title: P60Deaf2

city: Iowa City

first: Steven

middle: Haym

last: Green

state: Iowa

address: 143 Biology Building

department: Biology

institute: University of Iowa

data_processing:
Basecalls were made using bcl2fastq v2.20 software on the Illumina HiSeq4000 system.
Fastq files from technical replicates were merged so that there was one fastq file for each biological replicate. Reads were trimmed to remove adapter sequences and make all reads the same length using Trimmomatic with the following parameters: PE -phred 33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 CROP:100.
Trimmed reads were aligned to the rat genome (Rnor6.0.95) using STAR 2.7.0b with the following parameters: --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMtype BAM Unsorted --outFilterIntronMotifs RemoveNoncanonical
Mapped and unmapped reads were split into separate BAM files using samtools. Mapped reads were counted using featureCounts from the subread package (v1.6.3).
Raw counts were normalized and differential expression statistics calculated using DESeq2 v1.32.0 (Love MI, et al. 2014. Genome Biol 15(12), 550. doi: 10.1186/s13059-014-0550-8.)
Prinical components analysis revealed that the P32Hearing3 replicate was not clustering with the other P32Hearing replicates. Therefore, this replicate was not considered in the analysis and is not present in the normalized read counts matrix.
Genome_build: Rnor6.0.95
Supplementary_files_format_and_content: matrix table with raw read counts for each gene in each sample.
Supplementary_files_format_and_content: matrix table with DESeq2-normalized read counts for each gene in each sample.

organism: Rattus norvegicus

source_name: whole spiral ganglion

extract_protocol:
Cochleae were collected and removed from the temporal bone. Spiral ganglia were via microdissection by removing the bony tissue, spiral ligament, and organ of Corti. Ganglia were placed into RNAlater and flash frozen prior to RNA extraction. At the time of RNA extraction, the RNAlater was removed and replaced by Trizol and the tissue homogenized. The aqueous fraction was isolated using chloroform and phase lock tubes. RNA was then purified from the aqueous fraction using the RNeasy Kit (Qiagen) with on-column DNase treatment following manufacturer protocol.
Libraries were prepared using the Illumina Ribo-zero Gold Epidemiology library preparation kit

treatment_protocol: Sprague-Dawley rat pups were injected once daily from postnatal day 8 (P8) through P16 with kanamycin (400mg/kg, i.p.) to kill cochlear hair cells. Uninjected littermate rats were used as hearing controls. Uninjected hearing and injected deafened rats were euthanized at P32 or P60 for tissue collection and RNA extraction.

tag: condition

value: deaf

tag: replicate


title: input-Naive-rep2

status: Public on Jun 01 2024

type: SRA

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

country: China

institute: China Agricultural University

library_source: transcriptomic

data_processing:
FastQC was used to identify features of the raw data that may indicate quality problems
Trimmomatic was used to trim raw fastq files
Kallisto was used to mapped to GRCm38 cDNA sequences
DESeq2 was used to calculate differential expression of m6A levels for each gene
Assembly: mm10
Supplementary files format and content: xls format. Read counts for each gene

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Wild-type naïve (CD44-CD62L+) CD8+ T cells, effector  (CD44+CD62L-) CD8+ T cells and memory  (CD44+CD62L+) CD8+ T cells were sorted. Total RNAs were extracted from indicated cells and then submitted to SLIM-Seq protocol.
SLIM-Seq data were analyzed as previously described (Rong Yin et al., 2022)

tag: tissue

value: Spleen

tag: cell line

tag: cell type

value: naive CD8 (CD44-CD62L+CD8+)

tag: genotype

value: WT

tag: age

value: 6~8 weeks


title: HEK293CDK7as_TTseq_LabeledRNA_1-NM-PP1_30min_Rep1

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

country: Germany

institute: Max-Planck-Institute for Multidisciplinary Scienes

data_processing:
All sequencing data were demultiplexed with Illumina bcl2fastq demultiplexing software, provided the barcodes for each of the samples, and subsequently quality checked with FastQC (Babraham-Institute) (Andrews, 2010).
TT-seq: For all samples, paired-end 75 base reads were mapped using STAR (v 2.6.1b) (Dobin et al., 2013) to the GRCh38.p13 genome assembly merged with synthetic RNA spike-in sequences (Schwalb et al., 2016; Żylicz et al., 2019) with a maximum 2% mismatches [mapping parameters: --outFilterMismatchNoverLmax 0.02 --outFilterMultimapScoreRange 0 --alignIntronMax 500000]. SAMtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f2) were selected.  A spike-in (RNA) normalization strategy was used essentially as described (Schwalb et al., 2016). This spike-in normalization allows for calculating sequencing depth σ_j, cross-contamination rate ϵ_j, and antisense bias ratio c_j. Sequencing depth σ_j allows to observe global shifts. The read counts (kij) for spike-ins were calculated using HTSeq (Anders et al., 2015).
mNET-seq: For all samples, paired-end 45 base reads were trimmed for adapters (-a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACT), and low-quality bases (< Q20) were removed with Cutadapt (v 1.9.1) (Martin, 2011). The reads were then mapped to the GRCh38.p13 genome assembly merged with the yeast genome version SacCer3 using STAR (v 2.5.2b) (Dobin et al., 2013) with a maximum of 2% mismatches [mapping parameters: --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.02 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 500000 ]. Samtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, where alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f 2) were selected.   Read counts (kij) for yeast genes for each condition j (control or CDK7as inhibited) were calculated using HTSeq (Anders et al., 2015). The counts data was used to generate normalization factors with DESeq2 (Love et al., 2014) to normalize the mNET-seq data.
MNase-seq: For all samples, paired-end 45 base reads were trimmed for low-quality bases, random matches, and for a minimum length [trimming parameters: -q 20,20 -O 12 -m 25] with Cutadapt (v 1.9.1) (Martin, 2011). Processed reads were then mapped to the GRCh38.p13 genome assembly using STAR (v 2.6.1b) (Dobin et al., 2013) with maximum 2 percent mismatches [mapping parameters: --outFilterMismatchNoverLmax 0.02 --outFilterMultimapScoreRange 0 --alignIntronMax 1]. Samtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, where alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f 2) were selected.
MNase-ChIP-seq: For all samples, paired-end 43 base reads were mapped using Bowtie 2 (v 2.3.4.1) (Langmead and Salzberg, 2012) to the merged human hg38 (GRCh38.p13) and Drosophila (BDGP6.28) genome assembly [mapping parameters: --no-discordant --no-mixed --very-sensitive]. SAMtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. Duplicate fragments and fragments longer than 100 bp (70 bp for Pol II) were excluded from further analysis. MNase-ChIP-seq coverages were obtained from piled-up fragment midpoint counts for every genomic position. Pol II, Ser5P, and SPT5 coverages were normalized to the signal at untranscribed regions to allow for the detection of global changes. To this end, genome-wide coverage was calculated from all MNase-ChIP-seq fragment midpoints in consecutive 2 kbp bins throughout the non-transcribed human genome (i.e. excluding 32,789 transcribed units we annotated using GenoSTAN (Zacher et al., 2017) and everything annotated in GENCODE v31) and used to generate normalization factors with DESeq2 (Love et al., 2014). For all other factors, which exhibited a peak-like binding behavior, normalization factors were obtained from total human fragment counts. Bigwig files are for normalized (except Inputs), entire fragment coverages.
Assembly: GRCh38
Supplementary files format and content: bigwig files

organism: Homo sapiens

source_name: genome edited HEK293

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, 11960085) supplemented with 10% fetal bovine serum (Gibco, 10500–064) and 1 % GlutaMAX (Thermo Fisher Scientific, 35050087) in a humidified incubator at 37°C and 5% CO2. Cells were passaged every 2-3 days using 0.25% Trypsin-EDTA (Gibco, 25200056). Biological replicates were cultured separately. All cell lines were verified to be free of mycoplasma contamination with PlasmoTest Mycoplasma Detection Kit (InvivoGen).   Drosophila Schneider-2 (S2) cells, used for MNase-ChIP-seq spike-ins, were obtained from DSMZ (ATCC Cat# CRL-1963, RRID: CVCL_Z232) and cultured in Schneider's Drosophila-Medium (Gibco, 21720024) supplemented with 10% fetal bovine serum (Gibco, 10500–064) in a non-humidified incubator at 27°C, protected from light.  Yeast S. cerevisiae cells (BY4741 strain), used for mNET-seq spike-ins, were obtained from Euroscarf (ACC-Y00000) and cultured in yeast medium (YP + 2% glucose) at 30°C until OD595 of 0.8 was reached.

