title: HEK293T_Chromseq_TAF3_rep2

city: Xi'an

first: Wei

last: Sun

state: Shaanxi

address: No. 229 Taibai North Road, Beilin District

department: College of Life Sciences and Medicine

institute: Northwest University

description:
HEK293T_NLS_TAF3_rep2
Chromseq_allsamples_raw_counts.txt

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
Then, raw reads were trimmed using fastp(v0.23.1) with the options: fastp -A -f 11 -F 0 -t 0 -T 11.
Clean reads were aligned using HISAT2(v.2.1.0) to the hg19 genome with the options: hisat2 -q -t --no-unal.
The aligned reads were quantified by featureCounts(v2.0.1) using the options: featureCounts -t gene -g gene_id --extraAttributes gene_name,gene_type -s 1 -p -C
Differential expression analysis using DESeq2 (v1.34.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file include Chromseq three biological replicates raw counts for each sample
Supplementary files format and content: tab-delimited text file include RNAseq three biological replicates raw counts for each sample
Library strategy: Chrom-seq

growth_protocol: Plate HEK293T cells co-expressing the corresponding GCN4 and APEX2 fusion constructs for 48 hours.

extract_protocol:
The total RNA was isolated by using the NEB Next Poly A+Isolation Kit (NEB, #E7490S/L).1-5 μg of total RNA was used for the construction of sequencing libraries.
Libraries were built using the Smart-seq protocol.

treatment_protocol: Cells were changed the medium to fresh medium containing 500 µM biotin-aniline and incubate at 37℃ under 5% CO2 for 30 min. Then, H2O2 was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 min.

value: Human embryonic kidney


title: mCherry, D1, 2

status: Public on Jul 31 2024

type: SRA

city: Baltimore

first: Velinda

last: Vidaurre

state: Maryland

address: 3400 N Charles St

country: USA

institute: Johns Hopkins

library_source: transcriptomic

data_processing:
The sequencing reads were examined using the FastQC quality software (Galaxy Version 0.73+galaxy0)
Reads that passed the quality filter were then mapped to the Drosophila genome (D. melanogaster Aug 2014 (BDGP Release 6 + ISO11 MT/dm6)) using Bowtie 2 version 2.5.1
For gene mapping, the gene model (Drosophila_melanogaster.BDGP6.87.gtf) was utilized, and we followed an RNA-seq data analysis tutorial using Galaxy
Assembly: dm6
Supplementary files format and content: DESeq

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: testis

growth_protocol: Fly stocks were maintained in bottles containing a standard molassas recipe from the Bloomington Stock Center. Crosses to combine the nanos driver with the mCherry or Set1 RNAi transgenes were prepared in vials and maintained at 18°C. Upon eclosion, male progenies of the appropriate genotype were allowed to age for 0, 1, 3, or 5 days prior to sample preparation at 25°C.

extract_protocol:
Total RNA was purified following the manufacturers instruction of the Quick-RNA Microprep Kit (R1050, Zymo Research corporation).
The libraries were generated using the reagents provided in NEBNext Ultra II Directional RNA library Prep Kit for Illumina (E7760S, New England Biolabs Inc) and NEB Next Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs inc).

treatment_protocol: Male flies of the correct genotype were dissected in freshly prepared and filter sterilized Schneider's media containing 10% FBS. The biological replicates for each genotype and timepoint contain ~ 15 number of testis pairs. Following dissection, testes were digested in 200-300uL tissue digestion buffer composed of 2mg/mL collagenase disolved in TrypLE Express. The tissue was digested to completion in a 37°C water bath for 10-15 with agitation every 2-3 minutes. The suspended cells were next filtered with a 40um nylon mesh cell stainer. Cells were pelleted in 10 minute intervals at 1,200rpm until all digestion buffer was removed. The cells were washed with 200 ul of PBS and pelleted again for 5 min at 1,200 rpm.

tag: tissue

value: testis

tag: cell type

value: germ cell

tag: genotype

value: WT

tag: time

value: Day 1


title: VYS_MEHP_NEG_2

type: RNA

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

description: *** The raw data (CEL files) are not included because they were lost due to disk corruption ***

hyb_protocol: Samples were processed and scanned at the University of Michigan Microarray Core Facility (Ann Arbor, MI)

data_processing:
The affy, limma, and affyPLM packages of bioconductor were used in R (v2.15.1).
Background correction, normalization, and quantification of log2 expression was performed within-array using RMA, and quantile normalization was used across-arrays.

label: biotin - IVT Express Kit (Affymetrix)

molecule: total RNA

organism: Mus musculus

source_name: mouse visceral yolk sacs exposed to 100 μg/ml MEHP for 24 hours in whole embryo culture, without neural tube defect

label_protocol: RNA was processed using the IVT Express Kit (Affymetrix)

growth_protocol: Whole mouse conceptuses were manually extracted from untreated, pregnant dams on GD8. Conceptuses were transferred to whole embryo culture for 24 h, containing either 0.01% dimethyl sulfoxide (control) or 100 ug/ml mono-2-ethylhexyl phthalte. On GD9, conceptuses were removed from culture and manually dissected with watchmakers' forceps to yield embryos and visceral yolk sacs. Culture protocols were performed as described by Harris (2012; PMID: 22669667).

extract_protocol:
RNA extraction  was done immediately upon sampling using the RNeasy Mini Kit (Qiagen). RNA was stored at -80°C until use.
RNA purity and integrity were confirmed using the RNA 6000 Nano Kit for the Agilent 2100 Bioanalyzer. Other quality controls including PM chip density, RNA degradation, and standard error analyses were performed on the raw data.

