title: WT3 Naïve rep1 line 2

description:
WT3 sample technical replicate 1.  fastq read- pairs from lane 2
Y7_L002


title: Ranolazine_3

status: Public on Apr 16 2021

type: SRA

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

country: USA

institute: Weill Cornell Medical College

description: processed data file: CM.expression.xls

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Transcript abundances was estimated in Fragments Per Kilobase of exon per Million mapped reads (FPKM) by using Cufflinks v2.1.1 package.
Raw reads counts were extracted using htseq-count v0.11.2.
Genome_build: hg19
Supplementary_files_format_and_content: txt file storing raw read counts; excel file storing FPKM values or TMM-based normalized counts per gene per sample

molecule: total RNA

organism: Homo sapiens

source_name: SARS-CoV-2 infected_Ranolazine treated_ES-derived cardiomyocyte

growth_protocol: For monolayer-based differentiation of cardiomyocytes (CMs), hPSCs were cultured between P20-P40 and seeded at a density of 3x105 cells/well of a 6-well plate and grown for 48 hr to 90% confluence in a humidified incubator with 5% CO2 at 37℃. On day 0, the medium was replaced with RPMI 1640 supplemented with B27 without insulin and 6 µM CHIR99021. On day 1, the medium was changed to RPMI 1640 supplemented with B27 without insulin for 48 hr. Day 3, medium was refreshed to RPMI 1640 supplemented with B27 without insulin and 2 µM C59 for another 48 hr. On day 5, the medium was changed back to RPMI-B27 without insulin for 48 hr, and then switched to RPMI 1640 plus normal B27 until day 12 with a medium change every 2 days. On day 12, the medium was transiently changed to RPMI 1640 without D-glucose containing ascorbic acid, human albumin and DL-Lactate for two days to allow metabolic purification of CMs. From that day on, fresh RPMI 1640-B27 was changed every two days; Macrophages were derived from hPSCs by adapting a previously reported protocol28. hPSCs were cultured between P20-P40. First, H9 or H1 cells were lifted with ReLeSR (STEMCELL Technologies) as small clusters onto Matrigel-coated 6-well plates at low density. On day 0, IF9S medium was supplemented with 50 ng/ml BMP-4, 15 ng/ml Activin A and 1.5 µm CHIR99021. On day 2, medium was refreshed with IF9S medium with 50 ng/ml VEGF, 50 ng/ml bFGF, 50 ng/ml SCF (R&D Systems) and 10 µm SB431542 (Cayman Chemical). On day 5 and da y7, medium was changed to IF9S with 50 ng/ml IL-6 (R&D Systems), 12 ng/ml IL-3 (R&D Systems), 50 ng/ml VEGF, 50 ng/ml bFGF, 50 ng/ml SCF and 50 ng/ml TPO (R&D Systems). On day 9, cells were dissociated with TrypLE (Life Technologies) and re-suspended in IF9S medium with 50 ng/ml IL-6, 12 ng/ml IL-3 and 80 ng/ml M-CSF (R&D Systems). On day 13 and day 15, medium was changed and supplemented with 50 ng/ml IL-6, 12 ng/ml IL-3 and 80 ng/ml M-CSF. All differentiation steps were cultured at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: To analyze the gene expression of CMs co-cultured with H9-derived macrophages using RNA-seq, we used trans-well plates. CMs were seeded on the lower plate of 24 well plates and macrophages were seeded onto the upper chamber. After 24 hr, drug treatments were done to CMs and macrophages in the upper chamber were infected with SARS-CoV-2 (MOI=0.1). The trans-well chamber will allow cytokines to go through but not macrophages. 24 hpi, CMs were collected to extract total RNA. For analyzing macrophages infected with virus, macrophages were seeded onto 24 well plates and infected with SARS-CoV-2 (MOI=0.1). 24 hpi, macrophages were collected for total RNA.

tag: tissue/cell type

value: human ES-derived cardiomyocyte

tag: virus

value: SARS-CoV-2 infected

tag: treatment

value: Ranolazine treated


title: Ranolazine_2

description: processed data file: CM.expression.xls


title: VCaP INPUT

city: Pieve Emanuele

first: sarah

middle: natalia

last: mapelli

state: Milan

address: Via Rita Levi Montalcini 4

department: Experimental Immunopathology

country: Italy

institute: Humanitas research

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2
Duplicates were removed with picard-tools with MarkDuplicates.jar
Peaks were called with MACSversion 1.4, using pvalue threshold equal to 0.0005
Peaks were annotated with annotatePeaks.pl within the Homer software (on hg19 reference)
Genome_build: hg19
Supplementary_files_format_and_content: Annotated peak text files

molecule: genomic DNA

source_name: VCaP cells

growth_protocol: VCaP cells were cultured in T75 flasks by using regular growth medium. Briefly, to isolate chromatin, cells (120.000.000 per IP) were cross-linked using 1% Formaldehyde cross-link protein-DNA complexes and crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication, resulting in an average chromatin fragment size of 200 bp. Samples lysis was performed as previously described using MNase enzyme 1000 gel units=1 uL (Yokoyama, Y. et al. BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer. Cancer Res 76, 6320-6330, doi:10.1158/0008-5472.can-16-0854 (2016). After adding the MNase sonication buffer, the samples were sonicated for 30 cycles, 30 sec ON and 30 sec OFF at high voltage. ChIP and input DNA (50 ng) were used for indexed library preparation using NEBNext Ultra II DNA Library Prep kit and subjected to 75 bp single-end sequencing on the Illumina NextSeq500. Fragmented chromatin from VCaP cells was incubated with anti-IGG (Normal Mouse, Millipore, cat. 12-371) 2 µg or 10 µg, mERG (AB MART).

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with above mentioned antibodies.

tag: cell line

value: VCaP

tag: chip antibody

value: anti-IgG


title: 160726B_E6

type: RNA

city: Jinan

first: Yaru

last: Tian

address: Jiyan Road

country: China

institute: Shandong Cancer Hospital

hyb_protocol: 1 μg of total RNA was used for reverse transcription into cDNAs according to the manufacturer’s instructions. Then, the cDNA was labeled with Cy3-dCTP and hybridized to the Agilent Human CBC lncRNA + mRNA microarray V4.0

scan_protocol: The microarrays were washed and scanned using a G2505C Microarray Scanner (Agilent). Data were normalized and analyzed using GeneSpring software (Agilent).

source_name: SCLC without BM

label_protocol: The total RNAs was labeled to lncRNA + mRNA Human Gene Expression Microarray V4.0 (4x180K), each array contained a probe set comprising 40,916 human lncRNA transcripts and 34,235 human mRNAs.

growth_protocol: Peripheral blood anticoagulated by ethylenediaminetetraacetic acid was acquired from all SCLC patients.

extract_protocol: Total RNA was extracted from PBMCs using Trizol® reagent (Invitrogen, Grand Island, NY, USA).

treatment_protocol: Human PBMCs were isolated with Ficoll-Hypaque gradients.

tag: subject status

value: SCLC patient without BMs

tag: tissue

value: Peripheral blood


title: WT3 Naïve rep3 line 2

city: la Jolla

first: Juliana

middle: Maria

last: Navia-Pelaez

state: california

address: 9500 Gilman dr.

department: Medicine

institute: UCSD

description:
WT3 sample technical replicate 3.  fastq read- pairs from lane 2
Y9_L002

data_processing:
Illumina Casava1.7 software used for basecalling and Illumina bcl2fastq Conversion Software was then used to convert bcl files to fastq format
Splice aware alignment of FASTQ data was done using STAR (Dobin et al., 2013)
Quality control of sequenced data and alignment was performed by FASTQC v0.11.17,  QoRTs v1.3.0, and MultiQC v1.7 ( pmid: 27312411 )
Counting of genes associated with the reads was performed using STAR v2.6.0a (Dobin et al., 2013)
Comparisons of experimental groups were performed with DEseq2 binomial modeling using Wald test and accounting for an FDR of 10%. Volcano plots include genes significantly different with a fold change >1.5.
Pathway enrichment and GO analysis were performed in metascape.org using a minimum of 3 genes and P<0.05 (Zhou et al., 2019).
genome build: GRCm38 from ENSEMBL
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: table with normalized counts for expressed genes

organism: Mus musculus

source_name: Microglia

extract_protocol:
Microglia cells were sorted directtly into lysis buffer buffer containing Triton X-100, RNase Inhibitor, and Oligo(dT)30-VN and vortexed. Then lysates were hybridized with oligo(dT)+ to the poly(A) tails of the mRNA. Reagents for reverse transcription were added to construct cDNA libraries following addition of reagents for PCR amplification (qPCR was not performed at this point). Libraries were quantified and QC was performed using TapeStation high sensitivity D5000 screentape in addition to Qubit double stranded high sensitivity assay. All samples were adjusted to 1ng of cDNA for input into NexteraXT protocol. QC check was performed with TapeStation high sensitivity D1000 screen tape in addition to Qubit double stranded high sensitivity assay. The samples were subjected to qPCR and pooling and loaded onto the NovaSeq for paired-end 50x50 reads using NovaSeq S1 100 cycle kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell suspentions from lumbar spinal cord were stained, filtered, and FACS-sorted to collect resident microglia

value: Spinal Cord

tag: genotype

value: WT

value: naïve (no treatment)


title: 160726B_E3

data_processing: Data were normalized and analyzed using GeneSpring software (Agilent).


title: WT2 Naïve rep3 line 2

description:
WT2 sample technical replicate 3.  fastq read- pairs from lane 2
Y6_L002


title: 160726B_E2


title: Ranolazine_1

description: processed data file: CM.expression.xls


title: VCaP mERG

value: anti-mERG


title: 160726B_E1


title: 160726B_E4


title: DMSO_3

description: processed data file: CM.expression.xls

source_name: SARS-CoV-2 infected_DMSO treated_ES-derived cardiomyocyte

value: DMSO treated


title: WT2 Naïve rep3 line 1

description:
WT2 sample technical replicate 3.  fastq read- pairs from lane 1
Y6_L001


title: 160726B_L6

source_name: SCLC with BM

value: SCLC patient with BMs and 6


title: 160726B_E5


title: WT3 Naïve rep2 line 1

description:
WT3 sample technical replicate 2.  fastq read- pairs from lane 1
Y8_L001


title: 160726B_L5


title: WT2 Naïve rep2 line 2

description:
WT2 sample technical replicate 2.  fastq read- pairs from lane 2
Y5_L002


title: DMSO_2

description: processed data file: CM.expression.xls


title: hiNSC_scRNA

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to the human reference genome GRCh38 (Ensembl 93) v3.0.0, and counted following the Cell Ranger v.3.1.0 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R.
Genome_build: human reference genome GRCh38 (Ensembl 93) v3.0.0
Supplementary_files_format_and_content: three csv files containing raw count values for each cell in the two samples, respectively

source_name: hiNSC-GFP-TRAIL

growth_protocol: Cell lines were cultured in Dulbecco’s modified eagle’s medium (DMEM, Gibco) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, Millipore), 1% (v/v) Penicillin-Streptomycin (Gibco), and 0.2% (v/v) PlasmocinTM.

extract_protocol:
Single cell suspension of different samples was prepared using Accutase Cell Detachment Solution (STEMCELL Technologies). Cells were incubated with accutase at room temperature for 5 mins before centriguation and then single cells were resuspended with media and sent for sequencing.
Libraries were prepared using Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3.

value: skin

value: Lentivirus engineered


title: hiNeuroS_scRNA

source_name: hiNeuroS-TRAIL


title: 160726B_L3


title: 160726B_L4


title: DMSO_1

description: processed data file: CM.expression.xls


title: WT2 Naïve rep2 line 1

description:
WT2 sample technical replicate 2.  fastq read- pairs from lane 1
Y5_L001


title: fibroblast_scRNA

value: Wild type


title: LNA023

city: Singapore

first: Jinmiao

address: 8a Biomedical Grove

department: SigN

country: Singapore

institute: A*STAR

description: 10X Genomics

data_processing:
Cell Ranger pipeline version 3.1.0 was run on the raw paired-end fastq files (2x151 bp) on an Illumina HiSeq 4000 and NovaSeq 6000 using GRCh38 as the reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv: Tab-separated text files.
Supplementary_files_format_and_content: matrix.mtx: Matrix files.

