title: S53_adK

city: Charleston

first: Deanna

last: Baker Frost

state: SC

address: 96 Jonathan Lucas St room 822

department: Medicine

institute: Medical University of South Carolina

description:
Library name: S53_adK
PE150 6G raw data per sample

data_processing:
Novogene: Original image data file from HTS platforms is transformed to sequenced reads (Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
STAR software is used to accomplish the mapping. The alignment by STAR precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Gene expression level is calculated by the number of mapped reads with FeatureCounts. Read counts is proportional to gene expression level, gene length and sequencing depth, and is used for DE analysis.
Gene-level count data were generated by HTSeq and FeatureCounts. DE analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). Significance criteria q-value<0.1, log2FC>0.6 upregulation, log2FC<-0.6 downregulation
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-delimited .txt files generated by DESEQ2

source_name: lung

growth_protocol: Primary human SSc lung fibroblasts were outgrown from explanted lungs of SSc patients who underwent lung transplantation. SSc lung fibroblasts were plated in 6-well plates (125,000 cells/well) in complete DMEM media (Mediatech Inc., Manassas, VA, USA) with 10% FBS (Sigma-Aldrich, Saint Louis, MO, USA) and 1X Antibiotic/Antimycotic (ThermoFisher Scientific, Waltham, MA, USA) and allowed to recover for at least 48h.

extract_protocol:
48h post adenoviral infection, media was removed, and each well was washed with 1X cold PBS. RNA was extracted using 500uL of Trizol (Invitrogen, Carlsbad, CA, USA) following manufacturer’s instructions. For protein extraction, fibroblasts were culture for 72h post adenoviral infection. Conditioned media was saved, and each well was washed with 1X cold PBS. Lysates were harvested by scraping in 200uL of 2X SSB (125mM Tris pH 6.8, 10% glycerol, 3% SDS, 0.01% bromophenol blue, 715mM beta-mercaptoethanol).
mRNA library preparation with poly A enrichment/non-directional. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.

treatment_protocol: When 80% confluency was reached, media was removed, wells were washed 2 times with 1X sterile PBS. After the last wash, 500uL of 1X sterile PBS was added to each well, and 1uL of ad-KLF4 or ad-Null was added to the appropriate well(s)at a final multiplicity of infection (MOI) of 33. The plates were incubated at room temperature for 1h and rocked gently every 15min. After 1h, 1mL of complete media was added to each well and the plates were incubated at 37°C and 5% CO2. SSc lung fibroblasts were infected for 24h before the media was changed.

value: lung

value: human primary

value: fibroblasts

value: SSc lung fibroblasts


title: FLAM_IFNg_24H_2

status: Public on Jun 03 2026

type: SRA

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

country: USA

institute: Michigan State University

library_source: transcriptomic

data_processing:
RNASeq read quality assessment, mapping, and counting were performed using a custom pipeline built in Snakemake version 7.32.4 (https://github.com/kaylaconner/olivelab-rnaseq/tree/main)1. Read quality was assessed using FastQC version 0.12.12. Read mapping was performed against the GRCm39 mouse reference genome using Bowtie2 version 2.5.13. Aligned reads counts were assessed using the featurecounts function from the Subread package version 2.0.64. Differential gene expression analysis was conducted using the DESeq2 package version 1.42.0 in R version 4.3.25. Pre-filtering was performed to keep only genes that had >10 counts in 3 or more samples.
Assembly: Mouse GRCm39
Supplementary files format and content: RawCounts.csv - Contains raw read counts produced by Feature Counts for all samples combined into a single data matrix
Supplementary files format and content: normalizedcounts.csv - Contains normalized read counts produced by DESeq2 for all samples combined into a single data matrix

molecule: total RNA

organism: Mus musculus

source_name: Cell Line

extract_protocol:
A Direct-zol RNA Extraction Kit (Zymo Research, Cat no. R2072) was used to extract RNA according to the manufacturer’s protocol.
Illumina Sequencing was carried out by SeqCenter (Pittsburgh, PA).

tag: tissue

value: Cell Line

tag: cell line

value: FLAM

tag: cell type

value: Alveolar-Like Macrophage

tag: genotype

tag: treatment

value: IFNg + Mab Infected - 24H


title: Cannabis sativa L. Leaf, Putrescine 0.9mM treatment, RNA-seq, R3

city: Chuncheon-si

first: Byeong-Ryeol

last: Ryu

state: Gangwon-state

address: 1, Kangwondaehak-gil

department: Department of Bio-Health Convergence

country: South Korea

institute: Kangwon National Univsersity

description: Library name: Sample9

data_processing:
Sequencing-generated mRNA reads were quality-controlled using fastp (v0.24.0) to remove adapter sequences and low-quality reads.
Filtered reads were aligned to index the C. sativa reference genome (RefSeq: GCF_029168945.1) with STAR (v2.7.11b; --runmode genomeGenerate, --sjdbOverhang 150).
Gene-level read counts were obtained using featureCounts (v2.0.8).
The resulting count matrix was analyzed in DESeq2 (v1.44.0) to quantify gene expression.
Assembly: Cannabis sativa L. RefSeq genome (RefSeq: GCF_029168945.1)
Supplementary files format and content: tab-delimited text file includes featureCounts for each sample (header = T).
Supplementary files format and content: tab-delimited text file includes DESeq normalized counts for each sample (header = F).

organism: Cannabis sativa

source_name: Leaf

growth_protocol: C. sativa cv. Pink Pepper seeds were used in this experiment. Seeds were soaked in 1 % hydrogen peroxide solution (DAEJUNG Chemicals & Metals Co., Siheung, Korea) for 10 h, then sown in 105‐well seedling trays (42 mL per well) filled with potting soil (Anong Sangto, Asiaseed Co., Seoul, Korea). Seedlings were grown for 15 days under controlled conditions (25 ± 2°C; 43 ± 7% RH) and watered with 30 mL tap water per plant every 3 days. After germination, seedlings were transplanted into 600 mL pots and cultivated for 3 weeks at 23 ± 2°C and 43 ± 7% RH, with 300 mL tap water per plant every 3 days. Lighting was provided by red and blue LEDs (BISSOLLED, Seoul, Korea) at a photosynthetic photon flux density (PPFD) of 312.9 ± 0.5 µmol m-2 s-1 under an 18 h photoperiod.

extract_protocol:
Leaves collected for transcriptome analysis were immediately frozen in liquid nitrogen. Total RNA was extracted using the Rneasy Micro Kit (Qiagen, Hilden, Germany), and RNA concentration was measured with the Quant-iT™ RiboGreen RNA Assay Kit (ThermoFisher Scientific Inc., Waltham, MA, USA). RNA integrity was asseessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and samples with an RNA integrity number (RIN) of 7.0 were used.
mRNA libraries were prepared using the TruSeq Standard mRNA Library Prep Kit (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Plants were exposed to cold stress in a growth chamber (HanKuk Scientific Co., Ltd., Hwaseong, Korea) at 5 ± 1°C for 168 h. Control plants were maintained under the same conditions at 23 ± 1°C. Putrescine (Duchefa Biochemie, Haarlem, Netherlands) was dissolved in ultrapure water and foliar-sprayed at 5 mL per plant onto the shoots. To prevent cross-contamination, putrescine treated plants were allowed to air-dry for 5 min after spraying and then grown in an independent chanber. Relative humidity was maintained at 40 ± 3% RH for all treatments, and the PPFD was set to 150 µmol m-2 s-1.

value: Leaf

value: Cannabis sativa L. cv. Pink Pepper

value: Putrescine 0.9mM


title: IWP2_DIV40 n1

city: Paris

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, INSERM UMR1163

description:
Library name: B9
10xGenomics

library_source: transcriptomic single cell

data_processing:
The sequencing data was analyzed with the Cell Ranger software (version 6.0.1) provided by 10x Genomics. Demultiplexing of the sequencing reads was performed with cellranger mkfastq.
For each sample, FASTQ files generated with cellranger mkfastq were subsequently processed with cellranger count. Cellranger count performs alignment, filtering, barcode counting and UMI counting. Using the filtered barcodes, it also generates feature-barcode matrices
Assembly: GRCh38-3.0.0
Supplementary files format and content: cellranger output files for 'filtered_feature_bc_matrix' (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz)

molecule: polyA RNA

organism: Homo sapiens

source_name: iPSC-derived midbrain organoids

growth_protocol: Human induced pluripotent stem cells were used to generate human midbrain organoids (hMOs). iPSCs were dissociated into single cells and seeded at a density of 9,000 cells per well in U-bottom 96-well plates to form embryoid bodies (EBs). The initial neuroinduction medium consisted of a DMEM/F12 and Neurobasal base supplemented with N2, B27, NEAA, and was guided by dual SMAD inhibition (SB431542 and LDN) and Wnt activation (CHIR99021). From day 4, midbrain patterning was promoted by the addition of SHH and FGF8. On day 7, EBs were embedded in Matrigel and transferred to six-well plates. From day 8 onwards, organoids were cultured in a maturation medium containing neurotrophic factors, including BDNF and GDNF, as well as ascorbic acid and db-cAMP. On day 20, the organoids were mechanically freed from the Matrigel and transferred to either an orbital shaker or a spinning bioreactor for long-term dynamic culture.

extract_protocol:
Midbrain organoids were dissociated into single-cell suspension following the Worthington Papain Dissociation System kit instructions (Worthington Biochemical) with intermittent trituration steps. The final solution was centrifuge 300g per 7 min, cell pellet were resuspended in PBS-0,04% BSA and filtered twice (40um, 30um) to obtain single-cell suspensions.
Cells loaded to Chromium Chip (target cell recovery): 10,000 cells. Library Preparation Kit: Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics). Sequencing parameters: NovaSeq X, SP Flow Cell, 100 cycles. Read 1: 28 bp, i7-index: 10 bp, i5-index 10 bp, Read 2: 90 bp.

treatment_protocol: The Wnt-TriP protocol was developed as a modification of the standard growth protocol to investigate the role of temporal Wnt gradients on dopaminergic neuron development. Following the initial neuroinduction and midbrain patterning stages, a key treatment window was introduced between DIV 11 and DIV 18. During this period, the Wnt activator CHIR99021 was removed from the culture medium. Concurrently, the medium was supplemented with the Wnt-signalling inhibitor IWP-2 at a final concentration of 2.2 µM. Organoids in the "Standard" protocol, serving as the control, did not receive IWP-2 and were instead cultured with decreasing concentrations of CHIR99021 during this same timeframe. After DIV 18, the Wnt-TriP organoids were subsequently maintained in the final maturation medium, identical to that used for the standard condition.

