title: TERT-deleted DS_rep3

first: Kazuteru

last: Hasegawa

address: Lorry Lokey Stem Cell Research Building (SIM1), G2165 265 Campus Drive

description:
TERT-CKO3-P3
processed data file: readCount_matrix.txt

data_processing:
Fastq files were first trimmed to remove Illumina Nextera adapter sequence using Skewer. FastQC was used to validate proper trimming and check overall sequence data quality.
Bowtie2 was used for pre-alignments to remove reads that would map to chrM, alpha satellite repeats, Alu repeats, ribosomal DNA repeats, and other repeat regions. Bowtie2 was then used to align to the mm10 reference genome.
Samtools was used to sort and isolate uniquely mapped reads. Picard was used to remove duplicates.
The bam files were merged by conditions, and MAC2 was used to call peaks. The narrow peaks were then filtered by the ENCODE 7 hg19 blacklist, as well as peaks that extend beyond the ends of chromosomes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: readCount_matrix.txt: Tab-delimited text file includes read counts.

source_name: Differentiating spermatogonia

extract_protocol:
Genomic DNA was tagmented by using Tn5 transposase (Corces et al., 2017, Nat Methods).
DNA fragments were amplified with PCR reactions (Corces et al., 2017, Nat Methods).

treatment_protocol: Eight- to twelve-week-old mice were injected with tamoxifen. At day 7, cells were purified by FACS.

tag: age

value: 8-12 weeks

value: Differentiating spermatogonia

tag: time point

value: 7 days after tamoxifen injection

tag: marker expression


title: TERT-deleted DS_rep2

status: Public on Jul 11 2024

type: SRA

city: Stanford

country: USA

institute: Stanford University

description:
TERT-CKO2-P3
processed data file: readCount_matrix.txt

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: cell type

tag: genotype


title: TERT-deleted US-h_rep2

description:
TERT-CKO2-P1
processed data file: readCount_matrix.txt

source_name: Undifferentiated spermatogonia

value: Undifferentiated spermatogonia


title: TERT-deleted US-h_rep3

description:
TERT-CKO3-P1
processed data file: readCount_matrix.txt


title: TERT-deleted US-m_rep3

description:
TERT-CKO3-P2
processed data file: readCount_matrix.txt


title: TERT-deleted US-m_rep1

description:
TERT-CKO1-P2
processed data file: readCount_matrix.txt


title: TERT-deleted DS_rep1

description:
TERT-CKO1-P3
processed data file: readCount_matrix.txt


title: TERT-deleted US-h_rep1

description:
TERT-CKO1-P1
processed data file: readCount_matrix.txt


title: TERT-hetero_RoundSpermatids_rep3

description:
TERT-TdTom-Het1-SpermatocyteB-75k
processed data file: readCount_matrix.txt

source_name: Round Spermatid

value: Round Spermatid

value: TertTdtomato/+


title: CeD1_Sample1_freshtissue

status: Public on Jul 12 2024

first: Antonio

last: Santos

state: California

address: 265 Campus Dr.

department: Hematology

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequences from scRNA-seq were processed with Cell Ranger (v.3.0.2) software (10X Genomics) with demultiplexing, UMI (unique molecular identifier) collapsing and alignment to the GRCh38 human transcriptome. scRNA-seq data from CLIP versus gliadin treatment were loaded into Seurat objects following their standard pipeline
Assembly: GRCh38
Supplementary files format and content: mtx
Supplementary files format and content: clonotypes, contig_annotations

molecule: total RNA

organism: Homo sapiens

source_name: fresh tissue

extract_protocol:
Organoids were dissociated in 2030 units ml-1 collagenase IV (Worthington, LS004212) at 37°C for 40 min, washed twice in PBS, and digested in 400 μg ml-1 Liberase-TL (Roche, 5401020001) and 416 units ml-1 DNase I (Worthington, LS006328) at 37°C for 30 min with intermittent shaking. Samples were washed twice in FACS buffer (0.6 mM EDTA (Invitrogen, AM9261), 5% FBS, in PBS)
FACS-isolated organoid cells were subjected to droplet based scRNA-seq with the 10X Genomics Chromium single cell 5’ platform, with or without single-cell TCR/Ig V(D)J library, per the manufacturer’s protocol using Chromium Next GEM Single Cell 5' Kit v2 (PN-1000263), Library Construction Kit (PN-1000190), Chromium Single Cell Human TCR Amplification Kit (PN-1000252) and Chromium Single Cell Human BCR Amplification Kit (PN-1000253). Cell capture, library construction, and sequencing were performed as previously described

tag: patient

tag: batch

tag: stimulation

tag: tissue

value: fresh tissue

tag: culture medium

value: Live single cells


title: TERT-hetero_Spermatocytes_rep1

description:
TERT-TdTom-Het1-RoundSpermatidA-75k
processed data file: readCount_matrix.txt

source_name: Spermatocyte

value: Spermatocyte


title: TERT-hetero DS_rep2

description:
Ctrl2-P3-5
processed data file: readCount_matrix.txt


title: TERT-hetero_RoundSpermatids_rep1

description:
TERT-TdTom-Het1-RoundSpermatidC-150k
processed data file: readCount_matrix.txt


title: TERT-hetero US-m_rep2

description:
Ctrl2-P2-5
processed data file: readCount_matrix.txt


title: TERT-hetero_RoundSpermatids_rep2

description:
TERT-TdTom-Het1-SpermatocyteA-75k
processed data file: readCount_matrix.txt


title: adult forebrain, genome-wide, rep1

city: Baltimore

first: Mollie

last: Meffert

address: 725 N. Wolfe St.

institute: Johns Hopkins University School of Medicine

description:
Rep1
Forebrain_CIMERA-seq_sample_1-4_peakcalling.summary.txt
Forebrain_CIMERA-seq_sample_1-4_peaks.bed.txt
Forebrain_CIMERA-seq_sample_1-4_peaks.bed.mouse.annotation.txt

library_source: transcriptomic

data_processing:
Sequencing data were processed using SCRAP (SCRAP release 2.0) bioinformatic pipeline to identify the significant sncRNA:targetRNA interactions in each sample (Eadara et al. 2023; Mills et al. 2022), for which code is deposited at https://github.com/Meffert-Lab/SCRAP.
Peak calling was performed by setting SCRAP variables to consider only high confidence sncRNA binding sites across the genome supported by at least 3 chimeric sncRNA:target RNA reads in at least 2 sample libraries.  Peak calling was performed as groups: group1: Forebrain CIEMRA-seq sample 1-4 group 2: Forebrain CIMERA-seq sample 5-7 group 3: Excitatory neuron selective CIMERA-seq sample 1-3 group 4: IgG CIMERA-seq sample 1-2
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include counts for each chimeric RNA (sncRNA:target RNA pairs)
Library strategy: CIMERA-seq

source_name: forebrain

extract_protocol:
Mouse brain tissue in Homogenization buffer (1X HBSS supplemented with 5 mM MgCl2, 10 mM HEPES (pH 7.4) and 1X HALT protease/phosphatase inhibitor) is homogenized by 12 passes through a 21G needle. UV irradiate homogenates 3x with (4000 µJ/cm2 x 100) on a perfluoroalkoxy (PFA) petri dish, mixing samples between rounds. Transfer irradiated tissue homogenate to a microfuge tube and centrifuge 900 x g for 5 minutes at 4 °C.  Immunoprecipitation from the cell pellets were done with anti-Ago2 (2D4, Wako, 018-22021)  for total CIMERA-seq, anti-myc (9B11, Cell Signaling, 2276) for cell-selective CIMERA-seq, and anti-IgG1 (Invitrogen, 14-4714-82) for negative control.
Libraries were prepared by intermolecular ligation of small non-coding RNA and target RNA, RNA isolation from Ago protein, ligation of 3’ and 5’ adaptors, reverse transcription, minimal PCR amplification, gel purification and size selection.
custom sequencing libraries with 150 base-pair paired-end sequencing and a read depth of 61 – 138 million reads per sample (Illumina HiSeq X or NovaSeq)

treatment_protocol: The mouse line with conditional tAgo2 expression in excitatory neurons was generated by crossing B6Tg(Camk2a-Cre/ERT2) (Erdmann et al. 2007), and B6.Cg-Gt(ROSA)26Sortm1(CAG-GFP/Eif2c2)Zjh/J (Jackson Laboratory #017626). Tamoxifen (2 mg) was administered to mice intraperitoneally once per day for 5 days. Gene induction was allowed to occur for 14-21 days after the final injection before tissue harvest at 10-12 weeks of age.

value: forebrain


title: TERT-hetero DS_rep3

description:
Ctrl3-P3-6
processed data file: readCount_matrix.txt


title: TERT-hetero US-h_rep3

description:
Ctrl3-P1-6
processed data file: readCount_matrix.txt


title: TERT-hetero US-h_rep2

description:
Ctrl2-P1-5
processed data file: readCount_matrix.txt


title: TERT-hetero DS_rep1

description:
Ctrl1-P3-4
processed data file: readCount_matrix.txt


title: TERT-deleted US-m_rep2

description:
TERT-CKO2-P2
processed data file: readCount_matrix.txt


title: CeD3_AS9

description: 10X Genomics

source_name: organoid

value: organoid

value: WENR


title: TERT-hetero US-h_rep1

description:
Ctrl1-P1-4
processed data file: readCount_matrix.txt


title: ADF8_CUTtag_H3K4me3_96h_noPi_rep1

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

data_processing:
All amplified libraries were pooled and sequenced using paired-end 150 nt reads on an Illumina NovaSeq 6000 instrument. Data processing was performed with guidance from Zheng et al. 2020 (CUT&Tag data processing and analysis tutorial v1 Zheng Y, Ahmad K, Henikoff S. ZappyLab, Inc., 2020). Reads were trimmed of Nextera adapter content using Trimgalore and mapped to the Arabidopsis thaliana Col-PEK genome assembly using Bowtie2 with the following parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were converted to the BAM file format using Samtools. Duplicate reads were removed using Picard markDuplicates. Samples were filtered to exclude all read fragments less than 150 bp. Peaks were called on deduplicated BAM files using MACS2 with IgG as a control where applicable. For visualization, deduplicated BAM files of each sample were RPKM normalized using bamCoverage from deepTools. Mapped fragments overlapping with genes were counted using featureCounts.
Assembly: Col-PEK
Supplementary files format and content: text files with unique counts across the body of each Col-PEK gene from deduplicated bam files
Supplementary files format and content: RPKM normalized bigwig files from all fragments greater than 150bp
Library strategy: CUT&Tag

organism: Arabidopsis thaliana

source_name: root hair cell nuclei

growth_protocol: Seeds of Arabidopsis thaliana (ADF8:NTF, from pK7WG strain) were grown on half-strength Murashige and Skoog (½ MS) media agar plates supplemented with 1% sucrose. Plates were stratified in dark conditions for 3 days at 4°C followed by 10 days of vertical growth at 20°C under a 16 hour light/8 hour dark cycle.

extract_protocol:
Biotin tagged nuclei from ~100 mg from root tissue 1 cm above the root tip were captured on 25 uL of Streptavidin M280 Dynabeads according to the Isolation of Nuclei TAgged in specific Cell Types (INTACT) protocol. Bead bound nuclei for each timepoint in the starvation assay were counted in 1 mL of Nuclei Purification Buffer with 0.1% Triton X-100 (NPBt) and nuclei were split three ways to ~100,000 nuclei per sample in NPBt for three replicates.
CUT&Tag was performed on these bead bound nuclei according to the Epicypher CUT&Tag Protocol v1.7 with the following notes. All buffers were prepared without Digitonin. Bead bound nuclei were resuspended directly from NPBt into 50 uL of Antibody150 Buffer containing 0.5 ug of anti-H3K4me3 (Milipore 07-473) or anti-IgG (sigma I-5006) and incubated at 4°C overnight. Guinea pig anti-rabbit secondary (0.5 ug, Sigma SAB3700889) was incubated for 1 hr at room temperature in 50 uL Wash150 Buffer. Tagmented libraries were amplified using 17 PCR cycles.

