title: Green receptacle R2

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

institute: University of Cordoba

hyb_protocol: 600 ng of Cy3-labeled aRNA was hybridized on an 8x60K Sure Print G3 custom microarray (Agilent Technologies). After hybridization, arrays were  washed according to the manufacturer's protocol.

scan_protocol: Arrays were scanned with an Agilent Microarray Scanner. Images and intensity data were obtained using Agilent Feature Extraction v.10.7 software.

data_processing: The microarray datas were analyzed with the software for gene expression analysis ArrayStar 5 (DNASTAR).

organism: Fragaria x ananassa

source_name: Strawberry green unripen receptacle replicate 2

label_protocol: 200 ng of total RNA of each sample was labelled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Strawberry plants (F. x ananassa) were grown in plant chamber at 25 ºC, 10.000 lux and 80% humidity and afterwards maintained in a greenhouse.

extract_protocol: Total RNA was isolated from independent strawberry fruits as stated by Asif et al. (2000). The total RNA obtained was treated with DNase I (RNase free) (Invitrogen), in accordance with the manufacturer's instructions, to remove genomic DNA contamination, after which it was purified by using the RNeasy Mini kit (Qiagen).

treatment_protocol: Fruits were harvested in green and red stages.

tag: tissue

value: Inmature fruits


title: circRNA day_0_2D - donor#3 - replicate#2

status: Public on Oct 18 2019

type: RNA

city: Davos Platz

first: Martin

middle: J

last: Stoddart

address: Clavadelerstrasse 8

country: Switzerland

institute: AO Research Institute Davos

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA 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 using the Agilent Scanner G2505C.

data_processing: Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

molecule: total RNA

organism: Homo sapiens

source_name: Human mesenchymal stromal cells from bone marrow (vertebra)

label_protocol: the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

growth_protocol: MSCs were seeded at an initial cell density of 3x103 cells/cm2 and grown until passage 2 in α-MEM with 10% MSC-qualified FBS, 100 U/mL penicillin, 100 μg/mL streptomycin and 5 ng/ml basic Fibroblast Growth Factor. Cultures were maintained at 37°C/5% CO2, and the medium was refreshed every second day.

extract_protocol: Total RNA was isolated from day 0 2D and 3D samples collected in TRIreagent following manufacturer's instructions. Briefly, 100 µl of 1-Bromo-3-chloropropane (Sigma-Aldrich, St. Louis, MO, USA) were added to TRIreagent, mixed thoroughly and the samples were centrifuged at 12000 g for 15 min at 4°C. The recovered aqueous phase was mixed with 500 µl of 2-propanol (Sigma-Aldrich) and precipitation of RNA was carried out overnight at -20°C for enhanced recovery of small RNA species. RNA pellet was then washed with 75% EtOH (Sigma-Aldrich) and resuspended in 20 µl of DEPC-treated H2O. Total RNA concentration was measured with NanoDrop 1000 (Thermo Fisher) and purity was assessed by evaluation of the A260/280 and A260/230 ratios.

treatment_protocol: Cells were further expanded in the same expansion medium. When the cells were 70% confluent, cells were collected for RNA extraction. Monolayer of cells in triplicate, grown in 25 cm2 flasks (day 0 2D), were lysed directly with 1 ml of TRIreagent. The other cells were detached with 0.05% Trypsin-EDTA and counted. For each donor, three different aliquots of 1x106 cells each (day 0 3D) were lysed in 1 ml of TRIreagent within 30 minutes from trypsinization.

tag: age of donor

value: 55 years

tag: sex of donor

value: Female

tag: cell status

value: monolayer adhesion


title: breast cancer_1 [hoae149]

city: Chennai

first: Rajkumar

last: T

state: Tamilnadu

address: Adyar

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

hyb_protocol: The Cy3 and Cy5 labelled aRNA was used for hybridization onto the microarray chips from Stanford Functional Genomics Facility (SFGF, Stanford, CA) containing 44,544 spots, for 16 hrs in Lucidea SlidePro hybridization chamber. (GE Healthcare) at 42℃. The labeling for microarray experiments was standardized using the Amino Allyl MessageAmp II aRNA amplification kit (Ambion) as per the manufacturer’s instructions. Post hybridisation slides were washed in 0.1X SSC, 1X SSC followed by 0.1X SSC and dried

scan_protocol: The slides were scanned in ProScanArray (PerkinElmer, Shelton, CT, USA). Griding was done using Scan array Express software package (version -4). The integrated or mean intensity of signal within the spot was calculated. The files were saved as GPR files.

data_processing: The Foreground Median intensity for Cy3 and Cy5, Background Median intensity for Cy3 and Cy5, spot size data were imported into BRB-ArrayTools software using the Import wizard function. Background correction was not done. Global normalization was used to median centre the log-ratios on each array in order to adjust for differences in labelling intensities of the Cy3 and Cy5 dyes

source_name: tumour tissue from a patient with breast cancer

label_protocol: 1 µg of total RNA from the tumour sample and universal RNA (Stratagene; Cat no: 74000041) were reverse transcribed using Array script at 42°C for 2 hrs to obtain cDNA using the Amino Allyl MessageAmp II aRNA amplification kit (Ambion, Austin, Tx; Cat no: AM1797). The cDNA was amplified by in-vitro transcription in the presence of T7 RNA polymerase; aRNA thus obtained was purified and quantitated in NanoDrop (NanoDrop Technologies, Wilmington, DE, USA). 20 mg of tumour aRNA was labelled using NHS ester of Cy5 dye and control universal aRNA was labelled using NHS ester of Cy3 dye

extract_protocol: Total RNA extracted from tissue samples using RNeasy RNA extraction kit (Qiagen) according to manufacturer's instructions. Quantitated using Nanodrop and quality checked using Agilent BioAnalyzer

tag: age

tag: gender

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: IDC

tag: cancer stage

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: tissue origin

value: breast

tag: sample type

value: surgery (frozen tissue)

source_name: Universal reference RNA

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: circRNA day_0_2D - donor#3 - replicate#1

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.


title: PRE1_RNAi PRE1-RNAi-A3 (F)-Cy3

country: Spain

description:
raw data file: F.txt
FaPRE1-RNAi R3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

source_name: Strawberry fruit agroinjected with the FaPRE1-RNAi construct

label_protocol: 4 µg of total RNA were label following the Two-color microarray-bases Gen Expression Analysis v. 6.5 (Agilent)

growth_protocol: Strawberry plants (F. x ananassa) used for agro-infiltration were grown in plant chamber at 25 ºC, 10.000 lux and 80% humidity and afterwards maintained in a greenhouse.

extract_protocol: Total RNA was isolated from independent strawberry floral buds, as stated by Asif et al. (2000). The total RNA obtained was treated with DNase I (RNase free) (Invitrogen), in accordance with the manufacturer's instructions, to remove genomic DNA contamination, after which it was purified by using the RNeasy Mini kit (Qiagen).

treatment_protocol: The A. tumefaciens strain AGL0 (Lazo et al., 1991), containing the pFRN-FaPRE1 was used to inject the strawberry fruit receptacles (Fragaria × ananassa), according to Hoffmann et al. (2006). A total of 15-25 strawberry plants and 30-40 agroinfiltrated fruits were inoculated and analysed, respectively. As control, fruits agroinfiltrated with the empty pFRN vector were used.

tag: genotype/variation

value: overexpressing FaPRE1


title: apparent normal_6 [hov223]

source_name: apparent normal from a patient with benign phyllodes tumour

value: Morphologically normal

value: Apparent normal


title: d_whiA_Exponential_2

type: SRA

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description: ribosomal RNA depleted

library_source: transcriptomic

data_processing:
Torrent Suite version 5.2.2 was used for basecalling.
The sequenced reads were trimmed for adaptor sequences.
The sequenced reads were mapped using Tmap (mapall -f $db -r $readPath/$i.bam -g 3 -a 1 -n 30 -v stage1 map1 map2 map3), and counted using Htseq (-a 10 -t gene -i Name $i"_*.sam" *.gff > *_$i.txt).
The data was normalized and analysed for differential expression using R statistical software and the DESeq2 package(Love et al., 2014).
Genome_build: NC_000964.3
Supplementary_files_format_and_content: tab-delimited text files containing read counts per gene for each sample.

organism: Bacillus subtilis

source_name: batch culture

growth_protocol: Luria-Bertani (LB) medium was used for routine selection and maintenance of B. subtilis. The defined buffered minimal (Amber) medium consisted of 70 mM K2HPO4 and 30 mM KH2PO4 (adjusted to pH 7.4), 15 mM sodium chloride, 10 mM (NH4)2SO4, 0.002 mM of trace elements [ZnCl2, MnSO4, CuCl2, CoCl2 and Na2MoO4], 22 mM glucose, 0.25 mM tryptophan, 10 mM glutamate, 1 mM MgSO4, 0.1 mM calcium chloride and 0.01 mM ammonium ferric citrate. When indicated the medium was supplemented with 22 mM final concentration: malate, fumarate or citrate. All strains were grown at 37 oC at 250 rpm. B. subtilis strains used in this study are listed in Table S4.

extract_protocol:
Cells (2 ml cultures) were spun down (30 s Eppendorf centrifuge, 14,000 rpm, 4°C), resuspended in 0.4 ml ice-cold growth medium and added to a screw cap Eppendorf tube containing 1.5 g glass beads (0.1 mm), 500 ul phenol:chloroform:isoamyl alcohol (25:24:1), 50 ul 10% SDS and 50 ul RNAse free water (Hamoen et al., 2002). All solutions were prepared with diethylpyrocarbonate (DEPC)-treated water. After vortexing, tubes were frozen in liquid nitrogen and stored at -80°C. Cells were broken using a bead-beater for 4 min at room temperature. After centrifugation, the water phase was transferred to a clean tube containing 400 ul chloroform, after vortexing and centrifugation, the water phase was used for RNA isolation with High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany), yielding >3 ug total RNA per sample. TapeStation System (Agilent) was used for checking the integrity of the RNA, and RIN values of 8.3 – 9.2 were obtained.
For next-generation sequencing, a ribosomal RNA depletion was performed on the total RNA using the Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) (Illumina). Bar-coded RNA libraries were generated according to the manufacturers’ protocols using the Ion Total RNA-Seq Kit v2 and the Ion Xpress RNA-Seq barcoding kit (Thermo Fisher Scientific). The size distribution and yield of the barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). Sequencing templates were prepared on the Ion Chef System using the Ion PI Hi-Q Chef Kit (Thermo Fisher Scientific). Sequencing was performed on an Ion Proton System using a Ion PI v3 chip (Thermo Fisher Scientific) according to the instructions of the manufacturer.

tag: growth

value: Exponential

tag: experiment

value: whiA markerless mutant (KS696) (Surdova et.al. 2013)

tag: replicate


title: breast cancer_4 [hoae206]

value: trucut biopsy (frozen tissue)


title: PRE1_RNAi PRE1-RNAi-A2 (E)-Cy5

description:
raw data file: E.txt
FaPRE1-RNAi R2


title: apparent normal_4 [hoae199]

source_name: apparent normal from a patient with fibroadenoma


title: Green receptacle R1

source_name: Strawberry green unripen receptacle replicate 1

tag: tissue


title: circRNA day_0_2D - donor#2 - replicate#2

tag: age of donor

value: 80 years

value: Male


title: 168_Exponential_1

description: ribosomal RNA depleted

value: wild type


title: d_whiA_Exponential_1

description: ribosomal RNA depleted


title: apparent normal_5 [hov167]

source_name: apparent normal from a patient with fibrocystic disease


title: apparent normal_2 [hoae177]


title: apparent normal_3 [hoae182]

source_name: apparent normal froma a patient with benign phyllodes


title: Red receptacle R1

source_name: Strawberry red ripen receptacle replicate 1

value: Mature fruits


title: Red receptacle R2

source_name: Strawberry red ripen receptacle replicate 2


title: PRE1_RNAi PRE1-RNAi-A1 (D)-Cy3

description:
raw data file: D.txt
FaPRE1-RNAi R1


title: circRNA day_0_2D - donor#2 - replicate#1

tag: sex of donor


title: CA CA3 (F)-Cy5

description:
raw data file: F.txt
FaPRE1 Control R3

source_name: Strawberry fruit agroinjected with the empty vector

value: empty pFRN vector


title: Panc-1 TGF-β 2

status: Public on Oct 17 2019

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Total RNA was isolated from Panc-1 cells and analyzed miRNA expression by microarray.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Panc-1 TGF-β

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Panc-1 cells were obtained and cultured as recommended by the supplier.

extract_protocol: RNA samples were extracted from cells using miRNeasy mini kit (Qiagen).

treatment_protocol: Panc-1 cells were treated with 0 or 10 ng/ml of TGF-β for 72 hours.

tag: disease state

value: pancreatic ductal adenocarcinoma

tag: cell line

tag: agent

value: TGF-β


title: Panc-1 TGF-β 3


title: circRNA day_0_2D - donor#1 - replicate#1

value: 59 years

tag: cell status

value: monolayer adhesion


title: Panc-1 control1

source_name: Panc-1 control

value: control


title: circRNA day_0_2D - donor#1 - replicate#2


title: Panc-1 TGF-β 1


title: apparent normal_1 [hoae175]

tag: age

tag: gender

value: Female

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

tag: cancer stage

value: breast

value: surgery (frozen tissue)

