title: Methyl-Hi-C in neural stem cells from E17 somatosensory mouse cortex rep2

description: Library name: MethylHiC_NSC_E17_rep2

data_processing:
Raw reads of the joint Hi-C/DNA methylation data were aligned to the mm10 genome and processed using JuiceMe (Durand et al., 2016).
Assembly: mm10
Supplementary files format and content: Processed data file represents a tab-delimited text file containing processed interaction data.

extract_protocol:
Somatosensory cortices were isolated from E13, E15, E16 and E17 mouse embryos after removal of the meninges and dissociate using a papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628), following  the manufacturer's protocol. Single cells were then fixed at RT for 10 minutes in 1% Formaldehyde in PBS (ThermoFisher, Cat. N: 28908) and quenched with final 0.2M Glycine (Invitrogen, Cat. N: 15527013). Fixed cells were spun down with 500g at 4˚C for 5 minutes, washed once with 1% BSA (ThermoFisher, Cat. N: AM2618) in PBS and incubated at 4°C for 10minutes in permeabilization buffer (0.1% Saponin (Sigma-Aldrich, Cat. N: SAE0073), 0.2% BSA and 1% RNAsin plus RNase inhibitor (Promega, Cat. N: N261A) in PBS). Cells were washed at 2500g at 4˚C for 5minutes,  following the staining against Pax6 (1:40, BD 561664), Eomes (1:33, BD 566749) and Tubb3 (1:14, BD 560394) in staining buffer (0.1% saponin, 1% BSA, 0.1% RNAsin plus RNase inhibitor in PBS) at 4˚C for 1h with slow rotation. Cells were washed twice with permeabilization buffer, once with PBS with DAPI (1:1000; ThermoFisher, Cat. N: 62248) and a final wash with PBS containing 0.5% BSA. After the last wash the cells were resuspended in PBS with 1% BSA and 1% RNAsin plus RNase inhibitor, filtered with a 40µM cell strainer (ThermoFisher, Cat. N: 15342931) and FAC-sorted. Sorted Pax6+ cells (NSC) were flash frozen and stored at -80°C for Methyl-Hi-C.
Methyl-Hi-C was performed using a modified version of established protocols (Lee et al., 2019; Li et al., 2019). In brief, flash frozen NSC (Pax6+) pellets were thawed on ice, lysed in 0.2% Igepal-CA630 (Sigma-Aldrich, Cat. N: I3021) and permeabilized with 0.5% SDS (Invitrogen, Cat. N:AM9823). Chromatin was then digested at 37˚C  overnight with 200U DpnII (New England Biolabs, Cat. N: R0543). Following digestion, nuclei were incubated  at RT for 4h with DNA Polymerase I (New England Biolabs, Cat. N: M0210) and a nucleotide mix containing biotin-14-dATP (Life Technologies, Cat. N: 195245016) in DpnII buffer. Proximity ligation was then carried out at 16 °C for a minimum of 6h. After ligation, nuclei were lysed and the DNA was reverse-crosslinked by overnight incubation at 68˚C and purified by ethanol precipitation. Purified DNA was sheared to ~550 bp fragments using a Covaris S220 sonicator and end-repaired with T4 DNA Polymerase (New England Biolabs, Cat. N: M0203) at 20˚C for 4h. Prior to bisulfite treatment, sheared and biotinylated fully methylated pUC19 (Zymo Research, Cat. N: D5017) and unmethylated lambda DNA (Promega, Cat. N: D1521) was added to the samples (~ 0.01%). Bisulfite conversion was performed using the EZ DNA Methylation-Gold Kit (Zymo Research, Cat. N: D5005). Libraries were then prepared using the Accel-NGS® Methyl-Seq DNA Library Kit (Swift Bioscience, Cat. N: 30024), following the manufacturer's protocol up to the adapter ligation step. After adapter ligation, biotinylated fragments were enriched using MyOne Streptavidin T1 beads (ThermoFisher, Cat. N: 65602), followed by 5 washes with washing buffer (0.05% Tween-20 (Sigma-Aldrich, Cat. N: P9416)) and two final washes with low-TE water. Library amplification was carried out directly on the streptavidin beads using the EpiMark Hot Start Taq (New England Biolabs, Cat. N: M0490) using the following program: 95˚C 30s; {95˚C 15s, 61˚C 30s, 68 ˚C 60s} x14; 68˚C 5min; Hold at 10˚C. Beads were then pelleted on a magnetic rack and the amplified libraries in the supernatant were purified using 0.6x AMPure XP beads (Agencourt, Cat. N: A63881), reslting in a final average fragment size of approximately 500bp. Library concentration was quantified by qPCR using the NEBNext® Library Quant Kit (New England Biolabs, Cat. N: E7630S) and fragment size distribution was assessed using Agilent 2100 Bioanalyzer.


title: P14_LayerV_rep1

status: Public on Jun 10 2026

type: SRA

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

country: USA

institute: Harvard University

description:
scRNA_OL_layers_raw_counts.dge.txt
scRNA_OL_layers_metadata.txt

library_source: transcriptomic single cell

data_processing:
scRNA-seq sequencing and basecalling were performed with NextSeq 500 instrument (Illumina)
Cellranger mkfastq (10x Genomics v3.0.1) was used to demultiplex bcl files to fastq files using standard parameters
Cellranger count (10x Genomics v3.0.1) was used to produce an aligned single cell feature count matrix, using mm10 genome as a reference.
Seurat (v4.0.0) pipeline including SCTransform was used to normalize and scale the single cell data. Default parameters were used. The following parameters were used for regression: percent.mt, and sample.
PCA and UMAP were used to for dimensionality reduction and visualization of single cells data.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts
Supplementary files format and content: tab-delimited file with the metadata for each sample in the matrix

molecule: total RNA

organism: Mus musculus

source_name: S1 cortex

extract_protocol:
Tissue pieces were processed to obtain a single cell suspension using papain digestion  (30-90   min   according   to   the   mice   age),   following   an   adapted   protocol   from   the  Worthington Papain Dissociation System kit  (Worthington Biochemical).  Single cells  were   resuspended   in   ice-cold   Hibernate-A   containing   10%   fetal   bovine   serum.  Oligodendrocytes were isolated by fluorescence activated cells sorting. Sorted cells  were spun down and resuspended into 0.04% BSA in PBS. Cell were counted in a  hemocytometer chamber and immediately processed for single cell GE formation.
Library was performed according to the manufacter’s instructions with the single cell 3’  v2 protocol (or v3 for the second replicate) (10x Genomics).  Approximately 6-8,000  sorted oligodendrocytes were loaded onto  a Chromium™ Single Cell 3’ Chip and  processed   through   the   Chromium   Controller   to   generate   single-cell   gel   beads   in  emulsion.   cDNA   amplification   and   library   construction   were   done   following  10xGenomics instructions. Libraries were quantified in BioAnalyzer and sequenced  with a NextSeq 500 instrument (Illumina).

treatment_protocol: One male and one female Fezf2CreERT2/+; td-Tomato+/-; Plp1-eGFP+/- mice at each time  point were used. We dissected the brain and made 200-400um coronal sections in  Hybernate A (Brainbits) using a vibratome. Sections were transferred to another plate  and somatosensory cortex micro dissected into three sub-cortical regions (layer1-4,  layer5 and layer6) using the fluorescently labeled layer5 cells as landmark. Tissue was  kept in cold Hybernate A with B27 at all times. RNAse free techinique was used

tag: tissue

value: S1 cortex

tag: cell type

value: Oligodendrocyte

tag: genotype

value: Fezf2 CreERT2 +/- ; td-Tomato +/- ; Plp1-eGFP +/-


title: P14_LayerII-IV_rep1


title: Methyl-Hi-C in neural stem cells from E17 somatosensory mouse cortex rep1

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

description: Library name: MethylHiC_NSC_E17_rep1

library_source: genomic

molecule: genomic DNA

source_name: somatosensory cortex

value: somatosensory cortex

tag: age

value: neural stem cells (Pax6+)

value: C57BL/6JRj (Haplotype H2b)


title: P7_LayerV_rep1


title: Methyl-Hi-C in neural stem cells from E16 somatosensory mouse cortex rep2

description: Library name: MethylHiC_NSC_E16_rep2


title: P7_LayerVI_rep1


title: P7_LayerII-IV_rep1


title: GIST-882 cells, DMSO rep3

city: Changsha

first: Zhi

last: Li

address: NO. 87 Xiangya Road, Kaifu District

country: China

institute: Xiangya hospital, Central South University

description:
DMSO_3_1
gene_count 882.xls

library_source: transcriptomic

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quali
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

source_name: gastrointestinal stromal tissues

extract_protocol:
RNA was harvest using Trizol reagent (Invitrogen), total RNA was used for the construction of sequencing libraries.
Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: gastrointestinal stromal tissues

tag: cell line

value: gastrointestinal stromal tumor

tag: treatment

value: DMSO


title: Plasma, Frail, Subject16b

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

description:
Library name: Sample24
Column name in raw_counts_table.csv: I0PX.019

data_processing:
DIANA-microRNA-Analysis-Pipeline (DIANA-mAP) pipeline (v1.0)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (wihin DIANA-mAP pipeline).
Trimmed sequences were mapped using Bowtie and annotated with miRbase (wihin DIANA-mAP pipeline).
Read count extraction/quantification were performed with DIANA-mAP internal quantification module.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Plasma

extract_protocol:
Total RNA, including the small RNA fraction, was extracted from 800 ul of plasma EDTA using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN, Hilden, Germany). Briefly, samples were lysed with Buffer RPL to denature proteins and inhibit RNases. Inhibitors were precipitated using Buffer RPP, followed by centrifugation to recover the RNA-containing supernatant. Binding conditions were optimized with isopropanol and the mixture was processed through RNeasy UCP MinElute spin columns. After sequential washes with Buffer RWT, Buffer RPE and 80% ethanol to ensure high purity, the total RNA was eluted in 15 µl of nuclease-free water.
NGS libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN, Hilden, Germany). For each sample, the isolated RNA was used as starting material. The library preparation workflow involved the sequential ligation of specialized 3' and 5' adapters to the miRNAs. Following ligation, reverse transcription was performed to synthesize cDNA. During this step, Unique Molecular Indices (UMIs) were integrated into the cDNA molecules to enable unbiased quantification of miRNA expression and minimize PCR-induced bias. The resulting cDNA was purified using QIAseq miRNA NGS beads (QMN beads) and eluted in nuclease-free water.  The purified cDNA was then amplified via PCR using a universal forward primer and sample-specific indexing reverse primers (QIAseq miRNA NGS Index IL) to allow for multiplexing. The final libraries were purified again using a bead-based cleanup procedure. The quality and size distribution of the final miRNA libraries were assessed using the Agilent 2100 Bioanalyzer with a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA). A typical miRNA-sized library was identified by a peak at approximately 180 bp.