tag: strain

value: visceral yolk sacs

tag: exposure

value: Mono-2-ethylhexyl phthalate (MEHP) - 100 μg/ml for 24 hours in whole embryo culture

tag: ntd status

value: negative

tag: age


title: VYS_MEHP_POS_2

scan_protocol: Samples were processed and scanned at the University of Michigan Microarray Core Facility (Ann Arbor, MI)

source_name: mouse visceral yolk sacs exposed to 100 μg/ml MEHP for 24 hours in whole embryo culture, with a neural tube defect

value: positive


title: VYS_MEHP_NEG_3


title: VYS_MEHP_POS_1


title: EJ-vector control

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina PE150  software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples
Genome_build: hg38

organism: Homo sapiens

source_name: human bladder cancer cells

growth_protocol: Cells were cultured  in Dulbecco’s modified Eagle medium (Gibco, United States), which supplemented with 10% fetal bovine serum (Gibco, United States), 100 U/ml penicillin, and 100 μg/ml streptomycin. Then, incubating the cells at 37 °C in a humidified atmosphere (Thermo Fisher Scientific, MA, USA) with 5 % CO2.

extract_protocol:
Total RNA was extracted from all cells using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EJ, T24T, and UMUC3 cells transfected with circMGA and compaired vector. Transfection was carried out using Lipofectamine 2000 (Life Technologies) according to the manufacturer’s instructions. The transfected cells were then selected with neomycin (Invitrogen)

tag: treatment

value: EJ cell in control group

tag: vector


title: HEK293T_Chromseq_TAF3Control_rep3

description:
HEK293T_NLS_TAF3Control_rep3
Chromseq_allsamples_raw_counts.txt

tag: cell line


title: HEK293T_Chromseq_TAF3Control_rep2

description:
HEK293T_NLS_TAF3Control_rep2
Chromseq_allsamples_raw_counts.txt


title: VYS_CTL_NEG_3

source_name: mouse visceral yolk sacs exposed to DMSO for 24 hours in whole embryo culture, without neural tube defect

value: DMSO (0.01%) for 24 hours in whole embryo culture


title: 40_NRDE3_enri2_late_IP2

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

state: CA

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

description: size-selected small RNA

data_processing:
Small RNA libraries were sequenced on the Illumina NextSeq2000 (SE 75-bp reads) platform.
Sequences were parsed from adapters using FASTQ/A Clipper (options: -Q33 -l 17 -c -n -a TGGAATTCTCGGGTGCCAAGG) and quality filtered using the FASTQ Quality Filter (options: -Q33 -q 27 -p 65) from the FASTX-Toolkit
Contamination from reads mapping to 18-mer and 28-mer size standards were filtered out using Cutadapt (version 3.4)
Filtered reads were mapped to the C. elegans genome WS258 using Bowtie2 v. 2.5.0 (default parameters)
Reads were assigned to genomic features using featureCounts (options: -t exon -g gene_id -O --fraction –largestOverlap) which is part of the Subread v. 2.0.1 package.
Assembly: WS258
Supplementary files format and content: Processed data files are tab-delimited text files including total reads mapping to each gene generated by FeatureCounts.

organism: Caenorhabditis elegans

source_name: embryo

growth_protocol: Sychronized early adult animals were grown on enriched peptone plates seeded with OP50 E. coli at 17°C. Adult C. elegans stage was monitored carefully under DeltaVision microscope by live imaging. For early embryo collection (<=100-cell), adult animals were washed off from plates with H2O and bleached as soon as the first animals had 1-4 eggs (around 68-70 hours depending on the strain and the incubator temperature). For late embryo collection (>=300-cell), adult animals were washed off from plates with H2O and bleached when about half of the worms had 1~6 eggs (~70-72 hours depending on the strain and the incubator temperature). After bleaching, embryos were washed twice with M9 buffer, and filtered through 40µm cell strainers (Fisherbrand™ Sterile Cell Strainers, 40µm) twice to clear the residual worm body. To reach >=300-cell stage for late embryo collection, embryos were additionally incubated in M9 buffer at 20°C for 4.5 hours.

extract_protocol:
For immunoprecipitation followed by small RNA sequencing in embryos, ∼500,000 synchronized embryos were sonicated with Fisher Sonifier 550 with a microtip (15s on, 45s off, 10% power, total 2 minutes on time). After sonication, insoluble particulate was removed by centrifugation at 21,000g for 30 minutes. Immunoprecipitation was performed using anti-FLAG Affinity Matrix (Sigma Aldrich, A2220). NRDE-3-bound RNAs were isolated using TRIzol reagent (Thermo Fisher, 15596018), followed by chloroform extraction and isopropanol precipitation.
Small RNAs (18 to 30-nt) were size selected on homemade 10% Urea-polyacrylamide gels from total RNA samples. Small RNAs were treated with 5’ RNA polyphosphatase (Epicenter RP8092H) and ligated to 3’ pre-adenylated adapters with Truncated T4 RNA ligase (NEB M0373L). Small RNAs were then hybridized to the reverse transcription primer, ligated to the 5’ adapter with T4 RNA ligase (NEB M0204L), and reverse transcribed with Superscript III (Thermo Fisher 18080-051). Small RNA libraries were amplified using Q5 High-Fidelity DNA polymerase (NEB M0491L) and size selected on a homemade 10% polyacrylamide gel. Library concentration was determined using the Qubit 1X dsDNA HS Assay kit (Thermo Fisher Q33231) and quality was assessed using the Agilent BioAnalyzer. Libraries were sequenced on the Illumina NextSeq2000 (SE 75-bp reads) platform.