extract_protocol:
TT-seq: Total RNA was extracted using TRIzol reagent (Invitrogen, 15596026), 4sU-labeled RNA was extracted according to Gressel at al., protocols.io, 2019.
mNET-seq: mNET-seq was performed as previously described (Caizzi et al. 2021; Gressel et al. 2017; Nojima et al. 2016; Schlackow et al. 2017) with minor changes. 50 mio CDK7as cells were treated for 15 or 30 min with 7.5 μM of 1-NM-PP1 or DMSO (solvent control). After the treatment, chromatin isolation was performed as described in the protocol for cellular fractionation (Conrad et al. 2017) using 25 mio cells per reaction. All buffers were supplemented with 7.5 μM 1-NM-PP1 or respective amounts of DMSO, protease (Sigma-Aldrich, P8340), and phosphatase (Roche, 4906837001) inhibitors. After the fractionation, the chromatin pellet was digested in 100 μl MNase digest buffer (1x MNase buffer, 1x BSA, 100 mM NaCl, 50 units/μl MNase (NEB, M0247S)) at 37°C and 1,400 rpm for 2 min. The digestion was stopped by adding 11 μl of 250 mM EGTA, and samples were centrifuged at 13,000 g for 5 min at 4°C. Supernatants were pooled together for each sample and 8-fold diluted with IP buffer (50 mM Tris HCl pH 7.4, 150 mM NaCl, 0.05% NP-40, 0.3% empigen (Sigma-Aldrich, 30326)). 15 μg of anti-Pol II CTD antibody (Diagenode, C15200004) conjugated with 125 μl of Dynabeads M-280 Sheep Anti-Mouse IgG (Invitrogen, 11201D) were added to each sample and incubated on a rotating wheel at 4°C and 12 rpm for 1 h. After IP, beads were washed seven times with 1 ml of IP buffer and once with 300 μl of PNKT buffer (1x T4 PNK buffer (NEB, M0236L), 0.1% Tween-20). After washes, 5’ RNA ends were phosphorylated with T4 Polynucleotide Kinase (PNK) (3' phosphatase minus; NEB, M0236L) at 800 rpm for 10 min at 37°C. Next, beads were washed once with IP buffer, and 0.5 ml of TRIzol reagent (Invitrogen, 15596026) was added to the beads. 2.5 ng of S. cerevisiae spike-ins were added to each sample in TRIzol. RNA spike-ins for mNET-seq were obtained from S. cerevisiae cells as previously described (Caizzi et al. 2021). RNA was extracted from beads, followed by RNA precipitation with 100% ethanol and GlycoBlue coprecipitant (Invitrogen, AM9515) at -80°C overnight. RNA pellets were washed twice with 70% ethanol, air-dried, and dissolved in 7 M urea. In order to size select 25-110 nt RNA, samples were resolved on 6% polyacrylamide gel containing 7 M urea. RNA of corresponding sizes was extracted from the gel and precipitated with 100% ethanol and GlycoBlue coprecipitant.
MNase-seq: 5 mio CDK7as cells were treated for 15 min with 7.5 μM of 1-NM-PP1 or DMSO (solvent control) and centrifuged at 500 g for 3 min at 4°C. Cell pellets were resuspended in 50 μl of Buffer I (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 10 % sucrose, 0.5 mM CaCl2) and incubated at 37°C for 2 min. Next, we added 500 μl of Buffer II (50 mM Tris-HCl pH 7.5, 50 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 10 % sucrose, 2 mM CaCl2) supplemented with 3,000 U of MNase (NEB, M0247S) and incubated at 37°C for 9 min. MNase digestion was quenched with 11 μl of EGTA (500 mM). 550 μl of SDS Lysis Buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) was added, and samples were incubated on ice for 10 min. Samples were then treated with 0.1 μg/μl RNAse A (Thermo Scientific, EN0531) for 1.5 h at 37°C and 0.05 μg/μl Proteinase K (Life Technologies, AM2546) for 4 h at 65°C. DNA was extracted with an equal volume of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich, P2069), followed by DNA precipitation with an equal volume of 100% ethanol and 200 mM NaCl for 2 h at -20°C. DNA pellets were washed twice with 1 ml of 70% ethanol, air-dried, and dissolved in water.
MNase-ChIP-seq: MNase-ChIP-seq was performed as previously described (Skene et al. 2015) with the following changes. 40 mio CDK7as cells were treated for 30 min with 7.5 μM of 1-NM-PP1 or DMSO (solvent control), following 8 min crosslinking with 1% formaldehyde (16% formaldehyde (w/v), methanol-free, Thermo Fisher Scientific, 28908). The crosslinking was quenched for 5 min with 125 mM glycine, and cells were washed with 10 ml PBS at room temperature. 2 ml of ice-cold PBS was added to plates for cell scraping. Scraped cells were transferred to falcons, washed twice with 5 ml ice-cold PBS, and centrifuged at 200 g for 5 min at 4°C. All buffers were supplemented with protease (Sigma-Aldrich, P8340) and phosphatase (Roche, 4906837001) inhibitors. Cell pellets were lysed with 5 ml of Farnham Lysis buffer (5 mM Pipes pH 8, 85 mM KCl, 0.5% NP-40) for 10 min on ice. Nuclei were pelleted by centrifugation at 1,700 g for 5 min at 4°C and washed with ice-cold PBS. Nuclei pellets were resuspended in 200 μl of 1% SDS Lysis buffer (50 mM Tris HCl pH 8.0, 10 mM EDTA, 1% SDS) and incubated for 10 min at room temperature to permeabilize nuclei. The reaction was quenched with 1.8 ml of IP buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100) supplemented with 5 mM CaCl2 and incubated for 2 min at 37°C before the addition of 16,000U of MNase (NEB, M0247S) for 20 min at 37°C. MNase digestion was quenched with 40 μl of EDTA (500 mM) and 20 μl EGTA (500 mM). 1 ml of sample was transferred to AFA milliTubes (Covaris, 520135) and sonicated with a Covaris S220 Focused-ultrasonicator with the following parameters: 5% duty cycle, 140 W peak incident power, 200 cycles per burst, 600 sec processing time, 6°C bath temperature, continuous degassing mode, water level 8. Sonicated samples were centrifuged at 10,000 g for 15 min at 4°C, and supernatants were snap-frozen in liquid nitrogen and stored at −80°C before use. For each IP, 30 μg of sample chromatin and 200 ng of Drosophila S2 MNase-digested crosslinked chromatin were diluted in IP buffer to obtain a final concentration of 0.05% SDS and a final volume of 1.6 ml. Pre-clearing was carried out by adding 20 μl of Dynabeads Protein G (Thermo Fisher Scientific, 10009D) diluted in IP buffer, and incubating for 30 min at 4°C on the rotation wheel. Pre-cleared samples were incubated with 10 μg of Pol II (RPB1, Diagenode, C15200004), 10 μg of Ser5P (phospho-CTD Ser-5 of RPB1, Merck Millipore, 04-1572), 8 μl of Mediator (MED26, Cell Signaling, 14950), 6 μg of TFIIB (Santa Cruz, sc-271736), 5 μg of TFIIE (TFIIE-α, abcam, ab28177), 6 μg of NELF (NELF-E, Bethyl Laboratories, A301-913A) or 6 μg of SPT5 (Proteintech, 16511-1-AP) together with 1 μg of Spike-in (Active Motif, 61686) antibodies at 4°C overnight. The next day samples were centrifuged at 16,000g for 2 min at 4°C and inputs were taken for each sample. Samples were incubated for 2 h at 4°C with Dynabeads Protein G. Beads were washed once with Buffer 1 (20 mM Tris HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), four times with Buffer 2 (20 mM Tris HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with Buffer 3 (10 mM Tris HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% sodium-deoxycholate), and three times with TE buffer (10 mM Tris HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). After the last wash, 200 μl of elution buffer (0.1 M NaHCO3, 160 mM NaCl, 1% SDS) was added to the beads, and samples were de-crosslinked overnight at 65°C. Next, samples were diluted with 200 μl of PBS and treated with 0.02 μg/μl RNAse A (Thermo Scientific, EN0531) for 1.5 h at 37°C and 0.2 μg/μl Proteinase K (Life Technologies, AM2546) for 2 h at 45°C. DNA was extracted with an equal volume (400 μl) of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich, P2069), followed by DNA precipitation with 100% ethanol and 200 mM NaCl for 1 h at -80°C. DNA pellets were washed twice with 70% ethanol, air-dried, and dissolved in water.
TT-seq: Libraries were prepared from 100 ng of RNA with the strand-specific Ovation Universal RNA-Seq library kit (NuGEN, 0343-32).
mNET-seq: 8.4 ng of RNA for replicate 1 and 12.3 ng of RNA for replicate 2 were used for library preparation with TruSeq Small RNA Library Prep Kit (RS-200-0048) according to the manufacturer’s instructions.
MNase-seq: Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s instructions.
MNase-ChiP-seq: Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s instructions with adjusted for short fragments end repair, 5’ phosphorylation, and dA-tailing thermocycler program (30 min at 20°C, 1 h at 50°C; the heated lit set to 60°C). After amplification, libraries were double-sided (1.0 – 1.6x) size-selected with Agencourt AMPure XP beads (Beckman Coulter, A63881).

treatment_protocol: Cells were treated for 15, 30, or 60 min with 7.5 μM of 1-NM-PP1 (Sigma-Aldrich, St. Louis, MO USA) or an equal DMSO (solvent control; Sigma-Aldrich, St. Louis, MO USA) volume.

value: genome edited HEK293

value: Human embryonic kidney

value: analog-sensitive CDK7

tag: treatment

value: 30 min 1-NM-PP1, 10 min 4sU

tag: method

value: TT-seq


title: DLS439, SE, biol rep 1

city: Chapel Hill

first: Robert

middle: Houston

last: Dowen

state: NC

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

country: USA

institute: University of North Carolina at Chapel Hill

description:
Column names listed in line one for each txt file
FC_gene_read_counts_lin-29_study.txt
DESeq2_norm_gene_counts_lin-29_study.txt
DESeq2_DEGs_DLS439_v_N2_lin-29_study.txt
DESeq2_DEGs_DLS439_v_MT333_lin-29_study.txt
DESeq2_DEGs_DLS439_v_DLS440_lin-29_study.txt

data_processing:
The adapter-trimmed mRNA-Seq reads were mapped to the WS260 genome using the STAR aligner. The mapping was performed using a GTF obtained from Wormbase (c_elegans.PRJNA13758.WS260.canonical_geneset.gtf) with the parameter --outFilterIntronMotifs RemoveNoncanonical.
The gene-level read counts were calculated using the featureCounts algorithm of the subread package (Liao et al., Bioinformatics, 2014), using the following flags: -t exon -g gene_id -a c_elegans.PRJNA13758.WS260.canonical_geneset.gtf.
Differential expression was calculated relative to the N2 wild-type sample using the DESeq2 package using a 1% FDR cutoff (Love et al., 2014). Comparisons between individual mutants were also performed.
Assembly: WS260
Supplementary files format and content: FC_gene_read_counts_study_name.txt: A tab-delimited text file for each sub-study that includes gene level unnormalized read counts for each sample in matrix format generated using the featureCounts aligorithm.
Supplementary files format and content: DESeq2_norm_gene_counts_study_name.txt: A tab-delimited text file that for each sub-study includes gene level normalized read counts for each sample in matrix format generated using the DESeq2 aligorithm.
Supplementary files format and content: DESeq2_DEGs_sample1_v_sample2_study_name.txt: A tab-delimited text file that includes a list of differentially expressed genes, the log2 FC values, and the p values called by DESeq2 at a 1% FDR threshold for sample1 relative to sample2 for each sub-study.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole animals

growth_protocol: Wild-type and mutant C. elegans animals were synchronized at the L1 stage by egg prep and grown for ~72 hours at 20°C on 10cm NGM Agarose plates (5000 animals/plate) seeded with E. coli OP50 until they reached day 1 of adulthood. For RNAi experiments, synchronized animals were reared on E. coli HT115 bacteria expressing dsRNAs for ~72 hours at 20°C on 10cm NGM Agarose plates containing 5 mM isopropyl-β-D-thiogalactoside (IPTG) and 100 μg/ml ampicillin.

extract_protocol:
Animals were harvested in M9 buffer, washed three times, and flash frozen in liquid Nitrogen. Total RNA was isolated using Trizol.
mRNA-Seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation v2 kit. For the tra-1 and tir-1 studies, mRNA-Seq libraries were prepared by Novogene Inc.

tag: strain

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50

tag: developmental stage

value: Day 1 adults

value: Whole animals

tag: Sex

value: hermaphrodite


title: miCLIP-seq-IP-KO2

data_processing:
m6A-miCLIP-SMARTer-Seq data were analyzed as previously described (Michael J Moore et al., 2014)
Adapters were trimmed off for all raw reads and R1 beads were combined with R2 reads that transformed to reverse complementary sequences.
PolyA tails and duplicated reads were removed by Cutadapt and fastq2collapse.pl respectively; besides, the barcodes of reads were trimmed.
Reads were mapped to the reference genome (mm10) using BWA.
The mutation information was tracked and PCR duplicates were removed separately by parseA-lignment.pl and tag2collapse.pl based on BWA’s results. Further, the mutation site and transition number (m) were calculated through CIMS.pl. Mutation sites were kept with parameters, k/m ≥ 0.01 and k/m ≤ 0.5. The remaining sites within the RRACH motif sequence were regarded as m6A
Assembly: mm10
Supplementary files format and content: bw format

extract_protocol:
Total RNAs were isolated from effector CD8+ T cells of Mettl3ΔGzmb and control mice , and subjected to m6A-miCLIP-SMARTer-seq protocol.
The procedures of m6A-miCLIP-SMARTer-seq were according to the previously reported methods (Yao et al., 2021).

