title: B14_c2

city: Chicago

first: Sarah

middle: J

last: Sun

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

description: multiplexed 10X single-cell capture

data_processing:
Sample preprocessing was performed using the count function in cellranger (v6.0.2).
We demultiplexed cells into individuals and respective vaccination conditions using demuxlet (Kang et al 2018)
We included cells that featured: a “singlet” status called by demuxlet, percent mitochondrial reads < 15%, and RNA read count (nCount_RNA) > 500
We calcualted pseudobulk estimates for each major immune cell cluster  by summing the raw UMI counts across all cells assigned to that sample for each gene using the sparse_Sums function in textTinyR (v1.1.4)
We filtered out lowly-expressed genes with logCPM values < 1
We used the function voom from the R package limma (Ritchie et al., 2015) to normalize the pseudobulk data
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: .mtx files include count values for each multiplexed sample; .tsv files include the description of barcodes (cells) and features (genes)

source_name: bone marrow biopsy

extract_protocol:
Cells were collected, washed, and prepared for single-cell capture using the 10X workflow. Immediately prior to the capture, cells from samples were combined into two pools (2 or 3 samples per pool), so that each pool was balanced for vaccination cohort and cells from each individual processed that day combined in an equal ratio.
Single-cell GEMs were generated using a Chromium Controller instrument (10x Genomics).
Library preparation were performed as described in the Single Cell 3’ Reagent Kits v3.1 User Guide (10X Genomics). Briefly, cDNA was cleaned with DynaBeads MyOne SILANE beads (ThermoFisher Scientific) and amplified in a thermal cycler using the following program: 98°C for 3 min, 11 cycles x 98°C for 15 s, 63°C for 20 s, 72°C for 1 min, and 72°C 1 min. After cleanup with the SPRIselect reagent kit (Beckman Coulter), the libraries were constructed by performing the following steps: fragmentation, end-repair, A-tailing, SPRIselect cleanup, adaptor ligation, SPRIselect cleanup, sample index PCR (98°C for 45 s, between 11 and 13 cycles x 98°C for 20 s, 54°C for 30 s, 72°C for 20 s, and 72°C 1 min), and SPRIselect size selection. Prior to sequencing, all multiplexed single-cell libraries were quantified using the KAPA Library Quantification Kit for Illumina Platforms (Roche) and pooled in an equimolar ratio. Libraries were sequenced 100 base pair (read1: 28, i7: 10, i5: 10, read2: 90) on an Illumina NovaSeq.

value: bone marrow biopsy

value: HSPCs

value: naïve, 90 days post placebo, and 90 days post BCG vaccination


title: ESCC_KYSE30-Luc-GFP, CD44 Positive (CD44 High group), rep1

status: Public on Aug 21 2024

type: SRA

city: Hong Kong

first: Ching Ngar

last: Wong

state: Hong Kong

address: Lab Block, 21 Sassoon Road,

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

library_source: transcriptomic

data_processing:
Software from Illumina (bcl2fastq) was used
Assembly: Human Genome GRCh38

molecule: polyA RNA

organism: Homo sapiens

source_name: ESCC cell line

growth_protocol: In vitro cell culture

extract_protocol:
Total RNA extraction
cDNA libraries prepared by KAPA mRNA HyperPrep Kit, targeting Poly-A containing mRNA

treatment_protocol: Antibody staining, flow cytometry cell sorting

tag: tissue

value: ESCC cell line

tag: cell line

tag: treatment

value: FACS CD44 Positive


title: PTEN_notcastrated

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed by CellRanger (version 3.1.0)
To reduce the ‘dropout’ phenomenon, RMagic package was used on gene-counts71
To filter the cells, we removed those that had more than 25% expression on mitochondrial genes, fewer than 100 total genes expressed and we considered only protein-coding genes defined using getBM (biomaRt package). All the samples were integrated using Seurat package (FindIntegrationAnchors and IntegrateData functions). Principal component analysis (PCA) dimensionality reduction considered the top 2000 most variable features identified. Moreover, the dimensional reduction technique t-distributed stochastic neighbor embedding (t-SNE) and UMAP were applied using the RunTSNE and RunUMAP functions from Seurat.
Differentially expressed genes (DEGs) were identified using FindAllMarkers or FindMarker functions (test.use=MAST). Genes were identified as differentially expressed in a particular set of cells if FDR < 0.05 and minimum expression in at least 30% of cells.
Assembly: mm10
Supplementary files format and content: Rmagic counts of all samples

molecule: total RNA

organism: Mus musculus

source_name: prostate

growth_protocol: Ptenpc−/− mice were maintained under specific pathogen-free conditions.

extract_protocol:
All prostate lobes were collected and processed to obtain a single-cell suspension. Tumors were collected 16 weeks after either sham-operation or surgical castration. Tissues were digested in Digestion Buffer composed by RPMI 1640 Normal medium, Collagenase D (1 mg/mL), DNAse (100 U/mL) and HEPES (25 mM), in the presence of RNase Inhibitor Murine (New England Biolabs). The cell suspension was incubated for 40 min at 37 °C on a rocker. The digestion was stopped adding Normal medium and cell suspension was filtered by a 100 mm cell strainer and kept on ice for 4 min. After further filtering, cell suspension was spun down at 1500 rpm for 5 min at 4°C and Cell subsets were enriched by FACS sorting. Flow Cytometry staining of tumors was performed using the following antibodies: anti-Epcam-FITC (clone G8.8), anti-CD45-bv605 (clone 30-F11), and anti-CD11b-bv421 (clone M1/70); and anti-Gr1-APC (clone RB6-8C5), and 7AAD (eBioscience). the 7AAD negative cells were sorted: i) Epcam+, ii) Epcam-/CD45+ and iii) Epcam-/CD45-. After counting, cells were mixed together in ratio 1:1:1 to perform single-cells sequencing.
Single-cell suspensions were processed with Single Cell 3′ Reagent Kit v3 (Chromium Single Cell 3′ Library & Gel Bead Kit v3, Chromium Single Cell G Chip Kit, 10x Genomics) and Chromium Controller (10x Genomics) according to the protocol at the BIOS+ Genomics Facility in Bellinzona. The generated libraries were sequenced using Illumina NextSeq500 Systems accordingly with the 10x Genomics manual.

treatment_protocol: Surgical castration was performed on 8-week-old Ptenpc-/- mice under anesthesia with isoflurane. Prostate tumors were resected from either 10-week-old, sham-operated (hormone-sensitive, HS) or castration-resistant (16 weeks after surgical castration, CR) 24-week-old Ptenpc−/− mice.

value: prostate

value: untreated


title: WT, INPUT, 8

city: Daegu

first: Hong-Yeoul

last: Ryu

state: Buk-Gu

address: Daehak-ro 80

department: Biotechnology

country: South Korea

institute: Kyungpook National University

library_source: genomic

data_processing:
All FASTA RAW sequences were quality controlled using FastQC v0.11.7
ChIP-seq reads were trimmed using Trimmomatic v0.38
ChIP-seq reads were aligned to the Saccharomyces cerevisiae reference genome (sacCer3) using BowTie v1.1.2
Peaks were called using MACS2 v2.1.1.20160309
Assembly: sacCer3
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

extract_protocol:
Formaldehyde was added to mid-log phase cells to a final concentration of 1% for 20 min. Crosslinking was quenched by addition of glycine to 240 mM. Crosslinked cells were collected via centrifugation, washed twice in TBS, and then lysed with glass beads in FA lysis buffer (50 mM HEPES–KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS, protease inhibitor cocktail [Roche, 11697498001], and 1 mM PMSF [AmericanBio, AB01620]).
ChIP-seq libraries were prepared using the TruSeq DNA Sample prep kit according to manufacturer's protocols (TruSeq ChIP Sample preparation guide 15023092 Rev. B) and sequenced using 100 bp paired-end sequencing on an Illumina NovaSeq 6000 following manufacturer’s protocols.