value: embryo

tag: antibody

value: FLAG (Sigma Aldrich, A2220)

value: USC1593 - enri-2(cmp330) nrde-3(tor131[GFP::3xFLAG::nrde-3]) X

tag: Stage

value: late embryos (>=300cell)

tag: experimental temperature

tag: fraction

value: IP


title: 38_NRDE3_enri2_late_Input2

description: size-selected small RNA

value: input


title: VYS_CTL_POS_1

source_name: mouse visceral yolk sacs exposed to DMSO for 24 hours in whole embryo culture, with neural tube defect


title: 39_NRDE3_enri2_late_IP1

description: size-selected small RNA


title: RNAseq P. flava adult replicate 1

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
To quantify gene expression, reads were pseudo aligned against the set of longest transcripts per isoform per gene using Kallisto.
RNA-seq counts were corrected for batch effect and quantile normalised using edgeR and RUVSeq, taking the 10000 bottom-ranked genes in edgeR as in-silico empirical, invariable genes.
Pairwise Spearman correlation of replicates was done and visualised in R using base and ComplexHeatmap packages.
Assembly: Ptychodera flava genome: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA747109
Supplementary files format and content: Gene counts from Kallisto

organism: Ptychodera flava

source_name: whole animal

extract_protocol:
Total RNA of each developmental stage was isolated from one to three biological replicates using the RNeasy Micro Kit (Qiagen).
Library preparation for stranded polyA-based mRNA was then performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: whole animal

tag: developmental stage

value: adult

value: wild type


title: p3-1dpi

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

description:
L46080
RSEM_TPM_table.txt

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert (v 3.10.5). Reads were aligned to UCSC genome astMex_2.0 with STAR aligner (v 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (v 1.3.0)
Assembly: Astyanax mexicanus 2.0
Supplementary files format and content: TPM gene expression in text file

organism: Astyanax mexicanus

source_name: Skeletal Muscle

extract_protocol:
RNA from skeletal muscle was extracted using standard phenol/chloroform extraction. The subsequent RNA pellet was cleaned with the RNeasy Mini Kit (Qiagen #74104) with on-column DNAse digestion (Qiagen #79256).
Libraries were prepared according to the manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina #20020594)
The resulting libraries were quantified using a Bioanalyzer (Agilent Technologies) and Qubit fluorometer (Life Technologies). Libraries were normalized, pooled, multiplexed, and sequenced on an Illumina NextSeq-75-HO instrument as v2 Chemistry High Output 75bp single read runs.

treatment_protocol: Free Running Darkness

value: Skeletal Muscle

tag: group

value: troglobitic cavefish

tag: time point

value: cardiotoxin injection


title: HEK293T_Chromseq_TAF3_rep3

description:
HEK293T_NLS_TAF3_rep3
Chromseq_allsamples_raw_counts.txt

tag: cell type

value: Human embryonic kidney


title: T24T-vector control

value: T24T cell in control group


title: VYS_CTL_NEG_2

tag: tissue

value: visceral yolk sacs

value: negative


title: HEK293T_Chromseq_TAF3_rep1

description:
HEK293T_NLS_TAF3_rep1
Chromseq_allsamples_raw_counts.txt


title: HEK293T_Chromseq_TAF3Control_rep1

description:
HEK293T_NLS_TAF3Control_rep1
Chromseq_allsamples_raw_counts.txt


title: VYS_MEHP_NEG_1

value: Mono-2-ethylhexyl phthalate (MEHP) - 100 μg/ml for 24 hours in whole embryo culture


title: RNAseq P. flava Spengel replicate 2

value: Spengel

tag: genotype


title: VYS_CTL_NEG_1

tag: strain

value: DMSO (0.01%) for 24 hours in whole embryo culture


title: RNAseq P. flava Agassiz replicate 2

value: Agassiz


title: WT B cells #2, Stim

city: Buffalo

first: Lee

middle: Ann

last: Garrett-Sinha

state: NY

address: 955 Main St, Room 5124

department: Biochemistry

institute: University at Buffalo

description:
Cells cultured for 2 hours in RPMI-1640 media plus 10% fetal calf serum, penicillin-streptomycin, glutamax and 50 micromolar beta-mercaptoethanol with added anti-IgM antibody
1062_Stim_ATAC (BCR ligation)

library_source: genomic

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Spleen

growth_protocol: B cells were cultured in RPMI-1640 media with 10% fetal calf serum, penicillin/streptomycin, glutamax and 50 micromolar beta-mercaptoethanol at 37°C in a tissue culture incubator

extract_protocol:
100,000 unstimulated or stimulated B cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. Cells were thawed, permeabilized with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin detergents and then incubated with Tn5 transposase with adaptors, according to protocols established by Active Motif.
Cells were tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).

treatment_protocol: Some samples were left untreated (no treatment, NT). Other samples were stimulated (stim) via the B cell receptor (BCR) with 10 μg/ml goat F(ab')₂ fragment of goat anti-mouse IgM, µ chain specific antibody (Jackson ImmunoResearch) for two hours

value: Spleen

value: Purified primary B cells

value: wild-type

value: Culture for 2 hrs in media at 37°C with 10 μg/ml goat anti-IgM F(ab’)2 crosslinking antibody


title: 37_NRDE3_enri2_late_Input1

description: size-selected small RNA

value: embryo

value: FLAG (Sigma Aldrich, A2220)

value: USC1593 - enri-2(cmp330) nrde-3(tor131[GFP::3xFLAG::nrde-3]) X

value: late embryos (>=300cell)

value: input


title: RNAseq P. flava Agassiz replicate 1

value: whole animal

value: wild type


title: 34_NRDE3_enri2_early_Input2

description: size-selected small RNA

value: early embryos (<=100cell)


title: WT B cells #1, NT

description:
Cells cultured for 2 hours in RPMI-1640 media plus 10% fetal calf serum, penicillin-streptomycin, glutamax and 50 micromolar beta-mercaptoethanol
1060_NT_ATAC (No treatment)

value: Culture for 2 hrs in media at 37°C


title: EMB_MEHP_POS_3

source_name: mouse whole embryos exposed to 100 μg/ml MEHP for 24 hours in whole embryo culture, with a neural tube defect

value: whole mouse embryos

tag: exposure

value: Mono-2-ethylhexyl phthalate (MEHP) - 100 μg/ml for 24 hours in whole embryo culture

value: positive


title: WT B cells #2, NT

description:
Cells cultured for 2 hours in RPMI-1640 media plus 10% fetal calf serum, penicillin-streptomycin, glutamax and 50 micromolar beta-mercaptoethanol
1062_NT_ATAC (No treatment)


title: WT B cells #1, Stim

description:
Cells cultured for 2 hours in RPMI-1640 media plus 10% fetal calf serum, penicillin-streptomycin, glutamax and 50 micromolar beta-mercaptoethanol with added anti-IgM antibody
1060_Stim_ATAC (BCR ligation)


