title: Control, replicate 1, scRNAseq

city: 杭州市

first: 晓龙

last: 辛

address: 浙江省杭州市西湖区三墩镇浙江大学紫金港校区医学院

institute: 浙江大学

description: 10x Genomics

data_processing:
Cell, the official analysis software of 10x Genomics, was used Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) to the original data to identify the data filtering, alignment, quantitative, recycling cells, Finally, the gene expression matrix of each cell was obtained.
Follow-up the Seurat (https://satijalab.org/seurat/) for further cell filtration, standardization, the classification of the cells, each subgroup analysis and Marker gene screening differentially expressed genes.
The single-cell subpopulation classification analysis process includes the following steps:    (1) After removing low-quality cells, the LogNormalize method of "Normalization" function of Seurat software was used to homogenize the expression amount.    (2) Dimensionality was reduced by Principal component analysis (PCA), and the variables were reduced and then the homogenized expression values were used for PCA (Principal component analysis) analysis. The first 10 principal components were selected from the results of PCA analysis for subsequent clustering and grouping analyses.    (3) Clustering and grouping analysis: Seurat software used a clustering algorithm based on graph theory to cluster and group cells. It mainly includes the following steps:    a) Construct the clustering relationship between cells: construct the KNN clustering relationship graph based on Euclidean distance by using significant principal components;    b) Optimizing the weight value of clustering relationship distance between cells: using Jaccard similarity to optimize the weight value of intercellular distance;    c) Clustering and clustering: cell clusters were identified by clustering algorithm based on shared nearest neighbor (SNN) module optimization, that is, the k-nearest neighbors were first calculated and the SNN graph was constructed, and then the modularity function was optimized to determine the clusters.
Seurat was used to analyze differentially expressed genes in different cell populations by bimod likelihood ratio statistical test to screen genes that were up-regulated in different cell populations.    The screening conditions for up-regulated genes were as follows:    1. The gene is expressed in more than 10% of the cells in the target or control subsets;    (2) P value ≤0.01;    3. Gene expression fold logFC≥0.26, that is, gene up-regulation fold ≥2^0.26;
Gene Ontology(GO) is an international standardized classification system of gene functions. It provides a set of dynamically updated controlled vocabulary to comprehensively describe the properties of genes and gene products in organisms. There are three GO ontologies, which describe the molecular function, cellular component and biological process of a gene. The basic unit of GO is a term(entry, node), and each term corresponds to an attribute. GO functional significant enrichment analysis was performed by mapping all significantly differentially expressed genes to each term in the Gene Ontology database, calculating the number of genes in each term, and then applying hypergeometric test to find out the GO entries that were significantly enriched in significantly differentially expressed genes compared with the whole genome background.
Assembly: mm9
Supplementary files format and content: .rds, P14 single-cell data from WMI mice and control mice
Supplementary files format and content: .rds, Single cell data for P14 from WMI mice and control mice containing only glial cells

source_name: cerebral cortex

extract_protocol:
On postnatal day 14, the ligated cerebral cortex of the experimental group and the ipsilateral cerebral cortex of the control group were collected
(1) Nuclear quality inspection
After resuspension of the cell nuclei, the cells were collected by filtration through a 20um cell sieve and counted.
(2) 10X labeled cDNA fragments
Gel Beads containing barcode information are bound to a mixture of cells and enzymes and then coated with oil surfactant droplets located In a microfluidic "double cross" system to form GEMs (gel beads-in-emulsions). GEMs flow into the reservoir and are collected, gel beads dissolve to release Barcode sequences, reverse transcribe cDNA fragments, and label the samples. Gel beads were broken up and oil droplets were broken up, and cDNA was used as template for PCR amplification. The products of all GEMs were pooled to construct a standard sequencing library.
(3) Construction of standard sequencing library
First, the cDNA fragment was broken into 200-300 bp fragments by enzyme digestion, and the library construction process of traditional second generation sequencing was added, such as sequencing adapter and primer. Finally, the DNA library was amplified by PCR.
(4) Library sequencing
High-throughput sequencing was performed on the constructed library using the double-end sequencing mode of the Illumina sequencing platform.

treatment_protocol: On postnatal day 7, the right common carotid artery of mice was ligated under hypoxia for 1h

value: Neuron, Glia

value: cerebral cortex

value: 2 weeks old

value: Control


title: WT 4.3hpf Dome

status: Public on Mar 04 2023

type: SRA

city: Beijing

first: Weimin

last: Shen

address: Tsinghuayuan park

country: China

institute: School of life science, Tsinghua University

description: fpkm table.txt

library_source: transcriptomic

data_processing:
BGISEQ-500 platform was used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50, then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using software RSEM v1.2.8 from Langmead, B. et al., Nat. Methods, 2012, and Li, B. & Dewey, C. N., BMC Bioinformatics, 2011.
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Danio rerio

source_name: whole mount embryo

extract_protocol:
total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard protocols

tag: strain

value: AB

tag: tissue

value: whole mount embryo

tag: developmental stage

value: 4.3 hours post fertilization

tag: genotype

value: wild type


title: P0-4

city: Pittsburgh

first: Andrew

middle: Scott

last: Clugston

state: PA

address: 872 Mirror Street

department: Integrative Systems Biology

country: USA

institute: University of Pittsburgh

library_source: genomic

data_processing:
ATAC-seq data processing and IDR peak calling were performed using a custom Nextflow pipeline, available at https://bitbucket.org/clugstonA/mirna_enhancers/src/master/src/atacseq_pipeline/ATACseq_encode_pipeline_3.0.nf.
IDR peaks were annotated with overlapping enhancers from the FANTOM5 (available at https://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/) and Vista (available at https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=search&show=1&search.form=no&search.result=yes) using the R package GenomicRanges v1.38.0.
IDR peaks were annotated with overlapping genes, promoters, and exon annotations within the Ensemble R database package EnsDb.Mmusculus.v79 using the R package GenomicRanges v1.38.0.
IDR peaks were annotated with overlapping EnhancerAtlas 2.0 enhancer predictions (available at http://www.enhanceratlas.org/downloadv2.php) using the R package GenomicRanges v1.38.0.
Transcription factor footprints were detected using Regulatory Genomics' Hmm-based Identification of transcription factor footprints (HINT-RGT) ATAC-seq footprinting model, rgt-hint footprinting (settings: --organism=mm10 --atac-seq --paired-end).
Transcription factor footprints were annotated to known transcription factors using binding motifs from the HOCOMOCO11 DNA binding motif database (available at http://hocomoco11.autosome.ru/) using th HINT rgt-motifanalysis program (settings: --organism=mm10).
Genome_build: mm10
Supplementary_files_format_and_content: Bgzipped BED file containing mm10 IDR regions annotated with Tn5 insertion counts, differential accessibility statistics, transcription factor footprint results, and other genomic annotations.
Supplementary_files_format_and_content: Bgzipped BEDgraph files containing pileup scores for each sample.

molecule: genomic DNA

organism: Mus musculus

source_name: P0 mouse nephron progenitor replicate 2

extract_protocol:
Up to 24 kidneys from each litter were pooled for progenitor isolation, while one kidney was retained as a whole-kidney qPCR control for confirming enrichment of progenitor cells relative to surrounding cell types. Pools of kidneys were subjected to limited (15 min) digestion at 37C with a mixture of collagenase A and pancreatin to collect cortical cells. Cells were then washed, and nephron progentors isolated through positive selection using magnetic beads biotinylated with antibodies for Itga8. A fraction containing 50,000 cells was immediately subjected to suspension in ice-cold, non-ionic lysis buffer for 10 minutes to lyse cell membranes while maintaining the nuclear envelope. Nephron progenitor nuclei were washed and collected, then immersed in the sequencing library transposition reaction.
Libraries were prepared in accordance with that published by Buenrostro et. al (Nature Methods 2013). Nuclei were suspended in the Nextera DNA Flex Library Prep Kit (Illumina FC-121-1030) transposition reaction solution containing Tn5 transposase, and free DNA strands were collected and cleaned using the MinElute PCR Purification kit (Qiagen 28004). Forward (i7) and reverse (i5) Illumina indices were applied using PCR to add sample- and strand-specific molecular identifiers. The optimal number of amplification cycles for each sample was identified as the number of cycles required to  achieve 1/3 maximum fluorescence, measured in a 5uL PCR side reaction with a SYBR green reporter. Once determined, the remaining indexed DNA solutions were amplified using this many cycles. Libraries were then purified using Ampure XP magnetic beads (Beckman Coulter A63881).

treatment_protocol: Litters were sacrificed at either 14 days post fertilization (E14.5) or the day of birth (P0).

tag: cell type

value: Nephron progenitor

tag: embryonic day


title: WMI, replicate 1, scRNAseq

address: 浙江省杭州市西湖区三墩镇浙江大学紫金港校区医学院

description: 10x Genomics

library_source: transcriptomic single cell

tag: age

tag: treatment

value: cerebral white matter injury (WMI)


title: RIBO_seq_NPC_rep3

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

data_processing:
Adapters were trimmed using Cutadapt (v1.18)
RIBO-seq reads aligning to mitochondrial, ribosomal RNA, and tRNA sequences were filtered using Bowtie (v1.2)
Next, mRNA-seq and RIBO-seq reads were aligned to the human genome (hg38) with STAR (v2.7.1a)
Raw reads were counted using FeatureCounts (v1.6.4)
Assembly: GRCh38

organism: Homo sapiens

source_name: Neural progenitor cell

growth_protocol: Human ESC line HUES8 was grown in Matrigel-coated plates (MATRIGEL MATRIX HESC-QUALIFIED, BD Bioscience, #354277) with mTeSR1 media (Stemcell Technologies, #1000023391) and passaged with Accutase (Stemcell Technologies, #A1110501) until the density reached roughly 80-90%. The medium was replaced every day. Dual SMAD inhibition was used for neural differentiation according to a previous protocol(Meng et al., 2021). Briefly, human ESCs were replated at a density of 5 x 104 cells per well in 24-well plates. After two days of cultivation in mTeSR1, neuroectoderm differentiation was triggered by neural induction media for 7 days (KnockOutTM DMEM/F12 (Gibco, #12660012), 0.5× N2 (Shanghai BasalMedia Technologies, #M430721), 0.5× B27 without vitamin A (Shanghai BasalMedia Technologies, #B430805), 1% Penicillin/Streptomycin (Thermo Fisher Scientific, #15140163), 1% 2-Mercaptoethanol (Gibco, #2121115), 1% GlutaMAXTM Supplement (Thermo Fisher Scientific, #35050061), 1% NEAA (Gibco, #11140-050), plus 2.5 uM SB431542 (Selleck, #S1067), and 0.05 uM LDN193189 (Selleck, #S7507)). The medium was changed daily, and the TGF-β inhibitor SB431542 was withdrawn from the neural induction media for the last 2 days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Neural progenitor cell

tag: cell line

value: NPC

value: WT

tag: molecule type

value: ribosome bound total RNA


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t24, 2000U

status: Public on Mar 03 2023

city: New York

first: Andres

last: Mansisidor

state: NY

address: 1230 York Ave Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: Rockefeller University