source_name: PBMCs

extract_protocol:
PBMCs were thawed and stained for sorting on FACS Aria. Bulk cells were sorted into a 1.5mL Eppendorf tube containing PBS, 0.04% BSA for 10x processing.
About 8,700-14,000 cells were encapsulated in droplets using the 10X Genomics Chromium Controller. Single cell 5’ Gene Expression libraries, V(D)J Enriched libraries were prepared using the 10X Genomics Chromium Single Cell 5′ Library & Gel Bead Kit v1, V(D)J Enrichment Kit, Human T and B cell, A Chip Kit and i7 Multiplex Kit according to the manufacturer’s protocol (10X Genomics, Pleasanton, CA, USA).

tag: dengue infection status

value: Secondary

tag: serotype of infection

tag: sorted cell population


title: LNA014

description: 10X Genomics

value: Primary


title: 160726B_L2


title: non-COVID_5

description: processed data file: raw_counts_genes.clean.txt

value: human heart

value: Uninfected

value: unknown


title: 160726B_L1


title: WT2 Naïve rep1 line 2

description:
WT2 sample technical replicate 1.  fastq read- pairs from lane 2
Y4_L002


title: non-COVID_4


title: WT2 Naïve rep1 line 1

description:
WT2 sample technical replicate 1.  fastq read- pairs from lane 1
Y4_L001


title: LNA063-CD47pos

description: Smart-seq

data_processing:
Raw reads were aligned to the human reference genome GRCh38 from GENCODE release 22 using RSEM program version 1.2.19 with default parameters.
Gene expression values in transcripts per million (TPM) were calculated using the RSEM program and the human GENCODE annotation version 22.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing the TPM tables.

extract_protocol:
PBMCs were thawed and stained for sorting on FACS Aria. Single cells were sorted in wells containing 2 μl of 1 mg/ml Ultrapure BSA (ThermoFisher) and 1 μl of 10 mM dNTP mix (New England Biolabs).
cDNA library was prepared following Smart-Seq v2 protocol (Picelli et al., 2014) with the following modifications: 1. 1mg/ml BSA Lysis buffer (Ambion® ThermoFisher Scientific, Waltham, MA, USA); 2. Use of 250 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA).

value: Secondary infection


title: LNA054-CD47neg

description: Smart-seq


title: LNA063-CD47neg

description: Smart-seq


title: non-COVID_3


title: non-COVID_2


title: WT1 Naïve rep3 line 2

description:
WT1 sample technical replicate 3.  fastq read- pairs from lane 2
Y3_L002


title: WT1 Naïve rep3 line 1

description:
WT1 sample technical replicate 3.  fastq read- pairs from lane 1
Y3_L001


title: LNA054-CD47pos

description: Smart-seq


title: LNA036

description: Smart-seq


title: LNA018

description: Smart-seq


title: non-COVID_1


title: COVID_3

source_name: SARS-CoV-2 infected_heart

value: SARS-CoV-2 infected person


title: WT1 Naïve rep2 line 2

description:
WT1 sample technical replicate 2.  fastq read- pairs from lane 2
Y2_L002


title: WT1 Naïve rep2 line 1

description:
WT1 sample technical replicate 2.  fastq read- pairs from lane 1
Y2_L001


title: LNA002

description: Smart-seq

value: Primary infection


title: LNA006

description: Smart-seq


title: WT1 Naïve rep1 line 2

description:
WT1 sample technical replicate 1.  fastq read- pairs from lane 2
Y1_L002

value: Spinal Cord


title: COVID_1


title: COVID_2


title: WT1 Naïve rep1 line 1

description:
WT1 sample technical replicate 1.  fastq read- pairs from lane 1
Y1_L001

value: WT


title: E1481DK2

description: Smart-seq


title: OVA_GCBcell_gene expression

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
immunization
scRNA-seq
5'-end gene expression

data_processing:
scRNA-seq data: the 10x Genomics Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing and single cell UMI counting
Genome_build: mm10
Supplementary_files_format_and_content: mtx.tsv, a gene by cell count matrix in the tsv format
Supplementary_files_format_and_content: fasta, assembled BCR contig sequence of each cell
Supplementary_files_format_and_content: annotations.csv, high-level and detailed annotations of each contig

source_name: spleen

growth_protocol: primary GC B cells

extract_protocol:
RNA were extracted from cells using RNAClean XP beads (Backman)
10x 5'-end single cell RNA-seq

tag: strain

tag: age

value: 8 weeks

tag: Sex

value: male

tag: cell type

value: germinal center B cells


title: OVA_GCBcell_Ig

description:
immunization
scRNA-seq
5'-end immunoglobulin


title: MCF7/hMSC 4OHT, rep3

city: HOUSTON

first: Igor

middle: L.

last: Bado

state: Texas

address: One Baylor Plaza, Alkek Building N1130

department: Breast Center

institute: Baylor College of Medicine

data_processing:
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d).
RSEM (version 1.2.28) was used to quantify gene and isoform expression.
DEseq2 R package is used to normalize the gene/isoform expression matrix.
Genome_build: GRCh38.83
Supplementary_files_format_and_content: RSEM read counts and DESeq2 normalized gene expression matrix.

source_name: MCF7  organoids

growth_protocol: GFP-RPL10a-expressing MCF-7 cells were maintained in phenol red-free DMEM supplemented with 2% charcoal stripped FBS for 48 hours upon which, 1 million cells were seeded in 100 mm low attachment plates (Corning, cat #05-539-101) alone or in coculture with human mesenchymal stem cells (MSCs).

extract_protocol:
Cells were collected using  a Translating Ribosome Affinity Purification  (TRAP) assay
Library was prepared using illumina Nextera XT Kit and paired-end sequencing was performed on a Nextseq 550 System

treatment_protocol: Mammospheres were left to form for 24h before in 10nM 17β-estradiol, or fulvestrant or 100nM Tamoxifen treatment.

tag: culture conditions

value: coculture

value: 4-Hydroxytamoxifen (TAM)

tag: culture type


title: MCF7/hMSC 4OHT, rep2


title: SR_Ctrl_3

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Illumina Casava2.2 software used for basecalling.
Sequenced reads were mapped to hg38 whole genome using STAR v2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.26.8
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include rawcount values for each Sample …

source_name: human clear cell renal cell skin metastasis

growth_protocol: Caki-1 cells were grown in DMEM medium supplemented with 10% FBS and 1% Pen/Strep antibiotics. Cells were splitted twice per week and diluted at a 1:20, 1:25 ratio. Caki-1-SR cells were splitted following the same protocol and cultured in the same medium supplemented with 1 uM sunitinib

extract_protocol:
Protocol given by the manufacturer; QIAGEN Rneasy Plus Mini Kit (50); Ref 74134
RNA libraries were prepared for sequencing using Illumina TruSeqHT stranded mRNA kit

treatment_protocol: To establish Caki-1-SR cells chronic treatment with sunitinib was maintained for > 30 weeks; for RNA sequencing of Caki-1-SR cells the treatment with sunitnib was exchanged through normal culture medium. Caki-1 cells were cultured in culture medium and were not exposed to sunitinib treatment.

tag: disease

value: renal cell carcinoma


title: pancreatic_organoids_lane1_MULTI

city: San Francisco

first: Daniel

middle: N

last: Conrad

state: CA

institute: UCSF

description: Sample barcode data used to demultiplex samples in cDNA libraries

data_processing:
FASTQ files were generated directly from Illumina BCL files using Illumina bcl2fastq version 2.19
Cell Ranger 5.0.0 Pipeline was used for read alignment (w/ include-introns option) and generation of gene-barcode matrices
MULTI-seq barcode alignment and sample classification was performed using the deMULTIplex R package
Genome_build: GRCh38
Supplementary_files_format_and_content: cDNA Libraries: gene-cell matrices are provided in the format produced by Cell Ranger. The matrix itself is in matrix market exchange format, with the column (cell barcodes) and row (gene identities) labels given in TSV format as described in the cellranger documentation.   MULTI-seq Barcode Libraries: MULTI-seq barcode-cell matrices are provided in CSV format.

source_name: hESC

extract_protocol:
Nuclei were prepared from samples using a custom protocol, then nuclei were labeled with MULTI-seq barcodes and lysed in droplets using the 10X Chromium instrument according to the 10X Chromium Single Cell 3' v3 Reagent Kit User Guide Rev C.
Library preparation was performed according to the 10X Chromium Single Cell 3' v3 Reagent Kit User Guide Rev C and using the custom MULTI-seq protocol.

value: pancreatic organoids


title: pancreatic_organoids_lane2_MULTI


title: pancreatic_organoids_lane2_cDNA

description: 11 samples multiplexed into a single library (technical replicate 1)

molecule: polyA RNA


title: pancreatic_organoids_lane1_cDNA


title: SR_Ctrl_2

value: human clear cell renal cell skin metastasis


title: Caki1_Ctrl_3


title: MCF7/hMSC ICI, rep3

value: Fulvestrant (ICI)


title: MCF7_DVL3-WT

city: Lubbock

first: Kevin

last: Pruitt

address: 3601 4th Street

department: Immunology & Molecular Microbiology

institute: Texas Tech University Health Sciences Center

data_processing:
the RNA-Seq reads were normalized by RPKM and assembled by mapping reads directly to the annotated human reference genome using the DNASTAR SeqMan software (DNASTAR, Inc., Madison, WI).
Differential gene expression levels were quantified using Fisher’s Exact Test Signal Search in the DNASTAR ArrayStar software package (DNASTAR, Inc., Madison, WI).
Differentially expressed genes were filtered if they met the criterion for a two-fold change, a p-value that was less than .05 at a 95 % confidence interval.
Supplementary_files_format_and_content: For each comparison, genes were sorted based on fold change.  The results were ported into Excel spreadsheets where the log2 of the fold change for each gene was calculated.

growth_protocol: cells were cultured in RPMI 1640 (Gibco), supplemented with 1% pen-strep and 10% fetal bovine serum from GIBCO at 37℃ in 5% CO2

extract_protocol:
Total RNA was isolated using the Aurum™ Total RNA Mini Kit (Bio Rad)
NEBNext Ultra II Directional RNA Library Prep according to the manufacturer’s protocol (NEB # E7760L)

value: Epithelium

value: Breast

value: Overexpression


title: MCF7/hMSC 4OHT, rep1


title: MCF7/hMSC ICI, rep2


title: NP_GCBcell_2_gene expression


title: NP_GCBcell_1_Ig


title: NP_GCBcell_1_gene expression


title: Caki1_Ctrl_2


title: SR_Ctrl_1


title: MCF7_NTC

value: NTC


title: MCF7/hMSC E2, rep3

value: Estradiol (E2)


title: ATAC_S8

description: Bulk ATAC-seq

data_processing:
Analysis was conducted with a modified version of the Encode Consortium’s ATAC-Seq Pipeline
Adapters were trimmed from input FASTQ files using cutadapt
Alignment was performed using Bowtie2
The MACS2 was used for peak calling, and Peaks in the EncodeDCC consensus blacklist regions were also removed
IGV was used for peak visualization
Genome_build: human
Supplementary_files_format_and_content: bigwig

source_name: xenograft bone metastasis

growth_protocol: SCP2 cells were maintained in DMEM 10% FBS

extract_protocol:
Samples were processed as previously (https://doi.org/10.1038/nmeth.2688)
Library was prepared using customized primers as previously described (https://doi.org/10.1038/nmeth.2688)

value: SCP2 (MCF7_clone-derived)

tag: collection process

value: Bone-entrained

tag: passage


title: MCF7/hMSC ICI, rep1

tag: treatment


title: MCF7_EV

tag: cell line

value: EV


title: MCF7_DVL3_shB

value: Knockdown


title: MCF7/hMSC E2, rep2


title: NP_GCBcell_2_Ig

value: 8 weeks

value: male


title: Spleen_erythroid_M3_2_3

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

data_processing:
Library strategy: Micro Capture-C (MCC)
The raw fastq file is processed to reconstruct a single read from the paired end sequencing. This is then mapped to the 800bp sequence surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This allows the reads to be cut into ‘slices’ depending on whether they align to the sequence around the capture site. This strategy allows ligation junctions in the read to be determined with base pair accuracy. The resulting fastq file is aligned to the genome using bowtie.
The resulting fastq file is aligned to the genome using bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig of data from multipul viewpoints

source_name: Spleen erythroid cells

extract_protocol:
Qiagen DNeasy blood and tissue kit
7-10 µg of each 3C library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (1-3 cycles of 60s: duty cycle 10%; intensity 5; cycles per burst 200). The library size was assessed using an Agilent TapeStation (DNA 1000) and an Ampure XP (Beckman Coulter) bead clean-up was performed once the sample had been adequately sonicated. To maximise library complexity three aliquots, each containing 2 µg sonicated 3C library, were processed in parallel for each sample to add sequencing adaptors. NEB Ultra II reagents were used following the standard protocol with the following modifications: first, additional adapter was added into the ligation reactions (7.5 µl rather than 2.5 µl); no size selection was performed (Ampure XP bead clean ups were always performed with a sample:bead ratio of 1:1.8) and the final PCR to add indices was amplified in triplicate from each aliquot using the Herculase II PCR kit (Agilent) to maximise DNA yield. All parallel library preparations and PCR reactions were pooled for each reaction.

