title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 6h control, rep2

description:
Library name: Sample 8
Column name in Normalised_counts_qpro.xlsx: DNT6hcontrol_2

data_processing:
Pre-processing and removal of illumina adaptor sequences was performed on sequencing files using Fastp (v.0.23.2)(options:--umi --stdout --umi_loc=per_read --umi_len=6 -c --overlap_len_require 15)
Bowtie2(v12.3.0)(options: --fast-local --un-conc -- interleaved) was used to remove ribosomal RNA
Bowtie2(v12.3.0)(options: --local --sensitive-local) was used to align to the human hg38 genome
Samtools (v1.17) was used to filter reads with a mapq score of less than 10 and convert to BAM format
UMI-tools (v1.0.1)(options: --umi-separator=":" --paired) was used to deduplicate BAM files  before samtools was used to sort and index.
Deeptools (v3.5.1) bamCoverage (options: --skipNonCoveredRegions --binSize 1 --normalizeUsing None --Offset 1 --samFlagInclude 82 (forward) or 98 (reverse)) was then used to create bigwig files containing forward and reverse reads
DESeq2 (v1.44.0) was used to create normalised counts files and determine significant gene changes.
Assembly: hg38
Supplementary files format and content: Xcel matrix with normalised counts for each condition and replicate both pre- and post-filtering for low counts
Library strategy: PRO-Seq

molecule: nuclear RNA

extract_protocol:
Cells were washed x2 ice cold PBS and scraped into ice-cold permeabilisation buffer (10mM Tris/Cl pH 8, 10m KCl, 250mM sucrose, 5mM MgCl2, 1mM EGTA, 0.1% IGEPAL CA-630, 0.5mm DTT, 0.05% Tween-20, 10% glycerol, PIC and SUPERase-In RNase inhibitor). Cells were transferred to a falcon and incubated on ice for 5min. Permeabilised cells were collected by centrifugation at 700 rcf for 4min at 4C, washed twice (permeabilisation buffer without IGEPAL CA-630 and Tween-20) and resuspended in freeze buffer (50mM Tris/Cl pH 8, 40% glycerol, 5mM MgCl2, 1.1mM EDTA, 0.5mM DTT, SUPERase-In RNase inhibitor). Cells were counted, collected by centrifugation at 1000 rcf for 5min at 4C and resuspended freeze buffer at 1x10^6 cells/52ul for aliquoting and snap freezing. The run-on reaction was performed by mixing 50ul permeabilised cells 1:1 with 2x run-on master mix (10mM Tris/Cl pH 8, 5mM MgCl2, 1mM DTT, 300mM KCl, 40uM each of Biotin-11-(CTP/UTP/ATP/GTP), 1% sarkosyl, SUPERase-In RNase inhibitor) and incubating at 37C, 750rpm for exactly 5min and stopped by the addition of RL buffer. RNA was extracted using a Norgen RNA extraction kit (Norgen) and 1M NaOH used to hydrolyse bases. RNA was precipitated using ethanol and resuspended in  nuclease-free water.
The purified RNA was used to anneal a 3' adapter (/5Phos/rUrNrNrNrNrNNGATCGTCGGACTGTAGAACTCTGAAC/3InvdT/) before streptavidin bead binding, on-bead 5' hydroxy repair, on-bead 5' decapping. 5' adaptor ligation (/5InvddT/CCTTGGCACCCGAGAATTCCANrNrNrNrNrNrC) was performed on bead and RNA purified using TRIzol. Reverse transcription was performed using with RP1 primer (AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA). Test amplification was performed to calculate the required number of cycles for full-scale amplification using a single Illumina indexing primer (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA). Full-scale amplification was performed using 1 of 4 Illumina indexing primers for each sample (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA; CAAGCAGAAGACGGCATACGAGATAGATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA; CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA; CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA). DNA was purified after full-scale amplification using AMPure beads, quantified using the qubit HS dsDNA assay and profiled using a bioanalyzer.

treatment_protocol: Cells were seeded and allowed to settle for 24h prior to treatment with either DMSO (control) or 100nM dTAGv1. Treatments were timed so that harvesting of all time points was carried out simultaneously. Exeriments were repeated in duplicate.

value: DMSO


title: E90-2019_Hippocampus_AND_choroid

status: Public on Oct 13 2025

type: SRA

city: San Francisco

first: Alex

middle: A

last: Pollen

state: CA

address: 35 Medical Center Way

department: Neurology

country: USA

institute: UCSF

description:
Library name: E90-2019_Hippocampus_AND_choroid
10X Genomics (V3) 3 capture single cell RNA seq

library_source: transcriptomic single cell

data_processing:
fastq files
Kallisto gene expression quantification
Cellbender ambient RNA removal
Assembly: rheMac10
Supplementary files format and content: H5AD

molecule: polyA RNA

organism: Macaca mulatta

source_name: brain

extract_protocol:
Papain dissociated whole cells
10X Genomics (V3) 3 capture single cell RNA seq

tag: tissue

value: brain

tag: developmental stage


title: GPX4M-eGFP clone#11 unsorted

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

description: Library name: B06

library_source: genomic

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Galaxy: Clip adapter GTTTTAGA and CGGTGTTTC
Galaxy: Collapse sequences
Galaxy: FASTA-to-tabular
MAGeCK sgRNA enrichment analysis
Assembly: hg38
Supplementary files format and content: Table of normalized read counts of extracted sgRNAs
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cell lines were obtained from ATCC. HCT116 cells (male) were cultured in DMEM media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1X Penicillin-Streptomycin (Gibco)

extract_protocol:
Genomic DNA was isolated from unsorted cells using the MasterPure Complete DNA Purification kit (Lucigen). Genomic DNA from sorted cells was isolated by phenol-chlorofom extraction.
CRISPR screen custom DNA library. Sequencing libraries were generated using two sequential rounds of PCR using Herculase II Fusion DNA polymerase (Agilent). In the first round of PCR, 5µg of genomic DNA from unsorted cells was used in each of 24 100 µl reactions, and all recovered genomic DNA from sorted cells was split into two 100 µl reactions. Following 18 cycles of PCR1 amplification, 5 µl from the pooled reaction product was used in the second round of PCR (10 cycles), using primers containing barcodes and Illumina sequencing adaptors.

treatment_protocol: Transduced cells were selected with 1 µg/mL puromycin (Thermo Fisher Scientific)

tag: cell line

tag: cell type

value: colon cancer cell line

tag: genotype

value: GPX4M-eGFP Clone#11

tag: treatment

value: Unsorted


title: E90-2019_Midbrain

description:
Library name: E90-2019_Midbrain
10X Genomics (V3) 3 capture single cell RNA seq


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 6h dTAGv1, rep2

city: Leicester

first: John

last: Schwabe

state: Leicestershire

address: Lancaster Road

department: Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

description:
Library name: Sample 6
Column name in Normalised_counts_qpro.xlsx: DNT6hv1_2

library_source: transcriptomic

source_name: HCT 116

growth_protocol: HCT 116 cells were maintained in DMEM (high glocuse) supplememnted with 10% foetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C

value: HCT 116

value: Colon Carcinoma

value: DNTTIP1 knockdown

tag: time


title: E90-2019_Cerebellum

description:
Library name: E90-2019_Cerebellum
10X Genomics (V3) 3 capture single cell RNA seq


title: Water etracts of JGT (Low Dose) rep2

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description: Library name: JGW03_L_2

data_processing:
Read count and transcripts per million (TPM) were calculated as gene expression abundance using the RSEM software (v1.3.3) and gene annotation RN6 Gene Transfer Format (GTF) file from UCSC browser
Assembly: RN6
Supplementary files format and content: tab-delimited text files include count values for each Sample

molecule: total RNA

organism: Rattus norvegicus

extract_protocol:
One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI Tech, China) according to manufacturer’s instruction.
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

value: neuronal cell

value: Water etracts of JGT (Low Dose) rep2

tag: treatment dose


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 6h control, rep1

description:
Library name: Sample 7
Column name in Normalised_counts_qpro.xlsx: DNT6hcontrol_1


title: E80V1

description:
Library name: E80V1
10X Genomics (V3) 3 capture single cell RNA seq


title: GPX1-eGFP clone#1 unsorted

description: Library name: B01

value: GPX1-eGFP Clone#1


title: GPX4-eGFP clone#3 unsorted

description: Library name: B03

value: GPX4-eGFP Clone#3


title: GPX1-eGFP clone#10 unsorted

description: Library name: B02

value: GPX1-eGFP Clone#10


title: E80temporal

description:
Library name: E80temporal
10X Genomics (V3) 3 capture single cell RNA seq


title: GPX4M-eGFP clone#11 bright population

description: Library name: A12

value: Bright population


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 6h dTAGv1, rep1

description:
Library name: Sample 5
Column name in Normalised_counts_qpro.xlsx: DNT6hv1_1


title: E80somato

description:
Library name: E80somato
10X Genomics (V3) 3 capture single cell RNA seq


title: GPX4M-eGFP clone#6 bright population

description: Library name: A11

value: GPX4M-eGFP Clone#6


title: GPX4-eGFP clone#10 bright population

description: Library name: A8

value: GPX4-eGFP Clone#10


title: GPX4M-eGFP clone#11 dim population

description: Library name: A10

value: Dim population


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 2h control, rep1

description:
Library name: Sample 3
Column name in Normalised_counts_qpro.xlsx: DNT2hcontrol_1

value: DMSO


title: GPX4-eGFP clone#3 bright population

description: Library name: A7


title: GPX4M-eGFP clone#6 dim population

description: Library name: A9


title: E80motor

description:
Library name: E80motor
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: GPX1-eGFP clone#10 bright population

description: Library name: A4

value: colon cancer cell line


title: E80MGE

description:
Library name: E80MGE
10X Genomics (V3) 3 capture single cell RNA seq


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 2h dTAGv1, rep2

description:
Library name: Sample 2
Column name in Normalised_counts_qpro.xlsx: DNT2hv1_2


title: GPX4-eGFP clone#10 dim population

description: Library name: A6


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 2h dTAGv1, rep1

description:
Library name: Sample 1
Column name in Normalised_counts_qpro.xlsx: DNT2hv1_1


title: GPX4-eGFP clone#3 dim population

description: Library name: A5


title: GPX1-eGFP clone#1 dim population

description: Library name: A1


title: E80hippo

description:
Library name: E80hippo
10X Genomics (V3) 3 capture single cell RNA seq


title: GPX1-eGFP clone#1 bright population

description: Library name: A3


title: HIV infected (Donor 3)

