title: AMB_200609_9mo_5E_6E_1_P4-3-F15-K5


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-I6

status: Public on Dec 18 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain

tag: age

value: 9 months

tag: brain region

value: CP

tag: gender

value: M


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-E18


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-L6


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-I5


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-G5


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-D6


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-K6


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-H5


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-H17


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-G6


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-I18


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-D17


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-F6


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-G17


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-G18


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-F5


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-D18


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-C5


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-E6


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-F18


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-C17


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-E17


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-B6


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-B18


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-D5


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-P4


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-C6


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-O15


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-O3


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-O16


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-O4


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-C18


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-B5


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-N3


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-B17


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-A18


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-A17


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-M4


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-A6


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-L16


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-M3


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-P3


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-K4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-P16


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-A5


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-J4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-N4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-L4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-K15


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title: AMB_200609_9mo_5E_6E_1_P4-2-J15-J15


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title: AMB_200609_9mo_5E_6E_1_P4-2-J15-G15


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-I4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-I16


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-I15


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-F3


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-E16


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title: AMB_200609_9mo_5E_6E_1_P4-2-J15-E4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-C4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-E15


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-E3


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-D4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-F15


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-H16


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-H3


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-D16


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-D15


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-D3


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-C3


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-F4


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-C16


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title: AMB_200609_9mo_5E_6E_1_P4-2-J15-B16


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title: AMB_200609_9mo_5E_6E_1_P4-1-A15-P13


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-A16


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-P2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-O2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-P14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-O14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-O13


title: AMB_200609_9mo_5E_6E_1_P4-2-J15-A15


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-O1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-L14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-M14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-L2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-M13


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title: AMB_200609_9mo_5E_6E_1_P4-1-A15-M2


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title: AMB_200609_9mo_5E_6E_1_P4-1-A15-M1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-L13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-K13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-L1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-K2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-N13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-J14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-J2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-K1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-J13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-J1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-I2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-I14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-K14


title: AMB_200609_9mo_5E_6E_1_P4-3-F15-E5


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-I1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-H2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-I13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-H14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-H1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-G2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-G1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-F2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-G13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-F1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-E13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-E2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-E14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-F14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-G14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-F13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-D14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-D13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-E1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-C14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-C2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-H13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-D2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-B14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-B2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-C1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-C13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-B13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-D1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-A14


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-B1


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-A13


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-A2


title: AMB_200609_9mo_5E_6E_1_P4-1-A15-A1


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title: AMB_200609_9mo_5E_6E_1_P3-6-L16-O12


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title: AMB_200609_9mo_5E_6E_1_P3-6-L16-K23


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title: AMB_200609_9mo_5E_6E_1_P3-6-L16-H24


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-H11


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title: AMB_200609_9mo_5E_6E_1_P3-6-L16-M24


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-G11


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-F11


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-F23


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-H12


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-F24


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-E24


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-F12


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-E12


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-E11


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-D24


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-D11


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-D23


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-C23


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-D12


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-C24


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-C12


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-B23


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-E23


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-B12


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-B11


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-B24


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-A12


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-A23


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-A24


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-O9


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-P21


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-C11


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-P9


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-O21


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-O10


title: AMB_200609_9mo_5E_6E_1_P3-6-L16-A11


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-O22


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-N22


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-N9


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-L9


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-N10


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-M22


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-M21


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-P22


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-L22


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-M10


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-N21


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-L21


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-K9


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-K21


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-M9


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-K10


title: AMB_200609_9mo_5E_6E_1_P3-5-A16-K22


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title: AMB_200609_9mo_5E_6E_1_P1-1-O3-C13


