title: Peripheral organs, Stroke, scRNAseq, rep3

description:
10x Genomics
peripheral_barcodes.tsv
peripheral_genes.tsv
peripheral_matrix.mtx

source_name: Blood, Spleen, Liver, Lung, Heart

value: Blood, Spleen, Liver, Lung, Heart

value: Myeloid cells (CD45+, CD11b+)


title: Peripheral organs, Control, scRNAseq, rep4

status: Public on Jul 22 2024

type: SRA

city: Munich

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia (ISD)

country: Germany

institute: LMU Hospital

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

extract_protocol:
Three mouse single-cell RNA experiments were performed in this study: one on a pool of myeloid cells isolated from the heart, lung, liver, spleen and blood; and the other two on bone marrow myeloid cells, either from stroke and control mice, or from naïve recipients after BM transplantation. For the first experiment, mononuclear cell suspensions from peripheral organs were incubated with anti-CD16/CD32 antibody to block nonspecific binding and stained for CD45+CD11b+ myeloid cells (see antibodies list). Five unique cell hashtags antibodies were also used to label cells from each organ. All surface antibodies and hashtag antibodies were incubated for 30 min at 4ºC. Immediately prior to cell sorting, PI was added to all samples to label dead cells. Cells were sorted according to their surface markers (SH800S Cell Sorter, Sony Biotechnology). Sorted and organ-specific labeled cells from the heart, lung, liver, spleen and blood from the same animal were pooled together in the same collecting tube (cell ratio of 1:4:4:4:4, respectively). After sorting, all cells were centrifuged and cautiously resuspended to a final concentration of 1000 cells/l. Cells were then transferred to the Next GEM chip according to manufacturer’s instructions. ScRNA-seq and cell hashing libraries were prepared using the 10x Chromium Single Cell 3′ Solution combined with cell hashing, as per established protocols.10    For the second and third experiments, bone marrow cells suspensions were stained with a cocktail of antibodies against markers of the lymphoid lineage (CD3, CD4, CD8a, CD19 and Ter119) and mature neutrophils (Ly6G, see antibodies list). Immediately prior to cell sorting, PI or 7-AAD were also added to label dead cells. Cells were sorted according to the surface markers (SH800S Cell Sorter, Sony Biotechnology, or FACS Aria II Fusion cell sorter, BD Biosciences, Inc.) and the negative fraction of BM myeloid cells (depleted of lymphoid lineage cells and neutrophils) was collected. After sorting, cells were centrifuged and cautiously resuspended to a final concentration of 1000-1200 cells/l. Cells were then further processed according to manufacturer’s (10X) instructions. The scRNA-seq libraries were prepared using the 10x Chromium Single Cell 3′ Solution.   In all three experiments, quality control of all cDNA samples was performed with a Bioanalyzer 2100 (Agilent Technologies) and libraries were quantified with the Qubit dsDNA HS kit. Gene expression libraries were sequenced on an Illumina NextSeq 1000 using 20,000 reads per cell. Cell-surface protein expression libraries were sequenced on an Illumina NextSeq 1000 aiming for 5,000 reads per cell.
Libraries were performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol and single cell 3' v3.1 with feature barcoding technology for Cell surface protein, 10x Genomics).

tag: tissue

tag: cell type

tag: strain

tag: disease state

value: Control


title: Peripheral organs, Control, scRNAseq, rep3


title: Peripheral organs, Stroke, scRNAseq, rep4

value: Stroke


title: CLP_IgG_ctrl_16_07

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

library_source: transcriptomic

data_processing:
Reads were quality checked with package FastQC (version Version 0.11.9) then quality trimmed using Trimgalore (version 0.6.7)
Trimmed reads were mapped to mouse genome using STAR aligner (version 2.7.9a) with default settings.
Mapped reads were counted using RsubRead (version 2.8.1)
Raw counts were normalized using DESeq2 (version 1.36.0)
Assembly: ENSMBL Mus_musculus.GRCm39, release 104
Supplementary files format and content: txt matrix with log2 normalized values per sample.

molecule: polyA RNA

source_name: lung

extract_protocol:
Lung lobes were prepared and transferred to an enzyme mix to dissociate cells. CD45-positive cells were bound to CD45 antibody-coupled beads and then discarded. CD45-negative cells were bound to CD31 antibody-coupled magnetic beads for positive cell sorting. After washing, RNA was isolated from cells. PolyA+RNA was purified  from 100 ng total RNA using Poly(A) mRNA Magnetic Isolation module Kit (NEB E7490L, New England Biolabs).
The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).
Directional RNA Library Prep, single reads run 72 Nu with an average of 26.9 M reads per sample

treatment_protocol: Mice were anesthetized, the cecum mobilized after median laparotomy and the cecum ligated and punctured. The abdomen was closed and antibodies injected invtravenously. Mice were awakened and sacrificed after 18h.

value: lung

value: endothelial cells

tag: treatment


title: Peripheral organs, Stroke, scRNAseq,rep2


title: Peripheral organs, Control, scRNAseq, rep2


title: Peripheral organs, Stroke, scRNAseq, rep1


title: Bone marrow, Stroke-treated, snATACseq, rep3

description:
Sample 8
10x Genomics
barcodes.tsv
peaks.bed
matrix.mtx
fragments.tsv.gz.tbi
nuclear ATAC

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ATAC software v2.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: In barcodes.tsv, barcode-1 corresponds to Sample 1, barcode-2 corresponds to Sample 2, and so on.

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
Bone marrows were homogenized and filtered through 40 μm cell strainers to obtain single cell suspensions. Cell suspensions were were stained with a cocktail of antibodies against markers of the lymphoid lineage (CD3, CD4, CD8a, CD19 and Ter119) and mature neutrophils (Ly6G). Live, lymphoid lineage (CD3, CD4, CD8a, CD19 and Ter119) and neutrophil (Ly6G) negative BM cells were sorted using a FACS Aria II Fusion cell sorter (BD Biosciences, Inc.). Cells were centrifuged and incubated twice with Nuclei EZ Lysis Buffer on ice for 5 min each time. Lysed cells were washed and nuclei were incubated with 7AAD at 1g/ml for microscopic inspection of integrity before sorting on a FACS Aria II Fusion (BD Biosciences). Then, nuclei were further processed according to manufacturer’s (10X) protocols at a concentration of 1000-5000 nuclei/µl. Single nuclei ATAC libraries were prepared using the 10x Chromium Next GEM Single Cell ATAC kit
Libraries were performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol and single cell 3' v3.1 with feature barcoding technology for Cell surface protein, 10x Genomics).

value: Bone marrow

value: Lymphoid lineage (CD3, CD4, CD8a, CD19, Ter119) negative  and neutrophil (Ly6G) negative

value: Stroke-treated


title: Peripheral organs, Control, scRNAseq, rep1


title: Bone marrow, Control, snATACseq, rep2

description:
Sample 5
10x Genomics
barcodes.tsv
peaks.bed
matrix.mtx
fragments.tsv.gz.tbi
nuclear ATAC


title: Bone marrow, Stroke-treated, snATACseq, rep1

description:
Sample 4
10x Genomics
barcodes.tsv
peaks.bed
matrix.mtx
fragments.tsv.gz.tbi
nuclear ATAC


title: Bone marrow, Stroke, snATACseq, rep3

description:
Sample 6
10x Genomics
barcodes.tsv
peaks.bed
matrix.mtx
fragments.tsv.gz.tbi
nuclear ATAC


title: Bone marrow, Stroke-treated, snATACseq, rep2

description:
Sample 7
10x Genomics
barcodes.tsv
peaks.bed
matrix.mtx
fragments.tsv.gz.tbi
nuclear ATAC


title: Bone marrow, Stroke, snATACseq, rep1

description:
Sample 2
10x Genomics
barcodes.tsv
peaks.bed
matrix.mtx
fragments.tsv.gz.tbi
nuclear ATAC


title: Bone marrow, Stroke, snATACseq, rep2

description:
Sample 3
10x Genomics
barcodes.tsv
peaks.bed
matrix.mtx
fragments.tsv.gz.tbi
nuclear ATAC


title: ebax-1(null) pretzel stage embryo rep2

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

country: USA

institute: National Institutes of Health

data_processing:
Sequence analysis was performed on the NIH High Performance Computing Cluster. The 3′ adapter sequence was trimmed using Cutadapt 3.4 (Martin, 2011). The reads were mapped to a custom genome file which was comprised of C. elegans genome WS280 with an additional chromosome containing the sequences of the spike-in miRNAs and the mutant mir-35 precursors with flanking genomic sequence. Mapping was performed using bowtie2 2.4.4 (Langmead et al., 2009) with the following settings: --no-unal --end-to-end --sensitive. BAM files were sorted and indexed using samtools 1.13 (Danecek et al., 2021). Reads were assigned to miRNAs using htseq 0.13.5 (Anders et al., 2015) with the following settings: --mode union --nonunique fraction -a 0. The htseq analysis was performed using a gff file modified from mirGeneDB (Fromm et al., 2015) by replacing mirGeneDB IDs with miRbase IDs (Kozomara and Griffiths-Jones, 2014) and adding the intervals corresponding to the spike-in miRNAs and the mir-35 mutant miRNAs in the custom genome file. miRNA differential gene expression was analyzed using DESeq2 analysis with default settings (Love et al., 2014). For analysis of tailing and trimming, the Tailor package (Chou et al., 2015) was used with the genome file described above and FASTA files derived from mirGeneDB, but with IDs replaced by miRbase IDs and sequences for spike-in miRNAs and the mir-35 mutant miRNAs appended.
Assembly: genome_c_elegans.PRJNA13758.WS280.genomic_with_spike_mut_mir35.fa
Assembly: cel_mirGeneDB_spikeins_mutmir35s_010622.gff
Supplementary files format and content: Reads were normalized to total genome-mapping reads; reported values are reads per million. Note that, due to differences in efficiency of cloning different sequences (resulting from ligation biases), comparison of read numbers for different miRNAs is not meaningful. Analysis should be limited to comparisons between samples for the same sequence.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: For experiments in which bulk sample deep sequencing was performed (Figures 1 and 2), worms were grown in liquid culture as previously described and harvested with some modifications (Zanin et al., 2011). Briefly, the gravid worms were harvested by centrifugation at 3000xg for 2 min in 50mL conical tubes. They were washed once with room temperature water and then pelleted. The volume of the sample was brought up to 28mL with water, and then 4mL of 5M NaOH and 8mL of 4% sodium hypochlorite were added. The tubes were immediately shaken vigorously for 2 min and allowed to rest on the bench for 1 min, and this shaking and resting was repeated three times. The worms were immediately centrifuged at 3000xg for 2 min. The supernatant was decanted, and the worms were washed four times with 45mL of water. The synchronized embryos were either collected for the embryo samples, or M9 with cholesterol was added, and the worms were placed on a rocker at 20°C overnight to obtain a population of synchronized, starved L1 worms.

extract_protocol:
Samples were snap frozen, then resuspended in Trizol and vortexed for 15 minutes at room temperature. Thereafter, total RNA was purified according to the Trizol manufacturer’s instructions (ThermoFisher).
Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37°C.

