title: U48C - cells from uninfected well, seeded for 72 h

city: Seattle

first: Effie

middle: Efthimia

last: Bastounis

state: WA

address: UW Biology Life Sciences Bldg, Room 565, 4000 15th Ave NE

department: Biology

institute: University of Washington

description:
2x10^5 cells grown on 16 mm collagen I coated glass coverslips for 24 h were then exposed (or not) to Borrelia burdgorferi (MOI=200) for 4, 24 or 48 h. At the corresponding time post-infection cells where trypsinized and RNA was extraceted from all cells in the infected wells or from all cells in the corresponding uninfected wells.
In MCDB131 media supplemented with 10% FBS, 10 ng/mL epidermal growth factor, 1 μg/mL hydrocortisone, and 2 mM l-glutamine
Expression_Gene.xlsx
Expression_Transcript.xlsx
Differentially_Expressed_Genes.xlsx
Differentially_Expressed_Transcripts.xlsx

data_processing:
Raw sequencing data generated from Illumina NovaSeq 6000 that pass the Illumina chastity filter are used for following analysis. Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on alignment statistical analysis (mapping ratio, rRNA/mtRNA content, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤ 20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software.
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM (fragments per kilobase of transcript per million mapped reads) in group ≥ 0.5. FPKM is equal to the number of fragments that map a certain gene or transcipt times a million divided by the length of the gene in Kb and the fragmnets number that map to all genes/transcripts.
Differentially expressed gene and transcript analyses were performed with R package ballgown. Fold change (cutoff 1.5), p-value (≤ 0.05) and FPKM (≥ 0.5 mean in one group) were used for filtering differentially expressed genes and transcripts.
Genome_build: GRCh37
Supplementary_files_format_and_content: Expression_Gene.xlsx file contains in column A the Track_id which is the database name in gene level, in column B the name of the gene, in column C its locus, in column D the strand of the gene, in column E the gene type and in colunms F through U the FPKM of each gene for each one of the samples. Likewise, Expression_Transcript.xlsx file contains in column A the Track_id which is the database name in transcript level, in column B the name of the transcript, in column C the ENSEMBL gene id of the transcript, in column D the name of the gene, in column E the locus, in column F the strand, in column F the biological type of the transcript and in colunms H through W the FPKM of trasncript in samples. Differentially_Expressed_Genes.xlsx and Differentially_Expressed_Transcripts.xlsx show differentially expressed genes or transcripts when comparisons between different groups os samples are performed. Different groups compared are shown in different sheets within the xlsx file.

source_name: Human dermal microvascular endothelial cells (HMEC-1)

growth_protocol:
HMEC-1 (generous gift from the Welch lab, University of California, Berkeley) were cultured in MCDB 131 medium (Fisher Scientific; 10372–019) supplemented with 10% FBS (GemBio; 900-108), 10 ng/mL epidermal growth factor (Sigma; E9644), 1 μg/mL hydrocortisone (Sigma; H0888), and 2 mM l-glutamine (Sigma; 56-85-9). To generate confluent cell monolayers, 24-well plates glass-bottom for microscopy were coated with 50 µg/ml rat-tail collagen-I (diluted in 0.2 N acetic acid) for 1 h at 37°C, air-dried for 15 min, and UV-sterilized for 30 min in a tissue culture hood. HMEC-1 cells were seeded at a density of 2 × 10^5 cells/well for 24 h (or more depending on the condition).
GFP expressing Borrelia burgdorferi (Bb1286, obtained from Justin Radolf's lab, University of Connecticut Health Center) were grown to mid log phase (approximately 5x10^7 bacteria/mL) in BSK-H with 50 μg/mL gentamicin. Briefly, we added 10 uL of frozen glycerol stock into 1.5 mL of BSK-H media with 50 ug/mL gentamycin. We then placed that tube at 23oC. We waited until the concentration of the bacteria reached 2-5x10^6 and then dilute at 1x10^3 bacteria/mL and grew them at fresh BSK-H with antibiotics at 37oC until we get 5x10^7 bacteria/mL. That is what we used for infections and we did get single spirochetes at that point. For details please refer to: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786795/

extract_protocol:
Cells were harvested and lyzed using the QIAshredder Kit (Qiagen; 79656). mRNA was harvested using the RNeasy Plus Micro Kit (Qiagen; 74004) and eluted in 30 μL RNAase free water. RNA concentrations were measured using the nanodrop machine and were comparable between conditions. RNA quality and quantity were confirmed via bioanalyzer analysis performed by Arraystar Inc.
The total RNA was depleted of rRNAs by Arraystar rRNA Removal Kit. We used Illumina kits for the RNA-seq library preparation, which included procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Finally, the prepared RNA-seq libraries were qualified using Agilent 2100 Bioanalyzer and quantified by qPCR absolute quantification method
The DNA fragments in well mixed libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, loaded onto channels of the flow cell at 8 pM concentration, and amplified in situ using NovaSeq 6000 S4 Reagent Kit (300 cycles). Sequencing was carried out using the Illumina NovaSeq 6000 according to the manufacturer’s instructions. Sequencing was carried out by running 150 cycles.

treatment_protocol: 24 h post-seeding HMEC-1 cells were exposed to Borrelia burgdorferi (MOI=200) for various times (4, 24 or 38 h). . 2,24 or 48 h post-infection cells were trypsinized, span down, and then lyzed extract their RNA.

value: dermal microvascular endothelium

tag: sample type

value: immortalized

tag: source

value: Obtained from the Welch lab, UC Berkeley (previously obtained from Centers for Disease Control, Biological Products Branch)


title: U48D - cells from uninfected well, seeded for 72 h

status: Public on May 18 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: HCT-116_fixed43

city: Hong Kong

first: Xinlei

last: Wang

state: Hong Kong

address: Clear Water Bay, Sai Kung,

department: LIFS

country: China

institute: HKUST

data_processing:
Index and adapter were trimmed in data downloaded form Basespace
Quality control was done using Fastqc
Alignment and quantification were done by mapping raw reads to GRCh38 using kallisto 0.46.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression/Transcript expression matrix(TPM)

source_name: HCT-116 fixed43

growth_protocol: Both HepG2 and HCT-116 cell lines were culured with DMEM medium, supplemented with 1% Penicillin-Streptomycin and 10% Fetal Bovine Serum

extract_protocol: cDNA library was constructed using Smart-seq2 protocl, sequencing library was prepared using Illuminar Nextera DNA Library Prep Kit(Illumina, cat#FC-131-1096), we followed library contruction protocal provided by C1 Fluidigm(Fluidigm)

treatment_protocol: 80% methanol was used for cell fixation, fixed cells were stored in -80℃ for one week before further processing

tag: cell line


title: ESCs, Brg1-ChIP-WT-0h

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

library_source: genomic

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the mouse Genome mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells(mESCs)

growth_protocol: Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)

extract_protocol:
protein-DNA complexes were isolated with antibody and Tn5-proteinA/G.
The ChIP DNA library for sequencing was constructed with NovoNGS CUT&Tag 2.0 High-Sensitivity Kit  for Illumina (novoprotein) according to manufacturer’s instructions

treatment_protocol: Treated with 2µg/ml doxycycline or small molecules PFI-3 and BI-9564.

tag: cell type

value: OG2 transgenetic mouse embryonic stem cells(OG2ES)

tag: strain

tag: genotype

tag: chip antibody

value: CST no 52251

tag: treatment

value: no doxycycline


title: HCT-116_fixed39

source_name: HCT-116 fixed39


title: EPID17_838 [H5CV7BBXY_2_SI-GA-G2]

city: Barcelona

first: Laudanna

last: Carmelo

state: Barcelona

address: Baldiri i Reixac, 10

department: Aging and Metabolism

country: Spain

institute: Institute for Research in Biomedicine (IRB-Barcelona)

description:
H5CV7BBXY_SI-GA-G2
raw.counts.WT2.csv.gz

data_processing:
Sequencing of cDNA libraries was carried out on a HiSeq 4000 sequencer (Illumina) to obtain approximately 25,000-50,000 paired-end 75 bp reads per cell, respectively.
Alignment of scRNAseq analyses was completed utilizing 10x Genomics Cell Ranger pipeline (version 2.2.0).
Each library was aligned to an indexed mm10 genome (USCS) using Cell Ranger Count and processed using the Seurat pipeline (version 3.0.1) in R (version 3.5.2).
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts

source_name: Mammary gland cells

extract_protocol:
Cell concentration and viability were verified by counting with a TC20™ Automated Cell Counter (Bio-Rad Laboratories, S.A). Cells were partitioned into Gel Bead-In-Emulsions with a Target Cell Recovery of 5000 cells.
cDNA sequencing libraries were prepared using the NextGEM Single-cell 3’ mRNA kit (V3; 10X Genomics) following manufacturer's instructions.

value: Total mammary epithelium

value: Ctrl

tag: replicate


title: U48B - cells from uninfected well, seeded for 72 h


title: EPID17_837 [H5CV7BBXY_2_SI-GA-F2]

description:
H5CV7BBXY_SI-GA-F2
raw.counts.KO1.csv.gz


title: HCT-116_fixed41

source_name: HCT-116 fixed41


title: U48A - cells from uninfected well, seeded for 72 h


title: EPID17_837 [H5CV7BBXY_1_SI-GA-F2]


title: HCT-116_fixed38

source_name: HCT-116 fixed38


title: EPID17_837 [CD2ALANXX_8_SI-GA-F2]

description:
CD2ALANXX_SI-GA-F2
raw.counts.KO1.csv.gz


title: HCT-116_fixed36

source_name: HCT-116 fixed36


title: EB, Ss18-ChIP-seq

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the mouse Genome mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: mouse EBs

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions

treatment_protocol: Treated with 2µg/ml doxycycline

value: OG2 transgenetic mouse embryonic stem cells (OG2ES)

value: Hanging drop ,D4


title: EpiSCs, Ss18-ChIP-seq

source_name: mouse epiblast stem cells

value: OG2 transgenetic mouse epiblast stem cells (OG2ES)

value: OG2 transgenetic


title: Panc1 LS  rep4

city: Stockholm

first: Xinyuan

last: Liu

address: Hälsovägen 7

department: Department of Clinical Science, Intervention and Technology

country: Sweden

institute: Karolinska Institute

data_processing:
Reference genomes for human and mouse, GRCh38.87 and GRCm38.87 were downloaded from Ensembl and used to build respective indices for the species-based read classifier Xenome (1.0.1) and the short read aligner STAR (2.5.1b).
The program Xenome (1.0.1) was used to classify the fastq reads based on species origin using default settings.
Separated human and murine reads were subsequently aligned to their respective reference genomes by means of STAR (2.5.1b)  using default options with --sjdbGTFfile pointing to the respective reference annotation file and --outFilterMultimapNmax set to 1.
featureCounts from the package subread (1.5.2) was employed to quantify reads mapped to known features in the Ensembl database.
Genome_build: GRCh38.87 and GRCm38.87
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human pancreatic cancer cells

growth_protocol: Panc1 and imPSCc2 were cultivated either under high serum condition with DMEM/F12 medium supplemented with 10% FBS (high serum) and 0.5% penicillin/streptomycin or low serum condition supplemented with 0.1% FBS, 0.3% bovine serum albumin (only for Panc1 cells) , insulin-transferrin-selenium-sodium pyruvate solution (ITS-A) (1/10 of the recommended concentration was used to adapt insulin to more physiological concentrations) and 0.5% penicillin/streptomycin in a humidified incubator at 37°C and 5% CO2. Both Panc1 and imPSCc2 were stepwise adapted to low serum condition over a course of 6–8 weeks.

extract_protocol:
Total RNA was extracted directly from monospheroids and heterospheroids for RNA-sequencing using the RNeasy PLUS kit (Qiagen).
Library preparations were conducted using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, E7760S), including a poly-A enrichment step by the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S). The End Repaired DNA was subjected to Agencourt AMPure XP bead clean-up and size selection (NEB, E6260). Libraries from the samples were multiplexed using NEBNext® Multiplex Oligos for Illumina® (NEB, Index Primers Set 1; E7335S).

