title: 10x of HL60 differentiation, ADT sample tags, 1

library_source: genomic

data_processing:
Library strategy: CITE-seq
For the HL60 10x dataset, we followed the standard pipeline of kb-python to quantify the total, spliced and unspliced RNA. For the HL60 metabolic labeling based scRNA-seq experiment with clone tracing, we used the NASC-seq pipeline (https://github.com/sandberg-lab/NASC-seq) developed in to quantify the new and total RNA read counts.
For the scNT-seq experiment of the human hematopoiesis, we developed dynast (https://github.com/aristoteleo/dynast-release), an inclusive and efficient command-line toolkit for preprocessing data from metabolic labeling–based scRNA-seq experiments and quantifying the following four types of mRNA species: unspliced, spliced, labeled (or new), and total RNAs (details will be reported elsewhere). Samples from days 4 and 7 were each subjected to standard dynast runs, using human genome hg38 as the alignment reference. The resultant objects were first filtered to keep only high quality cells and then merged to obtain in total about 2,000 high-quality cells. This merged object was then used for all downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: file format is h5ad/csv. For h5ad files, they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our scSLAM-seq and scNT-seq experiment. Only spliced and unspliced RNA counts for each gene in each cell are available for the 10x dataset. For the edge_df.csv file, it is the clone linkage information between different cells, processed from the static barcodes.

molecule: protein

extract_protocol: HL60 differentiations were initialized on different days so that all samples could be harvested in a single scRNA-seq reaction to minimize batch effects. Cells were treated with 1 µM ATRA and differentiated for 0 (no ATRA treatment), 1, 2, 3, 4, or 5 days, with all differentiations performed in biological replicates. Samples were tagged or "cell hashed" (Stoeckius et al., 2018) with distinct BD sample tags (BD Bioscience, cat#PN 633780) to enable demultiplexing of cells, and then pooled for scRNA-seq. scRNA-seq was performed on one lane of the 10x Chromium™ Single Cell 3' v2 system following the standard library prep protocol (10x Genomics Single Cell 3’ Reagent Kits v2 User Guide, CG00052). Libraries were amplified with 10 cycles of cDNA amplification and 15 cycles of Sample Index PCR. BD Sample Tags were size-separated by SPRI selection after cDNA amplification and amplified according to standard protocols (BD User-Demonstrated Protocol: BD Single-Cell Multiplexing Kit—Human Doc ID: 179682 Rev. 1.0). Final cDNA and sample tag libraries were sequenced on a NovaSeq 6000 (Illumina).


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A10_MemorySeq028

status: Public on Feb 02 2022

type: SRA

city: Cambridge

first: Xiaojie

last: Qiu

state: MA

address: 455 Main St, Cambridge, MA

country: USA

institute: Whitehead Institute

description:
HL60_memory_seq.h5ad
NovaSeq 5000

library_source: transcriptomic

data_processing:
Library strategy: SLAM-seq
For the HL60 10x dataset, we followed the standard pipeline of kb-python to quantify the total, spliced and unspliced RNA. For the HL60 metabolic labeling based scRNA-seq experiment with clone tracing, we used the NASC-seq pipeline (https://github.com/sandberg-lab/NASC-seq) developed in to quantify the new and total RNA read counts.
For the scNT-seq experiment of the human hematopoiesis, we developed dynast (https://github.com/aristoteleo/dynast-release), an inclusive and efficient command-line toolkit for preprocessing data from metabolic labeling–based scRNA-seq experiments and quantifying the following four types of mRNA species: unspliced, spliced, labeled (or new), and total RNAs (details will be reported elsewhere). Samples from days 4 and 7 were each subjected to standard dynast runs, using human genome hg38 as the alignment reference. The resultant objects were first filtered to keep only high quality cells and then merged to obtain in total about 2,000 high-quality cells. This merged object was then used for all downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: file format is h5ad/csv. For h5ad files, they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our scSLAM-seq and scNT-seq experiment. Only spliced and unspliced RNA counts for each gene in each cell are available for the 10x dataset. For the edge_df.csv file, it is the clone linkage information between different cells, processed from the static barcodes.

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment

value: neutrophil lineage differentiation in the presence of  ATRA

tag: gender

value: female

tag: age

tag: ethnicity


title: sample.458_d6_TxM

city: St. Louis

first: Todd

last: Fehniger

state: MO

address: 660 S Euclid Ave, Campus Box 8007

department: Oncology

institute: Washington University School of Medicine

description: gene expression data

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimitted text file containing counts of uniquely aligned unambiguous reads per gene

source_name: NK cells

growth_protocol: In 1 experiment, NK cells from 3 different donors were isolated, activated for 16hrs with low-dose IL-15 or IL12/15/18, and incubated for six days in 1ng/mL IL-15

extract_protocol:
RNA was isolated using the Direct-zol RNA MicroPrep kit (zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time point

tag: tissue

value: blood

tag: donor

value: TxM (18/12/TxM molecule)


title: S12_057

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

description: countmtx.csv

data_processing:
[data processing step 10x Genomics samples]  Cellranger version 3.0.0
[data processing step Bulk alignment]  Hisat v0.1.5
[data processing step Bulk sorting reads]  samtools v1.2
[data processing step Bulk counting reads]  HTSeq v0.6.1
Genome_build: Bulk GRCh37, human SC GRCh38, mouse SC GRCm38
Supplementary_files_format_and_content: Countfiles with raw counts per sample (bulk) or droplet barcode (single-cell)

source_name: brain

extract_protocol:
[Macrophage isolation human]  Mechanical tissue dissociation followed by percoll gradient centrifugation. FACS sorting for CD45posCD11Bpos cells.
[Macrophage isolation mouse]  Enzymatic isolation at 4C using protease from Bacillus lichenformis and L-cysteine. FACS sorted on tdTomato Red cells.
Qiagen Rneasy lipid mini kit
3’ Quantseq FWD kit from Lexogen for bulk RNAseq. 3’ single cell RNAseq v2 from 10x Genomics for single cell.

treatment_protocol: [diet protocol mice]  Mice were fed 0.2% cuprizone in their diet ad libitum. Control animals received similarly prepared chow but without cuprizone

tag: group

value: NAWM

tag: cell type

value: total brain tissue

tag: postmortem delay

tag: rin

value: F

tag: cell isolation

tag: rna isolation

value: Qiagen Rneasy mini lipid kit

tag: sequencing method

value: 3’ Quantseq FWD


title: Plate11and12

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

data_processing:
Library strategy: CITE-seq
FASTQ files were processed using Seven Bridges Genomics pipeline
Doublet removal using doublet finder package in R
Genes_Raw.csv: Gene expression matrix
Antibodies_Raw.csv: Antibodies expression matrix
Metadata.csv: Metadata file listing all biological characteristics of cells

source_name: PBMCs

extract_protocol:
Blood from enrollees was centrifuged at 400 x g for 10 minutes at RT to remove platelet rich plasma. PBMCs were isolated by Ficoll-Paque PLUS gradient centrifugation using SepMate-50 tubes following the manufacturer’s protocol. PBMCs were cryopreserved in freezing solution (90% FBS/10% DMSO). Once all the samples were collected, PBMCs were thawed and washed with RPMI.
Library was prepared per BD's protocol. In brief, the reagents for PCR1 including the BD Human Immune Response Panel and a custom panel of 488 genes were added to the beads. Samples were aliquoted into  PCR tubes and incubated for 10 cycles according to BD’s protocol for PCR1. A double size selection was performed to remove high genomic DNA fragments. AMPure XP SPRI beads to the PCR products. After incubation, the supernatant is recovered followed by purifying the supernatant withan additional AMPure XP beads (sample tags and antibodies). The RNA tube was washed twice with 80 % ethanol. 550 μl of supernatant were removed from the antibody tube followed by two washes with 500 μL of 80 % ethanol. The cDNA was eluted off the beads using 30 μL of BD elution buffer and then transferred to a 1.5 mL tube.

value: PBMC

tag: condition

value: multiplexed sample:high and low CAD with and without IgE to alpha-gal sensitization


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

extract_protocol: To facilitate lineage tracing in scSLAM-seq libraries, cellular barcodes (GBCs) were introduced using a lentiviral transduction strategy (Adamson et al., 2016). Given that the success of this experiment critically depended on the uniqueness of barcode sequence to each cell at the start of the experiment, i.e. low barcode collision rate, and the capture of clone cells (clones with the same barcodes) across different days, we used an experimental scheme in which the starting population of the HL60 cells were infected at a low (2%) multiplicity of infection (MOI). This scheme has two benefits: first, we obtained a small number of barcoded single cells (~2000 in 1 ml of media in each well of a 24-well plate) so that we could capture clone cells via plate-based SLAM-seq (scRNA-seq augmented by metabolic labeling) characterized of low throughput; second, co-culturing the small number of infected cells with a large population of uninfected cells enabled us to differentiate infected cells more conveniently, as a small number of cells are difficult to grow and differentiate. Single cells carrying barcodes and expressing the blue fluorescent protein (BFP) reporter were sorted (Sony SH800) at five timepoints, days 0, 1, 2, 3, and 5, during differentiation in the presence of ATRA. cDNA from single cells was prepared in a 96-well format as previously described (Tabula Muris Consortium, 2020) following alkylation and RNA cleanup (Erhard et al., 2019; Hendriks et al., 2019). Sequencing libraries were either reformatted into a 384-well format and prepared using TTP Mosquito automated liquid handlers, or in a 96- well format using a multichannel pipette. GBC sequencing libraries were prepared by dual PCR amplification to enrich for GBC cDNA and to add Illumina adapters and dual indexes complimentary to that cell's transcriptome sequencing library indexes. GBC sequencing libraries were spiked into transcriptome libraries at 1:10 and sequenced on the NextSeq or MiSeq platform (Illumina). Transcriptome libraries were sequenced separately using a NovaSeq5000 S2 300-cycle kit.


title: S96_234

description: countmtx.csv

value: Lesion


title: 10x of HL60 differentiation, ADT sample tags, 2


title: S98_309

description: countmtx.csv


title: S13_022

description: countmtx.csv


title: S13_019

description: countmtx.csv


title: Human embryonal palatal mesenchyme cells_rep2

city: Bonn

first: Karharina

last: Ruff

address: Venusberg-Campus 1

country: Germany

institute: Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital

data_processing:
The Quality of the fastq files was checked using FastQC (v0.11.7).
Adapter sequences were trimmed using bbduk (BBMap v37.44).
The alignment of the reads to theGRCh37/hg19 reference genome was performed using STAR Aligner (v2.5.2b)
The gene expression with Ensembl Human GRCh37.p13 annotation as reference, was quantified using featureCounts (v1.5.1).
The quality of our data was checked using MultiQC (v1.2).
Genome_build: Human GRCh37.p13 - hg19
Supplementary_files_format_and_content: 3'RNA-seq read counts per gene

source_name: Human embryonal palatal mesenchyme cells (HEPM cells)

growth_protocol: Cells were cultivated in in DMEM-Dulbecco's Modified Eagle Medium (high Glucose), 10% heat inactivated fetal bovine serum (FBS) and Penicillin/Streptomycin, at a concentration of 1X at 37 °C and 5% CO2. The medium was changed every two days and the cells were split after five days with  0.25% Trypsin/EDTA.