treatment_protocol: For phosphate starvation conditions, seedlings were transferred to ½ MS media without potassium phosphate and supplemented with 1% sucrose and potassium sulfate to balance the ionic composition with phosphate rich plates. After 96 hours of starvation, seedlings were transferred back to ½ MS containing phosphate

value: root hair cell nuclei

value: ADF8:NTF, from pK7WG

tag: treatment

value: 96h Pi starvation


title: ADF8_CUTtag_H3K4me3_96h_noPi_rep3


title: ADF8_CUTtag_H3K4me3_96h_noPi_rep2


title: ADF8_CUTtag_H3K4me3_30m_rePi_rep3

value: 30m Pi resupply


title: ADF8_CUTtag_H3K4me3_4h_rePi_rep3

value: 4h Pi resupply


title: ADF8_CUTtag_H3K4me3_4h_rePi_rep1


title: TERT-hetero_Spermatocytes_rep2

description:
TERT-TdTom-Het1-RoundSpermatidB-75k
processed data file: readCount_matrix.txt

value: 8-12 weeks


title: ADF8_CUTtag_H3K4me3_1h_rePi_rep3

value: 1h Pi resupply


title: TERT-hetero US-m_rep1

description:
Ctrl1-P2-4
processed data file: readCount_matrix.txt

value: 7 days after tamoxifen injection


title: ADF8_CUTtag_H3K4me3_1h_rePi_rep2


title: ADF8_CUTtag_H3K4me3_1h_rePi_rep1


title: ADF8_CUTtag_H3K4me3_30m_rePi_rep1


title: ADF8_CUTtag_H3K4me3_0h_Pi_rep3

value: 10 Pi rich media


title: ADF8_CUTtag_IgG_0h_Pi


title: ADF8_CUTtag_H3K4me3_0h_Pi_rep2


title: ADF8_ATAC_96h_noPi_rep2

data_processing:
All amplified libraries were pooled and sequenced using paired-end 150 nt reads on an Illumina NovaSeq 6000 instrument. Data processing was performed with guidance from Zheng et al. 2020 (CUT&Tag data processing and analysis tutorial v1 Zheng Y, Ahmad K, Henikoff S. ZappyLab, Inc., 2020). Reads were trimmed of Nextera adapter content using Trimgalore and mapped to the Arabidopsis thaliana Col-PEK genome assembly using Bowtie2 with the following parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were converted to the BAM file format using Samtools. Duplicate reads were removed using Picard markDuplicates. Peaks were called on deduplicated BAM files using MACS2. For visualization, deduplicated BAM files of each sample were RPKM normalized using bamCoverage from deepTools. Mapped fragments overlapping with the TSS (-200bp +100bp from TSS) were counted using featureCounts for ATAC samples.
Assembly: Col-PEK
Supplementary files format and content: text files with unique counts across the TSS (-200bp, +100bp) of each Col-PEK gene from deduplicated bam files
Supplementary files format and content: RPKM normalized bigwig files

extract_protocol:
Biotin tagged nuclei from ~100 mg from root tissue 1 cm above the root tip were captured on 25 uL of Streptavidin M280 Dynabeads according to the Isolation of Nuclei TAgged in specific Cell Types (INTACT) protocol. Bead bound nuclei for each timepoint in the starvation assay were counted in 1 mL of Nuclei Purification Buffer with 0.1% Triton X-100 (NPBt) and nuclei were split three ways to ~100,000 nuclei per sample in NPBt for three replicates.
ATAC was performed in duplicate (~20k nuclei each) on these bead bound nuclei as previously described. (Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq, Bajic M,Maher KA,Deal RB. Methods Mol. Biol.,2018)


title: ADF8_ATAC_4h_rePi_rep2


title: ADF8_ATAC_4h_rePi_rep1


title: ADF8_ATAC_30m_rePi_rep2


title: ADF8_ATAC_96h_noPi_rep1


title: ADF8_ATAC_1h_rePi_rep1


title: ADF8_ATAC_0h_Pi_rep2


title: ADF8_ATAC_30m_rePi_rep1


title: ADF8_CUTtag_H3K4me3_30m_rePi_rep2


title: ADF8_CUTtag_H2AZ_96h_noPi_rep3

extract_protocol:
Biotin tagged nuclei from ~100 mg from root tissue 1 cm above the root tip were captured on 25 uL of Streptavidin M280 Dynabeads according to the Isolation of Nuclei TAgged in specific Cell Types (INTACT) protocol. Bead bound nuclei for each timepoint in the starvation assay were counted in 1 mL of Nuclei Purification Buffer with 0.1% Triton X-100 (NPBt) and nuclei were split three ways to ~100,000 nuclei per sample in NPBt for three replicates.
CUT&Tag was performed on these bead bound nuclei according to the Epicypher CUT&Tag Protocol v1.7 with the following notes. All buffers were prepared without Digitonin. Bead bound nuclei were resuspended directly from NPBt into 50 uL of Antibody150 Buffer containing 0.5 ug of anti-H2A.Z (Repression of Flowering in Arabidopsis Requires Activation of FLOWERING LOCUS C Expression by the Histone Variant H2A.Z Deal RB, Topp CN, McKinney EC, Meagher RB the Plant Cell Online, 2007) and incubated at 4°C overnight. Guinea pig anti-rabbit secondary (0.5 ug, Sigma SAB3700889) was incubated for 1 hr at room temperature in 50 uL Wash150 Buffer. Tagmented libraries were amplified using 17 PCR cycles.


title: ADF8_CUTtag_H2AZ_96h_noPi_rep1


title: ADF8_CUTtag_H3K4me3_4h_rePi_rep2


title: ADF8_ATAC_0h_Pi_rep1


title: ADF8_CUTtag_H2AZ_4h_rePi_rep1


title: ADF8_CUTtag_H2AZ_4h_rePi_rep3


title: ADF8_CUTtag_H2AZ_30m_rePi_rep2


title: ADF8_ATAC_1h_rePi_rep2


title: ADF8_CUTtag_H2AZ_1h_rePi_rep3


title: ADF8_CUTtag_H2AZ_30m_rePi_rep3


title: ADF8_CUTtag_H2AZ_96h_noPi_rep2


title: ADF8_CUTtag_H2AZ_4h_rePi_rep2


title: ADF8_CUTtag_H2AZ_1h_rePi_rep2


title: ADF8_CUTtag_H2AZ_1h_rePi_rep1


title: ADF8_CUTtag_H2AZ_0h_Pi_rep3


title: ADF8_CUTtag_H3K4me3_0h_Pi_rep1


title: nrde-3 PDPhe replicate 4

city: Syracuse

first: Maria

middle: C.

last: Ow

state: NY

address: 107 College Dr, LSC117

institute: Syracuse University

data_processing:
Data analysis was performed on the CLC Genomics Workbench (Qiagen) with differential expression assessed using EdgeR.
Assembly: WS235
Supplementary files format and content: tab-delimited text files contain raw counts and RPKM for each sample

organism: Caenorhabditis elegans

source_name: Neurons

growth_protocol: C. elegans ADL neurons from control one-day old adults and postdauer (pheromone) one-day old adults.

extract_protocol:
Total RNA extraction of FACS events was done using NEB Monarch Total RNA Miniprep (New England Biolabs [NEB] T2010).
RNA-Seq libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490S) and NEBNext® Ultra™ II RNA Library Prep with Sample Purification Beads (NEB E7775S) following the recommendations of the manufacturer. Indexing of libraries was done using NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB E7335S) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 2) (NEB E7500S) according to the manufacturer’s instructions.

value: Neurons

value: ADL neurons

value: PDPhe


title: ADF8_CUTtag_H2AZ_0h_Pi_rep2


title: nrde-3 PDPhe replicate 3


title: nrde-3 PDPhe replicate 2


title: ADF8_CUTtag_H2AZ_0h_Pi_rep1


title: ADF8_CUTtag_H3K27me3_96h_noPi_rep2a

extract_protocol:
Biotin tagged nuclei from ~100 mg from root tissue 1 cm above the root tip were captured on 25 uL of Streptavidin M280 Dynabeads according to the Isolation of Nuclei TAgged in specific Cell Types (INTACT) protocol. Bead bound nuclei for each timepoint in the starvation assay were counted in 1 mL of Nuclei Purification Buffer with 0.1% Triton X-100 (NPBt) and nuclei were split three ways to ~100,000 nuclei per sample in NPBt for three replicates.
CUT&Tag was performed on these bead bound nuclei according to the Epicypher CUT&Tag Protocol v1.7 with the following notes. All buffers were prepared without Digitonin. Bead bound nuclei were resuspended directly from NPBt into 50 uL of Antibody150 Buffer containing 0.5 ug of anti-H3K27me3 (Millipore 07-449) and incubated at 4°C overnight. Guinea pig anti-rabbit secondary (0.5 ug, Sigma SAB3700889) was incubated for 1 hr at room temperature in 50 uL Wash150 Buffer. Tagmented libraries were amplified using 17 PCR cycles.


title: nrde-3 CONPhe replicate 4

value: CONPhe


title: ADF8_CUTtag_H3K27me3_4h_rePi_rep3


title: ADF8_CUTtag_H2AZ_30m_rePi_rep1


title: nrde-3 CONPhe replicate 3


title: ADF8_CUTtag_H3K27me3_4h_rePi_rep2


title: nrde-3 CONPhe replicate 2


title: WT PDPhe replicate 4

value: WT


title: ADF8_CUTtag_H3K27me3_30m_rePi_rep3


title: WT PDPhe replicate 2


title: ADF8_CUTtag_H3K27me3_30m_rePi_rep2


title: ADF8_CUTtag_H3K27me3_30m_rePi_rep1


title: WT PDPhe replicate 1


title: ADF8_CUTtag_H3K27me3_4h_rePi_rep1


title: WT PDPhe replicate 3


title: ADF8_CUTtag_H3K27me3_1h_rePi_rep2


title: WT CONPhe replicate 3


title: WT CONPhe replicate 4


title: ADF8_CUTtag_H3K27me3_1h_rePi_rep1


title: ADF8_CUTtag_H3K27me3_96h_noPi_rep3


title: WT CONPhe replicate 2


title: nrde-3 PDPhe replicate 1


title: ADF8_CUTtag_H3K27me3_0h_Pi_rep2


title: ADF8_CUTtag_H3K27me3_0h_Pi_rep3


title: ADF8_CUTtag_H3K27me3_96h_noPi_rep1


title: ADF8_RNA_96h_noPi_rep3

data_processing:
All amplified libraries were pooled and sequenced using single-end 50 nt reads on an Illumina NextSeq 2000 instrument. Reads were mapped to the Arabidopsis thaliana TAIR10 genome assembly, converted to the BAM file format, and sorted by coordinate using the STAR aligner with the default parameters . Duplicate reads were removed using Picard markDuplicates. Strand specific fragment counting on genes was performed with a TAIR10 specific GTF file using featureCounts with the following parameters: -s 1 -t exon -g gene_id.
Assembly: TAIR10
Supplementary files format and content: text files with unique counts across the body of each TAIR10 gene from deduplicated bam files

molecule: nuclear RNA

extract_protocol:
Biotin tagged nuclei from ~100 mg from root tissue 1 cm above the root tip were captured on 25 uL of Streptavidin M280 Dynabeads according to the Isolation of Nuclei TAgged in specific Cell Types (INTACT) protocol . Bead bound nuclei for each timepoint in the starvation assay were counted in 1 mL of Nuclei Purification Buffer with 0.1% Triton X-100 (NPBt) and nuclei were split three ways to ~100,000 nuclei per sample in NPBt for three replicates. RNA was isolated from bead bound nuclei using the RNeasy plant micro kit (Qiagen) with on column DNase treatment and quantified via Quant-it™ RiboGreen RNA Assay Kit (Thermo-Fisher).
Libraries for RNA-seq were generated according to the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD V1 (Lexogen, cat.no. 015.24) following modified steps for low input samples.


title: ADF8_CUTtag_H3K27me3_0h_Pi_rep1


title: nrde-3 CONPhe replicate 1


title: ADF8_RNA_4h_rePi_rep3


title: motor cortex, stim on PD, rat2

city: Yeonsu-gu, Incheon

first: Johyeon

last: Nam

address: 265, Harmony-ro

department: Division of Life Sciences

country: South Korea

institute: Incheon National University

data_processing:
Low-quality adapter sequences were trimmed using TrimGalore.
The STAR 2-pass method was used to align the raw sequencing data to the rat reference genome (mRatBN7.2) using the STAR aligner.
Read count was extracted using featureCounts.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited text file includes normalized counts for each sample.