tag: sample id

tag: dev stage

value: pretzel stage embryo

tag: genotype

tag: alias in_text_and_figures

tag: Sex

value: hermaphrodite

value: whole animal


title: Bone marrow, Control, snATACseq, rep1

description:
Sample 1
10x Genomics
barcodes.tsv
peaks.bed
matrix.mtx
fragments.tsv.gz.tbi
nuclear ATAC


title: ebax-1(null) comma stage embryo rep2

value: comma stage embryo


title: wild type pretzel stage embryo rep2

value: wild type


title: wild type comma stage embryo rep2


title: ebax-1(null) 2-8 cell embryo rep2

value: 2-8 cell embryo


title: wild type 2-8 cell embryo rep2


title: wild type starved L1 rep2

value: starved L1


title: Bone marrow, Control, ScRNAseq, rep2

description:
10x Genomics
BM_barcodes.tsv
BM_genes.tsv
BM_matrix.mtx


title: wild type starved L1 rep1


title: ebax-1(null) pretzel stage embryo rep1


title: ebax-1(null) comma stage embryo rep1


title: ebax-1(null) 2-8 cell embryo rep1


title: wild type comma stage embryo rep1


title: ChIP-Seq Leaf_input_rep2

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

country: China

institute: Institute of Crop Sciences

library_source: genomic

data_processing:
We used fastp v0.21.0 for data quality control and Bowtie v2.3.5.1 to align reads to wheat reference genome (bowtie2 -X 1000 --very-sensitive).
Assembly: ChineseSpring v1.1
Supplementary files format and content: bigWig (except for Input sample).
Supplementary files format and content: Leaf.E1-9.segments.txt: Tab-delimited text file includes chromatin states of leaf.
Supplementary files format and content: Vernalized_leaf.E1-9.segments.txt: Tab-delimited text file includes chromatin states of vernalization leaf.

organism: Triticum aestivum

source_name: Leaf

extract_protocol: ChIP-seq was performed with antibodies for H3K27me3 (Abcam, ab6002), H3K4me3 (millipore, 07-473), H3K27ac (abclonal, A7253) and H3K36me3 (Abcam, ab9050). Libraries were constructed using Kit (TransGen Biotech, KP201-02), sequenced by Annoroad Gene Technology (Beijing, China).

value: Leaf


title: RNA-Seq Vernalized_shoot_apex_rep2

data_processing:
We used fastp v0.21.0 45 for data quality control and hisat2 with default parameters to align reads to wheat reference genome.
SAMtools v1.3.1 was used to sort bam, FeatureCounts to statistics read counts and TPMCalculator to calculate TPM.
Differential expressed genes (DEGs) were determined by DESeq2 (p-value < 0.01 and log2 (FoldChange) > 1).
Assembly: ChineseSpring v1.1
Supplementary files format and content: txt, TPM of all genes in different tissues

source_name: Vernalized shoot apex

growth_protocol: Wheat (Triticum aestivum; BBAADD, 2n = 6x = 42) cultivar AK58 was used in our study. Materials with no vernalization were taken from plants grown 2 weeks (day for 16h at 22°C, night for 8h at 19°C) after germination. Materials with vernalization were taken from plants planted in greenhouse after vernalization for 1 mouth in cold chamber (4℃, 16 h light/8 h dark) and grew in green house (day for 16h at 22°C, night for 8h at 19°C) for 1 day.

extract_protocol: RNA-Seq library was constructed by Berry Genomics (Beijing, China), and sequenced with Illumina NovaSeq 6000. All sequencing data were 150bp paired-end reads.

treatment_protocol: Total RNA was extracted with TRIzolTM Reagent (Invitrogen; 15596-026).

value: Vernalized shoot apex


title: RNA-Seq Vernalized_axillary_bud_rep2

source_name: Vernalized axillary bud

value: Vernalized axillary bud


title: RNA-Seq Vernalized_shoot_apex_rep1


title: ebax-1(null) starved L1 rep2


title: RNA-Seq Vernalized_leaf_rep2

source_name: Vernalized leaf

value: Vernalized leaf


title: RNA-Seq Vernalized_axillary_bud_rep1


title: RNA-Seq Vernalized_leaf_rep1


title: ebax-1(null) starved L1 rep1


title: RNA-Seq Shoot_apex_rep1

source_name: Shoot apex

value: Shoot apex


title: RNA-Seq Axillary_bud_rep2

source_name: Axillary bud

value: Axillary bud


title: ChIP-Seq Vernalized_leaf_input_rep2

data_processing:
We used fastp v0.21.0  for data quality control and Bowtie v2.3.5.1  to align reads to wheat reference genome (bowtie2 -X 1000 --very-sensitive).
We used fastp v0.21.0 for data quality control and Bowtie v2.3.5.1 to align reads to wheat reference genome (bowtie2 -X 1000 --very-sensitive).
Assembly: ChineseSpring v1.1
Supplementary files format and content: bigWig (except for Input sample).
Supplementary files format and content: Leaf.E1-9.segments.txt: Tab-delimited text file includes chromatin states of leaf.
Supplementary files format and content: Vernalized_leaf.E1-9.segments.txt: Tab-delimited text file includes chromatin states of vernalization leaf.

extract_protocol: ChIP-seq was performed  with antibodies for H3K27me3 (Abcam, ab6002), H3K4me3 (millipore, 07-473), H3K27ac (abclonal, A7253) and H3K36me3 (Abcam, ab9050). Libraries were constructed using Kit (TransGen Biotech, KP201-02), sequenced by Annoroad Gene Technology (Beijing, China).


title: ChIP-Seq Vernalized_leaf_input_rep1


title: RNA-Seq Leaf_rep2


title: RNA-Seq Leaf_rep1


title: ChIP-Seq Leaf_input_rep1


title: wild type pretzel stage embryo rep1


title: wild type 2-8 cell embryo rep1


title: Murine Spleen CD45+ Run 2

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

data_processing:
Fragment files were used to create Arrow files using the package ArchR (v.1.0.2) in R (v.4.0.0) and barcodes with >3000 fragments and a TSS enrichment score > 6 were maintained. Additionally, barcodes were excluded if they were flagged as gel bead multiplet, low-targeting barcode or barcode multiplet by Cell Ranger atac.
Potential cell doublets were identified with ArchR and barcodes with a DoubletScore >=2 were filtered out.
Dimensionality reduction with an iterative LSI  approach and UMAP and graph-based clustering were done with ArchR.
MACS2 (v.2.2.6) was used for peak calling at a cluster resolution of 0.1.
Gene activity scores were calculated with ArchR and transcription factor deviation scores were added using chromVAR (v.1.10.0). Fragments overlapping transposable elements were quantified based on integration sites from the RepeatMasker annotation available at http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz
Assembly: mm10
Supplementary files format and content: Output from Cell Ranger atac is described at https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac.
Supplementary files format and content: More information on the structure of Arrow files and ArchR projects is available at https://www.archrproject.com/bookdown/index.html

source_name: spleen

growth_protocol: SPF mice were housed under specified pathogen-free conditions at the central animal facility of the university clinics in Regensburg.

extract_protocol: Sorted cells were pelleted by centrifugation (300xg, 5min 4°C). Supernatant was removed and cells were resuspended in 50 µl - 100 µl 0.04%BSA-PBS buffer. Cells were centrifuged (300xg, 5 min 4°C), supernatant was completely removed and chilled nuclei lysis buffer (10 mM TRIS-HCL pH7.4, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA in nuclease-free water) was added. Lysis was performed for 2 min at 4°C, followed by addition of 50 µl washing buffer (10 mM TRIS-HCl ph7.4, 10 mM NaCl, 3 mM MgCL2, 1%BSA, 0.1% Tween-20 in nuclease-free water). After centrifugation (300xg, 5min 4°C), supernatant was removed and 45 µl chilled diluted nuclei buffer (10X Genomics) was added. After centrifugation (300xg, 5 min 4°C), supernatant was removed and 7µl chilled diluted nuclei buffer (10X Genomics) was added. Nuclei were counted (where applicable) and transposition mix was prepared with 5 µl of nuclei suspension based on the manufacturer’s protocol. Transposition was performed for one hour at 37°C, followed by supplementation of master mix and beads (Single Cell ATAC Gel Beads V1.0 or V1.1 and reagents, 10X Genomics #1000175), loading on 10X Chromium Next GEM Chip H (10X Genomics #1000161) and processing on 10X Chromium Controller (10X Genomics #120212). GEM incubation was performed with 11 cycles (mouse CD45) 10-11 cycles (human CD45) of PCR. All samples were processed in duplicate runs to increase total output of cells for analysis. Library was prepared according to the protocol with cycle numbers dependent on input nuclei concentration. scATAC libraries were sequenced on an Illumina NextSeqTM 550 with NextSeqTM 500/550 High Output Kit v2.5 (75 cycles, Illumina #20024906).

treatment_protocol: T cells were isolated and pre-enriched as described in the associated publication. Afterwards, they were stained with live/dead dye and surface antibodies as described. Cells were then sorted on an BDTM FACSAriaTM IIu or FACSAriaTM FUSION cell sorter using 85 µm nozzle size and 4-way-purity sort mode into 1.5 ml tubes filled with FACS buffer. Sample and post-sort quality control were recorded where applicable and are displayed in supplementary figures of the manuscript.

value: spleen

tag: cell line

value: CD45+ cells

value: Run 2


title: ChIP-Seq Vernalized_leaf_H3K4me3_rep2


title: ChIP-Seq Vernalized_leaf_H3K36me3_rep2


title: Murine Spleen CD45+ Run 1

value: Run 1


title: ChIP-Seq Vernalized_leaf_H3K4me3_rep1


title: ChIP-Seq Vernalized_leaf_H3K27me3_rep2


title: Sprague-Dawley_Male_Right_BiologicalReplicate2

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

data_processing:
Fastq files were produced from raw sequencing data or base call files (BCLs) using the bcl2fastq program from Illumina.
Genome sequence indexing and alignment of reads to the Ratticus Norvegicus reference genome were performed using STAR software.
The Subread R package feature count algorithm (featureCounts) was used to generate the count matrix of reads to genomic features, including genes and exons.
Genes that were present in less than 3 cells were filtered out.
Cells that expressed less than 200 genes or more than 10 percent mitochondrial genes were filtered out.
Assembly: mRatBN7
Supplementary files format and content: GZIP compressed Tab-delimited text file contains raw counts for each sample
Supplementary files format and content: GZIP compressed Tab-delimited text file contains normalized gene expression values for each sample

organism: Rattus norvegicus

source_name: DMV

extract_protocol:
Cell Lysates were directly processed for Reverse Transcription
Smart-3SEQ

tag: breed

value: Sprauge Dawley Rat

value: DMV

value: Male

tag: side

value: Right


title: Sprague-Dawley_Male_Left_BiologicalReplicate2

value: Left


title: ChIP-Seq Vernalized_leaf_H3K27me3_rep1


title: RNA-Seq Shoot_apex_rep2


title: Sprague-Dawley_Male_Left_BiologicalReplicate1


title: ChIP-Seq Vernalized_leaf_H3K27ac_rep2


title: ChIP-Seq Vernalized_leaf_H3K27ac_rep1


title: ChIP-Seq Leaf_H3K4me3_rep2


title: RNA-Seq Axillary_bud_rep1


title: Visium section 8

data_processing:
10X Genomics Space Ranger pipeline was used to generate FASTQ files
Genome sequence indexing and alignment of reads to the Ratticus Norvegicus reference genome were performed using Space Ranger's default settings.
Gene expression values were quantified using Space Ranger's default settings
Assembly: mRatBN7
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scale factors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: clusters.csv: file for reading in the clusters
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count data in Hierarchical Data Format
Library strategy: Spatial Transcriptomics

source_name: Brainstem

extract_protocol:
Fresh frozen tissue were OCT embedded and cryosectioned at 10  µm
Libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manfacturer's instruction

