title: pACYC184_Eco_DRT3_3b-intFLAG-1_ncRNAmut-C117G_rep1 biol rep 1

description: Library name: YW43_19_D


title: DMB006_control_rep1_batch2

status: Public on Jun 22 2026

type: SRA

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence, cleaned reads were mapped to hg38 (Gencode GRCh38.p12) using STAR
Assembly: hg38
Supplementary files format and content: Tab-separated files

molecule: total RNA

organism: Homo sapiens

extract_protocol:
For RNA-seq in Group 4 MB PDX, freshly isolated DMB006 cells from mouse brains were infected in triplicate with non-targeting control or KDM2B gRNA viruses at high MOI to ensure more than 90% of cells were infected. Cells were cultured for 7 days and then collected for RNA-seq. Infection efficiency was determined by flow cytometry analysis of GFP percentage on day 4. Editing efficiency was evaluated by targeted deep sequencing. For RNA-seq in D283, cells were infected in triplicate with non-targeting control or KDM2B gRNA viruses at high MOI to ensure more than 80% of cells were infected. Cells were cultured for 7 days. An aliquot of cells was collected on day 4 or day 7 for RNA-seq. Infection efficiency was determined by flow cytometry analysis of GFP percentage on day 4. Editing efficiency was evaluated by targeted deep sequencing.
RNA extraction was performed using RNeasy Plus kit (Qiagen) according to manufacturer’s instructions. RNA libraries for RNA-seq were prepared following manufacturer's protocols

tag: cell line

tag: cell type


title: pACYC184_Eco_DRT3_3b-intFLAG-1_ncRNAmut-G113C_rep2 biol rep 2

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

description: Library name: YW43_18_D

library_source: other

data_processing:
Raw reads were processed with Cutadapt (v5.0) to filter out adapter sequences, trim low-quality bases, and remove reads shorter than 15 bp. Cutadapt was run using a tiling approach across the 3′ adapter as previously described, with parameters -e 0.2, -O 10, -q 30, and -m 45 (error rate, minimum overlap, quality cutoff, and minimum length, respectively). Filtered reads were aligned with bwa-mem2 (v2.2.1) under default parameters to a composite reference comprising the E. coli MG1655 genome (NCBI: NC_000913.3), the relevant plasmid sequence, and either the λ-vir (NCBI: NC_001416.1) or T5 (NCBI: NC_005859.1) phage genome. Alignments were sorted and indexed using SAMtools (v1.17). Strand-specific coverage tracks were generated with bamCoverage (v3.5.6), normalized to sequencing depth based on the total number of reads passing trimming and length filtering. Reads that failed to align with bwa-mem2 were extracted using SAMtools fasta, and the fraction of unmapped reads was calculated using SAMtools flagstat. Genome build: E. coli MG1655 (NC_000913.3); λ-vir (NC_001416.1); T5 (NC_005859.1).
Assembly: ASM584v2
Supplementary files format and content: .fasta — Unmapped reads extracted from BAM alignments using SAMtools fasta. Each file contains all reads from a given sample that failed to align to the composite reference, used as input for downstream MEME motif enrichment analysis and motif counts per sample.

molecule: other

organism: Escherichia coli

extract_protocol:
cDIP elution was performed by removing the supernatant and resuspending beads with 80 µL of IP wash buffer containing 5 µg RNase A (Thermo Fisher Scientific). Inputs were resuspended with 70 µL of the same wash buffer. Both inputs and immunoprecipitation samples were incubated at 37 °C for 30 min. SDS was then added to a final concentration of 1%, along with 25 µg of proteinase K (Thermo Fisher Scientific). Supernatants containing eluted DNA were transferred to new tubes and DNA was isolated with the Monarch Spin PCR and DNA Cleanup kit (NEB), following the Oligonucleotide Cleanup protocol.
Eluted DNA samples were heated at 95 °C for 2 min and immediately placed on ice to denature DNA. Adapter ligation and conversion of ssDNA to dsDNA were performed using the xGen ssDNA & Low-Input DNA Library Prep Kit (IDT). Indexing PCR was performed using NEBNext Ultra II Q5 Master Mix (NEB). Libraries were sequenced on the Element AVITI system in single- or paired-end mode with 150 cycles per end.


title: in vivo Daxx KO microglia TAM 3dpi-2 [19781_S5]

city: Bonn

first: Paolo

last: Salomoni

address: Venusberg-Campus 1, Building 99

country: Germany

institute: DZNE

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19781_S5

data_processing:
Raw FASTQ files were trimmed by Trimgalore and aligned to genome mm10 by STAR. SAM files were filter by mapq>=10 and transformed to BAM by samtools. Gene count table was created by featureCounts.
Assembly: mm10
Supplementary files format and content: read counts from featureCounts

organism: Mus musculus

source_name: brain

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 5 ng of total RNA was used for contruction of sequencing libraries.
RNA library for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian following manufacturer's protocols.

tag: tissue

value: brain

value: microglia

tag: genotype

value: Cx3cr1CreERT,Daxx flox/flox

tag: treatment

value: Tamoxifen


title: pACYC184_Eco_DRT3_3b-intFLAG-1_ncRNAmut-G113C_rep1 biol rep 1

description: Library name: YW43_17_D


title: DMB006_gRNA10_rep3


title: in vivo Daxx KO microglia TAM 3dpi-1 [19780_S4]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19780_S4


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_rep2 biol rep 2

description: Library name: YW43_16_D


title: in vivo Daxx WT microglia TAM 3dpi-6 [19787_S11]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19787_S11

value: Cx3cr1CreERT,Daxx wt/wt


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_rep1 biol rep 1

description: Library name: YW43_15_D


title: DMB006_gRNA10_rep2


title: pACYC184_Eco_DRT3_3b-intFLAG-1_rep2 biol rep 2

description: Library name: YW43_14_D


title: in vivo Daxx WT microglia TAM 3dpi-5 [19786_S10]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19786_S10


title: DMB006_gRNA10_rep1


title: pACYC184_Eco_DRT3_3b-intFLAG-1_rep1 biol rep 1

description: Library name: YW43_13_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E262R_input_YW_rep2 biol rep 2

description: Library name: YW43_10i_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E262R_input_YW_rep1 biol rep 1

description: Library name: YW43_09i_D


title: in vivo Daxx WT microglia TAM 3dpi-4 [19785_S9]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19785_S9


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R170E_input_YW_rep1 biol rep 1

description: Library name: YW43_07i_D


title: DMB006_control_rep1


title: in vivo Daxx WT microglia TAM 3dpi-3 [19779_S3]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19779_S3


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E22A_R241A_input_YW_rep2 biol rep 2

description: Library name: YW43_06i_D


title: DMB006_control_rep2


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R170E_input_YW_rep2 biol rep 2

description: Library name: YW43_08i_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E22A_R241A_input_YW_rep1 biol rep 1

description: Library name: YW43_05i_D


title: in vivo Daxx WT microglia TAM 3dpi-2 [19778_S2]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19778_S2


title: D283_Day7_KDM2B_gRNA28_rep3

value: medulloblastoma cell line


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_input_YW_rep2 biol rep 2

description: Library name: YW43_04i_D


title: in vivo Daxx WT microglia TAM 3dpi-1 [19777_S1]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19777_S1


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_input_YW_rep1 biol rep 1

description: Library name: YW43_03i_D


title: D283_Day7_KDM2B_gRNA28_rep2


title: in vivo Daxx KO microglia TAM 1dpi-3 [24600]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24600


title: pACYC184_Eco_DRT3_3b-intFLAG-1_input_YW_rep2 biol rep 2

description: Library name: YW43_02i_D


title: D283_Day7_KDM2B_gRNA28_rep1


title: pACYC184_Eco_DRT3_3b-intFLAG-1_input_YW_rep1 biol rep 1

description: Library name: YW43_01i_D


title: in vivo Daxx KO microglia TAM 1dpi-2 [24599]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24599


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E262R_YW_rep1 biol rep 1

description: Library name: YW43_09_D


title: D283_Day7_KDM2B_gRNA10_rep3


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E262R_YW_rep2 biol rep 2

description: Library name: YW43_10_D


title: in vivo Daxx KO microglia TAM 1dpi-1 [24598]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24598


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R170E_YW_rep1 biol rep 1

description: Library name: YW43_07_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E22A_R241A_YW_rep1 biol rep 1

description: Library name: YW43_05_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E22A_R241A_YW_rep2 biol rep 2

description: Library name: YW43_06_D


title: D283_Day7_KDM2B_gRNA10_rep1


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_YW_rep2 biol rep 2

description: Library name: YW43_04_D


title: lib18_round2-R2

status: Public on Jun 23 2026

city: Hangzhou

first: Han

last: Guo

state: Zhejiang

address: Xiasha

department: Aptamer Selection Center

country: China

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

description:
Library name: lib18_round2-R2
This dataset contains sequencing data from aptamer selection against 24 individual protein targets.

data_processing:
Raw reads were quality-checked using FastQC. Adapter sequences and low-quality bases (Phred score < 20) were trimmed using Cutadapt. Reads shorter than 220 bp after trimming were discarded. Barcode and SELEX primer sequences were removed from the reads using custom scripts. Reads were demultiplexed based on round-specific barcodes. Clean reads were collapsed into unique sequences using fastx-collapser. The abundance of each unique aptamer sequence was counted across all target proteins. Read counts were normalized to reads per million (RPM) across samples.
FASTQ files named with the suffix round1-R5 contain sequencing data of aptamer libraries enriched against each target protein in round 5 of the preliminary screening process (round 1-R5). Each file corresponds to 24 protein targets derived from the same initial random library. We summed the read counts of each unique sequence across all sub-libraries and sorted the results in descending order. Unique sequences with prominent total read counts indicating significant enrichment were retained. The CSV files labeled raw_counts_round1-R5 document the read counts of these selected sequences in each individual sub-library.
FASTQ files named with round2-R2 contain sequencing data of aptamer libraries enriched against each target protein in round 2 of the secondary screening process (round 2-R2). Each file corresponds to 24 protein targets derived from the same top 3000 enriched library. Read counts of the original 3000 unique sequences across all sub-libraries were extracted and compiled into CSV files named raw_read_counts_round2-R2. Fewer than 3000 unique sequences were detected in each file. The missing sequences are likely false positives caused by matrix adsorption during the preliminary screening process, or result from limited sequencing throughput.
Total read counts of the 3000 unique sequences across 24 target-enriched libraries were normalized. For each unique sequence, we calculated the sum of read counts across 24 target libraries, and then computed the relative abundance ratio by dividing the read count of each library by the total read count. All results are presented in CSV files named relative_abundance_ratio_round2-R2. The relative abundance ratio reflect the binding capacity of each unique sequence to different target proteins and characterize sequence binding specificity.
Assembly: Not applicable.
Supplementary files format and content: All processed data are provided as CSV files. Files named with raw_count contain read counts of unique sequences in enriched libraries against each protein target. Files named with relative_abundance_ratio record the relative abundance ratios of corresponding read counts. Lib10, lib13, lib18 and lib25 represent four distinct random ssDNA libraries with different primer regions. Each library was used for aptamer selection against 24 protein targets. In these files, each row corresponds to one unique sequence, and each column represents one protein target. For round1-R5, since sample IDs in FASTQ files do not match protein names in CSV files, a supplementary file named round1-R5_fastq_SampleID_to_csv_Protein_Name_mapping is supplied to clarify the correspondence between sample IDs and protein names. Detailed data processing procedures are described in the Data Processing Steps section.