organism: Rattus norvegicus

source_name: Motor cortex

extract_protocol:
A library was independently prepared with 1ug of total RNA from each sample using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA).
Libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms (KAPA BIOSYSTEMS).

value: Motor cortex

value: stim on PD


title: motor cortex, stim on PD, rat3


title: ADF8_RNA_96h_noPi_rep2


title: ADF8_RNA_4h_rePi_rep1


title: ADF8_RNA_30m_rePi_rep3


title: ADF8_RNA_4h_rePi_rep2


title: motor cortex, PD, rat1

value: PD


title: motor cortex, PD, rat2


title: ADF8_CUTtag_H3K27me3_1h_rePi_rep3

value: root hair cell nuclei


title: motor cortex, PD, rat3


title: motor cortex, stim on ctrl, rat3

value: stim on ctrl


title: ADF8_RNA_30m_rePi_rep2

value: ADF8:NTF, from pK7WG


title: motor cortex, stim on PD, rat1


title: WT CONPhe replicate 1


title: ADF8_RNA_30m_rePi_rep1

value: 30m Pi resupply


title: ADF8_RNA_1h_rePi_rep3


title: motor cortex, stim on ctrl, rat1


title: ADF8_RNA_1h_rePi_rep2


title: motor cortex, ctrl, rat3

value: ctrl


title: ADF8_RNA_1h_rePi_rep1


title: motor cortex, stim on ctrl, rat2


title: motor cortex, ctrl, rat2


title: motor cortex, ctrl, rat1


title: ADF8_RNA_96h_noPi_rep1

value: 96h Pi starvation


title: DHD0 and DHD1 His+ Barcodes Biol Rep 1

city: Seattle

first: Alyssa

last: La Fleur

state: WA

address: Campus Box 352500 185 Stevens Way

institute: University of Washington

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  No 3-AT.
L39(2) His-

library_source: other

data_processing:
Trimmed fastq files are clustered with starcode
Clustered barcodes are matched to their proteins using the barcode to protein tables (see supplemental file), and PPIs are counted.
Autoactivators are detected and corrected (see methods of paper)
Deseq2 is used to get  fold changes for each PPI using the His+ and His- condition counts as inputs.
Assembly: N/A
Supplementary files format and content: Proccessed PPI counts per each selection stage (His+ and His-)
The first column of the csv file has the DBD associated protein name, while the columns have the AD associated protein  name.  The values in all other cells correspond to the count of the barcodes for the PPI being measured.
Library strategy: MP3-seq

molecule: other

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: 250uL of transformed yeast from gylcerol stock is first grown in 100mL of synthetic drop out media at 30C and 250rpm lacking tryptophan during an extended outgrowth step. Yeast are allowed to grow for at least 36 hours with periodic 1:250 dillutions into fresh media when optical density at 600nM reaches 1.0. 250uL of cells are used to inoculate 100mL of synthetic dropout media - Tryptophan -Histidine +3mM 3AT. Cells are allowed to incubate at same conditions before until OD600 of 1.0 is reached.

extract_protocol:
All plasmids are extracted after growth selection using a Zymoprep Yeast Plasmid Miniprep II Kit according to the manufacturer's protocol.
All proteins of interest are ordered as twist gene fragements. These fragments are ordered to contain the terminator, barcode, and overlap regions for assembly. These fragmetns are combined with the MP3-seq vector and assembled during yeast transformation through homologous recombination.

value: yeast cell

value: MATa AGA1::GAL1-AGA1::URA3 ura3-52 trp1 leu2-delta200 his3-delta pep4::BleoMX leu2::pGAL6z-HIS3 prbd1.6R can1 GAL


title: ADF8_RNA_0h_Pi_rep2

value: 10 Pi rich media


title: Adult hermaphrodite, prg-1(∆PAZ-domain), rep 1

city: Houston

first: Jacob

middle: Manuel

last: Ortega

state: Texas

address: 6550 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description: Small RNA sample

data_processing:
Raw data was evaluated for quality control by Novogene Co, Ltd by an in house data filtration process. In brief, raw reads are evaluated for poor base quality, 5' primer contaminants, lack of 3' primer, lack of insert tag, presence of polyA/T/G/C, and finally reads are trimmed of adapters. On average, 98% of reads for each sample were retained after Novogene filtration. Trimmed data was used for downstream analysis.
Reads were aligned to C. elegans piRNAs (piRNAdb.cel.v1_7_6.fa) and the C. elegans genome (ce11genome.fa) using a custom python script HQAlign (https://github.com/FireLabSoftware/HQAlign).
Aligned piRNA reads for each sample were normalized to total number of reads mapping to the C. elegans genome (per million).
Assembly: piRNAdb.cel.v1_7_6
Assembly: ce11genome
Supplementary files format and content: xlsx file includes includes raw counts of genome mapped reads and piRNA mapped reads
Supplementary files format and content: xlsx file includes normalization of piRNA reads to the total number of reads aligning to the C. elegans genome per million

source_name: Whole Animal

growth_protocol: Plates of C. elegans hermpahrodite stocks for each genotype were synchronized and cultured at 25°C. Once animals had reached adulthood, they were collected and a lysate was prepared from whole worms. This lysate was used to perform RNA IP of V5-tagged Wild Type or ∆PAZ mutant PRG-1 protein.

extract_protocol:
Small RNAs bound to PRG-1 protein were extracted from RNA IP samples by standard chloroform-phenol RNA extraction and sent to Novogene Co, Ltd for library construction and sequencing.
Libraries were constructed by Novogene Co, Ltd using an in house protocol.

value: Whole Animal


title: ADF8_RNA_0h_Pi_rep3


title: M12

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
FastQC for sequencing quality check
Adapter sequences were removed and 3 bp trimmed from read ends using cutadapt (1.14+)
Reads were aligned to the human referece genome Hg38 using STAR (2.5.2b+) with parameters ajusted to short reads and Integrative Genomics Viewer (IGV) alignment.
Duplicate reads were diagnosed with the Bioconductor package dupRadar.
Expression counts determined by edgeR
The remaining processing and normalization steps described in the paper were not performed on the provided processed data
Assembly: Hg38
Supplementary files format and content: csv

source_name: Kidney

extract_protocol:
Kidney tissue was obtained from a clinical biopsy, placed in Michels solution and frozen on OCT within 24 h. 10 um of cross-sectional biopsy tissue was cut on a cryotome and placed in PicoPure RNA extraction buffer. RNA was extracted according to protocol. Ribosomal RNA was removed using RiboGone – Mammalian Kit.
SMARTer® Universal Low Input RNA Kit for Sequencing, shearing by Covaris, Ion Plus Fragment Library Kit
Illumina HiSeq 4000 RNA seq, paired-end, 30 million reads per sample library

value: Kidney

tag: disease

value: Minimal change disease

tag: tissue source

value: Biopsy

tag: segment

value: Bulk

tag: storage

value: OCT at -80C

tag: gender

value: Male


title: ADF8_RNA_0h_Pi_rep1


title: M11


title: M9

value: Female


title: M8


title: 9-11 mm Juvenile Calvaria, sp7GFPdepleted, DAPI neg

city: Los Angeles

first: Claire

last: Arata

email: carata@usc.edu, clairearata@gmail.com

state: CA

address: 1425 San Pablo St

department: Stem Cell

institute: University of Southern California

description: 10x Genomics

data_processing:
Data analysis was performed with Seurat version 4.1.1, and datasets were filtered by nFeature_RNA > 200, nFeature_RNA < 2500, and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat (https://satijalab.org/seurat/archive/v3.0/integration.html). The data were processed using the FindNeighbors() and FindClusters() functions and data were visualized with UMAP (30 principal components). The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters (https://cole-trapnell-lab.github.io/monocle3/docs/trajectories/#learn-graph).
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files, matrix files and rds files

molecule: polyA RNA

organism: Danio rerio

source_name: calvaria

growth_protocol: The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments (Protocol 20771). Zebrafish embryos (Danio rerio) were raised in embryo media at 28.5°C. For adults, in the institute vivarium according to Protocol 20771.

extract_protocol:
We dissected the calvaria from 20 juvenile (9-11mm) from ecad:YFP (one dataset) or sp7:GFP (one dataset), and separately 10 adult (22-25 mm) ecad:YFP (one dataset) or Tubingen (one dataset), fish away from brain tissue in Ringer’s solution. 9-11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation (0.25% trypsin (Life Technologies, 15090-046), 1 mM EDTA, and 400 mg/mL Collagenase D (Sigma, 11088882001) in PBS). Tissue was incubated on a nutator at 28.5 °C for ~45 min and the enzymatic reaction was stopped by adding 6X stop solution (6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS).  Cells were pelleted by centrifugation (300 g) at 4 °C, rinsed in suspension media (1% FBS, 0.8 mM CaCl2 (Sigma-Aldrich, St. Louis, MO) in phenol red-free Leibovitz’s L15 medium (Life Technologies)), and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells, and cells were fluorescence-activated cell sorted (FACS) to isolate live cells that were DAPI negative and when applicative, ecad:YFP/sp7:GFP negative to deplete epithelial cells.
scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50,000 reads per cell for each library. Juvenile and adult stages were performed in replicates, and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.

value: various

value: calvaria

tag: age

value: juvenile (9-11 mm)

value: tubingen


title: 22-25 mm Adult Calvaria, DAPI neg

description: 10x Genomics

value: adult (22-25 mm)


title: M6


title: M7


title: M5

value: Thin basement membrane disease


title: M4


title: M3


title: M2


title: M1


title: Sample50

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

description: 10x Genomics single cell RNA-seq; CITE-seq: Totalseq-C Human Universal Cocktail v1.0 (399905, Biolegend), anti-human CD172a, CD366, Siglec10, CD206, CD258

data_processing:
Cell Ranger (v6.1.2) mkfastq method demultiplexed raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
Cell Ranger (v6.1.2) count method took FASTQ files from cellranger mkfastq and performs alignment to the Homo sapiens genome (GRCh38.92 assembly), filtering, barcode counting, and UMI counting.
Downstream analysis were perfored using R package Seurat v4.3.0 and scRepertoire package v1.8.0
Assembly: hg38
Supplementary files format and content: Gene matrix and barcode files for each samper were created by Cell Ranger (v6.1.2)

source_name: viable 60% CD45+EpCAM-, 20% CD45-EpCAM+, 20% CD45-EpCAM-

extract_protocol:
Cells were resuspended in PBS with 0.04% BSA. 10K CD45+/CD45- cells were loaded on the chromium single cell controller of 10X Genomics  as described in the manufacturers protocol and processed using the 3' scRNA-seq workflow.
We followed the protocol according to the manufacturers instructions with no adaptations.

value: CRC

value: Unstimulated


title: Sample610

description: 10x Genomics single cell RNA-seq; CITE-seq: Totalseq-C Human Universal Cocktail v1.0 (399905, Biolegend)

source_name: CD45+ cells

value: CD45+ cells

value: Healthy distant colon


title: Sample609


title: Microglia-like, Donor C, Treated with ATP at day 6, Treated with LPS at day 8, Collected day 10

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

data_processing:
Reads containing adapters or with low quality were removed to obtain the clean data.
Raw fastq files were aligned to the human genome (hg19) using HISAT2.
Count data was obtained using featureCounts.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample in a joined matrix.
Supplementary files format and content: indiviudal tab-delimited text files with raw counts for each sample separately.

source_name: In vitro Microglia-like cells

growth_protocol: Monocytes were isolated from peripheral blood using CD14+ MicroBeads (Miltenyi Biotec). Microglia-like cells were differentiated from monocytes cultured in RPMI Medium 1640 + GlutaMAXTM (Gibco, Thermo Fisher) containing 100 units/mL penicillin, 100 µg/mL streptomycin, and supplemented with 10 ng/mL human M-CSF, 10 ng/mL human GM-CSF, 10 ng/mL human β-NGF, 100 ng/mL human IL34, 100 ng/mL human CCL2, 2 ng/mL human TGF-β2 (PeproTech) and 1.5 µg/mL cholesterol solution dissolved in ethanol.

extract_protocol:
Total RNA was isolated using the Maxwell RSC simplyRNA Cells Kit (Promega). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA-seq libraries were prepared using the Illumina Sequencing PE150 strategy and sequenced with Novaseq 6000.