value: Brainstem

tag: age

value: 12 weeks


title: ChIP-Seq Leaf_H3K4me3_rep1

value: Leaf


title: ChIP-Seq Vernalized_leaf_H3K36me3_rep1


title: Visium section 6


title: ChIP-Seq Leaf_H3K36me3_rep1


title: Sprague-Dawley_Male_Right_BiologicalReplicate1


title: ChIP-Seq Leaf_H3K27me3_rep2


title: ChIP-Seq Leaf_H3K27me3_rep1


title: ChIP-Seq Leaf_H3K27ac_rep1


title: Visium section 4


title: ChIP-Seq Leaf_H3K27ac_rep2


title: Brainstem_247_Section_468-Sample_8

data_processing:
Fastq files were produced from raw sequencing data or base call files (BCLs) using the bcl2fastq program from Illumina.
Genome sequence indexing and alignment of reads to the Ratticus Norvegicus reference genome were performed using STAR software.
The Subread R package feature count algorithm (featureCounts) was used to generate the count matrix of reads to genomic features, including genes and exons.
Genes that were present in less than 3 cells were filtered out.
Cells that expressed less than 200 genes or more than 10 percent mitochondrial genes were filtered out.
Assembly: mRatBN7
Supplementary files format and content: Tab-delimited text file contains raw counts for each sample
Supplementary files format and content: Tab-delimited text file contains normalized gene expression values for each sample

value: Female

tag: connectivity

value: Non-FB

tag: cell state

tag: position

value: Caudal


title: Visium section 2

tag: tissue


title: Brainstem_247_Section_468-Sample_7


title: Visium section 1


title: Visium section 3


title: Brainstem_247_Section_468-Sample_6


title: ATAC-Seq Input_rep1

data_processing:
We used fastp v0.21.0 for data quality control and Bowtie v2.3.5.1 to align reads to wheat reference genome (bowtie2 -X 1000 --very-sensitive).
SAMtools v1.3.1 was used to sort and filter bam (samtools -q 10), Picard v2.16.0 to remove clonal duplicate, and MACS2 v 2.2.6 to call peak(macs2 --keep-dup all --nomodel --extsizes 150 --shift -75).
All the raw peaks were split into 150 bp bins with 50 bp overlapping, filtered by Tn5 integration site density, and merged by bedtools with “-d 200”.
Peaks overlapped with input and aligned to plant chloroplast DNA (NCBI) were discard, which guaranteed ACRs we identified were high-quality ACRs.
Assembly: ChineseSpring v1.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Input

extract_protocol: none provided

value: Input


title: ATAC-Seq Input_rep2


title: ATAC-Seq Vernalized_shoot_apex_rep2

value: Vernalized shoot apex


title: Visium section 7


title: ATAC-Seq Vernalized_shoot_apex_rep1


title: Brainstem_247_Section_468-Sample_4

value: FB


title: Brainstem_247_Section_468-Sample_20


title: Brainstem_247_Section_468-Sample_3


title: ATAC-Seq Vernalized_axillary_bud_rep1

value: Vernalized axillary bud


title: ATAC-Seq Vernalized_leaf_rep2

value: Vernalized leaf


title: Brainstem_247_Section_468-Sample_17


title: ChIP-Seq Leaf_H3K36me3_rep2


title: Visium section 5


title: ATAC-Seq Vernalized_leaf_rep1


title: ATAC-Seq Shoot_apex_rep2

value: Shoot apex


title: Brainstem_247_Section_468-Sample_16

value: Sprauge Dawley Rat


title: Brainstem_247_Section_468-Sample_19

value: DMV


title: ATAC-Seq Shoot_apex_rep1


title: Brainstem_247_Section_468-Sample_14


title: ATAC-Seq Axillary_bud_rep2

value: Axillary bud


title: Brainstem_247_Section_468-Sample_13

value: Right


title: Brainstem_247_Section_468-Sample_12


title: ATAC-Seq Leaf_rep2


title: ATAC-Seq Axillary_bud_rep1


title: Brainstem_247_Section_468-Sample_11


title: ATAC-Seq Vernalized_axillary_bud_rep2


title: ATAC-Seq Leaf_rep1


title: Brainstem_247_Section_468-Sample_15


title: Brainstem_247_Section_468-Sample_10

value: Left


title: Brainstem_247_Section_468-Sample_18


title: Brainstem_247_Section_464-Sample_3


title: Brainstem_247_Section_464-Sample_4


title: Brainstem_247_Section_464-Sample_2


title: Rius92_Takara_animal_19_6AM

city: Knoxville

first: Troy

last: Rowan

state: TN

address: 2506 River Dr

department: Animal Science Department

institute: University of Tennessee

description: Takara SMART-Seq v4 3′ DE

data_processing:
Takara reads sequenced on different lanes were concatenated to have one file per sample.
FastQC (v.0.11.9) and MultiQC (v.1.14) for quality control
Trimmomatic (v.0.39) with LEADING:5 TRAILING:5 SLIDINGWINDOW:5:20 MINLEN:30
STAR (v.2.7.10b): index Bos taurus genome (ARS-UCD2.0; Jul 2023) with sjdbOverhang of 149 bp.
STAR (v.2.7.10b): map to idenxed genome with quantMode “GeneCounts”.
Assembly: ARS-UCD2.0; Jul 2023
Supplementary files format and content: tab-delimited file with raw gene expression counts.

organism: Bos taurus

source_name: Whole blood

extract_protocol:
10 mL of blood was mixed with 30 mL of 1X NH4Cl red blood cell lysis buffer and was centrifuged at 2000 ×g for 10 minutes. The supernatant was aspirated and cell pellets resuspended in 1.2 mL of Trizol. RNA was isolated according to the protocol detailed in (Rio et al., 2010). RNA purification and genomic DNA removal were performed using the Zymo RNA Clean and Concentrator kit according to manufacturer protocol.
3` mRNA extraction with Takara SMART-Seq v4 3′ DE and Lexogen QuantSeq

treatment_protocol: Fifteen Holstein male calves housed under climate control rooms (Ríus et. al. 2022) in the East Tennessee Research and Education Center – JRTU undergoing an acute heat stress trial for an unrelated project (Yu et al., under revision). All animals were handled according to the University of Tennessee’s Institutional Animal Care and Use Committee Protocol 2851-0921. Fifteen whole blood samples were collected from the cattle at 6:30 before heat exposure, and 14 samples were collected at 18:30 immediately after 12 hours of heat exposure (Yu et al., under revision). Climate in the room was obtained following our previous work in heat-stressed claves  (Ríus et. al. 2022).

value: Whole blood

value: Normal

tag: hour

tag: sequencing library_kit

value: Takara SMART-Seq v4 3' DE


title: Rius96_Takara_animal_41_6AM

description: Takara SMART-Seq v4 3′ DE


title: Rius95_Takara_animal_40_6AM

description: Takara SMART-Seq v4 3′ DE


title: Rius91_Takara_animal_18_6AM

description: Takara SMART-Seq v4 3′ DE


title: Rius93_Takara_animal_23_6AM

description: Takara SMART-Seq v4 3′ DE


title: Rius90_Takara_animal_15_6AM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_464-Sample_5

tag: strain

value: 12 weeks

value: Female


title: Rius89_Takara_animal_12_6AM

description: Takara SMART-Seq v4 3′ DE

tag: treatment


title: Brainstem_247_Section_458-Sample_9

value: Non-FB

value: Caudal


title: Rius319_Takara_animal_32_6PM

description: Takara SMART-Seq v4 3′ DE

value: Heat Stress


title: Rius320_Takara_animal_36_6PM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_7


title: Brainstem_247_Section_458-Sample_6

value: FB


title: Brainstem_247_Section_458-Sample_8


title: Brainstem_247_Section_458-Sample_5


title: Brainstem_247_Section_458-Sample_4


title: Rius315_Takara_animal_14_6PM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_3


title: Rius314_Takara_animal_7_6PM

description: Takara SMART-Seq v4 3′ DE


title: Rius313_Takara_animal_3_6PM

description: Takara SMART-Seq v4 3′ DE


title: Rius318_Takara_animal_20_6PM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_1


title: Brainstem_247_Section_458-Sample_2


title: Brainstem_247_Section_458-Sample_19


title: Brainstem_247_Section_464-Sample_1


title: Rius284_Takara_animal_16_6AM

description: Takara SMART-Seq v4 3′ DE


title: Rius288_Takara_animal_36_6AM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_18


title: Rius287_Takara_animal_32_6AM

description: Takara SMART-Seq v4 3′ DE


title: Rius281_Takara_animal_3_6AM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_16


title: Rius282_Takara_animal_7_6AM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_17


title: Brainstem_247_Section_458-Sample_15


title: Rius120_Takara_animal_41_6PM

description: Takara SMART-Seq v4 3′ DE


title: Rius283_Takara_animal_14_6AM

description: Takara SMART-Seq v4 3′ DE


title: Rius316_Takara_animal_16_6PM

description: Takara SMART-Seq v4 3′ DE


title: Rius118_Takara_animal_29_6PM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_12


title: Rius119_Takara_animal_40_6PM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_13


title: Brainstem_247_Section_458-Sample_14


title: Rius116_Takara_animal_19_6PM

description: Takara SMART-Seq v4 3′ DE


title: Rius115_Takara_animal_18_6PM

description: Takara SMART-Seq v4 3′ DE


title: Rius113_Takara_animal_12_6PM

description: Takara SMART-Seq v4 3′ DE


title: Brainstem_247_Section_458-Sample_10


title: Brainstem_247_Section_452-Sample_9


title: Brainstem_247_Section_452-Sample_7


title: Rius96_Lexogen_animal_41_6AM

description: Lexogen QuantSeq 3′

value: Lexogen QuantSeq 3'


title: Brainstem_247_Section_452-Sample_8


title: Rius95_Lexogen_animal_40_6AM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_452-Sample_6


title: Rius92_Lexogen_animal_19_6AM

description: Lexogen QuantSeq 3′


title: Rius93_Lexogen_animal_23_6AM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_452-Sample_4


title: Rius94_Lexogen_animal_29_6AM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_452-Sample_5


title: Brainstem_247_Section_452-Sample_3


title: Rius91_Lexogen_animal_18_6AM

description: Lexogen QuantSeq 3′


title: Rius89_Lexogen_animal_12_6AM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_452-Sample_2


title: Rius320_Lexogen_animal_36_6PM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_452-Sample_16


title: Brainstem_247_Section_452-Sample_15


title: Brainstem_247_Section_458-Sample_11


title: Rius319_Lexogen_animal_32_6PM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_452-Sample_14


title: Brainstem_247_Section_452-Sample_13


title: Rius316_Lexogen_animal_16_6PM

description: Lexogen QuantSeq 3′


title: Rius318_Lexogen_animal_20_6PM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_452-Sample_11


title: Brainstem_247_Section_452-Sample_10


title: Rius313_Lexogen_animal_3_6PM

description: Lexogen QuantSeq 3′


title: Rius287_Lexogen_animal_32_6AM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_446-Sample_9


title: Brainstem_247_Section_446-Sample_7


title: Rius284_Lexogen_animal_16_6AM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_446-Sample_6


title: Rius288_Lexogen_animal_36_6AM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_446-Sample_5


title: Rius283_Lexogen_animal_14_6AM

description: Lexogen QuantSeq 3′


title: Rius282_Lexogen_animal_7_6AM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_446-Sample_4


title: Rius281_Lexogen_animal_3_6AM

description: Lexogen QuantSeq 3′


title: Rius120_Lexogen_animal_41_6PM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_446-Sample_3


title: Rius119_Lexogen_animal_40_6PM

description: Lexogen QuantSeq 3′


title: Rius315_Lexogen_animal_14_6PM

description: Lexogen QuantSeq 3′


title: Rius118_Lexogen_animal_29_6PM

description: Lexogen QuantSeq 3′


title: Rius117_Lexogen_animal_23_6PM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_446-Sample_2


title: Brainstem_247_Section_446-Sample_1


title: Brainstem_247_Section_446-Sample_12


title: Rius115_Lexogen_animal_18_6PM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_446-Sample_8


title: Rius114_Lexogen_animal_15_6PM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_446-Sample_13