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: Panc-1 control2


title: Panc-1 control3


title: CA CA1 (D)-Cy5

description:
raw data file: D.txt
FaPRE1 Control R1


title: CA CA2 (E)-Cy3

description:
raw data file: E.txt
FaPRE1 Control R2


title: LCL_1199

city: Ann Arbor

first: Lulu

last: Shang

state: Michigan

address: 1415 Washington Heights

department: Biostatistics

country: USA

institute: University of Michigan

hyb_protocol: Labeled cRNAs were hybridized onto the Affymetrix Human Transcriptome Array 2.0  according to Affymetrix protocol.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The African American samples were measured using Affymetrix Human Transcriptome Array 2.0. We used the Affymetrix Expression Console provided by Affymetrix for array quality control and all array images passed visual inspection. We focused on 1,205 samples for analysis after removing twenty-eight samples due to either low signal-to-noise ratio (N=1), abnormal polyadenylated RNA spike-in controls (Lys<Phe<Thr<Dap; N=24), sample mislabeling (N=2), or low RNA integrity (N=1). Specifically, raw intensity data were processed using the Affymetrix Power Tool software. Affymetrix CEL files were normalized using the Robust Multichip Average (RMA) algorithm in the Brainarray custom CDF version 19 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/), which included background correction, quantile normalization, log2-transformation, and probe set summarization. The algorithm also includes GC correction (GCCN), signal space transformation (SST), and gain lock (value = 0.75) to maintain linearity.

label: Biotin

source_name: Lymphoblastoid cell lines

label_protocol: One μg of RNA was labeled using the WT Expression labeling assay

growth_protocol: Cell lines established from peripheral blood samples by Epstein-Barr virus transformation

extract_protocol: Standard RNA extraction protocol using Trizol. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Foster City, CA) and quantified by spectrophotometry using the Nanodrop ND-1000 (Nanodrop Inc., Wilmington, DE). All RNA samples used in the present study yielded both anA260/A280 absorbance ratio greater than 2.0 and a RNA Integrity Number (RIN) ≥ 8.

value: peripheral blood

tag: age (yrs)