organism: synthetic construct

source_name: in vitro synthetic nucleic acid library; SELEX aptamer library, no native biological cell/tissue origin

growth_protocol: Not applicable. No biological cells or tissues were used in this study. All experoments were performed in vitro using synthetic oligonucleotide libraries and purified proteins.

extract_protocol:
Nucleotide sequences bound to target proteins were eluted using 100 μL of ddH2O by heating at 95 ℃ for 10 min.
Enriched ssDNA pools from each SELEX round were end-repaired, A-tailed, and ligated with sequencing adapters following standard Illumina library preparation protocols. Barcodes were incorporated for multiplexed sequencing. Libraries were amplified by limited-cycle PCR and purified to remove primer dimers and non-specific products before sequencing.

treatment_protocol: The preliminary screening procedure (round 1-R1 to round 1-R5) was conducted according to the classic magnetic bead-based SELEX process. For each target protein, an initial, artificially synthesized random ssDNA library, comprising approximately 10^15 molecules (1 OD), was employed. These ssDNA libraries were dissolved, denatured at 95 ℃ for 10 min, and cooled to 4 ℃ for 5 min to ensure optimal structural conformation. The prepared libraries were added into the histidine peptide-coupled plate for a 1 h counter selection process to eliminate the nonspecific binding. The supernatant was then transferred to the target protein-coupled plate and incubated for 1 h. To further reduce nonspecific binding through competitive interactions, BSA, HsDNA and histidine peptide were incorporated during the positive selection phase. The concentration of these agents was increased to augment selection pressure in subsequent rounds. Following this, unbound sequences present in the supernatant were discarded, and the plate was washed for four times with 200 μL of DPBS-T. Sequences bound to target proteins were eluted using 100 μL of ddH2O by heating at 95 ℃ for 10 min. The eluted ssDNA was then amplified and collected for the next round of selection. In the secondary screening procedure, the initial libraries comprised the corresponding 3000 sequences (top 3000 sequences). These top3000 sequences were derived from the NGS results of the round 1-R5, representing sequences that were significant enriched in the prior screening. Utilizing chip printing technology, the top 3000 sequences of the four libraries (a total of 12000 sequences) were synthesized in batches. Subsequently, emulsion PCR was performed using the corresponding primers to obtained uniformly amplified initial libraries for the secondary screening. The subsequent steps paralleled those of the preliminary screening.

value: lib18 ssDNA library, round 2 of the secondary screening process


title: in vivo Daxx WT microglia TAM 1dpi-2 [24596]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24596


title: D283_Day7_control_rep3


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_YW_rep1 biol rep 1

description: Library name: YW43_03_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_YW_rep2 biol rep 2

description: Library name: YW43_02_D


title: in vivo Daxx WT microglia TAM 1dpi-1 [24595]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24595


title: pACYC184_Eco_DRT3_3b-intFLAG-1_YW_rep1 biol rep 1

description: Library name: YW43_01_D


title: in vivo Daxx KO microglia TAM 0dpi-3 [24594]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24594


title: D283_Day7_control_rep2


title: Y666F_rep1_input biol rep 1

description: Library name: ST190_17i_D


title: 3b_mut_rep2_input biol rep 2

description: Library name: ST190_16i_D


title: in vivo Daxx KO microglia TAM 0dpi-2 [24593]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24593


title: 3b_mut_rep1_input biol rep 1

description: Library name: ST190_15i_D


title: D283_Day4_KDM2B_gRNA28_rep3


title: in vivo Daxx KO microglia TAM 0dpi-1 [24592]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24592


title: 3a_mut_rep2_input biol rep 2

description: Library name: ST190_14i_D


title: 3a_mut_rep1_input biol rep 1

description: Library name: ST190_13i_D


title: D283_Day4_KDM2B_gRNA28_rep2


title: 3a_3b_mut_rep2_lambda_input biol rep 2

description: Library name: ST190_12i_D


title: in vivo Daxx WT microglia TAM 0dpi-3 [24591]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24591


title: Y666F_rep2_input biol rep 2

description: Library name: ST190_18i_D


title: D283_Day4_KDM2B_gRNA28_rep1


title: 3a_3b_mut_rep1_lambda_input biol rep 1

description: Library name: ST190_11i_D


title: 3a_3b_mut_rep2_T5_input biol rep 2

description: Library name: ST190_10i_D


title: in vivo Daxx WT microglia TAM 0dpi-2 [24590]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24590


title: D283_Day4_KDM2B_gRNA10_rep3


title: 3a_3b_mut_rep2_uninfected_input biol rep 2

description: Library name: ST190_08i_D


title: 3a_3b_mut_rep1_uninfected_input biol rep 1

description: Library name: ST190_07i_D


title: D283_Day4_KDM2B_gRNA10_rep2


title: WT_rep2_lambda_input biol rep 2

description: Library name: ST190_06i_D


title: C10 tumor replicate 2

city: Bethesda

first: Jia

last: Nie

state: Maryland

address: Building 37, Room 3016

department: Center for Cancer Research

institute: National Cancer Institute

description: FFPE Visium CytAssist Spatial Gene Expression

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using spaceranger v2.0.1 (Bcl2fastq 2.20.0), and alignment was performed using spaceranger v2.0.1 (STAR 2.7.2a).
Assembly: mm10
Supplementary files format and content: .h5 files of raw/filtered gene-by-barcode matrces
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg:image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Library strategy: Spatial transcriptomics

source_name: tumor

extract_protocol:
C10 tumors on day 10 were dissected and were subjected to formalin-fixed and paraffin-embedded (FFPE) processing. Then 5 μm FFPE tissue sections were cut.
Spatial transcriptomics analysis was conducted using the Visium CytAssist Spatial Gene Expression Reagent Kits (10X Genomics) following the manufacturer's instructions (CG000520, CG000495)

value: tumor

value: PBS and Smarta


title: WT_rep1_lambda_input biol rep 1

description: Library name: ST190_05i_D


title: D283_Day4_KDM2B_gRNA10_rep1


title: WT_rep1_T5_input biol rep 1

description: Library name: ST190_03i_D


title: C10 tumor replicate 1


title: D283_Day4_control_rep3


title: WT_rep2_T5_input biol rep 2

description: Library name: ST190_04i_D


title: WT_rep2_uninfected_input biol rep 2

description: Library name: ST190_02i_D


title: Cortical neurons, shOpa1, shScrambled, Day 11, Rep5

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

description: SP flowcell PE50

library_source: genomic

data_processing:
fastq files were verified with multiQC.
Sequencing adaptors were trimmed and duplicates were removed.
ATAC peaks were called using MACS2.
Bigwig files were generated using bamCoverage for data visualization.
Assembly: mm10
Supplementary files format and content: Consensus peaks from all ATAC-seq samples, in BED format on the mm10 genome assembly. Peaks called with MACS2 and consensus peaks called with rmspc

molecule: genomic DNA

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

extract_protocol:
Cells were treated with DnaseI to eliminate DNA contamination. Tn5 transposomes were applied to lysed chromatin. Transposed chromatin was purified using Zymo DNA Clean & Concentrator-5 columns.
Transposed DNA libraries were prepared using NEBNext Ultra II Q5 Master Mix and Illumina-compatible unique 5′-i5 and 3′-i7 barcode sequences.

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

value: primary cell

value: cortical neurons

value: neuron differentiation


title: WT_rep1_uninfected_input biol rep 1

description: Library name: ST190_01i_D


title: D283_Day4_control_rep2


title: Cortical neurons, shOpa1, shScrambled, Day 11, Rep4

description: SP flowcell PE50


title: 3b_mut_rep2 biol rep 2

description: Library name: ST190_16_D


title: Cortical neurons, shOpa1, shScrambled, Day 11, Rep3

description: SP flowcell PE50


title: 3b_mut_rep1 biol rep 1

description: Library name: ST190_15_D


title: 3a_mut_rep2 biol rep 2

description: Library name: ST190_14_D


title: Cortical neurons, shOpa1, shScrambled, Day 11, Rep2

description: SP flowcell PE50


title: Whole testis, Bearded dragon, scRNAseq, Rep2

city: Cerdanyola del Vallès

first: Laia

last: Marín-Gual

address: Campus UAB

country: Spain

institute: Universitat Autònoma de Barcelona

description: Library name: Bearded_dragon_scRNAseq_Rep2

library_source: transcriptomic single cell

data_processing:
Cell Ranger (version 6.1.2) was used to map the single-cell RNAseq reads against the tammar wallaby (PRJNA1235426) and bearded dragon (PviZW2.1) genomes using default settings. Mapped data was subsequently analysed with the Seurat package (version 4.3).
Assembly: PRJNA1235426 (tammar wallaby), PviZW2.1 (bearded dragon)
Supplementary files format and content: Set of three-files containing genes, barcodes, and a matrix file of reads.

organism: Pogona vitticeps

source_name: Testis

extract_protocol:
Testicular disaggregation from tammar wallaby and bearded dragon were conducted as previously described (1). An aliquot of the single-cell solution was loaded into a ChromiumTM Single Cell Chip (10x Genomics®), aiming to recover between 5,000 and 6,000 cells.
Libraries were prepared following manufacturer’s instructions and sequenced on Illumina NovaSeq 6000 (50bp pair ends).

value: Testis

tag: Sex

value: Male


title: 3a_mut_rep1 biol rep 1

description: Library name: ST190_13_D


title: Whole testis, Bearded dragon, scRNAseq, Rep1

description: Library name: Bearded_dragon_scRNAseq_Rep1


title: 3a_3b_mut_rep2_lambda biol rep 2

description: Library name: ST190_12_D


title: Cortical neurons, shOpa1, shScrambled, Day 11, Rep1

description: SP flowcell PE50


title: 3a_3b_mut_rep1_lambda biol rep 1

description: Library name: ST190_11_D


title: D283_Day7_KDM2B_gRNA10_rep2


title: Round spermatids, Bearded dragon, HiC, rep2

description: Library name: RS_BeardedDragon_HiC_rep2

data_processing:
BBDuk (version 09/2019) was used for quality check and trimming. Basically, adapters and low-quality reads (i.e. reads with a minimum length of 35 bp and a minimum Phred quality score of 20) were removed. High-quality reads were then mapped against the tammar wallaby (PRJNA1235426) and bearded dragon (PviZW2.1) genomes using the GEM (version 3.6.1) mapper from TADbit (version 1.0.1).
Assembly: PRJNA1235426 (tammar wallaby), PviZW2.1 (bearded dragon)
Supplementary files format and content: GInteraction tables of Hi-C data at a 50 Kbp resolution, which include interaction values between all genomic bins genome-wide.