title: Brainstem_247_Section_446-Sample_11


title: Brainstem_247_Section_440-Sample_8


title: Rius116_Lexogen_animal_19_6PM

description: Lexogen QuantSeq 3′


title: Rius113_Lexogen_animal_12_6PM

description: Lexogen QuantSeq 3′


title: Brainstem_247_Section_440-Sample_4


title: Brainstem_247_Section_440-Sample_3


title: Brainstem_247_Section_440-Sample_11


title: Brainstem_247_Section_446-Sample_14


title: BamGal4_2

city: Stanford

first: Lorenzo

last: Gallicchio

state: california

address: Campus Drive W

department: developmental Biology

institute: Stanford University

data_processing:
Adapters and low-quality bases were trimmed with trimGalore: trim_galore –quality 20 –stringency 1 –length 30 –paired_end –clip_R1 3 $Input1 $Input2 –output_dir trim_PE/
Reads were mapped to the Drosophila melanogaster genome build dm6 using STAR. Reads that fell within gene regions were counted with STAR using Ensembl annotation BDGP6.28. star_pass1: STAR –runThreadN 4 –runMode alignReads –genomeDir $star_index –alignSJoverhangMin 10 –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –readFilesIn $Input1_trimmed $Input2_trimmed –outFileNamePrefix $pass1_prefix –outSAMtype None. star_pass2: STAR –runThreadN 4 –runMode alignReads –quantMode GeneCounts –genomeDir $star_index –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –sjdbFileChr- StartEnd $junction –readFilesIn $Input1_trimmed $Input2_trimmed –out- SAMtype BAM SortedByCoordinate –limitBAMsortRAM 10000000000 –outFileNamePrefix $pass2_prefix.
Samtools was used to create .bw files for visualization: bamCoverage -b $Input -o $Output –binSize 1 –normalizeUsing CPM -p 4
Assembly: Ensembl annotation BDGP6.28
Supplementary files format and content: STAR output: ReadsPerGene
Supplementary files format and content: bamCoverage output: bw fliles for visualization

organism: Drosophila melanogaster

source_name: Testes

growth_protocol: Crosses were maintained for 3 days at 25C, the adult flies removed and the progeny moved to 29C until dissection time.

extract_protocol:
total RNA was extracted using the kit: RNeasy Plus Mini Kit from QIAGEN
Library was constructed using the kit: NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760S) using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490S).

treatment_protocol: 150 pairs of testes per sample were dissected in PBS in a glass cyclops dish in batches of 50 pairs. Testes were transferred to a 1.7 ml tube with PBS using forceps. PBS was removed and the sample snap-frozen in liquid nitrogen. Samples were kept at −80°C until the next step.

value: Testes


title: cbcKD_RNAseq_rep2

value: bamGal4>cbcKD(BL 77426)


title: Pcf11KD_RNAseq_rep1

value: bamGal4>PCf11KD(VDRC 103710)


title: PCF11KD_2


title: mir-35(seed_rev_no_bulge) L1 rep3

tag: sample id

value: mir-35(cdb2 cdb 95)

value: hermaphrodite

value: whole animal


title: Brainstem_247_Section_440-Sample_10

value: Sprauge Dawley Rat

value: DMV

value: Right


title: mir-35(mut_3') L1 rep3

tag: dev stage

value: mir-35(cdb2 cdb72)


title: Brainstem_247_Section_440-Sample_5

value: 12 weeks

value: Middle


title: Brainstem_247_Section_440-Sample_7

value: Female

value: Left

value: Non-FB


title: Brainstem_247_Section_440-Sample_6

value: FB

value: Caudal


title: mir-35(mir-82_3') L1 rep3

tag: genotype

value: mir-35(cdb2 cdb 78)


title: mir-35(wild_type) L1 rep6

value: wild type

tag: alias in_text_and_figures


title: Brainstem_247_Section_440-Sample_2

tag: Sex


title: mir-35(seed_rev_no_bulge) embryo rep3

value: embryo


title: Rius114_Takara_animal_15_6PM

description: Takara SMART-Seq v4 3′ DE

value: Whole blood

value: Heat Stress

value: Takara SMART-Seq v4 3' DE


title: Brainstem_247_Section_446-Sample_10

value: Sprauge Dawley Rat


title: Brainstem_247_Section_440-Sample_1

value: DMV


title: cbcKD_RNAseq_rep1

value: Testes

value: bamGal4>cbcKD(BL 77426)


title: Brainstem_247_Section_440-Sample_9

value: 12 weeks

value: Right


title: mir-35(mir-82_3') embryo rep3

value: hermaphrodite

value: whole animal


title: mir-35(wild_type) embryo rep6


title: Brainstem_247_Section_434-Sample_9

value: Female

value: Left

value: Non-FB

value: Middle


title: mir-35(mut_3') embryo rep3

value: mir-35(cdb2 cdb72)


title: Brainstem_247_Section_434-Sample_8


title: Brainstem_247_Section_440-Sample_13

value: Caudal


title: BamGal4_1


title: Brainstem_247_Section_434-Sample_7


title: mir-35(seed_rev_no_bulge) L1 rep2

value: mir-35(cdb2 cdb 95)


title: Brainstem_247_Section_434-Sample_6


title: lung, MCT3

city: Changsha

first: Yusi

last: Chen

state: Hunan

address: 139 Renmin Road

institute: The Second Xiangya Hospital of Central South University

data_processing:
Trimmed reads (trimmed 5', 3'-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1mismatch only to precursor tRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
Based on alignment statistical analysis (mapping ratio, read length, fragment sequence bias), we determine whether the results can be used for subsequent data analysis.
If so, the expression profiling and differentially expressed tRFs & tiRNAs and miRNAs are calculated.
Principal Component Analysis (PCA), Correlation Analysis, Pieplots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics.
Assembly: mm10

source_name: lung tissue

extract_protocol:
Six lung tissue samples from PAH and normal rats were used to obtain total RNA using the manufacturer's instructions and TRIzol (Invitrogen). Then, using a NanoDrop ND-1000 spectrophotometer, the amount of RNA was determined, and the integrity of the RNA was evaluated using denaturing agarose gel electrophoresis. The RNA samples were processed using the rtStar tsRNA Pretreatment kit (Cat# AS-FS-005, Arraystar) to eliminate changes like acetylation and methylation that might interfere with the construction of tiny RNA microarray libraries. To create a 3-OH end, whole RNA (100 ng) was first dephosphorylated. Following the manufacturer's recommendations, the labelled sample mixes were hybridized on an array using the Arraystar Small RNA Microarray.
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and PCR finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer. amplified fragments were extracted and purified from the PAGE gel. And amplification primers. Subsequently, ~134-160 bp

value: lung tissue

value: monocrotaline


title: lung, MCT1


title: mir-35(mir-82_3') L1 rep2

value: mir-35(cdb2 cdb 78)


title: lung, MCT2


title: lung, control3

value: saline


title: Brainstem_247_Section_434-Sample_5

value: Sprauge Dawley Rat

value: DMV


title: mir-35(mut_3') L1 rep2


title: lung, control2


title: lung, control1


title: Brainstem_247_Section_434-Sample_4

value: 12 weeks


title: mir-35(seed_rev_no_bulge) embryo rep2

value: embryo


title: Brainstem_247_Section_434-Sample_3


title: mir-35(wild_type) L1 rep5

value: wild type

value: hermaphrodite


title: Brainstem_247_Section_434-Sample_2

value: Female

value: FB


title: Brainstem_247_Section_434-Sample_1

value: Left


title: AC109347.1 overexpressed mouse 3

city: Guangzhou

first: Cunyou

last: Zhao

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

data_processing:
The reads were aligned to the UCSC  Mus musculis reference genome mm9 with TopHat version 2.0.4, and multi-aligned reads were removed with SAMtools.
We then used HTSeq to generate mapping counts for the known annotated genes
We used Cuffdiff to convert the counts into total FPKM values, which represented the gene expression levels.
DEGs between AC109347.1 overexpressed and wild type were identified with the edgeR ver. 2.6.12 statistical package.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: brain

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

value: brain

value: AC109347.1 overexpressed

value: treated with a recombinant Adeno-associated-virus carrying lncRNA AC109347.1


title: AC109347.1 overexpressed mouse 4


title: Control mouse 2

value: treated with an empty Adeno-associated-virus vector with no insert


title: Control mouse 3


title: AC109347.1 overexpressed mouse 5


title: mir-35(mir-82_3') embryo rep2

value: whole animal


title: 2.5_BAT_C_FPKM

city: Nuthetal

first: Tim

middle: Julius

last: Schulz

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition

data_processing:
Read pre-processing: Demultiplexing of all libraries for each sequencing lane using the Illumina bcl2fastq 1.8.4 software: 1 or 2 mismatches or Ns were allowed in the barcode read when the barcode distances between all libraries on the lane allowed for it. Clipping of Illumina TruSeq™ adapters of all reads (folder 'AdapterClipped'): reads with final length < 20 bases were discarded. Filtering of rRNA sequences using RiboPicker 0.4.3 (http://ribopicker.sourceforge.net/) (folder 'RiboPicker')  Creation of FastQC reports for all FASTQ files
For data processing and analysis, FASTQC v0.11.8 was used for quality assessment and trimmgalore v0.6.4 was applied for filtering adapter sequences and small reads.
The clean reads were mapped to a reference genome (Genome Reference Consortium Mouse Build 38 mm10) using the alignment tools HISAT2 v2.1.0 and Bowtie2 v2.3.5.1 Expression levels were quantified Cufflinks v.2.2.1.
Assembly: Genome Reference Consortium Mouse Build 38 mm10
Supplementary files format and content: normalized_FPKM_gene_expression

source_name: brown adipose tissue

extract_protocol:
RNA was isolated from 50 mg of tissue that was homogenized by grinding frozen tissue on liquid nitrogen. A 50 mg aliquot of tissue powder was then removed for RNA isolation.
NGS sequencing was conducted using Illumina HiSeq 2000 with 2 x 100 bp reads (LGC genomics, Berlin, Germany).

treatment_protocol: Male C57Bl6J mice were housed under controlled conditions at 22 ±2 °C in an 12/12-hour light/dark cycle maintained on a standard chow diet (Ssniff, Soest, Germany). The animals were killed at 10 weeks of age by cervical dislocation. Brown adipose tissue depots were isolated and immediately frozen in liquid nitrogen.

value: brown adipose tissue

value: male

value: WT

value: 10 weeks


title: Control mouse 1


title: 2.5_BAT_B_FPKM


title: Brainstem_247_Section_434-Sample_13

value: Sprauge Dawley Rat

value: DMV

value: Right

value: Middle


title: mir-35(mut_3') embryo rep2

value: embryo

value: mir-35(cdb2 cdb72)

value: hermaphrodite


title: Brainstem_247_Section_434-Sample_12

value: 12 weeks

value: Female

value: FB


title: 2.5_BAT_D_FPKM


title: mir-35(seed_rev_no_bulge) L1 rep1

value: mir-35(cdb2 cdb 95)


title: Brainstem_247_Section_434-Sample_11


title: mir-35(wild_type) embryo rep5

value: wild type


title: 2.5_BAT_A_FPKM


title: mir-35(mir-82_3') L1 rep1

value: mir-35(cdb2 cdb 78)

value: whole animal


title: WT_20uM_iSB09_rep3

city: Valencia

first: Pedro

middle: L.