value: Plasma

tag: individual

tag: phenotype

value: Frail


title: Methyl-Hi-C in neural stem cells from E16 somatosensory mouse cortex rep1

description: Library name: MethylHiC_NSC_E16_rep1


title: Plasma, Frail, Subject11b

description:
Library name: Sample23
Column name in raw_counts_table.csv: HJ47.010


title: GIST-882 cells, DMSO rep2

description:
DMSO_2_1
gene_count 882.xls


title: Plasma, Frail, Subject10b

description:
Library name: Sample22
Column name in raw_counts_table.csv: H5B9.021


title: Methyl-Hi-C in neural stem cells from E15 somatosensory mouse cortex rep2

description: Library name: MethylHiC_NSC_E15_rep2


title: GIST-882 cells, DMSO rep1

description:
DMSO_1_1
gene_count 882.xls


title: Plasma, Frail, Subject4m

description:
Library name: Sample20
Column name in raw_counts_table.csv: C797.012


title: Plasma, Frail, Subject19m

description:
Library name: Sample19
Column name in raw_counts_table.csv: 8H07.011


title: GIST-882 cells, CS1 rep3

description:
CS1_3_1
gene_count 882.xls


title: Methyl-Hi-C in neural stem cells from E13 somatosensory mouse cortex rep2

description: Library name: MethylHiC_NSC_E13_rep2


title: Plasma, Frail, Subject17m

description:
Library name: Sample17
Column name in raw_counts_table.csv: 6NKR.004


title: GIST-882 cells, CS1 rep2

description:
CS1_2_1
gene_count 882.xls


title: Plasma, Frail, Subject12m

description:
Library name: Sample16
Column name in raw_counts_table.csv: 3UD6.017


title: Methyl-Hi-C in neural stem cells from E13 somatosensory mouse cortex rep1

description: Library name: MethylHiC_NSC_E13_rep1


title: Plasma, Frail, Subject11m

description:
Library name: Sample15
Column name in raw_counts_table.csv: 2LOH.005


title: GIST-882 cells, CS1 rep1

description:
CS1_1_1
gene_count 882.xls


title: Plasma, Frail, Subject3m

description:
Library name: Sample14
Column name in raw_counts_table.csv: 2KRT.023


title: scATAC-seq in E18 somatosensory mouse cortex rep2

description: Library name: scATAC_E18_rep2

library_source: genomic single cell

data_processing:
Raw sequencing data was converted to fastqs using cellranger-atac mkfastq (10x Genomics, v1.2.0). ScATAC reads were aligned to mm10 genome and quantified using cellranger-atac count (10x Genomics v1.2.0) using integrated doublet removal.
Assembly: mm10
Supplementary files format and content: Processed data files represent filtered peak-barcode matrix (*matrix.h5) stored in the Hierarchical Data Format (H5) as well as a gzipped BED-like tabular file containing the genomic position of the obtained fragments, their barcodes and duplication count.

extract_protocol:
Somatosensory cortices were isolated from E13, E15, E16, E17 and E18 mouse embryos after removal of the meninges and dissociated using a papain-based neural dissociation kit (Miltenyi Biotec, Cat. N.: 130-092-628), following the manufacturer’s protocol. Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen).
After tissue dissociation, library preparation for scATAC-seq (10x Genomics, Cat. N: PN-1000110, PN-1000086, PN-1000084) was performed according to the manufacturer's instructions, targeting a recovery of 6000 cells/nuclei per sample. Library concentration was quantified by qPCR using KAPA Library Quantification Kit (Roche, Cat. N: 07960298001) and fragment size distribution was assessed using Agilent 2100 Bioanalyzer.

value: whole tissue


title: Plasma, Not Frail, Subject7b

description:
Library name: Sample13
Column name in raw_counts_table.csv: 26Z6.001

value: Not Frail


title: GIST-T1 cells, DMSO rep3

description:
sample18
gene_count.xls


title: Plasma, Not Frail, Subject13b

description:
Library name: Sample12
Column name in raw_counts_table.csv: 23JN.010


title: scATAC-seq in E18 somatosensory mouse cortex rep1

description: Library name: scATAC_E18_rep1


title: Plasma, Not Frail, Subject12b

description:
Library name: Sample11
Column name in raw_counts_table.csv: 1SKX.013


title: GIST-T1 cells, DMSO rep2

description:
sample17
gene_count.xls


title: Plasma, Not Frail, Subject17b

description:
Library name: Sample10
Column name in raw_counts_table.csv: 0YBL.024


title: scATAC-seq in E17 somatosensory mouse cortex rep2

description: Library name: scATAC_E17_rep2


title: Plasma, Not Frail, Subject9b

description:
Library name: Sample9
Column name in raw_counts_table.csv: YZ62.012


title: GIST-T1 cells, DMSO rep1

description:
sample16
gene_count.xls


title: Plasma, Not Frail, Subject8b

description:
Library name: Sample8
Column name in raw_counts_table.csv: Q844.011


title: scATAC-seq in E17 somatosensory mouse cortex rep1

description: Library name: scATAC_E17_rep1


title: Plasma, Not Frail, Subject1b

description:
Library name: Sample7
Column name in raw_counts_table.csv: KU9N.016


title: GIST-T1 cells, CS1 rep3

description:
sample15
gene_count.xls


title: Plasma, Not Frail, Subject10m

description:
Library name: Sample6
Column name in raw_counts_table.csv: J3FQ.018


title: scATAC-seq in E16 somatosensory mouse cortex rep2

description: Library name: scATAC_E16_rep2


title: rc139-6-2-tscs-rc-ythdc1_rip

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

institute: UNC Chapel Hill

description: Library name: rc139-6-2-tscs-rc-ythdc1_rip

data_processing:
RIP-Seq reads were aligned using STAR v2.5.4b with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools.
Assembly: mm10
Supplementary files format and content: Wiggle tracks were normalized to q30 aligned reads to mm10

source_name: mouse TSCs 6-2

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three to four days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
Both input and immunoprecipitated RNA were purified with the Zymo Clean and Concentrator.
KAPA RNA Hyperprep Kit with RiboErase, 9uL of IP/input RNA + 1uL ERCC RNA spike-in

treatment_protocol: To induce RBP knockdown, TSCs were treated with 1000ng/mL of doxycycline for four days. For all RIP experiments, trypsinized cells were crosslinked with 0.3% formaldehyde (Thermo Fisher, cat #: 28908) in PBS for 30 minutes at 4C with rotation, then quenched with 200mM glycine for 5 minutes at room temperature with rotation. Crosslinked cells were then washed thrice with ice-cold PBS, followed by resuspension in ice-cold PBS and divided into 10-million cell aliquots.

tag: antibody

value: YTHDC1(Proteintech, 29441-1-AP)

value: mouse TSCs 6-2

value: WT


title: Plasma, Not Frail, Subject24m

description:
Library name: Sample5
Column name in raw_counts_table.csv: ISGQ.003


title: DNA of MPRA in neural stem cells from E16 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_NSC_E15_rep1

data_processing:
50xbp paired-end reads from the DNA or RNA libraries were trimmed using cutadapt with the following parameters: -u 1 -a GAATTCTCATTAC -A TCGACCGCAAGTTGG --discard-untrimmed. Count tables for DNA and RNA reads were generated using MPRAflow (--bc-length 12 and –mpranalyze).
Assembly: mm10
Supplementary files format and content: tab-seperated file containing the output from MRPA flow and MPRA analyze

extract_protocol:
Somatosensory cortices from E13, E14, E15, E16 and E17 mouse embryos (in utero electroporated at E12, E13, E14, E15 and E16, respectively) were isolated after the removal of the meninges and dissociated using a papain-based neural dissociation kit (Miltenyi Biotec, Cat. N.: 130-092-628) according to the manufacturer’s protocol. Single cells were then fixed at RT for 10 minutes in 1% Formaldehyde in PBS (ThermoFisher, Cat. N: 28908) and quenched with final 0.2M Glycine (Invitrogen, Cat. N: 15527013). Fixed cells were spun down with 500g at 4˚C for 5 minutes, washed once with 1% BSA (ThermoFisher, Cat. N: AM2618) in PBS and incubated at 4°C for 10minutes in permeabilization buffer (0.1% Saponin (Sigma-Aldrich, Cat. N: SAE0073), 0.2% BSA and 1% RNAsin plus RNase inhibitor (Promega, Cat. N: N261A) in PBS). Cells were washed at 2500g at 4˚C for 5minutes,  following the staining against Pax6 (1:40, BD 561664), Eomes (1:33, BD 566749) and Tubb3 (1:14, BD 560394) in staining buffer (0.1% saponin, 1% BSA, 0.1% RNAsin plus RNase inhibitor in PBS) at 4˚C for 1h with slow rotation. Cells were washed twice with permeabilization buffer, once with PBS with DAPI (1:1000; ThermoFisher, Cat. N: 62248) and a final wash with PBS containing 0.5% BSA. After the last wash the cells were resuspended in PBS with 1% BSA and 1% RNAsin plus RNase inhibitor, filtered with a 40µM cell strainer (ThermoFisher, Cat. N: 15342931) and FAC-sorted. Sorted Pax6+ cells (NSC) and Tbr2+ cells (IPC) were digested with Proteinase K (Proteinase K (New England Biolabs, Cat. N: P8107S) at 55˚C for 1 h and decrosslinked at 65 ˚C for 15 minutes. DNA and RNA were extracted using the Quick-DNA/RNA Microprep Plus Kit (Zymo Research; Cat. N: D7005). Purified RNA was treated with TURBO DNase (Thermo Fisher; Cat. N: AM1907) and reverse transcribed with Maxima H Minus RT (Thermo Fisher; Cat. N: EP0753) using Oligo(dT)18 Primer (Thermo Fisher; Cat. N: SO131). cDNA was purified with 1.5X vol. AMPure XP magnetic beads (Agencourt, Cat. N: A63881) and stored at -20 °C for later use.
Libraries were prepared from both DNA and cDNA using the same protcol. In brief, UMIs were incorporated by PCR using the primers RV_univ_MPRA (CGACGCTCTTCCGATCT) and FWD_mScar_Tn7_10UMI_3 (0.5 µM each; GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG NNNNNNNNNN TCGACCGCAAGTTGGAC) with the following conditions: 98°C 30s; {98°C 10s, 65°C 30s, 72°C 1min} x3; 72°C 3min; Hold at 4°C. P7 and P5 sequencing adapters were added in two separate PCRs using indexed Ad2.X(CAAGCAGAAGACGGCATACGAGAT XXXXXXXX GTCTCGTGGGCTCGGAGATGT) and P5NEXTPT5 primers (0.1 µM each; AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T) with the following conditions: 98°C 30s; {98°C 10s, 65°C 90s} x(10+X); 72°C 5min; Hold at 4°C. The required number of PCR cycles was determined by qPCR, using 1/10 of the second PCR product as input. All amplification steps were carried out using 1X NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs; Cat. N: M0544). PCR products were purified using AMPure XP magnetic beads at a volume ration of 0.8X to 1.2X.


title: GIST-T1 cells, CS1 rep2

description:
sample14
gene_count.xls


title: Plasma, Not Frail, Subject23m

description:
Library name: Sample4
Column name in raw_counts_table.csv: IJBS.007


title: DNA of MPRA in neural stem cells from E15 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_NSC_E14_rep2


title: scATAC-seq in E16 somatosensory mouse cortex rep1

description: Library name: scATAC_E16_rep1


title: Plasma, Not Frail, Subject21m

description:
Library name: Sample3
Column name in raw_counts_table.csv: IDL6.008


title: Patient 1 pre treatment scRNA-seq

city: Houston

first: Ziyi

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

data_processing:
Processing of raw reads was performed using the Cell Ranger software provided by 10X genomics and the hg38 human reference genome (GRCm38 v86 and corresponding GENCODE annotation file). During read alignment, PCR duplicates were removed. The UMI (unique molecular identifier) for each gene is counted to measure the gene expression levels. The cell doublet status is inferred by the software DoubletFinder. A number of quality-control metrics are evaluated to control the data quality, including the total UMI count, the total number of genes detected, the mitochondrial gene ratio, log10(gene number) per UMI, and the inferred status of cell doublet.  Low-quality cells with a total UMI count smaller than 500, a total number of genes smaller than 200, and a mitochondrial gene ratio greater than 50% are excluded for further analysis.
Assembly: GRCm38 v86
Supplementary files format and content: Filtered bc matrix from CellRanger and Parse pipelines.