value: effector CD8 (CD44+CD62L-EYFP+CD8+)

tag: rip antibody


title: DLS487, SE, biol rep 2

description:
Column names listed in line one for each txt file
FC_gene_read_counts_Hh_study.txt
DESeq2_norm_gene_counts_Hh_study.txt
DESeq2_DEGs_DLS487_v_N2_Hh_study.txt
DESeq2_DEGs_DLS487_v_MT333_Hh_study.txt
DESeq2_DEGs_DLS487_v_DLS490_Hh_study.txt


title: HEK293CDK7as_TTseq_LabeledRNA_1-NM-PP1_15min_Rep2

value: 15 min 1-NM-PP1, 10 min 4sU


title: P60Deaf1


title: input-memory-rep2

value: Memory CD8 (CD44+CD62L+CD8+)


title: miCLIP-seq-IP-WT2

value: Control


title: HEK293CDK7as_TTseq_LabeledRNA_1-NM-PP1_30min_Rep2


title: input-effector-rep3

value: Spleen

value: effector CD8 (CD44+CD62L-CD8+)


title: P60Hearing2

value: hearing


title: HEK293CDK7as_TTseq_LabeledRNA_1-NM-PP1_60min_Rep1

value: 60 min 1-NM-PP1, 10 min 4sU


title: HEK293CDK7as_TTseq_LabeledRNA_DMSO_60min_Rep2

value: genome edited HEK293

value: 60 min DMSO, 10 min 4sU


title: HEK293CDK7as_TTseq_TotalRNA_DMSO_15min_Rep1

value: Human embryonic kidney

value: analog-sensitive CDK7

value: 15 min DMSO, 10 min 4sU


title: P60Hearing3


title: P60Hearing1


title: input-effector-rep2

value: WT

value: 6~8 weeks


title: DLS439, SE, biol rep 2

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50

value: Day 1 adults

value: Whole animals


title: P32Hearing2


title: miCLIP-seq-IP-WT1

value: effector CD8 (CD44+CD62L-EYFP+CD8+)


title: miCLIP-seq-IP-KO1


title: P60Deaf3

value: deaf


title: P32Hearing1


title: MT333, SE, biol rep 1

description:
Column names listed in line one for each txt file
FC_gene_read_counts_lin-29_study.txt
DESeq2_norm_gene_counts_lin-29_study.txt
DESeq2_DEGs_MT333_v_N2_lin-29_study.txt
DESeq2_DEGs_DLS439_v_MT333_lin-29_study.txt
DESeq2_DEGs_DLS440_v_MT333_lin-29_study.txt
FC_gene_read_counts_Hh_study.txt
DESeq2_norm_gene_counts_Hh_study.txt
DESeq2_DEGs_MT333_v_N2_Hh_study.txt
DESeq2_DEGs_DLS487_v_MT333_Hh_study.txt
DESeq2_DEGs_DLS490_v_MT333_Hh_study.txt

value: hermaphrodite


title: P32Hearing3


title: MT333, SE, biol rep 3


title: P32Deaf3


title: N2 wild-type, SE, biol rep 2

description:
Column names listed in line one for each txt file
FC_gene_read_counts_lin-29_study.txt
DESeq2_norm_gene_counts_lin-29_study.txt
FC_gene_read_counts_Hh_study.txt
DESeq2_norm_gene_counts_Hh_study.txt

value: wild-type


title: miCLIP-seq-Input-KO1

value: Spleen

value: none (input)


title: MT333, SE, biol rep 2


title: HEK293CDK7as_TTseq_LabeledRNA_1-NM-PP1_15min_Rep1

value: 15 min 1-NM-PP1, 10 min 4sU

value: TT-seq


title: P32Deaf2


title: N2 wild-type, SE, biol rep 3


title: miCLIP-seq-Input-WT2

value: Control


title: HEK293CDK7as_TTseq_LabeledRNA_DMSO_60min_Rep1

value: genome edited HEK293

value: Human embryonic kidney

value: 60 min DMSO, 10 min 4sU


title: HEK293CDK7as_TTseq_LabeledRNA_DMSO_30min_Rep1

value: analog-sensitive CDK7

value: 30 min DMSO, 10 min 4sU


title: N2 wild-type, SE, biol rep 1

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50


title: P32Deaf1


title: miCLIP-seq-Input-WT1

value: 6~8 weeks


title: HEK293CDK7as_TTseq_LabeledRNA_DMSO_15min_Rep2

value: 15 min DMSO, 10 min 4sU


title: HEK293CDK7as_TTseq_LabeledRNA_DMSO_15min_Rep1


title: oligodendrocyte progenitor anti-miR145 replicate 2

status: Public on May 31 2024

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Align to Rnor6.0 using salmon v0.12.0
Fold change analysis using Deseq2
Assembly: Rnor6
Supplementary files format and content: Read counts table containing salmon read counts
Supplementary files format and content: Fold change analysis  table using deseq2

source_name: oligodendrocyte progenitor

growth_protocol: Primary rat OPCs were isolated and cultured as per Chen et al. First, MGCs were generated by dissecting cerebral cortices from P1-P3 Sprague-Dawley rat pups. Cortices were digested for 15 min at 37°C in 1% trypsin (Sigma-Aldrich) with 10.7 µ/mL Dnase I (Sigma-Aldrich) in Hank’s Balanced Salt Solution (HBSS). Digested tissue was triturated in MGC medium made up of Dulbecco’s Modified Eagle Medium (DMEM; Wisent) with 20% FBS, 2 mM L-glutamine (Invitrogen), 50 units/mL penicillin and 50 µg/mL streptomycin (Thermo-Fisher). Triturated tissue suspensions were allowed to settle on ice for 10 min followed by filtration through a 70 µm strainer and were then incubated in MGC medium on poly-L-lysine (PLL)-coated plates at 37°C and 5% CO2 for 7-10 days with 75% MGC medium changes every 2-3 days. To obtain enriched OPC cultures, MGCs were shaken for 18-20 h at 37°C and 5% CO2. Medium containing suspended OPCs was allowed to settle on coated culture plates (Corning) for 30 min at 37°C and 5% CO2 to remove contaminating cells by differential adhesion. OPCs were pelleted from suspension by centrifugation at 100 x g for 10 min and were then resuspended in appropriately supplemented SATO medium. SATO medium comprised 5 ug/mL insulin, 1 µg/mL bovine serum albumin (BSA), 0.05 µg/mL apo-transferrin, 0.03 µg/mL sodium selenite, 0.25 µg/mL D-biotin and 0.01 µg/mL hydrocortisone (all reagents from Sigma-Aldrich) in DMEM (Wisent) with 2 mM L-glutamine (Invitrogen) and 50 units/mL penicillin and 50 µg/mL streptomycin (Thermo-Fisher). OPCs were plated in SATO medium supplemented with 0.01 µg/mL basic fibroblast growth factor (FGF2; Millipore) and 0.01 µg/mL platelet-derived growth factor AA (PDGFAA; Millipore), and 50% media changes were done every 2 days. OPCs being differentiated into Ols were plated in SATO medium supplemented with 15 nM triiodothyronine (T3; Sigma-Aldrich), 0.01 µg/mL ciliary neurotrophic factor (CNTF; Peprotech) and 5 ng/mL N-acetyl L-cysteine (Sigma-Aldrich). To transition OPCs to Ols after plating, a 50% media change was done using 2X differentiation medium.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol. Primary Sprague-Dawley rat OPCs/OLs grown in a 6-well plate were lysed using 350 μl RLT lysis buffer per sample. Lysis buffer was added directly to washed cells, and lysate was then placed in a Qiashredder column (Qiagen) and spun at maximal speed for 2 min. Lysate was then mixed 1:1 with 70% ethanol in RNase-free H2O, transferred to the RNeasy spin column, and centrifuged at maximal speed for 25 s. Eluate was discarded, and the column was washed with 700 μl RW1 buffer by spinning at maximal speed for 25 s. Eluate was again discarded, and the column was washed with 500 μl RPE buffer at maximal speed for 25 s. The columns transferred to a clean collection tube and washed a second time with 500 μl RPE for 2 min. Columns were then placed in RNase-free microfuge tubes, and RNA was eluted in 20-30 μl RNase-free H2O by spinning at maximal speed for 1 min. Reverse transcription of mature miR-145-5p and snU6
Quality control and sequencing were performed  by StemCore Laboratories, Ottawa Hospital Research Institute. Samples were examined with  the Qubit HS RNA Assay (ThermoFisher) and Fragment Analyzer HS NGS assay (Agilent) to  determine sample concentration and RNA quality, respectively. Sequencing libraries were  constructed using 500 ng RNA from each sample. Library construction was performed using the TruSeq Stranded mRNA Library Prep (Illumina) and sequenced with a NextSeq 500 High Output 75 cycle kit (Illumina).

treatment_protocol: MiR-145-5p mimic, miR-219 mimic, scrambled miRNA mimic, miR-145-5p inhibitor, and scrambled miRNA inhibitor were all used at a concentration of 30 nM. MiR-145-5p mimic sequence is identical to mature miR-145-5p based on Sanger miRbase (miRbase.org).  Cells were transfected using INTERFERin siRNA transfection reagent (Polyplus) according to the manufacturer’s protocol. In brief, 30 pmol miRNA mimic or siRNA were prepared in 50 µl Opti-Mem serum-free media (Thermo-Fisher) and vortexed. To this, 1.5 µl INTERFERin was added, the mix was again vortexed, and lipid:RNA complexes were allowed to form for 10 min at room temperature. This transfection mix was added at a ratio of 50 ul for every 1 mL of cell media. For OPCs, transfected cells were assayed 24 h post transfection; for OLs, transfected cells were assayed 5 days post transfection.

value: Sprague-Dawley

value: oligodendrocyte progenitor


title: oligodendrocyte control replicate 1

source_name: oligodendrocyte

value: oligodendrocyte

value: control


title: oligodendrocyte miR-145 overexpression replicate 2

value: miR-145, miR-219 overexpression


title: oligodendrocyte miR-145, miR-219 overexpression replicate 2


title: oligodendrocyte control replicate 2


title: oligodendrocyte miR-145, miR-219 overexpression replicate 1


title: oligodendrocyte miR-145 overexpression replicate 1


title: oligodendrocyte progenitor anti-miR145 replicate 1


title: B16_gY2_2

city: Los Angeles

first: Sai

last: Xiao

state: California

address: 1500 E. Duarte Road

institute: City of Hope

description:
COHP_46324
poly-RNA-seq

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (v0.23.2) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (v2.2.1).
The gene expression levels were quantified using featureCounts (v2.0.6) based on the aligned BAM files generated by HISAT2.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes raw count values for each sample.

growth_protocol: WT and Ythdf2-KO B16-OVA tumor cells were grown in DMEM (Gibco) supplemented with 10% FBS (Gibco), 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA was isolated by TRIzol reagent. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). mRNA samples were fragmented into ~100-nucleotide-long fragments with RNA fragmentation reagents (Invitrogen).
RNA was enriched through RNA Clean & Concentration- 5 (Zymo Research) for library generation with a KAPA RNA HyperPrep Kit (Roche). Sequencing was performed at the City of Hope Genomics Facility on an Illumina NovaSeq 6000 machine with 100-bp paired-end reads (PE100).

value: tumor cells


title: oligodendrocyte progenitor control 1


title: HEK293CDK7as_TTseq_LabeledRNA_DMSO_30min_Rep2


title: B16_gY2_3

description:
COHP_46325
poly-RNA-seq


title: oligodendrocyte progenitor control 2


title: miCLIP-seq-Input-KO2

value: Spleen

value: effector CD8 (CD44+CD62L-EYFP+CD8+)

value: none (input)


title: B16_gNC_3

description:
COHP_46322
poly-RNA-seq

value: WT


title: B16_gNC_2

description:
COHP_46321
poly-RNA-seq


title: Female, Donor3, Day1

status: Public on May 30 2024

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

institute: University of Alberta

data_processing:
Partek Flow: Trim bases Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25)
Partek Flow: Alignment (STAR 2.7.3a) Default settings from Partek Flow
Partek Flow: Quantify to annotation model (Partek E/M) Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01
Partek Flow: Filter features Exclude features where maximum ≤ 50.0. Processed data file included with filtered raw gene counts
Partek Flow: Normalize counts Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis
Partek Flow: ANOVA for DEGs Factors: Donor(Random) + Timepoint*Sex. Shrinkage of error term variance: Limma-trend.
genome build/assembly: hg38
processed data files format and content: Normalized count

source_name: Primary Cell

growth_protocol: MFCs were isolated from fresh meniscus specimens obtained from 3 male subjects (22, 27, and 32 years old) and 3 female subjects (24, 32, and 38 years old) who had undergone partial meniscectomy. The MFCs were isolated by 22-hour digestion at 37°C using type II collagenase (0.15% w/v; 300 U/mg solid; Worthington, NJ, USA) in high glucose DMEM (4.5 mg/mL D-Glucose) supplemented with 5% v/v inactivated FBS (Sigma-Aldrich Co., MO, USA). Isolated primary cells were seeded at a density of 1x104 cells/cm2 on the ECM-coated plate and cultured in a standard DMEM-complete medium containing high glucose DMEM supplemented with 10% v/v FBS (Sigma-Aldrich), 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, and 10mM HEPES (Sigma-Aldrich) under normal oxygen tension (~21% O2) at 37°C for 48 hours.