value: yeast cells

tag: genotype

value: WT

tag: chip antibody


title: Rad21_CTCFAID_ESC_auxin2d_ns_2

city: Miami

first: Danny

last: Reinberg

state: Florida

address: 1501 NW 10th Ave

department: Sylvester Cancer Center/Human Genetics

country: USA

institute: University of Miami

data_processing:
Sequence reads were mapped to mm10 reference genome with Bowtie 2.
After normalization with the spike-in Drosophila read counts for all (except for normalization with total counts for RAD21), normalized ChIP-seq read densities were visualized in Easeq Software and/or Integrative Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: mESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)).

extract_protocol:
Cells were lysed as described in Oksuz et al., 2018 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Diagenode Bioruptor. ChIP was performed by using antibodies listed. Chromatin fromDrosophila(1:100 ratio to ESC or MN derived chromatin), andDrosophila-specific H2Av antibody were used as spike-in control in each sample.
Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).

tag: cell type

value: Embryonic stem cells


title: Rad21_CTCFAID_MAZKO_B2_ESC_auxin2d_ns


title: DBA_F_noFC_EtOH_325_B

city: University Park

first: Laurel

last: Seemiller

state: PA

address: 314 Mueller Laboratory

institute: Pennsylvania State University

data_processing:
Raw reads were trimmed using fastp software to remove the low quality bases and nextera adapter sequences
Trimmed reads were mapped to the reference genome using hisat2
Gene-level raw counts were obtained using featureCounts specifying '-t exon -s 2 -O -g gene_id' parameters
Transcript-level counts were obatined using salmon specifying library type as '--libType SR'
Differential expression analysis for the different pairwise comparisons at both gene-level and transcript-level were done using DESeq2 package in R
Assembly: GRCm38
Supplementary files format and content: tab-delimited file with gene-level read counts for all samples
Supplementary files format and content: tab-delimited file with transcript-level read counts for all samples

source_name: dorsal hippocampus

extract_protocol:
Trizol and Qiagen RNeasy Kits were used to extract RNA.
Library preparation was performed using the TruSeq Stranded mRNA kit and sequencing was conducted using Illumina NextSeq High Output 75 nt single read sequencing.

treatment_protocol: Dorsal hippocampus tissue was dissected and placed in RNAlater. Samples were stored at 4C for 48 hours before being dry-blotted and stored at -80C until later processing

value: dorsal hippocampus

tag: strain

tag: Sex

value: F

tag: drug condition

value: EtOH

tag: fear conditioning_condition

value: noFC


title: WT, INPUT, 2


title: tho2d, Nrd1-TAP, ChIP, 2

value: TAP(GE Healthcare, 17-0969-01)


title: DBA_F_FC_SAL_325_C

value: Saline

value: FC


title: B13_c2

description: multiplexed 10X single-cell capture

value: bone marrow biopsy


title: Channel 1

city: Washington

first: Bicna

last: Song

state: DC

address: 7144 13th Pl NW

institute: Children's National Hospital

data_processing:
For each of the 16 channels, all three types of sequencing libraries (mRNA, sgRNA, cell hashing) were uniquely indexed with the same Illumina index sequence. This results in a single pair of fastq files for each channel, necessitating computational separation of the three library types. Transcriptomic reads were mapped using STAR and STARsolo 2.7.10a against a custom gtf annotation based on gencode.v34.annotation.gtf (hg38). Reads that did not map to the transcriptome reference were subsequently mapped and counted using STARsolo against a custom fasta reference containing guide sequences and a fasta reference with hash label sequences.
The output transcriptome matrices from STARsolo underwent initial filtering, akin to the 10x Cell Ranger EmptyDrops filtering method. This retained cells with at least 10% UMI count of the 99th percentile UMI counts of the top expected cells number. From these filtered matrices, an initial Seurat object was created using CreateSeuratObject function with parameters min.cells = 5, min.features = 10, and all other parameters at default values. Mitochondrial and mRNA content (percent.mt, nCount_RNA) were used to filter out outlier cells. To identify cell multiplets and determine cell population (untreated or activated), cell labels (hashes) were called using MULTI-seq approach (deMULTIplex::classifyCells in R). Only cells with exactly one known label were retained. Then, sgRNA calling was performed using a binomial test, with total sgRNA UMI counts used to derive background frequencies. A threshold of 0.05 on Benjamini-Hochberg- corrected p-values (per channel) was used to generate the final calls.
The sgRNA assays produced sparse matrices where a value of 1 indicates that the respective cell is carrying the corresponding sgRNA, and 0 elsewhere. Following these steps, results from 16 channels were merged together, and the merged counts were normalized using NormalizeData and scaled using ScaleData. Cell cycle scoring was performed via CellCycleScoring , PCA was calculated using RunPCA, and UMAP was calculated on first 30 principal components using RunUMAP in Seurat.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Perturb-seq

source_name: Jurkat

extract_protocol:
We chose the Jurkat E6 cell line expressing dCas9-KRAB as our model to study. We transduced them with a genome-wide CRISPRi CROP-seq library at a high multiplicity of infection (MOI). The FACS-measured percentage of GFP positive cells was 99.6%, translating to an estimated MOI of ~6. From experience, we know that real MOI is typically higher than what is estimated from GFP positivity rate. After infection, we split the cells into two populations, including untreated cells and activated cells (cells treated with anti-TCR and anti-CD28 antibodies for approximately 24 hours to stimulate TCR signaling). Cells were then labelled with cell hashing antibodies. Multiple labels were used for the activated population to help with cell multiplet detection. Cells were loaded on 16 channels of 10x Chromium X instrument. We loaded on 115,000 cells per channel and the expected recovery rate was 60,000 cells per channel, including 24% multiplets. Samples were pooled unequally before they were loaded on the Chromium X: 10% untreated cells, 90% treated cells. A sequencing library was prepared using 3’Chemistry with a targeted primer panel: custom multiplex PCR step to enrich for specific transcript. Libraries were sequenced on NovaSeq S4 PE100 in asymetric read mode (R1: 28 cycles; R2: 172 cycles), with PhiX concentration of 1%. The expected coverage is around 9,000 to 10,000 input reads per cell.
The genome-wide CRISPRi sgRNA library was designed to target the transcription start site (TSS) coordinates, calculated from publicly available FANTOM CAGE peaks data. In total 18,595 genes were targeted, with 4 sgRNAs per gene. Additionally, we designed another CRISPRi library targeting 3,220 genes with 4 sgRNAs per gene. This library was designed using TSS data specific to Jurkat cells, calculated from publicly accessible Jurkat CAGE-seq datasets. Both libraries were combined into a final library targeting 3,220 genes with 8 sgRNAs per gene and 15,375 genes with 4 sgRNAs per gene.

value: Jurkat

value: T cell


title: tho2d, Nrd1-TAP, ChIP, 8


title: DBA_F_FC_EtOH_325_A


title: DBA_F_noFC_SAL_325_D


title: WT, Nrd1-TAP, ChIP, 8


title: Rad21_CTCFAID_MAZKO_B2_ESC_untreat_ns


title: ChIP-seq H3K14ac 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

data_processing:
Sequence reads were aligned to the neurospora crassa genome (OR74A) using Bowtie2 (version 2.3.3) with default option.
Reads with low mapping quality (MapQ < 10) and from repetitive seuqnces were discarded.
Pileup score were calculated using Homer software (version 4.10.1).
ChIP-seq scores correspond to the total number of mapped tags after normalizing to 10 million reads.
Assembly: neurospora crassa genome (OR74A)
Supplementary files format and content: bigwig of pileup graph

organism: Neurospora crassa

growth_protocol: 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32oC (supplemented with histidine for strain N6279).