treatment_protocol: We develop four experimental conditions of microglia-like cells: untreated and collected at day 7; treated with 100 uM of ATP at day 6 and collected at day 7; treated with 100 uM of ATP at day 6, treated with 100 ng/mL LSP at day 8,  and collected at day 10; treated with 100 ng/mL LSP at day 8,  and collected at day 10

value: In vitro Microglia-like cells

value: Microglia-like cells

value: Microglia-like ATP + LPS

value: ATP 100 uM at day 6 + LPS 100ng/uL at day 8


title: Microglia-like, Donor D, Treated with ATP at day 6, Collected day 7

value: Microglia-like ATP

value: ATP 100 uM at day 6


title: Microglia-like, Donor C, Treated with ATP at day 6, Collected day 7


title: Microglia-like, Donor D, Treated with ATP at day 6, Treated with LPS at day 8, Collected day 10


title: Monocytes, Donor D

source_name: Peripheral Blood Monocytes (CD14+)

value: Peripheral Blood Monocytes (CD14+)

value: Monocytes

value: Monocyte

value: Non-applicable


title: Monocytes, Donor C


title: M10

value: Kidney

value: Minimal change disease

value: Biopsy

value: Bulk

value: OCT at -80C

value: Female


title: Microglia-like, Donor D, Unreated with ATP, Treated with LPS at day 8, Collected day 10

value: Microglia-like LPS

value: LPS 100ng/uL at day 8


title: Microglia-like, Donor D, Untreated with ATP, Untreated with LPS, Collected day 7

value: In vitro Microglia-like cells

value: Microglia-like cells

value: Homeostatic Microglia-like


title: Microglia-like, Donor C, Untreated with ATP, Untreated with LPS, Collected day 7


title: Microglia-like, Donor B, Unreated with ATP, Treated with LPS at day 8, Collected day 10


title: Sample608

value: CD45+ cells

value: Healthy distant colon

value: Unstimulated


title: Sample214

description: 10x Genomics single cell RNA-seq

source_name: single cell suspension

value: single cell suspension

value: Healthy distant colon+CRC


title: Microglia-like, Donor B, Treated with ATP at day 6, Collected day 7

value: Microglia-like ATP

value: ATP 100 uM at day 6


title: Sample206


title: Sample62

description: 10x Genomics single cell RNA-seq, TCR⍺β, γδ-seq

source_name: CD45+/CD45- cells

value: CD45+/CD45- cells


title: Sample205


title: Microglia-like, Donor A, Treated with ATP at day 6, Treated with LPS at day 8, Collected day 10

value: Microglia-like ATP + LPS

value: ATP 100 uM at day 6 + LPS 100ng/uL at day 8


title: Monocytes, Donor B

value: Peripheral Blood Monocytes (CD14+)

value: Monocytes

value: Monocyte

value: Non-applicable


title: Microglia-like, Donor B, Untreated with ATP, Untreated with LPS, Collected day 7

value: In vitro Microglia-like cells


title: Microglia-like, Donor A, Unreated with ATP, Treated with LPS at day 8, Collected day 10

value: Microglia-like cells

value: Microglia-like LPS

value: LPS 100ng/uL at day 8


title: Sample60


title: Microglia-like, Donor A, Treated with ATP at day 6, Collected day 7


title: Sample61


title: Microglia-like, Donor C, Unreated with ATP, Treated with LPS at day 8, Collected day 10


title: Microglia-like, Donor B, Treated with ATP at day 6, Treated with LPS at day 8, Collected day 10


title: Sample37


title: Sample28


title: Microglia-like, Donor A, Untreated with ATP, Untreated with LPS, Collected day 7

value: Homeostatic Microglia-like


title: BRIC_shZNF598_10h_rep2

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

description: BRIC-Seq

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

growth_protocol: HEK293T cells expressing control or ZNF598-targeting shRNAs were cultured in DMEM at 37°C, 5% CO2.

extract_protocol:
Total RNAs were extracted using Trizol reagent and Direct-zol RNA MiniPrep Plus Kit (Zymo Research), mixed with BrU-containing spike-ins, and immunoprecipitated by magnetic beads with anti-BrdU antibody. RNAs on beads were purified using Direct-zol RNA MicroPrep Kit (Zymo Research).
Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina) and TruSeq Stranded Total RNA Kit (Illumina)

treatment_protocol: Cells were incubated in DMEM with 150 µM bromouridine (BrU) for 24 h. After washing with DMEM without BrU twice, cells were incubated in DMEM without BrU for 0, 2, 4, 6, 10, or 24 h.

tag: cell line

tag: shRNA


title: BRIC_shControl_24h_rep1

description: BRIC-Seq

value: shControl


title: BRIC_shZNF598_24h_rep1

description: BRIC-Seq


title: P03_PBMC,Post, scRNAseq

city: Guangzhou

first: Hao

last: Jin

state: Guangdong

address: No.72 of Second Zhongshan Road

country: China

institute: Sun Yat Sen Memorial Hospital

data_processing:
Raw sequencing data were processed using the 10X Genomics Cell Ranger v3.0.2 pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using CellRanger's default settings
Gene expression level of Refseq coding genes were quantified using CellRanger's default settings
Assembly: GRCh38
Supplementary files format and content: Tap-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
Freshly biopsied tumor tissues were flushed with 1×HBSS (Mg2+ Ca2+ free supplemented with 0.04% BSA) to remove any residual blood. Tumor-infiltrating cells isolation was performed by adding digestion buffer into tissues (1 mg/ml Collagenase I, 1mg /ml neutral protease, 0.2 mg/ml DNase I, and 0.01 % Hyaluronidase) in a shaking incubator at 37°C for 30 - 100 minutes. The isolated cells were resuspended with 1 × red blood cell removal solution and placed on ice for five minutes. Cells were washed and re-suspended in PBS then stained with a Viability Dye. The cell suspension was diluted with 1 × HBSS till a concentration of 700 - 1200 cells/μL was reached.
Library was constructed according to the manufacter's instructions (single-cell 3' v2 protocol, 10×Genomics). Briefly, tumor-infiltrating cells were resuspended in the master mix; they were then loaded with partioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate in every single GEM was retrotranscripted to DNA, which contained lumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10×barcode. The pooled barcoded cDNA was then cleaned up with Silane Dynabeads and amplified by PCR; the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, lumina R2 primer sequence, paired-end constructs with P5 +P7 sequences and a sample index were added.

value: peripheral blood

tag: tumor stage

value: post treatment


title: P03_TdLN,Post, scRNAseq

source_name: draining lymph node

value: draining lymph node


title: P03_tumor,Post, scRNAseq

source_name: triple-negative breast cancer

value: triple-negative breast cancer


title: P03_PBMC,Pre, scRNAseq

value: pre treatment


title: P02_TdLN,Post, scRNAseq


title: P03_tumor,Pre, scRNAseq


title: BRIC_shControl_10h_rep2

description: BRIC-Seq


title: P02_PBMC,Post, scRNAseq


title: BRIC_shControl_10h_rep1

description: BRIC-Seq


title: BRIC_shZNF598_10h_rep1

description: BRIC-Seq


title: Monocytes, Donor A

tag: cell type


title: BRIC_shZNF598_6h_rep2

description: BRIC-Seq


title: BRIC_shControl_6h_rep1

description: BRIC-Seq


title: P02_tumor,Post, scRNAseq


title: P02_PBMC,Pre, scRNAseq


title: BRIC_shZNF598_4h_rep2

description: BRIC-Seq


title: BRIC_shControl_6h_rep2

description: BRIC-Seq


title: BRIC_shZNF598_6h_rep1

description: BRIC-Seq


title: P03_TdLN,Pre, scRNAseq


title: Sample32

value: CD45+/CD45- cells

tag: genotype

value: Healthy distant colon+CRC

value: Unstimulated


title: P02_TdLN,Pre, scRNAseq


title: P02_tumor,Pre, scRNAseq


title: Sample 2-18_control

city: Hefei, Anhui Province

first: Baoyan

last: Wu

address: Science and Education Building, 8th floor, the First Affiliated Hospital of Anhui Medical University

data_processing:
High-throughput sequencing was performed on an Illumina Hiseq with a 2×150bp paired-end configuration.
To ensure sequencing quality, FastQC was employed, facilitating the exclusion of low-quality reads. FLASH executed joint paired-end sequencing, establishing a minimum acceptable length of 15bp and an error rate below 10%.
BLAST+ facilitated mapping to the human reference genome, defining a helpful sequence with a joint coverage fraction exceeding 90%.
Principal component analysis (PCA) using the R prompt function enabled sample clustering based on sperm methylation patterns.
Assembly: GRCH38

source_name: sperm

extract_protocol:
All individuals were required to provide a semen sample by masturbation that was collected after a previous ejaculation that occurred 3-7 days ago. Subsequently, semen samples were frozen at -80℃. Semen samples underwent washing with 10 mL of 1X phosphate-buffered saline, followed by centrifugation and resuspension of the pellet in 10 mL of somatic cell lysis buffer (0.1% SDS, 0.5% Triton X-100 in DEPC H2O; Sigma-Aldrich). Overnight incubation at 4℃ was followed by multiple centrifugations and resuspension of the pellet in 10 mL phosphate-buffered saline.
Sperm DNA underwent treatment using the sodium bisulfite-based EZ DNA Methylation-Gold™ Kit, effecting the conversion of unmethylated cytosine (C) to uridine (U) while preserving the methylated cytosine state. Specific primers targeting CpG island sequences were generated using Primer3. High-throughput sequencing was performed on an Illumina Hiseq with a 2×150bp paired-end configuration.

value: sperm

value: haploid cell

value: germ cell

value: WT


title: Sample 2-17_case

institute: First Affiliated Hospital of Anhui Medical University

value: MT


title: BRIC_shZNF598_4h_rep1

description: BRIC-Seq


title: Sample 2-14_case


title: BRIC_shZNF598_2h_rep1

description: BRIC-Seq


title: Sample 2-15_case


title: BRIC_shControl_2h_rep2

description: BRIC-Seq


title: Sample 2-12_case


title: Sample 2-13_case


title: Sample 2-11_case


title: nephritic kidney F480low MHC2low monocytes

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

data_processing:
Raw data were processed using the STAR aligner mapping to mouse genome build mm10.
Assembly: mm10
Supplementary files format and content: tab: ReadsPerGene in tab format

extract_protocol:
For bulk-seq analysis, we isolated kidney macrophages and monocytes from 2 healthy young and 4 nephritic NZB/W F1 mice. Kidneys were harvested, minced and placed into RPMI 1640 Medium with GlutaMAX (Gibco) with collagenase IV (Worthington Biochemical, 570 U/ml) and DNase I (Roche, 12,5 U/ml). Tissue digestion was performed using the gentleMACS™ Dissociator and incubation with the enzymes at 37°C for 20 minutes. Single cell suspensions were obtained by passing cells through a 70-µm and 40-µm strainer strainer and washing once with FACS buffer. Following centrifugation at 500g for 5 minutes at 4°C, erythrocytes were removed via resuspension in Red Blood Cell Lysing Buffer Hybri-Max® (Sigma Aldrich, R7757). Cells were plated in 96-well V-bottom plates. FcγRIII/II were blocked with purified anti-CD16/32 (FcγRIII/II, eBioscience) diluted 1:250 for 15 minutes at 4o degrees. Antibody mixes were added and incubated at 4°C in the dark for 30 minutes, then incubated with streptavidin conjugates for 20 minutes. Dead cells were excluded via staining with Fixable Viability Dye for 30 minutes. Cell sorting was performed using a BD Biosciences FACSAria II cell sorter achieving a purity rate of > 98%.
Total RNA was isolated using RNeasy Mini Kit (Qiagen; 217004), and cDNA libraries were generated for samples with high RNA integrity (RQN > 8), using the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) with up to 10 ng of RNA according to manufacturer’s instructions.
Paired-end sequencing (2 × 75 bp) of cDNA libraries was performed on an Illumina NextSeq2000 device.