last: Rodriguez

state: Valencia

address: C/ Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

data_processing:
After quality analysis with FastQC and read cleaning and adaptor trimming with cutadapt, clean reads were mapped to reference genome of Solanum lycopersicum SL4.0 using STAR. Read counts table produced by STAR was used to perform the differential expression analysis with DESeq2.
Assembly: SL4.0  (https://solgenomics.net/ftp/tomato_genome/assembly/build_4.00/)
Supplementary files format and content: tab-delimited text fille includes raw counts for each sample

organism: Solanum lycopersicum

source_name: whole seedlings

growth_protocol: Solanum lycopersicum seedlings (3 d.a.g.) were transferred from plates to flashes with liquid media during 8 days

extract_protocol:
RNA was harvested using E.Z.N.A.® Plant RNA Kit (Omega Biotek).
The library was constructed using the DNBSEQ Eukaryotic Strand-specific mRNA library kit (BGI Genomics, Shenzhen, China)

treatment_protocol: the medium was refreshed, and it was supplemented with 0.1% DMSO (mock) or 10 μM ABA or 20 μM iSB09 . Samples were collected after 3 hours of incubation

value: whole seedlings

value: 20uM iSB09


title: Brainstem_247_Section_434-Sample_10

value: Left

value: Non-FB


title: WT_20uM_iSB09_rep2

value: WT


title: mir-35(mut_3') L1 rep1

source_name: whole animal


title: WT_10uM_ABA_rep2

value: 10uM ABA


title: Brainstem_247_Section_428-Sample_7

value: Sprauge Dawley Rat

value: DMV

value: Middle


title: WT_10uM_ABA_rep1


title: Brainstem_247_Section_428-Sample_6


title: mir-35(wild_type) L1 rep4

value: hermaphrodite


title: WT_DMSO_rep3

value: 0.1% DMSO


title: WT_DMSO_rep2


title: mir-35(seed_rev_no_bulge) embryo rep1

value: embryo


title: Gut of flies fed E.coli (rep C)

city: Houston

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

data_processing:
kallisto v 0.44.0 (Bray et al., 2016) was used to perform pseudo alignment of RNA-seq reads to annotation release 102 of the house fly reference transcriptome from genome assembly v2.0.2 (Scott et al., 2014).
Transcripts were matched to their corresponding genes. Genes with alternative splicing will have multiple transcripts, and we measured the expression of a gene by summing over the count values of all of its transcripts.
Transcript per million (TPM) values were summed for genes with multiple transcripts to obtain gene-level TPM values
Genome_build: Annotation release 102 of the house fly reference transcriptome from genome assembly v2.0.2 (GCA_000371365.1)
Supplementary_files_format_and_content: Pseudomonas_infected_counts.csv
Supplementary_files_format_and_content: Ecoli_infected_counts.csv
Supplementary_files_format_and_content: Pseudomonas_infected_TPM.csv
Supplementary_files_format_and_content: Ecoli_infected_TPM.csv

organism: Musca domestica

source_name: Gut of infected house flies

growth_protocol: P. aeruginosa PAK-gfp and E. coli DH5ɑ were cultured and grown as described in Joyner et al. (2013, PLoS One 8:e79224) and Kumar and Nayduch (2016, Med Vet Entomol 30:218-228).

extract_protocol:
Flies were dissected 4 h post infection to separate the alimentary canal (i.e., gut) from the carcass (remainder of the body). For flies fed E.coli or the corresponding broth media, tissue samples from 3 individual flies were pooled for RNA extraction from each replicate. For flies fed P. aerugionas or the corresponding broth media, RNA was extracted from dissected tissues of individual flies, and RNA from 3 flies was pooled for each replicate. We collected three replicates per tissue (gut or carcass) for the E.coli treatment or corresponding control and four replicates per tissue for the P. aeruginosa treatment or corresponding control. RNA was extracted using Direct-zol miniprep plus kit (Zymo) following the manufacturer’s instructions with an optional TRIzol and BCP phase separation step prior to column purification.
RNA-seq libraries were constructed and sequenced by Novogene. Each RNA sample was normalized to a standard input concentration (1 μg of total RNA) using quantitative PCR, and an Illumina compatible sequencing library was prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer's recommended procedures. The resulting cDNA libraries were size validated on an Agilent 2100 Bioanalyzer System to ensure proper fragment distribution (∼260 bp) and effective removal of adapter dimers. Sequence libraries were multiplexed, and paired-end reads for each sample (2x150bp) were collected on an Illumina NovaSeq 6000 S4 flow cell to an approximate depth of 20 million read pairs for each sample.

treatment_protocol: One day old adult female house flies were fasted overnight and then individually housed and fed a 2 µl droplet of either P. aeruginosa (4.6 ×105 CFU), E. coli (3.8×105 CFU), or corresponding broth media (controls), as described in Nayduch et al. (2018, J Med Entomol 55:1264-1270).

value: Gut

tag: experimental group

value: Infected


title: mir-35(mir-82_3') embryo rep1


title: Brainstem_247_Section_428-Sample_5

value: 12 weeks

value: Female


title: Gut of flies fed E.coli (rep A)


title: Brainstem_247_Section_428-Sample_4

value: FB


title: Body of flies fed E.coli (rep C)

source_name: Body of infected house flies

value: Body


title: mir-35(mut_3') embryo rep1

value: mir-35(cdb2 cdb72)

value: whole animal


title: WT_DMSO_rep1

value: whole seedlings


title: Gut of flies fed E.coli (rep B)


title: WT_20uM_iSB09_rep1

value: WT

value: 20uM iSB09


title: Gut of flies fed control broth media for E.coli (rep C)

source_name: Gut of house flies

value: Control


title: WT_10uM_ABA_rep3

value: 10uM ABA


title: Body of flies fed E.coli (rep A)


title: Body of flies fed E.coli (rep B)


title: mir-35(seed_mut) L1 rep3

value: mir-35(cdb2 cdb6)


title: Brainstem_247_Section_428-Sample_1

value: Sprauge Dawley Rat

value: DMV

value: Right

value: Middle


title: Gut of flies fed control broth media for E.coli (rep B)

value: Gut


title: Brainstem_247_Section_428-Sample_2

value: 12 weeks


title: Gut of flies fed control broth media for E.coli (rep A)


title: Body of flies fed control broth media for E.coli (rep C)

source_name: Body of house flies


title: Brainstem_247_Section_428-Sample_11

value: Female

value: Non-FB


title: mir-35(seed_rev) L1 rep3

value: mir-35(cdb2 cdb4)

value: hermaphrodite


title: mir-35(wild_type) L1 rep3

value: wild type

value: whole animal


title: Body of flies fed control broth media for E.coli (rep A)

value: Body


title: Brainstem_247_Section_428-Sample_3

value: FB


title: Body of flies fed control broth media for E.coli (rep B)

value: Control


title: mir-35(wild_type) embryo rep4

value: embryo


title: Gut of flies fed P.aeruginosa (rep C)

value: Infected


title: Brainstem_247_Section_428-Sample_10

value: Sprauge Dawley Rat


title: mir-35(seed_mut) embryo rep3

value: mir-35(cdb2 cdb6)


title: Brainstem_247_Section_422-Sample_9

value: DMV

value: Left


title: mir-35(seed_rev) embryo rep3


title: Gut of flies fed P.aeruginosa (rep D)

value: Gut


title: Gut of flies fed P.aeruginosa (rep B)


title: Body of flies fed P.aeruginosa (rep D)


title: Brainstem_247_Section_422-Sample_8

value: 12 weeks

value: Middle


title: Gut of flies fed P.aeruginosa (rep A)


title: mir-35(wild_type) embryo rep3


title: Brainstem_247_Section_422-Sample_7

value: Female


title: Body of flies fed P.aeruginosa (rep C)


title: Brainstem_247_Section_422-Sample_6

value: Right

value: Non-FB


title: Gut of flies fed control broth media for P.aeruginosa (rep C)


title: Body of flies fed P.aeruginosa (rep B)


title: mir-35(seed_mut) L1 rep2

value: hermaphrodite


title: Body of flies fed P.aeruginosa (rep A)


title: mir-35(seed_rev) L1 rep2

value: mir-35(cdb2 cdb4)

value: whole animal


title: Gut of flies fed control broth media for P.aeruginosa (rep A)


title: Gut of flies fed control broth media for P.aeruginosa (rep B)


title: Brainstem_247_Section_422-Sample_5

value: FB


title: Body of flies fed control broth media for P.aeruginosa (rep D)

value: Body

value: Control


title: Brainstem_247_Section_422-Sample_4


title: mir-35(seed_mut) embryo rep2

value: embryo


title: Body of flies fed control broth media for P.aeruginosa (rep C)


title: Brainstem_247_Section_422-Sample_3

value: Sprauge Dawley Rat


title: Body of flies fed control broth media for P.aeruginosa (rep B)


title: Brainstem_247_Section_422-Sample_2


title: Body of flies fed control broth media for P.aeruginosa (rep A)


title: Brainstem_247_Section_422-Sample_1


title: mir-35(seed_mut) L1 rep1

value: mir-35(cdb2 cdb6)


title: Gut of flies fed control broth media for P.aeruginosa (rep D)


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, Biol Rep2

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

data_processing:
fastq files were quality checked with multiqc
fastq files were aligned using bowtie 2 with the local option in paired-end mode
read counts per exon were obtained using summarized overlaps
count normalization was performed using DESeq2
Assembly: GRCh38-hg38
Supplementary files format and content: BigWig
Supplementary files format and content: tab-delimited text file include normalized counts per sample

organism: Homo sapiens

source_name: WI38 (ATCC,CCL-75 )

growth_protocol: WI38 normal human lung fibroblasts (CCL-75, ATCC) were cultured in a DMEM (D629, Sigma) medium supplemented with 10% fetal bovine serum (#25-514, GenClone) at 37°C in a 5% CO2 and 2% O2 atmosphere.

extract_protocol:
Macherey-Nagel RNA Plus XS columns (#740990.250)
NEB UltraII Directional with poly A selection.

treatment_protocol: WI38-ER:RAS(G12V) cells were generated via retroviral transduction and were stimulated to with 400 nM 4-hydroxytamoxifen (4-OHT). Samples were collected and processed at indicated time-points post 4-OHT treatment.

tag: cell line

value: WI38 (ATCC,CCL-75 )

tag: cell type

value: normal lung fibroblasts

value: cells were retrovirally transduced with ER:RAS construct for inducible expression of oncogenic HRASG12V upon treatment with 4OHT

tag: time


title: Brainstem_247_Section_422-Sample_11

value: DMV

tag: age

value: 12 weeks

tag: side

value: Left

tag: connectivity


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, Biol Rep2


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, Biol Rep2


title: mir-35(seed_rev) L1 rep1

data_processing:
Sequence analysis was performed on the NIH High Performance Computing Cluster. The 3′ adapter sequence was trimmed using Cutadapt 3.4 (Martin, 2011). The reads were mapped to a custom genome file which was comprised of C. elegans genome WS280 with an additional chromosome containing the sequences of the spike-in miRNAs and the mutant mir-35 precursors with flanking genomic sequence. Mapping was performed using bowtie2 2.4.4 (Langmead et al., 2009) with the following settings: --no-unal --end-to-end --sensitive. BAM files were sorted and indexed using samtools 1.13 (Danecek et al., 2021). Reads were assigned to miRNAs using htseq 0.13.5 (Anders et al., 2015) with the following settings: --mode union --nonunique fraction -a 0. The htseq analysis was performed using a gff file modified from mirGeneDB (Fromm et al., 2015) by replacing mirGeneDB IDs with miRbase IDs (Kozomara and Griffiths-Jones, 2014) and adding the intervals corresponding to the spike-in miRNAs and the mir-35 mutant miRNAs in the custom genome file. miRNA differential gene expression was analyzed using DESeq2 analysis with default settings (Love et al., 2014). For analysis of tailing and trimming, the Tailor package (Chou et al., 2015) was used with the genome file described above and FASTA files derived from mirGeneDB, but with IDs replaced by miRbase IDs and sequences for spike-in miRNAs and the mir-35 mutant miRNAs appended.
Assembly: genome_c_elegans.PRJNA13758.WS280.genomic_with_spike_mut_mir35.fa
Assembly: cel_mirGeneDB_spikeins_mutmir35s_010622.gff
Supplementary files format and content: Reads were normalized to total genome-mapping reads; reported values are reads per million. Note that, due to differences in efficiency of cloning different sequences (resulting from ligation biases), comparison of read numbers for different miRNAs is not meaningful. Analysis should be limited to comparisons between samples for the same sequence.