tag: plateid

tag: plate

tag: rowname

tag: colname

value: C


title: LCL_1203


title: LCL_1200


title: LCL_1194

value: B


title: LCL_1191


title: LCL_1205


title: LCL_1197


title: LCL_1202


title: LCL_1198


title: LCL_1201


title: LCL_1204


title: LCL_1190

value: A


title: LCL_1189


title: LCL_1195


title: LCL_1196


title: LCL_1187


title: LCL_1188


title: LCL_1193


title: LCL_1192

value: Male


title: LCL_1185


title: LCL_1186


title: LCL_1182


title: LCL_1181


title: LCL_1180


title: LCL_1179


title: LCL_1177


title: LCL_1178


title: LCL_1184


title: LCL_1183


title: LCL_1174


title: LCL_1171


title: LCL_1170


title: LCL_1173


title: LCL_1168


title: LCL_1169


title: LCL_1161


title: LCL_1158


title: LCL_1166


title: LCL_1159


title: LCL_1172


title: LCL_1163


title: LCL_1165


title: LCL_1164


title: LCL_1157


title: LCL_1162


title: LCL_1155


title: LCL_1154


title: LCL_1167


title: LCL_1151


title: LCL_1156


title: LCL_1148


title: LCL_1175


title: LCL_1160


title: LCL_1150


title: LCL_1153


title: LCL_1149


title: LCL_1147


title: LCL_1152


title: LCL_1146


title: LCL_1145


title: LCL_1139


title: LCL_1136


title: LCL_1137


title: LCL_1134


title: LCL_1138


title: LCL_1133


title: LCL_1143


title: LCL_1131


title: LCL_1132


title: LCL_1130


title: LCL_1128


title: LCL_1127


title: LCL_1141


title: LCL_1142


title: LCL_1129


title: LCL_1135


title: LCL_1120


title: LCL_1123


title: LCL_1125


title: LCL_1124


title: LCL_1122


title: LCL_1126


title: LCL_1118


title: LCL_1121


title: LCL_1144


title: LCL_1115


title: LCL_1113


title: LCL_1109


title: LCL_1119


title: LCL_1114


title: LCL_1110


title: LCL_1105


title: LCL_1108


title: LCL_1112


title: LCL_1092

value: E


title: LCL_1107


title: LCL_1104


title: LCL_1103


title: LCL_1102


title: LCL_1101


title: LCL_1099


title: LCL_1116


title: LCL_1111


title: LCL_1117


title: LCL_1106


title: LCL_1097


title: LCL_1093


title: LCL_1100


title: LCL_1098


title: LCL_1096

value: F


title: LCL_1094


title: LCL_1089


title: LCL_1091


title: LCL_1088


title: LCL_1086


title: LCL_1085


title: LCL_1087


title: LCL_1084

value: D


title: LCL_1081


title: LCL_1079


title: LCL_1082


title: LCL_1076


title: LCL_1083


title: LCL_1072


title: LCL_1070


title: LCL_1074


title: LCL_1077


title: LCL_1078


title: LCL_1080


title: LCL_1066


title: LCL_1068


title: LCL_1069


title: LCL_1071


title: LCL_1075


title: LCL_1067


title: LCL_1065


title: LCL_1073


title: LCL_1063


title: LCL_1140


title: LCL_1057


title: LCL_1052


title: LCL_1055


title: LCL_1051


title: LCL_1062


title: LCL_1058


title: LCL_1048


title: LCL_1050


title: LCL_1046


title: LCL_1047


title: LCL_1053


title: LCL_1061


title: LCL_1049


title: LCL_1044


title: LCL_1056


title: LCL_1059


title: LCL_1060


title: LCL_1054


title: LCL_1045


title: LCL_1043


title: LCL_1176


title: LCL_1039


title: LCL_1042


title: LCL_1040


title: LCL_1037


title: LCL_1035


title: LCL_1036


title: LCL_1041


title: LCL_1038


title: LCL_1032


title: LCL_1030


title: LCL_1034


title: LCL_1031


title: LCL_1029


title: LCL_1027


title: LCL_1020


title: LCL_1023


title: LCL_1024


title: LCL_1026


title: LCL_1021


title: LCL_1025


title: LCL_1033


title: LCL_1022


title: LCL_1018


title: LCL_1014


title: LCL_1090


title: LCL_1012


title: LCL_1013


title: LCL_1011


title: LCL_1017


title: LCL_1010


title: LCL_1009


title: LCL_1095


title: LCL_1019


title: LCL_1016


title: LCL_1015


title: LCL_1007


title: LCL_1005


title: LCL_1006


title: LCL_1004


title: LCL_1008


title: LCL_1003


title: LCL_1002


title: LCL_1001


title: LCL_1000


title: LCL_0999


title: LCL_0997


title: LCL_0998


title: LCL_0996


title: LCL_0988


title: LCL_0993


title: LCL_0991


title: LCL_1064


title: LCL_0987


title: LCL_0990


title: LCL_0986


title: LCL_0985


title: LCL_0982


title: LCL_0983


title: LCL_0989


title: LCL_0984


title: LCL_0995


title: LCL_0981


title: LCL_0992


title: LCL_0980


title: LCL_0994


title: LCL_0979


title: LCL_0976


title: LCL_0977


title: LCL_0974


title: LCL_0972


title: LCL_0978


title: LCL_0970


title: LCL_0971


title: LCL_0975


title: LCL_0973


title: LCL_0969


title: LCL_0968


title: LCL_0966


title: LCL_0962


title: LCL_0967


title: LCL_0960


title: LCL_0965


title: LCL_0955


title: LCL_0956


title: LCL_0957


title: LCL_0959


title: LCL_0964


title: LCL_0961


title: LCL_0958


title: LCL_0954


title: LCL_0963


title: LCL_0950


title: LCL_0945


title: LCL_0953


title: LCL_0951


title: LCL_0939


title: LCL_0952


title: LCL_0944


title: LCL_0943


title: LCL_0941


title: LCL_0940


title: LCL_0938


title: LCL_0947


title: LCL_0936


title: LCL_0937


title: LCL_0933


title: LCL_0935


title: LCL_0948


title: LCL_0949


title: LCL_0942


title: LCL_0934


title: LCL_0930


title: LCL_0946


title: LCL_0929


title: LCL_0931


title: LCL_0932


title: LCL_0928


title: LCL_1028


title: LCL_0926


title: LCL_0925


title: LCL_0914


title: LCL_0923


title: LCL_0927


title: LCL_0921


title: LCL_0918


title: LCL_0910


title: LCL_0917


title: LCL_0911


title: LCL_0919


title: LCL_0912


title: LCL_0924


title: LCL_0915


title: LCL_0922


title: LCL_0913


title: LCL_0905


title: LCL_0908


title: LCL_0909


title: LCL_0904


title: LCL_0903


title: LCL_0907


title: LCL_0916


title: LCL_0920


title: LCL_0902


title: LCL_0900


title: LCL_0899


title: LCL_0901


title: LCL_0895


title: LCL_0892


title: LCL_0906


title: LCL_0898


title: LCL_0889


title: LCL_0897


title: LCL_0891


title: LCL_0887


title: LCL_0894


title: LCL_0896


title: LCL_0876


title: LCL_0886


title: LCL_0879


title: LCL_0888


title: LCL_0878


title: LCL_0893


title: LCL_0883


title: LCL_0875


title: LCL_0881


title: LCL_0890


title: LCL_0877


title: LCL_0880


title: LCL_0884


title: LCL_0882


title: LCL_0885


title: LCL_0874


title: LCL_0871


title: LCL_0870


title: LCL_0868


title: LCL_0873


title: LCL_0867


title: LCL_0864


title: LCL_0862


title: LCL_0859


title: LCL_0858


title: LCL_0860


title: LCL_0869


title: LCL_0853


title: LCL_0863


title: LCL_0866


title: LCL_0872


title: LCL_0857


title: LCL_0856


title: LCL_0861


title: LCL_0852


title: LCL_0849


title: LCL_0851


title: LCL_0855


title: LCL_0846


title: LCL_0854


title: LCL_0847


title: LCL_0850


title: LCL_0848


title: LCL_0843


title: LCL_0844


title: LCL_0840


title: LCL_0838


title: LCL_0839


title: LCL_0832


title: LCL_0842


title: LCL_0834


title: LCL_0829


title: LCL_0836


title: LCL_0837


title: LCL_0830


title: LCL_0831


title: LCL_0841


title: LCL_0828


title: LCL_0827


title: LCL_0825


title: LCL_0826


title: LCL_0833


title: LCL_0835


title: LCL_0822


title: LCL_0820


title: LCL_0824


title: LCL_0823


title: LCL_0821


title: LCL_0818


title: LCL_0815


title: LCL_0817


title: LCL_0819


title: LCL_0816


title: LCL_0813


title: LCL_0814


title: LCL_0812


title: LCL_0809


title: LCL_0808


title: LCL_0810


title: LCL_0806


title: LCL_0802


title: LCL_0803


title: LCL_0807


title: LCL_0811


title: LCL_0805


title: LCL_0804


title: LCL_0796


title: LCL_0793


title: LCL_0788


title: LCL_0799


title: LCL_0800


title: LCL_0798


title: LCL_0789


title: LCL_0801


title: LCL_0794


title: LCL_0795


title: LCL_0790


title: LCL_0792


title: LCL_0791


title: LCL_0787


title: LCL_0797


title: LCL_0865


title: LCL_0785


title: LCL_0780


title: LCL_0784


title: LCL_0781


title: LCL_0783


title: LCL_0776


title: LCL_0777


title: LCL_0786


title: LCL_0775


title: LCL_0782


title: LCL_0779


title: LCL_0774


title: LCL_0778


title: LCL_0772


title: LCL_0764


title: LCL_0763


title: LCL_0773


title: LCL_0756


title: LCL_0757


title: LCL_0767


title: LCL_0762


title: LCL_0755


title: LCL_0768


title: LCL_0766


title: LCL_0770


title: LCL_0759


title: LCL_0765


title: LCL_0754


title: LCL_0845


title: LCL_0771


title: LCL_0753


title: LCL_0760


title: LCL_0761


title: LCL_0752


title: LCL_0749


title: LCL_0769


title: LCL_0751


title: LCL_0758


title: LCL_0747


title: LCL_0746


title: LCL_0750


title: LCL_0748


title: LCL_0744


title: LCL_0745


title: LCL_0743


title: LCL_0742


title: LCL_0741


title: LCL_0734


title: LCL_0736


title: LCL_0738


title: LCL_0730


title: LCL_0737


title: LCL_0727


title: LCL_0724


title: LCL_0739


title: LCL_0733


title: LCL_0728


title: LCL_0725


title: LCL_0721


title: LCL_0722


title: LCL_0726


title: LCL_0723


title: LCL_0732


title: LCL_0731


title: LCL_0718


title: LCL_0735


title: LCL_0740


title: LCL_0729


title: LCL_0719


title: LCL_0720


title: LCL_0716


title: LCL_0713


title: LCL_0717


title: LCL_0715


title: LCL_0711


title: LCL_0712


title: LCL_0714


title: LCL_0709


title: LCL_0698


title: LCL_0708


title: LCL_0694


title: LCL_0696


title: LCL_0705


title: LCL_0703


title: LCL_0701


title: LCL_0697


title: LCL_0695


title: LCL_0691


title: LCL_0706


title: LCL_0704


title: LCL_0707


title: LCL_0702


title: LCL_0692


title: LCL_0693


title: LCL_0699


title: LCL_0700


title: LCL_0710


title: LCL_0686


title: LCL_0683


title: LCL_0687


title: LCL_0684


title: LCL_0680


title: LCL_0688


title: LCL_0685


title: LCL_0690


title: LCL_0681


title: LCL_0689


title: LCL_0677


title: LCL_0675


title: LCL_0672


title: LCL_0669


title: LCL_0670


title: LCL_0676


title: LCL_0671


title: LCL_0667


title: LCL_0678


title: LCL_0666


title: LCL_0673


title: LCL_0664


title: LCL_0682


title: LCL_0665


title: LCL_0663


title: LCL_0674


title: LCL_0657


title: LCL_0668


title: LCL_0679


title: LCL_0654


title: LCL_0662


title: LCL_0660


title: LCL_0647


title: LCL_0653


title: LCL_0656


title: LCL_0646


title: LCL_0658


title: LCL_0659


title: LCL_0661


title: LCL_0650


title: LCL_0655


title: LCL_0651


title: LCL_0636


title: LCL_0641


title: LCL_0637


title: LCL_0633


title: LCL_0638


title: LCL_0634


title: LCL_0652


title: LCL_0642


title: LCL_0648


title: LCL_0644


title: LCL_0632


title: LCL_0635


title: LCL_0643


title: LCL_0639


title: LCL_0645


title: LCL_0640


title: LCL_0631


title: LCL_0649


title: LCL_0628


title: LCL_0625


title: LCL_0620


title: LCL_0622


title: LCL_0630


title: LCL_0618


title: LCL_0617


title: LCL_0619


title: LCL_0627


title: LCL_0624


title: LCL_0614


title: LCL_0616


title: LCL_0611


title: LCL_0629


title: LCL_0626


title: LCL_0613


title: LCL_0623


title: LCL_0606


title: LCL_0610


title: LCL_0612


title: LCL_0602


title: LCL_0609


title: LCL_0607


title: LCL_0601


title: LCL_0605


title: LCL_0604


title: LCL_0608


title: LCL_0603


title: LCL_0599


title: LCL_0621


title: LCL_0600


title: LCL_0594


title: LCL_0593


title: LCL_0598


title: LCL_0591


title: LCL_0589


title: LCL_0587


title: LCL_0596


title: LCL_0592


title: LCL_0595


title: LCL_0583


title: LCL_0584


title: LCL_0588


title: LCL_0597


title: LCL_0585


title: LCL_0581


title: LCL_0578


title: LCL_0582


title: LCL_0577


title: LCL_0575


title: LCL_0580


title: LCL_0579


title: LCL_0571


title: LCL_0576


title: LCL_0567


title: LCL_0615


title: LCL_0564


title: LCL_0563


title: LCL_0562


title: LCL_0565


title: LCL_0590


title: LCL_0561


title: LCL_0573


title: LCL_0568


title: LCL_0570


title: LCL_0574


title: LCL_0569


title: LCL_0560


title: LCL_0557


title: LCL_0559


title: LCL_0566


title: LCL_0572


title: LCL_0558


title: LCL_0556


title: LCL_0549


title: LCL_0546


title: LCL_0548


title: LCL_0550


title: LCL_0547


title: LCL_0544


title: LCL_0554


title: LCL_0586


title: LCL_0540


title: LCL_0545


title: LCL_0551


title: LCL_0535


title: LCL_0555


title: LCL_0553


title: LCL_0552


title: LCL_0543


title: LCL_0542


title: LCL_0536


title: LCL_0530


title: LCL_0532


title: LCL_0539


title: LCL_0528


title: LCL_0526


title: LCL_0537


title: LCL_0541


title: LCL_0523


title: LCL_0525


title: LCL_0534


title: LCL_0520


title: LCL_0524


title: LCL_0515


title: LCL_0521


title: LCL_0538


title: LCL_0531


title: LCL_0533


title: LCL_0519


title: LCL_0516


title: LCL_0514


title: LCL_0522


title: LCL_0507


title: LCL_0529


title: LCL_0509


title: LCL_0527


title: LCL_0518


title: LCL_0513


title: LCL_0517


title: LCL_0510


title: LCL_0508


title: LCL_0512


title: LCL_0505


title: LCL_0511


title: LCL_0496


title: LCL_0490


title: LCL_0494


title: LCL_0485


title: LCL_0501


title: LCL_0503


title: LCL_0484


title: LCL_0489


title: LCL_0497


title: LCL_0502


title: LCL_0499


title: LCL_0504


title: LCL_0495


title: LCL_0492


title: LCL_0493


title: LCL_0487


title: LCL_0498


title: LCL_0506


title: LCL_0500


title: LCL_0486


title: LCL_0491


title: LCL_0488


title: LCL_0483


title: LCL_0482


title: LCL_0476


title: LCL_0474


title: LCL_0471


title: LCL_0477


title: LCL_0481


title: LCL_0475


title: LCL_0466


title: LCL_0479


title: LCL_0470


title: LCL_0467


title: LCL_0472


title: LCL_0469


title: LCL_0463


title: LCL_0459


title: LCL_0460


title: LCL_0473


title: LCL_0457


title: LCL_0464


title: LCL_0461


title: LCL_0458


title: LCL_0456


title: LCL_0455


title: LCL_0468


title: LCL_0465


title: LCL_0453


title: LCL_0462


title: LCL_0454


title: LCL_0452


title: LCL_0451


title: LCL_0450


title: LCL_0446


title: LCL_0443


title: LCL_0447


title: LCL_0440


title: LCL_0445


title: LCL_0442


title: LCL_0448


title: LCL_0436


title: LCL_0444


title: LCL_0438


title: LCL_0429


title: LCL_0434


title: LCL_0435


title: LCL_0439


title: LCL_0432


title: LCL_0433


title: LCL_0437


title: LCL_0431


title: LCL_0430


title: LCL_0449


title: LCL_0425


title: LCL_0428


title: LCL_0427


title: LCL_0426


title: LCL_0420


title: LCL_0419


title: LCL_0413


title: LCL_0417


title: LCL_0422


title: LCL_0423


title: LCL_0441


title: LCL_0421


title: LCL_0415


title: LCL_0418


title: LCL_0409


title: LCL_0412


title: LCL_0410


title: LCL_0406


title: LCL_0480


title: LCL_0405


title: LCL_0400


title: LCL_0414


title: LCL_0411


title: LCL_0402


title: LCL_0408


title: LCL_0407


title: LCL_0403


title: LCL_0398


title: LCL_0399


title: LCL_0401


title: LCL_0395


title: LCL_0391


title: LCL_0392


title: LCL_0390


title: LCL_0389


title: LCL_0388


title: LCL_0424


title: LCL_0404


title: LCL_0397


title: LCL_0478


title: LCL_0396


title: LCL_0394


title: LCL_0393


title: LCL_0386


title: LCL_0385


title: LCL_0387


title: LCL_0384


title: LCL_0381


title: LCL_0378


title: LCL_0375


title: LCL_0380


title: LCL_0382


title: LCL_0372


title: LCL_0379


title: LCL_0371


title: LCL_0377


title: LCL_0383


title: LCL_0362


title: LCL_0373


title: LCL_0376


title: LCL_0374


title: LCL_0359


title: LCL_0370


title: LCL_0367


title: LCL_0364


title: LCL_0368


title: LCL_0366


title: LCL_0365


title: LCL_0361


title: LCL_0360


title: LCL_0369


title: LCL_0357


title: LCL_0358


title: LCL_0363


title: HUVEC-siATOH8_2

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

institute: Teikyo University

hyb_protocol: Array hybridization was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

scan_protocol: Array scanning was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

data_processing: The CEL files were processed using the R package gcrma.

label: biotin

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and a T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeled cRNA by using a BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to the manufacturer’s instructions (Ishii et al, Genomics 68:136-143, 2000).

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were obtained from Lonza (Thermo Fisher Scientific) and cultured in EGM-2 medium (Lonza, Thermo Fisher Scientific)

extract_protocol: Total RNAs were extracted using RNeasy mini kit (QIAGEN).

treatment_protocol: HUVECs transfected with either siRNAs specific for ATOH8 or control siRNA were stimulated with BMP-9 (1 ng/ml, R&D) for 24 h or left untreated.

value: HUVEC

tag: cell type

value: human umbilical vein endothelial cells

tag: transfected with

tag: treated with

value: none (untreated)


title: HUVEC-siATOH8_2_BMP9

value: 1 ng/ml BMP9 for 24 h


title: LCL_0356

tag: tissue


title: HUVEC-siATOH8_1_BMP9


title: HUVEC-siControl

source_name: HUVEC-siControl

value: siControl


title: HUVEC-siATOH8_1


title: LCL_0350

value: Female


title: LCL_0355


title: LCL_0352


title: HUVEC-AdLacZ

hyb_protocol: 15 μg biotin-labelled cRNA was hybridized (16 h) to Human Genome U133 Plus 2.0 Array.

scan_protocol: Arrays were then washed and stained with streptavidin-phycoerythrin (PE) in GeneChip Fluidics Station 450, and then scanned using the Affymetrix Gene-Chip scanner 3000.

data_processing: Raw intensity data (CEL files) were generated using Affymetrix GeneChip Command Console Software (AGCC). The CEL files were processed using the R package gcrma.

source_name: HUVECs adenovirally expressing LacZ

label_protocol: Biotin-labelled cRNA was generated according to the standard Affymetrix protocol for one-cycle target labeling.

treatment_protocol: HUVECs were infected with either ATOH8 or control LacZ adenovirus for 72 h.

tag: infected with

value: control LacZ adenovirus for 72 h

value: endothelial cells


title: LCL_0347


title: HUVEC-siControl_BMP9

tag: cell line


title: LCL_0346


title: LCL_0353


title: LCL_0344


title: LCL_0343


title: LCL_0351


title: LCL_0354


title: LCL_0349


title: LCL_0348


title: astrocytoma_brain_50

city: Changsha

first: Chen-Xue

last: Mao

address: Xiangya road 110

department: Departments of Clinical Pharmacology

country: China

institute: Xiangya Hospital, Central South University

hyb_protocol: standard Agilent protocol

scan_protocol: mRNA and lncRNA expression was measured using LncRNA+mRNA Human Gene Expression Microarray V3.0, 4x180K, which contains 28,844 human mRNAs and 37,581 human lncRNAs. Slides were scanned by Agilent G2565CA Microarray Scanner.

data_processing: Scanned images of microarray were processed with Agilent Feature Extraction Software v10.7 (Agilent Technologies).

label_protocol: standard Agilent protocol

extract_protocol: Total RNA was isolated from tissue specimens using the TRIzol Reagent (Invitrogen) and purified with NucleoSpin RNA clean-up (MACHEREY- NAGEL) according to the manufacturer’s instructions. The quality and integrity of the RNA were verified by gel electrophoresis.

treatment_protocol: All astrocytoma patients underwent surgical resection and histologically confirmed, and their clinical and pathologic data were collected.

tag: subject status

value: astrocytoma patient

value: Astrocytoma


title: astrocytoma_brain_40


title: HUVEC-AdATOH8

source_name: HUVECs adenovirally expressing the transcription factor ATOH8

value: ATOH8 adenovirus for 72 h


title: astrocytoma_brain_43


title: astrocytoma_brain_39


title: LCL_0345

value: peripheral blood


title: astrocytoma_brain_42


title: astrocytoma_brain_49


title: astrocytoma_brain_41


title: astrocytoma_brain_37


title: LCL_0342


title: astrocytoma_brain_51


title: LCL_0416


title: astrocytoma_brain_38


title: astrocytoma_brain_35


title: LCL_0339


title: astrocytoma_brain_34


title: LCL_0341


title: astrocytoma_brain_28


title: LCL_0336


title: astrocytoma_brain_29


title: astrocytoma_brain_23


title: astrocytoma_brain_30


title: LCL_0333


title: LCL_0334


title: LCL_0330


title: astrocytoma_brain_17


title: LCL_0335


title: LCL_0331


title: LCL_0340


title: LCL_0338


title: astrocytoma_brain_19


title: LCL_0327


title: LCL_0329


title: LCL_0337


title: LCL_0332


title: astrocytoma_brain_16


title: astrocytoma_brain_22


title: LCL_0328


title: astrocytoma_brain_31


title: astrocytoma_brain_15


title: astrocytoma_brain_26


title: astrocytoma_brain_24


title: LCL_0325


title: astrocytoma_brain_27


title: astrocytoma_brain_12


title: LCL_0324


title: LCL_0322


title: astrocytoma_brain_14


title: LCL_0319


title: LCL_0315

value: C


title: LCL_0316


title: non-tumor_brain_13

value: Male

value: non-tumor brain tissues


title: non-tumor_brain_9


title: astrocytoma_brain_11


title: LCL_0313


title: LCL_0318


title: LCL_0323


title: non-tumor_brain_10


title: non-tumor_brain_7


title: astrocytoma_brain_10


title: non-tumor_brain_16


title: LCL_0320


title: LCL_0317


title: astrocytoma_brain_3


title: astrocytoma_brain_7


title: non-tumor_brain_17


title: non-tumor_brain_4


title: LCL_0314


title: LCL_0321


title: astrocytoma_brain_9


title: LCL_0312


title: LCL_0311


title: non-tumor_brain_3


title: LCL_0310

value: B


title: MM38_CD138N

city: Seoul

first: Daeun

last: Ryu

address: 81, Irwon-ro

country: South Korea

institute: Samsung Genome Institute

description:
Whole transcriptome sequencing
R_17_00367_RE_WTS
MM38_CD138N

data_processing:
A modified reference was generated by merging the three array control RNA spike-ins (ThermoFisher), 92 ERCC spike-ins and the human genome reference (hg19) with the GENCODE 19 annotations.
Paired-end 100bp reads were aligned to STAR_2.4.0b with default parameters.
Transcripts Per Million (TPM) values were estimated using RSEM v1.2.17 with default parameters.
hg19
Supplementary_files_format_and_content: A processed file is tab-delimited and contains the raw TPM values for 477 single cells and 11 CD138 negative bulk samples.

extract_protocol:
Plasma cells were purified using EasySep(®) CD138 Positive Selection kit before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 5-10um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). Two types of external sequence, 1,4,7 ArrayControl TM RNA Spikes and ERCC RNA Spike-In Control Mix (ThermoFisher) were added to the lysis mix for validation of array and batch effect. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies).
We analyzed single cell RNA sequencing(scRNA-seq) data after applied filtering criteria to remove cells with low sequencing quality. Also eleven CD138-negative bulk samples analyzed by the scRNA-seq pipeline.