value: Kidney

value: live FVD- CD45+ lineage(CD3 CD5 CD19 Ly6G NKp46 SiglecF)- CD11b+ CD45.2 iv-/intermediate F4/80low MHCIIlow

value: NZB/W F1

value: poly (I:C)


title: BRIC_shControl_2h_rep1

description: BRIC-Seq

value: shControl


title: nephritic kidney F480high MHC2high CD11bhi macrophages sample 3

value: live FVD- CD45+ lineage(CD3 CD5 CD19 Ly6G NKp46 SiglecF)- CD11b+ CD45.2 iv-/ intermediate F4/80high MHCIIhigh CD11bhigh


title: BRIC_shZNF598_0h_rep1

description: BRIC-Seq


title: nephritic kidney F480high MHC2high CD11bhi macrophages sample2


title: Sample 2-6_case


title: nephritic kidney F480high MHC2low CD11bhi macrophages

value: live FVD- CD45+ lineage(CD3 CD5 CD19 Ly6G NKp46 SiglecF)- CD11b+ CD45.2 iv-/ intermediate F4/80high MHCIIlow CD11bhigh


title: BRIC_shControl_4h_rep2

description: BRIC-Seq


title: BRIC_shZNF598_0h_rep2

description: BRIC-Seq


title: Sample 2-5_case


title: Sample 2-7_case


title: Sample 2-8_case


title: Sample 2-9_case


title: BRIC_shZNF598_2h_rep2

description: BRIC-Seq


title: Sample 2-16_case


title: BRIC_shControl_0h_rep2

description: BRIC-Seq


title: BRIC_shControl_4h_rep1

description: BRIC-Seq


title: Sample 1-22_case


title: Sample 1-21_control


title: Sample 2-1_case


title: nephritic kidney F480high MHC2high CD11bhi macrophages sample1


title: BRIC_shControl_0h_rep1

description: BRIC-Seq


title: Sample 1-20_case


title: PHPF_3, scRNAseq

city: Graz

first: Francesco

last: Valzano

address: Neue Stiftingtalstraße 6, 8010 Graz

institute: Ludwig Boltzmann Institute for lung vascular research

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Medium/small size pulmonary artery

extract_protocol:
Pulmonary arteries (PHPF_1, PHPF_2, PHPF_3, Donor_4, Donor_5) were dissected under stereomicroscope by following the branching pattern and including accompanying perivascular (adventitial) region. Arteries were minced and digested for 60 min at 37°C in phosphate-buffered saline (PBS) containing 2 mg/mL collagenase A (Roche) and DNase I (Sigma). Digest was filtered through 100 micron cell strainer into FBS and diluted with PBS. Following centrifugation, cell pellet was washed with PBS and passed through 40 micron cell strainer. The secondary, and tertiary pulmonary arteries from the left lung lobe were isolated from the lungs of 12 week old male mice kept under normobaric hypoxia (10% O2) or normoxia (21% O2) for three weeks minced and digested as described for the human counterpart.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: PA resident cells

value: Medium/small size pulmonary artery

tag: disease state

value: PHPF


title: healthy kidney F480high CD11b intermediate cells

value: live FVD- CD45+ lineage(CD3 CD5 CD19 Ly6G NKp46 SiglecF)- CD11b+ CD45.2 iv intermediate F4/80high CD11b intermediate


title: Sample 1-18_control


title: Sample 2-10_case


title: Tissue associated poly (I:C) kidney RORgt-FM+ NKp46+ ILC

data_processing:
Raw data were processed using cellranger-5.0.0 with mm10 pre-build reference refdata-cellranger-mm10-1.2.0. Mkfastq, count were used in default parameter settings with 3000 expected cells for demultiplexing, detection of intact cells and quantification of gene expression. Mapping quality was assessed using the CellRanger summary statistics.
Assembly: mm10
Supplementary files format and content: h5: aggregated gene count matrix in hdf5 format.

extract_protocol:
For scRNA-seq analysis, we isolated tissue (CD45.2iv.-) NKp46+ ILC from 12 untreated and 8 poly(I:C)-treated RORgt-FM mice. Kidneys were harvested, minced and placed into RPMI 1640 Medium with GlutaMAX (Gibco) with collagenase IV (Worthington Biochemical, 570 U/ml) and DNase I (Roche, 12,5 U/ml). Tissue digestion was performed using the gentleMACS™ Dissociator and incubation with the enzymes at 37°C for 20 minutes. Single cell suspensions were obtained by passing cells through a 70-µm and 40-µm strainer strainer and washing once with FACS buffer. Following centrifugation at 500g for 5 minutes at 4°C, erythrocytes were removed by centrifugation in Percoll gradient. For sorting of NKp46+NK1.1+ ILC leukocytes were further enriched by Percoll gradient centrifugation (Cytiva). The pellet was resuspended in 40% Percoll layered over 80% Percoll prior to density centrifugation (1306 g 20 min at 20ºC with no brake). Cells were plated in 96-well V-bottom plates. FcγRIII/II were blocked with purified anti-CD16/32 (FcγRIII/II, eBioscience) diluted 1:250 for 15 minutes at 4o degrees. Antibody mixes were added and incubated at 4°C in the dark for 30 minutes, then incubated with streptavidin conjugates for 20 minutes. For surface stains DAPI was added to stain dead cells before analysis. Cell sorting was performed using a BD Biosciences FACSAria II cell sorter achieving a purity rate of > 98%.
5' gene expression libraries were generated using Chromium Next GEM Single Cell 5' Kit v2 (10X Genomics) according to the manufacturer's instruction. Quality control of cDNA and final libraries was done using Bioanalyzer High Sensitivity DNA Analysis (Agilent) and the KAPA library quantification kit. Libraries were sequenced using NextSeq 2000 (Illumina).

value: live DAPI- CD45+ lineage(CD3 CD5 CD19 Ly6g)- NKp46+NK1.1+ CD45.2 iv-RORgt-FM+

value: RORgt-FM


title: Sample 1-17_control

value: sperm

value: haploid cell


title: PHPF_2, scRNAseq

description: 10x Genomics


title: Sample 1-16_control

value: germ cell

value: WT


title: Tissue associated poly (I:C) kidney RORgt-FM- NKp46+ ILC

value: Kidney

value: live DAPI- CD45+ lineage(CD3 CD5 CD19 Ly6g)- NKp46+NK1.1+ CD45.2 iv-RORgt-FM-


title: Sample 1-15_control


title: Sample 1-14_control


title: PHPF_1, scRNAseq

description: 10x Genomics


title: Donor_4, scRNAseq

description: 10x Genomics

value: control


title: Sample 1-12_control


title: Sample 1-13_control


title: Donor_5, scRNAseq

description: 10x Genomics


title: Tissue associated untreated kidney RORgt-FM-NKp46+ ILC


title: S2-UPF3KD-1

city: Birmingham

first: Matthew

last: Wright

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Sequences trimmed using TRIMMOMATIC PE
Sequences aligned to Dm6.56 using HISAT2
SAMtools to sort and convert sam files to BAM files
HTSeq to calculate raw counts from bam files
DESeq2 for differential expression analysis
Assembly: Dm6.56 FlyBase (https://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.56_FB2024_01/)
Supplementary files format and content: Raw gene counts in plain .txt files, annotated with FlyBase Gene ID or Gene name

organism: Drosophila melanogaster

source_name: S2 cell

growth_protocol: Flies were kept at 25 degrees celcius, testes were dissected out at 5-days of age. Cells grown at 27 degrees celcius, in Schneider's Insect Cell Media, supplemented with Fetal Bovine Serum and antibotics (Penicillin and Streptomycin).

extract_protocol:
RNA was extracted using TRIzol. The upper phase was taken, and RNA was precipitated. Precpitated RNA was dissolved in dH2O.
Library was constructed by Novogene, following polyA enrichment

value: S2 cell


title: Tissue associated untreated kidney RORgt-FM+ NKp46+ ILC


title: NKp46 blocking antibody treated kidney CD45+ cells including vessel-associated (CD45.2iv.+) NK cells

description: NKp46 blocking antibody treatment

extract_protocol:
For scRNA-seq analysis, we isolated kidney leukocytes, including vessel-associated (CD45.2iv.+) NK cells, isolated from 2 nephritic and 3 anti-NKp46 treated NZB/W F1 mice. Kidneys were harvested, minced and placed into RPMI 1640 Medium with GlutaMAX (Gibco) with collagenase IV (Worthington Biochemical, 570 U/ml) and DNase I (Roche, 12,5 U/ml). Tissue digestion was performed using the gentleMACS™ Dissociator and incubation with the enzymes at 37°C for 20 minutes. Single cell suspensions were obtained by passing cells through a 70-µm and 40-µm strainer strainer and washing once with FACS buffer. Following centrifugation at 500g for 5 minutes at 4°C, erythrocytes were removed by centrifugation in Percoll gradient. For sorting of NKp46+NK1.1+ ILC leukocytes were further enriched by Percoll gradient centrifugation (Cytiva). The pellet was resuspended in 40% Percoll layered over 80% Percoll prior to density centrifugation (1306 g 20 min at 20ºC with no brake). Cells were plated in 96-well V-bottom plates. FcγRIII/II were blocked with purified anti-CD16/32 (FcγRIII/II, eBioscience) diluted 1:250 for 15 minutes at 4o degrees. Antibody mixes were added and incubated at 4°C in the dark for 30 minutes, then incubated with streptavidin conjugates for 20 minutes. For surface stains DAPI was added to stain dead cells before analysis. Cell sorting was performed using a BD Biosciences FACSAria II cell sorter achieving a purity rate of > 98%.
5' gene expression libraries were generated using Chromium Next GEM Single Cell 5' Kit v2 (10X Genomics) according to the manufacturer's instruction. Quality control of cDNA and final libraries was done using Bioanalyzer High Sensitivity DNA Analysis (Agilent) and the KAPA library quantification kit. Libraries were sequenced using NextSeq 2000 (Illumina).

value: live DAPI- CD45+ lineage(CD3 CD5 CD19 Ly6g)- NKp46+NK1.1+ CD45.2 iv-

value: NZB/W F1


title: Nephritic kidney CD45+ cells including vessel-associated (CD45.2iv.+) NK cells

description: poly (I:C) + isotype control

value: live DAPI- CD45+ and live DAPI- CD45+ lineage(CD3 CD5 CD19 Ly6g)- NK1.1+ CD45.2 iv+ excluding live DAPI- CD45+ lineage(CD3 CD5 CD19 Ly6g)- NK1.1+ CD45.2 iv-


title: Damaged_rep_5

city: Adelaide

first: Katja

last: Hummitzsch

state: South Australia

address: Level 5, North Tce/George Street

department: Obstetrics & Gynaecology

country: Australia

institute: The University of Adelaide

description: RNA from oocyte

data_processing:
QC steps to remove adpater and low-quality reads in fastq files were done by using AfterQC software
Pseudoalignment and quantificantion were finished by Kallisto (version: 0.43)
For gene level analysis, Kallisto counts matrices were imported into R by using tximport package to generate matrcies at gene level. Then, filter counts and normalized counts were determined in limma-voom workflow
For isoform level analysis, IsoformSwitchR package was used to work with Kallisto counts matrices for importing data, filtering and all downstream analysis
Assembly: Sus_scrofa_Sscrofa11.1.cdna.all.fa.gz from Ensembl database
Supplementary files format and content: Raw Kallisto counts for each transcript and each sample in 'tsv' format

organism: Sus scrofa

source_name: oocyte

growth_protocol: For obtaining MII or 'damaged' oocytes, cumulus oocyte complexes (COCs) containing GV oocytes retrieved from fresh pig ovarian follicles were in vitro matured for 44h. Then, the COCs were treated with hyaluronidase to remove cumulus cells and then observed under a stereo-microscope to determine the presence of a first polar body. Oocytes with a first polar body were classified as ‘MII group’, whereas oocytes lacking a first polar body were classified as ‘damaged group’.

extract_protocol:
The SMART-Seq® HT kit (Takara Bio Inc., Shiga, Japan) was used for cDNA generation according to the manufacturer’s instructions using 13 PCR cycles across a total of 15 samples.
cDNAs were then converted to sequencing libraries using the Illumina DNA Prep kit (Illumina, San Diego, USA) according to the manufacturer’s instructions with 8 PCR cycles for the final amplification. An equimolar pool of libraries was sequenced by single-end RNA sequencing (1 x 75bp) on an Illumina Nextseq 500 at the South Australian Genomics Centre (SAGC; Adelaide, SA).

value: oocyte

tag: developmental stage

value: Damaged (not completely matured into MII after IVM)

tag: culture condition

value: IVM of GV oocytes for 44h

tag: 1st polar body detection

value: No


title: S2-UPF3KD-2


title: Sample 1-10_control

tag: tissue


title: Tissue associated kidney NKp46+ ILC treated with NKp46 blocking antibodies