extract_protocol:
The RNaeasy® kit (QIAGEN, Germany) was used according the manufacturer's protocol.
The QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Austria) was used according to the manufacturer's protocol. The samples were sequenced with 1x50 bp on an Illumina HiSeq2500 yielding ~20 mio reads per sample.
3'mRNA-seq

treatment_protocol: The cells were untreated

value: untreated


title: 10x of HL60 differentiation, scRNA-seq, 2


title: scNT-seq of HSPC day 7 timepoint, repeat

data_processing:
For the HL60 10x dataset, we followed the standard pipeline of kb-python to quantify the total, spliced and unspliced RNA. For the HL60 metabolic labeling based scRNA-seq experiment with clone tracing, we used the NASC-seq pipeline (https://github.com/sandberg-lab/NASC-seq) developed in to quantify the new and total RNA read counts.
For the scNT-seq experiment of the human hematopoiesis, we developed dynast (https://github.com/aristoteleo/dynast-release), an inclusive and efficient command-line toolkit for preprocessing data from metabolic labeling–based scRNA-seq experiments and quantifying the following four types of mRNA species: unspliced, spliced, labeled (or new), and total RNAs (details will be reported elsewhere). Samples from days 4 and 7 were each subjected to standard dynast runs, using human genome hg38 as the alignment reference. The resultant objects were first filtered to keep only high quality cells and then merged to obtain in total about 2,000 high-quality cells. This merged object was then used for all downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: file format is h5ad/csv. For h5ad files, they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our scSLAM-seq and scNT-seq experiment. Only spliced and unspliced RNA counts for each gene in each cell are available for the 10x dataset. For the edge_df.csv file, it is the clone linkage information between different cells, processed from the static barcodes.

source_name: Human hematopoietic stem and progenitor cells

extract_protocol: For the human hematopoiesis dataset, we cultured primary human CD34+ hematopoietic stem and progenitor cells obtained from the Fred Hutchinson Cancer Research Center. Cells were thawed and cultured in StemSpan SFEM II human hematopoietic stem cell expansion media (StemCell Technologies, Cat#02690) supplemented with StemSpan CC100 (StemCell Technologies, Cat#02690) and 50 ng/ml TPO (PeproTech, Cat#300-18-100UG). Cells were allowed to differentiate over the course of 1 week.

value: day 7, during differentiation in the presence of maintenance medium

value: Caucasian


title: 10x of HL60 differentiation, scRNA-seq, 1


title: sample.445_d6_TxM

description: gene expression data


title: S12_084

description: countmtx.csv

value: M


title: sample.458_overnight_ciml

description: gene expression data


title: Plate5and6


title: Plate1and2


title: sample.458_overnight_TxM

description: gene expression data


title: S12_027

description: countmtx.csv


title: S12_063

description: countmtx.csv


title: sample.458_overnight_ld

description: gene expression data

value: LD IL-15


title: sample.446_d6_TxM

description: gene expression data


title: Plate15and16


title: Plate13and14


title: GC3_VDJ

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8. The files for each sample can be analyzed and de-multiplexed directly using the 10X Genomics CellRanger software.
Reads were mapped to the human genome (GRCh38) using 10X Genomics CellRanger v3.1
Genome_build: grch38
Supplementary_files_format_and_content: Gene expression consists of UMI counts for cells/genes. VDJ analysis consists of V-REGION H-chain identity %, Heavy chain, V-REGION L-chain identity %, Light chain, and Cluster id for cells.

source_name: Tonsil

growth_protocol: Surgically removed tonsil tissue was immediately processed to isolate mononuclear cells by Ficoll.

extract_protocol:
Tonsillar dark zone (CD3-; IgD-; CD38+; CXCR4high; CD83low), light zone (CD3-; IgD-; CD38+; CXCR4low; CD83high) and total (CD3-; IgD-; CD38+) germinal center B cells were isolated by cytofluorimetric cell sorting. Cell suspension were diluted at the concentration of 1,000 cells/ul
Single cells were captured and analyzed in the Chromium Controller (10x Genomics) using the Chromium Single Cell 5’ kit v1.1 and the Chromium Single Cell V(D)J Enrichment Human B cell kit, following manufacturer's instructions.

value: Germinal Center B cells

value: Tonsil

tag: individual

value: GC donor 3


title: Plate9and10


title: GC1_VDJ

value: GC donor 1


title: Plate6and8


title: S11_110

description: countmtx.csv


title: DZ1_VDJ

value: Dark zone germinal center B cells

value: DZ and LZ donor 1


title: LZ2_VDJ

value: Light zone germinal center B cells

value: DZ and LZ donor 2


title: S12_032

description: countmtx.csv

value: NAWM

value: total brain tissue

value: Qiagen Rneasy mini lipid kit

value: 3’ Quantseq FWD


title: LZ1_GEX


title: Plate3and4

value: PBMC

value: multiplexed sample:high and low CAD with and without IgE to alpha-gal sensitization


title: sample.446_overnight_ciml

description: gene expression data

value: blood


title: GC2_VDJ

value: GC donor 2


title: LZ1_VDJ


title: sample.445_overnight_ciml

description: gene expression data


title: sample.446_overnight_ld

description: gene expression data

value: LD IL-15


title: S12_008

description: countmtx.csv

value: F


title: sample.446_overnight_TxM

description: gene expression data

value: TxM (18/12/TxM molecule)


title: DZ2_VDJ

value: Tonsil


title: GC2_GEX

value: Germinal Center B cells


title: S11_120

description: countmtx.csv

value: M


title: S10_273

description: countmtx.csv


title: DZ2_GEX

value: Dark zone germinal center B cells


title: sample.445_overnight_ld

description: gene expression data


title: S09_152

description: countmtx.csv


title: GC3_GEX

value: GC donor 3


title: LZ2_GEX

value: Light zone germinal center B cells

value: DZ and LZ donor 2


title: deltaD9 VACV 18 hr rep 3

city: Berkeley

first: Michael

last: Ly

address: 565 Li Ka Shing Center

institute: UC Berkeley

description:
MockvsdeltaD9_18hr.xlsx
deltaD9vsD9muD10mu_18hr.xlsx
deltaD9vsD9muD10mu_18hr_viralvshost.xlsx

data_processing:
Sequencing data was converted into fastq format using the Illumina bcl2fastq software on the sequencing center's local linux server
Sequenced reads were trimmed using TrimGalore v0.4.4 at default settings except --stringency 3 and mapped onto the concatenated genome using STAR v2.7.1a.
For differential gene expression analysis, CuffDiff (CuffLinks v2.2.1) was used to compare two conditions (e.g. untreated versus dox-induced), using all three biological replicates from each condition. The default settings for CuffDiff were mostly used except -library-type fr-firststrand, -library-norm-method classic-fpkm, and -p 20. All genes with FPKM value of 0 were removed, and for genes with multiple transcript isoforms, only the most highly expressed transcript isoform was used for downstream analysis.
Prior to calculating fold-change, the FPKM value for each transcript was normalized to the sum of ERCC spike-in FPKM values from each condition to control for differences in library size.
Genome_build: hg19 concatenated with vaccinia virus (Western Reserve strain; NC_006998.1) genome and ERCC RNA spike-in sequence
Supplementary_files_format_and_content: All files contain FPKM and fold-change values, and some contain exon information for host genes.
Supplementary_files_format_and_content: D10_WT_InducibleCells.xlsx: abundance measurements of host transcripts, exon information, and their fold-change values upon D10 WT induction
Supplementary_files_format_and_content: D10_MUT_InducibleCells.xlsx: abundance measurements of host transcripts and their fold-change values upon D10 E144Q/E145Q induction
Supplementary_files_format_and_content: D9_D10_ActivityViralGenes.xlsx: abundance measurements of viral transcripts and their fold-change values reflecting D9 or D10 activity
Supplementary_files_format_and_content: MockvsWT_3hr.xlsx: abundance measurements of host transcripts and their fold-change values with WT VACV infection at 3 hpi relative to mock
Supplementary_files_format_and_content: MockvsWT_6hr.xlsx: abundance measurements of host transcripts and their fold-change values with WT VACV infection at 6 hpi relative to mock
Supplementary_files_format_and_content: MockvsWT_18hr.xlsx: abundance measurements of host transcripts and their fold-change values with WT VACV infection at 18 hpi relative to mock
Supplementary_files_format_and_content: MockvsdeltaD9_18hr.xlsx: abundance measurements of host transcripts and their fold-change values with deltaD9 VACV infection at 18 hpi relative to mock
Supplementary_files_format_and_content: MockvsD9muD10mu_18hr.xlsx: abundance measurements of host transcripts and their fold-change values with D9muD10mu VACV infection at 18 hpi relative to mock
Supplementary_files_format_and_content: deltaD9vsD9muD10mu_18hr.xlsx: abundance measurements of host transcripts, exon information, and their fold-change values with D9muD10mu VACV infection relative to deltaD9 VACV infection at 18 hpi. Reflects D10 activity on host transcripts during infection.
Supplementary_files_format_and_content: deltaD9vsD9muD10mu_18hr_viralvshost.xlsx: abundance measurements of host and viral transcripts, and their fold-change values with D9muD10mu VACV infection relative to deltaD9 VACV infection at 18 hpi. Reflects D10 activity on host vs viral transcripts.

source_name: Tissue culture

extract_protocol:
Total RNA was extracted from samples using TRIzol and treated with TURBO DNase. Afterwards, the RNA was isolated using RNA Clean & Concentrator - 5 kit, and 2μL of ERCC RNA spike-ins (1:100 diluted) was added to each sample.
RNA-Seq libraries were prepared using services provided by QB3 UC Berkeley. Illumina Ribo-Zero rRNA Removal Kits were used to deplete the RNA. Subsequent   library preparation steps of fragmentation, adapter ligation and cDNA synthesis were  done on the depleted RNA using the KAPA RNA HyperPrep kit (KK8540).   Truncated universal stub adapters were used for ligation, and indexed primers were  used during PCR amplification to complete the adapters and to enrich the libraries for  adapter-ligated fragments. Samples were checked for quality on an Agilent  Fragment Analyzer. Samples were then transferred to the Vincent J. Coates Genomics  Sequencing Laboratory (GSL), another QB3-Berkeley Core Research Facility at UC Berkeley,  where Illumina sequencing library molarity was measured with quantitative PCR with the Kapa  Biosystems Illumina Quant qPCR Kits on a BioRad CFX Connect thermal cycler. Libraries were then  pooled evenly by molarity and sequenced.