value: iPSC-derived midbrain organoids

value: Wnt-TriP

tag: incubation

value: Standart

tag: days in_vitro

value: DIV 40


title: CTRL_DIV40 n2

description:
Library name: E9
10xGenomics


title: FLAM_IFNg_24H_3


title: Arabidopsis root control (replicate 1)

city: Toledo

first: Carolina

last: Escobar Lucas

state: Toledo

address: Avda Carlos III, s/n, Campus Fábrica de armas, Edificio Sabatini, laboratorio 08

department: Plant physiology

country: Spain

institute: University of Castilla-la Mancha

description:
Library name: RC_R1
Three biological replicates consisting of independent pools of gall (14 dpi) equivalent uninfected root segments.

data_processing:
Base-calling / raw read generation: Raw signal intensities from the Illumina HiSeq X platform were converted into base calls and stored as FASTQ files.
Quality control: Raw reads were evaluated for quality using FastQC v0.11.9, and summary reports were generated with MultiQC.
Trimming / filtering: Adapter sequences were removed using Cutadapt v3.4. Reads shorter than 20 bp after trimming were discarded.
Read alignment: Clean paired-end reads were aligned to a composite reference genome including Arabidopsis thaliana (TAIR10/Araport11 annotation) and Meloidogyne javanica using STAR aligner v2.7.10b.
Count table generation: Gene level read counts were obtained using HTSeq-count v0.13.5 in strand-specific mode against the Araport11 gene annotation.
Differential expression analysis: Statistical analysis was performed using edgeR with TMM normalization. Differential expression between galls and control roots was assessed using generalized linear models and likelihood ratio tests, with multiple testing correction by the Benjamini-Hochberg method (FDR < 0.05).
Assembly: Composite reference genome including Arabidopsis thaliana TAIR10 (Araport11 annotation) and Meloidogyne javanica genome.
Supplementary files format and content: Arabidopsis_14dpi_RNAseq_normalized_counts.txt.gz file containing normalized gene expression values. Each row corresponds to an Arabidopsis gene identifier (TAIR10 locus), and columns represent biological replicates from 14 dpi galls and uninfected root controls (three replicates per condition).
Supplementary files format and content: 14dpi_gall_vs_RC_deg.txt.gz file containing differential expression results. Each row corresponds to one gene and includes expression statistics metrics, log2 fold change between galls and control roots, statistical test values, raw p-values, and Benjamini-Hochberg adjusted p-values (FDR).

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis thaliana (Col-0) seeds were surface sterilized and germinated on Gamborg B5 medium supplemented with sucrose. Plants were grown in vitro under controlled environmental conditions (16 h light / 8 h dark photoperiod, 23 °C) prior to nematode inoculation.

extract_protocol:
Total RNA was extracted from hand-dissected galls and equivalent uninfected root segments using the AllPrep® DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions, as described in Silva et al. (2019). RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer.
Strand-specific mRNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) with poly(A) enrichment. Libraries were dual-indexed, pooled in equimolar amounts, and sequenced as 150 bp paired-end reads on an Illumina HiSeq X platform at Macrogen Inc. (Seoul, South Korea).

treatment_protocol: Seedlings were inoculated with Meloidogyne javanica to induce gall formation on the roots. Control plants were maintained under identical conditions without nematode infection. Root tissues containing galls and corresponding non infected root controls were collected at 14 days post-inoculation (dpi).

value: Root

tag: ecotype

value: Unifected


title: CTRL_DIV40 n3

description:
Library name: E8
10xGenomics


title: S53_adN

description:
Library name: S53_adN
PE150 6G raw data per sample

value: lung

value: control


title: FLAM_IFNg_24H_1


title: IWP2_DIV65 n2

description:
Library name: B7
10xGenomics

value: DIV 65


title: C4-2B Ola 1-2 5-day

city: Sacramento

first: Alan

last: Lombard

state: CA

address: 4500 2nd Avenue, Rm 4674

institute: University of California, Davis

description: Library name: LLG014

data_processing:
Raw sequencing data were processed using the nf-core/rnaseq pipeline (version 3.14.0, DOI 10.5281/zenodo.10471647), which includes quality control, alignment, and quantification steps
Reads were trimmed using Trim Galore
reads were mapped to the Homo sapiens reference genome (GRCh38) using STAR (Dobin et al., 2013). Gene-level quantification was performed using Salmon (Patro et al., 2017) against the GENCODE v45 gene annotation
Raw counts were extracted from the Salmon file outputs
Assembly: GRCh38 and GENCODE v45 gene annotation
Supplementary files format and content: tab-delimited text file contains raw counts for each sample and associated Ensembl gene id from the GENCODE v45 gene annotation.

growth_protocol: Cells are maintained in RPMI 1640 supplemented with 10% FBS and 1% pen/strep in humidified incubator at 5% CO2.

extract_protocol:
RNA was isolated from cultured cells using Trizol reagent (Thermofisher) following manufacturer’s instructions and further purified using the RNeasy kit (Qiagen) with the optional on-column DNase step according to the manufacturer’s protocols. Total RNA was eluted from the columns in nuclease-free water and stored at -80°C
Indexed, stranded mRNA-seq libraries were prepared from total RNA (1000 ng) using the KAPA Stranded mRNA-Seq Kit (Roche) according to the manufacturer’s standard protocol for mRNA capture, fragmentation, random-primed first strand synthesis, second strand synthesis with dUTP marking, A-tailing, adaptor ligation, and library amplification. Libraries were pooled and multiplex sequenced on an Illumina NovaSeqX Plus System

treatment_protocol: Cells were plated in 60mm and treated as indicated the following day. For LLG001-LLG018, treatment duration is indicated. For LLG037-LLG057, treatment was for 5-days.

value: Ola 1μM


title: Cannabis sativa L. Leaf, Putrescine 0.9mM treatment, RNA-seq, R2

description: Library name: Sample8


title: CTRL_DIV40 n1

description:
Library name: A9
10xGenomics


title: S66_adK

description:
Library name: S66_adK
PE150 6G raw data per sample

value: human primary

value: fibroblasts

value: SSc lung fibroblasts


title: FLAM_IFNg_6H_3

value: Cell Line

value: FLAM

value: Alveolar-Like Macrophage

value: IFNg + Mab Infected - 6H


title: IWP2_DIV25 n3

description:
Library name: F4
10xGenomics

value: iPSC-derived midbrain organoids

value: DIV 25


title: Cannabis sativa L. Leaf, Putrescine 0.9mM treatment, RNA-seq, R1

description: Library name: Sample7

value: Leaf

value: Cannabis sativa L. cv. Pink Pepper

value: Putrescine 0.9mM


title: S66_adN

description:
Library name: S66_adN
PE150 6G raw data per sample


title: Cannabis sativa L. Leaf, Putrescine 0.9mM treatment, miRNA-seq, R3

description: Library name: Sample9

data_processing:
Pre-processing was carried out using cutadapt (v4.6; --max-n 0, -m 18, -M 30, -q 20) to trim adapter sequences and discard low-quality reads.
miRNA libraries from related Rosaceae species (Fragaria vesca, Malus domestica, Prunus persica) were downloaded from miRbase (https://www.mirbase.org, accessed Jan 6, 2025). The Cannabis sativa reference genome was indexed for compatibility with miRDeep2 (v0.1.3) using Bowtie (v1.3.1)
To predict C. sativa miRNAs, trimmed small RNA reads were merged and collapsed into a unique FASTA file using mapper.pl (-c, -j, -m) against the genome index. Collapsed reads and Rosaceae miRNA libraries were then supplied to miRDeep2.pl to predict known and novel hairpin sequences. As these miRNAs lack in vitro validation, they were assigned temporary identifiers (e.g., Cannabis_001) rather than standard miR nomenclature.
For expression quantification, collapsed reads were remapped to the predicted miRNA reference using mapper.pl and quantifier.pl, and counts were used as input for DESeq2.
miRNA target prediction was performed with psRNATarget (Schema V2)
Assembly: Cannabis sativa L. RefSeq genome (RefSeq: GCF_029168945.1)
Supplementary files format and content: tab-delimited text file includes quantifier.pl (package of miRDeep2) result for each sample (header = T).
Supplementary files format and content: tab-delimited text file includes DESeq normalized counts for each sample (header = T).

extract_protocol:
Leaves collected for transcriptome analysis were immediately frozen in liquid nitrogen. Total RNA was extracted using the Rneasy Micro Kit (Qiagen, Hilden, Germany), and RNA concentration was measured with the Quant-iT™ RiboGreen RNA Assay Kit (ThermoFisher Scientific Inc., Waltham, MA, USA). RNA integrity was asseessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and samples with an RNA integrity number (RIN) of 7.0 were used.
Libraries were prepared with the TruSeq Small RNA Library Prep Kit (Illumina Inc., San Diego, CA, USA).


title: CTRL_DIV65 n2

description:
Library name: A7
10xGenomics

value: Standart


title: FLAM_IFNg_6H_2


title: C4-2B Ola 0-1 5-day

description: Library name: LLG010

value: DMSO


title: Cannabis sativa L. Leaf, Cold stress, RNA-seq, R3

description: Library name: Sample6

value: Cold stress


title: IWP2_DIV25 n2

description:
Library name: D4
10xGenomics

value: Wnt-TriP


title: S30_adK

description:
Library name: S30_adK
PE150 6G raw data per sample

value: lung


title: FLAM_IFNg_6H_1


title: Cannabis sativa L. Leaf, Cold stress, RNA-seq, R2

description: Library name: Sample5


title: IWP2_DIV25 n1

description:
Library name: B4
10xGenomics


title: S30_adN

description:
Library name: S30_adN
PE150 6G raw data per sample

value: human primary

value: control


title: FLAM_IFNg_Uninf_3

value: IFNg


title: S87_adK

description:
Library name: S87_adK
PE150 6G raw data per sample

value: fibroblasts

value: SSc lung fibroblasts


title: Cannabis sativa L. Leaf, Cold stress, RNA-seq, R1

description: Library name: Sample4


title: CTRL_DIV25 n3

description:
Library name: E4
10xGenomics


title: FLAM_IFNg_Uninf_2

value: Cell Line

value: FLAM

value: Alveolar-Like Macrophage


title: Cannabis sativa L. Leaf, Control, RNA-seq, R3

description: Library name: Sample3

value: Control


title: CTRL_DIV25 n2

description:
Library name: C4
10xGenomics

value: iPSC-derived midbrain organoids

value: DIV 25


title: S87_adN

description:
Library name: S87_adN
PE150 6G raw data per sample


title: FLAM_IFNg_Uninf_1


title: Cannabis sativa L. Leaf, Control, RNA-seq, R2

description: Library name: Sample2

value: Leaf

value: Cannabis sativa L. cv. Pink Pepper


title: BMDM_24H_1

source_name: Primary Cells

value: Primary Cells

value: Primary BMDM

value: Mab Infected - 24H


title: C4-2B Ola 5-1 1-day

description: Library name: LLG007

value: Ola 5μM


title: CTRL_DIV25 n1

description:
Library name: A4
10xGenomics

value: Standart


title: M_SSC24

description:
Library name: M_SSC24
PE150 6G raw data per sample

data_processing:
Novogene: Original image data file from HTS platforms is transformed to sequenced reads (Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
STAR software is used to accomplish the mapping. The alignment by STAR precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Gene expression level is calculated by the number of mapped reads with FeatureCounts. Read counts is proportional to gene expression level, gene length and sequencing depth, and is used for DE analysis.
Gene-level count data were generated by HTSeq and FeatureCounts. DE analysis of two conditions/groups was performed using the DESeq2 R package. Significance criteria q-value<0.05, log2FC>0.6 upregulation, log2FC<-0.6 downregulation
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-delimited .txt files generated by DESEQ2

source_name: whole lung tissue

growth_protocol: Pieces of whole lung tissue were flash frozen upon reception of a normal or SSc-PF lung

extract_protocol:
RNA was extracted from whole lung tissue in 1mL of Trizol (Invitrogen, Carlsbad, CA, USA) following manufacturer’s instructions.
mRNA library preparation with poly A enrichment/non-directional. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.

