title: het, 28hpf, WGS

city: Eugene

first: Samuel

last: Bertrand

state: OR

address: 1318 Franklin Blvd

department: IMB

institute: University of Oregon

description: Library name: sib

data_processing:
Trimming of adaptors and low-quality reads was performed by Cutadapt
Alignment, quantification, and analysis of RNA sequencing data was performed using the Rsubread
Reads were aligned to a comprehensive transcript annotation for zebrafish in R (Lawson et al., 2020)
Read counts and differential gene expression analysis were performed using the Deseq2 Bioconductor R package
Assembly: Lawson lab transcriptome assembly (Lawson et al., 2020) and GRCz11
Supplementary files format and content: tab delimited text file and raw counts for each file

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA extraction was performed using a DirectZol RNA kit following manufacturer instructions for n = 5 controls and n = 5 mutants for RNA seq and n = 1 control and mutant for whole genome sequencing
Libraries were sequenced on a HiSeq 2500 using a P3 flow cell according to the manufacturer’s instructions for paired end reads.

value: whole embryo

value: heterozygous


title: cebra, 28hpf, WGS

status: Public on Oct 10 2025

type: SRA

country: USA

description: Library name: ceb

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: genotype

value: cebra


title: Heart, miR122, replicate2

city: Beijing

first: Luzi

last: Yang

address: 38 Xueyuan Road, Haidian District

country: China

institute: Peking University Health Science Ce

data_processing:
The sequencing reads were analyzed by CRISPResso2
Experimentalparameter: FASTQ files for analysis(.fastq or .fastq.gz), Reference amplicon sequence, sgRNA used, quantification window size, quantification window center, Experiment name
code: CRISPResso \ --fastq_r1 base_editor.fastq.gz \ -a NNNNNNNNNNNNNN(private) \ -g NNNNNNNNNNNNNNNNNNNNN(Private) \ -w 20 \ -wc -10 \ --base_editor_output \ --write_cleaned_report \ --place_report_in_output_folder
Assembly: mm10
Supplementary files format and content: Nucleotide_percentage_table

organism: Mus musculus

source_name: Heart

extract_protocol:
Genomic DNA was extracted from tissues using TIANamp Genomic DNA Kit (DP304, Tiangen, China)
The sgRNA-targeted loci were amplified using Taq PCR MasterMix (KT211, Tiangen, China) and purified by TIANgel Purification Kit (DP219, TIANGEN).
Amplicon-seq

value: Heart

value: WT

tag: treatment

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk9d sgRNA


title: ATAC C-YTHDF3-4-Rep2

city: Guangzhou

first: Li

last: Xinhui

address: Guangzhou

institute: Sun Yat-sen university

data_processing:
The Paired-end raw reads were mapped to the human reference genome (hg19) with Bowtie2 after adapter sequences were trimmed.
The reads were then filtered for mitochondrial reads, low-quality reads, PCR duplicates, and black list regions. The peak calling of each sample was performed by MACS2.
Peak counts were combined into an N × M matrix and then be normalized by R package DiffBind, where N represents called peaks, M represents the samples, and each value Di,j represents the peak intensity for respective peak i in sample j.
The HOMER's promoter analysis was used to identify enriched motifs for differential peak set. The differential analysis was conducted using Wilcoxon's-test.
Assembly: hg19
Supplementary files format and content: bigWig

organism: Homo sapiens

source_name: breast

growth_protocol: All MDA-MB-231 cell lines were grown in DMEM medium (HyClone) with 10% FBS (ExCell Bio) and 1% penicillin-streptomycin (Gibco).

extract_protocol:
ATAC–seq of HOTAIR-Ctrl, HOTAIR-OE, HOTAIR-Ctrl YTHDF3-KO and HOTAIR-OE YTHDF3-KO cells were performed as previously described (Corces et al., 2017). Briefly, 50000 cells were pelleted, resuspended in 50 μl of lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% NP-40, and immediately centrifuged at 500g for 10 min at 4 °C. The nuclei pellets were resuspended in 50 μl of transposition buffer (25 μl of 2× TD buffer, 22.5 μl of distilled water, 2.5 μl of Illumina Tn5 transposase) and incubated at 37 °C for 30 min. Transposed DNA was purified with the DNA Clean & Concentrator-5 kit (Zymo Research), and eluted in 10 μl of EB buffer.
Library fragments were amplified using NEBnext PCR master mix as previously described (Corces et al., 2017)

value: breast

tag: cell line

value: MDA-MB-231 cell

tag: cell type

value: breast cancer cell

value: HOTAIR-Ctrl YTHDF3-KO


title: Control3

city: Hengyang City

first: Suzhen

last: Ma

state: Hunan Province

address: 28 Changsheng West Road, Hengyang City, Hunan Province

institute: University of South China

library_source: transcriptomic

data_processing:
Adapter and low-quality reads were first trimmed using Trim Galore (version 0.4.4) in paired-end mode with default parameters. Trimmed reads were then mapped to the hg38 reference genome to count mapped reads for all human transcripts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes log2(FPKM) values for each Sample

molecule: total RNA

growth_protocol: CAL27 cells were cultured in Dulbecco’s modified Eagle medium (DMEM), supplemented with 10% fetal bovine serum (FBS, Sigma, USA).

extract_protocol:
Extraction of total RNA following the manufacturer’s instruction of the AllPrep DNA/ RNA/miRNA Universal Kit (80224, Qiagen, USA).
For library preparation, 1 mg of total RNA from each sample was depleted for rRNA using the Ribo−Zero rRNA Removal Kit (RZH1046, EPICENTRE, USA), followed by construction of sequencing library using the TruSeq RNA Sample Prep Kit v2 (RS−122, Illumina, USA).

treatment_protocol: Constructing stable cell lines of CAL27 with overexpression of CNTNAP2-203:Lentiviral particles containing the control vector or CNTNAP2-203, were individually produced in HEK_x001E_293T cells. The supernatants containing the lentiviral particles were harvested. OSCC cells were infected with the respective lentiviruses, followed by selection with 5 μg/ml puromycin (Beyotime, China) for 2 weeks.

value: oral squamous cell carcinoma


title: het, 28hpf rep4

description: Library name: sibs-4


title: ATAC C-YTHDF3-4-Rep1


title: Muscle, miR122, replicate1

source_name: Muscle

value: Muscle

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk8d sgRNA


title: prefrontal cortex , MS group ,rep 5

city: Tokyo

first: Eman

middle: Abdo

last: Mady

address: Harumicho

department: veterinary medicine

country: Japan

institute: Tokyo university Of Agriculture and technology

description: Library name: MS5

data_processing:
Data integrity and quality control of the sequenced raw reads were checked by FastQC v0.11.7 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Overall reads’ quality, total bases, total reads, GC (%), and basic statistics were calculated. To reduce biases in the analysis, artifacts such as low-quality reads, adaptor sequences, contaminant DNA, or PCR duplicates were removed using Trimmomatic 0.38 software (http://www.usadellab.org/cms/?page=trimmomatic).
Trimmed readings are mapped to the reference genome with HISAT2 version 2.1.0 (https://ccb.jhu.edu/software/hisat2/index.shtml), a splice-aware aligner. To map cDNA fragments obtained from RNA sequencing, mm10 was used as a reference genome. After the read mapping, the transcript was assembled by StringTie version 2.1.3b (https://ccb.jhu.edu/software/stringtie/)  with aligned reads. Transcripts were additionally assembled from the results of mapped reads to predict novel transcripts and novel alternative splicing transcripts without the StringTie-e option. The assembled annotation (GTF file) of samples was merged into one merged file with the StringTie-merge option. Then, the abundances of samples were calculated for known and novel transcripts.
Expression profiles were represented as read count and normalization values which were calculated based on transcript length and depth of coverage. Normalization values were provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) / RPKM (Reads Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million)
In groups with different conditions, genes or transcripts that expressed differentially were filtered out through statistical hypothesis testing. Differentially Expressed Genes (DEG) analysis was performed on 4 comparison pairs as requested using DESeq2
Assembly: (Reads Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted from the prefrontal cortex using the ISOGEN II Reagent (Nippon Gene Co., Ltd, Tokyo, Japan). The quality of the isolated total RNA was confirmed and the grade of RNA in all samples was unified.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Mice were euthanized for brain sample collection and molecular assessments and then these samples Kept in dry ice during the collection and then these samples stored at - 80°C until further analysis

value: brain

value: prefrontal cortex

value: wild type

value: MS treatment


title: het, 28hpf rep3

description: Library name: sibs-3

value: whole embryo


title: Brain, miR122, replicate1

source_name: Brain

value: Brain

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk7d sgRNA


title: ATAC C-YTHDF3-2-Rep2


title: prefrontal cortex , MS group ,rep 4

description: Library name: MS4


title: prefrontal cortex ,MS group ,rep1

description: Library name: MS1


title: ATAC C-P18-Rep2

value: HOTAIR-Ctrl


title: het, 28hpf, rep1

description: Library name: sibs-1

value: heterozygous


title: Liver, miR122, replicate1

source_name: Liver

value: Liver

value: WT

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk3d sgRNA


title: cebra, 28hpf, rep3

description: Library name: CTD-3

value: cebra


title: Kindey, miR122, replicate1

source_name: Kindey

value: Kindey

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk6d sgRNA


title: ATAC C-puro-8-Rep2

value: breast

value: MDA-MB-231 cell

value: breast cancer cell


title: Lung, miR122, replicate1

source_name: Lung

value: Lung

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk5d sgRNA


title: prefrontal cortex , MS group ,rep 3

description: Library name: MS3

value: brain

value: prefrontal cortex

value: wild type

value: MS treatment


title: cebra, 28hpf, rep2

description: Library name: CTD-2

value: whole embryo


title: Heart, miR122, replicate1

value: Heart

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk2d sgRNA


title: ATAC C-YTHDF3-2-Rep1

value: HOTAIR-Ctrl YTHDF3-KO


title: het, 28hpf, rep2

description: Library name: sibs-2

value: heterozygous


title: ATAC C-P18-Rep1

value: HOTAIR-Ctrl


title: prefrontal cortex , control group,rep6

description: Library name: C6

value: no treatment


title: cebra, 28hpf, rep1

description: Library name: CTD-1

value: cebra


title: ATAC C-NT-1-1-Rep2

value: breast


title: prefrontal cortex , control group,rep5

description: Library name: C5


title: prefrontal cortex , control group, rep4

description: Library name: C4


title: Neonatal_sg2_Liver,S10

source_name: liver

value: liver

value: WT


title: Brain, sgRNA, replicate5

value: Brain

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk2d sgRNA


title: prefrontal cortex , MS group ,rep 6

description: Library name: MS6

value: brain


title: ATAC C-NT-1-1-Rep1

value: MDA-MB-231 cell

value: breast cancer cell


title: Bt-S4

city: Los Angeles

first: Benjamin

last: Macadangdang

state: CA

address: 10833 Le Conte Ave, MDCC B2-375

institute: University of California, Los Angeles

data_processing:
Raw sequencing reads from RNA-seq experiments were quality filtered and trimmed with fastp v0.23.4121 with default parameters, then mapped to the reference genome of each respective species with bwa-mem2122 with default parameters. Mapping statistics were generated with bamtools123 v2.5.1 and visualized with multiqc124 v1.21. Reads in gene features were counted with featureCounts125 function of the subread package at the fragment level (--countReadPairs) with fragments overlapping multiple features counted in both (-O).
Assembly: GCF_000154125.1, GCF_000210835.1, GCF_000304195.1, GCF_000011065.1, GCF_000154205.1
Supplementary files format and content: tab delimited file of raw counts for each gene

organism: Bacteroides thetaiotaomicron VPI-5482

growth_protocol: Bacteroides strains were grown in Brain Heart Infusion (BHI, BD Difco) medium at 37°C, supplemented with vitamin K (5 µg/mL) and hemin (5 µg/mL), and incubated in an anaerobic chamber (Coy) under 5% H2, 10% CO2, 85% N2 for 24 hours.