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 9_33_HIV-infected-24h_Donor-2_S27

data_processing:
Fatsq files were aligned to GRCh38 using Star aligner via RSEM V1.3.3 to obtain estimated raw counts. Those counts were used to get the differential expression using DESeq2 in R.
Assembly: GRCh38
Supplementary files format and content: Text file with Raw RSEM estimated counts

source_name: Primary CD4 T cells

extract_protocol:
Qiagen RNeasy mini kit
Stranded Total RNAseq with Ribo-zero Plus kit (Illumina)

value: Primary CD4 T cells

value: HIV infected

tag: subject id

value: Donor 3


title: Lp-1 treated, replicate 2

city: Boston

first: Vijay

middle: G

last: Sankaran

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital / Broad Institute

description: 10X Genomics

data_processing:
The raw scRNA-seq FASTQ files were processed with CellRanger (v8.0.1) pipeline to map in the reference genome (GRCh38). We excluded cells with unique molecular identifier (UMI) counts less than 1,000, or mitochondrial UMI fraction higher than 20%, and removed potential doublets by a threshold of doublet score > 0.2 using ScrubletR, which resulted in a total of 29,096 cells for the Lp-1 (replicate 1 = 5,991 and replicate 2 = 4,935) and Untreated (replicate 1 = 8,991 and replicate 2 = 9,179) groups. Symphony R package was used to project the cells on the human bone marrow reference (https://github.com/andygxzeng/BoneMarrowMap) and the scRNA-seq reference built from 10-day-expanded CD34+ cells in cytokine-free medium, and the predicted cell type was further curated to match the 12 hematopoietic cell types presented in the Sakurai et al. study (PMID: 36813966). A standard Seurat framework (v4.4.0) was used to conduct normalization, principal component analysis (PCA), and dimensionality reduction. The feature-barcode matrix was normalized by the total read count and log transformed, and the top 3,000 variable features were selected by the vst method in FindVariableFeatures function. The normalized expression was scaled by Seurat’s ScaleData function, and PCA was performed using the RunPCA function (npc = 30). The sample-dependent technical variation was corrected by using Harmony (PMID: 31740819). Uniform Manifold Approximation and Projection (UMAP) was conducted to reduce dimensions to embed the cells into two-dimensional space.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cord blood

extract_protocol:
CB-derived HSPCs were cultured in chemically defined cytokine-free conditions for 10 days in the presence or absence of Lp-1. Viable cells (negative to Apotracker) were sorted with a 100 mm nozzle – on a BD FACSAria Fusion (BD Biosciences) - according to the surface expression of CD34+CD45RA-CD90+ markers. Sorted cells were collected in 1.5 ml Eppendorf tubes containing 100 μl of 1xDPBS. The sorted cells were counted with Trypan Blue solution 0.4% (GIBCO) and roughly 2x104 viable cells from each sample were utilized for the subsequent procedure (estimated recovery: 104 cells/sample).
Libraries were prepared by Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to manufacturer’s instructions.

value: Cord blood

value: Ex vivo expanded HPSCs

value: WT

value: Lp-1 supplementation


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 2h control, rep2

description:
Library name: Sample 4
Column name in Normalised_counts_qpro.xlsx: DNT2hcontrol_2

value: HCT 116

value: Colon Carcinoma

value: DNTTIP1 knockdown


title: Untreated, replicate 2

description: 10X Genomics

value: Without Lp-1 supplementation


title: GPX1-eGFP clone#10 dim population

description: Library name: A2

value: GPX1-eGFP Clone#10


title: E80-2022_Myelencephalon_2

description:
Library name: E80-2022_Myelencephalon_2
10X Genomics (V3) 3 capture single cell RNA seq


title: LNCaP NE1m_IgG_replicate2

city: Paris

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Reads were mapped on human genome version GRCh38 with BWA version 0.7.17
Only unique mapped reads were kept for further analysis.
The peak calling was performed with MACS version 2.2.6, with the command "callpeak" and the parameters " -f BAMPE -g hs -B --keep-dup all" for each “target “and the associated IgG.
bam files were converted into bedgraph files followed by RPM normalization (reads per million of mapped reads) using bedtools version 2.29.0. The bedgraph files were successively converted into bigwig, wig, and tdf, files using respectively bedGraphToBigWig, bigWigToWig (from UCSC), and toTDF (igvtools).
Assembly: GRCh38
Supplementary files format and content: coverage files (reads per million normalization) for minus and plus strand in tdf format
Library strategy: CUT&RUN

source_name: prostate

growth_protocol: LNCaP cells were grown in P100 plate in RPMI 1640+GlutaMAX medium + 10% FBS + 2 nM DHT or phenol red-free RPMI 1664 + 10% dextran charcoal-stripped FBS for 1  month to 80% of confluency.

extract_protocol:
DNA fragments were purified with NEB Monarch PCR & DNA purification kit following the protocol enrichment for short DNA fragments and was quantified by Qubit HS DNA kit.
CUT & RUN libraries were prepared using the TruSeq ChIP-Sample Prep Kit-Set A and PCR Box (Illumina) from 5 ng of DNA with 10 PCR cycles for amplification following the manufacture’s procedures. Concentration and quality were assessed by Qubit with dsDNA HS Assay Kit (Thermo Fisher Scientific) and High Sensitivity DNA Analysis Chip Kit (Agilent Technologies).
CUT&RUN libraries were sequenced on a NovaSeq – S1 device in a pair-end 100 bp read length mode.

treatment_protocol: Cells were scrapped from plates collected by centrifugation. Pellets were resuspended in Wash buffer and washed twice before resuspending in volume 10^6 cells/100 µl. For each IP sample, 100 µl of cell suspension were aliquoted to 900 µl of Wash Buffer in 1.5ml eppendorf tube containing 10 µl of Concanavalin A beads (Epicypher) previously washed in Bead activation buffer (20mM HEPES pH 7.9, 10mM KCl,1mM CaCl2, 1mM MnCl2).  Cells were incubated with beads for 10 min with rotation at 15-20 rpm at room temperature (RT). Beads were separated from supernatant on a magnetic stand and resuspended in 50 µl of the antibody diluted in Antibody buffer (wash buffer with 0,1% digitonin and 2mM EDTA) (1:100 dilution for all antibodies and 1:1100 for IgG control). The beads were incubated with subtle agitation for 10 min for histone marks and 1h for Lsd1, Ezh2 and IgG antibodies at RT. Afterwards the beads were washed twice with Digitonin buffer (Wash buffer with 0,1% digitonin) and resuspended in pAG-MNase (CUTANA Epicypher) diluted 20 times in Digitonin buffer. After 10 min incubation with slight agitation at RT, beads were washed twice and resuspended in Digitonin buffer and chilled to 0°C (ice) for 5 min. To activate MNase, 2 µl of 100 mM CaCl₂ were added and incubated for additional 30 min on ice. To stop the reaction, 100 µl of Stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/ml RNase A, 50ug/ml Glycogen, 0.1% Digitonin, 10 pg/ml Spike-in DNA) was added and beads were incubate for 10 min at 37°C followed by centrifugation at 16k rcf at 4°C for 5 min. The supernatant with DNA fragments was rcovered in a new microtube.

value: prostate

value: LNCaP

value: tumor

value: ATCC (CRL-1740)

tag: cut and_run_antibody

value: Thermo Fisher, Ref. 31235


title: CD44 beads (Donor 1)

description: Library name: 2_8_UI-CD44-24h_Donor-1_S20

value: Primary CD4 T cells

value: CD44 beads

value: Donor 1


title: E80insula

description:
Library name: E80insula
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: Untreated, replicate 1

description: 10X Genomics

value: Cord blood

value: Ex vivo expanded HPSCs


title: CD44 beads (Donor 3)

description: Library name: 8_32_UI-CD44-24h_Donor-2_S26

value: Donor 3


title: E80PFC

description:
Library name: E80PFC
10X Genomics (V3) 3 capture single cell RNA seq


title: Uninfected (Donor 3)

description: Library name: 7_25_Control-0h_Donor-2_S25

value: Uninfected


title: HIV infected (Donor 2)

description: Library name: 6_21_HIV-infected-24h_Donor-2_S24

value: HIV infected

value: Donor 2


title: CD44 beads (Donor 2)

description: Library name: 5_20_UI-CD44-24h_Donor-2_S23


title: E80-2022_Myelencephalon_1

description:
Library name: E80-2022_Myelencephalon_1
10X Genomics (V3) 3 capture single cell RNA seq


title: Uninfected (Donor 2)

description: Library name: 4_13_Control-0h_Donor-2_S22


title: E80-2022_Metencephalon_2

description:
Library name: E80-2022_Metencephalon_2
10X Genomics (V3) 3 capture single cell RNA seq


title: HIV infected (Donor 1)

description: Library name: 3_9_HIV-infected-24h_Donor-1_S21


title: Pupa day 6, rep 3

city: Brighton

first: Andrew

last: Hesketh

state: East Sussex

address: Lewes Road

department: School of Applied Sciences

institute: University of Brighton

description: P6, rep 3

data_processing:
Basecalling and demultiplexing of raw signal data was performed using the GridION minKNOW software (version 22.07.9) using guppy 6.3.9 with the high accuracy basecalling model.
Reads were quality filtered with the default q-score setting of 9 and processed using pychopper (version 2.7.2) with option ‘ -k PCS111’ to identify, orient and trim full-length nanopore cDNA reads.
Full-length reads were first aligned to the reference genome GCF_947172395.1_ilBicAnyn1.1 using minimap2 (version 2.24-r1122). Novel transcripts not present in the reference genome were identified using espresso (version 1.4), increasing the –read_num_cutoff setting to 4 to require a minimum of 4 perfect reads to call de novo detected candidate splice junctions. The novel transcripts identified were subsequently merged with the existing annotation using stringtie (version 2.1.7) to create an updated annotation for use in transcriptome quantification.
Transcript abundances in each sample were counted by first aligning the pychopped RNA-seq reads to the updated transcriptome using minimap2 (version 2.24-r1122 ) with input options ‘-ax splice -uf -p 1.0’ , then quantifying with salmon (version 1.10.2) using the quant --ont alignment model for ONT long reads.
Salmon transcript quantifications were converted to gene level in R using the tximport package, then normalised and analysed for differential expression using DESeq2
Assembly: GCF_947172395.1_ilBicAnyn1.1
Supplementary files format and content: tab delimited text file of raw transcript-level counts for each sample
Supplementary files format and content: tab delimited text file of raw gene-level counts for each sample

organism: Bicyclus anynana

source_name: whole organism

growth_protocol: We used Bicyclus anynana  butterflies from a captive population maintained at 27oC with 65% humidity, and a 12h light/12h dark photoperiod. Larvae were fed ad libitum with young maize plants. In the 3rd/4th instar, 200 male larvae were selected and maintained in the same cage. Three specimens were collected from each of the following stages: 5th and final instar larvae (L5), and pupae on the day of pupation (P0), as well as 2 (P2), 4 (P4) and 6 (P6) days post-pupation. The P6 stage corresponds to what are essentially a fully formed butterfly that typically ecloses out of the pupal case on that same day. Each individual was placed inside a microtube, killed by flash freezing (30 seconds in liquid nitrogen), and subsequently stored at -80oC until further processing.

extract_protocol:
We extracted both DNA and RNA from the same individual butterfly sample. Disruption and homogenization of tissue were performed using TissueLyser (Qiagen) as per the manufacturer's instructions. Briefly, 1mL of cold PBS was added directly to each of the samples with autoclaved 3mm stainless steel beads and disruptions were carried out gently at 20Hz for 1 minute. To perform simultaneous RNA and DNA extractions using QIAzol and ATL buffer, we immediately divided the homogenate after homogenization, allocating portions for DNA extraction with the Qiagen DNeasy kit (Cat. No. 69504) and RNA extraction using the RNeasy Mini Kit (Cat. No. 74104). As described below, each suspension was subjected to a further cycle of homogenization at 20Hz for 30 seconds in the respective DNA or RNA extraction lysis buffers. The tissue homogenate was divided, not the tissue itself, to avoid any inconsistencies in mRNA profiling due to the uneven distribution of tissues and cell types. By splitting the tissue homogenate, we aim for a more random distribution of tissue types, ensuring consistent sampling. To prevent RNA degradation, we timed RNA extractions immediately after homogenization. RNA was extracted and purified using the QIAzol Lysis Reagent and Qiagen RNeasy Kits following the manufacturer's protocols. Briefly, 1mL of QIAzol was added to an aliquot of homogenate and an additional homogenization was performed for 30 seconds at 20Hz. The lysate was treated by addition of 0.3mL of chloroform per 1.3 mL of total lysate and the samples were then centrifuged at 12,000 x g for 15 minutes at 4°C. The supernatant was then removed to a clean tube and processed using Qiagen RNeasy spin columns according to the manufacturer’s RNA purification protocol. DNase treatment was performed using RNase-Free DNase Set (74104, Qiagen). RNA was eluted using 25µL of RNase-free water and the eluate reapplied to the column for a second round of elution to generate a concentrated sample. The final eluate was stored at −80°C.
RNA sequencing libraries representing full-length transcripts were prepared using the Oxford Nanopore Technology (ONT) PCR-cDNA Barcoding Kit (SQK-PCB111-24) according to the manufacturer's protocol.

