title: 4h_control (3b)

description:
development stage: cell culture on mid-log phase
T4neg3_L2

value: algae cell culture, time:4 h


title: 9p21+/- BM-MSCs-1, Day 0 [287M_0d_S25]

status: Public on Jun 06 2023

type: SRA

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

country: USA

institute: NYU Grossman School of Medicine

library_source: transcriptomic

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and read counting performed using HT-seq to make count tables
Assembly: mm10
Supplementary files format and content: txt. Formatted counts table

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: For bulk RNA-seq: To prepare BM-MSCs, femur and tibia were dissected from mice that were euthanized with CO2. Each cleaned bone was transferred into a single PCR tube with a whole at the bottom which was punched by an 18G needle. The combined PCR tube was inserted into a 1.5 ml Eppendorf tube and centrifuged at 16,000 g for 20 seconds. The flushed BM cells were suspended and cultured in 20 ml low glucose DMEM medium supplemented with 10% fetal bovine serum (FBS), 1% MEM-NEAA and 1% penicillin/streptomycin at 37°C in a humidified atmosphere at 5% CO2. The medium was replenished every 2-3 days for a week. For CITE-seq, no growth cultre

extract_protocol:
For bulk RNA-seq, total RNA were extracted using TRIzol Plus purification kit (ThermoFisher), and cDNA libraries were prepared with TruSeq Stranded Total RNA with Ribo-Zero Globin.RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. For CITE-seq, Post staining and sorting, cells were run through the standard 10x Chromium (v3) protocol up until cDNA amplification, with the following modification: during cDNA PCR and 1 pmol of hashtagging oligonucleotide (HTO) additive primer were added to the cDNA amplification master mix. Post cDNA amplification, a 0.6X Solid Phase Reversible Immobilisation (SPRI) bead clean-up was performed to separate the cDNA fraction (on beads) from HTO fraction (in supernatant). The cDNA fraction was converted into a 3’ tag gene expression library according to the 10x Genomics Single Cell Genomics Protocol (v3). Supernatant from cleanup was kept for ADT and HTO preparation. To the supernatant, another 1.4X SPRI was added to bring the total SPRI concentration to 2X. After washing the beads in 80% ethanol and eluting in water, a second round of 2X SPRI cleanup was performed to remove any residual primer carryover from the cDNA PCR.
RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For osteigenic differetiation:  The attached cells were collected and seeded at a density of 10,000 cells per well in a 24-well plate and switched into osteogenic medium (low glucose DMEM supplemented with 10% FBS plus 100 ug/ml ascorbic acid, 10 mM β-glycerophosphate, 1% MEM-NEAA and 1% penicillin/streptomycin) after reaching 80% confluency.

tag: tissue

value: bone marrow

tag: cell type

value: cultured mesenchymal stromal cells

tag: genotype

tag: treatment

value: osteogenic differentiation

tag: time

value: Day 0

tag: library type

value: mRNA


title: 9p21+/- BM-MSC-2s, Day 0 [1945M_0d_S27]


title: LIDAR, total, NPC, b3

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
counts.genes.txt
counts.biotypes.txt

data_processing:
For LIDAR, LIDAR3 and NEB samples: Adapter trimming with TrimGalore v0.6.4: --length 5 --paired --retain_unpaired -r 20 -r 100. For NEB samples, additional trimming step with Cutadapt v 4.2: cutadapt -A GATCGTCGG --minimum-length 5 --paired-filter any
Samples with UMI (LIDAR, LIDAR-3): UMIs were extracted using umi_tools v1.1.2 with the regex ".*(?<umi_1>.{7})CG(?P<umi_2>.{2})AG(?P<umi_3>.{2})GGG" and remaining constant bases were trimmed with Cutadapt (cutadapt --minimum-length 5 -g CGAGGGG), then TSO dimers were removed with Cutadapt (cutadapt -e 3 -b CGTCAGATGTGTATAAGAGACAG --discard-trimmed)
Reads were mapped sequentially with STAR v2.7.10a to consensus rRNA repeats (BK000964.3), snoRNA from GENCODE vM27, snRNA from GENCODE vM27, piRNA from piRbase v3.0 using bowtie2 ver2.5.0, and tRNA from GtRNAdb and tRNAscan-SE as curated by Nedialkova et al. using GSNAP ver 2019-02-26 with SNP database provided, then to a custom GRCm39 genome with all of the sequences above masked and provided as extra scaffolds, using STAR (paired reads with inserts > 100nt) or bowtie2 (paired reads with inserts < 100nt and single reads)
Samples with UMI (LIDAR, LIDAR-3): bam files were deduplicated using umi_tools dedup with method --unique
Only reads with fragment length >=15 were retained for downstream analysis
Assembly: GRCm39
Supplementary files format and content: tab delimited files include raw counts corresponding to each gene (counts.genes.txt) or biotype, including reads mapped to non-annotation regions (counts.biotypes.txt)

source_name: cells

extract_protocol:
For ESC and NPC, cell pellets were resuspended in 1ml of TriPure and RNA was extracted following standard protocol. DNA was digested with Turbo DNase-I at 37°C for 30min, RNA was re-purified using TriPure, and resuspend in 10mM Bis/Tris pH=6.7, 0.1mM EDTA. For mouse sperm, sperm were resuspended in 120 ul of water and 66 μl of Sperm_lysis_buffer were added [120mM Tris-HCl (pH=8), 6.4M Guanidine-HCl, 5% Tween-20, 5% Triton-X-100, 120mM EDTA]. Proteins were digested by adding 6.6 μl of 20 mg/ml proteinase K and 6.6 μl of 1M DTT, followed by incubation at 60°C for 15 min under 600 rpm constant shaking. Volume was adjusted with water to 400 μl and 400 μl of TriPure were added. RNA was extracted by adding 120 μl of BCP Phase Separation Reagent and precipitated with isopropanol. DNA was digested with Turbo DNase-I at 37°C for 30min, RNA was re-purified using TriPure, and resuspend in modBTE buffer (10mM Bis/Tris pH=6.7, 0.1mM EDTA). For enrichment of <200nt RNAs, the Zymo RNA Clean and Concentrator-5 kit was used, starting from 1ug of total RNA. For enrichment of <50nt RNAs, 18ug of total RNA were run on a denaturing 12% polyacrylamide-urea gel, and bands between 10nt and 50nt were excised. Gel pieces were shredded trough pierced 0.5ml tubes, and RNA was elute from the gel by overnight incubation in 400μl RNA elution buffer (10mM Bis/Tris pH=6.7, 300mM NaCl, 10mM EDTA) at 4°C with constant rotation. Eluate was filtered though 5μm PVDF spin filters, and RNA was precipitated by adding 1μl of Glycoblue, 40μl of 3M NaOAc pH=5.2, and 1.1ml of ice-cold 100% EtOH, followed by incubation at -80°C for 1h. RNA was pelleted at 20000g for 30min (4°C), washed once with 1ml of 70% EtOH, once with 1ml of 80% EtOH, air-dried for 5 min, and resuspended in modBTE buffer.
LIDAR and LIDAR-3 library preparation  The desired amount of total and fractionated RNAs was diluted to 1μl and mixed with 0.4μl of 10μM LIDAR_RT_primer (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNND). To anneal the LIDAR_RT_primer to the template RNA, samples were heated to 65°C for 5 min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix [25mM Tris-HCl pH=8.3, 20mM NaCl, 2.5mM MgCl2, 8mM DTT, 5% PEG-8000, 0.5mM dNTPs, 1mM GTP, 0.5 U/μl Murine RNase inhibitor, and 2U/μl Maxima H-minus Reverse Transcriptase – concentrations refer to a final volume of 8 μl] were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix (equimolar ratio of the following oligos: /5Biosg/CGTCAGATGTGTATAAGAGACAGtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhmtgNNcgNNagNNrGrGrG) were added, and samples were incubated at 42°C for 80 min, followed by 10 cycles at 50°C for 2 min and 42°C for 2 min, then at 85°C for 5 min. To pre-amplify and add adapters to cDNA, 12μl of KAPA_mix [1X KAPA HiFi HotStart buffer Ready Mix, 0.5μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.1μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl]  were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 18 cycles of amplification (98°C for 20s, 70°C for 30s, 72°C for 30s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 0.5μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase (Cat. No M0491, New England Biolabs) – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 18 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 2 min). Indexed libraries were purified using 2.3X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).  For LIDAR-3, the LIDAR-3_RT_oligo was generated by mixing equimolar amounts of LIDAR-3_RT_sense (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNNN) and LIDAR-3_RT_antisense (CdUGdUCdUCdUdUAdUACACAdUCdUCCGAG/3ddC/), followed by heating at 95°C for 5 min, and a slow cool down to 25°C (0.1°C/s). To prepare LIDARsp libraries, 1μl of input RNA was first denatured at 70°C for 2 min, then temperature was lowered to 50°C and 0.4μl of 1μM LIDAR-3_RT_oligo were added. Samples were incubated at 50°C for further 2min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix were added, and samples were incubated at 50°C for 80 min, followed by 10 cycles at 55°C for 2 min and 50°C for 2 min, then at 85°C for 5 min. LIDAR-3_RT_antisense was digested by adding 1ul of USER II enzyme and incubating at 37°C for 30 min. USER II was heat inactivated by incubation at 65°C for 10 min. To pre-amplify and add adapters to cDNA, 12μl of KAPAsp_mix [1X KAPA HiFi HotStart buffer Ready Mix, 2μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.5μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl] were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 6 cycles of 3-step amplification (98°C for 20s, 63°C for 30s, 72°C for 30s), 12 cycles of 2-step amplification (98°C for 20s, 72°C for 50s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 1μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5sp_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 7 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 5 min). Indexed libraries were purified using 2.4X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).   Small RNA-seq and mRNA-seq library preparation  Small RNA libraries were prepared using the NEBnext Small RNA Library Prep Set for Illumina (Cat. No E7330S, New England Biolabs), following the standard protocol with the following parameters: 1) 1:2 dilution of 3’SR Adaptor, SR RT Primer, and 5’SR Adaptor 2) 15 indexing PCR cycles 3) cleanup of final libraries with QIAgen MinElute PCR purification kit, followed by a second cleanup with 2X SPRI. Libraries were analyzed on a 6% non-denaturing polyacrylamide gel.  For mRNA-seq libraries, polyA RNA was enriched from 2 μg total RNA using Dynabeads Oligo(dT)25. Poly-A-enriched fraction was used for library construction using the NEBnext Ultra II Directional Library Prep Kit for Illumina (Cat. No. E7760L, New England Biolabs), following the standard protocol but using half the reaction volumes recommended. Libraries were analyzed on a 2% agarose gel.  Both small RNA-seq and mRNA-seq libraries were quantified using NEBNext Library Quant Kit for Illumina (Cat. No E7630L, New England Biolabs). Libraries were sequenced on an Illumina NextSeq500 instrument.