extract_protocol:
Cells were flash-frozen in a dry ice-ethanol slurry, then pelleted by centrifugation at 16,000xg for 1 minute at 4°C. The bacterial pellets were stored at −80°C until RNA extraction. RNA was extracted using TRIzol reagent and the PureLink™ RNA Mini Kit following the manufacturer’s instructions. Briefly, bacterial pellets were incubated with 1 mL of TRIzol for 5 minutes at room temperature, followed by the addition of 200 µL of chloroform. After 5 minutes at room temperature, the samples were centrifuged at 12,000xg for 15 minutes at 4°C. The aqueous phase was transferred to a new tube, and an equal volume of 100% ethanol was added. This mixture was transferred to a spin cartridge and centrifuged at 12,000xg for 15 seconds at room temperature. RNA samples were treated with PureLink™ DNase I, according to the manufacturer’s protocol. Following DNase treatment and four wash steps, RNA was eluted in 50 µL of RNase-free water by centrifugation at 12,000xg for 1 minute. Eluted RNA was transferred to RNase-free tubes and analyzed for quality by agarose gel electrophoresis. RNA integrity was assessed using the Bio-Rad ChemiDoc system, and RNA concentration was quantified with a NanoDrop One spectrophotometer (Thermo Fisher Scientific). Further RNA quality and concentration was validated on an Agilent 4200 TapeStation RNA ScreenTape, with all RIN scores above 8.0 and samples normalized to 250 ng starting mass.
Library preparation was performed using Illumina’s Stranded Total RNA Prep with Ribo-Zero Plus Microbiome, which targets depletion of microbiome rRNA prior to cDNA synthesis and library formation. Final libraries were validated using an Agilent 4200 TapeStation D1000 ScreenTape, with an average fragment size of 396bp. Libraries were quantified using Invitrogen’s Quant iT High Sensitivity dsDNA Kit and normalized during pooling.

tag: strain


title: prefrontal cortex ,MS group ,rep2

description: Library name: MS2

value: prefrontal cortex

value: wild type

value: MS treatment


title: Neonatal_sg2_Heart,S12

source_name: heart

value: heart


title: Bt-S2


title: Lung, sgRNA, replicate5

value: Lung


title: prefrontal cortex , control group ,rep 1

description: Library name: C1


title: Kindey, sgRNA, replicate5

value: Kindey


title: Neonatal_sg2_Heart,S11


title: Muscle, sgRNA, replicate5

value: Muscle


title: Neonatal_sg2_Liver,S9


title: Bt-S3


title: WT_L4h_PL_replicate_3

city: Taipei

first: Meng-Chun

last: Lin

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plant and Microbial Biology

data_processing:
Read mapping and RPKM calculation using RACKJ
RNA-seq reads were aligned to the TAIR10 genome assembly using BLAT with the following condition: >95% identity mapping
Calculation of reads per kilobase per million (RPKM) involved use of RACKJ software
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with RPKM values.

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 (WT) was surface sterilized, sown on half-strength MS medium plates (0.8% agar, pH 5.7), and kept at 4oC in darkness for 4 days for stratification

extract_protocol:
The aerial part of seedlings was harvested and ground by liquid nitrogen. Plant tissues were frozen and ground in liquid nitrogen and extracted by vortexing with eight volumes of extraction buffer [2% hexadecyltrimethylammonium bromide, 2% polyvinylpyrrolidone K 30, 100 mm 2-amino-2-(hydroxymethyl)-1,3-propanediol (TRIS)–HCl, pH 8.0, 25 mm EDTA, 2.0 m NaCl, 0.5 g l−1 spermidine, 2% 2-mercaptoethanol] prewarmed at 65°C. The homogenate was then extracted twice with an equal volume of chloroform:isoamyl alcohol (24:1) by vortexing and centrifugation for 10 min at 12 000 g. One-quarter volume of 10 m LiCl was then added to the aqueous phase for selective precipitation of RNA molecules. After overnight incubation at 4°C, the RNA pellet was harvested by centrifugation at 12 000 g for 20 min, washed with 75% ethanol (EtOH) and dissolved in 200 μl RNase-free water. The quality of RNA samples was assessed with use of the Agilent Bioanalyzer2100 and the Agilent RNA 6000 Nano Assay Kit.
Library construction protocol not provided.

treatment_protocol: The seeds were grown in darkness at 22 oC  for 4 days (Dark), further illuminated with white light (100 μmole m-2 s-1) for 4 h (L4h), or remained in the dark for 4 h (D4h)

value: Seedlings

tag: cultivar


title: Neonatal_sg2_Liver,S8


title: Spleen, sgRNA, replicate5

source_name: Spleen

value: Spleen


title: WT_L4h_PL_replicate_2


title: Bt-S1


title: Neonatal_sg2_Heart,S10


title: SUM159-CD36-Palmitate

city: Paris

first: Michèle

last: SABBAH

address: Hôpital Saint-Antoine, 34 rue Crozatier, Bâtiment Kourilsky, 1er étage

country: France

institute: INSERM U938

description: Library name: LC8

data_processing:
Sequencing depth ranged from 51 025 206 to 67 741 690 reads per sample. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low-quality reads from raw data.
Q20, Q30 and GC content of the clean data were calculated
Clean reads were mapped on the Homo Sapiens hg38 reference genome using HISAT2 v2.0.5 and featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab delimited text files include raw counts for each sample

molecule: polyA RNA

growth_protocol: Ham’s F12 medium supplemented with 2% heat inactivated FBS, 10 mM HEPES, 1 µg/mL hydrocortisone and 5 µg/mL of human insulin

extract_protocol:
RNA was extracted by TRIzol reagent, RNA integrity (RIN) was assessed using the RNA 6000 Nano kit (Agilent) and a Bioanalyzer 2100 system (Agilent).
PolyA mRNA selection, cDNA libraries preparation and sequencing were conducted by Novogene (Munich, Germany) using the Illumina NOVAseq X Plus platform

treatment_protocol: Cells were treated or not with 200microM palmitate for 24h

value: Palmitate


title: WT_L4h_PL_replicate_1


title: Neonatal_sg2_miR122_Liver,S4

value: liver


title: SUM159-CD36

description: Library name: LC7

value: No


title: SUM159-WT-Palmitate

description: Library name: LC6


title: cebra, 28hpf, rep4

description: Library name: CTD-4

value: whole embryo

value: cebra


title: Muscle, control, replicate1

value: WT

value: Control


title: Muscle, sgRNA, replicate4

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk2d sgRNA


title: prefrontal cortex , control group ,rep 3

description: Library name: C3

value: brain

value: prefrontal cortex

value: no treatment


title: WT_Dark_PL_replicate_3


title: Neonatal_sg2_miR122_Heart,S4

value: heart


title: Liver, sgRNA, replicate5

value: Liver


title: prefrontal cortex , control group, rep 2

description: Library name: C2

value: wild type


title: Spleen, miR122, replicate1

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk4d sgRNA


title: Brain, sgRNA, replicate4

value: Brain


title: MCF7-CD36-Palmitate

description: Library name: LC4


title: Heart, sgRNA, replicate5

value: Heart


title: WT_Dark_PL_replicate_1

value: Seedlings


title: WT_Dark_PL_replicate_2


title: MCF7-Palmitate

description: Library name: LC2

value: Palmitate


title: Spleen, sgRNA, replicate4

value: Spleen


title: Neonatal_sg2_miR122_Heart,S3


title: Neonatal_sg2_miR122_Liver,S2

value: liver


title: Neonatal_sg2_miR122_Liver,S3


title: Kindey, sgRNA, replicate4

value: Kindey


title: MCF7-CD36

description: Library name: LC3

value: No


title: WT_D4h_replicate_3

source_name: Arabidopsis seedlings_total RNA_D4h


title: WT_D4h_replicate_1


title: Neonatal_sg2_Liver,S7

value: WT


title: RNA OE-YTHDF3-4-Rep2

data_processing:
Raw reads were aligned to the human reference sequences build GRCh37/UCSC hg19 with HISAT2 aligner.
Expression levels of RefSeq annotated genes were calculated using featureCount.
The differential analysis was conducted using Wilcoxon's -test.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Total RNA of MDA-MB-231 cells with different treatments were extracted using Quick-RNA Miniprep Kit (Zymo Research).
Poly-A-selected RNA was isolated and the libraties were prepared with the dUTP protocol.

value: breast

value: MDA-MB-231 cell

value: breast cancer cell

value: HOTAIR-OE YTHDF3-KO


title: WT_D4h_replicate_2


title: Lung, sgRNA, replicate4

value: Lung

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk2d sgRNA


title: Heart, sgRNA, replicate4


title: Neonatal_sg2_miR122_Liver,S1


title: Neonatal_sg2_miR122_Heart,S2

value: heart


title: Muscle, sgRNA, replicate3

value: Muscle


title: WT_L4h_replicate_3

source_name: Arabidopsis seedlings_total RNA_L4h


title: RNA OE-YTHDF3-4-Rep1


title: WT_L4h_replicate_2


title: SUM159-WT

description: Library name: LC5


title: Neonatal_sg2_Heart,S9


title: Brain, sgRNA, replicate3

value: Brain


title: WT_L4h_replicate_1


title: RNA OE-YTHDF3-2-Rep2


title: Kindey, sgRNA, replicate3


title: RNA OE-YTHDF3-1-Rep2


title: Lung, sgRNA, replicate3


title: RNA OE-YTHDF3-2-Rep1


title: Neonatal_sg2_Heart,S7


title: Liver, sgRNA, replicate4

value: Liver


title: MCF7-WT

description: Library name: LC1


title: Spleen, sgRNA, replicate3


title: WT_Dark_replicate_3

source_name: Arabidopsis seedlings_total RNA_dark

value: Seedlings


title: Neonatal_sg2_Heart,S8


title: WT_Dark_replicate_1


title: WT_Dark_replicate_2


title: Neonatal_sg2_Liver,S5


title: Heart, sgRNA, replicate3

value: Heart


title: RNA OE-YTHDF3-1-Rep1


title: Muscle, sgRNA, replicate2


title: OVCAR5 cisplatin resistant cells, brequinar treatment, rep 3

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

description: Library name: OV5CRBQ3

data_processing:
Fastq files were pre-analyzed using FastQC (0.11.5)
Reads were aligned to the ENSEMBL human genome GRCh38 (release 91) using STAR (2.5.2)
BAM files from STAR alignment were sorted by name using Samtools (1.6)
HTSeq-count (anaconda 3.6) was used to generate raw counts for each BAM file
Assembly: GRCh38
Supplementary files format and content: counts

source_name: cell line

growth_protocol: OVCAR5 Cells were cultured in RPMI 1640 (Corning), 10% fetal bovine serum (FBS) (Corning), 1% penicillin/streptomycin (Sigma), and 1X GlutaMAX (Gibco). Cell lines were grown in a humidify atmosphere, 5% and 37°C.

extract_protocol:
RNA was isolated by using TRIzol (Invitrogen) according to the manufacturer’s instructions and quantified using a NanoDrop 3300 Fluorospectrometer.
The RNA-sequencing (RNA-seq) libraries were prepared from 1 μg of total RNA of OVCAR5. Libraries were generated using the NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs, Inc.). Library preparation was performed accoding to manufacter's protocol.