value: whole organism

tag: Sex

value: male

value: Pupa day 6


title: LNCaP NE1m_H3K4me3_replicate2

value: prostate

value: LNCaP

value: Millipore, 04745


title: E80-2022_Metencephalon_1

description:
Library name: E80-2022_Metencephalon_1
10X Genomics (V3) 3 capture single cell RNA seq


title: Pupa day 6, rep 1

description: P6, rep 1


title: LNCaP NE1m_IgG_replicate1

value: tumor

value: ATCC (CRL-1740)

value: Thermo Fisher, Ref. 31235


title: Pupa day 6, rep 2

description: P6, rep 2


title: Larva 5th Instar, rep 2

description: L5, rep 2

value: Larva 5th Instar


title: Uninfected (Donor 1)

description: Library name: 1_1_Control-0h_Donor-1_S19

value: Primary CD4 T cells

value: Donor 1


title: Larva 5th Instar, rep 1

description: L5, rep 1


title: E80-2022_Diencephalon_2

description:
Library name: E80-2022_Diencephalon_2
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: Pupa day 4, rep 3

description: P4, rep 3

value: Pupa day 4


title: E80-2022_Mesencephalon_2

description:
Library name: E80-2022_Mesencephalon_2
10X Genomics (V3) 3 capture single cell RNA seq


title: Larva 5th Instar, rep 3

description: L5, rep 3


title: LNCaP NE1m_H3K4me3_replicate1


title: Pupa day 4, rep 2

description: P4, rep 2


title: LNCaP NE1m_H3K27ac_replicate1

value: Millipore, MABE647


title: LNCaP NE1m_H3K27ac_replicate2


title: Lp-1 treated, replicate 1

description: 10X Genomics

value: Cord blood

value: Ex vivo expanded HPSCs

value: WT

value: Lp-1 supplementation


title: E80-2022_Mesencephalon_1

description:
Library name: E80-2022_Mesencephalon_1
10X Genomics (V3) 3 capture single cell RNA seq


title: Pupa day 4, rep 1

description: P4, rep 1

value: whole organism

value: male


title: E80-2022_Diencephalon_1

description:
Library name: E80-2022_Diencephalon_1
10X Genomics (V3) 3 capture single cell RNA seq


title: LNCaP NE1m_H3K27me3_replicate2

value: prostate

value: LNCaP

value: Cell signaling, C36B11


title: Pupa day 2, rep 3

description: P2, rep 3

value: Pupa day 2


title: E80-2019_Thalamus

description:
Library name: E80-2019_Thalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: Pupa day 2, rep 2

description: P2, rep 2


title: Pupa day 2, rep 1

description: P2, rep 1


title: LNCaP NE1m_H3K27me3_replicate1

value: tumor

value: ATCC (CRL-1740)


title: LNCaP DHT_IgG_replicate2

value: DHT

value: Thermo Fisher, Ref. 31235


title: Pupa day 0, rep 3

description: P0, rep 3

value: Pupa day 0


title: Pupa day 6, rep 2

description: P6, rep 2

data_processing:
Modified basecalling and alignment to the GCF_947172395.1_ilBicAnyn1.1 genome was performed using the epi2me labs wf-basecalling nextflow workflow (version 0.7.1, running dorado version 0.3.0 and minimap2 version 2.26-r1175) with the models --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac@v4.1.0 and --remora_cfg dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2.
The basecalled cram alignment files were analysed for CpG site methylation and 5-hydroxymethylation modifications using modkit (version 0.1.6), aggregating data across both strands using the –combine-strands option.
Assembly: GCF_947172395.1_ilBicAnyn1.1
Supplementary files format and content: gz compressed bedMethyl files output from modkit pileup. In column 4, m represents methylcytosine, and h represents 5-hydroxymethylcytosine. The fraction modified is given in column 11.

extract_protocol:
We extracted both DNA and RNA from the same individual butterfly sample. Disruption and homogenization of tissue were performed using TissueLyser (Qiagen) as per the manufacturer's instructions. Briefly, 1mL of cold PBS was added directly to each of the samples with autoclaved 3mm stainless steel beads and disruptions were carried out gently at 20Hz for 1 minute. To perform simultaneous RNA and DNA extractions using QIAzol and ATL buffer, we immediately divided the homogenate after homogenization, allocating portions for DNA extraction with the Qiagen DNeasy kit (Cat. No. 69504) and RNA extraction using the RNeasy Mini Kit (Cat. No. 74104). As described below, each suspension was subjected to a further cycle of homogenization at 20Hz for 30 seconds in the respective DNA or RNA extraction lysis buffers. DNA was extracted as per the manufacturer's instructions using the Qiagen DNeasy® Blood & Tissue Kit with the following modifications: after addition of the lysis buffer an additional homogenization cycle was performed for 30 seconds at 20Hz; centrifugation was performed at 17,000 x g for three minutes instead of 20,000 x g; and 100 µl of buffer AE was used during the elution step instead of 200µL. The final eluate was stored at −80°C.
DNA libraries were prepared from 1 mg aliquots of genomic DNA using the Oxford Nanopore Technology Native Barcoding Kit 24 V14 (SQK-NBD114.24) following the manufacturer's protocol.

value: Pupa day 6


title: E80-2019_Somatosensory

description:
Library name: E80-2019_Somatosensory
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: E80-2019_Pons

description:
Library name: E80-2019_Pons
10X Genomics (V3) 3 capture single cell RNA seq


title: E80-2019_V1

description:
Library name: E80-2019_V1
10X Genomics (V3) 3 capture single cell RNA seq


title: Pupa day 0, rep 2

description: P0, rep 2


title: Larva 5th Instar, rep 2

description: L5, rep 2

value: Larva 5th Instar


title: E80-2019_Temporal

description:
Library name: E80-2019_Temporal
10X Genomics (V3) 3 capture single cell RNA seq


title: Pupa day 0, rep 1

description: P0, rep 1


title: E80-2019_PFC

description:
Library name: E80-2019_PFC
10X Genomics (V3) 3 capture single cell RNA seq


title: Pupa day 6, rep 3

description: P6, rep 3


title: Pupa day 4, rep 3

description: P4, rep 3

value: Pupa day 4


title: Pupa day 4, rep 2

description: P4, rep 2


title: LNCaP DHT_IgG_replicate1


title: LNCaP DHT_H3K4me3_replicate2

value: Millipore, 04745


title: Pupa day 6, rep 1

description: P6, rep 1


title: Larva 5th Instar, rep 3

description: L5, rep 3


title: LNCaP DHT_H3K4me3_replicate1


title: LNCaP DHT_H3K27me3_replicate1


title: Pupa day 2, rep 2

description: P2, rep 2


title: Pupa day 0, rep 2

description: P0, rep 2


title: E80-2019_Midbrain

description:
Library name: E80-2019_Midbrain
10X Genomics (V3) 3 capture single cell RNA seq


title: E80-2019_Parietal

description:
Library name: E80-2019_Parietal
10X Genomics (V3) 3 capture single cell RNA seq


title: Larva 5th Instar, rep 1

description: L5, rep 1


title: LNCaP DHT_H3K27ac_replicate1

value: Millipore, MABE647


title: NE1m_IgG_rep2

value: Thermo Fisher, 31235


title: LNCaP DHT_H3K27ac_replicate2


title: Pupa day 4, rep 1

description: P4, rep 1

value: whole organism

value: male


title: E80-2019_Multi-seq

description:
Library name: E80-2019_Multi-seq
10X Genomics (V3) 3 capture single cell RNA seq


title: E80-2019_MGE

description:
Library name: E80-2019_MGE
10X Genomics (V3) 3 capture single cell RNA seq


title: ATACseq_MCF7_KO_Tam_rep1

city: Rehovot

first: Efrat

last: Shema

state: Israel

address: 234 Hertzel

department: Department of Immunology & Regenerative Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: KO_Tam_a

data_processing:
ATAC-seq analysis was performed using the UTAP transcriptome analysis pipeline. Reads were trimmed using cutadapt (parameters: -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT –times 2 -q 25 -m 30), and mapped to human genome (hg38) using bowtie2. Uniquely mapped reads were extracted using samtools (-F 4, -f 0x2, -q 39). Following alignment, mitochondrial genes were removed from the analysis, and duplicated reads were removed using picard-tools. Nucleosome-free fragments at the length <120bp were selected from the remaining unique reads.
Assembly: hg38
Supplementary files format and content: broadPeak - peak calling by MACS2
Supplementary files format and content: bw - coverage files by bamCoverage (deeptools)

source_name: Breast

growth_protocol: MCF7 cells were cultured in DMEM supplemented with 10% FBS, 1% P/S and 1% sodium pyruvate solution. Cells were maintained at 37°C with 5% CO2.

extract_protocol:
Sample preparation was conducted according to omni-ATAC protocol previously described by Grandi et al.  Briefly, 50,000 cells per sample were used, and for each condition three replicates were analyzed. Cell lysis was performed using ATAC-seq Lysis Buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin). Following washes (10 mM Tris–HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20) nuclei were incubated with 2.5ul of Nextera Tn5 enzyme (TDE1, Illumina) for 0.5h at 37°C. Transposition was terminated by adding 5 volumes of DNA Binding Buffer from the DNA Clean and Concentrator-5 Kit (Zymo Research, D4014) and tagmentated DNA was isolated using the same kit.
Libraries were prepared using NEBNext Ultra II Q5 2× Master Mix (New England Biolabs, M0544S), followed by library quantification using NEBNext Library Quant Kit (New England Biolabs, E7630) and additional amplification. DNA concentration was measured with a Qubit fluorometer (Life Technologies) and library sizes were determined using TapeStation (Agilent Technologies).

treatment_protocol: 5uM Tamoxifen for 48h

value: Breast

value: p53 KO

value: Tamoxifen


title: LNCaP DHT_H3K27me3_replicate2

value: prostate

value: LNCaP

value: tumor

value: Cell signaling, C36B11


title: E80-2019_LGE_AND_CGE

description:
Library name: E80-2019_LGE_AND_CGE
10X Genomics (V3) 3 capture single cell RNA seq


title: Pupa day 2, rep 3

description: P2, rep 3

value: Pupa day 2


title: ATACseq_MCF7_KO_NT_rep2

description: Library name: KO_NT_b

value: No treatment


title: E80-2019_Motor_1

description:
Library name: E80-2019_Motor_1
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: Pupa day 2, rep 1

description: P2, rep 1


title: Pupa day 0, rep 3

description: P0, rep 3

value: Pupa day 0


title: ATACseq_MCF7_KO_NT_rep1

description: Library name: KO_NT_a


title: Pupa day 0, rep 1

description: P0, rep 1


title: E80-2019_Hippocampus

description:
Library name: E80-2019_Hippocampus
10X Genomics (V3) 3 capture single cell RNA seq


title: NE1m_AR_rep2

value: ATCC (CRL-1740)

value: Abcam, ab108341


title: NE1m_IgG_rep1


title: ATACseq_MCF7_WT_Tam_rep3

description: Library name: WT_Tam_c

value: p53 WT


title: ATACseq_MCF7_KO_Tam_rep2

description: Library name: KO_Tam_b


title: E65-2019B_V1

description:
Library name: E65-2019B_V1
10X Genomics (V3) 3 capture single cell RNA seq


title: E65-2019B_Thalamus

description:
Library name: E65-2019B_Thalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: NE1m_AR_rep1


title: ATACseq_MCF7_KO_NT_rep3

description: Library name: KO_NT_c


title: E80-2019_Motor_2

description:
Library name: E80-2019_Motor_2
10X Genomics (V3) 3 capture single cell RNA seq


title: ATACseq_MCF7_WT_Tam_rep2

description: Library name: WT_Tam_b


title: DHT_IgG_rep2

value: Thermo Fisher, 31235


title: Delaminated sensory epithelium, Treated, Biol rep 3

city: Toronto

first: Alain

last: Dabdoub

state: Ontario

address: 2075 Bayview Ave., A3 42

country: Canada

institute: Sunnybrook Health Sciences Centre

data_processing:
Quality control of raw reads was performed using RNA-SeQC v1.1.7 for all six RNA-seq samples, and adapters were trimmed with cutadapt v1.9.1 using default parameters.
Reads were aligned to the appropriate reference genome (GRCh38) using STAR v2.5.2.
Gene abundances were quantified with RSEM v1.3.0 using default settings.
All estimated gene abundances were imported into R v4.1.1 with tximport, and genes with total counts < 10 across all samples were filtered out from the downstream analysis. The R package DESeq2 v1.28.1 was used for variance stabilizing transformation, normalization (DESeq2’s median of ratios method), and differential gene expression.
Assembly: GRCh38
Supplementary files format and content: The tab-delimited text file includes raw gene count values for each sample.