treatment_protocol: Cells were resuspended in aliquots of 1 x 107 in 10 ml media with 10% FCS in a 15-ml conical centrifuge tube using an automated cell counter (CountessII, Thermo Fisher).  Formaldehyde (37% (vol/vol)) was added to each aliquot to make a final concentration of 2% (vol/vol) and the cells were incubated on a roller mixer for 10 minutes at room temperature. The crosslinking reaction was quenched with cold 1 M glycine to a final concentration 130 mM and the sample was centrifuged (5 min at 220 g).  The supernatant was discarded and the cell pellet was washed with 10 ml cold Phosphate Buffered Saline (PBS) and reconstituted in 1 ml PBS. An automated cell count on was performed on 10 ml of the cell suspension to reconfirm the cell number. Digitonin (Sigma D-141) was prepared fresh for each experiment (0.5% in dimethylsulfoxide (DMSO) (wt/vol)). Each batch of digitonin was tested for its ability to permeabilise cells at a concentration of 0.005% (wt/vol). 10 ml digitonin was added to make a final concentration of 0.005% (wt/vol).

value: Spleen erythroid cells


title: Spleen_erythroid_M3_2_2


title: Spleen_erythroid_M3_2_1


title: MCF7/hMSC E2, rep1

value: coculture


title: ATAC_S6

description: Bulk ATAC-seq


title: MDA-MB-468_EV


title: MCF7/hMSC UT, rep3

value: Vehicle (UT)


title: Spleen_erythroid_M3_1_3


title: MCF7/hMSC UT, rep2


title: ATAC_S5

description: Bulk ATAC-seq

source_name: Parental

value: un-entrained


title: Spleen_erythroid_M3_1_2


title: Spleen_erythroid_M3_1_1


title: ATAC_S3

description: Bulk ATAC-seq


title: MDA-MB-468_DVL3-WT


title: ATAC_S4

description: Bulk ATAC-seq


title: MDA-MB-468_DVL3_shB


title: MDA-MB-468_NTC


title: WES2_S15

description: Whole Exome Seq

data_processing:
Library strategy: exome-seq
FastQC was used to evaluate data quality
adapters were removed using cutadapt and trim galore
BWA-MEM was used for read alignment using hg19 as reference genome
After QC of mapped reads, post alignment processing was performed using varscan for variant calling.
Genome_build: hg19
Supplementary_files_format_and_content: tabular.txt (CNV and SNP)

source_name: cell line

growth_protocol: MCF7 cells were maintained in DMEM 10% FBS

extract_protocol:
For DNA collection we used the Quick-DNA Miniprep Kit from Zymo (#D3024)
hgRNA was amplified using the KAPA SYBR FAST qPCR Kit before library preparation with the NEBNext Multiplex oligos for illumina (Dual Index Primers set1) kit (#NEB E7600S)

treatment_protocol: Bone-entrained cells were derived from bone lesions and cultured in in vitro.

tag: reporter gene

value: Bone-derived

tag: replicates


title: MCF7/hMSC UT, rep1


title: ATAC_S7

description: Bulk ATAC-seq


title: Spleen_erythroid_M2_2_3

tag: tissue


title: ATAC_S2

description: Bulk ATAC-seq


title: ATAC_S1

description: Bulk ATAC-seq


title: Spleen_erythroid_M2_2_2


title: WES2_S14

description: Whole Exome Seq


title: MCF7 4OHT, rep3

value: monoculture

value: 4-Hydroxytamoxifen (TAM)


title: WES2_S12

description: Whole Exome Seq

value: Parental


title: Spleen_erythroid_M2_2_1


title: MCF7 4OHT, rep2


title: MCF7 ICI, rep3

value: Fulvestrant (ICI)


title: LCM_19

description: Targeted hgRNA A21

data_processing:
Library strategy: Targeted Sequencing
Sequencing performed by Novogen
quality control and data normalization was performed using TraceQc ( https://github.com/LiuzLab/TraceQC.)

source_name: Xenograft bone lesion

extract_protocol:
For DNA collection we used the quick-dna/rna microprep plus kit from Zymo (#D7005)
hgRNA was amplified using the KAPA SYBR FAST qPCR Kit before library preparation with the NEBNext Multiplex oligos for illumina (Dual Index Primers set1) kit (#NEB E7600S)

value: LCM-derived


title: LCM_20

description: Targeted hgRNA A21


title: WES2_S11

description: Whole Exome Seq


title: Spleen_erythroid_M2_1_3


title: LCM_18

description: Targeted hgRNA A21


title: MCF7 ICI, rep2


title: MCF7 ICI, rep1


title: Spleen_erythroid_M2_1_2


title: Spleen_erythroid_M2_1_1


title: LCM_16

description: Targeted hgRNA A21


title: WES2_S8

description: Whole Exome Seq


title: WES2_S7

description: Whole Exome Seq


title: Spleen_erythroid_M1_2_3


title: MCF7 E2, rep3

value: Estradiol (E2)


title: WES2_S6

description: Whole Exome Seq


title: LCM_14

description: Targeted hgRNA A21


title: Spleen_erythroid_M1_2_2


title: LCM_15

description: Targeted hgRNA A21


title: Spleen_erythroid_M1_2_1


title: MCF7 E2, rep2


title: WES2_S5

description: Whole Exome Seq


title: MCF7 40HT, rep1


title: LCM_13

description: Targeted hgRNA A21


title: MCF7 E2, rep1


title: WES2_S10

description: Whole Exome Seq


title: Spleen_erythroid_M1_1_3


title: MCF7 UT, rep3


title: Spleen_erythroid_M1_1_2


title: LCM_17

description: Targeted hgRNA A21


title: LCM_12

description: Targeted hgRNA A21


title: WES2_S4

description: Whole Exome Seq


title: LCM_11

description: Targeted hgRNA A21


title: WES2_S9

description: Whole Exome Seq


title: WES2_S3

description: Whole Exome Seq


title: MCF7 UT, rep1


title: LCM_10

description: Targeted hgRNA A21


title: Spleen_erythroid_M1_1_1


title: WES2_S2

description: Whole Exome Seq


title: MCF7 UT, rep2


title: Tsga8-Y_LCM_late_early_R2

city: Yokohama

first: Keisuke

last: Minamizawa

address: Kanazawa

country: Japan

institute: Yokohama city university

data_processing:
Sequence reads were checked for quality with FastQC and trimmed with Trim Galore! (version 0.4.0) with default parameters.
RNA-seq reads were mapped onto mm10 using Hisat2 (version 2.1.0) with default parameters.
Read counts and quantification were performed using SeqMonk (version 0.30.2)
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated using SeqMonk contain normalised RNA-seq read count (RPKM) for all genes.

source_name: Testis

extract_protocol:
Total RNA from whole testis was isolated using Isogen (Nippon Gene) according to the manufacturer's instructions. For the LCM samples, tissue lysate was used for RNA extraction using Isogen (Nippon Gene).
For the whole testis samples, purified RNA was used for library preparation using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) . For the LCM samples, purified total RNA was used to prepare RNA-seq libraries with the SMART-seq2 protocol.

value: round spermatids (steps 1-3) and elongated spermatids (step 9-16)

tag: genotype

tag: gender


title: LCM_9

description: Targeted hgRNA A21


title: Tsga8-Y_LCM_late_early_R1


title: Tsga8+Y_LCM_late_early_R2


title: WES_S20

description: Whole Exome Seq


title: WES2_S1

description: Whole Exome Seq


title: LCM_7

description: Targeted hgRNA A21


title: LCM_8

description: Targeted hgRNA A21


title: WES_S19

description: Whole Exome Seq


title: FOB_R1881, rep2

data_processing:
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads derived from FOB coculture organoid materials containing a mixture of human and mouse reads were separated using Xenome (version 1.0.1).
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d).
RSEM (version 1.2.28) was used to quantify gene and isoform expression.
DEseq2 R package is used to normalize the gene/isoform expression matrix.
Genome_build: GRCh38.83 and GRCm38.83
Supplementary_files_format_and_content: RSEM read counts and DESeq2 normalized gene expression matrix.

growth_protocol: FOB cells were cultured in serum-free DMEM/F12 media in 3D monoculture or coculture (with 4T1 or TRAMP) platform

extract_protocol:
Total RNA was extracted for library preparation.
Library was prepared using illumina Nextera XT Kit and paired-end sequencing was performed on a Nextseq 550 System

treatment_protocol: Mammospheres were treated for 24 hours with 10nM 17β-estradiol or R1881


title: Tsga8+Y_LCM_late_early_R1


title: FOB_R1881, rep3


title: FOB_R1881, rep1


title: Tsga8-Y_LCM_early_mid_R2

value: round spermatids (steps 4-8)


title: LCM_6

description: Targeted hgRNA A21


title: WES_S18

description: Whole Exome Seq


title: LCM_5

description: Targeted hgRNA A21


title: WES_S17

description: Whole Exome Seq


title: FOB_E2, rep2

value: Estradiol


title: FOB_E2, rep1


title: WES_S16

description: Whole Exome Seq


title: FOB_UT, rep3

value: untreated


title: LCM_4

description: Targeted hgRNA A21


title: Tsga8+Y_LCM_early_mid_R1


title: FOB_UT, rep2


title: LCM_3

description: Targeted hgRNA A21


title: WES_S15

description: Whole Exome Seq


title: Tsga8+Y_LCM_early_mid_R2


title: FOB_E2, rep3


title: FOB_UT, rep1


title: LCM_1

description: Targeted hgRNA A21


title: FOB/TRAMP_R1881, rep3


title: WES_S13

description: Whole Exome Seq


title: WES_S14

description: Whole Exome Seq


title: WES_S12

description: Whole Exome Seq


title: Tsga8-Y_LCM_early_mid_R1


title: RKO_Cystine(25μM) rep3 [D3]

city: Kunming

first: Jiao

last: Wu

state: Yunnan

address: No.519 at Kunzhou Road

department: Department of the Second Medical Oncology

institute: The Third Affiliated Hospital of Kunming Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 or RKO cells were cultured for 48 hours in cystine-free or 25μM cystine-containing conditional media

value: RKO

value: Colon cancer cells

value: 25μM cystine-contained media for 48 hours


title: WES_S11

description: Whole Exome Seq


title: RKO_Cystine(25μM) rep2 [D2]


title: GNPs normal IgG rep 1

city: Kanazawa

first: Atsuki

last: Kawamura

state: Ishikawa

address: 13-1 Takaramachi

department: Department of Histology and Cell Biology

institute: Graduate School of Medical Sciences, Kanazawa University

data_processing:
Trimming of adapter sequences was performed with Trimmomatic (version 0.39).
RNA-seq: The total amount of each transcript was calculated with the use of a series of programs including HISAT2 (version 2.1.0), featureCounts (version 2.0.0) and DESeq2 (version 1.26.0). RNA-seq reads were mapped against the mouse (mm10) genome.
ChIP-seq: The pair-end reads were mapped to mm10 genome with bowtie (version 2.2.3), and duplicated reads were removed with samtools (version 1.9). Markedly enriched regions of the genome were identified with the MACS2 peak caller (version 2.1.0, with the option “-p 1e-5 --gsize mm --nomodel --extsize 160”). Peak annotation was identified with the ChIPseeker (1.22.1), and heatmap and density profiles were created using ngsplot (2.47).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS2; text file includes DESeq2 results

source_name: Granule neuron progenitors

extract_protocol: GNPs were isolated from the cerebellum of mice at P7 by Percoll density gradient centrifugation. RNA was harvested using Trizol reagent.  NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used with 1 µg of total RNA for the construction of sequencing libraries. ChIP was subjected with antibodies to CHD8 or normal IgG. Purified DNA was used to prepare a library with the use of SMARTer ThruPLEX DNA-Seq kit and SMARTer DNA unique dual index kit.