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-C14


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-B2


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-B14


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-B13


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-A2


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-A13


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-B1


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-A14


title: shTCF4, TCF4, HUVEC, IP-3

status: Public on Dec 03 2025

city: Boston

first: Kaifu

last: Chen

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Library name: si-TCF4 IP-3

data_processing:
The raw reads of CUT&RUN data were preprocessed by the CHIPs pipeline[https://doi.org/10.12688/f1000research.52878.1], which includes read trimming, read mapping to the mouse genome (hg38), read level quality control, and peak level quality control. DANPOS2 dpeak function was used to call peaks using BAM files of uniquely mapped reads
The BigWig files were generated by wigToBigWig based on wig files from DANPOS2 software
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

organism: Homo sapiens

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs were cultured in Endothelial Cell Medium (ECM; ScienCell) supplemented with 5% fetal bovine serum, 1% endothelial cell growth supplement (ECGS), and 1% penicillin/streptomycin. Cells were maintained at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Cells were harvested and subjected to CUT&RUN according to the Cell Signaling Technology (CST) protocol. Briefly, cells were immobilized on concanavalin A–coated magnetic beads, permeabilized, and incubated with specific antibody overnight at 4°C. Samples were then incubated with pA-MNase and activated by calcium addition. Digested chromatin was released and DNA purified using spin columns.
DNA was used to prepare sequencing libraries following a standard protocol for low-input samples. DNA fragments were end-repaired, A-tailed, and ligated to sequencing adapters. Libraries were amplified by PCR, size-selected (typically 150–400 bp), and quality checked using the Agilent High Sensitivity DNA Kit.

tag: cell type

value: Human Umbilical Vein Endothelial Cells

tag: chip antibody

tag: treatment


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-A1


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-E14


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-C1


title: TCF4, HUVEC, IP-3

description: Library name: TCF4 IP-3


title: TCF4, HUVEC, IP-2

description: Library name: TCF4 IP-2


title: TCF4, HUVEC, IP-1

description: Library name: TCF4 IP-1


title: shTCF4, TCF4, HUVEC, IP-1

description: Library name: si-TCF4 IP-1


title: smallRNA_siArmi_Rep3

status: Public on Nov 17 2025

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
Library name: smallRNA_siArmi_Rep3
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells

library_source: other

data_processing:
Illumina reads were processed by removing 3′ adapters with cutadapt {Martin, 2011 #646}, trimming 4 random nucleotides from each end and filtering for minimal length (>18 nt) and sequence complexity (bbduk, entropy = 0.35, entropy window = 18, k = 4) . Reads were first aligned to Drosophila rRNA precursor sequences and the mitochondrial genome using bowtie {Langmead, 2009 #656}. Remaining unmapped reads were mapped to the OSC_r1.01 genome using bowtie allowing for 1 mismatch. Alignments were separated into uniquely and all‑mapping fractions. For visualization, HOMER was used to generate tag directories (makeTagDirectory … -format bed -keepAll -single -fragLength given) and UCSC‑compatible tracks (makeUCSCfile … -fsize 1e20 -strand +/- -fragLength given -noadj -normLength 0) were generated per strand. Counts were normalized to 1M miRNAs and final BigWig tracks were created with bedGraphToBigWig (Kent Utilities), producing strand‑specific (sense and antisense) coverage profiles for genome browser display. For transposon histogram analysis, piRNA reads longer than 23 nucleotides were aligned to transposable element consensus sequences using bowtie (--best --strata -f -v 2 -a), permitting multiple mappings. Alignments were subsequently filtered to retain reads that mapped either uniquely or at most twice to a single transposon consensus, to account for long terminal repeat (LTR) redundancy. Reads mapping twice were assigned a fractional count of 0.5 to each location.
Assembly: OSC_r1.01.fa.gz
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: TE-histogram data for sense and antisense

molecule: other

organism: Drosophila melanogaster

source_name: OSC

growth_protocol: Ovarian somatic cells (OSCs) were maintained at 27 °C in a humidified incubator with 2.5% CO₂, as previously described (Niki, Yamaguchi et al. 2006, Saito, Inagaki et al. 2009) Cells were cultured in M3 basal medium supplemented with 10% fetal bovine serum (FBS), insulin, glutathione, and fly extract.

