancer cell line

value: Carboplatin treated (3 injections+2wk recovery)


title: 800 carboplatin treated (3injections+2inj post 2wk recovery)

value: Carboplatin treated (3injections+2inj post 2wk recovery)


title: 798 carboplatin treated (3injections+2inj post 2wk recovery)


title: 797 carboplatin treated (3 injections, one injection per week)

value: Carboplatin treated (3 injections, one injection per week)


title: 792-PBSCtrl mouse

value: PBS control treated mouse


title: A2780+siNT1-1; 1nM; 24h


title: 1441P

description:
Single Read
50bases
PR-5


title: 795 carboplatin treated (3 injections, one injection per week)


title: 793-PBSCtrl mouse


title: 794-PBSCtrl mouse


title: R5+PBS-1

data_processing:
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Counts were normalized to 1 million reads per sample, and reads with fewer than 6 normalized counts summed across all samples were discarded
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with read, seed (bp 2-7), cell viability based on seed, normalized read counts for each sample, and putative source based on blast

treatment_protocol: Cells were treated with PBS or 5 μM Cisplatin for 72hrs before RNA was extracted

value: Treated for 72 hrs with PBS


title: R5+CISP-2

value: Treated with 5 μM Cis for 72 hrs


title: R5+PBS-2

value: Ovaries


title: 791-Ctrl mouse

value: Untreated mouse


title: R5+CISP-1


title: A2780+CISP-1


title: 2065R

description:
Single Read
50bases
PR-2


title: R5+siMxy-2; 1nM; 24h


title: A2780+CISP-2


title: A2780+PBS-2


title: A2780-R5+cisp.rep2

data_processing:
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed, including 4N before pulldown sequence and 2N after
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Counts were normalized to 1 million reads per sample, and reads with fewer than 6 normalized counts summed across all samples were discarded
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with read, seed (bp 2-7), cell viability based on seed, normalized read counts for each sample, and putative source based on blast

extract_protocol:
Cells were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Cells were treated with PBS/water or 5μM cisplatin/1μg/ml carboplatin for 72hrs before being subjected to Ago pull down and smRNA Seq


title: PEO1+water.rep2

source_name: Lab of Daniela Matei Northwestern University)

value: Human ovarian cancer cell line derived from patient after receiving combination chemotherapy with Cis, chlorambucil and 5-fluorouracil (PMID:3583449)

value: Treated for 72 hrs with water


title: PEO4+water.rep1

value: Human ovarian cancer cell line derived from patient after receiving combination chemotherapy with Cis, chlorambucil and 5-fluorouracil and second relapse (PMID:3583449)


title: PEO4+carbo.rep2

value: Treated with 1 μg/ml carboplatin for 72 hrs


title: A2780+PBS-1


title: PEO1+carbo.rep2


title: A2780-R5+cisp.rep1

value: A2780 cells subjected to 5 cycles of cisplatin treatment as described (PMID:9041185).


title: PEO4+carbo.rep1


title: PEO4+water.rep2


title: PEO1+water.rep1


title: A2780R5+PBS.rep2


title: A2780+cisp.rep2

value: A2780 human  ovarian cancer cell line


title: A2780R5+PBS.rep1


title: A2780+PBS.rep2


title: A2780+PBS.rep1


title: CD45hi tumor infiltrating lymphocytes, Metformin

status: Public on Dec 04 2020

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Cell Ranger (10X genomics) was used
Samples were alinged using the mouse genome 10-3.0.0 (mm10, 10X genomics)
Further analysis was done by Seurat package.
Genome_build: 10-3.0.0 (mm10)
Supplementary_files_format_and_content: Feature, barcode, matrix

source_name: Murine brain tumor infiltrated cells

growth_protocol: C57BL/6 mice were housed in specific pathogen free (SPF) facility ijn KAIST. GL261 cells were cultured in RPMI medium.

extract_protocol:
After 20 days of injection, brain was isolated from mice. Tumor region was dissected. Cells were isolated from brain. CD45hi TILs were sorted by FACS Aria sorter.
Single cell 3' reagent kit v3 (10x genomics)

treatment_protocol: GL261 cells were intracranially injected into C57BL/6 mice. DW control water and metformin-containing water were given to mice through drinking.

value: mice were intracranially injected with GL261 cells

tag: time

value: 20 days post-injection

tag: drinking water

value: Metformin in drinking water

value: brain

tag: cell type

value: CD45hi TILs


title: CD45hi tumor infiltrating lymphocytes, DW

value: DW control water


title: A2780+cisp.rep1


title: A20_97_A1_ROI039

status: Public on Nov 01 2020

type: other

city: Seattle

first: Jason

middle: W

last: Reeves

state: WA

address: 530 Fairview Blvd

department: R&D

institute: Nanostring

description:
raw data file:
P1002220000325A.RCC
RCC Files from plexset are provided along with PKC. RCC files contain multiple samples collected by GeoMx. Because on-instrument processing is necessary for relationship between RCC & individual ROIs, the Raw Calibrated count matrix is included in addition to the analyzed count matrix.

hyb_protocol: Barcodes collected by GeoMx DSP were hybridized using standard nCounter protocols. For more information on nCounter hybridization protocols see nanostring.com

scan_protocol: Images related to samples included in this study were scanned using the GeoMx® Digital Spatial Profiling (DSP) platform. This platform includes a 20x microscope with 4 channels available for visualization of multiplexed immunoflorescent markers

data_processing:
nCounter RCC files were processed using the GeoMx DSP Software package to associate the PKC and CDF files with the RCC files and quantify the number of target counts observed for each region of interest collected.
RCC files can be processed with nSolver: https://www.nanostring.com/products/analysis-software/nsolver  which will provide the information about the well mapping for each sample + the protein ID measured.
RCC files can also be processed with the GeoMx software that manages the collection machine + data analysis. It’s an embedded software solution on the instrument and is not downloadable. Users can bring the RCC files to the GeoMx software that was used for collection on the samples to build the raw count matrices from the RCCs. This software manages the images and sample annotations natively.
Analyzed count matrix values represent the raw count values adjusted for background counts by normalizing the geometric mean of IgG controls (Ms IgG1 & Rb IgG) across the study.

molecule: protein

source_name: FFPE Rapid Autopsy Tissue

extract_protocol: Samples were incubated with DNA-oligo barcoded antibodies which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)

tag: case number

value: Case 5

tag: patient id

tag: roi

tag: segment

tag: covid-19 ish status

tag: tissue structure

value: LN

tag: tissue notes

tag: patient viral load

tag: roi x coordinate

tag: roi y coordinate

tag: segment type

value: Geometric

tag: surface area

tag: nuclei count

tag: qc flag - low signal

value: FALSE

tag: negative normalization factor

tag: hyb-code

value: D

tag: assayed molecule

value: DNA-oligonucleotide barcode


title: A20_97_A1_ROI036

tag: case number


title: A20_97_A1_ROI038

tag: patient id


title: A20_97_A1_ROI037

tag: roi


title: PEO1+carbo.rep1

tag: cell line

value: Human ovarian cancer cell line derived from patient after receiving combination chemotherapy with Cis, chlorambucil and 5-fluorouracil (PMID:3583449)

tag: tissue

value: Ovaries

tag: treatment


title: A20_97_A1_ROI034

tag: segment

tag: covid-19 ish status

tag: tissue structure

tag: tissue notes

value: Carbon_rich_macrophage rich region


title: A20_97_A1_ROI033

tag: patient viral load

tag: roi x coordinate

tag: roi y coordinate

tag: segment type


title: A20_97_A1_ROI032

tag: surface area

tag: nuclei count

tag: qc flag - low signal

tag: negative normalization factor


title: A20_97_A1_ROI031

tag: case number

tag: patient id

tag: hyb-code

value: C

tag: assayed molecule


title: A20-97 A1_ROI029-2PanCK-

tag: roi

value: Alveoli


title: A20_97_A1_ROI030

tag: segment


title: A20_97_A1_ROI035

tag: covid-19 ish status


title: A20-97 A1_ROI029-1PanCK+

tag: tissue structure


title: A20-97 A1_ROI021-Seg1

value: B


title: A20-97 A1_ROI027-1PanCK+

tag: tissue notes


title: A20-97 A1_ROI028-1PanCK+

tag: patient viral load


title: A20-97 A1_ROI023-Seg1

tag: roi x coordinate


title: A20-97 A1_ROI025-1PanCK+

tag: roi y coordinate


title: A20-97 A1_ROI025-2PanCK-

tag: segment type


title: A20-97 A1_ROI028-2PanCK-

tag: surface area


title: A20-97 A1_ROI026-1PanCK+

tag: nuclei count


title: A20-97 A1_ROI024-Seg1

tag: qc flag - low signal


title: A20-97 A1_ROI017-Seg1

tag: negative normalization factor


title: A20-97 A1_ROI019-Seg1

tag: case number


title: A20-97 A1_ROI016-Seg1

tag: patient id


title: A20-97 A1_ROI018-Seg1

tag: hyb-code


title: A20-97 A1_ROI020-Seg1

tag: assayed molecule


title: A20-97 A1_ROI026-2PanCK-

tag: roi


title: A20-97 A1_ROI027-2PanCK-

tag: segment


title: A20-97 A1_ROI022-Seg1

tag: covid-19 ish status


title: A20-97 A1_ROI015-Seg1

tag: tissue structure


title: A20-97 A1_ROI014-Seg1


title: A20-97 A1_ROI013-Seg1


title: A20-97 A1_ROI010-Seg1

value: A


title: A20-97 A1_ROI011-Seg1


title: A20-97 A1_ROI012-Seg1


title: A20-97 A1_ROI008-Seg1


title: A20-97 A1_ROI006-Seg1


title: A20-97 A1_ROI007-Seg1


title: A20-97 A1_ROI005-Seg1


title: A20-97 A1_ROI004-Seg1


title: A20-97 A1_ROI009-Seg1


title: A20-97 A1_ROI003-Seg1


title: A20-97 A1_ROI001-Seg1


title: A20-95 A1_ROI035-Seg1

description:
raw data file:
P1012301720326C.RCC
RCC Files from plexset are provided along with PKC. RCC files contain multiple samples collected by GeoMx. Because on-instrument processing is necessary for relationship between RCC & individual ROIs, the Raw Calibrated count matrix is included in addition to the analyzed count matrix.

value: Case 4

tag: tissue notes

value: Neg

value: F


title: A20-95 A1_ROI034-1PanCK+

tag: patient viral load

value: TRUE


title: A20-95 A1_ROI032-1PanCK+

tag: roi x coordinate


title: A20-95 A1_ROI034-2PanCK-

tag: roi y coordinate


title: A20-95 A1_ROI033-1PanCK+

tag: segment type


title: A20-95 A1_ROI033-2PanCK-

tag: surface area


title: A20-95 A1_ROI032-2PanCK-

tag: nuclei count


title: A20-95 A1_ROI036-Seg1

tag: qc flag - low signal


title: A20-95 A1_ROI029-1PanCK+

tag: negative normalization factor

value: E


title: A20-95 A1_ROI029-2PanCK-

tag: case number


title: A20-95 A1_ROI031-2PanCK-

tag: patient id


title: A20-95 A1_ROI030-2PanCK-

tag: hyb-code


title: A20-95 A1_ROI028-2PanCK-

tag: assayed molecule


title: A20-95 A1_ROI030-1PanCK+

tag: roi


title: A20-95 A1_ROI031-1PanCK+

tag: segment


title: A20-95 A1_ROI028-1PanCK+

tag: covid-19 ish status


title: A20-95 A1_ROI027-1PanCK+

tag: tissue structure


title: A20-95 A1_ROI026-2PanCK-

tag: tissue notes


title: A20-95 A1_ROI025-2PanCK-

tag: patient viral load


title: A20-95 A1_ROI026-1PanCK+

tag: roi x coordinate


title: A20-95 A1_ROI025-1PanCK+

tag: roi y coordinate


title: A20-97 A1_ROI002-Seg1

value: Case 5

tag: segment type


title: A20-95 A1_ROI027-2PanCK-

tag: surface area


title: A20-95 A1_ROI024-2PanCK-

tag: nuclei count


title: A20-95 A1_ROI023-2PanCK-

tag: qc flag - low signal


title: A20-95 A1_ROI024-1PanCK+

tag: negative normalization factor


title: A20-95 A1_ROI023-1PanCK+

tag: case number


title: A20-95 A1_ROI022-Seg1

tag: patient id

value: Geometric


title: A20-95 A1_ROI014-Seg1

value: FALSE

tag: hyb-code


title: A20-95 A1_ROI016-Seg1

value: D

tag: assayed molecule


title: A20-95 A1_ROI013-Seg1

tag: roi

value: DNA-oligonucleotide barcode


title: A20-95 A1_ROI020-Seg1

tag: segment


title: A20-95 A1_ROI019-Seg1

tag: covid-19 ish status


title: A20-95 A1_ROI007-Seg1

tag: tissue structure


title: A20-95 A1_ROI018-Seg1

tag: tissue notes


title: A20-95 A1_ROI002-Seg1

tag: patient viral load


title: A20-95 A1_ROI015-Seg1

tag: roi x coordinate


title: A20-95 A1_ROI017-Seg1

tag: roi y coordinate


title: A20-95 A1_ROI012-Seg1

tag: segment type


title: A20-90 A1_ROI033-2PanCK-

description:
raw data file:
P1002345000123A.RCC
RCC Files from plexset are provided along with PKC. RCC files contain multiple samples collected by GeoMx. Because on-instrument processing is necessary for relationship between RCC & individual ROIs, the Raw Calibrated count matrix is included in addition to the analyzed count matrix.