source_name: Tumor biopsy

extract_protocol:
The sample was incubated at 37 °C for 5 min. After dissociation, 2ml of advanced DMEM+10%FBS media was added to the sample and filtered through a 70 μm cell strainer (Fisher Scientific, cat.43-10070-40) into Eppendorf tubes
The filtrate was centrifuged at 500g for 5 min, and the supernatant was removed. If the pellet was bloody, red blood cell (RBC) removal was performed using RBC Lysis Solution (1x) (Miltenyi Biotec, cat. No. 130-094-183) for 10 min at RT. Sample was then centrifuged at 500g for 5 min and pellet was resuspended in 1ml of advanced DMEM, to be combined into one Eppendorf tube.
The single-cell suspension was visualized, counted, and stored at nitrogen until 10x Genomics Single-Cell sequencing was performed.

value: Tumor biopsy

value: Before


title: GIST-T1 cells, CS1 rep1

description:
sample13
gene_count.xls


title: Plasma, Not Frail, Subject20m

description:
Library name: Sample2
Column name in raw_counts_table.csv: 92YX.020


title: scATAC-seq in E15 somatosensory mouse cortex rep2

description: Library name: scATAC_E15_rep2


title: Plasma, Not Frail, Subject7m

description:
Library name: Sample1
Column name in raw_counts_table.csv: 1TCS.007


title: GIST-430 cells, DMSO rep3

description:
sample12
gene_count.xls


title: DNA of MPRA in neural stem cells from E14 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_NSC_E13_rep1


title: Patient 18 pre treatment scRNA-seq


title: DNA of MPRA in neural stem cells from E13 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_NSC_E12_rep2


title: scATAC-seq in E15 somatosensory mouse cortex rep1

description: Library name: scATAC_E15_rep1


title: A549 MT-2 SN 4

city: Leuven

first: Clément

middle: Jacques François

last: Heymann

address: 49 Herestraat

department: Microbiology, Immunology and Transplantation

country: Belgium

institute: Rega Institute (KU Leuven, Belgium)

description: Library name: GC154264.p4

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads' quality, total bases, total reads, GC (%) and basic statistics are calculated
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Assembly: Expression profiles are represented as read count.
Supplementary files format and content: GRCh38
Supplementary files format and content: tab-delimited text files include total counts values for each sample

source_name: lung

growth_protocol: A549 cells were maintained in HAM’s F-12K medium (Thermo Fisher Scientific [TFS], Waltham, MA, USA) supplemented with 5% fetal bovine serum (FBS, Cytiva, Marlborough, MA, USA) and 2mM L-Glutamine (TFS). MT-2, MT-4 and Jurkat cells were cultured in RPMI (TFS) supplemented with 10% FBS (Cytiva) and 2mM L-Glutamine (TFS).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Venlo, the Netherlands) and the samples were submitted to the Genomics core facility (KU Leuven) for RNA sequencing analysis.
Sequencing of the samples was performed by the Genomics core facility  of KU Leuven.

treatment_protocol: A549 were seeded at 4×10⁵cells/well 24 h prior co-culture or stimulation with cell culture supernatant. MT-2, MT-4 and Jurkat cells were treated with 5µM mitomycin C (Adooq Bioscience1) and added to the co-culture at a 1:1 ratio (4×10⁵ cells/well).

value: lung

value: Cancer epithelial cell

value: MT-2 SN co-culture


title: GIST-430 cells, DMSO rep2

description:
sample11
gene_count.xls


title: P30_LayerII-IV_rep1

description:
scRNA_OL_layers_raw_counts.dge.txt
scRNA_OL_layers_metadata.txt

value: S1 cortex

value: Oligodendrocyte

value: Fezf2 CreERT2 +/- ; td-Tomato +/- ; Plp1-eGFP +/-


title: Patient 16 post treatment scRNA-seq

value: After


title: A549 MT-2 SN 3

description: Library name: GC154258.p3


title: scATAC-seq in E13 somatosensory mouse cortex rep2

description: Library name: scATAC_E13_rep2

value: somatosensory cortex

value: C57BL/6JRj (Haplotype H2b)


title: A549 MT-2 SN 2

description: Library name: GC154252.p2


title: A549 MT-2 SN 1

description: Library name: GC154246.p1

value: MT-2 co-culture


title: GIST-430 cells, DMSO rep1

description:
sample10
gene_count.xls

value: gastrointestinal stromal tissues

value: gastrointestinal stromal tumor

value: DMSO


title: Patient 17 post treatment scRNA-seq


title: A549 MT-2 5

description: Library name: GC154269.p5


title: GIST-430 cells, CS1 rep3

description:
sample9
gene_count.xls


title: scATAC-seq in E13 somatosensory mouse cortex rep1

description: Library name: scATAC_E13_rep1

value: whole tissue


title: Patient 17 pre treatment scRNA-seq


title: A549 MT-2 4

description: Library name: GC154263.p4

value: WT


title: A549 MT-2 3

description: Library name: GC154257.p3


title: scRNA-seq in E18 somatosensory mouse cortex rep2

description: Library name: scRNA_E18_rep2

data_processing:
Raw sequencing data was converted to fastqs using cellranger mkfastq (10x Genomics, v3.1.0). ScRNA reads were aligned to mm10 genome and quantified using cellranger count (10x Genomics v3.1.0).
Assembly: mm10
Supplementary files format and content: Processed data files represent filtered feature-barcode matrix (*mtx.gz) stored in the Market Exchange Format (MEX) for sparse matrices as well as gzipped TSV files with feature and barcode sequences corresponding to row and column indices respectively.

molecule: polyA RNA

extract_protocol:
Somatosensory cortices were isolated from E13, E15, E16, E17 and E18 mouse embryos after removal of the meninges and dissociated using a papain-based neural dissociation kit (Miltenyi Biotec, Cat. N.: 130-092-628), following the manufacturer’s protocol. Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen).
After tissue dissociation, library preparation for scRNA-seq (v3, 10x Genomics, Cat. N: PN-1000075, PN-1000074, PN-120262) was performed according to the manufacturer's instructions, targeting a recovery of 6000 cells/nuclei per sample. Library concentration was quantified by qPCR using KAPA Library Quantification Kit (Roche, Cat. N: 07960298001) and fragment size distribution was assessed using Agilent 2100 Bioanalyzer.


title: A549 MT-2 2

description: Library name: GC154251.p2


title: GIST-430 cells, CS1 rep2

description:
sample8
gene_count.xls


title: scRNA-seq in E18 somatosensory mouse cortex rep1

description: Library name: scRNA_E18_rep1


title: A549 MT-2 1

description: Library name: GC154245.p1


title: GIST-430 cells, CS1 rep1

description:
sample7
gene_count.xls


title: A549 MT-4 SN 5

description: Library name: GC154268.p5

value: MT-4 SN co-culture


title: scRNA-seq in E17 somatosensory mouse cortex rep2

description: Library name: scRNA_E17_rep2


title: A549 MT-2 SN 5

description: Library name: GC154270.p5


title: GIST-48 cells, DMSO rep3

description:
sample6
gene_count.xls


title: A549 MT-4 SN 4

description: Library name: GC154262.p4


title: A549 MT-4 SN 1

description: Library name: GC154244.p1


title: scRNA-seq in E17 somatosensory mouse cortex rep1

description: Library name: scRNA_E17_rep1


title: A549 MT-4 6

description: Library name: GC154272.p6

value: MT-4 co-culture


title: scRNA-seq in E16 somatosensory mouse cortex rep2

description: Library name: scRNA_E16_rep2


title: GIST-48 cells, DMSO rep2

description:
sample5
gene_count.xls


title: A549 MT-4 5

description: Library name: GC154267.p5

value: lung


title: A549 MT-4 SN 3

description: Library name: GC154256.p3

value: Cancer epithelial cell


title: GIST-48 cells, DMSO rep1

description:
sample4
gene_count.xls


title: A549 MT-4 4

description: Library name: GC154261.p4


title: scRNA-seq in E16 somatosensory mouse cortex rep1

description: Library name: scRNA_E16_rep1


title: A549 MT-4 3

description: Library name: GC154255.p3


title: GIST-48 cells, CS1 rep3

description:
sample3
gene_count.xls


title: A549 MT-4 2

description: Library name: GC154249.p2


title: A549 MT-4 1

description: Library name: GC154243.p1


title: Plasma, Frail, Subject5b

description:
Library name: Sample21
Column name in raw_counts_table.csv: GIFQ.017

value: Plasma

value: Frail


title: scRNA-seq in E15 somatosensory mouse cortex rep2

description: Library name: scRNA_E15_rep2


title: GIST-48 cells, CS1 rep2

description:
sample2
gene_count.xls


title: Methyl-Hi-C in neural stem cells from E15 somatosensory mouse cortex rep1

description: Library name: MethylHiC_NSC_E15_rep1

value: neural stem cells (Pax6+)


title: A549 Jurkat 5

description: Library name: GC154266.p5

value: Jurkat co-culture


title: A549 Jurkat 4

description: Library name: GC154260.p4


title: scRNA-seq in E15 somatosensory mouse cortex rep1

description: Library name: scRNA_E15_rep1


title: GIST-48 cells, CS1 rep1

description:
sample1
gene_count.xls


title: A549 Jurkat 3

description: Library name: GC154254.p3


title: scRNA-seq in E13 somatosensory mouse cortex rep2

description: Library name: scRNA_E13_rep2


title: A549 Jurkat 2

description: Library name: GC154248.p2


title: RNA-seq of Pinus sylvestris, Embryo 48 hours after germination, tree 320

city: Helsingin yliopisto

first: Tanja

last: Pyhäjärvi

state: Finland

address: Department of Forest Sciences

department: Department of Forest Sciences

country: Finland

institute: University of Helsinki

description: Library name: 320A

data_processing:
We followed the Trinity Post-Transcriptome Assembly Downstream Analyses pipeline (Trinity v.2.6.6) (Haas et al., 2013, https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification) to generate quantification files at isoform level, and raw counts and normalized count matrices at putative-gene level.
To obtain independent transcript abundance estimates of each of the six individuals in each of the five tissues we used Salmon 0.9.1 (Patro et al., 2017) as implemented in the Trinity pipeline, with the --SS_lib_type (strand specific) and --trinity_mode options. The –trinity_mode option generated a transcript-to-gene map that allowed the estimation of counts from isoforms to generate counts at a putative gene level during the count matrix generation step.
We built three count matrices at the gene level based on the clean independent transcript quantification estimates with the script abundance_estimates_to_matrix.pl from the Trinity pipeline. For this, we generated a gene level raw counts matrix, which was then used to construct a transcript per million length normalized gene count matrix (TPM escalated matrix). The TPM escalated matrix accounts for differences in isoform lengths that otherwise could inflate FDR due to differential transcript usage (Soneson, Love & Robinson, 2015). Finally, the TPM escalated matrix was used to construct a gene counts matrix normalized using the Trimmed Mean of M values (TMM) method, which accounts for differences in the distribution of transcript expression that could lead to an increase in false positive rates, and decrease the power to detect truly differentially expressed genes (Robinson & Oshlack, 2010).
Assembly: P. sylvestris TRINITYguided transcriptome (Ojeda et al. 2019), GenBank: GILN000000000.1
Supplementary files format and content: TMM normalized gene counts used to asses patters of tissue preferential expression. A=embryo, KS=vegetative bud, M=megagametophyte, N=needle, Ni=phloem
Supplementary files format and content: TPM normalized gene counts of five different Scots pine tissues. A=embryo, KS=vegetative bud, M=megagametophyte, N=needle, Ni=phloem