extract_protocol:
sRNAseq libraries were prepared by first purifying Argonaute–sRNA complexes with TraPR resin columns. OSCs were harvested using trypsin, washed 2x with PBS and stored at -70°C after snap freezing cell-pellets in liquid nitrogen. OSCs were lysed by adding 330 µL of TraPR lysis buffer. OSC lysates were clarified, normalized to equal protein amounts (depending on the experiment 70-120 µg total protein) after Bradford measurements, applied to TraPR columns, and Argonaute-bound RNAs were eluted, followed by phenol–chloroform extraction and precipitation.
To minimize ligation bias and facilitate library multiplexing, adaptors were designed with random nucleotides placed adjacent to the ligating end. The 3′ adaptor carried six random bases at its 5′ terminus and contained sample barcodes (X) for multiplexing (5rApp/NNNNNNXXXXX–Adaptor–/3ddC). The 5′ adaptor was an RNA oligo bearing four random nucleotides at its 3′ terminus (…UCUNNNN). After 3′ adaptor ligation with T4 RNA ligase 2, truncated KQ, samples were pooled as necessary, spiked with fluorescently labeled and ligation-blocked oligos as size controls, and gel-purified on a 12.5% polyacrylamide–urea gel. Small RNAs were isolated using the Zymo ZR small RNA PAGE Recovery kit and subjected to 5′ adaptor ligation with T4 RNA ligase 1. Following cleanup with Zymo RCC5 columns, reverse transcription was performed. Libraries were PCR-amplified with KAPA HiFi polymerase and dual-index barcoded primers. Amplification was monitored in real time with EvaGreen, and reactions were stopped upon reaching 3,500–4,000 RFU to prevent overamplification. Final libraries were size-selected on low-melt agarose gels, gel-purified (Zymo), quantified with Qubit, multiplexed and sequenced (SE50, Illumina NovaSeq6000).

tag: cell line

value: OSC

value: ovarian somatic cells

tag: genotype

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: smallRNA_siArmi_Rep2

description:
Library name: smallRNA_siArmi_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells


title: smallRNA_siLuc_Rep3

description:
Library name: smallRNA_siLuc_Rep3
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells


title: smallRNA_siLuc_Rep1

description:
Library name: smallRNA_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells


title: smallRNA_flamenco-silencing_Gal4_Rep2

description:
Library name: smallRNA_flamenco-silencing_Gal4_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs isolated from FACS sorted OSC cells

value: wildtype besides a UAS-tethering construct integrated upstream of the flamenco promoter

value: Transfected with tethering plasmids encoding  Gal4. . Transfections were repeated after 48h to sustain tethering. At 6 and 7 days post transfection, cells were harvested by FACS, gated on reduced GFP reporter signal from the co-silenced selection cassette. For Gal4‑only controls, no FACS enrichment was applied.


title: smallRNA_siLuc_Rep2

description:
Library name: smallRNA_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells


title: smallRNA_siArmi_Rep1

description:
Library name: smallRNA_siArmi_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells


title: shTCF4, TCF4, HUVEC, IP-2

description: Library name: si-TCF4 IP-2


title: AMB_200609_9mo_5E_6E_1_P1-1-O3-D14


description:
Library name: smallRNA_flamenco-silencing_2x_Panx-IDR_6days
Sequencing of TraPR isolated Argonaute bound small RNAs isolated from FACS sorted OSC cells

value: Transfected with tethering plasmids encoding  Gal4 fused to the Panoramix IDR silencing domain . Transfections were repeated after 48h to sustain tethering. At 6 and 7 days post transfection, cells were harvested by FACS, gated on reduced GFP reporter signal from the co-silenced selection cassette. For Gal4‑only controls, no FACS enrichment was applied.


title: Cardiac, Heart Failure, DCM, s13

status: Public on Nov 08 2025

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Gasthuisberg

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

description:
Library name: GC108597
10x genomics

library_source: transcriptomic single cell

data_processing:
All processing steps were performed using Cell Ranger softwar (v6.01)
Assembly: hg38
Supplementary files format and content: TSV,rds, and matrix files