extract_protocol:
Lysates were cleared by centrifugation and 1/20th input was saved. H3K27me2/3 antibody (Active Motif, 2uL), H3K9ac antibody (Diagenode, 2 uL), or H3K14ac antibody (Millipore, 2 uL) was added and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl wash buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the Qiagen MinElute PCR purification kit and eluted in 30 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions. AMPure XP beads (Beckman Coulter A63881) were used for size selection of ~200-800 bp fragments. Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

treatment_protocol: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses.  Sonicated chromatin was lysed for 2 x 90s on a Mini-beadbeater-16 (Biospec Products) and then sheared using a Bioruptor (Diagenode) for 2 x 5 min with a cycle of 30 sec on followed by 30 sec off, at high power.

tag: antibody


title: Rad21_CTCFAID_ESC_untreat_ns_2


title: B12_c2

description: multiplexed 10X single-cell capture

value: HSPCs

value: naïve, 90 days post placebo, and 90 days post BCG vaccination


title: WT, Nrd1-TAP, ChIP, 2


title: MAZ_CTCFAID_MAZKO_B2_aux

value: MAZ (Abcam, ab85725)


title: DBA_M_noFC_EtOH_324_B

value: M


title: B13_c1

description: multiplexed 10X single-cell capture


title: DBA_M_noFC_SAL_324_D


title: ChIP-seq H3K14ac 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1


title: MAZ_CTCFAID_MAZKO_B2_ESC_auxin2d


title: B12_c1

description: multiplexed 10X single-cell capture


title: MAZ_CTCFAID_MAZKO_B2_noaux


title: DBA_M_FC_SAL_324_C


title: B14_c1

description: multiplexed 10X single-cell capture


title: B6_F_FC_SAL_323_C


title: ChIP-seq H3K14ac 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1


title: B11_c1

description: multiplexed 10X single-cell capture


title: ChIP-seq H3K9ac 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2


title: B10_c2

description: multiplexed 10X single-cell capture


title: B11_c2

description: multiplexed 10X single-cell capture


title: ChIP-seq H3K14ac 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2


title: DBA_M_FC_EtOH_324_A


title: B6_F_noFC_EtOH_323_B


title: B6_F_noFC_SAL_323_D


title: MAZ_CTCFAID_ESC_auxin2d_2


title: ChIP-seq H3K9ac 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1


title: MAZ_CTCFAID_MAZKO_B2_ESC_untreat


title: B10_c1

description: multiplexed 10X single-cell capture


title: MAZ_CTCFAID_aux


title: B6_M_noFC_SAL_322_D


title: MAZ_CTCFAID_noaux


title: ChIP-seq H3K9ac 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1


title: ChIP-seq H3K9ac 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2


title: MAZ_CTCFAID_ESC_untreat_2


title: B9_c2

description: multiplexed 10X single-cell capture


title: ChIP-seq H3K14ac ∆sds3 (∆NCU01599) strain: N8194

value: [delta]sds3 ([delta]NCU01599)


title: B6_M_FC_SAL_322_C


title: CTCF_CTCFAID_MAZKO_B2_aux

value: CTCF (Millipore, #07-729)


title: B8_c1

description: multiplexed 10X single-cell capture


title: ChIP-seq H3K14ac ∆sds3 (∆NCU01599) strain: N8193


title: B8_c2

description: multiplexed 10X single-cell capture


title: B7_c1

description: multiplexed 10X single-cell capture


title: B6_M_noFC_EtOH_322_B


title: B6_F_FC_EtOH_323_A


title: CTCF_CTCFAID_MAZKO_B2_ESC_auxin2d

value: Embryonic stem cells


title: B9_c1

description: multiplexed 10X single-cell capture


title: ChIP-seq H3K14ac ∆rlp2 (∆NCU02898) strain: N6708

value: [delta]rlp2 ([delta]NCU02898)


title: DBA_F_noFC_EtOH_321_B

value: dorsal hippocampus

value: F


title: DBA_F_FC_SAL_321_C


title: B7_c2

description: multiplexed 10X single-cell capture


title: ChIP-seq H3K14ac ∆rlp1 (∆NCU09007) strain: N8186

value: [delta]rlp1 ([delta]NCU09007)


title: DBA_F_noFC_SAL_321_D

value: noFC


title: ChIP-seq H3K14ac ∆rlp1 (∆NCU09007) strain: N8185


title: CTCF_CTCFAID_MAZKO_B2_ESC_untreat


title: B6_c2

description: multiplexed 10X single-cell capture


title: B6_M_FC_EtOH_322_A

value: EtOH


title: CTCF_CTCFAID_ESC_untreat_2


title: ChIP-seq H3K14ac ∆rlp2 (∆NCU02898) strain: N6706


title: CTCF_CTCFAID_noaux


title: B6_c1

description: multiplexed 10X single-cell capture


title: CTCF_CTCFAID_ESC_auxin2d_2


title: ChIP-seq H3K14ac WT strain: N3753

value: WT


title: B5_c1

description: multiplexed 10X single-cell capture

value: bone marrow biopsy


title: B5_c2

description: multiplexed 10X single-cell capture


title: CTCF_CTCFAID_aux


title: CTCF_CTCFAID_MAZKO_B2_noaux


title: DBA_M_FC_SAL_320_C

value: Saline

value: FC


title: DBA_M_noFC_SAL_320_D


title: DBA_M_noFC_EtOH_320_B


title: ChIP-seq H3K9ac ∆sds3 (∆NCU01599) strain: N8194


title: RAD21_E14_WT_rep2_ns_ch66


title: B4_c2

description: multiplexed 10X single-cell capture

value: HSPCs


title: RAD21_E14_Patz1KO_rep2_ns_ch65


title: RAD21_E14_WT_rep2_ns_ch65


title: B3_c1

description: multiplexed 10X single-cell capture

value: naïve, 90 days post placebo, and 90 days post BCG vaccination


title: ChIP-seq H3K9ac ∆rlp1 (∆NCU09007) strain: N8185


title: B6_F_noFC_SAL_319_D


title: ChIP-seq H3K9ac ∆sds3 (∆NCU01599) strain: N8193


title: B4_c1

description: multiplexed 10X single-cell capture


title: RAD21_E14_Patz1KO_rep2_ns_ch66


title: B3_c2

description: multiplexed 10X single-cell capture


title: B2_c2

description: multiplexed 10X single-cell capture


title: B6_F_FC_SAL_319_C


title: HA_E14_Patz1KO_rep2_ch66

value: HA (Abcam, ab9110)


title: B6_F_noFC_EtOH_319_B


title: ChIP-seq H3K9ac ∆rlp2 (∆NCU02898) strain: N6706


title: ChIP-seq H3K9ac ∆rlp2 (∆NCU02898) strain: N6708


title: ChIP-seq H3K14ac WT strain: N3752


title: DBA_F_FC_EtOH_321_A


title: B2_c1

description: multiplexed 10X single-cell capture


title: DBA_M_FC_EtOH_320_A

value: M


title: HA_E14_Patz1resc_rep2_ch66

source_name: PATZ1_Flag_HA_expressing WT E14 ESCs


title: B6_M_noFC_SAL_318_D


title: B6_F_FC_EtOH_319_A


title: ChIP-seq H3K9ac ∆rlp1 (∆NCU09007) strain: N8186


title: HA_E14_Patz1resc_rep3_ch68


title: HA_E14_Patz1KO_rep3_ch68


title: ChIP-seq H3K9ac WT strain: N3753


title: B1_c1

description: multiplexed 10X single-cell capture


title: B1_c2

description: multiplexed 10X single-cell capture


title: ChIP-seq H3K27me2me3 ∆sds3 (∆NCU01599) strain: N8193

value: [delta]sds3 ([delta]NCU01599)