description: MNase-seq

data_processing:
UMI demultiplexing (custom script)
adapter trimming (custom script)
alignment to HBV genome (Bowtie2 v2.3.4.3)
nucleosome coverage mapping (nucleoATAC)
Bedgraphs from both RNA- and MNase-seq were plotted using Sushi package v1.30.0 in R v4.1.0
Assembly: NC_003977.2 (offset by 500 bp)
Supplementary files format and content: bedgraph files that include coverage of fragment centers (50 bp windows)

extract_protocol:
In vivo MNase-seq was performed on purified nuclei at different timepoints after transfection with HBV cccDNA or on in vitro reconstituted chromatin.
For MNase-seq on in vitro reconstituted chromatin, titration of MNase was performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested chromatin arrays. Chromatinized DNA (100 ng) was digested using MNase (NEB) in 25 µL reactions with 2.5–25 units of enzymes that was incubated for 5 minutes at 37C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37C. The reaction was stopped by adding 20 mM EDTA and 1% SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index Barcodes or Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out using only 5 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). For MNase-seq on cell cultured samples, HEK293T cells were transfected with recombinant cccDNA 4 or 24-hours prior to harvest for MNase-seq. The nuclei of HEK293 cells were purified by incubating cells in Nuclei isolation buffer for 10 minutes (0.1% Igepal, 0.1% Triton X -100, 1 mM DTT in 1 X PBS), mechanically lysing with 10 strokes of loose (A) pestle Dounce homogenizer, and washing nuclei twice in 10 mL of Wash Buffer with Tween (10 mM Tris-HCl pH 7.5, 2.5 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Titration of MNase was similarly performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested genomic DNA. MNase (NEB) was added to 2 x 106 nuclei in 50 µL reaction volume with 250–2000 units of enzyme that was incubated for 5 minutes at 37 C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37 C. The reaction was stopped by adding 20 mM EDTA and 1 % SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). Libraries were then pooled and enriched for HBV-containing reads using custom-designed xGen Lockdown probes (Integrated DNA Technology) of 60 bp each tiling the entire HBV genome and oligo capture protocol was followed per manufacture’s protocol. Enriched libraries were subsequently amplified using 11 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and purified using Ampure XP beads.

value: Human embryonic kidney cells

value: HBV cccDNA transfected

value: 24 hr, 2000 Units MNase


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t24, 0500U

description: MNase-seq

value: 24 hr, 500 Units MNase


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t24, 1000U

description: MNase-seq

value: 24 hr, 1000 Units MNase


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t24, 0250U

description: MNase-seq

value: 24 hr, 250 Units MNase


title: E14-5

source_name: E14.5 mouse nephron progenitor replicate 2


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t04, 1000U

description: MNase-seq

value: 04 hr, 1000 Units MNase


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t04, 0500U

description: MNase-seq

value: 04 hr, 500 Units MNase


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t04, 0250U

description: MNase-seq

value: 04 hr, 250 Units MNase


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t04, 2000U

description: MNase-seq

value: 04 hr, 2000 Units MNase


title: RIBO_seq_ESC_rep2

source_name: Embryonic stem cell

value: Embryonic stem cell

value: ESC


title: MNase-seq,HEK293T cells, mock transfection, t0, 2000U

description: MNase-seq

value: mock transfection

value: 00 hr, 2000 Units MNase


title: RIBO_seq_ESC_rep1


title: MNase-seq,HEK293T cells, mock transfection, t0, 0500U

description: MNase-seq

value: 00 hr, 500 Units MNase


title: MNase-seq,HEK293T cells, mock transfection, t0, 0250U

description: MNase-seq

value: WT

value: 00 hr, 250 Units MNase


title: MNase-seq,HEK293T cells, mock transfection, t0, 1000U

description: MNase-seq

value: Human embryonic kidney cells

value: 00 hr, 1000 Units MNase


title: sfl1Δ_biofilm_vs_ SN76_biofilm_rep3

type: RNA

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

hyb_protocol: Six hundred nanograms of labelled cDNA were hybridized in the microarray. Hybridizations were carried out using Agilent gasket slides in a rotating oven for 17 h at 65°C.

scan_protocol: Slides were then washed following manufacturer’s instructions and scanned in an Agilent G2565AA microarrays scanner. Probes signal values were extracted using Agilent Feature Extraction Software.

data_processing: Data were normalized using median centering of signal distribution with Biometric Research Branch BRB-Array tools v3.4.o software 36. Final statistical analysis was carried out using LIMMA package in MeV software (MultiExperiment Viewer 4.8.0) 36 with a cut-off p-value of 0.1.

organism: Candida albicans

label_protocol: cDNA synthesis, hybridization, and scanning were performed using the Agilent protocol for two-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 (Agilent Technologies), according to the manufacturer’s instructions. One hundred nanograms of total RNA of each strain were used to synthesize labeled cDNA (with Cyanine 3-CTP and cyanine 5-CTP), using Agilent T7 Promoter Primer and T7 RNA polymerase Blend (Agilent Technologies, Cat.5190–2305).

growth_protocol: For the transcriptomic profiling an individual colony of C. albicans SN76 and sfl1Δ/sfl1Δ strains was inoculated in SDB at 37 ºC with orbital agitation (120 rev/min) overnight and then re-inoculated (at 1x105 cel/ml) in 25 ml of RPMI at pH 4 and left to grow for 24h at 37ºC and 120 rev/min orbital shake, inside Erlenmeyer flaks and microtiter plates, in order to induce planktonic and biofilm growth, respectively.

extract_protocol: The extraction of RNA from the cells was performed using the RiboPure – Yeast Kit (Life Technologies, CA), according to the manufacturer’s instructions.The concentration and purity of the extracted RNA were determined by spectrophotometry and its integrity was confirmed in an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Assay (Agilent Technologies, CA).

tag: growth mode

value: biofilm


title: sfl1Δ_plankt_vs_ SN76_plank_rep3

value: planktonic


title: sfl1Δ_biofilm_vs_ SN76_biofilm_rep1


title: sfl1Δ_biofilm_vs_ SN76_biofilm_rep2


title: sfl1Δ_plankt_vs_ SN76_plank_rep1


city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
PHPeB GfaABC1D-Cre systemic mouse, immunoprecipitated mRNA, rep 1
P1_IP

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

molecule: polyA RNA

source_name: ribosomally loaded, astrocyte-enriched

extract_protocol:
Immunoprecipitation was performed according to Sanz et al, PNAS 2009. RNA was harvested using RNeasy Micro Plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMART-Seq v4 RNA Ultra Low Input (Takara) + Nextera XT (Illumina) following manufacturer's protocols.

treatment_protocol:
Mice were injected with tamoxifen (Aldh1l1-CreERT2 samples, 100mg/kg in corn oil, i.p., daily for 5 days) or virus. Cortical brain tissue was harvested 2 weeks after the last tamoxifen injection.
Virus injections: systemic virus was delivered retroorbitally, 1x10^12 vg/mouse in saline. Intracortical virus was delivered via pulled glass micropipette; 500nl of 1x10^12vg/ml in saline at each of two sites (A/P 0.0mm, M/L 2.0mm, D/V:-0.75mm; A/P -1.2mm, M/L 2.0mm, D/V:-0.65mm)

value: ribosomally loaded, astrocyte-enriched

value: Ribotag

tag: virus

tag: viral delivery_route

value: systemic

tag: input or_ribosomally_loaded

value: ribosomally loaded


description:
Aldh1l1-CreERT2 mouse, immunoprecipitated mRNA, rep 4
A4_IP


description:
PHPeB GfaABC1D-Cre intracortical mouse, immunoprecipitated mRNA, rep 3
D3_IP

value: intracortical


description:
PHPeB GfaABC1D-Cre systemic mouse, immunoprecipitated mRNA, rep 3
P3_IP


description:
PHPeB GfaABC1D-Cre intracortical mouse, immunoprecipitated mRNA, rep 1
D1_IP


description:
PHPeB GfaABC1D-Cre intracortical mouse, immunoprecipitated mRNA, rep 2
D2_IP


description:
PHPeB GfaABC1D-Cre intracortical mouse, immunoprecipitated mRNA, rep 4
D4_IP


description:
Aldh1l1-CreERT2 mouse, immunoprecipitated mRNA, rep 3
A3_IP


description:
PHPeB GfaABC1D-Cre systemic mouse, immunoprecipitated mRNA, rep 4
P4_IP


description:
PHPeB GfaABC1D-Cre systemic mouse, immunoprecipitated mRNA, rep 2
P2_IP


description:
Aldh1l1-CreERT2 mouse, immunoprecipitated mRNA, rep 1
A1_IP


description:
AAV2/5 GfaABC1D-Cre mouse, immunoprecipitated mRNA, rep 3
5_3_IP


description:
AAV2/5 GfaABC1D-Cre mouse, immunoprecipitated mRNA, rep 4
5_4_IP


description:
AAV2/5 GfaABC1D-Cre mouse, immunoprecipitated mRNA, rep 1
5_1_IP


description:
AAV2/5 GfaABC1D-Cre mouse, immunoprecipitated mRNA, rep 2
5_2_IP


description:
Aldh1l1-CreERT2 mouse, immunoprecipitated mRNA, rep 2
A2_IP


title: TNBC Case 42

city: Seoul

first: Kyungsoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Biotechnoloty

country: South Korea

institute: Yonsei University

description: Gene expression data from tumor paraffin block

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human ST 2.0 Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT)

label: biotin

source_name: Triple-negative breast cancer

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT pico Terminal labeling kit.

extract_protocol: The RNA extraction of 147 FFPE tumor specimens was performed using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer's recommendations