molecule: nuclear RNA

source_name: Cardiac

extract_protocol:
70-100 mg of Snap frozen mid-myocardium tissues samples were mechanically homogenized gently using Miltenyi gentleMACS™ Tissue Dissociator with gentleMACS M tubes using the protocol “protein_01_01” in 5 ml lysis buffer solution (5 mM CaCL2, 3mM MgAc, 2mM EDTA, 0.5mM EGTA, 10mM Tris-HCL in water supplemented with 2mg/ml Actinomycin D, 1:1000 protease inhibitor cocktail, and 40 U/µl RNase OUT), then incubated on ice for 15 min with extra 5 ml of the same solution supplemented with 0.1% NP-40. Lysate was then gently filtered through a 30 μm filter into 15 ml conical tube, followed by rinsing the filter once with 2 ml lysis buffer supplemented with 0.1% NP-40. Nuclei were then centrifuged at 1000g for 5 min at 4 °C. Nuclei pellet was then resuspended in 2 ml of sucrose buffer solution (1 M sucrose, 3mM MgAc, and 10 mM Tris-HCL supplemented with 2mg/ml Actinomycin D, 1:1000 protease inhibitor cocktail, 40 U/µl RNase OUT, and 2µl/ml WGA) and layed over another 2 ml sucrose solution in 5 ml canonical tube. Centrifugation was repeated according to the above parameters. Supernatant was then removed and nuclei were resuspended in 400 μl nuclei wash buffer (PBS with 40 U/µl RNase OUT, 15 µl/ml UltraPure BSA,and 2µl/ml WGA) and centrifuged at 650g for 6 min at 4 °C. Another washing step repeated similar to the previous step with centrifugation speed of 500g, and a third wash was performed with 1 µl/ml DAPI and incubated for 10 min in 1.5 ml Eppendorf tube before centrifuging again at 500g speed. The pellet was then resuspended in 300 µl of PBS and filtered in FACS tubes with 35 µl strained. Nuclei were sorted based on size and DAPI positive staining into 40 µl PBS + 15 µl/ml UltraPure BSA using 100-µM nozzle, and collected in 1.5 ml tubes.
Single sorted nuclei were counted by LUNA automated counter in duplicates, then nuclei were centrifuged again and were gently resuspended to a target concentration of 1,000 nuclei/µl and loaded on the Chromium Controller (10X Genomics) with a targeted cell or nuclei recovery of 6,000–10,000 per reaction. 3′ gene expression libraries were prepared according to the manufacturer’s instructions of the v3 Chromium Single Cell Reagent Kits (10X Genomics). Quality control of cDNA and final libraries was done using Bioanalyzer High Sensitivity DNA Analysis (Agilent) and libraries were sequenced using NovaSeq 6000 (Illumina) at Genomics Core facility at KU Leuven targeting 80,000 read pairs nucleus. Nuclei were aligned to the human GRCh38-3.0.0 transcriptome with “Include-introns= TRUE” using the CellRanger- 6.0.1 software (10X Genomics) according to the 10X Genomics’ instructions.

tag: tissue

value: Cardiac

tag: Sex

value: F

tag: type

value: tissue

tag: batch


title: Cardiac, non-Failure , Donor, s15

description:
Library name: GC108599
10x genomics

value: M/F


title: Cardiac, Heart Failure, ICM-scar, s18

description:
Library name: GC123828
10x genomics


title: Cardiac, Heart Failure, ICM-scar, s9

description:
Library name: GC108593
10x genomics


title: Cardiac, Heart Failure, DCM, s14

description:
Library name: GC108598
10x genomics


title: Cardiac, Heart Failure, ICM, s11

description:
Library name: GC108595
10x genomics


title: Cardiac, Heart Failure, ICM-scar, s19

description:
Library name: GC123829
10x genomics


title: Cardiac, Heart Failure, DCM, s12

description:
Library name: GC108596
10x genomics


description:
Library name: smallRNA_flamenco-silencing_2x_Panx-IDR_7days
Sequencing of TraPR isolated Argonaute bound small RNAs isolated from FACS sorted OSC cells


title: Cardiac, Heart Failure, DCM, s20

description:
Library name: GC123830
10x genomics


title: Cardiac, Heart Failure, DCM, s8

description:
Library name: GC1003523
10x genomics


title: smallRNA_flamenco-silencing_Gal4_Rep1

description:
Library name: smallRNA_flamenco-silencing_Gal4_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs isolated from FACS sorted OSC cells


title: Cardiac, Heart Failure, ICM, s10

description:
Library name: GC108594
10x genomics


title: Cardiac, Heart Failure, ICM, s5

description:
Library name: GC1003520
10x genomics


title: IRBP_rep3

status: Public on Nov 01 2025

city: Milwaukee

first: Bo

last: Wang

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

description:
Library name: Sample 9
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression

library_source: transcriptomic

data_processing:
Bulk RNAseq: The aligment were done by STAR v2.7.11b, and transcripts count were done by FeatureCounts under Subread v2.0.8  package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: cell line

growth_protocol: BMSCs purchased from Lonza Bioscience were cultured in Mesenchymal Stem Cell Growth Medium (MSCGM, Lonza) under standard conditions (37°C, 5% CO₂, and 95% humidity), with media changes every three days.