value: Case 2

tag: surface area


title: A20-95 A1_ROI011-Seg1

tag: nuclei count


title: A20-90 A1_ROI034-2PanCK-

tag: qc flag - low signal


title: A20-90 A1_ROI033-1PanCK+

tag: negative normalization factor


title: A20-95 A1_ROI009-Seg1

tag: case number


title: A20-95 A1_ROI010-Seg1

tag: patient id


title: A20-95 A1_ROI008-Seg1

tag: hyb-code


title: A20-90 A1_ROI031-2PanCK-

tag: assayed molecule


title: A20-95 A1_ROI006-Seg1

tag: roi


title: A20-95 A1_ROI005-Seg1

tag: segment


title: A20-95 A1_ROI004-Seg1

tag: covid-19 ish status


title: A20-90 A1_ROI029-1PanCK+

tag: tissue structure


title: A20-90 A1_ROI035-Seg1

tag: tissue notes


title: A20-95 A1_ROI001-Seg1

tag: patient viral load


title: A20-90 A1_ROI034-1PanCK+

tag: roi x coordinate


title: A20-95 A1_ROI021-Seg1

tag: roi y coordinate


title: A20-90 A1_ROI032-2PanCK-

tag: segment type


title: A20-90 A1_ROI032-1PanCK+

tag: surface area


title: A20-90 A1_ROI031-1PanCK+

tag: nuclei count


title: A20-90 A1_ROI030-1PanCK+

tag: qc flag - low signal


title: A20-90 A1_ROI030-2PanCK-

tag: negative normalization factor


title: A20-90 A1_ROI024-1PanCK+

tag: case number


title: A20-90 A1_ROI028-2PanCK-

tag: patient id


title: A20-95 A1_ROI003-Seg1

tag: hyb-code


title: A20-90 A1_ROI028-1PanCK+

tag: assayed molecule


title: A20-90 A1_ROI029-2PanCK-

tag: roi


title: A20-90 A1_ROI027-1PanCK+

tag: segment


title: A20-90 A1_ROI025-1PanCK+

tag: covid-19 ish status


title: A20-90 A1_ROI022-1PanCK+

tag: tissue structure


title: A20-90 A1_ROI021-2PanCK-

value: Bronchial

tag: tissue notes


title: A20-90 A1_ROI024-2PanCK-

tag: patient viral load


title: A20-90 A1_ROI023-1PanCK+

tag: roi x coordinate


title: A20-90 A1_ROI025-2PanCK-

tag: roi y coordinate


title: A20-90 A1_ROI026-2PanCK-

tag: segment type


title: A20-90 A1_ROI020-2PanCK-

tag: surface area


title: A20-90 A1_ROI021-1PanCK+

tag: nuclei count


title: A20-90 A1_ROI016-Seg1

tag: qc flag - low signal


title: A20-90 A1_ROI017-Seg1

tag: negative normalization factor


title: A20-90 A1_ROI020-1PanCK+

tag: case number


title: A20-90 A1_ROI027-2PanCK-

tag: patient id


title: A20-90 A1_ROI013-Seg1

tag: hyb-code


title: A20-90 A1_ROI026-1PanCK+

tag: assayed molecule


title: A20-90 A1_ROI019-2PanCK-

tag: roi


title: A20-90 A1_ROI019-1PanCK+

tag: segment


title: A20-90 A1_ROI012-Seg1

tag: covid-19 ish status


title: A20-90 A1_ROI011-Seg1

tag: tissue structure


title: A20-90 A1_ROI015-Seg1

tag: tissue notes


title: A20-90 A1_ROI010-Seg1

tag: patient viral load


title: A20-90 A1_ROI014-Seg1

tag: roi x coordinate


title: A20-90 A1_ROI007-Seg1

tag: roi y coordinate


title: A20-90 A1_ROI008-Seg1

tag: segment type


title: A20-90 A1_ROI022-2PanCK-

tag: surface area


title: A20-90 A1_ROI023-2PanCK-

tag: nuclei count


title: A20-90 A1_ROI006-Seg1

value: Nearby_ROI_05; tissue bloody

tag: qc flag - low signal


title: A20-90 A1_ROI009-Seg1

tag: negative normalization factor


title: A20-90 A1_ROI005-Seg1

tag: case number


title: A20-90 A1_ROI002-Seg1

tag: patient id


title: A20-90 A1_ROI018-Seg1

tag: hyb-code


title: A20-87 A12_ROI030-2PanCK-

description:
raw data file:
P1010256001231A.RCC
RCC Files from plexset are provided along with PKC. RCC files contain multiple samples collected by GeoMx. Because on-instrument processing is necessary for relationship between RCC & individual ROIs, the Raw Calibrated count matrix is included in addition to the analyzed count matrix.

value: Case 1 LLL

tag: assayed molecule


title: A20-90 A1_ROI001-Seg1

tag: roi

value: Alveoli


title: A20-87 A12_ROI029-2PanCK-

tag: segment


title: A20-87 A12_ROI028-1PanCK+

tag: covid-19 ish status

value: Some CD68-POS


title: A20-87 A12_ROI027-1PanCK+

tag: tissue structure

value: lots of immune, but they don't stain positively for COVID-ISH


title: A20-87 A12_ROI026-2PanCK-

tag: tissue notes

value: lots of immune


title: A20-87 A12_ROI026-1PanCK+

tag: patient viral load


title: A20-87 A12_ROI029-1PanCK+

tag: roi x coordinate


title: A20-87 A12_ROI028-2PanCK-

tag: roi y coordinate


title: A20-87 A12_ROI025-2PanCK-

value: lots of immune that stained COVID-ISH positive

tag: segment type


title: A20-87 A12_ROI025-1PanCK+

tag: surface area

value: F


title: A20-87 A12_ROI022-Seg1

tag: nuclei count


title: A20-87 A12_ROI024-Seg1

tag: qc flag - low signal


title: A20-87 A12_ROI019-Seg1

tag: negative normalization factor


title: A20-87 A12_ROI018-Seg1

tag: case number


title: A20-87 A12_ROI014-Seg1

tag: patient id


title: A20-87 A12_ROI016-Seg1

tag: hyb-code


title: A20-87 A12_ROI030-1PanCK+

tag: assayed molecule


title: A20-87 A12_ROI017-Seg1

tag: roi


title: A20-87 A12_ROI015-Seg1

tag: segment


title: A20-87 A12_ROI012-Seg1

tag: covid-19 ish status


title: A20-87 A12_ROI011-Seg1

tag: tissue structure


title: A20-87 A12_ROI027-2PanCK-

tag: tissue notes


title: A20-87 A12_ROI009-Seg1

tag: patient viral load


title: A20-87 A12_ROI010-Seg1

tag: roi x coordinate


title: A20-87 A12_ROI007-Seg1

tag: roi y coordinate


title: A20-87 A12_ROI008-Seg1

tag: segment type


title: A20-87 A12_ROI023-Seg1

tag: surface area


title: A20-87 A12_ROI005-Seg1

tag: nuclei count


title: A20-87 A12_ROI021-Seg1

tag: qc flag - low signal


title: A20-87 A12_ROI006-Seg1

tag: negative normalization factor


title: A20-87 A12_ROI003-Seg1

tag: case number


title: A20-87 A12_ROI002-Seg1

tag: patient id


title: A20-87 A12_ROI004-Seg1

value: Fewer immune cells

tag: hyb-code


title: A20-87 A12_ROI013-Seg1

value: E

tag: assayed molecule


title: A20-87 A1_ROI030-1PanCK+

value: Case 1 LUL

tag: roi

value: C


title: A20-87 A1_ROI029-2PanCK-

tag: segment

value: FALSE


title: A20-87 A1_ROI030-2PanCK-

tag: covid-19 ish status


title: A20-87 A1_ROI029-1PanCK+

tag: tissue structure


title: A20-87 A1_ROI028-2PanCK-


title: A20-87 A1_ROI023-Seg1

tag: tissue notes

value: looks much like normal lung

value: Geometric

value: B


title: A20-87 A1_ROI028-1PanCK+

tag: patient viral load

value: DNA-oligonucleotide barcode


title: A20-87 A1_ROI024-Seg1

tag: roi x coordinate


title: A20-87 A1_ROI025-2PanCK-

tag: roi y coordinate


title: A20-87 A1_ROI027-1PanCK+

value: Bronchial

tag: segment type


title: A20-87 A1_ROI026-1PanCK+

tag: surface area


title: A20-87 A1_ROI026-2PanCK-

tag: nuclei count


title: A20-87 A1_ROI025-1PanCK+

tag: qc flag - low signal


title: A20-87 A1_ROI022-Seg1

tag: negative normalization factor


title: A20-87 A12_ROI001-Seg1

tag: case number

value: Case 1 LLL

value: D


title: A20-87 A1_ROI018-Seg1

tag: patient id

value: Alveoli


title: A20-87 A1_ROI021-Seg1

tag: hyb-code


title: A20-87 A1_ROI017-Seg1

tag: assayed molecule


title: A20-87 A1_ROI015-Seg1

tag: roi


title: A20-87 A1_ROI012-Seg1

tag: segment

value: A


title: A20-87 A1_ROI013-Seg1

tag: covid-19 ish status


title: A20-87 A1_ROI016-Seg1

tag: tissue structure


title: A20-87 A1_ROI014-Seg1

tag: tissue notes


title: A20-87 A1_ROI009-Seg1

tag: patient viral load


title: A20-87 A1_ROI011-Seg1

tag: roi x coordinate


title: A20-87 A1_ROI027-2PanCK-

tag: roi y coordinate


title: A20-87 A1_ROI010-Seg1

tag: segment type


title: A20-87 A1_ROI007-Seg1

tag: surface area


title: A20-87 A1_ROI004-Seg1

tag: nuclei count


title: A20-87 A1_ROI005-Seg1

tag: qc flag - low signal


title: A20-87 A1_ROI006-Seg1

tag: negative normalization factor


title: A20-87 A1_ROI008-Seg1

tag: case number


title: A20-87 A1_ROI003-Seg1

tag: patient id


title: A20-87 A1_ROI020-Seg1

tag: hyb-code


title: A20-87 A1_ROI002-Seg1

tag: assayed molecule


title: A20-87 A12_ROI020-Seg1

tag: roi


title: A20-87 A1_ROI001-Seg1

tag: segment


title: A20-49 A10 _ROI011-1PanCK+

description:
raw data file:
P1010256001230A.RCC
RCC Files from plexset are provided along with PKC. RCC files contain multiple samples collected by GeoMx. Because on-instrument processing is necessary for relationship between RCC & individual ROIs, the Raw Calibrated count matrix is included in addition to the analyzed count matrix.