value: cell line

value: OVCAR5 cisplatin resistant

value: High grade serous ovarian cancer

value: Brequinar


title: RNA OE-YTHDF3-5-Rep2

value: HOTAIR-OE


title: Neonatal_sg2_miR122_Heart,S1

value: WT


title: Neonatal_sg2_Liver,S6

value: liver


title: OVCAR5 cisplatin resistant cells, brequinar treatment, rep 2

description: Library name: OV5CRBQ2


title: RNA OE-YTHDF3-5-Rep1

value: breast

value: MDA-MB-231 cell

value: breast cancer cell


title: Neonatal_sg2_Liver,S4


title: RNA OE-puro-3-Rep1


title: OVCAR5 cisplatin resistant cells, control, rep 3

description: Library name: OV5CRC3

value: Control


title: Neonatal_sg2_Liver,S3


title: Brain, sgRNA, replicate2

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk2d sgRNA


title: Neonatal_sg2_Heart,S6

value: heart


title: OVCAR5 cisplatin resistant cells, brequinar treatment, rep 1

description: Library name: OV5CRBQ1


title: RNA OE-P18-Rep2


title: Liver, sgRNA, replicate3


title: Kindey, sgRNA, replicate2

value: Kindey


title: Neonatal_sg2_Heart,S5


title: OVCAR5 cisplatin resistant cells, control, rep 2

description: Library name: OV5CRC2


title: Neonatal_sg2_Heart,S4


title: Lung, sgRNA, replicate2

value: Lung


title: RNA C-YTHDF3-4-Rep2

value: HOTAIR-Ctrl YTHDF3-KO


title: RNA OE-P18-Rep1


title: Spleen, sgRNA, replicate2

value: Spleen


title: OVCAR5 cisplatin resistant cells, control, rep 1

description: Library name: OV5CRC1

value: cell line


title: RNA C-YTHDF3-4-Rep1


title: Neonatal_sg2_Heart,S3


title: RNA OE-puro-3-Rep2


title: OVCAR5 cisplatin sensitive cells, brequinar treatment, rep 3

description: Library name: OV5WTBQ3

value: OVCAR5 cisplatin sensitive


title: OVCAR5 cisplatin sensitive cells, brequinar treatment, rep 2

description: Library name: OV5WTBQ2

value: High grade serous ovarian cancer


title: Heart, sgRNA, replicate2

value: Heart


title: OVCAR5 cisplatin sensitive cells, brequinar treatment, rep 1

description: Library name: OV5WTBQ1

value: Brequinar


title: RNA C-YTHDF3-2-Rep2


title: Neonatal_sg2_Liver,S2

value: WT


title: Neonatal_sg2_Heart,S2


title: Neonatal_sg2_Liver,S1

value: liver


title: OVCAR5 cisplatin sensitive cells, control, rep 3

description: Library name: OV5WTC3


title: Brain, sgRNA, replicate1

value: Brain


title: RNA C-YTHDF3-2-Rep1

value: breast

value: MDA-MB-231 cell


title: Neonatal_sg2_Heart,S1


title: RNA C-puro-8-Rep2

value: breast cancer cell

value: HOTAIR-Ctrl


title: OVCAR5 cisplatin sensitive cells, control, rep 2

description: Library name: OV5WTC2

value: Control


title: OVCAR5 cisplatin sensitive cells, control, rep 1

description: Library name: OV5WTC1


title: Kindey, sgRNA, replicate1

value: Kindey

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk2d sgRNA


title: RNA C-puro-8-Rep1


title: Adult_sg2_1086_liver


title: RNA C-P18-Rep2


title: Spleen, sgRNA, replicate1


title: RNA C-P18-Rep1


title: E4.5 Sox2 KO rep 2, scRNAseq

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
We merged the GRCm39 reference genome with the eGFP reporter vector sequence to create a custom reference. We then used STAR version 2.7.10a to generate a reference genome index, with reporter features and Gencode annotations vM29.
FASTQ reads were mapped against the reference genome index using STAR with the settings “--soloType CB_UMI_Complex --soloCellFilter None --outSAMtype BAM SortedByCoordinate --soloFeatures GeneFull_Ex50pAS --soloCBmatchWLtype 1MM  --soloUMIlen 8 --runRNGseed 1 --soloMultiMappers EM --readFilesCommand zcat --outSAMattributes NH HI AS nM NM MD jM jI MC ch CB UB GX GN sS CR CY UR UY”.
Libraries using standard BD Rhapsody beads were mapped using the adapter parameters “--soloAdapterSequence NNNNNNNNNACTGGCCTGCGANNNNNNNNNGGTAGCGGTGACA --soloCBposition 2_0_2_8 2_21_2_29 3_1_3_9 --soloUMIposition 3_10_3_17 --soloCBwhitelist BD_CLS1.txt BD_CLS2.txt BD_CLS3.txt”, libraries with BD Rhapsody enhanced beads with --soloAdapterSequence NNNNNNNNNGTGANNNNNNNNNGACA --soloCBposition 2_0_2_8 2_13_2_21 3_1_3_9 --soloUMIposition 3_10_3_17 --soloCBwhitelist BD_CLS1_v2_draft.txt BD_CLS2_v2_draft.txt BD_CLS3_v2_draft.txt”.
Raw counts were imported as AnnData objects. We removed low complexity barcodes with the knee plot method, and further filtered out cells with a mitochondrial mRNA content, as well as unusually high total and gene counts using manually determined cutoffs for each sample. Doublets were scored with scrublet 0.2.3.
Finally, each sample’s gene expression matrix was normalized using scran (1.22.1) with Leiden clustering input at resolution 0.5.
Assembly: mm39
Supplementary files format and content: Tab-separated values files, MatrixMarket files, and AnnData files

source_name: Whole Embryo

extract_protocol:
Single cell suspension was obtained by dissociating embryos for 10-15min at 37 °C with TrypLE express enzyme. The cells were then loaded on to a microwell cartridge of BD Rhapsody Express system (BD Biosciences).
Single-cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using a BD Rhapsody WTA Reagent kit (BD Biosciences) and sequenced on the Illumina NextSeq 500 using the High Output Kit v2.5 (150 cycles, Illumina) or the Mid Output Kit (150 cycles, Illumina).

treatment_protocol: E2.5 Control and Sox2 KO embryos were collected by flushing the uterus with M2 medium. Embryos were then cultured in KSOM for the following 48hours till they developed into E4.5 embryos. Embryos were then subjected to zona removal via treatment with Tyrode's Solution and then washed in fresh PBS (without calcium and magnesium) and dissociated by TrypLE express enzyme (no phenol red, Thermo Fisher Scientific).

value: Whole Embryo

tag: age

value: 10-13 weeks

value: Sox2fl/ZP3Cre, Sox2 KO

tag: developmental stage


title: Lung, sgRNA, replicate1

value: Lung


title: E4.5 Sox2 KO rep 1, scRNAseq

description: BD Rhapsody

growth_protocol: E2.5 Control and Sox2 KO embryos were collected by flushing the uterus with M2 medium. Embryos were then cultured in KSOM for the following 48hours till they developed into E4.5 embryos.


title: Liver, sgRNA, replicate2

value: Liver


title: Liver, sgRNA, replicate1


title: Heart, sgRNA, replicate1

value: Heart


title: Adult_sg2_1085_heart

value: heart


title: Adult_sg2_1085_liver

value: WT


title: RNA C-NT-1-1-Rep1


title: Microglia, PLCG2 P522R, Basal, 3

status: Public on Oct 09 2025

city: Indianapolis

first: Logan

middle: Michael

last: Bedford

state: Indiana

address: 350 W 14th Street

department: Pharmacology and Toxicology

institute: Indiana University School of Medicine

description: Library name: Batch4-P522R-RNA

data_processing:
Sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK) for quality control.
The sequence data was then mapped to the human reference genome hg38 using the RNA-seq aligner STAR (v.2.7.10a).
Reads mapped to each gene were counted using featureCounts (v. 2.0.3).
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

growth_protocol: iPSCs were cultured on 6-well plates coated with hESC-qualified Matrigel (Fisher Scientific 8774552) and grown in mTeSR PLUS (STEMCELL Technologies 100-0276) media. Media were changed every two days. Colonies were grown to ~60-70% confluency before being passaged with ReLeSR (STEMCELL Technologies 100-0484), an enzyme-free method for colony dissociation. Colonies were then either replated at a 1:200 dilution for expansion or used for differentiation into human microglia-like cells (MGLs). Differentiation of iPSCs into MGLs was performed following previously established protocols [33]. In brief, iPSC colonies were cultured on Matrigel until they reached approximately 75% confluency. Then, enzyme-free dissociation with ReLeSR reagent was used to detach cells from the plate. The colonies (150-200 microns/colony) were then plated onto Matrigel-coated 6-well plates at a density of 35-40 colonies per well. Differentiation into hematopoietic progenitor cells (HPCs) was carried out using the STEMdiff Hematopoietic Kit (STEMCELL Technologies 5310). On day 12 of differentiation, HPCs were collected from the media, resuspended in Bambanker Freeze (Fujifilm Irvine Scientific 302-14686) at a density of 500,000 cells/mL, and cryopreserved in liquid nitrogen to create an HPC stock for subsequent MGL differentiation. To differentiate HPCs into MGLs, cryopreserved vials of HPCs were thawed and transitioned into Microglia Basal Media, which consisted of DMEM/F12 (Life Technologies 11330-057), 2% Insulin-Transferrin-Selenium (Life Technologies 41400045), 2% B27 (Life Technologies 17504001), 1% Antibiotic-Antimycotic (Life Technologies 15240062), 1% MEM NEAA (Life Technologies 11140050), 1% Glutamax (Life Technologies 35050061), 0.5% N2 (Life Technologies 17502048), 0.2 mg/mL insulin (Millipore-Sigma I2643), and 400 µM monothioglycerol (Millipore-Sigma M1753), supplemented with 100 ng/mL IL-34 (Peprotech 200-34-500ug), 50 ng/mL TGF-β1 (Peprotech 100-21-100µg), and 25 ng/mL M-CSF (Peprotech 300-25-100ug). HPCs in Microglia Basal Media were plated in parallel into two wells of a 6-well plate. Media was replenished every 48 h. After 25–28 days of maturation, MGLs were collected for analysis. differentiations.

extract_protocol:
In order to obtain RNA from both the adherent MGLs and the MGLs suspended in culture, the media from 28-day, mature MGLs in a 6-well plate were collected, centrifuged for 5 min at 300 x g, washed once with PBS and recentrifuged for 3 min at 500 x g. Adherent MGLs from the same plate were washed once with PBS. Then RNA was isolated directly from the well using Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific 2970541) according to manufacturer’s instructions. The adherent and nonadherent microglia were combined in RNA extraction buffer. One well per line was collected over four batches of differentiation.
RNA libraries were prepared from 100 nanograms of total RNA using Illumina Stranded mRNA Prep, Ligation kit (Illumina), following the manufacturer’s instructions.

value: iPSC derived Microglia-like cells

value: PLCG2 P522R

tag: batch


title: RNA C-NT-1-1-Rep2

value: breast


title: Microglia, PLCG2 P522R, Basal, 4

description: Library name: Batch5-P522R-RNA


title: Muscle, sgRNA, replicate1

value: Muscle


title: Microglia, PLCG2 P522R, Basal, 2

description: Library name: Batch3-P522R-RNA


title: Microglia, PLCG2 P522R, Basal, 1

description: Library name: Batch2-P522R-RNA


title: Microglia, PLCG2 M28L, Basal, 2

description: Library name: Batch3-M28L-RNA

value: PLCG2 M28L


title: Microglia, PLCG2 M28L, Basal, 3

description: Library name: Batch4-M28L-RNA


title: Microglia, PLCG2 M28L, Basal, 1

description: Library name: Batch2-M28L-RNA


title: Microglia, PLCG2 KO, Basal, 4

description: Library name: Batch5-KO-RNA

value: PLCG2 KO


title: Microglia, WT, Basal, 4

description: Library name: Batch5-WT-RNA


title: Microglia, PLCG2 KO, Basal, 3

description: Library name: Batch4-KO-RNA


title: Microglia, PLCG2 KO, Basal, 2

description: Library name: Batch3-KO-RNA


title: Microglia, WT, Basal, 2

description: Library name: Batch3-WT-RNA


title: Microglia, PLCG2 KO, Basal, 1

description: Library name: Batch2-KO-RNA


title: Microglia, WT, Basal, 1

description: Library name: Batch2-WT-RNA


title: MDA-MB-231, KIF20A OE1

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description: Library name: Sample 22

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Processed reads were aligned to the GRCh38 human reference genome.
Supplementary files format and content: tab delimited txt files include count values for each sample

source_name: Breast cancer

extract_protocol:
Total RNA was isolated from tumor cell lysates (biological triplicates per experimental group) using the RNeasy Mini Kit (QIAGEN, cat# 74104) following the manufacturer's protocol, with on-column DNase I treatment to eliminate genomic DNA contamination. RNA integrity was verified to meet stringent quality control standards for sequencing.
Stranded mRNA sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) through poly-A selection, followed by fragmentation, cDNA synthesis, end repair, adapter ligation, and PCR amplification.

value: Breast cancer

value: Breast cancer cell

value: KIF20A overexpression


title: Adult_sg2_1086_heart


title: E4.5 control, scRNAseq

description: BD Rhapsody

value: Whole Embryo

value: Oct4fl/Sox2fl, Control


title: MDA-MB-231, KIF20A OE3

description: Library name: Sample 24


title: MDA-MB-231, KIF20A OE2

description: Library name: Sample 23


title: MDA-MB-231, EV3

description: Library name: Sample 21

value: empty control vector


title: MDA-MB-231, EV2

description: Library name: Sample 20


title: MDA-MB-231, KIF20A SG3

description: Library name: Sample 18

value: KIF20A knockdown


title: MDA-MB-231, sgCTRL2

description: Library name: Sample 14

value: Control sgRNA


title: MDA-MB-231, KIF20A SG1

description: Library name: Sample 16


title: MDA-MB-231, KIF20A SG2

description: Library name: Sample 17


title: MDA-MB-231, sgCTRL1

description: Library name: Sample 13


title: MDA-MB-231, EV1

description: Library name: Sample 19


title: MDA-MB-231, sgCTRL3

description: Library name: Sample 15


title: Microglia, PLCG2 M28L, Basal, 4

description: Library name: Batch5-M28L-RNA


title: HCC70, POS3

description: Library name: Sample 12

value: sorted BCSC


title: HCC70, NEG3

description: Library name: Sample 9

value: sorted non-BCSC


title: HCC70, POS1

description: Library name: Sample 10

value: WT


title: HCC70, NEG2

description: Library name: Sample 8


title: HCC70, NEG1

description: Library name: Sample 7


title: Hs578T, POS3

description: Library name: Sample 6


title: Hs578T, POS2

description: Library name: Sample 5


title: HCC70, POS2

description: Library name: Sample 11


title: Microglia, WT, Basal, 3

description: Library name: Batch4-WT-RNA

value: iPSC derived Microglia-like cells


title: Hs578T, NEG3

description: Library name: Sample 3


title: Hs578T, NEG2

description: Library name: Sample 2


title: MmKidAt_20220810A_ATAC

city: Saint Louis

first: Madhurima

last: Kaushal

address: 1 Brookings Dr

institute: Washington University in St Louis

description: Library name: MmKidAt_20220810A_ATAC

library_source: genomic single cell

data_processing:
Raw fastq data were processed with the cellranger-arc (v2.0.2) software with the GRCm39 mouse genome reference.
Assembly: GRCm39
Supplementary files format and content: Genes expression files in the Market EXchange format (MEX) that is comprised of the tab seperated files for the columns which are cell ids (*barcodes.tsv.gz), the rows which are Ensembl gene ids (*features.tsv.gz) and gene expression counts (*matrix.mtx.gz).
Supplementary files format and content: Chromatin accessibility (ATAC-seq) processed files are the Hierarchical Data Format (H5), *feature_bc_matrix.h5 file containing the count of reads within individual called peaks and the tab separated file *fragments.tsv file containing the positions of mapped reads, cell ids which each reads are assigned and value representing the number of reads aligned to the same positions.