tag: patient id

value: female

tag: death(alive=0; death=1)

value: Multiple myeloma

tag: prep-site

value: Bone marrow

tag: facs sorting

value: CD138 negative


title: MM36EM_CD138N

description:
Whole transcriptome sequencing
R_17_00365_RE_WTS
MM36EM_CD138N

tag: gender

value: male

value: Ascites


title: MM34EM_CD138N

description:
Whole transcriptome sequencing
R_17_00364_RE_WTS
MM34EM_CD138N


title: MM33_CD138N

description:
Whole transcriptome sequencing
R_17_00284_RE_WTS
MM33_CD138N


title: MM28_CD138N

description:
Whole transcriptome sequencing
R_17_00282_RE_WTS
MM28_CD138N


title: MM17_CD138N

description:
Whole transcriptome sequencing
R_17_00279_RE_WTS
MM17_CD138N


title: MM25_CD138N

description:
Whole transcriptome sequencing
R_17_00281_RE_WTS
MM25_CD138N


title: MM30_CD138N

description:
Whole transcriptome sequencing
R_17_00366_RE_WTS
MM30_CD138N


title: MM16_CD138N

description:
Whole transcriptome sequencing
R_17_00278_RE_WTS
MM16_CD138N


title: MM38_93

description:
Single-cell RNA-seq
MM38_93_TCCTGAGC-AGAGTAGA
MM38_93

value: CD138 positive


title: MM38_91

description:
Single-cell RNA-seq
MM38_91_CGTACTAG-TAGATCGC
MM38_91


title: MM38_92

description:
Single-cell RNA-seq
MM38_92_TAAGGCGA-TATCCTCT
MM38_92


title: MM34_CD138N

description:
Whole transcriptome sequencing
R_17_00285_RE_WTS
MM34_CD138N


title: LCL_0308

tag: age (yrs)