source_name: Round spermatids

extract_protocol:
In nuclei Hi-C was adapted from previously described protocols.  Briefly, germ cells were incubated in lysis buffer containing 10 mM Tris, 10 mM NaCl, 0.2% Igepal and 1xPIC for 20 minutes at 4ºC. Subsequently, germ cells were incubated with 0.5% SDS in 1xNEBuffer 2 for 10 minutes at 4ºC and the reaction was quenched by adding 10% Triton X-100 and incubating for 30 minutes at 37ºC. Germ cells were then centrifuged at 5,000 xg for 5 minutes at 4ºC and resuspended in 300 µl 1xNEBuffer 2 containing 400 U of MboI. Chromatin was digested overnight at 37ºC and assessed the following day by comparing a digested and a non-digested control. Germ cells were then incubated at 65ºC for 20 minutes to inactivate the restriction enzyme and the reparation mix (0.05mM dCTP, 0.05mM dTTP, 0.5mM dGTP, 0.05mM biotin-dATP, 50U Klenow in 1xNEBuffer 2) was directly added into the cell suspension. Chromatin was repaired and biotinylated for 90 minutes at 37ºC, and then the enzyme was heat-inactivated at 65ºC for 10 minutes. Prior to ligation, germ cells were centrifuged for 5 minutes at 5,000 xg at 4ºC, resuspended in ligation buffer (0.8% Triton X-100, 0.1 mg/ml BSA, 10,000 U T4 DNA ligase in 1xNEB T4 ligase buffer) and incubated overnight at 16ºC. Lastly, germ cells were incubated with RNAse A for 15 minutes at 37ºC, and then with proteinase K overnight at 65ºC to reverse the crosslink, followed by a DNA extraction with Phenol:Chloroform. DNA concentration was quantified by Qubit and quality was assessed by running a 0.8% agarose gel.
For library preparation, samples were sonicated into fragments of 300 – 500 bp. The biotinylated fragments were pulled down using Dynabeades MyOne Streptavidin T1 beads, which were pre-washed with 2xbinding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl) and incubated with sonicated fragments for 30 minutes in rotation. Beads were then separated on a magnetic rack and washed with 1xbinding Buffer. Ends repair, adaptor ligation and amplification were performed with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® according to manufacturer’s recommendations. For size selection, DNA fragments were incubated with AMPure beads in a 1:1 proportion for 10 minutes at room temperature. Beads were then washed twice with 70% ethanol and DNA was eluted with Tris buffer for 10 minutes at room temperature. DNA concentration was quantified by Qubit and fragment size was assessed by running a Bioanalyzer. Libraries were submitted for Illumina sequencing (paired-end 150bp each side on NovaSeq 6000).

value: Round spermatids


title: 3a_3b_mut_rep1_T5 biol rep 1

description: Library name: ST190_09_D


title: 3a_3b_mut_rep2_uninfected biol rep 2

description: Library name: ST190_08_D


title: 3a_3b_mut_rep1_uninfected biol rep 1

description: Library name: ST190_07_D


title: Primary spermatocytes, Bearded dragon, HiC, rep2

description: Library name: SpcI_BeardedDragon_HiC_rep2

source_name: Primary spermatocytes

value: Primary spermatocytes


title: WT_rep2_lambda biol rep 2

description: Library name: ST190_06_D


title: WT_rep1_lambda biol rep 1

description: Library name: ST190_05_D


title: Primary spermatocytes, Bearded dragon, HiC, rep1

description: Library name: SpcI_BeardedDragon_HiC_rep1


title: WT_rep2_T5 biol rep 2

description: Library name: ST190_04_D


title: Cortical neurons, shOpa1, shAtf4, Day 11, Rep2

description: SP flowcell PE50


title: WT_rep1_T5 biol rep 1

description: Library name: ST190_03_D


title: TH199

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: ABMRM

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

value: heart biopsy


title: Cortical neurons, shOpa1, shAtf4, Day 11, Rep1

description: SP flowcell PE50

value: brain


title: WT_rep2_uninfected biol rep 2

description: Library name: ST190_02_D


title: WT_rep1_uninfected biol rep 1

description: Library name: ST190_01_D


title: UK1_15h_1

city: Boston

first: Carol

middle: A

last: Kumamoto

state: MA

address: 150 Harrison Ave.

department: Department of Molecular Biology and Microbiology

institute: Tufts University

description:
Library name: Sample 3
10x Genomics

data_processing:
Initial data analysis including demultiplexing, barcode processing and aligning reads to the human genome was performed using Cell Ranger.
Assembly: human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Clostridioides difficile
Homo sapiens

source_name: Colonoid line CJ50

growth_protocol: Preparation of colonoid monolayers on transwells. Colonoid line CJ50 was derived from colonic biopsies obtained from a 67 year old Chinese female undergoing routine outpatient colonoscopy for colorectal cancer screening at Tufts Medical Center (IRB #11652, principal investigator: Jatin Roper). The cells were propagated in Matrigel (Corning 356231) as described previously [29]. Medium compo-sition was as described [22] except that L-WRN conditioned medium (L-WRN cells ATCC CRL- 3276 [30]) was used at 65% instead of L-WNT3A, R-Spondin and Noggin conditioned media, Primocin (InvivoGen ant-pm-1) was used instead of pen-strep and 5 uM Y27632 (Rho kinase inhibitor, Sigma Y0503) was added for the first 48 hrs of culturing. For preparation of monolayers on transwells, colonoid spheres were recovered from Matrigel, washed with PBS and digested with TrypLE Express (Gibco 12605-010) for 2.5 min at 37oC. After digestion, cells were diluted with 1 volume advanced DMEM (Invi-trogen 12634-028), 1% Glutamax (Gibco 35050-061), 20% FBS (Fisher 26140079) and filtered through a 40 um cell strainer. Cells were diluted with 0.4% Trypan blue, counted with a Corning CytoSmart counter and diluted to 2.5 x 106 cells/ml with warmed 65% LWRN medium containing Y27632. Matrigel was diluted with CMGF- to 33 or 66 ug protein/mL, 125 ul was applied to each 6.5mm diameter, 0.4 um pore, polycarbonate filter transwell (Costar 3413) and incubated at 37oC for 2 hours. Liquid was removed from the transwell, the basolateral compartment was filled with 0.5 ml 65% medium and 50 ul of medium was added to the apical compartment. Cells (2.5 x 105 cells per 6.5 mm diameter transwell) were added and the seeded transwells were incubated in a tissue culture incubator with 5% CO2 at 37oC. The next day, transwells were given fresh 65% L-WRN medium containing 5 uM Y27632 (Sigma Y0503), replacing the basolateral medium and adding 0.2 ml to the apical compartment. The next day, the medium was changed to 65% without Y27632 (0.4 ml apically and 0.5 ml basolaterally) and was changed again after 2 days when the mono-layer was typically confluent. Confluent monolayers were differentiated by washing with CMGF-, followed by feeding with Differentiation Medium (DM) [22, 31] containing Primocin. Medium was changed the next day with DM containing Primocin. Monolayers were fed 2 days later (day 3) (DM without Primocin) and in the late afternoon of day 4 or in the morning of day 5 (DM without Primocin). Monolayers were inoculated with pre-germinated spores on day 5. For measurement of trans-epithelial electrical resistance (TEER), a Millicell ERS-2 volt/ohm meter was used following manufacturer’s protocol.

extract_protocol:
Monolayers were cultured on 12 mm diameter 0.4 um polycarbonate filters (Millicell PIHP01250) and differentiated as described above. Spores were treated with glycine and sodium cholate, as above, collected by centrifugation (Eppendorf 5415, 13200 rpm, 5 min) resuspended in PBS and 1 x 105 spores in 10 ul or PBS was added to the apical medium. Transwells were incubated as described above. After 4, 15, 20 or 25 hours of incubation, monolayers were washed with 100 ul PBS, EDTA 0.5 mM, pH 8 and incubated with TrypLE Express, 600 ul in the basolateral and 400 ul in the apical compartments at 37oC for 12 min. One hundred ul 50% FBS was added to the apical compartment and the cells were suspended by pipeting up and down several times. Cells were passed through a 40 um cell strainer and recovered in tubes precoated with 0.1% BSA. The transwells were then washed with 400 ul CMGF-, which was passed through the strainer and combined with the previous filtrate. Cells were collected by centrifugation at 300g x 5 min. Most of the supernatant was gently removed. Cells were resuspended in 1 ml of 0.04% BSA, 5 uM Y27632 and collected as above. Using a wide bore tip, the pellet was resuspended in the remaining supernatant by pipetting up and down. Cells were counted with a Corning Cytosmart counter and adjusted to 1 x 106 cells/ml.
The remaining steps were performed following manufacturer’s protocol. Briefly, the cell suspension was loaded along with reagents, barcoded Single Cell 3’ v3.1 Gel Beads and Partitioning Oil onto the Chromium Next GEM Chip G. Cells were partitioned into GEMS using the Chromium Controller. Gel beads were then dissolved, releasing primers, and the cells were lysed. Reverse transcription was performed to generate cDNA tagged with cell specific barcodes and Illumina TruSeq Read 1 sequencing primer. GEMS were broken and first strand cDNA was purified and PCR amplified. After enzymatic fragmentation followed by size selection, the cDNA was PCR amplified, incorporating a sample index and primers P5, P7, and TruSeq Read 2 for Illumina sequencing. Library quality was assessed using an Agilent Bioanalyzer. Paired end sequencing was performed by the Tufts University Genomics Core Facility.

treatment_protocol: Co-culturing C. difficile with colonoid monolayers. Pre-germinated spores (approximately 5 x 107 per ml) were prepared as above and 10ul of the preparation was added gently to the apical medium of the transwell. Control samples were inoculated with 10ul of buffer. The plates were wrapped with Parafilm and incubated in a standard tissue culture incubator (37oC, 5% CO2, room air). At various times, transwells were taken into the anaerobic chamber (2 transwells at a time) to estimate the number of bacteria per transwell. The first 170 ul of apical medium was carefully removed. This medium was not turbid and was discarded. The second approximately 170 ul of medium was collected into the pipet tip and used to wash the monolayer twice, then collected into a pre-weighed tube. For inoculated transwells, this sample was typically turbid. 10 ul of this sample was immediately diluted with 1 ml of pre-reduced PBS to measure CFU. The remainder of the sample was removed from the chamber and weighed to determine the volume recovered from each transwell after correction for the 10 ul removed for CFU. Transwell monolayers were removed from the chamber and fixed with 4% para-formaldehyde for 15 min at room temp, followed by washing 3 times with PBS at room temperature. Transwells were stored at 4oC in PBS. For some experiments, transwells were inoculated with vegetative C. difficile cells. Strains were grown in pre-reduced TY broth and harvested during log phase. A sample of each culture was diluted 1/50 into pre-reduced PBS. DM medium was pre-reduced and 0.4 ml was transferred to a gasketed screw cap tube for each inoculation. 10 ul of bacteria diluted in PBS was added to each tube (or PBS only for mock inoculation). The caps were screwed on tightly and tubes removed from the chamber. The transwells were inoculated by removing their apical medium and replacing it with the bacteria-containing medium. Transwells were inoculated with approximately 5 x 104 CFU.