extract_protocol:
After 7 days of culture, total RNA was extracted from all groups (n=3 per group) using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. RNA concentration was measured using the Nanodrop ND-1000, and quality was assessed via capillary electrophoresis (Agilent Technologies). RNA sequencing (RNA-Seq) was performed by Novogene Corporation Inc. Libraries were prepared using the KAPA Stranded RNA-Seq Library Prep Kit (Illumina), and sequencing was conducted on the NovaSeq 6000 platform (Illumina) to generate paired-end reads.
Total RNA from all groups were sent to Novogene Corporation Inc. (Sacramento, CA) for library preparation and sequencing. Only samples with an RNA integrity number (RIN) ≥ 7 were considered for cDNA library preparation. cDNA libraries were generated using TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), which included an rRNA suppression step.

treatment_protocol: After 24 hours of seeding, BMSCs in the IR and IRBP groups were exposed to a single 10 Gy dose of X-ray irradiation using a Precision CellRad X-ray source. After IR exposure, cells in the IR group were maintained in standard MSCGM medium. In the IR&BP group, BPs were resuspended in MSCGM medium by sonication (final concentration: 20 μg/mL, based on BP dry weight) and added to the cells 4 hours post-IR. The BP-containing medium was maintained for 24 hours before being replaced with fresh MSCGM without BPs.

value: cell line

value: LONZA PT-2501

value: Human Bone marrow Mesenchymal Stem Cells

value: exposed to a single 10 Gy dose of X-ray irradiation, 4 hours post-IR, bone nanoparticles were resuspended in MSCGM medium by sonication (final concentration:20 μg/mL, based on BP dry weight) and added to the cells and maintained for 24 hours before being replaced with fresh MSCGM without BPs.


title: Cardiac, Heart Failure, ICM, s1

description:
Library name: GC1003516
10x genomics


title: IRBP_rep2

description:
Library name: Sample 8
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: Cardiac, Heart Failure, ICM-scar, s2

description:
Library name: GC1003517
10x genomics


title: AMB_200609_9mo_5E_6E_1_P1-2-B16-E16

value: 9 months

value: CP

value: M


title: Cardiac, Heart Failure, DCM, s6

description:
Library name: GC1003521
10x genomics


title: IRBP_rep1

description:
Library name: Sample 7
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: IR_rep2

description:
Library name: Sample 5
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression

value: exposed to a single 10 Gy dose of X-ray irradiation


title: Cardiac, Heart Failure, ICM, s3

description:
Library name: GC1003518
10x genomics


title: IR_rep1

description:
Library name: Sample 4
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: Cardiac, non-Failure , Donor, s16

description:
Library name: GC108600
10x genomics


title: Con_rep3

description:
Library name: Sample 3
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression

value: No treatment


title: IR_rep3

description:
Library name: Sample 6
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: Con_rep2

description:
Library name: Sample 2
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: Cardiac, Heart Failure, ICM-scar, s4

description:
Library name: GC1003519
10x genomics


title: Con_rep1

description:
Library name: Sample 1
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: MuSC CUT&Tag control pSMAD1/5/9 biol rep 2

status: Public on Sep 17 2025

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
Library name: MuSC CUTTag vehicle pSMAD1/5/9 biol rep 2
HCl_pSMAD1_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-pSMAD1/5/9 ab, biol. rep2