treatment_protocol: Panc1 and imPSCc2 were trypsinized and grown either as monospheroids (2500 imPSCc2 or Panc1 cells) or heterospheroids (500 Panc1 cells and 2000 imPSCc2 in high serum; 1250 Panc1 cells and 1250 imPSCc2 in low serum) in non-treated, round-bottom 96-well microplates in DMEM/F12 medium supplemented with either 10% FBS (“high serum” condition) or 0.1% FBS, 0.3% BSA and ITS-A (“low serum” condition), and 0.5% penicillin/streptomycin as well as 0.24% methyl cellulose at 37°C and 5% CO2 humidified condition

tag: tag

value: low serum

value: human pancreatic cancer cells


title: HCT-116_fixed37

source_name: HCT-116 fixed37


title: EPID17_838 [CD2ALANXX_6_SI-GA-G2]

description:
CD2ALANXX_SI-GA-G2
raw.counts.WT2.csv.gz


title: HCT-116_fixed40

source_name: HCT-116 fixed40


title: EPID17_837 [CD2ALANXX_7_SI-GA-F2]


title: U24D - cells from uninfected well, seeded for 48 h


title: U24C - cells from uninfected well, seeded for 48 h


title: HCT-116_fixed35

source_name: HCT-116 fixed35


title: Panc1 LS  rep3


title: EPID17_838 [CD2ALANXX_8_SI-GA-G2]


title: EPID17_837 [CD2ALANXX_6_SI-GA-F2]


title: Panc1 LS  rep2


title: U24B - cells from uninfected well, seeded for 48 h


title: U24A - cells from uninfected well, seeded for 48 h


title: HCT-116_fixed33

source_name: HCT-116 fixed33


title: Panc1 LS  rep1


title: HCT-116_fixed34

source_name: HCT-116 fixed34


title: EPID17_836 [H5CV7BBXY_1_SI-GA-E2]

description:
H5CV7BBXY_SI-GA-E2
raw.counts.WT1.csv.gz


title: Panc1 HS rep4

value: high serum


title: HCT-116_fixed32

source_name: HCT-116 fixed32


title: U4D - cells from uninfected well, seeded for 28 h

source_name: Human dermal microvascular endothelial cells (HMEC-1)


title: U4C - cells from uninfected well, seeded for 28 h


title: EPID17_836 [CD2ALANXX_8_SI-GA-E2]

description:
CD2ALANXX_SI-GA-E2
raw.counts.WT1.csv.gz


title: EPID17_836 [CD2ALANXX_7_SI-GA-E2]


title: Panc1 HS rep2

description: outlier, not included in analysis


title: U4A - cells from uninfected well, seeded for 28 h


title: U4B - cells from uninfected well, seeded for 28 h


title: EPID17_836 [CD2ALANXX_6_SI-GA-E2]


title: HCT-116_fixed31

source_name: HCT-116 fixed31


title: HCT-116_fixed2

source_name: HCT-116 fixed2


title: H-2Kb+ TCRb+ transferred CD226-/- TIGIT-/- Treg cells and wild-type Tconv cells

city: Tsukuba

first: Akira

last: Shibuya

state: Ibaraki

address: 1-1-1 Tennodai

department: Immunology

country: Japan

institute: University of Tsukuba

description:
GVHD_DoubleKO_S4_L004
ADT_DoubleKO_S8_L004

data_processing:
Read alignment and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; features.tsv: feature ids per sample

molecule: polyA RNA

source_name: Spleen T cells

extract_protocol:
Freshly isolated spleens were gently rubbed back and forth applying slight pressure with slide glass to disperse spleen cells. The cell suspension was filtered through a 70 µm cell strainer and was treated with ACK lysis buffer to lyse red blood cells. PI- H-2Kb+ TCRb+ donor T cells were sorted by flow cytometry. Sorted donor T cells were stained with barcode sequence-conjugated anti-mouse CD45.1 (TotalSeq A0178, BioLegend) and CD45.2 (TotalSeq A0157, BioLegend).
10X Genomics, Chromium Single Cell 3’ Library and Gel Bead Kit v3.  BioLegend, TotalSeq™-A Antibodies with 10x Single Cell 3' Reagent Kit v3.

treatment_protocol: Recipient BALB/c mice were lethally irradiated (900 cGy) on day 0. T cell-depleted bone marrow (TCD-BM) cells from CD45.1+ CD45.2+ C57BL/6 mice were i.v. infused into recipient BALB/c mice with Treg cells (CD4+ Foxp3-GFP+ CD25hi) isolated by flow cytometry from the spleen of Foxp3-GFP CD45.2+ CD45.1- CD226+/+TIGIT+/+, CD226-/-TIGIT+/+, CD226+/+TIGIT-/-, or CD226-/-TIGIT-/- mice on the C57BL/6 background. Two days later, recipient mice were transferred with CD4+ and CD8+ Tconv cells isolated from the spleens of CD45.2- CD45.1+ WT mice on the C57BL/6 background.

tag: strain background

value: CD45.2+ CD45.1- CD226-/- TIGIT-/- Treg cells, CD45.2- CD45.1+ wild-type Tconv cells, and CD45.2+ CD45.1+ wild-type bone marrow derived T cells

value: Spleen

value: T cells


title: HCT-116_fixed29

source_name: HCT-116 fixed29


title: N2a_2

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

country: United Kingdom

institute: University of Bath

data_processing:
Library strategy: Capture-C
paired end reads were trimmed with trim_galore
then were aligned with flash
dpnII2E.pl was used to perform in silico digestion of capture/reporter fragments
the resulting fragments were aligned to mm10 using bowtie
the resulting sam files were analysed using Ccanalyser3.pl to determine captured interactions with the viewpoints Paupar, PAX6P0, PAX6P1 and SOX2.
the resulting sam files were analysed using r3Cseq to determine the significant fragments for each combination of viewpoint and replicate.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimitted table of captured fragments giving chromosome, start, end, width, nReads, RPMs, z, p.value and q.value

source_name: cell line

growth_protocol: DMEM supplemeted with 10% FBS

extract_protocol:
Re-suspend crosslinked pellet in 5 ml cold lysis buffer. Incubate for 20 min on ice. Centrifuge 5 min / 1,800 rpm / 4°C
Libraries were prepared using 1 ug of DNA according to Illumina's NEBNext DNA library Prep Reagent Set (New England: E6040S/L)

value: Mouse neuroblastoma


title: N2a_1


title: EPID17_836 [H5CV7BBXY_2_SI-GA-E2]

source_name: Mammary gland cells


title: Panc1 HS rep1


title: I48C - cells from well infected w/ B. burgdorferi MOI=200 seeded for 72 h out of w/c 48 h cells were exposed to bacteria

value: dermal microvascular endothelium

value: immortalized

value: Obtained from the Welch lab, UC Berkeley (previously obtained from Centers for Disease Control, Biological Products Branch)


title: H-2Kb+ TCRb+ transferred CD226+/+ TIGIT-/- Treg cells and wild-type Tconv cells

description:
GVHD_TIGITKO_S3_L004
ADT_TIGITKO_S7_L004

value: CD45.2+ CD45.1- CD226+/+ TIGIT-/- Treg cells, CD45.2- CD45.1+ wild-type Tconv cells, and CD45.2+ CD45.1+ wild-type bone marrow derived T cells


title: I48B - cells from well infected w/ B. burgdorferi MOI=200 seeded for 72 h out of w/c 48 h cells were exposed to bacteria


title: I48D - cells from well infected w/ B. burgdorferi MOI=200 seeded for 72 h out of w/c 48 h cells were exposed to bacteria


title: HCT-116_fixed30

source_name: HCT-116 fixed30


title: HCT-116_fixed28

source_name: HCT-116 fixed28


title: I48A - cells from well infected w/ B. burgdorferi MOI=200 seeded for 72 h out of w/c 48 h cells were exposed to bacteria


title: H-2Kb+ TCRb+ transferred CD226-/- TIGIT+/+ Treg cells and wild-type Tconv cells

description:
GVHD_DNAM1KO_S2_L003
ADT_DNAM1KO_S6_L003

value: CD45.2+ CD45.1- CD226-/- TIGIT+/+ Treg cells, CD45.2- CD45.1+ wild-type Tconv cells, and CD45.2+ CD45.1+ wild-type bone marrow derived T cells


title: HCT-116_fixed27

source_name: HCT-116 fixed27


title: Nst_2

source_name: neuronal stem cells

value: mouse cortical neural stem cells E14.5


title: Nst_1

growth_protocol: Dishes were pre-coated with Cell Start diluted in D-PBS with calcium and magnesium and cells plated in StemPro NSC SFM (Gibco) composed of: Knockout D-MEM / F12; Glutamax (2mM); bFGF (20ng/ml); EGF (20ng/ml); StemPro Neural Supplement (2%); All from (Gibco)


title: Panc1 HS rep3

source_name: human pancreatic cancer cells


title: I24D - cells from well infected w/ B. burgdorferi MOI=200 seeded for 48 h out of w/c 24 h cells were exposed to bacteria


title: HCT-116_fixed26

source_name: HCT-116 fixed26


title: H-2Kb+ TCRb+ transferred CD226+/+ TIGIT+/+ Treg cells and wild-type Tconv cells

description:
GVHD_WT_S1_L003
ADT_WT_S5_L003

value: CD45.2+ CD45.1- CD226+/+ TIGIT+/+ Treg cells, CD45.2- CD45.1+ wild-type Tconv cells, and CD45.2+ CD45.1+ wild-type bone marrow derived T cells


title: scRNA-seq. Chicken HH27 forelimb

city: Berlin

first: Christian

middle: A.

last: Feregrino

address: Ihnestraße 63

country: Germany

institute: MPI - Molecular Genetics

data_processing:
Cell count matrices generation using the Cell Ranger software v3 (10X Genomics).
cells filtered out based on UMI counts (>4*mean and <0.2*median of the sample) percentage of mitochondrial UMIs (> median + 3*MAD & > 0.1, except if UMI count > median), and relation of UMI count / genes detected (<0.15 & UMI count <2/3)
Genome_build: custom G. gallus genome based on the GRC Gg genome version 6.
Supplementary_files_format_and_content: Tab delimited text files. UMI count tables where cells are rows and genes are columns, additional meta-data columns

organism: Gallus gallus

source_name: Developing forelimb

extract_protocol:
Cells were dissociated using trypsin 0.25%. Single cells suspensions were fed into Chromium 10x controller systems
10x v2

tag: Stage

tag: dissection

value: Whole limb

tag: protocol


title: Neu_2

source_name: cortical neurons

value: Cortical neurons differentiated from E14.5 neuronal stem cells


title: HCT-116_fixed25

source_name: HCT-116 fixed25


title: I24C - cells from well infected w/ B. burgdorferi MOI=200 seeded for 48 h out of w/c 24 h cells were exposed to bacteria


title: scRNA-seq. Chicken HH24 forelimb


title: HCT-116_fixed24

source_name: HCT-116 fixed24


title: Neu_1

growth_protocol: Dishes were pre-coated with Poly-D-Lysine (20 microgram/ ml) and cells plated in Neurobasal B27 Medium supplemented with Glutamine (2mM)


title: I24B - cells from well infected w/ B. burgdorferi MOI=200 seeded for 48 h out of w/c 24 h cells were exposed to bacteria

source_name: Human dermal microvascular endothelial cells (HMEC-1)


title: Escells_2

source_name: embryonic stem cells

growth_protocol: Cultured on gelatin in serum and leukemia inhibitory factor (LIF)

value: Mouse embryonic stem cells


title: HCT-116_fixed23

source_name: HCT-116 fixed23


title: scRNA-seq. Chicken HH21 forelimb


title: Escells_1


title: HCT-116_fixed22

source_name: HCT-116 fixed22


title: I4D - cells from well infected w/ B. burgdorferi MOI=200 seeded for 28 h out of w/c 4 h cells were exposed to bacteria


title: HCT-116_fixed21

source_name: HCT-116 fixed21


title: I4C - cells from well infected w/ B. burgdorferi MOI=200 seeded for 28 h out of w/c 4 h cells were exposed to bacteria


title: Neuron wildtype , KCl treated --littermate control for Brg1-SE samples, rep 1

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

data_processing:
Kallisto (version 0.43.1) was used to quantify gene expression with GENCODE annotation M15 for GRCm38.
The parameter used in Kallisto is "--bias"
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The columns in Kallisto output are isoform_id, length, effective-length, estimated_read_count, TPM.