value: Colonoid line CJ50

tag: infection

value: infected


title: 3b_mut_rep2_input biol rep 2

description: Library name: ST190_16i_R

data_processing:
Raw reads were processed with Cutadapt (v5.0) to filter out adapter sequences, trim low-quality bases, and remove reads shorter than 15 bp. Filtered reads were aligned with bwa-mem2 (v2.2.1) under default parameters to a composite reference comprising the E. coli MG1655 genome (NCBI: NC_000913.3), the relevant plasmid sequence, and either the λ-vir (NCBI: NC_001416.1) or T5 (NCBI: NC_005859.1) phage genome. Alignments were sorted and indexed using SAMtools (v1.17). Strand-specific coverage tracks were generated with bamCoverage (v3.5.6), normalized to sequencing depth based on the total number of reads passing trimming and length filtering. Coverage tracks were visualized in IGV. Reads from total RNA–seq and RIP–seq libraries were assigned to annotated transcriptome features with featureCounts (v2.0.2), using the -s 1 flag to account for library strandedness. The resulting count matrices were passed to DESeq2 (v1.42.0) with default parameters, which estimated per-transcript fold-change and false-discovery rate between sample conditions indicated in the figure legend. Log2 fold-change estimates were shrunk using the apeglm estimator. For RNA–seq comparisons, phage-encoded genes were excluded from downstream analyses to focus on the host transcriptional response, with phage gene identifiers parsed from the corresponding RefSeq GFF3 annotation. Results were displayed as volcano plots generated in ggplot2, with log2[fold change] plotted as a function of -log10[padj]. Gene set enrichment analysis was performed on ranked log2 fold-change values using clusterProfiler (gseGO function) against GO Biological Process terms from the E. coli K-12 annotation database (org.EcK12.eg.db), with gene set sizes restricted to 5–500 members and significance assessed at FDR < 0.05.
Assembly: ASM584v2
Supplementary files format and content: Here's a cleaned-up version: ".txt — gene-level raw read count matrix generated by featureCounts. Rows correspond to annotated genes (Geneid from the GFF annotation), and columns correspond to individual samples. Values are unnormalized integer read counts representing the number of reads uniquely assigned to each gene. .bw — strand-specific BigWig coverage tracks generated from sorted BAM alignments, with separate files for forward (_fwd.bw) and reverse (_rev.bw) strands. Coverage values are normalized to sequencing depth.

extract_protocol:
Pellet was resuspended in 750 µL TRIzol and incubated for 5 min at room temperature. Next, 150 µL of chloroform was added to each sample, incubated for 2 min at room temperature, and then spun down at 12,000g for 15 min at 4 °C. Next, 360 µL of the aqueous phase was transferred to a clean tube and purified with the RNA Clean & Concentrator-5 kit (Zymo Research).
RNA was diluted in NEBuffer 2 and heated at 92 °C for 2 min for fragmentation by alkaline hydrolysis. The samples were then treated with TURBO DNase (Thermo Fisher Scientific), RppH (NEB), and T4 PNK (NEB) to remove DNA and prepare RNA ends for adapter ligation. RNA was purified using the Zymo RNA Clean & Concentrator-5 kit. Adapter ligation, reverse transcription, and indexing PCR were performed using the NEBNext Small RNA Library Prep kit. Libraries were sequenced on an Element AVITI system in paired-end mode with 150 cycles per end.


title: Cortical neurons, shControl, shScrambled, Day 11, Rep5

description: SP flowcell PE50


title: 3b_mut_rep1_input biol rep 1

description: Library name: ST190_15i_R


title: T98G

type: genomic

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hypridized to human Infinium MethylationEPIC array using standard Illumina protocols

scan_protocol: Arrays were imaged using BeadArray Reader and standard recommended Illumina scanner protocols

data_processing:
SeSAMe pipline (v1.24.0)
Average Beta values

label: Cy3 and Cy5

source_name: glioma

label_protocol: Standard Illumina Protocol

growth_protocol: The glioma cell lines LN18, LN229, LNZ308, and T98G were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Carlsbad, CA, USA) supplemented with 10% fetal calf serum (FCS; Thermo Fisher Scientific, Waltham, MA, USA) and 50 µg/mL gentamicin (Thermo Fisher Scientific, Waltham, MA, US). Glioma stem-like cells, GS-2 and GS-9, were cultured in Neurobasal®-A medium (Gibco, Carlsbad, CA, US), enriched with 2% B27 supplement without vitamin A (Invitrogen, Waltham, MA, USA), 1% GlutaMAX (Thermo Fisher Scientific, Waltham, MA, US), and 0.02 µg/mL each of recombinant human fibroblast growth factor (FGF) and epidermal growth factor (EGF) (PeproTech, Cranbury, NJ, USA).

extract_protocol: Genomic DNA from human cell lines was extracted using QIAamp DNA Blood Mini Kit

value: glioma


title: 3a_mut_rep2_input biol rep 2

description: Library name: ST190_14i_R


title: Cortical neurons, shControl, shScrambled, Day 11, Rep4

description: SP flowcell PE50


title: LNZ308


title: 3a_3b_mut_rep2_lambda_input biol rep 2

description: Library name: ST190_12i_R


title: Cortical neurons, shControl, shScrambled, Day 11, Rep3

description: SP flowcell PE50


title: LN229


title: 3a_3b_mut_rep2_uninfected_input biol rep 2

description: Library name: ST190_08i_R


title: 3a_3b_mut_rep1_uninfected_input biol rep 1

description: Library name: ST190_07i_R


title: Cortical neurons, shControl, shScrambled, Day 11, Rep2

description: SP flowcell PE50


title: LN18


title: LN229_DMSO_REP_B

description: Library name: 24049a002

data_processing:
The libraries were sequenced as paired-end 50bp reads on an Illumina NovaSeq6000 (Illumina) with a sequencing depth of approximately 25 million clusters per sample.
Raw data QC and processing was performed using megSAP (version 0.2-135-gd002274) combined with ngs-bits package (version 2019_11-42-gflb98e63).
Reads were aligned using STAR v2.7.3a
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read counts for each replicate.

source_name: tumor, central nervous system

growth_protocol: LN18 and LN229 glioma cell lines were cultured in DMEM (Gibco, Carlsbad, CA, US) supplemented with 10% fetal calf serum (Thermo Fisher Scientific, Waltham, MA, US) and 50 µg/mL Gentamicin (Thermo Fisher Scientific, Waltham, MA, US). GS-9 cells were grown in Neurobasal®-A medium (Gibco, Carlsbad, CA, US) supplemented with 2% B27 without vitamin A (Invitrogen, Waltham, MA, US), 1% GlutaMAX (Thermo Fisher Scientific, Waltham, MA, US), and 0.02 µg/mL fibroblast growth factor (FGF) and epidermal growth factor (EGF) (PeproTech, Cranbury, NJ, US).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were treated with 2µM (LN229), 0.75µM (LN18), or 3µM (GS-9) of abemaciclib for 48 hours, or corresponding concentration of DMSO solvent.

value: tumor, central nervous system

value: parental

value: DMSO


title: WT_rep2_lambda_input biol rep 2

description: Library name: ST190_06i_R


title: Cortical neurons, shControl, shScrambled, Day 11, Rep1

description: SP flowcell PE50


title: WT_rep1_lambda_input biol rep 1

description: Library name: ST190_05i_R


title: GS-9


title: Cortical neurons, shControl, shAtf4, Day 11, Rep3

description: SP flowcell PE50


title: WT_rep2_uninfected_input biol rep 2

description: Library name: ST190_02i_R


title: WT_rep1_uninfected_input biol rep 1

description: Library name: ST190_01i_R


title: Cortical neurons, shControl, shAtf4, Day 11, Rep2

description: SP flowcell PE50


title: CUT&RUN IgG control in SKLMS01

city: Houston

first: Zhao

last: Zheng

state: TX

address: 1901 East Rd

department: Genomic Medicine

institute: md anderson cancer center

description: Library name: CR-LMS-SKLMS01-C, IgG

data_processing:
1. Quality Control by using fastqc and multiqc, then trim the sequences if needed
2. aligning the sequences by Bowtie2
3. filtering the data and remove the duplicates, downsampling
4. calling the peaks by using macs1 for narrow peaks and macs2 for broad peaks
5. generating bigwig files
Assembly: hg38
Supplementary files format and content: peaks files: .narrowPeaks, .broadPeaks
Supplementary files format and content: bigwig files: .bw
Library strategy: CUT&RUN

growth_protocol: human cells were grown in DMEM/F12 with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Epicypher cut and run protocol v2.1
Epicypher CUTANA™ CUT&RUN Library Prep Kit

tag: disease state

value: Leiomyosarcoma

value: leiomyosarcoma cell


title: DMSO-3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA36624

data_processing:
Sequencing was performed on the NovaSeq 6000 platform in 101-base single-end mode.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.3.5.1 and SAMtools ver.1.2.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted from cells using the RNeasy Micro kit (QIAGEN N.V.) according to the enclosed instructions.
The cDNA libraries were constructed according to the manufacturer's instructions using the TruSeq Stranded mRNA Library Prep (Illumina, Inc., San Diego, CA).


title: DKOCr105_24hDMSO_3

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

description: Library name: Sample 6

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: mm10
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

source_name: Prostate

growth_protocol: SKO, DKO, DKOcr105, and TKO cells were cultured in DMEM/high glucose (Gibco 11995-065) with L-glutamine (Gibco 35050-061), sodium pyruvate (Gibco 11360-070), and 10% FBS (Corning MT35010CV). DKOcr298 was cultured in phenol-red free DMEM/high glucose (Gibco 31053-028) with L-glutamine (Gibco 35050-061), sodium pyruvate (Gibco 11360-070), and 10% charcoal-stripped FBS (Millipore Sigma F6765).

extract_protocol:
Total RNA was extracted using a Qiagen AllPrep RNA/DNA mini kit (Qiagen 80204) according to the manufacturer's protocol.
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

treatment_protocol: TKO and DKOcr298 cells were treated with BET inhibitors (500nM ZEN or 1µM JQ1) for 24hrs with corresponding vehicle (DMSO) controls; TKO and DKOcr298 were treated with BET inhibitor (500nM ZEN), DNA methyltransferase inhibitor (100nMdAZA), or the combination (500nM ZEN + 100nM dAZA) daily for 72 hrs with corresponding vehicle (DMSO) controls.

value: Prostate

value: Prostate Cancer Cell Line

value: DMSO 24hr


title: CUT&RUN NFIX in SKLMS01

description: Library name: CR-LMS-SKLMS01-L, Cut_Run


title: 3a_mut_rep1_input biol rep 1

description: Library name: ST190_13i_R


title: 3b_mut_rep1 biol rep 1

description: Library name: ST190_15_R


title: 3a_mut_rep2 biol rep 2

description: Library name: ST190_14_R


title: 3a_3b_mut_rep1_lambda_input biol rep 1

description: Library name: ST190_11i_R


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R170E_YW_rep2 biol rep 2

description: Library name: YW43_08_D


title: Cortical neurons, shControl, shAtf4, Day 11, Rep1

description: SP flowcell PE50

value: primary cell

value: cortical neurons

value: neuron differentiation


title: 3a_mut_rep1 biol rep 1

description: Library name: ST190_13_R


title: 3a_3b_mut_rep2_uninfected biol rep 2

description: Library name: ST190_08_R


title: Patient S3, normal tissue from fallopian tube

city: Castellón de la Plana

first: Guillermo

last: Peris

state: CAstellón

address: Av. Vicent Sos Baynat, s/n

department: Llenguatges i Sistemes Informàtics

institute: Universitat Jaume I

description: Library name: S3N

data_processing:
BBDuk from the BBMap toolkit for sequencing adapter removal and read trimming.
RNA paired-end reads were aligned to GRCh38.p14 human genome assembly with STAR v2.7.11b
Gene and transposable elements reads were quantified with TElocal  software from part of TEToolkit suite.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file with TElocal counts for genes and transposable elements for each sample.

source_name: Fallopian tube

extract_protocol:
FFPE (formalin-fixed paraffin-embedded) tumour and normal tissue were obtained from NovoPath, Newcastle Upon Tyne hospitals NHS foundation. RNA extraction of FFPE curls (10x10um) each tumour and normal tissue was performed by Genewiz, Azenta.
QC, library preparation and RNA-sequencing of each tumour and normal tissue was performed using standard RNA-seq paired end (2x150bp) sequencing service by Genewiz, Azenta.