title: B14

description: multiplexed 10X single-cell capture

data_processing:
Sample preprocessing was performed using the cellranger-atac (v2.0.0) function
We demultiplexed cells into individuals and respective vaccination conditions using demuxlet (Kang et al 2018)
We included cells with “singlet” demuxlet status and used parameters minTSS  = 4 and minFrags  = 1000 to further retain only cells with a sufficient signal to background ratio (high accessibility at transcription start sites) and at least 1000 unique nuclear fragments.
We called peaks using the ArchR function addReproduciblePeakSet which utilizes MACS2
We calculated pseudobulk estimates for each major immune cell cluster by summing the raw UMI counts across all cells assigned to that sample for each peak using the sparse_Sums function in textTinyR (v1.1.3)
We filtered out lowly-expressed peaks based on cluster-specific logCPM values (removed genes with a median logCPM < 1.25 for C12 and C15, 1.75 for C9 and C18, 2 for C23, 2.25 for C21, 2.5 for C17, and 1 for all other clusters)
We used the function voom from the R package limma (Ritchie et al., 2015) to normalize the pseudobulk data
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: .mtx files include count values for each multiplexed sample; .tsv file includes the description of barcodes (cells) and bed file describes peaks

extract_protocol:
Cells were collected, washed, and prepared for single-cell capture using the 10X workflow. Immediately prior to the capture, cells from samples were combined into two pools (2 or 3 samples per pool), so that each pool was balanced for vaccination cohort and cells from each individual processed that day combined in an equal ratio.
Single-cell GEMs were generated using a Chromium Controller instrument (10x Genomics).
Library preparation were performed as described in the Single Cell ATAC Reagent Kits v1.1 User Guide (10X Genomics). Briefly, post-incubation GEMs were cleaned up first with DynaBeads MyOne SILANE beads (ThermoFisher Scientific) and then with SPRIselect reagent (Beckman Coulter). Libraries were constructed by performing sample index PCR (98°C for 45 s, 9 or 10 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s, and 72°C 1 min) followed by SPRIselect size selection. Prior to sequencing, all multiplexed single-cell libraries were quantified using the KAPA Library Quantification Kit for Illumina Platforms (Roche) and pooled in an equimolar ratio. Libraries were sequenced 100 base pair (read1: 50, i7: 8, i5: 16, read2: 50) on an Illumina NovaSeq.


title: MAZ_E14_Patz1KO_rep3_ch68

value: MAZ (Abcam, ab85725)


title: B6_M_FC_EtOH_318_A


title: B12

description: multiplexed 10X single-cell capture


title: MAZ_E14_WT_rep2_ch66

value: Embryonic stem cells


title: RNA-seq 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2

description: Expression_change_after_TSA_treatment.xlsx

data_processing:
Sequence reads were aligned to the Neurospora crassa genome (OR74A) using STAR program (version 2.7.3a)
Total aligned reads per Neurospora gene were calculated using RSEM software (version 1.3.1) and normalized using DESeq2 software (version 1.24.0)
Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNaseI, amplification grade (Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
Assembly: Neurospora crassa genome (OR74A)
Supplementary files format and content: Excel file with average read count, log2FC, P-value, FDR and category (Up & Down)

growth_protocol: 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), supplemented with 1x histidine for N6279 strains, with TSA added to samples when indicated, shaking for 16 hours at 32oC.

extract_protocol:
Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNaseI, amplification grade (Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq kit (KAPA Biosystems).

treatment_protocol: Mycelia were harvested and added to a tube containing ~350uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at 4oC.

value: 0ul TSA


title: RNA-seq 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1

value: 5ul TSA


title: MAZ_E14_WT_rep3_ch68


title: CTCF_E14_Patz1KO_rep2_ch65

value: CTCF (Millipore, #07-729)


title: B13

description: multiplexed 10X single-cell capture


title: DBA_F_FC_EtOH_317_C

value: dorsal hippocampus

value: F


title: RNA-seq 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1


title: B10

description: multiplexed 10X single-cell capture


title: ChIP-seq H3K9ac WT strain: N3752


title: RNA-seq ∆sds3 (∆NCU01599) strain: N8193


title: CTCF_E14_Patz1KO_rep1_ch66


title: B6_M_FC_SAL_318_C


title: DBA_F_noFC_SAL_317_B

value: noFC


title: DBA_F_FC_SAL_317_A


title: B9

description: multiplexed 10X single-cell capture


title: RNA-seq ∆eaf-3 (∆NCU06788) strain: N6169

value: [delta]eaf-3 ([delta]NCU06788)


title: CTCF_E14_WT_rep2_ch65


title: B6_M_noFC_EtOH_318_B

value: EtOH


title: MAZ_E14_Patz1KO_rep2_ch66


title: DBA_M_noFC_EtOH_316_D


title: B8

description: multiplexed 10X single-cell capture

value: bone marrow biopsy


title: CTCF_E14_WT_rep1_ch66


title: RNA-seq 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2


title: RNA-seq ∆eaf-3 (∆NCU06788) strain: N5278


title: B11

description: multiplexed 10X single-cell capture


title: DBA_F_noFC_EtOH_317_D


title: PATZ1_KO_ESC rep2

data_processing:
Reads were aligned to mm10 reference genome using tophat 2.1.1 and bowtie2 2.3.1
Reads were assigned to the UCSC mm10 gene annotation
Counts were obtained by using featureCounts v1.6.2
Normalized differential expression (taking into account biological replicates) was calculated by using Deseq2.
Assembly: mm10
Supplementary files format and content: counts in txt format

source_name: E14 ESCs differentiated into cervical MNs

growth_protocol: mESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)). For motor neuron (MN) differentiation, the previously described protocol in Narendra et. al. (2015) was applied. Briefly, ESCs were differentiated into embryoid bodies in 2 days (Day 0) in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol). Medium was exchanged on Day 2 of differentiation, and further patterning of embryoid bodies was induced by supplementing the ANDFK media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

extract_protocol:
RNA was purified from cells with RNAeasy Plus Mini kit (Qiagen), and 1ug RNA was used for library preparation.
RNA was used to prepare automated TruSeq (Illumina) stranded RNAseq libraries by using RiboZero Gold library prepation according to manufacturer's protocols by NYU Genome Technology Center.

value: Motor Neurons

value: Patz1 -/-


title: B6

description: multiplexed 10X single-cell capture

value: HSPCs

value: naïve, 90 days post placebo, and 90 days post BCG vaccination


title: IVT, P1-cA

city: Suzhou

first: shaojun

last: Qi

address: B8, Lane 21, Dong Yan Li Rd, Suzhou Industry Park,Suzhou ,Jiang Su, China

department: Department of mRNA Sciences

country: China

institute: Suzhou Abogen Biosciences Co., Ltd.