title: 35_NRDE3_enri2_early_IP1

description: size-selected small RNA

value: IP


title: 32_NRDE3_simr1_late_IP3

description: size-selected small RNA

value: USC1512 - simr-1(cmp36) I; nrde-3(tor131[GFP::3xFLAG::nrde-3]) X


title: RNAseq P. flava Meschnikoff replicate 2

value: Meschnikoff


title: 31_NRDE3_simr1_late_IP2

description: size-selected small RNA


title: EMB_MEHP_POS_2

tag: ntd status


title: 33_NRDE3_enri2_early_Input1

description: size-selected small RNA


title: RNAseq P. flava Krohn replicate 1

value: Krohn


title: EMB_MEHP_POS_1

tag: age


title: EMB_MEHP_NEG_3

source_name: mouse whole embryos exposed to 100 μg/ml MEHP for 24 hours in whole embryo culture, without neural tube defect

value: negative


title: 36_NRDE3_enri2_early_IP2

description: size-selected small RNA

value: embryo


title: RNAseq P. flava Transforming larvae replicate 1

value: transforming larvae


title: RNAseq P. flava Spengel replicate 1

value: Spengel


title: 30_NRDE3_simr1_late_IP1

description: size-selected small RNA

value: FLAG (Sigma Aldrich, A2220)

value: late embryos (>=300cell)


title: RNAseq P. flava Meschnikoff replicate 1

value: whole animal


title: CD4+, 0.01pPCC, Day4, B

city: Doha

first: Nicholas

last: van Panhuys

state: State

address: Po Box 26999

department: Translational Medicine

country: Qatar

institute: Sidra Medicine

data_processing:
The initial quality of the sequencing was assessed with FASTQC (v.0.11.8).
Reads were aligned against the mouse genome mm10 in STAR v2.6.1d.
HTSeq-count (v0.9.1) was used to generate raw count
Assembly: mm10
Supplementary files format and content: Genes were median normalized by DESeq2 and are presented as normalized count values and uploaded in csv format.

source_name: Spleen/Lymph node

extract_protocol:
RNA was extracted using TRizol (ThermoFisher).
Lexogen QuantSeq3 mRNA-sequencing libraries were prepared according to the manufacturers instructions.
Libraries were pooled and sequenced on the Illumina NextSeq 500 system to a depth of 4 million reads per library.

value: Spleen/Lymph node

value: CD4+ T cell


title: CD4+, 0.01pPCC, Day4, C


title: CD4+, 0.01pPCC, Day4, A


title: CD4+, 0.1pPCC, Day4, C


title: RNAseq P. flava Krohn replicate 2

value: wild type


title: RNAseq P. flava Heider replicate 2

value: Heider


title: 29_NRDE3_simr1_late_Input3

description: size-selected small RNA

value: input


title: EMB_MEHP_NEG_2

value: whole mouse embryos

value: Mono-2-ethylhexyl phthalate (MEHP) - 100 μg/ml for 24 hours in whole embryo culture


title: EMB_CTL_POS_1

source_name: mouse whole embryos exposed to DMSO for 24 hours in whole embryo culture, with neural tube defect

value: DMSO (0.01%) for 24 hours in whole embryo culture

value: positive


title: 27_NRDE3_simr1_late_Input1

description: size-selected small RNA

value: USC1512 - simr-1(cmp36) I; nrde-3(tor131[GFP::3xFLAG::nrde-3]) X


title: EMB_CTL_NEG_3

source_name: mouse whole embryos exposed to DMSO for 24 hours in whole embryo culture, without neural tube defect

value: negative


title: OE2

city: Shanghai

first: Gao

last: yehui

address: No. 1239 Siping Road, Yangpu District

institute: Tongji University

data_processing:
To select cDNA fragments of 250–300 bp length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, USA).
3-μL USER Enzyme (New England Biolabs) was used with the size-selected, adaptor-ligated cDNA at 37 °C for 15 min, followed by 5 min at 95 °C before PCR. Next, PCR was performed with phusion high-fidelity DNA polymerase, universal PCR primers, and Index (X) Primer.
PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyser 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform, generating 150 bp paired-end reads.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

growth_protocol: The growth of N2, PHX6971, and PHX7528 strains was synchronised, and their eggs were allowed to hatch and develop to the young adult stage on NGM plates at 20 °C.

extract_protocol:
Extracting RNA using the Trizol (Tiangen) method.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: On day 5 of the adult stage, the nematodes were harvested in PBS.

tag: time

value: Day 5

value: gst-35 overexpress


title: RNAseq P. flava 72hpf tornaria replicate 1

value: 72hpf tornaria


title: CD4+, 0.1pPCC, Day4, B


title: CD4+, 1.0pPCC, Day4, C


title: KO2

value: gst-35 knockdown


title: RNAseq P. flava Heider replicate 1


title: CD4+, 1.0pPCC, Day4, B


title: RNAseq P. flava late gastrula replicate 2

value: late gastrula


title: CD4+, 0.1pPCC, Day4, A


title: 28_NRDE3_simr1_late_Input2

description: size-selected small RNA

value: embryo

value: FLAG (Sigma Aldrich, A2220)

value: late embryos (>=300cell)


title: EMB_CTL_NEG_2


title: EMB_MEHP_NEG_1


title: 25_NRDE3_simr1_early_IP2

description: size-selected small RNA

value: early embryos (<=100cell)

value: IP


title: KO1


title: RNAseq P. flava late gastrula replicate 1

value: whole animal

value: wild type


title: EMB_CTL_NEG_1

value: whole mouse embryos


title: RNAseq P. flava 72hpf tornaria replicate 2


title: RNAseq P. flava mid2 gastrula replicate 3

value: mid gastrula (after mesoderm migration)