organism: Pinus sylvestris

source_name: Embryo

extract_protocol:
mRNA was directly extracted from the embryo and megagametophyte using Dynabeads mRNA Direct Micro Kit according to manufacturer’s instructions, except for a minor modification (using 200 µl of lysis buffer). Total RNA was extracted from needles, vegetative buds, and phloem with the Spectrum Plant Total RNA Kit (Protocol B, Sigma). After total RNA extraction, mRNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc.). mRNA extractions were treated with Turbo DNA-free Kit (Thermo Fisher Scientific). RNA concentration was quantified using Qubit 2.0 (Invitrogen) and Qubit RNA HS Assay Kit (Thermo Fisher Scientific).
All libraries (6 trees × 5 tissues) were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs Inc.) with a fragmentation time of 5-12 min. An insert size selection of 300 bp was targeted using a concentration of 40-45 µl per 20 µl AMPure XP (Agencourt) and between 12-15 cycles of PCR during library preparation. Libraries were indexed using NEBNext Multiplex Oligos for Illumina, Single Index Set 1. RNA library concentrations were quantified using NEBNext Library Quant Kit for Illumina and LightCycler 480 (Roche). Fragment size distributions of mRNA, total RNA and libraries were verified with 2100 Bioanalyzer RNA 6000 Pico Kit and DNA 1000 kits (Agilent). 6-12 libraries were pooled in 5 runs of an Illumina NextSeq500 instrument using pair-end 2 × 150 bp and sequenced with Mid-Output Kit (Illumina) in the Biocenter Oulu Sequencing Center.

value: Embryo


title: Plasma, Frail, Subject18m

description:
Library name: Sample18
Column name in raw_counts_table.csv: 7IJD.009


title: scRNA-seq in E13 somatosensory mouse cortex rep1

description: Library name: scRNA_E13_rep1

value: somatosensory cortex


title: A549 Jurkat 1

description: Library name: GC154242.p1

value: Control


title: A549 control 6

description: Library name: GC154271.p6


title: RNA-seq of Pinus sylvestris, mature tree, vegetative bud, tree 320

description: Library name: 320KS

source_name: Vegetative bud

value: Vegetative bud


title: RNA-seq of Pinus sylvestris, mature tree, phloem, tree 251

description: Library name: 251Ni

source_name: Phloem

value: Phloem


title: A549 control 4

description: Library name: GC154259.p4


title: A549 control 2

description: Library name: GC154247.p2


title: A549 control 5

description: Library name: GC154265.p5


title: CD4cre_Dock2flox_2

city: Guangzhou

first: Shaoting

last: Xu

state: Outside of the US

address: 58 ZhongShan Second Road

institute: SYSU

description:
Library name: Sample 5
Column names in filter_annotation_all_Samples.csv: CD4cre_Dock2flox_2

data_processing:
Raw sequence data processing was conducted in QIIME2 and Dada2 following official tutorials. Briefly, raw sequence data were demultiplexed using the demux plugin followed by primers cutting with the cutadapt plugin. Sequences were then quality filtered, denoised, merged and chimera removed using the DADA2 plugin. Non-singleton amplicon sequence variants (ASVs) were aligned with mafft and used to construct a phylogeny with fasttree2.
Assembly: Greengenes2 2022.10
Supplementary files format and content: csv file includes the counts and taxonomic classification for each ASV in each sample
Supplementary files format and content: fna file includes the representative sequences of each ASV
Library strategy: 16S rRNA-seq

source_name: feces

extract_protocol:
Total genomic DNA was extracted using the OMEGA Soil DNA Kit (M5635-02). For fecal 16S rDNA sequencing, bacterial genomic DNA (>500 ng) was amplified targeting the V3-V4 region with primers (forward: ACTCCTACGGGAGGCAGCA; reverse: GGACTACHVGGGTWTCTAAT) containing 7-bp barcodes. PCR products were purified (Vazyme VAHTSTM DNA Clean Beads) and quantified (Quart-IT PicoGreen dsDNA Assay Kit).
Amplicons were pooled in equal amounts, and pair-end 2250 bp sequencing was performed on the Illumina NovaSeq platform (NovaSeq 6000 SP Reagent Kit).

value: feces

value: Untreated


title: A549 control 1

description: Library name: GC154241.p1


title: RNA-seq of Pinus sylvestris, Megagametophyte 48 hours after germination, tree 320

description: Library name: 320M

source_name: Megagametophyte

value: Megagametophyte


title: D57 Retina, SCR206, Temporal Central region, ATAC

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

description:
Library name: D57_Temporal_Central_Retina_ATAC
SCR206_filtered_feature_bc_matrix.h5

data_processing:
Cellranger arc count (v2.0.2) was used to align RNA and ATAC sequencing reads to the GRCh38 reference genome. MACS3 was called separately on the center and periphery samples to define ATAC peaks and then unified to create a single peak set. Low quality cells that had fewer than 100 ATAC reads in peaks and fewer than 500 RNA reads were removed.
Assembly: GRCh38
Supplementary files format and content: Gene and peak expression matrices generated from cellranger arc count are supplied for central and peripheral retina as filtered_feature_bc_matrix.h5 files.
Supplementary files format and content: Additionally, the ATAC fragment files generated from cellranger arc count are supplied as atac_fragments.tsv.gz files

source_name: Retina

extract_protocol:
We dissected the central temporal and the peripheral nasal regions of a human fetal retina at D57.
Nuclei from both samples were isolated using the Chromium Nuclei isolation kit (10x Genomics), following the manufacturer’s protocol. The isolated nuclei were then loaded onto a Chromium Chip J. and processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. Briefly, nuclei were encapsulated in a gel matrix and uniquely barcoded using the 10x Chromium Controller.

value: Retina

value: Retinal neurons and progenitors

value: Dissected from temporal central region

value: Fetal D57


title: CD4cre_Dock2flox_3

description:
Library name: Sample 6
Column names in filter_annotation_all_Samples.csv: CD4cre_Dock2flox_3


title: CD4cre_Dock2flox_1

description:
Library name: Sample 4
Column names in filter_annotation_all_Samples.csv: CD4cre_Dock2flox_1


title: D57 Retina, SCR206, Temporal Central region, RNA

description:
Library name: D57_Temporal_Central_Retina_RNA
SCR206_filtered_feature_bc_matrix.h5

molecule: nuclear RNA


title: RNA-seq of Pinus sylvestris, Megagametophyte 48 hours after germination, tree 251

description: Library name: 251M


title: D57 Retina, SCR205, Nasal Peripheral region, ATAC

description:
Library name: D57_Nasal_Peripheral_Retina_ATAC
SCR205_filtered_feature_bc_matrix.h5

value: Dissected from nasal peripheral region


title: Dock2flox_3

description:
Library name: Sample 3
Column names in filter_annotation_all_Samples.csv: Dock2flox_3


title: RNA-seq of Pinus sylvestris, Embryo 48 hours after germination, tree 251

description: Library name: 251A


title: D57 Retina, SCR205, Nasal Peripheral region, RNA

description:
Library name: D57_Nasal_Peripheral_Retina_RNA
SCR205_filtered_feature_bc_matrix.h5


title: Dock2flox_2

description:
Library name: Sample 2
Column names in filter_annotation_all_Samples.csv: Dock2flox_2


title: BATO3

city: HangZhou

first: Rong

last: Chen

state: Zhejiang

address: Fuchun Road

department: College of Pharmacy

institute: Zhejiang Chinese Medical University

description:
Library name: Sample12
BxPC-3.processed.data.xlsx

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quahty limit:0.05).
Trimmed saquence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parametars- mismath cost: 2 insertion  st: 3 doletion coat: 3 length fraction:0.8 similurity fraction 0.8.
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: hg38
Supplementary files format and content: AsPC-1.processed.data.xlsx
Supplementary files format and content: BxPC-3.processed.data.xlsx

source_name: tumor

extract_protocol:
RNA was harvested using Rneasy mini plug lt (Qiagen) 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq ware prepared using SMARTER mRNA-Seq Library Prep Kit folloing manulacturers protocols.

value: tumor

value: pancreatic ductal adenocarcinoma cell

value: WT


title: BATO1

description:
Library name: Sample10
BxPC-3.processed.data.xlsx


title: BCtrl3

description:
Library name: Sample9
BxPC-3.processed.data.xlsx


title: BATO2

description:
Library name: Sample11
BxPC-3.processed.data.xlsx


title: Dock2flox_1

description:
Library name: Sample 1
Column names in filter_annotation_all_Samples.csv: Dock2flox_1


title: RNA-seq of Pinus sylvestris, mature tree, needle, tree 251

description: Library name: 251N

source_name: Needle

value: Needle


title: RNA-seq of Pinus sylvestris, mature tree, vegetative bud, tree 251

description: Library name: 251KS


title: OE-B-H-R-3

city: wuhan

first: wu

last: chen

address: jiefang road

department: urology

institute: Renmin Hospital of Wuhan University

data_processing:
The sequencing data was processed using Cutadapt (version 2.7) to remove sequencing adapters, low-quality reads, short reads with more N, and reads shorter thn 16 bp.
Subsequently,perl5 (version 26) was used to process reads with UMIs shorter than 12 bp and reads without UMIs, and to identify UMIs.
The bowtie software (version 1.3.0) was then employed to compare the reads against the miRBase database.
Finally,small RNA quantification was performed by comparing the mapped reads to the miRBase.
The R package edgeR is used to calculate the expression difference based on grouping information from the obtained expression UMl counts matrix, aiming to identify miRNAs that are significantly differentially expressed (either being up-regulated or down-regulated).
Assembly: miRBase v22
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: kidney

growth_protocol: Mouse kidney tubular epithelial cells (TCMK-1, ATCC® CCL-139TM, Beijing Bnbio Co., Ltd., China) were cultivated in MEM/EBSS medium (HyClone, Cytiva) with 10% foetal bovine serum (FBS) (Gibco, USA) at 37 °C with 5% CO2.

extract_protocol:
Exosomes were isolated at 4 °C by differential centrifugation. Briefly, the medium supernatant of TCMK-1 cells was collected, and the cells and debris were removed by centrifugation at 300 × g for 10 min, 2000 × g for 20 min and 10,000 × g for 30 min. For exosome isolation, the supernatant was ultracentrifuged at 100,000 × g for 2 h (OptimaXE-100, Beckman). The precipitate was resuspended in phosphate‐buffered saline (PBS) and ultracentrifuged again at 100,000 × g to remove contaminating proteins. Finally, the exosomes were resuspended in PBS and quantified for subsequent experiments.Exosomes were identified by NTA,TEM, and Western blot, and total RNA was extracted.
MicroRNA libraries for miRNA-seq were prepared using the QlAseq miRNA Library Kit (Qiagen, USA) following the manufacturer's standard protocol.