value: HEK293T cells

value: Infected with deltaD9 VACV at MOI 3 and harvested at 18 hpi


title: GC1_GEX

value: GC donor 1


title: sample.458_purified NK

description: gene expression data

value: none (freshly isolated)


title: S11_077

description: countmtx.csv

value: Lesion

value: total brain tissue

value: Qiagen Rneasy mini lipid kit

value: 3’ Quantseq FWD


title: S09_115

description: countmtx.csv

value: NAWM


title: sample.446_purified NK

description: gene expression data

value: blood


title: DZ1_GEX

value: Tonsil

value: DZ and LZ donor 1


title: S09_149

description: countmtx.csv

value: M


title: sample.445_purified NK

description: gene expression data


title: S10_238

description: countmtx.csv

value: F


title: WT VACV 18 hr rep 3

value: Infected with WT VACV at MOI 3 and harvested at 18 hpi


title: WT VACV 6 hr rep 3

value: Infected with WT VACV at MOI 3 and harvested at 6 hpi


title: S08_295

description: countmtx.csv


title: D9muD10mu VACV 18 hr rep 3

description:
MockvsD9muD10mu_18hr.xlsx
deltaD9vsD9muD10mu_18hr.xlsx
deltaD9vsD9muD10mu_18hr_viralvshost.xlsx

value: Infected with D9muD10mu VACV at MOI 3 and harvested at 18 hpi


title: sample.445_overnight_TxM

description: gene expression data

value: TxM (18/12/TxM molecule)


title: Mock rep 3

description:
MockvsWT_3hr.xlsx
MockvsWT_6hr.xlsx
MockvsWT_18hr.xlsx
MockvsdeltaD9_18hr.xlsx
MockvsD9muD10mu_18hr.xlsx

value: HEK293T cells

value: Untreated


title: MCF-7 PD-L1-OE replicate 2

city: Tian jin

first: xu

last: feifei

address: weijinlu

country: China

institute: nankai univesity

description: gene.tpm.matrix.annot.xls

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: Ensemble GRCh38 version
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MCF-7 cells

growth_protocol: The breast cancer cell lines MCF-7 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum (FBS, Gibco), 100 units/ml of penicillin and streptomycin at 37 ℃ in a humidified environment with 5% CO2.

extract_protocol:
MCF-7 cells total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF-7 cells in 6-well plates were transfected with pCMV or pCMV-PD-L1 for 36 h with two biological replicates.

value: breast caner cells

value: transfected with PD-L1 overexpression plasmids for 36 hours


title: WT VACV 3 hr rep 3

value: Infected with WT VACV at MOI 3 and harvested at 3 hpi


title: deltaD9 VACV 18 hr rep 2

value: Infected with deltaD9 VACV at MOI 3 and harvested at 18 hpi


title: S08_228

description: countmtx.csv

value: total brain tissue

value: Qiagen Rneasy mini lipid kit

value: 3’ Quantseq FWD


title: S08_047

description: countmtx.csv

value: Lesion


title: MCF-7 PD-L1-OE replicate 1

description: gene.tpm.matrix.annot.xls


title: Mock rep 2


title: WT VACV 6 hr rep 2


title: D9muD10mu VACV 18 hr rep 1


title: D9muD10mu VACV 18 hr rep 2


title: S07_216

description: countmtx.csv

value: NAWM


title: WT VACV 3 hr rep 2


title: deltaD9 VACV 18 hr rep 1


title: MCF-7 control replicate 2

description: gene.tpm.matrix.annot.xls

value: transfected with control plasmids for 36 hours


title: MCF-7 control replicate1

description: gene.tpm.matrix.annot.xls


title: WT VACV 18 hr rep 1


title: S08_292

description: countmtx.csv

value: M


title: WT VACV 6 hr rep 1


title: S07_127

description: countmtx.csv

value: F


title: D4I: TO-02 ALI+NOG

city: Haikou

first: Yue

last: Hong

address: 58 Renmin Road

department: School of Life and Health Sciences

institute: Hainan University

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to hg38 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Tracheobronchial basal cells

growth_protocol: Tracheobronchial basal cells (2x105/well) were seeded on 6.5mm transwell with 0.4 µm pore polyester membrane insert and differentiated in PneumaCult-ALI Medium (STEMCELL Technologies).

extract_protocol:
RNA was isolated using Trizol reagent.  3 ug  total RNA was used to prepare  sequencing libraries by NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMP antagonist Noggin (200ng/ml) was added to differentiation medium during air-liquid interface throughout the course of differentiation.

value: Trachea-Bronchi

value: Epithelial stem cell

tag: passage

tag: cell status

value: Differentiated on ALI

value: treated


title: S07_182

description: countmtx.csv

tag: gender


title: WT VACV 18 hr rep 2

value: HEK293T cells

tag: treatment

value: Infected with WT VACV at MOI 3 and harvested at 18 hpi


title: WT VACV 3 hr rep 1


title: D20: NonTO-07

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to hg38 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

growth_protocol: Tracheobronchial basal cells from normal and TO-derived biopsies were cultured on a lawn of irradiated 3T3-J2 cells in Stem Culture medium made in house with a combinatorial supplement of trio inhibitors as previously described (Liu et al., 2012; Mou et al., 2016). To perform differentiation, basal cells (2x105/well) were seeded on 6.5mm transwell with 0.4 µm pore polyester membrane insert and maintained in PneumaCult-ALI Medium (STEMCELL Technologies).


title: D19: TO-06


title: S4: TO-02 Stem

value: Immature

value: untreated


title: S07_109

description: countmtx.csv

tag: age


title: S07_005

description: countmtx.csv


title: D18: PM-06


title: D17: TO-05


title: SD005_15

description: countmtx.csv

value: Control


title: Mock rep 1

value: Untreated


title: D15: TO-04


title: S06_208_WML

description: countmtx.csv

value: total brain tissue

value: Qiagen Rneasy mini lipid kit


title: S04_247

description: countmtx.csv

value: 3’ Quantseq FWD


title: D14: PM-04


title: D4: TO-02 ALI


title: D10: PM-03


title: D11: TO-03


title: D7: NonTO-04


title: D9: NonTO-06


title: MS069LESION

value: LESION

value: macrophages

value: mechanic

value: 3’ single cell RNAseq 10x Genomics v2


title: S09_104

description: countmtx.csv

value: Lesion

value: M


title: D8: NonTO-05

value: Trachea-Bronchi

value: Epithelial stem cell

value: Differentiated on ALI


title: S08_069

description: countmtx.csv


title: CAF_control_rep3

type: RNA

city: San Sebastian

first: Andrea

last: Abaurrea

state: Gipuzkoa

address: Paseo Doctor Begiristain, s/n, 20014 San Sebastián

country: Spain

institute: Biodonostia HRI

description:
Total RNA extracted from CAF-173 spheroids treated with PBS, set3
BT-173-C3

hyb_protocol: cDNAs were hybridized to the human Clariom S array on the GeneChip Hybridization Oven 640, and staining and washings were performed on the Affymetrix GeneChip Fluidics Station 450 following standard protocols

scan_protocol: GeneChips were scanned using the Scanner 3000 7G (Affymetrix)

data_processing: The data were analyzed using Transcriptome Analysis Console version 4.0 (TAC 4.0) using Affymetrix default analysis settings and global scaling as normalization method. Summarization method was gene level SST-RMA, and a probeset (Gene/Exon) was considered expressed if ≥ 50% samples had DABG<0.05.

label: biotin

source_name: Immortalised fibroblasts isolated from a human triple negative breast cancer tumour

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: CAF-173 cells were cultured in DMEM supplemented with 10% FBS, 1% glutamine and 1% penicillin/streptomycin in collagen-coated plates. 3D spheroids were generated by seeding CAF-173 cells in ultra-low attachment 96-well plates in DMEM supplemented with 10% FBS, 1% glutamine and 1% penicillin/streptomycin.

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

treatment_protocol: Spheroids were treated with 30 ng/ml OSM or PBS for 4 days and total RNA was extracted.

tag: cell line

value: Inmortalised fibroblasts isolated from a human triple negative breast cancer tumour

value: PBS


title: MS069NAWM

value: NAWM

value: F


title: D5: TO-01

tag: tissue


title: CAF_OSM_rep1

description:
Total RNA extracted from CAF-173 spheroids treated with OSM, set1
BT-173-OSM1

value: OSM


title: D16: PM-05


title: CAF_OSM_rep3

description:
Total RNA extracted from CAF-173 spheroids treated with OSM, set3
BT-173-OSM3


title: Cancer cells_OSM_rep3

description:
Total RNA extracted from MDA-MB-231 cells transfected with pUNO1-hOSM vector, set3
MDA-MB-231-hOSM3

source_name: Transfected MDA-MB-231 breast cancer cell line

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% FBS, 1% glutamine and 1% penicillin/streptomycin. Transfected MDA-MB-231 cells were cultured in the presence of 10 μg/ml blasticidin.

treatment_protocol: MDA-MB-231 breast cancer cells were stably transfected with 2 μg of  pUNO1-empty and pUNO1-hOSM vectors with turbofect and selected by 10 μg/ml blasticidin.

value: triple negative breast cancer cells

tag: genotype/treatment

value: stably transfected with pUNO1-hOSM vector (MDA-MB-231-hOSM)


title: CAF_control_rep1

description:
Total RNA extracted from CAF-173 spheroids treated with PBS, set1
BT-173-C1


title: CAF_OSM_rep2

description:
Total RNA extracted from CAF-173 spheroids treated with OSM, set2
BT-173-OSM2


title: CAF_control_rep2

description:
Total RNA extracted from CAF-173 spheroids treated with PBS, set2
BT-173-C2


title: MS069NAGM

tag: group

value: NAGM


title: D3: PM-02

tag: cell type


title: Cancer cells_OSM_rep2

description:
Total RNA extracted from MDA-MB-231 cells transfected with pUNO1-hOSM vector, set2
MDA-MB-231-hOSM2


title: Cancer cells_OSM_rep1

description:
Total RNA extracted from MDA-MB-231 cells transfected with pUNO1-hOSM vector, set1
MDA-MB-231-hOSM1


title: Cancer cells_control_rep3

description:
Total RNA extracted from MDA-MB-231 cells transfected with pUNO1-empty vector, set3
MDA-MB-231-hC3

value: stably transfected with pUNO1-empty vector (MDA-MB-231-hC)


title: D4: TO-02


title: D0: PM-01


title: Cancer cells_control_rep2

description:
Total RNA extracted from MDA-MB-231 cells transfected with pUNO1-empty vector, set2
MDA-MB-231-hC2


title: MS043LESION

value: LESION

value: macrophages

tag: postmortem delay


title: T3

city: Qingdao

first: Congpeng

last: Wang

state: Shandong

address: Changcheng Road

institute: Qingdao Agricultural University

data_processing:
The cDNA libraries were sequenced using an Illumina HiSeq4000 system with 150-bp paired-end reads.
The sequence data with base-pair qualities in the Q ≥ 20 were extracted by custom Perl scripts.
The filtered reads were mapped to the poplar genome (v.3.1) using the HISATA2 software45.
Quantification of transcript was done in terms of fragment per kilobase of transcript per Million mapped reads (FPKM).
Genome_build: poplar genome (v.3.1)
Supplementary_files_format_and_content: Excel files include Count and FPKM values for each Sample ...

organism: Populus deltoides x Populus x canadensis

source_name: Populus deltoedes × Populus euramericana

growth_protocol: Poplar was grown in a greenhouse at 22-24 °C with a photoperiod: 16 h of light/8 h of dark.