title: OE1


title: 24_NRDE3_simr1_early_IP1

description: size-selected small RNA


title: 26_NRDE3_simr1_early_IP3

description: size-selected small RNA


title: WT2

value: WT


title: CD4+, 10.0pPCC, Day4, B

value: Spleen/Lymph node

value: CD4+ T cell


title: CD4+, 1.0pPCC, Day4, A


title: 23_NRDE3_simr1_early_Input3

description: size-selected small RNA

value: USC1512 - simr-1(cmp36) I; nrde-3(tor131[GFP::3xFLAG::nrde-3]) X

value: input


title: WT1

value: Day 5


title: RNAseq P. flava mid2 gastrula replicate 2


title: 22_NRDE3_simr1_early_Input2

description: size-selected small RNA


title: RBNS_PKM2_Bound_A

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

description:
5'adapter: GTTCAGAGTTCTACAGTCCGACGATCrNrNrNrN
3'adapter: NNTGACTGTGGAATTCTCGGGTGCCAAGG

data_processing:
Library strategy: PAR-CLIP-Seq
bcl2fastq/2.20.0 was used to convert bcl to fastq
For RNA-Seq fastq files were aligned using star/2.7.2b.
differential expression was done using cuffdiff (cufflinks/2.2.1)
PARCLIP was analysed using Parpipes (https://github.com/ohlerlab/PARpipe)
Genome_build: hg38

organism: Escherichia coli BL21(DE3)

source_name: E. coli BL21(DE3) expressed Recombinant Protein

growth_protocol: HEK293 T-Rex Flp-In cells (Thermo Fisher Scientific, Cat# R78007) were cultured in DMEM medium (Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS), 100 μg/ml zeocin, and 10 μg/ml blasticidin (Gibco)

extract_protocol:
Trizol for RNA-Seq, For PARCLIP, the cytoplasm was extracted by resuspending cells in a modified hypotonic lysis buffer (10 mM Tris-HCl pH 7.5, 50 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 10% glycerol) for 2 min. The nuclear pellet was washed twice with the same buffer and lysed in NP-40 buffer(20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% (v/v) NP40, 0.5 mM DTT), followed by sonication.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

treatment_protocol: 2ug/ml Doxycycline

tag: molecule

value: Recombinant PKM2 bound RNA 29-mers


title: CD4+, 10.0pPCC, Day4, C


title: RNAseq P. flava mid1 gastrula replicate 3

value: mid gastrula (before mesoderm migration)


title: 21_NRDE3_simr1_early_Input1

description: size-selected small RNA

value: embryo


title: RBNS_PKM2_Bound_B


title: RNAseq P. flava mid1 gastrula replicate 2


title: CD4+, Naïve, C


title: RBNS_PKM2_Input_A

source_name: E. coli BL21(DE3)

value: Input random RNA 29-mers


title: CD4+, Naïve, B


title: CD4+, 10.0pPCC, Day4, A


title: 20_NRDE3_eri1_late_IP2

description: size-selected small RNA

value: FLAG (Sigma Aldrich, A2220)

value: USC1498 - eri-1(mg366) IV; nrde-3(tor131[GFP::3xFLAG::nrde-3]) X

value: late embryos (>=300cell)


title: 19_NRDE3_eri1_late_IP1

description: size-selected small RNA

value: IP


title: CD4+, Naïve, A


title: RBNS_PKM2_Input_B


title: RNAseq P. flava early gastrula replicate 3

value: whole animal

value: early gastrula

value: wild type


title: P13.9, C

tag: cell line

value: Fibroblast


title: RNAseq P. flava early gastrula replicate 2


title: Ri, root, nf-yc3 RNAi, sample 3

city: Taipei

first: Shu-Yi

last: Yang

address: Life Science Building, NTU. No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: Institute of Plant Biology

data_processing:
High-quality RNA samples (OD260/280 = 1.65~1.88, RQN ≥ 6.5) underwent library preparation and sequencing on an Illumina NovaSeq6000 platform, generating 150 bp paired-end reads with a read depth of 6 Gb. Raw fastq files were trimmed for adaptors and assessed for quality using FastQC and MultiQC (Ewels et al., 2016). Low-quality reads were filtered using Trimmomatic (Bolger et al., 2014). Reads were mapped to the tomato reference genome (SL3.0) using HISAT2, followed by quantification with featureCounts (Kim et al., 2015; Sahraeian et al., 2017) (Liao et al., 2013). DESeq2 (Love et al., 2014; Schurch et al., 2016) was used for differential gene analysis with DEGs identified based on a Fold change≥1.5 and p-value<0.05 threshold.
Assembly: tomato reference genome SL3.0 (GCF_000188115.4) (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000188115.4/)
Supplementary files format and content: tab-delimited excel files include raw count values for each Sample

organism: Solanum lycopersicum

source_name: root

extract_protocol:
Total RNA was extracted from 100 mg shoot or root tissue by using TRIzol Reagent (Invitrogen™) following the manufacturer’s instructions. A total amount of RNA (≥ 2 μg) per sample were used for transcriptome sequencing.
Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: root

value: nf-yc3 RNAi

tag: treatment

value: Rhizophagus irregularis

value: 3.2 uM Pi

value: 8 weeks post inoculation


title: Ri, root, nf-yc3 RNAi, sample 2


title: P13.9, B


title: RNAseq P. flava early gastrula replicate 1


title: 15_NRDE3_eri1_early_IP2

description: size-selected small RNA

tag: antibody

tag: Stage

value: early embryos (<=100cell)


title: RNAseq P. flava late blastula replicate 2

value: late blastula


title: Ri, root, EV, sample 3

value: empty vector


title: P13.9, A


title: Ri, root, nf-yc3 RNAi, sample 1


title: RNAseq P. flava mid1 gastrula replicate 1

value: mid gastrula (before mesoderm migration)


title: 14_NRDE3_eri1_early_IP1

description: size-selected small RNA

value: embryo

value: FLAG (Sigma Aldrich, A2220)

tag: experimental temperature

tag: fraction


title: Ri, root, EV, sample 2


title: POGZ_VC_8451

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

data_processing:
Raw reads were trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read were removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read were removed. Finally, reads shorter than 30 base pairs were dropped.
Cleaned reads were aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Gene expression levels were estimated by quantifying primary alignments mapping to at most 2 locations (MAPQ >= 3) to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4 and the mm10 ensGene annotation set from Ensembl.
Assembly: mm10
Supplementary files format and content: invivo_ensembl.ensGene.exon_raw_counts.tsv.gz and invitro_ensembl.ensGene.exon_raw_counts.tsv.gz: tab separated file containing the raw exonic counts for each in vivo or in vitro sample using the mm10 Ensembl annotation set.