library_source: other

data_processing:
basecalling by bcl2fastq v2.20.0.422
the first 10 bases at the head and the last base at the tail of sequence reads were trimmed using the Cutadapt tool (v4.5)
the universal Illumina adaptors were removed with Trimmomatic (v0.39)
low quality reads were filter out by NGSQCToolkit (v2.3)
aligned by BWA (v0.7.17) mem with default parameters
Assembly: CATGGCCGACAAGCAGAAGAACGGCATCAAGGCGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTGATAAACCGGTGCTGGAGCCTCGGTGGCCATGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCCTCGAGAAAAAAAAAAAACAAAAAAAAAAAACCAAAAAAAAAAAATAAAAAACTAATTAAAACAGCGGATGGGTACCCCACCATCCGACCCACTGGGTGTAGTACTCTGGTACTTCGTACCTTTGTACGCCTGTTCTTCCCATTGTACCCTTCCTGAACTTCCAACCCAAGTAACGTTAGAAGCTCAACATTTAGTACAACAGGAAGCACCACATCCAGTGGTGTTTAGTACAAGCACTTCTGTTTCCCCGGAGCGAGGTATAGGCTGTACCCACTGCCAAAAACCTTTAACCGTTATCCGCCAACCAACTACGTAAAAGCTAGTAGTATTATGTTTTTAACTAGGCGTTCGATCAGGTGGATTTCCCCTCCACTAGTTTGGTCGATGAGGCTAGGAATTCCCCACGGGTGACCGTGTCCTAGCCTGCGTGGCGGCCAACCCAGCTTATGCTGGGACGCCTTTTTATAGACATGGTGTGAAGACTCGCATGTGCTTGGTTGTGATTCCTCCGGCCCCTGAATGCGGCTAACCTTAACCCTGGAGCCTTGTGTCACAAACCAGTGATGATAAGGTCGTAATGAGCAATTCCGGGACGGGACCGACTACTTTGGGTGTCCGTGTTTCTTATTTTTCTTATTATTGTCTTATGGTCACAGCATATATATAACATATACTGTGATCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCTGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATAT
Supplementary files format and content: Excel file includes raw counts, counts covered the ligation point and indel ratio for each sample.

molecule: other

organism: synthetic construct

extract_protocol:
The RNA was purified either by precipitation with 7.5 M LiCl. 1 μg RNA was used for following library preparation.
The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina novaseq 6000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: synthetic RNA


title: DBA_M_noFC_SAL_316_B

value: M

value: Saline


title: IVT, ωA


title: B5

description: multiplexed 10X single-cell capture


title: IVT, ωU


title: DBA_M_FC_SAL_316_A

value: FC


title: B4

description: multiplexed 10X single-cell capture


title: WT_E14_ESC rep2

value: wild type


title: B3

description: multiplexed 10X single-cell capture


title: B6_F_noFC_EtOH_315_D


title: B6_F_FC_EtOH_315_C


title: WT_E14_ESC rep1


title: B7

description: multiplexed 10X single-cell capture


title: IVT, Arm-ωG

description: Sample 4

source_name: IVT, Arm-ωG


title: PATZ1_KO_ESC_rep2

data_processing:
Reads were aligned to mm10 reference genome using tophat 2.1.1 and bowtie2 2.3.1.0
Reads were assigned to the UCSC mm10 gene annotation
Counts were obtained by using featureCounts v1.6.2
Normalized differential expression (taking into account biological replicates) was calculated by using Deseq2.
Assembly: mm10
Supplementary files format and content: counts in txt format

value: Embryonic stem cells


title: B2

description: multiplexed 10X single-cell capture


title: IVT, ωC

description: Sample 5

source_name: IVT, ωC


title: B6_F_noFC_SAL_315_B


title: PATZ1_KO_ESC_rep3


title: IVT, Arm-Loop-ωG

description: Sample 3

source_name: IVT, Arm-Loop-ωG


title: DBA_M_FC_EtOH_316_C


title: B1

description: multiplexed 10X single-cell capture


title: PATZ1_KO_ESC_rep1


title: Jurkat HIV, unstimulated cells

description: 10x Genomics

data_processing:
The gene counting and CRISPR guide capture were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis).
Data normalization, dimensionality reduction, and clustering of data was performed using Seurat v4.3.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: We used a previously established cell line model of HIV latency. In this model, Jurkat cells were infected with an HIV vector with GFP tied to the LTR promoter, resulting in a positive GFP signal as a measurement of viral transcription reactivation and HIV latency reversal. These cells, which already express Cas9, were transduced with a lenti-sgRNA library.

extract_protocol:
Transduction was carried out on 850,000 cells at an MOI of 0.3 using 8ug/ml polybrene in 2 ml of RPMI containing 10% FBS and 1% penicillin-streptomycin. The media was replaced 24 hours later with fresh media without polybrene. Two days after transduction, the cells were selected for using 1.5 ug/ml puromycin for 5 days. After selection, the cell were split evenly into three groups. One third of the cells were kept in culture with no drug added, while two thirds of the cells were stimulated with PMA/I. After 16 hours, the stimulated cells were sorted into GFP+ and GFP- populations.
We designed Perturb-seq library that targets 10 protein-coding genes, which are either (1) known factors in HIV-1 virus expression and T cell activation (e.g., BIRC2), or (2) top hits from genome-scale CRISPR screens that we previously performed (e.g., BRD4).

value: Jurkat


title: IVT,  Loop-ωG

description: Sample 2

source_name: IVT,  Loop-ωG


title: PATZ1_KO_ESC rep1


title: B6_M_noFC_EtOH_314_D

value: dorsal hippocampus


title: WT_E14_ESC_rep3

source_name: WT E14 ESCs


title: B6_M_FC_EtOH_314_C


title: IVT, ΔSpacers-ωG

description: Sample 1

source_name: IVT, ΔSpacers-ωG


title: Jurkat HIV, stimulated cells, GFP-

description: 10x Genomics


title: WT_E14_ESC_rep2


title: B6_M_noFC_SAL_314_B


title: WT_E14_ESC_rep1


title: Jurkat HIV, stimulated cells, GFP+

description: 10x Genomics


title: 10 clones, pooled scRNA-seq

description: 10x Genomics

data_processing:
The gene counting and feature barcode processing were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis).
Data normalization, dimensionality reduction, and clustering of data was performed using Seurat v4.3.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: H1, HUES8

growth_protocol: The generation of KO hESCs were described in published studies, including HHEX KO H1 and HUES8 cell lines, FOXA1 KO HUES8 cell lines, OTUD5 KO HUES8 cell lines and CCDC6 KO H1 cell lines. Cells were regularly confirmed to be mycoplasma-free by the Memorial Sloan Kettering Cancer Center (MSKCC) Antibody & Bioresource Core Facility. KO and WT hESCs were maintained in Essential 8 (E8) medium (Thermo Fisher Scientific, A1517001) on vitronectin (Thermo Fisher Scientific, A14700) pre-coated plates at 37 °C with 5% CO2. The Rho-associated protein kinase (ROCK) inhibitor Y-276325 (5 µM; Selleck Chemicals, S1049) was added to the E8 medium the first day after passaging or thawing of hESCs.

extract_protocol:
One day before differentiation, each of 10 hESC barcoded clones were counted, mixed at the same cell number ratio and then seeded at a density of 2.3 × 105 cells/cm2 onto 12-well cell culture plate. At DE and PP2 stages, pooled differentiating cells were dissociated into single cell suspension by TrypLE Select for 5 min at 37 °C. Cells were then stored in BAMBANKER™ freezing medium for future experiments. For scRNA-seq, frozen cells were thawed and sorted to collect live GFP+ cells. Cellular suspensions were then loaded on a Chromium Controller following the manufacturer’s instructions (10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1 User Guide). cDNA libraries and targeted LARRY barcode libraries were generated separately using 10ul cDNA each. cDNA libraries were made under manufacturer’s instructions and targeted LARRY barcode libraries were amplified using specific primers (F: CTACACGACGCTCTTCCGATCT; R: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTtaaccgttgctaggagagaccataT).
Individual LARRY barcode constructs were cloned from LARRY barcode library (Addgene:140024) and transfected to 293T cells to generate lentivirus. Next, each KO and WT hESC clone was infected with a unique LARRY barcode at low MOI. One week after lentiviral infection, the barcoded cells, which expressed GFP, were sorted out and cultured in E8 medium as described in previous section.