source_name: Sensory epithelial cells

extract_protocol:
For RNA-seq, sensory epithelia were isolated from the underlying mesenchymal stroma using forceps and a 1mL insulin syringe. After dissection, utricles were immediately fixed with freshly prepared 4% paraformaldehyde (PFA) o.n. at 4°C for in situ validation and immunofluorescence; then processed for sectioning or used as whole mount. RNA from delaminated sensory epithelia was extracted using the Quick-RNATM Microprep kit according to the manufacturer’s guidelines.
Libraries were prepared following ribosomal RNA depletion using the Illumina Truseq Stranded mRNA Library Prep kit and then sequenced with the HiSeq 2000 platform (Illumina) using the 100-bp paired-end strategy

treatment_protocol: Utricles were cultured free-floating for 24 h in DMEM/F-12 GlutaMAXTM medium (Thermo Fisher Scientific, 10565042) supplemented with 10% FBS (Invitrogen, 12484028), 1% HEPES 1M (Gibco, 15630-080), 1% fungizone (Gibco, 15290018), 0.1% ciprofloxacin (Sigma-Aldrich, 17850-5G-F) at 37 °C in a humidified incubator with 5% CO2. Tissues were treated with 2 mM gentamicin (Gibco 15750-060 Gentamicin Reagent Solution, 50mg/mL) or distilled water as vehicle control. After 24 h, samples were washed in HBSS+/+ supplemented with 1% HEPES, then incubated for 5-10 min at 37 °C in a glass vial with Rubber-Lined Cap, 1 dram, 15x45mm (Fisher, 03-339-25B) containing an enzymatic solution, 2 mL of HBSS+/+ with 1mg/mL of thermolysin (Sigma-Aldrich, P1512), pre-heated for 10 min at 37 °C.

value: Sensory epithelial cells

value: 24h Gentamicin

value: Day 1

value: Female


title: DHT_AR_rep1


title: E65-2019B_Somatosensory

description:
Library name: E65-2019B_Somatosensory
10X Genomics (V3) 3 capture single cell RNA seq


title: PBMC_COVIDHC_CellPlex2_x8pool, CMO

city: Barcelona

first: Laura

last: Jiménez-Gracia

address: c/ Baldiri Reixac, 4  Barcelona Science Park - Tower I

country: Spain

institute: Centre Nacional d'Anàlisi Genòmic (CNAG)

description: Cell Multiplexing Oligos (CMO)

library_source: other

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A; v32; Ensembl98
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz and assignment_confidence_table.csv (for CMO libraries)
Library strategy: CMO

molecule: other

source_name: Blood

extract_protocol:
Cryopreserved PBMCs were thawed in a water bath at 37ºC and transferred to a 15 ml Falcon tube containing 10 ml of pre-warmed RPMI media supplemented with 10% FBS. Samples were centrifuged at 350 x g for 8 min at room temperature (RT), supernatant was removed and pellets resuspended with 1 ml of cold 1X PBS supplemented with 0.05% BSA. Samples were incubated during 10 min at RT with 0.1 mg/ml of DNAse I in order to eliminate ambient DNA and favor the resuspension of the pellet. Cells were filtered with a 40 µm strainer to remove eventual clumps and washed by adding 10 ml of cold PBS+0.05% BSA. Samples were centrifuged at 350 x g for 8 min at 4ºC and resuspended in an adequate volume of PBS+0.05% BSA in order to reach the desired concentration.
PBMCs samples were multiplexed with 10X Genomics Cell Plex kit following the Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocol (10x Genomics). Briefly, 0.2-1 million cells were centrifuged at 350x g at RT with a swinging-bucket rotor, resuspended in 100 µl of Cell Multiplexing Oligo and incubated at RT for 5 mins. Cells were washed 3 times with cold 1X PBS supplemented with 1% BSA, all centrifugations being performed at 350x g at 4C. Cells were finally resuspended in an appropriate volume of 1X PBS-1% BSA in order to obtain a final cell concentration. Multiplexed samples were encapsulated using the high throughput Chromium Next GEM Single Cell 3' HT Reagent Kit v3.1 in combination with the Chromium X instrument. Libraries were prepared following manufacturer’s instructions of protocols CG000419.  Sequencing was carried out on a NovaSeq6000 system (Illumina) and NextSeq500 using the following sequencing conditions: 28 bp (Read 1) + 10 bp (i7 index) + 10 bp (i5 index) + 90 bp (Read 2), to obtain approximately 40.000 read pairs per cell for the Gene Expression (GEX) library and 2000-4000 read pairs per cell for the CellPlex library (CMO).
scRNA-seq CellPlex 3’ HT

value: Blood

value: PBMC

tag: library type

value: CMO


title: ATACseq_MCF7_KO_Tam_rep3

description: Library name: KO_Tam_c

value: Breast

value: p53 KO

value: Tamoxifen


title: ATACseq_MCF7_WT_NT_rep2

description: Library name: WT_NT_b

value: No treatment


title: ATACseq_MCF7_WT_Tam_rep1

description: Library name: WT_Tam_a


title: ATACseq_MCF7_WT_NT_rep3

description: Library name: WT_NT_c


title: E80-2019_Cerebellum

description:
Library name: E80-2019_Cerebellum
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: Delaminated sensory epithelium, Treated, Biol rep 2


title: DHT_AR_rep2

value: prostate

value: LNCaP

value: tumor


title: PBMC_COVIDHC_CellPlex1_x8pool, CMO

description: Cell Multiplexing Oligos (CMO)


title: E65-2019B_Temporal

description:
Library name: E65-2019B_Temporal
10X Genomics (V3) 3 capture single cell RNA seq


title: E65-2019B_Parietal

description:
Library name: E65-2019B_Parietal
10X Genomics (V3) 3 capture single cell RNA seq


title: ATACseq_MCF7_WT_NT_rep1

description: Library name: WT_NT_a

value: p53 WT


title: Input ChIPseq, minus YM155, activated CD4 cells..

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

description: mapped to HG38

data_processing:
bcl conversion and demultiplexing (bcl2fastq), to fastq files
fastq mapping to hg38 reference (STAR, default parameters apart alignIntronMax flag set to 1 for end-to-end mapping)
quality control (MultiQC v.0.9dev0, default parameters)
peak calling (MACS2, narrow peaks, default parameters)
peak filtering and merging (MACS2, peaks with enrichment versus surrounding region and input (adjusted p<10-5) selected, >=1bp overlapping peaks in four samples merged to single annotation and further used as “survivin-ChIP peaks” (“cmd=annotatePeaks.pl peaks/peaksMrg.txt hg38 -pc 1 -noadj -d”  for all four samples))
Assembly: HG38
Supplementary files format and content: matrix with peak location (chromosome, strand, start, stop), peak score and sample redundancy in S1-S4

source_name: Primary activated CD4 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells, culture activated with ConA+LPS for 72h

extract_protocol:
EpiTect ChIP OneDay kit (Qiagen), quality control TapeStation (Agilent, Santa Clara, CA, USA)
ThruPLEX (Rubicon)

treatment_protocol: ChIP with anti-histone H3K4me3 (C15411003, Diagenode)/anti-histone H3K27ac (C15410196-10, Diagenode)/anti-histone H3K27me3 (C15410195-10, Diagenode) - 0.5 microg/mL

tag: stimulation

value: ConA+LPS

value: Control

tag: antibody

value: Input


title: PBMC_COVIDHC_CellPlex1_x8pool, GEX

description: polyA RNA

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A; v32; Ensembl98
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz and assignment_confidence_table.csv (for CMO libraries)

value: mRNA


title: AI_IgG_replicate2

description: total ribo-depleted RNA

data_processing:
Reads were mapped on human genome version GRCh38 with STAR version 2.7.
Only unique mapped reads were kept for further analysis.
Reads were divided with samtools 1.9 into plus strand bam files (flags -f128 -F16 for R2 and -f64 -f16 for R1) and minus strand bam files (flags -f128 -f16 for R2, and -f64 -F16 for R1).
The peak calling was performed for each strand, with MACS v3.0.0b1, with the command "callpeak" and the parameters " --broad --broad-cutoff 0.05" for each IP and the associated IgG.
bam files were converted into bedgraph files followed by RPM normalization (reads per million of mapped reads) using bedtools version 2.29.0. The bedgraph files were successively converted into bigwig, wig, and tdf, files using respectively bedGraphToBigWig, bigWigToWig (from UCSC), and toTDF (igvtools).
Assembly: GRCh38
Supplementary files format and content: coverage files (reads per million normalization) for minus and plus strand in tdf format

growth_protocol: LNCaP cells were grown in RPMI 1640+GlutaMAX medium + 10% FBS + 2 nM DHT or phenol red-free RPMI 1664+GlutaMAX medium + 10% dextran charcoal-stripped FBS for 1 or 6 months to 80% of confluency.

extract_protocol:
RNAs were extracted by adding Qiazol to the beads after immunoprecipitation and wash following the procedure of the miRNeasy kit (Qiagen) including the DNAse treatment step. Eluted RNA was quntified by Qubit and
Libraries were prepared by SMARTer Stranded Total RNA-seq Kit-Pico Input Mammalian using 10 ng of RNA.

treatment_protocol: 0.1 % formaldehyde in PBS for 10 min at room temperature and quenched with5 minutes at room temperature after adding glycine to a final concentration of 125 mM. Cell lysis and immunprecipitations were performed as described by Hendrickson et al. Genome Biology (2016).

value: ATCC (CRL-1740)

value: phenol red-free RPMI 1664+GlutaMAX medium + 10% dextran charcoal-stripped FBS, for 6 months

value: 6 months

tag: rip antibody

value: Abcam ab37415, 6 µg


title: Input ChIPseq, plus YM155, activated CD4 cells.

description: mapped to HG38


title: DHT_IgG_rep1

value: Thermo Fisher, 31235


title: Delaminated sensory epithelium, Control, Biol rep 2

value: Sensory epithelial cells

value: 24h Control

value: Day 1

value: Female


title: Delaminated sensory epithelium, Control, Biol rep 3

value: Male


title: Delaminated sensory epithelium, Treated, Biol rep 1

value: 24h Gentamicin


title: PBMC_COVIDHC_CellPlex2_x8pool, GEX

description: polyA RNA

value: Blood

value: PBMC


title: Input ChIPseq, plus YM155, activated CD4 cells..

description: mapped to HG38

value: ConA+LPS


title: 1m_IgG_replicate2

description: total ribo-depleted RNA

value: prostate

value: LNCaP

value: tumor

value: phenol red-free RPMI 1664+GlutaMAX medium + 10% dextran charcoal-stripped FBS for 1 month

value: 1 month


title: H3K27ac ChIPseq, activated CD4 cells

description: mapped to HG38

value: Control


title: E65-2019B_PFC

description:
Library name: E65-2019B_PFC
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: H3K4me3 ChIPseq, plus YM155, activated CD4 cells

description: mapped to HG38


title: E65-2019B_Motor_2

description:
Library name: E65-2019B_Motor_2
10X Genomics (V3) 3 capture single cell RNA seq


title: WT3

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

country: China

institute: PICB

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using Featurecounts
Assembly: mm10 (mouse)
Supplementary files format and content: tab-delimited text files include gene ID and expression level in reads count for each sample

organism: Mus musculus

source_name: striatum

growth_protocol: The mice were maintained under specific pathogen-free (SPF) conditions at the Center for New Drug Safety Evaluation and Research, China Pharmaceutical University.