value: Fallopian tube

tag: individual

value: Patient S3

value: Normal tissue


title: 3a_3b_mut_rep1_uninfected biol rep 1

description: Library name: ST190_07_R


title: Whole testis, Tammar wallaby, scRNAseq, Rep2

description: Library name: Tammar_wallaby_scRNAseq_Rep2

organism: Notamacropus eugenii

value: Testis

value: Male


title: in vivo Daxx WT microglia TAM 1dpi-3 [24597]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24597

value: brain

value: microglia

value: Cx3cr1CreERT,Daxx wt/wt

value: Tamoxifen


title: Patient S2, ovarian Sertoli Leydig tumor

description: Library name: S2T

source_name: Ovary

value: Ovary

value: Patient S2

value: Sertoli Leydig tumor


title: WT_rep2_uninfected biol rep 2

description: Library name: ST190_02_R


title: Whole testis, Tammar wallaby, scRNAseq, Rep1

description: Library name: Tammar_wallaby_scRNAseq_Rep1


title: Patient S1, uterine embryonal rhabdomyosarcoma

description: Library name: S1T

source_name: Uterus

value: Uterus

value: Patient S1

value: Embryonal rhabdomyosarcoma


title: WT_rep1_uninfected biol rep 1

description: Library name: ST190_01_R


title: Round spermatids, Tammar wallaby, HiC, rep3

description: Library name: RS_TammarWallaby_HiC_rep3

value: Round spermatids


title: ∆GreA DRT3 biol rep 3

description: Library name: HCL11_06

data_processing:
"Raw reads were processed with Cutadapt to filter out adapter sequences, trim low-quality bases, and remove reads shorter than 15 bp. Filtered reads were aligned with bwa-mem2 under default parameters to a composite reference comprising the E. coli MG1655 or BW25113 genome, and the DRT3 plasmid sequence. Alignments were sorted and indexed using SAMtools, and alignment statistics were assessed with samtools flagstat. Reads were assigned to annotated transcriptome features with featureCounts.
Assembly: ASM584v2
Supplementary files format and content: .txt file with gene-level raw read count matrix generated by featureCounts. Rows correspond to annotated genes (Geneid from the GFF annotation) and columns correspond to individual samples. Values are unnormalized integer read counts representing the number of reads uniquely assigned to each gene.

growth_protocol: E. coli K-12 MG1655 or BW25113 ∆GreA was transformed with DRT3 and three biological replicates were cultured overnight in LB containing the appropriate. Overnight cultures were back-diluted 1:100 into 3 mL of LB, grown to OD600 0.3, and pelleted by centrifugation at 4,000g for 5 min.

extract_protocol:
Pellet was resuspended in 750 µL TRIzol and incubated for 5 min at room temperature. Next, 150 µL of chloroform was added to each sample, incubated for 2 min at room temperature, and then spun down at 12,000g for 15 min at 4 °C. Next, 360 µL of the aqueous phase was transferred to a clean tube and purified with the RNA Clean & Concentrator-5 kit (Zymo Research).
RNA was diluted in NEBuffer 2 and heated at 92 °C for 2 min for fragmentation by alkaline hydrolysis. The samples were then treated with TURBO DNase (Thermo Fisher Scientific), RppH (NEB), and T4 PNK (NEB) to remove DNA and prepare RNA ends for adapter ligation. RNA was purified using the Zymo RNA Clean & Concentrator-5 kit. Adapter ligation, reverse transcription, and indexing PCR were performed using the NEBNext Small RNA Library Prep kit. Libraries were sequenced on an Element AVITI system in single or paired-end mode with 75 or 150 cycles per end.


title: Patient S1, normal tissue from lymph node.

description: Library name: S1N

source_name: Lymph node

value: Lymph node


title: GS-2

value: glioma


title: ∆GreA DRT3 biol rep 2

description: Library name: HCL11_05


title: D283_Day7_control_rep1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence, cleaned reads were mapped to hg38 (Gencode GRCh38.p12) using STAR
Assembly: hg38
Supplementary files format and content: Tab-separated files

extract_protocol:
For RNA-seq in Group 4 MB PDX, freshly isolated DMB006 cells from mouse brains were infected in triplicate with non-targeting control or KDM2B gRNA viruses at high MOI to ensure more than 90% of cells were infected. Cells were cultured for 7 days and then collected for RNA-seq. Infection efficiency was determined by flow cytometry analysis of GFP percentage on day 4. Editing efficiency was evaluated by targeted deep sequencing. For RNA-seq in D283, cells were infected in triplicate with non-targeting control or KDM2B gRNA viruses at high MOI to ensure more than 80% of cells were infected. Cells were cultured for 7 days. An aliquot of cells was collected on day 4 or day 7 for RNA-seq. Infection efficiency was determined by flow cytometry analysis of GFP percentage on day 4. Editing efficiency was evaluated by targeted deep sequencing.
RNA extraction was performed using RNeasy Plus kit (Qiagen) according to manufacturer’s instructions. RNA libraries for RNA-seq were prepared following manufacturer's protocols

value: medulloblastoma cell line


title: ∆GreA DRT3 biol rep 1

description: Library name: HCL11_04


title: LS8817, day3, Palbo, rep2, techrep2, ATAC

first: Viviana

middle: I.

last: Risca

state: NY

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

description: Library name: day3_Palbo_Biorep2.2

data_processing:
Adapters were trimmed using cutadapt
Reads were aligned with bowtie2 2.3.4.3 to the hg38 genome. Following this, duplicate reads and reads mapping to the mitochondrial genome were removed.
Bam files were converted to bedpe files, which were then converted to tagAlign files for MACS2 to call peaks on, areas of the genome enriched for aligned sequencing reads, indicating hyperaccessibility. MACS2 parameters were -g 2.7e9 -p 0.2 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits.
Reproducible peaks across technical replicates per condition were kept using Irreproducible Discovery Rate (Li et al. 2011)
A master nonredundant peak set was generated using a custom iterative peak filtering script which selects the peak with the lowest q-value generated by MACS2 from a set of overlapping peaks
Peaks were fixed to 500bp in length, with 250bp extending from the summit identified by MACS2
Fragment counts under peaks were counted using chromVAR’s getCounts function(Schep et al. 2017)
Assembly: hg38
Supplementary files format and content: Files ending in "scaleFactornorm.bw" are coverage bigwig tracks normalized by sequencing depth. Files ending in "scaleFactornorm_cutsCoverage.bw" are normalized coverage of Tn5 insertion sites (fragment ends). If the file contained the string "merged" it means that bams across biological and technical replicates for that condition were merged prior to generating the bigwig file.
Supplementary files format and content: .narrowPeak files are peaks called for each technical replicate by MACS2.
Supplementary files format and content: summits.bed files are the summits of peaks identified by MACS2

source_name: soft tissue sarcoma

growth_protocol: Cells were cultured in DMEM high glucose no glutamine (11960044, Gibco™), supplemented with 9% FBS (10082147, Gibco™), 1% of 100x GlutaMAX™ Supplement (35050061, Gibco™) and 1% of 10,000U/mL penicillin/streptomycin (15140122, Gibco™) and maintained at 37°C and 5% CO2.

extract_protocol:
Cells were treated in culture medium with DNase (Worthington cat# LS002007) at a final concentration of 200 U/mL at 37 °C for 30 mins, then washed twice with PBS at 500g, RT. Approximately ~50,000-60,000 cells were used for each transposition reaction. Following permeabilization, 2.5 µL of Illumina TDE1 enzyme was used for transposition at 37°C for 30 minutes.
Libraries were PCR amplified for 8-13 cycles with Illumina i5 or i7 barcoded primers and were cleaned up pre- and post-amplification following the manufacturer’s instructions using Zymo DNA Clean and Concentrator-5 Kit. Fragment length distribution and DNA amount was quantified via Tapestation and Qubit to assess for quality prior to sequencing.

treatment_protocol: Cells were passaged at a 1:3 ratio one day before drug treatment and treated with either 1 µM palbociclib or 100 nM doxorubicin, with media changes every 2–3 days until harvest.

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2

value: day3 palbociclib (1uM)


title: Round spermatids, Tammar wallaby, HiC, rep2

description: Library name: RS_TammarWallaby_HiC_rep2

value: Male


title: WT DRT3 biol rep 3

description: Library name: HCL11_03

value: WT


title: Round spermatids, Tammar wallaby, HiC, rep1

description: Library name: RS_TammarWallaby_HiC_rep1


title: DRT3_MUT_Glu_rep5

description:
Library name: HCL11_20
A3517

data_processing:
Raw reads were processed with BBDuk (v39.83) to filter for Himar transposon-end-containing reads, trim adapter sequences and low-quality bases, and trim transposon sequence to leave only the 16–17 bp of genomic sequence mappable to the E. coli MG1655 reference genome (NC_000913.3). Processed reads were aligned with Bowtie2 (v1.3.1) with no allowance for mismatches. Alignments were sorted and indexed using SAMtools (v1.17). Strand-specific coverage tracks were generated with bamCoverage (v3.5.6) with no normalization, using parameters that identified the TA dinucleotide within the read as the insertion site (bin size = 1, offset = –1). Mapped reads were assigned to annotated genes with featureCounts (v2.0.2) using the --read2pos 5 flag. The resulting count matrices were passed to PyDESeq2 (v0.5.3) for differential insertion analysis with default parameters. Five independent biological replicates were included for every comparison. Genome build: E. coli MG1655 (NC_000913.3).
Assembly: ASM584v2
Supplementary files format and content: .txt file with gene-level raw read count matrix generated by featureCounts. Rows correspond to annotated genes (Geneid from the GFF annotation) and columns correspond to individual samples. Values are unnormalized integer read counts representing the number of reads uniquely assigned to each gene.

extract_protocol:
Mutant library plates were grown at 37 °C for 18 hours, after which all colonies were scraped from the plates. Genomic DNA was extracted from these cells using the Wizard Genomic DNA Purification kit (Promega).
Extracted gDNA was digested with MmeI (2 U MmeI per 1 µg gDNA) at 37 °C for 1 hour, followed by enzyme inactivation at 65 °C for 20 min. Digested DNA was purified using QIAquick PCR Purification columns (Qiagen). Sequencing adaptors were ligated onto digested mini-transposons with T4 DNA ligase at 16 °C for 14 hours, followed by another QIAquick PCR purification cleanup. PCR amplification and Illumina barcoding were performed for 25 cycles with Q5 Hot Start HF DNA polymerase (NEB), using an annealing temperature of 65 °C and an extension time of 20 sec. The 173 bp product was gel-extracted using the QIAquick Gel Extraction kit (Qiagen) and sequenced on the Element AVITI system in single-end mode, 150 reads per end.


title: TH206

value: heart biopsy


title: Pachytene/Diplotene, Tammar wallaby, HiC, rep3

description: Library name: PD_TammarWallaby_HiC_rep3

source_name: Pachytene/Diplotene

value: Pachytene/Diplotene


title: Grp10, miRFP670 quartile sort, upper middle quartile

city: Cleveland

first: Kenneth

last: Matreyek

state: Ohio

address: 2103 Cornell Rd, Room 5104

department: Pathology

institute: Case Western Reserve University

description: Library name: Grp10, eeBxb1, miRFP670 bin 3

data_processing:
DNA was sequenced using a NextSeq 550 Mid output (130 million reads) 150 cycle kit (Illumina) at the Case Western Reserve University Genomics Core Facility
Reads were converted to fastq format and demultiplexed by the Case Western Reserve University Genomics Core Facility.  Paired-end reads were combined using PEAR (PMC3933873) using default statistical settings.
Each paired end read was tested for exact matches from the expected library and included as a read for the appropriate library member if applicable.  Read count relative to total number of reads in the sample was used to calculate read frequency for each expected library member.
Read frequencies for quartiles from the same fluorophore sort and the same group were used to calculate a weighted average Sort-Seq score for each fluorophore for expected library member.  Scores were averaged across groups to provide a final Sort-Seq score for each expected library member.  The Sort-Seq scores were used for further analysis in the manuscript.
Assembly: Synthetic Sequences
Supplementary files format and content: "processed_data_counts_frequencies.csv" is a comma separated values data table containing read counts and read frequencies for all observed DNA sequences (library_sequence, column 1).  Each row represents a DNA sequence of interest, and each column represents either a read count ("_counted") or a read frequency ("_freq") for each sample ("IXXXX", corresponding with IXXXX from file names as described in SAMPLES section).