tag: covid-19 ish status

value: Normal


title: A20-49 A10 _ROI012-2PanCK-

tag: tissue structure


title: A20-87 A1_ROI019-Seg1

tag: tissue notes


title: A20-49 A10 _ROI009-2PanCK-

tag: patient viral load


title: A20-49 A10 _ROI009-1PanCK+

tag: roi x coordinate


title: A20-49 A10 _ROI012-1PanCK+

tag: roi y coordinate


title: A20-49 A10 _ROI008-2PanCK-

tag: segment type


title: A20-49 A10 _ROI008-1PanCK+

tag: surface area


title: A20-49 A10 _ROI010-2PanCK-

tag: nuclei count


title: A20-49 A10 _ROI004-Seg1

tag: qc flag - low signal


title: A20-49 A10 _ROI005-Seg1

tag: negative normalization factor


title: A20-49 A10 _ROI007-1PanCK+

tag: case number


title: A20-49 A10 _ROI007-2PanCK-

tag: patient id


title: A20-49 A10 _ROI003-Seg1

tag: hyb-code


title: A20-39 A26 _ROI011-2PanCK-

tag: assayed molecule


title: A20-39 A26 _ROI012-1PanCK+

tag: roi


title: A20-39 A26 _ROI010-1PanCK+

tag: segment


title: A20-49 A10 _ROI011-2PanCK-

tag: covid-19 ish status


title: A20-39 A26 _ROI010-2PanCK-

tag: tissue structure


title: A20-49 A10 _ROI002-Seg1


title: A20-49 A10 _ROI010-1PanCK+


title: A20-49 A10 _ROI001-Seg1


title: A20-39 A26 _ROI011-1PanCK+


title: A20-39 A26 _ROI009-1PanCK+


title: A20-39 A26 _ROI009-2PanCK-


title: A20-39 A26 _ROI006-Seg1


title: A20-39 A26 _ROI007-1PanCK+


title: A20-39 A26 _ROI007-2PanCK-


title: A20-39 A26 _ROI008-2PanCK-


title: A20-39 A26 _ROI005-Seg1


title: A20-49 A10 _ROI006-Seg1


title: A20-39 A26 _ROI004-Seg1


title: A20-39 A26 _ROI002-Seg1


title: A20-39 A26 _ROI001-Seg1


title: A20-35 A11 _ROI012-2PanCK-


title: A20-35 A11 _ROI012-1PanCK+


title: A20-39 A26 _ROI012-2PanCK-


title: A20-35 A11 _ROI011-2PanCK-


title: A20-35 A11 _ROI010-2PanCK-


title: A20-35 A11 _ROI011-1PanCK+


title: A20-39 A26 _ROI008-1PanCK+


title: A20-35 A11 _ROI010-1PanCK+


title: A20-35 A11 _ROI009-2PanCK-


title: A20-35 A11 _ROI007-2PanCK-


title: A20-35 A11 _ROI008-2PanCK-


title: A20-35 A11 _ROI009-1PanCK+


title: A20-35 A11 _ROI008-1PanCK+


title: A20-35 A11 _ROI007-1PanCK+


title: A20-35 A11 _ROI004-Seg1


title: A20-35 A11 _ROI006-Seg1


title: A20-35 A11 _ROI005-Seg1


title: A20-35 A11 _ROI002-Seg1


title: A20-104 A31_ROI036-1PanCK+

description:
raw data file:
P1005210000188A.RCC
RCC Files from plexset are provided along with PKC. RCC files contain multiple samples collected by GeoMx. Because on-instrument processing is necessary for relationship between RCC & individual ROIs, the Raw Calibrated count matrix is included in addition to the analyzed count matrix.

value: Case 8

value: TRUE

value: H


title: A20-104 A31_ROI034-1PanCK+


title: A20-104 A31_ROI035-1PanCK+


title: A20-35 A11 _ROI001-Seg1


title: A20-104 A31_ROI033-1PanCK+


title: A20-104 A31_ROI031-1PanCK+


title: A20-104 A31_ROI030-1PanCK+


title: A20-104 A31_ROI028-2PanCK-


title: A20-104 A31_ROI028-1PanCK+


title: A20-104 A31_ROI027-1PanCK+


title: A20-104 A31_ROI027-2PanCK-


title: A20-104 A31_ROI032-1PanCK+


title: A20-104 A31_ROI026-2PanCK-

value: G


title: A20-104 A31_ROI025-2PanCK-


title: A20-35 A11 _ROI003-Seg1


title: A20-104 A31_ROI026-1PanCK+


title: A20-104 A31_ROI025-1PanCK+


title: A20-104 A31_ROI024-1PanCK+


title: A20-104 A31_ROI023-2PanCK-


title: A20-104 A31_ROI020-1PanCK+

value: F


title: A20-104 A31_ROI029-1PanCK+


title: A20-104 A31_ROI022-1PanCK+


title: A20-104 A31_ROI020-2PanCK-


title: A20-104 A31_ROI019-2PanCK-


title: A20-104 A31_ROI017-2PanCK-


title: A20-104 A31_ROI019-1PanCK+


title: A20-104 A31_ROI021-2PanCK-


title: A20-104 A31_ROI021-1PanCK+


title: A20-104 A31_ROI018-2PanCK-


title: A20-104 A31_ROI022-2PanCK-


title: A20-104 A31_ROI023-1PanCK+


title: A20-104 A31_ROI016-Seg1


title: A20-104 A31_ROI018-1PanCK+


title: A20-104 A31_ROI015-Seg1


title: A20-104 A31_ROI017-1PanCK+


title: A20-104 A31_ROI014-Seg1


title: A20-104 A31_ROI012-Seg1

value: E


title: A20-104 A31_ROI013-Seg1

value: FALSE


title: A20-104 A31_ROI010-Seg1


title: A20-104 A31_ROI024-2PanCK-


title: A20-104 A31_ROI008-Seg1


title: A20-104 A31_ROI006-Seg1


title: A20-104 A31_ROI007-Seg1


title: A20-104 A31_ROI009-Seg1


title: A20-104 A31_ROI005-Seg1


title: A20-104 A31_ROI001-Seg1


title: A20-102 A40_ROI031-1PanCK+

value: Case 7


title: A20-102 A40_ROI031-2PanCK-


title: A20-102 A40_ROI030-2PanCK-


title: A20-102 A40_ROI032-2PanCK-


title: A20-104 A31_ROI002-Seg1

value: Geometric


title: A20-104 A31_ROI011-Seg1


title: A20-102 A40_ROI025-2PanCK-

value: C


title: A20-102 A40_ROI025-1PanCK+

value: DNA-oligonucleotide barcode


title: A20-104 A31_ROI003-Seg1


title: A20-104 A31_ROI004-Seg1


title: A20-102 A40_ROI030-1PanCK+


title: A20-102 A40_ROI028-1PanCK+


title: A20-102 A40_ROI027-2PanCK-


title: A20-102 A40_ROI026-2PanCK-


title: A20-102 A40_ROI027-1PanCK+


title: A20-102 A40_ROI032-1PanCK+


title: A20-102 A40_ROI029-1PanCK+


title: A20-102 A40_ROI029-2PanCK-


title: A20-102 A40_ROI026-1PanCK+


title: A20-102 A40_ROI023-2PanCK-


title: A20-102 A40_ROI024-1PanCK+


title: A20-102 A40_ROI021-1PanCK+


title: A20-102 A40_ROI022-1PanCK+


title: A20-102 A40_ROI022-2PanCK-


title: A20-102 A40_ROI024-2PanCK-


title: A20-102 A40_ROI028-2PanCK-


title: A20-102 A40_ROI017-2PanCK-

value: B


title: A20-102 A40_ROI019-1PanCK+


title: A20-102 A40_ROI018-1PanCK+


title: A20-102 A40_ROI017-1PanCK+


title: A20-102 A40_ROI023-1PanCK+


title: A20-102 A40_ROI021-2PanCK-


title: A20-102 A40_ROI020-2PanCK-


title: A20-102 A40_ROI019-2PanCK-


title: A20-102 A40_ROI020-1PanCK+


title: A20-102 A40_ROI016-Seg1


title: A20-102 A40_ROI018-2PanCK-


title: A20-102 A40_ROI015-Seg1


title: A20-102 A40_ROI014-Seg1


title: A20-102 A40_ROI011-Seg1


title: A20-102 A40_ROI013-Seg1


title: A20-102 A40_ROI010-Seg1


title: A20-102 A40_ROI008-Seg1


title: A20-102 A40_ROI007-Seg1


title: A20-102 A40_ROI012-Seg1


title: A20-102 A40_ROI009-Seg1


title: A20-102 A40_ROI006-Seg1


title: A20-102 A40_ROI005-Seg1


title: A20-102 A40_ROI004-Seg1


title: A20-102 A40_ROI003-Seg1


title: A20-102 A40_ROI001-Seg1


title: A20-102 A40_ROI002-Seg1


title: A20-39 A26 _ROI003-Seg1


title: earlyOA145

status: Public on Oct 07 2020

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample.
UMI tags are extracted from raw files using UMI-tools software to remove duplicates in a later stage and aid in exact counting of miRNA reads.
The first round of alignment using Bowtie1 is performed against human miRBase (v22.1), and then unaligned reads from this step are aligned to the human reference genome to obtain reads falling in miRBase chromosomal coordinates only.
UMI-based counts, for each miRNA per sample, are generated from both these alignments and summed to generate a final table of miRNA expression levels for each sample.
Inference is performed on the raw counts using a negative binomial regression estimated by quasi-likelihood with trended dispersion and normalized by total aligned sequences.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1 combined tab-delimited text file includes raw count values for each Sample.

source_name: early OA_plasma

growth_protocol: No growth

extract_protocol:
RNA is extracted from 200 µL of human plasma using the QIAcube following Qiagen's instructions for sample setup of the miRNeasy Serum/Plasma Advanced Kit (Cat #217204).
miRNA libraries are prepared using QIAseq miRNA Library Kit optimized for biofluid samples (QIAseq miRNA, Cat # 331505). Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
Libraries are multiplexed and sequenced on Illumina NextSeq550 to generate 75bp SE UMI-tagged reads.

tag: gender

value: FEMALE

tag: Stage

value: early OA

tag: tissue

value: plasma

tag: molecule subtype

value: miRNA


title: earlyOA149


title: lateOA779

source_name: late OA_plasma

value: MALE

value: late OA


title: earlyOA124


title: lateOA784


title: earlyOA77


title: lateOA929


title: lateOA1068


title: earlyOA151


title: lateOA875


title: lateOA1033


title: lateOA754


title: earlyOA168


title: lateOA825


title: lateOA1140


title: lateOA748


title: earlyOA109


title: earlyOA102


title: earlyOA98


title: lateOA316R


title: lateOA1057R


title: lateOA105R


title: lateOA1009


title: lateOA998


title: lateOA968


title: lateOA903


title: earlyOA121


title: earlyOA116


title: earlyOA115W


title: earlyOA112


title: earlyOA58R


title: lateOA854


title: earlyOA53R


title: earlyOA54R


title: earlyOA56R


title: lateOA904


title: lateOA121


title: earlyOA150


title: lateOA425


title: earlyOA50


title: lateOA249


title: lateOA927


title: lateOA138R


title: lateOA251


title: earlyOA46


title: earlyOA161


title: lateOA48


title: lateOA341


title: lateOA305


title: lateOA40


title: lateOA506


title: lateOA259


title: earlyOA115


title: earlyOA107


title: earlyOA156


title: lateOA675


title: earlyOA19


title: lateOA65


title: earlyOA100


title: earlyOA101


title: lateOA275


title: lateOA69


title: lateOA97


title: earlyOA138


title: earlyOA93


title: lateOA411


title: lateOA370


title: lateOA77


title: lateOA141


title: earlyOA63


title: earlyOA31


title: lateOA280


title: earlyOA103


title: earlyOA88


title: earlyOA78


title: lateOA100


title: lateOA25


title: lateOA273


title: lateOA44


title: lateOA93


title: lateOA111


title: lateOA342


title: lateOA419


title: earlyOA30


title: earlyOA76


title: earlyOA29


title: Balb/c_4T1-ko54

status: Public on Jul 20 2020

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of read counts per gene

source_name: TNBC cell line

growth_protocol: 4T1 cells were grown in either NSG or Balb/c mice (injected into the fat pad) for up to 20 days and tumors were harvested