extract_protocol:
After removing the leaves, basal stems (2 cm) were sampled for RNA isolation. Thirty plants for each line were pooled as a sample and three biological replication were set. RNA purification, library construction and sequencing were conducted by Shanghai Applied Protein Technology Co., Ltd. (Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stem

tag: strain

value: Nanlin 895

tag: genotype

tag: development stage

value: 45 days


title: S17: TO-05

value: Trachea-Bronchi

value: Immature


title: T1


title: S19: TO-06

value: Epithelial stem cell


title: MS043NAGM

tag: rin

tag: cell isolation

value: mechanic

tag: rna isolation

tag: sequencing method

value: 3’ single cell RNAseq 10x Genomics v2


title: S18: PM-06

tag: passage

tag: cell status


title: T2


title: Cancer cells_control_rep1

description:
Total RNA extracted from MDA-MB-231 cells transfected with pUNO1-empty vector, set1
MDA-MB-231-hC1


title: D2: NonTO-02

value: Differentiated on ALI


title: S15: TO-04


title: S16: PM-05


title: D1: NonTO-01


title: CK3

value: WT


title: MS011LESION

tag: gender

value: M


title: MS011NAWM

value: NAWM

tag: age


title: MS011NAGM


title: MS043NAWM

value: F


title: CK2


title: MS116LESION


title: S6: NonTO-03


title: S10: PM-03


title: S7: NonTO-04


title: S8: NonTO-05


title: Whole transcriptome at normal salinity of MED4, rep3

city: guangzhou

first: he

middle: xia

last: yu

address: NO.164 xingang road

department: South China Sea Institute of Oceanology

institute: University of Chinese Academy of Sciences

description:
MED4-34-3
Replication 3
Prochlorococcus marinus MED4

data_processing:
Cutadapt (v1.9.1) was used to remove adapters, primers, and reads with a base quality < 20 based on FASTQ files. Clean data were aligned to the MED4 and NATL1A genomes via Bowtie2 software (v2.1.0). HTSeq (v0.6.1p1) was used to estimate gene expression levels from clean data. Differential expression analysis was performed using the DESeq Bioconductor package, a model based on negative binomial distribution. After adjusting using Benjamini and Hochberg’s approach for controlling the false discovery rate, differentially expressed genes were considered significant at P values < 0.05. Highly induced or suppressed genes were considered as meeting both false discovery rate P < 0.05 and magnitude of log2fold change with values greater than 2 (highly induced) or less than −2 (highly suppressed).
In order to cluster cyanobacteria genes based on their expression dynamics, the FPKM normalization of gene transcript level was used. The package EdgeR implemented in Bioconductor was used to analyze the differential expression of treat and control. The genes with log2FC ≥ 2 as well as P < 0.05 were considered to be upregulated.
Genome_build: not provided
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: Tab-delimited text files include differential expression of Prochlorococcus NATL1A and MED4, comparing the normal salinity control sample to salt stress treated samples.

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

source_name: normal salinity of MED4

growth_protocol: Cultures were maintained in Pro99 natural sea water medium with a salinity of 28% and 34%, at 21 °C and under a constant light intensity of 10 μE m−2 s−1. Canted neck polystyrene flask (Corning) with different volumes were used.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen). Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agarose gel. 1 μg total RNA with RIN value above 7 was used for following library preparation.
Next-generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®).

treatment_protocol: The cells under low salinity stress and normal salinity were collected after 5 generations.

tag: treatment

value: 34% salinity


title: S14: PM-04

tag: tissue


title: D6: NonTO-03


title: CK1


title: MS115LESION


title: S5: TO-01


title: Col0_3_rep1 (smRNA-seq)

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Control for Set 3

data_processing:
quality  trimming using sickle se (v0.940) and adapter removal using cutadapt (v1.9.dev6)
mapping with bowtie (v1.0.0) and sorting using samtools  (v1.1)
counting reads per gene with HTseq-count (v0.6.0) and differential accumulation analysis with DESeq2 (v1.8.2) package in R (v3.2.2)
bigwig files were generated using bedtools genomecov (v2.17.0) and bedGraphToBigWig (v4); Scores represent reads normalized to 1e7 reads
Genome_build: TAIR10
Supplementary_files_format_and_content: counts, bigwig

organism: Arabidopsis thaliana

source_name: 21 day old seedlings

growth_protocol: Seeds were stratified for 2 days at 4C and grown under a 16 h light/8 h dark (long-day) conditions.

extract_protocol:
Total plant RNA was isolated using Trizol reagent (Sigma) according to manufacturer’s instructions.
BGI

value: wild type (Col-0)

tag: growth protocol

value: soil

tag: developmental stage

value: 21 day old seedlings

value: total plant


title: MS116NAGM

tag: group

value: NAGM

tag: cell type

value: macrophages


title: cstf64_rep3 (smRNA-seq)

description: Set 3


title: S11: TO-03

value: Trachea-Bronchi


title: cstf64_rep2 (smRNA-seq)

description: Set 3


title: S20: NonTO-07

value: Immature


title: S4: TO-02

value: Epithelial stem cell


title: MS116NAWM

tag: postmortem delay

value: mechanic


title: Whole transcriptome at salt stress of MED4, rep2

description:
MED4-28-2
Replication 2
Prochlorococcus marinus MED4

source_name: salt stress of MED4

value: 28% salinity


title: Whole transcriptome at normal salinity of MED4, rep2

description:
MED4-34-2
Replication 2
Prochlorococcus marinus MED4


title: S2: NonTO-02


title: cstf64_rep1 (smRNA-seq)

description: Set 3

tag: genotype


title: Whole transcriptome at normal salinity of MED4, rep1

description:
MED4-34-1
Replication 1
Prochlorococcus marinus MED4


title: HVCF EXO TGF #4

city: Philadelphia

first: Steve

middle: R

last: Houser

state: PA

address: 3500 N Broad Street

institute: Temple University

description: diffexp_HVCF-TGF_cntrl.csv; diffexp_HVCF_cntrl.csv; diffexp_HVCF-EXO_cntrl.csv; diffexp_HVCF-EXOTGF_cntrl.csv

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,and for low-complexity or low-quality sequence.
High quality reads were mapped to hg38 whole genome using HISAT2 v2.1.0 and quantified using HTSeq v0.11.2
Differential expression was calculated using DESeq2 v1.22.2
Genome_build: hg38
Supplementary_files_format_and_content: comma separated format contains log2 fold change between experimental and control groups

source_name: cardiac fibroblast

growth_protocol: Human cardiac fibroblasts (Lonza CC2904) were plated at 1,800 cells per well in 96-well plate and grown in Lonza fibroblast medium (Lonza CC-4526) plus Fetal Bovine Serum (FBS) (Gibco10439024), fibroblast growth factor (Peprotech AF-100-18B), insulin-transferrin-selenium (ITS) (Lonza Biowhittaker 17838Z), and Penicillin streptomycin glutamine (PSG) (Gibco 10378016). Passage 1 cells were cultured in 10cm dishes and then passaged and plated at 200k cells per well in 6 well plates. Cells were allowed to adhere and grow for 24hrs in Lonza + 10% FBS media, and then were serum starved overnight in Lonza + 1% FBS. Following the overnight serum starvation, cell media was aspirated and replaced with Lonza + 1% FBS media.

extract_protocol:
RNA was isolated using the Qiagen miRNeasy isolation kit (Qiagen RNeasy Micro Kit 74004).
Takara SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian was used  for the construction of sequencing libraries. RNA libraries were prepared for sequencing using ribosomal cDNA removal protocols

treatment_protocol: Cells were treated with 2,000,000 particles/cell of hCBSC-derived exosomes +/- 10 ng/mL TGFβ (Invivogen rcyc-htgfb1). Following 72hrs of incubation at 37°C, cells were lysed and RNA was isolated.

value: normal human cardiac fibroblast

value: 10 ng TGFBeta + 2,000,000 particles hCBSC exosomes/fibroblast


title: Whole transcriptome at salt stress of MED4, rep1

description:
MED4-28-1
Replication 1
Prochlorococcus marinus MED4


title: Col0_3_rep3 (smRNA-seq)

description: Control for Set 3


title: Whole transcriptome at salt stress of MED4, rep3

description:
MED4-28-3
Replication 3
Prochlorococcus marinus MED4


title: MS115NAWM

value: M

value: 3’ single cell RNAseq 10x Genomics v2


title: Col0_3_rep2 (smRNA-seq)

description: Control for Set 3


title: S0: PM-01


title: TO-01: TO

data_processing:
Raw sequence reads were initially processed by FastQC for quality control, and then adapter sequences and poor quality reads were removed by using Trimmomatic.
Quality filtered reads were then mapped to mm10 reference genome using BWA(0.7.10), and only uniquely mapped reads were kept.
Sam files were converted to Bam format using Samtools and used for peak calling. MACS2(2.1.1)was used to call peaks and an initial threshold q-value of 0.05 as cutoff.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using MACS2

molecule: genomic DNA

growth_protocol: Tracheobronchial basal cells from normal and TO-derived biopsies were isolated and cloned on a lawn of irradiated 3T3-J2 cells in Stem Culture medium made in house with a combinatorial supplement of trio inhibitors as previously described (Liu et al., 2012; Mou et al., 2016).

extract_protocol:
Selected 50 average size islets were lysed in lysis buffer.Nuclei were then incubated with the Tn5 transposome and tagmentation.
Libaray was prepared according to protocols of TruePrep DNA Library Prep Kit V2 for illumina(Vazyme Biotech, Nanjing, China) .The libraries were sequenced on HiSeq platform and using PE150 sequencing strategy


title: rsr1_rep2 (smRNA-seq)

description: Set 2

source_name: 14 day old seedlings

value: MS

value: 14 day old seedlings


title: Whole transcriptome at normal salinity of NATL1A, rep2

description:
NATL1A-34-2
Replication 2

organism: Prochlorococcus marinus str. NATL1A

source_name: normal salinity of NATL1A

value: 34% salinity


title: S3: PM-02


title: Whole transcriptome at normal salinity of NATL1A, rep3

description:
NATL1A-34-3
Replication 3


title: rsr1_rep1 (smRNA-seq)

description: Set 2


title: HVCF EXO TGF #1


title: HVCF EXO TGF #3


title: S9: NonTO-06


title: PM-02: TO


title: Whole transcriptome at normal salinity of NATL1A, rep1

description:
NATL1A-34-1
Replication 1


title: S1: NonTO-01


title: fy_rep2 (smRNA-seq)

description: Set 2


title: HVCF EXO #4

value: 2,000,000 particles hCBSC exosomes/fibroblast


title: NonTO-02: Non-TO


title: rsr1_rep3 (smRNA-seq)

description: Set 2


title: pab_rep3 (smRNA-seq)

description: Set 2

value: pab2 pab4


title: NonTO-01: Non-TO


title: HVCF EXO TGF #2


title: Whole transcriptome at salt stress of NATL1A, rep3

description:
NATL1A-28-3
Replication 3

source_name: salt stress of NATL1A


title: fy_rep3 (smRNA-seq)

description: Set 2

value: total plant


title: HVCF EXO #3


title: fy_rep1 (smRNA-seq)

description: Set 2


title: HVCF EXO #2


title: HVCF EXO #1


title: Whole transcriptome at salt stress of NATL1A, rep1

description:
NATL1A-28-1
Replication 1


title: TO-02: TO


title: pab_rep2 (smRNA-seq)

description: Set 2


title: Whole transcriptome at salt stress of NATL1A, rep2

description:
NATL1A-28-2
Replication 2


title: IRF1 expressing replicate 3

first: Sibley

last: David

state: Missouri

address: 660 S. Euclid, CB 8230

institute: Washington University in St. Louis

description: irf1_3.CATATTGGAG-TACGGTATTC.HLGLYDSXY_CATATTGGAG-TACGGTATTC

data_processing:
Data was analyzed with Partek Flow Genomic Analysis software (v8.0). Reads less than 25 bp were not considered for alignment. 5 bp were trimmed from the 5' end of reads before alignment using STAR aligner. GSA analysis was used to identify differentially expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data is in .xlsx format and contains fold change gene expression for both IRF1 ectopically expressing and IFNγ treated cells relative to FLUC expressing untreated control.