value: Cerebellum

value: Postnatal day 7

value: wild type

tag: chip antibody

value: normal IgG

tag: antibody

value: IgG


title: GNPs normal IgG rep 2

tag: strain

tag: age


title: FOB/TRAMP_R1881, rep1

value: coculture


title: WES_S10

description: Whole Exome Seq

value: Parental


title: RKO_Cystine(25μM) rep1 [D1]

tag: cell type


title: FOB/TRAMP_UT, rep3

tag: culture conditions


title: LCM_2

description: Targeted hgRNA A21


title: GNPs input rep 2


title: FOB/TRAMP_UT, rep2

tag: culture type


title: GNPs input rep 1


title: RKO_Control rep3 [C3]

value: cystine-free media for 48 hours


title: GNPs CHD8 ChIP rep 2


title: WES_S8

description: Whole Exome Seq


title: FOB/TRAMP_UT, rep1


title: WES_S9

description: Whole Exome Seq


title: GNPs CHD8 CKO rep 4


title: GNPs CHD8 ChIP rep 1


title: RKO_Control rep2 [C2]


title: WES_S7

description: Whole Exome Seq


title: FOB/TRAMP_R1881, rep2


title: RKO_Control rep1 [C1]


title: GNPs CHD8 CKO rep 3


title: FOB/4T1_E2, rep3


title: HCT116_Cystine(25μM) rep3 [B3]


title: WES_S6

description: Whole Exome Seq


title: FOB/4T1_E2, rep2


title: HCT116_Cystine(25μM) rep2 [B2]


title: WES_S5

description: Whole Exome Seq


title: FOB/4T1_E2, rep1


title: GNPs CHD8 CKO rep 1


title: WES_S4

description: Whole Exome Seq


title: FOB/4T1_UT, rep3


title: GNPs control rep 4


title: WES_S3

description: Whole Exome Seq


title: HCT116_Control  rep3 [A3]


title: GNPs control rep 3


title: WES_S2

description: Whole Exome Seq


title: FOB/4T1_UT, rep2


title: FOB/4T1_UT, rep1


title: HCT116_Control  rep2 [A2]


title: GNPs CHD8 CKO rep 2


title: WES_S1

description: Whole Exome Seq


title: HCT116_Control  rep1 [A1]


title: H2A.Z_ATPminus_input_rep1

status: Public on Apr 15 2021

city: Shinagawa-ku

first: Hiroaki

last: Tachiwana

state: Tokyo

institute: Hoshi University

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie2 version 2.4.1
Duplicate reads were removed with picard using MarkDuplicates
Bigwig files were made with the BamCoverage of deeptools
Genome_build: hg38
Supplementary_files_format_and_content: bigqig file

source_name: HeLa cells

extract_protocol:
Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to ThruPLEX DNA-Seq Kit.

treatment_protocol: ANP32E knockdonw or ATP depletion

value: cervix epitheloid carcinoma

value: HeLa


title: H2A.Z_ATPplus_input_rep2


title: H2A.Z_ATPplus_input_rep1


title: H2A.Z_siANP32E_input_rep2


title: H2A.Z_siANP32E_input_rep1


title: HCT116_Cystine(25μM) rep1 [B1]


title: H2A.Z_siLuc_input_rep1


title: H2A.Z_siLuc_input_rep2


title: H2A.Z_ATPplus_ChIP_rep1


title: H2A.Z_ATPminus_ChIP_rep2


title: H2A.Z_ATPplus_ChIP_rep2


title: H2A.Z_siANP32E_ChIP_rep2


title: H2A.Z_ATPminus_ChIP_rep1


title: H2A.Z_siANP32E_ChIP_rep1


title: Cy3-Ps-Untrtd_Cy5-Ps-Mext_90dpi_rep1

city: Oulu

first: Janne

middle: J

last: Koskimäki

address: Pentti Kaiteran katu 1

department: Ecology and Genetics Research Unit

country: Finland

institute: University of Oulu

description:
Analysis used total RNA of the untreated Scots pine seedlings (Control) for comparison to the experimental samples, seedlings inoculated with M. extorquens DSM13060 (Treatment), harvested at 90 days post-inoculation.
PICME Pine 7K, custom cDNA microarray chip (Austrian Institute of Technology, Seibersdorf)

hyb_protocol: cDNAs of the M. extorquens-inoculated and control seedlings, were united and hybridized with custom cDNA microarray chips (PICME Pine 7K, Austrian Institute of Technology, Seibersdorf) in total of six times with two-color dye-swap approach to minimize technical variability and dye bias. The ESTs printed on the PICME_Pine arrays were produced by INRA (Dubos and Plomion 2003).  Microarray chips were prewashed in 2 x SSC, 0.2% SDS at 65°C for 10 min, followed by a wash in 0.2 x SSC at room temperature for 2 min and rinse in deionized water for 1 min at room temperature. The hybridization and washing procedures were performed according to the protocol of 3DNA Array 50 Expression Array Detection Kit (Genisphere) recommended for the PCR product (cDNA) arrays. Briefly, the cDNA hybridization mix consisted of 10µl of dye specific cDNAs from M. extorquens-inoculated and control pine seedling, 2 µl of locked nucleic acids dT blocker, 13 µl of nuclease free water and 25 µl of 2 x formamide-based hybridization buffer. The cDNA hybridization was carried out in a dark humidified hybridization chamber (Corning) at 45°C for 16 h. Hybridized microarray slides were washed in 2 x SSC, 0.2% SDS for 15 min at 65°C, 2 x SSC for 10min at room temperature and 0.2 x SSC for 10 min at room temperature with gentle agitation. Fluorescent labelling of the cDNAs by 3DNA hybridization was carried out in a total volume of 50 µl using a formamide-based buffer with 3h incubation at 48°C in a dark humidified hybridization chamber according to the manufacturer’s protocol recommended for the PCR product (cDNA) arrays. Hybridized microarray slides were washed as previously and immediately spin-dried in Falcon-tube by centrifugation at 250 x g for 2 min.

scan_protocol: Slide scanning was performed with ScanArray Gx microarray scanner (Perkin Elmer, Massachu¬setts, USA) with 90% laser power at 5 micron resolution. PMT values were adjusted accordingly for each scanning to minimize the background noise.

data_processing:
Fluorescent images were analyzed with ScanArray Express software (Perkin Elmer), and low-quality spots were flagged and removed during statistical analysis. Differential expression analysis was carried out with Limma (Ritchie et al., 2015). The raw intensities within each array was normalized with loess-method (with background subtraction) and quantile normalized among arrays. Differential expression was analyzed with linear regression (lmFit), using contrast between inoculation and control samples. The treatment was a fixed effect and technical variation among replicated probes was a random effect in the model (using duplicateCorrelation-function). The variance was smoothed with eBayes. The expression changes were false discover rate corrected with BH-method (Benjamini & Hochberg, 1995), and changes with adjusted p value (q value) of < 0.05 were considered significant. All differential analyses were carried out with the R software (R Core Team 2013).
Empty spots (null) had higher background compared to foreground intensity or had 0 weight (bad spot).

organism: Pinus sylvestris

source_name: Untreated Scots pine seedling control sample

label_protocol: Each total RNA sample (40µg/reaction) was reverse transcribed to cDNA using Superscript III reverse transcriptase (Life Technologies) with oligo-dT primers incorporated with dye specific (Cy3 or Cy5) capture sequences in according to the protocol of 3DNA Array 50 Expression Array Detection Kit (Genisphere).

growth_protocol: Seeds of Pinus sylvestris L. (elite line K884) were incubated in 55 °C for 72 h and transferred to sterile water overnight. Seeds were subsequently surface sterilized with 3% calcium hypochlorite (w/v) for 15 min and rinsed thoroughly three times with sterile water. Seeds were planted into glass jars containing sterile vermiculite with water and grown in 22 ± 1 °C with 16 h photoperiod and irradiance of 75 µmol m-2 s-1 for five days. For the bacterial inoculum, Methylorubrum extorquens DSM13060 was routinely grown to late-log phase in M9 minimal salts medium supplemented with 250 mM methanol and 10 mM sodium succinate, washed in PBS buffer, carefully re-suspended to sterile water, and adjusted to 2.5 x 107 CFU.

extract_protocol: RNA was isolated from the seedlings according to first part of the protocol of Jaakola et al. (2001). After LiCl2 precipitation, RNA pellet was treated with RNase-free DNase set (Qiagen) 15 min at 25°C to digest any contaminating DNA. Reactions with total RNA were subsequently purified using RNeasy Mini Kit (Qiagen). Total RNA concentrations were quantified using NanoDrop ND-1000 spectrofotometer (NanoDrop Technologies, USA). RNA quality was assessed by agarose gel electropherosis and using Bioanalyzer 2100 (Agilent technologies, USA) with RNA Nano 6000 chips.

treatment_protocol: After germination, half of the Pinus sylvestris (elite line K884) seedlings were inoculated by 2.5 x 10^6 CFU of Methylorubrum extorquens DSM13060 diluted in sterile water (TREATMENT), while the control seedlings were treated only with sterile water (CONTROL). Growing was continued for 90 days (days post-inoculation; dpi) in sterile glass jars containing vermiculite with water. Upon sample collection, all seedlings were immediately frozen in liquid nitrogen and stored at -80°C until gene expression and metabolomics analyses.

value: 90 days post-mock treatment (sterile H2O)

source_name: Scots pine seedling treated with Methylorubrum extorquens DSM13060

value: 90 days post inoculation Methylorubrum extorquens DSM13060


title: Cy3-Ps-Untrtd_Cy5-Ps-Mext_90dpi_rep2

source_name: Scots pine seedling treated with Methylorubrum extorquens DSM13061


title: Cy3-Ps-Mext_Cy5-Ps-Untrtd_90dpi_rep1

value: 90 days post-inoculation Methylorubrum extorquens DSM13060


title: H2A.Z_siLuc_ChIP_rep2


title: Cy3-Ps-Untrtd_Cy5-Ps-Mext_90dpi_rep3

source_name: Scots pine seedling treated with Methylorubrum extorquens DSM13062


title: H2A.Z_siLuc_ChIP_rep1


title: Cy3-Ps-Mext_Cy5-Ps-Untrtd_90dpi_rep2


title: Maxiprep_S80

city: Davis

first: Alexander

middle: Star

last: Nord

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

data_processing:
Library strategy: MPRA
PE reads were trimmed using Ngmerge (v0.2_dev) in adaptor removal mode.
Reads from were aligned to the human and mouse genomes (GRCh38, GRCm38) using bwa mem v0.7.17.
Aligned reads in SAM format were converted to BAM format, and duplicates were removed using Picard Tools MarkDuplicates, v2.23.3.
Reads per amplicon were counted using samtools view -F 0x0400 v1.10
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: CSV, read counts per MPRA amplicon