treatment_protocol: To achieve H/R conditions, TCMK-1 cells were cultured in exosome-free medium in a three-gas incubator containing 94% N2, 5% CO2 and 1% O2 for 24 h followed by reoxygenation (5% CO2, 21% O2, and 74% N2) for 12 h.For lentiviral infections, the lentiviral vector designated LV-BMAL1 (pcSLenti-EF1-EGFP-P2A-Puro-CMV-BMAL1-3xFlag-WPRE) was used for BMAL1 gene (NM_001368412.1) delivery and stable overexpression. The empty vector designated LV-NC (pcSLenti-EF1-EGFP-P2A-Puro-CMV-MSC-3xFlag-WPRE) was used as a negative control. The MOI was 100.

value: kidney

value: Mouse renal tubular epithelial cells

value: H/R culture was performed after transfection of lentivirus overexpressing BMAL1


title: BCtrl1

description:
Library name: Sample7
BxPC-3.processed.data.xlsx


title: BCtrl2

description:
Library name: Sample8
BxPC-3.processed.data.xlsx


title: RNA-seq of Pinus sylvestris, mature tree, phloem, tree 320

description: Library name: 320Ni


title: AATO3

description:
Library name: Sample6
AsPC-1.processed.data.xlsx


title: OE-B-H-R-2


title: AATO2

description:
Library name: Sample5
AsPC-1.processed.data.xlsx


title: RNA-seq of Pinus sylvestris, mature tree, needle, tree 320

description: Library name: 320N


title: AATO1

description:
Library name: Sample4
AsPC-1.processed.data.xlsx


title: ACtrl3

description:
Library name: Sample3
AsPC-1.processed.data.xlsx


title: OE-B-H-R-1


title: RNA-seq of Pinus sylvestris, mature tree, phloem, tree 397

description: Library name: 397Ni


title: VEC-H-R-3

value: H/R culture was performed after transfection with control lentivirus


title: ACtrl2

description:
Library name: Sample2
AsPC-1.processed.data.xlsx


title: VEC-H-R-2


title: RNA-seq of Pinus sylvestris, Embryo 48 hours after germination, tree 443

description: Library name: 443A

value: Embryo


title: bBL_oocytes,SAC-Seq treated (A site modified) sampes_Replicate2

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

description: Library name: bBL_T_B

data_processing:
Raw m6A-SAC-seq reads were adapter-trimmed using Trimmomatic v0.39. PCR duplicates were removed with fastx_collapser, and 5′/3′ barcodes were trimmed (5 and 11 bases, respectively). R1 reads >15 nt were retained for analysis.
Assembly: Preprocessed m6A-SAC-seq reads were aligned to the bovine genome (ARS-UCD1.3) using STAR v2.5.3a with default settings, allowing slightly relaxed mismatch criteria based on read length to capture potential base mutations.
Supplementary files format and content: txt; raw read counts

organism: Bos taurus

growth_protocol: Oocytes were collected from slaughterhouse-derived bovine ovaries. Cumulus-oocyte complexes (COCs) from 3–5 mm follicles were selected based on morphology and matured in BO-IVM medium at 38.5°C with 6% CO₂ for 22–23 hours. After confirming polar body extrusion, matured oocytes were fertilized in vitro using cryopreserved Holstein semen (2 × 10⁶ sperm/ml) for 18 hours. Presumptive zygotes were cultured in SOF-BE2 medium (30 embryos/50 µl drop) under mineral oil at 38.5°C in 5% CO₂, 5% O₂, and 90% N₂ until day 7.5.

extract_protocol:
samples were lysed in TRIsolution (Sigma), followed by phase separation with chloroform. The aqueous phase was collected, and RNA was precipitated with isopropanol, washed with ethanol, and resuspended in nuclease-free water.
Total RNA was directly subjected to Selectively Allyl-Chemically Labeled m6A Sequencing to achieve single-nucleotide resolution detection of m6A modifications. The RNA underwent selective allyl-chemical labeling of m6A sites, followed by reverse transcription using a modified primer designed to introduce mutation signatures indicative of m6A presence. cDNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs)


title: RNA-seq of Pinus sylvestris, mature tree, vegetative bud, tree 443

description: Library name: 443KS

value: Vegetative bud


title: ACtrl1

description:
Library name: Sample1
AsPC-1.processed.data.xlsx


title: bBL_oocytes,SAC-Seq treated (A site modified) sampes_Replicate1

description: Library name: bBL_T_A


title: VEC-H-R-1


title: bBL_embryo, SAC-Seq Input sampes_Replicate2

description: Library name: bBL_I_B


title: RNA-seq of Pinus sylvestris, Megagametophyte 48 hours after germination, tree 443

description: Library name: 443M


title: bBL_embryo, SAC-Seq Input sampes_Replicate1

description: Library name: bBL_I_A


title: RNA-seq of Pinus sylvestris, Megagametophyte 48 hours after germination, tree 397

description: Library name: 397M


title: bMorula_oocytes,SAC-Seq treated (A site modified) sampes_Replicate1

description: Library name: bMorula_T_A


title: bMorula_embryo, SAC-Seq Input sampes_Replicate2

description: Library name: bMorula_I_B


title: bMorula_embryo, SAC-Seq Input sampes_Replicate1

description: Library name: bMorula_I_A


title: VEC-N-2

value: Normal culture was performed after transfection with control lentivirus


title: VEC-N-1


title: NT30_Control (Rep-3)

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

data_processing:
Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software.
FastQC-quality controlled reads were mapped to the mouse transcriptome (GRCm39) based on Ensembl annotations using Kallisto v0.50.1
Assembly: GRCm39
Supplementary files format and content: Raw counts and TPMs computed by kallisto

source_name: Lymph nodes

extract_protocol:
RNA was isolated from TRI Reagent (Zymo Research) samples using Direct-zol RNA Microprep and Miniprep kits (Zymo Research) according to the manufacturer’s protocol.
Strand-specific RNA sequencing libraries were prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: We performed bulk RNA sequencing (RNAseq) from the dLN of mice at 1-, 3-, and 7-days after the priming with Comirnaty, the mannadjuvant and Comirnaty, alum and Comirnaty, or saline-injected controls

value: Lymph nodes

value: Non-treated Control


title: RNA-seq of Pinus sylvestris, mature tree, vegetative bud

description: Library name: 397KS


title: b16Cell_embryo, SAC-Seq Input sampes_Replicate1

description: Library name: b16Cell_I_A


title: NT29_Control (Rep-2)


title: RNA-seq of Pinus sylvestris, mature tree, phloem, tree 443

description: Library name: 443Ni

value: Phloem


title: b8Cell_oocytes,SAC-Seq treated (A site modified) sampes_Replicate1

description: Library name: b8Cell_T_A


title: NT28_Control (Rep-1)


title: RNA-seq of Pinus sylvestris, mature tree, needle, tree 443

description: Library name: 443N


title: b4Cell_oocytes,SAC-Seq treated (A site modified) sampes_Replicate2

description: Library name: b4Cell_T_B


title: b8Cell_embryo, SAC-Seq Input sampes_Replicate1

description: Library name: b8Cell_I_A


title: RNA-seq of Pinus sylvestris, mature tree, needle, tree 485

description: Library name: 485N


title: b4Cell_embryo, SAC-Seq Input sampes_Replicate1

description: Library name: b4Cell_I_A


title: RNA-seq of Pinus sylvestris, mature tree, phloem, tree 485

description: Library name: 485Ni


title: C25_Comirnaty+Alum_Day-7 (Rep-1)


title: All patients all timepoints PBMC scTCR-seq

library_source: other

molecule: protein

source_name: Peripheral Blood Mononuclear Cells (PBMC)

value: All - mulitplexed


title: b2Cell_oocytes,SAC-Seq treated (A site modified) sampes_Replicate2

description: Library name: b2Cell_T_B


title: RNA-seq of Pinus sylvestris, mature tree, phloem, tree 463

description: Library name: 463Ni


title: b2Cell_oocytes,SAC-Seq treated (A site modified) sampes_Replicate1

description: Library name: b2Cell_T_A


title: VEC-N-3


title: bMorula_oocytes,SAC-Seq treated (A site modified) sampes_Replicate2

description: Library name: bMorula_T_B


title: C24_Comirnaty+MA_Day-7 (Rep-3)


title: RNA-seq of Pinus sylvestris, Embryo 48 hours after germination, tree 485

description: Library name: 485A


title: b2cell_embryo, SAC-Seq Input sampes_Replicate1

description: Library name: b2cell_I_A


title: b2Cell_embryo, SAC-Seq Input sampes_Replicate2

description: Library name: b2Cell_I_B


title: b16Cell_oocytes,SAC-Seq treated (A site modified) sampes_Replicate1

description: Library name: b16Cell_T_A


title: RNA-seq of Pinus sylvestris, Embryo 48 hours after germination, tree 397

description: Library name: 397A


title: b16Cell_oocytes,SAC-Seq treated (A site modified) sampes_Replicate2

description: Library name: b16Cell_T_B


title: RNA-seq of Pinus sylvestris, mature tree, needle, tree 397

description: Library name: 397N


title: b16Cell_embryo, SAC-Seq Input sampes_Replicate2

description: Library name: b16Cell_I_B


title: C23_Comirnaty+MA_Day-7 (Rep-2)


title: bMII_oocytes,SAC-Seq treated (A site modified) sampes_Replicate2

description: Library name: bMII_T_B

source_name: Oocytes

value: Oocytes


title: RNA-seq of Pinus sylvestris, Megagametophyte 48 hours after germination, tree 485

description: Library name: 485M

value: Megagametophyte


title: C22_Comirnaty+MA_Day-7 (Rep-1)


title: bMII_oocytes,SAC-Seq treated (A site modified) sampes_Replicate1

description: Library name: bMII_T_A


title: b8Cell_oocytes,SAC-Seq treated (A site modified) sampes_Replicate2

description: Library name: b8Cell_T_B


title: b8Cell_embryo, SAC-Seq Input sampes_Replicate2

description: Library name: b8Cell_I_B


title: bMII_oocytes,SAC-Seq Input sampes_Replicate2

description: Library name: bMII_I_B


title: RNA-seq of Pinus sylvestris, mature tree, vegetative bud, tree 485

description: Library name: 485KS


title: bMII_oocytes,SAC-Seq Input sampes_Replicate1

description: Library name: bMII_I_A


title: C21_Comirnaty_Day-7 (Rep-3)


title: bGV_oocytes,SAC-Seq treated (A site modified) sampes_Replicate2

description: Library name: bGV_T_B


title: C27_Comirnaty+Alum_Day-7 (Rep-3)


title: RNA-seq of Pinus sylvestris, Embryo 48 hours after germination, tree 463

description: Library name: 463A


title: bGV_oocytes,SAC-Seq treated (A site modified) sampes_Replicate1

description: Library name: bGV_T_A


title: C20_Comirnaty_Day-7 (Rep-2)


title: bGV_oocytes,SAC-Seq Input sampes_Replicate2

description: Library name: bGV_I_B


title: bGV oocytes,SAC-Seq Input sampes_Replicate1

description: Library name: bGV_I_A


title: RNA-seq of Pinus sylvestris, Megagametophyte 48 hours after germination, tree 463

description: Library name: 463M


title: C19_Comirnaty_Day-7 (Rep-1)


title: b4Cell_oocytes,SAC-Seq treated (A site modified) sampes_Replicate1

description: Library name: b4Cell_T_A


title: RNA-seq of Pinus sylvestris, mature tree, vegetative bud, tree 463

description: Library name: 463KS


title: flagtagged_GFP_RMCE_hnrnpu_r1_rip_3

description: Library name: flagtagged_GFP_RMCE_hnrnpu_r1_rip_3

data_processing:
Wiggle tracks were generated using protocols and code from PMID: 39187382. Sequencing reads were aligned to the mm10 or Hg38 genome using STAR (v2.7.10a; 101). Replicates were downsampled and merged using SAMtools (v1.18; 95). Merged BAM files were filtered for MAPQ ≥ 30 and then split by strand with SAMtools and a custom script. Bam files were converted to BED12 format using Bedtools (v2.29; 98). Wiggle tracks were generated using a custom script which included normalizing wiggles to total aligned reads. WIG files were converted to BigWig format.
Assembly: mm10, hg36
Supplementary files format and content: bigwig files for mm10 alignment (hm_, m_) or hg38 alignment (hm_*hg38, h_). Replicated labels as "r1" or "r2". Merged files do not contain replicate information.