value: Female


title: LCL_0307

tag: plateid


title: LCL_0305

tag: plate


title: LCL_0306

tag: rowname


title: MM38_90

description:
Single-cell RNA-seq
MM38_90_TAAGGCGA-GTAAGGAG
MM38_90


title: LCL_0304

tag: colname


title: non-tumor_brain_1


title: LCL_0303


title: LCL_0301

value: A


title: MM38_89

description:
Single-cell RNA-seq
MM38_89_CTCTCTAC-TATCCTCT
MM38_89

tag: cell type


title: MM02_CD138N

description:
Whole transcriptome sequencing
R_17_00277_RE_WTS
MM02_CD138N


title: LCL_0302


title: LCL_0300


title: LCL_0297


title: MM38_86

description:
Single-cell RNA-seq
MM38_86_TAAGGCGA-AAGGAGTA
MM38_86


title: LCL_0299


title: MM38_83

description:
Single-cell RNA-seq
MM38_83_GGACTCCT-GTAAGGAG
MM38_83


title: MM38_78

description:
Single-cell RNA-seq
MM38_78_GGACTCCT-TAGATCGC
MM38_78


title: MM38_79

description:
Single-cell RNA-seq
MM38_79_CGTACTAG-CTAAGCCT
MM38_79


title: MM38_77

description:
Single-cell RNA-seq
MM38_77_TCCTGAGC-TAGATCGC
MM38_77


title: MM38_87

description:
Single-cell RNA-seq
MM38_87_TCCTGAGC-TATCCTCT
MM38_87


title: LCL_0296


title: MM38_73

description:
Single-cell RNA-seq
MM38_73_AGGCAGAA-CTAAGCCT
MM38_73


title: LCL_0294

value: F


title: MM38_70

description:
Single-cell RNA-seq
MM38_70_TCCTGAGC-AAGGAGTA
MM38_70


title: MM38_67

description:
Single-cell RNA-seq
MM38_67_AGGCAGAA-AGAGTAGA
MM38_67


title: MM38_65

description:
Single-cell RNA-seq
MM38_65_CGTACTAG-AGAGTAGA
MM38_65


title: MM38_68

description:
Single-cell RNA-seq
MM38_68_GGACTCCT-AGAGTAGA
MM38_68


title: MM38_63

description:
Single-cell RNA-seq
MM38_63_AGGCAGAA-TAGATCGC
MM38_63


title: MM38_71

description:
Single-cell RNA-seq
MM38_71_AGGCAGAA-AAGGAGTA
MM38_71


title: LCL_0309


title: MM38_61

description:
Single-cell RNA-seq
MM38_61_CTCTCTAC-AAGGAGTA
MM38_61


title: MM38_58

description:
Single-cell RNA-seq
MM38_58_CTCTCTAC-AGAGTAGA
MM38_58


title: MM38_59

description:
Single-cell RNA-seq
MM38_59_TCCTGAGC-GTAAGGAG
MM38_59


title: LCL_0291


title: LCL_0288


title: LCL_0292


title: MM38_66

description:
Single-cell RNA-seq
MM38_66_CGTACTAG-ACTGCATA
MM38_66


title: LCL_0293


title: LCL_0290


title: LCL_0289


title: LCL_0287

value: E


title: MM38_54

description:
Single-cell RNA-seq
MM38_54_TCCTGAGC-CTCTCTAT
MM38_54


title: MM38_56

description:
Single-cell RNA-seq
MM38_56_TAAGGCGA-CTAAGCCT
MM38_56


title: LCL_0298


title: LCL_0280


title: LCL_0277

value: D


title: LCL_0282

value: peripheral blood


title: LCL_0286


title: LCL_0285


title: LCL_0284


title: LCL_0283


title: LCL_0326


title: MM38_52

description:
Single-cell RNA-seq
MM38_52_GGACTCCT-ACTGCATA
MM38_52


title: LCL_0295


title: LCL_0278


title: LCL_0281


title: MM38_53

description:
Single-cell RNA-seq
MM38_53_CTCTCTAC-CTAAGCCT
MM38_53


title: LCL_0279


title: LCL_0274


title: LCL_0276


title: MM38_50

description:
Single-cell RNA-seq
MM38_50_TAAGGCGA-AGAGTAGA
MM38_50


title: MM38_51

description:
Single-cell RNA-seq
MM38_51_GGACTCCT-CTAAGCCT
MM38_51


title: LCL_0275


title: astrocytoma_brain_4

value: astrocytoma patient

value: Astrocytoma


title: MM38_47

description:
Single-cell RNA-seq
MM38_47_GGACTCCT-AAGGAGTA
MM38_47


title: MM38_40

description:
Single-cell RNA-seq
MM38_40_TCCTGAGC-ACTGCATA
MM38_40


title: MM38_39

description:
Single-cell RNA-seq
MM38_39_CGTACTAG-CTCTCTAT
MM38_39


title: LCL_0272


title: MM38_37

description:
Single-cell RNA-seq
MM38_37_AGGCAGAA-TATCCTCT
MM38_37


title: MM38_27

description:
Single-cell RNA-seq
MM38_27_CGTACTAG-AAGGAGTA
MM38_27


title: MM38_24

description:
Single-cell RNA-seq
MM38_24_AGGCAGAA-GTAAGGAG
MM38_24


title: MM38_22

description:
Single-cell RNA-seq
MM38_22_CGTACTAG-GTAAGGAG
MM38_22


title: MM38_20

description:
Single-cell RNA-seq
MM38_20_TAAGGCGA-TAGATCGC
MM38_20


title: LCL_0273

value: Male


title: MM38_19

description:
Single-cell RNA-seq
MM38_19_TCCTGAGC-CTAAGCCT
MM38_19


title: LCL_0270

value: C


title: MM38_16

description:
Single-cell RNA-seq
MM38_16_CTCTCTAC-ACTGCATA
MM38_16

value: female


title: MM38_15

description:
Single-cell RNA-seq
MM38_15_TAAGGCGA-ACTGCATA
MM38_15

value: Multiple myeloma


title: MM38_29

description:
Single-cell RNA-seq
MM38_29_GGACTCCT-TATCCTCT
MM38_29

value: Bone marrow


title: LCL_0271


title: LCL_0269


title: LCL_0266


title: LCL_0265


title: MM38_14

description:
Single-cell RNA-seq
MM38_14_CGTACTAG-TATCCTCT
MM38_14


title: LCL_0262

value: B


title: LCL_0263


title: LCL_0261


title: LCL_0260


title: MM38_13

description:
Single-cell RNA-seq
MM38_13_TAAGGCGA-CTCTCTAT
MM38_13


title: LCL_0267


title: LCL_0268


title: LCL_0264


title: LCL_0258


title: LCL_0256


title: LCL_0259


title: MM38_21

description:
Single-cell RNA-seq
MM38_21_AGGCAGAA-CTCTCTAT
MM38_21


title: MM38_5

description:
Single-cell RNA-seq
MM38_05_CTCTCTAC-GTAAGGAG
MM38_05


title: LCL_0255


title: MM36EM_96

description:
Single-cell RNA-seq
MM36A_96
MM36EM_96

value: male


title: MM36EM_93

description:
Single-cell RNA-seq
MM36A_93
MM36EM_93

value: Ascites


title: MM36EM_90

description:
Single-cell RNA-seq
MM36A_90
MM36EM_90

value: CD138 positive


title: MM38_3

description:
Single-cell RNA-seq
MM38_03_GGACTCCT-CTCTCTAT
MM38_03


title: MM36EM_89

description:
Single-cell RNA-seq
MM36A_89
MM36EM_89


title: MM36EM_82

description:
Single-cell RNA-seq
MM36A_82
MM36EM_82


title: MM36EM_76

description:
Single-cell RNA-seq
MM36A_76
MM36EM_76


title: MM36EM_71

description:
Single-cell RNA-seq
MM36A_71
MM36EM_71


title: MM36EM_70

description:
Single-cell RNA-seq
MM36A_70
MM36EM_70


title: MM38_12

description:
Single-cell RNA-seq
MM38_12_AGGCAGAA-ACTGCATA
MM38_12


title: MM38_41

description:
Single-cell RNA-seq
MM38_41_CTCTCTAC-CTCTCTAT
MM38_41


title: MM38_4

description:
Single-cell RNA-seq
MM38_04_CTCTCTAC-TAGATCGC
MM38_04


title: MM36EM_69

description:
Single-cell RNA-seq
MM36A_69
MM36EM_69


title: LCL_0257

value: Female


title: LCL_0253

value: A


title: LCL_0250


title: LCL_0251


title: LCL_0247

value: F


title: LCL_0244


title: LCL_0248


title: LCL_0245


title: LCL_0242


title: LCL_0243


title: LCL_0254


title: LCL_0252


title: LCL_0249


title: MM36EM_67

description:
Single-cell RNA-seq
MM36A_67
MM36EM_67


title: LCL_0241

value: E


title: MM36EM_77

description:
Single-cell RNA-seq
MM36A_77
MM36EM_77


title: MM36EM_66

description:
Single-cell RNA-seq
MM36A_66
MM36EM_66


title: MM36EM_62

description:
Single-cell RNA-seq
MM36A_62
MM36EM_62


title: MM36EM_60

description:
Single-cell RNA-seq
MM36A_60
MM36EM_60


title: MM36EM_59

description:
Single-cell RNA-seq
MM36A_59
MM36EM_59


title: MM36EM_55

description:
Single-cell RNA-seq
MM36A_55
MM36EM_55


title: MM36EM_54

description:
Single-cell RNA-seq
MM36A_54
MM36EM_54


title: MM36EM_52

description:
Single-cell RNA-seq
MM36A_52
MM36EM_52


title: LCL_0246


title: LCL_0239


title: MM36EM_53

description:
Single-cell RNA-seq
MM36A_53
MM36EM_53


title: MM36EM_47

description:
Single-cell RNA-seq
MM36A_47
MM36EM_47


title: MM36EM_48

description:
Single-cell RNA-seq
MM36A_48
MM36EM_48


title: LCL_0240


title: MM36EM_58

description:
Single-cell RNA-seq
MM36A_58
MM36EM_58


title: MM36EM_46

description:
Single-cell RNA-seq
MM36A_46
MM36EM_46


title: MM36EM_45

description:
Single-cell RNA-seq
MM36A_45
MM36EM_45


title: LCL_0237


title: MM36EM_44

description:
Single-cell RNA-seq
MM36A_44
MM36EM_44


title: MM36EM_41

description:
Single-cell RNA-seq
MM36A_41
MM36EM_41


title: LCL_0238


title: MM36EM_39

description:
Single-cell RNA-seq
MM36A_39
MM36EM_39


title: LCL_0235


title: LCL_0234


title: LCL_0236


title: MM36EM_38

description:
Single-cell RNA-seq
MM36A_38
MM36EM_38


title: LCL_0232

value: D


title: LCL_0231

value: peripheral blood


title: LCL_0229


title: LCL_0233


title: LCL_0228


title: LCL_0223


title: MM36EM_37

description:
Single-cell RNA-seq
MM36A_37
MM36EM_37


title: LCL_0230


title: MM36EM_33

description:
Single-cell RNA-seq
MM36A_33
MM36EM_33


title: MM36EM_32

description:
Single-cell RNA-seq
MM36A_32
MM36EM_32


title: MM36EM_26

description:
Single-cell RNA-seq
MM36A_26
MM36EM_26


title: MM36EM_25

description:
Single-cell RNA-seq
MM36A_25
MM36EM_25


title: MM36EM_23

description:
Single-cell RNA-seq
MM36A_23
MM36EM_23


title: LCL_0224


title: MM36EM_21

description:
Single-cell RNA-seq
MM36A_21
MM36EM_21


title: MM36EM_20

description:
Single-cell RNA-seq
MM36A_20
MM36EM_20


title: LCL_0220


title: LCL_0221


title: LCL_0222


title: MM36EM_16

description:
Single-cell RNA-seq
MM36A_16
MM36EM_16


title: LCL_0219


title: MM36EM_15

description:
Single-cell RNA-seq
MM36A_15
MM36EM_15


title: LCL_0216


title: MM36EM_11

description:
Single-cell RNA-seq
MM36A_11
MM36EM_11


title: LCL_0218


title: LCL_0215


title: LCL_0225


title: MM36EM_13

description:
Single-cell RNA-seq
MM36A_13
MM36EM_13


title: MM36EM_9

description:
Single-cell RNA-seq
MM36A_09
MM36EM_09


title: MM36EM_10

description:
Single-cell RNA-seq
MM36A_10
MM36EM_10


title: MM36EM_5

description:
Single-cell RNA-seq
MM36A_05
MM36EM_05


title: MM36EM_4

description:
Single-cell RNA-seq
MM36A_04
MM36EM_04


title: LCL_0217


title: LCL_0211


title: LCL_0212


title: MM36EM_3

description:
Single-cell RNA-seq
MM36A_03
MM36EM_03


title: LCL_0208


title: LCL_0214


title: LCL_0209


title: LCL_0206


title: MM33_66

description:
Single-cell RNA-seq
MM33_66_CTCTCTAC-GTAAGGAG
MM33_66


title: MM33_65

description:
Single-cell RNA-seq
MM33_65_CTCTCTAC-TAGATCGC
MM33_65


title: MM33_60

description:
Single-cell RNA-seq
MM33_60_CTCTCTAC-AGAGTAGA
MM33_60


title: MM33_90

description:
Single-cell RNA-seq
MM33_90_CTCTCTAC-CTAAGCCT
MM33_90


title: MM33_59

description:
Single-cell RNA-seq
MM33_59_CTCTCTAC-ACTGCATA
MM33_59


title: LCL_0213


title: LCL_0207


title: LCL_0210


title: MM33_58

description:
Single-cell RNA-seq
MM33_58_CTCTCTAC-AAGGAGTA
MM33_58


title: MM33_57

description:
Single-cell RNA-seq
MM33_57_TAGGCATG-CTAAGCCT
MM33_57


title: MM33_56

description:
Single-cell RNA-seq
MM33_56_CTCTCTAC-TATCCTCT
MM33_56


title: LCL_0205


title: LCL_0204


title: LCL_0201


title: LCL_0198


title: LCL_0203


title: LCL_0202


title: LCL_0199


title: MM33_11

description:
Single-cell RNA-seq
MM33_11_CAGAGAGG-CTCTCTAT
MM33_11


title: MM33_24

description:
Single-cell RNA-seq
MM33_24_CAGAGAGG-TATCCTCT
MM33_24


title: LCL_0197


title: MM30_94

description:
Single-cell RNA-seq
MM30_94_CTCTCTAC-TAGATCGC
MM30_94


title: MM33_41

description:
Single-cell RNA-seq
MM33_41_CAGAGAGG-TAGATCGC
MM33_41


title: MM33_55

description:
Single-cell RNA-seq
MM33_55_CTCTCTAC-CTCTCTAT
MM33_55


title: LCL_0200


title: MM30_89

description:
Single-cell RNA-seq
MM30_89_GGACTCCT-ACTGCATA
MM30_89


title: MM30_87

description:
Single-cell RNA-seq
MM30_87_CTCTCTAC-CTCTCTAT
MM30_87


title: LCL_0196


title: MM30_81

description:
Single-cell RNA-seq
MM30_81_CTCTCTAC-TATCCTCT
MM30_81


title: LCL_0194


title: MM30_92

description:
Single-cell RNA-seq
MM30_92_TAGGCATG-CTAAGCCT
MM30_92


title: LCL_0195


title: LCL_0193


title: MM30_67

description:
Single-cell RNA-seq
MM30_67_CAGAGAGG-AGAGTAGA
MM30_67


title: LCL_0192


title: LCL_0191


title: LCL_0190


title: LCL_0187


title: LCL_0189


title: LCL_0188


title: MM30_62

description:
Single-cell RNA-seq
MM30_62_CTCTCTAC-CTAAGCCT
MM30_62


title: MM30_57

description:
Single-cell RNA-seq
MM30_57_CTCTCTAC-GTAAGGAG
MM30_57


title: MM30_50

description:
Single-cell RNA-seq
MM30_50_GGACTCCT-CTAAGCCT
MM30_50


title: LCL_0185


title: MM30_55

description:
Single-cell RNA-seq
MM30_55_CTCTCTAC-ACTGCATA
MM30_55


title: MM30_47

description:
Single-cell RNA-seq
MM30_47_TAGGCATG-ACTGCATA
MM30_47


title: MM30_71

description:
Single-cell RNA-seq
MM30_71_TAGGCATG-GTAAGGAG
MM30_71


title: MM30_44

description:
Single-cell RNA-seq
MM30_44_GGACTCCT-TAGATCGC
MM30_44


title: LCL_0184


title: MM30_66

description:
Single-cell RNA-seq
MM30_66_GGACTCCT-GTAAGGAG
MM30_66


title: MM30_34

description:
Single-cell RNA-seq
MM30_34_GGACTCCT-CTCTCTAT
MM30_34


title: LCL_0186


title: MM30_33

description:
Single-cell RNA-seq
MM30_33_TAGGCATG-AAGGAGTA
MM30_33


title: LCL_0183


title: MM30_27

description:
Single-cell RNA-seq
MM30_27_TAGGCATG-TATCCTCT
MM30_27


title: MM30_28

description:
Single-cell RNA-seq
MM30_28_TCCTGAGC-CTAAGCCT
MM30_28


title: MM30_22

description:
Single-cell RNA-seq
MM30_22_TAGGCATG-TAGATCGC
MM30_22


title: LCL_0173


title: MM30_18

description:
Single-cell RNA-seq
MM30_18_GGACTCCT-AGAGTAGA
MM30_18


title: LCL_0174


title: MM30_19

description:
Single-cell RNA-seq
MM30_19_CTCTCTAC-AGAGTAGA
MM30_19


title: LCL_0175


title: MM30_41

description:
Single-cell RNA-seq
MM30_41_TCCTGAGC-AAGGAGTA
MM30_41


title: MM30_15

description:
Single-cell RNA-seq
MM30_15_GGACTCCT-TATCCTCT
MM30_15


title: LCL_0177


title: LCL_0179


title: LCL_0180


title: LCL_0181


title: LCL_0172


title: MM30_14

description:
Single-cell RNA-seq
MM30_14_GGACTCCT-AAGGAGTA
MM30_14


title: LCL_0182


title: LCL_0178


title: LCL_0176


title: LCL_0169


title: MM30_9

description:
Single-cell RNA-seq
MM30_09_TAGGCATG-AGAGTAGA
MM30_09


title: LCL_0171


title: LCL_0227


title: LCL_0226


title: LCL_0168


title: MM30_3

description:
Single-cell RNA-seq
MM30_03_TAGGCATG-CTCTCTAT
MM30_03


title: MM30_2

description:
Single-cell RNA-seq
MM30_02_CTCTCTAC-AAGGAGTA
MM30_02


title: MM30_1

description:
Single-cell RNA-seq
MM30_01_CAGAGAGG-TAGATCGC
MM30_01


title: MM28_93

description:
Single-cell RNA-seq
MM28_93_TCCTGAGC-AGAGTAGA
MM28_93


title: MM30_13

description:
Single-cell RNA-seq
MM30_13_CAGAGAGG-TATCCTCT
MM30_13


title: MM28_88

description:
Single-cell RNA-seq
MM28_88_TCCTGAGC-CTCTCTAT
MM28_88


title: MM28_72

description:
Single-cell RNA-seq
MM28_72_AGGCAGAA-CTAAGCCT
MM28_72


title: MM28_81

description:
Single-cell RNA-seq
MM28_81_TCCTGAGC-TAGATCGC
MM28_81


title: LCL_0165


title: LCL_0166


title: MM28_92

description:
Single-cell RNA-seq
MM28_92_TCCTGAGC-TATCCTCT
MM28_92


title: MM28_70

description:
Single-cell RNA-seq
MM28_70_AGGCAGAA-AAGGAGTA
MM28_70


title: MM30_7

description:
Single-cell RNA-seq
MM30_07_CAGAGAGG-CTCTCTAT
MM30_07


title: MM28_68

description:
Single-cell RNA-seq
MM28_68_AGGCAGAA-ACTGCATA
MM28_68


title: LCL_0170