tag: subclassification

value: B

tag: Sex

value: Female

tag: tstage

tag: nstage

tag: mstage

tag: Stage


description:
PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 3
P3_input

source_name: whole cortex

tag: tissue

value: whole cortex

tag: genotype

value: input


description:
PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 4
D4_input


title: PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 2

description:
PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 1
P2_input


description:
PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 1
P1_input


description:
PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 3
D3_input


title: Aldh1l1-CreERT2 mouse, input RNA, rep 3

description:
Aldh1l1-CreERT2 mouse, input RNA, rep 3
A3_input


title: Aldh1l1-CreERT2 mouse, input RNA, rep 4

description:
Aldh1l1-CreERT2 mouse, input RNA, rep 4
A4_input


description:
PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 1
D1_input


title: sfl1Δ_plankt_vs_ SN76_plank_rep2


title: Aldh1l1-CreERT2 mouse, input RNA, rep 1

description:
Aldh1l1-CreERT2 mouse, input RNA, rep 1
A1_input


description:
AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 4
5_4_input


title: AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 2

description:
AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 1
5_2_input


description:
AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 3
5_3_input


description:
PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 4
P4_input


title: NFO181-A549hACE2-SARSCoV2-5L

city: Copenhagen

first: Nicolas

last: Fossat

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

description: Single-end 1 x 150bp

data_processing:
CLEAR-CLIP_Preprocessing: Removal of adaptors and  quality trimming using Trimmomatic with settings 'SLIDINGWINDOW:4:20'. Collapsing of PCR duplicates, read demultiplexing and barcode/index/linker removal was aided by the R package CLIPflexR v0.1.20.
CLEAR-CLIP_Singleton reads: Sequenced reads were aligned to hg38/chlSab2/SARS-CoV-2 reference genomes using Rbowtie2, through the CLIPflexR wrapper with default settings. BED files and bedgraphs were created using CLIPflexR, and normalized to RPM for downstream analyses and coverage plots. Peak calling of aligned reads was done using Homer through the CLIPflexR wrapper, and peaks where annotated using GenomicFeatures v1.38.2, GenomicRanges v1.38 and ChiPseeker v1.22.1. Prediction of miRNA seed sites from 7mer-m8 or 7mer-A1 seed matches was done using a combination of CLIPflexR and custom methods.
CLEAR-CLIP_Chimera reads: Reads that remained unmapped after singleton alignment, were treated as potential chimeras. Unmapped reads were thus reverse aligned to the sequences of mature microRNAs and forward aligned to possible target sequences in hg38/chlSab2/SARS-CoV-2 reference genomes using Rbowtie2 and CLIPflexR. Chimeras were analysed for differential miRNA abundance (infected vs. non-infected), using edgeR, to indirectly scan for putative viral miRNA sequestration, by analysing loss of cell-bound miRNAsusing the edgeR package. Relative abundances of miRNAs for non-infected cells, were calculated as the average fraction of the three non-infected samples for each cell line.
RNA-Seq: Demultiplexed files were lane-merged and aligned to the SARS-CoV-2 reference genome using STAR (v2.7.9a). RPKM normalized genome coverage was generated from BAM files using deeptools genomecov. Average coverage was plotted against colored backgrounds, according to SARS-CoV-2 annotation regions in R.
Assembly: Green monkey: chlSab2; Human: hg38; SARS-CoV-2: Strain DK-AHH1 (PMID: 33903110). For each mutant, strain DK-AHH1 was also used but modified to carry the corresponding engineered point mutations.
Supplementary files format and content: Table_S1.xlsx - Number of reads per sample for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S2.txt - Singleton reads for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S3.txt - Chimeric reads for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S4.xlsx - List of miRNAs binding SARS-CoV-2 RNA in VeroE6 cells
Supplementary files format and content: Table_S5.xlsx - Functional miRNAs expressed in VeroE6 cells
Supplementary files format and content: Table_S6.xlsx - Number of reads per sample for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S7.txt - Singleton reads for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S8.txt - Chimeric reads for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S9.xlsx - List of miRNAs binding SARS-CoV-2 RNA in A549hACE2 cells
Supplementary files format and content: Table_S10.xlsx - Functional miRNAs expressed in A549hACE2 cells
Supplementary files format and content: Table_S11.xlsx - Differential expression of miRNAs in infected VeroE6 cells
Supplementary files format and content: Table_S12.xlsx - Differential expression of miRNAs in infected A549hACE2 cells
Supplementary files format and content: Table_S13.xlsx - Differential miRNA binding on cellular RNAs in infected VeroE6 cells
Supplementary files format and content: Table_S14.xlsx - Differential miRNA binding on cellular RNAs in infected A549hACE2 cells
Supplementary files format and content: Table S15.txt Differential gene expression in infected VeroE6 cells
Supplementary files format and content: Table S16.txt Differential gene expression in infected A549hACE2 cells (72 hpi)

source_name: Human lung A549hACE2 cells

growth_protocol: Cells were grown in standard conditions.

extract_protocol:
For CLEAR-CLIP, cells were washed twice with ice cold PBS, UV254 cross-linked or not, scrapped, collected, pelleted by centrifugation at 500 g for 5 min at 4C and snap frozen, before to be gently lysed and processed further as described in PMID: 26602609 with minor changes. For RNA-Seq, cells were washed twice with ice cold PBS, dissolved in ice-cold reagent and total RNA extracted using a RNA Clean & Concentrator-25 kit (Zymo Research Z1018) strictly following manufacturer instrcutions and adding a DNAse I step.
For CLEAR-CLIP, library was constructed following a custom-made protocol (see PMID: 26602609) and minor changes. For RNA-Seq, library was constructed strictly following the TruSeq Stranded Total RNA protocol from Illumina and using TruSeq RNA CD index plate (96 indexes, 96 samples).

treatment_protocol: Cells were infected or not with SARS-CoV-2 (Wild-type or engineered mutants) at MOI = 0.001 for 48 hours.

tag: infected

value: Yes

tag: sars-cov-2 genotype

value: Mutant 5L

tag: moi

tag: duration of infection

value: 48 hours

tag: experiment

value: CLEAR-CLIP

tag: cross-linked

tag: igg used for ip

value: anti-pan AGO

tag: molecule subtype

value: RNA obtained after CLEAR-CLIP


title: NFO181-A549hACE2-SARSCoV2-2L

description: Single-end 1 x 150bp

value: Mutant 2L


title: NFO181-A549hACE2-SARSCoV2-3G

description: Single-end 1 x 150bp

value: Mutant 3G


title: NFO181-A549hACE2-SARSCoV2-4L

description: Single-end 1 x 150bp

value: Mutant 4L


title: WT_IR24h2

city: Jinan

first: Meng

last: Jia

address: 44#, Wenhua Xi Road

institute: Shandong university

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38.91 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: MM10
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: renal cortex

growth_protocol: All mice (3-5 mice per cage) were housed under standard laboratory conditions (12 h on/off; lights on at 7:00 a.m.) and temperature (24°C) with ad libitum access to water and standard laboratory chow diet (Beijing KEAOXIELI feed company, Beijing, China). Water and cages were autoclaved. Cages with standard corncob bedding were changed three times a week.

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: A midline abdominal incision was made and bilateral renal pedicles were clipped for 30 min using microaneurysm clamps. At the end of the ischemic period, the vascular clamps were removed .  After reperfusion at 24 hours,  the mice were euthanized and the kidney tissue samples were harvested for RNA sequencing.

value: Mus kidney

value: renal cortex

tag: strain

tag: treatment

value: 24 h renal ischemia/reperfusion-induced AKI


title: PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 2

description:
PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 1
D2_input

value: Ribotag

tag: virus

tag: viral delivery_route

value: intracortical

tag: input or_ribosomally_loaded


title: NFO181-A549hACE2-SARSCoV2-1L

description: Single-end 1 x 150bp

value: Mutant 1L


title: WT_IR24h1


title: WT_Sham2

value: sham


title: SPM LPS+LCC-12

city: Paris Cedex 05

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Trimmed reads were then aligned on the mouse mm10 reference genome using the STAR mapper (2.6.1b), up to the generation of a raw count table per gene (GENCODE annotation v29).
The bioinformatics pipelines used for these tasks are available online (rawqc v2.1.0: https://github.com/bioinfo-pf-curie/raw-qc, RNA-seq v3.1.4: https://github.com/bioinfo-pf-curie/RNA-seq).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: sorted SPM (small peritoneal macrophages)

growth_protocol: Experiments were performed on 5-week-old male SWISS mice. Male littermates were randomly assigned to experimental groups. The experimental endotoxemic model was induced by intraperitoneal (IP) injection of LPS (20 mg/kg) )(Escherichia coli O55:B5, Sigma-Aldrich, L2880). All the animals were resuscitated with 30 mL/kg body weight of saline administered subcutaneously 6 h post LPS administration. Mice were intra-peritoneally injected with LCC-12 (0.3 mg/kg  6 h after LPS challenge). Mice were sacrificed 22 h post-LPS challenge.

extract_protocol:
The sorted SPM from 7 LPS-treated mice (102283 SPM)) and from 8 LPS+LCC-12-treated mice (66967 SPM) were centrifugated, then resuspended in 350 uL of TCL (Qiagen, 1031576) and 1% beta-mercapto-ethanol. Total RNas were extracted with the Norgen Single Cell RNA Purification kit (Norgen, 51800).
RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara, 634419). The input quantity of total RNA was 10 ng/each condition. A first step of RNA fragmentation, was applied using a proprietary fragmentation mix at 94° C for 4 minutes. After fragmentation, indexed cDNA synthesis was performed. Then the ribodepletion step was performed using probes specific to mammalian rRNA. PCR amplification (12 cycles) was done to amplify the cDNA libraries. Library quantification and quality assessment was performed using a Qubit fluorometric assay (Invitrogen, Q32854) with dsDNA HS (High Sensitivity) Assay Kit and LabChip GX Touch using a High Sensitivity DNA chip (Perkin Elmer, 760517, CLS760672). Libraries were then equimolarly pooled and quantified by qPCR using the KAPA library quantification kit (Roche, 07960336001). Sequencing was performed on a NovaSeq 6000 (Illumina) targeting 100 M clusters per sample and using paired-end 2 x 100 bp.

tag: individual

value: pool of SPM  from 8 mice (66967 SPM)

tag: cell type

value: small peritoneal macrophages

tag: Sex

value: male


title: NFO181-A549hACE2-SARSCoV2-5G

description: Single-end 1 x 150bp

value: Yes

value: Mutant 5G

value: 48 hours


title: SPM LPS

value: pool of SPM  from 7 mice (102283 SPM)

value: LPS


title: Aldh1l1-CreERT2 mouse, input RNA, rep 2

description:
Aldh1l1-CreERT2 mouse, input RNA, rep 1
A2_input

tag: tissue

value: whole cortex

tag: genotype

value: input


title: WT_Sham3

value: Mus kidney


title: NFO175_E-VeroE6-SARSCoV2-XL-IgG

description:
Single-end 1 x 150bp
Table_S5.xlsx; Table_S6.txt.gz; Table_S7.txt.gz; Table_S12.xlsx; Table_S14.xlsx

tag: infected

tag: sars-cov-2 genotype

value: Wild-type

value: CLEAR-CLIP

value: Unspecific

value: RNA obtained after CLEAR-CLIP


title: NFO175_G-VeroE6-XL-AGO

description:
Single-end 1 x 150bp
Table_S5.xlsx; Table_S6.txt.gz; Table_S7.txt.gz; Table_S10.xlsx; Table_S12.xlsx; Table_S14.xlsx

value: No

tag: moi

tag: duration of infection

value: anti-pan AGO


title: NFO181-A549hACE2-SARSCoV2-6L

description: Single-end 1 x 150bp

value: Mutant 6L

tag: experiment

tag: cross-linked


title: NFO175_F-VeroE6-XL-AGO

tag: igg used for ip

tag: molecule subtype


title: NFO181-A549hACE2-SARSCoV2-WT

description: Single-end 1 x 150bp


title: D889T16 [SARS-Cov-2 + LCC-12]

data_processing:
Raw sequencing reads were aligned on the Mouse mm10 reference genome using the STAR mapper, up to the generation of a raw count table per gene (Gencode annotation v22). The raw count table was then normalized using the TMM method from the edgeR R package, and the limma voom functions were applied to detect genes with differential expression between control, infected and infected treated by LCC samples. Genes with an adjusted pvalue < 0,05 were declared significant.
Genome_build: mm10

source_name: infected by SARS-Cov-2 and treated with LCC-12

growth_protocol: Eight week-old male K18-human ACE2 expressing C57BL/6 mice (B6.Cg-Tg(K18-hACE2)2Prlmn/J) were purchased from Jackson Laboratory. The mice were anesthetized by i.p. injection of ketamine (100 mg/kg) and xylazine (10 mg/kg) and then intranasally infected with 50 µl of DMEM containing, or not (mock sample), 5x102 TCID50 of hCoV-19_IPL_France strain of SARS-CoV-2 (NCBI MW575140). LCC-12 was inoculated intranasally (0.5 mg/ml, 50 µL) 6 h post-infection, and once a day until day 2. LCC-12 was inoculated intranasally (0.5 mg/ml, 50 µL) 6 h post-infection, and once a day until day 2. Mice were sacrificed at day 4 post-infection.