treatment_protocol: C57BL/6 mouse embryonic stem cells (ESC) were purchased from ATCC (SCRC-1002) and maintained onto 1% gelatin-coated dishes in DMEM knockout medium supplemented with 15% ES-grade Fetal Bovine Serum, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin solution, 110μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. Cells were passaged through trypsinization (0.05%) every 2–3 days. Prior to neuronal progenitor cells (NPC) differentiation, embryonic stem cells that were maintained in N2B27 serum-free medium consisting of 1:1 mix of Neurobasal medium and DMEM/F12, supplemented with 1X N2, 1X B27, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin, 55μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. For NPC differentiation differentiation, Epiblast-like cells (EpiLC) were induced from ESC in N2B27 serum-free medium (without 2i and LIF) supplemented with 40μg/ml of BSA, and 10ng/ml bFGF for 72h. EpiLC were treated with 500nM SAG in N2B27 serum-free medium (without 2i and LIF) for 48h to generate NPC.

value: cells

tag: cell line

value: NPC

tag: input amount_(ng)


title: LIDAR, total, NPC, b1

description:
counts.genes.txt
counts.biotypes.txt


title: WT BM-MSCs-2, Day 7 [1461WT_7d_S30]

value: WT

value: Day 7


title: 4h_control (3a)

city: Liberec

first: Alena

last: Sevcu

state: Liberec

address: Bendlova 1409/7

department: Applied Biology

country: Czech Republic

institute: Technical University of Liberec

description:
development stage: cell culture on mid-log phase
T4neg3_L1

data_processing:
Approximately five million 2 × 79-bp paired end reads were generated respectively from each library by the means of Illumina sequencing on a NextSeq 500/550 High Output v2 platform. The Illumina TruSeq adapter sequences (34 nucleotides) were then clipped by Illumina bcl2fastq2 Conversion Software v2.19.1 using standard parameters.
The FASTQ files were first trimmed (minimum quality 3, minimum read length to be kept 36 bp) using the Trimmomatic tool (http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014). The processed sequence reads were then mapped to R. subcapitata ATCC 22662 reference genome (GenBank Accession number: BDRX01000001.1) (Suzuki et al., 2018) using HISAT2 (Kim et al., 2019). SAMtools (Danecek et al., 2021) was then applied to access the transcripts level in order to get quantitative assignments and to generate the BAM files.
After that, BAM files were selected for the determination of read counts and identification of differentially expressed genes (DEGs). To define the transcripts abundance, read counts for each BAM file were determined by bedtools v2.27.1 and its option multicov (Quinlan and Hall, 2010). The established read count table was then imported into idep 1.0 (Ge et al., 2018). Then, the gene expression level in counts per million (CPMs) were calculated and visualized in box and PCA plot. To identify DEGs, the BAM files were loaded and processed in R using Rsamtools package (Morgan et al., 2022).
Prior than that, gene models were imported and queried using GenomicFeatures (Lawrence et al., 2013) package and followed by using GenomicAlignments (Lawrence et al., 2013) package to create the Summarized Experiment object that contains the fragment counts for each gene and sample.
Differential gene expression for each condition was illustrated using relative log expression function of the DESEQ2 (Love et al., 2014) package and statistical analysis was through the function p.adjust in R. Venn diagrams were plotted by VennDiagram (Chen and Boutros, 2011) package. Genes showing log2(fold change) ≥ 1.5 and ≤ −1.5, and adjusted p-value less than 0.05 were considered to be significantly expressed. Furthermore, a log2(fold change) ≥ 1.5 and ≤ −1.8 cutoff was applied only to the sample T1nZVI (nZVI exposure at 1 h) versus T1neg (control at 1 h), due to high number of DEGs. Clustering and visualization of the dissimilarity matrix was achieved using ClustVis – a web tool for visualizing clustering of multivariate data (http://biit.cs.ut.ee/clustvis/) (Metsalu and Vilo, 2015) and pheatmap packages. The heatmap function was applied with default setting (Manhattan distance and average linkage were used). Principal component analysis was performed based on PCAtools package. Following the differential gene expression analysis, functional annotation and genes classification into metabolic pathway subtypes were grouped using the KEGG database (https://www.kegg.jp/kegg/) (Kanehisa and Goto, 2000) and JGI Algal Genome Portal PhycoCosm (https://phycocosm.jgi.doe.gov) (Grigoriev et al., 2021; Nordberg et al., 2014). Annotation improvement was further performed using alpha version of protein sequence observation service (PSOS) (https://psos-staging.computational.bio/) and UniProtKB database (https://www.uniprot.org/) (Bateman et al., 2022). The differentially expressed genes were then co-analyzed using protein-protein interaction (PPI) software to analyze for possible gene interactions and was performed using STRING online database version 11.5 (https://string-db.org/) (Szklarczyk et al., 2021) with k-means clustering and interaction score of (medium confidence > 0.4) as the cut off criterion. For every p-value presented in PPI analysis, the false discovery rate (FDR) was controlled using the Benjamini–Hochberg method (Benjamini and Hochberg, 1995). Construction and visualization of PPI network was performed using Cytoscape software version 3.9.1 (Shannon et al., 2003) with Cytoscape stringApp 2.0 installed in the software (Doncheva et al., 2022).
Assembly: R. subcapitata ATCC 22662 genome (GenBank Accession number: BDRX01000001.1)
Supplementary files format and content: 50 genes with the highest variance across samples (rlog transformed counts).csv Format: csv Content: rlog transformed counts of 50 highly expressed genes
Supplementary files format and content: converted_counts_data.csv Format: csv Content: counts per million of all treatment conditions
Supplementary files format and content: T1Fe versus T1neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 1-Fe treatment versus Time 1 neg. control)
Supplementary files format and content: T1nZVI versus T1Fe DESEQ.csv Format: csv Differential gene expression for each condition (Time 1- nZVI treatment versus Time 1-Fe treatment)
Supplementary files format and content: T1nZVI versusT1neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 1- nZVI treatment versus Time 1-neg. control)
Supplementary files format and content: T4 versus T1 DESEQ.csv Format: csv Differential gene expression for each condition (Time 4 versus Time 1)
Supplementary files format and content: T4Fe versus T4neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 4-Fe treatment versus Time 4-neg. control)
Supplementary files format and content: T4nZVI versus T4Fe DESEQ.csv Format: csv Differential gene expression for each condition (Time 4-nZVI treatment versus Time 4-Fe treatment )
Supplementary files format and content: T4nZVI versus T4neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 4- nZVI treatment versus Time 4- neg. control)

organism: Raphidocelis subcapitata

source_name: R. subcapitata-nanoparticle free (4 h)

growth_protocol: Raphidocelis subcapitata ATCC 22662 (formerly known as Pseudokirchneriella subcapitata) was obtained from the Culture Collection of Autotrophic Organisms (CCALA, Czech Republic) and maintained in Bold’s Basal Medium (BBM) at 24°C.

extract_protocol:
RNA isolation of microalgae R. subcapitata involved two major steps: the cell lysis and then the RNA extraction procedure. RNA was harvested from three biological replicates after 1 and 4 h from R. subcapitata exposed with nZVI and nFe3O4 respectively. Cell pellets were obtained through centrifugation at 10,000 × g, 4°C for 2 min, followed by overnight cell lyophilization and phenol-chloroform extraction method adapted from a previous work (Yeap et al., 2021). The integrity and concentration of the RNA extracts were determined with an Agilent 2100 Bioanalyzer system (Agilent Technologies, Germany) and Nanodrop (Thermo Scientific, USA) was for RNA concentration quantification. All electropherogram of ribosomal RNA peaks were computed and analyzed by 2100 Expert software (Agilent Technologies, Germany).
To prepare for whole transcriptome sequencing of the directional RNA-seq library, up to 1 µg of total RNA (RIN > 6) was used with a TruSeq® stranded mRNA Library Prep kit (Illumina Inc., USA) after capturing poly-adenylated transcripts and mRNA fragmentation. The resulting cDNA libraries were pooled and sequenced in paired-end mode (2 × 79 bp) on an Illumina NextSeq 500/550 High Output v2 platform.

treatment_protocol: For NPs experiments, R. subcapitata was cultivated in Sueoka’s high salt medium (HSM) (Sueoka, 1960), with gentle mixture of 1% CO2 and air bubbling supply under a 130 µmol photons·m−2·s−1 of constant white light illumination at room temperature (24°C). The algae in mid-log exponential phase were harvested after 48 h at an initial cell density of 1.575 × 107 cells/mL for R. subcapitata, and then added to a flask containing NPs. R. subcapitata was exposed to two different forms of activated iron NPs (100 mg/L of nZVI and nFe3O4 respectively), while NP-free condition was served as a control. Three replicates for each condition were conducted in 550 mL of HSM, starting with 45 mL of pre-grown algal culture. 15 mL of the culture was sampled every 24 h before NPs exposure (up to 48 h) and after the start of NPs exposure at 0, 1, 4 h and thereafter every 24 h up to 120 h. Cultures (35 mL) were sampled after NPs exposure at 1 and 4 h for RNA extraction. All the measurements were recorded in three technical replicates per biological sample for each time point and averaged prior to data analysis.