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; DNAse digestion was done
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4T1 cells were either wt or had CD95 knock out using CRISPR/Cas9

tag: cell type

value: TNBC Breast cancer

tag: cell line

tag: mouse host strain

value: Balb/c

tag: cell line genotype

value: CD95 knock out clone #54

tag: cell line phenotype

value: CD95 KO


title: earlyOA24


title: earlyOA28


title: earlyOA87


title: Balb/c_4T1-ko69

value: CD95 knock out clone #69


title: NSG_4T1-ko54

value: NSG

value: CD95/Fas knock out clone #54


title: NSG_4T1-Par

value: parental

value: WT


title: 749ATX

status: Public on Jun 18 2020

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample.
Cutadapt (v1.18) is used to maintain minimum read length of 25 bp post trimming of adapters as well as trimming of N’s.
Splice-aware alignment of reads using a Hierarchical Graph FM index (HGFM) method is performed using HISAT2 software (v2.1.0) with parameters (--rna-strandness RF –dta) against human reference genome (vGRCh38).
To assemble the aligned reads into transcripts, StringTie software (v1.3.5) was used with parameters (--rf assuming it was a stranded library fr-firststrand).
To obtain the abundance of each of these transcripts based only on the known reference genome and transcriptome, StringTie was run again using different parameters (-e -B -G referencetranscripts.gtf) to generate output of Ballgown software as compatible table files.
A script named ‘prepDE.py’ by StringTie software was used to extract the read count information.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1 tab-delimited text file includes raw count values for each Sample.

source_name: Knee OA cartilage

growth_protocol: Chondrocytes are dissociated from OA cartilage of 4 separate patients undergoing total knee replacement surgery (Kellgren-Lawrence Grade III/IV) by sequential enzymatic digestion. Sub-confluent primary chondrocytes are passaged once (P1) and seeded in 6-well plates at a density of 3 × 105 in DMEM with 10% FBS.

extract_protocol:
Total RNA is extracted from vehicle or ATX-treated cells (n=4 per group) by standard Trizol method and quantified using the Qubit RNA BR assay (Denovix). Quality of RNA is assessed using the Agilent RNA Nano chips on a Bioanalyzer instrument. For all the samples, RNA integrity number (RIN) was >9.
mRNA libraries are prepared from 200 ηg total RNA  using the TruSeq Stranded mRNA library preparation kit (Illumina Cat# 20020594) as per manufacturer’s recommendations.  Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
Libraries are prepared for sequencing (volumetrically pooled, diluted and denatured): 75 paired end read-cycles on an Illumina NextSeq 550 sequencer.

treatment_protocol: Once the chondrocytes reach 80% confluency (~48h), cells are treated with 10 μM ATX inhibitor (PF-8380, Pfizer) or  vehicle (0.001% dimethyl sulphoxide) for 24 h.

value: Knee OA cartilage

tag: cells

value: primary chondrocytes

tag: treatment

value: 10 μM ATX inhibitor (PF-8380) for 24 h


title: A2058_scRNAseq

status: Public on Jun 22 2020

city: perth

first: Carlos

middle: A

last: Aya-bonilla

address: 32 kinship street

country: Australia

institute: Telethon Kids Institute

data_processing:
Bcl files were processed by the Cell Ranger software 2..0.2 using standard settings. A total of 2714 cells/barcodes passed filter.
Genome_build: hg19

source_name: Origin: ATCC

growth_protocol: A2058 cell line was grown in a media composed of Dulbecco’s modified Eagle’s (DMEM) medium (Thermo Fischer Scientific), 10% fetal calf serum (FCS) (Thermo Fischer Scientific) and 1% Pencillin-Streptavadin (Thermo Fischer Scientific) at 37°C in 5% CO2 atmosphere. Cells were passaged when ~80% confluent, twice a week using 5 mM EDTA.

extract_protocol:
Single cell libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v2 (10X Genomics). Library QC  was performed on a Bioanalyzer platform using the High sensitivity DNA kit (Agilent)
Library was sequenced on a NextSeq500 High Output run (26bp, 8bp, 98bp).

treatment_protocol: A2058 cells were harvested at ~80 % confluency by incubation with TrypLE Express reagent (Thermo Fischer Scientific). Cell viability and count were determined by Trypan blue staining using a hemocytometer. Single cell suspensions were filtered and 4513 cells were loaded onto a Chromium™ Single Cell A Chip.

value: Cultured melanoma cells


title: Balb/c_4T1-Par


title: NSG_4T1-ko69


title: earlyOA64

value: FEMALE

value: early OA

value: plasma


title: lateOA476

value: late OA

value: miRNA


title: 810CTL

value: 0.001% DMSO for 24 h


title: 810ATX


title: 766ATX


title: 789CTL


title: 766CTL


title: Balb/c_4T1-vCas9

value: TNBC Breast cancer

value: Balb/c

value: stably expressing vCas9


title: PB_HSC_21: CD71+ PB HSC Donor 4

status: Public on May 01 2020

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
gsnap version 2015-09-29 was used to map reads onto the human reference genome GRCh38. Parameters used: -A sam -B 5 -t 24 -n 1 -Q -N 1. The result output would be in the format of sam files.
A python HTSeq (version 0.5.3p3) was used to generate read counts text files using the output of gsnap sam files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: HTSeq counts (.csv)

source_name: peripheral blood derived CD71+ haematopoietic stem cells

extract_protocol:
Within CD34+ CD38- CD45RA- HSC/MPPs (purified as in Notta et al., Science 2011), we defined 2 subsets as follows:  CD71+ CD34lo cells (CD19- CD38- CD45RA- CD71+ CD34lo) and CD71- CD34hi cells (CD19- CD38- CD45RA- CD71+ CD34lo). To obtain samples for RNA-seq, subsets were purified from CD34+ enriched non-mobilised PB samples from platelet apheresis cones by FACS. 20 cells were directly sorted into lysis buffer according to the Smart-seq2 protocol published by Picelli et al., Nat. Protocol 2014.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fresh human peripheral blood

tag: donor

value: Donor 4

value: single cell CD71+ HSC


title: PB_HSC_20: CD71+ PB HSC Donor 4


title: PB_HSC_19: CD71+ PB HSC Donor 4


title: PB_HSC_18: CD71- PB HSC Donor 1

source_name: peripheral blood derived CD71- haematopoietic stem cells

value: Donor 1

value: single cell CD71- HSC


title: PB_HSC_23: CD71- PB HSC Donor 4


title: NSG_4T1-vCas9

value: NSG

value: WT


title: 749CTL

value: Knee OA cartilage

value: primary chondrocytes


title: 789ATX

value: 10 μM ATX inhibitor (PF-8380) for 24 h


title: PB_HSC_17: CD71- PB HSC Donor 1


title: PB_HSC_24: CD71- PB HSC Donor 4


title: PB_HSC_15: CD71+ PB HSC Donor 1


title: PB_HSC_14: CD71+ PB HSC Donor 1


title: PB_HSC_13: CD71+ PB HSC Donor 1


title: PB_HSC_07: CD71+ PB HSC Donor 3

value: Donor 3


title: PB_HSC_12: CD71- PB HSC Donor 3


title: PB_HSC_04: CD71- PB HSC Donor 2

value: Donor 2


title: PB_HSC_11: CD71- PB HSC Donor 3


title: PB_HSC_22: CD71- PB HSC Donor 4


title: PB_HSC_10: CD71- PB HSC Donor 3


title: PB_HSC_08: CD71+ PB HSC Donor 3


title: PB_HSC_06: CD71- PB HSC Donor 2


title: PB_HSC_05: CD71- PB HSC Donor 2


title: PB_HSC_02: CD71+ PB HSC Donor 2


title: PB_HSC_09: CD71+ PB HSC Donor 3


title: PB_HSC_01: CD71+ PB HSC Donor 2


title: PB_HSC_03: CD71+ PB HSC Donor 2


title: PB_HSC_16: CD71- PB HSC Donor 1


title: 14_microRNA: Kidney_male_nephrectomized_microRNA_rep4

status: Public on Apr 01 2020

type: RNA

city: Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa, JAPAN

first: Kohei

last: Matsushita

country: Japan

institute: National Institute of Health Sciences

hyb_protocol: We followed protocol of miRNA Complete Labeling Reagent and Hyb Kit (Agilent)

scan_protocol: We followed protocol of G2565BA microarray scanner (Agilent)

data_processing: Data acquisition and normalization were used Feature Extraction Software

organism: Rattus norvegicus

source_name: Right kidney_male_nephrectomized_after 2 day_microRNA

extract_protocol: We followed protocol of miRNeasy Mini Kit (Qiagen)

tag: strain

value: male

tag: age

value: kidney

tag: processing

value: nephrectomized


title: 4_microRNA: Kidney_male_sham operated_microRNA_rep4

source_name: Right kidney_male_sham operated_after 1 day_microRNA

label_protocol: We followed protocol of miRNA Complete Labeling Reagent and Hyb Kit (Agilent)

value: sham


title: 12_microRNA: Kidney_male_nephrectomized_microRNA_rep2


title: 32_mRNA: Kidney_female_nephrectomized_mRNA_rep2

hyb_protocol: We followed protocol of Gene Expression Hybridazation Kit (Agilent)

source_name: Right kidney_female_nephrectomized_after 2 day_mRNA

label_protocol: We followed protocol of Low Input Quick Amp Labeling Kit (Agilent)

extract_protocol: We followed protocol of RNeasy Mini Kit (Qiagen)

value: female


title: 34_mRNA: Kidney_female_nephrectomized_mRNA_rep4


title: 13_microRNA: Kidney_male_nephrectomized_microRNA_rep3


title: 24_mRNA: Kidney_female_sham operated_mRNA_rep4

source_name: Right kidney_female_sham operated_after 1 day_mRNA


title: 31_mRNA: Kidney_female_nephrectomized_mRNA_rep1


title: 3_microRNA: Kidney_male_sham operated_microRNA_rep3


title: 22_mRNA: Kidney_female_sham operated_mRNA_rep2


title: 11_microRNA: Kidney_male_nephrectomized_microRNA_rep1


title: 12_mRNA: Kidney_male_nephrectomized_mRNA_rep2

source_name: Right kidney_male_nephrectomized_after 2 day_mRNA


title: 33_mRNA: Kidney_female_nephrectomized_mRNA_rep3


title: 23_mRNA: Kidney_female_sham operated_mRNA_rep3


title: 1_microRNA: Kidney_male_sham operated_microRNA_rep1


title: 13_mRNA: Kidney_male_nephrectomized_mRNA_rep3


title: 3_mRNA: Kidney_male_sham operated_mRNA_rep3

source_name: Right kidney_male_sham operated_after 1 day_mRNA


title: 21_mRNA: Kidney_female_sham operated_mRNA_rep1


title: EpB2_WT1

status: Public on Dec 03 2019

city: Madrid

first: Jose Luis

last: de la Pompa

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Reads were pre-processed with a pipeline that used cutadapt v1.6 to remove Illumina adaptors, and FastQC to perform quality controls after each step.
Processed reads were mapped on the transcriptome and quantified using RSEM v1.2.3.
Genome_build: GRCm38, Ensembl genebuild 76
Supplementary_files_format_and_content: matrix_table.xls files contain ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

molecule: polyA RNA

source_name: Heart

growth_protocol: Experiments were conducted with WT and mutant mouse embryos at E12.5, E15.5 and E16.5.

extract_protocol:
RNA from whole hearts, collected at E12.5 from WT and Jag1Flox;Nfatc1-Cre and from WT and Delta4Flox;Nfatc1-Cre embryos, was isolated with the Arcturus Picopure RNA isolation kit (Applied Biosystems).   RNA from ventricles, collected at E15.5 from WT and D4Cdh5-CreER, from WT and Delta4GOF;Tie2-Cre and from E16.6 WT and Efnb2Flox;Nfatc1-Cre embryos was isolated with RNA Isolation Kit: RNeasy.
Libraries were prepared using the NEBNext Ultra RNA Library preparation kit (New England Biolabs)

value: Heart ventricles

tag: genotype

tag: developmental stage


title: EpB2_WT3


title: 2_microRNA: Kidney_male_sham operated_microRNA_rep2

tag: gender


title: EpB2_WT5


title: Epb2_KO3


title: 11_mRNA: Kidney_male_nephrectomized_mRNA_rep1


title: Epb2_KO2


title: D4Gof_WT4


title: D4Gof_TG4


title: 2_mRNA: Kidney_male_sham operated_mRNA_rep2


title: D4VE_WT2


title: D4VE_WT4


title: 14_mRNA: Kidney_male_nephrectomized_mRNA_rep4


title: 4_mRNA: Kidney_male_sham operated_mRNA_rep4


title: EpB2_WT2


title: D4VE_KO3


title: Epb2_KO1


title: 1_mRNA: Kidney_male_sham operated_mRNA_rep1


title: D4Pan_WT2

value: Heart


title: D4Gof_WT3


title: D4Gof_WT2


title: J1Pan_WT3


title: Epb2_KO4


title: D4VE_WT1


title: J1Pan_WT2


title: D4Gof_TG3


title: J1Pan_KO4


title: D4VE_KO4


title: J1Pan_KO3


title: D4Pan_KO2


title: D4Pan_WT4


title: D4VE_KO2


title: D4Pan_WT3


title: J1Pan_KO1


title: D4Pan_KO1


title: D4Gof_TG2


title: J1Pan_WT4


title: AM-95: mirVana pre-miR-16_rep1

status: Public on Nov 13 2019

description: sequenced everything above 140nts

data_processing:
Sequenced reads were mapped to hg19 human genome using STAR
raw counts were calculated by HTSeq and differential expression was done with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: text sheet of raw counts values for each Sample

source_name: Derived from from Hey cells, ref: Buick, R. N., Pullano, R., and Trent, J. M. (1985). Comparative properties of five human ovarian adenocarcinoma cell lines. Cancer Res. 45: 3668 – 3676.