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

extract_protocol:
For scRNA-seq analysis, we isolated kidney tissue (CD45.2iv.-) NKp46+ ILC from 10 healthy young, 8 nephritic and 3 anti-NKp46-treated NZB/W F1 mice. Kidneys were harvested, minced and placed into RPMI 1640 Medium with GlutaMAX (Gibco) with collagenase IV (Worthington Biochemical, 570 U/ml) and DNase I (Roche, 12,5 U/ml). Tissue digestion was performed using the gentleMACS Dissociator and incubation with the enzymes at 37°C for 20 minutes. Single cell suspensions were obtained by passing cells through a 70-µm and 40-µm strainer strainer and washing once with FACS buffer. Following centrifugation at 500g for 5 minutes at 4°C, erythrocytes were removed by centrifugation in Percoll gradient. For sorting of NKp46+NK1.1+ ILC leukocytes were further enriched by Percoll gradient centrifugation (Cytiva). The pellet was resuspended in 40% Percoll layered over 80% Percoll prior to density centrifugation (1306 g 20 min at 20ºC with no brake). Cells were plated in 96-well V-bottom plates. FcγRIII/II were blocked with purified anti-CD16/32 (FcγRIII/II, eBioscience) diluted 1:250 for 15 minutes at 4o degrees. Antibody mixes were added and incubated at 4°C in the dark for 30 minutes, then incubated with streptavidin conjugates for 20 minutes. For surface stains DAPI was added to stain dead cells before analysis. Cell sorting was performed using a BD Biosciences FACSAria II cell sorter achieving a purity rate of > 98%.
For kidney NK1.1+ NKp46+ ILC or NK1.1+ ILC, 5' gene expression libraries were generated using Chromium Next GEM Single Cell 5' Kit v2 (10X Genomics) according to the manufacturer's instruction. Quality control of cDNA and final libraries was done using Bioanalyzer High Sensitivity DNA Analysis (Agilent) and the KAPA library quantification kit. Libraries were sequenced using NextSeq 2000 (Illumina).
Chromium Next GEM Single Cell 5' Kit v2 (10X Genomics) were used.

tag: strain

tag: genotypes

tag: sorting strategy

value: live DAPI- CD45+ lineage(CD3 CD5 CD19 Ly6g)- NK1.1+ CD45.2 iv-

tag: Sex

value: female

value: treated with NKp46 blocking antibodies

tag: treatment

value: poly (I:C) + NKp46 blocking antibodies


title: Sample 1-11_control

value: sperm

value: haploid cell

value: germ cell


title: S2-UPF2KD-1


title: S2-UPF2KD-2


title: Sample 1-9_control

value: WT


title: Damaged_rep_3

description: RNA from oocyte


title: S2-WT2-1


title: Tissue associated nephritic kidney NKp46+ ILC, pic

value: Kidney

value: poly (I:C) nephritis

value: poly (I:C) +  isotype control


title: Sample 1-8_case

value: MT


title: Tissue associated nephritic kidney NKp46+ ILC

value: NZB/W F1

value: kidney

value: live DAPI- CD45+ lineage(CD3 CD5 CD19 Ly6g)- NKp46+NK1.1+ CD45.2 iv-

value: poly (I:C)


title: Sample 1-7_control


title: Damaged_rep_1

description: RNA from oocyte

value: oocyte

value: Damaged (not completely matured into MII after IVM)

value: IVM of GV oocytes for 44h

value: No


title: Sample 1-5_control


title: T-UPF1KD2-2

source_name: Testes

value: Testes


title: Tissue associated healthy kidney NKp46+ ILC

value: female

value: healthy


title: Damaged_rep_4

description: RNA from oocyte


title: MII_rep_5

description: RNA from oocyte

value: MII (metaphase II)

value: Yes


title: Sample 1-4_control

value: sperm

value: haploid cell

value: germ cell

value: WT


title: MII_rep_4

description: RNA from oocyte


title: Sample 1-3_control


title: T-UPF1KD1-2


title: MII_rep_3

description: RNA from oocyte


title: 293T W128A, ZBTB9, 0.1 Dox, rep2

city: Boston

first: Jared

last: Brown

state: MA

address: Mailtop CLS11007, 450 Brookline Ave

department: Data Science

institute: Dana Farber Cancer Institute

data_processing:
Alignment/filtering: All ChIP-seq samples were processed identically. Initial reads (.fastq) were screened for short/low quality sequences using fastp (v0.23.2) (options -q 16 -u 35 -e 22 -l 34). Filtered, paired .fastq file were aligned to the UCSC release of the hg38.p13 reference genome using the STAR aligner (v2.7.5b) in paired end mode (options –winAnchorMultimapNmax 100 –twopassMode Basic –outReadsUnmapped None –outSAMstrandField intronMotif –outSAMunmapped None –outMultimapperOrder Random –outSAMmultNmax 1 –alignIntronMax 1 –alignEndsType EndToEnd –alignMatesGapMax 1000). Aligned .bam files were filtered using SAMtools (v1.10) to initially remove mapped fragments fully contained within the ENCODE exclusion list for GRCh38 (dataset: ENCFF356LFX) followed by further filtering to remove optical (sequencing) duplicate alignments as identified by Picard (v1.2) and mapped fragments over 1kb. Duplicate fragments not identified as optical were downsampled to remove duplicate rates in excess of that expected by the local binding rates of duplicate and unique reads as fitted by a monotonic cubic spline on log counts; this is a slight modification of the approach described in Tian S., et al. (2019).
Normalization: Samples were rendered comparable within experiment and identifiable excess variation due to differences in sequending depth was removed/accounted for through the use of normalization scale factors. Factors were calculated through an approach integrating techniques from the TMM and Median-Ratio methods. Specifically, fragment counts across 75BP bins were tabulated and neighboring bins with similar length-normalized counts (less than 33% difference) were merged to increase per-bin information; the percent-change limit implicitly provides robustness to peaks, which tend to not be merged. Following merging, bin-specific pseudo-counts were calculated as the across-sample geometric mean of bin counts. Finally, sample-specific scale factors are estimated as the median of ratios between sample-bin-counts and bin-pseudo-counts. When necessary, normalized signal tracks are calculated by dividing the raw signal track by the sample-specific scale factor.
Peak calling: Per-sample peaks were called using a custom implementation of the MACS2 (v2.2.7.1) tools. ChIP fragments (.bam) were converted to a BedGraph using ‘pileup’ in paired-end mode then scaled by the previously estimated normalization factor with ‘bgdopt’.
Assembly: hg38
Supplementary files format and content: Processed *.bw files contain genome-wide signal tracks of aligned and filtered fragments, normalized by scaling with the sample-specific scale-factor.
Supplementary files format and content: Processed *peaks.bed files contain sample-specific peaks as called by MACS2.
Supplementary files format and content: Processed *MergedPeaks.bed files contain peak regions merged across those discovered in sample-specific testing.
Supplementary files format and content: Processed *MergedPeakCounts.csv files contain fragment counts corresponding to each merged peak across samples.
Supplementary files format and content: Processed *SampleMetaData.csv files contain sample-specific meta-data including sample-specific normalization size-factors.

source_name: HEK 293T - ZBTB9 KO

extract_protocol:
Cells were pelleted by centrifugation and resuspended in 8.25 ml of PBS and 8.25 ml of 2% formaldehyde and incubator for 10 minutes at room temperature. Cross-linking was quenched by the addition of 1665 µl of 1 M Tris/HCl pH 8.0 and 832.5 µl of 2.5 M glycine. Cells were pelleted and washed twice with PBS. Cross-linked cells were resuspended in LB1 Buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 in distilled water) and rotated for 10 minutes at 4°C. Cells were pelleted and resuspended in LB2 (10 mM Tris/HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA in distilled water) and rotated for 10 minutes at 4°C. Cells were pelleted and resuspended in home-made RIPA Buffer (50mM Tris/HCl pH 8.0, 150 mM NaCl, 5 mM EDTA, 0.5% Na-deoxycholate, 0.1% SDS, 1% Triton X-100, in distilled water) sonicated (Covaris, E220). Samples were transferred into DNA LoBind tubes (Eppendorf) and clarified by centrifugation. Antibody-bead conjugates were made with either Protein-A (ThermoFisher). Beads were washed twice with home-made RIPA Buffer and resuspended with the appropriate amount of beads (according to manufacturer’s instructions), and rotated overnight at 4°C. Antibody-bead complexes were applied to lysates and rotated overnight at 4°C. Beads were removed via magnet and washed twice with home-made RIPA Buffer , twice with Low salt wash Buffer (150 mM NaCl, 20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS in distilled water), twice with High salt wash Buffer (250 mM NaCl, 20 mM Tris/HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS in distilled water) and twice with LiCl Buffer (2.5 g deoxycholic acid, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 10 mM Tris/HCl pH 8.0, 0.02% NaN3 in distilled water). Beads were washed briefly with TE buffer and DNA was eluted in ChIP elution buffer (50mM Tris-HCl, pH 8.0, 10mM EDTA, 1% SDS in distilled water) and de-crosslinked overnight at 65°C. DNA was purified by column purification (DNA Clean and Concentration, Zymo Research) and quantified by ScreenTape HS D1000 (Agilent) and Qubit (ThermoFisher).
Library preparation was done using SMARTer® ThruPLEX® DNA-Seq Kit (Takara, #R400675).

value: HEK 293T - ZBTB9 KO

value: Kidney

tag: chip antibody


title: S2-WT2-2

value: S2 cell


title: T-WT-2


title: MII_rep_1

description: RNA from oocyte


title: MII_rep_2

description: RNA from oocyte


title: Sample 1-2_control


title: Sample 1-1_control


title: Damaged_rep_2

description: RNA from oocyte


title: 293T W128A, ZBTB9, 0.1 Dox, rep1


title: T-WT-1


title: preadipocytes, Sample 1, Day 14, replicate 4

first: Seung Hyuk

middle: T.

last: Lee

address: 695 Charles E. Young Drive South

institute: UCLA

data_processing:
We aligned reads with Bowtie2 v2.2.9 with parameters -k 4 -X 2000 --local.
We filtered out unpaired mapped reads and reads with MAPQ < 30 using (SAMtools) as well as duplicates (marked with Picard Tools).
We only retained reads from the autosomes and X chromosome were retained for downstream analyses.
To obtain list of consensus peaks, we first called peaks at each time point separately using MACS2 v2.2.7.1 and peaks with a q-value<0.01 were retained.
Peaks in blacklisted regions and those with fewer than one peak (bin) count per million mapped reads (BPM) in more than 20% of samples were filtered out
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes the raw counts for each Sample

source_name: subcutaneous adipose tissue

growth_protocol: Cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E) were seeded into PromoCell preadipocyte growth medium (PromoCell C-27410) with 1% Gibco Penicillin-Streptomycin (ThermoFisher 15140122) and  maintained in a monolayer culture at 37C and 5% CO2. Cells were cultured according to PromoCell preadipocyte culturing protocols and propagated for the full experiment, not cultured beyond 5 passages.

extract_protocol:
We followed the Omni-ATAC protocol. Cells were treated DNase I at 37 °C for 30 min and trypsinized, after which we tagmented and purified the DNA with the Qiagen MinElute kit.
We added Illumina sequencing adapters to the tagmented DNA samples for the sequencing library construction.
Illumina NovaSeq S4

treatment_protocol: To induce adipogenesis, we plated cells at confluency into 12-well plates for ATAC-seq (4 isogenic biological replicates per time point). The next day, we initiated adipogenesis using preadipocyte differentiation medium (PromoCell C-27436). We collected the 1d and 2d timepoints before any further media changes, while for all other differentiation timepoints, 72 hours after the preadipocyte differentiation medium was added, we replaced it with adipocyte nutrition medium (PromoCell C-27438), following the PromoCell preadipocyte differentiation protocols.