title: LCL_0163


title: MM28_67

description:
Single-cell RNA-seq
MM28_67_AGGCAGAA-GTAAGGAG
MM28_67


title: MM28_65

description:
Single-cell RNA-seq
MM28_65_AGGCAGAA-AGAGTAGA
MM28_65


title: LCL_0164


title: LCL_0157


title: LCL_0159


title: LCL_0161


title: LCL_0158


title: MM28_55

description:
Single-cell RNA-seq
MM28_55_AGGCAGAA-CTCTCTAT
MM28_55


title: MM28_49

description:
Single-cell RNA-seq
MM28_49_AGGCAGAA-TAGATCGC
MM28_49


title: LCL_0156


title: LCL_0160


title: MM28_45

description:
Single-cell RNA-seq
MM28_45_CGTACTAG-ACTGCATA
MM28_45


title: MM36EM_7

description:
Single-cell RNA-seq
MM36A_07
MM36EM_07


title: LCL_0153


title: MM28_43

description:
Single-cell RNA-seq
MM28_43_CGTACTAG-GTAAGGAG
MM28_43


title: LCL_0162


title: MM28_40

description:
Single-cell RNA-seq
MM28_40_CGTACTAG-TATCCTCT
MM28_40


title: MM28_34

description:
Single-cell RNA-seq
MM28_34_CGTACTAG-CTCTCTAT
MM28_34


title: MM28_60

description:
Single-cell RNA-seq
MM28_60_AGGCAGAA-TATCCTCT
MM28_60


title: LCL_0154


title: LCL_0155


title: MM28_47

description:
Single-cell RNA-seq
MM28_47_CGTACTAG-CTAAGCCT
MM28_47


title: LCL_0152


title: LCL_0149


title: LCL_0150


title: LCL_0146


title: LCL_0151


title: LCL_0147


title: LCL_0148


title: MM28_33

description:
Single-cell RNA-seq
MM28_33_CGTACTAG-TAGATCGC
MM28_33


title: LCL_0145


title: MM28_41

description:
Single-cell RNA-seq
MM28_41_CGTACTAG-AGAGTAGA
MM28_41


title: MM28_23

description:
Single-cell RNA-seq
MM28_23_TAAGGCGA-AAGGAGTA
MM28_23


title: MM28_29

description:
Single-cell RNA-seq
MM28_29_TAAGGCGA-CTAAGCCT
MM28_29


title: MM28_18

description:
Single-cell RNA-seq
MM28_18_TAAGGCGA-ACTGCATA
MM28_18


title: MM28_13

description:
Single-cell RNA-seq
MM28_13_TAAGGCGA-GTAAGGAG
MM28_13


title: MM28_7

description:
Single-cell RNA-seq
MM28_07_TAAGGCGA-CTCTCTAT
MM28_7


title: MM28_9

description:
Single-cell RNA-seq
MM28_09_TAAGGCGA-TATCCTCT
MM28_9


title: MM28_6

description:
Single-cell RNA-seq
MM28_06_TAAGGCGA-TAGATCGC
MM28_6


title: LCL_0144


title: MM25_96

description:
Single-cell RNA-seq
MM25_96_CTCTCTAC-TAGATCGC
MM25_96


title: LCL_0141


title: MM25_95

description:
Single-cell RNA-seq
MM25_95_TAGGCATG-AGAGTAGA
MM25_95


title: MM25_91

description:
Single-cell RNA-seq
MM25_91_AGGCAGAA-TAGATCGC
MM25_91


title: LCL_0142


title: LCL_0140


title: MM25_9

description:
Single-cell RNA-seq
MM25_9_AGGCAGAA-CTAAGCCT
MM25_9


title: LCL_0135


title: LCL_0139


title: LCL_0138


title: LCL_0143


title: LCL_0136


title: MM28_11

description:
Single-cell RNA-seq
MM28_11_TAAGGCGA-AGAGTAGA
MM28_11


title: MM25_88

description:
Single-cell RNA-seq
MM25_88_AGGCAGAA-AGAGTAGA
MM25_88


title: MM25_84

description:
Single-cell RNA-seq
MM25_84_AGGCAGAA-ACTGCATA
MM25_84


title: MM25_87

description:
Single-cell RNA-seq
MM25_87_TAGGCATG-TAGATCGC
MM25_87


title: MM25_8

description:
Single-cell RNA-seq
MM25_8_TAAGGCGA-ACTGCATA
MM25_8


title: LCL_0132


title: MM25_79

description:
Single-cell RNA-seq
MM25_79_TAGGCATG-CTAAGCCT
MM25_79


title: LCL_0134


title: LCL_0128


title: LCL_0129


title: LCL_0130


title: LCL_0137


title: LCL_0126


title: LCL_0127


title: MM25_83

description:
Single-cell RNA-seq
MM25_83_GGACTCCT-CTCTCTAT
MM25_83


title: LCL_0131


title: MM25_76

description:
Single-cell RNA-seq
MM25_76_TCCTGAGC-AAGGAGTA
MM25_76


title: LCL_0125


title: MM25_71

description:
Single-cell RNA-seq
MM25_71_GGACTCCT-CTAAGCCT
MM25_71


title: LCL_0133


title: LCL_0124


title: MM25_66

description:
Single-cell RNA-seq
MM25_66_AGGCAGAA-TATCCTCT
MM25_66


title: MM25_65

description:
Single-cell RNA-seq
MM25_65_TAGGCATG-TATCCTCT
MM25_65


title: MM25_61

description:
Single-cell RNA-seq
MM25_61_TCCTGAGC-GTAAGGAG
MM25_61


title: MM25_77

description:
Single-cell RNA-seq
MM25_77_GGACTCCT-TATCCTCT
MM25_77


title: MM25_60

description:
Single-cell RNA-seq
MM25_60_GGACTCCT-ACTGCATA
MM25_60


title: MM25_59

description:
Single-cell RNA-seq
MM25_59_TAGGCATG-CTCTCTAT
MM25_59


title: MM25_58

description:
Single-cell RNA-seq
MM25_58_TAGGCATG-ACTGCATA
MM25_58


title: LCL_0122


title: LCL_0119


title: MM25_57

description:
Single-cell RNA-seq
MM25_57_CGTACTAG-CTAAGCCT
MM25_57


title: LCL_0123


title: LCL_0116


title: LCL_0118


title: MM25_56

description:
Single-cell RNA-seq
MM25_56_TAAGGCGA-CTCTCTAT
MM25_56


title: MM25_55

description:
Single-cell RNA-seq
MM25_55_CTCTCTAC-TATCCTCT
MM25_55


title: LCL_0121


title: LCL_0120


title: MM25_52

description:
Single-cell RNA-seq
MM25_52_CGTACTAG-AAGGAGTA
MM25_52


title: MM25_48

description:
Single-cell RNA-seq
MM25_48_GGACTCCT-GTAAGGAG
MM25_48


title: MM25_46

description:
Single-cell RNA-seq
MM25_46_CGTACTAG-CTCTCTAT
MM25_46


title: MM25_49

description:
Single-cell RNA-seq
MM25_49_TCCTGAGC-TATCCTCT
MM25_49


title: MM25_45

description:
Single-cell RNA-seq
MM25_45_CTCTCTAC-AGAGTAGA
MM25_45


title: MM25_43

description:
Single-cell RNA-seq
MM25_43_CGTACTAG-TATCCTCT
MM25_43


title: LCL_0109


title: LCL_0108


title: LCL_0106


title: MM25_40

description:
Single-cell RNA-seq
MM25_40_GGACTCCT-TAGATCGC
MM25_40


title: MM25_39

description:
Single-cell RNA-seq
MM25_39_TAGGCATG-GTAAGGAG
MM25_39


title: LCL_0111


title: LCL_0112


title: LCL_0115


title: LCL_0167


title: MM25_37

description:
Single-cell RNA-seq
MM25_37_CGTACTAG-TAGATCGC
MM25_37


title: LCL_0117


title: MM25_70

description:
Single-cell RNA-seq
MM25_70_TCCTGAGC-AGAGTAGA
MM25_70


title: LCL_0110


title: MM25_33

description:
Single-cell RNA-seq
MM25_33_TAAGGCGA-AAGGAGTA
MM25_33


title: LCL_0114


title: LCL_0107


title: LCL_0113


title: MM25_32

description:
Single-cell RNA-seq
MM25_32_CGTACTAG-ACTGCATA
MM25_32


title: LCL_0105


title: MM25_28

description:
Single-cell RNA-seq
MM25_28_AGGCAGAA-AAGGAGTA
MM25_28


title: LCL_0104


title: LCL_0099


title: LCL_0101


title: LCL_0098


title: LCL_0100


title: MM25_27

description:
Single-cell RNA-seq
MM25_27_AGGCAGAA-CTCTCTAT
MM25_27


title: MM25_30

description:
Single-cell RNA-seq
MM25_30_TAAGGCGA-TATCCTCT
MM25_30


title: MM25_25

description:
Single-cell RNA-seq
MM25_25_TAGGCATG-AAGGAGTA
MM25_25


title: MM25_24

description:
Single-cell RNA-seq
MM25_24_GGACTCCT-AGAGTAGA
MM25_24


title: MM25_29

description:
Single-cell RNA-seq
MM25_29_AGGCAGAA-GTAAGGAG
MM25_29


title: LCL_0102


title: MM25_23

description:
Single-cell RNA-seq
MM25_23_TCCTGAGC-CTAAGCCT
MM25_23


title: MM25_21

description:
Single-cell RNA-seq
MM25_21_CGTACTAG-AGAGTAGA
MM25_21


title: MM25_22

description:
Single-cell RNA-seq
MM25_22_CGTACTAG-GTAAGGAG
MM25_22


title: MM25_17

description:
Single-cell RNA-seq
MM25_17_TAAGGCGA-TAGATCGC
MM25_17


title: MM25_20

description:
Single-cell RNA-seq
MM25_20_CTCTCTAC-CTCTCTAT
MM25_20


title: MM25_19

description:
Single-cell RNA-seq
MM25_19_TCCTGAGC-ACTGCATA
MM25_19


title: LCL_0097


title: LCL_0095


title: MM25_51

description:
Single-cell RNA-seq
MM25_51_TAAGGCGA-GTAAGGAG
MM25_51


title: LCL_0094


title: LCL_0096


title: LCL_0092


title: LCL_0091


title: MM25_13

description:
Single-cell RNA-seq
MM25_13_TAAGGCGA-AGAGTAGA
MM25_13


title: LCL_0088


title: LCL_0089


title: LCL_0093


title: MM25_1

description:
Single-cell RNA-seq
MM25_1_TAAGGCGA-CTAAGCCT
MM25_1


title: MM25_16

description:
Single-cell RNA-seq
MM25_16_GGACTCCT-AAGGAGTA
MM25_16


title: MM02_88

description:
Single-cell RNA-seq
MM2_88_AGGCAGAA-TAGATCGC
MM02_88


title: MM02_84

description:
Single-cell RNA-seq
MM2_84_CGTACTAG-CTAAGCCT
MM02_84


title: MM02_72

description:
Single-cell RNA-seq
MM2_72_CGTACTAG-AAGGAGTA
MM02_72


title: MM02_61

description:
Single-cell RNA-seq
MM2_61_CGTACTAG-ACTGCATA
MM02_61


title: MM02_51

description:
Single-cell RNA-seq
MM2_51_CGTACTAG-GTAAGGAG
MM02_51


title: MM02_7

description:
Single-cell RNA-seq
MM2_7_CGTACTAG-TAGATCGC
MM02_7


title: LCL_0087


title: MM25_14

description:
Single-cell RNA-seq
MM25_14_TCCTGAGC-CTCTCTAT
MM25_14


title: LCL_0086


title: LCL_0084


title: LCL_0083


title: LCL_0085


title: LCL_0080


title: LCL_0081


title: MM02_50

description:
Single-cell RNA-seq
MM2_50_CGTACTAG-AGAGTAGA
MM02_50


title: LCL_0082


title: MM02_5

description:
Single-cell RNA-seq
MM2_5_TAAGGCGA-CTAAGCCT
MM02_5


title: LCL_0079


title: MM02_38

description:
Single-cell RNA-seq
MM2_38_CGTACTAG-CTCTCTAT
MM02_38


title: LCL_0078


title: MM02_48

description:
Single-cell RNA-seq
MM2_48_CGTACTAG-TATCCTCT
MM02_48


title: MM17_94

description:
Single-cell RNA-seq
MM17_94_GGACTCCT-AGAGTAGA
MM17_94


title: MM17_95

description:
Single-cell RNA-seq
MM17_95_GGACTCCT-AAGGAGTA
MM17_95


title: MM17_92

description:
Single-cell RNA-seq
MM17_92_CTCTCTAC-TAGATCGC
MM17_92


title: MM17_85

description:
Single-cell RNA-seq
MM17_85_CTCTCTAC-CTCTCTAT
MM17_85


title: MM17_90

description:
Single-cell RNA-seq
MM17_90_GGACTCCT-CTCTCTAT
MM17_90


title: LCL_0076


title: LCL_0075


title: LCL_0077


title: LCL_0074


title: LCL_0073


title: LCL_0072


title: MM17_8

description:
Single-cell RNA-seq
MM17_8_TCCTGAGC-GTAAGGAG
MM17_8


title: MM17_84

description:
Single-cell RNA-seq
MM17_84_GGACTCCT-TATCCTCT
MM17_84


title: MM17_73

description:
Single-cell RNA-seq
MM17_73_GGACTCCT-GTAAGGAG
MM17_73


title: LCL_0068


title: MM17_7

description:
Single-cell RNA-seq
MM17_7_TCCTGAGC-AGAGTAGA
MM17_7


title: MM17_72

description:
Single-cell RNA-seq
MM17_72_TCCTGAGC-TATCCTCT
MM17_72


title: MM17_65

description:
Single-cell RNA-seq
MM17_65_TCCTGAGC-CTAAGCCT
MM17_65


title: LCL_0070


title: LCL_0067


title: LCL_0069


title: MM17_64

description:
Single-cell RNA-seq
MM17_64_TCCTGAGC-ACTGCATA
MM17_64


title: MM17_61

description:
Single-cell RNA-seq
MM17_61_TCCTGAGC-CTCTCTAT
MM17_61


title: LCL_0071


title: LCL_0064


title: LCL_0065


title: MM17_56

description:
Single-cell RNA-seq
MM17_56_CAGAGAGG-CTCTCTAT
MM17_56


title: LCL_0066


title: MM17_57

description:
Single-cell RNA-seq
MM17_57_TAGGCATG-AAGGAGTA
MM17_57


title: MM17_52

description:
Single-cell RNA-seq
MM17_52_TAGGCATG-GTAAGGAG
MM17_52


title: MM17_62

description:
Single-cell RNA-seq
MM17_62_CTCTCTAC-AAGGAGTA
MM17_62


title: MM17_5

description:
Single-cell RNA-seq
MM17_5_CTCTCTAC-TATCCTCT
MM17_5


title: MM17_42

description:
Single-cell RNA-seq
MM17_42_GGACTCCT-ACTGCATA
MM17_42


title: siBCat minus GSK 3

city: Rochester

first: Andre

last: van Wijnen

state: MN

address: 200 First Street SW

department: Orthopedic Surgery & Biochemistry and Molecular Biology

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

organism: Mus musculus

source_name: siBCat minus GSK

growth_protocol: MSCs were maintained in MEM alpha medium containing 10% fetal bovine serum and 100 μg/ml penicillin/streptomycin. For experiments, the cells were plated at a density of 10,000 cells/cm2 in 6-well culture plates (Fisher) and cultured for 1 day prior to addition of siRNAs and/or small molecule inhibitor GSK126. Cells were cultured in osteogenic media (50µg/ml ascorbic acid, 10mM β-glycerophosphate) for 4 days after addition of siRNAs. Cells were lysed on day 4 post-transfection.

extract_protocol:
Cells were lysed using TRIzol Reagent (Cat#: 15596026, Thermo Fisher) and stored at -80C until isolation. mRNA isolation was performed using the Direct-zol RNA Miniprep Kit (Cat#: R2052, Zymo Research) and quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher). Samples were assessed for RNA integrity (RIN) using the Agilent Bioanalyzer DNA 1000 chip (Invitrogen). Only samples with RIN scores > 6 and DV200 > 50% were selected for sequencing.
mRNA version 2 library prep kit (Illumina)

treatment_protocol: non-targeting siRNA, siRNA targeting B-Catenin, and/or small molecule inhibitor GSK126 were introduced into culture media one day after plating as indicated.

tag: strain background

value: MSC derived from adult mouse marrow

tag: treatment

value: B-Catenin siRNA and 5uM GSK126

tag: passage


title: MM17_4

description:
Single-cell RNA-seq
MM17_4_TAGGCATG-TAGATCGC
MM17_4


title: siBCat minus GSK 2


title: MM17_44

description:
Single-cell RNA-seq
MM17_44_TCCTGAGC-TAGATCGC
MM17_44


title: siBCat minus GSK 1


title: LCL_0061

tag: tissue


title: MM17_6

description:
Single-cell RNA-seq
MM17_6_TAGGCATG-ACTGCATA
MM17_6


title: siCTL plus GSK 3

description: siCTL_plus_G126-3.FCH2HTTBBXY_L2_R*_ICGTACG

source_name: siCTL plus GSK

value: non-targeting siRNA and 5uM GSK126


title: LCL_0057

value: Male


title: LCL_0060


title: siCTL plus GSK 1

description: siCTL_plus_G126-1.FCH2HTTBBXY_L2_R*_IGTGGCC


title: LCL_0054


title: LCL_0058


title: LCL_0055


title: LCL_0056


title: siCTL plus GSK 2

description: siCTL_plus_G126-2.FCH2HTTBBXY_L2_R*_IGTTTCG


title: LCL_0052


title: MM17_32

description:
Single-cell RNA-seq
MM17_32_GGACTCCT-TAGATCGC
MM17_32

value: female


title: MM17_30

description:
Single-cell RNA-seq
MM17_30_TCCTGAGC-AAGGAGTA
MM17_30

value: Multiple myeloma


title: siCTL minus GSK 3

source_name: siCTL minus GSK

value: non-targeting siRNA


title: siCTL minus GSK 2


title: MM17_3

description:
Single-cell RNA-seq
MM17_3_TAGGCATG-TATCCTCT
MM17_3

value: Bone marrow


title: MM17_29

description:
Single-cell RNA-seq
MM17_29_GGACTCCT-CTAAGCCT
MM17_29


title: siCTL minus GSK 1


title: 18:0 LPI [RNH-9-2]

city: Cleveland

first: J.

middle: Mark

last: Brown

state: OH

address: 99089 Carnegie Ave

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundaton

data_processing:
Single-ended 50 bp reads were trimmed with Trim Galore (v.0.3.3, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and controlled for quality with FastQC (v0.11.3, http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) before alignment to the Mus musculus genome (Mm10 using UCSC transcript annotations downloaded July 2016).
Reads were aligned using STAR in single-pass mode (v.2.5.2a_modified, https://github.com/alexdobin/STAR) with standard parameters but specifying "--alignIntronMax 100000 --quantMode GeneCounts".
Genome_build: GRCm38 / Mm10
Supplementary_files_format_and_content: counts

source_name: 18:0 LPI_liver homogenate

extract_protocol:
Rneasy RNA extraction
50bp single end

treatment_protocol: Saline or LPI 18:0 were injected into the portal vein of mice. 6 hours following these mice were sacked, livers harvested, and RNAseq run for global changes following acute LPI injection.