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen) and prepared into cDNA library according to the standard Illumina RNA-seq instruction.
The cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2500 by a 2X150 bp run.

treatment_protocol: Cgas deficiency or Sting deficiency mice on a C57BL/6J background were generated through CRISPR-Cas9 technology by Model Animal Research Center of Nanjing University as previously described

value: striatum

value: WT


title: H3K27me3 ChIPseq, plus YM155, activated CD4 cells

description: mapped to HG38


title: H3K4me3 ChIPseq, activated CD4 cells

description: mapped to HG38


title: E65-2019B_Motor_1

description:
Library name: E65-2019B_Motor_1
10X Genomics (V3) 3 capture single cell RNA seq


title: WT1


title: Delaminated sensory epithelium, Control, Biol rep 1

value: Sensory epithelial cells

value: 24h Control


title: AI_IgG_replicate1

description: total ribo-depleted RNA

value: ATCC (CRL-1740)

value: phenol red-free RPMI 1664+GlutaMAX medium + 10% dextran charcoal-stripped FBS, for 6 months

value: 6 months

value: Abcam ab37415, 6 µg


title: STINGKO3

value: STING KO


title: Input ChIPseq, minus YM155, activated CD4 cells.

description: mapped to HG38

value: ConA+LPS

value: Input


title: H3K27me3 ChIPseq, activated CD4 cells

description: mapped to HG38


title: E65-2019B_MGE

description:
Library name: E65-2019B_MGE
10X Genomics (V3) 3 capture single cell RNA seq


title: E65-2019B_Midbrain

description:
Library name: E65-2019B_Midbrain
10X Genomics (V3) 3 capture single cell RNA seq


title: Input ChIPseq, plus YM155, activated CD4 cells

description: mapped to HG38


title: AI_AR_replicate2

description: total ribo-depleted RNA

value: prostate

value: LNCaP

value: Abcam ab108341, 6 µg


title: Input ChIPseq, minus YM155, activated CD4 cells

description: mapped to HG38


title: H3K27ac ChIPseq, plus YM155, activated CD4 cells

description: mapped to HG38


title: 1m_IgG_replicate1

description: total ribo-depleted RNA

value: tumor

value: phenol red-free RPMI 1664+GlutaMAX medium + 10% dextran charcoal-stripped FBS for 1 month

value: 1 month


title: E65-2019B_Cerebellum_AND_Pons

description:
Library name: E65-2019B_Cerebellum_AND_Pons
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: STINGKO1

value: striatum


title: DHT_IgG_replicate2

description: total ribo-depleted RNA

value: RPMI 1640+GlutaMAX medium + 10% FBS + 2 nM DHT

value: up to 10 passages


title: E65-2019B_LGE

description:
Library name: E65-2019B_LGE
10X Genomics (V3) 3 capture single cell RNA seq


title: CGASKO2

value: cGAS KO


title: WT2

value: WT


title: CGASKO1


title: E65-2019B_Hypothalamus

description:
Library name: E65-2019B_Hypothalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: DHT_IgG_replicate1

description: total ribo-depleted RNA

value: ATCC (CRL-1740)


title: STINGKO2


title: E65-2019A_Temporal

description:
Library name: E65-2019A_Temporal
10X Genomics (V3) 3 capture single cell RNA seq


title: 1m_AR_replicate1

description: total ribo-depleted RNA


title: AI_AR_replicate1

description: total ribo-depleted RNA

value: phenol red-free RPMI 1664+GlutaMAX medium + 10% dextran charcoal-stripped FBS, for 6 months

value: 6 months


title: E65-2019B_Hippocampus_choroid

description:
Library name: E65-2019B_Hippocampus_choroid
10X Genomics (V3) 3 capture single cell RNA seq


title: E65-2019A_V1

description:
Library name: E65-2019A_V1
10X Genomics (V3) 3 capture single cell RNA seq


title: CGASKO3


title: 1m_AR_replicate2

description: total ribo-depleted RNA


title: E65-2019A_Thalamus

description:
Library name: E65-2019A_Thalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: vehicle2

treatment_protocol: Transient middle cerebral artery occlusion (tMCAO) model was established.

tag: strain

value: tMCAO+PBS


title: vehicle1


title: SN011-3


title: Liver tissue of ACLF rat treated with UTOpiA, bio rep 2

city: Suita

first: Yosuke

last: Yoneyama

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

country: Japan

institute: The University of Osaka

description: Library name: Uto_2

data_processing:
Sequencing was performed on NovaSeq6000 to target 26.7M reads per samples (13.3M pairs) (4Gb/sample).
Clean data were generated from the raw data by using Trimmomatic.
Trimmed sequence reads were mapped to rn6 by using  HISAT2.
Count matrix and TPM were generated with featureCounts.
Assembly: rn6
Supplementary files format and content: tab-separated value file includes raw counts for each sample.

source_name: Liver

extract_protocol:
RNA was harvested using FastGene RNA Premium Kit (NIPPON Genetics).
Library construction was performed with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext UltraTMII Directional RNA Library Prep Kit (New England Biolabs).

value: Liver


title: Liver tissue of ACLF rat treated with UTOpiA, bio rep 3

description: Library name: Uto_3


title: DHT_AR_replicate2

description: total ribo-depleted RNA

value: prostate


title: DHT_AR_replicate1

description: total ribo-depleted RNA

value: LNCaP


title: E65-2019A_PFC

description:
Library name: E65-2019A_PFC
10X Genomics (V3) 3 capture single cell RNA seq


title: SN011-2


title: E65-2019A_Somatosensory

description:
Library name: E65-2019A_Somatosensory
10X Genomics (V3) 3 capture single cell RNA seq


title: SN011-1


title: vehicle3


title: LNCaP_FV_NE_s_3_6m

description: total ribo-depleted RNA

data_processing:
Reads were mapped on human genome version GRCh38 with tophat version 2.1.1, with the following parameters : -g 1 -N 3 --read-edit-dist 3 -r 155 --mate-std-dev 80 –no-coverage-search --library-type fr-firststrand.
Only unique mapped reads were kept for further analysis.
New transcripts were discovered using scallop 0.10.5.
Read counting was performed using featureCounts version 1.6.0 on a combined annotation of gencode.v32 and new transcripts from scallop, with the following parameters : -F "GTF" -p -s 2 -O.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing raw read counts for each gene

growth_protocol: LNCaP cells were cultured at 37°C in a humid 5% CO2 atmosphere in either the RPMI 1640+GlutaMAX medium (Life Technologies) supplemented with 10% fetal bovine serum and 2 nM DHT (AD-cells, or +DHT) or the phenol red-free RPMI 1664+GlutaMAX medium supplemented with 10% dextran charcoal-stripped fetal bovine serum for 15 days, 1 month, 3 months, 6 months

extract_protocol:
Total RNA extraction was performed directly from cell cultures with miRNeasy kit according to the manufacture’ instructions including the DNase treatment step (Qiagen).
Trueseq stranded Total RNA-seq protocol with Ribo-zero depletion of rRNA from 500 ng of the total RNA extract sample

value: epithelial prostate cancer cells

value: ATCC CRL-1740

value: hormon depleted media (phenol red-free RPMI 1664+GlutaMAX medium supplemented with 10% dextran charcoal-stripped fetal bovine serum)


title: Liver tissue of ACLF rat treated with UTOpiA, bio rep 1

description: Library name: Uto_1


title: sham3

value: sham+PBS


title: Liver tissue of normal rat, bio rep 3

description: Library name: Normal_3


title: sham2


title: Liver tissue of normal rat, bio rep 2

description: Library name: Normal_2


title: E65-2019A_Motor_2

description:
Library name: E65-2019A_Motor_2
10X Genomics (V3) 3 capture single cell RNA seq

data_processing:
fastq files
Kallisto gene expression quantification
Cellbender ambient RNA removal
Assembly: rheMac10
Supplementary files format and content: H5AD

value: brain


title: LNCaP_FV_NE_s_1_6_m

description: total ribo-depleted RNA


title: E65-2019A_Motor_1

description:
Library name: E65-2019A_Motor_1
10X Genomics (V3) 3 capture single cell RNA seq


title: LNCaP_FV_NE_s_2_6_m

description: total ribo-depleted RNA


title: Liver tissue of normal rat, bio rep 1

description: Library name: Normal_1


title: sham1

value: striatum


title: Liver tissue of ACLF rat treated with empty, bio rep 3

description: Library name: Empty_3


title: E65-2019A_Midbrain

description:
Library name: E65-2019A_Midbrain
10X Genomics (V3) 3 capture single cell RNA seq


title: 3d-SN011-3


title: E65-2019A_Parietal

description:
Library name: E65-2019A_Parietal
10X Genomics (V3) 3 capture single cell RNA seq


title: Liver tissue of ACLF rat treated with empty, bio rep 2

description: Library name: Empty_2


title: E65-2019A_MGE

description:
Library name: E65-2019A_MGE
10X Genomics (V3) 3 capture single cell RNA seq


title: 3d-SN011-1


title: 3d-SN011-2


title: LNCaP_FV_NE_s_1_3m

description: total ribo-depleted RNA

value: 3 months


title: 7d_WT_2

value: ischemic stroke


title: LNCaP_FV_NE_s_2_1m

description: total ribo-depleted RNA

value: 1 month


title: LNCaP_FV_NE_s_3_1m

description: total ribo-depleted RNA


title: E65-2019A_Hypothalamus

description:
Library name: E65-2019A_Hypothalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: BMSCs,ST

city: Xi'an

first: Le

last: Wang

state: shanxi

address: Changle west road

institute: Air Force Medical University

data_processing:
Bowtie v1.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 v2.1.0
Read count extraction and normalization were performed using HTSeq (http://www-huber.embl.de/users/an ders/HTSeq/doc/overview.html)
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cells

growth_protocol: BMSCs were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol (TAKARA).3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: we respectively cultured BMMSCs on the surfaces of NT100(100-nanometer nanotubes) and ST (Smooth) for 6 hours.