extract_protocol:
The constructs collected at each time point were immediately preserved in Trizol reagent (Life Technologies, United States) and stored at -80°C until RNA extraction. The PuroSPIN Total RNA Purification KIT (Luna Nanotech, Canada) was used for RNA extraction and purification according to the manufacturer's instructions.
Raw input reads were trimmed and aligned to the reference human genome hg38 using the STAR 2.7.3a aligner. Genes with maximum read counts below 50 were filtered out, and normalization was performed using the Add 1.0, TMM, and Log 2.0 parameters. Statistical analysis was conducted using ANOVA with biological sex and time points as factors.

treatment_protocol: After 48 hours of pre-culture, the engineered tissue constructs were randomly allocated to static control and SMG group. The static control group was cultured in a tissue culture well plate while the SMG group was cultured using a commercially available bioreactor (RCCS-4; Synthecon Inc., TX, USA). The rotation speed of the bioreactor was adjusted to maintain the constructs in a free-falling position, with a speed of 30 rpm applied from day 1 to 2, and 34 rpm from day 3 to 7. Samples were collected at day 0 (common control), and from both groups at day 1, day 3, and day 7 (n=2 for each time point).

tag: individual

value: Female, Donor3

value: Primary Cell

value: Meniscus Fibrochondrocytes

value: Simulated Microgravity

tag: time

value: 1 day


title: Female, Donor2, Day7

value: Female, Donor2

value: 7 day


title: Female, Donor3, Day3

value: 3 day


title: B16_gNC_1

description:
COHP_46320
poly-RNA-seq


title: Female, Donor2, Day3


title: Female, Donor2, Day1


title: Male, Donor3, Day7

value: Male, Donor3


title: Female, Donor3, Day0

value: Static Control

value: 0 day


title: Male, Donor3, Day3


title: brain,total,nanopore,rep3

city: Ipswich

first: Zhiyi

last: Sun

state: MASSACHUSETTS

address: 240 County Road

department: Research

institute: New England Biolabs

data_processing:
PacBio consensus reads were generated using the SMRT tools (version 10.2.0.133434). Raw nanopore data were basecalled in high accuracy mode with Dorado 7.0.9 and filtered by average quality (≥ 7).
Sequencing reads in FASTQ format from either PacBio or Nanopore were first mapped to the rDNA reference sequences using minimap2 and the unmapped reads were kept for downstream circRNA analysis.
Then circular consensus sequences and candidate circRNAs were identified using the CIRI-long bioinformatics pipeline. We applied an additional filter to remove consensus sequences that were called from any read that contains fewer than 2 copies of repeat sequences. Candidate circRNA sequences were identified based on the GRCh38 reference genome sequence and annotation. Then all candidate circRNA sequences from the subsets were aggregated together using the CIRI-long collapse program to determine BSJ sites and calculate the relative isoform usage index of each BSJ.
Finally, for each BSJ, the read counts of its isoforms were calculated from the isoform usage index (*collapse.isoforms file) and the total read counts of that BSJ as isoform expression = isoform usage index * BSJ read counts.
Assembly: GRCh38/hg38
Supplementary files format and content: Tabular data file with circRNA isoform counts
Library strategy: Induro-RT mediated circRNA-sequencing (IMCR-seq)

source_name: brain

extract_protocol:
NEB Monarch Total RNA Miniprep Kit was used for home made HEK293 cell RNA, guanidine thiocyanate tecnniques were reported to be used for commercially obtained RNA and Quick-cfRNA Serum & Plasma Kit from Zymo Research was used for RNA extraction from plasma
Total RNA or rRNA depleted, RNaseR treated RNA were reverse transcribed with a group II intron RT then the cDNAs were sized selected with SPRI beads. Second strand synthesis and amplification were done with Phi29 DNA polymerase. T7 endonuclease I was used to digest the branched DNA into double stranded DNA and ONT and PacBio library preparation kits for dsDNA were used to make libraries for sequencing.

value: brain


title: B16_gY2_1

description:
COHP_46323
poly-RNA-seq

value: tumor cells


title: Male, Donor3, Day0


title: Female, Donor1, Day1

value: Female, Donor1


title: Male, Donor2, Day7

value: Male, Donor2


title: Male, Donor2, Day1


title: Female, Donor1, Day7


title: Male, Donor2, Day3


title: Male, Donor1, Day3

value: Male, Donor1


title: Male, Donor1, Day7

value: WT


title: Female, Donor1, Day3


title: Male, Donor1, Day1


title: S30, TCR/CD3+HVEM, 48h, rep3

status: Public on May 27 2024

city: Dublin

first: Muhammad Zainul

last: Arifin

state: Co. Dublin

address: University College Dublin

department: School of Medicine

country: Ireland

institute: Systems Biology Ireland

data_processing:
Raw sequence reads were quality checked using fastqc and low-quality reads were trimmed using BBDuk.
Alignment to the Human-Mouse reference genomes was performed using STAR v2.4.2a.
Counting of reads aligned over exonic features for the purpose of gene expression quantification was performed using the htseq-count script in the HTSeq package v0.6.1 in the ‘Union’ overlap resolution mode.
The Gene Transfer Format (GTF) file used for counting was a merged Homo sapiens and Mus musculus GTF file, both obtained from GENCODE (https://www.gencodegenes.org/pages/faq.html), and modified to ensure chromosomal compatibility with the Human-Mouse reference genome.
Counts were assembled using featureCounts.
Assembly: hg38 and mm39
Supplementary files format and content: Tab-delimited text file containing raw read counts of samples

source_name: Lymphoid

growth_protocol: Jurkat and Bw cells are suspension cells and they are grown at 37° C in a humidified atmosphere with 5% CO2 in RPMI supplemented with 10% fetal bovine serum, 100 μg/mL streptomycin, 100 U/mL penicillin.

extract_protocol:
RNA was isolated using RNeasy (Qiagen) according to the manfuacturers' instructions.
Purification of mRNA from total RNA was performed using poly-T oligo-attached magnetic beads. Following fragmentation, first strand cDNA was synthesized using random hexamer primers and subsequently subjected to second-strand cDNA synthesis. To prepare the sequencing library, end repair, A-tailing, adapter ligation, size selection, amplification, and purification were performed. The library was assessed using Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
The quantified libraries were pooled and sequenced on an Illumina platform NovaSeq 6000 S4, based on the effective library concentration and data amount. The libraries were sequenced with paired-end 2 ×150 bp runs with a depth of 50 million paired reads per sample.

treatment_protocol: Jurkat cells were control stimulated or stimulated with PDL1 or HVEM for 4h, 20h and 48h.

value: Lymphoid

value: T-Cell Jurkat

value: T-cell

value: TCR/CD3+BTLA stimulated


title: Female, Donor2, Day0

value: Primary Cell

value: Meniscus Fibrochondrocytes


title: Male, Donor1, Day0


title: S27, TCR/CD3+PD1, 48h, rep3

value: TCR/CD3+PD1 stimulated


title: S26, TCR/CD3+PD1, 48h, rep2


title: Female, Donor3, Day7

value: Female, Donor3

value: Simulated Microgravity

value: 7 day


title: S24, TCR/CD3, 48h, rep3

value: TCR/CD3 stimulated


title: S25, TCR/CD3+PD1, 48h, rep1


title: S22, TCR/CD3, 48h, rep1


title: S20, TCR/CD3+HVEM, 20h, rep2


title: Male, Donor3, Day1

value: Male, Donor3

value: 1 day


title: S19, TCR/CD3+HVEM, 20h, rep1


title: S23, TCR/CD3, 48h, rep2


title: Female, Donor1, Day0

value: Female, Donor1

value: Static Control

value: 0 day


title: S18, TCR/CD3+PDL1, 20h, rep3


title: S16, TCR/CD3+PDL1, 20h, rep1


title: S11, TCR/CD3+HVEM, 4h, rep2


title: S17, TCR/CD3+PDL1, 20h, rep2


title: S12, TCR/CD3+HVEM, 4h, rep3


title: S29, TCR/CD3+HVEM, 48h, rep2


title: S14, TCR/CD3, 20h, rep2


title: S9, TCR/CD3+PDL1, 4h, rep3


title: S10, TCR/CD3+HVEM, 4h, rep1


title: S8, TCR/CD3+PDL1, 4h, rep2


title: S28, TCR/CD3+HVEM, 48h, rep1


title: S6, TCR/CD3, 4h, rep3


title: S3, unstimulated, 0h, rep3

value: Unstimulated


title: S4, TCR/CD3, 4h, rep1

value: Lymphoid


title: S2, unstimulated, 0h, rep2

value: T-Cell Jurkat


title: S21, TCR/CD3+HVEM, 20h, rep3

value: T-cell


title: S5, TCR/CD3, 4h, rep2


title: S1, unstimulated, 0h, rep1


title: d21, bleo, 4b

status: Public on May 21 2024

city: Mölndal

first: Benjamin

last: Keith

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description: Day 21

library_source: transcriptomic single cell

data_processing:
FastQ files were processed using the Space Ranger 1.2.2 (10x Genomics) pipeline.
Manual alignment to the fiducial frame and identification of tissue-covered spots was performed using Loupe Browser (v.6, 10X Genomics)
Data filtering, processing, and analyses were performed in R (v.4.0.5) using the STUtility (v.1.1.1), Seurat (v.4.1.1), and semla (v. 1.1.6, under R v. 4.2.3 and Seurat v. 4.3.0.1) packages.
Assembly: mm10
Supplementary files format and content: aligned fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors json.json.gz: scalefactors in json format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format

source_name: Lung

extract_protocol:
Agarose-inflated mouse lungs were cryosectioned at 10 µm.
Sequencing libraries were prepared using Visium Spatial Gene Expression Slide & Reagent Kit (Cat. No. 1000184; 10X Genomics) with Dual Index Kit TT Set A (Cat. No. 1000215; 10X Genomics) according to the Visium Spatial Gene Expression User Guide (Rev C).
Spatial Transcriptomics

treatment_protocol: The left lung lobe was inflated with 0.4-0.5 mL 37°C low-melt agarose via the trachea.

value: Lung

value: Bleomycin


title: d21, bleo, 5b

description: Day 21


title: d21, bleo, 4a

description: Day 7


title: d21, bleo, 6b

description: Day 21


title: d21, bleo, 5a

description: Day 7


title: d21, bleo, 3

description: Day 7


title: S15, TCR/CD3, 20h, rep3


title: d21, bleo, 6a

description: Day 7


title: S7, TCR/CD3+PDL1, 4h, rep1


title: d21, bleo, 1

description: Day 7


title: d21, bleo, 2

description: Day 7


title: d21, ctrl, 3

description: Day 21

value: Control


title: S13, TCR/CD3, 20h, rep1


title: d21, ctrl, 2

description: Day 7


title: d21, ctrl, 1

description: Day 7


title: d7, bleo, 4a

description: Day 21


title: d7, bleo, 5a

description: Day 21


title: d7, bleo, 3

description: Day 7


title: d7, bleo, 4b

description: Day 21


title: d7, bleo, 5b

description: Day 21


title: d7, bleo, 6b

description: Day 21


title: B-cells_5_GEX

status: Public on May 14 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
GA49698
poly A RNA