extract_protocol:
RNA from lung homogenates were extracted using the NucleoSpin RNA kit (Macherey Nagel)
RNA sequencing libraries were prepared from 1 µg total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit, which allows strand specific sequencing to be performed. A first step of polyA selection using magnetic beads was performed to allow sequencing of polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. Sequencing was carried out on a NovaSeq 6000 instrument from Illumina based on a 2*100 cycle mode (paired-end reads, 100 bases).

treatment_protocol: The mouse was intranasally infected with 50 µl of DMEM containing 5x102 TCID50 of hCoV-19_IPL_France strain of SARS-CoV-2 (NCBI MW575140). LCC-12 was inoculated intranasally (0.5 mg/ml, 50 µL) 6 h post-infection, and once a day until day 2. The mouse was sacrified at day 4.

tag: strain

value: lung

tag: treatment


description:
AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 1
5_1_input

value: Ribotag

tag: virus

tag: viral delivery_route

value: intracortical


title: NFO181-A549hACE2-SARSCoV2-3L

description: Single-end 1 x 150bp

value: Yes

value: Mutant 3L


title: D889T18 [SARS-Cov-2 + LCC-12]

value: male

tag: individual

value: infected by SARS-Cov-2 and treated with LCC-12


title: WT_IR24h3

value: renal cortex

value: 24 h renal ischemia/reperfusion-induced AKI


title: WT_Sham1

value: Mus kidney

value: sham


title: D889T14 [SARS-Cov-2 + LCC-12]


title: D889T15 [SARS-Cov-2 + LCC-12]


title: NFO175_D-VeroE6-SARSCoV2-NoXL-AGO

value: Wild-type

value: 48 hours

value: CLEAR-CLIP


title: NFO175_C-VeroE6-SARSCoV2-XL-AGO

description:
Single-end 1 x 150bp
Table_S5.xlsx; Table_S6.txt.gz; Table_S7.txt.gz; Table_S8.xlsx; Table_S12.xlsx; Table_S14.xlsx

value: RNA obtained after CLEAR-CLIP


title: D889T13 [SARS-Cov-2 + LCC-12]


title: NFO175_H-VeroE6-XL-AGO

value: No

value: anti-pan AGO


title: D889T19 [SARS-Cov-2 + LCC-12]

value: lung


title: NFO175_A-VeroE6-SARSCoV2-XL-AGO


title: rdr6 premeiotic gynoecium replicate #2

city: Irapuato

first: Jean-Philippe

last: Vielle-Calzada

state: Guanajuato

address: Libramiento Norte carretera Leon Km 9.6

country: Mexico

institute: CINVESTAV

description: gynoecium rdr6 R2

data_processing:
Library adapters, the initial nine nucleotides (nt) from the 5' end, short sequences of less than 20 nt, and low-quality reads (Phred score less than 20) were discarded from all methylomes using the TrimGalore version 0.4.2 (Krueger F.https://github.com/FelixKrueger/TrimGalore)
Resulting reads were mapped to the Arabidopsis TAIR10 genome after in silico converting all sense cytosines to thymine, and all antisense guanines to adenine, allowing one mismatch per sequence and keeping only reads showing a single best alignment when using the Bismark version v0.19.0 (Krueger and Andrews, 2011).
Duplicate reads were removed using the Samtools version 1.9, rmdups option (Danecek et al., 2021)
After to asses biologial reproducibility of the biological replicates the reads were merged by genotype.
In each of the four resulting methylomes (wild-type, ago4, ago9 and rdr6) reads that showed a perfect match to the unconverted TAIR10 genome were eliminated by considering they represent DNA residues unaffected by bisulfite reactions (less than 1.1% of all sequences in all cases)
The total number of methylated and unmethylated cytosines were determined in each context (CG, CHH, and CHG) using the Bismark-methylation-extractor tool (Krueger and Andrews, 2011) in both sense and antisense genomic strands. The single nucleotide methylation frequency was calculated by estimating the number of cytosines over the number of cytosines and thymines at each individual genomic site.
Assembly: TAIR10
Supplementary files format and content: GFF format files, that include methylation frequency in genomic bins of 1nt for each sequence context (CG, CHG and CHH) per each one of the four genotypes

organism: Arabidopsis thaliana

source_name: rdr6 pre-meiotic gynoecium

extract_protocol:
For each biological replicate, 200 gynoecia of precisely 0.5 mm in length – and containing ovules at stages 1 and 2 (Rodríguez-Leal et al., 2015) - were isolated and collected under a Leica M80 stereomicroscope. Stage 9 and 10 flower buds (Schneitz, K. et al., 1995) were isolated using emasculation tweezers (Dumont #5 Tweezers; Electron Microscopy Sciences) and immobilized on a slide with double-sided adhesive tape. Gynoecia measuring 0.5 mm were isolated and collected using 1 ml insulin syringes (Terumo, USA), immediately placed 1.5 ml microcentrifuge tubes in liquid nitrogen, and stored at -80 C before DNA extraction. DNA extraction was performed with cetyltrimethyl ammonium bromide (CTAB) buffer adding a final incubation step with RNase (modified CTAB protocol on the base of Doyle and Doyle, 1987).
For bisulfite conversion of unmethylated cytosines to uracil, we used the EpiTect Fast Bisulfite Conversion kit (Qiagen, #59802). Library construction was performed using the Ovation Ultralow Methyl-Seq Library System kit (Nugen, #0336), following two rounds of bisulfite conversion (Walker et al., 2018). Two biological replicates were generated for each genotype. Wild-type replicate #1, ago4 replicate #1, ago9 replicate #1, and ago9 replicate #2 libraries were generated from 59 to 120 ng of total DNA that was treated with bisulfite as described above, and subsequently amplified with 10 cycles of PCR. Wild-type replicate #2 and ago4 replicate #2 libraries were generated from 70 ng of total DNA treated with bisulfite and subsequently amplified with 11 cycles of PCR. Finally, rdr6 replicate #1 and rdr6 replicate #2 were generated from 20 and 29 ng of total DNA, and amplified with 13 and 12 cycles of PCR, respectively.

tag: ecotype

tag: geo loc_name

value: Mexico:Guanajuato, Irapuato

value: rdr6 pre-meiotic gynoecium

tag: sample type

value: mix of whole pre-meiotic gynoecia

value: RNA-dependent RNA polymerase 6

value: RNA-DEPENDENT RNA POLYMERASE 6 homozygous mutant, biological replicate 2

tag: height or_length

value: 0.5mm pre-meiotic gynoecia

tag: isolation source

value: greenhouse


title: D889T17 [SARS-Cov-2 + LCC-12]

tag: Sex

value: male

tag: tissue

value: infected by SARS-Cov-2 and treated with LCC-12


title: D889T05 [SARS-Cov-2]

source_name: infected by SARS-Cov-2

treatment_protocol: The mouse was intranasally infected with 50 µl of DMEM containing 5x102 TCID50 of hCoV-19_IPL_France strain of SARS-CoV-2 (NCBI MW575140), and was sacrified at day 4.

value: infected by SARS-Cov-2


title: D889T09 [SARS-Cov-2]


title: D889T12 [SARS-Cov-2 + LCC-12]


title: ago9 premeiotic gynoecium replicate #1

description: gynoecium ago9 R1

source_name: ago9 pre-meiotic gynoecium

value: ago9 pre-meiotic gynoecium

tag: genotype

value: argonaute 9

value: ARGONAUTE 9 homozygous mutant, biological replicate 1


title: D889T04 [SARS-Cov-2]


title: rdr6 premeiotic gynoecium replicate #1

description: gynoecium rdr6 R1

value: RNA-DEPENDENT RNA POLYMERASE 6 homozygous mutant, biological replicate 1


title: ago4 premeiotic gynoecium replicate #2

description: gynoecium ago4 R2

source_name: ago4 pre-meiotic gynoecium

value: ago4 pre-meiotic gynoecium

value: argonaute 4

value: ARGONAUTE 4 homozygous mutant, biological replicate 2


title: ago9 premeiotic gynoecium replicate #2

description: gynoecium ago9 R2

value: Mexico:Guanajuato, Irapuato

value: ARGONAUTE 9 homozygous mutant, biological replicate 2


title: Wild-type premeiotic gynoecium replicate #2

description: gynoecium Wt R2

source_name: wild-type pre-meiotic gynoecium

value: wild-type pre-meiotic gynoecium

value: mix of whole pre-meiotic gynoecia

value: Wild-type

value: Wild-type, biological replicate 2


title: ago4 premeiotic gynoecium replicate #1

description: gynoecium ago4 R1

value: ARGONAUTE 4 homozygous mutant, biological replicate 1

value: 0.5mm pre-meiotic gynoecia

value: greenhouse


title: D889T07 [SARS-Cov-2]

value: male

value: lung

value: infected by SARS-Cov-2


title: D889T08 [SARS-Cov-2]


title: D889T11 [SARS-Cov-2]


title: D889T06 [SARS-Cov-2]


title: D889T10 [SARS-Cov-2]


title: Wild-type premeiotic gynoecium replicate #1

description: gynoecium Wt R1

value: Wild-type, biological replicate 1


title: D889T03 [mock]

source_name: non infected

treatment_protocol: The mouse received 50 µl of DMEM intranasally at day 0,  and was sacrificed at day 4.

value: non infected


title: D889T02 [mock]


title: NFO175_B-VeroE6-SARSCoV2-XL-AGO

tag: infected

value: Yes

tag: sars-cov-2 genotype

tag: moi

tag: duration of infection

value: 48 hours

tag: experiment

value: CLEAR-CLIP

value: anti-pan AGO

value: RNA obtained after CLEAR-CLIP


title: D889T01 [mock]

tag: strain

tag: treatment


title: HEK293T,Flag-TEAD2+SIRT4,rep3

city: beijing

first: lei

last: zhang

address: xueyuan road 38th

department: heath science center

institute: peking university

data_processing:
Hista2 for mapping sequence
Samtools for ordering sam file to bam file
FeatureCounts for counting gene reads
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: embryonic kidney

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
cell were lysised with trizol to extract RNA,
3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NovaSeq 6000 following manufacturer's protocols.

treatment_protocol: different groups of plasmid were transfected in cells with PEI for 6h, then cells were washed with warm PBS buffer and cultured with growth protocol for 48h.