tag: tissue


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, Biol Rep2


title: mir-35(wild_type) L1 rep2

value: wild type


title: mir-35(wild_type) L1 rep1


title: Brainstem_247_Section_416-Sample_7

value: Female

tag: cell state

tag: position

value: Middle


title: Brainstem_247_Section_422-Sample_10

tag: strain

value: Non-FB


title: mir-35(seed_mut) embryo rep1

value: hermaphrodite

value: whole animal


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, Biol Rep2

tag: treatment

value: EtOH (vehicle of 4-OHT)

value: control


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, Biol Rep1


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, Biol Rep1


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, Biol Rep1


title: Brainstem_247_Section_416-Sample_5

value: FB


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, Biol Rep1


title: mir-35(seed_rev) embryo rep2

tag: sample id

value: embryo

value: mir-35(cdb2 cdb4)


title: mir-35(seed_rev) embryo rep1

tag: dev stage


title: mir-35(wild_type) embryo rep2

tag: genotype


title: Brainstem_247_Section_416-Sample_4

value: Sprauge Dawley Rat


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, Biol Rep1

value: WI38 (ATCC,CCL-75 )

value: normal lung fibroblasts


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, Negative Control Rabbit IgG, Biol. Rep2

data_processing:
fastq files were quality checked with multiqc
fastq files were trimmed with trimmomatic te moreve adapters and aligned using bowtie 2 with the local option in paired-end mode
fastq files were trimmed with trimmomatic te moreve adapters and aligned using bowtie 2 with the local option in paired-end mode
Enriched regions were identified using macs v.2.2.7.1 (macs2 callpeak --nomodel --shiftsize --shift-control--gsize hs -p 1e-3)
Signal visualization tracks were generated with deeptools using the RPGC approach to obtain 1X coverage after merging time point replicates into a single bam file.
Assembly: GRCh38-hg38
Supplementary files format and content: BigWig and narrowPeak
Library strategy: CUT&Tag

extract_protocol:
DNA extraction and PCR amplification was performed and processed on Concavalin A bead immobilized nuclei using the CUTANA CUT&Tag kit (Epicypher:14–1102) according to manufacturer's instructions.
Libraries and library clean up per target per sample was performed according to CUTANA CUT&Tag kit (epicypher:14-1102) manufacturer's instructions (PCR amplification: 16 cycles). Library quality was assessed using an Agilent Tapestation 4200.

treatment_protocol: Nuclei from 100,000-200,000 cells per target per indicated timepoint were extracted and processed using the CUTANA CUT&Tag kit (Epicypher:14–1102) according to manufacturer's instructions. For the corresponding histone modications the following  antibodies were used: H3K4me1(Epicypher: 13–0057), H3K27me3 (Epicypher: 13–005), H3K27ac(Active Motif: 39,133) and rabbit IgG as a negative control(Epicypher: 13–0042), according to the manufacturer’s instructions.

value: cells were retrovirally transduced with ER:RAS construct for inducible expression of oncogenic HRASG12V upon treatment with 4OHT

tag: cut&tag antibody_target

value: rabbit IgG (Epicypher:13–0042)


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, Biol Rep2


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, Negative Control Rabbit IgG, Biol. Rep2


title: Brainstem_247_Section_416-Sample_3

value: DMV

value: 12 weeks

tag: Sex

value: Left


title: Brainstem_247_Section_416-Sample_1

value: Female

value: Right

value: Middle


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, Negative Control Rabbit IgG, Biol. Rep1


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, H3K27ace, Biol. Rep2

value: H3K27ac(Active Motif:39133)


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, Biol Rep1


title: Brainstem_247_Section_416-Sample_2

value: Non-FB


title: Brainstem_247_Section_416-Sample_14


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, H3K27ace, Biol. Rep2


title: 24 hpf embryo, H3K9me3_diag, rep 2

city: Athens

first: Mary

last: Goll

state: GA

address: 130 East Green Street

department: Genetics

institute: University of

description: E coli DNA spike in

data_processing:
Short reads (<20 bp) and adaptor sequences were removed using TrimGalore
Trimmed reads were aligned to the zebrafish genome assembly (GRCz.11 Ensemble release 98) using STAR with the following paramters: --readFilesCommand zcat –outSAMtype BAM SortedByCoordinate –outSAMmultNmax 1 –alignEndsType EndToEnd –alignIntronMax 1 –alignMatesGapMax 2000
Alignments were then filtered using SAMtools for a MAPQ score of 1 and PCR duplicates were removed using Picard MarkDuplicates
data was then normalized for library size and DNA spike-in using BEDtools “genomecov”
The Hypergeometric Optimization of Motif EnRichment (HOMER) software package was used to identify peaks over IgG using the following parameters: -style histone -minDist 1000 -gsize 1.5e9 -F 4
replicates were then analyzed using ChIPr with parameter -m 2 to identify reproducible peaks
Assembly: GRCz.11 release 98
Supplementary files format and content: bigwigs, averaged bigwigs, and peak files
Library strategy: CUT&RUN

organism: Danio rerio

source_name: embryo

extract_protocol: This is H3K9me3 CUT&RUN data isolated from zebrafish embryos. Genomic DNA libraries were prepared using an illumina protocol.

tag: timepoint

value: AB

tag: antibody

value: H3K9me3 Diagenode C15410056


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, H3K27ace, Biol. Rep2

tag: cell line

tag: cell type


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, H3K27ace, Biol. Rep2

value: EtOH (vehicle of 4-OHT)

tag: time

value: control


title: Brainstem_247_Section_416-Sample_13

value: Sprauge Dawley Rat

tag: age

tag: side


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, H3K4me, Biol. Rep2

value: WI38 (ATCC,CCL-75 )


title: 24 hpf embryo, H3K9me3_diag, rep 3

description: E coli DNA spike in

tag: tissue

value: embryo


title: mir-35(wild_type) embryo rep1

extract_protocol:
Samples were snap frozen, then resuspended in Trizol and vortexed for 15 minutes at room temperature. Thereafter, total RNA was purified according to the Trizol manufacturer’s instructions (ThermoFisher).
Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37°C.

value: wild type

tag: alias in_text_and_figures

value: hermaphrodite

value: whole animal


title: MUL1 -/- oocytes

type: RNA

city: Fukuoka

first: Takumi

last: Koshiba

address: 8-19-1 Nanakuma, Jonan-ku

country: Japan

institute: Fukuoka University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: oocyte, knockout

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated  and  purified  from cells using Rneasy Mini KIT (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Unfertalized oocytes were isolated by standard method.

value: unfertalized oocyte


title: Brainstem_247_Section_416-Sample_12

source_name: DMV

value: DMV

value: 12 weeks

tag: connectivity

tag: cell state

tag: position


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, H3K4me, Biol. Rep2

value: normal lung fibroblasts

value: cells were retrovirally transduced with ER:RAS construct for inducible expression of oncogenic HRASG12V upon treatment with 4OHT

tag: treatment


title: Brainstem_247_Section_416-Sample_11

tag: strain

value: Female

value: Right

value: Middle


title: 24 hpf embryo, H3K9me3_diag, rep 1

description: E coli DNA spike in

tag: genotype

value: AB

value: H3K9me3 Diagenode C15410056


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, H3K4me, Biol. Rep2

tag: cut&tag antibody_target


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, H3K27ace, Biol. Rep2

value: H3K27ac(Active Motif:39133)


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, H3K4me, Biol. Rep2


title: 4.5 hpf embryo, H3K9me3_diag, rep 1

description: E coli DNA spike in


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, Negative Control Rabbit IgG, Biol. Rep1

value: EtOH (vehicle of 4-OHT)

value: rabbit IgG (Epicypher:13–0042)

value: control


title: 4.5 hpf embryo, H3K9me3_diag, rep 2

description: E coli DNA spike in

value: embryo


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, H3K27me3, Biol. Rep2

value: WI38 (ATCC,CCL-75 )

value: H3K27me3 (Epicypher:13–005)


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, H3K27me3, Biol. Rep2


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, H3K27ace, Biol. Rep2


title: Brainstem_247_Section_410-Sample_7

value: Sprauge Dawley Rat

tag: Sex

value: Left

value: FB


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, H3K4me, Biol. Rep2

value: normal lung fibroblasts


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, H3K27me3, Biol. Rep2

value: cells were retrovirally transduced with ER:RAS construct for inducible expression of oncogenic HRASG12V upon treatment with 4OHT


title: 4.5 hpf embryo, H3K9me3_diag, rep 3

description: E coli DNA spike in

tag: timepoint


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, H3K27me3, Biol. Rep2


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, H3K4me, Biol. Rep2


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, H3K27me3, Biol. Rep2


title: 2.5 hpf embryo, H3K9me3_diag, rep 2

description: E coli DNA spike in

tag: antibody


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, H3K27me3, Biol. Rep2

tag: cell line


title: Brainstem_247_Section_410-Sample_12

value: DMV

value: 12 weeks

value: Female

value: Non-FB


title: 2.5 hpf embryo, H3K9me3_diag, rep 1

description: E coli DNA spike in

value: AB

value: H3K9me3 Diagenode C15410056


title: Brainstem_247_Section_410-Sample_8

value: Middle


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, H3K27ace, Biol. Rep1

tag: cell type

value: H3K27ac(Active Motif:39,133)


title: Brainstem_247_Section_410-Sample_10


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, H3K27ace, Biol. Rep1

tag: time


title: MUL1 +/+ oocytes

source_name: oocyte, wild-type

value: unfertalized oocyte


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, H3K27ace, Biol. Rep1


title: Brainstem_247_Section_410-Sample_9

tag: age


title: 24 hpf embryo, H3K9me3_active, rep 3

description: E coli DNA spike in

value: H3K9me3 Active Motif 39062

value: embryo


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, H3K27ace, Biol. Rep1

value: WI38 (ATCC,CCL-75 )


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, H3K27ace, Biol. Rep1


title: 2.5 hpf embryo, H3K9me3_diag, rep 3

description: E coli DNA spike in


title: Brainstem_247_Section_410-Sample_6

value: Sprauge Dawley Rat

tag: side

value: Right


title: 24 hpf embryo, H3K9me3_active, rep 2

description: E coli DNA spike in

tag: tissue


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, H3K27ace, Biol. Rep1

value: EtOH (vehicle of 4-OHT)

value: control


title: 24 hpf embryo, H3K9me3_active, rep 1

description: E coli DNA spike in


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, H3K4me, Biol. Rep1

value: normal lung fibroblasts

value: cells were retrovirally transduced with ER:RAS construct for inducible expression of oncogenic HRASG12V upon treatment with 4OHT