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: HeyA8 cells were plated at 50,000 cells per well in a 6-well plate; cells were tranfected with 25nM of either miRNAs or siRNAs, total RNA was harvested 48 hrs after treatment.

value: Ovaries

tag: treatment/infection

value: Transfected with mirVana pre-miR-16 for 48hrs

value: ovarian cancer


title: AM-94: kshv-miR-K12-6-5p_rep2

description: sequenced everything above 140nts

tag: tissue

value: Transfected with kshv-miR-K12-6-5p for 48hrs


title: AM-88: Pre-miR103-3p (seed GCAGCA)_rep2

description: sequenced everything above 140nts

value: Transfected with  Pre-miR103-3p (seed GCAGCA) for 48hrs


title: D4Gof_WT1

value: WT


title: D4VE_WT3


title: AM-80: mod-siSeed#1756 (AGCAGC)_rep2

description: sequenced everything above 140nts

value: Transfected with mod-siSeed#1756 (AGCAGC) for 48hrs


title: AM-87: Pre-miR103-3p (seed GCAGCA)_rep1

description: sequenced everything above 140nts


title: J1Pan_WT1


title: J1Pan_KO2


title: H8461

status: Public on Nov 21 2019

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

hyb_protocol: Hyb on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3.

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Array data were processed by Illumina’s BeadStudio software and expression levels exported for analysis.  The gene-wise, median correlation of each array compared to all other arrays was computed to ensure that no outliers existed within the data. The expression levels were then quantile normalized and non-informative probes (those with detection p-value >0.05 in all samples) were removed to reduce experimental noise. Ultimately, 27,167 probes were used in our analysis.

label: biotin

source_name: Human healthy donor PBMC

label_protocol: Biotin Labeling of RNA at 250ng with Ambion Illumina® TotalPrep RNA Amplification Kit(Cat #AMIL1791)

extract_protocol: Gene expression was analyzed in CD4 T cells from 6 SS patients and 3 healthy donors. Samples from patients included 3 clonal patients with a defined TCR Vbeta (85-99% of CD4 T cells) of Vbeta-7,Vbeta-13.2 and Vbeta-22. The remaining 3 samples were from non-clonal patients with medium to low circulating tumor cell burdens, as defined by 20%-50% of the patients lymphocytes identifiable as CD4+ CD26- cells and/or by one micron section analysis of fixed peripheral blood buffy coats. RNA was processed as previously described and hybridized on Illumina Human WG 8v2 microarray chips. All arrays were processed in the Wistar Institute Genomics Facility.

tag: class

value: healthy donor

tag: patient id

tag: replicates

value: no


title: H8491


title: D4Pan_WT1


title: AM-79: mod-siSeed#1756 (AGCAGC)_rep1

description: sequenced everything above 140nts

tag: cell line

tag: cell type


title: AM-96: mirVana pre-miR-16_rep2

description: sequenced everything above 140nts


title: Zfc3h1_KO_3_ESC_RPB1_ChIPseq

status: Public on Nov 12 2019

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

library_source: genomic

data_processing:
ChIPseq reads were aligned to mm10 using Bowtie, selecting only hits with the best stratum with up to two mismatches in the seed and reporting up to four good alignments per read
For visualization, ChIPseq reads were shifted to the centre of their fragment by half of fragment size deduced from the ChIP-Cor tool
SUZ12 peaks were called using MACS2 (version 2.1.1.20160309) with parameters --qvalue 0.05 --broad --broad-cutoff 0.3, ENCODE blacklisted peaks (Consortium, 2012) and low quality peaks (-log10(qvalue) ≤ 1) were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: ChIPseq reads bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: RIPseq reads bigwig files were generated using bamCoverage from deepTools (Ramírez et al., 2014), the score represents strand-specific per-base genome coverage which was normalized to the library size

molecule: genomic DNA

growth_protocol: ES cells were cultured on 0.2% gelatin coated plates in 2i/LIF containing medium.

extract_protocol:
ES cells were cross-linked by the addition of 1% formaldehyde for 10 minutes at RT before quenching with glycine. DNA was sheared to ~ 200 bp fragments by sonication using a Biorupter (Diagenode). ChIPs were carried out using 200 µg of chromatin and 2-3 µg of the indicated antibodies
ChIPseq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB) using AmpureXP beads (Beckman) for size selection.

value: Embryonic stem cells

tag: genotype/variation

tag: chip/rip antibody


title: WT_1_ESC_RPB1_ChIPSeq

value: Wildtype


title: H145


title: AM-92: mirVana control_rep2

description: sequenced everything above 140nts

value: Transfected with mirVana control for 48hrs


title: pLenti HCT116 Drosha KO cells rep 1 (# 2)

status: Public on Sep 20 2018

description:
ATCC CCL-247; Drosha KO cells provided by Narry Kim, ref: Kim Y.K., Kim B., Kim V.N. (2016). Re-evaluation of the roles of DROSHA, Export in 5, and DICER in microRNA biogenesis. Proc Natl Acad Sci U S A. 113(13):E1881-9.
Drosha k.o.

data_processing:
Sequenced reads were mapped to hg38 human genome using Tophat and bowtie2
raw counts were calculated by HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with normalized read counts for each sample comparison of interest, along with log2FoldChange values, p-values and adjusted p-values.

source_name: ATCC CCL-247; Drosha KO cells

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Cells were infected with either empty pLenti virus or pLenti-CD95L virus overnight and then treated with 3ug/mL puromycin for selection.  After selection cells were plated and total RNA harvested 50hrs after plating.

value: HCT116 Drosha k.o.

value: colon

value: Cells were infected with empty pLenti-GIII-CMV-RFP-2A-Puro and selected with 3 ug/mL puromycin for 2 days.  Total RNA was isolated 50hrs after puromycin selection.


title: pLenti HCT116 Drosha KO cells rep 2 (# 2)


title: HeyA8_FasL_50hr_rep1_sm pLenti-FasL rep 1

description:
Derived from from Hey cells, ref: Buick, R. N., Pullano, R., and Trent, J. M. (1985). Comparative properties of five human  ovarian adenocarcinoma cell lines. Cancer Res. 45: 3668 – 3676.
chr10:89,008,920-89,009,146 deletion

source_name: Derived from from Hey cell

value: HeyA8 CD95 k.o. cells clone #11

value: Cells were infected with  pLenti-GIII-CMV-RFP-2A-Puro-CD95L and selected with 3 ug/mL puromycin for 2 days.  Total RNA was isolated 50hrs after puromycin selection.


title: AM-91: mirVana control_rep1

description: sequenced everything above 140nts

value: Ovaries


title: pLenti-FasL HCT116 Drosha KO cells rep 2


title: AM-90: Pre-miR214-3p (seed CAGCAG)_rep2

description: sequenced everything above 140nts

value: Transfected with  Pre-miR214-3p (seed CAGCAG) for 48hrs


title: P106

source_name: Human cutaneous T cell lymphoma (CTCL)

value: Non-Clonal


title: P101

value: Clonal


title: AM-89: Pre-miR214-3p (seed CAGCAG)_rep1

description: sequenced everything above 140nts

value: Transfected with Pre-miR214-3p (seed CAGCAG) for 48hrs

value: ovarian cancer


title: AM-86: Pre-miR-15a-5p (seed AGCAGC)_rep2

description: sequenced everything above 140nts

value: Transfected with Pre-miR-15a-5p (seed AGCAGC) for 48hrs


title: pLenti-FasL HCT116 Drosha KO cells rep 1


title: DLD-1 si-NC

status: Public on Oct 27 2018

city: Guangzhou

first: han

last: kai

state: Guangdong

address: Dongfeng Road East

country: China

institute: Sun Yat-sen university cancer center

description:
microRNA
microRNA microarray in DLD-1 cells transfected with negative control siRNA

hyb_protocol: The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
Differentially expressed miRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed miRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts.

source_name: DLD-1 cells, negative control

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.

growth_protocol: Human colorectal carcinoma cell line DLD-1 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum.  The culture conditions were 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

treatment_protocol: DLD-1 cells transfected with circLONP2-specific siRNA or negative control siRNA were treated with Trizol reagent for further microRNA extraction.

value: colorectal carcinoma cell line

value: transfected with negative control siRNA


title: P102

value: no


title: P103


title: HeyA8_FasL_50hr_rep1_lg pLenti-FasL rep 1

description: Derived from from Hey cells, ref: Buick, R. N., Pullano, R., and Trent, J. M. (1985). Comparative properties of five human  ovarian adenocarcinoma cell lines. Cancer Res. 45: 3668 – 3676.

source_name: Derived from from Hey cells

extract_protocol:
Cells were lysed in NP40 lysis buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% (v/v) NP40, supplemented with phosphatase inhibitors) on ice for 15 minutes. The lysate was sonicated 3 times for 30 s at 60% amplitude (Sonics, VCX130) and cleared by centrifugation at 12,000g for 20 minutes. AGO1-4 were pulled down by using 500 mg of Flag-GST-T6B peptide (Hauptmann et al., 2015) and with 60 ml anti-Flag M2 magnetic beads (Sigma-Aldrich) for 2 hrs at 4°C. The pull-down was washed 3 times in NP40 lysis buffer. During the last wash, 10% of beads were removed and incubated at 95°C for 5 minutes in 2x SDS-PAGE sample buffer. Samples were run on a 4-12% SDS-PAGE and transferred to nitrocellulose membrane. The pull-down efficiency was determined by immunoblotting against AGO1 and AGO2 (Abcam 98056 and 32381). To the remaining beads 500 µl TRIzol reagent were added and the RNA extracted according to the manufacturer’s instructions. The RNA pellet was diluted in 20 µl of water. The sample was split and half of the sample was dephosphorylated with 0.5 U/μl of CIP alkaline phosphatase at 37°C for 15 min and subsequently radiolabeled with 0.5 μCi γ-32P-ATP and 1 U/μl of T4 PNK kinase for 20 min at 37°C. The AGO1-4 interacting RNAs were visualized on a 15% urea-PAGE. The remaining RNA was taken through a small RNA library preparation as previously descried (Hafner et al., 2012). Briefly, RNA was ligated with 3’ adenylated adapters and separated on a 15% denaturing urea-PAGE. The RNA corresponding to insert size of 19-35 nt was eluted from the gel, ethanol precipitated followed by 5’ adapter ligation. The samples were separated on a 12% Urea-PAGE and extracted from the gel. Reverse transcription was performed using Superscript III reverse transcriptase and the cDNA amplified by PCR. The cDNA was sequenced on Illumina HiSeq 3000. Adapter sequences: Adapter 1 – NNTGACTGTGGAATTCTCGGGTGCCAAGG; Adapter 2 – NNACACTCTGGAATTCTCGGGTGCCAAGG, Adapter 3 –  NNACAGAGTGGAATTCTCGGGTGCCAAGG, Adapter 4 – NNGCGATATGGAATTCTCGGGTGCCAAGG, Adapter 47 – NNTCTGTGTGGAATTCTCGGGTGCCAAGG, Adapter 48 – NNCAGCATTGGAATTCTCGGGTGCCAAGG, Adapter 49 – NNATAGTATGGAATTCTCGGGTGCCAAGG, Adapter 50 – NNTCATAGTGGAATTCTCGGGTGCCAAGG. RT primer sequence: GCCTTGGCACCCGAGAATTCCA; PCR primer sequences: CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA. To identify CD95L derived small RNAs all reads (4 conditions in duplicate) after removal of the adaptor sequences were BLASTED against the CD95L ORF (derived from NM_000639.1). Only reads were considered with an evalue of less than 0.05 and 100% identity across the entire length of the read.
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol. Two small RNA-SEQ sub-libraries were generated: one containing library fragments 140-150 bp in size and one containing library fragments 150-200 bp in size (both including the sequencing adator of about 130bp).
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: HeyA8 CD95 k.o clone 11 cells were infected with pLenti or pLenti-CD95L overnight; puromycin selection was done for 2 days and then cells were plated for 50hrs post selection before cells pellets were isolated and frozen; Ago pull-down was then done on the frozen pellets. Total time from addition of lentiviruses to freezing pellets was 122 hours.