value: embryonic kidney

tag: cell line

tag: cell type

value: Epithelial cell

value: WT

value: Transfected with Flag-TEAD2 and HA-SIRT4


title: HEK293T,Flag-TEAD2+SIRT4,rep2


title: platelet infarct KO rep1

city: Tübingen

first: Oliver

last: Borst

address: Otfried-Müller-Street 10

department: Internal Medicine III- Cardiology

country: Germany

institute: University Clinic Tübingen

data_processing:
FastQC (version 0.11.8)
adapter were trimmed using Trim Galore! (version 0.6.3)
Alignment against miRBase mature and hairpin was performed using Bowtie (version1.3.0)
Ensembl annotations miRBase mature and miRbase from the GRCm38
Post-alignment processing of miRBase hairpin was performed using SAMtools (version 1.10.2)
Analysis of miRBase counts was performed using edgeR (version 3.11) and TMM normalization
miRNA quality control was validated using mirtrace (version 1.0.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, matrix table with raw gene counts for every gene and every sample

source_name: platelet

extract_protocol:
purification of platelets was performed using immune-magnetic negative selection to completely deplete leukocytes. Total RNA including miRNA was isolated from murine platelets using the QIAsymphony RNA Kit.
The sequencing library was prepared using the QIAseq miRNA Library Kit with 10 to 20 ng input. The libraries were pooled in an equimolar fashion and sequenced on a NovaSeq6000 as paired-end reads with a sequencing depth of >12 Mio clusters (i.e. read-pairs) per sample.

value: platelet

value: KO

tag: condition

value: infarct


title: platelet infarct KO rep4


title: platelet infarct KO rep2


title: HEK293T,Flag-TEAD2+SIRT4,rep1


title: platelet infarct WT rep4


title: HEK293T,Flag-TEAD2-KR,rep2

value: Transfected with Flag-TEAD2-KR and HA-vector


title: platelet infarct WT rep2


title: platelet baseline KO rep3

value: baseline


title: platelet infarct WT rep3


title: platelet infarct WT rep1


title: HEK293T,Flag-TEAD2-KR,rep1


title: HEK293T,Flag-TEAD2,rep2

value: Transfected with Flag-TEAD2 and HA-vector


title: HEK293T,Flag-TEAD2-KR,rep3


title: platelet baseline KO rep2


title: HEK293T,Flag-TEAD2,rep1


title: platelet baseline KO rep4


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t24, Replicate3

description: RNA-seq

data_processing:
Pseudoalignment (kallisto v0.48.0) to hg38 (GRCh38.p13)
Differential Gene Expression (DESeq2 v1.32.0)
genomeCoverageBed -pc -strand - (Bedtools)
Bedgraphs were plotted using Sushi package v1.30.0 in R v4.1.0
Assembly: NC_003977.2 (offset by 500 bp)
Supplementary files format and content: a tab-delimited text file that includes tags per million (TPM) values for each sample
Supplementary files format and content: bedgraph files that include fragment coverage data

extract_protocol:
RNA-seq from  purified nuclei at different timepoints after transfection with HBV cccDNA.
Samples for RNA-sequencing were harvested into 1 mL TRIzol Reagent (ThermoFisher) and phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Mini Kit (Qiagen) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 38-42 µL RNase-free water. After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 9.9-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit), with 8 cycles of PCR.

value: Human embryonic kidney cells

value: HBV cccDNA transfected

tag: time

value: 24 hr


title: platelet baseline KO rep1


title: platelet baseline WT rep3


title: platelet baseline WT rep2


title: platelet baseline WT rep4


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t12, Replicate3

description: RNA-seq

value: 12 hr


title: platelet infarct KO rep3


title: platelet baseline WT rep1


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t24, Replicate1

description: RNA-seq


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t12, Replicate2

description: RNA-seq


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t12, Replicate1

description: RNA-seq


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t08, Replicate3

description: RNA-seq

value: 08 hr


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t08, Replicate1

description: RNA-seq


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t04, Replicate3

description: RNA-seq

value: 04 hr


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t08, Replicate2

description: RNA-seq


title: HEK293T,Flag-TEAD2,rep3


title: RNA-seq, HEK293T cells, mock transfection, t0, Replicate3

description: RNA-seq

value: mock transfection

value: 00 hr


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t24, Replicate2

description: RNA-seq


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t04, Replicate1

description: RNA-seq


title: IP_266_2

city: ChongQing

first: Xingyue

last: Zhang

institute: Southwest Hospitial

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using BWA(0.7.10)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 version 2.1.1 was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as cutoff
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS

source_name: C57BL/6J neonatal primary cardiomyocytes

growth_protocol: Neonatal CMs were isolated by enzymatic disassociation from 1-day-old neonatal mouse hearts; the crude method of collagenase type II enzymatic digestion was applied to isolate the cells. The final cell suspension including CMs was separated by allowing the cell suspension to sediment in an uncoated culture dish at 37 °C for 1 h. Preplating was performed to help fibroblasts adhere to the culture dish and separate them from the CMs, which remained floating in the suspension. To inhibit fibroblast proliferation, 0.1 mM bromodeoxyuridine was added. The cells were then used for experiments as stated. After separation, the cells were incubated  at 37 °C under 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and CD38-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The cells were subjected to hypoxia/ischemia at 37 °C under 5% CO2 and 1% O2 for 12 h.

value: neonatal primary cardiomyocytes

tag: chip antibody

value: CD38 (Biorbyt, orb557212)


title: IP_266_1


title: RNA-seq, HEK293T cells, mock transfection, t0, Replicate1

description: RNA-seq

value: WT


title: RNA-seq, HEK293T cells, mock transfection, t0, Replicate2, removed

description: RNA-seq


title: TBI_HuBrainCTL_Nuclei_529T_bulk_S10

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description: TruSeq Stranded mRNA LP (48 Spl)

data_processing:
Single cell/nuclei: Raw base calls were demultiplexed to obtained sample specific FastQ files using mkfastq in default parameters (10x Genomics), and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v6) with default parameters (--include-introns was used for nuclei mapping)
Bulk RNAseq: Raw base calls were demultiplexed to obtain sample specific FastQ files using bcl2fastq (Illumina). Reads were aligned using STAR aligner (version 2.6.0c) in default parameters to quantify gene expression, but using unique mapping (outFilterMultimapNmax 1, outFilterMismatchNoverLmax 0.03) for quantification of TEs. For mapping and quantification of individual TEs, we split BAM files per strand. Genes and TEs were quantified using featureCounts (subread package version 1.6.3). Genes were quantified using gencode annotation for hg38 version 36. TEs were quantified using a manually curated GTF file derived from repeatmasker (hg38) to avoid simple repeats, small RNAs and low-complexity regions; this GTF was retrieved from the authors of TEtranscripts (Jin et al., 2015). To quantify TE subfamilies, we mapped reads using STAR aligner (version 2.6.0c) with a multi-mapping approach (outFilterMultimapNmax 100, winAnchorMultimapNmax 200) and quantified using TEcounts from TEtoolkit (Jin et al., 2015).
Bulk RNAseq (pacbio): SMRTLink pipeline was ran using the default settings
Assembly: GRCh38
Supplementary files format and content: Single cell/nuclei: Cellranger count output matrices
Supplementary files format and content: Bulk RNAseq (truseq): Gene, TEs, and TE subfamilies read count matrices

source_name: temporal lobe

extract_protocol:
The nuclei isolation from the brain tissue was performed according to Jönsson et al., 2021. In brief, the tissue was thawed and dissociated in ice-cold lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) using a 1 ml tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl, pH 8.0, and 1 mM DTT) before centrifugation at 30,000 × g for 2 hours and 15 min. Pelleted nuclei were softened for 10 min in 100 ml of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) before being resuspended in 300 ml of dilution buffer (10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) and run through a cell strainer (70 mm). Cells were run through the FACS (FACS Aria, BD Biosciences) at 4°C at a low flow rate using a 100 mm nozzle (reanalysis showed >99% purity).
Single cell/nuclei: Nuclei/cells were directly loaded onto the Chromium Next GEM Chip G or Chromium Next GEM Chip K Single Cell Kit along with the reverse transcription mastermix following the manufacturer’s protocol for the Chromium Next GEM Single Cell 5’ Kit (10x Genomics, PN-1000263) to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics using 15 cycles of amplification.
Bulk RNAseq (truseq): Total RNA was isolated from nuclei using the RNeasy Mini Kit (Qiagen).
Bulk RNAseq (pacbio)Total RNA was obtained from tissue samples using miRNA Easy Mini Kit (Qiagen). RNA samples were subsequently put on dry ice and shipped to the National Genomics Infrastructure of Sweden. There, input QC of samples was performed on the Agilent Bioanalyzer instrument, using the Eukaryote Total RNA Nano kit to evaluate RIN and concentration. The sample libraries were prepared as described in "Procedure & Checklist – Iso-Seq™ Express Template Preparation for Sequel® and Sequel II Systems" (PN 101-763-800 Version 02 (October 2019)) using the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads (Promega) and the SMRTbell Express Template Prep Kit 2.0. 300 ng of total RNA was used for cDNA Synthesis followed by 12 + 3 cycles of cDNA Amplification. In the purification step of amplified cDNA the standard workflow was applied (sample is composed primarily of transcripts centered around 2 kb).
Single cell/nuclei: Sequencing libraries were generated with unique dual indices (TT set A) and pooled for sequencing on a Novaseq6000 using a 100-cycle kit and 28-10-10-90 reads.
Bulk RNAseq (truseq): Libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and sequenced on a NextSeq500 (PE 2×150bp).
Bulk RNAseq (pacbio): After purification the amplified cDNA went into the SMRTbell library construction. Quality control of the SMRTbell libraries was performed with the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. Primer annealing and polymerase binding was performed using the Sequel II binding kit 2.0. Finally, the samples were sequenced on Sequel II and Sequel IIe System using Sequel® II Sequencing Plate 2.0, with an On-Plate Loading Concentration of 110 pM, movie time 24 hours and pre-extension time 2 hours.

value: temporal lobe

tag: type

value: Bulk (sorted nuclei)

value: male

tag: age


title: In_266_1

value: none (input)


title: TBI_HuBrainCTL_Nuclei_529F_bulk_S9

description: TruSeq Stranded mRNA LP (48 Spl)

source_name: frontal lobe

value: frontal lobe

tag: Sex


title: Zyagen_D000_Skin.190507_long_S2 [Zyagen_D000_Skin.190507_long_S2]

city: Cambridge

first: Siddharth

last: Raju

state: Massachusetts

address: 415 Main Street

institute: Broad Institute

description:
Zyagen_D000_Skin.190507_long_S2
Rhesus monkey

data_processing:
Host transcriptomics data was processed using the umiRNAseq custom pipeline for Bulk RNA-seq Processing with UMI correction (https://github.com/broadinstitute/sabeti-host-txnomics-internal/blob/master/bulk-rna-seq/umiRNASeq.wdl).
Briefly, raw Fastq files were merged and tagged with their corresponding UMI barcode, then they were mapped using STAR to the Rhesus monkey (M. mulatta) reference genome and annotation (Mmul_10).
Resulting BAM files were filtered for multiple mapped reads, sorted and indexed using samtools. Then, PCR duplicates were removed by UMI-tools using the UMI barcodes of each transcript.
Furthermore, featureCounts were used to quantify expression from the aligned and processed RNA-Seq BAM files. Additionally, The BioMart R package was used to annotate the gene type, gene name, and gene function using the Ensembl M. mulatta database “mmulatta_gene_ensembl”.
Quality control over the sample was performed removing samples with low sequencing quality and mismatch sex assignment.
Assembly: Mmul_10
Supplementary files format and content: 20230121_counts_submission.txt: Tab-delimited format, raw counts.