tag: strain

value: Strain ATCC 22662

tag: replicate

value: biol rep 3

value: negative control:R. subcapitata


title: 4h_control (2d)

description:
development stage: cell culture on mid-log phase
T4neg2_L4

value: biol rep 2


title: WT BM-MSCs-1, Day 0 [289WT_0d_S24]


title: SMK_WT_TM2_SCI_EAE-1

city: Guangzhou

first: Han

last: Gao

state: Guangdong

address: 600 Tianhe RD

country: China

institute: The Third Affiliated Hospital of Sun Yat-sen University

description:
Sample multiplexing tag
SMK_2_2-1_S1_L004

data_processing:
Sequencing reads filtering and alignment were conducted using the BD RhapsodyTM Single-Cell Analysis system.
Read pairs with low sequencing quality are removed according to read length, mean base quality score, and highest single nucleotide frequency (SNF). Then the remaining reads were aligned to the mm10 genome by calling STAR.
BD Biosciences developed UMI adjustment recursive substitution error correction (RSEC) algorithm to remove artifact molecules.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
Supplementary files format and content: Metadata for every cell

molecule: polyA RNA

source_name: spinal cord myeloid cells

extract_protocol:
Spinal cords were enzymatically dissociated into single-cell suspensions with a papain-based Neural Dissociation Kits (Miltenyi, #130-092-628). Myeloid cells were enriched by positive selection with CD11b Microbeads (Miltenyi, #130-049-601) after myelin removal using Myelin Removal Beads (Miltenyi, #130-096-433), according to manufacturer’s protocols. Different single-cell suspension samples were mixed together using BDTM Single-cell Multiplexing Kits (BD, #633793) for high sample throughput and batch effects elimination purposes.
Library preparations were performed using the BD RhapsodyTM system according to the manufacturer’s protocol.
Sequencing was conducted using Illumina Novaseq 6000 PE150

value: WT and TREM2-/-

tag: disease state

value: SCI and EAE


title: fatbody_C_TP2G_rep1

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

country: United Kingdom

institute: University of East Anglia

description: NER0008751_obj1_exp1_fatbody_all_expressed_genes.csv

data_processing:
Sequencing reads were pseudoaligned to the Bombus terrestris transcriptome using Kallisto v0.46.1 with parameter --rf-stranded
Estimated transcript counts were summarised per gene in R v4.0.1 using the tximport package v1.16.1 with parameter type="kallisto"
Differential expression analysis was conducted in R v4.0.1 using the DESeq2 package v1.28.1, with technical replicates (sequencing the same library on different lanes of the sequencing machine) collapsed using the collapseReplicates() function.
Genome_build: Bombus_terrestris.Bter_1.0.cdna.all.fa
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in brain
CSV file with normalized abundance measurements from DESeq2 for all genes expressed in fat body (Represents the 22 samples used for the final analysis, as 2 samples did not meet our threshold for the number of reads pseudoaligned to the Bombus terrestris transcriptome with Kallisto. The 2 excluded samples had large numbers of bee virus reads present.)
CSV file with normalized abundance measurements from DESeq2 for all genes expressed in ovary

organism: Bombus terrestris

source_name: fat body

growth_protocol: Bumble bee colonies were maintained under standard conditions. See the publication for further details.

extract_protocol:
Bumble bee queens were flash-frozen in liquid nitrogen and stored at -80oC. Queens were then defrosted and the brain, fat body and ovaries were dissected out, flash-frozen in liquid nitrogen, and stored at -80oC. Each sample (one tissue from a single queen) was then ground in liquid nitrogen using a micropestle with the resulting powder resuspended in Tri-reagent (Sigma-Aldrich, UK). RNA was extracted using the Direct-zolTM RNA extraction kit (Zymo Research, USA) according to the manufacturer's protocol. An additional DNase treatment was performed using TurboTM DNA-free kit (Thermo Fisher Scientific, UK), according to the manufacturer's protocol.
Illumina TruSeq stranded mRNA-seq libraries constructed by Edinburgh Genomics (Edinburgh, UK)

treatment_protocol: Egg removal (R) treatment (to increase the costs of reproduction) and an egg removal and replacement (C) treatment (to control for the effects of disturbance caused by egg removal).

value: fat body

value: control (C), eggs removed and replaced

tag: time point

value: time point 2 (TP2G), after 60% of the members of the cohort had died

tag: biological replicate


title: fatbody_R_TP1G_rep6

value: removal (R), eggs removed

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: LIDAR, total, mES_serum-free, b3

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum-free


title: 4h_control (2c)

description:
development stage: cell culture on mid-log phase
T4neg2_L3

value: algae cell culture, time:4 h


title: WTA_WT_TM2_SCI_EAE-2

description:
Single-cell transcriptome part2
WTA_2_2-1_S1_L003


title: LIDAR, total, sperm, b1

description:
counts.genes.txt
counts.biotypes.txt

source_name: mouse sperm

value: mouse sperm

value: sperm

value: below detection


title: LIDAR, total, mES_serum-free, b2

description:
counts.genes.txt
counts.biotypes.txt

value: cells


title: fatbody_R_TP1G_rep5


title: LIDAR, total, NPC, b2

description:
counts.genes.txt
counts.biotypes.txt

value: NPC


title: 4h_control (2b)

description:
development stage: cell culture on mid-log phase
T4neg2_L2

value: Strain ATCC 22662


title: WTA_WT_TM2_SCI_EAE-1

description:
Single-cell transcriptome part1
WTA_2_2-2_S1_L004


title: LIDAR, total, mES_serum-free, b1

description:
counts.genes.txt
counts.biotypes.txt


title: fatbody_R_TP1G_rep4


title: 4h_control (1d)

description:
development stage: cell culture on mid-log phase
T4neg1_L4

value: biol rep 1

value: negative control:R. subcapitata


title: LIDAR, total, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum


title: LIDAR, total, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: 4h_control (2a)

description:
development stage: cell culture on mid-log phase
T4neg2_L1

value: biol rep 2


title: WTA_WT_TM2_NA

description:
Single-cell transcriptome
WTA_Naive4-1_S1_L004

value: WT and TREM2-/-

value: Nave


title: LIDAR, total, mES_serum, b1

description:
counts.genes.txt
counts.biotypes.txt


title: 4h_control (1c)

description:
development stage: cell culture on mid-log phase
T4neg1_L3


title: fatbody_R_TP1G_rep2

value: fat body


title: fatbody_R_TP1G_rep1

value: removal (R), eggs removed


title: 4h_control (1b)

description:
development stage: cell culture on mid-log phase
T4neg1_L2


title: Two-cell embryo, MYC_inhibited_rep1

city: KYOTO-SHI

first: Takuto

last: Yamamoto

state: (None)

address: Faculty of Agriculture main Bldg., Oiwake-tyo, Saikyo-ku

country: Japan

institute: Kyoto University

data_processing:
The sequencing reads were mapped to the mouse genome (mm10) using STAR aligner software (v2.7.10.a). The mapped reads were fed to RSEM (v1.3.3) to calculate the expression levels.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample generated by RSEM (v1.3.3).

source_name: Embryo

growth_protocol: mouse late two-cell stage embryos were in vitro produced by in vitro fertilization (IVF) and further cultured in KSOM up to 36 h post-insemination (hpi).

extract_protocol: RNA-seq library was generated from ten late two-cell embryos cultured in the DMSO-control and MYC-inhibited (10074-G5-treated) groups, respectively, by using SMART-Seq v4 PLUS Kit (Takara Bio USA) according to the manufacturer’s manual.

treatment_protocol: The culture was chemically semi-defined (bovine serum albumin was added). The one-cell stage embryos at 3 hpi were allocated to DMSO (a vehicle of 10074-G5) or MYC-inhibited (6 µM 10074-G5) groups and further cultured up to late two-cell stage (36 hpi).

value: Embryo

value: ICR

tag: developmental stage

value: two-cell embryo

tag: growth protocol

value: in vitro produced

value: inhibitor (10074-G5) treated from the one-cell stage


title: fatbody_C_TP1G_rep6

value: control (C), eggs removed and replaced

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: Two-cell embryo, MYC_inhibited_rep2


title: Two-cell embryo, DMSO_Control_rep2

value: vehicle treated from the one-cell stage


title: 4h_control (1a)

description:
development stage: cell culture on mid-log phase
T4neg1_L1

value: Strain ATCC 22662

value: algae cell culture, time:4 h


title: ConA72

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The FASTQ files and data processing were performed using 10x genomics CellRanger pipeline (version 6.0.0). Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A).
Seurat package (version 4.0) was used to further analyze single cell RNAseq data.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver Macrophages

extract_protocol:
The liver samples were homogenized with a gentleMACS Dissociator (Miltenyi), filtered through 70-μm cell strainers, and then centrifuged through a Percoll density gradient (40% and 70%), immune cells were collected and further sorted with BD FACSMelody to isolate CD45+ CD11b+ Ccr2+ Ly6G- liver MoMFs.   The sorted MoMFs from mouse livers were washed twice with PBS. The cell concentration and viability were assessed using the LUNA-FL Dual fluorescence cell counter (Logos Biosystems). The sorted MoMFs were loaded in the lanes according to the 10X Genomics 3’ Single Cell User Guide with a single capture lane per sample targeting recovery of 6,000 cells per lane. Cell partitioning completed successfully with uniform emulsion consistency and the reverse transcription PCR was run overnight.
All subsequent steps of library preparation and quality control were performed using 10X Chromium Next GEM Single Cell 3' Kit according to the manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 500.

value: Liver Macrophages

value: WT B6

value: ConA 72h


title: fatbody_C_TP1G_rep5


title: ConA48

description: 10x Genomics

value: ConA 48h


title: 1h_nZVI (3d)

description:
development stage: cell culture on mid-log phase
T1nZVI3_L4

source_name: R. subcapitata exposed to 100 mg/L nZVI (1 h)

value: biol rep 3

value: algae cell culture, time:1 h

value: R. subcapitata + nZVI


title: SMK_WT_TM2_NA

description:
Sample multiplexing tag
SMK_Naive4-1_S1_L002

value: WT and TREM2-/-

value: Nave


title: fatbody_R_TP1G_rep3

value: fat body

value: removal (R), eggs removed


title: Two-cell embryo, DMSO_Control_rep1

value: Embryo

value: ICR

value: two-cell embryo

value: in vitro produced


title: fatbody_C_TP1G_rep4

value: control (C), eggs removed and replaced

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: NAÏVE

description: 10x Genomics

value: Liver Macrophages

value: Control


title: PDO_rep3

city: Harbin

first: Miao

last: Liu

address: College of Life Sciences, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District,

institute: Northeast Forestry University

data_processing:
RNA concentration of library was measured using Qubit® RNA Assay Kit in  Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed  using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and  qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR  System (Library valid concentration＞10 nM).
The clustering of the index-coded samples was performed on a cBot cluster  generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the  manufacturer’s instructions. After cluster generation, the libraries were sequenced on  an Illumina platform and 150 bp paired-end reads were generated.
The reference genomes and the annotation file were downloaded from ENSEMBL  database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the  genome index, and Clean Data was then aligned to the reference genome using HISAT2  v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to  convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM  (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the  expression level of genes in each sample. the formula is shown as：FPKM=F*106/NL/103  F is the number of fragments in a certain sample that is assigned to a certain gene, N is  the total number of mapped reads in the certain sample and L is the length of the certain  gene.
Genome_build: http://www.ensembl.org/index.html
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: pancreatic duct organoids

growth_protocol: Mouse extrahepatic bile duct and pancreatic duct were obtained from C57BL/6 mouse by direct dissection under a dissecting microscope, and then were digested at 37 ℃ with collagenase IV for 20 min after mechanical mincing, washed and centrifuged to resuspend the cells in Matrigel , and 600 μL mouse expansion media was added to 24 wells. All cells were cultured in a humidified incubator with 95% air and 5% CO2 at 37°C. The main components of mouse expansion media included D/F12 basal media, 1% Glutamax, 1% penicillin-streptomycin , 2% B27 Supplement (minus VA), 30% Wnt3A condition media, 1 mM N-acetylcysteine , 50 ng/mL EGF , 100 ng/mL R-Spondin-1, 25 ng/mL Noggin , 100 ng/mL FGF10 , 10 mM Nicotinamide and 10 μM Y27632. When the luminal organoid obtained, the culture media was changed into mouse expansion mediawithout Wnt3A and Y27632.