source_name: A549 lung epithelial cells

extract_protocol:
Samples were harvested with RLT buffer. RNA was isolated using a Qiagen RNeasy mini kit according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line/type

value: A549 lung epithelial cells

tag: expressed gene

value: IFNγ 0 U/mL


title: PM-01: Non-TO

value: Trachea-Bronchi


title: HVCF TGF #4

value: 10 ng TGFBeta


title: IRF1 expressing replicate 2

description: irf1_2.CGAGTGATTA-CTTCAATAGC.HLGLYDSXY_CGAGTGATTA-CTTCAATAGC


title: MDA_MB_231_2

city: Beijing

first: Lulu

address: No. 10 You An Men Wai Xi Tou Tiao

department: Department of Human Anatomy

institute: Capital Medical University

data_processing:
RNA-Seq library preparation and sequencing were conducted in BGI Tech via BGISEQ-500 sequencer
The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing sequencing adapter, removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%, and removing reads whose unknown base ('N' base) ratio is more than 5%.
Clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set.
The expression level of gene was measured in the normalized read count (FPKM).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample.

source_name: human breast cancer cells

growth_protocol: The 231-BR cell line was maintained in Dulbecco's Modified Eagle Medium (DMEM), supplemented with 200 μg/mL G418 (Sigma-Aldrich), 10% Fetal Bovine Serum (FBS), and 1% penicillin-streptomycin. MDA-MB-231 was maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA from 231-BR and MDA-MB-231 cells was extracted using TRIzol reagent according to the manufacturer’s instructions.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB). DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform.

tag: cell line

value: human breast cancer cells


title: MDA_MB_231_3


title: MDA_MB_231_1


title: ccr4a_rep3 (smRNA-seq)

description: Set 2


title: HVCF TGF #3


title: pab_rep1 (smRNA-seq)

description: Set 2


title: HVCF TGF #2


title: IRF1 expressing replicate 1

description: irf1_1.CGCAAGACGT-GATAGGTGAA.HLGLYDSXY_CGCAAGACGT-GATAGGTGAA


title: ccr4a_rep2 (smRNA-seq)

description: Set 2


title: 231BR_3

value: human breast cancer brain metastasis cells


title: HVCF TGF #1


title: IFNγ treated FLUC expressing replicate 3

description: fluc_ifng_3.CATAATCCGG-TATAACTCCG.HLGLYDSXY_CATAATCCGG-TATAACTCCG

value: FLUC


title: 231BR_2


title: ahg2_rep3 (smRNA-seq)

description: Set 2


title: IFNγ treated FLUC expressing replicate 2

description: fluc_ifng_2.CGGAGAATTG-ACCAATCTGA.HLGLYDSXY_CGGAGAATTG-ACCAATCTGA


title: 231BR_1


title: IFNγ treated FLUC expressing replicate 1

description: fluc_ifng_1.AATCCATTGC-TAGCCTCATG.HLGLYDSXY_AATCCATTGC-TAGCCTCATG


title: FLUC expressing control replicate 3

description: fluc_3.GTAATACTCG-CTTCCAAGCT.HLGLYDSXY_GTAATACTCG-CTTCCAAGCT


title: ahg2_rep1 (smRNA-seq)

description: Set 2


title: HVCF #2

value: normal human cardiac fibroblast


title: HVCF #3


title: wild-type 1-HA (control)

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

institute: Ludwig Maximilian University of Munich

data_processing:
Libraries were pre-processed using the Hannon-lab fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/download.html) to remove poor quality reads (FASTQ quality filter), clip adaptors (FASTQ clipper) and filter duplicated reads (FASTQ collapser).
Pre-processed sequences were then aligned to the mouse genome (build GRCm38/mm10) using Tophat2 (Kim et al., 2013) (https://ccb.jhu.edu/software/tophat/index.shtml) with default options.
We predict statistically significant RIP regions (peaks) indicative of a physical interaction of an RNA transcript with CYFIP1 using the software RIPSeeker (Li et al., 2013).
Genome_build: GRCm38/mm10

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
RNA was extracted with Trizol reagent (invitrogen)
cDNA libraries for pulled-down RNA and input RNA were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina®.
cDNA libraries were sequenced on the Illumina Hiseq platform with 50 cycles single-end.

treatment_protocol: Mouse hippocampi were dissected out and homogenized in lysis buffer. Lysates were then incubated with mouse anti-HA antibody (Covance) or mouse control IgG for 2 hr at 4 °C. After antibody incubation, RNA-protein complexes were immunoprecipitated with Dynabeads Protein G (Thermo Fisher Scientific) for 2 hr, and the beads were washed 5 times with lysis buffer before extracting the RNA with Trizol (Invitrogen).

tag: strain

tag: rip antibody

value: HA antibody


title: ccr4a_rep1 (smRNA-seq)

description: Set 2


title: knock-in2-IgG (control)

value: IgG


title: CKO2_S55

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description: CKO

data_processing:
Individual FASTQ files were trimmed for adapter sequences using fastp v0.21.0. Alignment was performed against mouse genome reference GRCm38p5 using HISAT2 v2.1.0.
Gene expression values for genes described by the GENCODE Gene Transfer Format (GTF) release M14 (mouse) were quantified using the featureCounts tool of the Subread package v2.0.1 in unstranded mode.
Genome_build: GRCm38p5
Supplementary_files_format_and_content: voom normalized expression table for all detectable genes in all samples

source_name: Dental pulp

extract_protocol:
Teeth were dissected and pulp was removed from the mineralized structure and immersed in Lysis Buffer (Quiagen #79216).  Samples were pestled to break up tissue and RNA was isolated with RNA Sample Prep Tool (Zymo Research #R2072).
RNA Integrity Number (RIN) and RNA quantification for total RNA were determined by Agilent BioAnalyzer RNA 6000 Pico Kit (Cat. # 5067-1513) and Invitrogen Qubit RNA HS Assay kit ( Cat. # Q32852), respectively. Samples with RIN > 7 were used for global preamplification for the 1-ng low-input mRNA-seq using the Clontech SMAR-seq HT kit (Cat. # 634437). The resultant cDNA samples were used for library generation using the Illumina Nextera XT DNA Library Prep Kit (Cat. # 15031942) and sequenced on Illumina NovaSeq SP flowcell for 12-15 million PF clusters per sample.
1ng-Low Input mRNA-Seq


title: knock-in1-IgG (control)


title: HeLa Control RNAi

city: Nangjing

first: Ming

last: Fang

state: jiangsu

address: 2 Sipailou Road

institute: Southeast University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1).
The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute fold change of two were set as the threshold for significantly differential expression.
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: Differential expression analysis

source_name: HeLa cells

extract_protocol:
Total RNA was extracted according to the manufacturer’s instructions. Briefly, cells were lysed in 500 μl TRIzol® (Invitrogen; Thermo Fisher Scientific, Inc.) and 100 μl of chloroform was added to each lysate. The lysate was centrifuged at 12000 rpm for 15 min at 4˚C. Upper aqueous phase was collected in a fresh tube and RNA was precipitated with equal volume of isopropanol. Tubes were centrifuged again at 10000 rpm for 10 min at 4˚C. The pellet was washed twice with 75% ethanol at 7500 rpm for 5 min at 4˚C.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: HeLa cells were transfected with Control and MAGT1 siRNAs while plated onto 6 well plates using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. 48 hours later, RNA or protein was harvested for further analyses.

value: HPV18 positive cervical carcinoma

value: cervical carcinoma

value: HeLa

value: Control RNAi


title: CRE2_S51

description: CRE

value: Osterix-Cre control


title: CRE5_S52

description: CRE


title: Col0_2_rep1 (smRNA-seq)

description: Set 2

value: wild type (Col-0)

value: MS

value: 14 day old seedlings


title: ahg2_rep2 (smRNA-seq)

description: Set 2

value: total plant


title: CRE4_S50

description: CRE


title: CKO3_S56

description: CKO


title: CKO2_S54

description: CKO


title: FLUC expressing control replicate 2

city: St. Louis

description: fluc_2.AACATAGGTG-TATCTCTAGG.HLGLYDSXY_AACATAGGTG-TATCTCTAGG

value: A549 lung epithelial cells

value: IFNγ 0 U/mL


title: MS115NAGM

city: Groningen

first: Emma

address: Antonius Deusinglaan 1

institute: UMCG

data_processing:
[data processing step 10x Genomics samples]  Cellranger version 3.0.0
[data processing step Bulk alignment]  Hisat v0.1.5
[data processing step Bulk sorting reads]  samtools v1.2
[data processing step Bulk counting reads]  HTSeq v0.6.1
Genome_build: Bulk GRCh37, human SC GRCh38, mouse SC GRCm38
Supplementary_files_format_and_content: Countfiles with raw counts per sample (bulk) or droplet barcode (single-cell)

source_name: brain

extract_protocol:
[Macrophage isolation human]  Mechanical tissue dissociation followed by percoll gradient centrifugation. FACS sorting for CD45posCD11Bpos cells.
[Macrophage isolation mouse]  Enzymatic isolation at 4C using protease from Bacillus lichenformis and L-cysteine. FACS sorted on tdTomato Red cells.
Qiagen Rneasy lipid mini kit
3’ Quantseq FWD kit from Lexogen for bulk RNAseq. 3’ single cell RNAseq v2 from 10x Genomics for single cell.

value: NAGM

value: macrophages

tag: rin

value: M

tag: cell isolation

value: mechanic

tag: rna isolation

tag: sequencing method

value: 3’ single cell RNAseq 10x Genomics v2


title: CKO3_S53

description: CKO


title: Striatum WT Male (JB.26.3.S)

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR with default parameter settings
Raw counts were obtained with HTSeq using refSeq gene model (mm10) as reference.  Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38
Supplementary_files_format_and_content: Counts  for each sample

source_name: Striatum  WT 12 mon Male

extract_protocol:
Qiagen RNeasy kit with QIAshredder columns
TruSeq Stranded RNA (100 ng)

treatment_protocol: Mice were perfused with PBS in DEPC-treated H2O. Cortex, Striatum and cerebellum were dissected out and fresh frozen in dry ice immediately.

