title: IgG_Isotope_CS5415S_mm10_Rods_48h_Rep2

city: Berlin

first: Konrad

middle: Jakub

last: Chudzik

address: Hannoversche Str. 28

institute: MDC-BIMSB

description: Library name: IgG_Isotope_CS5415S_mm10_Rods_48h_Rep2

data_processing:
Sequencing adapters were trimmed using Trim Galore (v0.6.4) with the options --paired --nextera. Trimmed reads were aligned to the mouse genome (mm10) for rod cells or the human genome (hg38) for HeLa cells using Bowtie2 (v2.3.5.1) with --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 2000. Aligned reads were filtered for mapped, paired-end reads (MAPQ ≥ 20) using samtools (v1.10) with view -f 2 -q 20 and then sorted. ENCODE blacklisted regions were removed using bedtools (v2.29.2) with intersect -v.
Normalized coverage tracks (bigWig) were generated with deepTools2 (v3.4.1) using a bin size of 10 bp, read extension (-e), and CPM normalization, ignoring chrX and chrY. For merged tracks, FASTQ files were concatenated from biological replicates. To visualize enrichment relative to matched IgG controls, log2 ratio tracks were generated using deepTools bigwigCompare (v3.4.1). Analogous 20 kb binned subtraction bedGraphs were used as input for domain calling.
Domain calling was performed as previously described (Kefalopoulou et al., 2025) with minor changes in parameters. Specifically, 20 kb binned log2 matrices were binarized: bins above a signal threshold were considered positive (within domain) and below as negative. Adjacent segments separated by gaps ≤200 kb were merged, and regions smaller than 100 kb were removed. To evaluate biological replicate consistency, consensus domains were defined using bedtools intersect (v2.29.2). Consensus regions were used for all subsequent downstream analyses.
To characterize signal distribution across distinct chromatin environments, the genome was segmented into four categories based on the presence or absence of LMNB1 and ab1220 consensus domains: LMNB1+/ab1220+, LMNB1+/ab1220−, LMNB1−/ab1220+, and LMNB1−/ab1220−, using bedtools intersect and subtract (v2.29.2).
Assembly: mm10/hg38
Supplementary files format and content: bigWig (.bw): per-replicate CPM-normalized coverage tracks (10 bp bins, chrX/Y excluded), generated from blacklist-filtered alignments with deepTools2. Merged log2 ratio bigWigs (vs matched IgG, replicate-pooled) are provided as series-level supplementary files for visualization.
Supplementary files format and content: bedGraph (.bedgraph): per-replicate log2 ratio of signal vs matched IgG control, binned at 20 kb. Used as input for domain calling.
Supplementary files format and content: BED (.bed): per-replicate domain calls from the binarized 20 kb log2 bedGraphs (".bedgraph.bed"). Series-level supplementary BEDs include consensus domains per condition (intersection of biological replicates) and four genome-segmentation tracks (LMNB1+/ab1220+, LMNB1+/ab1220−, LMNB1−/ab1220+, LMNB1−/ab1220−)
Library strategy: CUT&Tag

source_name: retina

growth_protocol: All mice were housed in a centrally controlled environment with a 12 h light and 12 h dark cycle, temperature of 20-22.2°C, and humidity of 30–50%. All mice had access to food and water ad libitum. Bedding, food and water were routinely changed. All experiments involving animals were carried out following institutional guidelines as approved by LaGeSo Berlin and following the Directive 2010/63/EU of the European Parliament on the protection of animals used for scientific purposes. Biological replicates represent samples collected independently from different animals.  HeLa cells were cultured in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin at 37°C and 5% CO₂, and routinely tested for Mycoplasma contamination. Biological replicates represent HeLa cells grown independently from separate cryovials.

extract_protocol:
HeLa cells were collected using TrypLE (Gibco, 12604021) and following centrifugation (5 min, 300g, RT), resuspended in CUT&Tag wash buffer (20 mM HEPES pH 7.5 (Jena Bioscience, BU10675), 150 mM NaCl (Invitrogen, AM9760G), 0.5 mM spermidine (Sigma, S0266), 10 mM sodium butyrate (Sigma Aldrich, B5887), 1 mM PMSF (Thermo Scientific, 36978), Protease Inhibitor Cocktail (Roche, 04693132001)) and quantified using EVE automatic cell counter (NanoEntek). For sampling rod cells, retinas from 2-month-old NRL-GFP mice were dissociated using the Papain Dissociation System (Worthington, #130-094-802). Four retinas from two mice were used for one biological replicate. Briefly, retinas were dissociated in papain solution for 60 min at 37°C, while shaking at 700 rpm. Afterwards, retinas were triturated with a 1 ml micropipette and transferred to a new tube containing a mix of EBSS, DNase and albumin-ovomucoid inhibitor. Cell suspensions were triturated again with a glass Pasteur pipette ten times until tissue fragments were no longer visible. Finally, 250 µl of EBSS/albumin-ovomucoid inhibitor was added, and the single-cell suspension was cleared of cell clumps by filtration (pluriStrainer Mini 70 μm). FACS sorting of single cells was performed on the BD FACS Aria II or Aria III Cell Sorter System with sample and plate cooling at 4°C. Forward-side scatter gating was used to eliminate debris and identify intact cells, and GFP intensity was used to specifically isolate rod cells. Single cells were sorted into 15 ml falcons pre-coated with BSA and containing 5 ml of wash buffer for approximately 1 h. After sorting, rod cells were quantified using a haemocytometer. For each CUT&Tag reaction, 11 μl Concanavalin A beads (BioMag, 86057) were equilibrated twice with 100 μl and then concentrated in 11 μl of binding buffer (20 mM HEPES pH 7.5, 10 mM KCl (Invitrogen, AM9640G), 1 mM CaCl₂ (Merck, 102382), 1 mM MnCl₂ (Thermo, J63150.AD)). 100,000 cells were then bound to the beads by incubating for 10 min at RT with rotation. Beads were subsequently separated on a magnet and resuspended in 100 μl CUT&Tag Antibody buffer (Wash buffer with 0.05% Digitonin (Millipore, 30410) and 2 mM EDTA (Invitrogen, 15575-038)). Subsequently, 1 μl of primary antibody or IgG control was added and incubated on a rotator overnight (15 h) or for 48 h at 4°C. After magnetic separation, beads were resuspended in 100 μl of Dig-wash buffer containing 1 μl of matching secondary antibody (Abcam, ab46540 for mouse; Antibodies-online, ABIN101961 for rabbit) and incubated for 1 h at 4°C with rotation. Following three washes with CUT&Tag Dig-wash buffer (Wash buffer with 0.05% Digitonin), beads were resuspended in 100 μl CUT&Tag Dig-300 buffer (20 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 10 mM Sodium butyrate, 1 mM PMSF) with a 1:250 dilution of homemade 3xFLAG-pA-Tn5 preloaded with Mosaic-end adapters. After incubation for 1 h at 4°C with rotation, beads were washed four times with Dig-300 buffer and resuspended in 50 μl Tagmentation buffer (Dig-300 buffer with 10 mM MgCl₂ (Invitrogen, AM9530G)). Homemade spike-in-AmpR was added to the tagmentation buffer at a final concentration of 33.6 fM (Li et al., 2021). Tagmentation was performed for 1 h at 37°C and subsequently stopped by adding 2.25 μl EDTA, 2.75 μl 10% SDS (Invitrogen, 15553-035) and 0.5 μl Proteinase K (Invitrogen, 25530049). DNA fragments were solubilized for 16 h at 55°C followed by 30 min at 70°C to inactivate residual Proteinase K. DNA fragments were finally purified and eluted with 25 μl of elution buffer (Zymo, D5205).
NGS libraries were generated by PCR amplifying the CUT&Tag DNA fragments with barcoded i5 and i7 primers (Buenrostro et al., 2015) as described previously (Gjaltema et al. 2022). Briefly, DNA fragments with Nextera barcoded HPLC grade primers were loaded with NEBNext HiFi 2x PCR Master Mix (New England BioLabs, M0541S) into a thermocycler for 5 min at 72 °C, 30 sec at 98 °C, 10 sec at 98 °C, 10 sec at 63 °C (14 Cycles for steps 3-4) and 1 min at 72°C. Following PCR, 1x volume of Ampure XP beads (Beckman Coulter) were mixed with the NGS libraries and incubated at RT for 10 minutes. After magnetic separation, the beads were washed three times on the magnet with 80% ethanol, and the libraries were eluted with Tris-HCL, pH 8.0 (Roth, 9090.3). The quality of the purified NGS libraries was assessed with the D5000 tapestation (Agilent Technologies).

tag: tissue

value: retina

tag: cell type

value: rod photoreceptors

tag: genotype

tag: time

tag: chip antibody

value: Rabbit IgG isotype control (CS5415S, Cell Signaling)

tag: strain background

tag: age

value: 8-10 weeks


title: genomic DNA from maternal peripheral blood [4006-V2]

status: Public on Jun 30 2026

type: genomic

city: Kalyani

first: Arindam

last: Maitra

state: West Bengal

address: PO: NSS

country: India

institute: National institute of Biomedical Genomics

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using GenomeStudio using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software (Illumina) version 2011.1.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from peripheral blood samples using QIAamp blood midi kit (Qiagen) according to manufacturer’s protocol.

tag: Sex

value: Female

value: Peripheral blood

tag: status

value: Pregnant

tag: time point

value: Sampled during 18-20 weeks of gestation

tag: delivery

value: Term

tag: individual


title: genomic DNA from maternal peripheral blood [4006-V1]

value: Sampled during 11-14 weeks of gestation


title: Rabbit_IgG_CS27295_Rods_Rep2

type: SRA

country: Germany

description: Library name: Rabbit_IgG_CS27295_Rods_Rep2

library_source: genomic

organism: Mus musculus

value: Rabbit IgG (CS27295, Cell Signaling)


title: Jurkat BC06

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

country: USA

institute: Allen Institute

description:
Library name: FIX00561
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

library_source: transcriptomic single cell

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the Fixed RNA Profiling capability (version 9.0.1), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
scRNA counts matrices were normalized and scaled using Seurat. Cell populations were manually re-labelled via clustering using a combination of selected reference markers for each cell type. Doublets were identified and removed using Scrublet.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

molecule: total RNA

source_name: Cell Line

growth_protocol: VST culture and fixation: Culture was performed using GREX-10, 6 well plates (Wilson Wolf), largely following a previously published rapid expansion protocol (Lazarski 2021). Briefly, PBMC were thawed, pelleted at 400 xg and resuspended in 2% BSA/PBS for counting. Cells were pelleted once again and resuspended at 1.5x107 cells per mL in CTL culture media including 300ng/mL each of CMV derived pp65 and IE-1 peptide pools (Peptivator, Milltenyi) or vehicle control (water). CTL culture media contained 44% RPMI, 44% Clicks, 10% FBS, 1% PenStrep, 1x Glutamax. Cells were incubated/pulsed for 1h at 37C. Following peptide pulse, cells were distributed into GREX-10 6 well plates containing 30mL total volume CTL media. Media was supplemented with IL4 (400U/mL), IL7, and/or IL15 (10ng/mL) as indicated. On day 7 of culture, the upper 15mL of media was carefully removed from each well without disturbing cells and replaced with 15mL fresh CTL media including 2x cytokine addition. If applicable, treatment with metabolic inhibitors UK5099 (Sigma), TWS-119 (Selleck Chem.) or vehicle/DMSO, was initiated on day 1 of culture. Further addition of inhibitors was done at 1x concentration and occurred only during day 7 media exchange. Individual wells were harvested at indicated timepoints during VST culture. Upon harvest, cells were washed 1x with cold 0.4% BSA/PBS followed by 1x with cold PBS alone prior to pelleting and resuspension in cold 10x fixation buffer per the standard FLEX protocol. Cells were counted and fixed at a maximum of 1x107 per mL fixation buffer. Fixation occurred for 20-26 hours at 4C. After fixation, cells were pelleted at 850 xg and resuspended in 1mL ice cold quenching buffer per 10x FLEX guideline. 10x Enhancer and 50% glycerol were added, prior to storage at -80°C, per 10x FLEX guidelines.