data_processing:
Paired-end sequencing reads were subsampled to equal total depth per condition and sample to match read counts between replicates. Reads were then aligned to the mouse reference genome (GRCm39) using Bowtie2 version 2.5.4 with the following parameters: --very-sensitive --no-mixed --no-discordant. Aligned reads were subsequently filtered using samtools version 1.21 with options -b -h -f 2 -F 256 -F 2048 -F 1024 -q 30 to retain only properly paired reads (mapping quality ≥30) aligned to autosomes and sex chromosomes, while excluding reads mapped to ENCODE blacklisted regions. The filtered BAM files were converted to BED format using BEDTools version 2.31.1.
Peak calling was performed independently for each biological replicate using JAMM version 1.0.7.6 with the -r window parameter.
To establish consensus peak sets, per-replicate peaks were subjected to Irreproducible Discovery Rate (IDR) analysis using the IDR package version 2.0.3 with parameters --rank signal.value --idr-threshold 0.05. IDR was run on filtered peaks output from JAMM for transcription factors and on all peaks output for the H3K27ac modification. Only peaks meeting the IDR threshold of 0.05 were retained, generating consensus peak lists for each experimental condition.
Assembly: GENCODE M32 (GRCm39)
Supplementary files format and content: *_subsampled.bw => BigWig files to display the data in a genome browser
Supplementary files format and content: *.narrowPeak.bed => consensus peaks per condition and sample that passed the IDR threshold
Library strategy: CUT&Tag

source_name: skeletal muscle

growth_protocol: Mononucleated cells were isolated from forelimb, hindlimb, dorsal, and breast muscles of female 9-week-old mice and cultured in DMEM (Gibco, 41966029), 15% FBS (Gibco), 2.5 ng/mL basic FGF (Sigma, F3133), 10 ng/mL leukemia inhibitory factor (Sigma, ESG1106), and 1% Pen/Strep (Gibco) in Matrigel® (Corning, 356231)-coated dishes at 3% O2 and 5% CO2 at 37 °C for one day. After one day, the cells were detached, FACSed for GFP (PAX7-GFP reporter) to enrich for muscle stem cells, and cultured for another two days as before in medium additionally containing 1x B27 without vitamin A (Gibco, 12587010). In order to eliminate the effect of BMPs in the culture medium (e.g. from serum supplements), cells were then cultured in serum-free medium containing soluble BMP receptor (recombinant mouse BMPR-1A-Fc Chimera, R&D Systems, 437-MR) at a concentration of 200 ng/mL for 6 h.

extract_protocol:
Cells were washed, trypsinized, centrifuged, and resuspended in serum-free growth medium before fixing them in 0.1% formaldehyde for 2 minutes and subsequent quenching with glycine at twice the molar concentration of formaldehyde for 5 minutes. The cells were centrifuged at 4 °C for 4 minutes at 1,300 x g and the pellet was resuspended in CUT&Tag wash buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl (Sigma-Aldrich, 71386), 500 µM Spermidine (Sigma-Aldrich, S0266), 1x Complete protease inhibitor EDTA-free (Roche, 5056489001)) prior to slowly freezing the cells with 10% DMSO.
CUT&Tag was performed on 100,000 fixed frozen cells per condition as described by Kaya-Okur et al. 2019 and 2020. Briefly, cells were bound to concanavalin A-coated magnetic beads (Bangs Laboratories, 86057) and incubated with primary antibody overnight, followed by incubation with secondary antibody and later the CUTANA pAG-Tn5 enzyme (EpiCypher, 15-1017). Subsequently, the cleavage was induced and then the DNA was released, purified, and barcoded by amplification with barcoded primers for 13 cycles. Lastly, the libraries were purified and pooled.

treatment_protocol: Cells were stimulated with 100 ng/mL BMP4 or BMP6 or with vehicle (4 mM HCl containing 0.1% BSA) for 1 h.