tag: strain background

value: FvB

value: WT

tag: age

value: 12 mon

tag: Sex

value: Male

value: Striatum


title: knock-in2-HA (RIP)

value: HA antibody


title: Col0_2_rep3 (smRNA-seq)

description: Set 2

value: wild type (Col-0)

tag: growth protocol

tag: developmental stage

tag: tissue


title: upf3_rep3 (smRNA-seq)

description: Set 1

value: MS


title: KO2-hippocampus-before-FC-Technical_replicate2

city: Shanghai

first: Jin

last: Zheng

state: Shanghai

address: 800 Dongchuan RD

institute: sjtu

description: Transgenic mouse

data_processing:
Sequenced reads were trimmed for adaptor sequence sequence, then aligned to the reference mouse genome (mm10) using the Bowtie program (version 1).Hisat and cuffilinks softwares were used to handle data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hippocampus

growth_protocol: Transgenic mouse

extract_protocol:
Mouse tissues was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

value: KO


title: HVCF #4

tag: cell type

value: normal human cardiac fibroblast

tag: treatment


title: KO2-hippocampus-before-FC-Technical_replicate1

description: Transgenic mouse

tag: genotype


title: HeLa MAGT1 RNAi

value: HPV18 positive cervical carcinoma

value: cervical carcinoma

value: HeLa

value: MAGT1 RNAi


title: upf1_rep2 (smRNA-seq)

description: Set 1

value: 14 day old seedlings

value: total plant


title: CRE4_S49

description: CRE

value: Osterix-Cre control


title: Striatum WT Male (JB.14.3.S)

value: FvB


title: Col0_2_rep2 (smRNA-seq)

description: Set 2


title: upf3_rep1 (smRNA-seq)

description: Set 1


title: MS11 cells treated with Cef for 60 min, replicate 2

city: Cologne

first: Isabel

last: Rathmann

address: Zülpicher Str. 47 a

department: Institute for Biological Physics

institute: University of Cologne

data_processing:
reads were trimmed with Trimmomatic (version 0.36); Parameters: ILLUMINACLIP:IlluminaAdapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
reads were then mapped against the reference genome of  Neisseria gonorrhoeae MS11 (NCBI, CP003909.1) using STAR (2.5.3a); parameter:  --outSAMmultNmax 10
calling read counts with featureCounts from the subread package (version: 2.0.1); paramter: -p -O --minOverlap 20
Genome_build: NCBI, CP003909.1
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every gene and every sample

organism: Neisseria gonorrhoeae MS11

source_name: bacterial cells

growth_protocol: 1mL GC media was inoculated with approximately 3*10^6 cells in a 24 well plate. Cells were grown for 6h at 37°C, 5% C02 in an Infinite M200 plate reader with a shaking period of 2 min per OD cycle (OD was measured every 10 min).

extract_protocol:
RNA was extracted with the Qiagen RNeasy Protect Bacteria Mini Kit (Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (rRNA depletion and library construction were carried out by Cologne Center for Genomics (CCG), University of Cologne, Germany)
RNA-Seq (Carried out by CCG, University of Cologne, Germany)

treatment_protocol: After 6h growth, azithromycin or ceftriaxone were added at 2-fold MIC (0.256 µg/mL or 0.016 µg/mL, respectively). The same volume DMSO was added to the control, since this is the solvent of the used antibioitics. Afterwards, the cells were further incubated for 15min or 60min prior to RNA extraction.

value: ceftriaxone treatment, 60 min


title: MS11 cells treated with Cef for 60 min, replicate 3


title: HVCF #1


title: Striatum BAC-HD Male (JB.4.4.S)

source_name: Striatum  BACHD 12 mon Male

value: Tg

value: 12 mon


title: FLUC expressing control replicate 1

description: fluc_1.CCGCAGTATC-TACCTGGCAA.HLGLYDSXY_CCGCAGTATC-TACCTGGCAA

tag: cell line/type

value: A549 lung epithelial cells

tag: expressed gene

value: FLUC

value: IFNγ 0 U/mL


title: MS11 cells treated with Cef for 15 min, replicate 2

value: ceftriaxone treatment, 15 min


title: upf3_rep2 (smRNA-seq)

description: Set 1

value: MS


title: knock-in1-HA (RIP)

tag: strain

value: HA antibody


title: upf1_rep3 (smRNA-seq)

description: Set 1


title: WT2-hippocampus-before-FC-Technical_replicate2

description: Transgenic mouse

value: wild type


title: WT2-hippocampus-before-FC-Technical_replicate1

description: Transgenic mouse


title: KO1-hippocampus-before-FC-Technical_replicate2

description: Transgenic mouse

value: KO


title: MS11 cells treated with Cef for 60 min, replicate 1


title: MS11 cells treated with Azi for 60 min, replicate 2

value: azithromycin treatment, 60 min


title: Striatum BAC-HD Female (JB.3.5.S)

source_name: Striatum  BACHD 12 mon Female

value: Female

value: Striatum


title: lsm1_rep3 (smRNA-seq)

description: Set 1

value: lsm1a lsm1b

value: 14 day old seedlings

value: total plant


title: MS11 cells treated with Cef for 15 min, replicate 3


title: MS11 cells treated with Azi for 60 min, replicate 3


title: Striatum BAC-HD Female (JB.3.2.S)

value: FvB


title: ncb_rep3 (smRNA-seq)

description: Set 1


title: MS11 cells treated with Cef for 15 min, replicate 1


title: Striatum BAC-HD Male (JB.4.3.S)

value: Tg

value: Male


title: MS11 cells treated with Azi for 60 min, replicate 1


title: Striatum WT Female (JB.2.3.S)

source_name: Striatum  WT 12 mon Female

value: WT

value: 12 mon


title: ncb_rep1 (smRNA-seq)

description: Set 1


title: Striatum WT Female (JB.1.1.S)


title: MS11 cells treated with Azi for 15 min, replicate 3

value: azithromycin treatment, 15 min


title: WT1-hippocampus-before-FC-Technical_replicate1

description: Transgenic mouse


title: lsm1_rep2 (smRNA-seq)

description: Set 1


title: ncb_rep2 (smRNA-seq)

description: Set 1


title: KO1-hippocampus-before-FC-Technical_replicate1

description: Transgenic mouse


title: MS11 cells treated with Azi for 15 min, replicate 1


title: ILCs, Id1

city: Norman

first: KAILI

last: LIU

state: Oklahoma

address: 173 Felgar St

institute: The University of Oklahoma

description: blood Lin-Thy1+ cells enriched of ILCs

data_processing:
Sequencing reads were processed using the 10× Genomics CellRanger pipeline and further analyzed with the Seurat R package
Genes that were expressed in less than 5 cells or cells that expressed less than 200 genes were excluded.
Also, cells with a mitochondria percentage over 10% were excluded.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values (TSV) files include cell barcodes for each sample
Supplementary_files_format_and_content: Tab-separated values (TSV) files include features for each cell barcode
Supplementary_files_format_and_content: Matrix table with raw gene counts for each feature and each cell barcode

source_name: ILC

extract_protocol:
blood Lin-Thy1+ cells enriched of ILCs from 4 different strains of mice were obtained
RNA libraries were prepared for sequencing using standard Illumina protocols
single cell RNA-Seq

value: ILC


title: upf1_rep1 (smRNA-seq)

description: Set 1

value: MS


title: ILCs, WT_3

description: blood Lin-Thy1+ cells enriched of ILCs


title: lsm1_rep1 (smRNA-seq)

description: Set 1


title: Cortex WT Male (JB.14.3.C)

source_name: Cortex  WT 12 mon Male

value: Cortex


title: Col0_1_rep3 (smRNA-seq)

description: Set 1

source_name: 14 day old seedlings

value: wild type (Col-0)


title: ILCs, Nude

description: blood Lin-Thy1+ cells enriched of ILCs

value: Nude


title: Col0_1_rep1 (smRNA-seq)

description: Set 1


title: MS11 cells treated with DMSO for 60 min, replicate 1

value: DMSO added, 60 min


title: Cortex WT Male (JB.26.3.C)


title: Cortex BAC-HD Male (JB.4.4.C)

source_name: Cortex  BACHD 12 mon Male


title: ILCs, WT_2

description: blood Lin-Thy1+ cells enriched of ILCs


title: MS11 cells treated with DMSO for 60 min, replicate 3


title: Col0_1_rep2 (smRNA-seq)

description: Set 1


title: WT1-hippocampus-before-FC-Technical_replicate2

description: Transgenic mouse

value: wild type


title: MS11 cells treated with Azi for 15 min, replicate 2


title: Cortex BAC-HD Male (JB.4.3.C)


title: MS11 cells treated with DMSO for 15 min, replicate 3

value: DMSO added, 15 min


title: ILCs, WT_1

description: blood Lin-Thy1+ cells enriched of ILCs


title: Seedlings, wt_2

city: Sevilla

first: Myriam

last: Calonje

address: Americo Vespucio 49

institute: Institute for Plant Biochemistry and Photosynthesis (CSIC -  University of Sevilla)

description: wt.wig

data_processing:
The high quality of the raw sequencing data stored in the fastq files was verified using the software tool FastQC
Short sequence reads were mapped to the Arabidopsis reference genome version TAIR10 using BOWTIE allowing two mismatches to produce files in BAM format.
On the one hand, these BAM files were used for peak-calling in order to determine nucleosome positioning and occupancy in the different replicates of the two genotypes under study, namely WT and atbmi1a/b/c. This was performed with the Dpos utility from the software tool DANPOS2 using the clonalcut parameter. Nucleosome occupancy comparison between the two genotypes was represented using scatterplots generated with a custom R script.
On the other hand, the BAM files were further processed by removing PCR duplicates with the tool samtools rmdup, and converted into WIG format using the bioconductor R package nucleR. Specifically, files were imported and reads were trimmed using the function processReads with parameter trim=40. Next, noise removal and curve smoothing were applied with the function filterFFT using the parameter pcKeepComp=0.01. Finally, WIG files were generated by applying the function export.wig.
Genome_build: tair10
Supplementary_files_format_and_content: WIG files

source_name: Seedlings

growth_protocol: Arabidopsis Col-0 wild type (WT) and atbmi1a/b/c (Yang et al., 2013) seeds were germinated in one-half-strength Murashige and Skoog (MS) plates containing 1.5% sucrose and 0.8% agar for seven days. After seven days growing under long-day conditions at 21 °C, one gram of seedlings were collected and storage at -80 °C.

extract_protocol:
DNA was purified with phenol/chloroform extraction and precipitated with salts and ethanol. Purified DNA was run on a 2% agarose gel, and bands corresponding to approximately 150 bp were cut and purified with a Gel Purification kit (Qiagen, http://www.qiagen.com/).
Library was prepared using a TruSeq DNA Sample Prep Kit following the manufacturer’s instructions (Illumina). Sequencing was carried out as 50 bp of paired-end reads on an Illumina HiSeq 4000.