extract_protocol:
Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell FLEX GEM Library and Gel Bead kit.
REFLEX (Library prep, pre-amp): Following GEM incubation, 125 μL of Recovery Agent was added to break the GEM emulsion. Mixtures were inverted 10x and incubated for 2 minutes at room temperature. 125 μL of recovery agent was then carefully removed from the bottom of each well. The remaining approximately 65 μL of recovered GEM sample was combined with a master mix containing 27 μL of Amp Mix (10X PN-2000047), 10 μL of Pre-Amp Primers B (10XPN-20000529), 1.5 μL of TruSeq1 [1 μM], and 3 μL of a pre-mixed TCR Variable Primer Pool (See Supplemental Note [REF]) [0.66 μM] for a total volume of 106.5 μL of master mix plus recovered GEM. Samples were inverted 10x to mix and placed in a thermal cycler with the following cycling conditions: 98C for 3 minutes; 8 cycles of 98C/20 seconds, 60C for 30 seconds, 72C for 2 minutes; 72C for 5 minutes, 4C infinite hold. Upon completion of the PCR, tubes were pulsed briefly on a minifuge to collect liquid. 90 μL was then transferred into a new 1.5 mL Eppendorf tube. A 1.8X SPRI bead cleanup was performed and sample was eluted into 100 μL of elution solution in accordance with 10X User Guide CG000673 Rev B.
REFLEX (library prep, re-amplification): Pre-amplified library eluates were split into two or three pools for preparation of gene expression libraries,TCR libraries, and ADT libraries (when applicable). Gene expression and ADT libraries were prepared using 20uL pre-amp product and following 10x guidelines for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev B). Linear PCR master mix for TCR libraries consisted of 20 μL 1X KAPA HiFi HotStart (Roche, KK260), 10 uL molecular biology grade water (Fisher, BP2819100), and 0.5 μL TruSeq2 primer at 123.4 nM per reaction. TCR libraries utilized 40 μL of pre-amp product total, divided into 4, 10 μL aliquots. Each 10 μL aliquot was combined with 30.5 μL master mix in a PCR strip tube and incubated with the following PCR program: 95C/3min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeat x4 for 5 total cycles, 72C/5min final extension, hold 4C. After the 5 cycle linear PCR was completed, 0.5 μL TruSeq1, at 123.4 nM per reaction, was spiked into each reaction and an exponential PCR was performed with the following conditions: 95C/3 min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeated x7 for 8 total cycles, 72C/5min final extension, hold 4C. Following exponential PCR, each of the four 41 μL reactions per library condition were repooled for a total volume of 164 μL. Samples were SPRI cleaned at 0.8X ratio, eluted in 50 μL aforementioned “elution solution ”.
REFLEX (Indexing TCR Libraries): PCR indexing master mix was prepared with 50 μL 1X Kapa HiFi HotStart and 10 μL molecular biology grade water per reaction. Indexing reactions combined 20 μL cleaned re-amplified product, 60 μL master mix, and 20 μL Dual Index TT Set A (10X Genomics, PN-1000215). Each library used a unique TT index well enabling later identification via sequencing. Samples were inverted to mix and briefly spun down. Thermocycler conditions used were as follows: 98C/45s activation [98C/20s denaturation, 54C/30s annealing, 72C/90s] repeated x12-15 for 13-16 total cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. A final SPRIselect bead clean up was performed at a 0.7X ratio with cleaned product eluted into 40 μL Buffer EB (Qiagen, Cat No. 19086).
REFLEX (Indexing GEX libraries): GEX library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 4.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TS Set A primers (PN-3000511). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
REFLEX (Indexing ADT libraries): ADT library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 5.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TN Set A primers for the ADT libraries (10X, PN 1000250). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
Sequencing: Final scRNAseq libraries were sequenced using a NovaSeq X 25B PE300 or NextSeq2000 P4 300 cycle flow cell, Read1:80 Read2:200. A read depth of 5000 reads per cell for TCR libraries or 10,000 reads per cell for GEX libraries was targeted. ADT or CITEseq libraries were targeted at 5000 reads per cell.

treatment_protocol: Cell Lines: Parental Jurkat T cells were originally purchased from ATCC and were transduced with pMW39 lentivirus (CXCR4 sgRNA) + pMW5 lentivirus (dCas9 ) by our group for use in other studies. No modifications were made to the native Jurkat TCR. The Raji CCL-86 cell line was purchased from ATCC.

value: Cell Line

value: T cell Immortalized Cell Line

tag: treatment

tag: subject id

tag: age at_blood_drawn

value: Male

tag: ethnicity/race

tag: cmv stats

tag: treatment time

tag: batch id

tag: pool id

value: PA

tag: batch pool

tag: probe barcode_id


title: genomic DNA from maternal peripheral blood [3640-V5]

tag: tissue

value: Sampled at delivery

value: Preterm


title: Rabbit_IgG_CS27295_Rods_Rep1

description: Library name: Rabbit_IgG_CS27295_Rods_Rep1

value: retina

tag: cell type

tag: genotype

tag: time

tag: chip antibody

tag: strain background

tag: age


title: Jurkat BC05

description:
Library name: FIX00560
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: treatment

tag: Sex


title: genomic DNA from maternal peripheral blood [3640-V3]

tag: status

tag: time point

value: Sampled during 26-28 weeks of gestation

tag: delivery

tag: individual


title: Mouse_IgG_CS68860_Rods_Rep2

description: Library name: Mouse_IgG_CS68860_Rods_Rep2

value: rod photoreceptors

value: Mouse IgG (CS68860, Cell Signaling)


title: iPSC-vCMs + iPSC-vCM EVs #3

city: Boston

first: Worawan

middle: B

last: Limpitikul

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

description: Library name: E_C3

library_source: transcriptomic

data_processing:
Adapter sequences were trimmed from sequencing reads using Cutadapt (v4.8). Next, Quality assessment of both raw and adaptor-trimmed reads was carried out with FastQC (v0.12.1) (www.bioinformatics.babraham.ac.uk/projects/fastqc). Subsequently, the trimmed reads were aligned to the Gencode GRCh38.p13 reference genome using STAR (v2.7.11a). STAR was supplied with Gencode v38 gene annotations to enhance mapping precision, and gene-level read counts were obtained using featureCounts (v2.0.6)
Assembly: GRCh38.p13
Supplementary files format and content: csv files including cpm for each gene in each sample

source_name: ipsc-derived ventricular myocytes

extract_protocol:
per manufacturer's protocol - miRNeasy Micro Kit (Qiagen, cat. no. 217084)
per manufacturer's protocol - SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio USA, Inc., cat. no. 634413)

value: ipsc-derived ventricular myocytes

tag: cell line

value: human iPSCs

value: ventricular myocytes

value: wild type

value: iPSC-vCM EVs

tag: batch


title: N2 Celegans late stage embryos-replicate2

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

data_processing:
RNA-seq reads were aligned to the Caenorhabditis elegans reference genome (WBcel235/ce11) using the STAR aligner with default parameters
featureCounts was utilized to generate raw count matrices from aligned reads.
Within the DESeq2 framework, size factors were estimated to account for differences in library depth and sequencing run variations.
Low count genes (<10 in each samples) were filtered out to improve the robustness and accuracy of the statistical analysis.
DE gene were filtered out using pval <= 0.005 and qval <= 0.1
Assembly: ce11/WBcel235
Supplementary files format and content: bigwig and DESeq2 results

organism: Caenorhabditis elegans

source_name: late stage embryos

extract_protocol:
C. elegans RNA was extracted as described (Green and Sambrook, 2020). Briefly, late stage embryos were collected from worms grown on five NGM plates and flash frozen in liquid N2. The frozen pellet was grinded to a fine powder and dissolved in ten volumes of TRIzol™ (Invitrogen, USA). Total RNA was isolated according to the manufacturer’s protocol, flash frozen in liquid N2 and stored at -80 °C. For RNA-seq, library preparation and sequencing were performed by Novogene (Novogene Co, Hong Kong).
Poly-T oligo-attached magnetic beads (NEB Oligo d(T)25 Magnetic Beads, S1419S) were used to purify mRNA from total RNA. Random hexamer primers were used to synthesize first-strand cDNA (included in the library preparation kit), followed by second-strand cDNA synthesis using dUTP for strand-specific libraries. NEBNext® Ultra™II Directional RNA Library Prep Kit(Cat No. E7760) was used for library preparation. Qubit (Thermo fisher scientific) and real-time PCR were used for quantification and quality control. The size distribution of the library was analyzed using Agilent bioanalyzer (2100). Quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 PE150 platform.

value: late stage embryos


title: genomic DNA from maternal peripheral blood [3640-V2]

value: Female

value: Peripheral blood

value: Pregnant

value: Sampled during 18-20 weeks of gestation


title: ChIP-seq of hpl2 in condition CEC4, rep2

description:
rep2
hpl2_CEC4.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_CEC4_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_CEC4_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

data_processing:
ChIP-seq reads were aligned to the C. elegans WBcel235 reference genome using BWA with default parameters.
Fragment length and quality assessments were performed using PyMASC.
MACS2 was employed for peak calling using -q 0.5 to lower the threshold of reported peaks. Peak calling results from different replicates within a given IP and condition were then filtered using ChIP-R to assess the irreproducible discovery rate (IDR).
ChIP-seq samples were normalized using their respective input controls with bamCompare (deepTools), applying specific parameters including --minMappingQuality 20, --binSize 10, --smoothLength 30, --extendReads, --scaleFactorsMethod readCount, --operation log2, and --pseudocount 1.
Assembly: WBcel235/ce11
Supplementary files format and content: macs2 peak calling filtered by chipr
Supplementary files format and content: Input normalised bigwig
Supplementary files format and content: Differential zscore bigwig

source_name: embryos

growth_protocol: C. elegans were cultured on nematode growth medium (NGM) plates seeded with E. coli OP50-1 according to Lewis and Fleming (1995). NGM plates supplemented with ten times excess peptone were employed for growing worms destined for Hi-C and ChIP-seq experiments. The wild-type strain used was N2. The C. elegans strains utilized, along with their genotypes, are as follows: lin-61(tm2649) (Koester-Eiserfunke and Fischle, 2011), hpl-2(tm1489) (Schott et al., 2006), set-32(red11); met-2(n4256) set-25(n5021) (Kalinava et al., 2017), and cec-4(ok3124) (Gonzalez-Sandoval et al., 2015). The hpl-2(I158A) allele was created using a CRISPR/Cas9 approach; further details can be provided upon request. The genotypes of all C. elegans strains were routinely confirmed by single-worm PCR.