value: whole lung tissue

value: SSc-PF lung tissue

value: Male


title: FLAM_24H_3


title: Cannabis sativa L. Leaf, Control, RNA-seq, R1

description: Library name: Sample1


title: BasalPlate2

city: Trois-Rivières

first: Karen

middle: Cristine

last: Goncalves dos Santos

address: 3351 boul des Forges

department: Departement de Chimie, Biochimie, Physique et Sciences Forensiques

country: Canada

institute: Université du Québec à Trois-Rivières

description:
Library name: SRR24325013
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

data_processing:
Raw data were downloaded from the Sequencing Read Archive (SRA) using sra-toolkit 3.0.9, then quality control was performed using fastp 0.23.4 (mean quality = 20; unqualified percent limit = 30; cut-front window-size = 5; cut-right window size = 4; cut-right mean quality = 15; length required = 50).
Assembly was carried out with Trinity 2.14.0 default parameters, followed by removal of redundant transcripts with CD-HIT-EST 4.8.1 (-c 0.97, -l 200). Removal of contaminants was done through submission to NCBI TSA.
Expression quantification was performed using kallisto 0.46.1 and with Salmon 1.4.0, with the support scripts align_and_estimate_abundance.pl and abundance_estimates_to_matrix.pl from Trinity.
Assembly: TSA: DBNKRS000000000
Supplementary files format and content: Crinum_powellii_gene_counts.txt: Read count table, with genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Crinum_powellii_gene_TPM.txt: Transcripts per million table, with genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Crinum_powellii_isoform_counts.txt: Read count table, with isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Crinum_powellii_isoform_TPM.txt: Transcripts per million table, with isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Crinum_powellii_gene_counts_salmon.txt: Read count table, with genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Crinum_powellii_gene_TPM_salmon.txt: Transcripts per million table, with genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Crinum_powellii_isoform_counts_salmon.txt: Read count table, with isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Crinum_powellii_isoform_TPM_salmon.txt: Transcripts per million table, with isoforms in the rows and accession numbers of samples in the columns.

organism: Crinum x powellii

source_name: Basal plate

growth_protocol: C. x powellii “Album” bulbs were purchased from commercial market (Phoenix perennials, Canada). Bulbs were kept at 4 °C for 4 weeks, and then at room temperature for 24 h. Leaves, roots, and bulbs were separately flash frozen in liquid nitrogen and kept at −80 °C (extracted from 10.1016/j.phytochem.2023.113883)

extract_protocol:
Total RNA was extracted from different plant organs (roots, bulbs, basal plate, and leaves) and from in vitro tissues (callus developed with 2 mg/L and 4 mg/L of 2,4-D in light and dark conditions). For in vitro tissues, RNA was extracted by using a Qiagen RNeasy Plant Mini kit (Hildon, Germany), using approximately 100 mg callus samples according to the manufacturer's protocol. For in vivo tissues, total RNA was extracted using the method described in Meisel et al. (2005). Briefly, 1 g (fresh weight) of in vivo tissues were homogenized and the powder was transferred to a tube containing 5 mL of extraction buffer (20 mg/ml CTAB,100 mM of Tris-HCL pH 8, 20 mM EDTA, 1.4 M NaCl, 10 mg/ml of polyvinylpyrrodine, 100 μL of β-mercaptoethanol and 50 μl of spermidine trihydrochloride) at 65 °C. After agitation, extraction of nucleic acids was performed twice with chloroform:isoamyl alcohol 24:1. RNA was precipitated overnight with 0.25x of 10M LiCl at 4 °C. After centrifugation at 12 000 g for 35 min at room temperature, the pellet was resuspended in 0.5 mL of DEPC-treated H2O. Another extraction was performed with chloroform:isoamyl alcohol 24:1, and after centrifugation at 14 000g for 30 min at 4 °C, RNA was precipitated in the aqueous phase by adding 1 mL of 100% ice cold ethanol and incubating for 30 min at −80 °C. After centrifugation at 14 000 g for 20 min at 4 °C, the pellet was washed with 1 mL of 75% ethanol. Finally, RNA pellet was resuspended in 50 μL of DEPC-treated H2O. (extract from 10.1016/j.phytochem.2023.113883)
RNAseq

treatment_protocol: Bulbs were sterilized and dead scales removed. Then, ∼100–120 twin-scale size explants were obtained from each bulb. Basic media was prepared with MS supplemented with 3% of sucrose, 0.075% of PPM, 3 g/L of Phytagel, 0.5 mg/L of BAP, 0.5 mg/L of kinetin and 100 mg/L of yeast extract. The pH was adjusted to 5.7 ± 0.1 before adding phytagel and autoclaving. Plant growth hormones were added after sterilization. This basic media was used as a control to measure the effect of auxin in C. x powellii “Album” in vitro culture. During the experiment, the auxin 2,4-D was used at concentrations 2 or 4 mg/L. Five explants were cultured in each plate at 23 °C in light conditions (14hs:10hs light:dark, 100 μMol/m2) or in 24h dark conditions. Explants were sub-cultured every two weeks. (extracted from 10.1016/j.phytochem.2023.113883)

value: Basal plate

value: var Album

value: Not applicable


title: M_SSC87

description:
Library name: M_SSC87
PE150 6G raw data per sample


title: FLAM_24H_2

value: Cell Line

value: FLAM

value: Alveolar-Like Macrophage


title: FIP c_library

city: Shanghai

last: Liu

address: Dongchuan Road 500

country: China

institute: East china normal university

description: Library name: 3hF3_library

data_processing:
Raw paired-end fastq reads were filtered by Fastp discard the adapters and low quality bases. The clean reads obtained were then aligned to the  Candida albicans SC5314 genome using HISAT2.
Assembly: Candida albicans SC5314 Assembly 22 (GenBank accession: GCA_000182965.3)https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/182/965/GCF_000182965.3_ASM18296v3/
Supplementary files format and content: 1. quantify_annotation_merged_result.txt: Contains gene expression quantification and functional annotation for all genes across all samples. Columns include: Gene_ID (Systemic identifiers from Assembly 22), Raw_counts (mapped read counts), and TPM/FPKM values (normalized expression).
Supplementary files format and content: 2. 3hC-vs-3hF.DE_all.annotation.txt: Contains differential expression analysis results for the comparison between 3hC and 3hF. Columns include: Gene_ID, log2FoldChange, p-value, and padj (adjusted p-value).

organism: Candida albicans

source_name: fungi

growth_protocol: Single colonies of C. albicans strains was picked up from the SD agar plates and inoculated in the SD culture medium at 30°C until reaching logarithmic growth phase.

extract_protocol:
Total RNA was isolated using a Freezol Reagent (Vazyme,R711), which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry. High-quality RNA  with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing.
Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) following manufacturer’s recommendations. Poly (A) RNA is purified from 1 μg total RNA using Dynabeads Oligo (dT) . Then the poly(A) RNA was fragmented and reverse-transcribed to create the cDNA. Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA). After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 5300 Bioanalyzer (Agilent, USA).The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads.

treatment_protocol: 1 mL of logarithmic-phase C. albicans (2×107 CFU/mL) was treated with 16 μg/mL of FIP at 37 °C for 3 h, blank was untreated.

tag: strain

value: fungi

value: FIP treated


title: BasalPlate1

description:
Library name: SRR24325012
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: M_SSC66

description:
Library name: M_SSC66
PE150 6G raw data per sample


title: FIP b_library

description: Library name: 3hF2_library


title: FLAM_24H_1


title: Dark3A

description:
Library name: SRR24325011
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

source_name: Callus

value: Callus

value: in vitro culture 24h dark + 2mg/L 2,4-D


title: M_SSC53

description:
Library name: M_SSC53
PE150 6G raw data per sample


title: FLAM_6H_3

value: Mab Infected -- 6H


title: Dark3C

description:
Library name: SRR24325010
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: M_SSC26

description:
Library name: M_SSC26
PE150 6G raw data per sample


title: FIP a_library

description: Library name: 3hF1_library


title: FLAM_6H_2


title: Blank c_library

description: Library name: 3hC3_library

value: untreated


title: Dark4A

description:
Library name: SRR24325009
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

value: in vitro culture 24h dark + 4mg/L 2,4-D


title: M_SSC11

description:
Library name: M_SSC11
PE150 6G raw data per sample


title: FLAM_6H_1


title: BMDM_6H_1

value: Primary Cells

value: Primary BMDM


title: Blank b_library

description: Library name: 3hC2_library


title: FLAM_Uninf_3

value: Uninfected


title: Dark4B

description:
Library name: SRR24325008
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: F_SSC67

description:
Library name: F_SSC67
PE150 6G raw data per sample

value: whole lung tissue

value: SSc-PF lung tissue

value: Female


title: Blank a_library

description: Library name: 3hC1_library


title: Dark4C

description:
Library name: SRR24325007
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

value: var Album


title: F_SSC30

description:
Library name: F_SSC30
PE150 6G raw data per sample


title: FLAM_Uninf_2

value: Cell Line


title: COL 3

city: Richardson

first: Joseph

middle: Michael

last: Boll

state: TX

address: 800 W Campbell

department: Biological Sciences

institute: University of Texas at Dallas

description: Library name: COL_3_S117

data_processing:
CLC genomic workbench software (Qiagen) was used to process reads
Reads were aligned  to the A. baumannii ATCC 17978 genome annotation.
Baggerley’s test on proportions was used to generate a false discovery rate adjusted P-value.
Assembly: GCA_000015425.1
Supplementary files format and content: Each processed file is in MS Excel format and show the gene expresion levels.

organism: Acinetobacter baumannii

growth_protocol: Overnight culture of A. baumannii strains ATCC 17978 was backdiluted 1:100 in fresh LB at OD600 of ~0.5 in triplicate.

extract_protocol:
RNA was extracted with the Direct-Zol RNA miniprep kit (Zymo Research).
Done at SeqCenter - Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI). Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4)1.