organism: Macaca mulatta

source_name: Skin

extract_protocol:
Total RNA was extracted from tissue homogenates inactivated in TRIzol using the MagMAX MirVana total RNA kit (ThermoFisher) on a KingFisher FLEX instrument.
Ribosomal RNA was depleted using an RNase H-based method, RNA was then heat-fragmented, reverse transcription was performed, and strand-specific double-stranded cDNA was generated. xGen UDI-UMI (IDT) adapters were ligated and libraries were amplified.

tag: tissue

value: Skin

tag: monkey id


title: Zyagen_D000_Spleen.190507_long_S1 [Zyagen_D000_Spleen.190507_long_S1]

description:
Zyagen_D000_Spleen.190507_long_S1
Rhesus monkey

source_name: Spleen

value: Spleen


title: Zyagen_D000_Testis.160421_long_S16 [Zyagen_D000_Testis.160421_long_S16]

description:
Zyagen_D000_Testis.160421_long_S16
Rhesus monkey

source_name: Testis

value: Testis


title: Zyagen_D000_LN.190507_long_S6 [Zyagen_D000_LN.190507_long_S6]

description:
Zyagen_D000_LN.190507_long_S6
Rhesus monkey

source_name: Lymph node:NA

value: Lymph node:NA


title: In_266_2


title: TBI_HuBrainCTL_Nuclei_502T_bulk_S8

description: TruSeq Stranded mRNA LP (48 Spl)


title: TBI_HuBrainCTL_Nuclei_501T_bulk_S6

description: TruSeq Stranded mRNA LP (48 Spl)


title: Zyagen_D000_Ovary.160421_long_S15 [Zyagen_D000_Ovary.160421_long_S15]

description:
Zyagen_D000_Ovary.160421_long_S15
Rhesus monkey

source_name: Ovary

value: Ovary


title: TBI_HuBrainCTL_Nuclei_501F_bulk_S5

description: TruSeq Stranded mRNA LP (48 Spl)


title: Zyagen_D000_SpinalCord.190507_long_S8 [Zyagen_D000_SpinalCord.190507_long_S8]

description:
Zyagen_D000_SpinalCord.190507_long_S8
Rhesus monkey

source_name: SpinalCord

value: SpinalCord


title: Zyagen_D000_Liver.190507_long_S3 [Zyagen_D000_Liver.190507_long_S3]

description:
Zyagen_D000_Liver.190507_long_S3
Rhesus monkey

source_name: Liver

value: Liver


title: RNA-seq, HEK293T cells, HBV cccDNA transfection, t04, Replicate2

description: RNA-seq

value: Human embryonic kidney cells

tag: genotype

value: HBV cccDNA transfected

value: 04 hr


title: Zyagen_D000_Kidney.190507_long_S7 [Zyagen_D000_Kidney.190507_long_S7]

description:
Zyagen_D000_Kidney.190507_long_S7
Rhesus monkey

source_name: Kidney

value: Kidney


title: TBI_HuBrainCTL_Nuclei_502F_bulk_S7

description: TruSeq Stranded mRNA LP (48 Spl)


title: CR119_DA822_IgG_S18

description: Hyperprep kit (KAPA)

data_processing:
Single cell/nuclei: Raw base calls were demultiplexed to obtained sample specific FastQ files using mkfastq in default parameters (10x Genomics), and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v6) with default parameters (--include-introns was used for nuclei mapping)
bulk RNAseq: Raw base calls were demultiplexed to obtain sample specific FastQ files using bcl2fastq (Illumina). Reads were aligned using STAR aligner (version 2.6.0c) in default parameters to quantify gene expression, but using unique mapping (outFilterMultimapNmax 1, outFilterMismatchNoverLmax 0.03) for quantification of TEs. For mapping and quantification of individual TEs, we split BAM files per strand. Genes and TEs were quantified using featureCounts (subread package version 1.6.3). Genes were quantified using gencode annotation for hg38 version 36. TEs were quantified using a manually curated GTF file derived from repeatmasker (hg38) to avoid simple repeats, small RNAs and low-complexity regions; this GTF was retrieved from the authors of TEtranscripts (Jin et al., 2015). To quantify TE subfamilies, we mapped reads using STAR aligner (version 2.6.0c) with a multi-mapping approach (outFilterMultimapNmax 100, winAnchorMultimapNmax 200) and quantified using TEcounts from TEtoolkit (Jin et al., 2015).
CUT&RUN: Reads were aligned to the human genome (hg38) using bowtie2 (version 2.3.4.2; RRID:SCR_016368) (Langmead et al., 2012) (–local –very-sensitive-local –no-mixed –no-discordant –phred33 -I 10 -X 700), converted to bam files with samtools (version 1.4; RRID:SCR_002105) and sorted (samtools version 1.9; RRID:SCR_002105). RPKM normalized bigwig coverage tracks were made with bamCoverage (deepTools (version 2.5.4; RRID:SCR_016366)) (Ramírez et al., 2014).
Assembly: GRCh38
Supplementary files format and content: Single cell/nuclei: Cellranger count output matrices
Supplementary files format and content: bulk RNAseq: Gene, TEs, and TE subfamilies read count matrices
Supplementary files format and content: CUT&RUN: BigWig files

source_name: fetal forebrain

extract_protocol:
The nuclei isolation from the embryonic brain tissue was performed according to Jönsson et al., 2021. In brief, the tissue was thawed and dissociated in ice-cold lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) using a 1 ml tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl, pH 8.0, and 1 mM DTT) before centrifugation at 30,000 × g for 2 hours and 15 min. Pelleted nuclei were softened for 10 min in 100 ml of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) before being resuspended in 300 ml of dilution buffer (10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) and run through a cell strainer (70 mm). Cells were run through the FACS (FACS Aria, BD Biosciences) at 4°C at a low flow rate using a 100 mm nozzle (reanalysis showed >99% purity).
Single cell/nuclei: Nuclei/cells were directly loaded onto the Chromium Next GEM Chip G or Chromium Next GEM Chip K Single Cell Kit along with the reverse transcription mastermix following the manufacturer’s protocol for the Chromium Next GEM single cell 3’ kit (10X Genomics, PN-1000268) to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics using 13 cycles of amplification for 3’ libraries.
Bulk RNAseq: Total RNA was isolated from nuclei or tissue using the RNeasy Mini Kit (Qiagen).
CUT&RUN: We followed the protocol detailed by the Henikoff lab (Skene et al., 2017). Briefly, 100,000 sorted nuclei were washed twice (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x Roche cOmplete protease inhibitors) and attached to 10 ConA-coated magnetic beads (Bangs Laboratories) that had been pre-activated in binding buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Bead-bound cells were resuspended in 50 μL buffer (20 mM HEPES pH 7.5, 0.15 M NaCl, 0.5 mM Spermidine, 1x Roche complete protease inhibitors, 0.02% w/v digitonin, 2 mM EDTA) containing primary antibody (rabbit anti-H3K4me3 Active Motif 39159, RRID:AB_2615077; or goat anti-rabbit IgG, Abcam ab97047, RRID:AB_10681025) at 1:50 dilution and incubated at 4°C overnight with gentle shaking. Beads were washed thoroughly with digitonin buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete protease inhibitors, 0.02% digitonin). After the final wash, pA-MNase (a generous gift from Steve Henikoff) was added to the digitonin buffer and incubated with the cells at 4°C for 1 h. Bead-bound cells were washed twice, resuspended in 100 μL digitonin buffer, and chilled to 0-2°C. Genome cleavage was stimulated by the addition of 2 mM CaCl2 at 0°C for 30 min. The reaction was quenched by the addition of 100 μL 2x stop buffer (0.35 M NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% digitonin, 50 ng/μL glycogen, 50 ng/μL RNase A, 10 fg/μL yeast spike-in DNA (a generous gift from Steve Henikoff)) and vortexing. After 10 min of incubation at 37°C to release genomic fragments, cells and beads were pelleted by centrifugation (16,000 g, 5 min, 4°C) and fragments from the supernatant were purified.
Single cell/nuclei: Sequencing libraries were generated with unique dual indices (TT set A) and pooled for sequencing on a Novaseq6000 using a 100-cycle kit and 28-10-10-90 reads.
Bulk RNAseq: Libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and sequenced on a NextSeq500 (PE 2×150bp).
CUT&RUN: Illumina sequencing libraries were prepared using the Hyperprep kit (KAPA) with unique dual-indexed adapters (KAPA), pooled and sequenced on a Nextseq500 instrument (Illumina).

value: fetal forebrain

value: Bulk

value: 10 weeks


title: CR119_DA822_H3K4me3_S19

description: Hyperprep kit (KAPA)


title: CR118_DA817_IgG_S15

description: Hyperprep kit (KAPA)

value: 7 weeks


title: Zyagen_D000_Brain.190507_long_S5 [Zyagen_D000_Brain.190507_long_S5]

description:
Zyagen_D000_Brain.190507_long_S5
Rhesus monkey


title: HuEmCtxfresh8w_190319_bulk_DA094_S21

description: TruSeq Stranded mRNA LP (48 Spl)

value: 8 weeks


title: Zyagen_D000_Adrenal.190507_long_S4 [Zyagen_D000_Adrenal.190507_long_S4]

description:
Zyagen_D000_Adrenal.190507_long_S4
Rhesus monkey

source_name: Adrenal Gland

value: Adrenal Gland


title: HuEmCtxfresh8w6d_190416_bulk_DA140_S22

description: TruSeq Stranded mRNA LP (48 Spl)

value: 9 weeks


title: RA1803_PBMC-D6 [RA1803_PBMC_D006_S13]

description:
RA1803_PBMC_D006_S13
Rhesus monkey

source_name: PBMC

value: PBMC

value: infected with Ebola virus


title: RA1779_Liver-L [RA1779.Liver_S7]

description:
RA1779.Liver_S7
Rhesus monkey


title: RA1325_PBMC-D6 [RA1325_PBMC_D006_S12]

description:
RA1325_PBMC_D006_S12
Rhesus monkey


title: RA1074_PBMC-D6 [RA1074_PBMC_D006_S11]

description:
RA1074_PBMC_D006_S11
Rhesus monkey


title: RA0717_Liver-L [RA0717.Liver_S10]

description:
RA0717.Liver_S10
Rhesus monkey


title: HuEmCtxfresh40mm10-5w_201029_bulk_S23

description: TruSeq Stranded mRNA LP (48 Spl)

value: 10.5 weeks


title: HuEmCtx_40mm_190611_bulkB_S3

description: TruSeq Stranded mRNA LP (48 Spl)


title: HuEmCtxfresh7w4d_190416_bulk_DA103_S1

description: TruSeq Stranded mRNA LP (48 Spl)


title: RA0850_Liver-L [RA0850.Liver_S11]

description:
RA0850.Liver_S11
Rhesus monkey


title: RA0449_PBMC-D3 [RA0449.D003_S105_L002]

description:
RA0449.D003_S105_L002
Rhesus monkey


title: DA140_ctx_8wks6d_S4

description: Sample was sequenced twice. Chromium Next GEM Single Cell 3’ Kit

value: Cells


title: DA103_ctx_7wks4d_S2


title: HuEmCtx_40mm_190611_S5

description: Chromium Next GEM Single Cell 3’ Kit

value: Nuclei


title: DA094_ctx_8wks_S1


title: RA1803_WholeBlood-D6 [A0375_S50_L001]