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-7.1.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and B cell receptor repertoire profiling.
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 and refdata-gex-GRCh38-2020-A
Supplementary files format and content: features.tsv.gz : tab-delimited text file including the information of features (gene and ADT/HTO)
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the BCR clonotype information
Supplementary files format and content: matrix_B-cells_*.csv : comma-delimited text files including UMI counts for each feature (gene or ADT/HTO) and cell (barcode) conbination

source_name: PBMC

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Antibody-derived tags, hashtag oligonucleotides or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: PBMC

value: CD19+IgD- B-cells


title: d7, ctrl, 1

description: Day 7


title: d7, ctrl, 3

description: Day 21


title: d7, bleo, 1

description: Day 7


title: d7, bleo, 2

description: Day 7


title: B-cells_4_BCR

description:
GA49703
BCR V(D)J segments


title: B-cells_4_CITE

description:
GA49709
Antibody-derived tags (ADT) and Hashtag oligonucleotide (HTO)

library_source: other

molecule: protein


title: Male, Donor2, Day0

value: Male, Donor2

value: Primary Cell

value: Meniscus Fibrochondrocytes

value: WT


title: B-cells_3_CITE

description:
GA49707
Antibody-derived tags (ADT) and Hashtag oligonucleotide (HTO)


title: B-cells_3_GEX

description:
GA49695
poly A RNA


title: B-cells_3_BCR

description:
GA49701
BCR V(D)J segments


title: EHU-W1

status: Public on May 17 2024

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in 28+50-base paired-end mode.
Raw sequencing data for the sample was converted to a matrix of expression using Space Ranger version: 2.0.0 (10X Genomics).
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: prostatic cancer

extract_protocol:
The gene expressions of human prostatic cancer slide were detected by Visium CytAssist and 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared by using 10x Visium spatial protocols and standard MGI protocols.

value: prostatic cancer

tag: disease state

value: Adenocarcinoma pT2bN0M0, Gleason Score 4+5 with IDCP

value: Adenocarcinoma

value: male

value: robot-assisted laparoscopic radical prostatectomy


title: B-cells_5_BCR

description:
GA49704
BCR V(D)J segments


title: B-cells_2_GEX

description:
GA49694
poly A RNA


title: B-cells_1_CITE

description:
GA49705
Antibody-derived tags (ADT) and Hashtag oligonucleotide (HTO)


title: B-cells_1_GEX

description:
GA49693
poly A RNA


title: B-cells_2_BCR

description:
GA49700
BCR V(D)J segments


title: d7, bleo, 6a

description: Day 21


title: B-cells_1_BCR

description:
GA49699
BCR V(D)J segments


title: B-cells_2_CITE

description:
GA49706
Antibody-derived tags (ADT) and Hashtag oligonucleotide (HTO)


title: 24hr 1μM pyrvinium pamoate 3

status: Public on May 10 2024

city: Pittsburgh

first: Bokai

last: Zhu

state: PA

address: Bridgeside Point 1, 5th Floor, 100 Technology Drive

institute: Aging Institute of UPMC/University of Pittsburgh School of Medicine

data_processing:
Son - trimmomatic for quality control (QC) / Drugs - Trim Galore for QC
Son - HISAT2 for mapping / Drugs - Salmon for mapping
Son - Cufflinks for FPKM normalization / Drugs - Salmon for TPM normalization
Assembly: mm10
Supplementary files format and content: Son - FPKMs for all conditions in one XLSX file / Drugs - TPMs for all drugs in one XLSX file

source_name: MEF

extract_protocol:
Total RNA was extracted from cells using a PureLink™ RNA Mini Kit from ThermoFisher Scientific (catalog number 12183025)
Truseq Stranded mRNA (poly-A pulldown) - completed by the UPMC Genome Center

value: MEF

value: embryonic fibroblast

value: 1uM pyrvinium pamoate


title: 24hr 3μM proflavine hemisulfate 2

value: 3uM proflavine hemisulfate


title: 24hr 1μM pyrvinium pamoate 1


title: 24hr 1μM pyrvinium pamoate 2


title: 24hr 3μM proflavine hemisulfate 1


title: 24hr 3μM proflavine hemisulfate 3


title: B-cells_5_CITE

description:
GA49710
Antibody-derived tags (ADT) and Hashtag oligonucleotide (HTO)


title: B-cells_4_GEX

description:
GA49697
poly A RNA


title: 24hr 1μM ponatinib 2

value: 1uM ponatinib


title: d7, ctrl, 2

description: Day 21

value: Lung

value: Control


title: 24hr 1μM ponatinib 1


title: 24hr 3μM nintedanib 2

value: 3uM nintedanib


title: 24hr 3μM nintedanib 1


title: Son sgRNA (CRISPRa) tunicamycin 2

value: Son sgRNA (CRISPRa) / Son overexpression

value: tunicamycin


title: 24hr DMSO 3

value: DMSO


title: 24hr DMSO 2

value: WT


title: 24hr 1μM ponatinib 3


title: 24hr 3μM nintedanib 3


title: 24hr DMSO 1


title: Son sgRNA (CRISPRa) tunicamycin 3


title: Son sgRNA (CRISPRa) DMSO 3


title: Son sgRNA (CRISPRa) tunicamycin 1


title: Control sgRNA (CRISPRa) tunicamycin 3

value: control sgRNA (CRISPRa)


title: Control sgRNA (CRISPRa) tunicamycin 2


title: Control sgRNA (CRISPRa) tunicamycin 1


title: Son sgRNA (CRISPRa) DMSO 1


title: Control sgRNA (CRISPRa) DMSO 3


title: Control sgRNA (CRISPRa) DMSO 2


title: Son siRNA tunicamycin 4

value: Son siRNA / Son knockdown


title: Control sgRNA (CRISPRa) DMSO 1


title: Son siRNA tunicamycin 1


title: Son siRNA tunicamycin 2


title: Son siRNA DMSO 4


title: Son siRNA DMSO 1


title: Son siRNA DMSO 2


title: Son siRNA DMSO 3


title: Son sgRNA (CRISPRa) DMSO 2


title: Control siRNA tunicamycin 4

value: control siRNA


title: Control siRNA tunicamycin 2


title: Control siRNA tunicamycin 3


title: Control siRNA DMSO 3


title: Control siRNA DMSO 4


title: Control siRNA DMSO 1


title: Control siRNA DMSO 2


title: RNA-Seq of mus musculus: adult female brain,20μm

status: Public on May 01 2024

city: Changchun

first: Zhengyang

last: Jin

state: Jilin

address: No. 1163 Xinmin Street

institute: Jilin University

description: Well-ST-seq

data_processing:
*library strategy: Well-ST-seq
The filtered data was mapped to the mouse genome (mm10 mouse) using SpaceRanger V1.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Tissue was permeabilized with tissue permeabilizing enzyme for 12 minutes
RNA libraries for RNA-seq were prepared using Kapa HIFI HotStart ReadyMix PCR Kit following manufacturer's protocols.

value: Brain

value: Female

value: 12 weeks

value: Cryosection


title: Primary adipocytes, Mizoribine 2

status: Public on Apr 29 2024

city: Nashville

first: Elma

last: Zaganjor

state: TN

address: 2222 Pierce Ave

institute: Vanderbilt University

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023).
Trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter
Assembly: An alignment reference was generated from the mm10 mouse genome and refdata-gex-mm10-2020-A 10X gene annotations
Supplementary files format and content: HTSeq-formatted count files, one per sample

source_name: Primary adipocytes

extract_protocol:
Total RNA was isolated using TRIzol reagent as per the manufacturer's instructions.
RNAseq libraries were prepared using 200 ng of total RNA and the NEBNext rRNA Depletion Kit(NEB, Cat # E6310X) as per the manufacturer’s instructions.

value: Primary adipocytes

value: Mizoribine


title: RNA-Seq of mus musculus: adult female brain,10μm

description: Well-ST-seq


title: Primary adipocytes, Mizoribine 1


title: Primary adipocytes, Differentiated 2

value: Differentiated


title: Primary adipocytes, Mizoribine 3


title: Primary adipocytes, Differentiated 1


title: Primary adipocytes, Differentiated 3


title: Primary adipocytes, Undifferentiated 1

value: Undifferentiated


title: Primary adipocytes, Undifferentiated 2


title: WM266.4 cells, RIPK4.si_2 [R2]

status: Public on Apr 27 2024

city: Krakow

first: Ewelina

last: Madej

address: Gronostajowa 7

department: Department of Biophysics and Cancer Biology

country: Poland

institute: Jagiellonian University

data_processing:
Sequence reads were trimmed for adaptor/low quality sequence using the Cutadapt package. Filtering was performed using the quality parameter q 25 and the minimum length of the reading m 15. Quality reports were generated using FASTQC software. The reads were mapped with TopHat to the reference genome of Homo sapiens in the version GRCh38.p13.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw count for each sample

extract_protocol:
Total RNA was isolated using Total RNA Mini Plus (A&A Biotechnology, Gdansk, Poland). 2 μg of total RNA was used for the construction of sequencing libraries.
The library was prepared using the DNBSEQ mRNA library kit (BGI Genomics) following the manufacturer's protocol.

value: human melanoma cell line

value: RIPK4 silencing


title: WM266.4 cells, control.si_2 [K2]

value: control


title: Primary adipocytes, Undifferentiated 3


title: WM266.4 cells, RIPK4.si_3 [R3]


title: WM266.4 cells, control.si_3 [K3]


title: WM266.4 cells, RIPK4.si_1 [R1]


title: WM266.4 cells, control.si_1 [K1]


title: Control siRNA tunicamycin 1

value: MEF

value: embryonic fibroblast

value: tunicamycin


title: FL_cKO3_HSC_1222

description:
hematopoietic stem and progenitor cells from control FL
FL_cKO3_HSC_count

data_processing:
Sequencing was performed on MGISeq2000 platform in a 150+150 base paired-end mode.
We built the reference for STAR using the Gencode vM24 references.
After mapping reads on the genome using STAR (--twopassMode Basic --outSAMstrandField intronMotif --sjdbOverhang 100), extracted junctions using regtools junctions extract command (-a 8 -m 50 -M 500000 -s 0), and clustered them using leafcutter_cluster_regtools.py (-m50 -l 500000 --checkchrom --strand=False).
Then, we quantified differentially spliced genes by leafcutter_ds.R.
Visualization was performed by leafviz.
Assembly: mm10
Supplementary files format and content: leafcutter count file : per individual intron counts
Supplementary files format and content: leafcutter_ds_effect_sizes.txt : effect size for each intron quantified by leafcutter

source_name: fetal liver

growth_protocol: Single-cell suspensions were prepared by mechanical dissociation. Hematopoietic stem cell fractions were isolated by cell sorter.

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Each cDNA was generated using a Clontech SMART-Seq HT Kit (Takara Clontech, Mountain View, CA, USA), and each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).

treatment_protocol: Mice were housed in a specific-pathogen free animal facility.

value: fetal liver

value: hematopoietic stem and progenitor cells

value: Vav1-cre; Ahedfl/fl (cKO)

value: Single-cell suspensions were prepared by mechanical dissociation. Hematopoietic fractions were isolated by cell sorter.


title: FL_cKO2_HSC_1222

description:
hematopoietic stem and progenitor cells from control FL
FL_cKO2_HSC_count


title: FL_cKO1_HSC_1222

description:
hematopoietic stem and progenitor cells from control FL
FL_cKO1_HSC_count


title: FL_cKO_HSC

description: hematopoietic stem cells from cKO FL

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Fetal liver

value: Fetal liver

value: hematopoietic stem cells


title: FL_WT3_HSC_1222

description:
hematopoietic stem and progenitor cells from control FL
FL_WT3_HSC_count

value: Vav1-cre; Ahedfl/+ (control)


title: FL_WT_S1+2

description: pro-erythroblasts from control FL

value: pro-erythroblasts


title: BM_KO_S1+2

description: pro-erythroblasts from cKO BM

source_name: Bone marrow

value: Bone marrow

value: Rosa26-CreERT2; Ahedfl/fl (cKO)

value: tamoxifen intraperitoneally at 1 mg/day consecutively for 5 days


title: FL_WT2_HSC_1222

description:
hematopoietic stem and progenitor cells from control FL
FL_WT2_HSC_count


title: BM_KO_HSC

description: hematopoietic stem cells from cKO BM


title: FL_WT3_HSC_1201


title: FL_cKO3_HSC_1201


title: BM_WT_S1+2

description: pro-erythroblasts from control BM

value: Rosa26-CreERT2; Ahedwt/wt (control)


title: BM_WT_HSC

description: hematopoietic stem cells from control BM


title: FL_WT1_HSC_1201

description:
hematopoietic stem and progenitor cells from control FL
FL_WT1_HSC_count


title: FL_cKO1_HSC_1201


title: FL_WT_HSC

description: hematopoietic stem cells from control FL


title: JAKinhi_3

status: Public on Apr 18 2024

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Kidney

extract_protocol:
Total RNA was prepared from murine kidneys using QIAzol® Lysis Reagent (Qiagen).
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: Kidney

value: Balb/c

value: Male

value: Wild type


title: infection_3


title: FL_cKO_S1+2

description: pro-erythroblasts from cKO FL


title: FL_WT2_HSC_1201


title: JAKinhi_1


title: non-infection_3

value: non-treatment


title: FL_cKO2_HSC_1201

value: fetal liver


title: Son siRNA tunicamycin 3

value: MEF

value: embryonic fibroblast

value: Son siRNA / Son knockdown

value: tunicamycin


title: JAKinhi_2


title: infection_2


title: FL_WT1_HSC_1222

value: hematopoietic stem and progenitor cells

value: Single-cell suspensions were prepared by mechanical dissociation. Hematopoietic fractions were isolated by cell sorter.