molecule: other

organism: synthetic construct

source_name: plasmid DNA library

extract_protocol:
Bulk forebrains were dissected from postnatal day (P)7 mice injected with the viral library at P0. Dissection included whole forebrain, separated into left and right hemispheres, after removing surface tissue and skull. Hemispheres were stored in RNAlater Stabilization Solution (Thermo Fisher #AM7020) for downstream dual DNA and RNA collection. Hemispheres were then physically homogenized and processed using the AllPrep DNA/RNA Mini Kit (Qiagen #80204) to collect total RNA and genomic DNA from the same tissue. RNA was treated on-column with 1 µL RNase-Free DNase (Qiagen #79254). First strand cDNA was synthesized from purified total RNA using the SuperScript VILO cDNA Synthesis Kit (Invitrogen #11755050) with random primers.
We amplified the variable regions of the reporter library from cDNA and genomic (g)DNA using PCR with Phusion Hot Start II High Fidelity DNA polymerase (Invitrogen #F549S) using primers flanking the variable region within pscAAV-Hsp68-EGFP (forward primer, Amplicon PCR Primer F: GATCACTCTCGGCATGGAC; reverse primer, Amplicon PCR Primer R: GATGGCTGGCAACTAGAAGG). PCR consisted of 30 cycles (or 35, for technical replicate Sample 4-35) at 60 °C for annealing and 1 min for extension. PCRs were then loaded onto a 1.0% agarose gel, the ~1-1.1 kb fragment excised, and gel fragment purified using the Promega Gel & PCR Cleanup system (#A9282). Purified gel fragments were then re-purified using the Qiagen MinElute PCR Purification Kit (#28004) to remove residual chemical contamination, and concentration and quality assessed with Nanodrop and the Qubit dsDNA High Sensitivity assay kit (Thermo Fisher #Q33230). Purified amplicons were prepared for sequencing using the Nextera XT DNA Library Preparation Kit (Illumina #FC-131-1001) using 1 ng of purified amplicon library per sample. Quality and concentration of sequencing libraries was assessed using an Agilent BioAnalyzer instrument. Each library was quantified and pooled for sequencing on the Illumina HiSeq 4000 using a paired end 150-bp sequencing strategy. The miniMPRA was sequenced on a MiSeq instrument since lower coverage was required due to lower library complexity.

treatment_protocol: C57BL/6 mice from Jackson Laboratories were used for mouse experiments. All procedures were performed in accordance with the ARVO statement for the Use of Animals in Ophthalmic and Vision Research and were approved by the University of California Animal Care and Use Committee (AUP #R200-0913BC). Surgery was performed under anesthesia, and all efforts were made to minimize suffering. Neonatal mice (on a C57BL6/J background) were injected in the prefrontal cortex in 2 separate locations with 0.5 µL of virus. Only the left side of brain was injected. A beveled 34-gauge needle (Hamilton syringes) was used to push through the skull and to inject virus into the brain. Virus was delivered slowly by hand over the course of 1 min. Mice were anesthetized on ice for 3-4 min prior to injection, and after injection mice were heated on a warm pad before being returned to the cage.

tag: genetic material

value: plasmid DNA library

tag: developmental stage

tag: vehicle

value: AAV library


title: Cy3-Ps-Mext_Cy5-Ps-Untrtd_90dpi_rep3


title: LMS_23

city: Seville

first: Juan

last: Diaz-Martin

address: Av Manuel Siurot

country: Spain

institute: IBiS

data_processing:
Base-calling Illumina Basespace
Generation of read counts HTG Edgeseq Parser v. 5,2,823,5648
Normalization  R Bioconductor DESeq2 v. 1,28,1
Genome_build: hg19
Supplementary_files_format_and_content: fastq
Supplementary_files_format_and_content: Table with median transformation normalized counts
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: uterine leiomyosarcoma

extract_protocol:
Total RNA was prepared from 5µm FFPE tissue sections of microdissected ITF using the Agencourt FormaPure kit (A33341; Beckman Coulter, Indianapolis, IN, USA) and following the manufacturer’s instructions. RNA concentration was determined with Qubit 4 Fluorometer and Qubit® RNA HS Reagent (Thermo Fisher Scientific, Waltham, MA, USA).
HTG EdgeSeq Chemistry was employed to synthetize the RNA-Seq library. Briefly, target capture was performed by hybridizing the mRNA with Nuclease Protection Probes (NPPs). The S1 nuclease was added to the mix, producing a stoichiometric amount of target mRNA/NPP duplexes. This reaction was blocked by enzyme heat denaturation of S1. The samples were randomized before inclusion in the HTG EdgeSeq system to reduce potential biases in the run. Each hybridized sample was used as template to set up PCR reactions with specially designed tags, sharing common sequences that are complementary to both 5’-end and 3’-sequences of the probes, and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode used for sample identification and multiplexing. After PCR amplification, a clean-up procedure was performed using Agencourt AMPure XP (Beckman Coulter). The library was quantified by quantitative PCR, using KAPA Library Quantification (Roche), according to the manufacturer’s instructions. All samples and controls were quantified in triplicate and no template control was included in any run.

tag: tumor type

value: leiomyosarcoma

tag: tumor area

value: Invasive tumor front


title: LMS_21


title: LMS_15


title: LMS_13


title: LMS_11


title: LMS_20


title: LMS_16


title: H2A.Z_ATPminus_input_rep2

tag: cell line


title: LMS_07


title: CE_35

source_name: uterine adenocarcinoma

value: adenocarcinoma


title: LMS_05


title: CE_38


title: CE_30


title: CE_29


title: CE_25


title: CE_32


title: CE_28


title: CE_24


title: LMS_17


title: CE_16


title: CE_20


title: CE_22


title: CE_21


title: CE_09


title: CE_34


title: CE_02


title: CE_01


title: CE_26


title: EA.hy.RNA.AlincRNA.rep1

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

institute: A. I. Virtanen Institute

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.AlincRNA.rep1

data_processing:
Raw reads were trimmed and filtered using Trim Galore (v.0.4.4) with Phred quality score cutoff 30.
Processed reads were aligned to the GRCh37 genome assembly using STAR version 2.5.4b (Dobin et al. 2013) with options --outFilterMismatchNoverLmax 0.04 and --outFilterMultimapNmax 10.
Aligned reads mapping to features were assigned using featureCounts (Rsubread 1.32.4) with the Gencode V19 GTF.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

growth_protocol: EA.hy926 (ATCC; CRL-2922) were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM)-high glucose (D5671, Sigma) supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated from the cells using RNeasy Mini kit (74104 ;QIAGEN) and DNase treated with RNase-Free DNase Set (79254 ;QIAGEN).
Prior to RNA library preparation, the quality of the input RNA was assessed by Fragment Analyzer (Agilent)  using the RNA Kit (DNF-471; Agilent) and a threshold of RQN>9. RNA library preparation was carried out using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7765; New Englands BioLabs) according to manufacturer instructions. Briefly, 0.5 ug of DNAse-treated RNA was subjected to ribosomal RNA (rRNA) depletion, followed by RNA fragmentation, cDNA synthesis and 11 cycles of PCR amplification. The resultant library was quantified using Qubit dsDNA HS Assay Kit (Q32851; ThermoFisher Scientific) and its quality was checked with Bioanalyzer (Agilent). Individual libraries were pooled in equimolar amount (4 nM for each) and sequenced with the Nextseq 550 (Illumina) using single end 75 cycles for 10 million reads per sample.
Total RNA was isolated from the cells using RNeasy Mini kit (74104 ;QIAGEN) and DNase treated with RNase-Free DNase Set (79254 ;QIAGEN).
The quality of the input RNA was assessed by Fragment Analyzer (Agilent)  using the RNA Kit (DNF-471; Agilent) and a threshold of RQN>9. RNA library preparation was carried out using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7765; New Englands BioLabs) according to manufacturer instructions, using  0.5 ug of DNAse-treated RNA subjected to ribosomal RNA (rRNA) depletion, followed by RNA fragmentation, cDNA synthesis and 11 cycles of PCR amplification. The resultant library was quantified using Qubit dsDNA HS Assay Kit (Q32851; ThermoFisher Scientific) and its quality was checked with Bioanalyzer (Agilent). Individual libraries were pooled in equimolar amount (4 nM for each) and sequenced with the Nextseq 550 (Illumina) using single end 75 cycles for 10 million reads per sample.

treatment_protocol: CRISPR/Cas9-mediated deletion of target regions were performed using the Alt-R CRISPR-Cas9 System (Integrated DNA technology; IDT)

value: VEGFA_lincRNA knock-out


title: EA.hy.RNA.AlincRNA.rep2

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.AlincRNA.rep2


title: MALAT1_9

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute

description:
3’end RNA
MALAT1_knockdown_cpm.tsv

data_processing:
Fastq files were processed using an in-house RNAseq pipeline. First, FastQC (0.11.8) was used for data quality control after which adapter sequences, poly-A readthrough and low quality reads were removed via bbduk
Reads were mapped with STAR (v.2.6.0c) against the hg38 reference genome
Gene counts determined via HTSeq (v.0.11.0).
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file (tsv) contains counts per million (CPM) for all samples (columns) for 17,209 protein-coding genes

source_name: HEK-293T (dCas9-KRAB-MeCP2 positive)

growth_protocol: Nuclease deficient dCas9-KRAB-MeCP21 was stably introduced in HEK293T cells using the piggy-transposase system. dCas9-KRAB-MeCP2 positive HEK293T cells were selected using 10µg/ml of blasticidin. 12,000 cells per well were seeded in 96-well plates in 180 µl RPMI cell culture medium.

extract_protocol:
72 hours following the transfection, cells were lysed with SingleShot lysis buffer (Biorad, cat # 172-5081).
Quantseq RNAseq library preparation (Lexogen) was performed according to the manufacturer’s protocol using 5 ul of cell lysate as input. Libraries were quantified by qPCR, pooled, and sequenced on a Nextseq500 (Illumina).
3' end RNA-seq

treatment_protocol: single guide RNAs (sgRNA) targeting a window of 300bp up- and down-stream of the MALAT1 transcription start site (TSS), were designed using the DeskGen tool. Two control sgRNAs (GAACGACTAGTTAGGCGTGTA, GTGCGATGGGGGGGTGGGTAGC) were selected from Horlbeck et al. and Gilbert et al. 24 hours post seeding, sgRNAs were transfected with lipofectamine reagent CRISPRMAX to a final concentration of 0.5ng/µl in 200µl.

tag: treatment


title: EA.hy.RNA.AlincRNA.control.rep2

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.AlincRNA.control.rep2

value: control


title: EA.hy.RNA.ClincRNA.control.rep1

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.ClincRNA.control.rep1


title: EA.hy.RNA.ClincRNA.rep1

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.ClincRNA.rep1

value: VEGFC_lincRNA knock-out


title: MALAT1_7

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: MALAT1_8

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: CE_23


title: CE_19


title: MALAT1_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: MALAT1_4

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: MALAT1_10

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: MALAT1_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC2_SS6_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC2_SS5_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC2_SS5_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC2_SS4_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC2_SS4_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: EA.hy.RNA.ClincRNA.rep2

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.ClincRNA.rep2


title: EA.hy.RNA.AlincRNA.control.rep1

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.AlincRNA.control.rep1


title: NC2_SS3_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: EA.hy.RNA.ClincRNA.rep3