source_name: Neuron

growth_protocol: Primary cortical neurons were culture from E16.5 mouse embryo. Dissociated cortical neurons were plated on poly-L-ornithine- and fibronectin-coated wells. Culture media contained neurobasal plus with B27 plus supplement (Gibco).

extract_protocol:
Total RNA were expreact with TRIZOL and cleaned with a Qiagen RNeasy Kit.
RNA-seq libraries were prepared using the Illumina RNA-Seq Preparation Kit and sequenced at the University of Texas Southwestern Sequencing Core Facility.

treatment_protocol: For depolarization, the cultures were pretreated with TTX (1 µM) and APV (100 µM) to inhibit spontaneous activation on 5 div and 50 mM KCl was added to the cultures for 1 h on 6 div.

value: wild-type

value: primary cortical neurons

value: 50 mM KCl treatment for 1h


title: Neuron wildtype, Basal --littermate control for Brg1-SE samples, rep 1

value: Basal level of KCl


title: I4B - cells from well infected w/ B. burgdorferi MOI=200 seeded for 28 h out of w/c 4 h cells were exposed to bacteria


title: Neuron wildtype, Basal --littermate control for Brg1-SA samples, rep 2


title: ChIP_yw_haltere_input

city: New York

first: Ryan

last: Loker

state: NY

address: 3227 Broadway

institute: Columbia University

description: Input sample for haltere imaginal disc. Strain: yw

data_processing:
Reads taken from multiplexed Next-seq run were trimmed using the standard Basespace flowthrough (Bcl2Fastq) on pre-defined indices
Bigwig files generated from BAM files using Deeptools (bamCoverage) and normalized to genome coverage - RPGC (ATAC-seq) or reads-per-kilobase-per-million - RPKM (ChIP-seq). Paremeters: -bs 1 -e 200(ChIP-seq only)
For ATAC and ChIP Bowtie2 was used to map reads to Drosophila melanogaster genome (dm6) using default parameters with paired-end options (ATAC-seq) or single-end (ChIP-seq).
For RNA-seq HISAT2 was used to map reads to the Drosophila melanogaster genome (dm6) with default parameters
Genome_build: dm6
Supplementary_files_format_and_content: bigwig files generated from BAM files using Deeptools (bamCoverage) and normalized to genome coverage - RPGC (ATAC-seq) or reads-per-kilobase-per-million - RPKM (ChIP-seq). Read counts (RNA-seq)

organism: Drosophila melanogaster

source_name: L3 imaginal disc

growth_protocol: Drosophila larvae were raised on standard cornmeal food and kept at 25 degrees untill the wandering 3rd instar stage before harvesting of imaginal discs.

extract_protocol:
ChIP-seq was performed as previously described (Estella, Mckay, and Mann, 2008) with minor modifications.  Briefly third instar larval heads were dissected and inverted in PBS on ice. Heads were fixed for 20 minutes in 1.8% PFA in crosslinking medium (10 mM HEPES, pH=8.0; 100 mM NaCl; 1 mM EDTA, pH=8.0; 0.5 mM EGTA, pH=8.0) at room-temperature with rotation, and subsequently quenched (Quench solution: 1xPBS; 125 mM glycine; 0.1% Triton X-100). Fixed-heads were then washed 2X in buffer A (10 mM HEPES, pH=8.0; 10 mM EDTA, pH=8.0; 0.5 mM EGTA, pH=8.0, 0.25 % Triton X-100) and 2X buffer B (10 mM HEPES, pH=8.0; 200 mM NaCl; 1 mM EDTA, pH=8.0; 0.5 mM EGTA, pH=8.0; 0.01% Triton X-100) 10 minutes each at 4°C. Wing or haltere discs were then dissected and placed in sonication buffer (10 mM HEPES, pH = 8.0 ;1 mM EDTA, pH = 8.0; 0.5 mM EGTA, pH = 8.0, 0.1 % SDS). Chromatin sonication was performed using a Covaris S2 instrument at settings (105W; 2 % Duty; 15 minutes).  Sonicated chromatin was brought to 1X mild-RIPA (10 mM Tris-HCl, pH=8.0; 1 mM EDTA, pH=8.0; 150 mM NaCl; 1% Triton X-100) concentration and pre-cleared with Dynabeads for 1 hour at 4˚C with rotation. Pre-clearing beads were removed and antibody was added for incubation overnight. Dynabeads were added and incubated for 3 hrs. Bead bound antibody-chromatin complexes were washed as follows 2X RIPA LS (10 mM Tris-HCl, pH=8.0; 1 mM EDTA, pH=8.0; 150 mM NaCl; 1% Triton X-100; 0.1 % SDS; 0.1 % DOC), 2X RIPA HS (10 mM Tris-HCl, pH=8.0; 1 mM EDTA, pH=8.0; 500 mM NaCl; 1% Triton X-100; 0.1 % SDS; 0.1 % DOC), 1X LiCl (10mM Tris-HCl, pH=8.0; 1 mM EDTA, pH=8.0; 250 mM LiCl; 0.5 % IGEPAL CA-630; 0.5 % DOC), 1X TE (10 mM Tris-HCl, pH=8.0; 1 mM EDTA, pH=8.0). Samples were then treated with RNAse and proteinase K, and chromatin was isolated using phenol-chloroform.
Imaginal discs of 3rd instar larvae were dissected in PBS on ice.

value: Wing imaginal disc

tag: developmental stage

value: input

value: yw


title: ChIP_sdGFP_haltere_input

description: Input sample for haltere imaginal disc. Strain: sdGFP

value: sdGFP


title: HCT-116_fixed1

source_name: HCT-116 fixed1


title: HCT-116_fixed20

source_name: HCT-116 fixed20


title: I4A - cells from well infected w/ B. burgdorferi MOI=200 seeded for 28 h out of w/c 4 h cells were exposed to bacteria

value: dermal microvascular endothelium

value: immortalized


title: ChIP_sdGFP_wing_input

description: Input sample for wing imaginal disc. Strain: sdGFP


title: Neuron wildtype , KCl treated --littermate control for Brg1-SA samples, rep 2


title: ChIP_wing_Sd_rep1


title: ChIP_wing_Sd_rep2


title: HCT-116_fixed19

source_name: HCT-116 fixed19


title: A11: CRC, LMN-pos

city: Wuhan

first: Chao

last: Yang

state: Hubei

address: No. 99 ZhangZhiDong Street Wuchang District

department: Department of gastrointestinal surgery

institute: Remin Hospital of Wuhan University

data_processing:
TMM (trimmed mean of M-values) was used to normalize the gene expression
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt files include TMM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with gene reads count for every gene and every sample

source_name: primary colorectal cancer tissue

extract_protocol:
total RNA  was extracted with Takara RNAiso Plus (Takara, Dalian, China)
RNA-seq library was prepared with approximately 1μg of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® (Kapa Biosystems, Inc., Woburn, MA). Briefly, ribosomal RNA was removed from the total RNA. Next, the ribominus RNAs were fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. The library quality and concentration was assessed by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer.

value: primary colorectal cancer

tag: Sex

value: female

tag: age

value: LNM-positive


title: HCT-116_fixed18

source_name: HCT-116 fixed18


title: Neuron wildtype , KCl treated --littermate control for Brg1-SA samples, rep 1


title: T30: CRC, LMN-pos

value: male


title: I24A - cells from well infected w/ B. burgdorferi MOI=200 seeded for 48 h out of w/c 24 h cells were exposed to bacteria

tag: sample type

tag: source

value: Obtained from the Welch lab, UC Berkeley (previously obtained from Centers for Disease Control, Biological Products Branch)


title: HCT-116_fixed17

source_name: HCT-116 fixed17

tag: cell line


title: Neuron  Brg1-SE, Basall - rep2

tag: cell type


title: ChIP_haltere_Hth_rep2

tag: tissue

value: Haltere imaginal disc


title: ChIP_haltere_Sd_rep1

tag: genotype


title: Neuron  Brg1-SE, KCl treated - rep2


title: ChIP_haltere_Hth_rep1

tag: chip antibody


title: T29: CRC, LMN-pos


title: Neuron  Brg1-SE, Basal  - rep1

tag: treatment


title: T6: CRC, LMN-pos


title: T2: CRC, LMN-neg

value: LNM-negative


title: Neuron  Brg1-SE, KCl treated - rep1


title: ChIP_haltere_Ubx_rep2


title: Neuron wildtype, Basal --littermate control for Brg1-SA samples, rep 1

value: wild-type


title: HCT-116_fixed14

source_name: HCT-116 fixed14


title: HCT-116_fixed12

source_name: HCT-116 fixed12


title: HCT-116_fixed16

source_name: HCT-116 fixed16


title: A9: CRC, LMN-neg


title: ChIP_haltere_Sd_rep2


title: A17: CRC, LMN-neg


title: Neuron  Brg1-SA, Basal - rep2

value: primary cortical neurons


title: Neuron  Brg1-SA, KCl treated - rep2

value: 50 mM KCl treatment for 1h


title: RNA_wing_WT_nub_rep1

extract_protocol:
Total RNA was extracted from sorted wing or haltere nub+ or tsh+ cells using TRIZOL. RNA-seq libraries were made according to Nugen ovation Drosophila RNA-seq system
Imaginal discs of 3rd instar larvae were dissected in PBS on ice.


title: B1: Normal

source_name: normal colorectal tissue

value: normal colorectal


title: HCT-116_fixed11

source_name: HCT-116 fixed11


title: Neuron  Brg1-SA, Basal  - rep1

value: Basal level of KCl


title: RNA_wing_tsh_rep2

value: Wing imaginal disc


title: HCT-116_fixed10

source_name: HCT-116 fixed10


title: N1: Normal


title: HCT-116_fixed15

source_name: HCT-116 fixed15


title: Neuron  Brg1-SA, KCl treated - rep1


title: ChIP_haltere_Ubx_rep1

value: yw


title: HCT-116_fixed13

source_name: HCT-116 fixed13


title: A1: CRC, LMN-neg


title: RNA_wing_tsh_rep1


title: HepG2_3

city: Farmington

first: Scott

last: Adamson

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

description: Amplicon RT-PCR of splicing reporter cDNA from transfected HepG2 cells

data_processing:
Library strategy: RT-PCR sequencing (Vex-seq)
UMIs were extracted from read 2 using UMItools (v1.0.0) extract (with --bc-pattern=NNNNNNNNNN) using UMItools
Read pairs were aligned to variant specific references using hisat2 (2.1.0) with parameters -no-softclip --dta-cufflinks.
Duplicate reads were deduplicated using UMItools (v1.0.0) dedup.
Stringtie (v2.0.3) was used to detect novel splice junctions from aligned and deduplicated reads and all samples were merged
Pysam (v0.15.4) was used to extract junction counts from bam files for all stringtie detected junctions.
BWA-MEM (v0.7.17) was used to align plasmid DNA samples.
Samtools and htslb (v1.9) mpileup and bcftools were used to identify the number of novel variant reads and reference reads.
Genome_build: hg19
Supplementary_files_format_and_content: All processed data files are tab separated files. For the plasmid libraries, these contain total counts and counts of variant sequences (1o) as well as the allele frequency. For the Vex-seq libraries these are counts of included reads, excluded reads, percent spliced in, for each variant and identified isoform as well as characteristics about the splice junctions used (Stringtie outputs and pysam parsed junction counts).

growth_protocol: Cells were grown to a density of 0.7x10^6 for HepG2 and 1.0x10^6 for K562 and transfected with 5 micrograms of plasmid DNA

extract_protocol:
Total RNA was extracted 48 hours after transfection using Maxwell RSC simplyRNA kit (Promega).
cDNA was synthesized using Superscript III and a reporter-gene specific primer. Illumina primers and indices were added during PCR amplification.