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in  NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was  synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis  was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The  library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then  terminal repair,A-tailing and adapter added were implemented. The aimed products were  retrieved and PCR was performed, then the library was completed.

treatment_protocol: The extrahepatic bile duct and pancreatic duct epithelia obtained by separation and digestion were directly resuspended in Trizol, and the organoids used for sequencing and their replicates were cultured for 3-4 passages.

value: pancreatic duct


title: 1h_nZVI (3c)

description:
development stage: cell culture on mid-log phase
T1nZVI3_L3

value: Strain ATCC 22662


title: PDO_rep2


title: WT, Input, r3, RIP-seq

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were aligned to mouse genome and transcriptome (mm10, version M19, 2018-08-30) using HISAT (version 2.1.0).
Reads on each GENCODE annotated gene were counted using HTSeq and then differentially expressed genes were called using DESeq2 package
YTHDF2 target genes were identified as differentially up-regulated genes comparing YTHDF2 IP sample with the corresponding Input samples
Assembly: mm10
Supplementary files format and content: text files include read counts for each Sample

source_name: B16F10 tumors

growth_protocol: 3×105 B16F10 tumor cells in 100 μL DPBS were injected subcutaneously into the flank

extract_protocol:
Tumors were harvested and minced into small pieces. Tumor tissue was submerged in RPMI with 10 U/mL DNase I (Thermo Fisher Scientific, EN0521) and 1 mg/ml collagenase IV (Gibco, 17104019) and digested at 37 °C for 1 hour. The suspension was filtered through a 70-mm cell strainer. Red blood cells were lysed with ACK Lysing Buffer (Gibco, A1049201) and resuspended in FACS buffer (DPBS with 2% FBS). Tumor-infiltrating lymphocytes were enriched by CD4 (TIL) Microbeads (Miltenyi Biotec, 130-116-475).  Enriched lymphocytes were stained DAPI, CD45, and CD4. Live CD45+CD4+GFP+ Treg cells were sorted at 4 °C into into lysis buffer (50 mM HEPES, 150 mM KCl, 2 mM EDTA, 0.5% NP40, 0.5 mM DTT, protease inhibitor (Roche), and SUPERase·In RNase Inhibitor (Thermo Fisher Scientific, AM2696) and placed on ice for 30 minutes. 20 mL Protein A Dynabeads (Thermo Fisher Scientific, 10008D) were washed with lysis buffer and incubated with 2 mg anti-YTHDF2 for 30 minutes at 4 °C. Beads were washed twice with lysis buffer. Cell lysis was centrifuged at 20,000 × g for 15 minutes. 10% of the lysis was stored in Trizol as the input, and the rest was added to bead-antibody conjugates to rotate at 4 °C for 4 hours. After incubation, beads were washed with NT2 buffer (50mM HEPES, 200mM NaCl, 2mM EDTA, 0.05% NP40, 0.5mM DTT, protease inhibitor, and RNase inhibitor) 6 times and resuspended in Trizol. RNAs were isolated by chloroform and precipitated by isopropanol following the manufacturer’s protocol. Genomic DNA was removed by DNase I and purified by RNA Clean & Concentrator.
RNA libraries were constructed with the SMARTer Stranded Total RNA-Seq Kit v2 (Takara, 634412).

value: B16F10 tumors

value: CD45+ CD4+Foxp3-GFP+ Treg cells

value: WT

tag: rip antibody


title: fatbody_C_TP1G_rep3


title: WT, Input, r2, RIP-seq


title: fatbody_C_TP1G_rep2


title: WT, Input, r1, RIP-seq


title: 1h_nZVI (3a)

description:
development stage: cell culture on mid-log phase
T1nZVI3_L1

value: biol rep 3

value: algae cell culture, time:1 h

value: R. subcapitata + nZVI


title: fatbody_C_TP1G_rep1

value: fat body


title: PDO_rep1


title: 1h_nZVI (2d)

description:
development stage: cell culture on mid-log phase
T1nZVI2_L4

value: biol rep 2


title: brain_R_TP2G_rep5

description: NER0008751_obj1_exp1_brain_all_expressed_genes.csv

source_name: brain

value: brain

value: removal (R), eggs removed

value: time point 2 (TP2G), after 60% of the members of the cohort had died


title: 1h_nZVI (2c)

description:
development stage: cell culture on mid-log phase
T1nZVI2_L3


title: BDO_rep3

source_name: extrahepatic bile duct organoids

value: extrahepatic bile duct


title: WT, YTHDF2 IP, r2, RIP-seq

value: anti-mouse YTHDF2 antibody (Aviva Systems Biology, ARP67917_P050)


title: BDO_rep2


title: WT, YTHDF2 IP, r3, RIP-seq


title: brain_R_TP2G_rep4


title: 1h_nZVI (2b)

description:
development stage: cell culture on mid-log phase
T1nZVI2_L2


title: YoGI_261 before_drought_stress

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

institute: Centre for Novel Agricultural Products, University of York

description: Column B_YoGI_261 in processed files

data_processing:
After sequencing, quality control was carried out using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw reads were then filtered by trimming low quality sequences (average Phred score < 15), trimming short length reads (<36bp), and clipping Illumina adapters using Trimmomatic v0.39
Salmon was used to map reads to the Triticum aestivum reference genome v1.1  (IWGSC RefSeq v1.1). Salmon’s mapping-based mode was used to create an index from the reference genome, and then for quantification of the trimmed reads. Salmon output files were prepared for differential expression analysis using the R package TxImport, generating a table containing transcript abundance, counts, and length from the Salmon quantification files
Assembly: IWGSC V1.1 reference (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies)
Supplementary files format and content: Salmon output

organism: Triticum aestivum

source_name: Leaves

growth_protocol: Seeds fo the 14 wheat landraces were sown in Levington Advance Seed & Modular F2S compost mixed with Aggregate Industries Garside Sands 16/30 sand (80:20 ratio). The pots were treated with CaLypso insecticide (Bayer CropScience Ltd., 0.083ml mixed with 100ml water, applied to each litre of compost) and grown under long day (16/8h, 20°C/14°C) glasshouse conditions.

extract_protocol:
Each RNA extraction consisted in 6cm of leaf tissue. The before treatment were the wheat seedlings upon reaching GS13 whilst the after treatment was collected at the end of the drought period (13 days after GS13, 10 days draught stress+3 days recovery). Tissue was collected individually for each sample, and immediately immersed in liquid nitrogen to prevent nucleic acid degradation. Tissue samples were stored at -80°c for later processing. Total RNA was extracted from <100 mg of individual leaf tissue samples using the E.Z.N.A Plant RNA Kit (Omega Bio-Tek, GA, USA) including a DNase treatment, according to the manufacturer’s protocol.RNA was measured using NanoDrop ND-1000 Spectrophotometer (Thermo-Fisher Scientific, MA, USA) and a Qubit 4 Fluorometer (Life Technologies, CA, USA) whilst the quality was assessed by running 2 μl of sample on an Agilent Technology 2100 Bioanalyzer and only keeping samples with RIN>7. Replicates (4 plants) were pooled into 1 sample per landrace per treatment at equimolar proportions.
The library was obtained using TruSeq Stranded mRNA (Illumina). The mRNA was purified using poly-T oligo attached magnetic beads, fragmented and the first strand cDNA synthesized using random hexamer primers, whilst the second strand cDNA using dUTP for directional library. End-repair, A-tailing, adapter ligation, size selection,USER enzyme digestion to remove the UTP-containing second strand cDNA, PCR amplification and purification
TruSeq stranded mRNA run in the Illumina Novaseq 6000 platform (Illumina, CA, USA) with an 150bp paired-end sequencing strategy

treatment_protocol: Four plants of each accession were watered normally to maintain soil moisture, until they reached GS13 (Zadok’s growth scale) whereby stress was applied by withholding water for a ten-day period. Normal watering then resumed for three-days to serve as a recovery period. The negative control consisted in four replicates of each accession growing at the same time but not being exposed to drought stress. Plants were harvested 13 days after GS13.