extract_protocol:
ChIP was conducted with slight adjustments following the method described by Ercan et al. (2007). Post-crosslinking, C. elegans embryos underwent a wash with 100 mM Tris-HCl, pH 7.5, followed by two washes with FA buffer (50 mM HEPES-KOH, pH 7.5; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 150 mM NaCl; 1x protease inhibitor (cOmplete™, Sigma, Germany)). Nuclei were sheared as for Hi-C and then centrifuged at 13,000 xg for 15 minutes at 4°C to gather extracts. Immunoprecipitations were arranged using extracts equivalent to 3 mg along with 3–5 μg of antibodies in a total volume of 500 μL FA buffer. Prior to antibody addition, 10% of the reactions were kept aside as input. After 16 hours of incubation at 65°C with agitation, complexes were recovered by adding 20 μL of Protein A/G beads (Pierce™ Protein A/G Magnetic Beads, USA) and washed twice with FA buffer supplemented to 1 M NaCl, followed by two washes with FA buffer supplemented to 500 mM NaCl. Beads were treated with 1% (w/v) SDS in TE containing 250 mM NaCl at 65°C for 30 minutes to elute the complexes. Samples and inputs were treated with 2 μL of 10 mg/mL Proteinase K for 1 hour at 55°C. Decrosslinking was carried out at 65°C overnight in a thermomixer. DNA purification was executed with a PCR clean-up kit (Macherey-Nagel™, Germany) and quantified using Qubit Fluorometric Quantification. Library preparation followed the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, USA) protocol. Libraries were sequenced on Novaseq 6000 PE150 S4 flow cells. Various antibodies were employed for ChIP experiments: anti-HPL-2 (Novus Biologicals 38630002), anti-LIN-61 (Novus Biologicals 29590002), anti-LEM-2 (Novus Biologicals 48540002), anti-H3K9me2 (Abcam ab1220), anti-H3K9me3 (VWR 309M3-B), anti-H3K4me1 (Abcam ab8895), anti-H3K4me3 (Active Motif 39159), anti-H3K27me3 (Abcam ab6002), and anti-H3K27ac (Active Motif Ab39133). All ChIP-seq experiments were conducted as biological independent triplicates.
Immunoprecipitation of C. elegans nuclear extracts utilized anti-LIN-61 (Novus Biologicals 29590002), anti-HPL-2 (Novus Biologicals 38630002), and anti-T7 (Abcam ab9138) antibodies. The antibodies were crosslinked to dynabeads M-280 sheep anti-rabbit IgG (Pierce, USA) overnight at 4°C on a nutator, following the manufacturer’s instructions. Unbound antibodies were removed by washing the beads with 1xPBS three times. Beads were then resuspended in 1 mL 0.2 M triethanolamine, pH 8.2, 20 mM DMP at room temperature for 60 minutes. Cross-linking was halted by adding 1 mL 50 mM Tris-HCL, pH 7.5, at room temperature for 60 minutes. After three washes with 1xPBS, 5 mg of total protein C. elegans extracts in 500 μL were added to the beads and incubated for 30 minutes at room temperature. Subsequently, beads underwent six washes with buffer D (each wash involving incubation with 1 mL buffer D for 5 minutes followed by centrifugation at 2000 xg for 1 minute at room temperature). Bound proteins were released from the beads in SDS-PAGE sample buffer by incubating at 95°C for 10 minutes. The proteins were resolved on SDS-PAGE and subjected to analysis by western blotting following standard procedures.

treatment_protocol: Crosslinking of C. elegans embryos and nuclei preparation followed the protocol outlined by Crane et al. (2015). Gravid adult worms were harvested and bleached to yield a late-stage embryo pellet of at least 1 or 4 mL for ChIP-seq or Hi-C experiments, respectively. The embryos underwent two washes in 1xPBS, were flash-frozen in liquid nitrogen, and stored at -80 °C. Thawed on ice, the embryos were then crosslinked in 50 mL of 2% (v/v) formaldehyde in PBS for 30 minutes at room temperature on a nutator. Subsequent to crosslinking, they were sequentially washed in 100 mM Tris-HCl, pH 7.5, twice in 1xPBS, and once in lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 0.2% (v/v) Igepal CA-630 (Sigma, Germany); 5 mM DTT; 0.5 mM EGTA; 1x protease inhibitor (cOmplete™, Sigma, Germany)). The embryos were then dounced 25 times with pestle A and 25 times with pestle B (PYREX® 7 mL Dounce Tissue Grinder, Corning, USA) while kept on ice. The resulting extract was centrifuged at 100 xg at 4 °C, and the supernatant containing nuclei was collected. This extraction process was repeated up to six times, with each supernatant checked for the presence of DAPI-stained nuclei under a fluorescence microscope. Supernatants containing pure nuclei were combined and centrifuged for 5 minutes at 2000 xg at 4 °C to collect material for further experimentation.

value: embryos


title: Mouse_IgG_CS68860_Rods_Rep1

description: Library name: Mouse_IgG_CS68860_Rods_Rep1

value: 8-10 weeks


title: genomic DNA from maternal peripheral blood [4293-V3]

value: Preterm


title: Raji BC09

description:
Library name: FIX03047-001
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Cell Line

value: B lymphocyte, CCL-86

tag: subject id

tag: age at_blood_drawn

value: Male

tag: ethnicity/race

tag: cmv stats

tag: treatment time

tag: batch id

tag: pool id

value: PB

tag: batch pool


title: iPSC-vCMs + iPSC-vCM EVs #2

description: Library name: E_C2

tag: tissue

value: ipsc-derived ventricular myocytes

tag: cell type

tag: genotype


title: genomic DNA from maternal peripheral blood [3640-V1]

tag: Sex

tag: status

value: Sampled during 11-14 weeks of gestation


title: H3K9me2_CMA317_mm10_Rods_48h_Rep2

description: Library name: H3K9me2_CMA317_mm10_Rods_48h_Rep2

value: retina

value: rod photoreceptors

tag: time

tag: chip antibody

value: H3K9me2 (CMA317, Diagenode)

tag: strain background

tag: age


title: iPSC-vCMs + iPSC-vCM EVs #1

description: Library name: E_C1

tag: cell line

value: human iPSCs

value: ventricular myocytes

value: wild type

tag: treatment

value: iPSC-vCM EVs

tag: batch


title: genomic DNA from maternal peripheral blood [3501-V5]

value: Female

value: Peripheral blood

value: Pregnant

tag: time point

value: Sampled at delivery

tag: delivery

value: Term

tag: individual


title: iPSC-vCMs + VAT EVs #5

description: Library name: E_76V

value: VAT EVs


title: H3K9me2_CMA317_mm10_Rods_48h_Rep1

description: Library name: H3K9me2_CMA317_mm10_Rods_48h_Rep1

value: 8-10 weeks


title: iPSC-vCMs + VAT EVs #4

description: Library name: E_68V


title: genomic DNA from maternal peripheral blood [3501-V2]

value: Sampled during 18-20 weeks of gestation


title: H3K9me2_CMA317_Rods_Rep1

description: Library name: H3K9me2_CMA317_Rods_Rep1


title: iPSC-vCMs + VAT EVs #2

description: Library name: E_64V

value: ipsc-derived ventricular myocytes


title: genomic DNA from maternal peripheral blood [3501-V1]

value: Sampled during 11-14 weeks of gestation


title: genomic DNA from maternal peripheral blood [3248-V5]

value: Preterm


title: iPSC-vCMs + VAT EVs #1

description: Library name: E_63V


title: H3K9me2_AM39239_mm10_Rods_48h_Rep1

description: Library name: H3K9me2_AM39239_mm10_Rods_48h_Rep1

value: retina

value: rod photoreceptors

value: H3K9me2 (AM39239, Active Motif)


title: genomic DNA from maternal peripheral blood [3248-V3]

value: Sampled during 26-28 weeks of gestation


title: PRS CK STORM exosomes, Production batch 5 (miRNA)

city: Madrid

first: Daniel

last: Lapuente

address: Calle de Isabel Colbrand, 6, 4ª planta, Fuencarral-El Pardo

country: Spain

institute: Peaches Biotech

description: Library name: PRS_CK_STORM_Batch5

data_processing:
FastQC v0.11.9 was employed to evaluate raw read quality using default parameters.
Trim Galore! v0.6.10 was applied to remove adapter sequences, discard low-quality bases, and retain reads within the expected human microRNA length range.
UMI-tools v1.1.5 was used with the extract and dedup modules to remove PCR duplicates based on UMI sequences.
Deduplicated reads were aligned to the human reference genome (GRCh38) using miRDeep2 v2.0.1.2 with default settings.
Known human miRNA species were quantified via the quantifier.pl module of miRDeep2, using mature and hairpin reference sequences for Homo sapiens and Mus musculus obtained from miRBase release 22.1.
Assembly: GRCh38
Supplementary files format and content: The processed data file is a tab-delimited text (.txt) file containing raw read counts of known Homo sapiens miRNAs for each PRS CK STORM production batch. Each row corresponds to a mature miRNA species annotated with miRBase identifiers, and each column represents an individual sample.

source_name: Human primary M2 macrophages and adipose-derived stem cells (PRS CK STORM co-culture origin)

extract_protocol:
Total exosomal RNA was extracted from PRS CK STORM using the exoRNeasy Maxi Kit (QIAGEN), following the manufacturer’s instructions.
Small RNA libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN), incorporating UMIs during reverse transcription. Libraries were PCR-amplified (22 cycles), indexed, purified, quality-checked (TapeStation D1000), and pooled at equimolar concentrations based on insert size and qPCR quantification.

tag: production batch

value: Batch 5


title: genomic DNA from maternal peripheral blood [3248-V2]


title: H3K9me2_AM39239_Rods_Rep2

description: Library name: H3K9me2_AM39239_Rods_Rep2


title: genomic DNA from maternal peripheral blood [3248-V1]


title: H3K9me2_AM39239_Rods_Rep1

description: Library name: H3K9me2_AM39239_Rods_Rep1


title: Sample 3_#105 CANX SKO - #3

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

data_processing:
Fastqc was used for quality analysis of the sequences. Cutadapt was used to remove the illumina universal adapter sequence in the reads. miARma-seq pipeline as used for further analysis, tophat2 with bowtie algorithm was used as a mapper whereas gtf file of genome build HG38 from ensemble was used as annotation file. Read counts were generated from miARma-seq and Qlucore omics explorer 3.6 was used to convert read counts into expression value. Trimmed mean of M-values (TMM) normalization was performed using Qlucore Omics explorer 3.5, same gtf file was used to annotate genes. Gene with less than 5 read counts in a sample were removed, also if gene is not expressed in both replicates of a sample were also removed.
Assembly: hg38
Supplementary files format and content: tab delimited text file included TMM normalized values for each sample and have ensembl gene Ids and gene symbols

source_name: Embryonic Kidney

growth_protocol: Different cell line with specific knockouts where cultured until about 70% confluency in six well plates

extract_protocol:
RNA was purified using the PureLink™ RNA mini kit according to manufacturer’s instructions (Invitrogen 12183018A) from the collected cell pellets
The concentration of the RNA was determined by measuring absorbance at 260 nm using NanoDrop One (ThermoFisher Scientific). The RNA and subjected to the Illumina sequencing protocol
3' RNA-seq (Illumina HiSeq 2500 V4 platform)