treatment_protocol: Nuclei extracted from 1 gr of seven days old seedlings were resuspended in MNase digestion buffer (20 mM Tris–HCl, pH 8.0, 5 mM NaCl, and 2.5 mM CaCl2) and digested with 1 unit/µl of micrococcal nuclease (NEB) for 10 min at 37 °C. The digestion was stopped by adding EDTA and SDS to a final concentration of of 20 mM and 1%, respectively. Then samples were treated with 10 µl of RNase A at 37 °C and 20 µl Proteinase K at 45 °C each for 1 h.

tag: ecotype

value: Wild Type


title: MS11 cells treated with DMSO for 15 min, replicate 2


title: MS11 cells treated with DMSO for 15 min, replicate 1


title: MS11 cells treated with DMSO for 60 min, replicate 2


title: 16175X1 WT CD45

city: Salt Lake City

first: Alana

last: Welm

address: 2000 Circle of Hope

institute: University of Utah

description: Single-cell 3' RNA-Sequencing

data_processing:
For each sample, fastq files were demultiplexed with 10x Genomics' Single-Cell Gene Expression software, Cell Ranger, using the 'mkfastq version 3.1.0' pipeline to create I1 sample index, R1 cell barcode and UMI, R2 RNA sequence.
Reads were aligned to the 'refdata-cellranger-mm10-3.0.0' reference, prepared by 10x Genomics (see https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#mm10_3.0.0 for details).
Barcodes and UMIs were counted using cellranger count version 3.1.0 with expected-cells =10000.
Genome_build: mm10, M_musculus_Dec_2011, GRCm38
Supplementary_files_format_and_content: MEX-formatted UMI count matrices are available without normalization and are prefixed by sample identifiers (e.g. '16175X_'). Each sample's UMI count matrix contains the filtered gene-barcode output from 10x Genomics' Cell Ranger pipeline, which discards GEMs with insufficient total UMI count; details on this auto-filtering is available on 10x Genomics' website. More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

molecule: polyA RNA

source_name: CD45+ tumor infiltrating immune cells

extract_protocol: Lungs occupied by metastases were perfused with PBS (pH 7.4) and excised followed by transferred to Accumax cell/tissue dissociation solution (STEMCELL Technologies), and physically dissociated between frosted microscope slides. The suspension was then incubated at room temperature for 30 min with continuous agitation for enzymatic dissociation. Contaminating red blood cells were lysed using ammonium-chloride-potassium (ACK) lysis buffer and filtered through 100 μm nylon mesh filter to obtain a single-cell suspension. Single-cell suspensions were stained with anti-CD45-PE at 1:200 dilution and resuspended in PBS supplemented with 0.5% BSA), and incubated with DAPI. Live immune cells defined as DAPI(-)CD45(+) were sorted with the BD FACSAria flow cytometer. Equal numbers of sorted cells were processed with droplet-based 3’ end single-cell RNA sequencing using Chromium Single Cell 3’ Gene Expression Library Prep Kit V3 according to manufacturer’s protocol (10x Genomics).

value: FVB/NJ (WT)

value: MMTV-PyMT lung metastases

value: CD45+ tumor infiltrating immune cells


title: Cortex BAC-HD Female (JB.3.5.C)

source_name: Cortex  BACHD 12 mon Female

value: FvB

value: Tg

value: Female


title: Seedlings, abc_1

description: abc.wig

value: atbmi1abc triple mutant


title: ILCs, dKO

description: blood Lin-Thy1+ cells enriched of ILCs

value: dKO


title: Cortex WT Female (JB.2.3.C)

source_name: Cortex  WT 12 mon Female

value: WT

value: 12 mon


title: Cortex BAC-HD Female (JB.3.2.C)

value: Cortex


title: 16175X2 Ron SF-/- CD45

description:
Single-cell 3' RNA-Sequencing
DSF

value: Ron SF-/-


title: Seedlings, abc_2

description: abc.wig


title: Seedlings, wt_1

description: wt.wig


title: Cortex WT Female (JB.1.1.C)


title: kuf1-1, dehydrated 2h, replicate 4

status: Public on Feb 01 2022

city: Kaifeng

first: Weiqiang

last: Li

state: China

address: No.85 Minglun Street

department: School of Life Sciences

institute: Henan University

description: Gene expression data from dehydrated kuf1-1

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented at 60°C for 30 minutes following the manufacturer's instructions. Agilent hybridization buffer was then added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray slides were washed and dried immediately by a brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX12.6.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

source_name: kuf1-1, dehydrated 2h, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2  µg RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two-week-old WT and kuf1-1 mutant plants were transferred from GM plates to soil and grown for 10 additional day (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The aerial of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0, 2 or 4h.

value: rosette leaves

value: 24 day-old

value: dehydrated


title: kuf1-1, well-watered (0h), replicate 3

description: Gene expression data from well-watered kuf1-1

source_name: kuf1-1, well-watered, replicate 3

value: well-watered


title: kuf1-1, well-watered (0h), replicate 2

source_name: kuf1-1, well-watered, replicate 2


title: WT, dehydrated 4h, replicate 3

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 3


title: kuf1-1, dehydrated 4h, replicate 4

source_name: kuf1-1, dehydrated 4h, replicate 4


title: kuf1-1, dehydrated 4h, replicate 2

source_name: kuf1-1, dehydrated 4h, replicate 2


title: WT, dehydrated 4h, replicate 1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 1


title: kuf1-1, dehydrated 4h, replicate 1

source_name: kuf1-1, dehydrated 4h, replicate 1


title: kuf1-1, dehydrated 4h, replicate 3

source_name: kuf1-1, dehydrated 4h, replicate 3


title: WT, dehydrated 4h, replicate 4

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 4


title: WT, dehydrated 4h, replicate 2

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 2


title: kuf1-1, dehydrated 2h, replicate 3

source_name: kuf1-1, dehydrated 2h, replicate 3


title: WT, dehydrated 2h, replicate 3

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 3


title: kuf1-1, dehydrated 2h, replicate 1

source_name: kuf1-1, dehydrated 2h, replicate 1


title: WT, dehydrated 2h, replicate 2

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 2


title: kuf1-1, well-watered (0h), replicate 4

source_name: kuf1-1, well-watered, replicate 4


title: kuf1-1, dehydrated 2h, replicate 2

source_name: kuf1-1, dehydrated 2h, replicate 2


title: WT, well-watered (0h), replicate 2

description: Gene expression data from well-watered WT

source_name: WT, well-watered, replicate 2


title: kuf1-1, well-watered (0h), replicate 1

source_name: kuf1-1, well-watered, replicate 1


title: WT, dehydrated 2h, replicate 1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 1


title: WT, well-watered (0h), replicate 3

source_name: WT, well-watered, replicate 3


title: Control 3, WB α-casein stimulation

city: Maebashi

first: Yag

last: Hisako

address: 3-39-22 Showa-machi

country: Japan

institute: Department of Pediatrics, Gunma University Graduate School of Medicine

description: Gene expression, whole blood sample from control3 was stimulated with α-casein for 24 hours

hyb_protocol: 600 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25μl of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE Microarray 8 × 60 k ver. 2.0 (Design ID: 039494, Agilent Technologies) for 17 hours at 65°C.

scan_protocol: Fluorescence images of the hybridized arrays were generated using the Agilent Scanner (Scan control software ver. 8)

data_processing: The intensities were extracted with Agilent Feature Extraction software ver. 10.5.1.1

source_name: Control 3, WB α-casein stimulation

label_protocol: One-color spike-mix (Agilent Technology) was added to the total RNA prior to the labeling reaction. Labeling was performed using a Low lnput Quick Amp Labeling Kit (Agilent Technology) in the presence of cyanine-3 (Cy3)-CTP.

growth_protocol: Heparinized whole blood collected from patients with non-IgE GI-FAs and individuals who did not have non-IgE-GI-FAs or other immune diseases was diluted 4-fold with RPMI-1640 medium (Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol: Total RNAs were extracted from the blood sample, which unstimulated or stimulated with milk protein by using Nucleo Spin® RNA Blood (MACHEREY-NAGEL GmbH & Co. KG, Düren Germany).

treatment_protocol: The diluted blood was divided into each tube by 800 μL and it was incubated with α-casein (100 μg/mL; Sigma-Aldrich) or Pmix (100 μg/mL), which is a mixture of four milk protein components (α-casein, κ-casein, α-lactalbumin, or β-lactoglobulin; 100 µg/mL each; Sigma-Aldrich) at 37°C for 24 h

value: whole blood

tag: gender

value: male

tag: age(day)


title: Control 3, WB non stimulation

description: Gene expression, whole blood sample from control3 was not stimulated for 24 hours

source_name: Control 3, WB non stimulation


title: Control 1, WB Pmix stimulation

description: Gene expression, whole blood sample from control1 was stimulated with Pmix for 24 hours

source_name: Control 1, WB Pmix stimulation


title: Control 2, WB non stimulation

description: Gene expression, whole blood sample from control2 was not stimulated for 24 hours

source_name: Control 2, WB non stimulation


title: Control 1, WB non stimulation

description: Gene expression, whole blood sampls from control1 was not stimulated for 24 hours

source_name: Control 1, WB non stimulation


title: Control 2, WB Pmix stimulation

description: Gene expression, whole blood sample from control2 was stimulated with Pmix for 24 hours

source_name: Control 2, WB Pmix stimulation


title: Patient 4, WB Pmix stimulation

description: Gene expression, whole blood sample from patient4 was stimulated with Pmix for 24 hours

source_name: Patient 4, WB Pmix stimulation

value: female


title: Patient 4, WB α-casein stimulation

description: Gene expression, whole blood sample from patient4 was stimulated with α-casein for 24 hours

source_name: Patient 4, WB α-casein stimulation


title: Control 2, WB α-casein stimulation

description: Gene expression, whole blood sample from control2 was stimulated with α-casein for 24 hours

source_name: Control 2, WB α-casein stimulation


title: Control 3, WB Pmix stimulation

description: Gene expression, whole blood sample from control3 was stimulated with Pmix for 24 hours

source_name: Control 3, WB Pmix stimulation


title: kidney cell 2556

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

source_name: Kidney

extract_protocol:
The glomerular fraction was dissociated for 15min at 37°C using a buffer containing collagenase IV (1mg/ml) (Thermo Fisher), pronase E (1mg/ml) (Sigma Aldrich), and DNase I (50U/ml). Single cells were collected and non-digested glomeruli went through a second round of dissociation. Then, cells were filtered through a 50-µm cup falcon and centrifuged at 2000 rpm for 5 min. The pellet was resuspended, viable cells stained using CellTracker (CMFDA-Green, Thermo Fisher) and dye-positive cells sorted to 384-well plates using BD FACSAriaTM. The SmartSeq2 methodology was used for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: kidney

value: adult mice

value: IgAN


title: kidney cell 2555


title: kidney cell 2558


title: kidney cell 2559


title: Patient 2, WB Pmix stimulation

description: Gene expression, whole blood sample from patient2 was stimulated with Pmix for 24 hours