value: Leaves

value: YoGI_261=Watkins collection accession identifier 1190705


title: brain_R_TP2G_rep3


title: brain_R_TP2G_rep1


title: WT, YTHDF2 IP, r1, RIP-seq


title: 1h_nZVI (2a)

description:
development stage: cell culture on mid-log phase
T1nZVI2_L1


title: 1h_nZVI (3b)

description:
development stage: cell culture on mid-log phase
T1nZVI3_L2


title: PD

source_name: pancreatic duct epithelia

value: pancreatic duct


title: brain_C_TP2G_rep4

value: control (C), eggs removed and replaced


title: BDO_rep1


title: PE-hip-2

first: Wen-Long

last: Zhao

address: Guangyuan road 145#

institute: The International Peace Maternity and Child Health Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Hippocampus

extract_protocol:
adult hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus offspring from preeclampsia mother mice

tag: Sex

value: male

value: adult


title: PE-hip-3

tag: tissue


title: brain_C_TP2G_rep3


title: YoGI_164 before_drought_stress

description: Column B_YoGI_164 in processed files

value: YoGI_164=Watkins collection accession identifier 1190305


title: 1h_nZVI (1d)

description:
development stage: cell culture on mid-log phase
T1nZVI1_L4

value: Strain ATCC 22662

value: biol rep 1

tag: cell type

value: algae cell culture, time:1 h


title: brain_R_TP2G_rep2


title: 1h_nZVI (1c)

description:
development stage: cell culture on mid-log phase
T1nZVI1_L3

value: R. subcapitata + nZVI


title: 1h_nZVI (1a)

description:
development stage: cell culture on mid-log phase
T1nZVI1_L1


title: PE-hip-4


title: Control-hip-4

value: Hippocampus offspring from control mother mice


title: brain_C_TP2G_rep6

value: brain


title: ovary_C_TP1G_rep5

description: NER0008751_obj1_exp1_ovary_all_expressed_genes.csv

source_name: ovary

value: ovary

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: 1h_nZVI (1b)

description:
development stage: cell culture on mid-log phase
T1nZVI1_L2


title: WT-Y- primary BM stromal cells-1 [CITE-seq, HTO]

library_source: other

molecule: protein

source_name: bone marrow and bone (10-month-old mouse)

value: BM lin-CD31-CD71- cells

tag: genotype

value: WT

value: HTO

tag: antibodies/tags

value: CD45/H-2; BM lin-CD31-CD71- cells; 9p21+/- -Y-primary BM stromal cells-1 --/8526het_mutant


title: 1h_nFe3O4 (3d)

description:
development stage: cell culture on mid-log phase
T1Fe3_L4

source_name: R. subcapitata exposed to 100 mg/L nFe3O4  (1 h)

value: biol rep 3

tag: treatment

value: R. subcapitata + nFe3O4


title: BD

source_name: extrahepatic bile duct epithelia

value: extrahepatic bile duct


title: YoGI_059 before_drought_stress

description: Column B_YoGI_059 in processed files

value: Leaves

value: YoGI_059=CIMMYT collection accession identifier CWI 15005


title: YoGI_026 before_drought_stress

description: Column B_YoGI_026 in processed files

value: YoGI_026=CIMMYT collection accession identifier CWI 6118


title: YoGI_047 before_drought_stress

description: Column B_YoGI_047 in processed files

value: YoGI_047=CIMMYT collection accession identifier CWI 13432


title: PE-hip-1

value: Hippocampus offspring from preeclampsia mother mice

value: male

value: adult


title: YoGI_153 before_drought_stress

description: Column B_YoGI_153 in processed files

value: YoGI_153=Watkins collection accession identifier 1190254


title: YoGI_021 before_drought_stress

description: Column B_YoGI_021 in processed files

value: YoGI_021=CIMMYT collection accession identifier CWI 6075


title: YoGI_145 before_drought_stress

description: Column B_YoGI_145 in processed files

value: YoGI_145=Watkins collection accession identifier 1190224


title: brain_C_TP2G_rep2

value: brain

value: control (C), eggs removed and replaced

value: time point 2 (TP2G), after 60% of the members of the cohort had died


title: 1h_nFe3O4 (3c)

description:
development stage: cell culture on mid-log phase
T1Fe3_L3

value: Strain ATCC 22662

value: algae cell culture, time:1 h


title: 1h_nFe3O4 (3b)

description:
development stage: cell culture on mid-log phase
T1Fe3_L2

value: biol rep 3

value: R. subcapitata + nFe3O4


title: Control-hip-1

value: Hippocampus offspring from control mother mice


title: brain_C_TP2G_rep1


title: YoGI_161 before_drought_stress

description: Column B_YoGI_161 in processed files

value: Leaves

value: YoGI_161=Watkins collection accession identifier 1190292


title: 1h_nFe3O4 (3a)

description:
development stage: cell culture on mid-log phase
T1Fe3_L1


title: Control-hip-3


title: ovary_C_TP1G_rep2

value: ovary

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: Control-hip-2

value: male


title: 1h_nFe3O4 (2d)

description:
development stage: cell culture on mid-log phase
T1Fe2_L4

value: biol rep 2


title: 1h_nFe3O4 (2c)

description:
development stage: cell culture on mid-log phase
T1Fe2_L3


title: YoGI_017 before_drought_stress

description: Column B_YoGI_017 in processed files

value: YoGI_017=CIMMYT collection accession identifier CWI 3924


title: brain_R_TP1G_rep5

value: removal (R), eggs removed


title: brain_R_TP1G_rep4


title: YoGI_018 before_drought_stress

description: Column B_YoGI_018 in processed files

value: YoGI_018=CIMMYT collection accession identifier CWI 3926


title: YoGI_010 before_drought_stress

description: Column B_YoGI_010 in processed files

value: YoGI_010=CIMMYT collection accession identifier CWI 2165


title: brain_R_TP1G_rep6

value: brain


title: brain_R_TP1G_rep3


title: PE-cortex-1

source_name: Cortex

extract_protocol:
E17.5 cortexes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cortex offspring from preeclampsia mother mice

tag: devolopmental stage

value: fetus at E17.5 stage


title: 1h_nFe3O4 (2b)

description:
development stage: cell culture on mid-log phase
T1Fe2_L2

value: Strain ATCC 22662

value: algae cell culture, time:1 h


title: PE-cortex-3


title: PE-cortex-2


title: 1h_nFe3O4 (2a)

description:
development stage: cell culture on mid-log phase
T1Fe2_L1

value: R. subcapitata + nFe3O4


title: 1h_nFe3O4 (1b)

description:
development stage: cell culture on mid-log phase
T1Fe1_L2

value: biol rep 1


title: YoGI_002 before_drought_stress

description: Column B_YoGI_002 in processed files

value: Leaves

value: YoGI_002=CIMMYT collection accession identifier BW 7112


title: brain_R_TP1G_rep2

description: NER0008751_obj1_exp1_brain_all_expressed_genes.csv


title: YoGI_164 after_drought_stress

description: Column A_YoGI_164 in processed files

value: YoGI_164=Watkins collection accession identifier 1190305

value: drought


title: 1h_nFe3O4 (1c)

description:
development stage: cell culture on mid-log phase
T1Fe1_L3


title: Control-cortex-2

value: Cortex offspring from control mother mice


title: PE-cortex-4


title: brain_C_TP1G_rep6

value: control (C), eggs removed and replaced

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: brain_R_TP1G_rep1

value: removal (R), eggs removed


title: YoGI_261 after_drought_stress

description: Column A_YoGI_261 in processed files

value: YoGI_261=Watkins collection accession identifier 1190705


title: YoGI_007 before_drought_stress

description: Column B_YoGI_007 in processed files

value: YoGI_007=CIMMYT collection accession identifier BW 19498


title: Control-cortex-3


title: brain_C_TP1G_rep2

value: brain


title: brain_C_TP1G_rep4


title: 1h_nFe3O4 (1a)

description:
development stage: cell culture on mid-log phase
T1Fe1_L1


title: Control-cortex-1


title: 1h_control (3b)

description:
development stage: cell culture on mid-log phase
T1neg3_L2

source_name: R. subcapitata-nanoparticle free (1 h)

value: biol rep 3

value: negative control:R. subcapitata


title: 1h_control (3d)

description:
development stage: cell culture on mid-log phase
T1neg3_L4

value: Strain ATCC 22662


title: brain_C_TP1G_rep5


title: 1h_control (3c)

description:
development stage: cell culture on mid-log phase
T1neg3_L3

value: algae cell culture, time:1 h


title: brain_C_TP1G_rep1


title: HM3A

city: hefei

first: linlin

last: yan

state: anhui

address: No. 96, Jinzhai Road

institute: University of Science and Technology of China

data_processing:
SOAPnuke v1.5.2 software for reads filtration, Remove low-quality reads that containing joints, with unknown base N content greater than 5%,
The clean reads were mapped reference genome using HISAT2 v2.0.4
Bowtie2 v2.2.5 was used  to align Clean reads to the reference gene sequence
RSEM v1.2.8 was used to calculate the gene expression level of each sample
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include expression and FPKM values for each Sample

organism: Homo

source_name: Breast cancer

growth_protocol: The MCF-7 cell were cultured in 6-well palte for 48 hours

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: The MCF-7 cells were cultured with the CM derived from normoxia cells or hypoxia cells for 48 hours

value: Breast cancer

tag: cell line

value: Breast cancer cells

value: Cultured with hypoxia CM


title: blastocyst_Ribo-seq_rep1

city: Beijing

first: Wei

last: Xie

address: Zhongguancun street, Haidian

department: THU-PKU Center for Life Sciences

institute: Tsinghua University

description: Ribosome protected fragment

data_processing:
RNA-seq data of blastocyst was first trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1 based on the annotation of mm9 from UCSC genome browser.
Ribo-seq data was first trimmed with cutadapt v1.14 and the trimmed reads were mapped to mouse rRNAs sequences (mm9) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region, defined by mm9 refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: Gene expression table for RNA-seq and Ribo-seq data
Library strategy: Ribo-seq

source_name: Preimplantation embryo

extract_protocol: After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer. Samples were lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo DNase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8554G).

treatment_protocol: Blastocyst embryos were collected from 4-week-old C57BL/6J female mice that were mated with PWK/PhJ males. Embryos were collected at the 8-cell stage and cultured to blastocysts in vitro in KSOM medium (Millipore, MR-121-D). The blastocyst embryos were collected in the M2 medium (Sigma, M7167) and the zona pellucida was gently removed by treatment with acidic Tyrode’s solution (Sigma, T1788).

value: C57BL/6N x PWK

value: WT

value: untreated


title: 1h_nFe3O4 (1d)

description:
development stage: cell culture on mid-log phase
T1Fe1_L4

value: biol rep 1

value: R. subcapitata + nFe3O4


title: blastocyst_RNA-seq_rep2

data_processing:
RNA-seq data of blastocyst was first trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1 based on the annotation of mm9 from UCSC genome browser.
Ribo-seq data was first trimmed with cutadapt v1.14 and the trimmed reads were mapped to mouse rRNAs sequences (mm9) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region, defined by mm9 refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: Gene expression table for RNA-seq and Ribo-seq data

extract_protocol: After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer. RNA-Seq libraries were prepared using Smart-Seq2 protocol as described previously.