value: primary cells

value: Bone marrow mesenchymal stem cells

value: WT

value: Smooth


title: Liver tissue of ACLF rat treated with empty, bio rep 1

description: Library name: Empty_1


title: 7d_WT_1


title: LNCaP_FV_NE_s_1_1m

description: total ribo-depleted RNA


title: E65-2019A_Hippocampus_choroid

description:
Library name: E65-2019A_Hippocampus_choroid
10X Genomics (V3) 3 capture single cell RNA seq

extract_protocol:
Papain dissociated whole cells
10X Genomics (V3) 3 capture single cell RNA seq


title: BMSCs,ST2


title: E65-2019A_CGE_AND_LGE

description:
Library name: E65-2019A_CGE_AND_LGE
10X Genomics (V3) 3 capture single cell RNA seq


title: LNCaP_FV_NE_s_3_3m

description: total ribo-depleted RNA


title: LNCaP_FV_NE_s_3_15j

description: total ribo-depleted RNA

value: Day 15


title: E65-2019A_AND_E65-2019B_Multi-seq_3

description:
Library name: E65-2019A_AND_E65-2019B_Multi-seq_3
10X Genomics (V3) 3 capture single cell RNA seq


title: BMSCs,ST1


title: LNCaP_FV_NE_s_2_15j

description: total ribo-depleted RNA


title: BMSCs,NT

value: 100-nanometer nanotubes


title: LNCaP_FV_NE_s_2_3m

description: total ribo-depleted RNA

value: prostate


title: BMSCs,NT2


title: E65-2019A_Cerebellum_Pons

description:
Library name: E65-2019A_Cerebellum_Pons
10X Genomics (V3) 3 capture single cell RNA seq


title: LNCaP_FV_NE_s_3_0j

description: total ribo-depleted RNA

value: LNCaP

value: DHT, 2 nM

value: Day 0


title: BMSCs,NT1


title: E65-2019A_AND_E65-2019B_Multi-seq_2

description:
Library name: E65-2019A_AND_E65-2019B_Multi-seq_2
10X Genomics (V3) 3 capture single cell RNA seq


title: 7d_cGAS-KO_2

value: cGAS-KO


title: 14d_WT_2


title: E50_V1

description:
Library name: E50_V1
10X Genomics (V3) 3 capture single cell RNA seq


title: E65-2019A_AND_E65-2019B_Multi-seq_1

description:
Library name: E65-2019A_AND_E65-2019B_Multi-seq_1
10X Genomics (V3) 3 capture single cell RNA seq


title: 7d_STING-KO_1

value: STING-KO


title: LNCaP_FV_NE_s_1_15j

description: total ribo-depleted RNA

value: epithelial prostate cancer cells

value: ATCC CRL-1740

value: hormon depleted media (phenol red-free RPMI 1664+GlutaMAX medium supplemented with 10% dextran charcoal-stripped fetal bovine serum)


title: E50_thalamus

description:
Library name: E50_thalamus
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: 14d_WT_1

value: striatum

value: ischemic stroke


title: LNCaP_FV_NE_s_1_0j

description: total ribo-depleted RNA


title: E50_temporal

description:
Library name: E50_temporal
10X Genomics (V3) 3 capture single cell RNA seq


title: 7d_STING-KO_2


title: M5

city: Detroit

last: Pilsner

state: MI

address: 275 E Hancock St

department: Department of Obstetrics and Gynecology

institute: Wayne State University

data_processing:
Cutadapt was used for trimming reads <16 nts and filtering low quality reads (PHRED score<20). Potential sequencing contaminants were excluded using UniVec database.
The unmapped reads were then sequentially aligned to transcriptome databases for ncRNA biotypes in the order miRNA>tRNA>piRNA>rRNA> “other” RNA>circRNA>lncRNA. Filtered reads were sequentially mapped to mouse transcriptome databases in the orders that included mirBase 22.1 release (http://www.mirbase.org/ ) for both hairpin and mature miRNA, pirBase (http://bigdata.ibp.ac.cn/piRBase/) and GtRNAdb release 19 (http://gtrnadb.ucsc.edu/) for piRNA (gold standard) and tRNA using STAR (v.2.7.6a). The remaining unmapped reads were aligned to other transcriptomes including rRNA, lncRNA and other ncRNAs such as small nuclear RNA, small nucleolar RNA, Y_RNA, and misc_RNA extracted from ensembl ncRNA mouse transcriptome (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.20/). Lastly, the unmapped reads were aligned to circBase (http://www.circbase.org/) for circRNA transcript.
Epididymosomes ncRNA biotype-specific counts were normalized using weighted trimmed mean of M-values TMM and species with normalized count (RPM) ≥ 1 in all samples were utilized for downstream diffrenetial expression analysis using EdgeR
Assembly: mirBase 22.1 (http://www.mirbase.org/ ); pirBase (http://bigdata.ibp.ac.cn/piRBase/); GtRNAdb release 19 (http://gtrnadb.ucsc.edu/); ensembl ncRNA mouse transcriptome  (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.20/); circBase (http://www.circbase.org/)
Supplementary files format and content: Processed data file (columns N:T) are tab-delimited txt files and contain biotype-specific read count values for each sample

source_name: cauda epididymis extracellular vesicles

growth_protocol: Adult C57BL/6J (B6, JAX # 000664) male mice aged 7 – 8 weeks old were treated with vehicle (Control; 50% DMSO), 2.5 mg/kg/day of DBP or DEHP, and phthalate mixture (2.5 mg/kg/day of DBP and 2.5 mg/kg/day DEHP) for six weeks, using surgically implanted osmotic pumps (Alzet #2006).

extract_protocol:
Isolation of epididymosomes and total RNA was performed using Qiagen exoRNAeasy Midi Kit.
RNA libraries for small RNA-seq were prepared using Clontech SMARTER smRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Followin mice euthanizion, both cauda epididymides were collected, incised longitudinally and incubated at 37°C for 30 min in 1 mL of sperm wash buffer to suspend sperm and epididymal fluid in the solution. Large tissue was removed and tubes were centrifuged at 500 X g for 5 minutes to pellet and remove sperm. Remaining supernatant, which contained EVs, were immediately frozen on dry ice and stored at  -80°C until use for downstream analysis.

tag: field

value: small non-coding RNA (sncRNA)

value: cauda epididymis extracellular vesicles

value: DBP + DEHP (2.5 mg/kg/day/each)

value: 6 weeks


title: M6


title: 14d_STING-KO_2

tag: tissue


title: LNCaP_FV_NE_s_2_0j

description: total ribo-depleted RNA


title: COPD_P2_CellPlex_x8pool

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A; v32; Ensembl98
Supplementary files format and content: barcodes.tsv: cell barcodes
Supplementary files format and content: features.tsv: gene names (including CMOs for CellPlex_x8pool libraries)
Supplementary files format and content: matrix.mtx: count matrix

extract_protocol:
Cryopreserved PBMCs were thawed in a water bath at 37ºC and transferred to a 15 ml Falcon tube containing 10 ml of pre-warmed RPMI media supplemented with 10% FBS. Samples were centrifuged at 350 x g for 8 min at room temperature (RT), supernatant was removed and pellets resuspended with 1 ml of cold 1X PBS supplemented with 0.05% BSA. Samples were incubated during 10 min at RT with 0.1 mg/ml of DNAse I in order to eliminate ambient DNA and favor the resuspension of the pellet. Cells were filtered with a 40 µm strainer to remove eventual clumps and washed by adding 10 ml of cold PBS+0.05% BSA. Samples were centrifuged at 350 x g for 8 min at 4ºC and resuspended in an adequate volume of PBS+0.05% BSA in order to reach the desired concentration.
For ASTHMA + HC, PBMCs samples were evenly mixed in pools of 8 donors per library following a multiplexing approach based on donor’s genotype. For COPD + HC, PBMCs samples were multiplexed with 10X Genomics Cell Plex kit following the Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocol (10x Genomics). Briefly, 0.2-1 million cells were centrifuged at 350x g at RT with a swinging-bucket rotor, resuspended in 100 µl of Cell Multiplexing Oligo and incubated at RT for 5 mins. Cells were washed 3 times with cold 1X PBS supplemented with 1% BSA, all centrifugations being performed at 350x g at 4C. Cells were finally resuspended in an appropriate volume of 1X PBS-1% BSA in order to obtain a final cell concentration. Multiplexed samples were encapsulated using the high throughput Chromium Next GEM Single Cell 3' HT Reagent Kit v3.1 in combination with the Chromium X instrument. Libraries were prepared following manufacturer’s instructions of protocols CG000419.  Sequencing was carried out on a NovaSeq6000 system (Illumina) and NextSeq500 using the following sequencing conditions: 28 bp (Read 1) + 10 bp (i7 index) + 10 bp (i5 index) + 90 bp (Read 2), to obtain approximately 40.000 read pairs per cell for the Gene Expression (GEX) library and 2000-4000 read pairs per cell for the CellPlex library.
3’ scRNA-seq: with and without CellPlex

value: Blood


title: E50_somato

description:
Library name: E50_somato
10X Genomics (V3) 3 capture single cell RNA seq

tag: developmental stage


title: E50_septum

description:
Library name: E50_septum
10X Genomics (V3) 3 capture single cell RNA seq


title: 14d_cGAS-KO_2


title: 14d_STING-KO_1


title: COPD_P1_CellPlex_x8pool

description: 10x Genomics


title: M4


title: M3


title: E50_motor

description:
Library name: E50_motor
10X Genomics (V3) 3 capture single cell RNA seq


title: DH6

value: DEHP (2.5 mg/kg/day)


title: E50_MGE

description:
Library name: E50_MGE
10X Genomics (V3) 3 capture single cell RNA seq


title: 7d_cGAS-KO_1


title: ASTHMA_P2_Genotype_x8pool

description: 10x Genomics


title: 14d_cGAS-KO_1


title: M2


title: E50_PFC

description:
Library name: E50_PFC
10X Genomics (V3) 3 capture single cell RNA seq


title: M1


title: cirrhosis_CNAG_117

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A; v32; Ensembl98
Supplementary files format and content: barcodes.tsv: cell barcodes
Supplementary files format and content: features.tsv: gene names (including CMOs for CellPlex_x6pool libraries)
Supplementary files format and content: matrix.mtx: count matrix

extract_protocol:
Cryopreserved PBMCs were thawed in a water bath at 37ºC and transferred to a 15 ml Falcon tube containing 10 ml of pre-warmed RPMI media supplemented with 10% FBS. Samples were centrifuged at 350 x g for 8 min at room temperature (RT), supernatant was removed and pellets resuspended with 1 ml of cold 1X PBS supplemented with 0.05% BSA. Samples were incubated during 10 min at RT with 0.1 mg/ml of DNAse I in order to eliminate ambient DNA and favor the resuspension of the pellet. Cells were filtered with a 40 µm strainer to remove eventual clumps and washed by adding 10 ml of cold PBS+0.05% BSA. Samples were centrifuged at 350 x g for 8 min at 4ºC and resuspended in an adequate volume of PBS+0.05% BSA in order to reach the desired concentration.
PBMCs samples were multiplexed with 10X Genomics Cell Plex kit following the Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocol (10x Genomics). Briefly, 0.2-1 million cells were centrifuged at 350x g at RT with a swinging-bucket rotor, resuspended in 100 µl of Cell Multiplexing Oligo and incubated at RT for 5 mins. Cells were washed 3 times with cold 1X PBS supplemented with 1% BSA, all centrifugations being performed at 350x g at 4C. Cells were finally resuspended in an appropriate volume of 1X PBS-1% BSA in order to obtain a final cell concentration. Multiplexed samples were encapsulated using the high throughput Chromium Next GEM Single Cell 3' HT Reagent Kit v3.1 in combination with the Chromium X instrument. Libraries were prepared following manufacturer’s instructions of protocols CG000419.  Sequencing was carried out on a NovaSeq6000 system (Illumina) and NextSeq500 using the following sequencing conditions: 28 bp (Read 1) + 10 bp (i7 index) + 10 bp (i5 index) + 90 bp (Read 2), to obtain approximately 40.000 read pairs per cell for the Gene Expression (GEX) library and 2000-4000 read pairs per cell for the CellPlex library.
scRNA-seq CellPlex 3’ HT

tag: disease

value: cirrhosis


title: HealthyExercise2_PBMC_CellPlex_x4pool

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A; v32; Ensembl98
Supplementary files format and content: barcodes.tsv: cell barcodes
Supplementary files format and content: features.tsv: gene names (including CMOs for CellPlex_x4pool libraries)
Supplementary files format and content: matrix.mtx: count matrix

extract_protocol:
Cryopreserved PBMCs were thawed in a water bath at 37ºC and transferred to a 15 ml Falcon tube containing 10 ml of pre-warmed RPMI media supplemented with 10% FBS. Samples were centrifuged at 350 x g for 8 min at room temperature (RT), supernatant was removed and pellets resuspended with 1 ml of cold 1X PBS supplemented with 0.05% BSA. Samples were incubated during 10 min at RT with 0.1 mg/ml of DNAse I in order to eliminate ambient DNA and favor the resuspension of the pellet. Cells were filtered with a 40 µm strainer to remove eventual clumps and washed by adding 10 ml of cold PBS+0.05% BSA. Samples were centrifuged at 350 x g for 8 min at 4ºC and resuspended in an adequate volume of PBS+0.05% BSA in order to reach the desired concentration.
PBMCs samples were multiplexed with 10X Genomics Cell Plex kit following the Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocol (10x Genomics). Briefly, 0.2-1 million cells were centrifuged at 350x g at RT with a swinging-bucket rotor, resuspended in 100 µl of Cell Multiplexing Oligo and incubated at RT for 5 mins. Cells were washed 3 times with cold 1X PBS supplemented with 1% BSA, all centrifugations being performed at 350x g at 4C. Cells were finally resuspended in an appropriate volume of 1X PBS-1% BSA in order to obtain a final cell concentration. Multiplexed samples encapsulated using standard throughput Chromium Next GEM Single Cell 3’ Reagent Kit v3.1. Libraries were prepared following manufacturer’s instructions of protocols CG000390.  Sequencing was carried out on a NovaSeq6000 system (Illumina) using the following sequencing conditions: 28 bp (Read 1) + 10 bp (i7 index) + 10 bp (i5 index) + 90 bp (Read 2), to obtain approximately 40.000 read pairs per cell for the Gene Expression (GEX) library and 2000-4000 read pairs per cell for the CellPlex library.
scRNA-seq CellPlex 3’


title: E50_parietal

description:
Library name: E50_parietal
10X Genomics (V3) 3 capture single cell RNA seq


title: PLXDC2- human HSCs biol rep 2

city: Minato

last: Tanaka

state: Tokyo

address: Shirokanedai

institute: IMS, The University of Tokyo

description: Library name: Sample4

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2.
Read counts were quantified using featureCounts (Subread package) from BAM files aligned with HISAT2. Read alignment was performed against the human reference genome using HISAT2, and featureCounts was run with the corresponding gene annotation file (GTF format).
Assembly: hg38
Supplementary files format and content: read counts for each Sample