treatment_protocol: No treatment

value: Embryonic Kidney

value: human embryonic kidney 293 cells

value: KO-CANX

value: CRISPR-KO


title: CD68+, PDAC3, MGC WO-003

city: Rozzano

first: Anna Rita

last: Putignano

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description:
Library name: DSP-1001660035205-B-A12
CD68+ AOI from PDAC patient PDAC3, slide: CD68_Slide12, ROI: PDAC3-MGC_WO-003, area: 12517.48 um2, nuclei: 94

data_processing:
For each AOI, digital count conversion (.dcc) files were generated from fastqs using the GeoMx NGS Pipeline (version 3.1.1).
From each tissue under investigation DCC files were read into a NanoStringGeoMxSet object using the readNanoStringGeoMxSet function from GeomxTools R package (version 3.5, R version 4.3.3), and segments were assessed for sequence quality.
After generating gene-level counts, segments with high fraction of genes detected below the limit of quantification (LOQ) were removed. Count matrix, sample annotations, and feature annotations were read into a SpatialExperiment object and analyzed with standR package (version 1.6) workflow.
Genes with low expression levels were removed. Counts were normalized using the upper-quartile method from the edgeR package (version 4.0.16).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files containing raw expression values for each AOI/sample
Supplementary files format and content: DCC files containing raw probe read counts for each AOI/sample; RTS_IDs are interpretable using the accompanying PKC file

source_name: pancreas

extract_protocol:
After deparaffinization and target retrieval, slides were incubated with 0.1 μg/mL proteinase K for 15 minutes at 37°C and then post fixed for 5 minutes in 10% neutral buffered formalin followed by two washes in NBF stop buffer (24.5 g Tris base and 15 g Glycine in 2 L DEPC water). Slides were incubated with the Whole Transcriptome Atlas (WTA) RNA Probe set (121401102, NanoString), according to the manufacturer’s protocol.
Following probe incubation, slides were washed and incubated with the morphology marker solution: AlexaFluor™ 647 anti-human CD68 (BL13756, 375606 BioLegend, 1:400, RRID:AB_3097193) plus SYTO 13 (provided in GeoMx Nuclear Stain Morphology Kit, 121300303, NanoString) for 1 hour at RT and processed through the GeoMx® Digital Spatial Profiler instrument. Regions of interest (ROIs) with a circular shape and a diameter of 600 μm were selected, with an average of 3 ROIs without MGCs and 5 ROIs with MGCs per patient. For each ROI, the CD68+ area of interest (AOI) was selected to collect barcodes in a 96-well plate. Barcoded oligonucleotides were prepared for Illumina-based sequencing to generate target probe-specific count files, which were then saved in a digital count conversion format.

value: pancreas

value: macrophages


title: Sample 2_#105 CANX SKO - #2


title: H3K9me2_ab1220_Rods_Rep2

description: Library name: H3K9me2_ab1220_Rods_Rep2

value: H3K9me2 (ab1220, Abcam)


title: PRS CK STORM exosomes, Production batch 2 (miRNA)

description: Library name: PRS_CK_STORM_Batch2

value: Human primary M2 macrophages and adipose-derived stem cells (PRS CK STORM co-culture origin)

value: Batch 2


title: LaminB1_ab16048_Rods_Rep2

description: Library name: LaminB1_ab16048_Rods_Rep2

value: LaminB1 (ab16048, Abcam)

value: 8-10 weeks


title: genomic DNA from maternal peripheral blood [3138-V3]

value: Female

value: Peripheral blood

value: Pregnant

value: Term


title: PRS CK STORM exosomes, Production batch 1 (miRNA)

description: Library name: PRS_CK_STORM_Batch1

value: Batch 1


title: genomic DNA from maternal peripheral blood [3138-V2]

value: Sampled during 18-20 weeks of gestation


title: genomic DNA from maternal peripheral blood [3138-V1]

value: Sampled during 11-14 weeks of gestation


title: LaminB1_ab16048_Rods_Rep1

description: Library name: LaminB1_ab16048_Rods_Rep1

value: retina

value: rod photoreceptors


title: 7F2, eCLIP, Input, AD Int 3

city: Gainesville

first: John

last: Koren

state: FL

address: 1275 Center Dr

institute: University of Florida

description:
Library name: A20-022 Input
7F2 eCLIP

data_processing:
Eclipse's proprietary analysis pipeline (v1). UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2). Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the hg38 genome using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1). For each peak, IP versus input fold enrichments and p-values were calculated. Peaks were annotated using transcript information from GENCODE v41 with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron).
Assembly: Human (hg38)
Supplementary files format and content: excel filss with gene ID, ensemble ID, -log10(P-value), Log2 Fold Change, and feature
Library strategy: iCLIP

source_name: Hippocampus

extract_protocol:
Frozen human hippocampal samples tissue was disrupted by cryogrinder and UV crosslinked at 400 mJoules/cm2 with 254 nm radiation
Van Nostrand, E.L., et al., Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol, 2017. 1648: p. 177-200.

value: Hippocampus

value: ApoE 3/3


title: genomic DNA from maternal peripheral blood [1537-V5]

value: Sampled at delivery

value: Preterm


title: CD8+ T Cells, Sham or 6Gy, no infection or infected 4dpi or 7dpi

city: Washington

first: Henghong

last: Li

state: DC

address: 3700 Reservoir Rd. NW

department: Oncology

institute: Georgetown University

description:
Library name: Library C2
10X Genomics

data_processing:
The demultiplexing, barcode processing and gene counting were made using Cell Ranger software v7.1.0
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD8+ T Cells

extract_protocol:
Cells were recovered in phenol red free RPMI1640 complete medium (1% L-Glutamine, 5% HEPES, 1% NEAA, 1% Sodium Pyruvate, 50 μM 2-ME, and 0.1% Gentamicin) with 10% fetal bovine serum, and then subjected to red blood cell lysis in ACK lysis buffer. The reaction was neutralized with RPMI1640 complete medium and washed with RPMI1640 complete medium twice. Cell pellets were resuspended in RPMI1640 complete medium for T cell purification. Total CD8+ T cell purifications were performed using the MojoSort Mouse CD8 T Cell Isolation Kit (BioLegend) following manufacturer’s guidelines.
Library construction was performed according to the manufacturers instructions (single cell Chromium Fixed RNA Profiling Reagent Kit for Multiplexed Samples protocol, 10X Genomics)

treatment_protocol: Irradiation and/or Listeria monocytogenes infection

tag: strain

value: CD8+ T Cells


title: genomic DNA from maternal peripheral blood [1537-V3]

tag: tissue

value: Sampled during 26-28 weeks of gestation


title: CD8+ T Cells, 6Gy, no infection or infected 4dpi replicates

description:
Library name: Library B2
10X Genomics

tag: cell type


title: genomic DNA from maternal peripheral blood [1537-V2]


title: CD8+ T Cells, 6Gy, no infection or infected 4dpi

description:
Library name: Library A2
10X Genomics


title: 7F2, eCLIP, Input, AD High 4

description:
Library name: A21-007 Input
7F2 eCLIP

tag: genotype


title: genomic DNA from maternal peripheral blood [1537-V1]

tag: Sex


title: 7F2, eCLIP, Input, AD High 3

description:
Library name: A19-039 Input
7F2 eCLIP


title: genomic DNA from maternal peripheral blood [1031-V5]

tag: status


title: CD8+ T Cells, sham, no infection or infected 4dpi

description:
Library name: Library C1
10X Genomics


title: 7F2, eCLIP, Input, AD High 2

description:
Library name: A19-026 Input
7F2 eCLIP


title: genomic DNA from maternal peripheral blood [1031-V3]


title: CD8+ T Cells, 3Gy, infected 4dpi or 7dpi

description:
Library name: Library B1
10X Genomics


title: genomic DNA from maternal peripheral blood [1031-V2]


title: 7F2, eCLIP, Input, AD High 1

description:
Library name: A17-013 Input
7F2 eCLIP


title: CD8+ T Cells, sham or 3Gy, infected 4dpi or 7dpi

description:
Library name: Library A1
10X Genomics


title: 7F2, eCLIP, AD Int 4

description:
Library name: A20-001 IP
7F2 eCLIP


title: SKOV3-circ0005406 OE ovarian xenograft rep3

city: Nanjing

first: Xiyi

last: Chen

address: No.123 Mochou Road

country: China

institute: Women’s Hospital of Nanjing Medical University

description:
Library name: OE 3
B4

data_processing:
To identify DEGs (differential expression genes)between two different samples, the expression level of each transcript was calculated according to the transcripts permillion reads (TPM)method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2.
Assembly: hg38
Supplementary files format and content: gene.count.matrix.annot.txt lists the normalized read counts assessed by RNAseq of all samples listed.

source_name: xenograft ovarian cancer

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according to the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000(NanoDrop Technologies). Only high-quality RNAsample [Concentration≥20ng/μL, totalRNA>1μg,RQN>4.5 OR Concentration≥10ng/μL,total＞10ng,RIN>6.5] was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co.,Ltd. (Shanghai,China) according to the manufacturer’s instructions. The RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation(SanDiego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300-400bp use magnetic beads followed by PCR amplified for 10-15 PCRcycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: xenograft ovarian cancer

value: ovarian cancer

value: TP53 c.267delC; PIK3CA H1049R, circ_0005408 overexpression


title: 7F2, eCLIP, AD Int 3

description:
Library name: A20-022 IP
7F2 eCLIP


title: genomic DNA from maternal peripheral blood [1423-V5]

value: Female

value: Peripheral blood


title: SKOV3-circ0005406 OE ovarian xenograft rep2

description:
Library name: OE 2
B7

value: TP53 c.267delC; PIK3CA H1049R, circ_0005407 overexpression


title: genomic DNA from maternal peripheral blood [1423-V3]

value: Pregnant


title: 7F2, eCLIP, AD Int 1

description:
Library name: A17-006 IP
7F2 eCLIP


title: genomic DNA from maternal peripheral blood [1423-V2]

value: Sampled during 18-20 weeks of gestation


title: SKOV3 ovarian xenograft control rep3

description:
Library name: Ctrl 3
A5

value: TP53 c.267delC; PIK3CA H1049R


title: genomic DNA from maternal peripheral blood [1031-V1]

value: Sampled during 11-14 weeks of gestation

value: Term


title: Tau5, eCLIP, ANA 2

description:
Library name: 13473-IP
Tau5-eCLIP

source_name: hippocampus

value: hippocampus

value: UNK


title: Jurkat/Raji BC14

description:
Library name: FIX00567
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

source_name: Blood

value: Blood

value: Mixed Population

tag: subject id

tag: age at_blood_drawn

value: Male

tag: ethnicity/race

tag: cmv stats

tag: treatment time

tag: batch id

tag: pool id

value: PB

tag: batch pool

tag: probe barcode_id


title: genomic DNA from maternal peripheral blood [4293-V1]

tag: time point

tag: delivery

value: Preterm

tag: individual


title: 7F2, eCLIP, AD High 4

description:
Library name: A21-007 IP
7F2 eCLIP

tag: tissue

value: Hippocampus

value: ApoE 3/3


title: Raji BC10

description:
Library name: FIX03047-002
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Cell Line

tag: cell type

value: B lymphocyte, CCL-86

tag: treatment


title: genomic DNA from maternal peripheral blood [1423-V1]