value: H1, HUES8


title: IZE explants, ET 10d a

city: Katowice

first: Barbara

middle: Karolina

last: Wójcikowska

state: Silesia

address: Jagiellonska

department: Faculty of Natural Sciences; Institute of Biology, Biotechnology and Environmental Protection

country: Poland

institute: University of Silesia

data_processing:
Sequencing data were processed to obtain fastq files with bcl2fastq2 Conversion Software v2.19.0 (Illumina, San Diego, USA) including demultiplexing and adapter trimming steps.
The quality of the obtained sequencing data was assessed before the analysis and after each of its stages, using the FastQC tool (The Babraham Institue, Cambridge, United Kingdom) and MultiQC (Ewels et al., 2016) tools. All reads were trimmed to the length of 75 bp with BBduk (DOE Joint Genomes Institute, Walnut Creek, Ca, USA). Due to the high quality of the reads, they were only soft filtered and trimmed using Sickle tool (https://github.com/najoshi/sickle). The remaining ribosomal RNA reads were then removed using the SortMeRNA software.
Clean reads were mapped to the reference genome sequence assembly GCA_000001735.1 (TAIR10) with the splice-aware aligner STAR (Dobin et al., 2012) using two pass mode and parameters adjusted to the Arabidopsis thaliana genome annotation regarding mates gaps and intron lengths.
The quality of mapping was assessed with QualiMap (Okonechnikov et al., 2016) as well as SAMStat (Lassmann et al., 2011). Reads mapping to genes were counted using quantMode in STAR.
The analysis of differences in gene expression levels between samples was performed with the DESeq2 tool (Love et al., 2014) assuming negative binomial distribution and applying general linearized model with beta prior shrinkage.
Assembly: GCA_000001735.1 (TAIR10)
Supplementary files format and content: Raw feature counts with relation to genes: gene symbols are in rows, samples in columns.

organism: Arabidopsis thaliana

source_name: immature zygotic embryos

growth_protocol: Immature zygotic embryos (IZEs) at the cotyledonary stage of development were used as explants for the in vitro culture. A basal E0 medium contained 3.2 g L-1 of B5 micro and macro-elements (Duchefa Biochemie; #G0210), 20 g L-1 sucrose and 8 g L-l agar, pH 5.8. A standard medium for SE induction (EA) contained 5.0 μM of 2,4-D (Sigma-Aldrich #D7299). In addition, E0 medium supplemented with TSA (ET) (Sigma Aldrich; #T1952) at a concentration of 1.0 μM was applied for SE induction. Plant materials that were grown in sterile conditions were kept at 23°C under a 16 h photoperiod of 40 µM m-2 s-1 white, fluorescent light

extract_protocol:
An RNAqueous® Total RNA Isolation Kit (ThermoScientific) was used to isolate total RNA from the IZE explants induced on different media (E0, EA, ET) for 5 and 10 days. The freshly isolated tissues were wiped in frozen mortars. Depending on the age of the culture, from 250 (5th day) to 100 (10th day) explants were used for RNA isolation per repetition. RNA isolation, library preparation, and sequencing were produced in three biological replicates. The concentration and purity of RNA samples were evaluated with an ND-1000 spectrophotometer (NanoDrop Technologies). The integrity of the RNA was determined using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano chips (Agilent Technologies, Santa Clara, USA). RNA samples were treated with RNase-Free DNase and then purified using the Acid-Phenol: Chloroform with ammonium acetate method (ThermoScientific).
The sequencing libraries were prepared using Illumina ScriptSeq™ Complete Kit (Plant; Illumina, San Diego, USA) following the manufacturer’s protocol. Two micrograms of total RNA per sample were used as an input. Briefly, library prep involved the subsequent steps: ribosomal RNA removal with Ribo-Zero rRNA Removal Reagents (Plant Leaf; Illumina, San Diego, USA) followed by ethanol precipitation of the rRNA-depleted sample, RNA fragmentation, cDNA synthesis, RNA removal, terminal tagging of cDNA followed by bead cleanup, PCR amplification using Illumina indexes and final bead purification. The quality of the prepared Illumina libraries was analyzed using Agilent Bioanalyzer with the Agilent High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, USA), and the quantities were estimated using a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, USA). For cluster generation, the libraries were pooled with equimolar concentration and sequenced using the Illumina HiSeq 4000 system (Illumina, San Diego, USA) in 2x 76 cycles paired-end (PE) mode with 6 barcoded samples per lane.

treatment_protocol: IZE explants were treated by 5 or 10 day with 5.0 μM of 2,4-D (Sigma-Aldrich #D7299) (EA medium) or with TSA (ET) (Sigma Aldrich; #T1952) at a concentration of 1.0 μM.

value: immature zygotic embryos

tag: time

value: 10 day

tag: developmental stage

value: embryogenic culture

value: 1 µM TSA

tag: media

value: ET


title: B6_F_FC_SAL_315_A

value: F


title: DBA_F_FC_EtOH_313_C

value: EtOH


title: eCLIP_IgG_rep1

first: Mannan

last: Bhola

state: IL

address: 303 E Superior St

department: BMG

institute: Northwestern university

data_processing:
The quality control of raw data was evaluated with FastQC and MultiQC (Ewels et al., 2016b).
Reads were mapped uniquely with STAR v2.7.5 (Dobin et al., 2013) to the human genome (hg38).
FeatureCounts v2.0.3 (Liao et al., 2014) was used to get the read counts for eCLIP samples across all transcripts using GENCODE v45 annotation (Frankish et al., 2023).
Transcripts significantly enriched for TOP1 binding were determined by analyzing the differential enrichment of TOP1 IP over IgG using DESeq2 v1.38.3 (Love et al., 2014).
BigWig files were generated by calculating the log2 ratio as RPKM of the TOP1 IP with respect to IgG IP. The BigWig files were visualized in IGV (Thorvaldsdottir et al., 2013).
Assembly: hg38
processed data files format and content: BigWig
Library strategy: eCLIP-seq

growth_protocol: Human SW480 cells were grown at 37°C, supplied with 5% CO₂ in Dulbecco’s modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS.

extract_protocol:
TOP1-RNA complexes were separated by SDS-PAGE, transferred to a nitrocellulosemembrane, and RNA was extracted from the membrane using proteinase K (NEB).
3’ RNA adaptor was ligated onto the RNA with T4 RNA ligase. RNA was reverse transcribed with Superscript IV (Invitrogen), free primer was removed (ExoSap-IT, Affymetrix) and a 3’ DNA adaptor was ligated onto the cDNA product with T4 RNA ligase (NEB). Complementary DNA was amplified by PCR using Q5 Master Mix (NEB) and purified before Illumina sequencing. The sequencing was done using Illumina NextSeq 1000 with a read length configuration of 75bp for 40M reads per sample.

treatment_protocol: SW480 cells (20 × 10^6) were UV crosslinked (400 mJ/cm−2 at 254 nm) and saved at -80ºC until processing.

value: Colorectal Cancer Cell


title: WE_514-Trajectory

city: Qingdao

first: WEI

last: WANG

state: Shandong

address: 23 Hongkong east road haier building G zone

institute: Ocean University of China

data_processing:
Raw sequencing data was mapped to the reference genome using 10X Genomics’ Cell Ranger (Version 3.0.1) pipeline to generate UMI count matrix for the downstream analysis
Assembly: 20 SBC barcodes including the flanking sequences were added as pseudogenes to the Ciona robusta reference genome (http://ghost.zool.kyoto-u.ac.jp/download_ht.html).
Supplementary files format and content: Raw sequencing data was mapped to the reference genome using 10X Genomics' Cell Ranger (version 3.0.1) and three files including barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz were generated by Cell Ranger for downstream analysis.