title: HCC366_PKR-sg1_control2_Media_3

status: Public on Apr 17 2024

city: Boston

first: Tao

last: Zou

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
Quality check of RNA-sequencing FASTQ files was completed using FastQC v0.11.9 with default parameters.
After manual inspection, it was determined that the first three nucleotides of all reads should be removed before mapping. Adapter trimming was completed using cutadapt v2.8; Illumina Universal Adapter sequence “AGATCGGAAGAG” was used for both ends.
After trimming, reads shorter than 35 bp were discarded.
Reads were mapped to the Ensembl v99 hg38 gene annotation using the STAR aligner v2.7.5b.
Normalization was completed via RSEM to output TPMs and FPKMs
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing gene id, transcript id(s), length, effective length, expected count, TPM, and FPKM values from RSEM

growth_protocol: HCC366 and NCI-H1650 cell lines cell lines were grown and maintained in RPMI media supplemented with 10% FBS.

extract_protocol:
Total RNA extracted 7 days after gene knockout and rRNA depleted prior to strand-specific library preparation
RNA was isolated using the RNeasy Plus Kit (Qiagen) followed by ribosomal RNA depletion using the NEBNext rRNA Depletion Kit (E6310) or the QIAseq FastSelect -rRNA HMR Kit (Qiagen).
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760S).

treatment_protocol: Control genes, XRN1, PKR, or both XRN1 and PKR were deleted using CRISPR-Cas9 prior to total RNA extraction, followed by rRNA depletion prior to strand-specific library preparation.

value: Lung

value: Non-small cell lung cancer cell line, adenosquamous histology, derived from a female patient.

value: AAVS1 control gene and PKR double KO

value: AAVS1 and PKR double knockout with CRISPR-Cas9


title: HCC366_PKR-sg1_XRN1-sg2_Media_2

value: XRN1 and PKR double KO

value: XRN1 and PKR double knockout with CRISPR-Cas9


title: HCC366_PKR-sg1_XRN1-sg1_Media_2


title: HCC366_control1_control2_Media_2

value: AAVS1 control KO

value: AAVS1 control gene knockout with CRISPR-Cas9


title: HCC366_PKR-sg1_XRN1-sg2_Media_1


title: HCC366_PKR-sg1_control2_Media_1


title: H1650_Day7_XRN1-sg2_Rep3

value: Lung adenocarcinoma cell line derived from a 27 year old male patient.

value: XRN1 KO

value: XRN1 sg2 knockout with CRISPR-Cas9


title: HCC366_control1_control2_Media_1


title: H1650_Day7_control-sg2_Rep3

value: Chr2.2 control KO

value: Chr2.2 control gene knockout with CRISPR-Cas9


title: HCC366_control1_XRN1-sg2_Media_1

value: AAVS1 control gene and XRN1 double KO

value: AAVS1 and XRN1 double knockout with CRISPR-Cas9


title: non-infection_2

value: Kidney

value: Balb/c

value: Male

value: Wild type

value: non-treatment


title: H1650_Day7_control-sg1_Rep3

value: Lung


title: H1650_Day7_control-sg2_Rep2


title: H1650_Day7_XRN1-sg2_Rep1


title: HCC366_control1_XRN1-sg1_Media_2

value: Non-small cell lung cancer cell line, adenosquamous histology, derived from a female patient.


title: H1650_Day7_control-sg1_Rep1


title: infection_1


title: HCC366_Day7_XRN1-sg1_Rep3

value: XRN1 sg1 knockout with CRISPR-Cas9


title: HCC366_Day7_control-sg2_Rep3


title: HCC366_Day7_XRN1-sg1_Rep2


title: HCC366_Day7_control-sg2_Rep1


title: non-infection_1


title: HCC366_Day7_control-sg1_Rep2

value: AAVS1 control KO


title: HCC366_Day7_control-sg1_Rep1

value: AAVS1 control gene knockout with CRISPR-Cas9


title: PC-3 cells,  (sh-miR93#7) shRNA coding the full sequence of hsa-miR-93-5p [miRNA-seq PC-3]

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

data_processing:
The quality of RNA-Seq FASTQ files was assessed with FastQC v0.11.9.
Adapter sequences were removed with the use of cutadapt v2.10: AGATCGGAAGAGCACACGTCT -- miRNA-Seq 3'-adapter.
IsomiR read count matrices were obtained using IsomiRMap with miRBase v22 annotation.
The standard isomiR notation was utilized: A number after the first ``|'' character denotes the shift from the canonical 5'-end in 5'-3' direction (5'-isomiR notation); an additional ``|'' symbol followed by a number denoted 3'-end shifts (3'-isomiR notation); finally, symbols inside ``(.)'' denoted other nucleotides added to the shifted 3'-end.
Assembly: miRBase v22
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: prostate cancer

growth_protocol: The human prostate adenocarcinoma cell lines PC-3 were grown in DMEM medium containing 4.5g/L glucose (PanEco, Russia) supplemented with 4 mM L-Glutamine (PanEco, Russia), 10% fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and cultured under the standard cell culture conditions (37◦C, saturated humidity, 5% CO2).

extract_protocol:
According to the manufacturer's instructions, the total RNA was isolated from about $1 \times 10^6$ cells using miRNeasy Mini Kit (Qiagen, Germany). All RNA samples were treated with DNase I during the isolation procedure. The RNA yield was determined by UV absorbance using a NanoDrop 1000 spectrophotometer (Peqlab, Germany). The RNA quality was assessed by analyzing the ribosomal RNA integrity number (RIN) on an Agilent 2000 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, USA). The RIN values of the isolated RNA samples were 9.5 and higher. Libraries for miRNA sequencing were prepared from total RNA samples using NEBNext Multiplex Small RNA Library Prep Kit (Illumina, USA).
Libraries for miRNA sequencing were prepared from total RNA samples using NEBNext Multiplex Small RNA Library Prep Kit (Illumina, USA).

treatment_protocol: Stable overexpression of hsa-miR-93-5p isoforms was achieved by a shRNA-mediated approach. In particular, each of the two double-stranded DNA fragments containing a hsa-miR-93-5p sequence (5'-CAAAGTGCTGTTCGTGCAGGTAG for N8_2 and 5'-CAAAGTGCTGTTCGTGCAG for N4_3) was cloned into the BsmBI restriction sites of the LentiGuide-Hygro lentiviral vector (Addgene #139462, UK) without sgRNA scaffold. Nucleotide compositions of the obtained lentiviral vectors were confirmed by Sanger sequencing. Lentiviral particles were obtained as cell-free supernatants by transient transfection of HEK-293T and using GenJect-39 transfection reagent (Molecta, Russia). Briefly, lentiviral vectors based on pLentiGuide-Hygro were packaged using the second-generation packaging plasmid pCMV-dR8.2 dvpr (Addgene #8455, UK) and pCMV-VSV-G (Addgene #8454, UK) expressing the envelope protein of vesicular stomatitis virus. The supernatant was harvested 24h and 48h after transfection, 0.45 $\mu$m filtered and was immediately used for transduction or stored at -80C Target PC-3 cells were plated at 8 x 104 cells in 2 mL medium in each well of a 6-well plate 24 hours before transduction. After viral particles containing supernatant were added to the cells, the medium was replaced in 3 days, cells were seeded into a 25 cm^2 flask, and hygromycin was added at a concentration of 150 $\mu$g/mL. The hygromycin selection was carried out for at least two weeks.

value: prostate cancer


title: HCC366_PKR-sg1_XRN1-sg2_Media_3

value: XRN1 and PKR double KO

value: XRN1 and PKR double knockout with CRISPR-Cas9


title: HCC366_PKR-sg1_XRN1-sg1_Media_3


title: HCC366_control1_XRN1-sg2_Media_3


title: HCC366_control1_control2_Media_3


title: HCC366_PKR-sg1_control2_Media_2

value: AAVS1 control gene and PKR double KO

value: AAVS1 and PKR double knockout with CRISPR-Cas9


title: HCC366_control1_XRN1-sg1_Media_3

value: AAVS1 control gene and XRN1 double KO


title: lib77925

status: Public on Apr 15 2024

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3' end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0) (44).
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned using the STAR aligner (v2.4.2a) (45) with the GRCh38 reference genome and gene annotations from ensembl release 77.
Gene counts were generated using HTSeq-count (v0.4.1) (46).
Assembly: GRCh38
Supplementary files format and content: gene count matrix in .csv format

source_name: treg

growth_protocol: PBMCs were stained with an antibody cocktail (Supplemental Table 3B), 500 Tregs  were sorted into SMARTseq buffer, and stored at -80C until sequencing. Sorting was performed on FACSAria II (BD Biosceinces) cell sorter machine.

extract_protocol: To avoid batch effects, all samples underwent lysis, RT, and PCR on the same day. The double-stranded cDNA quality was tested on the Agilent Tapestation.

tag: study group

tag: donor id

value: TREX_ID 44

value: treg

tag: sample id

tag: timepoint

value: Day 0

tag: tregdose

value: high

tag: cpeptidechange


title: HCC366_control1_XRN1-sg2_Media_2

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: AAVS1 and XRN1 double knockout with CRISPR-Cas9


title: lib77927

value: Day 182


title: HCC366_PKR-sg1_XRN1-sg1_Media_1

value: Lung

tag: treatment


title: HCC366_control1_XRN1-sg1_Media_1

value: Non-small cell lung cancer cell line, adenosquamous histology, derived from a female patient.


title: lib77921

value: TREX_ID 108


title: lib77928

value: TREX_ID 65

value: Day -28

value: placebo


title: lib77919

value: TREX_ID 94


title: lib77918

value: Day 7


title: H1650_Day7_XRN1-sg2_Rep2

value: Lung adenocarcinoma cell line derived from a 27 year old male patient.

value: XRN1 KO

value: XRN1 sg2 knockout with CRISPR-Cas9


title: H1650_Day7_XRN1-sg1_Rep2

value: XRN1 sg1 knockout with CRISPR-Cas9


title: lib77912

value: TREX_ID 78

value: treg

value: Infusion product


title: H1650_Day7_control-sg2_Rep1

value: Chr2.2 control KO

value: Chr2.2 control gene knockout with CRISPR-Cas9


title: H1650_Day7_XRN1-sg1_Rep1

value: Lung


title: lib77911

value: TREX_ID 81

value: Day 182

value: high


title: lib77910


title: lib77909

value: Day 0


title: lib77907

value: TREX_ID 24


title: lib77908


title: HCC366_Day7_XRN1-sg2_Rep3

value: Non-small cell lung cancer cell line, adenosquamous histology, derived from a female patient.


title: lib77904


title: HCC366_Day7_XRN1-sg1_Rep1


title: HCC366_Day7_control-sg1_Rep3

value: AAVS1 control KO

value: AAVS1 control gene knockout with CRISPR-Cas9


title: HCC366_Day7_XRN1-sg2_Rep1

value: XRN1 KO


title: HCC366_Day7_XRN1-sg2_Rep2

value: XRN1 sg2 knockout with CRISPR-Cas9


title: lib77902

value: TREX_ID 71

value: Day 7


title: H1650_Day7_control-sg1_Rep2

value: Lung adenocarcinoma cell line derived from a 27 year old male patient.