source_name: breast tumor

growth_protocol: 4T1 cells were cultured in vitro with 10% FBS containing DMEM.

extract_protocol:
Qiagen RNAeasy Column
KAPA RNA Hyper Prep (Ribo-Erase rRNA Depletion)

treatment_protocol: 4T1 cells were subjected to RNA purification at 75% confluency. For tumors, cells were inoculated at 50k with in the MFP-4 in BalbC mice (8 weeks of age). Tumors grew for 28days and were resected at end point.

value: breast tumor

value: TNBC

value: POGZ WT

value: flash frozen

tag: group

value: in vivo


title: RNAseq P. flava early blastula replicate 2

value: whole animal

tag: developmental stage

value: early blastula

value: wild type


title: Ri, root, EV, sample 1

value: root

value: Rhizophagus irregularis


title: POGZ_VC_8447

tag: cell type


title: 12_NRDE3_eri1_early_Input2

description: size-selected small RNA

value: USC1498 - eri-1(mg366) IV; nrde-3(tor131[GFP::3xFLAG::nrde-3]) X

value: input


title: mock, root, nf-yc3 RNAi, sample 3

tag: tissue

value: nf-yc3 RNAi

value: mock

value: 3.2 uM Pi

value: 8 weeks post inoculation


title: RNAseq P. flava early blastula replicate 1

tag: genotype


title: POGZ_VC_8448


title: POGZ_VC_3

value: in vitro culture


title: 17_NRDE3_eri1_late_Input1

description: size-selected small RNA

value: embryo

value: FLAG (Sigma Aldrich, A2220)

tag: strain

value: late embryos (>=300cell)


title: 11_NRDE3_eri1_early_Input1

description: size-selected small RNA

value: early embryos (<=100cell)


title: RNAseq P. flava 16-32 cell replicate 2


title: mock, root, nf-yc3 RNAi, sample 2


title: POGZ_VC_2

value: TNBC

value: POGZ WT


title: 16_NRDE3_eri1_early_IP3

description: size-selected small RNA

value: IP


title: RNAseq P. flava 16-32 cell replicate 1

value: whole animal

value: wild type


title: 10_NRDE3_late_IP3

description: size-selected small RNA

value: JMC237 - nrde-3(tor131[GFP::3xFLAG::nrde-3]) X


title: 18_NRDE3_eri1_late_Input2

description: size-selected small RNA

value: USC1498 - eri-1(mg366) IV; nrde-3(tor131[GFP::3xFLAG::nrde-3]) X


title: mock, root, nf-yc3 RNAi, sample 1

value: root


title: RNAseq P. flava late blastula replicate 1

value: late blastula


title: RNAseq P. flava unfertilized replicate 1

value: unfertilized egg


title: 13_NRDE3_eri1_early_Input3

description: size-selected small RNA

value: input


title: ATACseq P. flava late gastrula replicate 2

data_processing:
Alignment of reads with Bowtie2.
Duplicated removal and correction of start position with Bedtools.
Peak calling with MACS2 and IDR algorithm.
Assembly: Ptychodera flava genome: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA747109
Supplementary files format and content: IDR peaks in BED format.

extract_protocol:
Animals at different stages were collected to reach 75,000 cells per sample, and treated with 0.1% N-acetylcysteine for 10 sec to remove the jelly coat, followed by incubating with 8.5 mM of DTT in seawater containing 5.7 mM of NaOH. The cells were then lysed for the transposition reaction and PCR amplification.
Transposition with Tn5 enzyme and PCR amplification.

value: late gastrula


title: ATACseq P. flava late gastrula replicate 1


title: POGZ_KO_8454

value: breast tumor

value: POGZ KO

value: flash frozen

value: in vivo


title: R_2HG_3

first: Xiang

last: Wang

address: 399 Wanyuan Road, Minhang District, Shanghai

department: Children’s Hospital and Institute of Biomedical Sciences

institute: Fudan University

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Differentially expressed genes were identified using Cuffdiff. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR). The fold-changes were also estimated according to the FPKM in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: peritoneal cavity

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse peritoneal macrophages


title: mock, root, EV, sample 3

value: empty vector

value: mock

value: 3.2 uM Pi

value: 8 weeks post inoculation


title: 7_NRDE3_late_Input3

description: size-selected small RNA

value: embryo

value: FLAG (Sigma Aldrich, A2220)

value: late embryos (>=300cell)


title: ATACseq P. flava mid gastrula replicate 1

value: whole animal

value: mid gastrula


title: mock, root, EV, sample 2

value: root


title: POGZ_KO_2

value: TNBC

value: in vitro culture


title: mock, root, EV, sample 1


title: 8_NRDE3_late_IP1

description: size-selected small RNA

value: JMC237 - nrde-3(tor131[GFP::3xFLAG::nrde-3]) X

value: IP


title: 6_NRDE3_late_Input2

description: size-selected small RNA

value: input


title: POGZ_KO_8459

value: breast tumor

value: POGZ KO

value: flash frozen

value: in vivo


title: POGZ_KO_8455


title: ATACseq P. flava mid gastrula replicate 2


title: R_2HG_1

value: mouse peritoneal macrophages


title: R_2HG_2


title: 5_NRDE3_late_Input1

description: size-selected small RNA


title: ATACseq P. flava early gastrula replicate 2

value: early gastrula


title: 4_NRDE3_early_IP2

description: size-selected small RNA

value: embryo

value: early embryos (<=100cell)


title: POGZ_KO_1


title: 3_NRDE3_early_IP1

description: size-selected small RNA

value: FLAG (Sigma Aldrich, A2220)


title: Control_3

value: vehicle, 24h


title: 2_NRDE3_early_Input2

description: size-selected small RNA


title: ATACseq P. flava early blastula replicate 2

value: whole animal

value: early blastula


title: POGZ_VC_1

value: TNBC

value: POGZ WT


title: LSK cells, sc_PPM1BCKO

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong Province

address: No.6699, Qingdao Road, Huaiyin District

institute: Shandong First Medical University

library_source: transcriptomic single cell

data_processing:
Raw data from each sample were processed via cellranger (version 3.1.0), aligning the reads to the mouse genome (mm10) and generating a gene-cell matrix for subsequent analyses
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Total RNA from pre-sorted cells was extracted following TRIzol™ Reagent (ThermoFisher).
libraries were assembled in accordance with the 10×Genomics 3' gene expression protocol, and sequencing was performed utilizing the Illumina NovaSeq sequencing platform.