tag: Sex

value: Female

value: Peripheral blood


title: IgG_Isotope_CS5415S_mm10_Rods_48h_Rep1

description: Library name: IgG_Isotope_CS5415S_mm10_Rods_48h_Rep1

value: retina

value: rod photoreceptors

tag: genotype

tag: time

tag: chip antibody

value: Rabbit IgG isotype control (CS5415S, Cell Signaling)

tag: strain background

tag: age

value: 8-10 weeks


title: SKOV3 ovarian xenograft control rep2

description:
Library name: Ctrl 2
A2

value: xenograft ovarian cancer

tag: cell line

value: ovarian cancer

value: TP53 c.267delC; PIK3CA H1048R


title: 7F2, eCLIP, AD High 3

description:
Library name: A19-039 IP
7F2 eCLIP


title: genomic DNA from maternal peripheral blood [1378-V5]

tag: status

value: Pregnant

value: Sampled at delivery

value: Term


title: SKOV3 ovarian xenograft control rep1

description:
Library name: Ctrl 1
A1

value: TP53 c.267delC; PIK3CA H1047R


title: 7F2, eCLIP, AD Int 2

description:
Library name: A15-011 IP
7F2 eCLIP

value: Hippocampus


title: 7F2, eCLIP, AD High 2

description:
Library name: A19-026 IP
7F2 eCLIP

value: ApoE 3/3


title: 150_REP14

city: Kuopio

first: Sini

middle: Anniina

last: Pitkänen

address: Neulaniementie 2

department: A. I. Virtanen -institute

country: Finland

institute: University of Eastern Finland

description:
Library name: Sample 54
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP14

data_processing:
The reads were preprocessed using nf-core/rnaseq pipeline (v. 3.14.0) using STAR, RSEM and Salmon packages combined with quality control, and annotated to the GRCm38 reference genome
Assembly: GRCm38
Supplementary files format and content: csv files including TPM counts for each Sample

molecule: polyA RNA

source_name: liver

extract_protocol:
Total RNA was extracted using NucleoSpin RNA kit (Macherey Nagel)
RNA sequencing libraries were prepared using QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen)

value: liver

value: WT

value: 150 mg/kg DINP


title: genomic DNA from maternal peripheral blood [1378-V3]

value: Female

value: Peripheral blood

value: Sampled during 26-28 weeks of gestation


title: 7F2, eCLIP, AD High 1

description:
Library name: A17-013 IP
7F2 eCLIP


title: SKOV3-circ0005406 OE ovarian xenograft rep1

description:
Library name: OE 1
B3

value: TP53 c.267delC; PIK3CA H1049R, circ_0005406 overexpression


title: genomic DNA from maternal peripheral blood [1378-V2]

value: Sampled during 18-20 weeks of gestation


title: 150_REP13

description:
Library name: Sample 53
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP13


title: genomic DNA from maternal peripheral blood [3501-V3]


title: H3K9me2_CMA317_Rods_Rep2

description: Library name: H3K9me2_CMA317_Rods_Rep2

value: retina

value: rod photoreceptors

value: H3K9me2 (CMA317, Diagenode)

value: 8-10 weeks


title: m6A, AD Int 4, Input

description:
Library name: A20-001 Input
RNA methylation m6A-IP

data_processing:
After sequencing, samples were processed with Eclipsebio's proprietary analysis pipeline (v1). UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2). Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the hg38 genome using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1). m6A peaks were identified within eCLIP samples using the peak caller CLIPper (v2.0.1). For each peak, IP versus input fold enrichments and p-values were calculated. For finer m6A site resolution, single nucleotide sites were also called. For this analysis, 5’ mismatches were trimmed from read alignments. Single nucleotide resolution sites were then called from trimmed reads using the tool PureCLIP (v1.3.1)[11]. PureCLIP was run using the input control data to identify sites enriched in the IP over the input. Peaks and single nucleotide sites were annotated using transcript information from GENCODE v41
Assembly: Human (hg38)
Supplementary files format and content: excel filss with gene ID, ensemble ID, -log10(P-value), Log2 Fold Change, and feature
Library strategy: MeRIP-Seq

extract_protocol:
mRNA was first isolated through poly(A) selection using oligo (dT) beads (ThermoFisher) followed by magnetic bead separation from 420 ng of total RNA. The mRNA was DNase treated at 37°C for 10 minutes then immediately sheared into 100-200nt fragments by heating at 95°C for 12 minutes in 1x Turbo DNase buffer (ThermoFisher).
Van Nostrand, E.L., et al., Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol, 2017. 1648: p. 177-200.


title: genomic DNA from maternal peripheral blood [1378-V1]

value: Pregnant

value: Sampled during 11-14 weeks of gestation


title: 150_REP12

description:
Library name: Sample 52
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP12


title: m6A, AD Int 3, Input

description:
Library name: A20-022 Input
RNA methylation m6A-IP


title: 150_REP11

description:
Library name: Sample 51
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP11


title: genomic DNA from maternal peripheral blood [1085-V5]

value: Sampled at delivery

value: Preterm


title: iPSC-vCMs + VAT EVs #3

description: Library name: E_67V

value: ipsc-derived ventricular myocytes

value: human iPSCs

value: ventricular myocytes

value: wild type

value: VAT EVs

tag: batch


title: m6A, AD Int 2, Input

description:
Library name: A15-011 Input
RNA methylation m6A-IP

value: Hippocampus

value: ApoE 3/3


title: H3K9me2_AM39239_mm10_Rods_48h_Rep2

description: Library name: H3K9me2_AM39239_mm10_Rods_48h_Rep2

value: H3K9me2 (AM39239, Active Motif)


title: genomic DNA from maternal peripheral blood [1085-V3]

value: Female

value: Peripheral blood

value: Sampled during 26-28 weeks of gestation


title: 150_REP10

description:
Library name: Sample 50
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP10

value: liver

value: WT

value: 150 mg/kg DINP


title: genomic DNA from maternal peripheral blood [1085-V2]

value: Pregnant

value: Sampled during 18-20 weeks of gestation


title: m6A, AD Int 1, Input

description:
Library name: A17-006 Input
RNA methylation m6A-IP


title: 150_REP9

description:
Library name: Sample 49
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP9


title: m6A, AD High 4, Input

description:
Library name: A21-007 Input
RNA methylation m6A-IP


title: genomic DNA from maternal peripheral blood [1085-V1]

value: Sampled during 11-14 weeks of gestation

value: Preterm


title: 150_REP8

description:
Library name: Sample 48
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP8


title: PRS CK STORM exosomes, Production batch 4 (miRNA)

description: Library name: PRS_CK_STORM_Batch4

value: Human primary M2 macrophages and adipose-derived stem cells (PRS CK STORM co-culture origin)

tag: production batch

value: Batch 4


title: m6A, AD High 3, Input

description:
Library name: A19-039 Input
RNA methylation m6A-IP


title: m6A, AD High 2, Input

description:
Library name: A19-026 Input
RNA methylation m6A-IP


title: 150_REP6

description:
Library name: Sample 46
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP6


title: genomic DNA from maternal peripheral blood [1131-V2]

value: Term


title: m6A, AD Int 4, IP

description:
Library name: A20-001
RNA methylation m6A-IP


title: 150_REP5

description:
Library name: Sample 45
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP5


title: genomic DNA from maternal peripheral blood [1131-V1]


title: 150_REP4

description:
Library name: Sample 44
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP4


title: m6A, AD Int 3, IP

description:
Library name: A20-022
RNA methylation m6A-IP


title: genomic DNA from maternal peripheral blood [0952-V5]

value: Sampled at delivery


title: 150_REP3

description:
Library name: Sample 43
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP3


title: m6A, AD Int 2, IP

description:
Library name: A15-011
RNA methylation m6A-IP

value: Hippocampus


title: 150_REP2

description:
Library name: Sample 42
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP2


title: genomic DNA from maternal peripheral blood [0952-V2]


title: m6A, AD Int 1, IP

description:
Library name: A17-006
RNA methylation m6A-IP

value: ApoE 3/3


title: 150_REP1

description:
Library name: Sample 41
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP1


title: 15_REP13

description:
Library name: Sample 40
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP13

value: 15 mg/kg DINP


title: m6A, AD High 3, IP

description:
Library name: A19-039
RNA methylation m6A-IP


title: genomic DNA from maternal peripheral blood [0733-V5]

value: Female


title: 15_REP12

description:
Library name: Sample 39
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP12


title: m6A, AD High 2, IP

description:
Library name: A19-026
RNA methylation m6A-IP


title: genomic DNA from maternal peripheral blood [0733-V3]

value: Peripheral blood


title: 15_REP11

description:
Library name: Sample 38
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP11


title: m6A, AD High 1, IP

description:
Library name: A18-027
RNA methylation m6A-IP


title: genomic DNA from maternal peripheral blood [0733-V2]


title: 15_REP10

description:
Library name: Sample 37
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP10


title: Tau5, input, AD Int 4

description:
Library name: A20-001 Input
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0733-V1]


title: Tau5, input, AD Int 3

description:
Library name: A20-022 Input
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0735-V5]


title: 15_REP8

description:
Library name: Sample 35
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP8


title: Tau5, input, AD Int 2

description:
Library name: A15-011 Input
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0735-V3]

value: Sampled during 26-28 weeks of gestation


title: Tau5, input, AD Int 1

description:
Library name: A17-006 Input
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0735-V2]


title: 15_REP6

description:
Library name: Sample 33
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP6

value: liver


title: Tau5, input, AD High 4

description:
Library name: A21-007 Input
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0735-V1]


title: 15_REP5

description:
Library name: Sample 32
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP5

value: WT


title: Tau5, input, AD High 3

description:
Library name: A19-039 Input
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0345-V5]


title: 15_REP4

description:
Library name: Sample 31
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP4


title: Tau5, input, AD High 2

description:
Library name: A19-026 Input
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0345-V3]


title: Tau5, input, AD High 1

description:
Library name: A17-013 Input
Tau5-eCLIP


title: 15_REP3

description:
Library name: Sample 30
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP3


title: genomic DNA from maternal peripheral blood [0345-V2]


title: 15_REP2

description:
Library name: Sample 29
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP2


title: Tau5, eCLIP, AD Int 4

description:
Library name: A20-001 IP
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0345-V1]


title: 1.5_REP13

description:
Library name: Sample 27
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP13

value: 1.5 mg/kg DINP


title: Tau5, eCLIP, AD Int 2

description:
Library name: A15-011 IP
Tau5-eCLIP


title: RKO_TQ_TREAMENT REP 3

type: RNA

city: Sosnowiec

first: Celina

last: Kruszniewska-Rajs

address: Jednosci 8

department: Molecular Biology

country: Poland

institute: Medical University of Silesia

description: Gene expression data from cells treated withTQ

hyb_protocol: 10 ul fragmented and labeled cRNA and Hybridization, Wash, and Stain Kit were used to prepare the Hybridization Cocktail. Microarrays were incubated with rotation at 60 rpm for 16 hours at 45°C.

scan_protocol: Hybridization, Wash, and Stain Kit and Fluidics Station 450 were used to wash and stain the probe arrays. Hybridized arrays were scanned using the GeneChip™ Scanner 3000 System

data_processing: september 2024, Expression Console, rma

label: biotin

label_protocol: The expression profiles were analyzed using the GeneChip™ Human Genome U133A 2.0 Array following the manufacturer’s instructions. Biotin-labeled complementary RNA (cRNA) was used  for hybridization.