value: subcutaneous adipose tissue

value: cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E)

value: primary white preadipocyte

tag: time

value: Day 14


title: GV_rep_5

description: RNA from oocyte

value: oocyte

value: GV (germinal vesicle)

value: No culture, dissect from fresh ovarian follicle

value: No


title: 293T W128A, ZBTB9, 0.01 Dox, rep2

tag: cell line


title: 2868300_wt_GMP_H3K27ac.3

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

description: H3K27ac Chipmentation in mouse GMP

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by BWA with the ENCODE DCC TF/Histone ChIP-Seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2, v1.1.6)
Signal strength relative to the control samples were generated using MACS2.
Broad peaks were called using MACS2, and overlapping peaks across pseudo-replicates were genereated using the same approach as that used by the ENCODE pipeline for overlap optimal peaks.
genome build/assembly: GRCm38/mm10
processed data files format and content: bigwig, broadPeak

source_name: bone marrow

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

treatment_protocol: PBS or G-CSF 5 mcg daily x2 days

value: bone marrow

value: GMP

value: wildtype


title: 293T W128A, ZBTB9, 0.01 Dox, rep1


title: preadipocytes, Sample 1, Day 14, replicate 3


title: T-UPF1KD2-1

value: Testes


title: GV_rep_4

description: RNA from oocyte


title: 293T W128A, ZBTB9, 1 Dox, rep1


title: 2868300_wt_GMP_H3K27ac.2

description: H3K27ac Chipmentation in mouse GMP


title: 293T W128A, ZBTB9, 1 Dox, rep2


title: 293T WT-ZBTB9, ZBTB9, 1 Dox, rep1


title: preadipocytes, Sample 1, Day 14, replicate 2


title: 2868300_wt_GMP_H3K27ac.1

description: H3K27ac Chipmentation in mouse GMP


title: T-UPF1KD1-1


title: preadipocytes, Sample 1, Day 14, replicate 1


title: GV_rep_3

description: RNA from oocyte


title: preadipocytes, Sample 1, Day 7, replicate 4

value: Day 7


title: 2868300_wt_GMP_H3K4me1.4

description: H3K4me1 Chipmentation in mouse GMP


title: GV_rep_2

description: RNA from oocyte


title: 2868300_wt_GMP_H3K4me1.2

description: H3K4me1 Chipmentation in mouse GMP


title: 293T WT-ZBTB9, ZBTB9, 0.1 Dox, rep2


title: 293T WT-ZBTB9, ZBTB9, 0.01 Dox, rep2


title: Sample13_C1D1

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Baseline for patient 13

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg19 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin (CTCL)

extract_protocol:
Total RNA from formalin-fixed paraffin-embedded (FFPE) skin from healthy controls and CTCL patients was extracted with miRNAeasy FFPE kit (Quiagen)
Kapa HyperPrep with RNAerase

treatment_protocol: Clinical protocol for patients with CTCL, on durvalumab and lenalidomide  (baseline/C1D1, C2D15 )

value: Skin (CTCL)

value: CTCL Tumor Cells


title: 2868300_wt_GMP_H3K4me1.1

description: H3K4me1 Chipmentation in mouse GMP


title: GV_rep_1

description: RNA from oocyte


title: preadipocytes, Sample 1, Day 7, replicate 3


title: Sample12_C2D15

description: Patient 12 treated

value: Durvalumab + lenalidomide


title: 293T WT-ZBTB9, ZBTB9, 0.01 Dox, rep1

value: HEK 293T - ZBTB9 KO

value: Kidney


title: 293T WT-ZBTB9, ZBTB9, 1 Dox, rep2


title: preadipocytes, Sample 1, Day 7, replicate 1

value: subcutaneous adipose tissue

value: cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E)


title: Sample12_C1D1

description: Baseline for patient 12


title: miCLIP_mESC_NSUN6_Eluent_rep1

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Zhejiang University

data_processing:
For batch paired-end reads of m5C-seq libraries, a sample-barcoded-sequence (Pos 1-6) and random-4-base (pos7-10) in Read1 and a 10nt unique molecular identifier (UMI) was included in the adaptor that ligates to the 3’end of cDNA so it locates in Read2 (Pos1-10). Firstly, m5C-seq batch libraries were demultiplexed into individual samples, using fastq-multx（with -m 1 parameters）that distributes reads into a sample FASTQ file(Read1.fq file and Read2.fq file) according to the sample-barcoded-sequence in Read1 (Pos 1-6). For every individual sample, only Read2 data with UMI was used for subsequent analyses. Illumina sequencing reads were first treated with trim_galore(version 0.6.4) for adapter removal and quality trimming. Work commands are as follows: trim_galore --fastqc --phred33 --length 30. We then used Seqkit (version 0.10.0) to deduplicate based on 10 bp UMI at the 5′ end of reads R2, key process parameters are as follows: seqkit rmdup -s. Finally, Fastp (version 0.23.2) was used to remove the 10 bp UMI in the deduplication read. 10 bases at the 3′ end of inserted sequences were also removed, using the key parameters: fastp -f 10 -t 10 -l 20.
Processed reads were mapped to reference genome (human GRCh19 reference / mouse mm10 reference) using HISAT2-3N (version 2.2.1-3n-0.0.3). The key parameters are as follows: hisat3n --base-change C,T --directional-mapping --repeat -p 20 -k 1. Considering a creditable m5C signal, the alignments are further filtering using python house-scripts, the alignments hosts >=3 C-to-T mismatches or >= 3 other type mismatches or the length of alignments < 20nt are filtered. Next, we parse BAM file using pysamstats (version 1.1.2), with commands as follow: pysamstats -D 100000 -S "nofilter" -t variation.
To identify the methyltransferase-dependent m5C sites, we calculated the C-to-T ratios for the m5C-TACseq-identified m5C sites in WT and all knockout/knockdown samples. Then, the fold change and difference of C-to-T ratio between KO/KD samples and WT/Control samples were calculated. For the identification of enzyme-dependent sites by comparing the KO and WT samples, the fold change in C-to-T ratio (KO sample/WT sample) was required to be less than 60% in two replicates, and the difference in C-to-T ratio (WT sample - KO sample) was required to be > 1.5%. Considering the presence of residual enzymes upon knockdown, to identify enzyme-dependent sites by comparing the KD and Control samples, the fold change in C-to-T ratio (KD sample/Control sample) was required to be less than 60% in at least one replicate.
The analysis of CLIP-seq data was performed using CLIP Tool Kit (CTK, v1.1.3). The processed reads were mapped to the mouse genome (Ensembl annotation of mm10) using hisat2 v2.2.1 with default settings.
Assembly: hg19(UCSC)/mm10(UCSC)/tRNA-referenece(tRNAdb)
Supplementary files format and content: tab-delimited text file includes every C base coverage and C-to-T signal
Supplementary files format and content: excel file,in xls file format
Library strategy: m5C-seq

source_name: cell line

growth_protocol: The mESC cell line was cultured in a complete ESC culture medium, comprising Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% heat-inactivated fetal bovine serum (FBS), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1000 U/mL recombinant leukemia inhibitory factor (LIF), and 100 U/mL penicillin/streptomycin. For differentiation assays, mESC cells were cultured without LIF for six days. HeLa and HEK 293T cell lines were cultured in DMEM supplemented with 10% FBS and 100 U/mL penicillin/streptomycin.

extract_protocol:
Total RNA extraction from the cell lines was accomplished using the RNA isolater total RNA extraction reagent (Vazyme, R401-01). Prior to size selection, RNA underwent DNase I treatment at 37 ℃ for 15 min and subsequently was purified using RNA isolater extraction and ethanol precipitation (Vazyme, EN401-01). The small RNA fraction, characterized by a size of less than 200nt, was enriched from the total RNA utilizing the RNA Clean & Concentrator-25 Kit (Zymo, R1018). For mRNA purification, two successive rounds of poly(A)+ selection were performed employing oligo(dT)25 dynabeads (Life Technologies, 61005). Additionally, chromatin-associated RNA was isolated following subcellular fractionation assay, DNase I treatment, and rRNA depletion (Vazyme, N406-01). Modification-free control RNAs were prepared from HeLa or mESC mRNA, adhering to a previously published protocol (PMID: 34594034, 36593412).
The RNA samples were initially dephosphorylated using T4 polynucleotide kinase (Vazyme, N102-01) at 37℃ for 1 hour, followed by ethanol precipitation. Subsequently, they were ligated to the 3' RNA linker using T4 RNA ligase 2, truncated at 25°C for 2 hours, followed by an overnight incubation at 16°C (Beyotime, R0635L). To remove excess adaptors, the samples underwent treatment with 5´ Deadenylase (NEB, M0331S), RecJf (NEB, M0264S), and Proteinase K (NEB, P8102). RNA samples intended for group comparisons were pooled and then purified through Tris-phenol extraction followed by ethanol precipitation. The barcoded and pooled samples were labeled by 5-(2-azidoethyl)-1,3-indandione (AI) and subsequently subjected to a click reaction. The m5C-modified RNA was subjected to RNA pull-down to be enriched, followed by reverse transcription using the HiScript III RT SuperMix (Vazyme, R323-01). The excess reverse transcription primer was digested with exonuclease I (NEB, M0293S). The cDNA was purified by silane beads and then performed to 5′ adapter ligation on beads with T4 RNA ligase 1, high concentration (NEB, M0437M). cDNA was purified using silane beads (Invitrogen, 37002D), and subsequently, the purified cDNA was amplified using the KAPA HiFi HotStart ReadyMix (Roche, KK2602). Finally, PCR products were purified using 1.8X VAHTS DNA Clean Beads (Vazyme, N411-02) and 7% TBE gel.

value: cell line

value: mESC

value: Mouse embryonic stem cells

value: NSUN6 C326A overexpression

value: Cells were lysed and followed by partial RNA digestion with RNase I. Then, FLAG immunoprecipitation was performed using anti-FLAG magnetic beads. The protein-RNA complex was eluted and a second biotin immunoprecipitation was conducted with streptavidin beads. The RNA was purified by RNA Isolater and subjected to library construction.


title: miCLIP_mESC_NSUN6_Eluent_rep2


title: 293T W128A, Input, 1 Dox, rep2

description: input for 293T-p404_ChIP_ZBTB9_dox-1-24h_REP2_230526_CTTGTA_S12_peaks.bed


title: 2868300_wt_GMP_H3K4me1.3

description: H3K4me1 Chipmentation in mouse GMP

value: bone marrow


title: preadipocytes, Sample 1, Day 4, replicate 2

value: primary white preadipocyte

value: Day 4


title: preadipocytes, Sample 1, Day 7, replicate 2


title: Sample13_C2D15

description: Patient 13 treated


title: 293T W128A, Input, 0.1 Dox, rep2

description: input for 293T-p404_ChIP_ZBTB9_dox-0-1-24h_REP2_230526_GGCTAC_S11_peaks.bed


title: preadipocytes, Sample 1, Day 4, replicate 4


title: preadipocytes, Sample 1, Day 4, replicate 1


title: 293T W128A, Input, 1 Dox, rep1

description: input for 293T-p404_ChIP_ZBTB9_dox-1-24h_REP1_230526_CAGATC_S6_peaks.bed


title: Sample11_C2D15

description: Patient 11 treated


title: Sample10_C2D15

description: Patient 10 treated


title: miCLIP_mESC_NSUN2_Eluent_rep2

value: NSUN2 C271A overexpression


title: Sample10_C1D1

description: Baseline for patient 10


title: 293T W128A, Input, 0.01 Dox, rep2

description: input for 293T-p404_ChIP_ZBTB9_dox-0-01-24h_REP2_230526_TAGCTT_S10_peaks.bed


title: miCLIP_mESC_NSUN2_Eluent_rep1


title: 293T W128A, Input, 0.01 Dox, rep1

description: input for 293T-p404_ChIP_ZBTB9_dox-0-01-24h_REP1_230526_TGACCA_S4_peaks.bed


title: preadipocytes, Sample 1, Day 2, replicate 3

value: Day 2


title: miCLIP_mESC_WT_Eluent_rep2

value: WT


title: Sample9_C2D15

description: Patient 9 treated

value: Skin (CTCL)

value: CTCL Tumor Cells


title: 293T WT-ZBTB9, Input, 1 Dox, rep2

description: input for 293T-p403_ChIP_ZBTB9_dox-1-24h_REP2_230526_GATCAG_S9_peaks.bed

value: HEK 293T - ZBTB9 KO


title: preadipocytes, Sample 1, Day 4, replicate 3


title: miCLIP_mESC_NSUN5_Eluent_rep2

value: NSUN5 C308A overexpression


title: 293T WT-ZBTB9, ZBTB9, 0.1 Dox, rep1

value: Kidney


title: Sample11_C1D1

description: Baseline for patient 11


title: miCLIP_mESC_NSUN5_Eluent_rep1


title: preadipocytes, Sample 1, Day 2, replicate 2

value: subcutaneous adipose tissue

value: cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E)