value: skeletal muscle

value: muscle stem cells

value: vehicle

tag: antibody

value: pSMAD1/5/9 (Cell Signalling, #13820)

value: biol rep 2


title: MuSC RNA-seq II BMP6 biol rep 2

description:
Library name: MuSC RNA-seq 2 BMP6 biol rep 2
TPM_joined.tab/.xlsx: TPM_BMP_TX_REP2
FPKM_joined.tab/.xlsx: FPKM_BMP_TX_REP2
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, biol. rep2

data_processing:
FASTQ files were aligned to the human genome (GENCODE GRCm39) using STAR v2.7.11a with the following settings: --runThreadN 20 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 50 --outFilterMatchNmin 150 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 36. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into two tables: output.tpm.csv and output.fpkm.csv.
Assembly: GENCODE M32 (GRCm39)
Supplementary files format and content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary files format and content: FPKM_joined.tab, FPKM_joined.xlsx, TPM_joined.tab, TPM_joined.xlsx => fused tables with all the samples of the experiment in TAB and XLSX format provided as TPM and FPKM values; transcript_count.csv => fused table with fragment counts mapped to transcript; gene_count.csv => fused table with fragment counts mapped to genes

molecule: polyA RNA

extract_protocol:
Cells were washed, trypsinized, centrifuged, and frozen at -80 °C for later RNA extraction. RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel, 740902) and residual DNA was removed using RNase-Free DNase from the NucleoSpin Mini RNA kit (Macherey-Nagel, 740955). RNA quantity and quality were assessed using a NanoDrop® 2000c spectrophotometer (Thermo Fisher Scientific)
Unstranded libraries were prepared by following the Smart-seq 2 protocol until the PCR amplification step and continued with the Nextera XT DNA library prep kit (Illumina, FC-131-1096) using the MGI universal and index primers for PCR amplification.

treatment_protocol: Cells were stimulated with 100 ng/mL BMP6 or with vehicle (4 mM HCl containing 0.1% BSA) for 1 h.


title: MuSC CUT&Tag BMP6 H3K27ac biol rep 2

description:
Library name: MuSC CUTTag BMP6 H3K27ac biol rep 2
BMP6_H3K27ac_on_all.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-H3K27ac ab, biol. rep2

value: H3K27ac (Abcam, ab4729)


title: MuSC CUT&Tag control SMAD4 biol rep 1

description:
Library name: MuSC CUTTag vehicle SMAD4 biol rep 1
HCl_SMAD4_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-SMAD4 ab, biol. rep1

value: SMAD4 (Cell Signalling, #38454)

value: biol rep 1


title: MuSC RNA-seq II BMP6 biol rep 1

description:
Library name: MuSC RNA-seq 2 BMP6 biol rep 1
TPM_joined.tab/.xlsx: TPM_BMP_TX_REP1
FPKM_joined.tab/.xlsx: FPKM_BMP_TX_REP1
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, biol. rep1


title: MuSC RNA-seq II control biol rep 1

description:
Library name: MuSC RNA-seq 2 vehicle biol rep 1
TPM_joined.tab/.xlsx: TPM_HCL_TX_REP1
FPKM_joined.tab/.xlsx: FPKM_HCL_TX_REP1
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, biol. rep1


title: MuSC CUT&Tag control negative control biol rep 1

description:
Library name: MuSC CUTTag vehicle negative control biol rep 1
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag without primary ab, biol. rep1


title: MuSC CUT&Tag control H3K27ac biol rep 2

description:
Library name: MuSC CUTTag vehicle H3K27ac biol rep 2
HCl_H3K27ac_on_all.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-H3K27ac ab, biol. rep2


title: MuSC CUT&Tag control SMAD4 biol rep 2

description:
Library name: MuSC CUTTag vehicle SMAD4 biol rep 2
HCl_SMAD4_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-SMAD4 ab, biol. rep2


title: MuSC CUT&Tag BMP6 pSMAD1/5/9 biol rep 2

description:
Library name: MuSC CUTTag BMP6 pSMAD1/5/9 biol rep 2
BMP6_pSMAD1_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-pSMAD1/5/9 ab, biol. rep2


title: MuSC CUT&Tag BMP6 SMAD4 biol rep 2

description:
Library name: MuSC CUTTag BMP6 SMAD4 biol rep 2
BMP6_SMAD4_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-SMAD4 ab, biol. rep2


title: MuSC CUT&Tag BMP6 SMAD4 biol rep 1

description:
Library name: MuSC CUTTag BMP6 SMAD4 biol rep 1
BMP6_SMAD4_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-SMAD4 ab, biol. rep1