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, H3K4me, Biol. Rep1


title: Brainstem_247_Section_410-Sample_4

value: DMV

value: 12 weeks


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, H3K4me, Biol. Rep1


title: Brainstem_247_Section_410-Sample_5

value: Female

value: FB


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, H3K4me, Biol. Rep1


title: 4.5 hpf embryo, H3K9me3_active, rep 3

description: E coli DNA spike in

value: AB


title: Brainstem_247_Section_410-Sample_3

value: Middle


title: 4.5 hpf embryo, H3K9me3_active, rep 2

description: E coli DNA spike in


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, H3K4me, Biol. Rep1


title: Brainstem_247_Section_410-Sample_2

value: Non-FB


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, H3K27me3, Biol. Rep1

value: H3K27me3 (Epicypher:13–005)


title: 4.5 hpf embryo, H3K9me3_active, rep 1

description: E coli DNA spike in

value: H3K9me3 Active Motif 39062


title: Brainstem_247_Section_410-Sample_1


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, H3K27me3, Biol. Rep1


title: 2.5 hpf embryo, H3K9me3_active, rep 3

description: E coli DNA spike in

value: embryo


title: Brainstem_247_Section_404-Sample_14


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, H3K27me3, Biol. Rep1

value: WI38 (ATCC,CCL-75 )


title: Brainstem_247_Section_404-Sample_13

value: Sprauge Dawley Rat


title: 2.5 hpf embryo, H3K9me3_active, rep 2

description: E coli DNA spike in


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, H3K27me3, Biol. Rep1


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, H3K27me3, Biol. Rep1


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, Biol. Rep2

data_processing:
fastq files were quality checked with multiqc
fastq files were trimmed with trimmomatic te moreve adapters and aligned using bowtie 2 with the local option in paired-end mode
fastq files were trimmed with trimmomatic te moreve adapters and aligned using bowtie 2 with the local option in paired-end mode
Enriched regions were identified using macs v.2.2.7.1 (macs2 callpeak --nomodel --shiftsize --shift-control--gsize hs -p 1e-3). The identified peaks were subsequently processed using the irreproducibility discovery rate (IDR) pipeline, generating time point-specific reproducible peak sets at each time point. Reproducible peaks were collapsed into master peaksets per histone modification analyzed.
Signal visualization tracks were generated with deeptools using the RPGC approach to obtain 1X coverage after merging time point replicates into a single bam file.
Assembly: GRCh38-hg38
Supplementary files format and content: BigWig and narrowPeak

extract_protocol:
DNA was extracted using a Qiagen MinElute kit.
Libraries were produced by PCR amplification (7 cycles) of tagmented DNA using the NEBNext Ultra II High-Fidelity 2× PCR Master Mix (#M0544, NEB). Library quality was assessed using an Agilent Tapestation 4200.

treatment_protocol: Nuclei from WI38-ER:RAS(G12V) cells were extracted at indicated time-points post stimulation with 400 nM 4-hydroxy-tamoxifen (4-OHT)  by incubating cells in nuclear extraction buffer (containing 10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuging at 500 × g at 4 °C for 5 min. The supernatant was carefully removed by pipetting, and the transposition was performed by resuspending nuclei in 50 µl of Transposition Mix containing 1× TD Buffer (Illumina, San Diego, CA) and 2.5 µl Tn5 (Illumina) for 30 min at 37 °C.


title: 2.5 hpf embryo, H3K9me3_active, rep 1

description: E coli DNA spike in


title: Brainstem_247_Section_404-Sample_9

value: Right


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, Biol. Rep2


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, H3K4me, Biol. Rep1

value: EtOH (vehicle of 4-OHT)


title: 24 hpf embryo, H3K9me3_abcam, rep 2

description: E coli DNA spike in

value: H3K9me3 Abcam 8898


title: 24 hpf embryo, H3K9me3_abcam, rep 3

description: E coli DNA spike in


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, Biol. Rep2

value: normal lung fibroblasts


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, Biol. Rep2

value: cells were retrovirally transduced with ER:RAS construct for inducible expression of oncogenic HRASG12V upon treatment with 4OHT

value: control


title: Brainstem_247_Section_404-Sample_8

value: DMV

value: 12 weeks


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, Biol. Rep2


title: 24 hpf embryo, H3K9me3_abcam, rep 1

description: E coli DNA spike in


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, Biol. Rep2


title: WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, Biol. Rep1


title: Brainstem_247_Section_404-Sample_7

value: Female

value: FB


title: WI38-ER:RASG12V, 24hrs post-treament with 4-OHT, Biol. Rep1


title: WI38-ER:RASG12V, 4hrs post-treament with 4-OHT, Biol. Rep1


title: 4.5 hpf embryo, H3K9me3_abcam, rep 3

description: E coli DNA spike in

value: AB


title: Brainstem_247_Section_404-Sample_6

value: Left

value: Middle


title: WI38-ER:RASG12V, 12hrs post-treament with 4-OHT, Biol. Rep1


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, H3K27me3, Biol. Rep1

value: H3K27me3 (Epicypher:13–005)


title: WI38-ER:RASG12V, 2hrs post-treament with 4-OHT, Biol. Rep1


title: Brainstem_247_Section_404-Sample_5

value: Non-FB


title: Brainstem_247_Section_404-Sample_4


title: 4.5 hpf embryo, H3K9me3_abcam, rep 2

description: E coli DNA spike in

value: embryo


title: WI38-ER:RASG12V, 2hrs post-treament with EtOH, Biol. Rep1

value: WI38 (ATCC,CCL-75 )


title: Brainstem_247_Section_404-Sample_3

value: Sprauge Dawley Rat


title: HSPCs, ADT-derived cDNA 4

city: San Francisco

first: Catherine

last: Smith

state: California

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description:
Mission Bio Tapestri
Experiment 11 Protein
Experiment11.genotypes.hdf5

library_source: other

data_processing:
FASTQ files from single-cell DAbseq samples were processed via an open-source pipeline. This analysis pipeline trims adaptor sequences, demultiplexes DNA panel amplicons and antibody tags into single cells, and aligns panel reads to the hg19 reference genome. Valid cell barcodes were called using the inflection point of the cell-rank plot in addition to the requirement that 60% of DNA intervals were covered by at least eight reads. Variants were called using GATK (v 4.1.3.0) according to GATK best practices. ITDseek was used to detect FLT3 internal tandem duplication (ITD) from amplicon sequencing reads. For each valid cell barcode, variants were filtered according to quality and sequence depth reported by GATK, with low quality variants and cells excluded based on the cutoffs of quality score < 30, read depth < 10, and alternate allele frequency < 20%. Cell-surface protein reads were normalized using centered log ratio transformation.
To de-multiplex individual patients combined into a single sample, we used a novel computational approach incorporating both patient-specific anti-CD45 oligo-conjugated “hash” antibody tags as well as single nucleotide polymorphisms (SNPs) covered by the SC DNA panel. Individual samples were multiplexed together into groups of 3 and all SNPs were treated as binary (mutated or wildtype). For each multiplexed run, to identify SNPs that maximally differ between samples we filtered all SNPs mutated in <10% or >80% of cells. We performed a series of hierarchical clustering steps to further refine antibody hash data.
Assembly: hg19
Supplementary files format and content: hdf5 files
Library strategy: DAbseq

molecule: protein

source_name: Bone Marrow/Peripheral Blood

extract_protocol:
We performed DAbseq on unsorted mononuclear cells using a microfluidic approach with molecular barcode technology using the Tapestri platform (MissionBio) as previously described .
Briefly, cryopreserved cells were blocked and stained with unique anti-CD45 oligo-conjugated antibodies to provide sample-level identifiers, and groups of 2-3 individual patients were pooled together for multiplexed runs. Pooled samples were run through Mission Bio Tapestri platform as previously described. DNA from barcoded cells was amplified via PCR using a targeted panel that included 288 amplicons associated with acute leukemia. DNA PCR products were isolated and purified with standard library preparation protocol. Protein PCR products were isolated from the supernatant from AmpureXP bead purification via incubation with a 5’ Biotin Oligo (ITD), and purified using Streptavidin C1 beads.

value: Bone Marrow/Peripheral Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: HSPCs, barcode-derived cDNA 4

description:
Mission Bio Tapestri
Experiment 11 DNA
Experiment11.genotypes.hdf5


title: Brainstem_247_Section_404-Sample_2

extract_protocol:
Cell Lysates were directly processed for Reverse Transcription
Smart-3SEQ


title: HSPCs, ADT-derived cDNA 2

description:
Mission Bio Tapestri
Experiment 9 Protein
Experiment9.genotypes.hdf5


title: 2.5 hpf embryo, H3K9me3_abcam, rep 3

description: E coli DNA spike in

value: H3K9me3 Abcam 8898


title: 2.5 hpf embryo, H3K9me3_abcam, rep 2

description: E coli DNA spike in


title: HSPCs, barcode-derived cDNA 3

description:
Mission Bio Tapestri
Experiment 10 DNA
Experiment10.genotypes.hdf5


title: Brainstem_247_Section_404-Sample_1


title: HSPCs, barcode-derived cDNA 2

description:
Mission Bio Tapestri
Experiment 9 DNA
Experiment9.genotypes.hdf5


title: HSPCs, barcode-derived cDNA 1

description:
Mission Bio Tapestri
Experiment 8 DNA
Experiment8.genotypes.hdf5


title: Brainstem_247_Section_404-Sample_12

value: Right


title: 2.5 hpf embryo, H3K9me3_abcam, rep 1

description: E coli DNA spike in


title: HSPCs, ADT-derived cDNA 3

description:
Mission Bio Tapestri
Experiment 10 Protein
Experiment10.genotypes.hdf5


title: Brainstem_247_Section_404-Sample_11


title: 24 hpf embryo, IgG

description:
E coli DNA spike in
mIgG.bw (CUTnRUN_conf_exps)

value: IgG


title: Brainstem_247_Section_404-Sample_10

value: DMV


title: 2.5 hpf embryo, IgG


title: HEK293_WT_6h

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

institute: USTC

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the reference genome with Bowtie2. For linear RNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels. For circRNA annotation, CIRI2 and Find_circ were used, and backspliced read per million (BRPM) was used to calculate circRNA levels.
Assembly: hg19 (human), mm10 (mouse) and ASM294v2 (yeast)
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: HEK293 cells

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) followed by RNase R treatment or not according to the manufacturer’s instructions.

value: HEK293 cells

value: WT


title: HEK293_ZC3H14_OE


title: HEK293_ZC3H14_KO_0h

value: ZC3H14 KO


title: HEK293_ZC3H14_KO_6h


title: HEK293_WT_0h


title: 4.5 hpf embryo, H3K9me3_abcam, rep 1

description: E coli DNA spike in

value: AB


title: HEK293_EV


title: Brainstem_247_Section_398-Sample_9

data_processing:
Fastq files were produced from raw sequencing data or base call files (BCLs) using the bcl2fastq program from Illumina.
Genome sequence indexing and alignment of reads to the Ratticus Norvegicus reference genome were performed using STAR software.
The Subread R package feature count algorithm (featureCounts) was used to generate the count matrix of reads to genomic features, including genes and exons.
Genes that were present in less than 3 cells were filtered out.
Cells that expressed less than 200 genes or more than 10 percent mitochondrial genes were filtered out.
Assembly: mRatBN7
Supplementary files format and content: Tab-delimited text file contains raw counts for each sample
Supplementary files format and content: Tab-delimited text file contains normalized gene expression values for each sample

value: 12 weeks

value: Female

value: FB


title: HEK293_siNC_mRNA


title: HEK293_siZC3H14_mRNA


title: Brainstem_247_Section_398-Sample_8

value: Left

value: Non-FB

value: Middle


title: 4 hpf embryo, H3K9me3, rep 3

description: E coli DNA spike in

value: embryo


title: 4 hpf embryo, H3K9me3, rep 2

description: E coli DNA spike in


title: Brainstem_247_Section_398-Sample_7

value: Sprauge Dawley Rat


title: CRKL-UTR-Mut

value: CRKL 3' UTR deletion


title: FBXW-UTR-Mut

value: FBXW4 3' UTR deletion


title: 4.5 hpf embryo, IgG


title: 4 hpf embryo, H3K9me3, rep 1

description: E coli DNA spike in

value: H3K9me3 Abcam 8898


title: Brainstem_247_Section_398-Sample_6


title: STARR-seq output, biological replicate 2

city: 津南区

first: An

last: Jiang

state: 天津市

address: 南开大学津南校区综合实验楼D413

institute: 南开大学

data_processing:
Paired-end 150 bp reads were merged into single amplicons using Flash v1.2.11[28]. Oligo sequences from the passing reads were then mapped back to the expected oligo sequences using BWA mem version 0.7.12[29]. Multi-mapped reads were discarded. Reads were filtered if not met the following conditions: 1) adaptor sequences ‘GCTAGCCATTGCGTGTAGAG’ was perfectly matched. 2) Exact 10bp barcode sequences between adaptors. 3) Only primary alignment would be included (-F 256).  Oligo with less than 5 unique barcodes in any replicate were discarded. The abundance of unqiue barcode counts for each oligo per replicate were provided as input to DESeq2[30] for normalization as well as for enhancer activity calculation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts the number of unique barcodes per oligo