source_name: B6/CAST F1-hybrid Rosa26-RMCE ESCs

value: FLAG (Sigma, F1804)

value: B6/CAST F1-hybrid Rosa26-RMCE ESCs

value: Mouse embryonic stem cells


title: C26_Comirnaty+Alum_Day-7 (Rep-2)


title: F18_tsc_NTG_1_nodox_input_chip

description: Library name: F18_tsc_NTG_1_nodox_input_chip

data_processing:
ChIP-Seq reads were aligned using bowtie2 with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools, and allele-specific read retention (i.e., reads that overlap at least one B6 or CAST SNP) was performed  using a custom Perl script (intersect_reads_snps16.pl).
Assembly: mm10
Supplementary files format and content: Total, non-allelic read counts are divided by total aligned reads to mm10 of the dataset in million (i.e. RPM) or normalized using ORI norm factor to calibrate to a human spike in (ori_norm).

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate and then cultured for three to four days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
ChIP beads were resuspended in Elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and placed on a 65°C heat block for 17 minutes with frequent vortexing. ChIP DNA was then reverse crosslinked in 0.5% SDS and 100mM NaCl overnight at 65°C, followed by a 1-h RNaseA (3L; Thermo Scientific EN0531) treatment at 37°C and a 2.5-h Proteinase K (10L; Invitrogen 25530015) treatment at 56°C. DNA was then extracted with 1 volume of phenol:chloroform:isoamyl alcohol (Sigma-Aldrich P3803) and precipitated with 2 volumes 100% ethanol, 1/10 volume 3M sodium-acetate pH 5.4, and 1/1000 volume linear acrylamide (Invitrogen AM9520) overnight at -20°C. Precipitated DNA was then extracted with a 30-minute max speed spin at 4°C, washed once with ice-cold 80% ethanol, and resuspended in TE.
ChIP-Seq libraries were prepared with NEBNext End Repair Module (NEB, cat #: E6050S), A-tailing by Klenow Fragment (3’--5’ exo-; NEB, cat #: M0212S), and TruSeq 6-bp index adaptor ligation by Quick ligase (NEB, cat #: M2200S), and NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat #: M0541S). All DNA clean-up steps were performed with AMPure XP beads (Beckman Coulter, cat #: A63880). Single-end, 150-bp sequencing was performed on an Illumina NextSeq1000 platform with a 100-cycle NextSeq 1000/2000 P2 Reagents v3 kit (Illumina 20046811)

treatment_protocol: Prior to crosslinking, TSC cell lines (with rtTA) were treated with 0-1000ng/mL doxycycline (1000ng/mL if not otherwise specified) for four days. Adhered cells were crosslinked with 0.6% formaldehyde (Fisher Scientific BP531-500) in RPMI media with 5% FBS for 10min at room temperature, then quenched with 125mM glycine for 5min at room temperature. Crosslinked cells were then washed twice with ice-cold PBS and scraped with ice-cold PBS with 0.05% Tween (Fisher Scientific EW-88065-31) and PIC (Sigma Aldrich P8340). The cells were then spun at 1,200 x g at 4°C to remove PBS, followed by resuspension in ice-cold PBS with PIC and divided into 10-million cell aliquots.

value: mouse TSCs 6-2

value: NTG sgRNA


title: B18_Comirnaty+Alum_Day-3 (Rep-3)


title: flagtagged_GFP_RMCE_hnrnpu_r2_rip_4

description: Library name: flagtagged_GFP_RMCE_hnrnpu_r2_rip_4


title: RNA-seq of Pinus sylvestris, mature tree, needle, tree 463

description: Library name: 463N

value: Needle


title: b4Cell_embryo, SAC-Seq Input sampes_Replicate2

description: Library name: b4Cell_I_B


title: F18_tsc_NTG_1_nodox_H2AK119ub_chip

description: Library name: F18_tsc_NTG_1_nodox_H2AK119ub_chip

value: Ubiquityl-Histone H2A (Lys119) (D27C4) (H2AK119ub) (Cell Signaling, cat #:8240)


title: B17_Comirnaty+Alum_Day-3 (Rep-2)


title: F18_tsc_NTG_1_Dox_input_chip

description: Library name: F18_tsc_NTG_1_Dox_input_chip

value: 4-day 1000ng/mL dox-treated


title: hVEC ALI + GBS repB

city: Aurora

first: Kelly

last: Doran

state: Colorado

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description:
Library name: 3B
Column name in hVEC_counts.tsv: hVEC_GBS_B; Column name in GBS_counts.tsv: GBS_hVEC_B

data_processing:
BCL convert v4.2.4 for demultiplexing, quality control, and adapter trimming
STAR v2.7.10b for read alignment
featureCounts v2.0.6 to assign counts
Assembly: GRCh38 (NCBI; human)
Assembly: Assembly 22 (CGD; C. albicans)
Assembly: NZ_HG939456.1 with sRNAs (S. agalactiae)
Supplementary files format and content: hVEC_counts.tsv is a tab-delimited text file of counts for human genes for each sample containing hVECs
Supplementary files format and content: Ca_counts.tsv is a tab-delimited text file of counts for C. albicans genes for each sample containing C. albicans
Supplementary files format and content: GBS_counts.tsv is a tab-delimited text file of counts for S. agalactiae genes for each sample containing S. agalactiae

organism:
Streptococcus agalactiae
Homo sapiens

growth_protocol: S. agalactiae (strain COH1) was grown statically in Todd Hewitt Broth at 37°C. C. albicans (strain 529L) was grown shaking in Yeast Peptone Dextrose Broth at 30°C. Human vaginal epithelial cells (hVEC; cell line VK2-E6/E7) were grown in Keratinocyte Serum-Free Medium supplemented with 0.05 mg/mL bovine pituitary extract and 0.5 ng/mL epidermal growth factor (KSFM). hVECs were grown in 6-well transwell inserts at an air-liquid interface for 16 days.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini Kit, then treated with Invitrogen Dnase.
Libraries were prepared with the Illumina Stranded Total RNA Prep ligation with Ribo-Zero Plus rRNA depletion kit.

treatment_protocol: 2x10^7 C. albicans yeast cells and/or 2x10^8 S. agalactiae CFU at mid-log were washed and resuspended in KSFM and added to hVEC air-liquid interface cultures in the apical compartment, then incubated at 37°C with 5% CO2 for six hours. Microbial mono- and co-cultures were grown in 6-well plates in KSFM at 37°C with 5% CO2 for six hours.

value: Vaginal epithelial cells

value: Bacteria

value: Epithelial cells grown at air-liquid interface, inoculated with S. agalactiae


title: F18_tsc_NTG_1_Dox_H2AK119ub_chip

description: Library name: F18_tsc_NTG_1_Dox_H2AK119ub_chip


title: B16_Comirnaty+Alum_Day-3 (Rep-1)

value: Lymph nodes


title: F18_tsc_HU_g5_nodox_input_chip

description: Library name: F18_tsc_HU_g5_nodox_input_chip

value: HNRNPU sgRNA 5 knockdown


title: F18_tsc_HU_g5_Dox_input_chip

description: Library name: F18_tsc_HU_g5_Dox_input_chip


title: F18_tsc_HU_g5_nodox_H2AK119ub_chip

description: Library name: F18_tsc_HU_g5_nodox_H2AK119ub_chip


title: B15_Comirnaty+MA_Day-3 (Rep-3)


title: F18_tsc_HU_g5_Dox_H2AK119ub_chip

description: Library name: F18_tsc_HU_g5_Dox_H2AK119ub_chip


title: hVEC ALI + GBS repA

description:
Library name: 3A
Column name in hVEC_counts.tsv: hVEC_GBS_A; Column name in GBS_counts.tsv: GBS_hVEC_A


title: siGLI1_3_T3

city: Tokyo

first: Tetsuya

last: Saito

state: Select state...

address: 1-5-45 Yushima Bunkyo-ku

department: Rheumatology

country: Japan

institute: Tokyo Medical and Dental University

description: Library name: SAMPLE 15

data_processing:
Raw reads were processed with SOAPnuke v1.5.6.
Clean reads were aligned to the GRCh38.p12 human reference genome using HISAT2 v2.2.1.
For gene-set realignment, Bowtie2 v2.4.5 was employed, and transcript abundance was estimated in transcripts per million (TPM) using RSEM v1.3.1.
Assembly: GRCh38.p12 human reference genome
Supplementary files format and content: xlsx files include average counts for all samples

source_name: Rheumatoid arthritis synovial fibroblasts

growth_protocol: DMEM with 10% FCS and P/S (passages < 5) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs were extracted with Qiagen Rneasy mini kit
RNA libraries were prepared using the BGI Optimal Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: RASFs (n=3) were treated with Veh or 4mix for 24 hours

value: TNF-alpha (10 ng/mL)


title: siGLI1_3_T2

description: Library name: SAMPLE 14

value: Rheumatoid arthritis synovial fibroblasts


title: F18_tsc_HK_g3_4_nodox_input_chip

description: Library name: F18_tsc_HK_g3_4_nodox_input_chip

source_name: mouse TSCs 6-2

value: HNRNPK sgRNAs 3+4 knockdown


title: F18_tsc_HK_g3_4_nodox_H2AK119ub_chip

description: Library name: F18_tsc_HK_g3_4_nodox_H2AK119ub_chip


title: B14_Comirnaty+MA_Day-3 (Rep-2)


title: B13_Comirnaty+MA_Day-3 (Rep-1)


title: F18_tsc_HK_g3_4_Dox_input_chip

description: Library name: F18_tsc_HK_g3_4_Dox_input_chip


title: siGLI1_3_T1

description: Library name: SAMPLE 13


title: B12_Comirnaty_Day-3 (Rep-3)


title: F18_tsc_HK_g3_4_Dox_H2AK119ub_chip

description: Library name: F18_tsc_HK_g3_4_Dox_H2AK119ub_chip


title: siGIL3_T3

description: Library name: SAMPLE 12


title: F14_tsc_HU_g1_3_nodox_input_chip

description: Library name: F14_tsc_HU_g1_3_nodox_input_chip

value: HNRNPU sgRNAs 1+3 knockdown


title: F14_tsc_HU_g1_3_nodox_H3K27me3_chip

description: Library name: F14_tsc_HU_g1_3_nodox_H3K27me3_chip

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) (H3K27me3) (Cell Signaling, cat #:9733)