description:
A0375_S50_L001
Rhesus monkey

source_name: Whole blood

value: Whole blood


title: RA1803_WholeBlood-D2 [A0373_S52_L001]

description:
A0373_S52_L001
Rhesus monkey


title: HuEmCtxfresh40mm10-5w_201029_S8

description: Chromium Next GEM Single Cell 3’ Kit


title: RA1803_WholeBlood-BL [A0372_S53_L001]

description:
A0372_S53_L001
Rhesus monkey


title: CR118_DA817_H3K4me3_S16

description: Hyperprep kit (KAPA)


title: LV3627_3_h6_NPCday14_S13

description: TruSeq Stranded mRNA LP (48 Spl)

data_processing:
Organoids: Raw base calls were demultiplexed to obtained sample specific FastQ files using mkfastq in default parameters (10x Genomics), and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v6) with default parameters (--include-introns was used for nuclei mapping)
fbNPCs: Raw base calls were demultiplexed to obtain sample specific FastQ files using bcl2fastq (Illumina). Reads were aligned using STAR aligner (version 2.6.0c) in default parameters to quantify gene expression, but using unique mapping (outFilterMultimapNmax 1, outFilterMismatchNoverLmax 0.03) for quantification of TEs. Genes and TEs were quantified using featureCounts (subread package version 1.6.3). Genes were quantified using gencode annotation for hg38 version 36. TEs were quantified using a manually curated GTF file derived from repeatmasker (hg38) to avoid simple repeats, small RNAs and low-complexity regions; this GTF was retrieved from the authors of TEtranscripts (Jin et al., 2015).
Assembly: GRCh38
Supplementary files format and content: Organoids: Cellranger count output matrices. fbNPCs: gene and TE count matrices

source_name: forebrain neural progenitor cells

extract_protocol:
fbNPCs: iPSCs were differentiated into forebrain neural progenitors (fbNPCs) as previously described Johansson et al., 2022 and Grassi et al., 2020. Upon dissociation at 70-90% confluency, the cells were plated on LN111 (1.14µg/cm2; Biolamina) coated Nunc multidishes at a density of 10.000 cells/cm2 and grown in N2 medium (1:1 DMEM/F-12 (21331020; GIBCO) and Neurobasal (21103049; GIBCO) supplemented with 1% N2 (GIBCO), 2 mM L-glutamine (GIBCO), and 0.2% penicillin/streptomycin). 10 μM SB431542 (Axon) and 100 ng/ml noggin (Miltenyi) were given for dual SMAD inhibition. The media was changed every 2-3 days. On day 9, N2 media without dual SMAD inhibitors were used. On day 11, cells were dissociated and replated on LN111 coated Nunc multidishes at a density of 800.000 cells/cm2 in B27 medium (Neurobasal supplemented with 1% B27 without vitamin A (GIBCO), 2 mM L-glutamine and 0.2% penicillin/streptomycin Y27632 (10 μM), BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2 mM; Sigma). Cells were kept in the same media until day 14 when cells were harvested for downstream analysis.
Organoids: To generate the human cerebral-like organoids we followed the protocol detailed in Johansson et al., 2022. We used three hIPSC6-derived lines obtained by transduction and FACS sorting as described above: one control line (guide against LacZ) and two LINC01876 CRISPRi KD lines (guide 2 and guide 3). Briefly, 8000 cells/well were plated in a 96-wells plate (Costar, Ultra Low Attachment, round bottom; REF 7007) with 250 μL of mTeSR1 (StemCell Technologies, Inc.) and RY27632 10 μM. This is considered day −5 of the differentiation of the iPSCs-derived hFB organoids. On days −3 and −1 the medium was changed (150 μL and 200 μL of mTeSR1, respectively). At day 0 the cells are fed with Neural Induction Medium (NIM; DMEM/F12 media, N2 Supplement (1:100), L-Glutamine (2mM), Penicillin/Streptomycin (1:500), Non-Essential Amino acids (1:100) and Heparin (2ug/ml).) enriched with 3% KSR. On days 2, 4, and 6, the organoids were fed with NIM with no added KSR. On day 8 the organoids were embedded in 30-50 μL of Matrigel (Corning) and incubated at 37°C for 25 minutes to allow the Matrigel to solidify. The organoids were then transferred in Corning REF 3471 6-well plates with flat bottoms containing 4  ml/well of Cortical Differentiation Medium (CDM; F12 Media (-Glut) (48.5%), Neurobasal (48.5%), N2 Supplement (1:200), B27 Supplement (-Vit.A, 1:100), L-Glutamine (2mM), Penicillin/Streptomycin (1:500), Non-Essential Amino acids (1:200), Beta MercaptoEtOH (50uM) and Insulin (2.5 ug/mL)). On days 10 and 12 of the differentiation, the media was changed exchanging 3 ml/well for 3 mL of fresh CDM. On days 15, 17, 19, 21 and 23, ∼4 mL of the medium was replaced with 4 mL of Improved Differentiation Medium + A (IDM, F12 Media (-Glut) (48.5%), Neurobasal (48.5%), N2 Supplement (1:200), B27 Supplement (+Vit.A, 1:50), L-Glutamine (2mM), Penicillin/Streptomycin (1:500), Non-Essential Amino acids (1:200), Beta MercaptoEtOH (50uM), Insulin (2.5 ug/mL) and Ascorbic Acid (400uM)). From day 25, the media was changed every 3 days with 3-4 mL of Cortical Terminal Differentiation Medium (CTDM, F12 Media (-Glut) (48.5%), Neurobasal (48.5%), N2 Supplement (1:200), B27 Supplement (+Vit.A) – (1:50) 800uL, L-Glutamine (2mM), Penicillin/Streptomycin (1:500), Non-Essential Amino acids (1:200), Beta MercaptoEtOH (50uM), Insulin (2.5 ug/mL) and Ascorbic Acid (400uM), BDNF (10ng/uL), cAMP (200uM), GDNF (10ng/uL)). All the diameter measurements of the organoids were taken with the Measure tool from Image J. The chosen measuring unit was mm.
Organoids: The nuclei isolation from the organoids was performed according to Jönsson et al., 2018. In brief, the tissue and organoids were thawed and dissociated in ice-cold lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) using a 1 ml tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl, pH 8.0, and 1 mM DTT) before centrifugation at 30,000 × g for 2 hours and 15 min. Pelleted nuclei were softened for 10 min in 100 ml of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) before being resuspended in 300 ml of dilution buffer (10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) and run through a cell strainer (70 mm). Cells were run through the FACS (FACS Aria, BD Biosciences) at 4°C at a low flow rate using a 100 mm nozzle (reanalysis showed >99% purity). Nuclei were directly loaded onto the Chromium Next GEM Chip G or Chromium Next GEM Chip K Single Cell Kit along with the reverse transcription mastermix following the manufacturer’s protocol for the Chromium Next GEM single cell 3’ kit (10X Genomics, PN-1000268) to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics using 13 cycles of amplification for 3’ libraries.
fbNPCs: Total RNA was isolated from nuclei, cell culture samples, or tissue using the RNeasy Mini Kit (Qiagen).
Organoids: Sequencing libraries were generated with unique dual indices (TT set A) and pooled for sequencing on a Novaseq6000 using a 100-cycle kit and 28-10-10-90 reads.
fbNPCs: Libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and sequenced on a NextSeq500 (PE 2×150bp).

value: forebrain neural progenitor cells

tag: timepoint

value: 14 days


title: LV3629_3_h6_NPCday14_S16

description: TruSeq Stranded mRNA LP (48 Spl)

tag: target

value: LINC01876 (guide 2)


title: LV3627_1_h6_NPCday14_S12

description: TruSeq Stranded mRNA LP (48 Spl)


title: RA1803_WholeBlood-BL [A0371_S54_L001]

description:
A0371_S54_L001
Rhesus monkey


title: RA1803_WholeBlood-D4 [A0374_S51_L001]

description:
A0374_S51_L001
Rhesus monkey


title: LV3627_2_h6_NPCday14_S17

description: TruSeq Stranded mRNA LP (48 Spl)


title: LV3629_2_h6_NPCday14_S19

description: TruSeq Stranded mRNA LP (48 Spl)


title: HuEmCtx_40mm_190611_bulkA_S2

description: TruSeq Stranded mRNA LP (48 Spl)


title: RA1325_WholeBlood-D4 [A0369_S56_L001]

description:
A0369_S56_L001
Rhesus monkey


title: RA0717_PBMC-D4 [RA0717_PBMC_D004_S9]

description:
RA0717_PBMC_D004_S9
Rhesus monkey


title: RA0452_PBMC-D5 [RA0452_PBMC_D005_S10]

description:
RA0452_PBMC_D005_S10
Rhesus monkey


title: LV3628_3_h6_NPCday14_S15

description: TruSeq Stranded mRNA LP (48 Spl)

value: LINC01876 (guide 1)


title: RA1325_WholeBlood-D6 [A0370_S55_L001]

description:
A0370_S55_L001
Rhesus monkey


title: RA1325_WholeBlood-BL [A0367_S58_L001]

description:
A0367_S58_L001
Rhesus monkey


title: RA1325_WholeBlood-D2 [A0368_S57_L001]

description:
A0368_S57_L001
Rhesus monkey


title: LV3599_4_h6_NPCday14_S23

description: TruSeq Stranded mRNA LP (48 Spl)

value: LacZ


title: LV3628_1_h6_NPCday14_S14

description: TruSeq Stranded mRNA LP (48 Spl)


title: LV3628_2_h6_NPCday14_S18

description: TruSeq Stranded mRNA LP (48 Spl)


title: RA1325_WholeBlood-BL [A0366_S59_L001]

description:
A0366_S59_L001
Rhesus monkey


title: RA1074_WholeBlood-D6 [A0365_S60_L001]

description:
A0365_S60_L001
Rhesus monkey


title: RA1074_WholeBlood-D4 [A0364_S61_L001]

description:
A0364_S61_L001
Rhesus monkey


title: LV3599_3_h6_NPCday14_S22

description: TruSeq Stranded mRNA LP (48 Spl)


title: LV3599_2_h6_NPCday14_S21

description: TruSeq Stranded mRNA LP (48 Spl)


title: DA641_H6_LV3629_Day60_organoids_S29

description: Chromium Next GEM Single Cell 3’ Kit

source_name: neural organoid

value: neural organoid

value: 60 days


title: RA1074_WholeBlood-BL [A0362_S63_L001]

description:
A0362_S63_L001
Rhesus monkey


title: DA639_H6_LV3628_Day60_organoids_S28

description: Chromium Next GEM Single Cell 3’ Kit


title: RA1074_WholeBlood-D2 [A0363_S62_L001]

description:
A0363_S62_L001
Rhesus monkey


title: RA1074_WholeBlood-BL [A0361_S64_L001]

description:
A0361_S64_L001
Rhesus monkey


title: RA1849_WholeBlood-D4 [A0360_S65_L001]

description:
A0360_S65_L001
Rhesus monkey


title: DA637_H6_LV3599_Day60_organoids_S27

description: Chromium Next GEM Single Cell 3’ Kit


title: RA1849_WholeBlood-BL [A0358_S67_L001]