tag: sequenced molecule

value: Reporter RNA


title: RNA_haltere_WT_nub_rep2


title: HepG2_2


title: RNA_haltere_WT_nub_rep1


title: HepG2_1


title: WT m6A IP rep 2

city: Chicago

first: Caraline

last: Sepich

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

data_processing:
Library strategy: MeRIP-seq
Base calling was performed with Illumina bcl2fastq software.
Quality of sequenced reads was assessed with FastQC v0.11.5.
Trimmomatic 0.39 was used to remove the 3 bases at the start of all R2 reads (per SMARTer kit manual instructions) using the option HEADCROP: 3. Then adapter trimming and quality filtering were performed with Trimmomatic 0.39 using paired-end mode with the options LEADING: 3, TRAILING: 3, SLIDINGWINDOW: 4:15, and MINLEN:21.
Files were aligned to the human genome hg38 using hisat2 in splice-aware paired-end mode. Resulting bam files were sorted with samtools version 1.7.
Using the MeRIPTools package, reads were counted with the function CountReads, and peaks were called using Fisher's exact test with the function callPeakFisher. The R package QNB was used for inferential testing and differentially methylated peaks were called with an adjusted P-value of < 0.1.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Sepich-Poore_METTL5_m6A-seq_all_peaks.txt: Tab-delimited text file includes information about m6A peak locations, probability of a peak in wild-type and METTL5 knockout cells, log2 relative ratios, a beta coefficient associated with the predictor variable (interpretable as Log2 Fold Change), and P-values.

source_name: HeLa

growth_protocol: HeLa cells were obtained from ATTCC (cat# CCL-2). METTL5 knockout was performed using CRISPR/Cas9 technology with guide RNAs designed for excision of exons 2-3. All cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum, sodium pyruvate, and penicillin/streptomycin.

extract_protocol:
Cells were lysed in Trizol (Invitrogen) and total RNA was purified by chloroform extraction followed by isopropanol precipitation. Ribosomal RNA depletion was performed using the RiboMinus Eukaryote Kit v2 (Life Technologies) per manufacturer instructions.
Total RNA was fragmented using the Bioruptor Pico sonicator (Diagenode) 30 sec on, 30 sec off, 30 cycles. m6A immunoprecipitation was performed using the EpiMark N6-methyladenosine Enrichment Kit (NEB) as per manufacturer's instructions. Input at m6A IP samples were used to create libraries using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) as per manufacturer's instructions.

value: HeLa

value: WT

tag: condition

value: anti-m6A immunoprecipitate


title: RNA_wing_WT_nub_rep2


title: XBDR2

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Spinacia_oleracea whole genome using hisat2-2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts
Differeantial expression analysis with DEseq2
Genome_build: Spinacia_oleracea V1.0
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

organism: Spinacia oleracea

source_name: Root

growth_protocol: Spinach varieties; Bloomsdale and USDA accession PI175311 were selected for the study. The seeds of both varieties were grown in an environmentally controlled growth chamber at the Texas A&M  AgriLife Research and Extension Center in Uvalde, Texas, in plastic containers using Turface () as a growing medium. Plants were grown in 200 μmol·m-2·s -1 for 12 h.at 23°C. The plants were fertilized with with Peter’s professional mix (5-11-26) (0.974 g/L) and nitrogen level was mainatained at 200 ppm with addition of calcium Nitrate (Ca(NO3)2). Each treatment had six independent containers, each with independent plants. Plant samples from 6-week old plants were frozen in liquid nitrogen and stored at −80 °C until subsequent analyses. Three independent plants were used for oxalate analysis, total RNA extractions and physiological analysis.

extract_protocol:
The flash-frozen plant samples in liquid nitrogen were ground to a fine powder using a paint shaker (Harbil, Wheeling, IL, USA) and 3-mm-diameter steel balls (Abbott Ball, West Hartford, CT, USA). Total RNA was extracted using an RNeasy® Plant Mini Kit (QIAGEN Sciences, Germantown, MD, USA) as per the manufacturer’s protocol and treated with DNase1 (QIAGEN Sciences, Germantown, MD, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Bloomsdale

value: Root

tag: oxalate content

value: Low Oxalate


title: XBDL3

source_name: Leaf

value: Leaf


title: RNA_haltere_tsh_rep1

source_name: L3 imaginal disc

value: Haltere imaginal disc


title: M5 KO m6A IP rep 1

source_name: METTL5 knockout HeLa

value: METTL5 KO


title: XBDR1


title: XBDL2


title: XBDR3


title: K562_2

description: Amplicon RT-PCR of splicing reporter cDNA from transfected K562 cells


title: K562_3


title: RNA_haltere_tsh_rep2


title: M5 KO input rep 2

value: input


title: WT m6A IP rep 1


title: M5 KO input rep 1


title: ATAC_wing_RNAi_nub_rep2

extract_protocol:
ATAC libraries made according to Buenrostro et al. 2015
Imaginal discs of 3rd instar larvae were dissected in PBS on ice.


title: K562_1


title: ATAC_wing_RNAi_nub_rep1


title: M5 KO m6A IP rep 2


title: XBDL1


title: WT input rep 2


title: XS1R3

value: High Oxalate


title: WT input rep 1


title: 12_TRANS4_siJARID2

first: Jurga

last: Laurencikiene

institute: Karolinska Institutet

data_processing:
Sample demultiplexing was performed using bcl2fastq (v2.20.0).
Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7).
Reads were aligned to a reference built from Ensembl GRCh38 genome sequences using STAR (v2.6.1d).
Counts for each gene were obtained using featureCounts (v1.5.1) using the GRCh38.99 GTF file from Ensembl
Bioconductor package DESEq2 was used for count normalization and sample group comparisons, generating log2 fold changes, Wald test p-values and p-values adjusted for multiple testing (Benjamini-Hochberg method).
Supplementary_files_format_and_content: raw and normlized counts

source_name: human adipose tissue derived stem cells

growth_protocol: Human mesenchymal stem cells (hMSCs) were isolated from adipose tissue of a male donor (16 years old, BMI 24 kg/m2). Adipose tissue was collagenased and the SVF isolated. The SVF cells were plated in flasks at 3500 cells/cm2 and cultured for 12-14 hours in proliferation medium consisting of low glucose DMEM (Lonza, Verviers, Belgium) supplemented with 10% FBS (Hyclone, Thermo Scientific, Cramlington, UK), penicillin (50 U/ml; Gibco, Life Technologies), streptomycin (50 mg/ml; Gibco, Life Technologies), Hepes (0.5 M) and 2 mmol/l glutamine (Hyclone). The cells were cultured until ~80% confluence, trypsinised and seeded at 4500 cells/cm2 for propagation or at 30 000 cells/cm2 for differentiation. From passage two, FGF2 (5 ng/ml; Sigma-Aldrich) was added to the proliferation medium. The cells were cultured for three days until confluent. FGF2 was then removed from the medium and the cells were incubated for another 24 h. Differentiation medium was prepared by mixing 1:1 of Ham’s F12 (Gibco) and low glucose DMEM supplemented with penicillin (50 U/ml; Gibco, Life Technologies), streptomycin (50 mg/ml; Gibco, Life Technologies), Hepes (0.5 mol/l) and 2 mmol/l glutamine (Sigma- Aldrich). The 1:1 mix was further supplemented with 860 nmol/l insulin, 10 μg/ml transferrin and 0.2 nmol/l triiodothyronine, rosiglitazone (1 μmol/l), IBMX (100 μmol/l) and dexamethasone (1 μmol/l), all from Sigma-Aldrich. The differentiation medium contained 7.8 mmol/l glucose. Differentiation medium was added on day 0 after washing cells twice with PBS. IBMX and dexamethasone were removed after 3 days, and rosiglitazone after 10 days. Full differentiation was reached at day 13. Media were exchanged every 2-3 days.

extract_protocol:
Total RNA from hASC was extracted with Nucleospin RNA mini kit from Macherey Nagel (Macherey Nagel, Dueren, Germany)
Illumina TruSeq stranded mRNA sample
The yield and quality of the amplified libraries were analyzed using Qubit (Thermo Fisher) and the Agilent Tapestation (Agilent). The indexed cDNA libraries were normalized, combined and the pools were sequenced on the Illumina Nextseq 550 (Illumina) for a 75-cycle v2 sequencing run generating 75bp single-end reads

treatment_protocol: Transfection was performed using NEON electroporation system (Invitrogen, Carlsbad, USA). 1600V/20ms pulse and 100μl electroporation tips were used to transfect 106 cells.  Final concentration of 20nM siRNA was used (JARID2 siRNA L-009244-00-0010 and non-targeting siRNA D-001810-10-20 from Dharmacon). After electroporation, cells were seeded in a density of 40,000 cells/cm2.

tag: sirna

value: Adipose tissue

tag: time point

value: day 13 (full differentiation)


title: ATAC_haltere_RNAi_nub_rep2

tag: developmental stage


title: 11_TRANS3_siJARID2


title: XS1R2


title: ATAC_haltere_RNAi_nub_rep1


title: 10_TRANS2_siJARID2


title: 9_TRANS4_D13_NegC

value: Negative control


title: XS1R1


title: ATAC_wing_unsorted_rep2

value: Wing imaginal disc


title: ATAC_wing_unsorted_rep1

value: yw


title: 8_TRANS3_D13_NegC


title: ATAC_haltere_unsorted_rep2


title: 6_HG23_2_D6_siJARID2

value: day 6 (mid differentiation)


title: XS1L1


title: XS1L2


title: ATAC_wing_WT_nub_rep2


title: ATAC_haltere_unsorted_rep1


title: ATAC_wing_WT_nub_rep1


title: 7_TRANS2_D13_NegC_


title: 5_HG24_D6_siJARID2


title: ATAC_wing_tsh_rep2


title: 4_HG23_D6_siJARID2


title: 3_HG23_2_D6_NegC


title: ATAC_wing_tsh_rep1


title: 2_HG24_D6_NegC


title: XS1L3


title: ATAC_haltere_WT_nub_rep2


title: llama_RBD_before

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: VHH sequencing

data_processing:
base calling: illumina CASAVA 1.8.2
nanobody diversity analysis: trim : sickle (v1.33) with  “pe -t sanger -q 30 -l 180-188 –no-fiveprime” option
nanobody diversity analysis: merge : flash (v1.2.11) with  “-m 20 -M 200 -x 0.1” option
nanobody diversity analysis: unique nucleotide and protein sequence extracted by in-house perl script
nanobody diversity analysis: IMGT numbering on VHH genes: ANARCI unix version
nanobody diversity analysis: CDR3 clustering: cd-hit (v4.6.8) with "-c 0.7" option
VHH usage analysis: merge: Ngmerge program with default setting
VHH usage analysis: trim pMES4 vector seqeunce: pTrimmer
VHH usage analysis: clean: remove reads with undtermined nucleotide N, low quality or less than 300nt with fastp with " -n 0 -q 30 -u 10 -l 300 -A" option
VHH usage analysis: fastq to fasta: sed -n '2~4p' - | sed = | sed '1-2s/^/>vhh_1_/'.
VHH usage analysis: BLAST database with 30 VHH genes with BLAST+
VHH usage analysis: alignment: igblast -germline_db_V to 30 VHH genes
VHH usage analysis: usage calculation by in-house python script
Genome_build: NA
Supplementary_files_format_and_content: nanobody diversity analysis: fasta file for protein sequences
Supplementary_files_format_and_content: VHH usage analysis: text file for VHH gene identification

organism: Lama glama

source_name: spleen

growth_protocol: Two modified ESCs clones that have 40 normal chromosomes determined by karyotyping, negative for both mycoplasma and virus infection (mouse antibody production test) were injected into blastocysts from C57BL/6 strain by standard procedures. Injected blastocysts were transferred to the uteri of pseudopregnant female C56BL/6 recipients. High percentage chimeras were mated with C57BL/6 mice and offspring were genotyped for VHH minigene knock-in and Cuand Cgamma1 exon deletion. One out of three chimeras produced germline transmitted F1 offspring. Three F1 male mice with all three loci in Igh gene modified were backcrossed with C57BL/6 mice. F2 heterozygous mice were inbred to produce mice homozygous for all three loci modifications. Homozygous offspring were inbred to establish the mouse strain named as “nanomouse”. Two F1 offspring from the same chimera founder mouse were genotyped to only have CH1 exon of Cu deleted, while VH and CH1 exon of Cgamm1 awere intact. The two F1 mice were backcrossed with C57BL/6 miceand F2 heterozygous mice were inbred to produce mice homozygous for CH1 exon of Cu deletion. This stain was named “IguCh1-/-".