source_name: mature,Male,wt

extract_protocol:
10x Chromium Nuclei Isolation Kit (Sample User Guide, CG000505 Rev A)
Single nuclei suspensions were generated from OCT embedded tissue sections following manufacturer's protocols using the 10X Genomics Chromium Nuclei Isolation Kit (PN-1000494). Single nuclei ATAC and Genes Expression libraries were generated from nuclei suspensions following manufacturer's protocols using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (PN-1000283).

value: kidney

tag: Sex

value: Male

value: mature

value: wildtype


title: MmKidAt_20220810A_RNA

description: Library name: MmKidAt_20220810A_RNA


title: Hs578T, POS1

description: Library name: Sample 4


title: 99866_mast1_rep_A

city: Worcester

first: Athma

last: Pai

state: MA

address: 368 Plantation Street, AS5-2057

department: RNA Therapeutics Institute

institute: UMASS Medical School

description: Library name: 99866_mast1_rep_A

data_processing:
Quality control of fastqs were performed using fastqc. Fastqs were trimmed using bbduk from the BBmap package to remove adapter comtamination and rRNA and poly-A artifacts. Fastqs were aligned to GRCh38 via STAR.
Assembly: GRCh38
Supplementary files format and content: featureCounts v.2.0.3 was used to count reads based on the meta exon file, produced from genome version Ensembl_GRCh38.p14_GCA_000001405.29. Meta exon gtf was created according to https://github.com/thepailab/HITindex command used to obtain featurecounts: # Program:featureCounts v2.0.3; Command:“featureCounts” “-T” “4” “-p” “-s” “2" “-O” “-f” “-t” “exon”

growth_protocol: HEK293 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing D-Glucose (4.5 g/L), L-Glutamine and 10% fetal bovine serum (FBS).

extract_protocol:
48 hours post transfection, total RNA was extracted using RNeasy Mini Kit according to the manufacturer’s instructions. Reverse transcription was performed in a reaction mix containing 1 μg of total RNA, using Maxima H Minus First Strand cDNA Synthesis Kit (Thermo Scientific, K1652) according to the manufacturer’s instructions.
Samples 1-15: Samples 16-24: Novogene Directional mRNA library preparation (poly A enrichment),NovaSeq X Plus Series (PE150)

treatment_protocol: Cells were seeded into 6-well plates and transiently transfected ~16 hours later, at ~80% confluency, using lipofectamine3000 (Invitrogen L3000001) CRISPR activaton experiments were transfected with either UniSAM empty vector (Addgene #99866) or UniSAM vector containing sgRNA targeting the promoter region of the targeted first exon. CRISPR inteference experiments were transfected with either dCas9-P2A-EGFP empty vector (Addgene #159086) or dCas9-P2A-EGFP vector containing sgRNA targeting downstream of the transcription start site of the targeted first exon.

value: embryonic kidney cells

value: CRISPRa against the second first exon of MAST1


title: 99866_mast1_rep_B

description: Library name: 99866_mast1_rep_B


title: TFX_99866_TP53_AFE1_rep_C

description: Library name: TFX_99866_TP53_AFE1_rep_C

value: CRISPRa against the first first exon of TP53


title: 99866_znf638_rep_A

description: Library name: 99866_znf638_rep_A

value: CRISPRa against the first first exon of ZNF638


title: 99866_control_rep_A

description: Library name: 99866_control_rep_A

value: CRISPRa control


title: 99866_znf638_rep_B

description: Library name: 99866_znf638_rep_B


title: TFX_99866_TP53_AFE1_rep_B

description: Library name: TFX_99866_TP53_AFE1_rep_B


title: 99866_znf638_rep_C

description: Library name: 99866_znf638_rep_C


title: 99866_control_rep_B

description: Library name: 99866_control_rep_B


title: TFX_99866_TP53_AFE1_rep_A

description: Library name: TFX_99866_TP53_AFE1_rep_A


title: TFX_99866_SYT9_AFE2_rep_C

description: Library name: TFX_99866_SYT9_AFE2_rep_C

value: CRISPRa against the second first exon of SYT9


title: 99866_control_rep_C

description: Library name: 99866_control_rep_C


title: TFX_99866_SYT9_AFE2_rep_A

description: Library name: TFX_99866_SYT9_AFE2_rep_A


title: TFX_99866_control_rep_B

description: Library name: TFX_99866_control_rep_B


title: TFX_159086_SWI5_AFE2_rep_C

description: Library name: TFX_159086_SWI5_AFE2_rep_C

value: CRISPRi against the second first exon of SWI5


title: TFX_159086_SWI5_AFE2_rep_B

description: Library name: TFX_159086_SWI5_AFE2_rep_B


title: TFX_159086_SWI5_AFE2_rep_A

description: Library name: TFX_159086_SWI5_AFE2_rep_A


title: TFX_99866_control_rep_C

description: Library name: TFX_99866_control_rep_C


title: TFX_159086_control_rep_B

description: Library name: TFX_159086_control_rep_B

value: CRISPRi control


title: Hs578T, NEG1

description: Library name: Sample 1

value: Breast cancer

value: Breast cancer cell


title: siDIC-DRO Uninduced Replicate 5

city: Pavia

first: Sofia

last: Francia

address: Via Abbiategrasso, 207

country: Italy

institute: Istituto di Genetica Molecolare - Consiglio Nazionale delle Ricerche (IGM-CNR)

data_processing:
The reads for RNA-seq experiments were aligned to the GRCh37/hg19 assembly human reference genome using the nextflow nf-core RNA-seq pipeline with default parameters and singularity profile
Assembly: GRCh37/hg19
Supplementary files format and content: Matrix table with raw gene count ontain unsing nf-core RNA-seq pipeline (Ewels et al, Nat Biotechnol. 2020 Feb 13)

growth_protocol: DIvA (AsiSI-ER-U20S) cell line (Iacovoni et al 2010) was cultured in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% pyruvate, HEPES 25mM and 1% Penicillin/Streptomycin (P/S). Cells were grown at 37°C in 5% CO2 and selected on a semi-regular basis with puromycin at a final concentration of 1ug/ml.

extract_protocol:
Total RNA was isolated using the RNeasy Kit (Qiagen), according to the manufacturer’s instructions.
mRNA-seq indexed library preparation was performed starting from total mRNA (Illumina, TruSeq Stranded mRNA) according to the manufacturer’s instructions. Library quality and quantity was assessed on the 2100 Bioanalyzer High Sensitivity DNA kit (Agilent), quantified on Qubit dsDNA HS Assay, normalized and pooled to perform a multiplexed sequencing run. Clusters were generated on the Illumina flow cell and sequencing was carried out on NextSeq 550 System with paired-end 75 bp.

treatment_protocol: Cells were seeded on a 6-well plate and transfected with RNAi max reagentsfor the introduction of 20nMolar final concentration of the indicated siRNA 72 hours before DNA damage induction and collection. To induce DNA damage, cells were treated with 300 nM 4-OHT (Sigma-Aldrich; H7904) for 4 hours.

value: DiVA cells transfected with siDICER/siDROSHA


title: TFX_159086_control_rep_A

description: Library name: TFX_159086_control_rep_A


title: 99866_mast1_rep_C

description: Library name: 99866_mast1_rep_C


title: siCTL uninduced Replicate 5

source_name: DIvA (AsiSI-ER-U20S) cell line (Iacovoni et al 2010)

value: DiVA cells transfected with siCTL


title: siDIC-DRO Induced Replicate 5

value: DIvA (AsiSI-ER-U20S) cell line (Iacovoni et al 2010)

value: DiVA cells transfected with siDICER/siDROSHA, treated with 300 nM 4-OHT


title: TFX_99866_SYT9_AFE2_rep_B

description: Library name: TFX_99866_SYT9_AFE2_rep_B


title: siDIC-DRO Uninduced Replicate 1

data_processing:
The reads for RNA-seq experiments were aligned to the GRCh37/hg19 assembly human reference genome using the STAR aligner (Dobin et al. 2013) using default settings with the parameter --quantMode GeneCounts in order to obtain gene counts.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample


title: siDIC-DRO Induced Replicate 1


title: siDIC-DRO Induced Replicate 3


title: TFX_99866_control_rep_A

description: Library name: TFX_99866_control_rep_A


title: siCTL uninduced Replicate 4


title: siDIC-DRO Uninduced Replicate 2


title: siCTL Uninduced Replicate 3


title: siCTL Uninduced Replicate 2


title: siDIC-DRO Uninduced Replicate 3


title: siCTL induced Replicate 4

value: DiVA cells transfected with siCTL, treated with 300 nM 4-OHT


title: siCTL Induced Replicate 1


title: siCTL induced Replicate 5


title: siCTL Induced Replicate 3


title: siATM Uninduced Replicate 2

value: DiVA cells transfected with siATM


title: siCTL Uninduced Replicate 1


title: siATM Uninduced Replicate 3


title: siATM Induced Replicate 3

value: DiVA cells transfected with siATM, treated with 300 nM 4-OHT


title: siATM Uninduced Replicate 1


title: siDIC-DRO Uninduced Replicate 4


title: siATM Induced Replicate 1


title: Algae untreated

city: Houston

first: Tao

middle: P.

last: Wu

address: One Baylor Plaza, MS BCM225

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3) and customed python scripts
SNPs information at AT positions are generated by GATK (4.1.7.0)
Assembly: NC_000913.3; CP023448.1; Creinhardtii_281_v5.0; hg38
Supplementary files format and content: Comma-separated values, base content after nitrite treatment
Supplementary files format and content: BED, SNP information to filter 6mA

organism: Chlamydomonas reinhardtii

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 500-800 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was subjected to nitrite treatment. The treated DNA was used to construct sequencing library by customed protocol.
Methyl-seq

value: Unicellular eukarytoes

value: Wild-type


title: siATM Induced Replicate 2


title: A1_plate 6A

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

description:
Library name: BSSE-QGF-120967
Smart-seq2

data_processing:
Libraries were sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2.5 kit).
Sequence reads were trimmed for quality control with trim_galore (v.0.6.5) and uniquely aligned to mouse reference genome (GRCm38) using kallisto pseudo-mode(v.0.46.1).
Transcript-level counts were converted into gene-level counts using tximport (v1.18.0) with mm10 Refseq
Assembly: UCSC, mm 10 (GRCm38)
Supplementary files format and content: TSV text file including a table of genes (rows) x cells (columns) showing counts  per single cell. Processed data file includes only samples that passed QC check.

source_name: Dorsal Pancreas

extract_protocol:
Dorsal pancreatic tissue (E12.5) was dissected from Tg(Prox1-EGFP), Tg(Nkx2.5-Cre;mTmG) and Tg(Nkx3.2-Cre;mTmG) transgenic mice and dissociated into single-cell suspensions. GFP+ cells were FACS-sorted at 4°C using an Aria II or Aria III flow cytometer (BD) into 96-well plates containing cell lysis buffer. Plates containing FACS-sorted cells were then frozen and kept at -80°C until shipment to the Genomic Facility for library preparation and sequencing.
Libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina) protocols.