treatment_protocol: Cutltures were growth in LB at 37°C

value: dmla dpldA LOS-

value: 10 μg/mL Colsitin


title: Light3A

description:
Library name: SRR24325006
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

value: in vitro culture 14h:10h light:dark + 2mg/L 2,4-D


title: F_SSC29

description:
Library name: F_SSC29
PE150 6G raw data per sample


title: FLAM_Uninf_1

value: FLAM

value: Alveolar-Like Macrophage


title: COL 2

description: Library name: COL_2_S116


title: F_SSC27

description:
Library name: F_SSC27
PE150 6G raw data per sample


title: Light3B

description:
Library name: SRR24325005
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

value: Callus


title: COL 1

description: Library name: COL_1_S115


title: WT, replicate 4, scRNAseq

city: Milwaukee

first: Karin

last: Hoffmeister

state: WI

address: 8727 Watertown Plank Road

institute: Versiti Blood Research Institute

data_processing:
Fastqs processed with 10x Genomics Cell Ranger v7.0.0 which yielded features, matrix, and barcode files
features, matrix, and barcodes read into the R environment using the Seurat version 4.4.0 suite of tools
Assembly: mm10
Supplementary files format and content: output from cellranger: features, matrix, and barcode files
Supplementary files format and content: Rdata file: processed file, annotations according to this project (see publication)

source_name: Bone Marrow

extract_protocol:
Bone marrow (BM) cells were obtained by flushing mice tibia and femur shafts in 1×PBS supplemented with 3% FBS and 5 mM EDTA (flushing buffer) through a 70 mm filter, followed by erythrocyte lysis 1× RBC Lysis Buffer (eBiosciences).
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3′ v2 Reagent Kit (10X Genomics) according to the manufacturer’s instructions

value: Bone Marrow

value: LSK


title: Light3C

description:
Library name: SRR24325004
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: F_SSC25

description:
Library name: F_SSC25
PE150 6G raw data per sample


title: LOS 3

description: Library name: LOS_3_S114


title: WT, replicate 3, scRNAseq


title: Light4A

description:
Library name: SRR24325003
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

value: in vitro culture 14h:10h light:dark + 4mg/L 2,4-D


title: WT, replicate 2, scRNAseq


title: F_SSC19

description:
Library name: F_SSC19
PE150 6G raw data per sample


title: LOS 2

description: Library name: LOS_2_S113


title: Light4B

description:
Library name: SRR24325002
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: M_NL146

description:
Library name: M_NL146
PE150 6G raw data per sample

value: normal lung tissue

value: Male


title: LOS 1

description: Library name: LOS_1_S112


title: Bulb1

description:
Library name: SRR24325001
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

source_name: Bulb

value: Bulb

value: Not applicable


title: M_NL133

description:
Library name: M_NL133
PE150 6G raw data per sample

value: whole lung tissue


title: dd 3

description: Library name: dd_3_S111

value: dmla dpldA


title: WT, replicate 1, scRNAseq


title: B4galt1 KO, replicate 3, scRNAseq


title: Light4C

description:
Library name: SRR24325000
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

value: var Album


title: M_NL132

description:
Library name: M_NL132
PE150 6G raw data per sample


title: B4galt1 KO, replicate 2, scRNAseq


title: dd 2

description: Library name: dd_2_S110


title: Bulb2

description:
Library name: SRR24324999
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: M_NL126

description:
Library name: M_NL126
PE150 6G raw data per sample


title: B4galt1 KO, replicate 1, scRNAseq


title: Bulb3

description:
Library name: SRR24324998
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: M_NL9

description:
Library name: M_NL9
PE150 6G raw data per sample


title: dd 1

description: Library name: dd_1_S109


title: WT 3

description: Library name: WT_3_S108

value: wild-type


title: Leaves1

description:
Library name: SRR24324997
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

source_name: Leaves

value: Leaves


title: BALI_multiomic_RNA_DG_vs_CA1_adult_rep3

city: Cambridge

first: Dario

last: Bressan

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description:
BALI RNA-Seq with 4-digit barcode, 2 areas, adult fresh frozen mousebrain
BALI spatial profiling - RNA-Seq
BALI_multiomic_RNA_DG_vs_CA1_adult_barcoding_stats.xslx
BALI_multiomic_RNA_DG_vs_CA1_adult_UMI_data.csv, where:
1_bc5 matches BALI_multiomic_RNA_DG_vs_CA1_adult_rep1_DG
2_bc5 matches BALI_multiomic_RNA_DG_vs_CA1_adult_rep2_DG
3_bc5 matches BALI_multiomic_RNA_DG_vs_CA1_adult_rep3_DG
1_bc6 matches BALI_multiomic_RNA_DG_vs_CA1_adult_rep1_CA1
2_bc6 matches BALI_multiomic_RNA_DG_vs_CA1_adult_rep2_CA1
3_bc6 matches BALI_multiomic_RNA_DG_vs_CA1_adult_rep3_CA1

data_processing:
The fastq files produced by high-throughput sequencing were processed through the following pipeline using custom bash shell scripts: 1) UMI extraction and annotation using the umitools package (v0.5.5) with the command umi_tools extract --bc-pattern=NNNNNN, 2) extraction of reads including each first (spatial) BALI barcode from both paired fastq files using the cutadapt package (v4.1) (options -g ^[barcode], -e 1, --pair-filter-both, --match-read-wildcards), 3) Extraction of successive BALI barcodes from the output of step 2, using the same command and options, 4) Extraction of the final adapter placed before the sequencing library itself (Tn5 mosaic end for ATAC-seq) using the same command as above. The strategy was performed iteratively to produce a pair of read1/read2 fastq files for each complete BALI barcode, as well as to produce fastq files for “partial” barcodes caused by incomplete ligations (i.e. in cases in which position 1 of a barcode ligated to the overhang-compatible position 4 rather than to position 2). Further analysis was performed on all reads featuring full barcodes, as well as on those featuring a complete barcode fragment including position 4 (the spatially defined one) as well as position 3, plus the end adapter (mosaic end). These reads corresponded to molecules that could be reliably assigned to a specific region.
ATAC PROCESSING: Both read 1 and read 2 files from each spatial region were mapped to the mm10 reference genome (source: Illumina igenomes) using the bowtie2 package (v2.5.1) using the following options: --local --very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed -q --no-discordant --phred33 -I 10 -X 1000
ATAC PROCESSING: The resulting SAM files were converted to BAM, sorted and indexed using the samtools package (v1.9)
ATAC PROCESSING: Genome coverage was calculated using the bamCoverage command from the deeptools package (v3.5.1) with the following options -normalizeUsing None --binSize 3 --scaleFactor [scale_factor]. The scale factor was calculated as 1 / total mapped reads  for each library.
ATAC PROCESSING: Peaks were identified using the macs2 package (v2.2.9.1) using the following options -f BAMPE --nomodel --keep-dup=all.
RNA PROCESSING: The read 1 fastq file from each spatial region was mapped on the mm10 reference genome (source: Illumina igenomes) using the STAR package (v 2.7.9a) with the following options: --outReadsUnmapped Fastx –outSAMtype BAM Unsorted --quantmode GeneCounts
RNA PROCESSING: The resulting BAM files were then sorted and indexed using the samtools package (v1.9) commands
RNA PROCESSING: To produce UMI counts for each gene (as opposed to the raw counts produced by STAR), each BAM file was ran through the featureCounts command from the Subread package (v2.0.3) with default options against the same mm10 genome annotation described above
RNA PROCESSING: The resulting annotated BAM file was sorted again using samtools sort.
RNA PROCESSING: UMIs counts per gene were calculated using the umi_tools count command (from the umitools package v0.5.5) with options --per-gene --gene-tag=XT --assigned-status-tag=XS, and UMIs were deduplicated using the umi_tools group command (to produce an overall quantification of all UMIs in each region) and umi_tools dedup command (to produce a deduplicated BAM file)
RNA PROCESSING: The deduplicated BAM files were sorted and indexed a third time, and genome coverage was calculated using the bamCoverage command from the deeptools package (v3.5.1) with the following options --normalizeUsing RPKM --binSize 1.
RNA PROCESSING: To perform Differential Expression analysis, the UMI count matrices from each area and replicate were merged and normalized as above, and the fold and log10 change ratios calculated using the average expression across replicates.
Assembly: mm10
Supplementary files format and content: Excel file including the number of reads filtered by each subsequent barcode trimming step: p1-p4 correspond to barcode position. Lig1-4 correspond to different ligation steps. DG/CA1 correspond to the areas. Per-cycle barcoding efficiency, as well as cumulative efficiency and fraction of partial barcodes, are reported
Supplementary files format and content: ATAC: Bigwig coverage file for all mapped reads in the Dentate Gyrus area (normalized by total number of mapped reads)
Supplementary files format and content: ATAC: Bigwig coverage file for all mapped reads in the CA1 area (normalized by total number of mapped reads)
Supplementary files format and content: RNA: Csv file including the UMI counts for each gene in each spatial area, as well as the normalized counts (normalized by total number of UMI), and the fold and log10 expression ratios between the two spatial areas.
Library strategy: BALI MultiOmic-Seq (RNA-Seq + ATAC-Seq)

source_name: Brain

growth_protocol: All animal procedures were performed in accordance with the Animal (Scientific Procedures) Act 1986 under UK Home Office project license PAD85403A. Animals were housed under standard husbandry conditions per UK Home Office and Institute regulations. Individually ventilated cages housed four to five animals under a 12-h light, 12-h dark cycle at the CRUK Cambridge Institute animal facility. Relative humidity was kept between 45 and 65% with a temperature range of 20-24°C. Animals had free access to water and pelleted food. Adult samples were collected from ethically euthanised 8-12 month old animals.