title: PC-3 cells,  (sh-miR93#8) shRNA coding 4 nuclotides 3'-end shortened version of hsa-miR-93-5p [miRNA-seq PC-3]

value: prostate cancer


title: lib77929

value: TREX_ID 10

value: treg

value: placebo


title: lib77899

value: TREX_ID 46


title: lib77930

value: TREX_ID 65

value: Day 182


title: HCC366_Day7_control-sg2_Rep2

value: Lung

value: Chr2.2 control KO

value: Chr2.2 control gene knockout with CRISPR-Cas9


title: lib77926

value: TREX_ID 44

value: high


title: lib77897

value: Day 0


title: lib77923

value: TREX_ID 108


title: lib77920

value: Infusion product


title: lib77924


title: lib77917

value: TREX_ID 94


title: lib77892

value: TREX_ID 53

value: Day 28


title: lib77893


title: lib77922

value: Day 7


title: lib77913

value: TREX_ID 78

value: treg


title: lib77915


title: lib77890

value: TREX_ID 76


title: lib77916


title: lib77914

value: Day 14


title: H1650_Day7_XRN1-sg1_Rep3

value: Lung adenocarcinoma cell line derived from a 27 year old male patient.

value: XRN1 KO

value: XRN1 sg1 knockout with CRISPR-Cas9


title: lib77906

value: TREX_ID 24


title: lib77885

value: TREX_ID 10

value: Day -28

value: placebo


title: lib77884

value: TREX_ID 65


title: lib77905

value: Day 0

value: high


title: lib77903

value: TREX_ID 71

value: Day 182


title: lib77883


title: lib77898

value: TREX_ID 46

value: Day 7


title: lib77881

value: TREX_ID 64

value: treg


title: lib77900

value: Infusion product


title: lib77895

value: TREX_ID 57


title: lib77894


title: lib77891

value: TREX_ID 53


title: lib77896


title: lib77879

value: TREX_ID 89


title: lib77878


title: lib77889

value: TREX_ID 76

value: Day 28


title: lib77874

value: TREX_ID 11


title: lib77876

value: TREX_ID 60

value: placebo


title: lib77873

value: Day 0


title: lib77888

value: high


title: lib77875

value: Day -28


title: lib77886

value: TREX_ID 10


title: lib77887


title: lib77872

value: TREX_ID 49

value: Day 182


title: lib77867

value: TREX_ID 69

value: Day 7


title: lib77869

value: treg

value: Infusion product


title: lib77870


title: lib77868


title: lib77880


title: lib77866


title: lib77882

value: TREX_ID 64


title: lib77865

value: TREX_ID 113


title: lib77861

value: TREX_ID 112


title: lib77860


title: lib77859


title: lib77862


title: lib77858


title: lib77854

value: TREX_ID 77


title: lib77877


title: lib77857


title: lib77855


title: lib77856

value: Day 14


title: lib77853

value: TREX_ID 86


title: lib77852


title: lib77871


title: lib77901

value: TREX_ID 71


title: lib77848

value: TREX_ID 5


title: lib77851

value: high


title: lib77850


title: lib77863

value: Day 0


title: lib77849


title: lib77845

value: TREX_ID 100


title: lib77847


title: lib77846


title: lib77843


title: lib77864


title: lib77841

value: TREX_ID 3

value: placebo


title: lib77840


title: lib77842


title: lib77838

value: TREX_ID 90


title: lib77844

value: Day 7


title: lib77839

value: treg


title: lib77836

value: TREX_ID 80


title: lib77835

value: TREX_ID 111


title: lib77834


title: lib77837


title: lib77833

value: TREX_ID 83


title: lib77831

value: TREX_ID 35

value: low


title: lib77832


title: lib77826

value: TREX_ID 75

value: Day -28


title: lib77828

value: TREX_ID 52


title: lib77827


title: LNCaP_NT2_H3K27ac_ChIP

status: Public on Apr 01 2024

city: Salt Lake City

first: Xiaoyang

last: Zhang

state: Utah

address: 1950 Circle of Hope Drive

department: Oncological Sciences

institute: University of Utah

library_source: genomic

data_processing:
Bowtie2 to align sequencing reads
MACS2 to identify ChIP-seq peaks and calculate Signal Per Million Reads (SPMR)
Assembly: hg19
Supplementary files format and content: bigWig (bw)

molecule: genomic DNA

source_name: LNCaP-clone FGC

extract_protocol:
Chromatin immunoprecipitation using antibodies to enrich DNA fragments
NEBNext DNA Ultra II library prep kit (E7645S)

value: LNCaP-clone FGC

value: Prostate adenocarcinoma cell line

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: H2170_CRISPRi_NT2_HiChIP_rep2

data_processing:
HiC-Pro to align sequencing reads
hichipper to identify chromatin loops connecting H3K27ac anchors
Assembly: hg19
Supplementary files format and content: intra-chromosomal interaction counts text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, FDR (blank), PETs
Supplementary files format and content: inter-chromosomal interaction counts text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, FDR (blank), PETs
Library strategy: HiChIP

extract_protocol:
HiChIP protocol (Mumbach et al., 2016, Nature Methods) to enrich DNA fragments that are in proximity with each other
Illumina Tagment DNA Enzyme and Buffer Kit (Illumina 20034197)

value: Lung squamous cancer cell line

tag: hichip antibody


title: H2170_CRISPRi_NT1_RNA_seq

data_processing:
Bowtie2 to align sequencing reads
RSEM to quanitfy expression for each GENCODE gene
Assembly: hg19
Supplementary files format and content: RSEM text file

extract_protocol:
Quick-RNA miniprep kit (ZYMO R1055)
NEBNext Ultra Directional RNA library prep kit (NEB E7760S)

value: CRISPRi sg_d103


title: H2170_CRISPRi_NT2_RNA_seq

value: CRISPRi sg_d98


title: HF-46773 SAM24436426

status: Public on Mar 28 2024

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Neuroinformatics

institute: Genentech, Inc.

data_processing:
Reads were aligned to the genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Splicing analysis was done using the SGSeq and DEXseq Bioconductor packages.
Assembly: GRCh38
Supplementary files format and content: Each sample has a TSV data file with counts, gene exonic size (width) and RPKM as provided by HTSeqGenie

source_name: Lumbar Spinal Cord

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on TapeStation 4200 (Agilent Technologies). For sequencing library generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies).

value: Lumbar Spinal Cord

tag: diagnosis

value: Control

tag: Sex

value: M

value: Elderly

value: Years


title: HF-39053 SAM24436429

value: F

value: crestor, celebrex, lipinopril, advair, actonel

tag: race

value: White


title: HF-37902 SAM24436430


title: HF-32327-(1) SAM24436428

value: Adult


title: HF-46775 SAM24436427


title: HF-43950-(1) SAM24436423


title: HF-43960-(1) SAM24436425


title: HF-47156 SAM24436419

value: ALS

value: Levsin, Morphine, Xanax, Prozac, Rilutek


title: HF-40651-(1) SAM24436421


title: HF-39862 SAM24436418


title: HF-43959-(1) SAM24436424


title: HF-40655-(1) SAM24436422


title: HF-39861 SAM24436417


title: HF-113410 SAM24436420

value: Tizanidine, Rilutek, Radicava, Nuedexta, Ativan, Morphine, Tylenol, Cuvposa, Vitamins


title: HF-39860 SAM24436416


title: HF-47150 SAM24436413

value: Riluzole, Protonix, Synthroid, Xanax, Neudexta, Botox

value: Asian


title: lib77829

value: TREX_ID 52

value: treg

value: Day 7

value: placebo


title: HF-47151 SAM24436414

value: Lumbar Spinal Cord

value: Riluzole, Methadone, Morphine, Oxycodone, Tribenzor, Atropine, Diazepam, Lorazepam, Ativan, Prochlorperazine


title: HF-43957 SAM24436412

value: M

value: Elderly


title: H2170_CRISPRi_NT2_HiChIP_rep1

value: Lung squamous cancer cell line

value: H3K27ac (Abcam ab4729)


title: lib77830

value: TREX_ID 35

value: Day 0

value: low


title: ERa_BRCa_patient_5

status: Public on Mar 27 2024

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Reads were aligned to the human genome build GRCh37 using BWA
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis
Enrichment over input control was determined using both MACS2. Only peaks identified by both methods, and not overlapping with the ENCODE GRCh37/Hg19 blacklisted regions, were retained.
Deeptools bamCoverage was used to egnerate Reads-Per-Genomic-Contact (RPGC) normalized bigwig files.
Raw data vailable at EGA: EGAS50000000008
Assembly: Hg19/GRCh37
Supplementary files format and content: .bed, peaks
Supplementary files format and content: .bw, BigWig of RPGC normalized ChIP-seq signal

source_name: primary breast tumor

extract_protocol:
Fresh frozen tumor material was cryosectioned, collected in Eppendorf tubes and stored at -80C until processing. An H&E slide was assessed by pathologist to confirm tumor cell content. For ChIP, tissue was thawed on ice and cross-linked in solution A (50 mM Hepes, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, pH = 7.4) containing 2 mM DSG (Sigma) and incubated at room temperature for 25 min while rotating. Next, formaldehyde was added to 1% final concentration and rotation was continued for 20 min. Reaction was quenched by 0.2 M glycine. Samples were pelleted, washed with cold PBS and tissue architecture was disrupted by a pellet pestle (Sigma) and subsequently sonicated (Diagenode PicoBioruptor). IP was performed by overnight incubation with 5 ug ER antibody (SC-543, Santa Cruz) to 50uL dynabeads (Invitrogen) in blocking buffer (5% BSA in PBS), then washed 10 times with RIPA (50 mM HEPES, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-DOC, pH = 7.6), washed in TBS, reverse cross-linked at 65C in Elution Buffer (50mM Tris, 10mM EDTA, 1% SDS) and DNA eluted.
ChIP DNA was prepared for Illumina multiplex-sequencing with 10 samples per lane and sequenced on Illumina HiSeq 2500 (Illumina) at 65bp single-end.

value: primary breast tumor

tag: disease state

value: breast cancer

tag: individual

value: Era (SX-543, Santa Cruz)


title: ERa_BRCa_patient_2


title: ERa_BRCa_patient_3


title: ERa_BRCa_patient_4


title: ERa_BRCa_patient_1


title: Mt1ko technical replicate 16

status: Public on Mar 26 2024

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Sequence reads were trimmed with Trimmomatic (v0.35) using defulat settings and universal Illumina adapters.
Sequence reads were aligned to reference genome GRCm38 with RSEM (v1.3.3).
Expected counts were rounded to nearest integer and counts for technical replicates were summed as a representative biological sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each biological sample
Supplementary files format and content: tab-delimited text file including raw counts for all technical replicates

extract_protocol:
Total RNA was isolated using the RNeasy Micro kit (Qiagen) including the optional DNase digest step.
Libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2-Pico (Takara)

value: Bone marrow

value: Dnmt3aR878H/+;Npm1cA/+ Mt1 knockdown


title: Mt1ko technical replicate 17


title: Mt1ko technical replicate 18


title: control technical replicate 15


title: HF-47152 SAM24436415

value: ALS

value: F

value: Adult

value: Years

value: Zoloft, Klonopin, Amitriptyline, Riluzole

value: White


title: Mt1ko technical replicate 12


title: control technical replicate 14


title: control technical replicate 7


title: Mt1ko technical replicate 10


title: control technical replicate 8


title: Mt1ko technical replicate 5


title: control technical replicate 9


title: Mt1ko technical replicate 11


title: RPMs, Tm_1

status: Public on Mar 24 2024

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA 3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: 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 with RNeasy micro kit (QIAGEN).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina) or a combination of SMART-Seq HT Kit (Takara Bio, Japan) and NexteraXT DNA Library Preparation Kit (Illumina).

value: peritoneal cavity

value: resident peritoneal macrophages

value: Wildtype

value: Tm culture


title: HF-43956 SAM24436411

value: Lumbar Spinal Cord

value: M


title: Mt1ko technical replicate 6


title: RPMs, med_2

value: medium culture


title: RPMs, CT_1

value: CT culture


title: RPMs, med_1


title: RNAseq_So(d18:1)_4

status: Public on Mar 21 2024

city: Beijing

first: Chuan

last: Ye

address: 38 Xueyuan Road, Haidian District

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling. Trim-galore v0.6.7 was used for adapter trimming and low-quality reads. Clean reads mapping was conducted by Hisat2 v2.2.1, and mm10 was used as mouse reference genome. Gene expression was quantified by featureCounts v2.0.1.
Assembly: mm10
Supplementary files format and content: For RNA-Seq data, tab-delimited text files contian normalized count values for each gene of each sample.