description:
A0358_S67_L001
Rhesus monkey


title: DA616_H6_LV3628_Day60_organoids_S19

description: Chromium Next GEM Single Cell 3’ Kit


title: RA1849_WholeBlood-D2 [A0359_S66_L001]

description:
A0359_S66_L001
Rhesus monkey


title: DA595_H6_LV3629_Day60_organoids_S23

description: Chromium Next GEM Single Cell 3’ Kit


title: DA593_H6_LV3628_Day60_organoids_S22

description: Chromium Next GEM Single Cell 3’ Kit


title: DA612_H6_LV3599_Day60_organoids_S17

description: Chromium Next GEM Single Cell 3’ Kit


title: RA1849_WholeBlood-BL [A0357_S68_L001]

description:
A0357_S68_L001
Rhesus monkey


title: RA0850_WholeBlood-BL [A0354_S71_L001]

description:
A0354_S71_L001
Rhesus monkey


title: RA0850_WholeBlood-D4 [A0356_S69_L001]

description:
A0356_S69_L001
Rhesus monkey


title: DA560_H6_LV3629_Day30_organoids_S16

description: Chromium Next GEM Single Cell 3’ Kit

value: 30 days


title: DA591_H6_LV3599_Day60_organoids_S21

description: Chromium Next GEM Single Cell 3’ Kit


title: DA554_H6_LV3628_Day30_organoids_S14

description: Chromium Next GEM Single Cell 3’ Kit


title: RA0850_WholeBlood-BL [A0353_S74_L001]

description:
A0353_S74_L001
Rhesus monkey


title: LV3599_3_h6_NPCday14_S11

description: TruSeq Stranded mRNA LP (48 Spl)


title: RA0717_WholeBlood-D2 [A0351_S76_L001]

description:
A0351_S76_L001
Rhesus monkey


title: RA0717_WholeBlood-D4 [A0352_S75_L001]

description:
A0352_S75_L001
Rhesus monkey


title: RA0717_WholeBlood-BL [A0350_S77_L001]

description:
A0350_S77_L001
Rhesus monkey


title: RA0850_WholeBlood-D2 [A0355_S70_L001]

description:
A0355_S70_L001
Rhesus monkey


title: RA0717_WholeBlood-BL [A0349_S78_L001]

description:
A0349_S78_L001
Rhesus monkey


title: DA548_H6_LV3599_Day30_organoids_S12

description: Chromium Next GEM Single Cell 3’ Kit


title: DA516_H6_LV3599_day30_organoids_S11

description: Chromium Next GEM Single Cell 3’ Kit


title: DA518_H6_LV3628_day30_organoids_S12

description: Chromium Next GEM Single Cell 3’ Kit


title: RA1639_WholeBlood-D1 [A0346_S81_L001]

description:
A0346_S81_L001
Rhesus monkey


title: DA520_H6_LV3629_day30_organoids_S13

description: Chromium Next GEM Single Cell 3’ Kit


title: RA1639_WholeBlood-D5 [A0348_S79_L001]

description:
A0348_S79_L001
Rhesus monkey


title: RA1639_WholeBlood-BL [A0345_S82_L001]

description:
A0345_S82_L001
Rhesus monkey


title: RA0522_WholeBlood-D1 [A0341_S86_L001]

description:
A0341_S86_L001
Rhesus monkey


title: RA0522_WholeBlood-D3 [A0342_S85_L001]

description:
A0342_S85_L001
Rhesus monkey


title: HG3 Control Input, rep2

city: Monrovia

first: Lili

last: Wang

state: CALIFORNIA

address: 1218 South Fifth Ave.

department: Systems biology

institute: City of Hope

data_processing:
Reads were aligned to the human reference genome (GRCh38/hg38) using STAR with default parameters. m6A peak calling, quantification, annotation and differential m6A sites analysis were performed using R package exomePeak.
Assembly: hg38
Supplementary files format and content: Peak track file (tdf)

source_name: B cells

extract_protocol:
Methylated RNA immunoprecipitation was processed by using EpiMark® N6-Methyladenosine Enrichment Kit (#E1610S, NEB).
Purified RNA fragments were used for library construction using Stranded Total RNA Prep with Ribo-Zero Plus Kit (#20040529, Illumina)

value: chronic lymphocytic leukemia cell line

value: WT

tag: rip antibody


title: HG3 METTL3 KO Input, rep1

value: METTL3 knockout


title: HG3 METTL3 KO Input, rep2


title: HG3 Control MeRIP seq, rep2


title: HG3 METTL3 KO MeRIP seq, rep1


title: HG3 METTL3 KO MeRIP seq, rep2


title: HG3 Control MeRIP seq, rep1


title: HG3_Ctrl_Riboseq

data_processing:
Reads aligned to rRNA sequences were removed from further analysis using alignment tool Bowtie. Remaining reads were aligned to human reference genome (GRCh38/hg38) using HISAT2 with default parameters. Multiple alignment reads were filtered out for downstream analysis.
For the calculation of translation efficiency (TE), the ribosome protected fragments (RPF) were counted in CDS regions with read length between 28 to 34 nt and not aligned to the first 15 and last 5 codons. RPFs and RNA-seq reads for each transcript were normalized by trimmed mean of M values (TMM) from edgeR . TE was calculated as ratio between normalized RPFs and normalized RNA-seq reads. Fisher’s exact test was used to test the significance of independent distribution of RPFs relative to RNA-seq reads. P values for multiple comparisons were adjusted using the Benjamini-Hochberg correction. Genes with more than 2-fold change and FDR less than 0.05 were used as significance cutoff.
Assembly: hg38
Supplementary files format and content: Differential translation efficiency table (txt) reporting TPMs
Library strategy: RIBO-seq

extract_protocol:
NA
Ribosome profiling was carried out following protocol from Illumina TruSeq Ribo Profiler (Mammalian) kit (Illumina).


title: RA0452_WholeBlood-D5 [A0338_S89_L001]

description:
A0338_S89_L001
Rhesus monkey


title: RA0522_WholeBlood-BL [A0339_S88_L001]

description:
A0339_S88_L001
Rhesus monkey


title: HG3 METTL3 KO RNAseq, rep3

data_processing:
RNAseq:Reads were aligned to the human reference genome (GRCh38/hg38) using STAR with default parameters. Differentially expression of mRNA analysis was performed using DESeq2 R package. Genes with more than 2-fold change and FDR less than 0.05 were used as significance cutoff.
Assembly: hg38
Supplementary files format and content: Hg3_METTL3KO_diff.txt

extract_protocol:
Stranded Total RNA Prep
Ribo-Zero Plus Kit (Illumina)


title: HG3_METTL3KO_Riboseq


title: BSR159-Ep-1234

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

data_processing:
Sequencing and base calling: RNA-seq libraries were sequenced on an Illumina HiSeq 2500 equipment (Illumina, San Diego, CA, USA) with base calling by CASAVA software (version 1.8.2, Illumina, San Diego, CA, USA).
Read alignment: Raw data were processed by TrimGalore package (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to trim the adapters, in following the RNA-seq library reads processed by FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016) and performed analysis of detection of differential expression in EPN using processed reads aligned with the reference genome (Genome Reference Consortium Human GRCh38) through STAR package (Dobin and Gingeras, 2015). Alignment performance was assessed with Picard and Qualimap tools.
Gene specific read counts: Gene specific read counts were determined with to FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016). DESeq2 (v1.26.0) (Love et al., 2014) was used to estimate the change in feature expression between conditions.
Genome_build: Reads are in .fastq.gz format and contain the raw base calls from sequencing. Alignment files are in .bam format and contain mapped reads.
Supplementary_files_format_and_content: Normalized abundance measurements are in .txt format as the output from DESeq2.

source_name: Frozen ependymal tumor tissue

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/Protein Mini kit (QIAGEN, Hilden, Germany) and RNA integrity was evaluated by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) following manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Frozen ependymal tumor tissue

tag: primary/relapse

value: primary

tag: brain location

value: posterior fossa

tag: age at diagnosis years

tag: histological grade

value: III

tag: gender

value: male

tag: molecular subgroup


title: RA0452_WholeBlood-D3 [A0337_S90_L001]

description:
A0337_S90_L001
Rhesus monkey

value: Whole blood

tag: treatment

value: infected with Ebola virus

tag: time


title: BSR148-Ep-186

value: II

value: female


title: HG3_METTL3KO_RNAseq

tag: cell line

tag: cell type


title: RA0452_WholeBlood-D1 [A0336_S91_L001]

description:
A0336_S91_L001
Rhesus monkey


title: HG3 METTL3 KO RNAseq, rep1


title: HG3 METTL3 KO RNAseq, rep2


title: HG3 Control RNAseq, rep3


title: RA0522_WholeBlood-BL [A0340_S87_L001]

description:
A0340_S87_L001
Rhesus monkey


title: RA0452_WholeBlood-BL [A0334_S93_L001]

description:
A0334_S93_L001
Rhesus monkey


title: BSR132-Ep-556

value: relapse

value: supratentorial

value: ST-EPN-RELA


title: RA0452_WholeBlood-BL [A0335_S92_L001]

description:
A0335_S92_L001
Rhesus monkey


title: BSR141-Ep-735


title: HG3 Control RNAseq, rep2


title: HG3_Ctrl_RNAseq


title: BSR134-Ep-162


title: RA1834_WholeBlood-D1 [A0332_S95_L001]

description:
A0332_S95_L001
Rhesus monkey


title: BSR136-Ep-2078


title: BSR131-Ep-107


title: BSR151-Ep-835


title: bam mutant Mei-P26 RNAi rep2

first: Tamsin

middle: Joy

last: Samuels

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description:
gene_exp.diff_bam_KD_meiP26_vs_bam_OE_meiP26.txt
gene_exp.diff_bam_vs_bam_KD_meiP26.txt

data_processing:
RNA- sequencing data was first aligned to ribosomal RNA using Bowtie2 (Langmead & Salzberg, 2012)
Non-rRNA reads were mapped to the Drosophila melanogaster genome (dm6) using STAR (Dobin et al., 2013)
transcript abundance was quantified and differentially expressed genes were identified using Cufflinks (Trapnell et al., 2010)
Assembly: dm6
Supplementary files format and content: genes_fpkm.txt files are output off cuflinks, showing fpkm per gene for each sample
Supplementary files format and content: gene_exp.diff are .txt files output of cufflinks, showing differential expression test between two samples for each gene

organism: Drosophila melanogaster

source_name: whole ovary

extract_protocol:
120 pairs of ovaries were dissected for each sample and immediately stored at -80°C after dissection. Frozen samples were homogenized in TRIzol Reagent (Invitrogen) using an electrical pestle and further disrupted by passing 15 times through a 26-gauge syringe. Total RNA was isolated using TRIzol Reagent (Invitrogen) following the manufacturer9s protocol.
Poly(A)-selected RNA-sequencing (RNA- seq) libraries were generated using 2.5 μg of purified RNA with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®. Libraries were multiplexed using the NEBNext® Multiplex Oligos for Illumina® and sequenced in single-end, 50-nt-long reads on an Illumina HiSeq 2500.

value: whole ovary

tag: age

value: adult

tag: Sex

value: nosgal4/UAS-Mei-P26 RNAi;bam86