growth_protocol: DMEM + 10% FBS (Thermo Fisher Scientific)

extract_protocol:
Total RNA was extracted from transfected ARPE-19 cells using M5 HiPer Universal RNA Mini Kit (Mei5bio), and followed by poly (A) tail mRNA isolation using Dynabeads® Oligo (dT) kit (ThermoFisher Scientific). mRNA was treated with TURBO™ DNase (ThermoFisher Scientific) and purified by Agencourt RNAClean XP beads (Beckman Coulter). Target-specific first strand complementary DNA (cDNA) synthesis was performed with SuperScript III (ThermoFisher Scientific; 1.5 μg mRNA/reaction) to specifically reverse transcribe plasmid transcribed mRNAs (RT primer: 5’- CAAACTCATCAATGTATCTTATCATG-3’). All mRNA from the 10 million transfected cells was used in reverse transcription. After reverse transcription, reactions were treated with RNase A + H and pooled.
Then the first round of amplification, every 5 μL cDNA reaction was used as a template in every 50 μL PCR reaction using KAPA HiFi HotStart ReadyMix (Roche). Target amplification primers were used(gia-starrseq-2-f: 5’- ACACTCTTTCCCTACACGACGCTCTTCCGATCTattagattgatctagagcatgcaccggt-3’; gia-starrseq-2-r: 5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtcgaagcggccggccgaattcgtcga-3’). In the final round of amplification, the enzyme used is the same as that used in the first round, but 4 sets of primer combinations with different indexes are set to complete the final construction of the library. Illumina HiSeq platform compatible primers were used (forward: 5’-  AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; reverse: 5’- CAAGCAGAAGACGGCATACGAGAT-index-GTGACTGGAGTTCAGACGTG-3’). A total of 4 duplicated PCR reactions were performed for each indexing PCR. PCR products were cleaned up by DNA pure beads (VDOBIOTECH) and submitted for Illumina sequencing. Input library for sequencing was generated using similar PCR setup. Products from 4 duplicated PCR reactions were pooled (10 ng plasmid/reaction, 16 cycles of PCR).

treatment_protocol: Input plasmid library was electroporated into ARPE-19 cells using the Nucleofector™ platform (Lonza) according to manufacturer’s protocol (1 μg DNA/1 million cells). A total of 10 million cells were electroporated in each replicate and two biological replicates were generated. After transfection, cells were further cultured for 29 h until harvest.

tag: group

value: output


title: STARR-seq input, biological replicate 4

address: 南开大学津南校区综合实验楼D413

value: input


title: STARR-seq output, biological replicate 1

address: 南开大学津南校区综合实验楼D413


title: STARR-seq input, biological replicate 3

address: 南开大学津南校区综合实验楼D413


title: 4 hpf embryo, IgG, rep 2

description:
E coli DNA spike in
mIgG.bw (CUTnRUN_timecourse)

value: IgG


title: 4 hpf embryo, IgG, rep 1


title: Brainstem_247_Section_398-Sample_5

value: DMV

tag: connectivity

value: Rostral


title: Brainstem_247_Section_398-Sample_4

tag: cell state


title: C10orf53 siRNA knockdown-control, biological rep 2

address: 南开大学津南校区综合实验楼D413

data_processing:
RNA sequencing data were obtained from samples and sequenced using the Illumina platform to generate FASTQ files. Quality control was performed with FastQC, followed by trimming of adapters and low-quality bases using Trimmomatic. Reads were aligned to the reference genome using HISAT2, which efficiently handles known splice sites. The aligned reads were then quantified at the gene level using featureCounts, based on exon regions from the genome annotation.Differential expression analysis was conducted using DESeq2 in R, where raw counts were normalized and analyzed using a negative binomial distribution model. Statistical significance of differentially expressed genes was determined and adjusted for multiple comparisons with the Benjamini-Hochberg method. Functional enrichment analysis of significant genes was performed to interpret biological implications.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts of each gene

value: control siRNA transfection (C10orf53)


title: WT-UTR

value: HEK293 cells

value: WT


title: 4.5 hpf embryo, H3K9me3, rep 3

description: E coli DNA spike in

value: AB


title: STARR-seq input, biological replicate 1

address: 南开大学津南校区综合实验楼D413


title: Brainstem_247_Section_398-Sample_3

value: 12 weeks

value: Female

value: Left

value: FB

tag: position


title: Brainstem_247_Section_398-Sample_2

value: Sprauge Dawley Rat

value: Non-FB


title: C10orf53 siRNA knockdown-control, biological rep 3

address: 南开大学津南校区综合实验楼D413

tag: treatment


title: 4.5 hpf embryo, H3K9me3, rep 2

description: E coli DNA spike in

value: embryo


title: Brainstem_247_Section_398-Sample_1

tag: strain


title: 4.5 hpf embryo, H3K9me3, rep 1

description: E coli DNA spike in

tag: genotype

value: H3K9me3 Abcam 8898


title: C10orf53 siRNA knockdown-treat, biological rep 3

address: 南开大学津南校区综合实验楼D413

value: C10orf53 siRNA transfection


title: C10orf53 siRNA knockdown-control, biological rep 1

address: 南开大学津南校区综合实验楼D413


title: Brainstem_247_Section_398-Sample_15

value: Right


title: PLEKHA7 siRNA knockdown-control, biological rep 2

address: 南开大学津南校区综合实验楼D413

value: control siRNA transfection (PLEKHA7)


title: C10orf53 siRNA knockdown-treat, biological rep 2

address: 南开大学津南校区综合实验楼D413


title: PLEKHA7 siRNA knockdown-control, biological rep 3

address: 南开大学津南校区综合实验楼D413


title: 4.5 hpf embryo, IgG, rep 1

value: IgG


title: Brainstem_247_Section_398-Sample_14

value: DMV

value: Rostral


title: 4.5 hpf embryo, IgG, rep 2


title: STARR-seq input, biological replicate 2

address: 南开大学津南校区综合实验楼D413

value: input


title: PLEKHA7 siRNA knockdown-treat, biological rep 3

address: 南开大学津南校区综合实验楼D413

value: PLEKHA7 siRNA transfection


title: Brainstem_247_Section_398-Sample_13


title: 3 hpf embryo, H3K9me3, rep 3

description: E coli DNA spike in

value: AB


title: 3 hpf embryo, H3K9me3, rep 2

description: E coli DNA spike in


title: PLEKHA7 siRNA knockdown-treat, biological rep 2

address: 南开大学津南校区综合实验楼D413


title: Iris ATAC-seq, biological rep 3

address: 南开大学津南校区综合实验楼D413

description:
Iris_ATAC.bed
Iris_ATAC.bw

data_processing:
The ATAC-seq data were processed as previously described, with two biological replicates collected for iris tissue. After quality control by Fastp, 150 bp paired-end ATAC-Seq reads were aligned to the human reference genome (GRCh38/hg38) using Bowtie2 with default parameters. After filtering reads from mitochondrial DNA and removing duplicate reads, we included properly paired reads with high mapping quality (MAPQ score >10, qualified reads) through SAMTools for further analysis.Deeptools was performed to check pearson correlation between 2 biological replicates and to summarize signal intensities across transcriptional starting sites. Because a high correlation rate was observed(R=0.99), the bam file were grouped for further calling peak using MACS2 with parameters --nomodel --shift -100 --extsize 200
Assembly: hg38
Supplementary files format and content: bigwig file

source_name: Iris

extract_protocol:
The tissue were re-suspended in cold PBS according to ATAC-Seq protocol. Transposition was performed at 37℃ for 60 min with gentle shaking.
DNA was purified with the Qiagen DNA miniElute column and amplified for 16 cycles with indexed S5 and N7 primers. The final library was size-selected for products between 200-600 bp using the AMPure XP bead and subjected to pair-end sequencing (PE150) on a Novaseq6000 platform.

value: Iris

value: No treatment


title: Iris ATAC-seq, biological rep 2

address: 南开大学津南校区综合实验楼D413

description:
Iris_ATAC.bed
Iris_ATAC.bw


title: Iris ATAC-seq, biological rep 1

address: 南开大学津南校区综合实验楼D413

description:
Iris_ATAC.bed
Iris_ATAC.bw


title: ARPE-19 ATAC-seq, biological rep 2

address: 南开大学津南校区综合实验楼D413

description:
ARPE_atac.bed
ARPE_ATAC.bw


title: ARPE-19 ATAC-seq, biological rep 1

address: 南开大学津南校区综合实验楼D413

description:
ARPE_atac.bed
ARPE_ATAC.bw


title: 3 hpf embryo, H3K9me3, rep 1

description: E coli DNA spike in


title: 3 hpf embryo, IgG, rep 2


title: Brainstem_247_Section_398-Sample_12

value: 12 weeks

value: Female


title: 3 hpf embryo, IgG, rep 1


title: Brainstem_247_Section_398-Sample_10

value: Sprauge Dawley Rat

value: FB


title: C10orf53 siRNA knockdown-treat, biological rep 1

address: 南开大学津南校区综合实验楼D413


title: ENU_C

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

data_processing:
Raw sequence reads were processed using the nf-core RNA-Seq pipeline (https://nf-co.re/rnaseq/3.10) to obtain gene expression levels.
Gene filtering was performed using the zPKM program.
Count normalization and differential expression testing was performed using the DESeq2 program.
Assembly: hg19
Supplementary files format and content: *.genes.results files are tab-delimmited text files that contain unnormalized gene expression levels for each sample
Supplementary files format and content: counts.filtered.normalized.csv is comma-delimmited textr file that contains filtered and normalized counts for all samples

source_name: lung

growth_protocol: Human IMR-90 primary fibroblasts were obtained from the American Tissue Culture Collection (ATCC; LOT number 70020198). They were cultured in DMEM (Dulbecco’s Modified Eagle Medium, from ATCC) supplemented with 10% fetal bovine serum (FBS, Gibco/Life Technologies) and 1% Penicillin-Streptomycin solution (Gibco/Life Technologies) at 3% oxygen and 37°C. Cells obtained from ATCC were at passage 11 upon arrival and were cultured for an additional 5 passages before the start of the experiment.

extract_protocol:
RNA was extracted from frozen cell pellets using the Zymo DNA/RNA extraction kit (Microprep plus D7005) according to the manufacturer’s instructions and quantified using a Qubit kit (Thermo Fisher Scientific, USA).
Libraries were prepared by using the mRNA-Seq service from Novogene Corp Inc., CA

treatment_protocol: Cells were then treated for a total of 9 times over the course of several months with ENU. Cells were treated with medium containing 50 µg/ml ENU 24 hours after seeding 1 million cells in a 10 cm dish. After 3 days cells were counted, 1 million cells re-seeded, and any remaining cells were collected and stored at -80°C. The same procedure was repeated 7 days after treatment. All downstream analysis was performed on samples collected 7 days after the last treatment unless stated otherwise.

value: lung

value: ATCC IMR-90 CCL-192

value: fibroblast

value: WT

value: ENU 50 µg/mL cycle 9

tag: batch

value: Batch C


title: PLEKHA7 siRNA knockdown-control, biological rep 1

address: 南开大学津南校区综合实验楼D413

value: control siRNA transfection (PLEKHA7)


title: Brainstem_247_Section_392-Sample_9

value: DMV

tag: Sex

value: Left

value: Rostral


title: 3.5 hpf embryo, H3K9me3, rep 3

description: E coli DNA spike in

tag: timepoint

value: AB

value: H3K9me3 Abcam 8898

value: embryo


title: Brainstem_247_Section_392-Sample_8

value: 12 weeks

value: Non-FB