growth_protocol: DMEM with 10% FBS, 1 % Penicillin / Streptomycin, and 2 ug/mL doxycycline.

extract_protocol:
Genomic DNA was extracted using a Dneasy Blood and Tissue Kit (Qiagen, 69506) and DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265)
Extracted genomic DNA was used as a template to produce a 1564 nucleotide amplicon spanning the genomic integration junction.  Samples were run with gel electrophoresis, the appropriate band was extracted using a Bio-Rad Freeze 'N Squeeze DNA Gel Extraction Spin Column (Bio-Rad, 7326165) and cleaned using a Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4004).  The resulting DNA was used as the template for to produce a 299 nudleotide amplicon surrounding the DNA sequence of interest using distinct indices for each quartile to be run on the same Illumina NextSeq 550 kit run.  Samples were again run with gel electrophoresis, extracted, and cleaned.  DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265).  DNA amplicons were pooled to a final concentration of 10-20ng/uL in 21uL of nuclease free water using 15-20ng of DNA from each quartile prior to running the Illumina NextSeq 550 kit.

value: Cultured Cells

value: Recombination into


title: Grp10, miRFP670 quartile sort, upper quartile

description: Library name: Grp10, eeBxb1, miRFP670 bin 4


title: Grp10, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp10, eeBxb1, miRFP670 bin 2


title: DRT3_MUT_Glu_rep4

description:
Library name: HCL11_18
A3540


title: WT DRT3 biol rep 2

description: Library name: HCL11_02


title: WT DRT3 biol rep 1

description: Library name: HCL11_01


title: in vivo Daxx WT microglia TAM 0dpi-1 [24589]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24589

data_processing:
Raw FASTQ files were trimmed by Trimgalore and aligned to genome mm10 by STAR. SAM files were filter by mapq>=10 and transformed to BAM by samtools. Gene count table was created by featureCounts.
Assembly: mm10
Supplementary files format and content: read counts from featureCounts

source_name: brain

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 5 ng of total RNA was used for contruction of sequencing libraries.
RNA library for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian following manufacturer's protocols.

value: brain

value: microglia

value: Cx3cr1CreERT,Daxx wt/wt

value: Tamoxifen


title: 3a_3b_mut_rep1_T5_input biol rep 1

description: Library name: ST190_09i_D

data_processing:
Raw reads were processed with Cutadapt (v5.0) to filter out adapter sequences, trim low-quality bases, and remove reads shorter than 15 bp. Cutadapt was run using a tiling approach across the 3′ adapter as previously described, with parameters -e 0.2, -O 10, -q 30, and -m 45 (error rate, minimum overlap, quality cutoff, and minimum length, respectively). Filtered reads were aligned with bwa-mem2 (v2.2.1) under default parameters to a composite reference comprising the E. coli MG1655 genome (NCBI: NC_000913.3), the relevant plasmid sequence, and either the λ-vir (NCBI: NC_001416.1) or T5 (NCBI: NC_005859.1) phage genome. Alignments were sorted and indexed using SAMtools (v1.17). Strand-specific coverage tracks were generated with bamCoverage (v3.5.6), normalized to sequencing depth based on the total number of reads passing trimming and length filtering. Reads that failed to align with bwa-mem2 were extracted using SAMtools fasta, and the fraction of unmapped reads was calculated using SAMtools flagstat. Genome build: E. coli MG1655 (NC_000913.3); λ-vir (NC_001416.1); T5 (NC_005859.1).
Assembly: ASM584v2
Supplementary files format and content: .fasta — Unmapped reads extracted from BAM alignments using SAMtools fasta. Each file contains all reads from a given sample that failed to align to the composite reference, used as input for downstream MEME motif enrichment analysis and motif counts per sample.

extract_protocol:
cDIP elution was performed by removing the supernatant and resuspending beads with 80 µL of IP wash buffer containing 5 µg RNase A (Thermo Fisher Scientific). Inputs were resuspended with 70 µL of the same wash buffer. Both inputs and immunoprecipitation samples were incubated at 37 °C for 30 min. SDS was then added to a final concentration of 1%, along with 25 µg of proteinase K (Thermo Fisher Scientific). Supernatants containing eluted DNA were transferred to new tubes and DNA was isolated with the Monarch Spin PCR and DNA Cleanup kit (NEB), following the Oligonucleotide Cleanup protocol.
Eluted DNA samples were heated at 95 °C for 2 min and immediately placed on ice to denature DNA. Adapter ligation and conversion of ssDNA to dsDNA were performed using the xGen ssDNA & Low-Input DNA Library Prep Kit (IDT). Indexing PCR was performed using NEBNext Ultra II Q5 Master Mix (NEB). Libraries were sequenced on the Element AVITI system in single- or paired-end mode with 150 cycles per end.


title: DRT3_WT_Glu_rep5

description:
Library name: HCL11_19
A3525


title: Pachytene/Diplotene, Tammar wallaby, HiC, rep2

description: Library name: PD_TammarWallaby_HiC_rep2

data_processing:
BBDuk (version 09/2019) was used for quality check and trimming. Basically, adapters and low-quality reads (i.e. reads with a minimum length of 35 bp and a minimum Phred quality score of 20) were removed. High-quality reads were then mapped against the tammar wallaby (PRJNA1235426) and bearded dragon (PviZW2.1) genomes using the GEM (version 3.6.1) mapper from TADbit (version 1.0.1).
Assembly: PRJNA1235426 (tammar wallaby), PviZW2.1 (bearded dragon)
Supplementary files format and content: GInteraction tables of Hi-C data at a 50 Kbp resolution, which include interaction values between all genomic bins genome-wide.

extract_protocol:
In nuclei Hi-C was adapted from previously described protocols.  Briefly, germ cells were incubated in lysis buffer containing 10 mM Tris, 10 mM NaCl, 0.2% Igepal and 1xPIC for 20 minutes at 4ºC. Subsequently, germ cells were incubated with 0.5% SDS in 1xNEBuffer 2 for 10 minutes at 4ºC and the reaction was quenched by adding 10% Triton X-100 and incubating for 30 minutes at 37ºC. Germ cells were then centrifuged at 5,000 xg for 5 minutes at 4ºC and resuspended in 300 µl 1xNEBuffer 2 containing 400 U of MboI. Chromatin was digested overnight at 37ºC and assessed the following day by comparing a digested and a non-digested control. Germ cells were then incubated at 65ºC for 20 minutes to inactivate the restriction enzyme and the reparation mix (0.05mM dCTP, 0.05mM dTTP, 0.5mM dGTP, 0.05mM biotin-dATP, 50U Klenow in 1xNEBuffer 2) was directly added into the cell suspension. Chromatin was repaired and biotinylated for 90 minutes at 37ºC, and then the enzyme was heat-inactivated at 65ºC for 10 minutes. Prior to ligation, germ cells were centrifuged for 5 minutes at 5,000 xg at 4ºC, resuspended in ligation buffer (0.8% Triton X-100, 0.1 mg/ml BSA, 10,000 U T4 DNA ligase in 1xNEB T4 ligase buffer) and incubated overnight at 16ºC. Lastly, germ cells were incubated with RNAse A for 15 minutes at 37ºC, and then with proteinase K overnight at 65ºC to reverse the crosslink, followed by a DNA extraction with Phenol:Chloroform. DNA concentration was quantified by Qubit and quality was assessed by running a 0.8% agarose gel.
For library preparation, samples were sonicated into fragments of 300 – 500 bp. The biotinylated fragments were pulled down using Dynabeades MyOne Streptavidin T1 beads, which were pre-washed with 2xbinding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl) and incubated with sonicated fragments for 30 minutes in rotation. Beads were then separated on a magnetic rack and washed with 1xbinding Buffer. Ends repair, adaptor ligation and amplification were performed with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® according to manufacturer’s recommendations. For size selection, DNA fragments were incubated with AMPure beads in a 1:1 proportion for 10 minutes at room temperature. Beads were then washed twice with 70% ethanol and DNA was eluted with Tris buffer for 10 minutes at room temperature. DNA concentration was quantified by Qubit and fragment size was assessed by running a Bioanalyzer. Libraries were submitted for Illumina sequencing (paired-end 150bp each side on NovaSeq 6000).


title: DRT3_WT_Glu_rep4

description:
Library name: HCL11_17
A3541


title: Grp10, miRFP670 quartile sort, lower quartile

description: Library name: Grp10, eeBxb1, miRFP670 bin 1


title: 3b_mut_rep2 biol rep 2

description: Library name: ST190_16_R


title: DRT3_MUT_Glu_rep3

description:
Library name: HCL11_16
A3574


title: DRT3_WT_Glu_rep3

description:
Library name: HCL11_15
A3599


title: Pachytene/Diplotene, Tammar wallaby, HiC, rep1

description: Library name: PD_TammarWallaby_HiC_rep1


title: Grp10, mKG quartile sort, upper quartile

description: Library name: Grp10, eeBxb1, mKG bin 4


title: DRT3_WT_Glu_rep2

description:
Library name: HCL11_13
A3543


title: Grp10, mKG quartile sort, upper middle quartile

description: Library name: Grp10, eeBxb1, mKG bin 3


title: Spermatogonia, Tammar wallaby, HiC, rep2

description: Library name: Spermatogonia_TammarWallaby_HiC_rep2

source_name: Spermatogonia

value: Spermatogonia


title: DRT3_WT_Glu_rep1

description:
Library name: HCL11_11
A3595


title: Spermatogonia, Tammar wallaby, HiC, rep1

description: Library name: Spermatogonia_TammarWallaby_HiC_rep1


title: DRT3_MUT_Glu_rep1

description:
Library name: HCL11_12
A3589


title: Grp10, mKG quartile sort, lower middle quartile

description: Library name: Grp10, eeBxb1, mKG bin 2


title: DRT3_MUT_Ara_rep5

description:
Library name: HCL11_10
A3601


title: DRT3_MUT_Glu_rep2

description:
Library name: HCL11_14
A3531


title: DRT3_WT_Ara_rep5

description:
Library name: HCL11_09
A3527


title: Grp10, mKG quartile sort, lower quartile

description: Library name: Grp10, eeBxb1, mKG bin 1


title: SKLMS01 ChIP-seq for NFIC

description: Library name: LMS SKLMS01 NFIC, ChIP

data_processing:
1. Quality Control by using fastqc and multiqc, then trim the sequences if needed
2. aligning the sequences by BMA
3. filtering the data and remove the duplicates, downsampling
4. calling the peaks by using macs2 for narrow peaks and macs2 for broad peaks
5. generating bigwig files
Assembly: hg38
Supplementary files format and content: .bigwig