extract_protocol:
Diversity: Llama nanobody phage library was constructed as described before (PMID:24577359) with some modifications. Briefly, 300 ml of whole blood was collected from llama and peripheral blood mononuclear cells (PBMC) were isolated using Ficoll-Paque plus (GE Healthcare, 17-1440-03) according to manufacturer’s instruction. Total RNA e  xtracted from PBMC was used as starting material for RT-PCR to amplify the variable domains of immunoglobulin heavy chain (VHH) by two steps of PCR reactions. 50ug of RNA was reverse transcribed to cDNA with random hexamers and 2.5ul of cDNA (corresponding to about 0.9ug of original RNA) was used for first round PCR with gene-specific primers CALL001 and CALL002. The PCR reaction was repeated in 12 individual tubes with cDNA added into reactions separately. PCR fragment of about 700 bp long was gel purified and used as template (30 ng for each reaction, repeated in 12 individual tubes) for second round PCR with nested primers VHH-Back and VHH-For to amplify nanobody-encoding genes. PCR product from individual reactions werepooled, gel purified. Nanobody fragments and pMES4 phagmid were digested with PstI-HF and BstEII-HF restriction enzymes (NEB R3140L, R3162L) and ligated (1ug and 2ug respectively) with T4 ligase at 16 °C overnight. Ligation product was column purified (into 12ul of H2O) and electroporated into 360ul of TG1 cells. After 1 hour of recovery in 37 °C in shaker incubator, cells were plated on 6 of 245mm x 245mm dish (Thermo Fisher Scientific,431301) containing 2-YT Agar supplemented with 100ug/ml carbenicillin and 2% (wt/vol) glucose. Plates were placed in 37 °C bacteria incubator overnight and then bacteria scaped off plates. Cells were infected with VSCM13 helper phage (Agilent Technologies, 200251) and nanobody phage library preprepared as described before (PMID: 24577359). Nanomouse nanobody phage libraries were constructed the same way as nanomouse VHH(D)J region phagemid library construction with some modifications. Briefly, total RNA was extracted from splenic cells, bone marrow (femur and tibia) cells and PBMC of immunized mice and processed separately until TG1 cell electroporation step. RNA from splenic cells, bone marrow and PBMC (50ug, 50ug and all respectively) were reversed transcribed to cDNA with Ighg1 CH2-specific primer in separate tubes. 2ul of cDNA was used as template for BCR variable domains amplification (12 reactions each), using unmodified  TSO and Ighg1 CH2-specific oligonucleotide as primers. Second PCR was repeated in 12 reactions with 30 ng of the first-step PCR product as template 30 FR1 and 4 JH oligonucleotide mix as primers. PCR products were gel purified, digested with SfiI and ligated with pMES4 (200 ng and 400 ng respectively). Ligation products from splenic cells, bone marrow and PBMC samples were pooled and column purified (into 12ul of H2O) and electroporated into 360ul of TG1 cells and phage libraries prepared as described above.  VHH usage analysis: BCR VHH(D)J region phage library of unimmunized nanomouse was constructed and deep sequenced by Illumina Miseq for VHH usage analysis. Briefly, total RNA was extracted from nanomouse splenic cells by Trizol Reagent (Thermo Fisher Scientific,15596026) and reverse transcribed to cDNA with SuperScript™ III First-Strand Synthesis SuperMix (Thermo Fisher Scientific, 18080400) according to manufacturer’s instructions with some modifications.10ug of total RNA was denatured and annealed with gene specific primer corresponding to CH2 of Ighm gene. After elongation at 50 °C for 50 minutes, template switching oligonucleotide (TSO, 3’-propyl modified) linker was added to the 3’ end of the first strand cDNA with 90 minutes incubation at 42 °C as described before (Fernando Lopes Pinto et al. 2010, Anal Biochem. PMID: 19837043). Reaction was inactivated at 85 °C for 5 minutes and 2ul of cDNA was used as template for BCR variable domains amplification by two-step PCR with CloneAmp HiFi PCR Premix (Takara, 639298). For the first-step PCR, unmodified TSO and Ighm CH2-specific oligonucleotide were used as primers. 30 ng of the first-step PCR product was used as template for second-step nested PCR with a primer mix of 30 forward primers corresponding to framework (FR1) of 30 VHH genes and 4 reverse primers corresponding to JH1~JH4 of Igh gene. pMES4 phagemid was amplified with primers to introduce two different SfiI sites on two ends. Both VHH(D)J and pMES4 fragments were digested with restriction enzyme SfiI (NEB, R0123L) and ligated (100 and 200 ng respectively) with T4 ligase (NEB, M0202L) at 16 °C overnight. Ligation product was purified with DNA Clean & Concentrator (Zymo Research, D4014) and eluted into 12ul of H2O. 3ul of DNA was electroporated into 60ul of TG1 cells (Lucigen, 60502-2) in 1.0 mm cuvette (HARVARD Apparatus, 450134) with BTX electroporation system ECM 630 at the setting of 25uF, 200 Ohms, 1600 Volts. After 1 hour of recovery in 37 °C in shaker incubator, TG1 cells were plated on 5 of 10-cm LB Agar plates supplemented with 100ug/ml carbenicillin (KD Medical, BPL-2400). Plates were placed in 37 °C bacteria incubator overnight and then bacteria scaped off plates and phagemid library DNA extracted with Zymo Plasmid Miniprep kit (Zymo Research, D4054).
Phagemid DNA extracted from TG1 cell libraries was used as starting material for constructing MiSeq libraries for both VHH usage and nanobody diversity analysis. Briefly, 1.2 ug of phagemid DNA was used as template and VHH(D)J inserts were amplified by two primers recognizing pMES4 backbone with CloneAmp HiFi PCR Premix (Takara, 639298) in 50 ul reaction volume (9 cycles). To avoid MiSeq failure due to low complexity at initial cycles and to enable multiplex sequencing, 1-9 nt long staggers were introduced into forward primers. Without purification, 5 ul of the first PCR product was used as template for a second PCR (9 cycles) to add Illumina P5 and P7 primers on DNA ends. PCR product was then loaded onto 2% agarose gel and ~580 bp size band was purified with Zymoclean Gel DNA Recovery Kit (Zymo Research, D4002). DNA concentration was determined by Qubit 4  Fluorometer (Thermo Fisher Scientific, Q33238) and average DNA size was determined by TapeStation 4150 (Agilent). DNA was then adjusted to 2 nM in elution buffer containing 0.1% Tween-20. For unimmunized nanomice VHH(D)J library, DNA (2nM) from 3 mice were mix at 1:1:1 ratio and loaded for MiSeq run. For immunized llama and nanomice nanobody diversity analysis, DNA (2nM) of pre-selection and post-selection library were mixed at 10:1 ratio first and then samples from individual animals were pooled at 1:1 ratio before loading for MiSeq Sequencing (Illumina). 270 cycles of paired-end sequencing data were acquired  for VHH usage analysis and 300 cycles of paired-end sequencing data were acquired for nanobody diversity analysis.

treatment_protocol: One llama was immunized subcutaneously with SARS-CoV-2 virus antigens (recombinant protein of RBD and Spike) in the presence of Freund’s adjuvant according to the scheme described in the table below. Day 0 Bleed for test serumImmu. 1 Day 01 mg RBD, CFAImmu. 2 Day 140.5 mg RBD, IFADay 24Bleed for test serumImmu. 3 Day 280.5 mg RBD, IFADay 38Bleed for test serumImmu. 4 Day 420.5 mg RBD, IFADay 52Bleed for test serumImmu. 5 Day 560.5 mg Spike, IFADay 66Bleed for test serumImmu. 6 Day 700.5 mg Spike, IFADay 80500 ml bloodTwo groups of Nanomice (5 mice in group1, 6 mice in group2) were immunized with SARS-CoV-2 virus antigens (recombinant protein of RBD and Spike) in the presence of Freund’s adjuvant according to the scheme described in the table below.   Group1.  Day 0.   Bleed for test serum  Immu. 1  Day 0    50 ug RBD, CFA, i.p.  Immu. 2. Day 14. 25 ug RBD, IFA, i.p.                   Day 21. Bleed for test serum  Immu. 3.  Day 28. 25 ug RBD, IFA, i.p.                    Day 35. Bleed for test serum  Immu. 4   Day 42.  25 ug RBD, IFA, i.p.                   Day 49.  Bleed for test serum  Immu. 5.  Day 56.  25 ug Spike in PBS, i.p.  Immu. 6.  Day 59.  25 ug Spike in PBS, i.v.                    Day 62.  Harvest Experiment  Group 2    Day 0.    Bleed for test serum  Immu. 1.    Day 0.   50 ug Spike, CFA, i.p.  Immu. 2.   Day 14.  25 ug Spike, IFA, i.p.                    Day 21   Bleed for test serum  Immu. 3.   Day 28.  25 ug Spike, IFA, i.p.                    Day 35.  Bleed for test serum  Immu. 4.   Day 42. 25 ug Spike, IFA, i.p.                    Day 49.  Bleed for test serum  Immu. 5.   Day 56.  25 ug Spike in PBS, i.p.  Immu. 6.   Day 59.  25 ug Spike in PBS, i.v.                    Day 62.  Harvest Experiment.

value: peripheral blood mononuclear cells

value: wt

value: spleen

value: SARS-CoV-2 RBD + Spike infection


title: ATAC_haltere_WT_nub_rep1


title: llama_RBD_after

description: VHH sequencing

value: SARS-CoV-2 RBD + Spike infection, selection


title: ATAC_haltere_tsh_rep3


title: ATAC_haltere_tsh_rep2


title: WT methionine 1 rep 2

city: Beijing

first: Jing-Ren

last: Zhang

state: Beijing

address: Room 312, Renhuan Building, Tsinghua University

department: School of Medicine

institute: Tsinghua University

description: Transcriptome_of pneumococcus_D39_and_metR_mutant_in_1 μg_per_ml_methionine

data_processing:
Base calliing: Illumina Casava software version 1.8
Quality control: FastQC v0.11.5
Trimming: Trimmomatic v0.32
S. pneumoniae reads were mapped with Tophat 2.1.1 and Bowtie 2.3.1
Trans Per Million (TPM) were calculated using a custom script
Genome_build: Streptococcus pneumoniae D39 (accession NC_008533.2, assembly  GCA_000014365.2) was used directly in the analysis.
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae D39 WT cultured in CDM with 1 µg/ml methionine for 5.5 hours (replicate 2)

growth_protocol: Both strains were grown in 8 ml of TSB to OD620-0.5; spin in microfuge (1.8 ml/tube x 4) and wash 2 times with Ringer's solution; suspended the final pellet in 1 ml of ringer's solution and adjusted the OD620 to 0.5 with ringer's solution  in a 20-ml glass tube. Mixed 300 ul of  bacterial suspension with 30 ml of fresh (not prewarmed) chemically defined medium supplemented with 1 ug/ml methionine or 50 µg/ml methionine. Spit the suspension into four 20-ml glass tubes (7 ml/tube). Incubated at 37 ℃ with 5 % CO2 for 5.5 hrs.

extract_protocol:
Total RNA was purified from cultures at the 5.5 hr point. Total RNA was extracted using TIANGEN kit (TIANGEN, Beijing, China) and purified using QIAGEN kit (QIAGEN, Beijing, China).
The ribosomal RNA was removed from total RNA (~1.5 µg) using poly-T oligo-attached magnetic beads. Fragmentation of mRNAs and sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The cDNA molecules were ligated with the NEBNext Adaptor, and further processed for selected, purifed, and sequence amplification.