extract_protocol:
For adult brain collection, mice were euthanised by cervical dislocation followed by confirmation of death by permanent cessation of circulation. Animals were then decapitated and the brain dissected and frozen in OCT resin and stored as above. Cryosections were cut using a XXXX cryostat under RNAse free conditions. Cryosections were cut using a XXXX cryostat under RNAse free conditions. The instrument was wiped with RNAse-ZAP prior to use and between different blocks. A different blade was used for each block. Sample blocks were equilibrated to the chamber temperature for 15 minutes prior to sectioning, and then mounted on the object holder. Sections were cut at a thickness of 10 uM and collected on RNAse-free SuperFrost Plus microscope slides (one section per slide). Slides were left at room temperature for 20-30 seconds to help tissue adhesion and then stored on dry ice (short term) or at -80C (long term).
The adapters for transposome assembling were annealed at 50 uM each in 1x Annealing buffer (40 mM TrisHCl pH 8.0, 50 mM NaCl) with the following thermocycling protocol: 95C for 5 minutes, slow ramp to 65C (0.1C/sec), 65C for 5 minutes, slow ramp to 10C (0.1C/sec). The oligos pairs used were BL699/BL538 (BALI-adapter, universal ligation root) and BL515/BL538 (A-adapter, single modality ATAC) or BLXXX/BL538 (A-adapter, multi-omics). The transposomes were assembled by mixing 3 uL of BALI-adapter, 3 uL of A-adapter, 6 uL of unloaded Tn5 and incubating the mix at 23C for 30 minutes and then used immediately afterwards. All steps were performed under RNAse-free conditions. Cryosections of adult brain were retrieved from cold storage and equilibrated for 5 minutes at room temperature and then heated for 5 minutes at 37C on a metal heat block. Pap-pen was used to draw a hydrophobic boundary around each section, and let dry for 5 minutes at room temperature. Sections were incubated with 500 uL PBS to dissolve and remove the OCT embedding matrix, and fixed with 500 uL of 0.5% PFA in PBS for exactly 5 minutes at room temperature. Fixation was quenched by removing the PFA and promptly adding 1.25M Glycine in PBS, one quick wash and one wash for 5 minutes at room temperature. After washing twice in PBS for 5 minutes each, the sections were permeabilised in Permeabilization buffer (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% IGEPAL, 0.001% Digitonin, 1% BSA, 10 uL murine RNAse Inhibitor) for 15 minutes at room temp. The sections were washed in 1x Wash Buffer (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 10 uL murine RNAse Inhibitor) once quickly and once for 5 minutes, then in PBS twice for 5 minutes. For each section, 200 uL of transposition mix were prepared as follows: 2uL of loaded Tn5 in 10 mM Tris-HCl pH 7.6, 5 mM MgCl2, 10% Dimethyl Formamide, 0.33x PBS, 0.1% Tween-20, 0.01% Digitonin. Each section was sealed with an adhesive hybridization chamber and incubated with 200 uL of tagmentation mix for 35 minutes at 37C in a humid chamber. The slides were retrieved and washed with 40 mM EDTA once quickly, and once for 5 minutes, then with PBS for 3 times for 5 minutes. The sections were heated for 5 minutes in pre-warmed PBS at 65C in a hybridization oven, and then snap-cooled in ice-cold PBS on ice for 10 minutes. For each slide, an first RT mix (14uL) was prepared containing 2.5 uL of dNTPs (stock 10 mM each), 1.5uL of phosphorilated RT primer (BL730, 100 uM stock) in water, denatured for 5 minutes in 65C and the snap cooled on ice for >2 minutes. A second RT mix (36 uL) was prepared with 10 uL of 5x SuperScript-IV buffer, 2.5uL SuperScript-IV enzyme, 1 uL of RNAsin, 3uL of 100 uM TSO oligo (BL617),  5 uL of 5M Betaine, 2.5 uL of 100 mM DTT in nuclease free water, and added to the first mix, up to a total RT reaction volume of 50uL. Any excess PBS was removed from the slides, and 50 uL of RT mix was added directly on top of the sections, which were then covered with a 22x22 mm coverslip and incubated overnight (~16hrs) at 42C in a sealed humid chamber. The slides were retrieved from the RT reaction, washed one in PBS then twice in 2xSSC for 5 minutes each.The index oligos for the ligations were annealed at 45uM final in 1xSSC in the following pairs: BL680/BL676(cycle 1, bulk), BL681/BL677 (cycle 2, bulk), BL683/BL642 (cycle 3, bulk), BL732/BL601 (cycle 4A, Dentate Gyrus), BL733/BL677 (cycle 4B, CA1), BL732/BL641 (cycle 1, single ligation bulk). The annealing thermocycler conditions were as follows: 1) 95C for 5 minutes, 2) ramp down to 65 at 0.1C/second, 3) hold at 65C for 5 minutes, 4) ramp down to 12C at 0.1C/second, 5) hold at 12C.. The spatial barcodes were encoded in the tissue with the following protocol, which was conducted under light protected condition for its entirety: cycle 1 ligation, cycle 2 uncaging (bulk), cycle 2 ligation, cycle 3 uncaging (bulk), cycle 3 ligation, cycle 4A uncaging (Dentate Gyrus), cycle 4A ligation, cycle 4B uncaging (CA1), cycle 4B ligation. Bulk uncaging was performed with a UV transilluminator fitted with 365 nm bulbs for 15 minutes at room temperature, with the section covered with 500 uL of 2x SSC. Spatial uncaging was performed on a SP5 Leica confocal system fitted with a 30mW 405nm solid state laser, illuminating each ROI for 10 minutes with the 405nm laser at maximum power. Following uncaging, the slides were washed in 2xSSC, once quickly and once for 5 minutes. Ligations were performed as follows. Sections were incubated for 5 minutes in 1x Ligation buffer (50 mM TrisHCl pH7.4, 10 mM MgCl2, 10 mM DTT, 1mM ATP). For each sample, a ligation mix (50 uL) was prepared as follows: index oligos (3 uM, as appropriate), T4 ligase (100U/uL, NEB) in 1x T4 ligation buffer. The ligation mix was added directly to the sections, covered with a 22x22mm glass coverslip, and the reactions were incubated for 30 minutes (45 minutes for cycle 1) at 25C in a humid chamber. The slides were then washed in 2xSSC+Draq5 (1:1000) once for 10 minutes, 2xSSC+10%EC once for 5 minutes and 2xSSC once for 5 minutes. After the serial ligations, an adhesive hybridization chamber was mounted on the slides, and the sections were lysed in 200 uL of Lysis Buffer (0.8 U/mL in RIPA buffer) at 60C overnight (~16 hrs) in a sealed humid chamber. All the following steps were not carried out under light protected conditions. The lysate (200 uL) was collected and an aliquote (150 uL) was treated with 10 uL of 100 mM PMSF for 10 minutes at room temperature to inactivate the proteinase K prior to biotin pulldown to separate the Tn5 fragments (biotinylated) from cDNA. For each sample, 10uL of myOne C1 beads were washes 3 times in 1xB&W-T buffer, and then resuspended in 150 uL of 2xB&W-T buffer. The lysate was then added and incubated with the beads for 60 minutes at room temperature. After this incubation we collected the supernatant as our cDNA enriched fraction for RNA libraries, while the beads represented our Tn5 fragments enriched fraction for ATAC libraries. The beads were washed 3 times in 1xB&W-T buffer for 5 minutes, once in 1xST buffer for 5 minutes and then directly used as input for library amplification via precise PCR as follows. For each sample, a 50 uL PCR mix was prepared mixing 25 uL of 2x Q5 mastermix, 2.5 uL of 10 uM P5 primer (BL727), 2.5 uL of 10 uM indexed P7 primer (Ad2.X) in nuclease free water, and adding it directly to the washed bead pellet. The reaction was incubated in a thermocycler at 72C for 5 minutes (gap-fill), 98C for 3 minutes, then 5 cycles at 98C for 20 seconds, 68C for 20 seconds, 72C for 20 seconds. The pre-amplified products was kept on ice, and 5 uL were used as input for qPCR to determine the optimal number of additional cycles, The qPCR reactions were set up as follows: 5 uL of the preamplified material (after removal of the beads), 5 uL of 2x Q5 master mix, 0.5 uL of 10 uM P5 primer (BL727), 0.5 uL of 10 uM indexed P7 primer (Ad2.X), 2.5 uL of 20x EVA-Green in nuclease free water. The cycling protocol was 98C for 3 minutes, 40 cycles of 98C for 20 seconds, 68C for 20 seconds, 72C for 20 seconds with a plate reading step. The number of cycles required to reach 1/3 of the amplification curve plateau was selected for the final amplification of the libraries. The PCR reactions were purified with AmpureXP beads (1.2x) and eluted in 20 uL of EB buffer. The libraries were analysed on a Tapestation (D5000 cartridge) and quantified with KAPA library quantification kit prior to pooling. Sequencing was performed on a Novaseq (Illumina) instrument.  Separately, the cDNA fraction was purified using Monarch Reaction clean-up columns and eluted in 12.5uL. The cDNA was treated with RNAseH by adding 1.5 uL of 10x RNAseH buffer and 1 uL RNAseH enzyme to each sample, and then incubating the mix at 37C for 30 minutes, 65C for 20 minutes. The cDNA was amplified to via precise PCR as follows. For each sample, a 50 uL PCR mix was prepared mixing 15 uL of RNAseH treated sample, 25 uL of 2x Q5 mastermix, 2.5 uL of 10 uM forward primer (BL753), 2.5 uL of 10 uM reverse primer in nuclease free water. The reaction was incubated in a thermocycler at 98C for 3 minutes, then 5 cycles at 98C for 15 seconds, 67C for 20 seconds, 72C for 60 seconds. The pre-amplified products was kept on ice, and 5 uL were used as input for qPCR to determine the optimal number of additional cycles, The qPCR reactions were set up as follows: 5 uL of the preamplified material, 5 uL of 2x Q5 master mix, 0.5 uL of 10 uM forward primer (BL753), 0.5 uL of 10 uM reverse primer (BL752), 2.5 uL of 20x EVA-Green in nuclease free water. The cycling protocol was 98C for 3 minutes, 40 cycles of 98C for 15 seconds, 67C for 20 seconds, 72C for 60 seconds with a plate reading step. The number of cycles required to reach 1/3 of the amplification curve plateau was selected for the final amplification of the libraries. The PCR reactions were purified with AmpureXP beads (0.8x) and eluted in 20 uL of EB buffer. A small aliquote (2 uL) was analysed on a Tapestation. The amplified cDNA fraction was then tagmented with Tn5 loaded with a single adapter (BL371/BL515) in a reaction set up as follows: 50 ng of pre-amplified cDNA, 0.5uL loaded Tn5 enzyme in 10 mM Tris-HCl pH 7.6, 5 mM MgCl2, 10% Dimethyl Formamide, 0.33x PBS, 0.1% Tween-20, 0.01% Digitonin in 50uL final. The tagmentation reaction was incubated at 37C for 30 minutes, and inactivated adding 50 uL of 80 mM EDTA and 2.5uL of 2% SDS solution for 15 minutes at room temperature. The reactions were purified were purified with AmpureXP beads (0.8x) and eluted in 20 uL of EB buffer. A small aliquote (2 uL) was analysed on a Tapestation. The purified reaction was amplified to generate ATAC libraries as follows: 18 uL of Tn5-cDNA, 2.5 uL of 10uM P5 primer (BL727), 2.5 uL of 10 uM indexed P7 primer (Ad2.X) in nuclease free water. The cycling protocol was 72C for 5 minutes (gap-fill), then 98C for 1 minutes and 5 cycles of 98C for 10 seconds, 68C for 20 seconds, 72C for 45 seconds, with a final extension at 72C for 5 minutes. The PCR reactions were purified with AmpureXP beads (0.8x) and eluted in 20 uL of EB buffer. The libraries were analysed on a Tapestation (D5000 cartridge) and quantified with KAPA library quantification kit prior to pooling. Sequencing was performed on a Novaseq (Illumina) instrument.