title: HM2A


title: YoGI_059 after_drought_stress

description: Column A_YoGI_059 in processed files

value: Leaves

value: YoGI_059=CIMMYT collection accession identifier CWI 15005

value: drought


title: brain_C_TP1G_rep3

value: control (C), eggs removed and replaced

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: YoGI_153 after_drought_stress

description: Column A_YoGI_153 in processed files

value: YoGI_153=Watkins collection accession identifier 1190254


title: HM1A


title: blastocyst_RNA-seq_rep1


title: 1h_control (2d)

description:
development stage: cell culture on mid-log phase
T1neg2_L4

value: biol rep 2

value: negative control:R. subcapitata


title: YoGI_026 after_drought_stress

description: Column A_YoGI_026 in processed files

value: YoGI_026=CIMMYT collection accession identifier CWI 6118


title: YoGI_145 after_drought_stress

description: Column A_YoGI_145 in processed files

value: YoGI_145=Watkins collection accession identifier 1190224


title: blastocyst_Ribo-seq_rep2

description: Ribosome protected fragment


title: 1h_control (2c)

description:
development stage: cell culture on mid-log phase
T1neg2_L3

value: Strain ATCC 22662

value: algae cell culture, time:1 h


title: Juvenille Danio rerio 2

city: Muttenz

first: Armin

middle: K.

last: Zenker

state: Baselland

address: Hofackerstrasse 30

department: School of Life Sciences - Institute for Ecopreneurship

country: Switzerland

institute: University of Applied Sciences and Arts Northwestern Switzerland

data_processing:
All data analyses steps were carried out using the Galaxy server (usegalaxy.org) (Jalili et al., 2020). Data from transcript sequencing was mapped to the GRCz11 reference genome (GCA_000002035.4) using HISAT2 (Galaxy Version 2.1.0+galaxy4) (Kim et al., 2019).
Transcripts were assembled and merged from the mapped reads with StringTie (Galaxy Version 1.3.4) (Pertea et al., 2015).
After determining gene expression with featureCount (Galaxy Version 1.6.3+galaxy2), the NGS data was normalised and differential gene expression analysis of juvenile, male and female zebrafish was carried out using DESeq2 (Galaxy Version 2.11.40.2) (Love et al., 2014; King et al., 2020). Normalisation was based on the ‘median of ratios’ - the counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene, to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data, genes expressed at juvenile-stage (28dpf) which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish.
Assembly: StringTie (Galaxy Version 1.3.4) (Pertea et al., 2015).
Supplementary files format and content: Tables of gene expression

organism: Danio rerio

source_name: Whole body

growth_protocol: NGS data was collected from 28-day-old and adult zebrafish, which had already been euthanised with Tricaine by the breeder.

extract_protocol:
RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin (Life Sciences Training Facility (LSTF), Basel), according to Illumina’s standard protocol for RNA sequencing (Illumina Inc., San Diego, USA, Cat. # RS-100-0801).
Galaxy server (usegalaxy.org)

treatment_protocol: No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly, animal welfare guidelines were followed while zebrafish were kept by the breeder.

value: Whole body

value: Juvenille


title: YoGI_021 after_drought_stress

description: Column A_YoGI_021 in processed files

value: YoGI_021=CIMMYT collection accession identifier CWI 6075


title: Juvenille Danio rerio 1


title: 1h_control (2b)

description:
development stage: cell culture on mid-log phase
T1neg2_L2


title: NM2A

value: Breast cancer

value: Breast cancer cells

value: Cultured with normoxia CM


title: YoGI_018 after_drought_stress

description: Column A_YoGI_018 in processed files

value: Leaves

value: YoGI_018=CIMMYT collection accession identifier CWI 3926


title: 1h_control (1d)

description:
development stage: cell culture on mid-log phase
T1neg1_L4

value: biol rep 1


title: 1h_control (2a)

description:
development stage: cell culture on mid-log phase
T1neg2_L1


title: Adult female Danio rerio 2

value: female

value: Adult


title: YoGI_017 after_drought_stress

description: Column A_YoGI_017 in processed files

value: YoGI_017=CIMMYT collection accession identifier CWI 3924

value: drought


title: NM1A


title: YoGI_047 after_drought_stress

description: Column A_YoGI_047 in processed files

value: YoGI_047=CIMMYT collection accession identifier CWI 13432


title: YoGI_010 after_drought_stress

description: Column A_YoGI_010 in processed files

value: YoGI_010=CIMMYT collection accession identifier CWI 2165


title: ChIP-seq of Plasmodium berghei hepatic merozoites: input

city: San Antonio

first: Evelien

middle: M

last: Bunnik

state: TX

address: 7703 Floyd Curl Dr.

department: Microbiology, Immunology, and Molecular Genetics

institute: University of Texas Health Science Center at San Antonio

description: Pb input

library_source: genomic

data_processing:
Paired-end data generated for histone PTM ChIP-seq was treated as single-end data so that all ChIP-seq data could be processed in the same way, and only read one was processed for analysis. Following quality assessment of the reads using FastQC (v0.11.8) (reads with a quality score ³ 30 were retained), adaptor sequences were trimmed using Trim-galore (v0.5.0). ChIP-seq data were mapped to the P. falciparum 3D7 genome v3.0, release 44 or the P. berghei ANKA genome v3.0, release 49 with Bowtie2 (v2.3.5). Reads were filtered with SAMtools (v1.9) to remove sequences that aligned to the genome more than once (option -q 10) and duplicates were removed using markduplicates from Picard (v2.18.29-SNAPSHOT). Using bamCompare from the deeptools suite (v3.2.0), log2(ChIP/input) bigwig files with reads extended to 150 bp were generated from bam files. Input and no antibody bigwig files were generated with bamCoverage from deeptools (v3.2.0).
Assembly: P. falciparum 3D7 genome v3.0, release 44 or P. berghei ANKA genome v3.0, release 49
Supplementary files format and content: bigwig files showing log2(ChIP/input), except for input and no antibody samples which not normalized

molecule: genomic DNA

organism: Plasmodium berghei

source_name: ANKA

extract_protocol:
Parasites were crosslinked with 1% paraformaldehyde. Crosslinked parasites were washed with 1 ml cold PBS containing protease inhibitors (cOmplete protease inhibitor cocktail) then incubated on ice with 1 ml nuclear extraction buffer [f.c.: 10 mM HEPES, 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1 mM DTT, 200 mM AEBSF, cOmplete protease inhibitor cocktail, Phos Stop phosphatase inhibitor in nuclease-free water]. After 35 min., NP-40/IGEPAL was added to a final concentration of 0.25% and the solution was homogenized by passing the mixture seven times through a 26 G needle. Extracted nuclei were pelleted by centrifugation at 2,100 × g for 20 min. at 4°C. Supernatant was removed and the pelleted nuclei were resuspended in 130 µl of cold shearing buffer [f.c.: 0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 7.5, cOmplete protease inhibitor cocktail, Phos Stop phosphatase inhibitor in nuclease-free water] and transferred to a microTUBE. Chromatin was fragmented with an M220 sonicator (Covaris) with the following settings: 5% duty cycle, 75 W peak incident power, 200 cycles per burst at 6°C for 300 sec. Fragmented chromatin was transferred to a pre-lubricated, low binding 1.5 ml tube. The microTUBE was washed with 70 µl of shearing buffer after which the solution was combined with the fragmented chromatin for a total volume of 200 µl. For each developmental stage (schizont, merozoite, ring, and hepatic merozoite) 30 µl of sheared chromatin was collected at this point for use as an input sample and stored at -70°C until decrosslinking. Chromatin was diluted 1:1 in ChIP dilution buffer [f.c.: 30 mM Tris-HCl pH 8.0, 3 mM EDTA, 0.1% SDS, 300 mM NaCl, Triton X-100, supplemented with cOmplete protease inhibitor cocktail and Phos Stop phosphatase inhibitor in nuclease-free water] then precleared by incubation with protein A agarose/salmon sperm DNA beads (50 µl beads per 1 ml sheared chromatin) for 1 hour at 4°C with agitation to reduce non-specific background. Following the incubation, the beads were pelleted by centrifugation at 100 × g for 1 min. at RT. The supernatant containing the chromatin was moved to a new low-binding tube and incubated overnight at 4°C with agitation with 2 µg of antibody against the histone PTM of interest. Protein A agarose/salmon sperm DNA beads (25 µl beads per 500 µl sonicated chromatin) were washed with 500 µl ChIP dilution buffer and blocked with 1 mg/ml BSA for 1 hour at 4°C with agitation to reduce non-specific binding. Agarose beads were washed 3 times with 500 µl ChIP dilution buffer, then added to the chromatin suspension and incubated for 1 hour at 4°C with agitation. Agarose beads were pelleted by centrifugation at 100 × g for 1 min. at RT, and the supernatant was discarded. Beads were washed twice at 4°C for 15 min. with agitation 1 ml high salt wash buffer [f.c.: 1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 nM NaCl in nuclease-free water], 1 ml low salt wash buffer [f.c.: 1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, in nuclease-free water], and 1 ml lithium chloride wash buffer [f.c.: 0.25 M LiCl, 1% NP-40/IGEPAL, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0 in nuclease-free water]. Beads were then washed twice for 15 min. with TE buffer [f.c.: 10 mM Tris-HCl pH 8.0, 1 mM EDTA in nuclease-free water] at RT with agitation. Chromatin bound to agarose beads was eluted by incubating with 125 µl elution buffer [f.c.: 1% SDS, 0.1 M NaHCO3 in nuclease-free water] for 15 min. at RT with agitation. The elution was repeated, and fractions combined for a total of 250 µl. Samples were reverse crosslinked by adding NaCl to a final concentration of 0.5 M and incubating overnight at 45°C. RNase A was then added to a final concentration of 0.6 μg/ml and incubated at 37°C for 30 min. Samples were then incubated with EDTA (f.c.: 1 mM), Tris-HCl pH 7.5 (f.c.:4 mM), and proteinase K (0.8 U) for 2 hours at 45°C. DNA was isolated using 2 volumes sparQ beads according to manufacturer’s instructions. ChIP DNA was stored at -20°C until library preparation. Input samples were incubated with 0.6 μg RNase A per µl for 30 min. at 37°C, then incubated with 0.8 U proteinase K overnight at 45°C. DNA was isolated using 2 volumes sparQ beads according to manufacturer’s instructions and stored at -20°C until library preparation.
Libraries from ChIP samples were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB #E6040) or the NEBNext Ultra II DNA library prep kit for Illumina (NEB #E7645) according to manufacturer’s instructions with the following modification. Libraries were amplified using i7 index primers and i5 universal primer (NEBNext multiplex oligos for Illumina index primers set 1 and 2, NEB #E7335 and #E7500) with KAPA HiFi hot start ready mix with the following program: initial denaturation at 98°C for 45 sec.; 15 cycles of (98°C for 15 sec., 55°C for 30 sec., 62°C for 30 sec.); and final extension at 62°C for 5 min. Libraries were purified using 0.9 volumes sparQ beads according to manufacturer’s instructions. Libraires were sequenced with the Illumina HiSeq 2500 or Illumina NextSeq500 to generate 50 bp single-end reads or 75 bp paired-end reads, respectively.