organism: Ciona robusta

source_name: Embryo

extract_protocol:
Whole embryo cell suspension was loaded onto 10X Chromium chip for GEM generation
Expression Library was prepared according to the 10X Chromium Single Cell 3' Reagent Kits protocol

value: Embryo

value: whole embryo cell suspension

tag: age


title: eCLIP_TOP1_rep2


title: translocation_HSPC

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

country: Germany

institute: DKFZ (German Cancer Research Center)

data_processing:
Data was processed using the nfcore/hic v2.1.0 pipeline.
Reads were aligned to the reference genome using bowtie2.
Genome-wide contact maps were created using cooler.
Assembly: GRCh37/hg19
Supplementary files format and content: Multiresolution contact maps (.mcool format, resolution: 10000bp, 20000bp, 50000bp and 250000bp)

growth_protocol: Cell line ChiPSC22 and its t(7;12) derivatives were grown in the feeder free DEF-CS culture system (Cellartis/Takara Bio Europe) under standard conditions.

extract_protocol:
DNA was extracted and prepared as described in Rao et al. 2014. DNA was digested with the DpnII restriction enzyme.
Library construction was performed as described in Rao et al. 2014.

treatment_protocol: Before differentiation of CHIPSC22 and its t(7;12) derivatives to HSPCs, they were transferred to Matrigel (BD Biosciences, Stockholm, Sweden) and mTeSR1 medium (StemCell Technologies Inc., Grenoble, France) for 2-3 passages. They were then grown for 3-4 passages as clusters using Gentle Cell Dissociation Reagent (Stemcell Technologies Inc.). The STEMdiff Hematopoietic kit (Stemcell Technologies Inc.) was used for the differentiations according to the protocol. On day 12 of the differentiation, the hematopoietic cells were harvested and analyzed by ATAC-seq.

value: HSPC

value: translocation t(7;12)


title: IZE explants, ET 5d c

value: 5 day


title: DBA_F_noFC_SAL_313_B

value: Saline

value: noFC


title: wt_HSPC

value: wt


title: DBA_F_FC_SAL_313_A

value: dorsal hippocampus

value: FC


title: eCLIP_TOP1_rep1


title: IZE explants, ET 5d b

value: immature zygotic embryos


title: IZE explants, ET 5d a

value: embryogenic culture


title: DBA_M_noFC_EtOH_312_D

value: M


title: E3

city: Beijing

first: Ting

last: Zhang

address: Dongcheng District

institute: Beijing Municipal Key Laboratory of Child Development and Nutriomics

data_processing:
quality control with MultiQC
adapter and quality trimming with Cutadapt
transcript quantification with featureCounts
differential expression analysis (p value <0.05 and |log2foldchange| >1)
Assembly: grcm38.p6
Supplementary files format and content: fpkm,  tpm, read counts

source_name: hind leg muscles

extract_protocol:
The mice in the EX group were euthanized and killed by cervical dislocation 24 h after the last training. We used phosphate buffered saline (PBS) for transcardial perfusion and cadavers disinfected with 70% ethanol and placed the dissection table with the abdomen facing up. The hind leg muscles were removed and placed in the prepared petri dish, and eliminated the intermuscular fat removed [21]. The tissue samples were packaged and stored according to the requirements of each omics sequence: the size of soybean grains was required for transcription, the amount of tissue was required to reach 50-100 mg for metabolomics, >200 mg for proteomics and >500 mg for modified proteomics. The collected tissue samples were quickly frozen in liquid nitrogen and finally transferred to -80 °C for subsequent trials.
First, TRIzol reagent was used to extract total RNA from muscle tissue samples and purify it to ensure that the quality and concentration of RNA samples met the requirements of subsequent sequencing. Library was constructed and sequenced based on DNBseq platform (PE150 strategy). Low-quality sequences, such as head sequence, sequence with mass score <20, original reads with N-base ratio >10% and sequence less than 25bp, were removed from the RNA sequencing results.

value: hind leg muscles

value: the running distance of each mouse is 22 kilometers


title: IZE explants, ET 10d c

value: 10 day

value: 1 µM TSA

value: ET


title: IZE explants, EA 10d c

value: EA


title: translocation_iPSC

value: iPSC


title: wt_iPSC


title: DBA_M_FC_EtOH_312_C

value: EtOH


title: RPE p53-/-, CCAR1 knockout, replicate 5

city: Boston

first: Huy

last: Nguyen

state: MA

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

description:
C5
CCAR1_rnaseq_raw_counts.txt

data_processing:
Kallisto (version 0.48.0) was used to map the raw RNA-seq reads against the GENCODE human reference gene annotation (Release 44) and generate raw transcript abundance estimates.
The tximport Bioconductor R package was used to summarize the transcript abundance estimates to produce gene-level estimated counts.
Assembly: hg38
Supplementary files format and content: tab-delimited file with matrix table of raw gene counts for every gene and every sample

source_name: Eye; Pigmented epithelium; Retina

growth_protocol: RPE p53-/-  parental and CCAR1 knockout cells were grown in DMEM/F12 containing GlutaMAX (Gibco) and supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich).

extract_protocol:
RNA samples were prepared using RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN). RNA samples were quantified using Qubit 2.0 Fluorometer, and the RNA integrity was checked with 4200 TapeStation.
NEBNext Ultra II RNA Library Prep Kit for Illumina was used following the manufacturer’s recommendations (New England BioLabs). Briefly, mRNAs were initially enriched with Oligo d(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3´ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as by quantitative PCR (KAPA Biosystems). The sequencing libraries were clustered on flowcell lanes. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions.

value: Eye; Pigmented epithelium; Retina

value: epithelial cell

value: RPE p53-/-, CCAR1 knockout


title: IZE explants, EA 10d b


title: IZE explants, ET 10d b


title: RPE p53-/-, parental control, replicate 5

description:
P5
CCAR1_rnaseq_raw_counts.txt

value: RPE p53-/-, parental control


title: DBA_M_noFC_SAL_312_B

value: dorsal hippocampus

value: Saline

value: noFC


title: DBA_F_noFC_EtOH_313_D

value: F


title: E1


title: IZE explants, EA 10d a

value: immature zygotic embryos

value: embryogenic culture


title: DBA_M_FC_SAL_312_A

value: M

value: FC


title: IZE explants, EA 5d c

value: 5 day


title: C3

value: hind leg muscles

value: Con mice did not use treadmill training for hours.


title: RPE p53-/-, parental control, replicate 4

description:
P4
CCAR1_rnaseq_raw_counts.txt


title: C2


title: B6_F_noFC_EtOH_311_D


title: B6_F_FC_EtOH_311_C


title: B6_F_noFC_SAL_311_B


title: C1


title: E2

value: the running distance of each mouse is 22 kilometers


title: IZE explants, E0 10d c

value: 10 day

value: non-embryogenic culture

value: lack


title: IZE explants, EA 5d b

value: EA


title: B6_F_FC_SAL_311_A


title: IZE explants, EA 5d a


title: B6_M_noFC_EtOH_310_D

value: EtOH


title: nanos2

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

description: 10x Genomics

data_processing:
cellranger pipeline using default parameters with forced recovery of 10000 cells for each library
Assembly: PRJNA667495 from Zimmerman et al 2023 doi:10.1038/s41467-023-44080-7
Supplementary files format and content: extracted barcodes representing captured cells: barcodes
Supplementary files format and content: gene designation: features
Supplementary files format and content: extracted count matrix: matrix

organism: Nematostella vectensis

source_name: 2 month non-sexed animal

extract_protocol:
Whole juvenile was dissociated with collagenase.  Mechanical force was used to disrupt the tissues and obtain single-cell suspensions. Cell suspensions were washed with 0.1% BSA (bovine serum albumin), and cell viability and counts were assayed with a Cellometer X2 (Nexcelom). Cell suspensions were diluted to 1000 cells/ microliter and loaded into a 10x Genomics single cell platform using vs3 reagents.
10X Genomics Chromium v2/v3 chemistry according to manufacturer protocols

value: 2 month non-sexed animal

value: nanos2 mutant


title: tho2D-4

city: Ansan

first: Yan

last: Liu

state: Gyeonggi-do

address: 55 Hanyangdeahak-ro

department: Department of Molecular and Life Science

institute: Hanyang University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to Saccharomyces cerevisiae S288C (GCA_000146045.2_R64) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4d, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: Saccharomyces cerevisiae S288C (GCA_000146045.2_R64)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Saccharomyces cerevisiae S288C

source_name: yeast cell

growth_protocol: The yeast strains were grown in YPD until mid-log phase.