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages were isolated from the bone marrow of C57BL/6J wild-type mice. The bone marrow collected from the femur and tibia of mice was inoculated on sterile petri dishes and cultured in RPMI 1640 containing 10% FBS, 100 units/ml penicillin, 100 mg/ml streptomycin and 10 ng/ml macrophage-colony stimulating factor (M-CSF) for 5-6 days.

extract_protocol:
The polyA mRNA isolation was performed using Oligo(dT) beads
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 μM sphingosine was dissolved in methanol and added to BMDMs for 6 h. Methanol was added to control group for 6 h too.

tag: strain

value: Bone marrow-derived macrophages


title: RNAseq_So(d18:1)_3


title: RNAseq_So(d18:1)_1


title: RNAseq_Control_4

value: Control


title: RNAseq_Control_2


title: RNAseq_Control_1


title: RNAseq_Control_3


title: Mt1ko technical replicate 4

value: Bone marrow

value: Dnmt3aR878H/+;Npm1cA/+ Mt1 knockdown


title: H24 [miRNA-seq]

status: Public on Mar 15 2024

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 101-base single-end mode.
Before analysis of the small RNA-Seq data, reads were trimmed the 3' adapter sequence (AGATCGGAAGAGCACACGTCT).
Trimmed reads were mapped on miRBase human miRNA dataset using miRDeep2 software.
Quantification was also performed with miRDeep2 software.
Supplementary files format and content: miRBase human miRNA dataset
Supplementary files format and content: tab-delimited text files include count data for each sample

source_name: peripheral blood

extract_protocol:
Total RNA isolation was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Each library was prepared using NEBNext Multiplex Small RNA Library Prep Set for illumina (New England Biolabs).

value: peripheral blood

value: peripheral blood mononuclear cells

value: healthy donor


title: Female_baseline, HTO

status: Public on Mar 18 2024

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description: processed data linked to GEX sample

data_processing:
Cell Ranger (10x Genomics, v6.0.1) was used to performalignment (GRCm38, Ensembl 84), filtering, barcode counting and UMI counting of sequencing reads from fastq files
Assembly: GRCm38
Supplementary files format and content: Tab -separated values files and matrix files

source_name: carotid plaque

extract_protocol:
Digested tissue was filtered through a 70-µm strainer, washed with cold PBS, centrifuged at 500 g for 5 min. at 4 °C and resuspended in PBS supplemented with 1% vol/vol BSA. Single-cell suspensions were placed on ice and stained with eFluor 780 Fixable Viability Dye (eBioscience, 65-0865-14) for 30 min., washed, blocked with TruStain FcX (anti-mouse CD16/32) Antibody (Biolegend, 101319) for 5 min. and then stained with PerCP/Cyanine5.5 anti-mouse CD45 Antibody (Biolegend, 103132) for 30 min. Live, CD45+ cells were purified by fluorescence-activated cell sorting using a BD FACSAria II instrument at the Cytometry and Cell Sorting Laboratory at the NYU Grossman School of Medicine at NYU Langone Health. For sorting, specimens were pooled by experimental group. The sorter was equipped with a 100 µm nozzle.
scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 reagent, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics; 1000268, 1000215 and 100127, respectively) according to the manufacturer’s instructions.

value: carotid plaque

value: Female

tag: condition

value: baseline

tag: library type

value: hashtag-derived oligonucleotide (HTO)


title: Male_baseline, HTO

description: processed data linked to GEX sample

value: Male


title: Male_baseline, mRNA

value: polyA-RNA


title: RPMs, Tm_2

value: peritoneal cavity

value: resident peritoneal macrophages

value: Wildtype

value: Tm culture


title: H21 [miRNA-seq]


title: control technical replicate 2


title: RPMs, CT_2

value: CT culture


title: H16 [miRNA-seq]


title: Female_baseline, mRNA


title: H20 [miRNA-seq]


title: H25 [miRNA-seq]


title: control technical replicate 1


title: control technical replicate 3


title: RNAseq_So(d18:1)_2

value: Bone marrow-derived macrophages


title: H15 [miRNA-seq]


title: H8 [miRNA-seq]


title: H14 [miRNA-seq]


title: H16

data_processing:
Sequencing was performed on a MGISEQ-2000RS platform in 2 x 100 bp paired-end mode.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.0.13, in combination with Bowtie2, version 2.2.3, and SAMtools, version 0.1.19.
Mapped read counts were calculated using featureCounts (in subread-2.0.0) with option -M -O --fraction.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include mapped read counts for each sample

extract_protocol:
Total RNA isolation was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions. DNA libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).


title: H9 [miRNA-seq]


title: H7 [miRNA-seq]


title: H11 [miRNA-seq]


title: H19 [miRNA-seq]


title: H25


title: H2 [miRNA-seq]


title: H22


title: H24


title: H1 [miRNA-seq]


title: A28 [miRNA-seq]

value: Acute respiratory distress syndrome


title: H20


title: A10 [miRNA-seq]


title: H19


title: A9 [miRNA-seq]


title: H11


title: A7 [miRNA-seq]


title: H21


title: H15


title: H14


title: A8 [miRNA-seq]


title: H8


title: H9


title: A4 [miRNA-seq]


title: A108 [miRNA-seq]


title: A97 [miRNA-seq]


title: A16


title: A13 [miRNA-seq]


title: A16 [miRNA-seq]


title: A13


title: A2 [miRNA-seq]


title: H22 [miRNA-seq]


title: H7


title: A8


title: A75 [miRNA-seq]


title: A81 [miRNA-seq]


title: A28


title: A102 [miRNA-seq]


title: A7


title: H1


title: A112 [miRNA-seq]


title: H2


title: A87 [miRNA-seq]


title: A10


title: A9


title: A86 [miRNA-seq]


title: A53 [miRNA-seq]


title: A73 [miRNA-seq]


title: A4


title: A72 [miRNA-seq]


title: A38 [miRNA-seq]


title: A73


title: A2


title: A112


title: A33 [miRNA-seq]


title: A70 [miRNA-seq]


title: A108


title: A68 [miRNA-seq]


title: A97


title: A59 [miRNA-seq]


title: A90 [miRNA-seq]


title: A72


title: A87


title: A43 [miRNA-seq]


title: A81


title: A102


title: A90


title: A57 [miRNA-seq]


title: A45 [miRNA-seq]


title: A75


title: A27 [miRNA-seq]


title: A1 [miRNA-seq]


title: A68


title: A65 [miRNA-seq]


title: A86


title: A65


title: A59


title: A70


title: A45


title: A41 [miRNA-seq]


title: A33


title: A38


title: A57


title: A43


title: A53


title: A6 [miRNA-seq]


title: A27


title: A41


title: A6


title: mNPC, V2, 2D, Day44, biol rep 1

status: Public on Mar 14 2024

city: Los Angeles

first: Zhongwei

last: Li

address: 1425 San Pablo St

department: Keck medicine

institute: University of Southern California

description:
mNPC DESeq2 Medium ratio
2D NPC (D44) #1

data_processing:
For Bulk RNA-Seq
Partek Flow Genomic Analysis Software
FASTQ files were trimmed from both ends based on a minimum read length of 25 bps and an end mininum quality score (Phred) of 20 or higher
For mouse samples, reads were aligned to mm39 - GENCODE Genes - release M28 GENCODE mm10 (release M24) using STAR 2.7.8a.
For human samples, reads were aligned to hg38 - GENCODE Genes - release 40 using STAR 2.7.8a.
Aligned reads were quantified to the Partek E/M annotation model. Gene counts were normalized using DESeq2 Median ratio.
For CRISPR Screen
MAGeCKFlute
1798 genes from CRISPR screen replicate #1, and 1627 genes from CRISPR screen replicate #2, with beta scores > 1.5 or < -1.5, and p-values < 0.05, were identified as potential hits
These hits were further analysed using Canonical Pathway Analysis tools of the Ingenuity Pathway Analysis (IPA) platform
Assembly: mm39 and hg38
Supplementary files format and content: Tab-delimited excel files include DESeq2 Median ratio for each Sample
Supplementary files format and content: Tab-delimited excel files include beta scores for each genes
Supplementary files format and content: Tab-delimited excel files include read counts for each genes

source_name: Embryonic Kidney

growth_protocol: Nephron progenitor cells cultured in NPSR V1 or V2 medium, 37C, 5% CO2

extract_protocol:
Total RNA was extract using the Zymo Research Quick-RNA Microprep kit, 200-400 ug total RNA was used for the construction of sequencing library
All the single-end data library were prepared using Roche KAPA Standed mRNA-seq Kit. All the paired-end data library were constructed by NovoGene with total RNA we provided.

value: Embryonic Kidney

value: 2D mNPC

value: Nephron Progenitor Cell

value: mNPSR-v2 culture

tag: time

value: Clonal mNPC line was derived from one single NPC of mNPC lines cultured for 44 days with mNPSR-v2 medium


title: mNPC, V2, 3D-2D, biol rep 2

description:
mNPC DESeq2 Medium ratio
3D-to-2D NPC #2

treatment_protocol: Nephron progenitor cells cultured in NPSR V1 or V2 medium, 37C, 5% CO2

value: 3D-to-2D mNPC

value: 28 days


title: A1

value: peripheral blood

value: peripheral blood mononuclear cells


title: CRISPR screen, biol rep 2

description:
CRISPR screen beta scores (All genes)
Normalized sgRNA read counts in CRISPR screen

value: Virus infection

value: 3 weeks after infection


title: D24 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D24_2

data_processing:
Partek Flow Genomic Analysis Software
FASTQ files were trimmed from both ends based on a minimum read length of 25 bps and an end mininum quality score (Phred) of 20 or higher
For mouse samples, reads were aligned to mm39 - GENCODE Genes - release M28 GENCODE mm10 (release M24) using STAR 2.7.8a.
For human samples, reads were aligned to hg38 - GENCODE Genes - release 40 using STAR 2.7.8a.
Aligned reads were quantified to the Partek E/M annotation model. Gene counts were normalized using DESeq2 Median ratio or TMM.
Assembly: mm39 and hg38
Supplementary files format and content: Tab-delimited excel file include TMM for each Sample

source_name: hPSC-derived cells

growth_protocol: SIX2- cells or SIX2-/PODXL+ podocytes isolated iNPC-derived nephron organoids were cultured with hNPSR-v2 medium. Kidney organoids were cultured with Stage II medium (STEMdiffTM APELTM2 medium with 50 ng/mL FGF9 and 1 μg/mL heparin) or Stage III medium (Advanced RPMI 1640 medium with 1X B27 and 200nM A83-01), 37C, 5% CO2

extract_protocol:
Total RNA was extracted using Direct-zol RNA MicroPrep Kit (Zymo) or Quick-RNA Microprep Kit (Zymo) following the kit instruction.
RNA-Seq library were constructed by NovoGene with total RNA we provided.

value: H1 hESC

value: Kidney cells

value: iNPCLCs were cultured with hNPSR-v2 medium