tag: Stage

value: Hepatic merozoite

tag: chip antibody

value: ANKA

tag: isolation

value: HepG2 liver cells were cultured according to standard practices in complete DMEM medium (Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) fetal bovine serum, 1X glutaMAX, 100 U/ml penicillin, and 100 µg/ml streptomycin) at 37°C and 5% CO2. The day prior to infection, HepG2 cells were seeded at 75,000 cells per well in a volume of 500 µl of complete DMEM in a 24-well plate. The day of infection, salivary glands containing P. berghei sporozoites were dissected from live mosquitos (obtained from the University of Georgia insectary, GA, USA) and ground with a small pellet pestle to release sporozoites. Released sporozoites were filtered through a 40 µm filter and counted using a hemocytometer. Sporozoites were diluted to 40,000 sporozoites per 300 µl in infection medium (complete DMEM supplemented with 100 U/ml penicillin, 50 µg/ml streptomycin, and 150 µlg/ml neomycin and 50 µg/ml kanamycin, and 7.5 µg/ml of the antifungal amphotericin B. Culture medium was removed from the wells containing the adherent HepG2 cells and 300 µl of the sporozoite dilution was added to each well. The plate was centrifuged at 2,000 × g for 5 min. at RT. Two hours post infection, all medium was removed and replaced with 1 ml infection medium. At 48 hpi the medium replaced once more with 1 ml fresh infection medium. Infected cells were cultured under normal conditions until merosomes were harvested 68 – 75.5 hpi. To harvest merosomes, the culture medium was collected in a 15-ml tube. Next, the empty wells were rinsed with 500 µl of infection medium and this medium was added to the original collection. Merosomes were pelleted by centrifugation at 4,000 × g for 5 min. at RT. Supernatant was removed until roughly 100 µl remained. The merosome pellet was resuspended in the remaining supernatant and transferred to a 1.5-ml tube. PBS was added to the merosomes to a final volume of 1 ml. Merozoites were released from merosomes by incubation with 1% saponin in milliQ water for 2 min. at RT. Merozoites were pelleted by centrifugation at 4,000 × g for 4 min. at RT. Supernatant was removed until roughly 100 µl remained, and merozoites were resuspended in the remaining medium. PBS was added to the resuspended merozoites to a final volume of 1 ml.


title: 1h_control (1c)

description:
development stage: cell culture on mid-log phase
T1neg1_L3

tag: strain

value: Strain ATCC 22662

tag: replicate

value: algae cell culture, time:1 h

value: negative control:R. subcapitata


title: Adult male Danio rerio 2

value: Whole body

value: male


title: ChIP-seq of Plasmodium berghei hepatic merozoites: H3K9ac

description: Pb H3K9ac


title: NM3A

value: Breast cancer

value: Breast cancer cells

value: Cultured with normoxia CM


title: 1h_control (1a)

description:
development stage: cell culture on mid-log phase
T1neg1_L1

value: biol rep 1


title: YoGI_007 after_drought_stress

description: Column A_YoGI_007 in processed files

value: Leaves

value: YoGI_007=CIMMYT collection accession identifier BW 19498


title: 1h_control (1b)

description:
development stage: cell culture on mid-log phase
T1neg1_L2


title: Adult male Danio rerio 1

value: Adult


title: HCT116 cells, shSMC4_1

status: Public on Jun 05 2023

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

data_processing:
Clean reads were aligned to hg38 reference genome with Hisat2 using default parameters. Gene expression levels were counted with HT-seq using default. Differential expression analysis of two groups was performed using the DESeq2 R package.
Assembly: hg38

organism: Homo sapiens

extract_protocol:
Total RNA was extracted by phenol/chloroform.
RNA-Seq was performed using BGISEQ platform (BGI) and  Illumina HiSeq .

value: Colorectal cancer cell line


title: YoGI_002 after_drought_stress

description: Column A_YoGI_002 in processed files

value: YoGI_002=CIMMYT collection accession identifier BW 7112

value: drought


title: HCT116 cells, shSMC4_2


title: ChIP-seq of Plasmodium berghei hepatic merozoites: H3K4me3

description: Pb H3K4me3

value: Hepatic merozoite

value: ANKA


title: HCT116 cells, shControl_1

value: shControl


title: HCT116 cells, shControl_2


title: Topo-seq-B Replicate 2

city: Barcelona

first: Joaquim

last: Roca

address: Baldiri Reixach 4-15

department: IBMB

country: Spain

institute: CSIC

data_processing:
Nucleosome DNA sequences were then mapped to the S. Cerevisiae reference genome (R64-1-1 from Ensembl Genomes) using bowtie (v1.1.2). Read counting and alignment statistics were calculated using SAMTools and Picard.
Assembly: bwa.scerevisiae.S288c_R64
Supplementary files format and content: Tables (xls) indicating: Read counts-Chromosome-Start-End coordinates of the Nucleosomes for each Sample.
Library strategy: Topo-seq (Sequencing libraries of DNA topoisomers eluted from electrophoresis gels)

organism: Saccharomyces cerevisiae

growth_protocol: S. cerevisiae strain FY251 was grown at 28ºC in 250 ml of rich medium (YPD+dex) until OD 1.0.

extract_protocol:
Cells were converted to spheroplasts and lysed in hypotonic buffer. Chromatin was digested with 30 units of micrococcal nuclease at 24oC for different time points (3 to 30 min).
Mono-nucleosome DNA fragments were gel-purified, their ends repaired and ligated to adaptors. Nucleosome DNA fragments were inserted into the yeast circular minichromosome YCp1.3 and introduced via transformation into yeast cells. About 10 e4 transformant were collected, each containing a YCp1.3 minichromosome hosting one nucleosome of the library (NucLib sample). DNA of circular minichromosomes hosting the nucleosome library were electrophoresed in an agarose gel to resolve the topology (Lk distributions) of the DNAs. Lk distributions above the Lk average were gel eluted and their nucleosome DNAs sequenced (Topo-seq-A sample). Lk distributions below the Lk average were gel eluted and their nucleosome DNAs sequenced (Topo-seq-B sample).


title: Topo-seq-B Replicate 1


title: MINI_76, PBMCs, Control

city: Bethesda

first: Peter

middle: J

last: McGuire

address: 10 Center Dr, Building 10, Room 7N260A

department: NHGRI

institute: NIH

data_processing:
NIH HPC Biowulf
Sequence reads were examined for quality with QoRTs (1.3.6) and fastp (0.23.2).
Sequence reads were mapped to GRCh38 with STAR (2.7) and counts were extracted with RSEM (1.3.3).
Read count extraction was performed in R using DESeq2 (1.38.3)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts (from RSEM) for each sample

source_name: PBMCs

extract_protocol:
PBMC were isolated from 5mL whole blood using LeucoSep tubes (Greiner Bio-one) and Ficoll-Paque Plus (GE Healthcare) for density gradient centrifugation, before lysis in TRIzol (Thermo Fisher).
Total RNA was isolated and purified with miRNeasy kit (Qiagen), with RNA quality and quantity estimated using Nanodrop (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies). 500ng of total RNA was used for the construction of sequencing libraries.
Stranded cDNA sequencing libraries were generated with TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s instructions.

value: PBMCs

tag: diagnosis

value: Control

tag: age

value: M


title: MINI_80, PBMCs, Control


title: MINI_77, PMBCs, MD

value: Case


title: MINI_78, PBMCs, Control

value: F


title: NucLib Replicate 1


title: MINI_81, PBMCs, Control


title: Topo-seq-A Replicate 2


title: Topo-seq-A Replicate 1


title: MINI_74, PBMCs, Control


title: NucLib Replicate 2


title: MINI_75, PBMCs, Control


title: Adult female Danio rerio 1

value: Whole body

value: female

tag: developmental stage


title: MINI_73, PBMCs, Control


title: MINI_72, PBMCs, Control


title: MINI_71, PBMCs, Control


title: MINI_70, PBMCs, Control


title: MINI_66, PBMCs, Control


title: MINI_69, PBMCs, Control


title: MINI_68, PBMCs, Control


title: MINI_79, PBMCs, Control


title: MINI_63, PBMCs, Control


title: MINI_64, PBMCs, Control


title: MINI_65, PBMCs, Control


title: MINI_67, PBMCs, Control


title: MINI_62, PBMCs, Control


title: MINI_60, PBMCs, Control


title: MINI_59, PBMCs, Control


title: MINI_56, PMBCs, MD


title: MINI_57, PMBCs, MD


title: MINI_54, PMBCs, MD


title: MINI_55, PMBCs, MD


title: MINI_58, PBMCs, Control


title: MINI_53, PMBCs, MD


title: MINI_52, PMBCs, MD


title: MINI_50, PMBCs, MD


title: MINI_49, PMBCs, MD


title: MINI_51, PMBCs, MD


title: MINI_48, PMBCs, MD


title: MINI_45, PMBCs, MD


title: MINI_44, PMBCs, MD


title: MINI_61, PBMCs, Control


title: MINI_42, PMBCs, MD


title: MINI_46, PMBCs, MD


title: MINI_47, PMBCs, MD


title: MINI_43, PMBCs, MD


title: MINI_41, PMBCs, MD


title: MINI_37, PMBCs, MD


title: MINI_36, PBMCs, Control


title: MINI_35, PBMCs, Control


title: MINI_34, PBMCs, Control


title: MINI_33, PBMCs, Control


title: MINI_31, PBMCs, Control


title: MINI_30, PBMCs, Control


title: MINI_29, PBMCs, Control


title: MINI_28, PBMCs, Control


title: MINI_32, PBMCs, Control


title: MINI_26, PMBCs, MD


title: MINI_25, PMBCs, MD


title: MINI_24, PMBCs, MD


title: MINI_40, PBMCs, Control


title: MINI_23, PMBCs, MD


title: MINI_22, PMBCs, MD


title: MINI_39, PBMCs, Control


title: MINI_21, PMBCs, MD


title: MINI_18, PMBCs, MD


title: MINI_20, PMBCs, MD


title: MINI_16, PBMCs, Control


title: MINI_19, PMBCs, MD


title: MINI_14, PBMCs, MD


title: MINI_38, PBMCs, Control


title: MINI_17, PMBCs, MD


title: MINI_15, PBMCs, MD


title: MINI_13, PMBCs, Control


title: 1h_control (3a)