value: Brain

tag: age

value: 12 weeks

tag: area 1

value: Dentate gyrus granular layer

tag: area 2

tag: barcode length


title: BALI_multiomic_RNA_DG_vs_CA1_adult_rep2


title: WT 2

description: Library name: WT_2_S107


title: Leaves2

description:
Library name: SRR24324996
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: F_NL140

description:
Library name: F_NL140
PE150 6G raw data per sample

value: Female


title: BALI_multiomic_RNA_DG_vs_CA1_adult_rep1


title: WT 1

description: Library name: WT_1_S106


title: Leaves3

description:
Library name: SRR24324995
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: F_NL129

description:
Library name: F_NL129
PE150 6G raw data per sample


title: w10 control blastocyst

city: Napoli

first: Francesco

last: Cecere

state: Napoli

address: Via Posillipo 226

department: UOC Ricerca Clinica e Traslazionale

country: Italy

institute: AORN Santobono-Pausilipon

description: Library name: w10

data_processing:
Libraries was adapted and quality-trimmed (Phred score <20) using Trim Galore version 0.4.4. The good quality reads were aligned to the Genome Reference Consortium mouse genome build 39 (GRCm39) with HiSat2 version 2.1.0 in paired-end mode. The data were quantified and analyzed in Rstudio.
Assembly: mm39
Supplementary files format and content: Log normalized counts

source_name: Blastocist

growth_protocol: Blastocysts were cultured in a medium supplemented with 15% FBS in 0.5% gelatin-coated plates and incubated at 37°C in a humidified atmosphere with 5% CO2 for 72 h. Trophoblast outgrowth was evaluated by measuring the area occupied (mm²) using ZEN 3.9 software. To evaluate ICM expansion, blastocysts were further cultured for one week in 2i medium.

extract_protocol:
DNA and RNA were separated using the G&T protocol [59]. Magnetic beads (MyOne C1, Life Technologies) were washed and annealed to oligo dTs and then used to capture polyadenylated mRNA from individual cell lysates. The supernatant containing the DNA was transferred to a new tube, and the beads washed three times in 1× FSS buffer (SuperScript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma), and 0.4 U/μl RNasin (Promega) to remove all DNA residues. Each washing solution was added to the DNA tube to maximize recovery.
The mRNA bound to the beads was processed further for cDNA conversion. This involved the resuspension of the beads in 10 μl of reverse transcriptase master mix (100 U of SuperScript II [Invitrogen], 10 U of RNasin [Promega], 1× Superscript II first-strand buffer, 5 mM DTT [Invitrogen], 1 M betaine [Sigma], 9 mM MgCl2 [Invitrogen], 1 μM template-switching oligo [TSO; Eurogentec], 1 mM dNTP mix [Roche]). The mRNA mixture was reverse-transcribed by incubation for 60 min at 42°C followed by 30 min at 50°C and 10 min at 60°C. The cDNA obtained was subjected to PCR amplification by adding 11 μl of 2× KAPA HiFi HotStart ReadyMix and 1 μl of 2 μM ISPCR primer. The amplification was performed in a thermocycler for 3 min at 98°C, followed by 17 cycles of 15 sec at 98°C, 20 sec at 67°C, and 6 min at 72°C, and a final extension step of 5 min at 72°C. The amplified product was purified using Ampure XP beads with a 1:1 ratio and eluted into 20 μl of water. Libraries were prepared from 100–400 pg of cDNA using the Nextera XT kit (Illumina) following the manufacturer's instructions but with one-fifth volumes. All 20 single-blastocyst RNA-seq libraries were pooled together and sequenced on an Illumina NovaSeq X platform to an average depth of 4.2 million reads using paired-end 75-bp read length settings.

value: Blastocist

value: Control


title: BALI_multiomic_DNA_DG_vs_CA1_adult_rep3

description:
BALI ATAC-Seq with 4-digit barcode, 2 areas, adult fresh frozen mousebrain
BALI spatial profiling / ATAC-Seq
BALI_multiomic_RNA_DG_vs_CA1_adult_barcoding_stats.xslx

library_source: genomic

molecule: genomic DNA


title: Root1

description:
Library name: SRR24324994
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).

value: Root


title: F_NL62

description:
Library name: F_NL62
PE150 6G raw data per sample


title: w9 control blastocyst

description: Library name: w9


title: BALI_multiomic_DNA_DG_vs_CA1_adult_rep2


title: F_NL57

description:
Library name: F_NL57
PE150 6G raw data per sample


title: Root3

description:
Library name: SRR24324993
Koirala, M. et al. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry 216, 113883, doi:10.1016/j.phytochem.2023.113883 (2023).


title: BALI_multiomic_DNA_DG_vs_CA1_adult_rep1


title: w8 control blastocyst

description: Library name: w8


title: Fugu spinal cord, C5, scRNA-seq 2

city: Dalseong-gun

first: Tery

last: Yun

state: Daegu

address: 333 Technojungang-daero, Hyeonpung-eup

department: Department of Brain Sciences

institute: DGIST

description: Library name: C5-fugu

data_processing:
Raw FASTQ files were processed using Cell Ranger v7.2.0. Fugu reads were mapped to Takifugu rubripes genome (Ensembl release 113). Mudskipper reads were mapped to Periophthalmus magnuspinnatus genome (Ensembl release 113). Chicken reads were mapped to Gallus gallus genome (Ensembl release 113). Empty droplets removed using emptyDrops (FDR ≤ 0.01, DropletUtils v1.26.0). Doublets identified using scDblFinder v1.23.4. Downstream analysis performed in Seurat v5.3.0 with Monocle3 pseudotime and CAME cross-species cell type mapping.
Assembly: Fugu: Takifugu rubripes (Ensembl release 113); Mudskipper: Periophthalmus magnuspinnatus (Ensembl release 113); Chicken: Gallus gallus (Ensembl release 113)
Supplementary files format and content: Tab-separated gzipped files in 10x Genomics sparse matrix format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene IDs and names), and matrix.mtx.gz (UMI count matrix). Generated by Cell Ranger v7.2.0.

organism: Takifugu obscurus

source_name: spinal cord

growth_protocol: Fugu (Takifugu obscurus) and mudskipper (Periophthalmus magnuspinnatus) were dissected approximately one month post-hatching. Chicken (Gallus gallus) spinal cord was collected at embryonic days 10-11 (Hamburger-Hamilton stage 36-37). All procedures were approved by IACUC of DGIST (Approval No: DGIST-IACUC-23052304-0002).

extract_protocol:
Spinal cord tissue from multiple individuals was pooled per library. Cell dissociation was performed by incubation in pronase solution for 40 min at room temperature, followed by trituration in 100 µL ACSF containing 1% FBS. Volume was adjusted to 3 mL and live cells were enriched by FACS (BD FACSAria III) using propidium iodide (1 µg/mL) exclusion. Cell viability exceeded 80%. Sorted cells were resuspended in 1× DPBS containing 0.04% BSA.
Libraries were prepared using the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics). Target cell recovery was 1,000-9,000 cells per replicate depending on tissue availability. Reverse transcription was performed using a C1000 Touch Thermal Cycler (Bio-Rad). Libraries were sequenced on an Illumina HiSeq X platform (paired-end 100 bp reads) targeting an average of 20,000 read pairs per cell.

value: spinal cord


title: BALI_DNA_DG_vs_CTX_adult_rep2

description:
BALI ATAC-Seq with 4-digit barcode, 2 areas, adult fresh frozen mousebrain
BALI spatial profiling / ATAC-Seq
BALI_DNA_DG_vs_CTX_adult_barcoding_stats.xlsx

data_processing:
The fastq files produced by high-throughput sequencing were processed through the following pipeline using custom bash shell scripts: 1) UMI extraction and annotation using the umitools package (v0.5.5) with the command umi_tools extract --bc-pattern=NNNNNN, 2) extraction of reads including each first (spatial) BALI barcode from both paired fastq files using the cutadapt package (v4.1) (options -g ^[barcode], -e 1, --pair-filter-both, --match-read-wildcards), 3) Extraction of successive BALI barcodes from the output of step 2, using the same command and options, 4) Extraction of the final adapter placed before the sequencing library itself (Tn5 mosaic end for ATAC-seq) using the same command as above. The strategy was performed iteratively to produce a pair of read1/read2 fastq files for each complete BALI barcode, as well as to produce fastq files for “partial” barcodes caused by incomplete ligations (i.e. in cases in which position 1 of a barcode ligated to the overhang-compatible position 4 rather than to position 2). Further analysis was performed on all reads featuring full barcodes, as well as on those featuring a complete barcode fragment including position 4 (the spatially defined one) as well as position 3, plus the end adapter (mosaic end). These reads corresponded to molecules that could be reliably assigned to a specific region.
Both read 1 and read 2 files from each spatial region were mapped to the mm10 reference genome (source: Illumina igenomes) using the bowtie2 package (v2.5.1) using the following options: --local --very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed -q --no-discordant --phred33 -I 10 -X 1000
The resulting SAM files were converted to BAM, sorted and indexed using the samtools package (v1.9)
Genome coverage was calculated using the bamCoverage command from the deeptools package (v3.5.1) with the following options -normalizeUsing None --binSize 3 --scaleFactor [scale_factor]. The scale factor was calculated as 1 / total mapped reads  for each library.
Peaks were identified using the macs2 package (v2.2.9.1) using the following options -f BAMPE --nomodel --keep-dup=all.
Assembly: mm10
Supplementary files format and content: Excel file including the number of reads filtered by each subsequent barcode trimming step: p1-p4 correspond to barcode position. Lig1-4 correspond to different ligation steps. DG/CTX correspond to the areas. Per-cycle barcoding efficiency, as well as cumulative efficiency and fraction of partial barcodes, are reported
Supplementary files format and content: Bigwig coverage file for all mapped reads in the Dentate Gyrus area (normalized by total number of mapped reads)
Supplementary files format and content: Bigwig coverage file for all mapped reads in the Auditory Cortex area (normalized by total number of mapped reads)
Library strategy: BALI ATAC-Seq