growth_protocol: The human colorectal adenocarcinoma cell line RKO (ATCC® CRL-2577) was cultured in Eagle’s Minimum Essential Medium (Sigma-Aldrich, Merck, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (Euroclone SpA, Pero, Italy) and gentamicin (50 µg/L; Sigma-Aldrich, Merck, St. Louis, MO, USA). Cells were maintained at 37 °C in a humidified atmosphere containing 5% CO₂

extract_protocol: Cells were used for global gene expression profiling. Total RNA was isolated using the TRIzol reagent according to the manufacturer’s protocol. RNA integrity was assessed by agarose gel electrophoresis and spectrophotometric analysis.

treatment_protocol: Cells were grown in standard tissue culture flasks, and experiments were performed using cultures within six passages to ensure phenotypic stability and reproducibility. Cells were plated in six-well culture plates at a density of 3 × 10⁵ cells per well and incubated for 48 h to allow proper attachment. Following the stabilization period, cells were treated with thymoquinone, 5-fluorouracil, or their combination. Thymoquinone  was applied at a final concentration of 20 µM, while 5-fluorouracil  was used at 10 µg/mL (approximately 76.8 µM. In the combined treatment group, both compounds were administered simultaneously at the indicated concentrations These concentrations were selected based on preliminary cytotoxicity testing and previously reported studies to enable reliable evaluation of dose-dependent effects.

value: RKO


title: 1.5_REP12

description:
Library name: Sample 26
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP12


title: RKO_TQ_TREAMENT REP 2

source_name: The human colorectal adenocarcinoma cell line RKO (ATCC® CRL-2577)


title: Tau5, eCLIP, AD Int 1

description:
Library name: A17-006 IP
Tau5-eCLIP


title: 1.5_REP11

description:
Library name: Sample 25
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP11


title: Tau5, eCLIP, AD High 4

description:
Library name: A21-007 IP
Tau5-eCLIP


title: RKO_TQ_TREAMENT REP 1


title: 1.5_REP10

description:
Library name: Sample 24
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP10


title: Tau5, eCLIP, AD High 3

description:
Library name: A19-039 IP
Tau5-eCLIP


title: RKO_MIX_TREATMENT REP 3

description: Gene expression data from cells treated with 5-FU and TQ


title: 15_REP1

description:
Library name: Sample 28
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP1


title: Tau5, eCLIP, AD Int 3

description:
Library name: A20-022 IP
Tau5-eCLIP


title: 1.5_REP9

description:
Library name: Sample 23
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP9


title: Tau5, eCLIP, AD High 2

description:
Library name: A19-026 IP
Tau5-eCLIP


title: RKO_MIX_TREATMENT REP 2


title: 1.5_REP8

description:
Library name: Sample 22
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP8


title: RKO_MIX_TREATMENT REP 1


title: Tau5, eCLIP, AD High 1

description:
Library name: A17-013 IP
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [1131-V5]

value: Pregnant


title: genomic DNA from maternal peripheral blood [1131-V3]


title: 150_REP7

description:
Library name: Sample 47
column name in AllSamples_Countsmatrix_TPM.csv: 150_REP7

value: 150 mg/kg DINP


title: 1.5_REP7

description:
Library name: Sample 21
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP7


title: PBMCs from patient 7 and 8 with Mock and EV treatment, scRNAseq_pool4

city: New Orleans

first: Tony

last: Hu

state: LA

address: 333 S Liberty St

department: Biochemistry and Molecular Biology

institute: Tulane University

data_processing:
Cell Ranger Version 7.0.1 (10x Genomics) was used to process raw sequencing data. In addition, R (Version 4.3.1) based package Seurat suite version 5.0.1 was used for further quality control and downstream analysis. Filtering was performed to remove multiplets and broken cells, and uninteresting sources of variation were regressed out. Batch effect was corrected using “rPCA” from Seurat. High variable genes were determined by iterative selection based on the dispersion versus average expression of the gene.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
PBMCs analyzed in flow cytometry and gene expression experiments were isolated from mixed anticoagulated blood of 3 healthy volunteers by adding 10 volumes of 1× red blood cell (RBC) lysis buffer (8.02 g l-1 NH4Cl, 0.84 g l-1 NaHCO3, 0.37 g l-1 EDTA), incubate for 10 – 15 min at room temperature on a shaker at 90 rpm. Stop the reaction by adding 20 – 30 volumes of 1× PBS. PBMCs were pelleted at 400 g for 5 min at 4 °C, washed with 1× PBS, and resuspended in RPMI-1640 with 10% heat-inactivated FBS and 100 U ml-1 penicillin and streptomycin for culture or in 90% FBS and 10% DMSO for long-term storage in liquid nitrogen.
The fixed cells were next subjected to 4-multiplexed probe hybridization, single-cell gel beads in the emulsion (GEM) generation and barcoding, GEM recovery and pre-amplification, fixed RNA-Gene expression library construction and finally sequencing using Chromium fixed RNA profiling reagent kits for multiplexed samples (10x Genomics, PN-1000415, PN-1000420, PN-1000421) and Chromium next GEM chip Q single cell kit (10x Genomics, PN-1000422) according to the manufacturer’s protocol.

treatment_protocol: EVs (30 μg, protein content) were added into 1 ml of 1 × 106 cells ml-1 PBMC cells, and co-incubated for 48 h.

value: PBMC

value: Mock,EV


title: m6A, AD High 1, Input

description:
Library name: A18-027 Input
RNA methylation m6A-IP


title: RKO_5FU TREATMENT REP 3

description: Gene expression data from cells treated with 5-FU


title: 1.5_REP6

description:
Library name: Sample 20
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP6


title: PBMCs from patient 3 and 4 with Mock and EV treatment, scRNAseq_pool2


title: PBMCs from patient 5 and 6 with Mock and EV treatment, scRNAseq_pool3


title: 1.5_REP5

description:
Library name: Sample 19
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP5


title: RKO_5FU TREATMENT REP 2


title: genomic DNA from maternal peripheral blood [0952-V3]

value: Preterm


title: 1.5_REP4

description:
Library name: Sample 18
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP4


title: RKO_5FU TREATMENT REP 1


title: PBMCs from patient 1 and 2 with Mock and EV treatment, scRNAseq_pool1


title: RKO_CONTROL CELLS REP 3

description: Gene expression data from untreated cells.


title: genomic DNA from maternal peripheral blood [0952-V1]

value: Sampled during 11-14 weeks of gestation


title: m6A, AD High 4, IP

description:
Library name: A21-007
RNA methylation m6A-IP


title: 1.5_REP3

description:
Library name: Sample 17
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP3


title: SUM159PT, ZSWIM8 KD, AGO2 miR-eCLIP, replicate 2

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

description:
chimeric_peak_info_SUM159.xlsx
SUM_ZSWIM8_KD.ago2_reproducible_peaks.bed
SUM_ZSWIM8_KD.mir_targets_reproducible_clusters.bed

data_processing:
*library strategy: miR-eCLIP
After sequencing, samples were processed with Eclipsebio's proprietary analysis pipeline (v1). UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2).
Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the genome (UCSC version GRCh38/hg38) using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1).
AGO2 eCLIP peaks were identified within eCLIP samples using the peak caller CLIPper (v2.0.1). For each peak, IP versus input fold enrichments and p-values were calculated. miRNAs from miRBase (v22.1) were "reverse mapped" to any reads that did not map to repetitive elements or the genome using bowtie (v1.2.3). The miRNA portion of each read was then trimmed, and the remainder of the read was mapped to the genome using STAR (v2.7.7a). PCR duplicates were resolved using umi_tools (v1.1.1), and miRNA target clusters were identified using CLIPper (v2.0.1).
Each cluster was annotated with the names of miRNAs responsible for that target. Peaks were annotated using transcript information from GENCODE release 41 (GRCh38.p13) with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron).
We used DESeq2 to confidently identify statistically significant differences between sample groups (ZSWIM8 vs Ctrl)
Assembly: GRCh38
Supplementary files format and content: ago2_clusters.bed: Input normalized file of AGO2 eCLIP clusters; mir_targets_clusters.bed: Locations of miRNA target read clusters called using the CLIPper algorithm; reproducible_peaks.bed: AGO2 eCLIP peaks or miR target clusters found to be reproducible and significant in all replicates
Supplementary files format and content: chimeric_peak_info_SUM159.xlsx: excel file containing the coordinates of each chimeric peak, and which gene and miRNA is associated with the peak. The average columns list the average, normalized chimeric read counts in each sample group. The associated fold change (ZSWIM8 vs Ctrl) and -log10-transformed significance was calculated with DESeq2

growth_protocol: Cells were treated infected with lentivirus expressing the sgRNAs and then treated with 1 ug/mL doxycycline, to activate the dCas9-KRAB transgene, for 10 days

extract_protocol:
Cell pellets were then lysed with 1 mL of eCLIP lysis mix and sonicated (QSonica Q800R2) for 5 minutes, 30 seconds on / 30 seconds off with an energy setting of 75% amplitude, followed by digestion with RNase-I (Ambion).
The standard eCLIP protocol [PMID 27018577] was modified to enable chimeric ligation of miRNA and mRNA according to bioRxiv preprint by Manakov et al, 2022 [10.1101/2022.02.13.480296].

treatment_protocol: While plated, approximately 20 x 106 cells were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation, pelleted, snap frozen on ice dry and stored until use at -80°C.

value: breast cancer cell line

tag: source gender

value: female

tag: eclip antibody

value: sc-53521, Santa Cruz Biotechnology

value: ZSWIM8 knock down


title: 1.5_REP2

description:
Library name: Sample 16
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP2


title: SUM159PT, ZSWIM8 KD, AGO2 miR-eCLIP, replicate 1


title: RKO_CONTROL CELLS REP 2


title: Day5_Het1A cells_Bile acid_3 (biol rep 3)

city: LEEDS

first: SAFOURA

last: ZAHED MOHAJERANI

state: -- Please select --

address: 7.10, T. C. Miall Building

department: LIRMM

country: United Kingdom

institute: UNIVERSITY OF LEEDS

description: Library name: D5_Het_BA_3

data_processing:
Raw sequencing reads were quality filtered to generate clean reads. Reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.0.5). Gene-level counts were generated using featureCounts. Differential gene expression analysis was performed using DESeq2 with thresholds of FDR < 0.05 and |log2 fold change| ≥ 1. KEGG pathway enrichment analysis was conducted using the clusterProfiler R package, and gene set enrichment analysis (GSEA) was performed using the Broad Institute GSEA software.
Assembly: GRCh38 (human reference genome)
Supplementary files format and content: Tab-delimited text files (.txt or .tsv) containing gene-level expression quantification generated from RNA-seq data. Clean paired-end (150 bp) reads were aligned to the GRCh38 reference genome using HISAT2 (v2.0.5), and gene counts were quantified using featureCounts. Processed files contain gene identifiers (Ensembl gene IDs and/or gene symbols) and corresponding raw read counts for each sample. Differential gene expression analysis was performed using DESeq2 (FDR < 0.05, |log2FC| ≥ 1). Additional processed outputs include normalized expression matrices and differential expression results containing log2 fold change, p-values, and adjusted p-values (FDR).