title: Sample7_C2D15

description: Patient 7 treated

value: Durvalumab + lenalidomide


title: 293T W128A, Input, 0.1 Dox, rep1

description: input for 293T-p404_ChIP_ZBTB9_dox-0-1-24h_REP1_230526_ACAGTG_S5_peaks.bed


title: preadipocytes, Sample 1, Day 2, replicate 4


title: small_RNA_DM_mESC_Tet2_KO_Label_rep2

description: RNA fraction below 200 nt

value: cell line

value: mESC

value: Mouse embryonic stem cells

value: Tet2 knockout

value: TET2 oxidation and AI Labeling


title: small_RNA_DM_mESC_Tet2_KO_Label_rep1

description: RNA fraction below 200 nt


title: small_RNA_DM_mESC_Tet2_KO_Ctrl_rep2

description: RNA fraction below 200 nt

value: control


title: 293T WT-ZBTB9, Input, 0.01 Dox, rep2

description: input for 293T-p403_ChIP_ZBTB9_dox-0-01-24h_REP2_230526_GCCAAT_S7_peaks.bed


title: small_RNA_DM_mESC_Tet2_KO_Ctrl_rep1

description: RNA fraction below 200 nt


title: preadipocytes, Sample 1, Day 2, replicate 1

value: primary white preadipocyte


title: 293T WT-ZBTB9, Input, 0.01 Dox, rep1

description: input for 293T-p403_ChIP_ZBTB9_dox-0-01-24h_REP1_230526_ATCACG_S1_peaks.bed


title: preadipocytes, Sample 1, Day 1, replicate 3

value: Day 1


title: Sample9_C1D1

description: Baseline for patient 9


title: Sample6_C2D15

description: Patient 6 treated


title: Sample5_C2D15

description: Patient 5 treated


title: small_RNA_DM_mESC_Tet2_WT_Label_rep2

description: RNA fraction below 200 nt

value: WT


title: preadipocytes, Sample 1, Day 1, replicate 4


title: preadipocytes, Sample 1, Day 0, replicate 4

value: Day 0


title: 293T WT-ZBTB9, Input, 0.1 Dox, rep1

description: input for 293T-p403_ChIP_ZBTB9_dox-0-1-24h_REP1_230526_CGATGT_S2_peaks.bed


title: 293T WT-ZBTB9, Input, 0.1 Dox, rep2

description: input for 293T-p403_ChIP_ZBTB9_dox-0-1-24h_REP2_230526_ACTTGA_S8_peaks.bed


title: Sample6_C1D1

description: Baseline for patient 6

value: Skin (CTCL)

value: CTCL Tumor Cells


title: preadipocytes, Sample 1, Day 1, replicate 2


title: 293T K166A, ZBTB3, 1 Dox, rep2

source_name: HEK 293T - ZBTB3 KO

value: HEK 293T - ZBTB3 KO


title: 293T K166A, ZBTB3, 1 Dox, rep1

value: Kidney


title: preadipocytes, Sample 1, Day 1, replicate 1

value: subcutaneous adipose tissue


title: preadipocytes, Sample 1, Day 0, replicate 3

value: cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E)


title: Sample7_C1D1

description: Baseline for patient 7


title: Sample4_C2D15

description: Patient 4 treated

value: Durvalumab + lenalidomide


title: 293T K166A, ZBTB3, 0.1 Dox, rep2


title: 293T WT-ZBTB9, Input, 1 Dox, rep1

description: input for 293T-p403_ChIP_ZBTB9_dox-1-24h_REP1_230526_TTAGGC_S3_peaks.bed

value: HEK 293T - ZBTB9 KO


title: small_RNA_DM_mESC_Tet2_WT_Label_rep1

description: RNA fraction below 200 nt

value: cell line

value: mESC


title: preadipocytes, Sample 1, Day 0, replicate 2


title: Sample4_C1D1

description: Baseline for patient 4


title: Sample5_C1D1

description: Baseline for patient 5


title: miCLIP_mESC_WT_Eluent_rep1

value: Mouse embryonic stem cells

value: Cells were lysed and followed by partial RNA digestion with RNase I. Then, FLAG immunoprecipitation was performed using anti-FLAG magnetic beads. The protein-RNA complex was eluted and a second biotin immunoprecipitation was conducted with streptavidin beads. The RNA was purified by RNA Isolater and subjected to library construction.


title: small_RNA_DM_mESC_Tet2_WT_Ctrl_rep2

description: RNA fraction below 200 nt

value: control


title: small_RNA_DM_mESC_Tet2_WT_Ctrl_rep1

description: RNA fraction below 200 nt


title: 293T K166A, ZBTB3, 0.1 Dox, rep1


title: preadipocytes, Sample 1, Day 0, replicate 1

value: primary white preadipocyte


title: Sample3_C2D15

description: Patient 3 treated


title: 293T K166A, ZBTB3, 0.01 Dox, rep2


title: SAT7

description:
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
meta_data.tsv.gz

data_processing:
Sequence reads were aligned to the GRCh37 human genome reference using STARSolo in STAR v2.7.5a with the the ‘--soloFeatures GeneFull’ parameter to account for full pre-mRNA transcripts
We used demuxlet, implemented in the popscle software tool, to assign droplets to the one of the 8 donors.
Assembly: hg19
Supplementary files format and content: Matrix market format for gene counts
Supplementary files format and content: Tab-separated text file for meta data, barcodes (column names), and gene names (row names).

extract_protocol:
To isolate nuclei, the tissue was minced over dry ice and transferred into ice-cold lysis buffer consisting of 0.1% IGEPAL, 10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl2. After a 10 minute incubation period, the lysate was gently homogenized with a dounce homogenizer and filtered through a 70-μm MACS smart strainer (Miltenyi Biotec #130-098-462) for debris removal. Nuclei were centrifuged at 500g for 5 min at 4 °C and washed in 1 ml of resuspension buffer (RSB) consisting of 1× PBS, 1.0% BSA, and 0.2 U/μl RNase inhibitor. Nuclei were then further filtered using a 40-μm Flowmi cell strainer (Sigma Aldrich # BAH136800040), centrifuged at 500g for 5 min at 4 °C, and re-suspended in wash buffer.
Libraries were prepared using the 10x Single Cell 3’ Reagent Kit v3.1
Illumina NovaSeq SP


title: Sample3_C1D1

description: Baseline for patient 3


title: adult forebrain, IgG negative control, rep1

city: Baltimore

first: Mollie

last: Meffert

address: 725 N. Wolfe St.

institute: Johns Hopkins University School of Medicine

description:
NegC Rep1
IgG_CIMERA-seq_sample_1-2_peakcalling.summary.txt
IgG_CIMERA-seq_sample_1-2_peaks.bed.txt
IgG_CIMERA-seq_sample_1-2_peaks.bed.mouse.annotation.txt

data_processing:
Sequencing data were processed using SCRAP (SCRAP release 2.0) bioinformatic pipeline to identify the significant sncRNA:targetRNA interactions in each sample (Eadara et al. 2023; Mills et al. 2022), for which code is deposited at https://github.com/Meffert-Lab/SCRAP.
Peak calling was performed by setting SCRAP variables to consider only high confidence sncRNA binding sites across the genome supported by at least 3 chimeric sncRNA:target RNA reads in at least 2 sample libraries.  Peak calling was performed as groups: group1: Forebrain CIEMRA-seq sample 1-4 group 2: Forebrain CIMERA-seq sample 5-7 group 3: Excitatory neuron selective CIMERA-seq sample 1-3 group 4: IgG CIMERA-seq sample 1-2
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include counts for each chimeric RNA (sncRNA:target RNA pairs)
Library strategy: CIMERA-seq

source_name: forebrain

extract_protocol:
Mouse brain tissue in Homogenization buffer (1X HBSS supplemented with 5 mM MgCl2, 10 mM HEPES (pH 7.4) and 1X HALT protease/phosphatase inhibitor) is homogenized by 12 passes through a 21G needle. UV irradiate homogenates 3x with (4000 µJ/cm2 x 100) on a perfluoroalkoxy (PFA) petri dish, mixing samples between rounds. Transfer irradiated tissue homogenate to a microfuge tube and centrifuge 900 x g for 5 minutes at 4 °C.  Immunoprecipitation from the cell pellets were done with anti-Ago2 (2D4, Wako, 018-22021)  for total CIMERA-seq, anti-myc (9B11, Cell Signaling, 2276) for cell-selective CIMERA-seq, and anti-IgG1 (Invitrogen, 14-4714-82) for negative control.
Libraries were prepared by intermolecular ligation of small non-coding RNA and target RNA, RNA isolation from Ago protein, ligation of 3’ and 5’ adaptors, reverse transcription, minimal PCR amplification, gel purification and size selection.
custom sequencing libraries with 150 base-pair paired-end sequencing and a read depth of 61 – 138 million reads per sample (Illumina HiSeq X or NovaSeq)

value: forebrain


title: Sample2_C2D15

description: Patient 2 treated


title: SAT6


title: adult forebrain, cell-selective, rep3

description:
CSRep3
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peakcalling.summary.txt
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peaks.bed.txt
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peaks.bed.mouse.annotation.txt


title: 293T WT-ZBTB3, ZBTB3, 1 Dox, rep2


title: adult forebrain, cell-selective, rep2

description:
CSRep2
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peakcalling.summary.txt
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peaks.bed.txt
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peaks.bed.mouse.annotation.txt


title: Sample1_C2D15

description: Patient 1 treated


title: 293T WT-ZBTB3, ZBTB3, 1 Dox, rep1


title: SAT5


title: adult forebrain, cell-selective, rep1

description:
CSRep1
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peakcalling.summary.txt
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peaks.bed.txt
Excitatory_neuron_specific_CIMERA-seq_sample_1-3_peaks.bed.mouse.annotation.txt


title: SAT4


title: Sample1_C1D1

description: Baseline for patient 1


title: 293T WT-ZBTB3, ZBTB3, 0.1 Dox, rep2


title: SAT3


title: adult forebrain, genome-wide, rep6

description:
Rep6
Forebrain_CIMERA-seq_sample_5-7_peakcalling.summary.txt
Forebrain_CIMERA-seq_sample_5-7_peaks.bed.txt
Forebrain_CIMERA-seq_sample_5-7_peaks.bed.mouse.annotation.txt


title: HCV_DAA_DMSO3

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

data_processing:
Reads in fastq format were aligned against human genome using RNA-STAR (--sjdbOverhang 49)
Human genes in ENSEMBL file Homo_sapiens.GRCh38.87.gtf were quantified using QoRTs.jar QC command (--stranded  --singleEnded)
Assembly: GRCh38
Supplementary files format and content: Text-tabulated file containing raw counts for each sample and gene annotations

source_name: Human hepatoma

extract_protocol:
Total RNA was extracted using  guanidiium thyocyanate and acid phenol a phase separation, with a final isopropanol precipitation. Total RNA was treated with DNAseI and re-extracted using the same method. Total RNA was depleted from ribosomal RNA using RiboZero following manufacturer´s instructions.
TruSeq Stranded Total RNA library Prep kit (Illumina)

value: Human hepatoma

tag: infection

value: HCV

tag: state

value: quiescent

value: DAA


title: 293T WT-ZBTB3, ZBTB3, 0.1 Dox, rep1

value: HEK 293T - ZBTB3 KO

tag: cell type


title: 293T WT-ZBTB3, ZBTB3, 0.01 Dox, rep2

value: Kidney


title: SAT8

value: subcutaneous adipose tissue


title: HCV_DAA_DMSO2


title: adult forebrain, genome-wide, rep5

description:
Rep5
Forebrain_CIMERA-seq_sample_5-7_peakcalling.summary.txt
Forebrain_CIMERA-seq_sample_5-7_peaks.bed.txt
Forebrain_CIMERA-seq_sample_5-7_peaks.bed.mouse.annotation.txt


title: adult forebrain, IgG negative control, rep2

description:
NegC Rep2
IgG_CIMERA-seq_sample_1-2_peakcalling.summary.txt
IgG_CIMERA-seq_sample_1-2_peaks.bed.txt
IgG_CIMERA-seq_sample_1-2_peaks.bed.mouse.annotation.txt


title: 293T K166A, ZBTB3, 0.01 Dox, rep1


title: SAT1


title: Sample2_C1D1

description: Baseline for patient 2

value: Skin (CTCL)

value: CTCL Tumor Cells