title: MuSC CUT&Tag control pSMAD1/5/9 biol rep 1

description:
Library name: MuSC CUTTag vehicle pSMAD1/5/9 biol rep 1
HCl_pSMAD1_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-pSMAD1/5/9 ab, biol. rep1


title: MuSC CUT&Tag control H3K27ac biol rep 1

description:
Library name: MuSC CUTTag vehicle H3K27ac biol rep 1
HCl_H3K27ac_on_all.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-H3K27ac ab, biol. rep1


title: MuSC CUT&Tag BMP6 pSMAD1/5/9 biol rep 1

description:
Library name: MuSC CUTTag BMP6 pSMAD1/5/9 biol rep 1
BMP6_pSMAD1_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-pSMAD1/5/9 ab, biol. rep1


title: MuSC CUT&Tag BMP6 negative control biol rep 1

description:
Library name: MuSC CUTTag BMP6 negative control biol rep 1
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag without primary ab, biol. rep1


title: 48hpa-LY

status: Public on Sep 15 2025

first: Juan

middle: Daniel

last: Montenegro

state: Vienna

address: Djerassiplatz 1

department: Department of neurobiology and developmental biology

institute: University of Vienna

description: Library name: F10_2d_LY

data_processing:
Sequencing reads were mapped to the Nematostella vectensis genome (Zimmermann et al. 2023) using standard parameters of Cellranger v7.1.0 (Zheng et al. 2017). Filtered matrices were then used to proceed with analysis using Seurat v5 (Butler et al. 2018; Stuart et al. 2019). The libraries were filtered for cells with low read and feature counts and analyzed using our scripts (complete details at https://github.com/technau/Gast ruloids ).
Assembly: Nvec200 (https://simrbase.stowers.org/starletseaanemone)
Supplementary files format and content: Seurat object
Supplementary files format and content: RData: GO enrichment analysis of gene modules obtained from the original single cell object and using the package hdWGCNA.

organism: Nematostella vectensis

source_name: aggregates

extract_protocol:
Samples were washed with ice cold Calcium Magnesium Free (CMF) seawater briefly and the samples were allowed to settle. The CMF was then removed and they were resuspended in ACME (ACetic-MEthanol) prepared as described previously (Garcia-Castro et al. 2021) and tubes were left on the rocker for 20 min. The samples were then dissociated using a cut pipette tip every 5 min during the 20 min window and their dissociation status was checked until sufficient. Tubes were then spun at 400 rcf for 4 min at 4℃ and the supernatant was carefully removed without disturbing the loose cell pellet. The pellet was then resuspended with 1xPBS + 0.5% BSA + RNaseOUT (40U/ml) and DMSO was added to be 10% of the final volume. This cell mix was then stored at -80℃ until the day of  library preparation. On library preperation day, the tubes were left to thaw at RT and then spun again at 400 rcf for 4 min at 4℃ after which the cell pellet was resuspended in 1xPBS + 0.5% BSA + RNaseOUT (40U/ml) and the viability and concentration were then quantified using ViaStain™AOPI staining solution (Nexcelom) and the Cellometer X2.
Libraries for sequencing were prepared using the standard 10X pipeline for scRNAsequencing

value: aggregates

value: LY


title: 24hpa-run2

description: Library name: Nvagg24

value: wt


title: 48hpa-DMSO

description: Library name: F9_2d_DMSO

value: DMSO


title: MuSC CUT&Tag BMP6 H3K27ac biol rep 1

description:
Library name: MuSC CUTTag BMP6 H3K27ac biol rep 1
BMP6_H3K27ac_on_all.narrowPeak: includes high confidence peaks that agree between the replicates
Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-H3K27ac ab, biol. rep1


title: 48hpa-run2

description: Library name: Nvagg48


title: 48hpa-run1

description: Library name: D4_48hrAggSN


title: 24hpa-run1

description: Library name: 18_NvAgg24hr


title: MuSC RNA-seq II control biol rep 2

description:
Library name: MuSC RNA-seq 2 vehicle biol rep 2
TPM_joined.tab/.xlsx: TPM_HCL_TX_REP2
FPKM_joined.tab/.xlsx: FPKM_HCL_TX_REP2
Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, biol. rep2


title: 12hpa

description: Library name: 17_NvAgg12hr