title: HeyA8_FasL_50hr_rep2_lg pLenti-FasL rep 2


title: AM-82: Pre-miRNT1_rep2

description: sequenced everything above 140nts

value: Transfected with  Pre-miRNT1 for 48hrs


title: AM-81: Pre-miRNT1_rep1

description: sequenced everything above 140nts


title: AM-93: kshv-miR-K12-6-5p_rep1

description: sequenced everything above 140nts

value: Transfected with kshv-miR-K12-6-5p for 48hrs


title: AM-85: Pre-miR-15a-5p (seed AGCAGC)_rep1

description: sequenced everything above 140nts

value: Transfected with  Pre-miR-15a-5p (seed AGCAGC) for 48hrs


title: AM-78: mod-siNT1_rep2

description: sequenced everything above 140nts

value: Transfected with  mod-siNT1 for 48hrs


title: P104


title: HeyA8_pLenti_50hr_rep1_sm pLenti rep 1

value: Cells were infected with empty pLenti-GIII-CMV-RFP-2A-Puro and selected with 3 ug/mL puromycin for 2 days.  Total RNA was isolated 50hrs after puromycin selection.


title: HeyA8_pLenti_50hr_rep2_sm pLenti rep 2

value: HeyA8 CD95 k.o. cells clone #11


title: AM-77: mod-siNT1_rep1

description: sequenced everything above 140nts


title: HeyA8_FasL_50hr_rep2_sm pLenti-FasL rep 2

value: Cells were infected with  pLenti-GIII-CMV-RFP-2A-Puro-CD95L and selected with 3 ug/mL puromycin for 2 days.  Total RNA was isolated 50hrs after puromycin selection.


title: P105


title: DLD-1 si-circLONP2

description:
microRNA
microRNA microarray in DLD-1 cells transfected with circLONP2 siRNA

source_name: DLD-1 cells, circLONP2 knockdown

value: transfected with circLONP2 siRNA


title: HeyA8_vec_50hr_rep2_lg pLenti rep 2

value: Ovaries


title: HeyA8_vec_50hr_rep1_lg pLenti rep 1


title: HSC/MPP Subset2 SLX.15684.i728_i516

status: Public on Sep 14 2018

source_name: cord blood derived haematopoietic stem cells

extract_protocol:
CD49f+ HSCs were purified by FACS from CD34+ cord blood samples obtained as in Notta et al., Science 2011. Novel HSC subsets were defined as follows:  CD49f+ Subset2 cells (CD19- CD38- CD45RA- CD90+ CD49f+ CD34hi CLEC9Alo),  HSC/MPP Subset2 (CD19- CD38- CD45RA- CD34hi CLEC9Alo). Myelo-lymphoid restricted progenitors were defined as follows: LMPP (CD19- CD38- CD34+ CD45RA+ CD10-), MLP (CD19- CD38- CD34+ CD45RA+ CD10+). Single cells were directly sorted into lysis buffer according to the Smart-seq2 protocol published by Picelli et al., Nat. Protocol 2014.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human cord blood