value: Dorsal Pancreas


title: B1_plate 6A

description:
Library name: BSSE-QGF-120968
Smart-seq2


title: siCTL Induced Replicate 2


title: D1_plate 6A

description:
Library name: BSSE-QGF-120970
Smart-seq2


title: siDIC-DRO Induced Replicate 2


title: E2_plate 6A

description:
Library name: BSSE-QGF-120979
Smart-seq2


title: C2_plate 6A

description:
Library name: BSSE-QGF-120977
Smart-seq2


title: G1_plate 6A

description:
Library name: BSSE-QGF-120973
Smart-seq2


title: H2_plate 6A

description:
Library name: BSSE-QGF-120982
Smart-seq2


title: D2_plate 6A

description:
Library name: BSSE-QGF-120978
Smart-seq2


title: B3_plate 6A

description:
Library name: BSSE-QGF-120984
Smart-seq2


title: H1_plate 6A

description:
Library name: BSSE-QGF-120974
Smart-seq2


title: TFX_159086_control_rep_C

description: Library name: TFX_159086_control_rep_C

value: embryonic kidney cells


title: H3_plate 6A

description:
Library name: BSSE-QGF-120990
Smart-seq2


title: A3_plate 6A

description:
Library name: BSSE-QGF-120983
Smart-seq2


title: B4_plate 6A

description:
Library name: BSSE-QGF-120992
Smart-seq2


title: G3_plate 6A

description:
Library name: BSSE-QGF-120989
Smart-seq2


title: C1_plate 6A

description:
Library name: BSSE-QGF-120969
Smart-seq2


title: E1_plate 6A

description:
Library name: BSSE-QGF-120971
Smart-seq2


title: E3_plate 6A

description:
Library name: BSSE-QGF-120987
Smart-seq2


title: D4_plate 6A

description:
Library name: BSSE-QGF-120994
Smart-seq2


title: A2_plate 6A

description:
Library name: BSSE-QGF-120975
Smart-seq2


title: D3_plate 6A

description:
Library name: BSSE-QGF-120986
Smart-seq2


title: siDIC-DRO Induced Replicate 4


title: F2_plate 6A

description:
Library name: BSSE-QGF-120980
Smart-seq2


title: F1_plate 6A

description:
Library name: BSSE-QGF-120972
Smart-seq2


title: A4_plate 6A

description:
Library name: BSSE-QGF-120991
Smart-seq2


title: E4_plate 6A

description:
Library name: BSSE-QGF-120995
Smart-seq2


title: B2_plate 6A

description:
Library name: BSSE-QGF-120976
Smart-seq2


title: F3_plate 6A

description:
Library name: BSSE-QGF-120988
Smart-seq2


title: C4_plate 6A

description:
Library name: BSSE-QGF-120993
Smart-seq2


title: C3_plate 6A

description:
Library name: BSSE-QGF-120985
Smart-seq2


title: G4_plate 6A

description:
Library name: BSSE-QGF-120997
Smart-seq2


title: F4_plate 6A

description:
Library name: BSSE-QGF-120996
Smart-seq2


title: D5_plate 6A

description:
Library name: BSSE-QGF-121002
Smart-seq2


title: F5_plate 6A

description:
Library name: BSSE-QGF-121004
Smart-seq2


title: H4_plate 6A

description:
Library name: BSSE-QGF-120998
Smart-seq2


title: G2_plate 6A

description:
Library name: BSSE-QGF-120981
Smart-seq2


title: B5_plate 6A

description:
Library name: BSSE-QGF-121000
Smart-seq2


title: C5_plate 6A

description:
Library name: BSSE-QGF-121001
Smart-seq2


title: E5_plate 6A

description:
Library name: BSSE-QGF-121003
Smart-seq2


title: A5_plate 6A

description:
Library name: BSSE-QGF-120999
Smart-seq2


title: B6_plate 6A

description:
Library name: BSSE-QGF-121008
Smart-seq2


title: A6_plate 6A

description:
Library name: BSSE-QGF-121007
Smart-seq2


title: H5_plate 6A

description:
Library name: BSSE-QGF-121006
Smart-seq2


title: G5_plate 6A

description:
Library name: BSSE-QGF-121005
Smart-seq2


title: G6_plate 6A

description:
Library name: BSSE-QGF-121013
Smart-seq2


title: F6_plate 6A

description:
Library name: BSSE-QGF-121012
Smart-seq2


title: E6_plate 6A

description:
Library name: BSSE-QGF-121011
Smart-seq2


title: A7_plate 6A

description:
Library name: BSSE-QGF-121015
Smart-seq2


title: B7_plate 6A

description:
Library name: BSSE-QGF-121016
Smart-seq2


title: G7_plate 6A

description:
Library name: BSSE-QGF-121021
Smart-seq2


title: C7_plate 6A

description:
Library name: BSSE-QGF-121017
Smart-seq2


title: D7_plate 6A

description:
Library name: BSSE-QGF-121018
Smart-seq2


title: C6_plate 6A

description:
Library name: BSSE-QGF-121009
Smart-seq2


title: F7_plate 6A

description:
Library name: BSSE-QGF-121020
Smart-seq2


title: H7_plate 6A

description:
Library name: BSSE-QGF-121022
Smart-seq2


title: A8_plate 6A

description:
Library name: BSSE-QGF-121023
Smart-seq2


title: C8_plate 6A

description:
Library name: BSSE-QGF-121025
Smart-seq2


title: H6_plate 6A

description:
Library name: BSSE-QGF-121014
Smart-seq2


title: D6_plate 6A

description:
Library name: BSSE-QGF-121010
Smart-seq2


title: D8_plate 6A

description:
Library name: BSSE-QGF-121026
Smart-seq2


title: E7_plate 6A

description:
Library name: BSSE-QGF-121019
Smart-seq2


title: E8_plate 6A

description:
Library name: BSSE-QGF-121027
Smart-seq2


title: G8_plate 6A

description:
Library name: BSSE-QGF-121029
Smart-seq2


title: H8_plate 6A

description:
Library name: BSSE-QGF-121030
Smart-seq2


title: C9_plate 6A

description:
Library name: BSSE-QGF-121033
Smart-seq2


title: F8_plate 6A

description:
Library name: BSSE-QGF-121028
Smart-seq2


title: F9_plate 6A

description:
Library name: BSSE-QGF-121036
Smart-seq2


title: D9_plate 6A

description:
Library name: BSSE-QGF-121034
Smart-seq2


title: E9_plate 6A

description:
Library name: BSSE-QGF-121035
Smart-seq2


title: A10_plate 6A

description:
Library name: BSSE-QGF-121039
Smart-seq2


title: H9_plate 6A

description:
Library name: BSSE-QGF-121038
Smart-seq2


title: C10_plate 6A

description:
Library name: BSSE-QGF-121041
Smart-seq2


title: B9_plate 6A

description:
Library name: BSSE-QGF-121032
Smart-seq2


title: B10_plate 6A

description:
Library name: BSSE-QGF-121040
Smart-seq2


title: B8_plate 6A

description:
Library name: BSSE-QGF-121024
Smart-seq2


title: E10_plate 6A

description:
Library name: BSSE-QGF-121043
Smart-seq2


title: F10_plate 6A

description:
Library name: BSSE-QGF-121044
Smart-seq2


title: H10_plate 6A

description:
Library name: BSSE-QGF-121046
Smart-seq2


title: A11_plate 6A

description:
Library name: BSSE-QGF-121047
Smart-seq2


title: B11_plate 6A

description:
Library name: BSSE-QGF-121048
Smart-seq2


title: D11_plate 6A

description:
Library name: BSSE-QGF-121050
Smart-seq2


title: D10_plate 6A

description:
Library name: BSSE-QGF-121042
Smart-seq2


title: E11_plate 6A

description:
Library name: BSSE-QGF-121051
Smart-seq2


title: C11_plate 6A

description:
Library name: BSSE-QGF-121049
Smart-seq2


title: G10_plate 6A

description:
Library name: BSSE-QGF-121045
Smart-seq2


title: H11_plate 6A

description:
Library name: BSSE-QGF-121054
Smart-seq2


title: G11_plate 6A

description:
Library name: BSSE-QGF-121053
Smart-seq2


title: F11_plate 6A

description:
Library name: BSSE-QGF-121052
Smart-seq2


title: E12_plate 6A

description:
Library name: BSSE-QGF-121059
Smart-seq2


title: C12_plate 6A

description:
Library name: BSSE-QGF-121057
Smart-seq2


title: F1_plate 6B

description:
Library name: BSSE-QGF-121068
Smart-seq2


title: G12_plate 6A

description:
Library name: BSSE-QGF-121061
Smart-seq2


title: F12_plate 6A

description:
Library name: BSSE-QGF-121060
Smart-seq2


title: B1_plate 6B

description:
Library name: BSSE-QGF-121064
Smart-seq2


title: C1_plate 6B

description:
Library name: BSSE-QGF-121065
Smart-seq2


title: A2_plate 6B

description:
Library name: BSSE-QGF-121071
Smart-seq2


title: G9_plate 6A

description:
Library name: BSSE-QGF-121037
Smart-seq2


title: H12_plate 6A

description:
Library name: BSSE-QGF-121062
Smart-seq2


title: E1_plate 6B

description:
Library name: BSSE-QGF-121067
Smart-seq2


title: G1_plate 6B

description:
Library name: BSSE-QGF-121069
Smart-seq2


title: A1_plate 6B

description:
Library name: BSSE-QGF-121063
Smart-seq2


title: D1_plate 6B

description:
Library name: BSSE-QGF-121066
Smart-seq2


title: D2_plate 6B

description:
Library name: BSSE-QGF-121074
Smart-seq2


title: D12_plate 6A

description:
Library name: BSSE-QGF-121058
Smart-seq2


title: A3_plate 6B

description:
Library name: BSSE-QGF-121079
Smart-seq2


title: B2_plate 6B

description:
Library name: BSSE-QGF-121072
Smart-seq2


title: A12_plate 6A

description:
Library name: BSSE-QGF-121055
Smart-seq2


title: E2_plate 6B

description:
Library name: BSSE-QGF-121075
Smart-seq2


title: B12_plate 6A

description:
Library name: BSSE-QGF-121056
Smart-seq2


title: H2_plate 6B

description:
Library name: BSSE-QGF-121078
Smart-seq2


title: B3_plate 6B

description:
Library name: BSSE-QGF-121080
Smart-seq2


title: F3_plate 6B

description:
Library name: BSSE-QGF-121084
Smart-seq2


title: C3_plate 6B

description:
Library name: BSSE-QGF-121081
Smart-seq2


title: G2_plate 6B

description:
Library name: BSSE-QGF-121077
Smart-seq2


title: A9_plate 6A

description:
Library name: BSSE-QGF-121031
Smart-seq2


title: G3_plate 6B

description:
Library name: BSSE-QGF-121085
Smart-seq2


title: D3_plate 6B

description:
Library name: BSSE-QGF-121082
Smart-seq2


title: D4_plate 6B

description:
Library name: BSSE-QGF-121090
Smart-seq2


title: C2_plate 6B

description:
Library name: BSSE-QGF-121073
Smart-seq2


title: H4_plate 6B

description:
Library name: BSSE-QGF-121094
Smart-seq2


title: A5_plate 6B

description:
Library name: BSSE-QGF-121095
Smart-seq2


title: F4_plate 6B

description:
Library name: BSSE-QGF-121092
Smart-seq2


title: G4_plate 6B

description:
Library name: BSSE-QGF-121093
Smart-seq2


title: B5_plate 6B

description:
Library name: BSSE-QGF-121096
Smart-seq2


title: H3_plate 6B

description:
Library name: BSSE-QGF-121086
Smart-seq2


title: E4_plate 6B

description:
Library name: BSSE-QGF-121091
Smart-seq2


title: F2_plate 6B

description:
Library name: BSSE-QGF-121076
Smart-seq2


title: D5_plate 6B

description:
Library name: BSSE-QGF-121098
Smart-seq2


title: C5_plate 6B

description:
Library name: BSSE-QGF-121097
Smart-seq2


title: B4_plate 6B

description:
Library name: BSSE-QGF-121088
Smart-seq2


title: G5_plate 6B

description:
Library name: BSSE-QGF-121101
Smart-seq2


title: A4_plate 6B

description:
Library name: BSSE-QGF-121087
Smart-seq2


title: E5_plate 6B

description:
Library name: BSSE-QGF-121099
Smart-seq2


title: F5_plate 6B

description:
Library name: BSSE-QGF-121100
Smart-seq2


title: E3_plate 6B

description:
Library name: BSSE-QGF-121083
Smart-seq2


title: H5_plate 6B

description:
Library name: BSSE-QGF-121102
Smart-seq2


title: C6_plate 6B

description:
Library name: BSSE-QGF-121105
Smart-seq2


title: E6_plate 6B

description:
Library name: BSSE-QGF-121107
Smart-seq2


title: F6_plate 6B

description:
Library name: BSSE-QGF-121108
Smart-seq2


title: G6_plate 6B

description:
Library name: BSSE-QGF-121109
Smart-seq2


title: A6_plate 6B

description:
Library name: BSSE-QGF-121103
Smart-seq2


title: H6_plate 6B

description:
Library name: BSSE-QGF-121110
Smart-seq2


title: A7_plate 6B

description:
Library name: BSSE-QGF-121111
Smart-seq2


title: D6_plate 6B

description:
Library name: BSSE-QGF-121106
Smart-seq2


title: B7_plate 6B

description:
Library name: BSSE-QGF-121112
Smart-seq2


title: C4_plate 6B

description:
Library name: BSSE-QGF-121089
Smart-seq2


title: C7_plate 6B

description:
Library name: BSSE-QGF-121113
Smart-seq2


title: F7_plate 6B

description:
Library name: BSSE-QGF-121116
Smart-seq2


title: D7_plate 6B

description:
Library name: BSSE-QGF-121114
Smart-seq2


title: E7_plate 6B

description:
Library name: BSSE-QGF-121115
Smart-seq2


title: H7_plate 6B

description:
Library name: BSSE-QGF-121118
Smart-seq2


title: B8_plate 6B

description:
Library name: BSSE-QGF-121120
Smart-seq2


title: A8_plate 6B

description:
Library name: BSSE-QGF-121119
Smart-seq2


title: H8_plate 6B

description:
Library name: BSSE-QGF-121126
Smart-seq2


title: E8_plate 6B

description:
Library name: BSSE-QGF-121123
Smart-seq2


title: G8_plate 6B

description:
Library name: BSSE-QGF-121125
Smart-seq2


title: C8_plate 6B

description:
Library name: BSSE-QGF-121121
Smart-seq2


title: A9_plate 6B

description:
Library name: BSSE-QGF-121127
Smart-seq2


title: B9_plate 6B

description:
Library name: BSSE-QGF-121128
Smart-seq2


title: D8_plate 6B

description:
Library name: BSSE-QGF-121122
Smart-seq2


title: B6_plate 6B

description:
Library name: BSSE-QGF-121104
Smart-seq2


title: F9_plate 6B

description:
Library name: BSSE-QGF-121132
Smart-seq2


title: E9_plate 6B

description:
Library name: BSSE-QGF-121131
Smart-seq2


title: G9_plate 6B

description:
Library name: BSSE-QGF-121133
Smart-seq2


title: C9_plate 6B

description:
Library name: BSSE-QGF-121129
Smart-seq2


title: B10_plate 6B

description:
Library name: BSSE-QGF-121136
Smart-seq2


title: A10_plate 6B

description:
Library name: BSSE-QGF-121135
Smart-seq2


title: D9_plate 6B

description:
Library name: BSSE-QGF-121130
Smart-seq2


title: D10_plate 6B

description:
Library name: BSSE-QGF-121138
Smart-seq2


title: G7_plate 6B

description:
Library name: BSSE-QGF-121117
Smart-seq2


title: E10_plate 6B

description:
Library name: BSSE-QGF-121139
Smart-seq2


title: C10_plate 6B

description:
Library name: BSSE-QGF-121137
Smart-seq2


title: F10_plate 6B

description:
Library name: BSSE-QGF-121140
Smart-seq2


title: H9_plate 6B

description:
Library name: BSSE-QGF-121134
Smart-seq2


title: F8_plate 6B

description:
Library name: BSSE-QGF-121124
Smart-seq2


title: B11_plate 6B

description:
Library name: BSSE-QGF-121144
Smart-seq2


title: G10_plate 6B

description:
Library name: BSSE-QGF-121141
Smart-seq2


title: C11_plate 6B

description:
Library name: BSSE-QGF-121145
Smart-seq2


title: A11_plate 6B

description:
Library name: BSSE-QGF-121143
Smart-seq2


title: D11_plate 6B

description:
Library name: BSSE-QGF-121146
Smart-seq2


title: H11_plate 6B

description:
Library name: BSSE-QGF-121150
Smart-seq2


title: A12_plate 6B

description:
Library name: BSSE-QGF-121151
Smart-seq2


title: E11_plate 6B

description:
Library name: BSSE-QGF-121147
Smart-seq2


title: F11_plate 6B

description:
Library name: BSSE-QGF-121148
Smart-seq2


title: B12_plate 6B

description:
Library name: BSSE-QGF-121152
Smart-seq2


title: G11_plate 6B

description:
Library name: BSSE-QGF-121149
Smart-seq2


title: F12_plate 6B

description:
Library name: BSSE-QGF-121156
Smart-seq2


title: G12_plate 6B

description:
Library name: BSSE-QGF-121157
Smart-seq2


title: E12_plate 6B

description:
Library name: BSSE-QGF-121155
Smart-seq2


title: D12_plate 6B

description:
Library name: BSSE-QGF-121154
Smart-seq2


title: H12_plate 6B

description:
Library name: BSSE-QGF-121158
Smart-seq2


title: A1_plate 7A

description:
Library name: BSSE-QGF-121159
Smart-seq2


title: E1_plate 7A

description:
Library name: BSSE-QGF-121163
Smart-seq2


title: C1_plate 7A

description:
Library name: BSSE-QGF-121161
Smart-seq2


title: F1_plate 7A

description:
Library name: BSSE-QGF-121164
Smart-seq2


title: H10_plate 6B

description:
Library name: BSSE-QGF-121142
Smart-seq2


title: H1_plate 7A

description:
Library name: BSSE-QGF-121166
Smart-seq2


title: G1_plate 7A

description:
Library name: BSSE-QGF-121165
Smart-seq2


title: B2_plate 7A

description:
Library name: BSSE-QGF-121168
Smart-seq2


title: C12_plate 6B

description:
Library name: BSSE-QGF-121153
Smart-seq2


title: F2_plate 7A

description:
Library name: BSSE-QGF-121172
Smart-seq2


title: D2_plate 7A

description:
Library name: BSSE-QGF-121170
Smart-seq2


title: G2_plate 7A

description:
Library name: BSSE-QGF-121173
Smart-seq2


title: C2_plate 7A

description:
Library name: BSSE-QGF-121169
Smart-seq2


title: C3_plate 7A

description:
Library name: BSSE-QGF-121177
Smart-seq2


title: E2_plate 7A

description:
Library name: BSSE-QGF-121171
Smart-seq2


title: E3_plate 7A

description:
Library name: BSSE-QGF-121179
Smart-seq2


title: D3_plate 7A

description:
Library name: BSSE-QGF-121178
Smart-seq2


title: D1_plate 7A

description:
Library name: BSSE-QGF-121162
Smart-seq2


title: B3_plate 7A

description:
Library name: BSSE-QGF-121176
Smart-seq2


title: A3_plate 7A

description:
Library name: BSSE-QGF-121175
Smart-seq2


title: B1_plate 7A

description:
Library name: BSSE-QGF-121160
Smart-seq2


title: C4_plate 7A

description:
Library name: BSSE-QGF-121185
Smart-seq2


title: G3_plate 7A

description:
Library name: BSSE-QGF-121181
Smart-seq2


title: H2_plate 7A

description:
Library name: BSSE-QGF-121174
Smart-seq2


title: B4_plate 7A

description:
Library name: BSSE-QGF-121184
Smart-seq2


title: H3_plate 7A

description:
Library name: BSSE-QGF-121182
Smart-seq2


title: A4_plate 7A

description:
Library name: BSSE-QGF-121183
Smart-seq2


title: F4_plate 7A

description:
Library name: BSSE-QGF-121188
Smart-seq2


title: G4_plate 7A

description:
Library name: BSSE-QGF-121189
Smart-seq2


title: H4_plate 7A

description:
Library name: BSSE-QGF-121190
Smart-seq2


title: A2_plate 7A

description:
Library name: BSSE-QGF-121167
Smart-seq2


title: F3_plate 7A

description:
Library name: BSSE-QGF-121180
Smart-seq2


title: F5_plate 7A

description:
Library name: BSSE-QGF-121196
Smart-seq2


title: C5_plate 7A

description:
Library name: BSSE-QGF-121193
Smart-seq2


title: H5_plate 7A

description:
Library name: BSSE-QGF-121198
Smart-seq2


title: E5_plate 7A

description:
Library name: BSSE-QGF-121195
Smart-seq2


title: D5_plate 7A

description:
Library name: BSSE-QGF-121194
Smart-seq2


title: G5_plate 7A

description:
Library name: BSSE-QGF-121197
Smart-seq2


title: B5_plate 7A

description:
Library name: BSSE-QGF-121192
Smart-seq2


title: D6_plate 7A

description:
Library name: BSSE-QGF-121202
Smart-seq2


title: C6_plate 7A

description:
Library name: BSSE-QGF-121201
Smart-seq2


title: B6_plate 7A

description:
Library name: BSSE-QGF-121200
Smart-seq2


title: F6_plate 7A

description:
Library name: BSSE-QGF-121204
Smart-seq2


title: E6_plate 7A

description:
Library name: BSSE-QGF-121203
Smart-seq2


title: G6_plate 7A

description:
Library name: BSSE-QGF-121205
Smart-seq2


title: H6_plate 7A

description:
Library name: BSSE-QGF-121206
Smart-seq2


title: A7_plate 7A

description:
Library name: BSSE-QGF-121207
Smart-seq2


title: E4_plate 7A

description:
Library name: BSSE-QGF-121187
Smart-seq2


title: C7_plate 7A

description:
Library name: BSSE-QGF-121209
Smart-seq2


title: E7_plate 7A

description:
Library name: BSSE-QGF-121211
Smart-seq2


title: F7_plate 7A

description:
Library name: BSSE-QGF-121212
Smart-seq2


title: D7_plate 7A

description:
Library name: BSSE-QGF-121210
Smart-seq2


title: B7_plate 7A

description:
Library name: BSSE-QGF-121208
Smart-seq2


title: G7_plate 7A

description:
Library name: BSSE-QGF-121213
Smart-seq2


title: H7_plate 7A

description:
Library name: BSSE-QGF-121214
Smart-seq2


title: H1_plate 6B

description:
Library name: BSSE-QGF-121070
Smart-seq2


title: A5_plate 7A

description:
Library name: BSSE-QGF-121191
Smart-seq2


title: B8_plate 7A

description:
Library name: BSSE-QGF-121216
Smart-seq2


title: A8_plate 7A

description:
Library name: BSSE-QGF-121215
Smart-seq2


title: C8_plate 7A

description:
Library name: BSSE-QGF-121217
Smart-seq2


title: A6_plate 7A

description:
Library name: BSSE-QGF-121199
Smart-seq2


title: A9_plate 7A

description:
Library name: BSSE-QGF-121223
Smart-seq2


title: H8_plate 7A

description:
Library name: BSSE-QGF-121222
Smart-seq2


title: E8_plate 7A

description:
Library name: BSSE-QGF-121219
Smart-seq2


title: G8_plate 7A

description:
Library name: BSSE-QGF-121221
Smart-seq2


title: B9_plate 7A

description:
Library name: BSSE-QGF-121224
Smart-seq2


title: C9_plate 7A

description:
Library name: BSSE-QGF-121225
Smart-seq2


title: D9_plate 7A

description:
Library name: BSSE-QGF-121226
Smart-seq2


title: G9_plate 7A

description:
Library name: BSSE-QGF-121229
Smart-seq2


title: E9_plate 7A

description:
Library name: BSSE-QGF-121227
Smart-seq2


title: F9_plate 7A

description:
Library name: BSSE-QGF-121228
Smart-seq2


title: A10_plate 7A

description:
Library name: BSSE-QGF-121231
Smart-seq2


title: B10_plate 7A

description:
Library name: BSSE-QGF-121232
Smart-seq2


title: C10_plate 7A

description:
Library name: BSSE-QGF-121233
Smart-seq2


title: G10_plate 7A

description:
Library name: BSSE-QGF-121237
Smart-seq2


title: F10_plate 7A

description:
Library name: BSSE-QGF-121236
Smart-seq2


title: H10_plate 7A

description:
Library name: BSSE-QGF-121238
Smart-seq2


title: A11_plate 7A

description:
Library name: BSSE-QGF-121239
Smart-seq2


title: D10_plate 7A

description:
Library name: BSSE-QGF-121234
Smart-seq2


title: C11_plate 7A

description:
Library name: BSSE-QGF-121241
Smart-seq2


title: B11_plate 7A

description:
Library name: BSSE-QGF-121240
Smart-seq2


title: D8_plate 7A

description:
Library name: BSSE-QGF-121218
Smart-seq2


title: E11_plate 7A

description:
Library name: BSSE-QGF-121243
Smart-seq2


title: D11_plate 7A

description:
Library name: BSSE-QGF-121242
Smart-seq2


title: H9_plate 7A

description:
Library name: BSSE-QGF-121230
Smart-seq2


title: A12_plate 7A

description:
Library name: BSSE-QGF-121247
Smart-seq2


title: G11_plate 7A

description:
Library name: BSSE-QGF-121245
Smart-seq2


title: F11_plate 7A

description:
Library name: BSSE-QGF-121244
Smart-seq2


title: B12_plate 7A

description:
Library name: BSSE-QGF-121248
Smart-seq2


title: C12_plate 7A

description:
Library name: BSSE-QGF-121249
Smart-seq2


title: C1_plate 7B

description:
Library name: BSSE-QGF-121257
Smart-seq2


title: D12_plate 7A

description:
Library name: BSSE-QGF-121250
Smart-seq2


title: E12_plate 7A

description:
Library name: BSSE-QGF-121251
Smart-seq2


title: B1_plate 7B

description:
Library name: BSSE-QGF-121256
Smart-seq2


title: A1_plate 7B

description:
Library name: BSSE-QGF-121255
Smart-seq2


title: E10_plate 7A

description:
Library name: BSSE-QGF-121235
Smart-seq2


title: G12_plate 7A

description:
Library name: BSSE-QGF-121253
Smart-seq2


title: E1_plate 7B

description:
Library name: BSSE-QGF-121259
Smart-seq2


title: G1_plate 7B

description:
Library name: BSSE-QGF-121261
Smart-seq2


title: F1_plate 7B

description:
Library name: BSSE-QGF-121260
Smart-seq2


title: H1_plate 7B

description:
Library name: BSSE-QGF-121262
Smart-seq2


title: A2_plate 7B

description:
Library name: BSSE-QGF-121263
Smart-seq2


title: D2_plate 7B

description:
Library name: BSSE-QGF-121266
Smart-seq2


title: B2_plate 7B

description:
Library name: BSSE-QGF-121264
Smart-seq2


title: C2_plate 7B

description:
Library name: BSSE-QGF-121265
Smart-seq2


title: H11_plate 7A

description:
Library name: BSSE-QGF-121246
Smart-seq2


title: G2_plate 7B

description:
Library name: BSSE-QGF-121269
Smart-seq2


title: E2_plate 7B

description:
Library name: BSSE-QGF-121267
Smart-seq2


title: F2_plate 7B

description:
Library name: BSSE-QGF-121268
Smart-seq2


title: F12_plate 7A

description:
Library name: BSSE-QGF-121252
Smart-seq2


title: H12_plate 7A

description:
Library name: BSSE-QGF-121254
Smart-seq2


title: H2_plate 7B

description:
Library name: BSSE-QGF-121270
Smart-seq2


title: A3_plate 7B

description:
Library name: BSSE-QGF-121271
Smart-seq2


title: D3_plate 7B

description:
Library name: BSSE-QGF-121274
Smart-seq2


title: C3_plate 7B

description:
Library name: BSSE-QGF-121273
Smart-seq2


title: E3_plate 7B

description:
Library name: BSSE-QGF-121275
Smart-seq2


title: F3_plate 7B

description:
Library name: BSSE-QGF-121276
Smart-seq2


title: D1_plate 7B

description:
Library name: BSSE-QGF-121258
Smart-seq2


title: C4_plate 7B

description:
Library name: BSSE-QGF-121281
Smart-seq2


title: A4_plate 7B

description:
Library name: BSSE-QGF-121279
Smart-seq2


title: E4_plate 7B

description:
Library name: BSSE-QGF-121283
Smart-seq2


title: F4_plate 7B

description:
Library name: BSSE-QGF-121284
Smart-seq2


title: G4_plate 7B

description:
Library name: BSSE-QGF-121285
Smart-seq2


title: B5_plate 7B

description:
Library name: BSSE-QGF-121288
Smart-seq2


title: A5_plate 7B

description:
Library name: BSSE-QGF-121287
Smart-seq2


title: C5_plate 7B

description:
Library name: BSSE-QGF-121289
Smart-seq2


title: E5_plate 7B

description:
Library name: BSSE-QGF-121291
Smart-seq2


title: F5_plate 7B

description:
Library name: BSSE-QGF-121292
Smart-seq2


title: G5_plate 7B

description:
Library name: BSSE-QGF-121293
Smart-seq2


title: H5_plate 7B

description:
Library name: BSSE-QGF-121294
Smart-seq2


title: B3_plate 7B

description:
Library name: BSSE-QGF-121272
Smart-seq2


title: A6_plate 7B

description:
Library name: BSSE-QGF-121295
Smart-seq2


title: C6_plate 7B

description:
Library name: BSSE-QGF-121297
Smart-seq2


title: F8_plate 7A

description:
Library name: BSSE-QGF-121220
Smart-seq2


title: F6_plate 7B

description:
Library name: BSSE-QGF-121300
Smart-seq2


title: G6_plate 7B

description:
Library name: BSSE-QGF-121301
Smart-seq2


title: H3_plate 7B

description:
Library name: BSSE-QGF-121278
Smart-seq2


title: G3_plate 7B

description:
Library name: BSSE-QGF-121277
Smart-seq2


title: B6_plate 7B

description:
Library name: BSSE-QGF-121296
Smart-seq2


title: B4_plate 7B

description:
Library name: BSSE-QGF-121280
Smart-seq2


title: H6_plate 7B

description:
Library name: BSSE-QGF-121302
Smart-seq2


title: A7_plate 7B

description:
Library name: BSSE-QGF-121303
Smart-seq2


title: B7_plate 7B

description:
Library name: BSSE-QGF-121304
Smart-seq2


title: H4_plate 7B

description:
Library name: BSSE-QGF-121286
Smart-seq2


title: D4_plate 7B

description:
Library name: BSSE-QGF-121282
Smart-seq2


title: F7_plate 7B

description:
Library name: BSSE-QGF-121308
Smart-seq2


title: E7_plate 7B

description:
Library name: BSSE-QGF-121307
Smart-seq2


title: D5_plate 7B

description:
Library name: BSSE-QGF-121290
Smart-seq2


title: C7_plate 7B

description:
Library name: BSSE-QGF-121305
Smart-seq2


title: D7_plate 7B

description:
Library name: BSSE-QGF-121306
Smart-seq2


title: G7_plate 7B

description:
Library name: BSSE-QGF-121309
Smart-seq2


title: B8_plate 7B

description:
Library name: BSSE-QGF-121312
Smart-seq2


title: H7_plate 7B

description:
Library name: BSSE-QGF-121310
Smart-seq2


title: C8_plate 7B

description:
Library name: BSSE-QGF-121313
Smart-seq2


title: snmCT_mar2025_mbd567_P6

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

description: Library name: snmCT_mar2025_mbd567_P6

library_source: other

data_processing:
Libraries were sequenced using a paired-end 100x100bp protocol on Novaseq 6000. Each 384 well plate was sequenced separately, and the sequencing data were  processed using a custom pipeline (available here: TODO: TBD), which handled demultiplexing, quality filtering, alignment, and initial processing (obtaining gene counts etc.). These are briefly described below.
Read pairs were initially demultiplexed to assign each to a well according to its well barcode, with the same list of barcodes used for each plate. See supplementary file feature_README.txt.
As recommended in Luo et al. 2017 Science, to remove bias due to random priming and adaptase behavior, paired-end reads were  hard trimmed by 10bp at both 5’ and 3’ ends, and the 5’ end of read 1 (containing the well barcode) was trimmed by an additional 8 bp to remove the barcodes. Demux reads were trimmed for adapter sequences and filtered to remove low quality sequences using trim_galore with options -a AGATCGGAAGAG -q 25 --stringency 3 (Babraham Institute).
High quality reads were aligned to the transcriptome using STAR with options --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapNmax 1 --winAnchorMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.05 --alignIntronMin 70 --alignIntronMax 5000 --outFilterIntronMotifs RemoveNoncanonical, and only unique alignments were kept.
Reads that did not align to the (unconverted) transcriptome  were then aligned to the bisulfite-converted genome using Bismark with options -N 0 -L 20 --non_directional, again retaining only unique alignments. All alignments were then filtered to remove PCR duplicates using picard tools’ MarkDuplicates function (Broad Institute).
Assembly: RNA-seq read counts per gene were obtained using htseq-count, while per-site  bisulfite-seq data was extracted from the bismark BAM file using the bismark_methylation_extractor function.
Supplementary files format and content: TAIR10
Supplementary files format and content: RNA-seq count matrices contain one row per gene, and one column per nucleus. Column labels are P[plate #]_[well ID], so P8_J18 is plate 8, well J18. Note that only wells that passed basic QC were included.
Supplementary files format and content: WGBS processed data files are BED-like files containing data pseudobulked across all nuclei of indicated genotype in indicated cluster and sequence context (CG, CHG and CHH). Columns indicate (1) chromosome, (2) cytosine location (0-based), (3) location + 1, (4) # reads unmethylated at this position, (5) # reads methylated at this position, (6) % methylation (methylated / (meth + unmeth)), (7) number of nuclei that had 1+ reads overlapping this position, (8) number of samples that had 1+ reads overlapping this position (either 1 or 2, since we have 2 replicates/samples)

molecule: other

source_name: pollen

growth_protocol: Plants were grown on soil in greenhouse under long-day conditions (16h light / 8h dark)

extract_protocol:
Nuclei extraction from pollen was performed as in Ichino et al. 2022 Cell Rep. We harvested ~ 5 mL unopened flower buds + 1 open flower per inflorescence, and ground buds in 0.1M mannitol in a mortar on ice by gently tapping. The suspension was transferred to a 50mL conical tube and vortexed intermittently for 30 sec to release spores, then filtered through a 100 um nylon membrane, then two 60 um membranes. Samples were spun 10 min 900 g at 4C with slow acceleration and braking. Pellets were resuspended in ice-cold 0.1 M mannitol, and layered above 3 mL 20% Percoll diluted in 0.1M mannitol, then centrifuged 450 g 10 min 4C. This was repeated twice. Spores were pelleted 5 min 500 g 4C, and resuspended in 800 uL Glbraith buffer + bMe. This mixture was transferred to 1.5 mL tubes containing 100 uL acid-washed 0.5 mm glass beads (Sigma), and vortexed max speed 2 min total in cold, alternating 7 sec vortex, 3 sec invert for 1st min, then 7s vortex, 2s invert for second min. Nuclei were filtered through a 10um nylon filter. Nuclei were spun 5 min 500 g 4C, and pellets were gently resuspended in Sysmex nuclei extraction buffer and DAPI buffer (1:8 ratio). Nuclei were filtered through a 35 um nylon mesh into a FACS tube and immediately sorted, using DAPI to detect nuclei. Individual nuclei were sorted into a 384 well plate pre-filled with the buffer for reverse transcription (see library construction protocol).
Each 384 well plate was processed separately, with 8 plates prepared per sample (note plate 8 of Col rep 2 and 1 of mbd56 rep 2 failed and were not sequenced). Library preparation was performed as described in Luo et al. 2022 Cell Genomics, omitting the accessibility portion of the assay (the GpC methyltransferase treatment). Briefly, RNA was first reverse-transcribed using a template-switching reaction (see SMART-seq protocols) with an oligo-dT primer in the presence of 5'-methyl-dCTP, so that all cytosines in cDNA are methylated. cDNA amplification was performed using KAPA2G DNA polymerase for TODO: TBD cycles. DNA was digested into smaller fragments using Uracil DNA gycosylase + Endonuclease VIII. then bisulfite converted using the Zymo EZ-96 DNA methylation-direct kit with reduced volume.

value: pollen

tag: ecotype

value: mbd5 mbd6 mbd7


title: E6_plate 7B

description:
Library name: BSSE-QGF-121299
Smart-seq2


title: D6_plate 7B

description:
Library name: BSSE-QGF-121298
Smart-seq2


title: snmCT_mar2025_mbd567_P4

description: Library name: snmCT_mar2025_mbd567_P4


title: snmCT_mar2025_mbd567_P3

description: Library name: snmCT_mar2025_mbd567_P3


title: D8_plate 7B

description:
Library name: BSSE-QGF-121314
Smart-seq2


title: A8_plate 7B

description:
Library name: BSSE-QGF-121311
Smart-seq2


title: snmCT_mar2025_mbd567_P2

description: Library name: snmCT_mar2025_mbd567_P2


title: snmCT_mar2025_mbd567_P1

description: Library name: snmCT_mar2025_mbd567_P1


title: F8_plate 7B

description:
Library name: BSSE-QGF-121316
Smart-seq2


title: E8_plate 7B

description:
Library name: BSSE-QGF-121315
Smart-seq2


title: snmCT_mar2025_mbd7_P6

description: Library name: snmCT_mar2025_mbd7_P6


title: H8_plate 7B

description:
Library name: BSSE-QGF-121318
Smart-seq2


title: G8_plate 7B

description:
Library name: BSSE-QGF-121317
Smart-seq2


title: A9_plate 7B

description:
Library name: BSSE-QGF-121319
Smart-seq2


title: snmCT_mar2025_mbd7_P4

description: Library name: snmCT_mar2025_mbd7_P4


title: B9_plate 7B

description:
Library name: BSSE-QGF-121320
Smart-seq2


title: snmCT_mar2025_mbd7_P5

description: Library name: snmCT_mar2025_mbd7_P5


title: snmCT_mar2025_mbd7_P3

description: Library name: snmCT_mar2025_mbd7_P3


title: C9_plate 7B

description:
Library name: BSSE-QGF-121321
Smart-seq2


title: snmCT_mar2025_mbd7_P2

description: Library name: snmCT_mar2025_mbd7_P2


title: snmCT_mar2025_mbd7_P1

description: Library name: snmCT_mar2025_mbd7_P1


title: snmCT_mar2025_mbd567_P5

description: Library name: snmCT_mar2025_mbd567_P5


title: snmCT_mar2025_mbd56_P6

description: Library name: snmCT_mar2025_mbd56_P6

value: mbd5 mbd6


title: D9_plate 7B

description:
Library name: BSSE-QGF-121322
Smart-seq2


title: E9_plate 7B

description:
Library name: BSSE-QGF-121323
Smart-seq2


title: F9_plate 7B

description:
Library name: BSSE-QGF-121324
Smart-seq2


title: snmCT_mar2025_mbd56_P4

description: Library name: snmCT_mar2025_mbd56_P4


title: snmCT_mar2025_mbd56_P5

description: Library name: snmCT_mar2025_mbd56_P5


title: snmCT_mar2025_mbd56_P3

description: Library name: snmCT_mar2025_mbd56_P3


title: G9_plate 7B

description:
Library name: BSSE-QGF-121325
Smart-seq2


title: H9_plate 7B

description:
Library name: BSSE-QGF-121326
Smart-seq2


title: snmCT_mar2025_mbd56_P2

description: Library name: snmCT_mar2025_mbd56_P2


title: B10_plate 7B

description:
Library name: BSSE-QGF-121328
Smart-seq2


title: snmCT_mar2025_mbd56_P1

description: Library name: snmCT_mar2025_mbd56_P1


title: A10_plate 7B

description:
Library name: BSSE-QGF-121327
Smart-seq2


title: C10_plate 7B

description:
Library name: BSSE-QGF-121329
Smart-seq2


title: snmCT_mar2025_Col_P6

description: Library name: snmCT_mar2025_Col_P6

value: Col


title: snmCT_mar2025_Col_P5

description: Library name: snmCT_mar2025_Col_P5


title: D10_plate 7B

description:
Library name: BSSE-QGF-121330
Smart-seq2


title: snmCT_mar2025_Col_P3

description: Library name: snmCT_mar2025_Col_P3


title: F10_plate 7B

description:
Library name: BSSE-QGF-121332
Smart-seq2


title: snmCT_mar2025_Col_P2

description: Library name: snmCT_mar2025_Col_P2


title: snmCT_mar2025_Col_P4

description: Library name: snmCT_mar2025_Col_P4


title: E10_plate 7B

description:
Library name: BSSE-QGF-121331
Smart-seq2


title: G10_plate 7B

description:
Library name: BSSE-QGF-121333
Smart-seq2


title: ChIP_MBD7_mbd7sln_T2_9_r2

description: Library name: ChIP_MBD7_mbd7sln_T2_9_r2

data_processing:
Reads were filtered for adapter sequenced and poor quality ends, then aligned to TAIR10 using bowtie2 with standard parameters and allowing max fragment size 1000 bp. PCR duplicates were removed using MarkDuplicates from the picard tools suite.
Coverage tracks were obtained using the bamCoverage function from DeepTools with parameters --binSize 10 --normalizeUsing CPM --extendReads, and blacklisting the chloroplast and mitochondrial genomes.
Tracks were normalized to the no-FLAG control track (Col0) using bigwigCompare (DeepTools) with default operation 'log2' and bin size 10 bp.
Assembly: TAIR10
Supplementary files format and content: Files named *_cov.bw are RPM-normalized coverage tracks generated by bamCoverage (deeptools) with bin size 10 and the extendReads option. Files named *_log2_over_noFLAG.bw are coverage tracks normalized (log2 fold change) to the "no FLAG" control using bamCompare.

source_name: flower buds

extract_protocol:
ChIP was performed as in Wang et al. 2024 Nature Plants. Each sample used approximately 2g flash-frozen, unopened flower buds. Briefly, tissue was ground 2x for 90 sec in TissueLyser II and powder was resuspended in nuclei isolation buffer without formaldehyde. Once fully dissolved, 37% formaldehyde was added to final conc. 1%, and samples were incubated 12 min. Crosslinking was quenched with 2M glycine, and nuclei were purified and then lysed. Chromatin was sheared using a Bioruptor Plus (Diagenode) 30s on/30s off on high x 22 cycles. Sheared chromatin was incubated with 7 uL anti-FLAG antibody (1:600 dilution, Sigma) overnight at 4C. Antibody-bound chromatin was recovered using a 1:1 mix of protein A and protein G dynabeads (Invitrogen) for 2h at 4C. Beads were washed 5x before eluting bound chromatin at 65C twice. Reverse crosslinking was performed using NaCl at 65C overnight and proteins were digested using Tris pH 6.5. DNA was purified using standard phenol:chloroform:isoamyl alcohol extraction and precipitated with sodium acetate and ethanol o/n at -20C.
Precipitated DNA from ChIP was processed using the Ovation Ultra Low System V2 kit (NuGEN), and sequenced on NovaSeq X Plus.

value: flower buds

value: sln mbd7 + MBD7-3xF


title: snmCT_mar2025_Col_P1

description: Library name: snmCT_mar2025_Col_P1


title: ChIP_MBD7_mbd7sln_T2_1

description: Library name: ChIP_MBD7_mbd7sln_T2_1


title: ChIP_MBD7_mbd7sln_T2_3

description: Library name: ChIP_MBD7_mbd7sln_T2_3


title: H10_plate 7B

description:
Library name: BSSE-QGF-121334
Smart-seq2


title: B11_plate 7B

description:
Library name: BSSE-QGF-121336
Smart-seq2


title: ChIP_MBD7_mbd567_T2_4

description: Library name: ChIP_MBD7_mbd567_T2_4

value: mbd5 mbd6 mbd7 + MBD7-3xF


title: ChIP_MBD7_mbd7_T2_18

description: Library name: ChIP_MBD7_mbd7_T2_18

value: mbd7 + MBD7-3xF


title: ChIP_MBD7_mbd567_T2_19

description: Library name: ChIP_MBD7_mbd567_T2_19


title: G11_plate 7B

description:
Library name: BSSE-QGF-121341
Smart-seq2


title: ChIP_MBD7_mbd7_T2_10

description: Library name: ChIP_MBD7_mbd7_T2_10


title: ChIP_MBD7_mbd7_T2_2

description: Library name: ChIP_MBD7_mbd7_T2_2


title: H11_plate 7B

description:
Library name: BSSE-QGF-121342
Smart-seq2


title: ChIP_MBD6_T2_9

description: Library name: ChIP_MBD6_T2_9

value: mbd6 + MBD6-3xF


title: ChIP_MBD6_T2_4

description: Library name: ChIP_MBD6_T2_4


title: B12_plate 7B

description:
Library name: BSSE-QGF-121344
Smart-seq2


title: ChIP_Col0

description: Library name: ChIP_Col0

value: wild-type


title: E11_plate 7B

description:
Library name: BSSE-QGF-121339
Smart-seq2


title: C11_plate 7B

description:
Library name: BSSE-QGF-121337
Smart-seq2


title: C12_plate 7B

description:
Library name: BSSE-QGF-121345
Smart-seq2


title: A11_plate 7B

description:
Library name: BSSE-QGF-121335
Smart-seq2


title: Panel II_E17.5_13

type: RNA

description: HybISS, Cartana

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: After quality control samples were processed by CARTANA Sweden (a subsidiary of 10X Genomics), for in situ barcode sequencing, imaging, and data processing. CSV files contain reads coordinates and gene information of segmented spots. The coordinates are in pixel unit. Scaling factor is 0.32 um/pixel. (0,0) is at northwest (top-left corner). Downstream processing  was performed using either SSAM pipeline (https://github.com/pnucolab/ssam) or a pipeline involving nuclear segmentation using Cellpose 2.0 (https://github.com/MouseLand/cellpose), reads to cell assignment using pciSeq (https://github.com/acycliq/pciSeq) and single-cell mapping into the spatial data using Tangram (https://github.com/broadinstitute/Tangram).

label: not applicable

source_name: E17.5_Pancreas, spleen, duodenum

label_protocol: not applicable

growth_protocol: Standard mouse housing conditions

extract_protocol: E12.5, E14.5 and E17.5 embryonic pancreas were dissected and fixed overnight in 4% PFA. Samples were equilibrated in 20% sucrose solution and embedded in OCT compound (Sakura). 10 mm-thick cryosections were stored at -80°C. The starting day of the experiment, sections were kept at 60°C for an hour before post-fixation with 4% PFA for 5 minutes. After washes, sections were serially dehydrated in 50%, 70% and 100% Ethanol and then subjected to antigen retrieval in Citrate buffer. Gene panels were then hybridized overnight at 37°C. Ligation and following steps were performed using the High Sensitivity Library Preparation Kit from CARTANA AB (10x Genomics). Incubations were performed in SecureSealTM chambers (Grace Biolabs, Bend, OR, USA). Slow Fade Antifade Mountant (Thermo Fisher Scientific, Waltham, MA, USA, ref S36936) was used for optimal handling and imaging of tissue sections.

treatment_protocol: not applicable

value: Pancreas, spleen, duodenum


title: D12_plate 7B

description:
Library name: BSSE-QGF-121346
Smart-seq2


title: scATAC-seq of mus musclus: E12.5 embryo male lung

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

description: Library name: scATAC_ARC

data_processing:
We used the FASTQ files from both snATAC and snRNA as input files for CellRanger ARC (v2.0.2) to achieve mm10 mouse genome aligning, real cells identifying, cell barcode demultiplexing and molecular counting for both ATAC and GEX (Gene Expression). We employed the resulting files (filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz and per_barcode_metrics.csv), as input files for the creation of a new Seurat object using the R packages Seurat (v4.4.0) and Signac (v1.13.0).
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix
Supplementary files format and content: fragment files

source_name: lung

extract_protocol:
Single cell multiomics libraries were constructed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics, PN-1000283) according to the manufacturer’s protocol. Briefly, after dissociation, cells (epithelia cells: whole lung cells= 1:10) were collected and resuspended in chilled Lysis Buffer to isolate nuclei. After washing, nuclei suspensions underwent incubation in a Transposition Mix containing Transposase. The Transposase penetrated the nuclei and selectively cleaved DNA within the open chromatin regions. Simultaneously, adapter sequences were appended to the ends of the DNA fragments. The Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library
Single cell multiomics libraries were constructed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics, PN-1000283) according to the manufacturer’s protocol. Briefly, after dissociation, cells (epithelia cells: whole lung cells= 1:10) were collected and resuspended in chilled Lysis Buffer to isolate nuclei. After washing, nuclei suspensions underwent incubation in a Transposition Mix containing Transposase. The Transposase penetrated the nuclei and selectively cleaved DNA within the open chromatin regions. Simultaneously, adapter sequences were appended to the ends of the DNA fragments. The Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library

value: lung

value: whole lung cells

value: WT


title: F12_plate 7B

description:
Library name: BSSE-QGF-121348
Smart-seq2


title: E12_plate 7B

description:
Library name: BSSE-QGF-121347
Smart-seq2


title: Panel II_E17.5_10

description: HybISS, Cartana


title: Panel II_E17.5_11

description: HybISS, Cartana


title: Panel II_E17.5_9

description: HybISS, Cartana


title: G12_plate 7B

description:
Library name: BSSE-QGF-121349
Smart-seq2


title: Panel II_E17.5_8

description: HybISS, Cartana


title: D11_plate 7B

description:
Library name: BSSE-QGF-121338
Smart-seq2


title: F11_plate 7B

description:
Library name: BSSE-QGF-121340
Smart-seq2


title: H12_plate 7B

description:
Library name: BSSE-QGF-121350
Smart-seq2


title: Panel II_E17.5_7

description: HybISS, Cartana


title: A1_Plate 8A

description:
Library name: BSSE-QGF-131162
Smart-seq2


title: Panel II_E17.5_5

description: HybISS, Cartana


title: B1_Plate 8A

description:
Library name: BSSE-QGF-131163
Smart-seq2


title: C1_Plate 8A

description:
Library name: BSSE-QGF-131164
Smart-seq2


title: Panel II_E17.5_6

description: HybISS, Cartana


title: A12_plate 7B

description:
Library name: BSSE-QGF-121343
Smart-seq2


title: D1_Plate 8A

description:
Library name: BSSE-QGF-131165
Smart-seq2


title: E1_Plate 8A

description:
Library name: BSSE-QGF-131166
Smart-seq2


title: Panel II_E17.5_3

description: HybISS, Cartana


title: Panel II_E17.5_1

description: HybISS, Cartana


title: Panel II_E14.5_22

description: HybISS, Cartana

source_name: E14.5_Pancreas, spleen, duodenum