growth_protocol: Het1A human oesophageal epithelial cells (ATCC) were cultured in Keratinocyte Serum-Free Medium (KSFM; Gibco) supplemented with 10% fetal bovine serum (FBS), bovine pituitary extract (50 mg/mL), and epidermal growth factor (EGF; 5 μg/mL). Cells were seeded at 0.3 × 10^6 cells per well in 6-well plates and serum-starved in 1% FBS-containing medium for 48 h before treatment and throughout the experiment.

extract_protocol:
Total RNA was extracted from Het1A cells 24 h after the fifth bile acid exposure according to the manufacturer's instructions. RNA quality and integrity were assessed prior to library preparation.
RNA library preparation, quality control, and sequencing were performed by Novogene. Libraries were prepared from total RNA and sequenced on an Illumina platform using paired-end 150 bp reads.

treatment_protocol: Cells were exposed to acidified KSFM (pH 4.0) containing 100 μM mixed bile acids (glycocholic acid, taurocholic acid, glycodeoxycholic acid, glycochenodeoxycholic acid, and deoxycholic acid) for 10 min daily for 5 consecutive days. Control cells received 0.1% DMSO vehicle. Fresh culture medium was added after each exposure cycle. Cells were harvested 24 h after the final treatment.

value: Oesophageal epithelial cells

value: Bile acid


title: 1.5_REP1

description:
Library name: Sample 15
column name in AllSamples_Countsmatrix_TPM.csv: 1.5_REP1


title: RKO_CONTROL CELLS REP 1


title: SUM159PT, control cells, AGO2 miR-eCLIP, replicate 2

description:
chimeric_peak_info_SUM159.xlsx
SUM_CTRL.ago2_reproducible_peaks.bed
SUM_CTRL.mir_targets_reproducible_clusters.bed

value: untreated


title: Day5_Het1A cells_Bile acid_2 (biol rep 2)

description: Library name: D5_Het_BA_2


title: CONTROL_REP14

description:
Library name: Sample 14
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP14

value: liver

value: Control


title: SUM159PT, control cells, AGO2 miR-eCLIP, replicate 1


title: Day5_Het1A cells_Bile acid_1 (biol rep 1)

description: Library name: D5_Het_BA_1


title: SUM159PT, ZSWIM8 KD, input, replicate 2


title: Day5_Het1A cells_Control_3 (biol rep 3)

description: Library name: D5_Het_C_3

value: control


title: CONTROL_REP13

description:
Library name: Sample 13
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP13

value: WT


title: CONTROL_REP12

description:
Library name: Sample 12
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP12


title: Day5_Het1A cells_Control_2 (biol rep 2)

description: Library name: D5_Het_C_2


title: SUM159PT, ZSWIM8 KD, input, replicate 1


title: CONTROL_REP11

description:
Library name: Sample 11
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP11


title: SUM159PT, control cells, input, replicate 2


title: 15_REP9

description:
Library name: Sample 36
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP9

value: 15 mg/kg DINP


title: CONTROL_REP10

description:
Library name: Sample 10
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP10


title: SUM159PT, control cells, input, replicate 1


title: Day5_Het1A cells_Control_1 (biol rep 1)

description: Library name: D5_Het_C_1


title: HSPA6-NC3

city: Beijing

first: Huayuan

last: Liu

state: Beijing

address: New Student Apartment Building, No. 17, South Panjiayuan, Chaoyang District, Beijing

institute: Chinese Academy of Medical Sciences Cancer Hospital

description: Library name: sample 7

data_processing:
Gene Set Enrichment Analysis  Gene Set Enrichment Analysis (GSEA) is a computational approach to  determine if a pre-defined Gene Set can show a significant consistent  difference between two biological states. The genes were ranked  according to the degree of differential expression in the two samples,  and then the predefined Gene Set were tested to see if they were  enriched at the top or bottom of the list. Gene set enrichment analysis  can include subtle expression changes. We use the local version of the  GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO,  KEGG, Reactome, DO, DisGeNET data set were used for GSEA  independently
Assembly: GRh38
Supplementary files format and content: Tab-delimited table contains information on RNA modification sites identified in each sample, RNA counts, and standardized values.

source_name: CD4+T cells

extract_protocol:
RNAquantification andqualification  ①RNAdegradation and contamination was monitored on 1% agarose gels.  ② RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA) .  ③RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for Transcriptome sequencing  Atotal amount of 1 µg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached  magnetic beads. Fragmentation was carried out using divalent cations under elevated  temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand  cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments of  preferentially 250~300 bp in length, the library fragments were purified with AMPure  XP system (Beckman Coulter, Beverly, USA). Then 3 µlUSER Enzyme (NEB, USA)  was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5  min at 95 °Cbefore PCR. Then PCR was performed with Phusion High-Fidelity DNA  polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products  were purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system

value: CD4+T cells


title: CONTROL_REP9

description:
Library name: Sample 9
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP9


title: DEH2 under drought condition replicate3

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Library name: DEH2_DR_3
RNA-seq of DEH2 promoter driven TaTOR transgenic plants under drought condition replicate 3

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped toIWGSC Version 2.1 genome assembly reference genome using STAR.
Reads quantification was performed by Salmon.
Normalized counts were obtained from R tximport and DESeq2 package.
Assembly: IWGSC Version 2.1 genome assembly reference genome
Supplementary files format and content: Matrix table files include normalized counts for each sample

organism: Triticum aestivum

source_name: Leaf

growth_protocol: Spring wheat (T. aestivum) line Fielder regarded as wild-type was used in genetic transformation for generation of TOR expression lines UBQ/TOR, DREM/TOR and DEH2/TOR. Depending on the experiment, plants were grown either in soil or hydroponic solution. Uniform seeds of different wheat lines were surface sterilized with 20% bleach containing 0.1% Tween 20 (v/v) for 10 min, rinsed 4 times with deionized H2O and soaked in deionized water overnight at 4℃, seeds were then germinated in petri dish with wet filter paper. After 7 days, uniform seedlings were selected and transferred to soil or hydroponic solution. All the plants were grown in a growth chamber with light intensity of 300μmol photons m-2 s-1 and a relative humidity of 60%, the photoperiod cycle and temperature were set as 24 ℃, 16-h-light /18 ℃, 8-h-dark.

extract_protocol:
RNA was extracted from 0.1 g of each sample using a Qiagen RNeasy Mini Kit, and checked for quality using a Thermo Scientific NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer.
RNA-seq libraries were prepared using the Illumina TruSeq UD V1.5 Kit. Libraries were prepared by using RNA according to manufacturer's instruction and then loaded on an Illumina NovaSeq 6000 platform for pair-end sequencing with 150 cycles.

treatment_protocol: For the drought tolerance assessment, wheat lines were initially grown under well-watered condition (80% field capacity) until they reached 4-week-old. Subsequently, water was withheld for a period of 12 days to induce drought stress, after which the plants were re-watered, the plant survival rates were assessed 7 days later.

value: Leaf

value: Drought treated


title: CONTROL_REP8

description:
Library name: Sample 8
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP8


title: HSPA6-NC1

description: Library name: sample 5


title: DEH2 under drought condition replicate2

description:
Library name: DEH2_DR_2
RNA-seq of DEH2 promoter driven TaTOR transgenic plants under drought condition replicate 2


title: HSPA6-NC2

description: Library name: sample 6


title: CONTROL_REP7

description:
Library name: Sample 7
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP7


title: DEH2 under drought condition replicate1

description:
Library name: DEH2_DR_1
RNA-seq of DEH2 promoter driven TaTOR transgenic plants under drought condition replicate 1


title: 15_REP7

description:
Library name: Sample 34
column name in AllSamples_Countsmatrix_TPM.csv: 15_REP7


title: HSPA6-OE3-L3

description: Library name: sample 4


title: genomic DNA from maternal peripheral blood [3138-V5]

city: Kalyani

first: Arindam

last: Maitra

address: PO: NSS

institute: National institute of Biomedical Genomics

data_processing: GenomeStudio software (Illumina) version 2011.1.

source_name: peripheral blood

extract_protocol: Genomic DNA was extracted and purified from peripheral blood samples using QIAamp blood midi kit (Qiagen) according to manufacturer’s protocol.

value: Female

value: Peripheral blood

value: Pregnant

tag: time point

value: Sampled at delivery

tag: delivery

value: Term


title: CONTROL_REP6

description:
Library name: Sample 6
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP6

tag: tissue


title: DREM under drought condition replicate3

description:
Library name: DREM_DR_3
RNA-seq of DREM promoter driven TaTOR transgenic plants under drought condition replicate 3

value: DREM


title: HSPA6-OE3-L2

description: Library name: sample 3


title: DREM under drought condition replicate2

description:
Library name: DREM_DR_2
RNA-seq of DREM promoter driven TaTOR transgenic plants under drought condition replicate 2


title: CONTROL_REP5

description:
Library name: Sample 5
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP5


title: HSPA6-OE2

description: Library name: sample 2


title: CONTROL_REP4

description:
Library name: Sample 4
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP4


title: DREM under drought condition replicate1

description:
Library name: DREM_DR_1
RNA-seq of DREM promoter driven TaTOR transgenic plants under drought condition replicate 1


title: UBQ under drought condition replicate3

description:
Library name: UBQ_DR_3
RNA-seq of UBQ promoter driven TaTOR transgenic plants under drought condition replicate 3

value: UBQ


title: HSPA6-OE1

description: Library name: sample 1


title: Western diet, subcutaneous white adipose, Sphk2 deleted repicate 3

city: Richmond

first: Christopher

last: Green

state: Virginia

address: 1101 E. Marshall St.

institute: Virginia Commonwealth University

description: Library name: RB36

data_processing:
Fastq files were subsequently generated with Illumina BaseSpace. Raw fastq files were checked for quality using FastQC and collated using MultiQC.
Adapters were trimmed using CutAdapt and reads were aligned using STAR (Aligner) version 2.7.9a to the mouse GRCm39/mm39 mouse primary assembly genome (https://ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/) using default parameters
Raw counts were generated using the FeatureCounts tool from the SourceForge Subread package and subsequently counted genes using the ensembl gtf file for Mus musculus, GRCm39 assembly, version release 108. Raw counts were then analysed using the EdgeR package.
Assembly: mm39vM30
Supplementary files format and content: comma separated text file includes raw counts for each Sample

source_name: subcutaneous white adipose

extract_protocol:
RNA was extracted from equal weights of frozen tissue using TRIzol (#15596026, Fisher). 1ug of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were constructed from poly(A) isolated RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490S/L, New England BioLabs) and enriched with a SMARTer Apollo Library Prep System (#640078, Takara). The library was prepared using a dUTP-based stranded NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7760S, New England BioLabs), indexed and amplified with 8 PCR cycles. Uniquely barcoded libraries were then analyzed and sequenced with the paired end read 2x61 base pair setting.

treatment_protocol: Mice were fed chow diet or Western diet for 18 weeks.