growth_protocol: Mouse melanoma cells were grown in DMEM/F12 with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Following the protocol on: Terranova, Christopher, et al. "An integrated platform for genome-wide mapping of chromatin states using high-throughput ChIP-sequencing in tumor tissues." Journal of visualized experiments: JoVE 134 (2018).
NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina

value: Leiomyposarcoma

value: Human leiomyosarcoma cell line

tag: chip antibody

value: ChIP-seq for NFIC


title: DRT3_MUT_Ara_rep4

description:
Library name: HCL11_08
A3562


title: Skin, Individual 7, Summer (N2)

city: Santiago

first: Rorigo

last: Maldonado

address: Avenida Pedro de Valdivia 1509

country: Chile

institute: Universidad Finis Terrae

description: Library name: ss_7_N2

data_processing:
Processed data files were generated from raw small RNA sequencing reads following standard quality control and preprocessing steps. Raw FASTQ files provided at the lane level were concatenated per sample, and only read 1 (R1) files were retained, as small RNA inserts are fully contained within R1 reads.
Assembly: https://doi.org/10.6084/m9.figshare.28726535.v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include raw counts for each Sample

organism: Orestias ascotanensis

source_name: Skin

growth_protocol: Specimens were collected from the Ascotan Salt Pan (21°29'46.5"S 68°15'26.3"W) at an elevation of 3,740 meters above sea level in July 2019 (n=7) and January 2020 (n=7) using a fishing net. Euthanasia was performed by administering an overdose of tricaine methanesulphonate (MS-222, 500 mg L−1; Sigma-Aldrich). Tissue samples from gills, skin, and muscle were harvested on-site. Each tissue sample was individually preserved in RNAlater (Invitrogen) immediately after dissection to stabilize and protect RNA. The samples were transported on ice to the laboratory and subsequently stored at -80°C until RNA extraction.

extract_protocol:
For small RNA sequencing, total RNA samples were enriched for short RNA species by size selection using denaturing polyacrylamide gel electrophoresis on Novex™ TBE–Urea gels (Invitrogen) run in TBE Running Buffer (LC6675). Gel fragments corresponding to the expected size range of small RNAs, including mature microRNAs, were excised and purified.
Small RNA libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina, 15016911) according to the manufacturer’s instructions. Libraries were sequenced by Quick Biology (Pasadena, CA, USA) on an Illumina NextSeq 500 platform using paired-end 75 bp reads. Although paired-end sequencing was performed, only read 1 (R1), which fully covers the mature small RNA insert, was used for downstream analyses.

value: Skin

value: summer

tag: batch


title: Grp10, mCherry quartile sort, upper quartile

description: Library name: Grp10, eeBxb1, mCherry bin 4


title: DRT3_WT_Ara_rep4

description:
Library name: HCL11_07
A3504


title: DRT3_MUT_Ara_rep3

description:
Library name: HCL11_06
A3500


title: DRT3_WT_Ara_rep3

description:
Library name: HCL11_05
A3501


title: Grp10, mCherry quartile sort, upper middle quartile

description: Library name: Grp10, eeBxb1, mCherry bin 3


title: DRT3_WT_Ara_rep2

description:
Library name: HCL11_03
A3552


title: Grp10, mCherry quartile sort, lower middle quartile

description: Library name: Grp10, eeBxb1, mCherry bin 2


title: Skin, Individual 6, Summer (N2)

description: Library name: ss_6_N2


title: DRT3_WT_Ara_rep1

description:
Library name: HCL11_01
A3585


title: DRT3_MUT_Ara_rep1

description:
Library name: HCL11_02
A3579


title: Muscle, Individual 6, Summer (N2)

description: Library name: sm_6_N2

source_name: Muscle

value: Muscle


title: Control_H3K4me3_positive_control

first: Norihiro

last: Goto

address: 413 East 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

description:
Library name: Control_H3K4me3
Control_H3K4me3

data_processing:
Paired-end sequencing reads were mapped to the UCSC mm9 mouse genome build (genome.ucsc.edu) using Bowtie.
To drop duplicate alignments, BAM files were processed with Picard MarkDuplicates.
BAM files were sorted and merged using Samtools.
Peaks were called using SEACR
Read counts per peak per sample were quantified using BEDTools.
Assembly: mm9
Supplementary files format and content: H3K27ac_peak_counts.txt.gz is a tab delimited text of counts for filtered peaks
Library strategy: CUT&Run

source_name: Colon cancer organoids

extract_protocol:
Organoids were dissociated using TrypLE Express for 10 min at 37 °C, filtered through a 40 μm cell strainer, and 500,000 cells were collected, centrifuged, and washed twice with PBS. H3K27ac CUT&RUN libraries were prepared using the CUTANA CUT&RUN kit (EpiCypher, 14-1048) according to the manufacturer’s instructions.
CUT&RUN libraries were PCR amplified using NEBNext High-Fidelity 2X PCR Master Mix for the appropriate numbers of cycles determined by qRT-PCR as previously described. Paired-end sequencing was performed on an Illumina NextSeq 2000.

value: Colon cancer organoids

tag: recipient mice

value: AKP


title: Control_H3K27ac_replicate3

description:
Library name: Control_H3K27ac_3
Control_H3K27ac


title: Grp9, miRFP670 quartile sort, upper quartile

description: Library name: Grp9, eeBxb1, miRFP670 bin 4


title: Grp9, miRFP670 quartile sort, upper middle quartile

description: Library name: Grp9, eeBxb1, miRFP670 bin 3


title: Control_H3K27ac_replicate1

description:
Library name: Control_H3K27ac_1
Control_H3K27ac


title: Skin, Individual 5, Summer (N2)

description: Library name: ss_5_N2


title: Gills, Individual 5, Summer (N2)

description: Library name: sg_5_N2

source_name: Gills

value: Gills


title: Gata6KO_H3K27ac_replicate3

description:
Library name: Gata6KO_H3K27ac_3
Gata6KO_H3K27ac


title: Gata6KO_H3K27ac_replicate2

description:
Library name: Gata6KO_H3K27ac_2
Gata6KO_H3K27ac


title: Grp9, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp9, eeBxb1, miRFP670 bin 2


title: Muscle, Individual 5, Summer (N2)

description: Library name: sm_5_N2


title: Gata6KO_H3K27ac_replicate1

description:
Library name: Gata6KO_H3K27ac_1
Gata6KO_H3K27ac


title: Grp9, miRFP670 quartile sort, lower quartile

description: Library name: Grp9, eeBxb1, miRFP670 bin 1


title: orgCorti_Casz1-WT_rep5

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description: Library name: WT5

data_processing:
Paired fastq files were processed to filter out low quality reads using Trimmomatic (sliding window trimming); filtered reads were mapped using STAR aligner, and mapped reads were quantified using featureCounts; genes were filtered out if expression was not higher than 1 count per million in at least 3 samples; feature counts were analyzed for differential gene expression between genotype groups using edgeR.
Assembly: mm10; GRCm38.M23
Supplementary files format and content:
FeatureCounts.txt: columns = read counts for each sample; rows = entrezgene_ids
edgeR_Casz1cKOvsWT.txt:  entrezgene_ids, logFC, logCPM, Pvalues, FDR

extract_protocol:
RNA was isolated from organ of Corti samples using the RNeasy Micro Kit (Qiagen).
Total RNA was reverse-transcribed with Maxima H- RT with oligo-dT and template switching oligo primers. Full length cDNA was tagmented with Illumina Nextera XT Library Prep kits, and sequenced on a NextSeq2000 DNA sequencer (Illumina).


title: orgCorti_Casz1-WT_rep4

description: Library name: WT4


title: Grp9, mKG quartile sort, upper quartile

description: Library name: Grp9, eeBxb1, mKG bin 4


title: Gills, Individual 4, Summer (N2)

description: Library name: sg_4_N2


title: orgCorti_Casz1-WT_rep3

description: Library name: WT3


title: orgCorti_Casz1-WT_rep2

description: Library name: WT2


title: Skin, Individual 4, Summer (N2)

description: Library name: ss_4_N2


title: Grp9, mKG quartile sort, upper middle quartile

description: Library name: Grp9, eeBxb1, mKG bin 3


title: orgCorti_Casz1-WT_rep1

description: Library name: WT1


title: Muscle, Individual 4, Summer (N2)

description: Library name: sm_4_N2


title: Grp9, mKG quartile sort, lower middle quartile

description: Library name: Grp9, eeBxb1, mKG bin 2


title: orgCorti_Casz1-KO_rep5

description: Library name: KO5


title: orgCorti_Casz1-KO_rep3

description: Library name: KO3


title: Gills, Individual 3, Summer (N2)

description: Library name: sg_3_N2


title: Grp9, mKG quartile sort, lower quartile

description: Library name: Grp9, eeBxb1, mKG bin 1


title: Skin, Individual 3, Summer (N2)

description: Library name: ss_3_N2


title: orgCorti_Casz1-KO_rep2

description: Library name: KO2


title: orgCorti_Casz1-KO_rep1

description: Library name: KO1


title: Grp9, mCherry quartile sort, upper quartile

description: Library name: Grp9, eeBxb1, mCherry bin 4


title: Muscle, Individual 3, Summer (N2)

description: Library name: sm_3_N2


title: Grp9, mCherry quartile sort, upper middle quartile

description: Library name: Grp9, eeBxb1, mCherry bin 3


title: Smarta CD4 T cells, replicate 2, ScRNAseq

description: 10x Genomics

data_processing:
The demuliplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger softwere v6.1.2
Assembly: mm10
Supplementary files format and content: .h5 files of raw/filtered gene-by-barcode matrces

source_name: dLN and tumor

extract_protocol:
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with feature barcode technology for cell surface protein per the manufacturer instructions (10X genomics)
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with feature barcode technology for cell surface protein per the manufacturer instructions (10X genomics) were used for library. Libraries were pooled and sequenced on NextSeq2000 ( Kit V3, 100 cycle, parameter: R1: 26bp, I7: 10bp, I5: 10bp,  and R2: 90bp).

value: dLN and tumor

value: Immune cells

value: PBS or Smarta


title: Gills, Individual 2, Summer (N2)

description: Library name: sg_2_N2


title: Smarta CD4 T cells, replicate 1, ScRNAseq

description: 10x Genomics


title: Leio012 ChIP-seq for NFIX

description: Library name: LMS Leio012 NFIX, ChIP

value: ChIP-seq for NFIX


title: Sacubitrilat and Endothelin-1-treated hiPSC-CMs, biological replicate 3

city: Chicago

first: Jacob

middle: D

last: Cunningham

state: IL

address: 1500 W Monroe St. Unit 221

department: Cell & Molecular Physiology

institute: Loyola University Chicago

description:
Library name: HS7VFC_12_et1_Sac_rep3
hiPSC-CMs treated with Sac and ET1

data_processing:
FASTQ files were generated and demultiplexed using BCL Convert v4.3.6 and fqtk v0.3.1.
Reads were filtered using fastp v0.24.0 with poly-X tail trimming, 3-prime quality-based tail trimming, a minimum Phred quality score of 15, and a minimum retained read length of 50 bp.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text matrix containing UMI-deduplicated, strand-specific gene-level counts for all 12 samples. Rows represent genes identified by gene_id, with gene annotation fields where available, and columns represent the GEO library names. Counts were generated using featureCounts from UMI-deduplicated aligned reads.