title: siGIL3_T2

description: Library name: SAMPLE 11


title: F14_tsc_HU_g1_3_nodox_H2AK119ub_chip

description: Library name: F14_tsc_HU_g1_3_nodox_H2AK119ub_chip


title: F14_tsc_HU_g1_3_Dox_input_chip

description: Library name: F14_tsc_HU_g1_3_Dox_input_chip


title: F14_tsc_HU_g1_3_Dox_H3K27me3_chip

description: Library name: F14_tsc_HU_g1_3_Dox_H3K27me3_chip


title: F14_tsc_HU_g1_3_Dox_H2AK119ub_chip

description: Library name: F14_tsc_HU_g1_3_Dox_H2AK119ub_chip


title: A9_Comirnaty+Alum_Day-1 (Rep-3)


title: B11_Comirnaty_Day-3 (Rep-2)


title: B10_Comirnaty_Day-3 (Rep-1)


title: siGIL3_T1

description: Library name: SAMPLE 10


title: F14_tsc_HK_g1_nodox_H3K27me3_chip

description: Library name: F14_tsc_HK_g1_nodox_H3K27me3_chip

value: HNRNPK sgRNAs 1 knockdown


title: F14_tsc_HK_g1_nodox_input_chip

description: Library name: F14_tsc_HK_g1_nodox_input_chip


title: siGLI1_T3

description: Library name: SAMPLE 9


title: F14_tsc_HK_g1_nodox_H2AK119ub_chip

description: Library name: F14_tsc_HK_g1_nodox_H2AK119ub_chip


title: A8_Comirnaty+Alum_Day-1 (Rep-2)


title: siGLI1_T2

description: Library name: SAMPLE 8


title: F14_tsc_HK_g1_Dox_input_chip

description: Library name: F14_tsc_HK_g1_Dox_input_chip


title: A7_Comirnaty+Alum_Day-1 (Rep-1)


title: F14_tsc_HK_g1_Dox_H3K27me3_chip

description: Library name: F14_tsc_HK_g1_Dox_H3K27me3_chip


title: siGLI1_T1

description: Library name: SAMPLE 7


title: F11_tsc_XRN2_g1_nodox_H3K27me3_chip

description: Library name: F11_tsc_XRN2_g1_nodox_H3K27me3_chip

value: XRN2 sgRNA 1 knockdown


title: A6_Comirnaty+MA_Day-1 (Rep-3)


title: F14_tsc_HK_g1_Dox_H2AK119ub_chip

description: Library name: F14_tsc_HK_g1_Dox_H2AK119ub_chip

value: mouse TSCs 6-2


title: F11_tsc_XRN2_g1_Dox_H3K27me3_chip

description: Library name: F11_tsc_XRN2_g1_Dox_H3K27me3_chip


title: A5_Comirnaty+MA_Day-1 (Rep-2)


title: siCtrl_T3

description: Library name: SAMPLE 6

value: siCtrl


title: F11_tsc_NTG_1_nodox_input_chip

description: Library name: F11_tsc_NTG_1_nodox_input_chip

value: NTG sgRNA


title: F11_tsc_NTG_1_nodox_H3K27me3_chip

description: Library name: F11_tsc_NTG_1_nodox_H3K27me3_chip


title: A4_Comirnaty+MA_Day-1 (Rep-1)


title: F11_tsc_NTG_1_Dox_input_chip

description: Library name: F11_tsc_NTG_1_Dox_input_chip


title: A3_Comirnaty_Day-1 (Rep-3)


title: F11_tsc_NTG_1_Dox_H3K27me3_chip

description: Library name: F11_tsc_NTG_1_Dox_H3K27me3_chip


title: siCtrl_T1

description: Library name: SAMPLE 4


title: siCtrl_T2

description: Library name: SAMPLE 5


title: F11_tsc_HU_g5_nodox_input_chip

description: Library name: F11_tsc_HU_g5_nodox_input_chip


title: F11_tsc_HU_g5_nodox_H3K27me3_chip

description: Library name: F11_tsc_HU_g5_nodox_H3K27me3_chip


title: A2_Comirnaty_Day-1 (Rep-2)


title: siCtrl_Veh3

description: Library name: SAMPLE 3

value: Veh


title: siCtrl_Veh2

description: Library name: SAMPLE 2


title: F11_tsc_HU_g5_Dox_H3K27me3_chip

description: Library name: F11_tsc_HU_g5_Dox_H3K27me3_chip

value: 4-day 1000ng/mL dox-treated


title: A1_Comirnaty_Day-1 (Rep-1)


title: F11_tsc_HU_g5_Dox_input_chip

description: Library name: F11_tsc_HU_g5_Dox_input_chip


title: F11_tsc_HK_g3_4_nodox_input_chip

description: Library name: F11_tsc_HK_g3_4_nodox_input_chip


title: siCtrl_Veh1

description: Library name: SAMPLE 1


title: F11_tsc_HK_g3_4_nodox_H3K27me3_chip

description: Library name: F11_tsc_HK_g3_4_nodox_H3K27me3_chip


title: Cortical neurons, shControl, Day 11, Input DNA

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
fastq files were verified with multiQC.
Sequencing adaptors were trimmed and duplicates were removed.
ChIP peaks were called using MACS2.
Bigwig files were generated using bamCoverage for data visualization.
Assembly: mm10

source_name: brain

growth_protocol: Primary cortical neurons were prepared from embryonic cortices at day E14.5-15 of CD1 mice and cultured in vitro for 11 days.

extract_protocol:
Chromatin were cross-linked with formaldehyde for 30 minutes. Chromatin was lysed and sonicated (Covaris) into average 150bp fragments.
ChIP-seq library was prepared using Illumina ChIP-seq library preparation kit.

treatment_protocol:
Cells were seeded at a density of 1 million cells/ml. Neurons were cultured in neurobasal media containing 1X B27; 1X N2; 100 Units/mL Penicillin/Streptomycin, and 0.6 mM L-glutamine. Cells were treated with the mitotic inhibitor cytosine arabinoside at 2uM.
A 50 % Media change is performed every 3-4 days and a full media change 3 days following Ara-C treatment. Lentiviral transduction was performed at day 6 and cells were harvested for RNA extraction on day 11.

value: brain

value: primary cell

value: cortical neurons

value: WT

value: neuron differentiation


title: F11_tsc_HK_g3_4_Dox_input_chip

description: Library name: F11_tsc_HK_g3_4_Dox_input_chip


title: Biological replicate 2, technical replicate 2, naive SW620s

city: San Francisco

first: Balyn

last: Zaro

address: 555 Mission Bay Blvd S, Rm 484

institute: UCSF

description:
Library name: Sample 20
B2T2_SW620_S20_L001.counts

data_processing:
RNA-seq reads were trimmed to remove sequencing adapters using Trimmomatic (v0.39) with the TruSeq3-PE-2 adapter sequences. Low-quality bases and short reads were filtered using the parameters LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36. Trimmed reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b). Gene expression levels were quantified using HTSeq-count, where aligned reads were counted against gene features defined in the Gencode v45 GTF annotation.
Assembly: human reference genome (hg38) using STAR (v2.7.11b)
Supplementary files format and content: Processed data file for all samples is: RNA_seq_raw_reads_count_all and contains columns with raw counts for each individua sample outlined above. Rows represent ensembl gene ids.

extract_protocol:
Cells were sorted via FACS following co-incubation as indicated. Following PBS washing steps to remove excess FBS, samples were lysed into TRI Reagent (Zymo Research, R2071) and then snap frozen and stored at -80°C until RNA extraction was performed. RNA extraction was performed using Direct-zol RNA MiniPrep Plus (Zymo Research, R2071) following manufacturer’s instructions.
Two biological replicates of each cell type (Eaters, Non-eaters, Uneaten, SW620, and Naive macrophages) were used for RNA sequencing, with each biological replicate consisting of two technical replicates. RNA-seq libraries were prepared using the Single Cell/Low Input RNA Library Prep Kit (NEB, E6420), following the manufacturer's protocol. In brief, 200 ng of total RNA was used as input. First, reverse transcription was performed, followed by 7 cycles of cDNA amplification and clean-up. The cDNA was then fragmented, repaired, ligated with NEBNext adaptors, and enriched using 4-5 cycles of PCR. Libraries were sequenced on a NovaSeq X 10B platform using paired-end 150 bp (PE150) reads.

value: Human colorectal cancer cells


title: F11_tsc_HK_g3_4_Dox_H3K27me3_chip

description: Library name: F11_tsc_HK_g3_4_Dox_H3K27me3_chip


title: Cortical neurons, shOpa1, Day 11, ATF4 ChIP

value: Opa1 knock-down


title: F11_tsc_DC1_g4_nodox_H3K27me3_chip

description: Library name: F11_tsc_DC1_g4_nodox_H3K27me3_chip

value: YTHDC1 sgRNA 4 knockdown


title: Biological replicate 2, technical replicate 2, Non-Eater macrophages

description:
Library name: Sample 19
B2T2_Noneat_S19_L001.counts

source_name: Human monocyte derived macrophages

value: Human monocyte derived macrophages

value: Isolated following co-incubation with live SW620 colorectal cancer cells


title: F11_tsc_DC1_g4_Dox_H3K27me3_chip

description: Library name: F11_tsc_DC1_g4_Dox_H3K27me3_chip

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) (H3K27me3) (Cell Signaling, cat #:9733)


title: G1_tsc_HU_Dox_r2_ring1b_rip

description: Library name: G1_tsc_HU_Dox_r2_ring1b_rip

data_processing:
RIP-Seq reads were aligned using STAR v2.5.4b with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools.
Assembly: mm10
Supplementary files format and content: Wiggle tracks were normalized to q30 aligned reads to mm10

extract_protocol:
Both input and immunoprecipitated RNA were purified with the Zymo Clean and Concentrator.
KAPA RNA Hyperprep Kit with RiboErase, 9uL of IP/input RNA + 1uL ERCC RNA spike-in

value: RING1B(Cell Signaling, #5694S)

value: HNRNPU sgRNA 5 knockdown


title: Cortical neurons, shControl, Day 11, ATF4 ChIP


title: Biological replicate 2, technical replicate 2, Eater macrophages

description:
Library name: Sample 18
B2T2_Eat_S18_L001.counts

value: Isolated following co-incubation and phagocytosis of live SW620 colorectal cancer cells


title: G1_tsc_HU_Dox_r2_input_rip

description: Library name: G1_tsc_HU_Dox_r2_input_rip

value: mouse TSCs 6-2


title: G1_tsc_HU_Dox_r1_ring1b_rip

description: Library name: G1_tsc_HU_Dox_r1_ring1b_rip


title: Biological replicate 2, technical replicate 2, naive human macrophages

description:
Library name: Sample 17
B2T2_Mac_S17_L001.counts


title: G1_tsc_HU_Dox_r1_input_rip

description: Library name: G1_tsc_HU_Dox_r1_input_rip


title: Mmrn1-high LT-HSCs, rep3

city: Chongqing

first: Naicheng

state: Chongqing

address: Gaotanyan Street 30

department: College of Preventive Medicine

institute: Third Military Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the GRCm38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of  Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample

source_name: Mmrn1-high long term hematopoietic stem cells from murine bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

value: Bone marrow

value: stem cells

value: Mmrn1-GFP type

tag: mmrn1 status


title: Biological replicate 2, technical replicate 2, Uneaten SW620s

description:
Library name: Sample 16
B2T2_UE_S16_L001.counts

value: Isolated following co-incubation with human monocyte derived macrophages


title: Mmrn1-high LT-HSCs, rep2


title: Biological replicate 2, technical replicate 1, naive SW620s

description:
Library name: Sample 15
B2T1_SW620_S15_L001.counts


title: F8_tsc_HU_g5_dox_RNA

description: Library name: F8_tsc_HU_g5_dox_RNA

data_processing:
RNA-Seq reads were aligned using STAR v2.5.4b with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools.
Assembly: mm10
Supplementary files format and content: Wiggle tracks were normalized to q30 aligned reads to mm10