tag: strain

value: WT

tag: antibiotic resistance

value: rpsL1 (StreptomycinR)

tag: culture time

value: 5.5 hours


title: ΔmetR methionine 50 rep 2

description: Transcriptome_of pneumococcus_D39_and_metR_mutant_in_50 μg_per_ml_methionine

source_name: Streptococcus pneumoniae D39 ΔmetR cultured in CDM with 50 µg/ml methionine for 5.5 hours (replicate 2）

value: deltametR


title: ΔmetR methionine 50 rep 1

source_name: Streptococcus pneumoniae D39 ΔmetR cultured in CDM with 50 µg/ml methionine for 5.5 hours (replicate 1）


title: ΔmetR methionine 1 rep 1

source_name: Streptococcus pneumoniae D39 ΔmetR cultured in CDM with 1 µg/ml methionine for 5.5 hours (replicate 1)


title: ATAC_haltere_tsh_rep1

value: Haltere imaginal disc


title: WT methionine 50 rep 1

source_name: Streptococcus pneumoniae D39 WT cultured in CDM with 50 µg/ml methionine for 5.5 hours (replicate 1)


title: ΔmetR methionine 1 rep 2

source_name: Streptococcus pneumoniae D39 ΔmetR cultured in CDM with 1 µg/ml methionine for 5.5 hours (replicate 2)


title: WT methionine 1 rep 1

source_name: Streptococcus pneumoniae D39 WT cultured in CDM with 1 µg/ml methionine for 5.5 hours (replicate 1)


title: 1_HG23_D6_NegC


title: DNA213

type: genomic

city: Zhengzhou

first: Bianling

last: Xu

address: 91 Ruhe Road, Zhongyuan District, Zhengzhou City, Henan Province, China

institute: Zhengzhou Hospital of Traditional Chinese Medicine

description: Gene expression in hyperlipidemic liver

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA

data_processing: The expression value of green fluorescence signal in a sample after standardized treatment.

source_name: liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Normal control group consisted of wild-type (WT) C57BL/6J mice with a regular mouse diet ; HLP group,apolipoprotein-E-deficient (ApoE-/-) mice ,were fed with high-fat diet containing 2.5% cholesterol, 15% fat.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: male

tag: age

tag: group

value: hyperlipidemic


title: DNA222

description: Gene expression in hyperlipidemic liver


title: DNA214

description: Gene expression in hyperlipidemic liver


title: DNA212

description: Gene expression in hyperlipidemic liver


title: DNA223

description: Gene expression in hyperlipidemic liver


title: Old ASC1_sRNA

status: Public on May 17 2021

city: wuhan

first: sen

last: ren

state: hubei

address: donghu road

department: Department of Neurosurgery

institute: Zhongnan Hospital of Wuhan University

description:
Sample 4-O_ASC1
miRNA

data_processing:
Illumina Xten software used for basecalling.
Transcriptome sequencing uses high-throughput sequencing technology to sequence the cDNA after total RNA reverse transcription, and obtains most transcripts of samples in this state.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome, TPM and FPKM were calculated using Bowtie2 (Langmead B et al., 2012)
Genome_build: hg19
Supplementary_files_format_and_content: text files include counts,  FPKM and TPM values

source_name: adipose stem cells

extract_protocol:
Adipose stem cell samples were randomly selected from old group (n = 3), young group (n = 3) and diabetic group (n = 3), rinsed with PBS twice and total RNA was isolated by using miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Subcutaneous adipose tissue

tag: disease state

value: Normal

tag: age/years old


title: Young ASC3_sRNA

description:
Sample 9-Y_ASC3
miRNA


title: Young ASC2_sRNA

description:
Sample 8-Y_ASC2
miRNA


title: DNA113

description: Gene expression in the liver

value: control


title: Diabetic ASC1_sRNA

description:
Sample 1-D_ASC1
miRNA

value: Diabetes mellitus


title: Diabetic ASC2_sRNA

description:
Sample 2-D_ASC2
miRNA


title: DNA112

description: Gene expression in the liver


title: DNA124

description: Gene expression in the liver


title: DNA111

description: Gene expression in the liver


title: Old ASC2_sRNA

description:
Sample 5-O_ASC2
miRNA


title: Old ASC3_sRNA

description:
Sample 6-O_ASC3
miRNA


title: WT methionine 50 rep 2

source_name: Streptococcus pneumoniae D39 WT cultured in CDM with 50 µg/ml methionine for 5.5 hours (replicate 2)

tag: genotype


title: Diabetic ASC3_sRNA

description:
Sample 3-D_ASC3
miRNA


title: H78hfq mutant rep2

city: Shanghai

first: Xianqing

last: Huang

address: DongChuan RD, Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.82 software used for basecalling.
Sequenced reads were trimmed by Trimmomatic（v0.30） for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pseudomonas protegens H78 whole genome using tophat (v2.0.9 ).
Fragments Per Kilobase per Megabase of library size (FPKM) were calculated using Htseq(V 0.6.1).
Genome_build: Pseudomonas protegens H78  (Genbank Accession No. CP013184)
Supplementary_files_format_and_content: Excel file include FPKM values for each sample and differential expression analysis of all genes in the hfq mutant relative to the wild-type H78 strain...

organism: Pseudomonas protegens

source_name: Pseudomonas protegens H78hfq mutant

growth_protocol: Pseudomonas protegens H78 and its hfq mutant, which were grown to the late exponential phase (OD600 = 5.0 to 6.0) in the KMB media at 28 °C

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit (Cat.4106), purified by the Qiagen RNeasy micro kit (Cat.74004) and the Qiagen RNase-Free DNase Set (Cat.79254)
According to  standard Illumina protocols, mRNA was enriched by removing rRNA and further fragmented to be used for synthesizing the first and second strands of cDNAs and constructing the sequencing library.

value: H78hfq mutant

tag: growth phase

value: the late exponential phase


title: DNA131

description: Gene expression in the liver


title: H78hfq mutant rep3


title: H78 Wildtype rep3

source_name: Pseudomonas protegens H78

value: H78 wild-type

value: wild-type


title: H78hfq mutant rep1


title: GK73

type: RNA

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description:
29_N
microRNA expression profiles from papillary thyroid carcinoma

hyb_protocol: Hybridization was performed according to manufacturer’s standard protocols.

scan_protocol: miRNA microarrays were scanned with Agilent SureScan Microarray Scanner

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the limma package. Spot-level raw intensities were background-corrected using the normexp method and normalized with quantile normalization.

source_name: non-neoplastic thyroid

label_protocol: RNA was labeled and processed according to manufacturer’s recommended protocols.

extract_protocol: RNA was extracted from snap-frozen tissues using Qiagen miRNeasy Mini Kit and quantified by Qubit 2.0 Fluorometer (Thermo Fisher).

treatment_protocol: Patients RAI treatment following tumor surgical resection (thyroidectomy)

tag: histological variant

value: non-neoplastic thyroid

tag: tissue type

tag: collection before/after rai

value: Before

tag: patient id

tag: patient rai responce

value: Refractory

tag: rai uptake at the metastatic site

value: No

tag: disease

value: Persistence

tag: lesion by ptc-ma

tag: lesion class

tag: patients with available multiple tumor tissues

tag: tumor purity class by cibersort

value: low purity


title: H78 Wildtype rep2

tag: strain


title: H78 Wildtype rep1


title: Young ASC1_sRNA

description:
Sample 7-Y_ASC1
miRNA

tag: tissue


title: GK64

description:
25_N
microRNA expression profiles from papillary thyroid carcinoma

value: high purity


title: GK69

description:
27_N
microRNA expression profiles from papillary thyroid carcinoma


title: GK71

description:
28_N
microRNA expression profiles from papillary thyroid carcinoma


title: GK42

description:
11_N
microRNA expression profiles from papillary thyroid carcinoma

value: Yes


title: GK24

description:
2_N
microRNA expression profiles from papillary thyroid carcinoma

value: Avid

value: Remission


title: GK46

description:
13_N
microRNA expression profiles from papillary thyroid carcinoma


title: GK93

description:
42_L2
microRNA expression profiles from papillary thyroid carcinoma

source_name: papillary thyroid carcinoma

value: Classical

value: lymph node metastasis_2 post RAI

value: After


title: GK99

description:
46_L
microRNA expression profiles from papillary thyroid carcinoma

value: lymph node metastasis post RAI

value: WT


title: GK32

description:
7_N
microRNA expression profiles from papillary thyroid carcinoma


title: GL00

description:
47_L
microRNA expression profiles from papillary thyroid carcinoma


title: GK90

description:
41_L1
microRNA expression profiles from papillary thyroid carcinoma

value: lymph node metastasis_1 post RAI


title: GK92

description:
42_L1
microRNA expression profiles from papillary thyroid carcinoma


title: GK22

description:
1_N
microRNA expression profiles from papillary thyroid carcinoma


title: GK89

description:
40_L2
microRNA expression profiles from papillary thyroid carcinoma


title: GK87

description:
39_L
microRNA expression profiles from papillary thyroid carcinoma

value: pTERT


title: GK98

description:
45_L
microRNA expression profiles from papillary thyroid carcinoma

value: Follicular

value: BRAFV600E + TERT228

value: BRAFV600E +pTERT


title: GK63

description:
25_P
microRNA expression profiles from papillary thyroid carcinoma

value: Primary tumor

value: Before

value: Refractory

value: No


title: GK66

description:
26_N
microRNA expression profiles from papillary thyroid carcinoma

value: non-neoplastic thyroid

value: Persistence

value: high purity


title: GK80

description:
34_L2
microRNA expression profiles from papillary thyroid carcinoma

value: Classical

value: low purity


title: GK88

description:
40_L1
microRNA expression profiles from papillary thyroid carcinoma

value: After


title: GK72

description:
29_P
microRNA expression profiles from papillary thyroid carcinoma


title: GK82

description:
35_syn
microRNA expression profiles from papillary thyroid carcinoma

value: synchronous lymph node metastasis


title: GK60

description:
22_L
microRNA expression profiles from papillary thyroid carcinoma

value: lymph node metastasis post RAI

value: Yes

value: Fusion


title: GK70

description:
28_P
microRNA expression profiles from papillary thyroid carcinoma


title: GK68

description:
27_P
microRNA expression profiles from papillary thyroid carcinoma


title: GK58

description:
21_syn
microRNA expression profiles from papillary thyroid carcinoma

value: WT


title: GK59

description:
22_syn
microRNA expression profiles from papillary thyroid carcinoma


title: GK77

description:
32_P
microRNA expression profiles from papillary thyroid carcinoma


title: GK85

description:
37_syn
microRNA expression profiles from papillary thyroid carcinoma


title: GK55

description:
19_L
microRNA expression profiles from papillary thyroid carcinoma


title: GK97

description:
44_L
microRNA expression profiles from papillary thyroid carcinoma

value: Follicular


title: GK49

description:
15_P
microRNA expression profiles from papillary thyroid carcinoma


title: Plasmablastic lymphoma 35

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

institute: IDIBAPS

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix OncoScan™ FFPE Assay kit

data_processing:
Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.
Nexus biodiscovery software 9.0
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: Anal