extract_protocol:
For adult brain collection, mice were euthanised by cervical dislocation followed by confirmation of death by permanent cessation of circulation. Animals were then decapitated and the brain dissected and frozen in OCT resin and stored as above. Cryosections were cut using a XXXX cryostat under RNAse free conditions. Cryosections were cut using a XXXX cryostat under RNAse free conditions. The instrument was wiped with RNAse-ZAP prior to use and between different blocks. A different blade was used for each block. Sample blocks were equilibrated to the chamber temperature for 15 minutes prior to sectioning, and then mounted on the object holder. Sections were cut at a thickness of 10 uM and collected on RNAse-free SuperFrost Plus microscope slides (one section per slide). Slides were left at room temperature for 20-30 seconds to help tissue adhesion and then stored on dry ice (short term) or at -80C (long term).
The adapters for transposome assembling were annealed at 50 uM each in 1x Annealing buffer (40 mM TrisHCl pH 8.0, 50 mM NaCl) with the following thermocycling protocol: 95C for 5 minutes, slow ramp to 65C (0.1C/sec), 65C for 5 minutes, slow ramp to 10C (0.1C/sec). The oligos pairs used were BL699/BL538 (BALI-adapter, universal ligation root) and BL515/BL538 (A-adapter, single modality ATAC) or BLXXX/BL538 (A-adapter, multi-omics). The transposomes were assembled by mixing 3 uL of BALI-adapter, 3 uL of A-adapter, 6 uL of unloaded Tn5 and incubating the mix at 23C for 30 minutes and then used immediately afterwards. Cryosections of adult brain were retrieved from cold storage and equilibrated for 5 minutes at room temperature and then heated for 5 minutes at 37C on a metal heat block. Pap-pen was used to draw a hydrophobic boundary around each section, and let dry for 5 minutes at room temperature. Sections were incubated with 500 uL PBS to dissolve and remove the OCT embedding matrix, and fixed with 500 uL of 0.5% PFA in PBS for exactly 5 minutes at room temperature. Fixation was quenched by removing the PFA and promptly adding 1.25M Glycine in PBS, one quick wash and one wash for 5 minutes at room temperature. After washing twice in PBS for 5 minutes each, the sections were permeabilised in Permeabilization buffer (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% IGEPAL, 0.001% Digitonin, 1% BSA, 10 uL murine RNAse Inhibitor) for 15 minutes at room temp. The sections were washed in 1x Wash Buffer (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 10 uL murine RNAse Inhibitor) once quickly and once for 5 minutes, then in PBS twice for 5 minutes. For each section, 200 uL of transposition mix were prepared as follows: 2uL of loaded Tn5 in 10 mM Tris-HCl pH 7.6, 5 mM MgCl2, 10% Dimethyl Formamide, 0.33x PBS, 0.1% Tween-20, 0.01% Digitonin. Each section was sealed with an adhesive hybridization chamber and incubated with 200 uL of tagmentation mix for 35 minutes at 37C in a humid chamber. The slides were retrieved and washed with 40 mM EDTA once quickly, and once for 5 minutes, then with PBS 3 times for 5 minutes and with 2xSSC 2 times for 5 minutes. The index oligos for the ligations were annealed at 45uM final in 1xSSC in the following pairs: BL680/BL676(cycle 1, bulk), BL681/BL677 (cycle 2, bulk), BL683/BL642 (cycle 3, bulk), BL732/BL601 (cycle 4A, Dentate Gyrus), BL733/BL677 (cycle 4B, cortex), BL732/BL641 (cycle 1, single ligation bulk). The annealing thermocycler conditions were as follow: 1) 95C for 5 minutes, 2) ramp down to 65 at 0.1C/second, 3) hold at 65C for 5 minutes, 4) ramp down to 12C at 0.1C/second, 5) hold at 12C.. The spatial barcodes were encoded in the tissue with the following protocol, which was conducted under light protected condition for its entirety: cycle 1 ligation, cycle 2 uncaging (bulk), cycle 2 ligation, cycle 3 uncaging (bulk), cycle 3 ligation, cycle 4A uncaging (Dentate Gyrus), cycle 4A ligation, cycle 4B uncaging (cortex), cycle 4B ligation. Bulk uncaging was performed with a UV transilluminator fitted with 365 nm bulbs for 15 minutes at room temperature, with the section covered with 500 uL of 2x SSC. Spatial uncaging was performed on a SP5 Leica confocal system fitted with a 30mW 405nm solid state laser, illuminating each ROI for 10 minutes with the 405nm laser at maximum power. Following uncaging, the slides were washed in 2xSSC, once quickly and once for 5 minutes. Ligations were performed as follows. Sections were incubated for 5 minutes in 1x Ligation buffer (50 mM TrisHCl pH7.4, 10 mM MgCl2, 10 mM DTT, 1mM ATP). For each sample, a ligation mix (50 uL) was prepared as follows: index oligos (3 uM, as appropriate), T4 ligase (100U/uL, NEB) in 1x T4 ligation buffer. The ligation mix was added directly to the sections, covered with a 22x22mm glass coverslip, and the reactions were incubated for 30 minutes (45 minutes for cycle 1) at 25C in a humid chamber. The slides were then washed in 2xSSC+Draq5 (1:1000) once for 10 minutes, 2xSSC+10%EC once for 5 minutes and 2xSSC once for 5 minutes. After the serial ligations, an adhesive hybridization chamber was mounted on the slides, and the sections were lysed in 200 uL of Lysis Buffer (0.8 U/mL in RIPA buffer) at 60C overnight (~16 hrs) in a sealed humid chamber. All the following steps were not carried out under light protected conditions. The lysate was collected and purified with MinElute Reaction Clean-up column, and eluted in 25 uL of EB buffer. Libraries were amplified via quantitative PCR as follows. For each sample, a 50 uL PCR mix was prepared mixing 5 uL of purified sample, 25 uL of 2x Q5 mastermix, 1.25 uL of 50 uM P5 primer (BL727), 1.25 uL of 50 uM indexed P7 primer (Ad2.X) in nuclease free water. The reaction was incubated in a thermocycler at 72C for 5 minutes (gap-fill), 98C for 3 minutes, then 5 cycles at 98C for 20 seconds, 68C for 20 seconds, 72C for 20 seconds. The pre-amplified products was kept on ice, and 5 uL were used as input for qPCR to determine the optimal number of additional cycles, The qPCR reactions were set up as follows: 5 uL of the preamplified material, 5 uL of 2x Q5 master mix, 0.25 uL of 50 uM P5 primer (BL727), 1.25 uL of 50 uM indexed P7 primer (Ad2.X), 2.5 uL of 20x EVA-Green in nuclease free water. The cycling protocol was 98C for 3 minutes, 40 cycles of 98C for 20 seconds, 68C for 20 seconds, 72C for 20 seconds with a plate reading step. The number of cycles required to reach 1/3 of the amplification curve plateau was selected for the final amplification of the libraries. The PCR reactions were purified with AmpureXP beads (0.8x) and eluted in 20 uL of EB buffer. The libraries were analysed on a Tapestation (D5000 cartridge) and quantified with KAPA library quantification kit prior to pooling. Sequencing was performed on a Novaseq (Illumina) instrument.

value: Auditory Cortex


title: Fugu spinal cord, C4, scRNA-seq 1

description: Library name: C4-fugu


title: F_NL41

description:
Library name: F_NL41
PE150 6G raw data per sample

value: normal lung tissue


title: w7 control blastocyst

description: Library name: w7


title: w6 control blastocyst

description: Library name: w6


title: F_NL24

description:
Library name: F_NL24
PE150 6G raw data per sample


title: WT-B4, WT SARS-CoV-2 infected

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Cell Ranger v7.0.0 pipeline was run on the samples following 10x Genomics guidelines. Seurat v4 was used to perform data processing and analysis.
Assembly: mm10
Supplementary files format and content: Count matrices for cell barcodes in Hierarchical Data Format HDF5.

source_name: Lung

extract_protocol:
In brief, the freshly collected whole lungs were dissected into single lobes to isolate single cells using a mouse lung dissociation kit (Miltenyi Biotec) and a gentleMACS™ Dissociator (Miltenyi Biotec), and red blood cells were lysed with 1X RBC lysis buffer (eBioscience). Cell suspensions were processed for single-cell sequencing following the protocol for Chromium Next GEM Single Cell 5’ Version 2 (dual index). 10,000 cells were targeted. The transcriptome of each cell was indexed with a pool of 750,000 barcodes by partitioning each cell into Gel beads-in-emulsion (GEMs) combined with a Master Mix containing reverse transcription (RT) reagents and poly(dT) RT primers. The emulsion was generated using Next GEM chips and the Chromium Controller device (10x Genomics). The RT reaction to the generated emulsion produced 10x Barcoded full-length cDNA from poly-adenylated mRNA. This initial cDNA was PCR amplified to produce material for 5’ gene expression sequencing. After PCR amplification, bioanalyzer Quality Control (QC) was performed for all the samples using the Agilent Bioanalyzer High Sensitivity DNA assay in the 2100 expert software (Agilent). All the samples passed the initial QC with a cDNA size 700-1,500 bp.
Amplified full-length cDNA from polyadenylated mRNA was used to generate 5’ gene expression (GEX) libraries. The cDNA was enzymatically fragmented, and size selected to optimize the cDNA amplicon size. P5, P7, i5 and i7 sample indexes, and Illumina R2 sequences (read 2 primer sequences) were added via End Repair, A-tailing, Adaptor ligation and sample index PCR. A second QC was performed for each library before sequencing with an expected library size 500 – 900 bp.