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate. For RNA-seq, cells were then split off of feeders for a second time, but without pre-plating and then cultured for three to four days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
RNA was harvested with trizol and purified with the Zymo Clean and Concentrator kit.
KAPA RNA Hyperprep Kit with RiboErase, 9uL of 100ng/ul RNA + 1uL ERCC RNA spike-in

treatment_protocol: To induce RBP knockdown, TSCs were treated with 1000ng/mL of doxycycline for four days.

value: 4-day 1000ng/mL dox-treated


title: F8_tsc_HK_g3_4_nd_RNA

description: Library name: F8_tsc_HK_g3_4_nd_RNA

value: HNRNPK sgRNAs 3+4 knockdown


title: F8_tsc_HU_g5_nd_RNA

description: Library name: F8_tsc_HU_g5_nd_RNA


title: F8_tsc_HK_g3_4_dox_RNA

description: Library name: F8_tsc_HK_g3_4_dox_RNA


title: Biological replicate 2, technical replicate 1, Non-Eater macrophages

description:
Library name: Sample 14
B2T1_Noneat_S14_L001.counts


title: F8_tsc_DC1_g4_nd_RNA

description: Library name: F8_tsc_DC1_g4_nd_RNA


title: Biological replicate 2, technical replicate 1, Eater macrophages

description:
Library name: Sample 13
B2T1_Eat_S13_L001.counts


title: Mmrn1-high LT-HSCs, rep1


title: Biological replicate 2, technical replicate 1, naive human macrophages

description:
Library name: Sample 12
B2T1_Mac_S12_L001.counts


title: F18_tsc_HU_g5_nodox_r2_RNA

description: Library name: F18_tsc_HU_g5_nodox_r2_RNA


title: F8_tsc_DC1_g4_dox_RNA

description: Library name: F8_tsc_DC1_g4_dox_RNA


title: F18_tsc_HU_g5_nodox_r1_RNA

description: Library name: F18_tsc_HU_g5_nodox_r1_RNA


title: Mmrn1-low LT-HSCs, rep1

source_name: Mmrn1-low long term hematopoietic stem cells from murine bone marrow


title: Biological replicate 2, technical replicate 1, Uneaten SW620s

description:
Library name: Sample 11
B2T1_UE_S11_L001.counts


title: cortical brain tissue, IfnarM2

city: Copenhagen

first: Shohreh

last: Issazadeh-Navikas

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

data_processing:
Raw data were demultiplexed, aligned, and quantified using Cell Ranger version (v)3.1.0. To allow for counting of unspliced pre-mRNA, a custom version of the mm10-3.0.0 mouse reference genome provided by 10x Genomics was used, where the feature ‘type of transcripts’ was changed from ‘transcript’ to ‘exon’.
Data analysis was performed in R using Seurat v3.1.5 and Conos v1.2.1. The -barcode matrices were filtered to include cells meeting the following criteria: 200<nFeature_RNA<6000, nCount_RNA>1000, and percent_MT<10. Doublets were filtered out using the Scrublet package
Data were log-normalized, and individual samples were integrated using the fast mutual nearest neighbors (fastMNN) method based on the top 3,000 variable features. Clustering and UMAP visualization were performed using the first 40 dimensions of the MNN reduction.
The integrated dataset was annotated using canonical correlation analysis (CCA) based label transfer in Seurat with the Allen Brain Map Mouse Whole Cortex and Hippocampus SMART-seq dataset [https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-smart-seq] as the reference
Assembly: mm10-3.0.0
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Cortex (brain)

extract_protocol:
16,000 nuclei per sample were loaded on the 10x Chromium chip for library preparation using the Single Cell 3’ v3 chemistry according to manufacturer instructions. For cDNA amplification, 12 PCR cycles were applied. For each sample, 230 ng of purified cDNA was used for library construction.
The libraries were diluted to a concentration of 10 nM and pooled for sequencing. After denaturation, the library pool was diluted to a loading concentration of 300 pM and sequenced on a Novaseq6000 in paired-end mode (2x100) (read 1:28 cycles, read 2:91 cycles, and i7 index: 8 cycles) at an average depth of 50,000 reads per nucleus.
single nuclei (sn)RNA-seq

value: Cortex (brain)

value: Cortical cells

value: 6 week old

tag: gender

value: Male

tag: strain

value: naive


title: F18_tsc_HK_g3_4_nodox_r2_RNA

description: Library name: F18_tsc_HK_g3_4_nodox_r2_RNA


title: F18_tsc_HK_g3_4_Dox_r2_RNA

description: Library name: F18_tsc_HK_g3_4_Dox_r2_RNA


title: Biological replicate 1, technical replicate 2, Non-Eater macrophages

description:
Library name: Sample 9
B1T2_Noneat_S9_L001.counts

value: Human monocyte derived macrophages

value: Isolated following co-incubation with live SW620 colorectal cancer cells


title: F18_tsc_HK_g3_4_Dox_r1_RNA

description: Library name: F18_tsc_HK_g3_4_Dox_r1_RNA


title: cortical brain tissue, IfnarF2

value: Female


title: Biological replicate 1, technical replicate 2, Eater macrophages

description:
Library name: Sample 8
B1T2_Eat_S8_L001.counts

value: Human colorectal cancer cells


title: F14_tsc_HU_g1_3_Dox_RNA

description: Library name: F14_tsc_HU_g1_3_Dox_RNA

value: HNRNPU sgRNAs 1+3 knockdown


title: F14_tsc_HK_g1_nodox_RNA

description: Library name: F14_tsc_HK_g1_nodox_RNA

value: mouse TSCs 6-2

value: HNRNPK sgRNAs 1 knockdown


title: Biological replicate 1, technical replicate 2, naive human macrophages

description:
Library name: Sample 7
B1T2_Mac_S7_L001.counts


title: F14_tsc_HK_g1_Dox_RNA

description: Library name: F14_tsc_HK_g1_Dox_RNA


title: cortical brain tissue, B6M2


title: CD34+ day4 Transduced - patient 4

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

institute: SR-TIGET

description: Library name: E08

data_processing:
Raw fastq data were preprocessed using Cell Ranger (v7.1.0, 10X Genomics) to produce features-barcodes matrices. GRCh38 genome and genes annotations provided by the manufacturer were used as reference data for reads mapping and gene expression quantification. Genes expression matrices were then processed within the R environment (v4.0.3) using the Seurat package (v4.1.1).
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Sparse raw UMI counts matrix ( barcodes + features + .mtx)

source_name: mPB

extract_protocol:
Chromium(TM) Single Cell 3' Library (10xGENOMICS) according to manufacturer’s instructions (v2 chemistry).
Chromium(TM) Single Cell 3' Library (10xGENOMICS) according to manufacturer’s instructions (v2 chemistry).

value: mPB

tag: patient

tag: timepoint

value: day 4


title: Biological replicate 1, technical replicate 2, Uneaten SW620s

description:
Library name: Sample 6
B1T2_UE_S6_L001.counts

value: Isolated following co-incubation with human monocyte derived macrophages


title: hTERT-HM cells, day 6 rep3

city: St. Louis

first: Ritu

last: Dave

address: 425 S Euclid Ave

institute: Washington University School of Medicine

description:
Library name: sample10
column name in all.gene_counts.xlsx: sample.Day_6_C

data_processing:
Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s DRAGEN BCLconvert version 4.3.13.
RNA-seq reads were then aligned to the Ensembl GRCh38.113 primary assembly with STAR version 2.7.11b.
Gene counts were derived from the number of uniquely aligned unambiguous fragments by Subread:featureCount version 2.0.8. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.10.0.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 5.04.
Assembly: GRCh38.113
Supplementary files format and content: xlsx file includes raw counts for each Sample

source_name: myometrium

extract_protocol:
RNA was extracted using the Zymo Research RNA Miniprep kit. Library preperation was done with 1ug of total RNA.
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (NEBNext Poly(A) mRNA Magnetic Isolation module, New England Biolabs). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: myometrium

value: hTERT-HM

value: myometrial cell

value: WT


title: hTERT-HM cells, day 6 rep2

description:
Library name: sample9
column name in all.gene_counts.xlsx: sample.Day_6_B


title: cortical brain tissue, B6F2

value: Cortex (brain)

value: Cortical cells

value: 6 week old


title: hTERT-HM cells, day 3 rep4

description:
Library name: sample7
column name in all.gene_counts.xlsx: sample.Day_3_E


title: hTERT-HM cells, day 3 rep3

description:
Library name: sample6
column name in all.gene_counts.xlsx: sample.Day_3_D


title: shRUNX2-2+TGF-β

city: Birmingham

first: Lin

last: Jin

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

description: Library name: Jin_E11

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
Raw paired-end FASTQ files were quality- and adapter-trimmed using Trimmomatic v0.36 in paired-end mode with parameters: PE -threads 8 -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Paired trimmed reads were retained for downstream analysis.
Trimmed paired-end reads were aligned to the human hg38 reference genome using STAR v2.7.3a with parameters: --readFilesCommand zcat --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonical --quantMode GeneCounts --limitBAMsortRAM 64000000000.
Gene-level read counts were generated from STAR coordinate-sorted BAM files using htseq-count with the hg38 refGene GTF annotation file and parameters: -f bam -r pos -s reverse -t exon -i gene_id -m union -a 10.
Count tables were used for downstream differential gene expression analysis.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text file consisting of raw counts (transcript abundances) for each sample for each Ensembl Gene ID

source_name: immortalized skin fibroblast

growth_protocol: Immortalized human skin fibroblasts or primary human skin fibroblasts (passages 2–5) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Cells were maintained by replacing the medium every 2–3 days and subcultured before reaching full confluence to preserve normal morphology and proliferative capacity.

extract_protocol:
Total RNA was extracted from cultured fibroblasts using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and purity were assessed by spectrophotometry, and samples were stored at –80°C until further use
Using the NEBNext Ultra II RNA Library Prep Kit for Illumina with poly(A) selection, we begin with high-quality total RNA and enrich mRNA using oligo-dT magnetic beads to capture polyadenylated transcripts, followed by washing and elution; we then fragment the purified mRNA under heat and prime it for reverse transcription to generate first-strand cDNA, after which we perform second-strand synthesis to produce double-stranded cDNA (optionally incorporating strand specificity), and subsequently carry out end repair and dA-tailing to create adapter-compatible ends; we ligate sequencing adapters, purify the library using magnetic beads (with optional size selection), and amplify it by PCR with indexed primers to enrich adapter-ligated fragments, and finally we assess library size distribution and concentration before pooling and sequencing on an Illumina platform.

treatment_protocol: Cells were treated either with or without TGF‑β or with compoound F05650303 for 48 hours.

value: immortalized skin fibroblast

value: fibroblast

value: wt

value: TGF-β


title: hTERT-HM cells, day 3 rep2

description:
Library name: sample5
column name in all.gene_counts.xlsx: sample.Day_3_C