label_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

value: Plasmablastic Lymphoma

tag: gender

value: Male

value: FFPE


title: Plasmablastic lymphoma 28

source_name: Thyroid mass

value: Female


title: Plasmablastic lymphoma 33

source_name: submaxilar LN


title: Plasmablastic lymphoma 32

source_name: palate


title: Plasmablastic lymphoma 30

source_name: testis


title: Plasmablastic lymphoma 25

source_name: Testis


title: Plasmablastic lymphoma 27

source_name: Suprapubic areas


title: GK45

description:
13_P
microRNA expression profiles from papillary thyroid carcinoma

value: Primary tumor

value: Before

value: Refractory

value: No


title: GK29

description:
5_P
microRNA expression profiles from papillary thyroid carcinoma

value: Classical

value: Avid

value: Remission

value: high purity


title: GK34

description:
7_L
microRNA expression profiles from papillary thyroid carcinoma

value: lymph node metastasis post RAI

value: After

value: Persistence

value: low purity


title: GK35

description:
8_P
microRNA expression profiles from papillary thyroid carcinoma

value: Yes

value: RET/PTC1 e NTRK-T1

value: Fusion


title: GK23

description:
2_P
microRNA expression profiles from papillary thyroid carcinoma

value: WT


title: Plasmablastic lymphoma 22

source_name: Abdominal mass

value: Plasmablastic Lymphoma

value: Male

value: FFPE


title: Plasmablastic lymphoma 19

source_name: Ethmoid mass


title: Plasmablastic lymphoma 20

source_name: Small bowel


title: GK33

description:
7_syn
microRNA expression profiles from papillary thyroid carcinoma

value: synchronous lymph node metastasis

value: Before

value: Refractory


title: GK25

description:
3_P
microRNA expression profiles from papillary thyroid carcinoma

value: Classical

value: Primary tumor

value: Avid

value: No


title: GK61

description:
23_L
microRNA expression profiles from papillary thyroid carcinoma

value: lymph node metastasis post RAI

value: After

value: pTERT

value: high purity


title: GK43

description:
12_P
microRNA expression profiles from papillary thyroid carcinoma

value: Yes

value: Persistence

value: NTRK


title: Plasmablastic lymphoma 31

source_name: maxilar

value: Plasmablastic Lymphoma


title: GK41

description:
11_P
microRNA expression profiles from papillary thyroid carcinoma

value: Fusion


title: Plasmablastic lymphoma 26

source_name: LN cervical

value: Female

value: FFPE


title: Plasmablastic lymphoma 18

source_name: Oral mucosa

value: Male


title: Plasmablastic lymphoma 14

source_name: oral mucosa


title: Plasmablastic lymphoma 10

source_name: not available


title: Plasmablastic lymphoma 17

source_name: Small and large bowel


title: Plasmablastic lymphoma 24

source_name: Mediastinal mass


title: GK47

description:
14_P
microRNA expression profiles from papillary thyroid carcinoma

source_name: papillary thyroid carcinoma

value: Before

value: Refractory


title: Plasmablastic lymphoma 23

source_name: Stomach mass


title: Plasmablastic lymphoma 3

source_name: Mesenteric LN


title: Plasmablastic lymphoma 5

source_name: Nasal Mucosa


title: Plasmablastic lymphoma 21

source_name: Tongue


title: Plasmablastic lymphoma 29

source_name: Colon


title: Plasmablastic lymphoma 12


title: GK31

description:
7_P
microRNA expression profiles from papillary thyroid carcinoma

value: Classical

value: Primary tumor

value: low purity


title: Plasmablastic lymphoma 6

source_name: Sigma


title: GK21

description:
1_P
microRNA expression profiles from papillary thyroid carcinoma

value: Avid

value: Remission

value: WT

value: No


title: ExVivoBlood_sepsis_rep1 [SC2]

city: Hohhot, Inner Mongolia

first: Jingping

address: Jinshan Development Zone

institute: Inner Mongolia Medical University

description:
SC2
Gene expression in peripheral blood.

hyb_protocol: The labeled RNA was purified and hybridized to miRNA arrays (Agilent-070156 Human miRNA Microarray, Release 21.0, 8x60K). The miRNA profiling was performed using Agilent miRNA array. The Agilent array was designed with eight identical arrays per slide (8 x 60K format), with each array containing probes interrogating 2006 human mature miRNAs, both from miRBase R19.0. Each miRNA was detected by probes repeat for 30 times. The array also contain 2164 Agilent control probes.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The miRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V12 (Agilent). The default 90th percentile normalization method were performed for date preprocessing. To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a Benjamini-Hochberg corrected p value of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

source_name: Peripheral Blood, sepsis

label_protocol: Microarray experiments were conducted according to the manufacturer's instructions. Briefly, the miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (100 ng) was dephosphorylated and ligated with pCp-Cy3.

extract_protocol:
Total RNA containing small RNA was extracted from peripheral blood from volunteers by using Qiagen miRNeasy Mini kit (217004) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacturer’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.
RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only RNA extracts with RNA integrity number values >6 underwent in further analysis.

treatment_protocol: Patients: Forty patients admitted to the department of respiratory and critical care medicine of the Third Affiliated Hospital of Inner Mongolia Medical University from January 1st 2015 to October 31th 2015 were enrolled according to the following inclusion and exclusion criteria. This study was approved by the Research Ethics Committee of the Third Affiliated Hospital of Inner Mongolia Medical University and written informed consent was obtained from all patients. Inclusion criteria: Patients diagnosed as sepsis according to the standard of Sepsis 3.0, that is, clinical suspicion of infection complicated with infection-induced sequential organ failure assessment (SOFA) score ≥2; see table 1. Exclusion criteria: 1)＜18 or＞80 years old; 2) Patients with liver and kidney failure; 3) Pregnant or lactating women; 4) Patients with tumors, hematological diseases, etc.; 5) Agranulocytosis (< 0.5 × 109/L); 6) Patients complicated with HIV infection; 7) People withdrawal due to special circumstances. Forty healthy control individuals came from physical examination donors (male/female: 20/20; aged 20-80 years). There was no significant difference in mean values of gender and age between the test group and the control group. All protocols were approved by the local ethics committee of the Third Affiliated Hospital of Inner Mongolia Medical University, and signed informed consent was obtained from all subjects who were promised to withdraw from clinical observation at any time for any reason. The whole blood samples of all subjects were collected into a sterilized Eppendorf tubes.

tag: diagnosis

value: sepsis

value: whole blood

value: male

tag: age


title: Plasmablastic lymphoma 1

source_name: Sinus

value: Plasmablastic Lymphoma


title: ExVivoBlood_sepsis_rep1 [SC3]

description:
SC3
Gene expression in peripheral blood.


title: ExVivoBlood_sepsis_rep1 [S9]

description:
S9
Gene expression in peripheral blood.


title: ExVivoBlood_healthy_rep1 [N8]

description:
N8
Gene expression in peripheral blood.

source_name: Peripheral Blood, healthy

value: healthy


title: ExVivoBlood_healthy_rep1 [N10]

description:
N10
Gene expression in peripheral blood.


title: GK75

description:
30_N
microRNA expression profiles from papillary thyroid carcinoma

source_name: non-neoplastic thyroid

value: non-neoplastic thyroid

value: Persistence

value: high purity


title: ExVivoBlood_sepsis_rep1 [S4]

description:
S4
Gene expression in peripheral blood.


title: ExVivoBlood_healthy_rep1 [N11]

description:
N11
Gene expression in peripheral blood.


title: ExVivoBlood_sepsis_rep1 [S3]

description:
S3
Gene expression in peripheral blood.


title: H78 Wildtype replicate 2

data_processing:
Base-calling software:BGISEQ-500.
Data filtering software: SOAPnuke.
Clean reads were aligned to the Reference genes using Bowtie2 and the Reference genome usiong HISAT.
Gene expression was quantified as Fragments Per Kilobase per Megabase of library size (FPKM) using RSEM.
Genome_build: Pseudomonas protegens H78  (Genbank Accession No. CP013184)
Supplementary_files_format_and_content: Excel file include FPKM values for each sample and differential expression analysis of all genes in the crc-deleted mutant relative to the wild-type H78 strain...

source_name: Pseudomonas protegens H78

growth_protocol: Pseudomonas protegens H78 and its crc-deleted mutant (Δcrc), which were grown to the late exponential phase (OD600 = 4.0 to 5.0) in the KMB media at 28 °C

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit (Cat.4106), purified by the Qiagen RNeasy micro kit (Cat.74004) and the Qiagen RNase-Free DNase Set (Cat.79254)
According to standard BGISEQ-500 RNA sequencing protocols, mRNA was enriched by removing rRNA and further fragmented to be used for synthesizing the first and second strands of cDNAs and constructing the sequencing library.

value: H78 wild-type

tag: growth phase

value: the late exponential phase

tag: genotype

value: wild-type


title: H78 Wildtype replicate 3


title: Plasmablastic lymphoma 16

description: Hybridized to Affymetrix OncoScan FFPE Assay

source_name: Soft tissue perirectal

value: Male

value: FFPE


title: JB_99

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

data_processing:
Unstranded single-end reads with 51 bp in length were trimmed for adaptor and low quality sequences using Cutadapt (v 1.18) with parameters -q 20 -O 7 -m 16 –trim-n
Trimmed reads were mapped to the human genome (hg38 UCSC) using Bowtie2 (v 2.2.6) with parameters -p 6 -N 1 –un-gz
Mapped reads were summarized using featureCounts (v 1.6.3) with parameters -s 0 -T 6 -t miRNA -g ID and miRBase (v 22) annotations.
Normalized gene expression was achieved using R/edgeR (v 3.28) by applying TMM normalization of read counts.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Neuroblastoma_tumor_miRNA_TMM.csv: Comma-separated text file including TMM normalized abundance measurements (CPM, counts per million mapped reads) for each sample.

source_name: primary neuroblastoma tumor

extract_protocol:
Total RNA was extracted from 30 micrograms of primary tumor tissue using the Qiagen ALLprep tumour protocol with miRNeasy kits. 500 ng of total RNA was used in the small RNA protocol with the TruSeq™ Small RNA sample prepkit v2 (Illumina) according to the instructions of the manufacturer.
The barcoded libraries were size restricted between 140 and 165bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 50 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell according to the instructions of the manufacturer. Demultiplexing of raw reads, adapter trimming and quality filtering was done according to Stokowy et al. (PMID: 2462507).

value: Primary neuroblastoma tumor

tag: Stage

tag: mna (cn>5)

value: no


title: Plasmablastic lymphoma 15

source_name: Oral mucosa


title: Plasmablastic lymphoma 13

source_name: Gastrostomy

value: Female


title: H78Δcrc mutant rep2

source_name: Pseudomonas protegens H78Δcrc mutant

value: H78 deltacrc mutant

value: crc-deleted mutant


title: JB_97


title: Plasmablastic lymphoma 9

source_name: not available


title: Plasmablastic lymphoma 8

source_name: Skin


title: JB_95


title: JB_96


title: Plasmablastic lymphoma 7

source_name: Submandibular Mass


title: Plasmablastic lymphoma 4

source_name: Abdominal Mass


title: JB_93

value: yes


title: JB_98


title: ExVivoBlood_sepsis_rep1 [SP4]

description:
SP4
Gene expression in peripheral blood.

value: sepsis

value: whole blood

value: male


title: JB_91


title: JB_90


title: Plasmablastic lymphoma 2

source_name: Cervical LN

value: Plasmablastic Lymphoma


title: ExVivoBlood_sepsis_rep1 [SP1]

description:
SP1
Gene expression in peripheral blood.


title: ExVivoBlood_sepsis_rep1 [SC1]

description:
SC1
Gene expression in peripheral blood.


title: ExVivoBlood_sepsis_rep1 [S8]

description:
S8
Gene expression in peripheral blood.


title: JB_87


title: ExVivoBlood_sepsis_rep1 [S5]

description:
S5
Gene expression in peripheral blood.


title: ExVivoBlood_healthy_rep1 [N9]

description:
N9
Gene expression in peripheral blood.

value: healthy


title: JB_82


title: ExVivoBlood_healthy_rep1 [N7]

description:
N7
Gene expression in peripheral blood.


title: H78Δcrc mutant rep1


title: ExVivoBlood_sepsis_rep1 [SP2]

description:
SP2
Gene expression in peripheral blood.


title: JB_80


title: H78Δcrc mutant rep3


title: ExVivoBlood_sepsis_rep1 [S10]

description:
S10
Gene expression in peripheral blood.


title: JB_100


title: JB_79


title: JB_78


title: H78 Wildtype replicate 1


title: JB_76


title: ExVivoBlood_healthy_rep1 [N1]

description:
N1
Gene expression in peripheral blood.


title: JB_94


title: JB_75


title: JB_74


title: JB_92


title: JB_72


title: JB_89


title: JB_88


title: JB_85


title: JB_84


title: JB_83


title: JB_69


title: JB_66


title: JB_81


title: JB_64


title: JB_65


title: JB_77


title: JB_61


title: JB_86


title: JB_56


title: JB_57


title: JB_71


title: JB_70


title: JB_54


title: JB_50


title: JB_67


title: JB_68


title: JB_63


title: JB_60


title: JB_62


title: JB_59


title: JB_58


title: JB_46


title: JB_45


title: JB_73


title: JB_53


title: JB_42


title: JB_51


title: JB_52


title: JB_40


title: JB_48


title: JB_47


title: JB_44


title: JB_41


title: JB_39


title: JB_32


title: JB_33


title: JB_37


title: JB_36


title: JB_35


title: JB_28


title: JB_25


title: JB_34


title: JB_30


title: JB_31


title: JB_29


title: JB_20


title: JB_21


title: JB_27


title: JB_23


title: JB_24


title: JB_18


title: JB_26


title: JB_43


title: JB_22


title: JB_19


title: JB_16


title: JB_12


title: JB_13


title: JB_11


title: JB_14


title: JB_10


title: JB_9


title: JB_6


title: JB_2


title: JB_3


title: JB_8


title: JB_1


title: JB_17


title: JB_15


title: EC_RNA_YS_cell735

first: Haiqing

last: Xiong

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

source_name: yolk sac (YS)

extract_protocol:
Following CoTECH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Organs were digested with 0.06 Collagenase II + 0.08% Trypsin and 0.09% Collagenase II + 0.12% Trypsin  at 37 °C.