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.ClincRNA.rep3


title: EA.hy.RNA.ClincRNA.control.rep2

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.ClincRNA.control.rep2


title: EA.hy.RNA.AlincRNA.rep3

description:
Clones
total RNA, rRNA depleted
EA.hy.RNA.AlincRNA.rep3


title: NC2_SS2bis_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC2_SS2bis_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: LMS_19


title: NC1_SS6_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: MALAT1_6

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC2_SS1bis_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS3_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS5_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS4_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS5_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS4_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS3_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS2bis_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC2_SS6_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS2bis_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS1bis_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: NC1_SS1bis_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: Cell 94 from tonsillectomy sample 5

city: Chicago

first: Yuta

last: Asano

state: IL

address: 924 E 57th Street

institute: The University of Chicago

data_processing:
Illumina bcl2fastq2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence.
Before mapping, reference human transcriptome was masked for low-complexity or low-quality sequence by RepeatMasker with -noint -norna -qq options.
Reads were mapped to masked human transcriptome by kallisto. For single-end reads, -l 200 -s 50 options were used.
High quality cells were selected by detected gene count (> 3,000 for the first, and > 1,000 for the second cohort) and antibody gene expression (sum of log2-cpm values of Ig heavy constant region genes > 5).
Data of the first cohort was normalized by RUVSeq using ERCC-mapped reads as negative controls, and normalized by log2-cpm. The second cohort data were also log2-cpm-normalized and combined with the first cohort data by ComBat and SCTransform in Seurat to generate the integrated data.
Genome_build: GRCh38
Supplementary_files_format_and_content: Csv files of the normalized first cohort and integrated data

source_name: Tonsil

extract_protocol:
Tissues were minced and digested by Liberase TL, stained and sorted by FACS Fusion at -80 ˚C and frozen until library preparation.
Smart-Seq 2
single-cell RNA-seq

tag: patient

value: Tonsil 5

tag: plate

tag: well

tag: batch

value: Batch 5

tag: cohort

value: Second


title: Cell 96 from tonsillectomy sample 5


title: Cell 93 from tonsillectomy sample 5


title: Cell 95 from tonsillectomy sample 5


title: Cell 92 from tonsillectomy sample 5


title: NC2_SS3_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: Cell 89 from tonsillectomy sample 5


title: Cell 91 from tonsillectomy sample 5


title: NC2_SS1bis_2

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: Cell 90 from tonsillectomy sample 5