source_name: WTC-mEGFP-ACTN2-cl85 (AICS-0075-085)

growth_protocol: Human iPSCs were maintained on Matrigel-coated culture plates in mTeSR Plus medium. At approximately 70%–80% confluence, cardiac differentiation was initiated with RPMI 1640 containing B-27 supplement without insulin and 7.5 µM CHIR99021. On differentiation day 2, medium was replaced with RPMI 1640 containing B-27 supplement without insulin and 5 µM IWP-2. On day 4, cells were maintained in RPMI 1640 containing B-27 supplement without insulin. From days 6–14, cells were maintained in RPMI 1640 containing complete B-27 supplement, with medium changed every other day. Cardiomyocytes were metabolically enriched using glucose-free RPMI 1640 containing B-27 supplement without insulin and 10 mM sodium L-lactate. After selection, cardiomyocytes were dissociated with TrypLE, replated on Matrigel-coated plates at 3 × 10^6 cells/mL, and maintained in RPMI 1640 containing complete B-27 supplement.

extract_protocol:
Total RNA was extracted by Plasmidsaurus from cells preserved in Zymo DNA/RNA Shield
Poly(A) mRNA was captured from total RNA using a poly(dT)VN primer containing a sample barcode, a unique molecular identifier (UMI), and the Read 1 sequence. Reverse transcription and second-strand cDNA synthesis were followed by tagmentation. Libraries were indexed and amplified to add unique dual indexes and Illumina P5/P7 adapter sequences. Libraries were prepared as stranded, single-end, approximately 90-bp 3-prime-end-counting RNA-sequencing libraries.

treatment_protocol: Human iPSC-derived cardiomyocytes were assigned to four experimental conditions: vehicle control, sacubitrilat alone, endothelin-1 alone, or endothelin-1 plus sacubitrilat. Cells were treated with 10 nM endothelin-1 and/or 16 uM sacubitrilat for 48 hours simultaneously with endothelin-1. Control cells received the corresponding vehicle treatment.

value: WTC-mEGFP-ACTN2-cl85 (AICS-0075-085)

value: induced pluripotent stem cell-derived cardiomyocyte

value: heterozygous endogenous C-terminal ACTN2-mEGFP tag

value: 16 uM Sacubitrilat and 10 nM endothlin 1, 48 hours

value: Biological replicate 3


title: CD11b+NK1.1– CD45+ TILs, replicate 1, ScRNAseq

description: 10x Genomics

source_name: Tumor

value: Tumor


title: Skin, Individual 2, Summer (N2)

description: Library name: ss_2_N2


title: Sacubitrilat and Endothelin-1-treated hiPSC-CMs, biological replicate 2

description:
Library name: HS7VFC_11_et1_Sac_rep2
hiPSC-CMs treated with Sac and ET1

value: Biological replicate 2


title: Grp9, mCherry quartile sort, lower quartile

description: Library name: Grp9, eeBxb1, mCherry bin 1

value: Cultured Cells

value: Recombination into


title: Sacubitrilat-treated hiPSC-CMs, biological replicate 3

description:
Library name: HS7VFC_9_sac_rep3
hiPSC-CMs treated with ET1

value: 16 uM Sacubitrilat, 48 hours


title: Grp8, miRFP670 quartile sort, upper quartile

description: Library name: Grp8, eeBxb1, miRFP670 bin 4


title: CD11b+NK1.1– CD45+ TILs, replicate 2, ScRNAseq

description: 10x Genomics


title: Sacubitrilat-treated hiPSC-CMs, biological replicate 2

description:
Library name: HS7VFC_8_sac_rep2
hiPSC-CMs treated with ET1


title: Gills, Individual 1, Summer (N2)

description: Library name: sg_1_N2

value: summer


title: Sacubitrilat-treated hiPSC-CMs, biological replicate 1

description:
Library name: HS7VFC_7_sac_rep1
hiPSC-CMs treated with ET1

value: Biological replicate 1


title: Grp8, miRFP670 quartile sort, upper middle quartile

description: Library name: Grp8, eeBxb1, miRFP670 bin 3


title: Endothelin-1-treated hiPSC-CMs, biological replicate 3

description:
Library name: HS7VFC_6_et1_rep3
hiPSC-CMs treated with Sacubitrilat

value: 10 nM endothlin 1, 48 hours


title: Skin, Individual 1, Summer (N2)

description: Library name: ss_1_N2

value: Skin


title: Grp8, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp8, eeBxb1, miRFP670 bin 2


title: Endothelin-1-treated hiPSC-CMs, biological replicate 1

description:
Library name: HS7VFC_4_et1_rep1
hiPSC-CMs treated with Sacubitrilat


title: Endothelin-1-treated hiPSC-CMs, biological replicate 2

description:
Library name: HS7VFC_5_et1_rep2
hiPSC-CMs treated with Sacubitrilat


title: Vehicle-treated hiPSC-CMs, biological replicate 3

description:
Library name: HS7VFC_3_control_rep3
hiPSC-CMs treated with vehicle

value: 16 uM DMSO, 48 hours


title: Grp8, miRFP670 quartile sort, lower quartile

description: Library name: Grp8, eeBxb1, miRFP670 bin 1


title: Vehicle-treated hiPSC-CMs, biological replicate 1

description:
Library name: HS7VFC_1_control_rep1
hiPSC-CMs treated with vehicle


title: Gills, Individual 7, Summer (N1)

description: Library name: sg_7_N1

value: Gills

value: winter


title: Grp8, mKG quartile sort, upper quartile

description: Library name: Grp8, eeBxb1, mKG bin 4


title: hiSCs, lenti-MNDA, rep2

city: Beijing

first: Haihan

last: Xiao

address: Building N5, Jinyu Intelligent Manufacturing Factory, Haidian District, Beijing, China

institute: Everlife Biomed Co. Ltd. China

description: Library name: MNDA-rep2

data_processing:
Raw reads were processed with quality control to remove low-quality reads with a Phred quality score below 20, adapter sequences, and reads containing more than 5% ambiguous bases (N), thereby producing high-quality clean reads. The clean reads were aligned to the human reference genome Homo_sapiens.GRCh38.p13 (Gencode) using the HISAT2 software with default parameters, and the number of reads mapped to each gene was counted using FeatureCounts to obtain the raw gene expression counts.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: human induced pluripotent stem cell-derived Sertoli-like cells

growth_protocol:
The protein-coding sequences of NR5A1 and GATA4 were cloned into the transactivator vector of the Tet-On 3G Tetracycline Inducible Gene Expression System (Clonetech). Subsequently, the modified transactivator vector and response vector were co-introduced into commercially available human iPSCs via electroporation. Doxycycline (DOX)-induced expression cassette of NR5A1 and GATA4 was integrated into the cellular genome through homologous recombination. Genetically engineered founder cells were obtained after puromycin selection.
The founder cells were cultured on plates coated with iMatrix-511 SILK extracellular matrix in StemFit Basic03 medium (Ajinomoto) supplemented with human basic fibroblast growth factor (bFGF). Differentiation was initiated by switching the culture medium to DOX-conditioned medium, consisting of MEM Alpha medium supplemented with 10% KnockOut Serum Replacement, 1 × GlutaMAX, 1 × non-essential amino acids, and 5 μg/mL DOX. After 3 days of differentiation induction, cells were dissociated with TrypLE Express solution and re-plated onto LN521-precoated culture plates. DOX-conditioned medium was refreshed every other day, and differentiation was maintained for another 6 days to obtain mature hiSCs.

extract_protocol:
Total cellular RNA was extracted using Trizol reagent. Messenger RNA (mRNA) was specifically enriched from the total RNA using oligo(dT) capture beads.
RNA-seq libraries were constructed using the RNA-seq Library Prep Kit for Illumina (Cat. No. NR605, Vazyme, China), following the kit’s recommended procedures, including RNA fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adapter ligation, and PCR amplification.

treatment_protocol: hiSCs were transduced with MNDA-overexpressing lentivirus or empty control lentivirus at an MOI of 100 for 48 h. The culture medium was subsequently exchanged for G418 selection medium (final concentration 300 μg/mL), and cells were cultured for another 48 h. MNDA-overexpressing hiSCs and control cells were harvested after drug selection.

value: MNDA overexpression


title: Skin, Individual 7, Summer (N1)

description: Library name: ss_7_N1


title: hiSCs, lenti-control, rep2

description: Library name: Control-rep2

value: human induced pluripotent stem cell-derived Sertoli-like cells

value: control


title: Muscle, Individual 7, Summer (N1)

description: Library name: sm_7_N1

value: Muscle


title: hiSCs, lenti-control, rep1

description: Library name: Control-rep1


title: Grp8, mKG quartile sort, lower middle quartile

description: Library name: Grp8, eeBxb1, mKG bin 2


title: Gills, Individual 6, Summer (N1)

description: Library name: sg_6_N1


title: Grp8, mKG quartile sort, lower quartile

description: Library name: Grp8, eeBxb1, mKG bin 1


title: Skin, Individual 6, Summer (N1)

description: Library name: ss_6_N1


title: PEO1_Cis_DAC_R3

city: Bloomington

first: Heather

last: O'Hagan

state: Indiana

institute: Indiana University

description:
Library name: Sample 12
Column name in PEO1_RNA_seq_raw_count.txt: Combo_3

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.9)
Reads were aligned to the hg38 genome followed by calculation of raw read counts using STAR (version 2.7.11a)
Assembly: hg38
Supplementary files format and content: Tab-deliminated file includes raw counts for each sample from STAR

growth_protocol: PEO1 cells were cultured in RPMI media with 10% fetal bovine serum (FBS) and 2μM sodium pyruvate in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNAs were collected using RNeasy Mini Kit (QIAgen, 74106)
RNA libraries for RNA-seq were preparing using Plasmidsaurus in-house RNA-Seq pipeline

treatment_protocol: PEO1 cells were mock-treated or treated with cisplatin (13μM, 16h) and/or DAC (100nM, 72h)

value: Primary ovarian cancer cells

value: Cisplatin + DAC

tag: time

value: 72 hour


title: Grp8, mCherry quartile sort, upper quartile

description: Library name: Grp8, eeBxb1, mCherry bin 4

value: Cultured Cells


title: Grp8, mKG quartile sort, upper middle quartile

description: Library name: Grp8, eeBxb1, mKG bin 3

value: Recombination into


title: Muscle, Individual 6, Summer (N1)

description: Library name: sm_6_N1


title: PEO1_Cis_DAC_R1

description:
Library name: Sample 10
Column name in PEO1_RNA_seq_raw_count.txt: Combo_1


title: Grp8, mCherry quartile sort, upper middle quartile

description: Library name: Grp8, eeBxb1, mCherry bin 3


title: PEO1_DAC_R3

description:
Library name: Sample 9
Column name in PEO1_RNA_seq_raw_count.txt: DAC_3

value: DAC


title: Gills, Individual 5, Summer (N1)

description: Library name: sg_5_N1


title: PEO1_Cis_DAC_R2

description:
Library name: Sample 11
Column name in PEO1_RNA_seq_raw_count.txt: Combo_2


title: Sacubitrilat and Endothelin-1-treated hiPSC-CMs, biological replicate 1

description:
Library name: HS7VFC_10_et1_Sac_rep1
hiPSC-CMs treated with Sac and ET1

value: WTC-mEGFP-ACTN2-cl85 (AICS-0075-085)

value: induced pluripotent stem cell-derived cardiomyocyte

value: heterozygous endogenous C-terminal ACTN2-mEGFP tag

value: 16 uM Sacubitrilat and 10 nM endothlin 1, 48 hours