source_name: Patient 2, WB Pmix stimulation


title: kidney cell 2554


title: WT, dehydrated 2h, replicate 4

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 4


title: kidney cell 2551


title: kidney cell 2557


title: kidney cell 2560


title: kidney cell 2549


title: Control 1, WB α-casein stimulation

description: Gene expression, whole blood sample from control1 was stimulated with α-casein for 24 hours

source_name: Control 1, WB α-casein stimulation


title: kidney cell 2561


title: Patient 3, WB non stimulation

description: Gene expression, whole blood sample from patient3 was not stimulated for 24 hours

source_name: Patient 3, WB non stimulation


title: Patient 3, WB α-casein stimulation

description: Gene expression, whole blood sample from patient3 was stimulated with α-casein for 24 hours

source_name: Patient 3, WB α-casein stimulation


title: kidney cell 2548


title: kidney cell 2553


title: WT, well-watered (0h), replicate 4

source_name: WT, well-watered, replicate 4


title: kidney cell 2547


title: Patient 4, WB non stimulation

description: Gene expression, whole blood sample from patient4 was not stimulated for 24 hours

source_name: Patient 4, WB non stimulation


title: kidney cell 2541


title: Patient 1, WB Pmix stimulation

description: Gene expression, whole blood sample from patient1 was stimulated with Pnux for 24 hours

source_name: Patient 1, WB Pmix stimulation


title: kidney cell 2550


title: kidney cell 2539


title: Patient 2, WB non stimulation

description: Gene expression, whole blood sample from patient2 was not stimulated for 24 hours

source_name: Patient 2, WB non stimulation


title: kidney cell 2538


title: WT, well-watered (0h), replicate 1

description: Gene expression data from well-watered WT

source_name: WT, well-watered, replicate 1


title: kidney cell 2546


title: kidney cell 2540


title: kidney cell 2552


title: kidney cell 2545


title: kidney cell 2544


title: kidney cell 2542


title: kidney cell 2533


title: kidney cell 2536


title: kidney cell 2534


title: kidney cell 2543


title: kidney cell 2532


title: kidney cell 2531


title: kidney cell 2530


title: kidney cell 2528


title: kidney cell 2562


title: kidney cell 2537


title: kidney cell 2526


title: kidney cell 2522


title: kidney cell 2527


title: kidney cell 2523


title: kidney cell 2519


title: kidney cell 2524


title: kidney cell 2521


title: kidney cell 2518


title: kidney cell 2520


title: kidney cell 2535


title: kidney cell 2517


title: kidney cell 2515


title: kidney cell 2516


title: kidney cell 2511


title: kidney cell 2510


title: kidney cell 2512


title: kidney cell 2514


title: kidney cell 2513


title: kidney cell 2505


title: kidney cell 2504


title: kidney cell 2508


title: kidney cell 2506


title: kidney cell 2501


title: Patient 2, WB α-casein stimulation

description: Gene expression, whole blood sample from patient2 was stimulated with α-casein for 24 hours

source_name: Patient 2, WB α-casein stimulation


title: kidney cell 2509


title: kidney cell 2498


title: Patient 1, WB non stimulation

description: Gene expression, whole blood sample from patient1 was not stimulated for 24 hours

source_name: Patient 1, WB non stimulation


title: kidney cell 2502


title: kidney cell 2503


title: kidney cell 2494


title: kidney cell 2493


title: kidney cell 2496


title: kidney cell 2495


title: kidney cell 2491


title: kidney cell 2490


title: kidney cell 2499


title: kidney cell 2525


title: Patient 3, WB Pmix stimulation

description: Gene expression, whole blood sample from patient3 was stimulated with Pmix for 24 hours

source_name: Patient 3, WB Pmix stimulation


title: kidney cell 2500


title: kidney cell 2507


title: kidney cell 2486


title: kidney cell 2484


title: kidney cell 2492


title: kidney cell 2487


title: kidney cell 2483


title: kidney cell 2488


title: kidney cell 2497


title: kidney cell 2489


title: kidney cell 2485


title: kidney cell 2481


title: kidney cell 2477


title: kidney cell 2480


title: kidney cell 2476


title: kidney cell 2475


title: kidney cell 2479


title: kidney cell 2474


title: kidney cell 2471


title: kidney cell 2468


title: kidney cell 2466


title: kidney cell 2478


title: kidney cell 2463


title: kidney cell 2470


title: kidney cell 2472


title: kidney cell 2461


title: kidney cell 2460


title: kidney cell 2458


title: kidney cell 2459


title: kidney cell 2457


title: kidney cell 2464


title: kidney cell 2469


title: kidney cell 2473


title: kidney cell 2482


title: kidney cell 2450


title: kidney cell 2529


title: kidney cell 2453


title: kidney cell 2448


title: kidney cell 2465


title: kidney cell 2452


title: kidney cell 2442


title: kidney cell 2444


title: kidney cell 2462


title: kidney cell 2454


title: kidney cell 2446


title: kidney cell 2451


title: kidney cell 2443


title: kidney cell 2439


title: kidney cell 2445


title: kidney cell 2447


title: kidney cell 2434


title: kidney cell 2441


title: kidney cell 2437


title: kidney cell 2467


title: kidney cell 2440


title: kidney cell 2429


title: kidney cell 2456


title: kidney cell 2430


title: kidney cell 2435


title: kidney cell 2449


title: kidney cell 2455


title: kidney cell 2431


title: kidney cell 2438


title: kidney cell 2427


title: kidney cell 2432


title: kidney cell 2424


title: kidney cell 2428


title: kidney cell 2433


title: kidney cell 2426


title: kidney cell 2419


title: kidney cell 2425


title: kidney cell 2417


title: kidney cell 2423


title: kidney cell 2421


title: kidney cell 2420


title: kidney cell 2422


title: kidney cell 2413


title: kidney cell 2415


title: kidney cell 2410


title: kidney cell 2405


title: kidney cell 2403


title: kidney cell 2407


title: kidney cell 2408


title: kidney cell 2411


title: kidney cell 2412


title: kidney cell 2416


title: kidney cell 2402


title: kidney cell 2404


title: kidney cell 2414


title: kidney cell 2406


title: kidney cell 2400


title: kidney cell 2436


title: kidney cell 2399


title: kidney cell 2418


title: kidney cell 2401


title: kidney cell 2397


title: kidney cell 2393


title: kidney cell 2392


title: kidney cell 2396


title: kidney cell 2398


title: kidney cell 2409


title: kidney cell 2390


title: kidney cell 2389


title: kidney cell 2391


title: kidney cell 2388


title: kidney cell 2387


title: kidney cell 2382


title: kidney cell 2379


title: kidney cell 2385


title: kidney cell 2381


title: kidney cell 2377


title: kidney cell 2395


title: kidney cell 2370


title: kidney cell 2372


title: kidney cell 2369


title: kidney cell 2371


title: kidney cell 2368


title: kidney cell 2383


title: kidney cell 2366


title: kidney cell 2364


title: kidney cell 2380


title: kidney cell 2376


title: kidney cell 2378


title: kidney cell 2373


title: kidney cell 2362


title: kidney cell 2375


title: kidney cell 2357


title: kidney cell 2384


title: kidney cell 2358


title: kidney cell 2394


title: kidney cell 2360


title: kidney cell 2386


title: kidney cell 2352


title: kidney cell 2350


title: kidney cell 2359


title: kidney cell 2348


title: kidney cell 2374


title: kidney cell 2344


title: kidney cell 2349


title: kidney cell 2345


title: kidney cell 2340


title: kidney cell 2341


title: kidney cell 2343


title: kidney cell 2339


title: kidney cell 2338


title: kidney cell 2336


title: kidney cell 2354


title: kidney cell 2356


title: kidney cell 2347


title: kidney cell 2337


title: kidney cell 2355


title: kidney cell 2351


title: kidney cell 2361


title: kidney cell 2367


title: kidney cell 2353


title: kidney cell 2363


title: kidney cell 2346


title: kidney cell 2342


title: kidney cell 2330


title: kidney cell 2328


title: kidney cell 2325


title: kidney cell 2334


title: kidney cell 2335


title: kidney cell 2365


title: kidney cell 2332


title: kidney cell 2331


title: kidney cell 2333


title: kidney cell 2319


title: kidney cell 2320


title: kidney cell 2318


title: kidney cell 2321


title: kidney cell 2326


title: kidney cell 2315


title: kidney cell 2329


title: kidney cell 2327


title: kidney cell 2313


title: kidney cell 2311


title: kidney cell 2324


title: kidney cell 2314


title: kidney cell 2312


title: kidney cell 2309


title: kidney cell 2317


title: kidney cell 2323


title: kidney cell 2308


title: kidney cell 2316


title: kidney cell 2310


title: kidney cell 2307


title: kidney cell 2302


title: kidney cell 2300


title: kidney cell 2299


title: kidney cell 2301


title: kidney cell 2298


title: kidney cell 2305


title: kidney cell 2297


title: kidney cell 2294


title: kidney cell 2306


title: kidney cell 2288


title: kidney cell 2287


title: kidney cell 2286


title: kidney cell 2304


title: kidney cell 2322


title: kidney cell 2284


title: kidney cell 2280

value: Control


title: kidney cell 2278


title: kidney cell 2296


title: kidney cell 2293


title: kidney cell 2291


title: kidney cell 2290


title: kidney cell 2273


title: kidney cell 2289


title: kidney cell 2295


title: kidney cell 2292


title: kidney cell 2285


title: kidney cell 2271


title: kidney cell 2272


title: kidney cell 2282


title: kidney cell 2277


title: kidney cell 2303


title: kidney cell 2281


title: kidney cell 2268


title: kidney cell 2279


title: kidney cell 2283


title: kidney cell 2274


title: kidney cell 2275


title: kidney cell 2276


title: kidney cell 2264


title: kidney cell 2261


title: kidney cell 2262


title: kidney cell 2265


title: kidney cell 2267


title: kidney cell 2270


title: kidney cell 2269


title: kidney cell 2266


title: kidney cell 2259


title: kidney cell 2254


title: kidney cell 2263


title: kidney cell 2256


title: kidney cell 2258


title: kidney cell 2257


title: kidney cell 2260


title: kidney cell 2251


title: kidney cell 2249


title: kidney cell 2247


title: kidney cell 2253


title: kidney cell 2241


title: kidney cell 2252


title: kidney cell 2243


title: kidney cell 2242


title: kidney cell 2250


title: kidney cell 2245


title: kidney cell 2246


title: kidney cell 2244


title: kidney cell 2255


title: kidney cell 2237


title: kidney cell 2248


title: kidney cell 2235


title: kidney cell 2236


title: kidney cell 2239


title: kidney cell 2233


title: kidney cell 2232


title: kidney cell 2238


title: kidney cell 2234


title: kidney cell 2225


title: kidney cell 2240


title: kidney cell 2231


title: kidney cell 2228


title: kidney cell 2230


title: kidney cell 2222


title: kidney cell 2215


title: kidney cell 2213


title: kidney cell 2223


title: kidney cell 2219


title: kidney cell 2227


title: kidney cell 2221