value: Bone marrow

value: Lsk cells


title: ATACseq P. flava early gastrula replicate 1


title: 9_NRDE3_late_IP2

description: size-selected small RNA

value: JMC237 - nrde-3(tor131[GFP::3xFLAG::nrde-3]) X

value: late embryos (>=300cell)

value: IP


title: POGZ_KO_3

value: POGZ KO

value: in vitro culture


title: 1_NRDE3_early_Input1

description: size-selected small RNA

value: input


title: Control_1

value: mouse peritoneal macrophages


title: Prolif,HNECS,PneumaEx,Donor538

status: Public on Jul 30 2024

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: No HTO

data_processing:
CellRanger v7.0.0. count
No CITE-seq-Count
Assembly: GRCh38/hg38
Supplementary files format and content: CellRanger output files:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CITE-seq Count output files :  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: nasal airways

growth_protocol: Proliferation in PneumaEx medium

extract_protocol:
Cells were incubated in trypsin 0.05%-EDTA for 5 min at 37°C. Then, cells were gently detached by pipetting and transferred into a 50mL tube and An excess of HBSS containing 2% BSA was added. Cells were centrifuged at 150 g for 5 min and resuspended in 500 µL of supplemented HBSS containing 2% BSA, centrifuged again at 150 g for 5 min and resuspended in 500 µL HBSS with 10% FBS and dissociated mechanically 4 times through a 26G syringe. Finally, cell suspensions were filtered through a 40 µm porosity FlowmiTM Cell Strainer (Bel-Art), centrifuged at 150 for 5 min and resuspended in 500 µL of HBSS. Cell concentration and viability were measured with a CountessTM automated cell counter (Thermo Fisher Scientific), after incubation with NucGreen to detect dead cells (Thermo Fisher scientific). All steps, except trypsin incubation were performed on ice.  Cell concentration of each cell suspension (4 conditions per time point) was determined, and 500 000 cells of each were centrifuged and resuspended in 100 µL of HBSS containing 2% BSA. Each cell suspension was then incubated with 0.5 µg of a distinct hashtag antibody (TotalSeqTM-A0251, A0252, A0253 and A0254, BioLegend). Each cell suspension was washed twice with HBSS, and cell concentration was measured again. Cells from each of the 4 conditions were pooled in order to obtain a final cell suspension containing identical cell concentration of each condition. We aimed at reaching a total concentration of 300 cells/mL in HBSS for the cell capture by 10X genomics Chromium.
The manufacturer’s protocol (Chromium™ Single Cell 3’ Reagent Kits, v3) was followed to obtain single cell 3’ libraries for Illumina sequencing.

value: nasal airways

value: Human Nasal Epithelial Cells (HNECS)

tag: differentiation day

value: Prolif

tag: hto

value: No HTO


title: Prolif,HNECS,PneumaExPlus,Donor538

description: No HTO

growth_protocol: Proliferation in PneumaExPlus medium


title: Prolif,HNECS,PneumaExPlus,Donor467

description: No HTO


title: Prolif,HNECS,PneumaEx,Donor543

description: No HTO


title: Prolif,HNECS,BEGM,Donor467

description: No HTO

growth_protocol: Proliferation in BEGM medium


title: Prolif,HNECS,PneumaExPlus,Donor543

description: No HTO


title: ATACseq P. flava early blastula replicate 1

value: whole animal


title: 995479-1 db/m

city: Indianapolis

first: Neha

last: Mahajan

state: Indiana

address: 1160 W Michigan St

department: Ophthalmology

institute: Indiana University

description: 6 months post-diabetes

data_processing:
The sequence reads were mapped to the designated reference genome using the Qiagen GeneGlobe RNA-seq Analysis Portal with default parameters for miRNA.
Differential expression analysis was performed using edgeR (v.3.41.9) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: The excel table including fold change, log2 fold change, p-values, FDR, log2CPM, and raw counts

source_name: LSK Cells

extract_protocol:
The LSK cells were sorted using flow cytometry followed by RNA isolation using Trizol method.
Qiaseq miRNA

value: LSK Cells

value: B6.BKS(D)-Leprdb/+ db/m

value: LSK cells derived from bone marrow

value: heterozygous for Leptin receptor


title: 995475-1 db/m

description: 6 months post-diabetes

value: homozygous for Leptin receptor


title: LSK cells, sc_PPM1Bfl/fl

value: Bone marrow

value: Lsk cells


title: 995477-2 db/m

description: 6 months post-diabetes


title: 995478-3 db/m

description: 6 months post-diabetes


title: 995478-1 db/m

description: 6 months post-diabetes


title: 995477-1 db/m

description: 6 months post-diabetes


title: 995475-2 db/m

description: 6 months post-diabetes


title: JTMD8,  single cell

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

institute: Transgene SA

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
single cell: raw data processing using cellranger-7.1.0
Assembly: GRCm39
Supplementary files format and content: raw readcount matrix in .mtx format

source_name: CT26-induced tumour

extract_protocol:
Tumors were dissociated mechanically using sterile scissors, then enzymatically using Tumor Dissociation Kit (mouse, Miltenyi Biotec; 130-096-730). Cells were isolated on a 10X Genomics Chromium Instrument.
Single cell libraries were generated using the Single Cell 3' Reagent Kit v3.1 chemistry following the guidelines of the 10X Genomics user manual (10X Genomics, Leiden, The Netherlands). Cell number and viability were determined by a Trypan Blue exclusion assay on a Buerker Chamber. Single cell suspensions with 90 percent of viable cells (or single nuclei suspensions) were processed on the 10X Genomics Chromium iX targeting 6000 captured cells per sample. Full length cDNA amplification was carried out using 12 cycles of PCR. Dual index library construction was performed with 13 cycles during sample index PCR.  Final library quantification and quality control were completed using Bioanalyzer 2100 (Agilent Technologies, Les Ulis, France).

