title: nuclei

status: Public on Jan 31 2022

type: SRA

city: Leuven

first: Ruth

last: Styfhals

address: Naamsestraat 61

department: Biology

country: Belgium

institute: KU Leuven

library_source: transcriptomic

data_processing:
Mapping, barcode assingment and counting was done with 10x Genomics Cell Ranger 5.0.1 (introns were retained and expected cells parameter was set at 8000).
Filtering and subsetting steps were done in Seurat v3.2.3. Nuclei and cells with too high (>4000) or low gene counts were filtered out (<400 for nuclei, <800 for cells).  Cells with a higher percentage (>5) of mitochondrial RNA were regressed out. Genes expressed in less than 10 cells were excluded.
The SCTransform scaling method was used and data integration of the cells and nuclei was done following the Seurat vignette.
The package scclusteval was used to assess optimal clustering parameters to obtain the highest number of stable clusters (Tang et al., 2020). Reclustering according to these optimal parameters (dims =150, k.param =10, resolution =2) resulted in the highest number of stable clusters.
Differentially expressed genes were calculated for all clusters compared to all other clusters (logfc.threshold = 0.25).
Genome_build: 3' extended genome annotation for Octopus sinensis (ASM634580v1).
Supplementary_files_format_and_content: 3'-extended_genome_annotation.gtf: We improved the genome annotation for octopus sinensis based on publically available full-length RNAseq data (IsoSeq and FLAM-seq).
Supplementary_files_format_and_content: countmatrix.csv: After filtering and quality control we obtained the following raw count matrix (17961 genes x 17081 cells).
Supplementary_files_format_and_content: cell_level_metadata.csv: All cell barcodes and corresponding cell type annotation.
Supplementary_files_format_and_content: seurat_object_with_annotation.rds: Resulting seurat object that contains both the count matrix and the cell level metadata.
Supplementary_files_format_and_content: cells_barcodes.tsv.gz
Supplementary_files_format_and_content: cells_matrix.mtx.gz
Supplementary_files_format_and_content: cells_features.tsv.gz
Supplementary_files_format_and_content: nuclei_barcodes.tsv.gz
Supplementary_files_format_and_content: nuclei_matrix.mtx.gz
Supplementary_files_format_and_content: nuclei_features.tsv.gz

molecule: nuclear RNA

organism: Octopus vulgaris

source_name: nuclei of one day old paralarval brain

growth_protocol: Octopus embryos were housed until hatching in a stand-alone system with artificial sea water.

extract_protocol:
Nuclei isolation: The brains were immediately transferred to a dounce homogenizer (Sigma) containing 0.5 mL of ice-cold homogenization buffer (HB) (320 mM Sucrose, 5 mM CaCl2, 3 mM Mg(OAc)2, 10 mM Tris 7.8, 0.1 mM EDTA, 0.1% IGEPAL CA-360, 0.1 mM Phenylmethylsulfonyl fluoride, 1 mM β-mercaptoethanol with 5µl Rnasin Plus). It was left in the HB for 5 min before starting homogenization. The tissue was homogenized with 10 manual gentle strokes (pestle A) + 10 manual gentle strokes (pestle B). The tissue homogenate was filtered through a 70 µm cell mesh strainer. Leftover contents on the strainer were washed with an additional 0.5 ml HB buffer. The homogenized tissue was incubated in HB on ice for 5 mins. Leftover contents on the strainer were washed with an additional 1.65 ml HB and added to a final volume of 2.65 ml. The nuclei homogenate in the HB was mixed with 2.65 ml of Gradient Medium (GM) (5 mM CaCl2, 50% Optiprep, 3 mM Mg(OAc)2, 10 mM Tris 7.8, 0.1 mM Phenylmethylsulfonyl fluoride, 1 mM β-mercaptoethanol). 29% density cushion was prepared by dilution of Optiprep with Optiprep Diluent Medium (150 mM KCl, 30 mM MgCl2, 60 mM Tris pH 8.0, 250 mM sucrose). The nuclei suspension in the HB + GM mix was layered over the 29 % cushion and centrifuged in an SW41Ti rotor (Beckman Coulter) at 7.700 rpm and 4°C for 30 minutes. The supernatant was removed with a Pasteur pipette, and the removal of the lower supernatant was done with a P200. The nuclei pellet was resuspended in 50 uL Resuspension Buffer (PBS, 1% BSA) and transferred to a new tube. The resuspended nuclei were counted using a LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems).
Single cell suspension: Paralarval brains were enzymatically dissociated by adding 20 µl of Collagenase/Dispase (100 mg/ml, Roche) to 500 µl L15-adapted medium and incubating for two hours at 25°C, 500 rpm. Every 15 minutes, a P100 was used to pipet slowly up and down until the tissue was fully dissociated. After a 5 min centrifugation step (200 rcf, 4°C), the supernatant was discarded and the pellet was resuspended in 1 ml of Mg-Ca-Free filtered sea water with 0,04% BSA (449 mM NaCl, 33 mM Na2SO4, 9 mM KCL, 2.15 mM NaHC03, 10 mM Tris-Cl pH 8.2, 2.5 mM EGTA, filter sterilized). The cells were pulled through a strainer (35 µm) by a brief spin, followed by a wash with 400 µl Ca-Mg-Free filtered seawater. Cells were centrifuged again for 5 min (200 rcf, 4°C), supernatant was removed and the pellet was resuspended in 100 µl Ca-Mg-Free filtered sea water with 0,04% BSA.  The cell viability and concentration was assessed by the LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems). Average cell size was 9.1 µm. We obtained a single cell suspension with a multiplet cell percentage of 2.6%. The cell suspension was further diluted to reach appropriate cell counts, and a final viability of 84.9% was obtained before proceeding with 10X genomics.
Chromium Single Cell 3’ Solution V3 Chemistry
Library preparations for the sc/snRNA-seq experiments were performed using 10X Genomics Chromium Single Cell 3’ Kit, v3 chemistry (10X Genomics, Pleasanton, CA, USA). We aimed for a targeted cell recovery of 6000-10 000 cells/nuclei. Post cell count and QC, the samples were immediately loaded onto the Chromium Controller. Single cell or single nuclei RNAseq libraries were prepared using manufacturers recommendations (Single cell 3’ reagent kits v3.1 user guide; CG000204 Rev D), and at the different check points the library quality was assessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent).

treatment_protocol: Brains were dissected in L15 medium with additional salts.

tag: protocol

value: nuclei isolation

tag: tissue

value: a pool of 30 paralarval brains

tag: molecule subtype

value: nuclear RNA


title: cells

molecule: total RNA

source_name: cells of one day old paralarval brain

value: single cell suspension

value: total RNA


title: Root at time 24 control experiment 3

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

data_processing:
Base calling was made with the HiSeq Control Software HD 3.4.0.38, RTA 2.7.7 and bcl2fastq2.17 v2.17.1.14 softwares (Illumina).
The read quality trimming and the miRNA identification was made using Mirnovo software with universal plant prediction model without a reference species (Vitsios et al., 2017, Nucleic Acids Research 45: e177). The miRNA read count was improved with CD-HIT (Fu et al., 2012, Bioinformatics 28: 3150-3152).
The differential expression analysis of the miRNA was made using the edgeR package for R, the miRNAs were normalised by cpm and filtered; 20 cpm in at least 2 samples (Robinson et al., 2010). Only the miRNAs with P values < 0.05 and the three experimental replicates with the same expression sense than the final logFC (positive or negative) were considered as differentially expressed.
Genome_build: Identified miRNAs (total_mirna_id.fasta)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample.The column id is the sequence identifier.

organism: Pinus pinaster

source_name: Roots

growth_protocol: Seeds from maritime pine (Pinus pinaster Ait.) from “Sierra Segura y Alcaraz” (Albacete, Spain) were provided by from the Área de Recursos Genéticos Forestales of the Spanish Ministerio de Agricultura, Pesca y Alimentación. Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were grown in vermiculite in plant growth chambers under 16 h light photoperiod, a luminal intensity of 100 μmol m−2 s−1, a constant temperature of 25 °C and watered twice a week with distilled water.

extract_protocol:
Total RNA was isolated using Norgen Biotek Plant/Fungi Total RNA Purification kit (Norgen Biotek, Thorold, ON, Canada). Total RNA concentration and purity were determined with a Nanodrop ND1000 (Thermo Scientific, Waltham, MA, USA). Purity was determined through the 260/280 and 260/230 ratios. The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA BR, Broad-Range, Assay Kit (Invitrogen, Paisley, UK). RNA quality was further confirmed using agarose gel electrophoresis and using the RNA Pico Assay for the 2100 Bioanalyzer (Agilent, USA). RNA samples with an RNA integrity number (RIN) higher than 7 were used for miRNA-Seq.
The miRNA isolation and sequencing were carried out by Fasteris (Plan-les-Ouates, Switzerland). Three micrograms of total RNA were used to isolated miRNAs by poliacrilamide gels in order to select sequences with a size between 18 and 30 bp. RNA libraries for sequencing were prepared using the TruSeq small RNA kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The 21 samples were sequenced on an Illumina HiSeq 4000 as single-end reads of 50 bp length.

treatment_protocol: One-month old maritime pine seedlings were used for this experiment. Pine seedlings were randomly subdivided into three different groups, relocated into forestall seedbeds and irrigated with 80 mL of a solution that contains macro- and micronutrients without any nitrogen source (1.16 mM KCl; 0.63 mM KH2PO4; 0.35 mM MgSO4·7H2O; 0.17 mM CaCl2·H2O; 80 μM EDTA-FeSO4; 25.9 μM H3BO3; 10.2 μM MnCl2·4H2O; 1.3 μM ZnSO4·7H2O; 0.7 μM CuSO4·5H2O; 0.1 μM Na2MoO4·2H2O). After three days of acclimation, the control group was irrigated with 80 mL of water, the second group was supplied with 80 mL of 0.1 mM NH4Cl and the third group was supplied with 80 mL of 3 mM NH4Cl. Root samples were collected before the irrigation and at two different time points after the treatments (2 and 24 hours) and immediately frozen in liquid nitrogen. Ten seedlings were collected and pooled per each sample. This experiment was carried out three independent times.

value: roots

tag: provenance

value: Segura-Alcaraz

tag: developmental stage

value: 1 month-old seedling

tag: treatment

tag: time

value: 24 hours

tag: experimental replicate


title: Root at time 24 control experiment 2


title: Root at time 24 control experiment 1


title: Root at time 24 ammonium 3 mM experiment 3

value: Ammonium 3 mM


title: Root at time 24 ammonium 3 mM experiment 2


title: Root at time 24 ammonium 3 mM experiment 1


title: Root at time 24 ammonium 0.1 mM experiment 2

value: Ammonium 0.1 mM


title: Root at time 24 ammonium 0.1 mM experiment 3


title: Root at time 24 ammonium 0.1 mM experiment 1


title: Root at time 2 control experiment 3

value: 2 hours


title: Root at time 2 control experiment 2


title: Root at time 2 ammonium 3 mM experiment 2


title: Root at time 2 ammonium 3 mM experiment 3


title: Root at time 2 control experiment 1


title: Root at time 2 ammonium 3 mM experiment 1


title: Root at time 2 ammonium 0.1 mM experiment 2


title: Root at time 2 ammonium 0.1 mM experiment 3


title: Root at time 2 ammonium 0.1 mM experiment 1


title: MUT 0.1 IU/g rep3

city: Syracuse

first: Jessica

last: MacDonald

state: NY

address: 107 College Place

country: USA

institute: Syracuse University

data_processing:
Analysis was performed in PartekFlow: sequenced reads were trimmed for adaptor sequence and aligned with STAR 2.7.3a index (assembly: mus musculus mm10, aligner index: whole genome) and quantified to model (GENCODE M25).
Data was quantified in R using the normalization strategy to remove unwanted variation (RUV) described by Risso et al., Nature Biotechnology, 2014.
After normalization, the data was extracted from R and analyzed in PartekFlow in two separate projects (filtering and analyzing  1 IU/g and 10 IU/g vitamin D separate from 1 IU/g and 0.1 IU/g vitamin D).
Genome_build: mm10
Supplementary_files_format_and_content: Csv file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Csv file with RUV normalized gene counts for every gene and every sample

organism: Mus musculus

source_name: Cortex

extract_protocol:
Total cortices were dissected and RNA was extracted with Trizol (Invitrogen, 15596-018) combined with columns (Qiagen, 74104 and 79254).
1 ug of RNA was used for the construction of sequencing libraries, which were prepared using Lexogen protocols (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina - Cataloge number 015)

treatment_protocol: Mice were fed chow with varying defined concentrations of vitamin D starting at 4 weeks of age. All other components of the chow were identical. Mice remained on the diet until they were dissected at 7 months of age.

tag: strain

tag: vitamin d treatment

value: Deficient (0.1 IU/g Vitamin D)

tag: genotype

value: Heterozygous (Mecp2+/-)


title: Root at time 0 experiment 3

value: 0 hours


title: Root at time 0 experiment 1


title: Root at time 0 experiment 2


title: MUT 0.1 IU/g rep1


title: MUT 0.1 IU/g rep2


title: WT 0.1 IU/g rep3

value: Wildtype (Mecp2+/+)


title: WT 0.1 IU/g rep1


title: MUT 10 IU/g rep3

value: Supplemented (10 IU/g Vitamin D)


title: WT 10 IU/g rep3


title: MUT 10 IU/g rep2


title: MUT 1 IU/g rep3

value: Control (1 IU/g Vitamin D)


title: MUT 10 IU/g rep1


title: WT 10 IU/g rep2


title: MUT 1 IU/g rep1


title: MUT 1 IU/g rep2


title: WT 0.1 IU/g rep2


title: WT 1 IU/g rep2


title: WT 1 IU/g rep1


title: WT 1 IU/g rep3


title: WT 10 IU/g rep1


title: SK08-B4

city: Boston

first: Matthew

last: Booker

state: MA

address: 21-27 Burlington Ave.

department: Informatics

institute: Dana Farber Cancer Institute

data_processing:
Gene count quantifications were performed with RSEM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count for each Sample

source_name: Carm1 KO

growth_protocol: OT-I CD8 T cells were isolated from spleens and inguinal lymph nodes harvested from OT-I mice and placed in ice-cold 2% FBS [FBS (Sigma) + PBS (GIBCO)]. These organs were prepared by mashing through a 70 μm filter. Splenocytes were suspended in 2% FBS. Using EasySep mouse CD8+ T cell negative selection kit (StemCell Technologies), naïve CD8 T cells were isolated using manufacturer’s instructions. Naive CD8 T cells were resuspended with cRPMI (RPMI-1640 + 10% FBS + 2mM L-Glutamine + 100U Pen/Strep (ThermoFisher) + 49nM b-mercaptoethanol (Sigma)) to a final concentration of 1-2x10^6 cells/ml. cRPMI medium was supplemented with 2.5ng/ml IL-7 + 50ng/ml IL-15.

extract_protocol:
4 technical replicates were used to extract total using RNA RNeasy Plus Mini Kit (Qiagen # 74134) according to the manufacturer’s protocol.
Total RNA was quality-checked using an Agilent BioAnalyzer 2000 instrument.  RNA with an integrity number of greater than 9.5 was used for subsequent analyses. Total RNA was submitted to GeneWiz for RNA-seq analysis. The standard mRNA library preparation TruSeq RNA Sample Prep Kit v2 (Illumina) was used for library preparation. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing. Pair-end 150bp sequencing was performed on Illumina NextSeq 500 instrument. Gene count quantifications were performed with RSEM.
Standard bulk RNA-Seq (Pair-end 150bp sequencing)

treatment_protocol: CRISPR-Cas9 editing OT-CD45.1 CD8 T was performed by nucleofection of respective crRNA using P3 primary cell 96-well nucleofector kit (Lonza). Gene editing efficiency was determined by TIDE analysis using genomic DNA and Western blotting. 7-days post editing and culture 2X10^6 tumor or OT-I CD45.1 CD8 T cells were pelleted and used for total RNA extraction. OT-I CD8 T cells were edited by crRNA targeting LacZ or Carm1 were validated for the complete loss of Carm1 protein by western blotting.

tag: cell type

value: OT-I CD8 T cells

tag: genotype/variation

value: Carm1 KO


title: SK04-A4

source_name: Control KO

value: Control KO; WT


title: SK06-B2


title: SK03-A3


title: SK07-B3


title: SK01-A1


title: SK05-B1


title: SK02-A2


title: Control Ser2_mNETseq

data_processing:
Library strategy: mNET-Seq
Adapters were removed using cutadapt (version 1.18).
Reads were then aligned to the mouse genome (mm10) using TopHat (version 2.1.1).
Location and strand of the 5’ end of the second read among properly paired reads was determined using an Rsamtools version 1.34.1.
Ser2-P reads and CTD reads were normalized for library size and the ratio of Ser2-P reads to CTD reads were calculated.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: TSS_change_ser2_fraction.txt: Tab-delimited text file
Supplementary_files_format_and_content: TES_change_ser2_fraction.txt: Tab-delimited text file

source_name: B16F10 melanoma cells

growth_protocol: B16F10 parental cell lines were purchased from American Type Culture collection (ATCC) and were grown in DMEM media supplemented with 10%FBS and 1% Penicillin/Streptomycin at 37oC with 5% CO2.

extract_protocol:
The samples were processed as recommended previously (Nojima et al., 2016). Briefly, three sets of 8x10e6 cells per experimental condition were processed separately and pooled after MNase treatment. Protein G Dynabeads (ThermoFisher, 10004D) were coupled with the following antibodies: RNAPII Ser2-P (Abcam, Rabbit Poly Ab 5095, 5mg/IP), RNAPII CTD (clone 8WG16, Biolegend 664912, 5mg/IP).
NEBNext Small RNA-seq Library Prep kit (E7300S) was used for library synthesis. Prior to library preparation, sample quality assessed using the Agilent RNA 6000 Pico Kit (#5067-1513). Samples were processed per manufacturer’s protocol for Next-Generation Sequencing (NGS) with the exception of the size selection step, which was performed as described previously (Nojima et al., 2016). We selected barcoded fragments of 150-250bp, which correspond to RNA fragments of 23bp-123bp. Samples were sequenced on the Illumina Nextseq500 platform using a PE75 flow cell. Analysis was performed by the Molecular Biology Core Facility at Dana Farber Cancer Institute as described previously (Nojima et al., 2016).

tag: cell line

value: Melanoma cell line

value: WT

tag: mnet antibody


title: Carm1 KO Pol II_mNETseq

value: RNAPII CTD (clone 8WG16, Biolegend 664912, 5mg/IP)


title: Control Pol II_mNETseq


title: 3D7_KO

city: Braga

first: Nuno

middle: S.

last: Osório

address: Campus de Gualtar

country: Portugal

institute: ICVS

data_processing:
Transcriptome datasets for both 3D7 and Dd2 were mapped against the 3D7 v3 (Böhme, U. et al., Wellcome Open Res., 2019) reference sequence using HISAT2 2-2.0.0-beta (Kim, D. et al., Nat.Biotechnol, 2019) (--rna-strandness RF --max-intronlen 5000).
Read counts were determined using HTSEQ v0.6.0 (Anders, S. et al., Oxf. Engl., 2015) (-r pos -s no). Deconvolution analysis was performed as described previously in Aunin, E. et al., PLOS Pathogens, 2020.
Differentially expressed genes were determined using edgeR (Robinson, M.D. et al.,  Bioinforma, 2010), with genes expressed at <=3 counts per million (cpm) excluded.
Because there were no biological replicates for any condition, we used the exact test with dispersion set to 0.01, as suggested for data concerning genetically identical model organisms (https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf).
We used a false discovery rate (FDR) cut off of 0.01 and a fold change cut off of 2 to call differentially expressed genes.
Genome_build: 3D7 v3 reference sequence (Böhme, U. et al., Wellcome Open Res., 2019)
Supplementary_files_format_and_content: Table with genes up or down in KO relative to WT  with FDR <= 0.01 and fold change > 2. Direction of up or downregulation, gene ID, false discovery rate (FDR), log counts per million (logCPM), log fold change (logFC), and gene description (Desc).

organism: Plasmodium falciparum 3D7

source_name: Red blood cells infected P. falciparum

growth_protocol: P. falciparum 3D7 and Dd2 strains (MRA-120 and MRA-156, MR4-Malaria Resources) were maintained at 4% hematocrit in RBCs with RPMI-1640 (Gibco) supplemented with 2 g/L sodium bicarbonate, 2 mM L-glutamine, 25 mM HEPES (Gibco), 25 µg/mL gentamycin (Gibco), 100 µM hypoxanthine (Sigma-Aldrich) and 0.25% (w/v) AlbuMAXII (Gibco) with daily medium changes. Parasites were maintained at 37 °C in an airtight environment with 3% O2, 5% CO2 and 92% of N2.

extract_protocol:
RNA was extracted from trophozoite stages, estimated between 28 to 32 hours old, using a RNeasy Mini Kit (Qiagen)
Libraries and sequencing were outsourced (Macrogen Inc), using TruSeq RNA Illumina Library v2 construction (nonstranded polyA enrichment) and HiSeq2500 Illumina 2x100bp 2Gb (20M pair-end reads) throughput-based sequencing.

treatment_protocol: Parasites were tightly synchronized with 5% sorbitol in intervals of 20 hours for 3 consecutive life cycles.

tag: age

value: 28-32h after cycle initiation

value: knock-out of PfMRP1 transporter


title: 3D7_WT

value: wild-type


title: Retinoic_Acid_80uM

city: Bangalore

first: Rajarshi

last: Pal

address: CCAMP, NCBS

country: India

institute: Eyestem research

data_processing:
Adapter Trimming was performed using Trimmomatic (v-0.36)
Contamination removal was performed using Bowtie2 (2.2.4).The unwanted sequences like - mitochondrial genome sequences, ribosomal RNAs, transfer RNAs are removed in this step.
The paired-end reads are aligned to the reference human genome (hg19). Alignment was performed using HISAT2 (2.1.0).
The aligned reads are used for estimating expression of the genes. The raw read counts were estimated using FeatureCount (1.5.2). Read count data were normalized using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include  rawcounts for each Sample

organism: Homo sapiens

source_name: Induced pluripotent stem cells

growth_protocol: Pluripotent stem cells were allowed to form forced aggregates calld embryoid body which mimics the gastrulation stage of developing embryo. This platform is used to screen various drugs (at IC50 concentration) and assess embryotoxicity using developmental toxicity assays

extract_protocol:
RNA was isolated from the cells using Qiagen miRNeasy kit as per kit protocol
NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used to prepare libraries for total RNA sequencing (NEB, Cat# E7530L). 500ng was taken for mRNA enrichment using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490L). Following purification, the enriched mRNA was fragmented using divalent cations under elevated temperatures. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase. Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H enzyme. The cDNA fragments were then subjected to a series of enzymatic steps that repair the ends, tails the 3’ end with a single ‘A’ base, followed by ligation of the adapters (Refer, Table 1.0 Sample-Index Details). The adapter-ligated products were then purified and enriched using the following thermal conditions: initial denaturation 98°C for 30sec; 13 cycles of - 98°C for 10sec, 65°C for 75sec; final extension of 65°C for 5mins. PCR products are then purified and checked for fragment size distribution on Fragment Analyzer using HS NGS Fragment Kit (1-6000bp) (Agilent, Cat# DNF-474-1000).
mRNA enrichment followed by library preparation using non-directional library protocol

treatment_protocol: Drug compounds were added to the cells at the time of embryoid body formation until the differentiation end point with alternate day media change (with drugs)

value: pluripotent stem cell derived embryoid bodies


title: Dexamethasone_500uM


title: Valproic_Acid_2.5mM


title: pb104-rep1-BTZ-T1

city: TAMPA

first: Camilla

middle: Valente

last: Pires

address: 3720 Spectrum Blvd, 404

institute: University of South Florida

data_processing:
RNAseq reads from each sample were aligned to the P. falciparum reference genome usinf HISAT2.
Mapped reads were used to assemble known transcripts from the reference and their abundances were estimated using SAMtools and the abundances were estimated using Feature Counts
Genome_build: P. falciparum reference genome (PlasmoDB version 47)
Supplementary_files_format_and_content: RNAseq_data_processed_counts.txt is the output of Fecture counts and contains ID (Geneid), chromosome (Chr),vcoordenadenades (Start and End), Strand (+ or -), Length and rhe counts (number of reads), for each mapped gene from each RNAseq sample.

organism: Plasmodium falciparum

growth_protocol: Parasite cultures were maintained according to standard methods with gassing (5% O2 and 5% CO2, nitrogen balanced) and 5% hematocrit (O+ blood; Interstate Blood Bank) in RPMI 1640 medium (Invitrogen) supplemented with 0.5% Albumax II (Invitrogen), 0.25% sodium bicarbonate, and maintained at 37°C.

extract_protocol:
Parasites were separated from red blood cells via incubation with 0.015% saponin at room temperature for 5 min. Cultures were then pelleted and washed three times in 10 mL room temperature PBS. Samples were stored at − 80 °C in 1 mL TRIzol reagent (Fisher Scientific, Hampton, NH) until extraction. At RNA extraction, 200 μl of chloroform was added and samples were vortexed vigorously for 15 seconds, followed by incubation at room temperature for up to 5 minutes. Samples were then spun down at 12000×g (10,800 rpm) at 4 °C for 10 minutes and the supernatant discarded. 1 mL of 75% ethanol was added to the pellet, and samples were spun down at 10000×g (9800 rpm) for 5 minutes. The resulting supernatant was discarded and the pellet briefly allowed to dry. The RNA pellet was then dissolved in 20–50 μl of DEPC-treated water while being incubated at 55 °C for 10–15 min.
0.5 μg–1.0 μg of RNA samples were prepped for sequencing using the Illumina TruSeq Stranded mRNA Kit as per kit protocol. Library quantification was measured by qPCR and TapeStation (Agilent Technologies). Sequencing was performed on an Illumina NextSeq V2.5 mid-output 300-cycle.

treatment_protocol: Cultures of wildtype NF54 and pB- mutant pB104  were  highly synchronous rings, then split equally into two control and two experiments T75 flasks each. T0 samples were harvested. All parasites were grown at the normal human body temperature (37C) to early ring-stage. Two flasks of were then exposed to 3-cycles growth of low-dose of each antimalarial drug (dihydroartemisin-DHA and Bortezomib-BTZ), while the remaining two flasks without any drug exposure. After the third cycles-growth (T1), RNA was harvested simultaneously from all conditions for RNAseq.

value: piggyBac mutant

tag: disrupted gene id

tag: drug treatment

value: Bortezomib (BTZ) exposure


title: pb104-rep2-DHA-T1

value: dihydroartemisin (DHA) exposure


title: pb104-rep2-nodrug-ctrl-T1

value: no drug control


title: Carm1 KO Ser2_mNETseq

value: RNAPII Ser2-P (Abcam, Rabbit Poly Ab 5095, 5mg/IP)


title: Folic_Acid_2000uM


title: pb104-rep2-BTZ-T1


title: Control

value: Control


title: pb104-rep1-DHA-T1


title: pb104-rep2-T0


title: YFP+ Memory Rep2

city: London

first: Maria

last: Vila de Mucha

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

data_processing:
Reads were filtered to remove adaptors and low-quality bases and aligned to mm9 using TopHat2. PCR duplicates were removed using the NuGEN duplicate marking tool and read counts generated using featureCounts.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of raw read counts for every sample and every gene as generated by featureCounts

source_name: CD4+ T cell

extract_protocol:
CD4+ cells were purified using LS positive selection magnetic-activated columns (MACS) and anti-CD4 (L3T4) beads (Miltenyi Biotec). YFP- and YFP+ Naive and Memory CD4+ MACs sorted cells were further purified by fluorescence activated cell sorting using a FACS Aria to purify Naïve (CD4+ CD25- CD44low CD62Lhigh) or memory (CD4+ CD25- CD44high CD62Llow) cells based on the basis of YFP expression. RNA was extracted using the RNAeasy Micro kit (Qiagen) and RNA samples were then checked for the quality, contamination and concentration using a NanoDrop, Qubit spectrophotometer and Agilent Bioanalyzer.
Libraries were prepared using the Ovation SoLo RNA-seq library preparation kit (NuGEN genomics) according to the manufacturer’s protocol and were sequenced on an Illumina HiSeq 3000 to generate 2x75 bp paired-end reads.

value: YFP+ Memory CD4+ effector T cell

value: T-bet cre/+ Rosa26 YFP/+


title: YFP+ Memory Rep3


title: NF54-rep2-DHA-T1

value: wildtype


title: NF54-rep1-DHA-T1


title: YFP+ Memory Rep1


title: NF54-rep2-BTZ-T1


title: YFP- Memory Rep3

value: YFP- Memory CD4+ effector T cell


title: NF54-rep1-BTZ-T1


title: YFP+ Naïve Rep3

value: YFP+ Naive CD4+ effector T cell


title: pb104-rep1-T0


title: NF54-rep2-nodrug-ctrl-T1


title: YFP+ Naïve Rep2


title: YFP+ Naïve Rep1


title: pb104-rep1-nodrug-ctrl-T1


title: NF54-rep2-T0


title: YFP- Naïve Rep2

value: YFP- Naive CD4+ effector T cell


title: YFP- Naïve Rep3


title: NF54-rep1-T0


title: B16-F10 cells, RNA-seq wild-type rep3

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with tophat2 v2.1.0 (RNA-seq) or bowtie2 v2.2.6 (sDRIP-seq).
HTseq-count v0.11.2 was then used to count the total number of reads at exon of genes (RNA-seq) or whole gene and gene binned by 1kb (sDRIP-seq).
Gencode vM1 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions with adj.pvalue of at least 0.05 and log2FC of at least +/- 1
Genome_build: mm9
Supplementary_files_format_and_content: Both sDRIP-seq and RNA-seq wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).

molecule: polyA RNA

source_name: B16-F10 cells, RNA-seq wild-type

growth_protocol: B16-F10 cells were obtained from ATCC and grown in high-glucose Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin / streptomycin. Cells were seeded 1-2 days prior to experiments and were grown to 40-60% confluency

extract_protocol:
RNA-seq: Total RNA was extracted using Trizol and poly(A) selected using poly(T) beads.
sDRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
RNA-seq: Standard paired-end TruSeq protocol.
sDRIP-seq: Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

treatment_protocol: Extracted DNA was subjected to mock or enzymatic treatments (RNase H1, RNase III, RNase T1, or RNase T1+RNase III) prior to immunoprecipitation with the S9.6 antibody.

value: skin melanoma cells


title: YFP- Naïve Rep1


title: S Day+15 scRNAseq

city: Munich

first: Moritz

middle: J

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

country: Germany

data_processing:
Demultiplexed with Illumina's bcl2fastq
Cell barcodes/UMIs in Read 1 were identified and added as XC/XM tag to Read 2 with ddSeeker
Reads were aligned with STAR aligner (v2.7.5) using default settings for thresholds
Aligned data was merged with unaligned/tagged data with Drop-seq tools (v2.3.0)
Ensembl Annotation was added with Drop-seq tools
Cell barcodes were checked for remaining synthesis and substitution errors and repaired with Drop-seq tools.
The provided UMI count tables were computed as digital gene expression with Drop-seq tools for the 2000 most abundant cell barcodes in each sample
To acquire separate count tables for spliced and unspliced reads (in the loom files provided), DropEst (v0.8.6) was used instead of Drop-seq's Digital Expression function. The corresponding configuration file of Velocyto was used in following command , in accordance with the suggestions of the developers of Velocyto (La Manno et al. 2018): dropest -m -V -b -f -g %GTF file from Drop-seq metabundle% -L eiEIBA -m -c %FILEPATH%/ dropEst/configs/drop_seq_velocyto.xml
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Two files are provided per sample: A UMI count matrix from Drop-seq's digital expression analysis disregarding splicing detection & a loom file containing separate count tables for spliced & unspliced counts

source_name: hiPSC-derived oligodendroglial culture

growth_protocol: Lentiviral infection of hiPSCs, with cistronic contructs containing SOX10 (S) or SOX10-OLIG2-NKK6.2 (SON) and constitutive expression units for the reversed tetracycline transactivator (rtTA) and a puromycin selection cassette, was performed in StemMACS iPS-Brew.  hiPSC media was changed to mTESR1. 12 days neural induction was initiated by medium exchange to N2B27 media, supplemented with 10 µM SB431542 (StemCell), 1 µM LDN193189 (StemCell) and 0.1 µM retinoic acid (RA, Sigma) until day 8 and 0.1 µM RA and 1 µM SAG until day 12. Directed OL differentiation (Day +0) was initiated by adding OL differentiation medium (OL-DM), which consists of N2B27 supplemented with 10 ng/mL PDGF-AA (PeproTech), 10 ng/mL IGF1 (PeproTech), 5 ng/mL HGF (PeproTech), 10 ng/mL NT3 (Peprotech), 0.1 ng/mL Biotin (Sigma), 1 mM dbcAMP (Sigma), 60 ng/mL T3 (Sigma) and 1 µg/mL doxycycline (Clontech).

extract_protocol: SureCell 3' WTA Library Prep Kit Manufacturer's Protocol (Illumina)

treatment_protocol: To reveal the transcriptional architecture of individual induced cells from S- and SON-directed differentiation, we applied single-cell RNA sequencing (scRNAseq) after completion of neural induction (NPC Day+0) and 15 days after S (S Day+15) and SON (SON Day +15) induction.

value: hiPSC-derived oligodendroglial culture

tag: timepoint

value: Day 15

tag: expressed tf combination


title: SON Day+15 scRNAseq

value: Sox10, Olig2, Nkx6.2


title: YFP- Memory Rep2


title: B16-F10 cells, RNA-seq wild-type rep1

value: wild-type


title: B16-F10 cells, RNA-seq carm1-/- rep3

source_name: B16-F10 cells, RNA-seq carm1-/-


title: NPC Day+0 scRNAseq

source_name: hiPSC-derived NPCs

value: hiPSC-derived NPCs

value: Day 0


title: B16-F10 cells, RNA-seq wild-type rep2


title: B16-F10 cells, RNA-seq carm1-/- rep2


title: B16-F10 cells, RNA-seq carm1-/- rep1


title: YFP- Memory Rep1


title: NF54-rep1-nodrug-ctrl-T1


title: 203806760152_R02C01

type: genomic

city: Ann Arbor

first: Maureen

last: Sartor

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

institute: University of Michigan

description:
normal neonatal dried bloodspot sample
Sample passed quality control

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Processed in R (Bioconductor - Enmix and minfi)
processed data file includes quantile normalized average beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: neontatal bloodspot 149

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen EZ1 DNA Investigator Kit according to standard instructions

tag: infant sex

value: Female

tag: tissue

value: neonatal blood spot

tag: arch id


title: 203516060077_R01C01

source_name: neontatal bloodspot 146

value: Male


title: 203486190008_R01C01

source_name: neontatal bloodspot 150


title: 203486190008_R03C01

source_name: neontatal bloodspot 151


title: 203516060078_R03C01

source_name: neontatal bloodspot 148


title: 203806760138_R03C01

source_name: neontatal bloodspot 152


title: 203483530044_R03C01

source_name: neontatal bloodspot 144


title: Non Tumor region 16

city: Montpellier

first: Damien

last: Grégoire

address: 1919, route de Mende

country: France

institute: CNRS

data_processing:
Base calling was performed with Illumina RTA software. FastQC was used to perform quality control of the sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg38 whole genome using bowtie v2.29 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Calculations for raw counts were done using featureCounts, using the optioon "stranded" (-s 1) in order to assess the read orientation.
Genome_build: Hg38
Supplementary_files_format_and_content: txt

source_name: liver section (laser capture)

extract_protocol:
Serial 10 µM sections of human liver tissue were mounted on PET-membrane steel frame slides (Leica) and stored at −80 °C until use. For laser dissection, slides were fixed for 20 min in 70% ethanol at +4 °C followed by dissection using a PALM MicroBeam laser UV dissector (Zeiss). Serial section alignment of the smiFISH and unstained slides was carried out at the Laser Microdissection platform at Bordeaux Neurocampus using an automated serial section alignment and microdissection (PALM 4 technology, Zeiss). RNA was extracted and purified from each sample (circa 100–200 cells) using the RNeasy® Micro kit (Qiagen) with on-column DNAse I digestion. RIN values were calculated using the Agilent Bioanalyzer with RNA pico chips. RNA samples containing a minimum of 1 ng RNA and a RIN >4 were used for further RNAseq analysis.
RNA was amplified using the Ovation® SoLo RNA-seq library preparation kit (NuGEN) used for low input or single-cell sequencing according to manufacturer’s instructions, including a ribosomal RNA depletion step (Insert Dependent Adaptor Cleavage). Libraries were then monitored for concentration and fragment sizes using a Fragment Analyzer (kit Standard Sensitivity NGS) and by qPCR (ROCHE Light Cycler 480) prior sequencing on Illumina HiSeq2000 platform (single end 50 bp length).

tag: hcv status

value: HCV negative

tag: disease state

value: Non Tumor

value: liver


title: 203516060071_R04C01

source_name: neontatal bloodspot 143


title: Control cells Replicate 1

type: RNA

city: Newhaven

first: Jiangbing

last: zhou

address: 310 Cedar Street, Ste LH 412A

institute: Yale university

description: Biological replicate 1 of 4. Control  cells.

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to Affymetrix GeneChip arrays.

scan_protocol: After hybridization, slides were washed and scanned by GeneChip Scanner 3000.

data_processing: The Expression Console software also acquires and converts hybridization intensity data into a presence/absence call for each gene using appropriate algorithms.

label: biotin

source_name: Control  cells

label_protocol: 10 µg of total RNA was primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: Cells were grown in Neurobasal-A media (Invitrogen) supplemented with B27 nutritional supplement (Gibco), basic fibroblast growth factor (bFGF), and epidermal growth factor (EGF), and were maintained at 37°C and 5% CO2.own in Dulbecco’s modified Eagle’s medium (HyClone, Logan, UT, USA) with 10% fetal bovine serum (Biological Industries, Beit Haemek, Israel ) and 1% penicillin and streptomycin, and were maintained at 37°C and 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Using ZNF117 sgRNA to knockout the ZNF117

value: human glioblastoma stem cells

value: Control


title: Control cells Replicate 4


title: Control cells Replicate 3


title: ZNF117 knockout cells Replicate 3

description: Biological replicate 1 of 3. Stable ZNF117-knockout GS5 cells.

source_name: ZNF117 knockout cells

value: ZNF117 knockout


title: Non Tumor region 11

value: HCV positive


title: Tumor region 10

value: Tumor


title: Tumor region 9


title: Tumor region 6


title: ZNF117 knockout cells Replicate 1


title: MIPCC-DSP-20210909A-03 020

type: protein

city: Changsha

first: Lin

last: Ye

address: 139 Renmin Middle Road, Furong district, Changsha

country: China

institute: Central South University

hyb_protocol: The slides were incubated with multi-channel fluorescence staining combination with additional target specific oligos probe sets (1833 genes with 8659 pairs of probes, provided in supplementary Table S2), which is similar to conventional immunofluorescence or IHC.

scan_protocol: The slides were stained with Texas red-labeled CD45 antibody (GMX-PRO-MORPH-HST-12, Nanostring), Alexa Fluor 555-labeled Collagen IV and Syto13, together with the DSP antibody barcodes

data_processing: Protein counts were normalized using housekeeping proteins (histone H3 and ribosomal protein S6).

label: antibody

molecule: protein

source_name: Kidney

label_protocol: Target retrieval was performed in a water bath with 1M Tris-EDTA buffer (pH=9.0) for 15 min. The FFPE samples were stained with primary mouse CD45 antibody (Cat NO. 13917, Cell signaling Technology), subsequently with Alexa Fluor 594 secondary mouse antibody (A-11012, Thermo), and Alexa Fluor 555-labeled Collagen IV antibody and DNA stain Syto13 (GMX-PRO-MORPH-HST-12, Nanostring) to facilitate the identification of tissue morphology.

extract_protocol: Formalin-fixed paraffin-embedded renal tissues were used.

tag: disease

value: ANCA

value: 67 years

tag: gender


title: MIPCC-DSP-20210909A-03 023


title: MIPCC-DSP-20210909A-03 022


title: MIPCC-DSP-20210909A-03 021


title: Control cells Replicate 2

tag: genotype


title: 203516060078_R07C01

source_name: neontatal bloodspot 147


title: Tumor region 5


title: Non Tumor region 17

source_name: tumor section (laser capture)


title: MIPCC-DSP-20210909A-03 024


title: 203516060071_R06C01

source_name: neontatal bloodspot 145


title: Non Tumor region 12


title: 203806760138_R02C01

source_name: neontatal bloodspot 140


title: MIPCC-DSP-20210909A-03 018


title: 203486190008_R08C01

source_name: neontatal bloodspot 139


title: 203483530045_R08C01

source_name: neontatal bloodspot 142


title: MIPCC-DSP-20210909A-03 016


title: 203483530042_R01C01

source_name: neontatal bloodspot 136


title: MIPCC-DSP-20210909A-03 013

value: 51 years


title: SiHa-si-NC-3

city: Wuhan

first: Chunjiang

last: He

address: Donghu Road 185

department: School of Basic Medical Sciences

institute: Wuhan University

data_processing:
Basecalls performed using bcl2fastq2
Using trim-galore to remove low-quality reads and sequencing adapters
Reads were mapped to the human reference genome (GRCh38.p13/hg38, UCSC Genome Browser) using STAR v2.77.a
Using CLEAR to obtain the circular transcript data like raw counts, circular/linear ratio
Gene counts data was quantified with FeatureCounts
Genome_build: GRCh38.p13/hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and cervical sample

source_name: cell line

growth_protocol: All cells were maintained in DMEM (HyClone, USA) supplemented with 10% fetal bovine serum (Gibco, South America), 1% penicillin-streptomycin (Gibco, USA), and were kept at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit 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: SiHa

tag: transfection

value: si-NC


title: 203483530043_R01C01

source_name: neontatal bloodspot 137


title: SiHa-si-circYPEL2-3


title: SiHa-si-circYPEL2-2


title: SiHa-si-NC-2


title: MIPCC-DSP-20210909A-03 011


title: 203483530042_R08C01

source_name: neontatal bloodspot 133


title: HeLa-si-NC-3

value: HeLa


title: MIPCC-DSP-20210909A-03 019


title: 203806760152_R04C01

source_name: neontatal bloodspot 141


title: HeLa-si-NC-2


title: 203806760152_R01C01

source_name: neontatal bloodspot 134


title: MIPCC-DSP-20210909A-03 017


title: HeLa-si-circYPEL2-3


title: Tumor region 1

source_name: liver section (laser capture)


title: 203483530043_R04C01

source_name: neontatal bloodspot 132


title: HeLa-si-NC-1


title: HeLa-si-circYPEL2-2


title: 203483530045_R07C01

source_name: neontatal bloodspot 138


title: 203516060077_R04C01

source_name: neontatal bloodspot 135


title: MIPCC-DSP-20210909A-03 012

source_name: Kidney

value: Female


title: SiHa-si-NC-1


title: MIPCC-DSP-20210909A-03 015


title: SiHa-si-circYPEL2-1


title: MIPCC-DSP-20210909A-03 014


title: 203486190008_R04C01

source_name: neontatal bloodspot 131

value: neonatal blood spot


title: HeLa-si-circYPEL2-1


title: 203516060078_R05C01

source_name: neontatal bloodspot 130

value: Male


title: Normal cervical-3

source_name: tissue

tag: individual

value: normal patient 3

value: normal cervical tissue


title: Normal cervical-1

value: normal patient 1


title: MIPCC-DSP-20210909A-03 007

value: 56 years


title: MIPCC-DSP-20210909A-03 006


title: MIPCC-DSP-20210909A-03 010


title: 203806760152_R06C01

source_name: neontatal bloodspot 129


title: Normal cervical-2

value: normal patient 2


title: MIPCC-DSP-20210909A-03 005


title: Cervical cancer-3

value: cervical cancer patient 3

value: cervical cancer


title: Cervical cancer-2

value: cervical cancer patient 2


title: MIPCC-DSP-20210909A-03 004

value: ANCA


title: 203486190008_R07C01

source_name: neontatal bloodspot 128


title: Cervical cancer-1

value: cervical cancer patient 1


title: ZNF117 knockout cells Replicate 2

source_name: ZNF117 knockout cells

tag: cell line

tag: cell type

value: human glioblastoma stem cells

value: ZNF117 knockout


title: 203483530045_R02C01

source_name: neontatal bloodspot 126


title: MIPCC-DSP-20210909A-03 003

tag: age


title: MIPCC-DSP-20210909A-03 009

value: 51 years


title: 203490640037_R04C01

source_name: neontatal bloodspot 127


title: 203516060072_R07C01

source_name: neontatal bloodspot 125


title: MIPCC-DSP-20210909A-03 002


title: 203483530042_R04C01

source_name: neontatal bloodspot 124


title: MIPCC-DSP-20210909A-03 008


title: MIPCC-DSP-20210909A-03 001


title: CHD8sh4_H3K36me3

city: Basel

first: Emanuela

last: Kerschbamer

state: Basel Stadt

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

library_source: genomic

data_processing:
ChIP-seq reads were aligned on the human genome reference assembly GRCh38 using BWA (version 0.7.15) (Li and Durbin 2009). Aligned reads were filtered to discard unmapped, multiply mapped, PCR duplicates reads (Picard tools MarkDuplicates version: 2.3.0, Picard Toolkit.” 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/) along with low quality alignments (samtools view -q 1, samtools version 1.7) (Li et al. 2009).
Peak calling was performed with MACS2 (version 2.1.0) using a minimum FDR threshold 0.00001. The same settings with the addition of the --broad option were used for H3K27me3 and H3K36me3 marks (Zhang et al. 2008). Peaks localized to blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/) or unplaced contigs were filtered out. Narrow peaks (for H3K27ac, H3K4me1, H3K4me2, H3K4me3 histone marks) closer than 350 bp were merged into a single peak.
Genome_build: GRCh38
Supplementary_files_format_and_content: narrowPeak files for H3K4me1, H3K4me2, H3K4me3 and H3K27ac; broadPeak files for H3K27me3 and H3K36me3

source_name: Neural progenitor cells CHD8 KD

growth_protocol: Human iPSC-derived NPC lines were cultured on poly-L-ornithine hydrobromide/laminin - coated plates in hiNPC medium (70% v/v DMEM completed with 30% v/v HAM F12 , 2% v/v B27, 1% v/v Penicillin-Streptomycin solution, 1% v/v L-Glutamine and supplemented with EGF, bFGF and Heparin). Semi-confluent monolayers of hiNPCs were maintained in 5% CO2, 37°C humidified incubator.

extract_protocol:
Chromatin immunoprecipitation was performed using the protocol described by (33); with minor modifications. Sonication of the samples was accomplished using a Bioruptor sonicator. Sheared-chromatin was diluted 10 fold in ChIP dilution buffer, supplemented with protease inhibitor. 50 μl of sheared chromatin was removed and stored at 4°C as control aliquot (INPUT).  Each sample was incubated overnight with antibodies (20 ug/ChIP) of interest. The following primary antibodies were used: H3K27me3 (07-449, Millipore), H3K4me3 (AB8580, Abcam), H3K36me3 (Ab9050, Abcam), H3K4me2 (AB7766, Abcam), H3K4me1 (AB8895, Abcam) and H3K27ac (AB4729, Abcam). Chromatin–Antibody complexes were then precipitated, washed eluted. DNA isolation was performed by phenol:chloroform:isoamyl alcohol, precipitated with NaCl, supplemented with glycogen, washed with EtOH and then treated with RNase I. Finally, DNA was purified with MinElute Kit.
Libraries were prepared according to NEBNext UltraII DNA Library preparation kit (Illumina).

treatment_protocol: Human iPSC-derived NPC line GM8330-8 (Sheridan et al., 2011), Sh1-CHD8, Sh2-CHD8, Sh4-CHD8 and Sh-GFP lines, were previously generated by lentiviral delivery of shRNAs targeting CHD8 and GFP coding sequences respectively (Sugathan et al., 2014).

value: iPSC-derived neural progenitor cells

value: CHD8sh4 (knock-down treatment)

tag: chip antibody

value: H3K36me3 (Ab9050, Abcam)


title: 203483530042_R07C01

source_name: neontatal bloodspot 123

value: Male

value: neonatal blood spot


title: GFP2_H3K36me3

source_name: Neural progenitor cells control

value: GFPsh (knock-down treatment)


title: CHD8sh1_H3K36me3

value: CHD8sh1 (knock-down treatment)


title: CHD8sh2_H3K36me3

value: CHD8sh2 (knock-down treatment)


title: GFP2_H3K27me3

value: H3K27me3 (07-449, Millipore)


title: GFP_H3K36me3


title: 203486190008_R05C01

source_name: neontatal bloodspot 122


title: Liver_Steatosis_4

city: Zaragoza

first: Luis

middle: Vicente

last: Herrera-Marcos

state: Zaragoza

address: C/Miguel servet nº177

department: Bioquimica y biologia molecular y celular

institute: Universidad de Zaragoza. Facultad de Veterinaria

data_processing:
This library was read through on the DNBseq platform using Combinational Probe-Anchor Synthesis Sequencing Method.
Regarding the bioinformatic analysis. Firstly, SOAPnuke v1.5.2 was used to filter reads, and HISAT2 v2.0.4 to do the genome mapping step.
Then, in order to study the transcriptome, clean reads were aligned to the reference genome using Bowtie2 v2.2.5 and then calculate gene expression level with RSEM v1.2.12.
Finally to detect differentialy expressed genes (DEG) PossionDis was used.
Genome_build: Ensembl Sus scrofa genome 10.2
Supplementary_files_format_and_content: Excel tables containing the genes differentialy expressed in each animal before and after the experiment.
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

organism: Sus scrofa

source_name: liver from pigs

extract_protocol:
liver biospies were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. RNA from each liver was isolated using Tri-reagent (Ambion). DNA contaminants were removed by TURBO DNAse treatment using the DNA removal kit from Ambion. RNA was quantified by absorbance at A260/280. The integrity, concentration and purity of RNA was verified by a Biorad experion chip (Hercules, CA, USA)
8 liver RNA samples from representative individuals were pooled in 4 pools for each condition.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into 100 bp pieces.
The cleaved RNA fragments are copied into doble strand cDNA.containing the addition of a single 'A' base and the subsequent ligation of the adapter.
After purification and enrichment by PCR, samples were pooled to make single strand DNA circle(ssDNA circle), which gave the final library.
DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process.
The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study.

value: liver

tag: breed

value: Landrace x Large White

value: 6 months

tag: Sex

value: male

tag: condition

value: steatosis


title: Liver_Steatosis_3


title: CHD8sh4_H3K27me3


title: 203483530044_R01C01

source_name: neontatal bloodspot 121

tag: infant sex

value: Female


title: Liver_Steatosis_2

tag: tissue


title: Liver_Steatosis_1


title: CHD8sh2_H3K27me3


title: GFP2_H3K27ac

value: H3K27ac (AB4729, Abcam)


title: CHD8sh4_H3K27ac


title: 203806760152_R05C01

source_name: neontatal bloodspot 120

tag: arch id


title: GFP_H3K27ac


title: CHD8sh2_H3K27ac


title: CHD8sh1_H3K27me3


title: CHD8sh1_H3K27ac


title: Liver_Control_4

value: 4 months

value: healthy


title: 203483530045_R01C01

source_name: neontatal bloodspot 118


title: 203516060077_R06C01

source_name: neontatal bloodspot 117


title: Liver_Control_3


title: GFP_H3K4me3

value: iPSC-derived neural progenitor cells

value: H3K4me3 (AB8580, Abcam)


title: GFP2_H3K4me3


title: GFP_H3K27me3


title: CHD8sh2_H3K4me3


title: 203483530042_R06C01

source_name: neontatal bloodspot 116

value: Male


title: CHD8sh1_H3K4me3


title: CHD8sh4_H3K4me3

value: CHD8sh4 (knock-down treatment)


title: Liver_Control_1


title: 203483530042_R05C01

source_name: neontatal bloodspot 115

value: neonatal blood spot


title: 203483530045_R03C01

source_name: neontatal bloodspot 119


title: GFP2_H3K4me2

value: GFPsh (knock-down treatment)

value: H3K4me2 (AB7766, Abcam)


title: 203516060072_R01C01

source_name: neontatal bloodspot 113


title: CHD8sh4_H3K4me2


title: GFP2_H3K4me1

value: H3K4me1 (AB8895, Abcam)


title: GFP_H3K4me1


title: CHD8sh2_H3K4me1

value: CHD8sh2 (knock-down treatment)


title: Testicular extracellular vesicles 1

city: New Territories

first: Ellis

last: Fok

address: Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: Chinese University of Hong Kong

description: replicate 1

data_processing:
BGISEQ-500 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality reads, then mapped to genome using Bowtie 2 and cmsearch with -q -L 16 --phred64 -p 6 and --cpu 6 --noali, respectively.
Small RNAs were classified with priority rule: MiRbase > pirnabank > snoRNA > Rfam > other sRNA
miRDeep2 used for predict novel miRNA
Supplementary_files_format_and_content: count and tpm

source_name: testis

extract_protocol:
RNA was extracted by Rneasy mini kit
Libraries were prepared according to BGISEQ-500 platform. Briefly, small RNAs were segmented by PAGE. 3' adaptor was added by ligation followed by reverse primer annealing. Then, 5' adaptor was added by ligation. Strand cDNAs were synthesized followed by PCR amplification to enrich cDNA with both 3' and 5' adaptors.

treatment_protocol: Proteinase K and RNase A treated

tag: strain

value: adult


title: CHD8sh2_H3K4me2


title: CHD8sh1_H3K4me2

value: CHD8sh1 (knock-down treatment)


title: CHD8sh4_H3K4me1


title: Testicular extracellular vesicles 2

description: replicate 2


title: 203483530042_R02C01

source_name: neontatal bloodspot 111


title: 203806760152_R03C01

source_name: neontatal bloodspot 110


title: DU145_Lactate_iBET_4

city: Bellinzona

first: Giada

last: Sandrini

address: Via Chiesa 5

institute: IOR

data_processing:
Sequencing reads were aligned to the GRch38.p12 release of the human genome
Reads were quantified using STAR aligner (STAR-2.6.1c)
Rawcounts were processed according to DESeq pipeline
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file

extract_protocol:
RNA was isolated from DU145 cells in four independent replicates, marked with Illumina total prep 96 RNA amplification kit (Ambion).
RNA sequencing was performed using Next Ultra II Directional RNA Library Prep Kit for Illumina starting from 800ng of total RNA each sample and sequenced on the Illumina NextSeq500 with single-end, 75 base pair long reads

tag: treatment

tag: replicate


title: CHD8sh1_H3K4me1


title: 203806760152_R07C01

source_name: neontatal bloodspot 109


title: DU145_Lactate_iBET_2


title: 203516060072_R06C01

source_name: neontatal bloodspot 112


title: DU145_Lactate_iBET_3


title: Liver_Control_2

value: liver

value: Landrace x Large White

value: male


title: 203516060072_R04C01

source_name: neontatal bloodspot 108

value: Female


title: DU145_Lactate_iBET_1


title: DU145_iBET_4

value: iBET


title: DU145_iBET_3


title: DU145_iBET_2


title: GFP_H3K4me2

source_name: Neural progenitor cells control


title: 203516060071_R01C01

source_name: neontatal bloodspot 107


title: 203516060072_R03C01

source_name: neontatal bloodspot 114


title: DU145_iBET_1


title: 203516060071_R03C01

source_name: neontatal bloodspot 106


title: DU145_Lactate_3

value: Lactate


title: DU145_Lactate_4


title: DU145_Lactate_2


title: 203516060077_R02C01

source_name: neontatal bloodspot 105


title: 203483530044_R08C01

source_name: neontatal bloodspot 104


title: DU145_Lactate_1


title: DU145_Ctrl_4

value: Ctrl


title: 203516060077_R03C01

source_name: neontatal bloodspot 103


title: DU145_Ctrl_2


title: DU145_Ctrl_3


title: DU145_Ctrl_1


title: Lab-WT 23 °C under blue light

city: Seoul

first: Jihye

last: Yang

address: Anam-ro 145

department: Department of Environmental Science and Ecological Engineering

country: South Korea

institute: Korea University

data_processing:
RNA sequencing was performed on an Illumina Novaseq 6000 platform.
The reference genome sequence was retrieved from the NCBI database.
Quality-filtered reads were aligned to the reference genome sequence using Bowtie2.
The relative abundance of transcripts is presented as FPKM (Fragments Per Kilobase of transcript per Million).

organism: Acinetobacter baumannii

source_name: Proteobacteria cells

growth_protocol: Exponential phase at 23°C under blue light irradiated (LB media)

extract_protocol:
Using an RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
Illumina sequencing library was constructed by the TruSeq Stranded Total RNA with Ribo-Zero Plus (Illumina, San Diego, CA, USA) following the manufacturer's protocol

tag: growth phase

value: Mid-exponential phase

value: Lab-WT


title: Lab-WT 23 °C dark


title: 203806760138_R04C01

source_name: neontatal bloodspot 101


title: sEVs derived from senescent hUCMSCs

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

institute: Korea Univ.

description: S-UCMSC

data_processing:
Sequence reads mapped by bowtie2 software to obtain alignment file.
Read counts mapped on mature miRNA sequence extracted from alignment file using bedtools (v2.25.0) and R (version 3.2.2).
Read counts used to determine miRNA expression levels.
Genome_build: Mature miRNA sequences available on miRBase was used as reference for mapping.
Supplementary_files_format_and_content: Excel files contain gene symbol, fold change, normalized data, raw data, mature id, start, end, width, strand, type, alias, derives from, sequence, and target prediction based on miRBase search.

source_name: umbilical cord

growth_protocol: Human umbilical cord mesenchymal stem cells were maintained in growth media (DMEM supplemented with 10% FBS and 1% non-essential amino acids).

extract_protocol:
Small extracellular vesicles were isolated using ExoSpin kit according to the manufacturer protocol. Total RNA from the small extracellular vesicles were extracted using Trizol reagent.
NEBNext Multiplex Small RNA Library Prep Kit

treatment_protocol: Human umbilical cord mesenchymal stem cells were seeded in T75 flasks using serum-free media supplemented with exosome-free FBS and incubated for 48 hours.

value: human umbilical cord mesenchymal stem cells (hUCMSCs)

tag: cellular phenotype

value: senescent

tag: passages


title: 203486190008_R02C01

source_name: neontatal bloodspot 102

value: neonatal blood spot


title: WT_PolProf.Rep_3

city: BOSTON

first: Laura

middle: Elisabeth

last: Wester

state: Massachusetts

address: 677 Huntington Ave

institute: Harvard T.H. Chan School of Public

description:
RNA from polysome profiling experiment Rep. 3
WT.deseq2_results.tsv

data_processing:
Raw reads were mapped with kallisto version 0.46.1 to reference genome ce11 ENSEMBL build 103 (kallisto quant)
Transcript Abundances were quantified in the same step (kallisto quant)
Differential gene expression was calculated using DESeq2 version 1.30.1 in R version 4.0.4 (model:  ~Library + Replicate )
kept genes with at least 10 reads over all samples
counts(dds, normalized = TRUE)
Genome_build: ce11, ensembl build 103
Supplementary_files_format_and_content: tab separated files with normalized counts and differential gene expression

organism: Caenorhabditis elegans

source_name: Polysome profiling of whole tissue lysate

growth_protocol: All C. elegans strains were generated and maintained at 20 °C on nematode growth medium (NGM) agar plates, seeded with the Escherichia coli (E. coli) strain OP50-1 (CGC). After CRISPR engineering, all new alleles were outcrossed against the wildtype Bristol N2 strain.  Before  collections for RNAseq, all strains were bleached to E. coli strain OP50 and grown to day 1 of adulthood.

extract_protocol:
Polysome profiling: For the analysis of mRNA translation via polysome profiling based on Großhans and Ding (2009), synchronized gravid day 1 adults were grown on NGM plated seeded with OP50 (Ding and Großhans, 2009). Per genotype and replicate, about 12000 worms were harvested and washed twice with M9, once with M9 supplemented with 1 mM cycloheximide (Sigma) and once with lysis buffer (20 mM Tris pH 8.5, 140 mM KCl, 1.5 mM MgCl2, 0.5 % Nonidet P40, 1 mM DTT, 1 mM cycloheximide). Worms were pelleted and resuspended in 350 μL cold lysis buffer, supplemented with 1 % sodiumdeoxycholate (DOC, Sigma). Resuspended worms were lysed using a chilled Dounce homogenizer. Ribonuclease inhibitor RNasin (Promega) was added to samples used for RNA sequencing at a concentration of 0,4 U/μL. Samples were then mixed and incubated on ice for 30 min, followed by a centrifugation step (12000 g, 10 min, 4 °C) for clearance. The pellet was discarded and the RNA concentration of the supernatant was estimated by absorbance measurement at 260 nm. At least 50 µl of lysate were taken aside as corresponding total RNA at this point, diluted in an equal amount of TRI reagent (Zymo Research) and frozen at -80 °C. To prepare sucrose gradients, 15 % (w/v) and 60 % (w/v) sucrose solutions were prepared in basic lysis buffer (20 mM Tris pH 8.5, 140 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM cycloheximide). Linear sucrose gradients were produced using a Gradient Master (Biocomp). Equivalent amounts of sample (around 400 μg RNA) were loaded onto the gradient and centrifuged at 39000 g for 3 h at 4 °C, using an Optima L-100 XP Ultracentrifuge (Beckman Coulter) and the SW41Ti rotor. To analyze the sample on the gradient during fractionation, absorbance at 254 nm was measured and recorded (Econo UV monitor EM-1, Biorad), using the Gradient Profiler software (version 2.07). Gradient fractionation was performed from the top down using a Piston Gradient Fractionator (Biocomp) and a fraction collector (Model 2110, Biorad). Gradients were fractionated in 20 fractions of equal volume. In an initial experiment, the ribosomal fractions were validated by analyzing RNA from each fraction via agarose gel electrophoresis. The 18 S and 28 S rRNA signals were used as indicators for the 40 S ribosomal subunit, the 60 S ribosomal subunit and fully assembled ribosomes. For more precise analysis of ribosomal fractions, they were collected by hand according to their absorbance profile.  For RNA sequencing experiments, one single fraction comprising all polysomal fractions (corresponding to Figure 1, polysome profiling sequencing A) or one fraction comprising the 60 S ribosomes, the 80 S ribosomes and polysomes (corresponding to Figure 2 and Sup. Figure 2, polysome profiling sequencing B) was collected per sample. RNA extraction from total lysates and polysome fractions was performed using the Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer´s recommendations.
SKI TRIP experiments: SKI TRIP experiments were optimized based on previous TRAP models (McLachlan and Flavell, 2019; Sanz et al., 2009). Per SKI TRIP sample, 50 µl Protein G coated dynabeads (ThermoFisher) were washed with 1 ml PBS and incubated with 1 ml PBS and 0.1 μg monoclonal anti- FLAG antibody (Sigma F1804) per μL of dynabeads at 4 °C and constant rotation overnight. Per FLAG IP, 30000 synchronized day 1 worms were collected in M9 buffer, washed two times in M9 and one final time in M9 including 1 mM cycloheximide (Sigma). Samples were then washed with lysis buffer prepared in nuclease free water (10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) pH 7.4, 150 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 1 mM cycloheximide, EDTA free Protease Inhibitor). Worms were pelleted at 2000 g for 2 min and the supernatant was discarded. The residual worm pellet (about 500 μL) was shock frozen by dropping it into liquid nitrogen in fractions of approximately 20 μL using a P200 pipette. The resulting frozen worm pearls were carefully lysed using the TissueLyserII (Qiagen) or the CryoMill (Retsch) for twice 1 min at 30 Hz, using metal beads of 5 mm diameter. Keeping all parts and the samples RNase-free and frozen using dry ice and liquid nitrogen at all times was crucial. Lysed worm powder was thawed on ice in a final volume of 3.75 ml lysis buffer including 0.5 % v/v NP-40 (Sigma), 0.4 U/μL RNasin (Promega), 10 mM ribonucleoside vanadyl complex (RVC by NEB), 33 mM 1,2-diheptanoylsn-glycero-3-phosphocholine (DHPC by Merck) and 1 % w/v sodium deoxycholate (Sigma). It is crucial to add the mentioned lysis buffer in a volume to reach approximately 8 worms/μL, taking the starting volume of the ~500 µl worm pellet into account. In case of varying worm or pellet amounts, the volume of added lysis buffer should be adjusted in this step. Samples were incubated for 30 min on ice. After centrifugation at 12000 g for 10 min at 4 °C, the supernatant was transferred to new tubes (kept on ice at all times) and the pellet was discarded. As corresponding total RNA sample, 100 μL of supernatant was mixed with 100 μL of RLT buffer (Qiagen RNeasy Kit) including 1 % v/v ß-mercaptoethanol. This total RNA sample was then vortexed, incubated for 10 min at room temperature and stored at -80 °C. The remaining supernatant was pre-cleared with washed 10 μL protein G coated Dynabeads (washed once with low-KCl wash buffer: 10 mM HEPES pH 7.4, 150 mM KCl, 5 mM MgCl2, 1 % v/v NP-40) without coupled antibody for at least 1 h. Samples were then incubated with washed FLAG-antibody-coupled beads (washed once with low-KCl wash buffer) for at least 2 h at 4 °C and constant rotation. Beads were washed four times with high-KCl wash buffer (10 mM HEPES pH 7.4, 350 mM KCl, 5 mM MgCl2, 1 % v/v NP-40, 0.04 U/μL RNasin).  For RNA elution, the beads were incubated in 350 μL of RLT buffer (Qiagen RNeasy Kit) including 1 % v/v ß-mercaptoethanol for 10 min at room temperature. The eluate was separated from the beads and RNA purification was performed using the Qiagen RNeasy Kit following the manufacturer’s protocol, analyzed using Agilent Technologies 2200 TapeStation System and further processed in RNA sequencing experiments.
For sequencing of RNA obtained from polysome profiling and FLAG IP samples, RNA was eluted and purified as described above in three replicates per experiment. RNA sequencing was performed at the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute (Boston, USA). All RNA samples were processed with a Kapa mRNA library preparation using a starting amount of 200 ng RNA per sample. The RNA libraries were sequenced on an Illumina NoveSeq with the following parameters: at least 20 M reads, 50 bp paired-end sequencing for sample batch AL7663 and 150 bp paired end sequencing for sample batches AL8842 and AL9212.

treatment_protocol: No special treatments.

value: Wildtype Bristol N2

tag: genotype

value: x

tag: promotor driving flag

value: All tissues

tag: fraction

value: RNA from polysome fractions


title: sEVs derived from nonsenescent hUCMSCs

description: NS-UCMSC

tag: cell type

value: nonsenescent


title: 203516060077_R08C01

source_name: neontatal bloodspot 100

value: Male


title: waste (cells from droplets that were not sorted)

city: San Francisco

first: Russell

last: Cole

address: 953 Indiana Street

institute: Scribe Biosciences

data_processing:
Sequencing data was aligned to the human GRCh38 reference genome using 10X Genomics Cell Ranger 3.1.0 pipeline. The FMC63 gene encoding the a CD19 CAR was appended to the GRCh38 reference genome prior to alignment.
Sequencing data was analyzed using 10X Genomics Loupe Browser 5.1.0
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: 10X Genomics CellRanger outputs

growth_protocol: CAR-T cells were cultured in 75-cm2 flasks in X-VivoTM 15 Serum-free Hematopoietic Cell Medium (Lonza BE02-060Q) supplemented with IL-2 (Peprotech cat. 200-02) at 33-66 units/mL. RAJI (ATCC CCL-86TM) and PBMC (StemCell cat. # 70025.1) were cultured in 75-cm2 flasks in RPMI-1640 medium (ATCC 30-2001TM) supplemented with 5% FBS and antibiotics

extract_protocol:
Sorted droplet and waste droplet emulsions were broken using an anti-static gun, and the aqueous phase of each sample removed for sequencing and image analysis. Samples were prepared for single-cell RNA-sequencing using the 10X Chromium Next GEM Single Cell 5’ Library Kit (10X catalog no. 1000265) according to the manufacturer’s instructions.
10X Chromium Next GEM Single Cell 5’ Library Kit

treatment_protocol: cells were combined in 1:1 ratio in microfluidic droplets

value: mixture of Primary human T lymphocytes and RAJI cells

value: waste


title: sorted (cells from droplets that were sorted based on IFN-γ signal)

source_name: Primary human T lymphocytes and RAJI cells

value: sorted


title: WT_PolProf.Rep_1

description:
RNA from polysome profiling experiment Rep. 1
WT.deseq2_results.tsv


title: 203516060071_R07C01

source_name: neontatal bloodspot 99


title: EC transfected with scrambled precursor Rep1

city: Maastricht

first: Jana

last: Hegenbarth

state: Limburg

address: Universiteitssingel 50

department: Department of Molecular Genetics

country: Netherlands

institute: Maastricht University

data_processing:
Read trimming with trimmomatic v. 0.36 (Parameters: LEADING:3 TRAILING:3 MINLEN:15 -phred33)
Quality control with FastQC
Read mapping with hisat2 v. 2.1.0 (Parameters: only mapped reads were used, all QC params used as default.)
Gene assembly with stringtie v.1.3.4 and file conversion to countmatrix as recommended in stringtie manual (Parameters: -v -p 8 --rf -e)
Genome_build: Ensembl Release90 (Homo_sapiens.GRCh38)
Supplementary_files_format_and_content: CSV-file, contains gene read counts as Deseq2 input

source_name: HUVECS

growth_protocol: Cells were cultured in EGM-2 media consisting of EBM-2 Basal Medium supplemented with Endothelial Cell Growth Medium-2 Bullet Kit (and cultured at 37oC with 5% CO2.

extract_protocol:
Total RNA was isolated from cultured cells using Direct-zol RNA MiniPrep according to manufacturer’s instructions.
RNA library preparation was performed according to the manufacturer’s instructions using the NEBNext rRNA depletion and RNA Ultra II library prep kit

treatment_protocol: Cells in passage number 6-7 were used. 15*104 HUVECs were cultured in 6-well plates and upon reaching 70% confluency, they were transfected with 10 nm of either a precursor molecule for hsa-miR-200c-3p or a scramble precursor, as control, for 24h.

value: human umbilical vein endothelial cells

tag: transfected with

value: precursor-scrambled

tag: disease state

value: healthy


title: EC transfected with precursor-200c Rep3


title: WT_Total_PP.Rep_3

description:
Total RNA for normalization Rep. 3
WT.deseq2_results.tsv

source_name: Whole tissue lysate


title: EC transfected with scrambled precursor Rep3


title: EC transfected with scrambled precursor Rep2


title: EC transfected with precursor-200c Rep2


title: 203483530042_R03C01

source_name: neontatal bloodspot 98


title: EC transfected with precursor-200c Rep1


title: WT_Total_PP.Rep_2

description:
Total RNA for normalization Rep. 2
WT.deseq2_results.tsv


title: 203483530044_R06C01

source_name: neontatal bloodspot 97


title: 203516060078_R06C01

source_name: neontatal bloodspot 96


title: WT_Total_PP.Rep_1

description:
Total RNA for normalization Rep. 1
WT.deseq2_results.tsv


title: Population Control 10

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

data_processing:
FASTQ files were processed by HTG EdgeSeq parser software
Parser produces text file of counts per target miRNA
Genome_build: NA - set of 2083 targets used, plus 5 negative controls, 1 positive control and 13 housekeeping genes - total of 2102 observations per sample
Supplementary_files_format_and_content: txt files with target-level counts

source_name: serum

extract_protocol:
Samples were lysed with a 1:1 ratio of HTG biofluids lysis buffer, according to manufacturer's instructions.
Lysates input into nuclease protection assays run on the HTG EdgeSeq processor. Sequence adapters were added to the samples in a 16-cycle PCR reaction. PCR products were purified using AMPure XP beads (Beckman Coulter, High Wycombe, UK).

value: peripheral blood

value: Population Control

tag: nas

tag: saf activity

tag: fibrosis stage

tag: disease group

value: Control


title: Population Control 7

tag: tissue


title: Population Control 9


title: Population Control 8


title: Population Control 6


title: Ubiquitous_PolProf_2.Rep_3

description:
RNA from polysome profiling experiment Rep. 3
UbiquitousB.deseq2_results.tsv

tag: strain

value: :rpl-22:endogenous rpl-22

value: RNA from 60S, 80S and polysome fractions


title: Population Control 5


title: 203516060072_R02C01

source_name: neontatal bloodspot 95

tag: infant sex

value: neonatal blood spot

tag: arch id


title: Ubiquitous_PolProf_2.Rep_2

description:
RNA from polysome profiling experiment Rep. 2
UbiquitousB.deseq2_results.tsv


title: 203516060071_R05C01

source_name: neontatal bloodspot 94


title: Population Control 4


title: WT_PolProf.Rep_2

description:
RNA from polysome profiling experiment Rep. 2
WT.deseq2_results.tsv

value: Wildtype Bristol N2

value: x


title: Population Control 3


title: 203483530043_R06C01

source_name: neontatal bloodspot 93

value: Female


title: Population Control 2


title: Ubiquitous_PolProf_2.Rep_1

description:
RNA from polysome profiling experiment Rep. 1
UbiquitousB.deseq2_results.tsv

value: All tissues


title: Population Control 1


title: 203483530044_R05C01

source_name: neontatal bloodspot 92

value: Male


title: NAFLD Patient 98

value: Chronic Liver Disease (NAFLD)


title: Ubiquitous_Total_PP_2.Rep_3

description:
Total RNA for normalization Rep. 3
UbiquitousB.deseq2_results.tsv


title: NAFLD Patient 99


title: Ubiquitous_Total_PP_2.Rep_2

description:
Total RNA for normalization Rep. 2
UbiquitousB.deseq2_results.tsv


title: NAFLD Patient 97


title: NAFLD Patient 96


title: 203516060077_R07C01

source_name: neontatal bloodspot 91


title: Ubiquitous_Total_PP_2.Rep_1

description:
Total RNA for normalization Rep. 1
UbiquitousB.deseq2_results.tsv


title: NAFLD Patient 94


title: 203010900023_R04C01

description:
normal neonatal dried bloodspot sample
Sample failed quality control. No processed data provided.

source_name: neontatal bloodspot 90


title: NAFLD Patient 93


title: 203483530043_R08C01

source_name: neontatal bloodspot 89


title: Ubiquitous_PolProf.Rep_1

description:
RNA from polysome profiling experiment Rep. 1
UbiquitousA.deseq2_results.tsv

source_name: Polysome profiling of whole tissue lysate

value: RNA from polysome fractions


title: NAFLD Patient 90


title: NAFLD Patient 95


title: Ubiquitous_PolProf.Rep_2

description:
RNA from polysome profiling experiment Rep. 2
UbiquitousA.deseq2_results.tsv


title: sgRNA

city: Minneapolis

first: Jakub

last: Tolar

state: Minnesota

address: 2001 6th St SE

department: Pediatrics

institute: University of Minnesota - Twin Cities

data_processing:
Cutadapt was used to filter reads based on the presence of the 'CACCG' sequence that appears directly 5' to the sgRNA sequence; this "adapter" and any bases preceding it were removed.
Cutadapt was used to trim reads from the 3' end such that only the first 20 bases (the sgRNA sequence) remained.
Galaxy was used to convert FASTQ files into FASTA files and FASTA files into tab-delimited text files.
Galaxy was used to filter the text files such that only the column containing the sgRNA sequence was retained.
Matlab was used to map the reads to the sgRNA library and calculate mapping efficiency (% of reads that mapped to an sgRNA); no mismatches were allowed.
Matlab was used to calculate the counts-per-million (CPM) value for each sgRNA; CPM was calculated based on the number of sgRNA reads, not the total number of reads.
Matlab was used to calculate fold change (FC) and log2FC for each sgRNA relative to the input material (plasmid DNA).
Genome_build: List of sgRNA sequences in the library.
Supplementary_files_format_and_content: COL7A1_CRISPRaScreen_Data.xlsx
Supplementary_files_format_and_content: COL7A1_CRISPRaScreen_sgRNA.tabular.txt

organism: synthetic construct

source_name: sgRNA

growth_protocol: Cells were expanded in normal growth media, put into selection media after transduction with lenti-dCas9-VP64 (blasticidin) and the sgRNA library (puromycin), then returned to normal growth media after selection.

extract_protocol:
Cells were pelleted and genomic DNA was extracted using the Gentra Puregene Cell Kit from QIAGEN according to manufacturer's instructions.
The region of the sgRNA lentiviral construct containing the sgRNA sequence was PCR-amplified from genomic DNA using primers containing Illumina P5 and P7 adapters. Product size was confirmed via gel electrophoresis. PCR products were cleaned up using AMPure XP beads. Library concentrations were determined with a NanoDrop.

treatment_protocol: Cells were trypsinized, resuspended, and sorted with FACS based on tdTomato fluorescence; gates were established such that the top 10% of cells (by mean fluorescence intensity) were sorted separately.

tag: sample type

value: sgRNA


title: Ubiquitous_PolProf.Rep_3

description:
RNA from polysome profiling experiment Rep. 3
UbiquitousA.deseq2_results.tsv


title: NAFLD Patient 9

value: NAFL


title: Ubiquitous_Total_PP.Rep_3

description:
Total RNA for normalization Rep. 3
UbiquitousA.deseq2_results.tsv


title: NAFLD Patient 89


title: 202253630092_R07C01

description:
normal neonatal dried bloodspot sample
Sample passed quality control

source_name: neontatal bloodspot 88


title: NAFLD Patient 91


title: Ubiquitous_Total_PP.Rep_2

description:
Total RNA for normalization Rep. 2
UbiquitousA.deseq2_results.tsv


title: NAFLD Patient 88


title: 202298850259_R02C01

source_name: neontatal bloodspot 85


title: CTV labeled memory T cells

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

institute: Sanquin

data_processing:
Feature-barcode matrices were generated using the Cell Ranger software of the 10X Genomics Chromiumä pipeline, resulting in 13,064 single-cell transcriptomes.
Resulting 10x files were combined into a Seurat object in the R environment, and hashtag assignment was performed using HTOdemux
Subsequent analysis was performed using the MetaCell package in the R environment.
Cells that could be ascribed to multiple samples or to no sample (inferred from the detection of multiple or no Hashtags), cells with a transcript (UMI) count lower than 2,000 and cells with a mitochondrial-gene fraction higher than 0.12 were excluded from downstream analysis.
Finally, cells with a gene-count of >2,800 were additionally excluded from further analysis. Subsequent analysis of the remaining 9,702 cells was performed using the Seurat47 and MetaCell30 R packages.
Genome_build: mm10-3.0.0
Supplementary files:
10x_files.tar: 10x file output from CellRanger.
metacell_objects.tar: relevant output files generated by the MetaCell R package.
Metadata_table_CTV.tsv: Table containing metadata on all cells profiled by scRNAseq.
seurat_object_CTVexp.rds: Seurat object, produced by the Seurat R package.

source_name: Spleen

extract_protocol:
Spleens from OT-I and GFP;OT-I mice were harvested and CD8+ T cells were isolated using the Mouse CD8 T Lymphocyte Enrichment Set (BD Biosciences) using the manufacturers protocol. The obtained cells were mixed in a 1:1 ratio and transferred to 4 primary recipient C57BL/6J-Ly5.1 mice (1.5x106 T cells per recipient), and 24 hours later recipients were infected with 5,000-10,000 CFU Lm-OVA. 30 days post-infection spleens  were harvested from the primary recipients and were enriched for early memory CD8+ T cells using the Mouse CD8 T Lymphocyte Enrichment Set (BD Biosciences), replacing the manufacturers supplied antibody-cocktail with a mixture of anti-mouse CD19, CD20 and CD4 biotinylated antibodies (used 1:200 each, See Supplementary Table 7 for information on antibody clones). The enriched cell pool was subsequently stained with CellTraceä Violet (Thermofisher) and re-transferred into 4 infection-matched secondary C57BL/6J-Ly5.1 recipients. 74 after secondary transfer (104 days post-infection) spleens  were harvested from the secondary recipients and stained with anti-mouse KLRG1-PE, CD27-APC, and CD45.2-AF700 (See Supplementary Table 7 for information on antibody clones). Next, stained cell-pools were first enriched for transferred cells (i.e. CD45.2+) through FACS using the BD FACSAria™ Fusion Flow Cytometer (BD Biosciences), and subsequently sorted again to obtain 4 populations of TCM based on their GFP expression and CTV dilution: KLRG1-CD27+GFP+Division0-2, KLRG1-CD27+GFP+Division5+, KLRG1-CD27+GFP-Division0-2, KLRG1-CD27+GFP-Division5+. Each cell pool obtained by cell-sorting was barcode-labeled with distinct anti-mouse TotalSeq Hashtag antibodies (TotalSeq-A0301-0304, Biolegend), and subsequently pooled.
Single-cell RNA isolation and library preparation was performed according to the manufacturer’s protocol of the 10X Genomics Chromiumä Single Cell 3’ kit, and the cDNA library was sequenced on a NextSeqTM 550 Sequencing System (Illumina). Feature-barcode matrices were generated using the Cell Ranger software of the 10X Genomics Chromium pipeline.

value: OT-I and GFP;OT-I

tag: time point

value: 104 days post LM-OVA infection

value: CD8 T cells


title: Ubiquitous_Total_PP.Rep_1

description:
Total RNA for normalization Rep. 1
UbiquitousA.deseq2_results.tsv

source_name: Whole tissue lysate


title: 203516060078_R04C01

first: Maureen

last: Sartor

address: 100 Washtenaw Ave

institute: University of Michigan

data_processing:
Processed in R (Bioconductor - Enmix and minfi)
processed data file includes quantile normalized average beta

source_name: neontatal bloodspot 84

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen EZ1 DNA Investigator Kit according to standard instructions


title: 203516060078_R02C01

source_name: neontatal bloodspot 86


title: 202298850217_R05C01

source_name: neontatal bloodspot 87


title: NAFLD Patient 87

source_name: serum

value: peripheral blood


title: Mouse Embryonic Fibroblasts - BRD4-T20-Input

city: New York

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

data_processing:
ChIP-seq reads were mapped to the mouse reference genome (mm10) using Bowtie2 v.2.3.4.1 with the following parameters: --sensitive-local.
The clonal reads from the aligned reads were removed using PCARD MarkDuplicates and REMOVE_DUPLICATES=true for further analysis.
The peak calling was performed using macs2/2.1.1.20160309 program using the following command: macs2 callpeak -t $i.bam -c $i.input.bam -g mm -n $i --outdir $i-Macs-BroadPeak -B -f BAM --broad --keep-dup auto --nomodel --extsize 200.
The bam files were converted to 1x sequence depth normalized bigWig files as reads per genomic content (RPGC) using deeptools v2.5.46 15 bamCoverage command.
Genome_build: mm10
Supplementary_files_format_and_content: The BAM files were converted to 1x sequence depth normalized bigWig files as reads per genomic content (RPGC) using deeptools v2.5.46 15 bamCoverage command for visualization on genome browsers.
Supplementary_files_format_and_content: BroadPeak files macs2 command (macs2 callpeak -t Brd4.bam -c Input.bam -g mm -n Brd4 --outdir Brd4_Macs-BroadPeak -B -f BAM --broad --keep-dup auto --nomodel --extsize 200)

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Embryonic fibroblasts were prepared from Brd4f/f ER2-Cre mice and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% penicillin-streptomycin (Invitrogen).

extract_protocol:
MEFs (~ 5 x106 in 15-cm plate) were fixed with 1% formaldehyde (Sigma) in buffer A (50 mM HEPES, pH 7.5, 100 mM NaCl, 1 mM EDTA, and 0.5 mMEGTA) for 10 min and quenched with 0.125 M glycine for 5 min. Cells were washed and incubated in nucleus isolation buffer (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25 % Triton x-100). Nuclear pellets (~2 x 107) were re-suspended in 1 ml shearing buffer (1 x TE, pH 8, and 0.1% SDS) and transferred to Covaris millitubes and sonicated in Covaris ME200 sonicator. Sonicated chromatin was precipitated with anti-BRD4 antibody (IgG) pre-bound to Dynabeads Protein G (Thermo Fisher). Immunoprecipitated DNA was de-crosslinked, digested with proteinase K, and purified using QIAquick PCR Purification Kit (Qiagen). Precipitated DNA was validated by qChIP.
Precipitated DNA (~ 20 ng) was used for library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolab). Library DNA with fragment length of 200-400 bp was subjected to single end sequencing on a Nextseq system (Illumina).

treatment_protocol: To delete Brd4, cells were treated with 2 µM 4-hydroxytamoxifen (TMX, Sigma) for 96 h.

value: Mouse Embryonic Fibroblasts

tag: chip antibody

value: Input

tag: treatment

value: Time 20h


title: 202253630092_R06C01

city: Ann Arbor

source_name: neontatal bloodspot 83

value: neonatal blood spot


title: Mouse Embryonic Fibroblasts - BRD4-T16-Input

value: Time 16h


title: UBI_total.Rep_3

description:
Total RNA for normalization Rep. 3
Ubiquitous.deseq2_results.tsv

tag: genotype

tag: promotor driving flag

value: :rpl-22:endogenous rpl-22


title: NAFLD Patient 86


title: UBI_total.Rep_2

description:
Total RNA for normalization Rep.2
Ubiquitous.deseq2_results.tsv


title: Mouse Embryonic Fibroblasts - BRD4-T8-Input

tag: cell type

value: Time 8h


title: NAFLD Patient 85


title: Mouse Embryonic Fibroblasts - BRD4-T0-Input

value: Time 0h


title: NAFLD Patient 84


title: 203490640037_R05C01

source_name: neontatal bloodspot 82

value: Male


title: NAFLD Patient 92

value: Chronic Liver Disease (NAFLD)


title: 202262730027_R03C01

source_name: neontatal bloodspot 81


title: UBI_IP.Rep_3

description:
RNA from SKI TRIP experiment Rep. 3
Ubiquitous.deseq2_results.tsv

source_name: SKI TRIP from all tissues

value: All tissues

tag: fraction

value: RNA from ribosome IP


title: UBI_total.Rep_1

description:
Total RNA for normalization Rep. 1
Ubiquitous.deseq2_results.tsv


title: Mouse Embryonic Fibroblasts - BRD4-T20

value: In house BRD4 antibody


title: NAFLD Patient 83

tag: disease state


title: 203483530043_R07C01

source_name: neontatal bloodspot 80


title: Mouse Embryonic Fibroblasts - BRD4-T16


title: NAFLD Patient 82

tag: nas


title: UBI_IP.Rep_2

description:
RNA from SKI TRIP experiment Rep. 2
Ubiquitous.deseq2_results.tsv


title: 203490640037_R06C01

source_name: neontatal bloodspot 79


title: Soma_total.Rep_3

description:
Total RNA for normalization Rep. 3
Soma.deseq2_results.tsv


title: Mouse Embryonic Fibroblasts - BRD4-TO


title: 203009240151_R08C01

source_name: neontatal bloodspot 78

value: Female


title: NAFLD Patient 81

tag: saf activity


title: NAFLD Patient 80

tag: fibrosis stage


title: Mouse Embryonic Fibroblasts - BRD4-T8


title: CD8+ T cells_Genital Tract rep3

city: New Haven

first: HIROMITSU

last: ASASHIMA

state: CT

address: 114 Canner St, 3

institute: Yele School of Medicine

data_processing:
low quality ends (less than phred score=30) and short read length (minimum length=30) was trimmed using PRINSEQ++(version1.2).
Trimmed reads were aligned to the mm39 genome reference using STAR(v2.7.1), and subsequently RSEM (RNA-Seq by Expectation-Maximization) was used to count reads mapping to the mouse genes from Ensembl release 104.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: genital tract

extract_protocol:
Each data point reflects pooled cells from two mice.  Spleens were bisected, ½ spl from each mouse mechanically disaggregated between frosted glass slides then pooled.  Gt from same two mice were processed together using a modification of a collagenase/hyaluronidase cocktail and mechanical disaggregation protocol. CD3+CD4+CD8-Ig-, CD3+CD8+CD4-Ig- cells were sorted from each tissue.
RNA libraries were prepared for sequencing with TruSeq Stranded mRNA Kit (Illumina)

treatment_protocol: 1 week prior to primary infection mice were treated with 2.5mg medroxyprogesterone subcutaneously.  Primary challenge was 5x104 IFU delivered intravaginally in 10µl of sucrose phosphate glutamate buffer (visual confirmation).  Mice cleared infection (~28d), then 10-weeks later were treated with medroxyprogesterone and reinfected with 5x105 IFU intravaginally 5d later. Spleen and gt were harvested 6d after secondary infection.

value: genital tract

tag: condition

value: 6d after secondary infection of Chlamydia muridarum


title: 202298850217_R01C01

source_name: neontatal bloodspot 77

tag: tissue


title: Soma_total.Rep_2

description:
Total RNA for normalization Rep.2
Soma.deseq2_results.tsv

tag: strain


title: NAFLD Patient 8

value: peripheral blood

tag: disease group

value: NAFL


title: UBI_IP.Rep_1

description:
RNA from SKI TRIP experiment Rep. 1
Ubiquitous.deseq2_results.tsv


title: CD8+ T cells_Genital Tract rep2


title: Soma_total.Rep_1

description:
Total RNA for normalization Rep. 1
Soma.deseq2_results.tsv


title: NAFLD Patient 79


title: 203010900023_R05C01

description:
normal neonatal dried bloodspot sample
Sample failed quality control. No processed data provided.

source_name: neontatal bloodspot 76

tag: infant sex

tag: arch id


title: CD8+ T cells_Genital Tract rep1


title: 202262730027_R02C01

source_name: neontatal bloodspot 75


title: NAFLD Patient 78


title: CD4+ T cells_Genital Tract rep3


title: 202298850259_R04C01

source_name: neontatal bloodspot 73


title: Soma_IP.Rep_2

description:
RNA from SKI TRIP experiment Rep. 2
Soma.deseq2_results.tsv

source_name: SKI TRIP from soma

value: Soma

value: RNA from soma-specific ribosome IP


title: 202298850217_R08C01

source_name: neontatal bloodspot 74

value: neonatal blood spot


title: NAFLD Patient 76


title: CD4+ T cells_Genital Tract rep2


title: Soma_IP.Rep_3

description:
RNA from SKI TRIP experiment Rep. 3
Soma.deseq2_results.tsv


title: Soma_IP.Rep_1

description:
RNA from SKI TRIP experiment Rep. 1
Soma.deseq2_results.tsv


title: NAFLD Patient 77


title: 202253630017_R08C01

source_name: neontatal bloodspot 72


title: NAFLD Patient 74

source_name: serum


title: 203010900023_R01C01

source_name: neontatal bloodspot 70


title: 202262730027_R07C01

source_name: neontatal bloodspot 71


title: CD8+ T cells_Spleen rep3

source_name: Spleen

value: Spleen


title: NeuroB_total.Rep_1

description:
Total RNA for normalization Rep. 1
NeuroB.deseq2_results.tsv

source_name: Whole tissue lysate


title: NAFLD Patient 75


title: CD8+ T cells_Spleen rep1


title: 203483530044_R07C01

description:
normal neonatal dried bloodspot sample
Sample passed quality control

source_name: neontatal bloodspot 69


title: NAFLD Patient 73


title: 202253630016_R08C01

source_name: neontatal bloodspot 68


title: NeuroB_IP.Rep_3

description:
RNA from SKI TRIP experiment Rep. 3
NeuroB.deseq2_results.tsv

source_name: SKI TRIP from neurons (B)

value: Neurons

value: RNA from neuron-specific ribosome IP


title: NeuroB_IP.Rep_2

description:
RNA from SKI TRIP experiment Rep. 2
NeuroB.deseq2_results.tsv


title: NAFLD Patient 72


title: CD4+ T cells_Genital Tract rep1


title: NAFLD Patient 71


title: NeuroB_total.Rep_2

description:
Total RNA for normalization Rep.2
NeuroB.deseq2_results.tsv


title: CD4+ T cells_Spleen rep3


title: 202253630092_R01C01

source_name: neontatal bloodspot 67


title: 203010900023_R02C01

source_name: neontatal bloodspot 66


title: NeuroB_IP.Rep_1

description:
RNA from SKI TRIP experiment Rep. 1
NeuroB.deseq2_results.tsv


title: NeuroB_total.Rep_3

description:
Total RNA for normalization Rep. 3
NeuroB.deseq2_results.tsv


title: CD8+ T cells_Spleen rep4


title: NAFLD Patient 70


title: 202262730027_R01C01

source_name: neontatal bloodspot 65


title: NAFLD Patient 7


title: CD4+ T cells_Spleen rep1


title: 202298850217_R03C01

source_name: neontatal bloodspot 64


title: 202259490093_R03C01

source_name: neontatal bloodspot 63


title: Olfr160 OSN replicate 3

city: Worcester

first: I-Hao

last: Wang

address: 370 Sunderland Rd, Unit D24

department: PMM

institute: UMMS

data_processing:
The sequencing reads were processed using the DolphinNext RNAseq pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=732). The default settings were employed except STAR v2.6.1 and RSEM v1.3.1 were used for alignment and quantification, respectively
Differential analysis were conducted in DEseq2. The significant genes were deducted by computing Wald tests with corrected p < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrix/ TPM matrix was generated by RSEM

source_name: Olfr160 expressing olfactory sensory neurons

extract_protocol:
RNA was extracted with an RNeasy micro kit (QIAGEN).
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s guidelines with one alteration, which was to increase the insert length to ~300 base pair

treatment_protocol: Mice were euthanized according to IACUC protocol, and then main olfactory epithelia were dissected and quickly immersed in ice-cold HBSS (Worthington). Olfactory epithelia were separated from the bone under a dissection microscope and then were minced into small pieces using forceps.  Each epithelium was then washed once with HBSS and resuspended in 2 ml of EBSS containing papain (20 U/mL, Worthington) and DNase I (2000 U/mL, Worthington). After 40 minutes of incubation with gentle agitation at 37°C, the suspension was washed with 5 ml of PBS + 0.02% BSA twice and passed through a 30 μm cell strainer (Miltenyi Biotec). The cell suspension was stained with 3 μM of DAPI and subjected to FACS to isolate the GFP/mCherry high and DAPI low population of cells

value: mature olfactory sensory neuron


title: NAFLD Patient 68


title: Olfr160 OSN replicate 2


title: CD4+ T cells_Spleen rep2


title: NAFLD Patient 69


title: NeuroA_IP.Rep_3

description:
RNA from SKI TRIP experiment Rep. 3
NeuroA.deseq2_results.tsv

source_name: SKI TRIP from neurons (A)


title: NeuroA_total.Rep_2

description:
Total RNA for normalization Rep.2
NeuroA.deseq2_results.tsv


title: NAFLD Patient 67


title: Olfr1507 OSN replicate 3

source_name: Olfr1507 expressing olfactory sensory neurons


title: Olfr160 OSN replicate 1


title: CD8+ T cells_Spleen rep2


title: 202253630017_R01C01

source_name: neontatal bloodspot 61

value: Male


title: Olfr1507 OSN replicate 2


title: Muscle_total.Rep_3

description:
Total RNA for normalization Rep. 3
Muscle.deseq2_results.tsv


title: NeuroA_IP.Rep_1

description:
RNA from SKI TRIP experiment Rep. 1
NeuroA.deseq2_results.tsv


title: NeuroA_total.Rep_3

description:
Total RNA for normalization Rep. 3
NeuroA.deseq2_results.tsv


title: NAFLD Patient 65

source_name: serum

value: Chronic Liver Disease (NAFLD)


title: NAFLD Patient 64


title: NeuroA_total.Rep_1

description:
Total RNA for normalization Rep. 1
NeuroA.deseq2_results.tsv

value: All tissues


title: 202253630017_R02C01

source_name: neontatal bloodspot 59


title: Olfr1507 OSN replicate 1


title: 202259490093_R07C01

source_name: neontatal bloodspot 57


title: NAFLD Patient 62


title: 203483530045_R05C01

source_name: neontatal bloodspot 62


title: Olfr73 OSN replicate 3

source_name: Olfr73 expressing olfactory sensory neurons


title: NAFLD Patient 66


title: NAFLD Patient 61


title: Muscle_total.Rep_2

description:
Total RNA for normalization Rep.2
Muscle.deseq2_results.tsv

source_name: Whole tissue lysate


title: NAFLD Patient 63


title: 203483530043_R02C01

source_name: neontatal bloodspot 60


title: Olfr73 OSN replicate 1


title: 202262730027_R05C01

source_name: neontatal bloodspot 56


title: Muscle_IP.Rep_3

description:
RNA from SKI TRIP experiment Rep. 3
Muscle.deseq2_results.tsv

source_name: SKI TRIP from muscle

value: Muscle

value: RNA from muscle-specific ribosome IP


title: Muscle_IP.Rep_1

description:
RNA from SKI TRIP experiment Rep. 1
Muscle.deseq2_results.tsv


title: Muscle_IP.Rep_2

description:
RNA from SKI TRIP experiment Rep. 2
Muscle.deseq2_results.tsv


title: NAFLD Patient 6


title: 203010900023_R03C01

description:
normal neonatal dried bloodspot sample
Sample failed quality control. No processed data provided.

source_name: neontatal bloodspot 54

value: Female