value: Lysophosphatidylinositol 18:0

value: liver


title: 18:0 LPI [RNH-10-2]


title: 18:0 LPI [RNH-8-2]


title: LCL_0059

value: B


title: MM17_25

description:
Single-cell RNA-seq
MM17_25_CTCTCTAC-GTAAGGAG
MM17_25

value: CD138 positive


title: LCL_0051

value: A

value: Female


title: LCL_0062

value: C


title: 18:0 LPI [RNH-7-2]


title: LCL_0050


title: LCL_0049


title: LCL_0090


title: LCL_0103


title: MM17_19

description:
Single-cell RNA-seq
MM17_19_CTCTCTAC-CTAAGCCT
MM17_19


title: Saline [RNH-3-2]

source_name: Saline_liver homogenate

value: saline


title: Saline [RNH-2-2]


title: Saline [RNH-5-2]


title: LCL_0053

value: peripheral blood


title: MM17_20

description:
Single-cell RNA-seq
MM17_20_TAGGCATG-CTAAGCCT
MM17_20


title: MM17_18

description:
Single-cell RNA-seq
MM17_18_CAGAGAGG-TAGATCGC
MM17_18


title: Saline [RNH-1-2]


title: LCL_0063


title: MBOAT7 ASO [RNH-10]

data_processing:
Single-ended 50 bp reads were trimmed with Trim Galore (v.0.3.3, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and controlled for quality with FastQC (v0.11.3, http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) before alignment to the Mus musculus genome (Mm10 using UCSC transcript annotations downloaded July 2016).
Reads were aligned using STAR in single-pass mode (v.2.5.2a_modified, https://github.com/alexdobin/STAR) with standard parameters but specifying "--alignIntronMax 100000 --quantMode GeneCounts".
Genome_build: GRCm38 / Mm10
Supplementary_files_format_and_content: counts file

source_name: MBOAT7 ASO_liver homogenate

treatment_protocol: Selective knockdown of Mboat7 was accomplished using 2-O-ethyl (cET) modified antisense oligonucleotides (ASO). All ASOs used in this work were synthesized, screened, and purified  by Ionis Pharmaceuticals, Inc. (Carlsbad, CA). For Mboat7 knockdown studies, adult (8 week old) male C57BL/6 mice were purchased from Jackson Labs (Bar Harbor, ME USA), and maintained on either a standard rodent chow diet or a high fat diet (HFD, D12492 from Research Diets Inc.) and injected intraperitoneally biweekly with 12.5 mg/kg of either non-targeting control ASO or one of two independent ASOs directed against murine Mboat7 for a period of 20 weeks. After 20 weeks, a necropsy was performed including harvesting the a portion of liver for RNAseq.

tag: genotype/variation

value: MBOAT7 ASO knockdown

value: Severe Fatty Liver


title: Saline [RNH-4-2]


title: MM17_17

description:
Single-cell RNA-seq
MM17_17_TAGGCATG-AGAGTAGA
MM17_17


title: MBOAT7 ASO [RNH-9]


title: 18:0 LPI [RNH-6-2]


title: MBOAT7 ASO [RNH-8]


title: MM17_16

description:
Single-cell RNA-seq
MM17_16_CAGAGAGG-AGAGTAGA
MM17_16


title: MBOAT7 ASO [RNH-6]


title: MBOAT7 ASO [RNH-7]


title: MM17_15

description:
Single-cell RNA-seq
MM17_15_CTCTCTAC-AGAGTAGA
MM17_15


title: LCL_0046


title: LCL_0048


title: LCL_0045


title: Control ASO [RNH-5]

source_name: Control ASO_liver homogenate

value: MBOAT7 Control ASO

value: Normal Liver


title: LCL_0047


title: MM17_14

description:
Single-cell RNA-seq
MM17_14_TAGGCATG-CTCTCTAT
MM17_14

value: female


title: Control ASO [RNH-3]


title: Control ASO [RNH-1]


title: MM17_12

description:
Single-cell RNA-seq
MM17_12_CTCTCTAC-ACTGCATA
MM17_12

value: Multiple myeloma


title: LCL_0044

value: Male


title: LCL_0043


title: Control ASO [RNH-4]


title: Control ASO [RNH-2]


title: MM17_10

description:
Single-cell RNA-seq
MM17_10_CAGAGAGG-GTAAGGAG
MM17_10

value: Bone marrow


title: CK306 - DMPA

city: Hamilton

first: Jocelyn

middle: M

last: Wessels

state: Ontario

address: 1280 Main Street West

department: Obstetrics and Gynecology

country: Canada

institute: McMaster University

library_source: genomic

data_processing:
Paired-end alignment using PANDAseq
FASTQ Trimming using Cutadept/sickle
FASTQ Culling using Chimera checking
OTU picking - de novo (AbundantOTU+, CD-HIT, DNACLUST, UCLUST, UPARSE) and closed reference (BLAST, UCLUST-ref, UCLUST-ref-strict)
Genome_build: Taxon Assignment - assigment algorithm (BLAST, RDP) and reference database (Greengenes 2011, Greengenes 2013, Silva 111)

molecule: genomic DNA

source_name: Cervico-vaginal lavage

extract_protocol:
Genomic DNA was extracted from the CVL supernatants using a modified DNA isolation method as described in Stearns et al. (Stearns et al., 2015). CVL supernatants were inverted to mix and transferred to screw cap tubes containing 2.8mm ceramic beads, 0.1mm glass beads, GES, and sodium phosphate buffer. Samples were bead beat and centrifuged as described in Stearns et al., 2015 and the resulting supernatant was further processed using the robotic MagMAX Express 96-Deep Well Magnetic Particle Processor (Applied Biosystems, Foster City, CA) with the Multi-Sample kit (Life Technologies #4413022, Burlington, Canada).
sl1p pipeline (Whenlan and Surette, 2017, BMC Microbiome)
16S rRNA gene sequencing

value: Cervico-vaginal lavage

tag: material sequenced

value: 16S rRNA gene

tag: group

value: DMPA


title: CK305 - OCP

value: OCP


title: CK308 - NH

value: NH


title: CK307 - DMPA


title: MM17_1

description:
Single-cell RNA-seq
MM17_1_CAGAGAGG-TATCCTCT
MM17_1

tag: patient id

tag: death(alive=0; death=1)

value: CD138 positive


title: MM02EM_95

description:
Single-cell RNA-seq
MM02P_95_CAGAGAGG-ACTGCATA
MM02EM_95

value: male

tag: prep-site

value: Pleural effusion

tag: facs sorting


title: CK303 - OCP


title: CK304 - DMPA


title: LCL_0042

value: peripheral blood

tag: age (yrs)

value: B

tag: gender


title: CK302 - DMPA


title: LCL_0039

tag: plateid

tag: plate

value: Female


title: LCL_0040

tag: rowname

tag: colname


title: LCL_0037

value: C


title: LCL_0041


title: LCL_0038


title: LCL_0036


title: MM02EM_90

description:
Single-cell RNA-seq
MM02P_90_TCCTGAGC-CTCTCTAT
MM02EM_90

tag: cell type


title: CK299 - NH


title: CK297 - OCP


title: MM02EM_87

description:
Single-cell RNA-seq
MM02P_87_CGTACTAG-ACTGCATA
MM02EM_87


title: CK295 - OCP


title: CK171 - DMPA


title: CK173 - NH


title: CK301 - NH


title: MM02EM_91

description:
Single-cell RNA-seq
MM02P_91_TAAGGCGA-TATCCTCT
MM02EM_91


title: CK170 - NH


title: CK300 - DMPA


title: CK298 - NH


title: CK174 - DMPA


title: MM02EM_92

description:
Single-cell RNA-seq
MM02P_92_CAGAGAGG-CTAAGCCT
MM02EM_92


title: MM02EM_85

description:
Single-cell RNA-seq
MM02P_85_TCCTGAGC-AAGGAGTA
MM02EM_85


title: MM02EM_86

description:
Single-cell RNA-seq
MM02P_86_TAGGCATG-ACTGCATA
MM02EM_86


title: CK165 - NH


title: CK164 - OCP


title: MM02EM_84

description:
Single-cell RNA-seq
MM02P_84_AGGCAGAA-GTAAGGAG
MM02EM_84


title: LCL_0034

value: A


title: LCL_0035


title: LCL_0031


title: CK296 - OCP


title: LCL_0030


title: MM02EM_89

description:
Single-cell RNA-seq
MM02P_89_TAAGGCGA-TAGATCGC
MM02EM_89


title: LCL_0032


title: CK163 - OCP


title: MM02EM_83

description:
Single-cell RNA-seq
MM02P_83_TCCTGAGC-ACTGCATA
MM02EM_83


title: LCL_0033


title: CK169 - NH


title: CK160 - DMPA


title: CK159 - DMPA


title: CK158 - OCP


title: CK162 - DMPA


title: MM02EM_81

description:
Single-cell RNA-seq
MM02P_81_CGTACTAG-CTCTCTAT
MM02EM_81


title: CK150 - DMPA


title: CK148 - DMPA


title: MM02EM_80

description:
Single-cell RNA-seq
MM02P_80_CAGAGAGG-AAGGAGTA
MM02EM_80


title: CK144 - DMPA


title: LCL_0029


title: CK143 - NH


title: MM02EM_79

description:
Single-cell RNA-seq
MM02P_79_TAAGGCGA-GTAAGGAG
MM02EM_79


title: CK140 - NH


title: CK141 - NH


title: CK161 - OCP


title: LCL_0027


title: LCL_0026


title: MM02EM_78

description:
Single-cell RNA-seq
MM02P_78_CAGAGAGG-GTAAGGAG
MM02EM_78


title: LCL_0024


title: CK142 - NH


title: LCL_0028


title: MM02EM_76

description:
Single-cell RNA-seq
MM02P_76_TAAGGCGA-CTAAGCCT
MM02EM_76


title: LCL_0025


title: CK138 - OCP


title: LCL_0022


title: CK136 - NH


title: MM02EM_74

description:
Single-cell RNA-seq
MM02P_74_CGTACTAG-TAGATCGC
MM02EM_74


title: MM02EM_75

description:
Single-cell RNA-seq
MM02P_75_AGGCAGAA-CTAAGCCT
MM02EM_75


title: MM02EM_73

description:
Single-cell RNA-seq
MM02P_73_GGACTCCT-CTCTCTAT
MM02EM_73


title: CK134 - OCP


title: CK133 - NH


title: wt Cd100 rep 3

city: Cologne

first: Timothy

middle: Owen

last: Jobe

state: DE

address: Zulpicher Str 47b

department: Botanical Institute

country: Germany

institute: University of Cologne

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: expression normalized using RMA

organism: Arabidopsis thaliana

source_name: 14 day old Col-0 seedling on 100uM Cd rep 3

label_protocol: standard Affymetrix protocol

growth_protocol: Minimal media

extract_protocol: Qiagen Rneasy kit

treatment_protocol: no treatment for 12 days, then transferred to 20uM As(III) for 48 hours

tag: genotype

tag: developmental stage

value: 14 day old seedling

tag: growth

value: 100uM Cd

value: seedling


title: MM02EM_71

description:
Single-cell RNA-seq
MM02P_71_CGTACTAG-CTAAGCCT
MM02EM_71

value: Multiple myeloma


title: wt Cd100 rep 2

source_name: 14 day old Col-0 seedling on 100uM Cd rep 2

tag: tissue


title: wt Cd100 rep 1

source_name: 14 day old Col-0 seedling on 100uM Cd rep 1


title: LCL_0023


title: LCL_0020


title: LCL_0021


title: LCL_0018


title: LCL_0019


title: CK132 - DMPA

value: Cervico-vaginal lavage

tag: material sequenced


title: slim1 Cd100 rep 2

source_name: 14 day old slim1-1 seedling on 100uM Cd rep 2


title: slim1 Cd100 rep 3

source_name: 14 day old slim1-1 seedling on 100uM Cd rep 3


title: MM02EM_70

description:
Single-cell RNA-seq
MM02P_70_TAGGCATG-AGAGTAGA
MM02EM_70


title: MM02EM_68

description:
Single-cell RNA-seq
MM02P_68_CAGAGAGG-CTCTCTAT
MM02EM_68


title: MM02EM_67

description:
Single-cell RNA-seq
MM02P_67_CTCTCTAC-CTCTCTAT
MM02EM_67


title: MM02EM_65

description:
Single-cell RNA-seq
MM02P_65_GCTACGCT-CTCTCTAT
MM02EM_65


title: CK129 - OCP

value: 16S rRNA gene

tag: group


title: CK127 - NH


title: MM02EM_82

description:
Single-cell RNA-seq
MM02P_82_TAGGCATG-TATCCTCT
MM02EM_82

tag: patient id


title: CK126 - DMPA

value: DMPA


title: wt 20As rep 3

source_name: 14 day old Col-0 seedling on 20uM As(III) rep 3

value: 20uM As(III)


title: LCL_0016

source_name: Lymphoblastoid cell lines

value: Male


title: MM02EM_63

description:
Single-cell RNA-seq
MM02P_63_CTCTCTAC-ACTGCATA
MM02EM_63

tag: death(alive=0; death=1)

value: CD138 positive


title: LCL_0017


title: wt 20As rep 2

source_name: 14 day old Col-0 seedling on 20uM As(III) rep 2


title: wt 20As rep 1

source_name: 14 day old Col-0 seedling on 20uM As(III) rep 1


title: CK131 - DMPA


title: slim1 Cd100 rep 1

source_name: 14 day old slim1-1 seedling on 100uM Cd rep 1


title: CK125 - NH

value: NH


title: LCL_0014


title: MM02EM_62

description:
Single-cell RNA-seq
MM02P_62_TCCTGAGC-AGAGTAGA
MM02EM_62

value: male

tag: prep-site

value: Pleural effusion


title: MM02EM_61

description:
Single-cell RNA-seq
MM02P_61_GGACTCCT-AGAGTAGA
MM02EM_61

tag: facs sorting


title: CK123 - DMPA


title: CK124 - DMPA


title: MM02EM_60

description:
Single-cell RNA-seq
MM02P_60_GGACTCCT-TATCCTCT
MM02EM_60


title: CK118 - OCP

value: OCP


title: MM02EM_59

description:
Single-cell RNA-seq
MM02P_59_AGGCAGAA-AAGGAGTA
MM02EM_59


title: LCL_0012

value: peripheral blood

tag: age (yrs)

value: B


title: slim1 As20 rep 2

source_name: 14 day old slim1-1 seedling on 20uM As(III) rep 2


title: slim1 As20 rep 1

source_name: 14 day old slim1-1 seedling on 20uM As(III) rep 1


title: LCL_0011

tag: gender


title: slim1 As20 rep 3

source_name: 14 day old slim1-1 seedling on 20uM As(III) rep 3


title: LCL_0013

tag: plateid


title: CK115 - DMPA


title: LCL_0010

tag: plate

value: Female


title: MM02EM_58

description:
Single-cell RNA-seq
MM02P_58_CTCTCTAC-TATCCTCT
MM02EM_58


title: CK114 - NH


title: MM02EM_54

description:
Single-cell RNA-seq
MM02P_54_TAAGGCGA-CTCTCTAT
MM02EM_54


title: CK112 - NH


title: CK113 - DMPA


title: LCL_0009

tag: rowname


title: MM02EM_53

description:
Single-cell RNA-seq
MM02P_53_TCCTGAGC-GTAAGGAG
MM02EM_53


title: LCL_0008

tag: colname


title: Sorted CD45RO+ TMEM cell subset from healthy donor 7

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

hyb_protocol: Samples were hybridized to GeneChip Human Transcriptome Arrays 2.0 (Thermo Scientific) following the Encore Biotin Module user guide (NuGen Technlogies) and Affymetrix's Hybridization procedures