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

value: Cord blood

tag: cell line

value: Primary

tag: cell type

value: Hematopoietc stem cells

value: Wild type

tag: sorted fraction

value: PLXDC2- human HSCs


title: ASTHMA_P1_Genotype_x8pool

description: 10x Genomics


title: E50_hindbrain

city: San Francisco

last: Pollen

address: 35 Medical Center Way

institute: UCSF

description:
Library name: E50_hindbrain
10X Genomics (V3) 3 capture single cell RNA seq


title: DH2

tag: treatment

tag: time


title: PLXDC2+ human HSCs biol rep 4

description: Library name: Sample7

tag: genotype

value: PLXDC2+ human HSCs


title: cirrhosis1_PBMC_CellPlex_x6pool

description: 10x Genomics


title: cirrhosis2_PBMC_CellPlex_x6pool

description: 10x Genomics


title: PLXDC2- human HSCs biol rep 3

description: Library name: Sample6


title: E50_choroid

description:
Library name: E50_choroid
10X Genomics (V3) 3 capture single cell RNA seq


title: DH5


title: PLXDC2+ human HSCs biol rep 3

description: Library name: Sample5


title: cirrhosis_CNAG_118

description: 10x Genomics


title: E50_hypo

description:
Library name: E50_hypo
10X Genomics (V3) 3 capture single cell RNA seq


title: DH4


title: DB6

value: DBP (2.5 mg/kg/day)


title: PLXDC2+ human HSCs biol rep 1

description: Library name: Sample1


title: E50hippo

description:
Library name: E50hippo
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: E50_cerebellum

description:
Library name: E50_cerebellum
10X Genomics (V3) 3 capture single cell RNA seq


title: BRCA_PBMC_P497_Time0

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A; v32; Ensembl98
Supplementary files format and content: barcodes.tsv: cell barcodes
Supplementary files format and content: features.tsv: gene names
Supplementary files format and content: matrix.mtx: count matrix

extract_protocol:
Cryopreserved PBMCs were thawed in a water bath at 37ºC and transferred to a 15 ml Falcon tube containing 10 ml of pre-warmed RPMI media supplemented with 10% FBS. Samples were centrifuged at 350 x g for 8 min at room temperature (RT), supernatant was removed and pellets resuspended with 1 ml of cold 1X PBS supplemented with 0.05% BSA. Samples were incubated during 10 min at RT with 0.1 mg/ml of DNAse I in order to eliminate ambient DNA and favor the resuspension of the pellet. Cells were filtered with a 40 µm strainer to remove eventual clumps and washed by adding 10 ml of cold PBS+0.05% BSA. Samples were centrifuged at 350 x g for 8 min at 4ºC and resuspended in an adequate volume of PBS+0.05% BSA in order to reach the desired concentration.
Cellular suspensions were loaded in a standard assay with a target recovery of 6000 cells per sample using the Chromium Next GEM Single Cell 5' Reagent Kit v2  Libraries were prepared following manufacturer’s instructions of protocols CG000331. Sequencing was carried out on a NovaSeq6000 system (Illumina) using the following sequencing conditions: 28 bp (Read 1) + 10 bp (i7 index) + 10 bp (i5 index) + 90 bp (Read 2), to obtain approximately 40.000 read pairs per cell for the Gene Expression (GEX) library.
5’ scRNA-seq (only GEX)

value: BRCA


title: PLXDC2- human HSCs biol rep 4

description: Library name: Sample8


title: PLXDC2+ human HSCs biol rep 2

description: Library name: Sample3


title: DH3


title: Delaminated sensory epithelium, Control, Biol rep 2

data_processing:
Quality control metrics for all FASTQ reads were obtained using RNA-SeQC v1.1.7. The CellRanger v3.0.2 pipeline was used for primary data processing and the production of gene-barcode matrices, with settings as recommended by the manufacturer (10x Genomics).
The raw gene-barcode matrices for all groups (Time0, Control, and Treated; two samples per group) were processed as follows: first, cell quality was determined by examining the distribution of library sizes, the number of expressed genes across cells, and the fraction of reads mapped to mitochondrial (MT) genes. Second, we filtered out doublets using DoubletFinder v2.0. Cells with log-library sizes that were more than three median absolute deviations (MADs) below the median log-library size were also filtered out. The MAD approach was also used to determine mitochondrial expression cut-offs for each group. Genes detected in less than three cells were removed.
The data set was normalized and scaled using Seurat’s (v4.0) SCTransform function. Unwanted sources of variation (e.g., batch effects) were regressed out of the aggregated data using Harmony in PCA space. The resulting Harmony embeddings were used downstream.
Assembly: GRCh38
Supplementary files format and content: The tab-delimited text files (for each sample) include raw gene count values for all cells.

extract_protocol:
Sample preparation and cell capture were performed using the 10x Genomics Chromium Single Cell 3’ v3 Reagent Kits user guide. Briefly, two washes were done to exchange sample buffer for one recommended for loading on the Chromium Controller. Samples were spun at 0.3G for 6 min at 4oC and resuspended in a solution of 250 µL RPMI-1640 Medium with 0.04% BSA and 5U/µL RNase Inhibitor. Cell viability was assessed via Trypan Blue (Thermo Fisher) and using a haemocytometer (Thermo Fisher). A second spin was performed under identical conditions, and cells were resuspended in 55 µL final volume. Following counting, cell suspension (46.6 µL) was loaded onto the Chromium Single Cell B Chip Kit. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed, and incubated overnight in a Veriti 96-well thermos cycler (Thermo Fisher) for the reverse transcriptase reaction. Following this reaction, cDNA was recovered using the Recovery Agent provided by 10x Genomics and subsequently cleaned up using a Silane DynaBead (Thermo Fisher) as outlined by the user guide
The molarity of each library was calculated based on library size as measured by BioAnalyzer (Agilent Technologies), qPCR amplification data (Sigma) or Illumina MiSeq clustering data (Illumina). Briefly, samples were normalized, then diluted using elution buffer (Qiagen) with 0.1% Tween® 20 (Sigma-Aldrich), and each pool denaturated at r.t.. Library pools were further diluted before being diluted to a final loading concentration. 100 µL from each pool were loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. All samples were sequenced with the following run parameters: read 1 - 28 cycles, read 2 - 91 cycles, and index 1 - 8 cycles. A median sequencing depth of 60,000 reads/cell was targeted for each sample.

value: Sensory epithelial cells

value: 24h Control (distilled water)

value: Day 1

value: Male


title: DH1

value: small non-coding RNA (sncRNA)

value: cauda epididymis extracellular vesicles

value: 6 weeks


title: HealthyExercise1_PBMC_CellPlex_x4pool

description: 10x Genomics

value: Blood


title: BRCA_PBMC_P474_Time0

description: 10x Genomics


title: DB4


title: PLXDC2- human HSCs biol rep 1

description: Library name: Sample2

value: Cord blood


title: BRCA_PBMC_P560_Time0

description: 10x Genomics


title: E50_CGE-LGE

description:
Library name: E50_CGE-LGE
10X Genomics (V3) 3 capture single cell RNA seq


title: E40_thalamus

description:
Library name: E40_thalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: Delaminated sensory epithelium, Uncultured, Biol rep 1

data_processing: The data set was normalized and scaled using Seurat’s (v4.0) SCTransform function. Unwanted sources of variation (e.g., batch effects) were regressed out of the aggregated data using Harmony in PCA space. The resulting Harmony embeddings were used downstream.

value: Time 0 (untreated)

value: Day 0


title: DB5


title: E40_V1

description:
Library name: E40_V1
10X Genomics (V3) 3 capture single cell RNA seq


title: E40_somato

description:
Library name: E40_somato
10X Genomics (V3) 3 capture single cell RNA seq


title: BRCA_PBMC_ P498_Time0

description: 10x Genomics


title: DB2


title: DB3


title: E40_Pre-optic

description:
Library name: E40_Pre-optic
10X Genomics (V3) 3 capture single cell RNA seq


title: TAC_heart

city: Rouen

first: Ebba

last: Brakenhielm

address: Inserm U1096

institute: Inserm

description:
Library name: TAC_C57
10xGenomics

data_processing:
Raw FASTQ files were generated and demultiplexed from BCL data using bcl2fastq (v2.20.0). Quality control with FastQC (v0.11.9) indicated >98% perfect index and 86% of bases >= Q30, requiring no treatment. Reads were aligned to the mouse reference genome (GRCm39.111) using STARsolo RNA-seq aligner (v2.7) to produce raw UMI count matrix. Data filtering, normalization, integration, principal component-based unsupervised clustering, and differential analysis were performed using the Seurat package (version 5.0.2) in R (version 4.1.2). Among 4178 total sequenced cells, 3436 cells remained post-filtering, including 1932 cells from sham-operated controls and 1504 cardiac cells from TAC mice. Functional enrichment analysis was performed with the R package clusterProfiler (v3.2).
Assembly: mouse reference genome (GRCm38)
Supplementary files format and content: expression_data.xlsx
Supplementary files format and content: barcodes-sham.tsv
Supplementary files format and content: barcodes-TAC.tsv
Supplementary files format and content: C57_scRNAseq_ref_README.txt
Supplementary files format and content: UMAP_Projection.csv

source_name: Cardiac

extract_protocol:
Hearts were digested and cardiac endothelial cells sorted by FACS to generate cells for inclusion in scRNAseq experiment
The 10X Genomics Chromium Next Gem Single Cell 3' library kit v.3.1 was used to prepare barcoded mRNA following the guidelines from the supplier. Single Index kit T Set A was used to label each reaction. Samples were loaded onto 3 separate Illumina kit High-throughput 2x75 (<400 million reads) flow-cells and sequenced using Illumina Nextseq, using the settings of: Read1: 28 cycles; Read2: 8 cycles; Read3 (i7): 114 cycles

treatment_protocol: TAC or sham surgery was performed in adult female C57BL6/J

value: Cardiac

value: female

value: Endothelial cells

value: TAC-operated

tag: batch


title: BRCA_PBMC_P571_Time0

description: 10x Genomics


title: C6

value: Control (50% DMSO)


title: BRCA_PBMC_ P473_Time0

description: 10x Genomics

value: BRCA


title: DB1

value: DBP (2.5 mg/kg/day)


title: E40_parietal

description:
Library name: E40_parietal
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: Delaminated sensory epithelium, Treated, Biol rep 2

value: Sensory epithelial cells

value: 24h Gentamicin

value: Day 1

tag: Sex

value: Female


title: Sham_heart

description:
Library name: SHAM_C57
10xGenomics

value: sham-operated


title: E40_PFC

description:
Library name: E40_PFC
10X Genomics (V3) 3 capture single cell RNA seq


title: MCF7_KO-p53_Tam_rep3

description: Library name: EA9b_20240606

data_processing:
Reads were trimmed using cutadapt and mapped to the hg38 genome using STAR v2.4.2a (default parameters). The pipeline quantifies the genes annotated in Gencode (that have been expanded with 1000 bases toward the 5’ edge and 100 bases toward the 3’ bases). Counting was done using htseq-count (union mode). Further analysis was done only for genes having a minimum of 5 reads in at least one sample. Normalization of the counts and differential expression analysis was performed using DESeq2 with the parameters: betaPrior = True, cooksCutoff = FALSE, independentFiltering = FALSE. Differentially expressed genes were defined using FC > 1.5 and raw p-value < 0.05 as a significance cutoff.
Assembly: hg38
Supplementary files format and content: Deseq2 - differential analysis output

extract_protocol:
RNA was isolated using the NucleoSpin kit (Macherey Nagel).
RNA-seq libraries were prepared from 30 ng of input RNA from each sample and were barcoded during reverse transcription and pooled. Following Agencourt AMPure XP beads cleanup (Beckman Coulter), the pooled samples underwent second-strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR. Sequencing was done with a Nextseq 75 cycles high output kit (Illumina).