description:
development stage: cell culture on mid-log phase
T1neg3_L1

data_processing:
Approximately five million 2 × 79-bp paired end reads were generated respectively from each library by the means of Illumina sequencing on a NextSeq 500/550 High Output v2 platform. The Illumina TruSeq adapter sequences (34 nucleotides) were then clipped by Illumina bcl2fastq2 Conversion Software v2.19.1 using standard parameters.
The FASTQ files were first trimmed (minimum quality 3, minimum read length to be kept 36 bp) using the Trimmomatic tool (http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014). The processed sequence reads were then mapped to R. subcapitata ATCC 22662 reference genome (GenBank Accession number: BDRX01000001.1) (Suzuki et al., 2018) using HISAT2 (Kim et al., 2019). SAMtools (Danecek et al., 2021) was then applied to access the transcripts level in order to get quantitative assignments and to generate the BAM files.
After that, BAM files were selected for the determination of read counts and identification of differentially expressed genes (DEGs). To define the transcripts abundance, read counts for each BAM file were determined by bedtools v2.27.1 and its option multicov (Quinlan and Hall, 2010). The established read count table was then imported into idep 1.0 (Ge et al., 2018). Then, the gene expression level in counts per million (CPMs) were calculated and visualized in box and PCA plot. To identify DEGs, the BAM files were loaded and processed in R using Rsamtools package (Morgan et al., 2022).
Prior than that, gene models were imported and queried using GenomicFeatures (Lawrence et al., 2013) package and followed by using GenomicAlignments (Lawrence et al., 2013) package to create the Summarized Experiment object that contains the fragment counts for each gene and sample.
Differential gene expression for each condition was illustrated using relative log expression function of the DESEQ2 (Love et al., 2014) package and statistical analysis was through the function p.adjust in R. Venn diagrams were plotted by VennDiagram (Chen and Boutros, 2011) package. Genes showing log2(fold change) ≥ 1.5 and ≤ −1.5, and adjusted p-value less than 0.05 were considered to be significantly expressed. Furthermore, a log2(fold change) ≥ 1.5 and ≤ −1.8 cutoff was applied only to the sample T1nZVI (nZVI exposure at 1 h) versus T1neg (control at 1 h), due to high number of DEGs. Clustering and visualization of the dissimilarity matrix was achieved using ClustVis – a web tool for visualizing clustering of multivariate data (http://biit.cs.ut.ee/clustvis/) (Metsalu and Vilo, 2015) and pheatmap packages. The heatmap function was applied with default setting (Manhattan distance and average linkage were used). Principal component analysis was performed based on PCAtools package. Following the differential gene expression analysis, functional annotation and genes classification into metabolic pathway subtypes were grouped using the KEGG database (https://www.kegg.jp/kegg/) (Kanehisa and Goto, 2000) and JGI Algal Genome Portal PhycoCosm (https://phycocosm.jgi.doe.gov) (Grigoriev et al., 2021; Nordberg et al., 2014). Annotation improvement was further performed using alpha version of protein sequence observation service (PSOS) (https://psos-staging.computational.bio/) and UniProtKB database (https://www.uniprot.org/) (Bateman et al., 2022). The differentially expressed genes were then co-analyzed using protein-protein interaction (PPI) software to analyze for possible gene interactions and was performed using STRING online database version 11.5 (https://string-db.org/) (Szklarczyk et al., 2021) with k-means clustering and interaction score of (medium confidence > 0.4) as the cut off criterion. For every p-value presented in PPI analysis, the false discovery rate (FDR) was controlled using the Benjamini–Hochberg method (Benjamini and Hochberg, 1995). Construction and visualization of PPI network was performed using Cytoscape software version 3.9.1 (Shannon et al., 2003) with Cytoscape stringApp 2.0 installed in the software (Doncheva et al., 2022).
Assembly: R. subcapitata ATCC 22662 genome (GenBank Accession number: BDRX01000001.1)
Supplementary files format and content: 50 genes with the highest variance across samples (rlog transformed counts).csv Format: csv Content: rlog transformed counts of 50 highly expressed genes
Supplementary files format and content: converted_counts_data.csv Format: csv Content: counts per million of all treatment conditions
Supplementary files format and content: T1Fe versus T1neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 1-Fe treatment versus Time 1 neg. control)
Supplementary files format and content: T1nZVI versus T1Fe DESEQ.csv Format: csv Differential gene expression for each condition (Time 1- nZVI treatment versus Time 1-Fe treatment)
Supplementary files format and content: T1nZVI versusT1neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 1- nZVI treatment versus Time 1-neg. control)
Supplementary files format and content: T4 versus T1 DESEQ.csv Format: csv Differential gene expression for each condition (Time 4 versus Time 1)
Supplementary files format and content: T4Fe versus T4neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 4-Fe treatment versus Time 4-neg. control)
Supplementary files format and content: T4nZVI versus T4Fe DESEQ.csv Format: csv Differential gene expression for each condition (Time 4-nZVI treatment versus Time 4-Fe treatment )
Supplementary files format and content: T4nZVI versus T4neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 4- nZVI treatment versus Time 4- neg. control)

extract_protocol:
RNA isolation of microalgae R. subcapitata involved two major steps: the cell lysis and then the RNA extraction procedure. RNA was harvested from three biological replicates after 1 and 4 h from R. subcapitata exposed with nZVI and nFe3O4 respectively. Cell pellets were obtained through centrifugation at 10,000 × g, 4°C for 2 min, followed by overnight cell lyophilization and phenol-chloroform extraction method adapted from a previous work (Yeap et al., 2021). The integrity and concentration of the RNA extracts were determined with an Agilent 2100 Bioanalyzer system (Agilent Technologies, Germany) and Nanodrop (Thermo Scientific, USA) was for RNA concentration quantification. All electropherogram of ribosomal RNA peaks were computed and analyzed by 2100 Expert software (Agilent Technologies, Germany).
To prepare for whole transcriptome sequencing of the directional RNA-seq library, up to 1 µg of total RNA (RIN > 6) was used with a TruSeq® stranded mRNA Library Prep kit (Illumina Inc., USA) after capturing poly-adenylated transcripts and mRNA fragmentation. The resulting cDNA libraries were pooled and sequenced in paired-end mode (2 × 79 bp) on an Illumina NextSeq 500/550 High Output v2 platform.

value: Strain ATCC 22662

value: biol rep 3

value: algae cell culture, time:1 h

value: negative control:R. subcapitata


title: MINI_12, PMBCs, Control


title: MINI_11, PMBCs, Control


title: MINI_10, PMBCs, Control


title: MINI_09, PMBCs, Control


title: MINI_07, PMBCs, Control


title: MINI_04, PMBCs, Control


title: MINI_08, PMBCs, Control


title: MINI_06, PMBCs, Control


title: MINI_05, PMBCs, Control


title: MINI_01, PMBCs, Control


title: MINI_02, PMBCs, Control


title: Esr2-KO rep2

city: Nanjing

first: Wentao

last: Fan

address: Tongwei road 6

institute: Nanjing Agricultural University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Colon

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.Part of RNA was utilized to construct rRNA depletion(NEBNext Ultra Directional RNA Library Prep Kit),The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: Colon

value: post natal day 21


title: Esr2-KO rep1


title: WT rep1

value: wild type


title: MINI_03, PMBCs, Control

tag: Sex


title: WT rep2

tag: tissue


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH9

city: Silver Spring

first: Rasmi

last: Thomas

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

data_processing:
Sequencing reads were trimmed with Trimmomatic(v0.36) (options: SLIDINGWINDOW:15:30 MINLEN:50)
Trimmed reads were aligned to the Macaca mulatta (reference assembly 8.0.1) plus SIVmac251 or SIVmac239 genomes (for AY69/T034, respectively) using HISAT2 (v2.1.0).
Global gene expression was quantified using htseq-count(v0.9.1) (options: -s no -a 2 -t exon)
Assembly: Mmul_8.0.1
Supplementary files format and content: tab-delimited text files include raw counts for each library

organism: Macaca mulatta

source_name: lymph node

extract_protocol:
Single cells in 96-well plates were lysed in SMART-Seq lysis buffer supplemented with RNAse inhibitor for 2 minutes at room temperature, vortexed, centrifuged, and frozen at -80C until cDNA library preparation.
Whole cDNA library was prepared using the SMART-Seq Ultra Low Input RNA kit.

value: lymph node

tag: cell type

value: Memory CD4 T cell

tag: macaque id

tag: cell number

tag: d1a5 splice_characterization

value: no D1-A5 splice detected

tag: tatrev splice_characterization

value: no tat-rev splice detected

tag: siv presence

value: no SIV detected

tag: siv percent

value: SIV not > 1%


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH8


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH9

value: SIV detected


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH9


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH9


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH9


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH8


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH9


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH8


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH8


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH9


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH8


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH7


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH7


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH7


title: YoGI_161 after_drought_stress

description: Column A_YoGI_161 in processed files

value: Leaves

tag: genotype

value: YoGI_161=Watkins collection accession identifier 1190292

tag: treatment

value: drought


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH6

value: D1-A5 splice detected

value: tat-rev splice detected

value: SIV > 1%


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH6


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH6


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH7


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH8


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH7


title: Control-cortex-4

tag: strain

value: Cortex offspring from control mother mice

tag: devolopmental stage

value: fetus at E17.5 stage


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH6


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH7


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH6


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH7


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH8


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH5


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH5


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH5


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH6


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH4


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH4


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH5


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH5


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH4


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH5


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH4


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH4


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH4


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH3


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH3


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH3


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH3


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH2


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH2


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH3


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH3


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH2


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH2


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH2


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH1


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH6


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH2


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH5


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH1


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH2


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH1


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH12


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH1


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH1


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH3


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH1


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH12


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH12


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH11


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH12


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH1


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH10


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH10


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate6 wellH11


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH12


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate3 wellH10


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH10


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH4


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH12


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellH11


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate4 wellH11


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate5 wellH11


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate1 wellH11


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate2 wellH11


title: Memory CD4 T cell gene expression from macaque AY69 lymph node, plate7 wellG9