value: Lung


title: BALI_DNA_DG_vs_CTX_adult_rep1

growth_protocol: The adapters for transposome assembling were annealed at 50 uM each in 1x Annealing buffer (40 mM TrisHCl pH 8.0, 50 mM NaCl) with the following thermocycling protocol: 95C for 5 minutes, slow ramp to 65C (0.1C/sec), 65C for 5 minutes, slow ramp to 10C (0.1C/sec). The oligos pairs used were BL699/BL538 (BALI-adapter, universal ligation root) and BL515/BL538 (A-adapter, single modality ATAC) or BLXXX/BL538 (A-adapter, multi-omics). The transposomes were assembled by mixing 3 uL of BALI-adapter, 3 uL of A-adapter, 6 uL of unloaded Tn5 and incubating the mix at 23C for 30 minutes and then used immediately afterwards. Cryosections of adult brain were retrieved from cold storage and equilibrated for 5 minutes at room temperature and then heated for 5 minutes at 37C on a metal heat block. Pap-pen was used to draw a hydrophobic boundary around each section, and let dry for 5 minutes at room temperature. Sections were incubated with 500 uL PBS to dissolve and remove the OCT embedding matrix, and fixed with 500 uL of 0.5% PFA in PBS for exactly 5 minutes at room temperature. Fixation was quenched by removing the PFA and promptly adding 1.25M Glycine in PBS, one quick wash and one wash for 5 minutes at room temperature. After washing twice in PBS for 5 minutes each, the sections were permeabilised in Permeabilization buffer (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% IGEPAL, 0.001% Digitonin, 1% BSA, 10 uL murine RNAse Inhibitor) for 15 minutes at room temp. The sections were washed in 1x Wash Buffer (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 10 uL murine RNAse Inhibitor) once quickly and once for 5 minutes, then in PBS twice for 5 minutes. For each section, 200 uL of transposition mix were prepared as follows: 2uL of loaded Tn5 in 10 mM Tris-HCl pH 7.6, 5 mM MgCl2, 10% Dimethyl Formamide, 0.33x PBS, 0.1% Tween-20, 0.01% Digitonin. Each section was sealed with an adhesive hybridization chamber and incubated with 200 uL of tagmentation mix for 35 minutes at 37C in a humid chamber. The slides were retrieved and washed with 40 mM EDTA once quickly, and once for 5 minutes, then with PBS 3 times for 5 minutes and with 2xSSC 2 times for 5 minutes. The index oligos for the ligations were annealed at 45uM final in 1xSSC in the following pairs: BL680/BL676(cycle 1, bulk), BL681/BL677 (cycle 2, bulk), BL683/BL642 (cycle 3, bulk), BL732/BL601 (cycle 4A, Dentate Gyrus), BL733/BL677 (cycle 4B, cortex), BL732/BL641 (cycle 1, single ligation bulk). The annealing thermocycler conditions were as follow: 1) 95C for 5 minutes, 2) ramp down to 65 at 0.1C/second, 3) hold at 65C for 5 minutes, 4) ramp down to 12C at 0.1C/second, 5) hold at 12C.. The spatial barcodes were encoded in the tissue with the following protocol, which was conducted under light protected condition for its entirety: cycle 1 ligation, cycle 2 uncaging (bulk), cycle 2 ligation, cycle 3 uncaging (bulk), cycle 3 ligation, cycle 4A uncaging (Dentate Gyrus), cycle 4A ligation, cycle 4B uncaging (cortex), cycle 4B ligation. Bulk uncaging was performed with a UV transilluminator fitted with 365 nm bulbs for 15 minutes at room temperature, with the section covered with 500 uL of 2x SSC. Spatial uncaging was performed on a SP5 Leica confocal system fitted with a 30mW 405nm solid state laser, illuminating each ROI for 10 minutes with the 405nm laser at maximum power. Following uncaging, the slides were washed in 2xSSC, once quickly and once for 5 minutes. Ligations were performed as follows. Sections were incubated for 5 minutes in 1x Ligation buffer (50 mM TrisHCl pH7.4, 10 mM MgCl2, 10 mM DTT, 1mM ATP). For each sample, a ligation mix (50 uL) was prepared as follows: index oligos (3 uM, as appropriate), T4 ligase (100U/uL, NEB) in 1x T4 ligation buffer. The ligation mix was added directly to the sections, covered with a 22x22mm glass coverslip, and the reactions were incubated for 30 minutes (45 minutes for cycle 1) at 25C in a humid chamber. The slides were then washed in 2xSSC+Draq5 (1:1000) once for 10 minutes, 2xSSC+10%EC once for 5 minutes and 2xSSC once for 5 minutes. After the serial ligations, an adhesive hybridization chamber was mounted on the slides, and the sections were lysed in 200 uL of Lysis Buffer (0.8 U/mL in RIPA buffer) at 60C overnight (~16 hrs) in a sealed humid chamber. All the following steps were not carried out under light protected conditions. The lysate was collected and purified with MinElute Reaction Clean-up column, and eluted in 25 uL of EB buffer. Libraries were amplified via quantitative PCR as follows. For each sample, a 50 uL PCR mix was prepared mixing 5 uL of purified sample, 25 uL of 2x Q5 mastermix, 1.25 uL of 50 uM P5 primer (BL727), 1.25 uL of 50 uM indexed P7 primer (Ad2.X) in nuclease free water. The reaction was incubated in a thermocycler at 72C for 5 minutes (gap-fill), 98C for 3 minutes, then 5 cycles at 98C for 20 seconds, 68C for 20 seconds, 72C for 20 seconds. The pre-amplified products was kept on ice, and 5 uL were used as input for qPCR to determine the optimal number of additional cycles, The qPCR reactions were set up as follows: 5 uL of the preamplified material, 5 uL of 2x Q5 master mix, 0.25 uL of 50 uM P5 primer (BL727), 1.25 uL of 50 uM indexed P7 primer (Ad2.X), 2.5 uL of 20x EVA-Green in nuclease free water. The cycling protocol was 98C for 3 minutes, 40 cycles of 98C for 20 seconds, 68C for 20 seconds, 72C for 20 seconds with a plate reading step. The number of cycles required to reach 1/3 of the amplification curve plateau was selected for the final amplification of the libraries. The PCR reactions were purified with AmpureXP beads (0.8x) and eluted in 20 uL of EB buffer. The libraries were analysed on a Tapestation (D5000 cartridge) and quantified with KAPA library quantification kit prior to pooling. Sequencing was performed on a Novaseq (Illumina) instrument.


title: siEMD replicate 3

first: Bilian

last: Ke

address: No. 160 Pujian Road, Shanghai

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

description: Library name: Scleral_FB_siEMD_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

source_name: sclera

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: sclera

value: primary cell

value: fibroblast


title: Celf2_het newborn mouse hemi brain

city: San Antonio

first: Zhijie

middle: Jason

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

description: Library name: Celf2_het

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell ranger tool.
Seurat was used for data pre-processing and analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing genes by barcode counts matrices

molecule: nuclear RNA

source_name: mouse hemi brain

extract_protocol:
A 10 µm thick frozen section was placed on the Visium Spatial Gene Expression Slide (10x Genomics, USA) and processed with the Visium Spatial Gene Expression Reagent kit (10x Genomics, USA) according to the manufacture’s protocol.
Libraries were construct with 10X genomic Visium library kits with Dual Index Plate TT Set A- B1 and C1

value: mouse hemi brain

value: Celf2 Het


title: w5 control blastocyst

description: Library name: w5


title: Celf2_KO newborn mouse hemi brain

description: Library name: Celf2_KO

value: Celf2 KO


title: siEMD replicate 2

description: Library name: Scleral_FB_siEMD_2


title: WT-B3, WT SARS-CoV-2 infected


title: w4 control blastocyst

description: Library name: w4


title: siEMD replicate 1

description: Library name: Scleral_FB_siEMD_1


title: Col_monosome_rep4

city: Kaifeng

first: Xiaohong

last: Zhu

address: Jinming Street

institute: Henan University

data_processing:
Library strategy: Ribo-seq
illumina Novaseq6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: seedling

growth_protocol: Seedlings were grown vertically on 1/2 MS medium with 1% sucrose and 1.2% agar.

extract_protocol:
Total RNA of polysome or monosome fractions was precipitated and pooled for RNA-seq analysis. 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

treatment_protocol: Ten day old Col-0, 2OX and sextuple seedlings grown vertically on 1/2 MS agar plates were collected for monosomal and polysomal RNA isolation. Ten day old Col-0 seedlings were transferred from MS plates to 9-well plate containing 1mL 1/2 liquid MS medium per well and treated with 50uM antimycin for 5 hours (sample named as Col_AA), or treated with DMSO (sample named as Col_CK)

value: whole seedling

value: ten day old

value: wild type Col-0

tag: molecule subtype

value: monosomal RNA


title: Celf2_ctrl NB#11

description: Library name: Celf2_ctrl NB#11

data_processing:
Basecalls performed using Illuminal CASAVA software.
Cutadapt was used to remove the first 9 bases and N’s on both ends of reads. Reads with minimum of 25 bases were kept. Reads were aligned to human genome (hg19) using STAR. Duplicated reads were marked and removed by Picard. The bam files were transformed into bed12 format by bedtools, and then shifted to 200nt by a custom script and transformed back to bed6 format. Macs2 bdgopt sub-command was used to normalize each sample to a 10 million total reads.
exomePeak was used to call m6A enriched peaks by combining both replicates with default parameters.
Assembly: mm9
Supplementary files format and content: bigWig file

source_name: newborn mouse brain

extract_protocol:
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara-Clontech, 634413), according to the manufacturer’s instructions.

value: newborn mouse brain

value: Celf2 +/-


title: WT-B2, WT SARS-CoV-2 infected


title: WT-B1, WT SARS-CoV-2 infected


title: Celf2_ctrl NB#7

description: Library name: Celf2_ctrl NB#7


title: w2 control blastocyst

description: Library name: w2

value: Blastocist

value: Control


title: siLMNA replicate 3

description: Library name: Scleral_FB_siLMNA_3


title: w3 control blastocyst

description: Library name: w3


title: Celf2_ctrl NB#6

description: Library name: Celf2_ctrl NB#6


title: siLMNA replicate 2

description: Library name: Scleral_FB_siLMNA_2


title: NSP15-D4, NSP15 mutant SARS-CoV-2 infected


title: w1 control blastocyst

description: Library name: w1


title: Celf2KO NB#10

description: Library name: Celf2KO NB#10

value: Celf2 -/-


title: siLMNA replicate 1

description: Library name: Scleral_FB_siLMNA_1


title: NSP15-D3, NSP15 mutant SARS-CoV-2 infected


title: m10 Padi6 mutant blastocyst

description: Library name: m10


title: Celf2KO NB#4

description: Library name: Celf2KO NB#4


title: NSP15-D2, NSP15 mutant SARS-CoV-2 infected


title: Celf2KO NB#2

description: Library name: Celf2KO NB#2


title: m9 Padi6 mutant blastocyst

description: Library name: m9


title: siNC replicate 2

description: Library name: Scleral_FB_siNC_2


title: NSP15-D1, NSP15 mutant SARS-CoV-2 infected


title: siNC replicate 3

description: Library name: Scleral_FB_siNC_3


title: m8 Padi6 mutant blastocyst

description: Library name: m8


title: HCIEC23_DMSO_SOX17

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

description: Library name: Sample 4

data_processing:
Reads were aligned to the hg19 build of the human genome using Bowtie: -m1 -t -best -q -S -l 32 -e 80 -n 2
SAMtools was used to sort and convert SAM files to BAM files
MACS2 was used to call peaks with a P-value cutoff of 1x10-10 and mfold parameter between 15 and 100
Assembly: hg19
Supplementary files format and content: BigWig files
Supplementary files format and content: narrowPeak files from MACS2

growth_protocol: Cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. 5 days prior to treatment, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific) with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Cells were fixed using 1% formaldehyde (Sigma Aldrich, 252549) for 10 minutes at room temperature to cross-link DNA and proteins. Cross-linking was stopped by addition of glycine (Fisher Scientific, BP381) to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via scraping in Farnham lysis buffer supplemented with protease and phosphatase inhibitors (Thermo Scientific, A32959).
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009.

treatment_protocol: Cells were treated with 0.1% DMSO for one hour (SOX17 ChIP), or 10 nM 17beta-estradiol for one hour (ER ChIP), or 0.1% DMSO for 8 hours (H3K4me1)

value: endometrial adenocarcinoma

value: WT

value: DMSO


title: siNC replicate 1

description: Library name: Scleral_FB_siNC_1

value: sclera

value: primary cell


title: NSP1-C4, NSP1 mutant SARS-CoV-2 infected

value: Lung


title: m7 Padi6 mutant blastocyst

description: Library name: m7