treatment_protocol: 5uM Tamoxifen for 48h or 5uM Nutlin for 24h

value: Breast

value: p53 KO

value: Tamoxifen


title: Delaminated sensory epithelium, Treated, Biol rep 1

value: Male


title: UPAR- Male

city: Cold Spring Harbor

first: Vyom

last: Shah

state: New York

address: 1 bungtown road

department: Beyaz Lab

institute: Cold Spring Harbor Laboratory

description:
10x Genomics
UPAR_sort_scrna_metadata.csv

data_processing:
cDNA and libraries were checked for quality on Agilent Bioanalyzer, quantified by KAPA qPCR, and sequenced on a NextSeq500 (Illumina) to an average depth of approximately 33,000 reads per cell.
The Cellranger pipeline (v4.0.0 10X Genomics) was used to align FASTQs to the mouse reference genome (gex-mm10-2020-A, 10X Genomics) and produce digital gene-cell counts matrices with default parameters.
Cells with more than 15% mitochondrial transcripts as well as cells that had fewer than 100 feature counts or expressed fewer than 8000 genes were removed using Seruat (v4.0.3)
Using Seurat (v4.0.3) normalization, graph-based clustering and differential expression analysis. Each dataset was normalized using SCTransform and the 2500 most variable genes were identified with SelectIntegrationFeatures. All samples were integrated into a singular dataset via using the PrepSCTIntegration, FindIntegrationAnchors, and IntegrateData functions
Assembly: mm10
Supplementary files format and content: h5 and comma seperated value files

source_name: Intestinal Epithelium

extract_protocol:
Small intestine was removed, washed with cold PBS, opened laterally and cut into 3-5mm fragments. Pieces were washed multiple times with ice cold PBS until clean, washed 2-3 with PBS+EDTA (7.5mM), and incubated with mild agitation for 30 minutes at 4C. Crypts were then mechanically separated from the connective tissue by shaking, and filtered through a 70-μm mesh into a 50mL conical tube to remove villus material and tissue fragments. For Epcam+ cell isolation, the crypt suspensions were dissociated to individual cells with TrypLE Express (Thermo Fisher Scientific, 12604039) and stained for flow cytometry. Epithelial cells were isolated as SYTOX-, CD45- Epcam+ with a BD FACS Aria II SORP cell sorter into supplemented crypt culture medium for culture. uPAR+ and uPAR- populations were isolated as DAPI-, uPAR+/- with a SONY cell sorter(SH800S).
Single cell libraries were prepared using a 10X Genomics Chromium Controller (cat Chromium Next GEM Single Cell 3' Gene Expression kit (cat #1000268) according to the manufacturer's instructions. Cell suspensions were adjusted to target a yield of 8,000 cells per sample. Single cell 3' digital gene expression with cell barcodes and unique molecular identifiers (UMIs).

value: Intestinal Epithelium

tag: age


title: UPAR+ Male


title: MCF7_KO-p53_Tam_rep2

description: Library name: EA9b


title: UPAR- Female


title: C2

value: small non-coding RNA (sncRNA)

value: cauda epididymis extracellular vesicles

value: 6 weeks


title: C3

value: Control (50% DMSO)


title: E40_motor

first: Alex

description:
Library name: E40_motor
10X Genomics (V3) 3 capture single cell RNA seq


title: E40_MGE

description:
Library name: E40_MGE
10X Genomics (V3) 3 capture single cell RNA seq


title: UPAR+ Female


title: C4


title: intest_UT_M_old

description: 10x Genomics

extract_protocol:
Organoids were dissociated into single cell suspensions at 37C using TrypLE, and passed through a 100 um FlowMi cell strainer.  Cells were stained with DAPI and sorted on a Sony SH800S sorter. DAPI-negative viable cells were sorted into a chilled microcentrifuge tube containing PBS. Viability was confirmed to be >75% using a Countess FL II cell counter (Life Technologies #AMQAF1000) before proceeding to single cell library preparation.
Single cell libraries were prepared using a 10X Genomics Chromium Controller (cat Chromium Next GEM Single Cell 3' Gene Expression kit (cat #1000268) according to the manufacturer's instructions. Cell suspensions were adjusted to target a yield of 8,000 cells per sample. Single cell 3' digital gene expression with cell barcodes and unique molecular identifiers (UMIs).


title: MCF7_KO-p53_Tam_rep4

description: Library name: ED4


title: MCF7_KO-p53_NT_rep4

description: Library name: ED3

value: No treatment


title: intest_UT_M_young

description: 10x Genomics


title: MCF7_KO-p53_Tam_rep1

description: Library name: EA9a


title: 196a_stage_17_MM-74

city: Norwich

first: Alice

last: Godden

state: Not applicable

address: School of Biological Sciences, University of East Anglia, Norwich Research Park

institute: University of East Anglia

description: Library name: B212T17

data_processing:
Raw fastq files were trimmed to remove adapter sequences. Following this RNA-sequencing reads were mapped to the X. laevis v10.1 genome assembly using STAR (v.2.7.3a).
Assembly: X. laevis v10.1
Supplementary files format and content: Differential and mean expression of genes using DESeq2 normalised read counts in Rstudio.

organism: Xenopus laevis

source_name: Neural crest

growth_protocol: Wild-type Xenopus laevis embryos were injected at the 4-cell stage and grown to NF st. 14 and 17.

extract_protocol:
RNA extraction kit standard
Illumina RNA-seq library prepation kit, unstranded

treatment_protocol: Use of morpholino and mismatch morpholinos at a concentration of 60 ng.

value: Neural crest

value: wild-type

value: mismatch morpholino

value: NF st 17


title: C1


title: 196a_stage_17_MM-58

description: Library name: B212T07


title: C5


title: E40_Hindbrain

description:
Library name: E40_Hindbrain
10X Genomics (V3) 3 capture single cell RNA seq

source_name: brain

value: brain


title: intest_UT_F_old

description: 10x Genomics

value: Female


title: intest_UT_F_young

description: 10x Genomics


title: MCF7_KO-p53_NT_rep3

description: Library name: EA6b_20240606


title: E40_Midbrain

description:
Library name: E40_Midbrain
10X Genomics (V3) 3 capture single cell RNA seq


title: MCF7_KO-p53_NT_rep2

description: Library name: EA6b


title: MCF7_KO-p53_NT_rep1

description: Library name: EA6a


title: 196a_stage_17_196a_MO-55

description: Library name: B212T09

value: morpholino


title: E40_Choroid

description:
Library name: E40_Choroid
10X Genomics (V3) 3 capture single cell RNA seq


title: E40hippo

description:
Library name: E40hippo
10X Genomics (V3) 3 capture single cell RNA seq


title: 196a_stage_17_MM-57

description: Library name: B212T25


title: E40_DRG

description:
Library name: E40_DRG
10X Genomics (V3) 3 capture single cell RNA seq


title: 196a_stage_17_196a_MO-54

description: Library name: B212T14


title: intest_uPAR_M_young

description: 10x Genomics


title: MCF7_WT-p53_Tam_rep4

description: Library name: ED2

value: Breast

value: p53 WT


title: E40_CGE-LGE

description:
Library name: E40_CGE-LGE
10X Genomics (V3) 3 capture single cell RNA seq


title: E40_Hypo

description:
Library name: E40_Hypo
10X Genomics (V3) 3 capture single cell RNA seq


title: 196a_stage_17_196a_MO-138

description: Library name: B212T26


title: E100V1

description:
Library name: E100V1
10X Genomics (V3) 3 capture single cell RNA seq


title: intest_uPAR_F_young

description: 10x Genomics


title: MCF7_WT-p53_Tam_rep1

description: Library name: EA4a_20240606

value: Tamoxifen


title: intest_uPAR_F_old

description: 10x Genomics


title: E100somato

description:
Library name: E100somato
10X Genomics (V3) 3 capture single cell RNA seq


title: MCF7_WT-p53_Tam_rep3

description: Library name: EA4b_20240606


title: ovary tissue of polycystic ovary syndrome (PCOS) mouse M2

type: RNA

city: Changsha

first: Waixing

last: Li

address: Tongzipo

institute: The Third Xiangya Hospital of Central South University

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Hierarchical clustering heatmap analysis was performed for differentially m6A-methylated RNAs. Differentially m6A-methylated mRNAs were analyzed for GO and pathway enrichment.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and/or Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

label_protocol: Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated "IP" fraction contained enriched m6A methylated RNAs, and the supernatant " Sup" fraction contained unmodified RNAs."IP" and "Sup" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

extract_protocol: Total RNA extracted using Trizol reagent.The purity and amount of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.

tag: subject

value: Female C57BL/6J mice aged 7 weeks

tag: sample type


title: 196a_stage_14_MM-48

description: Library name: B212T22

value: NF st 14


title: 196a_stage_14_MM-66

description: Library name: B212T12


title: 196a_stage_14_MM-47

description: Library name: B212T19


title: ovary tissue of polycystic ovary syndrome (PCOS) mouse M3


title: MCF7_WT-p53_Tam_rep2

description: Library name: EA4b


title: MCF7_WT-p53_NT_rep4

description: Library name: EA1b_20240606


title: MCF7_WT-p53_NT_rep5

description: Library name: ED1


title: E100temporal

description:
Library name: E100temporal
10X Genomics (V3) 3 capture single cell RNA seq


title: E100PFC

description:
Library name: E100PFC
10X Genomics (V3) 3 capture single cell RNA seq


title: 196a_stage_14_196a_MO-45

description: Library name: B212T28


title: ovary tissue of normal mouse C3

source_name: ovary tissue of normal mouse


title: ovary tissue of polycystic ovary syndrome (PCOS) mouse M1


title: MCF7_WT-p53_NT_rep3

description: Library name: EA1b


title: 196a_stage_14_196a_MO-44

description: Library name: B212T04


title: MCF7_WT-p53_NT_rep2

description: Library name: EA1a_20240606


title: ovary tissue of normal mouse C2


title: ovary tissue of normal mouse C1


title: E100insula

description:
Library name: E100insula
10X Genomics (V3) 3 capture single cell RNA seq


title: MCF7_WT-p53_NT_rep1

description: Library name: EA1a


title: 196a_stage_14_196a_MO-137

description: Library name: B212T06


title: Delaminated sensory epithelium, Uncultured, Biol rep 2

value: Sensory epithelial cells

value: Time 0 (untreated)

value: Day 0


title: E100hippo

description:
Library name: E100hippo
10X Genomics (V3) 3 capture single cell RNA seq


title: intest_uPAR_M_old

description: 10x Genomics

value: Male

value: Intestinal Epithelium