tag: cell type

value: endothelial cells

value: yolk sac (YS)

tag: antibody


title: EC_RNA_YS_cell736


title: EC_RNA_YS_cell734


title: EC_RNA_YS_cell733


title: EC_RNA_YS_cell729


title: EC_RNA_YS_cell727


title: EC_RNA_YS_cell725


title: EC_RNA_YS_cell732


title: EC_RNA_YS_cell724


title: JB_4


title: JB_7


title: EC_RNA_YS_cell722


title: EC_RNA_YS_cell721


title: EC_RNA_YS_cell723


title: EC_RNA_YS_cell720


title: EC_RNA_YS_cell719


title: EC_RNA_YS_cell717


title: EC_RNA_YS_cell716


title: EC_RNA_YS_cell718


title: EC_RNA_YS_cell714


title: EC_RNA_YS_cell715


title: EC_RNA_YS_cell731


title: EC_RNA_YS_cell712


title: EC_RNA_YS_cell713


title: EC_RNA_YS_cell710


title: EC_RNA_YS_cell711


title: EC_RNA_YS_cell706


title: EC_RNA_YS_cell704


title: EC_RNA_YS_cell708


title: EC_RNA_YS_cell707


title: EC_RNA_YS_cell728


title: EC_RNA_YS_cell705


title: EC_RNA_YS_cell709


title: EC_RNA_YS_cell701


title: EC_RNA_YS_cell700


title: EC_RNA_YS_cell698


title: EC_RNA_YS_cell697


title: EC_RNA_YS_cell696


title: EC_RNA_YS_cell694


title: EC_RNA_YS_cell695


title: EC_RNA_YS_cell693


title: EC_RNA_YS_cell692


title: EC_RNA_YS_cell699


title: EC_RNA_YS_cell690


title: EC_RNA_YS_cell689


title: EC_RNA_YS_cell686


title: EC_RNA_YS_cell688


title: EC_RNA_YS_cell703


title: EC_RNA_YS_cell685


title: EC_RNA_YS_cell702


title: EC_RNA_YS_cell687


title: EC_RNA_YS_cell684


title: EC_RNA_YS_cell681


title: EC_RNA_YS_cell682


title: EC_RNA_YS_cell680


title: EC_RNA_YS_cell683


title: EC_RNA_YS_cell679


title: EC_RNA_YS_cell676


title: EC_RNA_YS_cell678


title: EC_RNA_YS_cell670


title: EC_RNA_YS_cell691


title: EC_RNA_YS_cell669


title: EC_RNA_YS_cell668


title: EC_RNA_YS_cell674


title: JB_5


title: EC_RNA_YS_cell675


title: EC_RNA_YS_cell667


title: EC_RNA_YS_cell666


title: EC_RNA_YS_cell665


title: EC_RNA_YS_cell671


title: EC_RNA_YS_cell661


title: EC_RNA_YS_cell660


title: EC_RNA_YS_cell663


title: EC_RNA_YS_cell664


title: EC_RNA_YS_cell662


title: EC_RNA_YS_cell658


title: EC_RNA_YS_cell657


title: EC_RNA_YS_cell659


title: EC_RNA_YS_cell677


title: EC_RNA_YS_cell654


title: EC_RNA_YS_cell672


title: EC_RNA_YS_cell656


title: EC_RNA_YS_cell652


title: EC_RNA_YS_cell653


title: EC_RNA_YS_cell651


title: EC_RNA_YS_cell650


title: EC_RNA_YS_cell649


title: EC_RNA_YS_cell648


title: EC_RNA_YS_cell646


title: EC_RNA_YS_cell647


title: EC_RNA_YS_cell673


title: EC_RNA_YS_cell645


title: EC_RNA_YS_cell643


title: EC_RNA_YS_cell655


title: EC_RNA_YS_cell644


title: EC_RNA_YS_cell642


title: EC_RNA_YS_cell641


title: EC_RNA_YS_cell637


title: EC_RNA_YS_cell629


title: EC_RNA_YS_cell631


title: EC_RNA_YS_cell633


title: EC_RNA_YS_cell640


title: EC_RNA_YS_cell632


title: EC_RNA_YS_cell634


title: EC_RNA_YS_cell638


title: EC_RNA_YS_cell636


title: EC_RNA_YS_cell639


title: EC_RNA_YS_cell635


title: EC_RNA_YS_cell630


title: EC_RNA_YS_cell627


title: EC_RNA_YS_cell625


title: EC_RNA_YS_cell624


title: EC_RNA_YS_cell626


title: EC_RNA_YS_cell623


title: EC_RNA_YS_cell621


title: EC_RNA_YS_cell622


title: EC_RNA_YS_cell618


title: EC_RNA_YS_cell616


title: EC_RNA_YS_cell617


title: EC_RNA_YS_cell615


title: EC_RNA_YS_cell628


title: EC_RNA_YS_cell613


title: EC_RNA_YS_cell612


title: EC_RNA_YS_cell611


title: EC_RNA_YS_cell606


title: EC_RNA_YS_cell610


title: EC_RNA_YS_cell607


title: EC_RNA_YS_cell605


title: EC_RNA_YS_cell602


title: EC_RNA_YS_cell600


title: EC_RNA_YS_cell603


title: EC_RNA_YS_cell620


title: EC_RNA_YS_cell599


title: EC_RNA_YS_cell619


title: EC_RNA_YS_cell598


title: EC_RNA_YS_cell596


title: EC_RNA_YS_cell595


title: EC_RNA_YS_cell597


title: EC_RNA_YS_cell594


title: EC_RNA_YS_cell592


title: EC_RNA_YS_cell593


title: EC_RNA_YS_cell614


title: EC_RNA_YS_cell591


title: EC_RNA_YS_cell590


title: EC_RNA_YS_cell589


title: EC_RNA_YS_cell604


title: EC_RNA_YS_cell609


title: EC_RNA_YS_cell587


title: EC_RNA_YS_cell583


title: EC_RNA_YS_cell585


title: EC_RNA_YS_cell584


title: EC_RNA_YS_cell586


title: EC_RNA_YS_cell588


title: EC_RNA_YS_cell581


title: EC_RNA_YS_cell580


title: EC_RNA_YS_cell582


title: EC_RNA_YS_cell577


title: EC_RNA_YS_cell579


title: EC_RNA_YS_cell576


title: EC_RNA_YS_cell578


title: EC_RNA_YS_cell574


title: EC_RNA_YS_cell572


title: EC_RNA_YS_cell573


title: EC_RNA_YS_cell571


title: EC_RNA_YS_cell568


title: EC_RNA_YS_cell567


title: EC_RNA_YS_cell570


title: EC_RNA_YS_cell566


title: EC_RNA_YS_cell564


title: EC_RNA_YS_cell565


title: EC_RNA_YS_cell563


title: EC_RNA_YS_cell730


title: EC_RNA_YS_cell601


title: EC_RNA_YS_cell726


title: EC_RNA_YS_cell575


title: EC_RNA_YS_cell562


title: EC_RNA_YS_cell558


title: EC_RNA_YS_cell559


title: EC_RNA_YS_cell560


title: EC_RNA_YS_cell555


title: EC_RNA_YS_cell569


title: EC_RNA_YS_cell556


title: EC_RNA_YS_cell551


title: EC_RNA_YS_cell554


title: EC_RNA_YS_cell552


title: EC_RNA_YS_cell553


title: EC_RNA_YS_cell545


title: EC_RNA_YS_cell548


title: EC_RNA_YS_cell549


title: EC_RNA_YS_cell543


title: EC_RNA_YS_cell544


title: EC_RNA_YS_cell550


title: EC_RNA_YS_cell542


title: EC_RNA_YS_cell561


title: EC_RNA_YS_cell540


title: EC_RNA_YS_cell557


title: EC_RNA_YS_cell538


title: EC_RNA_YS_cell539


title: EC_RNA_YS_cell537


title: EC_RNA_YS_cell535


title: EC_RNA_YS_cell536


title: EC_RNA_YS_cell541


title: EC_RNA_YS_cell534


title: EC_RNA_YS_cell531


title: EC_RNA_YS_cell532


title: EC_RNA_YS_cell533


title: EC_RNA_YS_cell546


title: EC_RNA_YS_cell529


title: EC_RNA_YS_cell530


title: EC_RNA_YS_cell547


title: EC_RNA_YS_cell528


title: EC_RNA_YS_cell527


title: EC_RNA_YS_cell526


title: EC_RNA_YS_cell523


title: EC_RNA_YS_cell525


title: EC_RNA_YS_cell521


title: EC_RNA_YS_cell520


title: EC_RNA_YS_cell519


title: EC_RNA_YS_cell514


title: EC_RNA_YS_cell517


title: EC_RNA_YS_cell518


title: EC_RNA_YS_cell516


title: EC_RNA_YS_cell512


title: EC_RNA_YS_cell513


title: EC_RNA_YS_cell515


title: EC_RNA_YS_cell507


title: EC_RNA_YS_cell511


title: EC_RNA_YS_cell506


title: EC_RNA_YS_cell524


title: EC_RNA_YS_cell503


title: EC_RNA_YS_cell510


title: EC_RNA_YS_cell509


title: EC_RNA_YS_cell500


title: EC_RNA_YS_cell505


title: EC_RNA_YS_cell508


title: EC_RNA_YS_cell502


title: EC_RNA_YS_cell504


title: EC_RNA_YS_cell497


title: EC_RNA_YS_cell496


title: EC_RNA_YS_cell522


title: EC_RNA_YS_cell495


title: EC_RNA_YS_cell494


title: EC_RNA_YS_cell498


title: EC_RNA_YS_cell493


title: EC_RNA_YS_cell491


title: EC_RNA_YS_cell492


title: EC_RNA_YS_cell487


title: EC_RNA_YS_cell501


title: EC_RNA_YS_cell488


title: EC_RNA_YS_cell485


title: EC_RNA_YS_cell482


title: EC_RNA_YS_cell489


title: EC_RNA_YS_cell499


title: EC_RNA_YS_cell483


title: EC_RNA_YS_cell480


title: EC_RNA_YS_cell481


title: EC_RNA_YS_cell476


title: EC_RNA_YS_cell477


title: EC_RNA_YS_cell475


title: EC_RNA_YS_cell479


title: EC_RNA_YS_cell472


title: EC_RNA_YS_cell490


title: EC_RNA_YS_cell473


title: EC_RNA_YS_cell484


title: EC_RNA_YS_cell471


title: EC_RNA_YS_cell486


title: EC_RNA_YS_cell478


title: EC_RNA_YS_cell470


title: EC_RNA_YS_cell465


title: EC_RNA_YS_cell468


title: EC_RNA_YS_cell467


title: EC_RNA_YS_cell464


title: EC_RNA_YS_cell463


title: EC_RNA_YS_cell466


title: EC_RNA_YS_cell469


title: EC_RNA_YS_cell462


title: EC_RNA_YS_cell460


title: EC_RNA_YS_cell457


title: EC_RNA_YS_cell456


title: EC_RNA_YS_cell458


title: EC_RNA_YS_cell461


title: EC_RNA_YS_cell453


title: EC_RNA_YS_cell454


title: EC_RNA_YS_cell451


title: EC_RNA_YS_cell455


title: EC_RNA_YS_cell452


title: EC_RNA_YS_cell450


title: EC_RNA_YS_cell449


title: EC_RNA_YS_cell448


title: EC_RNA_YS_cell446


title: EC_RNA_YS_cell444


title: EC_RNA_YS_cell443


title: EC_RNA_YS_cell447


title: EC_RNA_YS_cell445


title: EC_RNA_YS_cell442


title: EC_RNA_YS_cell459


title: EC_RNA_YS_cell441


title: EC_RNA_YS_cell440


title: EC_RNA_YS_cell439