scan_protocol: Arrays were scanned following the GCS 3000 7G User guide (Thermo Scientific)

data_processing: RMA of .CEL files using affy Bioconductor library and Brainarray: hta20hsentrezgcdf v21.0.0 custom CDF. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: sorted CD8+ T cell subset from human PBMCs

label_protocol: Samples were amplified an labeled according to Ovation Pico WTA System V2 and Encore Biotin Module user guides (NuGen Technlogies)

extract_protocol: Toral RNAs were isolated following the microRNeasy kit guidelines (Qiagen)

tag: cell type

value: Sorted CD45RO+ TMEM cell subset


title: Sorted TNR3– cell subset from healthy donor 8

value: Sorted TNR3– cell subset


title: LCL_0015


title: LCL_0007

value: A


title: LCL_0006


title: MM02EM_49

description:
Single-cell RNA-seq
MM02P_49_AGGCAGAA-AGAGTAGA
MM02EM_49

value: Multiple myeloma


title: CK104 - DMPA

value: Cervico-vaginal lavage


title: MM02EM_45

description:
Single-cell RNA-seq
MM02P_45_CGTACTAG-AAGGAGTA
MM02EM_45


title: CK103 - NH

value: 16S rRNA gene


title: Sorted TNR3+ cell subset from healthy donor 8

value: Sorted TNR3+ cell subset


title: LCL_0005


title: Sorted TNR3+ cell subset from healthy donor 7


title: LCL_0004


title: MM02EM_52

description:
Single-cell RNA-seq
MM02P_52_TAGGCATG-CTAAGCCT
MM02EM_52


title: CK100 - NH


title: MM02EM_43

description:
Single-cell RNA-seq
MM02P_43_TAGGCATG-AAGGAGTA
MM02EM_43


title: LmnaG609G/G609G

city: Shenzhen

first: yuan

last: meng

address: College avenue 1066#

department: Department of Medicine

institute: Shenzhen University

data_processing:
The reads were mapped to the mouse mm9 genome and analyzed using STAR: >90% reads mapped confidently to genomic regions and >50% mapped to exonic regions.
Cell Ranger 2.1.0 was employed to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis. >80,000 mean reads and 900 median genes per cell were obtained.
The UMI (unique molecular identifier) counts were used to quantify the gene expression levels and the t-SNE algorithm was used for dimensionality reduction.
The cell population was then clustered by k-means clustering (k = 4).
The Log2FoldChange was the ratio of gene expression of one cluster to that of all other cells. The p-value was calculated using the negative binomial test and the false discovery rate was determined by Benjamini-Hochberg procedure.
Genome_build: mm9
Supplementary_files_format_and_content: “cloupe” files include UMI values for each sample.

source_name: Lung endothelial cells (MLECs) from LmnaG609G/G609G

growth_protocol: Mice were housed and handled in accordance with protocols approved by the Committee on the Use of Live Animals in Teaching and Research of Shenzhen University, China.

extract_protocol:
CD31+ cells isolated from murine lung by FACS (>90% viability) were used for single-cell RNA sequencing.  The cDNAs were quantified using an Agilent Bioanalyzer 2100 DNA Chip, and the library was sequenced using an Illumina Hiseq PE150 with ~10-30M raw data assigned for each cell.
A sequence library was built according to the Chromium Single Cell Instrument library protocol (49). Briefly, single-cell RNAs were barcoded and reverse-transcribed using the Chromium™ Single Cell 3’ Reagent Kits v2 (10 × Genomics), then fragmented and amplified to generate cDNAs.

treatment_protocol: Lmnaf/+ allele (LmnaG609G mutation flanked by 2 loxP sites) was generated by Cyagen Biosciences Inc., China. Briefly, the 5’ and 3’ homology arms were amplified from BAC clone RP23-21K15 and RP23-174J9, respectively. The G609G (GGC to GGT) mutation was introduced into exon 11 in the 3’ homology arm. C57BL/6 embryonic stem cells were used for gene targeting. To obtain ubiquitous expression of progerin (LmnaG609G/G609G), Lmnaf/f mice were bred with E2A-Cre mice. To obtain VE-specific expression of progerin, Lmnaf/f mice were bred with Tie2-cre mice.

value: Lung endothelial cells (MLECs)

tag: cell population

value: CD31+ cells purified by fluorescence activated cell sorting (FACS)


title: CK99 - DMPA

value: DMPA


title: LCL_0003


title: Sorted TNR3– cell subset from healthy donor 7


title: CK108 - NH

value: NH


title: Lmnaf/f

source_name: Lung endothelial cells (MLECs) from Lmnaf/f


title: MM02EM_40

description:
Single-cell RNA-seq
MM02P_40_AGGCAGAA-TAGATCGC
MM02EM_40

value: male

value: CD138 positive


title: MM02EM_44

description:
Single-cell RNA-seq
MM02P_44_TAAGGCGA-AGAGTAGA
MM02EM_44

value: Pleural effusion


title: CK98 - NH

source_name: Cervico-vaginal lavage


title: CK97 - OCP

value: OCP


title: LCL_0001

value: peripheral blood


title: MM02EM_39

description:
Single-cell RNA-seq
MM02P_39_TCCTGAGC-TAGATCGC
MM02EM_39


title: Sorted CD45RO+ TMEM cell subset from healthy donor 4


title: Sorted TNR3– cell subset from healthy donor 1


title: LCL_0002

value: Female


title: Sorted TNR3– cell subset from healthy donor 4


title: Sorted CD45RO+ TMEM cell subset from healthy donor 1

value: Sorted CD45RO+ TMEM cell subset


title: MM02EM_37

description:
Single-cell RNA-seq
MM02P_37_GCTACGCT-TAGATCGC
MM02EM_37


title: FLAG-ATOH8 ChIP-seq, HPAEC-FA8, rep2

data_processing:
Reference files of the human genome hg19 (NCBI build 37, Feb. 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie (version 1.1.2) (Langmead et al., 2009) with the command "-S -a --best --strata -n 1 -m 1".
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
SMAD1/5 and FLAG-ATOH8 binding regions were identified using MACS2 software (Model based analysis of ChIP-seq) (version 2.1.0.20151222) (Zhang et al., 2008) with a q-value threshold of 0.05 (default).
WIG to bigWig conversion was performed  using UCSC wigToBigWig.
To reduce the size of the bigWig files, regions with value less than 2 were removed using bwtool (Pohl and Beato, 2014) with the command "remove less 2".
Genome_build: hg19
Supplementary_files_format_and_content: BED files (which are derived from .narrowPeak output files) and WIG files were generated using MACS2 (version 2.1.0.20151222). The detail of "BED6+4 format" is described in the README for MACS.

source_name: pulmonary arterial endothelial cells

growth_protocol: Human pulmonary artery endothelial cells (HPAECs) were obtained from Lonza (Thermo Fisher Scientific) and were cultured in EGM-2 medium (Lonza). The endothelial cells were used at passage number 4-8 for all experiments.

extract_protocol:
Chromatin isolation, sonication, immunoprecipitation using anti-SMAD1/5 antibody (913C1b; Bio Matrix Research, Chiba, Japan) and anti-FLAG M2 antibody (F3165; Sigma-Aldrich, Merck) were performed essentially as described previously (Morikawa et al., 2016). For cells stably expressing FLAG-ATOH8, we conducted nuclei isolation by NEXSON (Nuclei EXtraction by SONication) (Arrigoni et al., 2016) with slight modifications in order to reduce possible non-specific binding of exogenous protein.
The libraries were constructed as described (Murai et al, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: Recombinant human BMP-9 (R&D Systems) was used for stimulation of cells.

tag: cell line

tag: lentiviral infection

tag: treated with

value: none (untreated)

tag: chip antibody

value: anti-FLAG M2 (Sigma-Aldrich, Merck, catalog# F3165)


title: input DNA, HPAEC

value: Human pulmonary artery endothelial cells (HPAECs)


title: MM02EM_41

description:
Single-cell RNA-seq
MM02P_41_CGTACTAG-TATCCTCT
MM02EM_41

value: Multiple myeloma


title: EST KO AKI 1-6

city: Pittsburgh

first: Anne

last: Barbosa Diniz

state: PA

address: 3501 Terrace St

department: Pharmaceutical Sciences

institute: University of Pittsburgh

description: A total of 124mg of frozen renal tissues from 6 different mice in the same group were pooled together

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array. GeneChips were washed and stained in the Affymetrix Gene Scanner 7G.

scan_protocol: GeneChips were scanned using the Affymetrix Gcos/Genechip operating software.

data_processing: GeneChips were processed using the Affymetrix Gcos/Genechip operating software.

source_name: Renal tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 8 weeks old C57BL/6 (WT) mice underwent a sham or 30 minutes of warm bilateral renal ischemia-reperfusion injury (IRI). These mice were sacrificed 24 hours later and their kidneys were harvested and frozen at -80C. 180mg of frozen kidneys from 3 different mice in the WT AKI group were pooled together in the same tube. 124mg of frozen livers from 6 different mice in the EST KO AKI group were pooled together in the same tube.

tag: tissue

value: kidney

tag: strain

tag: treatment

value: acute kidney injury

tag: genotype

value: EST KO


title: MM02EM_36

description:
Single-cell RNA-seq
MM02P_36_GGACTCCT-GTAAGGAG
MM02EM_36

tag: patient id

tag: death(alive=0; death=1)

tag: prep-site

tag: facs sorting


title: FLAG-ATOH8 ChIP-seq, HPAEC-FA8, rep1


title: MM02EM_34

description:
Single-cell RNA-seq
MM02P_34_GGACTCCT-CTAAGCCT
MM02EM_34

tag: gender


title: TH 518

city: Homburg Saar

first: Masood

last: Abu-Halima

address: Kirrberger St 60

department: Human Genetics

institute: Univeristy of Saarland

description: univentricular heart (UVH)

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized

label: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

source_name: Blood

extract_protocol: Total RNA including miRNAs was isolated using the Qiagen PAXgene™ Blood miRNA  according to manufacturers recommendations.

tag: disease state

value: healthy control

value: blood


title: TH 465

description: univentricular heart (UVH)

label_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations


title: TH 437

description: univentricular heart (UVH)


title: MM02EM_32

description:
Single-cell RNA-seq
MM02P_32_CGTACTAG-GTAAGGAG
MM02EM_32


title: SMAD1/5 ChIP-seq, HPAEC BMP-9 1.5h, rep2

value: anti-SMAD1 (Bio Matrix Research, Japan, catalog# 913C1b, lot# 913C1b-3), which detects both SMAD1 and SMAD5


title: WT AKI 1-3 female

description: 100mg of frozen livers from 3 different mice in the same group were pooled together

source_name: Hepatic tissue

treatment_protocol: 8 weeks old C57BL/6 (WT) mice underwent a sham or 30 minutes of warm bilateral renal ischemia-reperfusion injury (IRI). These mice were sacrificed 24 hours later and their livers were harvested and frozen at -80C. 100mg of frozen livers from 3 different mice in the AKI group were pooled together in the same tube. 100mg of frozen livers from 3 different mice in the Sham group were pooled together in the same tube.

value: liver

value: female

value: wt


title: SMAD1/5 ChIP-seq, HPAEC BMP-9 1.5h, rep1


title: MM02EM_31

description:
Single-cell RNA-seq
MM02P_31_TAAGGCGA-ACTGCATA
MM02EM_31

value: male

value: Pleural effusion

value: CD138 positive


title: TH 436

description: univentricular heart (UVH)


title: TH 426

description: univentricular heart (UVH)


title: MM02EM_28

description:
Single-cell RNA-seq
MM02P_28_GGACTCCT-TAGATCGC
MM02EM_28


title: TH 424

description: univentricular heart (UVH)


title: TH 433

description: univentricular heart (UVH)


title: B7_pGSN_D9_R4

city: Boston

first: Lester

last: Kobzik

state: MA

address: 665 Huntington Ave

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

data_processing:
FASTQ files with basecalls were generated using Illumina bcl2fastq software with the arguments --create-fastq-for-index-reads --ignore-missing-bcls --minimum-trimmed-read-length 0 --mask-short-adapter-reads 0
DriverMap read counts were determined using Cellecta DriverMap Data Alignment Software, as detailed in https://manuals.cellecta.com/drivermap-targeted-expression-profiling-kits/v1/en/topic/run-data-extraction
The resulting data matrix of counts for genes analyzed (columns B & C) shows counts for each sample as a column (see raw data file, DriverMapDay9LungRawDataMatrix.txt)
Read counts were normalized using total counts per column (sample) to calculate scaling factors used to multiply all column values to result in identical total counts per column for all columns (samples), see processed data file DriverMapDay9LungProcessedData.txt
Supplementary_files_format_and_content: tab-delimited text file

source_name: Lung

extract_protocol:
Lung tissue RNA was isolated using the QIAGEN RNeasy mini kit (Cat. # 74104).
RNA Samples were processed using the DriverMap targeted sequencing platform and protocol developed by Cellecta, Inc (https://www.cellecta.com/products-3/drivermap-targeted-rna-sequencing/). The DriverMap platform combines multiplex PCR for ~4700 gene coding regions and quantitation by next generation sequencing.

treatment_protocol: Mice were treated by intraperitoneal injection with rhu-pGSN (2 mg/day days 3-6, then 5 mg per day days 7-9 after influenza infection) or vehicle

tag: Sex

value: Male

tag: age

value: 6-8 weeks old

tag: infection

value: influenza

value: pGSN

tag: day of lung harvest


title: B8_pGSN_D9_R5