tag: passages

value: fresh

value: single haematopoietic stem cell


title: HSC/MPP Subset2 SLX.15684.i728_i522


title: HSC/MPP Subset2 SLX.15684.i728_i520


title: HSC/MPP Subset2 SLX.15684.i727_i518


title: HSC/MPP Subset2 SLX.15684.i728_i521


title: HSC/MPP Subset2 SLX.15684.i727_i520


title: HSC/MPP Subset2 SLX.15684.i729_i518


title: HSC/MPP Subset2 SLX.15684.i729_i522


title: HSC/MPP Subset2 SLX.15684.i729_i516


title: HSC/MPP Subset2 SLX.15684.i727_i522


title: HSC/MPP Subset2 SLX.15684.i729_i521


title: HSC/MPP Subset2 SLX.15684.i727_i517


title: HSC/MPP Subset2 SLX.15684.i727_i521


title: HSC/MPP Subset2 SLX.15684.i729_i520


title: HSC/MPP Subset2 SLX.15684.i728_i513


title: HSC/MPP Subset2 SLX.15683.i719_i522


title: HSC/MPP Subset2 SLX.15683.i718_i522


title: HSC/MPP Subset2 SLX.15684.i729_i517


title: HSC/MPP Subset2 SLX.15684.i728_i518


title: HSC/MPP Subset2 SLX.15684.i727_i513


title: HSC/MPP Subset2 SLX.15684.i727_i516


title: HSC/MPP Subset2 SLX.15684.i727_i515


title: HSC/MPP Subset2 SLX.15684.i728_i515


title: HSC/MPP Subset2 SLX.15684.i729_i515


title: HSC/MPP Subset2 SLX.15684.i728_i517


title: HSC/MPP Subset2 SLX.15684.i729_i513


title: HSC/MPP Subset2 SLX.15683.i719_i513


title: HSC/MPP Subset2 SLX.15683.i718_i516


title: HSC/MPP Subset2 SLX.15683.i718_i513


title: HSC/MPP Subset2 SLX.15682.i721_i522


title: HSC/MPP Subset2 SLX.15682.i722_i521


title: HSC/MPP Subset2 SLX.15682.i721_i520


title: HSC/MPP Subset2 SLX.15683.i716_i517


title: HSC/MPP Subset2 SLX.15683.i719_i516


title: HSC/MPP Subset2 SLX.15683.i716_i521


title: HSC/MPP Subset2 SLX.15683.i719_i521


title: HSC/MPP Subset2 SLX.15683.i718_i521


title: HSC/MPP Subset2 SLX.15683.i719_i518


title: HSC/MPP Subset2 SLX.15683.i719_i517


title: HSC/MPP Subset2 SLX.15683.i718_i518


title: HSC/MPP Subset2 SLX.15683.i716_i522


title: HSC/MPP Subset2 SLX.15683.i716_i516


title: HSC/MPP Subset2 SLX.15683.i718_i515


title: HSC/MPP Subset2 SLX.15683.i718_i520


title: HSC/MPP Subset2 SLX.15683.i716_i520


title: HSC/MPP Subset2 SLX.15683.i716_i518


title: HSC/MPP Subset2 SLX.15683.i719_i520


title: HSC/MPP Subset2 SLX.15683.i719_i515


title: HSC/MPP Subset2 SLX.15683.i718_i517


title: HSC/MPP Subset2 SLX.15682.i722_i517


title: HSC/MPP Subset2 SLX.15682.i722_i522


title: HSC/MPP Subset2 SLX.15682.i720_i518


title: HSC/MPP Subset2 SLX.15683.i716_i515


title: HSC/MPP Subset2 SLX.15682.i720_i522


title: HSC/MPP Subset2 SLX.15682.i721_i521


title: HSC/MPP Subset2 SLX.15682.i720_i521


title: HSC/MPP Subset2 SLX.15682.i720_i520


title: HSC/MPP Subset2 SLX.15682.i722_i520


title: HSC/MPP Subset2 SLX.15682.i721_i518


title: HSC/MPP Subset2 SLX.15682.i721_i517


title: HSC/MPP Subset2 SLX.15682.i722_i518


title: HSC/MPP Subset2 SLX.15682.i722_i515


title: HSC/MPP Subset2 SLX.15682.i720_i513


title: HSC/MPP Subset2 SLX.15684.i707_i508


title: HSC/MPP Subset2 SLX.15682.i721_i515


title: HSC/MPP Subset2 SLX.15682.i721_i513


title: HSC/MPP Subset2 SLX.15682.i722_i513


title: HSC/MPP Subset2 SLX.15682.i720_i515


title: HSC/MPP Subset2 SLX.15682.i720_i517


title: HSC/MPP Subset2 SLX.15684.i708_i508


title: HSC/MPP Subset2 SLX.15682.i721_i516


title: HSC/MPP Subset2 SLX.15682.i722_i516


title: HSC/MPP Subset2 SLX.15682.i720_i516


title: HSC/MPP Subset2 SLX.15684.i709_i507


title: HSC/MPP Subset2 SLX.15684.i708_i506


title: HSC/MPP Subset2 SLX.15684.i709_i506


title: HSC/MPP Subset2 SLX.15684.i709_i508


title: HSC/MPP Subset2 SLX.15684.i707_i507


title: HSC/MPP Subset2 SLX.15684.i709_i505


title: HSC/MPP Subset2 SLX.15684.i707_i506


title: HSC/MPP Subset2 SLX.15684.i707_i505


title: HSC/MPP Subset2 SLX.15684.i708_i505


title: HSC/MPP Subset2 SLX.15684.i709_i504


title: HSC/MPP Subset2 SLX.15684.i707_i504


title: HSC/MPP Subset2 SLX.15684.i709_i503


title: HSC/MPP Subset2 SLX.15684.i707_i503


title: HSC/MPP Subset2 SLX.15684.i708_i507


title: HSC/MPP Subset2 SLX.15684.i708_i502


title: HSC/MPP Subset2 SLX.15684.i709_i502


title: HSC/MPP Subset2 SLX.15684.i709_i517


title: HSC/MPP Subset2 SLX.15684.i707_i517


title: HSC/MPP Subset2 SLX.15684.i708_i517


title: HSC/MPP Subset2 SLX.15683.i712_i508


title: HSC/MPP Subset2 SLX.15683.i711_i508


title: HSC/MPP Subset2 SLX.15683.i710_i508


title: HSC/MPP Subset2 SLX.15683.i712_i507


title: HSC/MPP Subset2 SLX.15683.i712_i505


title: HSC/MPP Subset2 SLX.15684.i707_i502


title: HSC/MPP Subset2 SLX.15683.i710_i507


title: HSC/MPP Subset2 SLX.15683.i711_i506


title: HSC/MPP Subset2 SLX.15683.i710_i506


title: HSC/MPP Subset2 SLX.15683.i711_i507


title: HSC/MPP Subset2 SLX.15683.i712_i504


title: HSC/MPP Subset2 SLX.15683.i710_i505


title: HSC/MPP Subset2 SLX.15683.i712_i506


title: HSC/MPP Subset2 SLX.15683.i711_i504


title: HSC/MPP Subset2 SLX.15683.i711_i503


title: HSC/MPP Subset2 SLX.15683.i710_i504


title: HSC/MPP Subset2 SLX.15683.i712_i502


title: HSC/MPP Subset2 SLX.15683.i712_i503


title: HSC/MPP Subset2 SLX.15683.i710_i503


title: HSC/MPP Subset2 SLX.15683.i711_i502


title: HSC/MPP Subset2 SLX.15683.i710_i502


title: HSC/MPP Subset2 SLX.15683.i712_i517


title: HSC/MPP Subset2 SLX.15683.i710_i517


title: HSC/MPP Subset2 SLX.15683.i711_i517


title: HSC/MPP Subset2 SLX.15683.i711_i505


title: HSC/MPP Subset2 SLX.15682.i703_i507


title: HSC/MPP Subset2 SLX.15682.i702_i507


title: HSC/MPP Subset2 SLX.15682.i703_i508


title: HSC/MPP Subset2 SLX.15682.i701_i507


title: HSC/MPP Subset2 SLX.15682.i703_i506


title: HSC/MPP Subset2 SLX.15682.i701_i506


title: HSC/MPP Subset2 SLX.15682.i701_i508


title: HSC/MPP Subset2 SLX.15682.i702_i508


title: HSC/MPP Subset2 SLX.15682.i702_i505


title: HSC/MPP Subset2 SLX.15682.i703_i504


title: HSC/MPP Subset2 SLX.15682.i701_i505


title: HSC/MPP Subset2 SLX.15682.i703_i503


title: HSC/MPP Subset2 SLX.15682.i701_i504


title: HSC/MPP Subset2 SLX.15682.i703_i505


title: HSC/MPP Subset2 SLX.15682.i702_i506


title: HSC/MPP Subset2 SLX.15682.i702_i502


title: HSC/MPP Subset2 SLX.15682.i703_i502


title: HSC/MPP Subset2 SLX.15682.i703_i517


title: HSC/MPP Subset2 SLX.15682.i701_i502


title: HSC/MPP Subset2 SLX.15682.i702_i503


title: MLP SLX.15684.i721_i522

source_name: cord blood derived multi lymphoid progenitors

value: single cell multi lymphoid progenitor


title: MLP SLX.15684.i720_i522


title: HSC/MPP Subset2 SLX.15682.i702_i517


title: MLP SLX.15684.i722_i521


title: MLP SLX.15684.i721_i521


title: HSC/MPP Subset2 SLX.15682.i702_i504


title: MLP SLX.15684.i720_i521


title: MLP SLX.15684.i721_i520


title: MLP SLX.15684.i722_i518


title: MLP SLX.15684.i722_i520


title: MLP SLX.15684.i722_i522


title: HSC/MPP Subset2 SLX.15682.i701_i503


title: MLP SLX.15684.i720_i520


title: MLP SLX.15684.i720_i516


title: MLP SLX.15684.i720_i517


title: MLP SLX.15684.i721_i517


title: MLP SLX.15684.i721_i515


title: MLP SLX.15684.i722_i517


title: MLP SLX.15684.i720_i513


title: MLP SLX.15684.i720_i515


title: MLP SLX.15684.i721_i513


title: MLP SLX.15684.i722_i513


title: MLP SLX.15684.i721_i516


title: MLP SLX.15683.i726_i522


title: MLP SLX.15683.i724_i522


title: MLP SLX.15683.i726_i521


title: MLP SLX.15683.i724_i521


title: MLP SLX.15683.i723_i521


title: MLP SLX.15684.i722_i516


title: MLP SLX.15683.i726_i520


title: MLP SLX.15684.i720_i518


title: MLP SLX.15684.i721_i518


title: MLP SLX.15684.i722_i515


title: MLP SLX.15683.i724_i518


title: MLP SLX.15683.i723_i518


title: MLP SLX.15683.i723_i520


title: MLP SLX.15683.i726_i517


title: MLP SLX.15683.i723_i517


title: MLP SLX.15683.i723_i516


title: MLP SLX.15683.i726_i518


title: MLP SLX.15683.i724_i517


title: MLP SLX.15683.i723_i522


title: MLP SLX.15683.i724_i516


title: MLP SLX.15683.i723_i515


title: MLP SLX.15683.i723_i513


title: MLP SLX.15683.i724_i515


title: MLP SLX.15683.i726_i515


title: MLP SLX.15683.i726_i516


title: MLP SLX.15682.i729_i522


title: MLP SLX.15682.i728_i522


title: MLP SLX.15682.i727_i522


title: MLP SLX.15682.i729_i521


title: MLP SLX.15682.i728_i521


title: MLP SLX.15683.i724_i520


title: MLP SLX.15682.i727_i521


title: MLP SLX.15682.i728_i520


title: MLP SLX.15682.i727_i520


title: MLP SLX.15682.i729_i520


title: MLP SLX.15682.i729_i518


title: MLP SLX.15683.i726_i513


title: MLP SLX.15683.i724_i513


title: MLP SLX.15682.i727_i518


title: MLP SLX.15682.i729_i516


title: MLP SLX.15682.i727_i517


title: MLP SLX.15682.i727_i515


title: MLP SLX.15682.i728_i515


title: MLP SLX.15682.i729_i515


title: MLP SLX.15682.i728_i517


title: MLP SLX.15682.i727_i516


title: MLP SLX.15682.i729_i517


title: MLP SLX.15682.i728_i516


title: MLP SLX.15684.i703_i508


title: MLP SLX.15682.i727_i513


title: MLP SLX.15684.i701_i508


title: MLP SLX.15684.i701_i507


title: MLP SLX.15684.i702_i507


title: MLP SLX.15684.i703_i506


title: MLP SLX.15684.i702_i505


title: MLP SLX.15684.i702_i506


title: MLP SLX.15684.i703_i505


title: MLP SLX.15684.i701_i506


title: MLP SLX.15684.i701_i505


title: MLP SLX.15682.i728_i518


title: MLP SLX.15684.i703_i504


title: MLP SLX.15682.i728_i513


title: MLP SLX.15684.i702_i504


title: MLP SLX.15682.i729_i513


title: MLP SLX.15684.i701_i502


title: MLP SLX.15684.i703_i503


title: MLP SLX.15684.i701_i503


title: MLP SLX.15684.i703_i502


title: MLP SLX.15684.i702_i508


title: MLP SLX.15683.i705_i508


title: MLP SLX.15684.i702_i502


title: MLP SLX.15684.i703_i517


title: MLP SLX.15684.i703_i507


title: MLP SLX.15683.i706_i507


title: MLP SLX.15684.i701_i504


title: MLP SLX.15683.i705_i507


title: MLP SLX.15683.i706_i508


title: MLP SLX.15683.i704_i507


title: MLP SLX.15683.i706_i506


title: MLP SLX.15683.i705_i506


title: MLP SLX.15683.i704_i506


title: MLP SLX.15683.i706_i505


title: MLP SLX.15683.i704_i505


title: MLP SLX.15683.i705_i505


title: MLP SLX.15683.i705_i504


title: MLP SLX.15683.i706_i504


title: MLP SLX.15683.i706_i503


title: MLP SLX.15683.i705_i503


title: MLP SLX.15684.i702_i503


title: MLP SLX.15684.i702_i517


title: MLP SLX.15683.i704_i504


title: MLP SLX.15683.i704_i508


title: MLP SLX.15683.i704_i503


title: MLP SLX.15683.i706_i517


title: MLP SLX.15683.i705_i517


title: MLP SLX.15683.i705_i502


title: MLP SLX.15683.i704_i517


title: MLP SLX.15682.i707_i508


title: MLP SLX.15682.i708_i508


title: MLP SLX.15682.i709_i507


title: MLP SLX.15682.i707_i507


title: MLP SLX.15682.i708_i507


title: MLP SLX.15682.i708_i506


title: MLP SLX.15682.i709_i505


title: MLP SLX.15682.i708_i505


title: MLP SLX.15682.i707_i506


title: MLP SLX.15682.i707_i505


title: MLP SLX.15682.i709_i504


title: MLP SLX.15683.i706_i502


title: MLP SLX.15682.i708_i504


title: MLP SLX.15683.i704_i502


title: MLP SLX.15682.i707_i502


title: MLP SLX.15682.i707_i503


title: MLP SLX.15682.i708_i503


title: MLP SLX.15682.i708_i502


title: MLP SLX.15682.i707_i504


title: MLP SLX.15682.i709_i503


title: MLP SLX.15682.i709_i502


title: MLP SLX.15682.i709_i508


title: MLP SLX.15682.i708_i517


title: LMPP SLX.15684.i718_i521

source_name: cord blood derived lymphoid primed multipotent progenitors

value: single cell lymphoid primed multipotent progenitor


title: LMPP SLX.15684.i716_i522