title: Cell 88 from tonsillectomy sample 5


title: Cell 87 from tonsillectomy sample 5


title: NC1_SS6_1

description:
3’end RNA
MALAT1_knockdown_cpm.tsv


title: Cell 84 from tonsillectomy sample 5


title: Cell 83 from tonsillectomy sample 5


title: Cell 86 from tonsillectomy sample 5


title: Cell 82 from tonsillectomy sample 5


title: Cell 85 from tonsillectomy sample 5


title: Cell 77 from tonsillectomy sample 5


title: Cell 79 from tonsillectomy sample 5


title: Cell 75 from tonsillectomy sample 5


title: Cell 76 from tonsillectomy sample 5


title: Cell 78 from tonsillectomy sample 5


title: Cell 74 from tonsillectomy sample 5


title: Cell 73 from tonsillectomy sample 5


title: Cell 81 from tonsillectomy sample 5


title: Cell 72 from tonsillectomy sample 5


title: Cell 80 from tonsillectomy sample 5


title: Cell 71 from tonsillectomy sample 5


title: Cell 70 from tonsillectomy sample 5


title: Cell 68 from tonsillectomy sample 5


title: Cell 67 from tonsillectomy sample 5


title: Cell 69 from tonsillectomy sample 5


title: Cell 65 from tonsillectomy sample 5


title: Cell 64 from tonsillectomy sample 5


title: Cell 63 from tonsillectomy sample 5


title: Cell 66 from tonsillectomy sample 5


title: Cell 60 from tonsillectomy sample 5


title: Cell 61 from tonsillectomy sample 5


title: Cell 58 from tonsillectomy sample 5


title: Cell 62 from tonsillectomy sample 5


title: Cell 57 from tonsillectomy sample 5


title: Cell 59 from tonsillectomy sample 5


title: Cell 56 from tonsillectomy sample 5


title: Cell 54 from tonsillectomy sample 5


title: Cell 55 from tonsillectomy sample 5


title: Cell 51 from tonsillectomy sample 5


title: Cell 52 from tonsillectomy sample 5


title: Cell 53 from tonsillectomy sample 5


title: Cell 50 from tonsillectomy sample 5


title: Cell 49 from tonsillectomy sample 5


title: Cell 48 from tonsillectomy sample 5


title: Cell 45 from tonsillectomy sample 5


title: Cell 47 from tonsillectomy sample 5


title: Cell 44 from tonsillectomy sample 5


title: Cell 43 from tonsillectomy sample 5


title: Cell 42 from tonsillectomy sample 5


title: Cell 41 from tonsillectomy sample 5


title: Cell 40 from tonsillectomy sample 5


title: Cell 39 from tonsillectomy sample 5


title: Cell 37 from tonsillectomy sample 5


title: Cell 36 from tonsillectomy sample 5


title: Cell 33 from tonsillectomy sample 5


title: Cell 38 from tonsillectomy sample 5


title: Cell 35 from tonsillectomy sample 5


title: Cell 34 from tonsillectomy sample 5


title: Cell 31 from tonsillectomy sample 5


title: Cell 29 from tonsillectomy sample 5


title: Cell 32 from tonsillectomy sample 5


title: Cell 28 from tonsillectomy sample 5


title: Cell 27 from tonsillectomy sample 5


title: Cell 30 from tonsillectomy sample 5


title: Cell 26 from tonsillectomy sample 5


title: Cell 25 from tonsillectomy sample 5


title: Cell 24 from tonsillectomy sample 5


title: Cell 46 from tonsillectomy sample 5


title: Cell 21 from tonsillectomy sample 5


title: Cell 20 from tonsillectomy sample 5


title: Cell 23 from tonsillectomy sample 5


title: Cell 16 from tonsillectomy sample 5


title: Cell 18 from tonsillectomy sample 5


title: Cell 22 from tonsillectomy sample 5


title: Cell 15 from tonsillectomy sample 5


title: Cell 19 from tonsillectomy sample 5


title: Cell 12 from tonsillectomy sample 5


title: Cell 13 from tonsillectomy sample 5


title: Cell 14 from tonsillectomy sample 5


title: Cell 17 from tonsillectomy sample 5


title: Cell 11 from tonsillectomy sample 5


title: Cell 9 from tonsillectomy sample 5


title: Cell 10 from tonsillectomy sample 5


title: Cell 7 from tonsillectomy sample 5


title: Cell 5 from tonsillectomy sample 5


title: Cell 8 from tonsillectomy sample 5


title: Cell 6 from tonsillectomy sample 5


title: Cell 4 from tonsillectomy sample 5


title: Cell 3 from tonsillectomy sample 5


title: Cell 96 from renal allograft sample 7

source_name: Kidney

value: Kidney 7


title: Cell 1 from tonsillectomy sample 5


title: Cell 95 from renal allograft sample 7


title: Cell 2 from tonsillectomy sample 5


title: Cell 94 from renal allograft sample 7


title: Cell 91 from renal allograft sample 7


title: Cell 90 from renal allograft sample 7


title: Cell 93 from renal allograft sample 7


title: Cell 89 from renal allograft sample 7


title: Cell 92 from renal allograft sample 7


title: Cell 83 from renal allograft sample 7


title: Cell 85 from renal allograft sample 7


title: Cell 84 from renal allograft sample 7


title: Cell 78 from renal allograft sample 7


title: Cell 80 from renal allograft sample 7


title: Cell 81 from renal allograft sample 7


title: Cell 79 from renal allograft sample 7


title: Cell 77 from renal allograft sample 7


title: Cell 75 from renal allograft sample 7


title: Cell 74 from renal allograft sample 7


title: Cell 71 from renal allograft sample 7


title: Cell 70 from renal allograft sample 7


title: Cell 72 from renal allograft sample 7


title: Cell 68 from renal allograft sample 7


title: Cell 67 from renal allograft sample 7


title: Cell 65 from renal allograft sample 7


title: Cell 66 from renal allograft sample 7


title: Cell 69 from renal allograft sample 7


title: Cell 64 from renal allograft sample 7


title: Cell 88 from renal allograft sample 7


title: Cell 87 from renal allograft sample 7


title: Cell 63 from renal allograft sample 7


title: Cell 86 from renal allograft sample 7


title: Cell 62 from renal allograft sample 7


title: Cell 82 from renal allograft sample 7


title: Cell 61 from renal allograft sample 7


title: Cell 60 from renal allograft sample 7


title: Cell 76 from renal allograft sample 7


title: Cell 54 from renal allograft sample 7


title: Cell 59 from renal allograft sample 7


title: Cell 52 from renal allograft sample 7


title: Cell 53 from renal allograft sample 7


title: Cell 58 from renal allograft sample 7


title: Cell 57 from renal allograft sample 7


title: Cell 56 from renal allograft sample 7


title: Cell 55 from renal allograft sample 7


title: Cell 51 from renal allograft sample 7


title: Cell 50 from renal allograft sample 7


title: Cell 48 from renal allograft sample 7


title: Cell 49 from renal allograft sample 7


title: Cell 46 from renal allograft sample 7


title: Cell 73 from renal allograft sample 7


title: Cell 47 from renal allograft sample 7


title: Cell 45 from renal allograft sample 7


title: Cell 44 from renal allograft sample 7


title: Cell 41 from renal allograft sample 7


title: Cell 42 from renal allograft sample 7


title: Cell 43 from renal allograft sample 7


title: Cell 39 from renal allograft sample 7


title: Cell 36 from renal allograft sample 7


title: Cell 37 from renal allograft sample 7


title: Cell 38 from renal allograft sample 7


title: Cell 40 from renal allograft sample 7


title: Cell 34 from renal allograft sample 7


title: Cell 35 from renal allograft sample 7


title: Cell 33 from renal allograft sample 7


title: Cell 32 from renal allograft sample 7


title: Cell 31 from renal allograft sample 7


title: Cell 25 from renal allograft sample 7


title: Cell 28 from renal allograft sample 7


title: Cell 27 from renal allograft sample 7


title: Cell 29 from renal allograft sample 7


title: Cell 30 from renal allograft sample 7


title: Cell 26 from renal allograft sample 7


title: Cell 23 from renal allograft sample 7


title: Cell 19 from renal allograft sample 7


title: Cell 20 from renal allograft sample 7


title: Cell 17 from renal allograft sample 7


title: Cell 11 from renal allograft sample 7


title: Cell 16 from renal allograft sample 7


title: Cell 15 from renal allograft sample 7


title: Cell 13 from renal allograft sample 7


title: Cell 18 from renal allograft sample 7


title: Cell 14 from renal allograft sample 7


title: Cell 12 from renal allograft sample 7


title: Cell 10 from renal allograft sample 7


title: Cell 9 from renal allograft sample 7


title: Cell 6 from renal allograft sample 7


title: Cell 4 from renal allograft sample 7


title: Cell 7 from renal allograft sample 7


title: Cell 5 from renal allograft sample 7


title: Cell 22 from renal allograft sample 7


title: Cell 21 from renal allograft sample 7


title: Cell 24 from renal allograft sample 7


title: Cell 89 from tonsillectomy sample 4

value: Tonsil 4

value: Batch 4

value: First


title: Cell 87 from tonsillectomy sample 4


title: Cell 88 from tonsillectomy sample 4


title: Cell 83 from tonsillectomy sample 4


title: Cell 82 from tonsillectomy sample 4


title: Cell 86 from tonsillectomy sample 4


title: Cell 81 from tonsillectomy sample 4


title: Cell 84 from tonsillectomy sample 4


title: Cell 80 from tonsillectomy sample 4


title: Cell 78 from tonsillectomy sample 4


title: Cell 77 from tonsillectomy sample 4


title: Cell 73 from tonsillectomy sample 4


title: Cell 8 from renal allograft sample 7


title: Cell 76 from tonsillectomy sample 4


title: Cell 74 from tonsillectomy sample 4


title: Cell 71 from tonsillectomy sample 4


title: Cell 72 from tonsillectomy sample 4


title: Cell 75 from tonsillectomy sample 4


title: Cell 70 from tonsillectomy sample 4


title: Cell 68 from tonsillectomy sample 4


title: Cell 67 from tonsillectomy sample 4


title: Cell 65 from tonsillectomy sample 4


title: Cell 66 from tonsillectomy sample 4


title: Cell 69 from tonsillectomy sample 4


title: Cell 64 from tonsillectomy sample 4


title: Cell 63 from tonsillectomy sample 4


title: Cell 85 from tonsillectomy sample 4


title: Cell 62 from tonsillectomy sample 4


title: Cell 56 from tonsillectomy sample 4


title: Cell 61 from tonsillectomy sample 4


title: Cell 53 from tonsillectomy sample 4


title: Cell 57 from tonsillectomy sample 4


title: Cell 60 from tonsillectomy sample 4


title: Cell 59 from tonsillectomy sample 4


title: Cell 55 from tonsillectomy sample 4


title: Cell 58 from tonsillectomy sample 4


title: Cell 79 from tonsillectomy sample 4


title: Cell 52 from tonsillectomy sample 4


title: Cell 50 from tonsillectomy sample 4


title: Cell 51 from tonsillectomy sample 4


title: Cell 43 from tonsillectomy sample 4


title: Cell 47 from tonsillectomy sample 4


title: Cell 42 from tonsillectomy sample 4


title: Cell 41 from tonsillectomy sample 4


title: Cell 46 from tonsillectomy sample 4


title: Cell 48 from tonsillectomy sample 4


title: Cell 44 from tonsillectomy sample 4


title: Cell 39 from tonsillectomy sample 4


title: Cell 38 from tonsillectomy sample 4


title: Cell 49 from tonsillectomy sample 4


title: Cell 40 from tonsillectomy sample 4


title: Cell 54 from tonsillectomy sample 4


title: Cell 36 from tonsillectomy sample 4


title: Cell 37 from tonsillectomy sample 4


title: Cell 35 from tonsillectomy sample 4


title: Cell 34 from tonsillectomy sample 4


title: Cell 33 from tonsillectomy sample 4


title: Cell 31 from tonsillectomy sample 4


title: Cell 27 from tonsillectomy sample 4


title: Cell 32 from tonsillectomy sample 4


title: Cell 29 from tonsillectomy sample 4


title: Cell 28 from tonsillectomy sample 4


title: Cell 45 from tonsillectomy sample 4


title: Cell 25 from tonsillectomy sample 4


title: Cell 24 from tonsillectomy sample 4


title: Cell 26 from tonsillectomy sample 4


title: Cell 22 from tonsillectomy sample 4


title: Cell 23 from tonsillectomy sample 4


title: Cell 20 from tonsillectomy sample 4


title: Cell 19 from tonsillectomy sample 4


title: Cell 17 from tonsillectomy sample 4


title: Cell 18 from tonsillectomy sample 4


title: Cell 15 from tonsillectomy sample 4


title: Cell 16 from tonsillectomy sample 4


title: Cell 12 from tonsillectomy sample 4


title: Cell 11 from tonsillectomy sample 4


title: Cell 14 from tonsillectomy sample 4


title: Cell 10 from tonsillectomy sample 4


title: Cell 9 from tonsillectomy sample 4


title: Cell 7 from tonsillectomy sample 4


title: Cell 8 from tonsillectomy sample 4


title: Cell 13 from tonsillectomy sample 4


title: Cell 30 from tonsillectomy sample 4


title: Cell 5 from tonsillectomy sample 4


title: Cell 4 from tonsillectomy sample 4


title: Cell 6 from tonsillectomy sample 4


title: Cell 3 from tonsillectomy sample 4


title: Cell 93 from tonsillectomy sample 3

value: Tonsil 3


title: Cell 94 from tonsillectomy sample 3


title: Cell 2 from tonsillectomy sample 4


title: Cell 92 from tonsillectomy sample 3


title: Cell 90 from tonsillectomy sample 3


title: Cell 21 from tonsillectomy sample 4


title: Cell 89 from tonsillectomy sample 3


title: Cell 84 from tonsillectomy sample 3


title: Cell 86 from tonsillectomy sample 3


title: Cell 83 from tonsillectomy sample 3


title: Cell 1 from tonsillectomy sample 4


title: Cell 95 from tonsillectomy sample 3


title: Cell 96 from tonsillectomy sample 3


title: Cell 78 from tonsillectomy sample 3


title: Cell 82 from tonsillectomy sample 3


title: Cell 77 from tonsillectomy sample 3


title: Cell 76 from tonsillectomy sample 3


title: Cell 81 from tonsillectomy sample 3


title: Cell 91 from tonsillectomy sample 3


title: Cell 73 from tonsillectomy sample 3


title: Cell 71 from tonsillectomy sample 3


title: Cell 75 from tonsillectomy sample 3


title: Cell 66 from tonsillectomy sample 3


title: Cell 65 from tonsillectomy sample 3


title: Cell 70 from tonsillectomy sample 3


title: Cell 67 from tonsillectomy sample 3


title: Cell 68 from tonsillectomy sample 3


title: Cell 64 from tonsillectomy sample 3


title: Cell 72 from tonsillectomy sample 3


title: Cell 88 from tonsillectomy sample 3


title: Cell 87 from tonsillectomy sample 3


title: Cell 85 from tonsillectomy sample 3


title: Cell 74 from tonsillectomy sample 3


title: Cell 62 from tonsillectomy sample 3


title: Cell 61 from tonsillectomy sample 3


title: Cell 80 from tonsillectomy sample 3


title: Cell 79 from tonsillectomy sample 3


title: Cell 57 from tonsillectomy sample 3


title: Cell 56 from tonsillectomy sample 3


title: Cell 58 from tonsillectomy sample 3


title: Cell 55 from tonsillectomy sample 3


title: Cell 69 from tonsillectomy sample 3


title: Cell 54 from tonsillectomy sample 3


title: Cell 50 from tonsillectomy sample 3


title: Cell 49 from tonsillectomy sample 3


title: Cell 51 from tonsillectomy sample 3


title: Cell 53 from tonsillectomy sample 3


title: Cell 63 from tonsillectomy sample 3


title: Cell 48 from tonsillectomy sample 3


title: Cell 45 from tonsillectomy sample 3


title: Cell 60 from tonsillectomy sample 3


title: Cell 47 from tonsillectomy sample 3


title: Cell 41 from tonsillectomy sample 3


title: Cell 43 from tonsillectomy sample 3


title: Cell 40 from tonsillectomy sample 3


title: Cell 37 from tonsillectomy sample 3


title: Cell 44 from tonsillectomy sample 3


title: Cell 38 from tonsillectomy sample 3


title: Cell 39 from tonsillectomy sample 3


title: Cell 33 from tonsillectomy sample 3


title: Cell 35 from tonsillectomy sample 3


title: Cell 34 from tonsillectomy sample 3


title: Cell 42 from tonsillectomy sample 3


title: Cell 36 from tonsillectomy sample 3


title: Cell 52 from tonsillectomy sample 3


title: Cell 32 from tonsillectomy sample 3


title: Cell 30 from tonsillectomy sample 3


title: Cell 28 from tonsillectomy sample 3


title: Cell 29 from tonsillectomy sample 3


title: Cell 27 from tonsillectomy sample 3


title: Cell 31 from tonsillectomy sample 3


title: Cell 46 from tonsillectomy sample 3


title: Cell 26 from tonsillectomy sample 3


title: Cell 24 from tonsillectomy sample 3


title: Cell 23 from tonsillectomy sample 3


title: Cell 25 from tonsillectomy sample 3


title: Cell 22 from tonsillectomy sample 3


title: Cell 21 from tonsillectomy sample 3


title: Cell 20 from tonsillectomy sample 3


title: Cell 18 from tonsillectomy sample 3


title: Cell 19 from tonsillectomy sample 3


title: Cell 16 from tonsillectomy sample 3


title: Cell 11 from tonsillectomy sample 3


title: Cell 13 from tonsillectomy sample 3


title: Cell 17 from tonsillectomy sample 3


title: Cell 15 from tonsillectomy sample 3


title: Cell 14 from tonsillectomy sample 3


title: Cell 9 from tonsillectomy sample 3


title: Cell 7 from tonsillectomy sample 3


title: Cell 12 from tonsillectomy sample 3


title: Cell 10 from tonsillectomy sample 3


title: Cell 8 from tonsillectomy sample 3


title: Cell 6 from tonsillectomy sample 3