value: subcutaneous white adipose

value: Sphk2 deleted


title: CONTROL_REP2

description:
Library name: Sample 2
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP2

value: liver


title: UBQ under drought condition replicate2

description:
Library name: UBQ_DR_2
RNA-seq of UBQ promoter driven TaTOR transgenic plants under drought condition replicate 2


title: Western diet, subcutaneous white adipose, Sphk2 deleted repicate 2

description: Library name: RB35


title: CONTROL_REP1

description:
Library name: Sample 1
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP1

value: Control


title: UBQ under drought condition replicate1

description:
Library name: UBQ_DR_1
RNA-seq of UBQ promoter driven TaTOR transgenic plants under drought condition replicate 1


title: WT under drought condition replicate3

description:
Library name: WT_DR_3
RNA-seq of WT under drought condition replicate 3


title: Western diet, subcutaneous white adipose, wild-type repicate 3

description: Library name: RB33

value: wild-type


title: WT under drought condition replicate2

description:
Library name: WT_DR_2
RNA-seq of WT under drought condition replicate 2

value: WT


title: Western diet, subcutaneous white adipose, wild-type repicate 2

description: Library name: RB32


title: INPUT_Female_E13.5,rep2

city: Guangzhou

first: Zhenyi

last: Huang

state: GuangDong

address: ShaTaiNan Street 1023-1063,Baiyun

department: Development

institute: Southern Medical University

description:
Library name: INPUT_Female_E13.5,rep2
targeted DNA fragments

data_processing:
For CUT&Tag, the adaptor sequence were removed using bbduk (v 38.18) and low-quality reads were trimmed by trimmomatic (v 0.39), with the length cut-off 35 bp.
The clean reads were aligned to GRCm38 genome (Ensembl version) using bowtie2 (v 2.3.5.1) with the options (--very-sensitive --end-to-end). Then, low quality mapping reads were removed using samtools with the option (-q 35). The duplicated sequences were removed using picard (v 2.23.0) and biological replicates were merged.
MACS2 (v 2.2.6) was used to call narrow peaks with the options (-g mm -f BAMPE -B --call-summits).
Bigwig files were generated using genomeCoverageBed from bedtools (v 2.29.2) and bedGraphToBigWig (v 2.8).
Assembly: mm10
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

source_name: Female fetal ovaries

growth_protocol: Mice were housed under specific pathogen-free (SPF) conditions on a standard 12 h light/12 h dark cycle with free access to food and water. The ambient temperature was maintained at 20–25°C with 40%–70% relative humidity.

extract_protocol:
BVSC⁺ germ cells were purified from E13.5 ovaries and immobilized on ConA beads. Beads were incubated with rabbit anti-GATA2 antibody (1:100; Abclonal, A0677) followed by anti-rabbit secondary antibody (1:100; Abcam, ab6702) After washing, pA-Tn5 transposomes were applied, and activation was performed with Mg²⁺ for 1 h at 37 °C. Reactions were stopped with 0.5 M EDTA, 10% SDS and 20 mg/ml Proteinase K. DNA was extracted by phenol-chloroform and used for library preparation.
Library was quantified using the Equalbit dsDNA HS Assay Kit (Vazyme, EQ111-01) according to the manufacturer’s instructions.

treatment_protocol: Female C57BL/6J mice in natural estrus were mated with male BVSC mice, and the day on which a vaginal plug was detected was designated as embryonic day 0.5 (E0.5).

value: Female fetal ovaries

value: BVSC (Blimp1-mVenus and Stella-ECFP) transgenic mice

tag: cell type

value: BVSC+ germ cells

value: BVSC

value: Trypsin digestion

tag: cut&tag antibody

value: Replicate 2


title: CONTROL_REP3

description:
Library name: Sample 3
column name in AllSamples_Countsmatrix_TPM.csv: CONTROL_REP3

tag: treatment


title: INPUT_Female_E13.5,rep1

description:
Library name: INPUT_Female_E13.5,rep1
targeted DNA fragments

tag: genotype

value: Replicate 1


title: WT under drought condition replicate1

description:
Library name: WT_DR_1
RNA-seq of WT under drought condition replicate 1

value: Leaf

value: Drought treated


title: Western diet, subcutaneous white adipose, Sphk2 deleted repicate 1

description: Library name: RB34


title: GATA2_Abclnal_Female_E13.5,rep2

description:
Library name: GATA2_Abclnal_Female_E13.5,rep2
targeted DNA fragments

value: anti-GATA2 antibody (1:100; Abclonal, A0677)


title: Western diet, subcutaneous white adipose, wild-type repicate 1

description: Library name: RB31


title: GATA2_Abclnal_Female_E13.5,rep1

description:
Library name: GATA2_Abclnal_Female_E13.5,rep1
targeted DNA fragments


title: DEH2 under well-watered condition replicate3

description:
Library name: DEH2_CK_3
RNA-seq of DEH2 promoter driven TaTOR transgenic plants under well-watered condition replicate 3

value: Well watered


title: Western diet, gonadal white adipose, Sphk2 deleted repicate 3

description: Library name: RB30

source_name: gonadal white adipose

value: gonadal white adipose


title: 7F2, eCLIP, Input, AD Int 1

description:
Library name: A17-006 Input
7F2 eCLIP

value: Hippocampus

value: ApoE 3/3


title: cKO_E14.5_Female,rep2

description:
Library name: cKO_E14.5_Female,rep2
Accessible DNA

data_processing:
For ATAC-seq, the adaptor sequence were removed using bbduk (v 38.18) and low-quality reads were trimmed by trimmomatic (v 0.39), with the length cut-off 35 bp.
The clean reads were aligned to GRCm38 genome (Ensembl version) using bowtie2 (v 2.3.5.1) with the options (--very-sensitive --end-to-end). Then, low quality mapping reads were removed using samtools with the option (-q 35). The duplicated sequences were removed using picard (v 2.23.0) and biological replicates were merged.
MACS2 (v 2.2.6) was used to call narrow peaks with the options (-g mm -f BAMPE -B --call-summits).
Bigwig files were generated using genomeCoverageBed from bedtools (v 2.29.2) (scale factor = 20 million / <each sample’s total unique reads>) and bedGraphToBigWig (v 2.8).
Assembly: mm10
Supplementary files format and content: bigWig,narrowPeak

extract_protocol:
Germ cells were enriched using anti-SSEA1 MicroBeads (Miltenyibiotec, 130-094-530). Approximately 10,000 cells were resuspended in lysis buffer and lysed on ice to release nuclei.
Libraries were constructed using the High-Sensitivity Open Chromatin Profile Kit 2.0 (Novoprotein, N248) according to the manufacturer’s instructions.

treatment_protocol: Gata2flox/+ Prdm1-Cre males were crossed with Gata2flox/flox females. Female embryos were collected at E14.5 from pregnant mice and genotyped.Ovaries from Gata2WT and Gata2cKO embryos were dissociated using 0.05% Trypsin at 37 °C, and the reaction was quenched with DMEM containing 10% FBS and 1% SP. The cell suspension was filtered through 40 μm strainers

tag: strain

value: Ovarian cells

tag: Sex

value: female

tag: time


title: DEH2 under well-watered condition replicate2

description:
Library name: DEH2_CK_2
RNA-seq of DEH2 promoter driven TaTOR transgenic plants under well-watered condition replicate 2


title: Western diet, gonadal white adipose, Sphk2 deleted repicate 2

description: Library name: RB29

value: Sphk2 deleted


title: WT_E14.5_Female,rep2

description:
Library name: WT_E14.5_Female,rep2
Accessible DNA

value: Female fetal ovaries


title: cKO_E14.5_Female,rep1

description:
Library name: cKO_E14.5_Female,rep1
Accessible DNA


title: Western diet, gonadal white adipose, wild-type repicate 3

description: Library name: RB27

value: wild-type


title: WT_E14.5_Female,rep1

description:
Library name: WT_E14.5_Female,rep1
Accessible DNA


title: DEH2 under well-watered condition replicate1

description:
Library name: DEH2_CK_1
RNA-seq of DEH2 promoter driven TaTOR transgenic plants under well-watered condition replicate 1


title: Western diet, gonadal white adipose, Sphk2 deleted repicate 1

description: Library name: RB28


title: DREM under well-watered condition replicate3

description:
Library name: DREM_CK_3
RNA-seq of DREM promoter driven TaTOR transgenic plants under well-watered condition replicate 3

value: DREM


title: DREM under well-watered condition replicate2

description:
Library name: DREM_CK_2
RNA-seq of DREM promoter driven TaTOR transgenic plants under well-watered condition replicate 2


title: Western diet, gonadal white adipose, wild-type repicate 2

description: Library name: RB26


title: E15.5 cortex, 12DIV, WT ACM, rep4

city: Syracuse

first: Jessica

middle: L.

last: MacDonald

state: NY

address: 107 College Place

department: Biology

institute: Syracuse University

description:
Library name: Sample 12
Column Name in "ACM_Raw_Counts": WT.ACM.5

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36
Trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featurecounts from the Subread package v.1.5.2.
Sequence reads underwent batch correction R using RUVseq and differentially expressed genes were calculated using edgeR
Assembly: mm10
Supplementary files format and content: .csv file includes mapped raw counts
Supplementary files format and content: .xlsx files include fold change comparisons between treatments

source_name: Neocortex

growth_protocol: E15.5 primary cortical cultures were maintained in neurobasal media supplemented with N2, B27, Glutamax and containing PenStrep in a humidified chamber at 37C with 5% C02

extract_protocol:
Neurons were harvested in TRIzol at 12DIV and total RNA extracted with RNeasy Mini kit (Qiagen)
RNA libraries were prepared by Azenta Life Sciences using the NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol:
Cultures were treated with AraC at 3DIV to deplete astrocytes
Astrocyte Cultured Media (ACM) from either Mecp2 +/y or Mecp2 -/y or NonConditioned Media (NCM) was added to cultures at 6DIV

value: Neocortex

value: E15.5 primary cortical culture

tag: in vitro_stage

value: WT

value: WT ACM


title: Western diet, gonadal white adipose, wild-type repicate 1

description: Library name: RB25


title: DREM under well-watered condition replicate1

description:
Library name: DREM_CK_1
RNA-seq of DREM promoter driven TaTOR transgenic plants under well-watered condition replicate 1

value: Leaf


title: E15.5 cortex, 12DIV, WT ACM, rep3

description:
Library name: Sample 11
Column Name in "ACM_Raw_Counts": WT.ACM.4

tag: cell line


title: UBQ under well-watered condition replicate3

description:
Library name: UBQ_CK_3
RNA-seq of UBQ promoter driven TaTOR transgenic plants under well-watered condition replicate 3

value: UBQ


title: Western diet, brown adipose, Sphk2 deleted repicate 3

description: Library name: RB24

source_name: brown adipose

value: brown adipose


title: E15.5 cortex, 12DIV, WT ACM, rep2

description:
Library name: Sample 10
Column Name in "ACM_Raw_Counts": WT.ACM.3


title: UBQ under well-watered condition replicate2

description:
Library name: UBQ_CK_2
RNA-seq of UBQ promoter driven TaTOR transgenic plants under well-watered condition replicate 2

value: Well watered


title: Western diet, brown adipose, Sphk2 deleted repicate 2

description: Library name: RB23


title: Western diet, brown adipose, Sphk2 deleted repicate 1

description: Library name: RB22


title: UBQ under well-watered condition replicate1

description:
Library name: UBQ_CK_1
RNA-seq of UBQ promoter driven TaTOR transgenic plants under well-watered condition replicate 1


title: E15.5 cortex, 12DIV, WT ACM, rep1

description:
Library name: Sample 9
Column Name in "ACM_Raw_Counts": WT.ACM.1