title: MLP SLX.15682.i709_i517


title: MLP SLX.15682.i709_i506


title: MLP SLX.15682.i707_i517


title: LMPP SLX.15684.i719_i521


title: LMPP SLX.15684.i718_i522


title: LMPP SLX.15684.i716_i521


title: LMPP SLX.15684.i718_i520


title: LMPP SLX.15684.i716_i520


title: LMPP SLX.15684.i718_i518


title: LMPP SLX.15684.i719_i520


title: LMPP SLX.15684.i716_i518


title: LMPP SLX.15684.i719_i518


title: LMPP SLX.15684.i719_i517


title: LMPP SLX.15684.i718_i517


title: LMPP SLX.15684.i719_i516


title: LMPP SLX.15684.i716_i517


title: LMPP SLX.15684.i718_i516


title: LMPP SLX.15684.i719_i515


title: LMPP SLX.15684.i716_i516


title: LMPP SLX.15684.i719_i522


title: LMPP SLX.15684.i718_i515


title: LMPP SLX.15684.i716_i515


title: LMPP SLX.15684.i719_i513


title: LMPP SLX.15683.i721_i522


title: LMPP SLX.15683.i722_i522


title: LMPP SLX.15684.i718_i513


title: LMPP SLX.15683.i720_i522


title: LMPP SLX.15683.i722_i521


title: LMPP SLX.15683.i722_i520


title: LMPP SLX.15683.i721_i521


title: LMPP SLX.15683.i720_i520


title: LMPP SLX.15683.i721_i520


title: LMPP SLX.15683.i720_i518


title: LMPP SLX.15683.i722_i517


title: LMPP SLX.15683.i721_i518


title: LMPP SLX.15683.i721_i517


title: LMPP SLX.15683.i720_i521


title: LMPP SLX.15683.i722_i516


title: LMPP SLX.15683.i720_i517


title: LMPP SLX.15683.i721_i516


title: LMPP SLX.15683.i722_i515


title: LMPP SLX.15683.i721_i515


title: LMPP SLX.15683.i720_i516


title: LMPP SLX.15683.i720_i513


title: LMPP SLX.15682.i726_i522


title: LMPP SLX.15683.i720_i515


title: LMPP SLX.15683.i721_i513


title: LMPP SLX.15682.i723_i522


title: LMPP SLX.15682.i726_i521


title: LMPP SLX.15682.i724_i521


title: LMPP SLX.15683.i722_i513


title: LMPP SLX.15682.i723_i521


title: LMPP SLX.15682.i724_i522


title: LMPP SLX.15682.i726_i520


title: LMPP SLX.15682.i726_i518


title: LMPP SLX.15683.i722_i518


title: LMPP SLX.15682.i724_i520


title: LMPP SLX.15682.i724_i518


title: LMPP SLX.15682.i723_i518


title: LMPP SLX.15682.i726_i517


title: LMPP SLX.15682.i724_i517


title: LMPP SLX.15682.i724_i515


title: LMPP SLX.15682.i726_i516


title: LMPP SLX.15682.i726_i515


title: LMPP SLX.15682.i723_i515


title: LMPP SLX.15682.i723_i516


title: LMPP SLX.15682.i723_i517


title: LMPP SLX.15682.i724_i516


title: LMPP SLX.15682.i726_i513


title: LMPP SLX.15682.i724_i513


title: LMPP SLX.15684.i712_i508


title: LMPP SLX.15682.i723_i513


title: LMPP SLX.15684.i711_i508


title: LMPP SLX.15684.i710_i508


title: LMPP SLX.15684.i712_i507


title: LMPP SLX.15682.i723_i520


title: LMPP SLX.15684.i712_i506


title: LMPP SLX.15684.i710_i507


title: LMPP SLX.15684.i711_i506


title: LMPP SLX.15684.i710_i506


title: LMPP SLX.15684.i711_i504


title: LMPP SLX.15684.i712_i505


title: LMPP SLX.15684.i711_i505


title: LMPP SLX.15684.i710_i505


title: LMPP SLX.15684.i710_i504


title: LMPP SLX.15684.i711_i507


title: LMPP SLX.15684.i711_i503


title: LMPP SLX.15684.i712_i503


title: LMPP SLX.15684.i710_i503


title: LMPP SLX.15684.i711_i517


title: LMPP SLX.15684.i710_i502


title: LMPP SLX.15684.i712_i502


title: LMPP SLX.15684.i711_i502


title: LMPP SLX.15684.i710_i517


title: LMPP SLX.15683.i703_i508


title: LMPP SLX.15683.i701_i508


title: LMPP SLX.15683.i702_i508


title: LMPP SLX.15683.i701_i507


title: LMPP SLX.15683.i703_i507


title: LMPP SLX.15683.i702_i507


title: LMPP SLX.15684.i712_i517


title: LMPP SLX.15684.i712_i504


title: LMPP SLX.15683.i703_i506


title: LMPP SLX.15683.i702_i506


title: LMPP SLX.15683.i703_i505


title: LMPP SLX.15683.i701_i505


title: LMPP SLX.15683.i701_i506


title: LMPP SLX.15683.i703_i504


title: LMPP SLX.15683.i702_i505


title: LMPP SLX.15683.i703_i503


title: LMPP SLX.15683.i701_i504


title: LMPP SLX.15683.i702_i504


title: LMPP SLX.15683.i701_i503


title: LMPP SLX.15683.i702_i503


title: LMPP SLX.15683.i702_i502


title: LMPP SLX.15683.i703_i502


title: LMPP SLX.15683.i703_i517


title: LMPP SLX.15682.i705_i508


title: LMPP SLX.15683.i701_i502


title: LMPP SLX.15682.i706_i507


title: LMPP SLX.15682.i704_i508


title: LMPP SLX.15683.i702_i517


title: LMPP SLX.15682.i705_i507


title: LMPP SLX.15682.i704_i507


title: LMPP SLX.15682.i706_i506


title: LMPP SLX.15682.i704_i506


title: LMPP SLX.15682.i706_i505


title: LMPP SLX.15682.i705_i506


title: LMPP SLX.15682.i705_i505


title: LMPP SLX.15682.i704_i505


title: LMPP SLX.15682.i706_i504


title: LMPP SLX.15682.i705_i504


title: LMPP SLX.15682.i706_i503


title: LMPP SLX.15682.i705_i503


title: LMPP SLX.15682.i704_i504


title: LMPP SLX.15682.i704_i503


title: LMPP SLX.15682.i706_i502


title: LMPP SLX.15682.i704_i502


title: LMPP SLX.15682.i705_i502


title: LMPP SLX.15682.i705_i517


title: LMPP SLX.15682.i706_i517


title: LMPP SLX.15682.i706_i508


title: LMPP SLX.15682.i704_i517


title: CD49f+ HSC Subset2 SLX.15684.i724_i522

source_name: cord blood derived CD49f+ haematopoietic stem cells

value: single cell CD49f+ HSC Subset2


title: CD49f+ HSC Subset2 SLX.15684.i724_i521


title: CD49f+ HSC Subset2 SLX.15684.i723_i521


title: CD49f+ HSC Subset2 SLX.15684.i726_i521


title: CD49f+ HSC Subset2 SLX.15684.i726_i520


title: CD49f+ HSC Subset2 SLX.15684.i724_i520


title: CD49f+ HSC Subset2 SLX.15684.i726_i518


title: CD49f+ HSC Subset2 SLX.15684.i723_i522


title: CD49f+ HSC Subset2 SLX.15684.i723_i518


title: CD49f+ HSC Subset2 SLX.15684.i724_i518


title: CD49f+ HSC Subset2 SLX.15684.i723_i520


title: CD49f+ HSC Subset2 SLX.15684.i726_i517


title: CD49f+ HSC Subset2 SLX.15684.i724_i517


title: CD49f+ HSC Subset2 SLX.15684.i726_i516


title: CD49f+ HSC Subset2 SLX.15684.i724_i516


title: CD49f+ HSC Subset2 SLX.15684.i726_i515


title: CD49f+ HSC Subset2 SLX.15684.i723_i517


title: CD49f+ HSC Subset2 SLX.15684.i723_i515


title: CD49f+ HSC Subset2 SLX.15684.i726_i513


title: CD49f+ HSC Subset2 SLX.15684.i724_i515


title: CD49f+ HSC Subset2 SLX.15683.i729_i522


title: CD49f+ HSC Subset2 SLX.15684.i726_i522


title: CD49f+ HSC Subset2 SLX.15684.i723_i516


title: CD49f+ HSC Subset2 SLX.15683.i727_i522


title: CD49f+ HSC Subset2 SLX.15683.i728_i521


title: CD49f+ HSC Subset2 SLX.15683.i727_i521


title: CD49f+ HSC Subset2 SLX.15683.i729_i520


title: CD49f+ HSC Subset2 SLX.15683.i729_i518


title: CD49f+ HSC Subset2 SLX.15683.i727_i520


title: CD49f+ HSC Subset2 SLX.15683.i728_i518


title: CD49f+ HSC Subset2 SLX.15683.i727_i517


title: CD49f+ HSC Subset2 SLX.15683.i728_i517


title: CD49f+ HSC Subset2 SLX.15683.i729_i516


title: CD49f+ HSC Subset2 SLX.15683.i728_i516


title: CD49f+ HSC Subset2 SLX.15683.i727_i516


title: CD49f+ HSC Subset2 SLX.15683.i729_i515


title: CD49f+ HSC Subset2 SLX.15683.i727_i515


title: CD49f+ HSC Subset2 SLX.15684.i724_i513


title: CD49f+ HSC Subset2 SLX.15684.i723_i513


title: CD49f+ HSC Subset2 SLX.15683.i729_i513


title: CD49f+ HSC Subset2 SLX.15683.i728_i513


title: CD49f+ HSC Subset2 SLX.15683.i727_i513


title: CD49f+ HSC Subset2 SLX.15683.i729_i521


title: CD49f+ HSC Subset2 SLX.15682.i718_i522


title: CD49f+ HSC Subset2 SLX.15682.i716_i522


title: CD49f+ HSC Subset2 SLX.15682.i719_i521


title: CD49f+ HSC Subset2 SLX.15683.i728_i522


title: CD49f+ HSC Subset2 SLX.15683.i728_i520


title: CD49f+ HSC Subset2 SLX.15682.i719_i520


title: CD49f+ HSC Subset2 SLX.15683.i727_i518


title: CD49f+ HSC Subset2 SLX.15683.i729_i517


title: CD49f+ HSC Subset2 SLX.15682.i718_i520


title: CD49f+ HSC Subset2 SLX.15682.i716_i520


title: CD49f+ HSC Subset2 SLX.15682.i719_i518


title: CD49f+ HSC Subset2 SLX.15682.i718_i518


title: CD49f+ HSC Subset2 SLX.15682.i716_i518


title: CD49f+ HSC Subset2 SLX.15683.i728_i515


title: CD49f+ HSC Subset2 SLX.15682.i719_i517


title: CD49f+ HSC Subset2 SLX.15682.i718_i517


title: CD49f+ HSC Subset2 SLX.15682.i716_i517


title: CD49f+ HSC Subset2 SLX.15682.i719_i513


title: CD49f+ HSC Subset2 SLX.15682.i719_i515


title: CD49f+ HSC Subset2 SLX.15682.i719_i516


title: CD49f+ HSC Subset2 SLX.15682.i718_i515


title: CD49f+ HSC Subset2 SLX.15682.i716_i516


title: CD49f+ HSC Subset2 SLX.15682.i716_i515


title: CD49f+ HSC Subset2 SLX.15682.i719_i522


title: CD49f+ HSC Subset2 SLX.15682.i718_i521


title: CD49f+ HSC Subset2 SLX.15684.i704_i508


title: CD49f+ HSC Subset2 SLX.15684.i705_i508


title: CD49f+ HSC Subset2 SLX.15684.i706_i508


title: CD49f+ HSC Subset2 SLX.15682.i718_i513


title: CD49f+ HSC Subset2 SLX.15684.i706_i507


title: CD49f+ HSC Subset2 SLX.15682.i716_i521


title: CD49f+ HSC Subset2 SLX.15684.i705_i507


title: CD49f+ HSC Subset2 SLX.15684.i706_i506


title: CD49f+ HSC Subset2 SLX.15684.i706_i505


title: CD49f+ HSC Subset2 SLX.15684.i704_i507


title: CD49f+ HSC Subset2 SLX.15684.i705_i506


title: CD49f+ HSC Subset2 SLX.15682.i718_i516


title: CD49f+ HSC Subset2 SLX.15684.i706_i504


title: CD49f+ HSC Subset2 SLX.15684.i705_i505


title: CD49f+ HSC Subset2 SLX.15684.i706_i503


title: CD49f+ HSC Subset2 SLX.15684.i704_i504


title: CD49f+ HSC Subset2 SLX.15684.i704_i505


title: CD49f+ HSC Subset2 SLX.15684.i705_i503


title: CD49f+ HSC Subset2 SLX.15684.i705_i504


title: CD49f+ HSC Subset2 SLX.15684.i706_i502


title: CD49f+ HSC Subset2 SLX.15684.i705_i502


title: CD49f+ HSC Subset2 SLX.15684.i706_i517


title: CD49f+ HSC Subset2 SLX.15684.i704_i502


title: CD49f+ HSC Subset2 SLX.15684.i705_i517


title: CD49f+ HSC Subset2 SLX.15684.i704_i517


title: CD49f+ HSC Subset2 SLX.15683.i708_i507


title: CD49f+ HSC Subset2 SLX.15683.i709_i507


title: CD49f+ HSC Subset2 SLX.15683.i708_i508


title: CD49f+ HSC Subset2 SLX.15683.i709_i506


title: CD49f+ HSC Subset2 SLX.15684.i704_i506


title: CD49f+ HSC Subset2 SLX.15683.i707_i507


title: CD49f+ HSC Subset2 SLX.15683.i709_i508


title: CD49f+ HSC Subset2 SLX.15683.i708_i505


title: CD49f+ HSC Subset2 SLX.15683.i709_i505


title: CD49f+ HSC Subset2 SLX.15683.i707_i506


title: CD49f+ HSC Subset2 SLX.15683.i708_i506


title: CD49f+ HSC Subset2 SLX.15683.i707_i505


title: CD49f+ HSC Subset2 SLX.15683.i709_i504


title: CD49f+ HSC Subset2 SLX.15684.i704_i503


title: CD49f+ HSC Subset2 SLX.15683.i708_i503


title: CD49f+ HSC Subset2 SLX.15683.i707_i503


title: CD49f+ HSC Subset2 SLX.15683.i709_i503


title: CD49f+ HSC Subset2 SLX.15683.i709_i502


title: CD49f+ HSC Subset2 SLX.15683.i708_i502


title: CD49f+ HSC Subset2 SLX.15683.i707_i502


title: CD49f+ HSC Subset2 SLX.15683.i709_i517


title: CD49f+ HSC Subset2 SLX.15683.i708_i517


title: CD49f+ HSC Subset2 SLX.15682.i712_i508


title: CD49f+ HSC Subset2 SLX.15683.i707_i508


title: CD49f+ HSC Subset2 SLX.15682.i710_i507


title: CD49f+ HSC Subset2 SLX.15682.i711_i507


title: CD49f+ HSC Subset2 SLX.15682.i710_i508


title: CD49f+ HSC Subset2 SLX.15682.i712_i507


title: CD49f+ HSC Subset2 SLX.15682.i712_i506


title: CD49f+ HSC Subset2 SLX.15683.i708_i504


title: CD49f+ HSC Subset2 SLX.15682.i710_i506


title: CD49f+ HSC Subset2 SLX.15682.i712_i505


title: CD49f+ HSC Subset2 SLX.15682.i712_i504


title: CD49f+ HSC Subset2 SLX.15682.i710_i504


title: CD49f+ HSC Subset2 SLX.15682.i711_i504


title: CD49f+ HSC Subset2 SLX.15682.i710_i505


title: CD49f+ HSC Subset2 SLX.15683.i707_i504


title: CD49f+ HSC Subset2 SLX.15682.i712_i503