title: Cell 5 from tonsillectomy sample 3


title: Cell 4 from tonsillectomy sample 3


title: Cell 3 from tonsillectomy sample 3


title: Cell 96 from renal allograft sample 3

value: Kidney 3

value: Batch 3


title: Cell 95 from renal allograft sample 3


title: Cell 2 from tonsillectomy sample 3


title: Cell 92 from renal allograft sample 3


title: Cell 91 from renal allograft sample 3


title: Cell 90 from renal allograft sample 3


title: Cell 94 from renal allograft sample 3


title: Cell 93 from renal allograft sample 3


title: Cell 88 from renal allograft sample 3


title: Cell 87 from renal allograft sample 3


title: Cell 89 from renal allograft sample 3


title: Cell 86 from renal allograft sample 3


title: Cell 84 from renal allograft sample 3


title: Cell 82 from renal allograft sample 3


title: Cell 83 from renal allograft sample 3


title: Cell 81 from renal allograft sample 3


title: Cell 85 from renal allograft sample 3


title: Cell 78 from renal allograft sample 3


title: Cell 72 from renal allograft sample 3


title: Cell 75 from renal allograft sample 3


title: Cell 70 from renal allograft sample 3


title: Cell 74 from renal allograft sample 3


title: Cell 80 from renal allograft sample 3


title: Cell 79 from renal allograft sample 3


title: Cell 69 from renal allograft sample 3


title: Cell 77 from renal allograft sample 3


title: Cell 71 from renal allograft sample 3


title: Cell 76 from renal allograft sample 3


title: Cell 1 from tonsillectomy sample 3


title: Cell 73 from renal allograft sample 3


title: Cell 68 from renal allograft sample 3


title: Cell 67 from renal allograft sample 3


title: Cell 66 from renal allograft sample 3


title: Cell 61 from renal allograft sample 3


title: Cell 62 from renal allograft sample 3


title: Cell 64 from renal allograft sample 3


title: Cell 60 from renal allograft sample 3


title: Cell 65 from renal allograft sample 3


title: Cell 63 from renal allograft sample 3


title: Cell 58 from renal allograft sample 3


title: Cell 59 from renal allograft sample 3


title: Cell 57 from renal allograft sample 3


title: Cell 56 from renal allograft sample 3


title: Cell 55 from renal allograft sample 3


title: Cell 53 from renal allograft sample 3


title: Cell 54 from renal allograft sample 3


title: Cell 46 from renal allograft sample 3


title: Cell 49 from renal allograft sample 3


title: Cell 48 from renal allograft sample 3


title: Cell 44 from renal allograft sample 3


title: Cell 40 from renal allograft sample 3


title: Cell 39 from renal allograft sample 3


title: Cell 38 from renal allograft sample 3


title: Cell 59 from tonsillectomy sample 3


title: Cell 35 from renal allograft sample 3


title: Cell 33 from renal allograft sample 3


title: Cell 31 from renal allograft sample 3


title: Cell 29 from renal allograft sample 3


title: Cell 45 from renal allograft sample 3


title: Cell 26 from renal allograft sample 3


title: Cell 25 from renal allograft sample 3


title: Cell 51 from renal allograft sample 3


title: Cell 24 from renal allograft sample 3


title: Cell 23 from renal allograft sample 3


title: Cell 22 from renal allograft sample 3


title: Cell 20 from renal allograft sample 3


title: Cell 21 from renal allograft sample 3


title: Cell 19 from renal allograft sample 3


title: Cell 47 from renal allograft sample 3


title: Cell 50 from renal allograft sample 3


title: Cell 18 from renal allograft sample 3


title: Cell 16 from renal allograft sample 3


title: Cell 42 from renal allograft sample 3


title: Cell 43 from renal allograft sample 3


title: Cell 41 from renal allograft sample 3


title: Cell 37 from renal allograft sample 3


title: Cell 32 from renal allograft sample 3


title: Cell 36 from renal allograft sample 3


title: Cell 13 from renal allograft sample 3


title: Cell 14 from renal allograft sample 3


title: Cell 34 from renal allograft sample 3


title: Cell 30 from renal allograft sample 3


title: Cell 52 from renal allograft sample 3


title: Cell 28 from renal allograft sample 3


title: Cell 9 from renal allograft sample 3


title: Cell 10 from renal allograft sample 3


title: Cell 17 from renal allograft sample 3


title: Cell 8 from renal allograft sample 3


title: Cell 15 from renal allograft sample 3


title: Cell 27 from renal allograft sample 3


title: Cell 2 from renal allograft sample 3


title: Cell 5 from renal allograft sample 3


title: Cell 202 from renal allograft sample 4

value: Kidney 4


title: Cell 12 from renal allograft sample 3


title: Cell 200 from renal allograft sample 4


title: Cell 11 from renal allograft sample 3


title: Cell 201 from renal allograft sample 4


title: Cell 199 from renal allograft sample 4


title: Cell 197 from renal allograft sample 4


title: Cell 198 from renal allograft sample 4


title: Cell 7 from renal allograft sample 3


title: Cell 6 from renal allograft sample 3


title: Cell 4 from renal allograft sample 3


title: Cell 1 from renal allograft sample 3


title: Cell 3 from renal allograft sample 3


title: Cell 204 from renal allograft sample 4


title: Cell 203 from renal allograft sample 4


title: Cell 195 from renal allograft sample 4


title: Cell 189 from renal allograft sample 4


title: Cell 186 from renal allograft sample 4


title: Cell 185 from renal allograft sample 4


title: Cell 188 from renal allograft sample 4


title: Cell 190 from renal allograft sample 4


title: Cell 184 from renal allograft sample 4


title: Cell 196 from renal allograft sample 4


title: Cell 191 from renal allograft sample 4


title: Cell 193 from renal allograft sample 4


title: Cell 182 from renal allograft sample 4


title: Cell 187 from renal allograft sample 4


title: Cell 180 from renal allograft sample 4


title: Cell 179 from renal allograft sample 4


title: Cell 177 from renal allograft sample 4


title: Cell 175 from renal allograft sample 4


title: Cell 176 from renal allograft sample 4


title: Cell 181 from renal allograft sample 4


title: Cell 192 from renal allograft sample 4


title: Cell 174 from renal allograft sample 4


title: Cell 178 from renal allograft sample 4


title: Cell 168 from renal allograft sample 4


title: Cell 194 from renal allograft sample 4


title: Cell 172 from renal allograft sample 4


title: Cell 170 from renal allograft sample 4


title: Cell 169 from renal allograft sample 4


title: Cell 167 from renal allograft sample 4


title: Cell 171 from renal allograft sample 4


title: Cell 183 from renal allograft sample 4


title: Cell 166 from renal allograft sample 4


title: Cell 164 from renal allograft sample 4


title: Cell 165 from renal allograft sample 4


title: Cell 159 from renal allograft sample 4


title: Cell 162 from renal allograft sample 4


title: Cell 161 from renal allograft sample 4


title: Cell 160 from renal allograft sample 4


title: Cell 158 from renal allograft sample 4


title: Cell 173 from renal allograft sample 4


title: Cell 156 from renal allograft sample 4


title: Cell 152 from renal allograft sample 4


title: Cell 149 from renal allograft sample 4


title: Cell 150 from renal allograft sample 4


title: Cell 151 from renal allograft sample 4


title: Cell 155 from renal allograft sample 4


title: Cell 144 from renal allograft sample 4


title: Cell 143 from renal allograft sample 4


title: Cell 153 from renal allograft sample 4


title: Cell 154 from renal allograft sample 4


title: Cell 142 from renal allograft sample 4


title: Cell 148 from renal allograft sample 4


title: Cell 147 from renal allograft sample 4


title: Cell 146 from renal allograft sample 4


title: Cell 145 from renal allograft sample 4


title: Cell 141 from renal allograft sample 4


title: Cell 139 from renal allograft sample 4


title: Cell 163 from renal allograft sample 4


title: Cell 132 from renal allograft sample 4


title: Cell 157 from renal allograft sample 4


title: Cell 138 from renal allograft sample 4


title: Cell 125 from renal allograft sample 4


title: Cell 137 from renal allograft sample 4


title: Cell 136 from renal allograft sample 4


title: Cell 135 from renal allograft sample 4


title: Cell 134 from renal allograft sample 4


title: Cell 122 from renal allograft sample 4


title: Cell 133 from renal allograft sample 4


title: Cell 121 from renal allograft sample 4


title: Cell 140 from renal allograft sample 4


title: Cell 131 from renal allograft sample 4


title: Cell 119 from renal allograft sample 4


title: Cell 130 from renal allograft sample 4


title: Cell 128 from renal allograft sample 4


title: Cell 129 from renal allograft sample 4


title: Cell 126 from renal allograft sample 4


title: Cell 116 from renal allograft sample 4


title: Cell 124 from renal allograft sample 4


title: Cell 127 from renal allograft sample 4


title: Cell 114 from renal allograft sample 4


title: Cell 113 from renal allograft sample 4


title: Cell 123 from renal allograft sample 4


title: Cell 115 from renal allograft sample 4


title: Cell 118 from renal allograft sample 4


title: Cell 112 from renal allograft sample 4


title: Cell 111 from renal allograft sample 4


title: Cell 108 from renal allograft sample 4


title: Cell 107 from renal allograft sample 4


title: Cell 106 from renal allograft sample 4


title: Cell 120 from renal allograft sample 4


title: Cell 104 from renal allograft sample 4


title: Cell 117 from renal allograft sample 4


title: Cell 103 from renal allograft sample 4


title: Cell 109 from renal allograft sample 4


title: Cell 102 from renal allograft sample 4


title: Cell 101 from renal allograft sample 4


title: Cell 98 from renal allograft sample 4


title: Cell 99 from renal allograft sample 4


title: Cell 97 from renal allograft sample 4


title: Cell 96 from renal allograft sample 4


title: Cell 105 from renal allograft sample 4


title: Cell 94 from renal allograft sample 4


title: Cell 90 from renal allograft sample 4


title: Cell 92 from renal allograft sample 4


title: Cell 91 from renal allograft sample 4


title: Cell 93 from renal allograft sample 4


title: Cell 86 from renal allograft sample 4


title: Cell 88 from renal allograft sample 4


title: Cell 110 from renal allograft sample 4


title: Cell 89 from renal allograft sample 4


title: Cell 87 from renal allograft sample 4


title: Cell 85 from renal allograft sample 4


title: Cell 82 from renal allograft sample 4


title: Cell 81 from renal allograft sample 4


title: Cell 83 from renal allograft sample 4


title: Cell 80 from renal allograft sample 4


title: Cell 100 from renal allograft sample 4


title: Cell 79 from renal allograft sample 4


title: Cell 75 from renal allograft sample 4


title: Cell 77 from renal allograft sample 4


title: Cell 76 from renal allograft sample 4


title: Cell 74 from renal allograft sample 4


title: Cell 78 from renal allograft sample 4


title: Cell 71 from renal allograft sample 4


title: Cell 95 from renal allograft sample 4


title: Cell 69 from renal allograft sample 4


title: Cell 68 from renal allograft sample 4


title: Cell 67 from renal allograft sample 4


title: Cell 72 from renal allograft sample 4


title: Cell 70 from renal allograft sample 4


title: Cell 66 from renal allograft sample 4


title: Cell 64 from renal allograft sample 4


title: Cell 63 from renal allograft sample 4


title: Cell 62 from renal allograft sample 4


title: Cell 59 from renal allograft sample 4


title: Cell 58 from renal allograft sample 4


title: Cell 60 from renal allograft sample 4


title: Cell 84 from renal allograft sample 4


title: Cell 57 from renal allograft sample 4


title: Cell 56 from renal allograft sample 4


title: Cell 55 from renal allograft sample 4


title: Cell 54 from renal allograft sample 4


title: Cell 53 from renal allograft sample 4


title: Cell 73 from renal allograft sample 4


title: Cell 52 from renal allograft sample 4


title: Cell 50 from renal allograft sample 4


title: Cell 49 from renal allograft sample 4


title: Cell 48 from renal allograft sample 4


title: Cell 47 from renal allograft sample 4


title: Cell 45 from renal allograft sample 4


title: Cell 65 from renal allograft sample 4


title: Cell 44 from renal allograft sample 4


title: Cell 43 from renal allograft sample 4


title: Cell 41 from renal allograft sample 4


title: Cell 42 from renal allograft sample 4


title: Cell 40 from renal allograft sample 4


title: Cell 61 from renal allograft sample 4


title: Cell 37 from renal allograft sample 4


title: Cell 36 from renal allograft sample 4


title: Cell 35 from renal allograft sample 4


title: Cell 31 from renal allograft sample 4


title: Cell 32 from renal allograft sample 4


title: Cell 28 from renal allograft sample 4


title: Cell 29 from renal allograft sample 4


title: Cell 27 from renal allograft sample 4


title: Cell 51 from renal allograft sample 4


title: Cell 46 from renal allograft sample 4


title: Cell 21 from renal allograft sample 4


title: Cell 25 from renal allograft sample 4


title: Cell 22 from renal allograft sample 4


title: Cell 24 from renal allograft sample 4


title: Cell 19 from renal allograft sample 4


title: Cell 23 from renal allograft sample 4


title: Cell 18 from renal allograft sample 4


title: Cell 16 from renal allograft sample 4


title: Cell 39 from renal allograft sample 4


title: Cell 17 from renal allograft sample 4


title: Cell 13 from renal allograft sample 4


title: Cell 15 from renal allograft sample 4


title: Cell 33 from renal allograft sample 4


title: Cell 20 from renal allograft sample 4


title: Cell 11 from renal allograft sample 4


title: Cell 38 from renal allograft sample 4


title: Cell 34 from renal allograft sample 4


title: Cell 10 from renal allograft sample 4


title: Cell 12 from renal allograft sample 4


title: Cell 8 from renal allograft sample 4


title: Cell 7 from renal allograft sample 4


title: Cell 9 from renal allograft sample 4


title: Cell 30 from renal allograft sample 4


title: Cell 26 from renal allograft sample 4


title: Cell 5 from renal allograft sample 4


title: Cell 6 from renal allograft sample 4


title: Cell 4 from renal allograft sample 4


title: Cell 2 from renal allograft sample 4


title: Cell 3 from renal allograft sample 4


title: Cell 1 from renal allograft sample 4


title: Cell 48 from tonsillectomy sample 2

value: Tonsil 2


title: Cell 47 from tonsillectomy sample 2


title: Cell 14 from renal allograft sample 4


title: Cell 46 from tonsillectomy sample 2


title: Cell 45 from tonsillectomy sample 2


title: Cell 43 from tonsillectomy sample 2


title: Cell 44 from tonsillectomy sample 2


title: Cell 46 from tonsillectomy sample 1

value: Tonsil 1


title: Cell 43 from tonsillectomy sample 1


title: Cell 45 from tonsillectomy sample 1


title: Cell 48 from tonsillectomy sample 1


title: Cell 39 from tonsillectomy sample 2


title: Cell 41 from tonsillectomy sample 2


title: Cell 40 from tonsillectomy sample 2


title: Cell 42 from tonsillectomy sample 1


title: Cell 44 from tonsillectomy sample 1


title: Cell 42 from tonsillectomy sample 2


title: Cell 40 from tonsillectomy sample 1


title: Cell 41 from tonsillectomy sample 1


title: Cell 39 from tonsillectomy sample 1


title: Cell 37 from tonsillectomy sample 2


title: Cell 38 from tonsillectomy sample 1


title: Cell 47 from tonsillectomy sample 1


title: Cell 37 from tonsillectomy sample 1


title: Cell 35 from tonsillectomy sample 2


title: Cell 33 from tonsillectomy sample 2


title: Cell 32 from tonsillectomy sample 2


title: Cell 34 from tonsillectomy sample 2


title: Cell 31 from tonsillectomy sample 2


title: Cell 36 from tonsillectomy sample 1


title: Cell 35 from tonsillectomy sample 1


title: Cell 33 from tonsillectomy sample 1


title: Cell 34 from tonsillectomy sample 1


title: Cell 32 from tonsillectomy sample 1


title: Cell 31 from tonsillectomy sample 1


title: Cell 38 from tonsillectomy sample 2


title: Cell 30 from tonsillectomy sample 2


title: Cell 29 from tonsillectomy sample 2


title: Cell 25 from tonsillectomy sample 2


title: Cell 28 from tonsillectomy sample 2


title: Cell 26 from tonsillectomy sample 2


title: Cell 30 from tonsillectomy sample 1


title: Cell 28 from tonsillectomy sample 1


title: Cell 36 from tonsillectomy sample 2


title: Cell 22 from tonsillectomy sample 2


title: Cell 24 from tonsillectomy sample 2