value: CT26-induced tumour

value: BALB/c

tag: timepoint


title: JTMD7, single cell

value: untreated


title: 995478-2 db/m

description: 6 months post-diabetes


title: 6122023_X61707703_S104_F9R28_R3C2_12I_S409_R1_001

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

institute: Lunenfeld-Tanenbaum Research Institute

description: positive sample

data_processing:
Samples sequenced using Illumina NextSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie to standard amplicons from original screens, as well as two rounds of trimming and mapping to forward and reverse 5 bp barcode references.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were used to aggregate the forward and reverse barcodes.
Final analysis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1) as well as customized sequences for our forward and reverse 5 bp barcode sequences
Supplementary files format and content: run27_R1BCrpt_count_table.txt; run31_R1BCrpt_count_table.txt; run38_R1BCrpt_count_table.txt; run46_R1BCrpt_count_table.txt; run139_R1BCrpt_count_table.txt; run141p3_R1BCrpt_count_table.txt; run141p6_R1BCrpt_count_table.txt
Supplementary files format and content: run27_R2BCrpt_count_table.txt; run31_R2BCrpt_count_table.txt; run38_R2BCrpt_count_table.txt; run46_R2BCrpt_count_table.txt; run139_R2BCrpt_count_table.txt; run141p3_R2BCrpt_count_table.txt; run141p6_R2BCrpt_count_table.txt
Supplementary files format and content: run27_BCrpt_count_table.txt; run31_BCrpt_count_table.txt; run38_BCrpt_count_table.txt; run46_BCrpt_count_table.txt; run139_BCrpt_count_table.txt; run141p3_BCrpt_count_table.txt; run141p6_BCrpt_count_table.txt
Supplementary files format and content: run27_BCrpt_pair_analysis_filenames.txt; run31_BCrpt_pair_analysis_filenames.txt; run38_BCrpt_pair_analysis_filenames.txt; run46_BCrpt_pair_analysis_filenames.txt; run139_BCrpt_pair_analysis_filenames.txt; run141p3_BCrpt_pair_analysis_filenames.txt; run141p6_BCrpt_pair_analysis_filenames.txt

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: human nasopharyngeal swab

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample) and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library) (A66514, Beckman Coulter)
Other: RNAseq with limited amplicons.

value: human nasopharyngeal swab

tag: bc run_id

tag: pipeline version

value: BC


title: 6122023_X61707705_S35_F3R28_R3C2_12C_S340_R1_001

description: positive sample


title: 6122023_X61707652_S126_F11R28_R3C2_12K_S431_R1_001

description: positive sample


title: 6122023_X61707656_S170_F15R28_R3C2_12O_S475_R1_001

description: positive sample


title: 6122023_X61707680_S81_F7R28_R3C2_12G_S386_R1_001

description: positive sample


title: 6122023_X61707706_S58_F5R28_R3C2_12E_S363_R1_001

description: positive sample


title: Control_2

value: mouse peritoneal macrophages

value: vehicle, 24h


title: 6122023_X61707632_S12_F1R28_R3C2_12A_S317_R1_001

description: positive sample


title: 6122023_X61704287_S75_F7R22_R3C2_6G_S380_R1_001

description: positive sample


title: 6122023_X61707036_S102_F9R26_R3C2_10I_S407_R1_001

description: positive sample


title: 6122023_X61704379_S50_F5R20_R3C2_4E_S355_R1_001

description: positive sample


title: 6122023_X61705789_S1_F1R17_R3C2_1A_S306_R1_001

description: positive sample


title: 6122023_X61703839_S140_F13R20_R3C2_4M_S445_R1_001

description: positive sample


title: 6122023_X61703692_S52_F5R22_R3C2_6E_S357_R1_001

description: positive sample


title: 6122023_X61703776_S162_F15R20_R3C2_4O_S467_R1_001

description: positive sample


title: 6122023_X61703792_S6_F1R22_R3C2_6A_S311_R1_001

description: positive sample


title: 6122023_X61703416_S48_F5R18_R3C2_2E_S353_R1_001

description: positive sample


title: 6122023_X61703862_S98_F9R22_R3C2_6I_S403_R1_001

description: positive sample


title: 6122023_X61703802_S29_F3R22_R3C2_6C_S334_R1_001

description: positive sample


title: 6122023_X61703773_S142_F13R22_R3C2_6M_S447_R1_001

description: positive sample


title: 6122023_X61703398_S160_F15R18_R3C2_2O_S465_R1_001

description: positive sample


title: 6122023_X61703575_S120_F11R22_R3C2_6K_S425_R1_001

description: positive sample


title: 6122023_X61703152_S71_F7R18_R3C2_2G_S376_R1_001

description: positive sample


title: 6122023_X61703396_S25_F3R18_R3C2_2C_S330_R1_001

description: positive sample


title: 6122023_X61703305_S4_F1R20_R3C2_4A_S309_R1_001

description: positive sample


title: 6122023_X61707650_S168_F15R26_R3C2_10O_S473_R1_001

description: positive sample


title: 6122023_X61702776_S10_F1R26_R3C2_10A_S315_R1_001

description: positive sample


title: 6122023_X61703337_S73_F7R20_R3C2_4G_S378_R1_001

description: positive sample


title: 6122023_X61702023_S164_F15R22_R3C2_6O_S469_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample