title: TNBC002|ROI-002|PanCK-

description:
Library name: DSP-1001660016068-D-B06
TNBC002 - 002 - PanCK-
TNBC002-slide.png
TNBC002 - 002.png
TNBC002 - 002 - Segments.png


title: total RNAs from dZfc3h1 and dZcchc7 KD in OSCs with rRNA depletion (ribo-zero) replicate1

status: Public on Dec 19 2025

type: SRA

city: Vienna

first: Julius

middle: Fabian

last: Brennecke

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA-Institute for Molecular Biotechnology

library_source: transcriptomic

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

molecule: total RNA

organism: Drosophila melanogaster

source_name: OSCs

growth_protocol: OSCs were grown in M3 medium supplemented with 10% fetal bovine serum, insulin, glutathion and fly extract in hunidified incubator with 2.5% CO2 at 27º C

extract_protocol:
RNA was extracted using NucleoSpin® RNA Kit from Macherey-Nagel
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)

tag: cell line

value: OSCs

tag: treatment


title: STD DAT, rep 5 long term

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

description:
Library name: GEN52_21_15
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

data_processing:
Quality control analyses, FASTQ generation files, adapters trimming and filtering of sequencing were performed using FASTQ toolkit v1.0.0 and basespace.
Differeintal analysis was performed using DESeq2 from Illumina.
Assembly: Mus_musculus (UCSC mm10)
Supplementary files format and content: Files include raw counts for each sample

organism: Mus musculus

source_name: Liver

growth_protocol: Male mice were purchased and fed with different diets (standard healthy diet, high fat diet, high sucrose diet or high fot diet with high sucrose). Treatments in each diet were of 1 week for short term and 18 weeks for long term. Liver were frozen in liquid nitrogen and stored at -80 ºC.

extract_protocol:
RNA extraction was performed using RNAeasy mini Kit (Qiagen).
RNA-seq libreries were made using the Illumina Stranded mRNA prep ligation kit

treatment_protocol: Mice were treated with DAD or DAT at 150 mg/kg of food for long term studies. DAS were provided by oral gavage (200 mg/Kg) 3 hours before euthanization.

tag: tissue

value: Liver

tag: genotype

value: Wild type

value: STD DAT


title: TNBC001|ROI-025|PanCK-

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

state: CA

address: 1500 E Duarte Rd

department: Population Sciences

country: USA

institute: City of Hope

description:
Library name: DSP-1001660016068-D-B02
TNBC001 - 025 - PanCK-
TNBC001-slide.png
TNBC001 - 025.png
TNBC001 - 025 - Segments.png

data_processing:
The "GeomxTools" library in R was used to read in the DCC files using the .pkc file, and the raw counts were output into the "raw_counts.tsv" file
Assembly: Hg38
Supplementary files format and content: "Hs_R_NGS_WTA_v1.0.pkc" is the GeoMx probe code file used to map probes to gene names when producing the "raw_counts.tsv" file
Supplementary files format and content: "raw_counts.tsv" is a gene by sample expression matrix of raw counts where each sample is the "library name" and corresponds to ether a PanCK+/- segmented ROI (AOI); NTC control samples and samples that failed QC are not included

organism: Homo sapiens

source_name: Breast

extract_protocol:
Tissue sections were prepared following the instruction of GeoMx slide preparation, and the slides were processed using the protocol of RNA slide preparation  for  formalin-fixed paraffin-embedded (FFPE) samples as described in the GeoMx DSP Manual Slide Preparation User Manual (NanoString Technologies, GeoMx-DSP-Manual-Slide-Preparation, MAN-10150). Briefly, deparaffinization and rehydration, antigen retrieval (Invitrogen, IHC Antigen Retrieval Solution, Cat#00-4956-58), and proteinase K digestion (1ug/ml, at 37°C) were performed. Human whole transcriptome atlas (WTA) probes (GeoMx WTA, Mouse RNA Probe for NGS, catalog #121401103) were hybridized in Buffer R (GeoMx RNA Slide Prep Kit PCLN catalog #121300313) and incubated in a hybridization humidity chamber (UVP, HB-1000 Hybridizer) overnight at 37°C. To remove nonspecifically bound probes, slides were washed in 50% Formamide/2x SSC (Thermo Fisher, catalog AM9763, USA) at 37°C (2 washes/25 min each), then slides were blocked and incubated with antibodies diluted with 200 μL Buffer W (GeoMx RNA Slide Prep Kit PCLN catalog 121300313). Then, immunostaining was performed for detection of the region of interest (ROI) . Briefly, Morphology Marker Solution was prepared in the following proportions per slide: 22 μL SYTO (GeoMx Nuclear Stain Morphology Kit, catalog 121300303), 5.5 μL Pan-CK, 5.5 μL CD45 (GeoMx Solid Tumor TME Morphology, Human FFPE RNA Compatible, catalog 121300315), and 181.5 μL Buffer W (GeoMx RNA Slide Prep Kit PCLN catalog 121300313) for a total volume of 220 μL/slide. Slides were incubated in this solution at room temperature for 1 hour followed by 2 consecutive SSC washes, then, slides were loaded into the for ROI selection following GeoMxTM Digital Spatial Profiler Instrument User Manual.
After ROI selection, the WTA probe tags were selectively isolated (UV-cleaved) and collected from each of these ROIs, then transferred to individual wells of a collection plate on the DSP. The collections were processed for library preparation following the manual of MANUAL GeoMx® DSP NGS Readout (MAN-10153-06). The quality of library was assessed by the Bioanalyzer DNA 1000 assay (Agilent, catalog 5067-1504). The library was then sequenced on Illumina NextSeq2000. The fastq files were converted to .DCC files using the software of GeoMx-NGS Pipeline; the DCC files were loaded on GeoMx DSP for QC, normalization.  Q3 data was generated and used for all the analysis.

value: Breast

tag: prognosis

value: PPx


title: total RNAs from dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: STD DAD, rep 2 long term

description:
Library name: GEN52_21_17
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: STD DAD


title: HFD, rep 5 long term

description:
Library name: GEN52_21_25
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: HFD control


title: STD DAT, rep 4 long term

description:
Library name: GEN52_21_14
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: Thap1_mKO_nt_Rrm1_L2C_embryo_RNA_rep2

city: Beijing

first: xi

last: wu

address: Tsinghua univesity

country: China

institute: Tsinghua university

description: Library name: Sample 3

data_processing:
Paired-end RNA-seq reads were trimmed and mapped to the mm9 genome by TopHat v2.1.1 (Trapnell et al., 2009). FPKM (Fragments per kilobase per million of sequenced reads) for gene expression was calculated using Cufflinks v2.2.1 (Trapnell et al., 2012) based on mm9 refFlat from the UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: bigWig

molecule: polyA RNA

source_name: 2C embryo

extract_protocol:
Embryos were lysed and used directly as input materials for subsequent RNA-seq library prepararion.
All RNA libraries were prepared using the Smart-seq2 method as previously reported (Picelli et al., 2014), and were sequenced by the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s instructions.

value: 2C embryo

value: Thap1 maternal knockout


title: STD DAT, rep 3 long term

description:
Library name: GEN52_21_13
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from dZcchc7 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: total RNAs from dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: PBMC, No vaccine, 6343, Day 42

city: Lincoln

first: Hiep

last: Vu

state: Nebraska

address: 4240 Fair St

department: Animal Science and Nebraska Center for Virology

institute: University of Nebraska-Lincoln

description:
Library name: No vaccine 4
Column name in raw_counts_All_Sample.txt: NV_6343

data_processing:
Raw read datasets were utilized as input for the nf-core/rnaseq pipeline (version 3.14), employing STAR (version 2.7.9a) as the alignment tool with default settings. The reference genome and transcript annotation in Gene Transfer Format (GTF) for pigs were retrieved from the Sus scrofa genome (Sscrofa11.1; GenBank assembly number GCF_000003025.6) and Ensembl (https://ftp.ensembl.org/pub/release-112/fasta/sus_scrofa/dna/). The data matrix containing gene counts and gene lengths obtained from this pipeline served as input for nf-core/differentialabundance (version 1.5.0), where DESeq2 (version 1.34.0) was used for differential gene expression analysis, following the default parameters of the pipeline
Assembly: Sscrofa11.1 (GCF_000003025.6)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Sus scrofa

source_name: Blood

extract_protocol:
One million PBMC cells were shipped to GENEWIZ (Azenta Life Sciences) for Standard RNA-Seq service, where total RNA and polyA+ transcripts were isolated and prepared per their in-house protocols.
RNA-seq library was prepared per their in-house protocols.

value: Blood

tag: cell type

value: PBMC

tag: group

value: No vaccine


title: STD DAD, rep 3 long term

description:
Library name: GEN52_21_18
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: TNBC002|ROI-002|PanCK+

description:
Library name: DSP-1001660016068-D-B05
TNBC002 - 002 - PanCK+
TNBC002-slide.png
TNBC002 - 002.png
TNBC002 - 002 - Segments.png

value: GPx


title: STD DAT, rep 2 long term

description:
Library name: GEN52_21_12
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: TNBC001|ROI-024|PanCK-

description:
Library name: DSP-1001660016068-D-A12
TNBC001 - 024 - PanCK-
TNBC001-slide.png
TNBC001 - 024.png
TNBC001 - 024 - Segments.png


title: WT_aph_L2C_RNA_rep2

description: Library name: Sample 6

value: WT


title: total RNAs from dZcchc7 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: STD DAD, rep 1 long term

description:
Library name: GEN52_21_16
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: TNBC002|ROI-001|PanCK+

description:
Library name: DSP-1001660016068-D-B03
TNBC002 - 001 - PanCK+
TNBC002-slide.png
TNBC002 - 001.png
TNBC002 - 001 - Segments.png


title: TNBC002|ROI-001|PanCK-

description:
Library name: DSP-1001660016068-D-B04
TNBC002 - 001 - PanCK-
TNBC002-slide.png
TNBC002 - 001.png
TNBC002 - 001 - Segments.png


title: WT_nt_L2C_RNA_rep2

description: Library name: Sample 5


title: total RNAs from dZcchc7 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: total RNAs from dZcchc7 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: Thap1_mKO_Rrm1_OE_L2C_embryo_RNA_rep2

description: Library name: Sample 4


title: total RNAs from dZcchc7 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: STD DAT, rep 1 long term

description:
Library name: GEN52_21_11
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: Ctrl_Rrm1_OE_L2C_embryo_RNA_rep2

description: Library name: Sample 2


title: TNBC001|ROI-025|PanCK+

description:
Library name: DSP-1001660016068-D-B01
TNBC001 - 025 - PanCK+
TNBC001-slide.png
TNBC001 - 025.png
TNBC001 - 025 - Segments.png


title: TNBC001|ROI-023|PanCK-

description:
Library name: DSP-1001660016068-D-A10
TNBC001 - 023 - PanCK-
TNBC001-slide.png
TNBC001 - 023.png
TNBC001 - 023 - Segments.png


title: total RNAs from Dis3 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: TNBC001|ROI-024|PanCK+

description:
Library name: DSP-1001660016068-D-A11
TNBC001 - 024 - PanCK+
TNBC001-slide.png
TNBC001 - 024.png
TNBC001 - 024 - Segments.png


title: TNBC001|ROI-023|PanCK+

description:
Library name: DSP-1001660016068-D-A09
TNBC001 - 023 - PanCK+
TNBC001-slide.png
TNBC001 - 023.png
TNBC001 - 023 - Segments.png


title: Thap1_mKO_Rrm1_OE_L2C_embryo_RNA_rep1

description: Library name: Sample 16

source_name: L2C embryo

value: L2C embryo


title: Ctrl_nt_Rrm1_L2C_embryo_RNA_rep2

description: Library name: Sample 1


title: STD, rep 4 long term

description:
Library name: GEN52_21_4
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: STD control


title: total RNAs from dZcchc7 KD in OSCs with rRNA depletion (ribo-zero) replicate3

value: OSCs


title: total RNAs from Dis3 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: TNBC001|ROI-022|PanCK-

description:
Library name: DSP-1001660016068-D-A08
TNBC001 - 022 - PanCK-
TNBC001-slide.png
TNBC001 - 022.png
TNBC001 - 022 - Segments.png


title: Thap1_mKO_nt_Rrm1_L2C_embryo_RNA_rep1

description: Library name: Sample 15


title: STD, rep 5 long term

description:
Library name: GEN52_21_5
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: Liver


title: STD, rep 3 long term

description:
Library name: GEN52_21_3
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: Wild type


title: TNBC001|ROI-022|PanCK+

description:
Library name: DSP-1001660016068-D-A07
TNBC001 - 022 - PanCK+
TNBC001-slide.png
TNBC001 - 022.png
TNBC001 - 022 - Segments.png


title: STD, rep 2 long term

description:
Library name: GEN52_21_2
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from Dis3 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: Ctrl_Rrm1_OE_L2C_embryo_RNA_rep1

description: Library name: Sample 14


title: TNBC001|ROI-021|PanCK-

description:
Library name: DSP-1001660016068-D-A06
TNBC001 - 021 - PanCK-
TNBC001-slide.png
TNBC001 - 021.png
TNBC001 - 021 - Segments.png


title: TNBC001|ROI-021|PanCK+

description:
Library name: DSP-1001660016068-D-A05
TNBC001 - 021 - PanCK+
TNBC001-slide.png
TNBC001 - 021.png
TNBC001 - 021 - Segments.png


title: Thap1_mKO_Thap1_OE_L2C_embryo_RNA_rep1

description: Library name: Sample 12


title: total RNAs from CG7065 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: total RNAs from CG7065 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: STD, rep 1 long term

description:
Library name: GEN52_21_1
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from CG7065 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: Thap1_mKO_nt_Thap1_L2C_embryo_RNA_rep1

description: Library name: Sample 11


title: WT_Nfkb1-KO_BMDC_Day5, HTO

city: Los Angeles

first: Alexander

last: Hoffmann

state: United States

address: 611 Charles E Young Drive East

institute: University of California, Los Angeles

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

data_processing:
Gene expression data were counted using 10X Genomics CellRanger v3.0. Cell hashing data were counted using CITE-seq-count (v1.4.2) python package.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Bone-marrow derived dendritic cells

growth_protocol: Grown for 3-5 days in RPMI + 10% FBS + 2-BME + Pen/Strep and 100ng/mL of Flt3L at 1x10^6 cells/mL. Media replenished on day 3

extract_protocol:
On day 3 or day 5, three wells of cells were harvested, pooled before staining with surface antibodies for CD3/CD19/CD49b/Ter119-FITC, Gr-1-PECy7, CD45.1-BV711, CD45.2 APCCy7 and DAPI. Live Dump-(CD3/CD19/CD49b/TER119/Gr-1-) CD45.1+CD45.2- (WT) cells and live Dump-CD45.1-CD45.2+ (Nfkb1-/-) cells were sorted by BD FACS Aria II (UCLA JCCC Flow Core). Sorted cells were stained with unique TotalSeq™-A anti-mouse Hashtag Antibodies (TotalSeq™-A #1,2,3,5 were used, BioLegend, San Diego, CA) for multiplexing. On each day, stained CD45.1 WT cells and CD45.2 Nfkb1-/- cells were washed once, counted, mixed at 1:1 ratio and resuspended in PBS with 10% fetal bovine serum while the concentration was adjusted to 1200 cells/μL.
The cells were then submitted to UCLA Technology Center for Genomics & Bioinformatics for 10X Genomics (Pleasaton, CA) Chromium captures. Each independent sample was loaded into a separate GEM wells and TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 protocol was applied.

value: Bone-marrow derived dendritic cells

value: mixed sample (Wild-type, Nfkb1-/-)

tag: time

value: Flt3 Differentiation:Day 5

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0305 anti-mouse Hashtag 1，TotalSeq-A0305 anti-mouse Hashtag 2，TotalSeq-A0305 anti-mouse Hashtag 3，TotalSeq-A0305 anti-mouse Hashtag 5


title: TNBC001|ROI-020|PanCK-

description:
Library name: DSP-1001660016068-D-A04
TNBC001 - 020 - PanCK-
TNBC001-slide.png
TNBC001 - 020.png
TNBC001 - 020 - Segments.png

value: Breast

value: PPx


title: total RNAs from CG31510 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: WT_Nfkb1-KO_BMDC_Day5, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: TNBC001|ROI-020|PanCK+

description:
Library name: DSP-1001660016068-D-A03
TNBC001 - 020 - PanCK+
TNBC001-slide.png
TNBC001 - 020.png
TNBC001 - 020 - Segments.png


title: total RNAs from CG31510 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: total RNAs from CG31510 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: Pat-16-CVD-CTL

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: Library name: Sample 5

library_source: genomic

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 109.
Assembly: hg38
Supplementary files format and content: ext429_atac_processed.txt

molecule: genomic DNA

extract_protocol:
50.000 cells were used for ATAC library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina).
Cells were pelleted and resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and was incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq2000 platform (Illumina) using P3 flowcell with 2x 36bp paired-end setup.

tag: disease

value: ASCVD

value: Blood

value: monocytes

tag: patient id


title: WT_Nfkb1-KO_BMDC_Day3, GEX

value: Flt3 Differentiation:Day 3


title: TNBC001|ROI-019|PanCK-

description:
Library name: DSP-1001660016068-D-A02
TNBC001 - 019 - PanCK-
TNBC001-slide.png
TNBC001 - 019.png
TNBC001 - 019 - Segments.png


title: Ctrl_nt_Rrm1_L2C_embryo_RNA_rep1

description: Library name: Sample 13

value: L2C embryo

value: WT


title: WT_nt_L2C_RNA_rep1

description: Library name: Sample 39

source_name: late two-cell embryo

value: late two-cell embryo


title: Ctrl_nt_Thap1_L2C_embryo_RNA_rep1

description: Library name: Sample 9


title: Thap1_mKO_L2C_embryo_RNA_rep2

description: Library name: Sample 28

value: Thap1 maternal knockout


title: total RNAs from CG31510 and CG7065 KD in OSCs with rRNA depletion (ribo-zero) replicate3

value: OSCs


title: Pat-15-CVD-CTL

description: Library name: Sample 4


title: WT_aph_L2C_RNA_rep1

description: Library name: Sample 40

value: Aphidicolin 3ug/ul


title: DOX treated islets, withdrawal 4 days, replicate 2

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
3’ mRNA (v3.1 NextGem 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Metadata_Full_dataset.csv
Metadata_Beta.cell.subset.csv

library_source: transcriptomic single cell

data_processing:
Raw data binary base call (BCL) scRNAseq files were demultiplexed into FASTQ files for the individual samples using CellRanger mkfastq.
Demultiplexed FASTQ files were processed using kb-python
Assembly: GRCm38 (Ensembl 98) including the sFLT1 transgene
Supplementary files format and content: .tar.gz files containing raw unfiltered UMI counts in kallisto output format and comma-delimited text files including metadata per cell

source_name: Pancreatic islets

extract_protocol:
All methods listed in Bourgeois et al., ER stress relief drives ß-cell proliferation.
All methods listed in Bourgeois et al., ER stress relief drives ß-cell proliferation.

value: Pancreatic islets

value: 14 days doxycycline, withdrawal 4 days


title: aac2(A128P,A137D) rep3

city: Syracuse

first: Dr. Xin Jie

last: Chen

state: NY

address: 750 East Adams St

department: Biochemistry and Molecular Biology

institute: State University of New York Upstate Medical University

description:
Library name: CY6471-C_S12
CY6471-C_S12

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, using Cutadapt-1.2.1 and low-quality (q < 25) sequence
Trimmed sequences were mapped to sacCer3 whole genome using Bowtie 2 and quantified to Saccharomyces Genome Database (SGD) annotation, using strict paired-end compatibility, with requirement of junction reads to match introns, minimum feature overlap of 95%, and minimum reads of 1.
Assembly: sacCer3
Supplementary files format and content: tab-delimited text files include normalized alignment counts per gene for each sample. Features on columns

organism: Saccharomyces cerevisiae

source_name: Single-cell eukaryote (haploid)

growth_protocol: Cells were grown at 25°C in 1% yeast extract +2% peptone +2% glycerol +2% ethanol

extract_protocol:
Total RNA was extracted using glass beads and phenol/chloroform/isoamyl alcohol (25:24:1). RNA was precipitated, and the quality and quantity of RNA was assessed with the Bioanalyzer. 1 mg RNA was used as input to the Illumina Stranded mRNA kit for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Stranded mRNA prep kit following the manufacturers protocol.

tag: strain

value: Single-cell eukaryote (haploid)

value: AAC2; aac2A128P, A137D

tag: medium

value: 1%Yeast extract +2%peptone +2% glycerol +2% ethanol


title: Ctrl_Thap1_OE_L2C_embryo_RNA_rep1

description: Library name: Sample 10


title: Pat-11-CTRL-CTL

description: Library name: Sample 1

value: Control


title: aac2(A128P,A137D) rep2

description:
Library name: CY6471-B_S11
CY6471-B_S11


title: Ctrl_L2C_embryo_RNA_rep1

description: Library name: Sample 25


title: total RNAs from CG31510 and CG7065 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: DOX treated islets, withdrawal 4 days, replicate 1


title: Control islets, no DOX, replicate 2

value: No doxycycline


title: Pat-14-CVD-CTL

description: Library name: Sample 3

value: ASCVD


title: aac2(A128P,A137D) rep1

description:
Library name: CY6471-A_S10
CY6471-A_S10


title: Ctrl_E2C_embryo_RNA_rep2

description: Library name: Sample 23

source_name: early two-cell embryo

value: early two-cell embryo


title: dMFB1; aac2(A128P, A137D) rep3

description:
Library name: CY6470-C_S9
CY6470-C_S9

value: AAC2; aac2A128P, A137D; mfb1{delta}


title: Ctrl_L2C_embryo_RNA_rep2

description: Library name: Sample 27


title: total RNAs from CG31510 and CG7065 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: dMFB1; aac2(A128P, A137D) rep2

description:
Library name: CY6470-B_S8
CY6470-B_S8


title: SAM24418487 Mm  intest organ Slit3 72h 4

city: South San Fracisco

last: Castillo-Azofeifa

address: 1 DNA Way

institute: Genentech

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie (Pau and Reeder, 2012) in BioConductor (Huber et al., 2015)
first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed
The remaining reads were aligned to the mouse (GRCm38.p5) reference genome using GSNAP (PMID:20147302, 27008021) version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000')
Transcript annotation was based on the Gencode genes data base (mouse: GENCODE M15).
To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated.
Assembly: GRCm38
Supplementary files format and content: Tab-delimeted file that includes raw counts for each gene in a feature by sample matrix

source_name: Small intestine

extract_protocol:
After treatment organoids were lysed, and RNA was isolated (RNAeasy Mini Kit, 74104, Qiangen).
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific catalog#: Q32852) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies catalog#: 5067-5576). cDNA library was generated from 2 nanograms of total RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara catalog#: 634894). 150 picograms of cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina catalog#: FC-131-1024). Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific catalog#: Q32851) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies catalog#: 5067-5582).Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pairreads for each sample.

treatment_protocol: Organoids were treated with 10 ug/mL of recombinant Slit3 (or control) for 3, 24 and 72 hours.

value: Small intestine

value: organoid

value: WT BL6, *LDLR.ko.BL6- MNV.Helico Free

value: 72 hours


title: Thap1_mKO_E2C_embryo_RNA_rep1

description: Library name: Sample 22

value: Thap1 maternal knockout


title: Mock, HMEC-1 cells, bio rep 1, dual RNA-seq

city: Taipei City

first: Shu-Wei

middle: Marcia

last: Su

address: No. 155, Sec. 2, Linong St, Beitou District

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: Total RNA treated with DNase I and ribosomal RNA depletion

data_processing:
Raw sequencing data quality was analyzed using Fastp (version 0.23.2), and the sequencing adapters and low-quality reads were trimmed and removed using STAR (version 2.7.9a). The reads were aligned to the GAS NZ131 reference genome (NCBI accession number, NC_011375.1) and human reference genome (hg38) using the featureCounts (version 2.0.4). The differential gene expression analysis was performed separately for HMEC-1 cells and GAS and normalized using DESeq2. The genes with a Padj < 0.05 and a log2 fold change ≥ 1 or ≤ −1 were considered to be differentially expressed genes (DEGs). Gene ontology (GO) term enrichment analysis of the DEGs was performed using the Blast2GO tool.
Assembly: GAS NZ131 reference genome (NCBI accession number, NC_011375.1) and human reference genome (hg38)
Supplementary files format and content: Tab-delimited text files including raw counts for each sample

growth_protocol: HMEC-1 cells were cultured in endothelial cell growth medium M200 (Thermo Fisher Scientific) with addition of low serum growth supplement (Thermo Fisher Scientific) and 10% fetal bovine serum and incubated at 37°C in 5% CO2. For GAS infection model, HMEC-1 cells were seeded in 6-well (3 × 105 cells per well) culture plates for overnight. Next day, the refreshed GAS (OD600=0.5; mid-log phase) grown in tryptic soy broth containing 0.5% yeast extract (TSBY) were collected, washed, and resuspended in M200 medium.

extract_protocol:
To extract total RNAs of HMEC-1 cells and intracellular GAS, we resuspended the cell pellets in the lysozyme buffer (Geneaid) containing acid-treated silica beads (0.1 mm) (Sigma). The cells were mechanically broken by vortexing, followed by the RNA isolation procedure of GENEzol TriRNA Bacterial Kit (Geneaid), according to the manufacturer’s recommendation. The total RNAs for dual RNA-seq analysis were further evaluated using the Eukaryote Total RNA Nano Kit for 2100 Bioanalyzer system (Agilent). The RNAs that obtained the RNA integrity number greater than 9 were used for subsequent library preparation of dual RNA-seq analysis.
The high quality total RNAs (HMEC-1 cells and GAS) were treated with DNase I and ribosomal RNA depletion (Ribo-Zero rRNA Removal Kits; Illumina), prior to library preparation (Stranded Total RNA Prep kit; Illumina) and NextSeq2000 sequencing (2x100 bp paired-end sequencing) (Illumina).

treatment_protocol: To infect HMEC-1 cells, we then added the freshly prepared GAS in the seeded cell wells at a multiplicity of infection (MOI) of 50 for infection. After 30 min of infection, the extracellular GAS in the medium was removed, and the cells were washed twice with PBS buffer. Subsequently, the cells were inoculated for another half of hour (in total 1 h post-infection point) with M200 containing antibiotic gentamicin (125 µg/mL). For dual RNA-seq analyses, HMEC-1 cells containing intracellular GAS were collected from 6-well plates at 1 h post-infection, followed by trypsin-EDTA detachment and washed in M200 medium. The cell pellets were then preserved in the RNAlater stabilization solution (Thermo Fisher Scientific) at -80ºC until use.

value: not applicable

value: Human microvascular endothelial cell line-1

value: non-infection


title: Thap1_mKO_L2C_embryo_RNA_rep1

description: Library name: Sample 26

value: late two-cell embryo


title: DOX treated islets, replicate 2

value: Pancreatic islets

value: 14 days doxycycline


title: Ctrl_E2C_embryo_RNA_rep1

description: Library name: Sample 21

value: WT


title: DOX treated islets, replicate 1


title: WT rep3

description:
Library name: CY6469-C_S6
CY6469-C_S6

value: Single-cell eukaryote (haploid)

value: 1%Yeast extract +2%peptone +2% glycerol +2% ethanol


title: WT_Nfkb1-KO_BMDC_Day3, HTO

value: Bone-marrow derived dendritic cells

value: mixed sample (Wild-type, Nfkb1-/-)

value: Flt3 Differentiation:Day 3

value: HTO

value: TotalSeq-A0305 anti-mouse Hashtag 1，TotalSeq-A0305 anti-mouse Hashtag 2，TotalSeq-A0305 anti-mouse Hashtag 3，TotalSeq-A0305 anti-mouse Hashtag 5


title: PROseq measurement of nascent RNA from dZcchc8 KD OSCs, replicate2

description: Library name: PROseq_siZC8_rep2

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 0 mismatches for genome wide analysis
set flat to force processing of only the 1nd mate of paired end data
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Library strategy: PRO-seq

molecule: nuclear RNA

extract_protocol:
RNA was extracted using Trizol
Precision Run-On Sequencing (PRO-seq) procedure was according to Mahat et al. (2016)

value: OSCs


title: Thap1_mKO_E2C_embryo_RNA_rep2

description: Library name: Sample 24

value: early two-cell embryo


title: Mock, HMEC-1 cells, bio rep 4, dual RNA-seq


title: Control islets, no DOX, replicate 1

value: No doxycycline


title: Ctrl_PN5_1C_embryo_RNA_rep4

description: Library name: Sample 19

source_name: PN5 one-cell embryo

value: PN5 one-cell embryo


title: SAM24418483 Mm  intest organ anti-gD 72h 4

value: Small intestine

value: organoid

value: WT BL6, *LDLR.ko.BL6- MNV.Helico Free

value: anti-gD control

value: 72 hours


title: WT rep1

description:
Library name: CY6469-A_S4
CY6469-A_S4


title: Mock, HMEC-1 cells, bio rep 3, dual RNA-seq

value: not applicable

value: Human microvascular endothelial cell line-1

value: non-infection


title: Mock, HMEC-1 cells, bio rep 2, dual RNA-seq


title: PROseq measurement of nascent RNA from dZcchc7 KD OSCs, replicate1

description: Library name: PROseq_siZC7_rep1


title: Pat-8-CTRL-CTL

description: Library name: Sample 2

value: Control

value: Blood

value: monocytes


title: Thap1_mKO_PN5_1C_embryo_RNA_rep3

description: Library name: Sample 18

value: Thap1 maternal knockout


title: SAM24418481 Mm  intest organ anti-gD 72h 2

value: WT


title: SAM24418486 Mm  intest organ Slit3 72h 3


title: dMFB1; aac2(A128P, A137D) rep1

description:
Library name: CY6470-A_S7
CY6470-A_S7

value: Single-cell eukaryote (haploid)

value: AAC2; aac2A128P, A137D; mfb1{delta}

value: 1%Yeast extract +2%peptone +2% glycerol +2% ethanol


title: SAM24418480 Mm  intest organ anti-gD 72h 1


title: SAM24418485 Mm  intest organ Slit3 72h 2


title: Thap1_mKO_PN5_1C_embryo_RNA_rep4

description: Library name: Sample 20

value: PN5 one-cell embryo


title: PROseq measurement of nascent RNA from dZfc3h1 KD OSCs, replicate1

description: Library name: PROseq_siZC1_rep1

value: OSCs


title: Ctrl_PN5_1C_embryo_RNA_rep2

description: Library name: Sample 15


title: SAM24418479 Mm  intest organ Slit3 24h 4

value: Small intestine

value: organoid

value: 24 hours


title: SAM24418484 Mm  intest organ Slit3 72h 1

value: WT BL6, *LDLR.ko.BL6- MNV.Helico Free

value: 72 hours


title: PROseq measurement of nascent RNA from Rrp41 KD OSCs, replicate2

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 0 mismatches for genome wide analysis
set flat to force processing of only the 2nd mate of paired end data
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Library strategy: PRO-seq


title: PROseq measurement of nascent RNA from dZcchc8 KD OSCs, replicate1

description: Library name: PROseq_siZC8_rep1


title: SAM24418478 Mm  intest organ Slit3 24h 3


title: WT rep2

description:
Library name: CY6469-B_S5
CY6469-B_S5


title: dMFB1 rep3

description:
Library name: CY6468-C_S3
CY6468-C_S3

value: AAC2; mfb1{delta}


title: PROseq measurement of nascent RNA from CG7065 KD OSCs, replicate1

description: Library name: PROseq_siCG7065_rep1


title: SAM24418482 Mm  intest organ anti-gD 72h 3

value: anti-gD control


title: SAM24418477 Mm  intest organ Slit3 24h 2


title: Ctrl_PN5_1C_embryo_RNA_rep3

description: Library name: Sample 17


title: PROseq measurement of nascent RNA from dZcchc7 KD OSCs, replicate2

description: Library name: PROseq_siZC7_rep2


title: PROseq measurement of nascent RNA from dZfc3h1 KD OSCs, replicate2

description: Library name: PROseq_siZC1_rep2


title: dMFB1 rep2

description:
Library name: CY6468-B_S2
CY6468-B_S2


title: PROseq measurement of nascent RNA from CG31510 KD OSCs, replicate1

description: Library name: PROseq_siCG31510_rep1


title: SAM24418475 Mm  intest organ anti-gD 24h 4


title: PROseq measurement of nascent RNA from Rrp40 KD OSCs, replicate1


title: Ctrl_MII_oocyte_RNA_rep2

description: Library name: Sample 11

source_name: MII oocyte

value: MII oocyte


title: PROseq measurement of nascent RNA from Piwi KD OSCs, replicate2

value: siPiwi


title: Thap1_mKO_PN5_1C_embryo_RNA_rep2

description: Library name: Sample 16


title: SAM24418474 Mm  intest organ anti-gD 24h 3


title: dMFB1 rep1

description:
Library name: CY6468-A_S1
CY6468-A_S1


title: PROseq measurement of nascent RNA from CG7065 KD OSCs, replicate2

description: Library name: PROseq_siCG7065_rep2


title: PROseq measurement of nascent RNA from Rrp41 KD OSCs, replicate1


title: PROseq measurement of nascent RNA from Piwi KD OSCs, replicate1


title: PROseq measurement of nascent RNA from CG31510 KD OSCs, replicate2

description: Library name: PROseq_siCG31510_rep2


title: Ctrl_PN5_1C_embryo_RNA_rep1

description: Library name: Sample 13


title: input DNA used for ChIP with anti-Pol II antibody from Piwi KD OSCs, replicate2

description: Library name: input_Pol_II_siPiwi_rep2

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 0 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006)
with NEBNext Ultra DNA Library Prep Kit Illumina (NEB)


title: PROseq measurement of nascent RNA from Rrp40 KD OSCs, replicate2


title: Thap1_mKO_MII_oocyte_RNA_rep2

description: Library name: Sample 12


title: PROseq measurement of nascent RNA from Mtr4 KD OSCs, replicate2


title: input DNA used for ChIP with anti-Pol II antibody from Piwi KD OSCs, replicate1

description: Library name: input_Pol_II_siPiwi_rep1


title: PROseq measurement of nascent RNA from Mtr4 KD OSCs, replicate1


title: PROseq measurement of nascent RNA from control KD OSCs, replicate2

description: Library name: PROseq_siCtrl_rep2


title: Thap1_mKO_PN5_1C_embryo_RNA_rep1

description: Library name: Sample 14


title: Ctrl_D60_FGO_RNA_rep2

description: Library name: Sample 7

source_name: D60 FGO

value: D60 FGO


title: SAM24418470 Mm  intest organ Slit3 3h 3

value: 3 hours


title: SAM24418471 Mm  intest organ Slit3 3h 4

value: WT


title: Thap1_mKO_MII_oocyte_RNA_rep1

description: Library name: Sample 10

value: Thap1 maternal knockout


title: PROseq measurement of nascent RNA from dZfc3h1 and dZcchc8 KD OSCs, replicate2


title: PROseq measurement of nascent RNA from control KD OSCs, replicate1

description: Library name: PROseq_siCtrl_rep1


title: SAM24418469 Mm  intest organ Slit3 3h 2


title: SAM24418476 Mm  intest organ Slit3 24h  1


title: PROseq measurement of nascent RNA from dZfc3h1 and dZcchc8 KD OSCs, replicate1


title: input DNA used for ChIP with anti-Pol II antibody from Zfc3h1 and Zcchc8 KD OSCs, replicate1

description: Library name: input_Pol_II_siZfc3h1_Zcchc8_rep1


title: Thap1_mKO_D60_FGO_RNA_rep2

description: Library name: Sample 8


title: Ctrl_MII_oocyte_RNA_rep1

description: Library name: Sample 9


title: Ctrl_D60_FGO_RNA_rep1

description: Library name: Sample 5


title: SAM24418473 Mm  intest organ anti-gD 24h 2


title: Thap1_mKO_D14_oocyte_RNA_rep2

description: Library name: Sample 4

source_name: D14 oocyte

value: D14 oocyte


title: SAM24418468 Mm  intest organ Slit3 3h 1


title: SAM24418472 Mm  intest organ anti-gD 24h 1


title: input DNA used for ChIP with anti-Pol II antibody from Zfc3h1 and Zcchc8 KD OSCs, replicate2

description: Library name: input_Pol_II_siZfc3h1_Zcchc8_rep2


title: input DNA used for ChIP with anti-Pol II antibody from CG7065 KD OSCs, replicate2

description: Library name: input_Pol_II_siCG7065_rep2


title: Thap1_mKO_D60_FGO_RNA_rep1

description: Library name: Sample 6


title: input DNA used for ChIP with anti-Pol II antibody from CG31510 and CG7065 KD OSCs, replicate2

description: Library name: input_Pol_II_siCG31510_CG7065_rep2


title: input DNA used for ChIP with anti-Pol II antibody from CG7065 KD OSCs, replicate1

description: Library name: input_Pol_II_siCG7065_rep1


title: input DNA used for ChIP with anti-Pol II antibody from CG31510 and CG7065 KD OSCs, replicate1

description: Library name: input_Pol_II_siCG31510_CG7065_rep1


title: PROseq measurement of nascent RNA from Dis3 KD OSCs, replicate1


title: SAM24418465 Mm  intest organ anti-gD 3h 2


title: D235_bladder

type: RNA

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: Custom probe panel #QK9QBG

hyb_protocol: A custom probe panel #QK9QBG and control probes were added to the slide at a concentration of 10 nM and hybridized at 50°C overnight in a thermocycler. Stringent post-hybridization washes were performed, followed by ligation of probes at 37°C for 2 hr and primer annealing. Rolling circle amplification of probes was performed for 2 hr at 37°C, thereby generating copies of the gene-specific barcode for each RNA-binding event. After washing and chemically quenching the background fluorescence, nuclei were stained with DAPI, and the slide was loaded onto a Xenium Analyzer.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Data processed using Xenium Ranger software.
Supplementary files format and content: morphology_focus/morphology_focus_0000.ome.tif: DAPI image
Supplementary files format and content: morphology_focus/morphology_focus_0001.ome.tif: boundary (ATP1A1/E-Cadherin/CD45) image
Supplementary files format and content: morphology_focus/morphology_focus_0002.ome.tif: interior - RNA (18S) image
Supplementary files format and content: morphology_focus/morphology_focus_0003.ome.tif: interior - protein (alphaSMA/Vimentin) image
Supplementary files format and content: analysis_labeled_edited.zarr.zip: compressed secondary analysis results, including cell annotations that can be loaded in Xenium Explorer
Supplementary files format and content: cell_feature_matrix.zarr.zip: compressed cell expression matrices
Supplementary files format and content: cells.zarr.zip: compressed cell and nucleus segmentation data
Supplementary files format and content: experiment.xenium: JSON file for opening the experiment in Xenium Explorer
Supplementary files format and content: morphology.ome.tif: slide image
Supplementary files format and content: transcripts.zarr.zip: compressed transcript data

source_name: bladder

label_protocol: The Xenium slide was permeabilized using 1% SDS for 2 min, followed by 2 PBS washes and immersed in pre-chilled 70% methanol for 60 min on ice and washed 2 times in PBS.

extract_protocol: A 10 µm, FFPE bladder sample from a deceased organ donor was sectioned onto a Xenium slide.

value: bladder

tag: Sex

value: Female

tag: age

value: 42 years


title: Ctrl_D14_oocyte_RNA_rep1

description: Library name: Sample 1


title: Ctrl_D14_oocyte_RNA_rep2

description: Library name: Sample 3


title: Thap1_mKO_D14_oocyte_RNA_rep1

description: Library name: Sample 2


title: SAM24418467 Mm  intest organ anti-gD 3h 4

value: Small intestine


title: SAM24418464 Mm  intest organ anti-gD 3h 1

value: organoid


title: PROseq measurement of nascent RNA from Dis3 KD OSCs, replicate2

source_name: OSCs

value: OSCs


title: SAM24418466 Mm  intest organ anti-gD 3h 3

value: WT BL6, *LDLR.ko.BL6- MNV.Helico Free


title: B. burgdorferi, BSK + PG, exponential phase, rep3

city: Boston

first: Peter

last: Gwynne

state: MA

address: 136 Harrison Ave

department: Molecular and Microbiology

institute: Tufts University

description: Library name: PG 3

data_processing:
A B. burgdorferi B31 genome was built using ASM868v2 (GCF_000008685.2) and a custom gene transfer format (gtf) file (gift from Philip Adams) using STAR23 v. 2.6.1.
Reads were mapped to the genome of B. burgdorferi (GCF_000008685.2) using STAR v. 2.6.1 and gene expression was summarized using RSEM24 v. 1.3.1.
Differential expression analysis was performed using DESeq225 v. 4.3.1 in R
Assembly: ASM868v2 (GCF_000008685.2)
Supplementary files format and content: Exp1TPM: transcript counts for each of the nine conditions
Supplementary files format and content: PCDEGs: differential expression for each transcript comparing the average of the media + PC counts to the average of the BSK (media only) counts
Supplementary files format and content: PGDEGs: differential expression for each transcript comparing the average of the media + PG counts to the average of the BSK (media only) counts

organism: Borreliella burgdorferi B31

source_name: Exponential phase

growth_protocol: B. burgdorferi B31 was grown in Barber-Stoenner-Kelly medium (BSK). Cells from a stationary phase culture were back-diluted to 2x10^5 cells/mL in 10 mL BSK and incubated at 32C with 4% CO2 for 4-5 days until cultures reached between 1 and 6 x 10^7. Cell density was counted by Petroff-Hausser.

extract_protocol:
RNA was extracted from 10mL exponential phase cell pellets using an miRNeasy mini kit (QIAGEN). gDNA was digested using TURBO DNase (Invitrogen), and RNA was repurified using the Monarch Spin 10 µg RNA Cleanup Kit (NEB).
Samples were submitted to Azenta Life Sciences/Genewiz for RNA quality assessment, library preparation, and sequencing (Illumina NovaSeqX+ 2x150bp).

treatment_protocol: Cultures were grown in either standard BSK or BSK supplemented with 100 uM phospholipid, either phosphatidylcholine or phosphatidylglycerol.

value: Exponential phase


title: PROseq measurement of nascent RNA from control KD OSCs, replicate1

value: siCtrl


title: input DNA used for ChIP with anti-Pol II antibody from control KD OSCs, replicate1

description: Library name: input_Pol_II_siCtrl_rep1


title: P06_tb_neg_hiv_pos

city: Dublin

first: Gina

last: Leisching

address: St James's Hospital, Trinity College Dublin

country: Ireland

institute: Trinity Translational Medicine Institute

description: nCounter Metabolic Pathways Panel [NS_Hs_Metabolism_v1.0]

hyb_protocol: NanoString nCounter Metabolic Pathways Panel

data_processing: Data were analysed using the NanoString nSolver Data Analysis Software

source_name: Human alveolar macrophages

label_protocol: NanoString

extract_protocol: Total RNA was harvested from human macrophages 24 hr following H37Rv Mtb infection and isolated and purified by silica-membrane column centrifugation.

tag: pair

value: U1 + Uninfected

tag: tb

value: negative

tag: hiv

value: positive


title: B. burgdorferi, BSK + PG, exponential phase, rep1

description: Library name: PG 1


title: P05_tb_pos_hiv_neg

scan_protocol: NanoString nCounter Metabolic Pathways Panel

value: U937 + Infected


title: input DNA used for ChIP with anti-Pol II antibody from CG31510 KD OSCs, replicate1

description: Library name: input_Pol_II_siCG31510_rep1

tag: cell line


title: input DNA used for ChIP with anti-Pol II antibody from control KD OSCs, replicate2

description: Library name: input_Pol_II_siCtrl_rep2


title: small RNA-seq analyis of small RNA expression changes in CG7065 germline KD fly ovary replicate2

description: Library name: TraPR_MTD_shCG7065_rep2

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 0 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

source_name: fly ovaries

growth_protocol: flies were maintained at 25 °C under a 12-hour light/dark cycle. For ovary sample collections, flies were aged for 2-3 days and placed on apple juice agar supplemented with fresh yeast paste for 2 days.

extract_protocol:
small RNAs were purified though TrapR column, followed by pheno Chloroform extraction
Small RNA-seq was performed according to the TraPR method, Grentzinger et al. (2020)

tag: tissue

value: fly ovaries


title: PROseq measurement of nascent RNA from CG31510 and CG7065 KD OSCs, replicate2

tag: treatment


title: input DNA used for ChIP with anti-Pol II antibody from CG31510 KD OSCs, replicate2

description: Library name: input_Pol_II_siCG31510_rep2


title: PROseq measurement of nascent RNA from CG31510 and CG7065 KD OSCs, replicate1


title: B. burgdorferi, BSK + PG, exponential phase, rep2

description: Library name: PG 2

tag: cell type


title: B. burgdorferi, BSK + PC, exponential phase, rep3

description: Library name: PC 3


title: small RNA-seq analyis of small RNA expression changes in CG7065 germline KD fly ovary replicate1

description: Library name: TraPR_MTD_shCG7065_rep1


title: ChIP with anti-Pol II antibody from Zfc3h1 and Zcchc8 KD OSCs, replicate2

description: Library name: Pol_II_8WG16_siZfc3h1_Zcchc8_rep2


title: small RNA-seq analyis of small RNA expression changes in control germline KD fly ovary replicate2

description: Library name: TraPR_MTD_shWhite_rep2


title: B. burgdorferi, BSK + PC, exponential phase, rep2

description: Library name: PC 2


title: B. burgdorferi, BSK + PC, exponential phase, rep1

description: Library name: PC 1


title: ChIP with anti-Pol II antibody from Zfc3h1 and Zcchc8 KD OSCs, replicate1

description: Library name: Pol_II_8WG16_siZfc3h1_Zcchc8_rep1


title: P04_tb_neg_hiv_pos

tag: group


title: P04_tb_pos_hiv_pos

value: U1 + Infected


title: ChIP with anti-Pol II antibody from CG31510 and CG7065 KD OSCs, replicate2

description: Library name: Pol_II_8WG16_siCG31510_CG7065_rep2


title: P06_tb_pos_hiv_pos


title: small RNA-seq analyis of small RNA expression changes in CG31510 germline KD fly ovary replicate2

description: Library name: TraPR_MTD_shCG31510_rep2


title: P03_tb_pos_hiv_neg


title: ChIP with anti-Pol II antibody from Piwi KD OSCs, replicate1

description: Library name: Pol_II_8WG16_siPiwi_rep1


title: PROseq measurement of nascent RNA from control KD OSCs, replicate2


title: ChIP with anti-Pol II antibody from Piwi KD OSCs, replicate2

description: Library name: Pol_II_8WG16_siPiwi_rep2


title: P05_tb_neg_hiv_neg

value: U937 + Uninfected


title: B. burgdorferi, BSK, exponential phase, rep2

description: Library name: BSK 2


title: TTseq measurement of nascent RNA from dZfc3h1 and dZcchc8 (ZC1_ZC8) KD OSCs after incubuation with 4sU, replicate3

description: Library name: siZC1_ZC8_day4_3

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

extract_protocol:
RNA was extracted using NucleoSpin® RNA Kit from Macherey-Nagel, the TT-seq experiment was performed following the protocol in (B. Schwalb et al., 2016) with modifications
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)


title: ChIP with anti-Pol II antibody from CG7065 KD OSCs, replicate2

description: Library name: Pol_II_8WG16_siCG7065_rep2


title: input DNA used for ChIP with anti-H3K9me3 antibody from Piwi KD OSCs, replicate2


title: small RNA-seq analyis of small RNA expression changes in CG31510 germline KD fly ovary replicate1

description: Library name: TraPR_MTD_shCG31510_rep1


title: B. burgdorferi, BSK, exponential phase, rep3

description: Library name: BSK 3


title: small RNA-seq analyis of small RNA expression changes in control germline KD fly ovary replicate1

description: Library name: TraPR_MTD_shWhite_rep1


title: TTseq measurement of nascent RNA from dZcchc8 (ZC8) KD OSCs after incubuation with 4sU, replicate3

description: Library name: siZC8_day4_3


title: B. burgdorferi, BSK, exponential phase, rep1

description: Library name: BSK 1


title: ChIP with anti-Pol II antibody from CG31510 and CG7065 KD OSCs, replicate1

description: Library name: Pol_II_8WG16_siCG31510_CG7065_rep1


title: TTseq measurement of nascent RNA from dZcchc8 (ZC8) KD OSCs after incubuation with 4sU, replicate2

description: Library name: siZC8_day4_2


title: P03_tb_neg_hiv_neg


title: P02_tb_pos_hiv_pos


title: input DNA used for ChIP with anti-H3K9me3 antibody from siLuc control KD OSCs, replicate2


title: P01_tb_pos_hiv_neg


title: TTseq measurement of nascent RNA from dZfc3h1 and dZcchc8 (ZC1_ZC8) KD OSCs after incubuation with 4sU, replicate1

description: Library name: siZC1_ZC8_day4_1


title: TTseq measurement of nascent RNA from dZfc3h1 and dZcchc8 (ZC1_ZC8) KD OSCs after incubuation with 4sU, replicate2

description: Library name: siZC1_ZC8_day4_2


title: ChIP with anti-Pol II antibody from CG31510 KD OSCs, replicate2

description: Library name: Pol_II_8WG16_siCG31510_rep2


title: input DNA used for ChIP with anti-H3K9me3 antibody from siLuc control KD OSCs, replicate1


title: ChIP with anti-Pol II antibody from control KD OSCs, replicate2

description: Library name: Pol_II_8WG16_siCtrl_rep2


title: P02_tb_neg_hiv_pos


title: ChIP with anti-Pol II antibody from CG31510 KD OSCs, replicate1

description: Library name: Pol_II_8WG16_siCG31510_rep1


title: input DNA used for ChIP with anti-H3K9me3 antibody from Piwi KD OSCs, replicate1


title: TTseq measurement of nascent RNA from dZcchc8 (ZC8) KD OSCs after incubuation with 4sU, replicate1

description: Library name: siZC8_day4_1


title: TTseq measurement of nascent RNA from dZcchc7 (ZC7) KD OSCs after incubuation with 4sU, replicate3

description: Library name: siZC7_day4_3


title: input DNA used for ChIP with anti-H3K9me3 antibody from CG31510 and CG7065 KD OSCs, replicate2


title: Siberian Hamster, POA, 32wk, Rep 6

city: Glasgow

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

country: United Kingdom

institute: University of Glasgow

description: Library name: POA_161

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated  using Salmon
Assembly: GRCm39
Supplementary files format and content: Expression matrix (CPM)

organism: Phodopus sungorus

source_name: POA

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus mini-kit
RNA Libraries were constructed using the PCR_cDNA sequencing barcoding kit (SQK-PCB109, Oxford Nanopore) as per manufacturers instructions

value: POA

value: 32wk SD


title: ChIP with anti-Pol II antibody from CG7065 KD OSCs, replicate1

description: Library name: Pol_II_8WG16_siCG7065_rep1


title: Siberian Hamster, POA, 32wk, Rep 5

description: Library name: POA_113


title: TTseq measurement of nascent RNA from dZcchc7 (ZC7) KD OSCs after incubuation with 4sU, replicate1

description: Library name: siZC7_day4_1


title: input DNA used for ChIP with anti-H3K9me3 antibody from CG31510 and CG7065 KD OSCs, replicate1


title: ChIP with anti-Pol II antibody from control KD OSCs, replicate1

description: Library name: Pol_II_8WG16_siCtrl_rep1


title: P01_tb_neg_hiv_neg


title: TTseq measurement of nascent RNA from dZcchc7 (ZC7) KD OSCs after incubuation with 4sU, replicate2

description: Library name: siZC7_day4_2


title: ChIP with anti-H3K9me3 antibody from Piwi KD OSCs, replicate2

tag: antibody

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: Siberian Hamster, POA, 32wk, Rep 2

description: Library name: POA_160


title: Siberian Hamster, POA, 32wk, Rep 4

description: Library name: POA_152


title: K562 GATA1 bulk D&D-seq primary Ab

city: New York

first: Dan

last: Landau

address: 413 East 69th Street

institute: Weill Cornell Medicine

description:
Library name: Bulk D_D-seq GATA1 primary antibody
D&D deamination targeting GATA1 binding loci

data_processing:
Data quality of raw fastq data was analyzed using FastQC (v0.12.1).
Nextera transposaes adapter sequences and homo polymer G were trimmed using CutAdapt (4.0) with minimum read length 20bp.
Trimmed reads were aligned to the human reference genome (GRCh38) using bwa-mem2 (2.1).
Duplicated reads, non-primary and low quality alignments were filtered using picard MarkDuplicates (3.3.0).
Peaks were called using MACS2 (2.2.9.1) with -f BAM --nomodel and peaks found in the blacklist annotation were filtered out using bedtools (v2.31.1).
Motif enrichment analysis was performed using MEME SEA (v5.5.5) with the HOCOMOCO v11 core human motif database. Target peaks with motif sequence were resized to 200bp (+/-100bp from the motif center).
C>T variants were collected using bcftools mpileup and highly frequent variants (>10%) and germlines (gnomAD) were filtered out.
C>T variants were overlapped with target peaks and annotated as D&D edits using bedtools intersect.
Assembly: GRCh38
Supplementary files format and content: narrowPeak, vcf (D&D edits)

source_name: Bone marrow

growth_protocol: Human K562 (ATCC, CCL-243) cell line was maintained according to standard procedures in RPMI-1640 (Thermo Fisher Scientific, 11-875-119) with 10% FBS (Thermo Fisher Scientific, 10-437-028) at 37 °C with 5% CO2. Cell lines in culture were screened biweekly for mycoplasma contamination using the MycoAlert PLUS Mycoplasma Detection Kit (Lonza, LT07-703).

extract_protocol:
For all the following centrifugations, cells were centrifuged in a swing-bucket centrifuge at 300g for 5 minutes before fixation and 600g for 5 minutes after fixation. About 200K to 1 million cells were collected and resuspended in 400 µl PBS. Then, 16% methanol-free formaldehyde (Thermo Fisher Scientific, PI28906) was added for fixation (final concentration 0.1%) at room temperature for 5 minutes. Glycine (final concentration 125 mM) was added to stop the cross-linking, followed by a wash with 1 ml of PBS. Fixed cells were permeabilized in 200 µl permeabilization buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 1% BSA, 1× protease inhibitors) on ice (7 minutes for cell lines, 5 minutes for primary cells), followed by a wash with 200 µl cold wash buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors). After cell counting, 100K-400K cells were transferred to PCR tubes and resuspended in 100 µl antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors), with 1 µl (1:100 dilution) of the antibodies. The cells were incubated at 4 °C with slow rotation overnight. For experiments with secondary antibodies, the cells were washed with antibody buffer and resuspended in 100 ul antibody buffer with 1 µl (1:100 dilution) of the secondary antibodies and incubated at room temperature for 1 hour. The cells were washed once with 200 ul wash buffer, and another time with 200 ul D&D binding buffer. The cells were resuspended in 50 ul D&D activation buffer with 100 uM DddA_NT, and incubated at room temperature on a rotator for 1 hour. The cells were then washed with 200 ul D&D binding buffer, resuspended in 50 ul DnD activation buffer, and incubated at 37 °C for 1 hour for deamination.
After D&D activation, the cells were washed once with 200 ul 1x Tris-TD buffer and resuspended in 50 ul 1x Tris-TD buffer with loaded TnY or Tn5 (volume depends on its  concentration and needs to be titrated to get the optimal tagmentation). To initiate tagmentation, the reaction was incubated at 37°C for 1 hour. To extract DNA, 1 ul 10% SDS, 2 ul proteinase K (NEB, P8107S), and 3 ul 0.5M EDTA were added to the reactions, which were then incubated at 55°C for 1 hour, followed by column-based DNA purification per the manufacturer’s instruction (Zymo, D5205). For library preparation PCR, we used uracil-tolerant DNA polymerase (NEBNext Q5U Master Mix, NEB M0597S) and Nextera-compatible indexing primers to amplify the purified DNA. To increase the efficiency of the initial gap fill-in step, we spiked in 1 ul of non-hot-start polymerase Bst 3.0 (NEB, M0374). The PCR steps are: 72°C for 5 min; 98°C for 30 s; 12 cycles of 98°C for 10 s, 55°C for 30 s and 72 °C for 30 s; followed by 72 °C for 5 min. Bulk samples are sequenced PE150 or PE100 for about 40M reads per sample.

value: Bone marrow

value: Erythroleukemia

tag: genotype

value: WT

value: GATA1 D&D


title: ChIP with anti-H3K9me3 antibody from Piwi KD OSCs, replicate1

value: OSCs


title: K562 CTCF bulk D&D-seq secondary Ab

description:
Library name: Bulk D_D-seq CTCF secondary antibody
D&D deamination targeting CTCF binding loci with secondary antibody

value: CTCF D&D


title: TTseq measurement of nascent RNA from dZfc3h1 (ZC1) KD OSCs after incubuation with 4sU, replicate2

description: Library name: siZC1_day4_2


title: K562 GATA1 bulk D&D-seq secondary Ab

description:
Library name: Bulk D_D-seq GATA1 secondary antibody
D&D deamination targeting GATA1 binding loci with secondary antibody


title: TTseq measurement of nascent RNA from dZfc3h1 (ZC1) KD OSCs after incubuation with 4sU, replicate3

description: Library name: siZC1_day4_3


title: K562 CTCF bulk D&D-seq primary Ab

description:
Library name: Bulk D_D-seq CTCF primary antibody
D&D deamination targeting CTCF binding loci


title: ChIP with anti-H3K9me3 antibody from siLuc control KD OSCs, replicate2


title: Siberian Hamster, POA, 32wk, Rep 1

description: Library name: POA_149


title: TTseq measurement of nascent RNA from control KD OSCs after incubuation with 4sU, replicate3

description: Library name: siLuc_day4_3


title: K562 CTCF bulk D&D-seq

description:
Library name: Bulk D_D-seq CTCF
D&D deamination targeting CTCF binding loci

growth_protocol: Human K562 (ATCC, CCL-243) and CA46 (ATCC, CRL-1648) cell lines were maintained according to standard procedures in RPMI-1640 (Thermo Fisher Scientific, 11-875-119) with 10% FBS (Thermo Fisher Scientific, 10-437-028) at 37 °C with 5% CO2. Cell lines in culture were screened biweekly for mycoplasma contamination using the MycoAlert PLUS Mycoplasma Detection Kit (Lonza, LT07-703).

extract_protocol:
For all the following centrifugations, cells were centrifuged in a swing-bucket centrifuge at 300g for 5 minutes before fixation and 600g for 5 minutes after fixation. About 200K to 1 million cells were collected and resuspended in 400 µl PBS. Then, 16% methanol-free formaldehyde (Thermo Fisher Scientific, PI28906) was added for fixation (final concentration 0.1%) at room temperature for 5 minutes. Glycine (final concentration 125 mM) was added to stop the cross-linking, followed by a wash with 1 ml of PBS. Fixed cells were permeabilized in 200 µl permeabilization buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 1% BSA, 1× protease inhibitors) on ice (7 minutes for cell lines, 5 minutes for primary cells), followed by a wash with 200 µl cold wash buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors). After cell counting, 100K-400K cells were transferred to PCR tubes and resuspended in 100 µl antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors), with 1 µl (1:100 dilution) of the antibodies. The cells were incubated at 4 °C with slow rotation overnight. The cells were washed once with 200 ul wash buffer, and another time with 200 ul D&D binding buffer. The cells were resuspended in 50 ul D&D activation buffer with 100 uM DddA_NT, and incubated at room temperature on a rotator for 1 hour. The cells were then washed with 200 ul D&D binding buffer, resuspended in 50 ul DnD activation buffer, and incubated at 37 °C for 1 hour for deamination.
After D&D activation, the cells were washed once with 200 ul 1x Tris-TD buffer and resuspended in 50 ul 1x Tris-TD buffer with loaded TnY or Tn5 (volume depends on its  concentration and needs to be titrated to get the optimal tagmentation). To initiate tagmentation, the reaction was incubated at 37°C for 1 hour. To extract DNA, 1 ul 10% SDS, 2 ul proteinase K (NEB, P8107S), and 3 ul 0.5M EDTA were added to the reactions, which were then incubated at 55°C for 1 hour, followed by column-based DNA purification per the manufacturer’s instruction (Zymo, D5205). For library preparation PCR, we used uracil-tolerant DNA polymerase (NEBNext Q5U Master Mix, NEB M0597S) and Nextera-compatible indexing primers to amplify the purified DNA. To increase the efficiency of the initial gap fill-in step, we spiked in 1 ul of non-hot-start polymerase Bst 3.0 (NEB, M0374). The PCR steps are: 72°C for 5 min; 98°C for 30 s; 12 cycles of 98°C for 10 s, 55°C for 30 s and 72 °C for 30 s; followed by 72 °C for 5 min. Bulk samples are sequenced PE150 or PE100 for about 40M reads per sample.


title: TTseq measurement of nascent RNA from dZfc3h1 (ZC1) KD OSCs after incubuation with 4sU, replicate1

description: Library name: siZC1_day4_1


title: Siberian Hamster, POA, 28wk, Rep 6

description: Library name: POA_175

value: 28wk SD


title: ChIP with anti-H3K9me3 antibody from siLuc control KD OSCs, replicate1


title: Siberian Hamster, POA, 28wk, Rep 4

description: Library name: POA_163


title: Siberian Hamster, POA, 28wk, Rep 5

description: Library name: POA_172


title: ChIP with anti-H3K9me3 antibody from CG31510 and CG7065 KD OSCs, replicate2


title: TTseq measurement of nascent RNA from control KD OSCs after incubuation with 4sU, replicate1

description: Library name: siLuc_day4_1


title: HeLa cells, esiDNAJC19_5

city: Cologne

first: Lara

last: Kroczek

address: Joseph-Stelzmann-Straße 9B

institute: Max-Planck Institute for Biology of Ageing

description:
Library name: JC19n5_MKRN240014793-1A_227WMFLT4
JC19_KD.Rep_5

data_processing:
removal rRNA transcripts: grep -v -i rrna <gtf> > <no.rRNA.gtf>
Index building (cufflinks/2.2.1): gffread -w <cdna_fasta> -g <fasta> <no.rRNA.gtf>
cDNA index was build using kallisto (kallisto/0.46.1): kallisto index -i <kallisto_index> <cdna_fasta>
Alignment and quantification (kallisto/0.46.1): kallisto quant -t 18 -i <kallisto_index> <--rf-stranded|--fr-stranded|unstranded> --genomebam -g <gtf> -c <chromosomes> -o <read_name> -b 100 <read_1> <read_2>
After normalization of read counts by making use of the standard median-ratio for estimation of size factors, pair-wise differential gene expression was performed using DESeq2/1.24.0 After removal of genes with less then 10 overall reads log2 fold changes were shrank using approximate posterior estimation for GLM coefficients.
Assembly: Ensembl Homo sapiens release 110 / hg38
Supplementary files format and content: tab-delimited file of deseq2 normalized counts

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco‘s Modified Eagle‘s Medium (DMEM), containing 4.5 g/L D-Glucose (Thermo Fisher, Cat# 61965-059) and 10% fetal bovine serum (Sigma, Cat# F7524). Cells were maintained at 37°C and 5% CO2 in a humidified incubator. Prior to each experiment, cells were seeded at equal densities and continuously monitored for mycoplasma contamination.

extract_protocol:
Cells were harvested and washed with ice-cold PBS prior to cell lysis using the lysis buffer provided in the RNA isolation kit (Macherey-Nagel, Cat# 740955.250). The experiment was performed according to the manufacturer’s instructions. RNA isolation was quantified using a NanoDrop spectrophotometer (Thermo Fisher, Cat# ND-ONE-W)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: For transient transfection of siRNA, a reverse transfection was conducted with a total cell number of 4x105 cells per well in a 6-well plate. The experiments were conducted 48 h after transfection with RNAiMAXX transfection reagent (Invitrogen, Cat# 56532). The following siRNA/esiRNA targeting sequences against human proteins were utilized: siRNA DNAJC19 (SASI_Hs01_00055864, Sigma) siRNA DNAJC15 (SASI_Hs01_00246981, Sigma)

value: HeLa

value: cervical cancer, immortalized

tag: batch


title: HeLa cells, esiDNAJC19_3

description:
Library name: JC19n3_MKRN240014791-1A_227WMFLT4
JC19_KD.Rep_3


title: RNA-seq Control rep2

city: Kansas City

first: Melanie

last: Weilert

state: MO

institute: Stowers Institute for Medical Research

description: Library name: kc167_dmso_totalRNA_2

data_processing:
All RNA-seq pair-ended sequencing data were aligned to the dm6 genome using STAR (2.7.1a) and raw read counts per gene were quantified with “--quantMode GeneCounts” option. RNA-seq levels are TPM-normalized across samples using the  dm6 annotation gtf file available at: https://hgdownload.soe.ucsc.edu/goldenPath/dbutbefm6/bigZips/genes/dm6.ensGene.gtf with the annotated transcript length.
Assembly: Drosophila melanogaster UCSC dm6
Supplementary files format and content: TPM table counts in tab-delimited text format in the file : RNA-seq_counts_tpm_replicates_combined.tsv. STAR output (Raw reads counts per gene) for each replicate is available under each sample.

source_name: Kc167 cells

growth_protocol: Drosophila melanogaster Kc167 cells were grown at 25 °C in HyClone SFX-Insect Cell Culture Media.

extract_protocol:
Total mRNA were extracted for Drosophila melanogaster Kc167 cells using Invitrogen TRIzol reagent.
cDNA libraries are prepared using Illumina TruSeq Stranded mRNA Preparation Kit with polyA enrichment and sequenced on Illumina NextSeq 500.

treatment_protocol: Cells were treated with DMSO (2%) for 1 hour as the control.

value: Kc167 cells

value: DMSO


title: TTseq measurement of nascent RNA from non 4sU treated control OSCs, replicate3

city: Vienna

first: Julius

last: Brennecke

address: Dr. Bohr Gasse 3

institute: IMBA-Institute for Molecular Biotechnology

description: Library name: siLuc_day4_3_no4sU_input


title: Siberian Hamster, POA, 32wk, Rep 3

description: Library name: POA_153


title: Siberian Hamster, POA, 28wk, Rep 3

description: Library name: POA_165


title: TTseq measurement of nascent RNA from control KD OSCs after incubuation with 4sU, replicate2

description: Library name: siLuc_day4_2


title: ChIP with anti-H3K9me3 antibody from CG31510 and CG7065 KD OSCs, replicate1


title: total RNAs from CG31510 and CG7065 germline KD in fly ovary harboring P element with polyA selection replicate3

description: Library name: nanosGal4_P_element_shCG31510_CG7065_rep3

extract_protocol:
RNA was extracted using NucleoSpin® RNA Kit from Macherey-Nagel
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)

value: fly ovaries


title: HeLa cells, esiDNAJC19_4

description:
Library name: JC19n4_MKRN240014792-1A_227WMFLT4
JC19_KD.Rep_4


title: Siberian Hamster, POA, 24wk, Rep 5

description: Library name: POA_188

value: 24wk SD


title: TRF2 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_trf2_nexus_1

data_processing:
ChIP-nexus data were first preprocessed by trimming and reassigning fixed and random barcode sequence information, stored as read names for use in downstream processing.
Reads were next trimmed to remove adapter sequences using Cutadapt (v.4.2) and aligned to the dm6 genome assembly using bowtie2 (v.2.3.5.1)
Using aligned coordinates alongside the stored fixed and random barcode sequence information, reads were deduplicated. Coverage was generated by collecting only the first “stop” base of each aligned read.
Across each relevant condition and TF, ChIP-nexus reads were pooled across replicates to generate the final high-coverage samples. Normalized reads-per-million (RPM) coverage was generated by scaling all base-resolution ChIP-nexus coverage relative to the total aligned reads, described previously.
Assembly: Drosophila melanogaster UCSC dm6
Supplementary files format and content: Bigwig files of positive and negative strands for each replicate and single base-pair resolution.

extract_protocol:
10e7 Kc167 cells were fixed with 1% formaldehyde in culture media at room temperature for 10 min with rotation. Fixed cells were washed with cold PBS, incubated with Orlando and Paro’s Buffer (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0, with freshly added Protease Inhibitor) for 10 min at room temperature with rotation, and then centrifuged and re-suspended in ChIP Buffer (10 mM Tris-HCl, pH 8.0; 140 mM NaCl; 0.1% SDS; 0.1% sodium deoxycholate; 0.5% sarkosyl; 1% Triton X-100, with freshly added Protease Inhibitor). Sonication was performed with a Bioruptor Pico for five rounds of 30 s on and 30 s off. Chromatin extracts were then centrifuged at 16,000 g for 5 min at 4° C. Supernatants were used for ChIP.
NOTE: This sample was prepared following a previous version of the ChIP-nexus protocol. Chromatin extracts were added to the antibody-bound beads (10 ug antibody per 50 ul Dynabeads Protein A + 50 ul Dynabeads Protein G) and incubated at 4°C overnight with rotation and then washed with Nexus washing buffer A to D (wash buffer A: 10 mM Tris-EDTA, 0.1% Triton X-100, wash buffer B: 150 mM NaCl, 20 mM Tris-HCl, pH 8.0, 5 mM EDTA, 5.2% sucrose, 1.0% Triton X-100, 0.2% SDS, wash buffer C: 250 mM NaCl, 5 mM Tris-HCl, pH 8.0, 25 mM HEPES, 0.5% Triton X-100, 0.05% sodium deoxycholate, 0.5 mM EDTA, wash buffer D: 250 mM LiCl, 0.5% IGEPAL CA-630, 10 mM Tris-HCl, pH 8.0, 0.5% sodium deoxycholate, 10 mM EDTA). End repair and dA-tailing were performed using the NEBNext End Repair Module and the NEBNext dA-Tailing Module. ChIP-nexus adaptors with mixed fixed barcodes (CTGA, TGAC, GACT, ACTG) were ligated with Quick T4 DNA ligase and converted to blunt ends with Klenow fragment and T4 DNA polymerase. The samples were treated with lambda exonuclease and RecJf exonuclease. After each enzymatic reaction, the chromatin was washed with the Nexus washing buffers A to D and Tris buffer (10 mM Tris, pH 7.5, 8.0, or 9.5, depending on the next enzymatic step). The chromatin was then eluted and subjected to reverse crosslinking and ethanol precipitation. Purified single-stranded DNA was then circularized with CircLigase, annealed with oligonucleotides complementary to the BamHI restriction site and linearized by BamHI digestion. The linearized single-stranded DNA was purified by ethanol precipitation and subjected to PCR amplification with NEBNext High-Fidelity 2X PCR Master Mix and ChIP-nexus primers.

treatment_protocol: Transcription inhibitors were added directly into SFX media. Cells were treated with 10 μM triptolide (TOCRIS Bioscience, 3253; dissolved in DMSO) at room temperature for 1h. Equivalent amounts of DMSO treatment (2%) were used as the control.

tag: chip antibody

value: custom anti-TRF2 rabbit polyclonal, Kadonaga Lab, TRF2_275

value: 10 uM Triptolide


title: Siberian Hamster, POA, 28wk, Rep 2

description: Library name: POA_162

value: POA


title: Siberian Hamster, POA, 24wk, Rep 4

description: Library name: POA_180


title: HeLa cells, esiDNAJC19_2

description:
Library name: JC19n2_MKRN240014790-1A_227WMFLT4
JC19_KD.Rep_2


title: HeLa cells, esiDNAJC19_1

description:
Library name: JC19n1_MKRN240014789-1A_227WMFLT4
JC19_KD.Rep_1


title: TRF2 ChIP-nexus Control rep1

description: Library name: kc167_dmso_trf2_nexus_1


title: total RNAs from dZfc3h1 and dZcchc7 germline KD in fly ovary harboring P element with polyA selection replicate3

description: Library name: nanosGal4_P_element_shZfc3h1_Zcchc7_weak_rep3


title: Siberian Hamster, POA, 24wk, Rep 2

description: Library name: POA_187


title: Siberian Hamster, POA, 24wk, Rep 6

description: Library name: POA_178


title: TTseq measurement of nascent RNA from non 4sU treated control OSCs, replicate1

description: Library name: siLuc_day4_1_no4sU_input


title: TRF2 ChIP-nexus 1 h Triptolide treatment rep2

description: Library name: kc167_triptolide_trf2_nexus_2


title: Siberian Hamster, POA, 24wk, Rep 1

description: Library name: POA_181


title: HeLa cells, esiScrambled_5

description:
Library name: WTn5_MKRN240014788-1A_227WMFLT4
WT.Rep_5


title: total RNAs from CG31510 and CG7065 germline KD in fly ovary harboring P element with polyA selection replicate2

description: Library name: nanosGal4_P_element_shCG31510_CG7065_rep2


title: HeLa cells, esiDNAJC15_4

description:
Library name: JC15n4_MKRN240014782-1A_227WMFLT4
JC15_KD.Rep_4


title: HeLa cells, esiDNAJC15_3

description:
Library name: JC15n3_MKRN240014781-1A_227WMFLT4
JC15_KD.Rep_3


title: total RNAs from dZfc3h1 and dZcchc7 germline KD in fly ovary harboring P element with polyA selection replicate2

description: Library name: nanosGal4_P_element_shZfc3h1_Zcchc7_weak_rep2


title: HeLa cells, esiScrambled_4

description:
Library name: WTn4_MKRN240014787-1A_227WMFLT4
WT.Rep_4


title: AKP_tumors

city: Lausanne

first: Maxim

last: Norkin

address: SV Station 19

country: Switzerland

institute: EPFL

description: Library name: AKP_tumors

data_processing:
star/2.7.11b
Assembly: GRCm39
Supplementary files format and content: Annotation.csv contains file annotations and Counts_processed.csv contains normalized counts

source_name: sc tumors

growth_protocol: AKP cells originate from a genetically engineered mouse model (GEMM). 14 days post-treatment

extract_protocol:
Mouse tumor samples harvested after termination were washed in PBS and mechanically minced into small fragments using sterile blades. Subsequently, tumor fragments were enzymatically incubated in a digestion buffer containing collagenase II at 2.5 mg/ml (Sigma-Aldrich, C6885-1G), collagenase IV at 2.5 mg/ml (Sigma-Aldrich, C5138-1G), and DNase I at 0.5 mg/ml (Roche; #11284932001) for 40 minutes at 37°C on a gently rotating platform to enhance enzymatic activity. Following digestion, the tumor suspension was filtered through a 100 µm cell strainer. FBS was immediately added to the collected fraction to neutralize enzymatic activity. The samples were centrifuged at 320 × g for 5 minutes, after which the supernatant was discarded. Cell pellets were washed three times with sterile PBS, centrifuging at 320 × g for 5 minutes between washes. After the final wash, cells were resuspended in 200 µL sterile PBS. RNA was then extracted using the High Pure RNA Isolation Kit (Roche; #11828665001), following the manufacturer’s protocol.
Purified RNA samples were subjected to bulk RNA sequencing using the Mercurius BRB-seq platform from Alithea Genomics (reference), according to the manufacturer's instructions. Sequencing was performed on an Illumina NovaSeq instrument (Aviati platform) with a sequencing depth of 5 million reads per sample, using a single-end 150 bp (SE150) configuration at the Genomic Technologies Facility (GTF), University of Lausanne (UNIL), Lausanne, Switzerland

treatment_protocol: Treatment was initiated when palpable tumors had formed (approximately 80-100 mm3) on day 7 for a maximum of 30 days following treatment planning.

value: sc tumors

value: AKP organoids

value: tumor

value: AKP

value: Ctrl, IgG, ODC, PD1, OXA, OXA PD1, ODC PD1


title: NC2beta ChIP-nexus non treated rep2

description: Library name: kc167_nt_nc2b_15_nexus_2

value: custom anti-NC2b rabbit polyclonal, Kadonaga Lab, NC2b_14915

value: Non treated


title: Siberian Hamster, POA, 24wk, Rep 3

description: Library name: POA_196


title: total RNAs from dZfc3h1 and dZcchc7 germline KD in fly ovary harboring P element with polyA selection replicate1

description: Library name: nanosGal4_P_element_shZfc3h1_Zcchc7_weak_rep1


title: HeLa cells, esiDNAJC15_2

description:
Library name: JC15n2_MKRN240014780-1A_227WMFLT4
JC15_KD.Rep_2


title: total RNAs from CG31510 and CG7065 germline KD in fly ovary harboring P element with polyA selection replicate1

description: Library name: nanosGal4_P_element_shCG31510_CG7065_rep1


title: Siberian Hamster, POA, 28wk, Rep 1

description: Library name: POA_174

value: 28wk SD


title: HeLa cells, esiDNAJC15_1

description:
Library name: JC15n1_MKRN240014779-1A_227WMFLT4
JC15_KD.Rep_1

value: HeLa


title: TTseq measurement of nascent RNA from non 4sU treated control OSCs, replicate2

description: Library name: siLuc_day4_2_no4sU_input

value: OSCs


title: RNA-seq Control rep1

description: Library name: kc167_dmso_totalRNA_1

value: Kc167 cells


title: total RNAs from CG7065 germline KD in fly ovary of the P element genetic background with polyA selection replicate3

description: Library name: nanosGal4_P_element_shCG7065_rep3


title: Siberian Hamster, POA, 20wk, Rep 5

description: Library name: POA_217

value: 20wk SD


title: NC2alpha ChIP-nexus non treated rep3

description: Library name: kc167_nt_nc2a_40_nexus_3

value: custom anti-NC2a rabbit polyclonal, Kadonaga Lab, NC2a_14940


title: Mot1 ChIP-nexus non treated rep3

description: Library name: kc167_nt_mot1_60_nexus_3

value: custom anti-Mot1 rabbit polyclonal, Kadonaga Lab, Mot1_3860


title: Siberian Hamster, POA, 20wk, Rep 4

description: Library name: POA_216


title: Siberian Hamster, POA, 20wk, Rep 6

description: Library name: POA_213


title: NC2alpha ChIP-nexus non treated rep1

description: Library name: kc167_nt_nc2a_40_nexus_1


title: Siberian Hamster, POA, 20wk, Rep 3

description: Library name: POA_231


title: HeLa cells, esiScrambled_2

description:
Library name: WTn2_MKRN240014785-1A_227WMFLT4
WT.Rep_2

value: cervical cancer, immortalized

value: WT


title: HeLa cells, esiScrambled_3

description:
Library name: WTn3_MKRN240014786-1A_227WMFLT4
WT.Rep_3


title: HeLa cells, esiScrambled_1

description:
Library name: WTn1_MKRN240014784-1A_227WMFLT4
WT.Rep_1


title: TRF2 ChIP-nexus Control rep2

description: Library name: kc167_dmso_trf2_nexus_2

value: custom anti-TRF2 rabbit polyclonal, Kadonaga Lab, TRF2_275

value: DMSO


title: NC2beta ChIP-nexus non treated rep1

description: Library name: kc167_nt_nc2b_15_nexus_1


title: Siberian Hamster, POA, 20wk, Rep 2

description: Library name: POA_226

value: POA


title: TAF13 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf13_nexus_3

value: custom anti-TAF13 rabbit polyclonal, Zeitlinger Lab, TAF13 - U3982CL190-3

value: 10 uM Triptolide


title: K562 bulk CTCF D&D with WGS, primary template amplification (PTA)

description:
Library name: Bulk WGS with CTCF D_D-seq
D&D deamination targeting CTCF binding loci

data_processing:
Data quality of raw fastq data was analyzed using FastQC (v0.12.1).
Nextera transposaes adapter sequences and homo polymer G were trimmed using CutAdapt (4.0) with minimum read length 20bp.
Trimmed reads were aligned to the human reference genome (GRCh38) using bwa-mem2 (2.1).
Duplicated reads, non-primary and low quality alignments were filtered using picard MarkDuplicates (3.3.0).
C>T variants were collected using bcftools mpileup and highly frequent variants (>10%) and germlines (gnomAD) were filtered out.
C>T variants were overlapped with CTCF ChIP-seq (Encode) and annotated as D&D edits using bedtools intersect.
Assembly: GRCh38
Supplementary files format and content: narrowPeak, vcf (D&D edits)

growth_protocol: K562 cells were grown in RPMI 1640 Medium, GlutaMAX™ Supplement + 10% FBS + Pen/Strep

extract_protocol:
Followed Bioskryb ResolveDNA protocol for DNA extraction/nuclei lysis
KAPA HiFi HotStart Library Amp Kit

treatment_protocol: Followed DnD protocol

value: Bone marrow

value: Erythroleukemia

value: CTCF D&D


title: total RNAs from CG7065 germline KD in fly ovary of the P element genetic background with polyA selection replicate1

description: Library name: nanosGal4_P_element_shCG7065_rep1

value: fly ovaries


title: total RNAs from CG7065 germline KD in fly ovary of the P element genetic background with polyA selection replicate2

description: Library name: nanosGal4_P_element_shCG7065_rep2


title: TAF13 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf13_nexus_3


title: total RNAs from CG31510 germline KD in fly ovary of the P element genetic background with polyA selection replicate3

description: Library name: nanosGal4_P_element_shCG31510_rep3


title: Siberian Hamster, POA, 16wk, Rep 6

description: Library name: POA_244

value: 16wk SD


title: total RNAs from CG31510 germline KD in fly ovary of the P element genetic background with polyA selection replicate1

description: Library name: nanosGal4_P_element_shCG31510_rep1


title: K562 SP1 bulk D&D-seq

description:
Library name: Bulk D_D-seq SP1
D&D deamination targeting SP1 binding loci

value: SP1 D&D


title: Siberian Hamster, POA, 16wk, Rep 5

description: Library name: POA_265


title: TAF13 ChIP-nexus Control rep1

description: Library name: kc167_dmso_taf13_nexus_1

value: Kc167 cells


title: TAF13 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf13_nexus_1


title: total RNAs from CG31510 germline KD in fly ovary of the P element genetic background with polyA selection replicate2

description: Library name: nanosGal4_P_element_shCG31510_rep2


title: K562 TAL1 bulk D&D-seq

description:
Library name: Bulk D_D-seq TAL1
D&D deamination targeting TAL1 binding loci

value: TAL1 D&D


title: total RNAs from Piwi germline KD in fly ovary of the P element genetic background with polyA selection replicate3

description: Library name: nanosGal4_P_element_shPiwi_rep3


title: TAF12 ChIP-nexus 1 h Triptolide treatment rep2

description: Library name: kc167_triptolide_taf12_nexus_2

value: custom anti-TAF12 rabbit polyclonal, Zeitlinger Lab, TAF12 - U7970DB220-1


title: K562 P300 bulk D&D-seq

description:
Library name: Bulk D_D-seq P300
D&D deamination targeting P300 binding loci


title: total RNAs from Piwi germline KD in fly ovary of the P element genetic background with polyA selection replicate2

description: Library name: nanosGal4_P_element_shPiwi_rep2


title: Siberian Hamster, POA, 16wk, Rep 4

description: Library name: POA_283


title: single-cell D&D-seq, CA46 (CTCF) and K562 (GATA1) mixed

description:
Library name: Cell mix scD_D-seq
D&D deamination targeting CTCF or GATA1 binding loci

library_source: genomic single cell

data_processing:
Raw fastq files were quantified using cellranger-atac (2.1.0).
Preprocess, normalization, and clustering were preformed using Signac (1.13.0)
Reads for each cell line were extracted using sinto (0.10.0).
Duplicated reads, non-primary and low quality alignments were filtered using picard MarkDuplicates (3.3.0).
Peaks were called using MACS2 (2.2.9.1) with -f BAM --nomodel and peaks found in the blacklist annotation were filtered out using bedtools (v2.31.1).
Motif enrichment analysis was performed using MEME SEA (v5.5.5) with the HOCOMOCO v11 core human motif database. Target peaks with motif sequence were resized to 200bp (+/-100bp from the motif center).
C>T variants were collected using bcftools mpileup and highly frequent variants (>10%) and germlines (gnomAD) were filtered out.
C>T variants were overlapped with target peaks and annotated as D&D edits using bedtools intersect.
Assembly: GRCh38
Supplementary files format and content: seurat object (full dataset and D&D edits)

extract_protocol:
For all the following centrifugations, cells were centrifuged in a swing-bucket centrifuge at 300g for 5 minutes before fixation and 600g for 5 minutes after fixation. About 200K to 1 million cells were collected and resuspended in 400 µl PBS. Then, 16% methanol-free formaldehyde (Thermo Fisher Scientific, PI28906) was added for fixation (final concentration 0.1%) at room temperature for 5 minutes. Glycine (final concentration 125 mM) was added to stop the cross-linking, followed by a wash with 1 ml of PBS. Fixed cells were permeabilized in 200 µl permeabilization buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 1% BSA, 1× protease inhibitors) on ice (7 minutes for cell lines, 5 minutes for primary cells), followed by a wash with 200 µl cold wash buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors). After cell counting, 100K-400K cells were transferred to PCR tubes and resuspended in 100 µl antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors), with 1 µl (1:100 dilution) of the antibodies. The cells were incubated at 4 °C with slow rotation overnight. The cells were washed once with 200 ul wash buffer, and another time with 200 ul D&D binding buffer. The cells were resuspended in 50 ul D&D activation buffer with 100 uM DddA_NT, and incubated at room temperature on a rotator for 1 hour. The cells were then washed with 200 ul D&D binding buffer, resuspended in 50 ul DnD activation buffer, and incubated at 37 °C for 1 hour for deamination.
After D&D activation, the cells were resuspended in 1x nuclei buffer and counted using trypan blue and a Countess II FL Automated Cell Counter. For the remaining steps, we follow single-cell ATAC-seq per 10x protocol (version CG000209 Rev F, 10x Genomics) with the following modifications: During the GEM generation and barcoding reaction (step 2.1), 2 ul of uracil-tolerant DNA polymerase (NEBNext Q5U Master Mix, NEB M0597S) was added to the barcoding reaction mixture to facilitate the first few rounds of PCR, where we expect to have some uridine in the reaction. Samples are sequenced PE150 or PE100.

value: CTCF & GATA1 D&D


title: TAF12 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf12_nexus_1


title: K562 JUN bulk D&D-seq

description:
Library name: Bulk D_D-seq JUN
D&D deamination targeting JUN binding loci

value: JUN D&D


title: total RNAs from Piwi germline KD in fly ovary of the P element genetic background with polyA selection replicate1

description: Library name: nanosGal4_P_element_shPiwi_rep1


title: Siberian Hamster, POA, 20wk, Rep 1

description: Library name: POA_214

value: 20wk SD


title: Siberian Hamster, POA, 16wk, Rep 3

description: Library name: POA_255


title: K562 GATA2 bulk D&D-seq

description:
Library name: Bulk D_D-seq GATA2
D&D deamination targeting GATA2 binding loci

value: WT

value: GATA2 D&D


title: total RNAs from control germline KD in fly ovary of the P element genetic background with polyA selection replicate3

description: Library name: nanosGal4_P_element_shwhite_rep3


title: TAF12 ChIP-nexus Control rep2

description: Library name: kc167_dmso_taf12_nexus_2

value: DMSO


title: TAF12 ChIP-nexus Control rep1

description: Library name: kc167_dmso_taf12_nexus_1


title: K562 GATA1 bulk D&D-seq

description:
Library name: Bulk D_D-seq GATA1
D&D deamination targeting GATA1 binding loci

value: GATA1 D&D


title: total RNAs from control germline KD in fly ovary of the P element genetic background with polyA selection replicate2

description: Library name: nanosGal4_P_element_shwhite_rep2


title: Siberian Hamster, POA, 16wk, Rep 1

description: Library name: POA_252

value: POA


title: total RNAs from control germline KD in fly ovary of the P element genetic background with polyA selection replicate1

description: Library name: nanosGal4_P_element_shwhite_rep1


title: Siberian Hamster, POA, 12wk, Rep 6

description: Library name: POA_277

value: 12wk SD


title: TAF11 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf11_nexus_3

value: custom anti-TAF11 rabbit polyclonal, Zeitlinger Lab, TAF11 - U1266BL120-9

value: 10 uM Triptolide


title: TAF11 ChIP-nexus 1 h Triptolide treatment rep2

description: Library name: kc167_triptolide_taf11_nexus_2


title: small RNA-seq analyis of small RNA expression changes in Rrp40 KD OSCs

value: OSCs


title: small RNA-seq analyis of small RNA expression changes in Rrp41 KD OSCs


title: total RNAs from GFP-CG31510_delta_PRD and GFP-CG7065_delta_PRD fly ovary with polyA selection replicate3

description: Library name: CG31510_CG7065_delta_PRD_rep3

value: fly ovaries


title: Siberian Hamster, POA, 12wk, Rep 4

description: Library name: POA_278


title: TAF11 ChIP-nexus Control rep2

description: Library name: kc167_dmso_taf11_nexus_2


title: small RNA-seq analyis of small RNA expression changes in control KD (4 days KD) OSCs


title: TAF11 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf11_nexus_3


title: total RNAs from GFP-CG31510_delta_PRD and GFP-CG7065_delta_PRD fly ovary with polyA selection replicate2

description: Library name: CG31510_CG7065_delta_PRD_rep2


title: total RNAs from GFP-CG31510_delta_PRD and GFP-CG7065_delta_PRD fly ovary with polyA selection replicate1

description: Library name: CG31510_CG7065_delta_PRD_rep1


title: Siberian Hamster, POA, 12wk, Rep 3

description: Library name: POA_289


title: TAF10 ChIP-nexus 1 h Triptolide treatment rep2

description: Library name: kc167_triptolide_taf10_nexus_2

value: custom anti-TAF10 rabbit polyclonal, Zeitlinger Lab, TAF10 - U7970DB220-5


title: small RNA-seq analyis of small RNA expression changes in control KD (2 days KD) OSCs


title: Siberian Hamster, POA, 16wk, Rep 2

description: Library name: POA_251

value: 16wk SD


title: total RNAs from GFP-CG7065_delta_PRD fly ovary with polyA selection replicate3

description: Library name: CG7065_delta_PRD_rep3


title: Siberian Hamster, POA, 12wk, Rep 2

description: Library name: POA_276


title: TAF10 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf10_nexus_1

value: Kc167 cells


title: small RNA-seq analyis of small RNA expression changes in dZfc3h1 and dZcchc8 KD OSCs


title: Siberian Hamster, POA, 12wk, Rep 1

description: Library name: POA_292


title: total RNAs from GFP-CG7065_delta_PRD fly ovary with polyA selection replicate2

description: Library name: CG7065_delta_PRD_rep2


title: Siberian Hamster, POA, 8wk, Rep 6

description: Library name: POA_305

value: 8wk SD


title: TAF10 ChIP-nexus Control rep2

description: Library name: kc167_dmso_taf10_nexus_2


title: TAF10 ChIP-nexus Control rep1

description: Library name: kc167_dmso_taf10_nexus_1


title: small RNA-seq analyis of small RNA expression changes in CG7065 KD OSCs


title: small RNA-seq analyis of small RNA expression changes in Dis3 KD OSCs


title: Siberian Hamster, POA, 8wk, Rep 5

description: Library name: POA_397


title: Siberian Hamster, POA, 8wk, Rep 4

description: Library name: POA_306


title: total RNAs from GFP-CG7065_delta_PRD fly ovary with polyA selection replicate1

description: Library name: CG7065_delta_PRD_rep1


title: total RNAs from GFP tagged CG7065 fly ovary with polyA selection replicate3

description: Library name: GFP_CG7065_rep3


title: Siberian Hamster, POA, 12wk, Rep 5

description: Library name: POA_280


title: small RNA-seq analyis of small RNA expression changes in Mtr4 KD OSCs


title: TAF9 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf9_nexus_1

value: custom anti-TAF9 rabbit polyclonal, Zeitlinger Lab, TAF9 - 529220-34


title: TAF9 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf9_nexus_3


title: total RNAs from GFP tagged CG7065 fly ovary with polyA selection replicate1

description: Library name: GFP_CG7065_rep1


title: Siberian Hamster, POA, 8wk, Rep 3

description: Library name: POA_398


title: Siberian Hamster, POA, 8wk, Rep 2

description: Library name: POA_399


title: total RNAs from GFP-CG31510_delta_PRD fly ovary with polyA selection replicate3

description: Library name: CG31510_delta_PRD_rep3


title: TAF9 ChIP-nexus Control rep1

description: Library name: kc167_dmso_taf9_nexus_1


title: total RNAs from GFP-CG31510_delta_PRD fly ovary with polyA selection replicate2

description: Library name: CG31510_delta_PRD_rep2


title: small RNA-seq analyis of small RNA expression changes in CG31510 KD OSCs


title: Siberian Hamster, POA, 8wk, Rep 1

description: Library name: POA_310


title: TAF8 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf8_nexus_3

value: custom anti-TAF8 rabbit polyclonal, Zeitlinger Lab, TAF8 - U7893CL140-7


title: total RNAs from GFP-CG31510_delta_PRD fly ovary with polyA selection replicate1

description: Library name: CG31510_delta_PRD_rep1


title: Siberian Hamster, POA, 4wk, Rep 6

description: Library name: POA_356

value: 4wk SD


title: TAF8 ChIP-nexus 1 h Triptolide treatment rep2

description: Library name: kc167_triptolide_taf8_nexus_2


title: total RNAs from GFP tagged CG7065 fly ovary with polyA selection replicate2

description: Library name: GFP_CG7065_rep2