extract_protocol:
Total RNA was extracted from the cells with the use of an RNeasy Mini Kit (Qiagen) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Yeast cells were grown at 30°C in YPD.

value: yeast cell

value: THO2 knockout

value: YPD at 30℃


title: IZE explants, E0 10d b

value: immature zygotic embryos


title: RPE p53-/-, CCAR1 knockout, replicate 3

description:
C3
CCAR1_rnaseq_raw_counts.txt

value: Eye; Pigmented epithelium; Retina

value: epithelial cell

value: RPE p53-/-, CCAR1 knockout


title: IZE explants, E0 10d a


title: RPE p53-/-, parental control, replicate 3

description:
P3
CCAR1_rnaseq_raw_counts.txt

value: RPE p53-/-, parental control


title: B6_M_FC_EtOH_310_C

data_processing:
Raw reads were trimmed using fastp software to remove the low quality bases and nextera adapter sequences
Trimmed reads were mapped to the reference genome using hisat2
Gene-level raw counts were obtained using featureCounts specifying '-t exon -s 2 -O -g gene_id' parameters
Transcript-level counts were obatined using salmon specifying library type as '--libType SR'
Differential expression analysis for the different pairwise comparisons at both gene-level and transcript-level were done using DESeq2 package in R
Assembly: GRCm38
Supplementary files format and content: tab-delimited file with gene-level read counts for all samples
Supplementary files format and content: tab-delimited file with transcript-level read counts for all samples

source_name: dorsal hippocampus

extract_protocol:
Trizol and Qiagen RNeasy Kits were used to extract RNA.
Library preparation was performed using the TruSeq Stranded mRNA kit and sequencing was conducted using Illumina NextSeq High Output 75 nt single read sequencing.

value: dorsal hippocampus

value: M

value: FC


title: RPE p53-/-, CCAR1 knockout, replicate 2

description:
C2
CCAR1_rnaseq_raw_counts.txt


title: RPE p53-/-, CCAR1 knockout, replicate 4

description:
C4
CCAR1_rnaseq_raw_counts.txt


title: RPE p53-/-, CCAR1 knockout, replicate 1

description:
C1
CCAR1_rnaseq_raw_counts.txt


title: tho2D-3


title: IZE explants, E0 5d c

value: 5 day

value: non-embryogenic culture


title: WT-4

value: WT


title: B6_M_noFC_SAL_310_B

value: Saline

value: noFC


title: RPE p53-/-, parental control, replicate 1

description:
P1
CCAR1_rnaseq_raw_counts.txt


title: B6_M_FC_SAL_310_A


title: WT-3


title: IZE explants, E0 5d b

value: lack


title: CYGB-overexpression rep3

city: Antwerpen

first: Joey

last: De Backer

state: Antwerpen

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

data_processing:
mRNA sequencing via polyA selection
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38/hg38
Supplementary files format and content: Comma separated values file containing unique hit counts for each sampe

growth_protocol: A375 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum and antibiotics in a humidified atmosphere with 5% CO2 at 37 degrees celcius

extract_protocol:
RNA extraction and purification was performed using a PureLink RNA Mini Kit (Invitrogen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers,followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: No treatment was performed

value: melanoma

value: CYGB-overexpression

value: Untreated


title: RPE p53-/-, parental control, replicate 2

description:
P2
CCAR1_rnaseq_raw_counts.txt


title: AVC Group

city: Shanghai City

first: Yue

last: Dong

address: 800 Xiangyin Road

institute: Naval Medical University

description: metatranscriptomic sequence

data_processing:
The data were first cleaned by trimming adapters, removing low-quality sequences, and removing host reads, and the clean reads of each sample were mapped to reference sequence that was spliced by Trinity v2.4.0 (Cambridge, MA).
Assembly: For the clean reads obtained by preprocessing each sample, de novo assembly was performed with Trinity, then the sequence of all samples was integrated and repeat (set sequence identity threshold 0 .95) was deleted using CORSET to obtain unigene dataset.
Supplementary files format and content: The data were first cleaned by trimming adapters, removing low-quality sequences, and removing host reads, and the clean reads of each sample were mapped to reference sequence that was spliced by Trinity v2.4.0 (Cambridge, MA).

source_name: Nasal lavage fluid (NLF)

extract_protocol:
Total RNA was extracted from NLF using Trizol, and the RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
Upon confirming the RNA quality standards (total RNA ≥ 500ng, RNA integrity number ≥ 5.8), the RNA library for meta-transcriptome sequencing was prepared by depleting ribosomal RNA using an rRNA Removal Kit, fragmenting the RNA into 250-300 bp pieces, and reverse-transcribing these into cDNA. Subsequent steps included end repair, adenylation, and adaptor ligation. The library was then size-selected, amplified, and its concentration and insert size were validated using Qubit® fluorometer, Agilent 2100 Bioanalyzer, and qPCR before sequencing.

value: Nasal lavage fluid (NLF)

value: Ribavirin


title: CYGB-overexpression rep2


title: PBS Group

description: metatranscriptomic sequence

value: Vehicle


title: WT rep3


title: OPA1+/- cornea, 6 months, replicate #3

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

description:
M63_S14
M63_S14

data_processing:
For the RNA sequencing analysis, data analysis was performed with R, using the DESeq2 package. Corrected P-values (P-adjusted) were used, and P<0.05 was considered as significant.
Assembly: mm10
Supplementary files format and content: tab delimited files

source_name: cornea

extract_protocol:
Total RNA was extracted usingTrizol reagent and purified afterwards with Qiagen RNeasy kit following the manufacturer's procedure. Total RNA concentrations were measured with Qubit and quality was assessed using RNA ScreenTape Assay (Agilent TapeStation 4200).
500 ng of good quality (RIN >8.8) total RNA was ribo-depleted using Illumina's mammalian Ribo-Zero Magnetic Gold Kit HMN/Mouse/Rat (MRZG12324). Library preparation was completed on ribo-depleted RNA using the NEBNext Ultra Directional RNA Library prep kit (NEB, #E7420L) using 8 cycles of PCR amplification and indexed using single (i7) indexing. Indexed library preps from each sample were then pooled and sequenced with 75SE reads at a pool concentration of 1.4 pM on the NextSeq 500 using a NextSeq High Output 75 cycle flow cell (Illumina).

value: cornea

value: 6 months


title: IZE explants, E0 5d a

value: immature zygotic embryos


title: CYGB-overexpression rep1


title: OPA1+/- cornea, 6 months, replicate #4

description:
M64_S15
M64_S15


title: WT rep2


title: OPA1+/- cornea, 6 months, replicate #1

description:
M61_S12
M61_S12


title: OPA1+/+ cornea, 6 months, replicate #3

description:
C63_S11
C63_S11


title: OPA1+/+ cornea, 6 months, replicate #2

description:
C62_S10
C62_S10


title: OPA1+/+ cornea, 6 months, replicate #1

description:
C61_S9
C61_S9


title: Tissue sample from ccRCC patient ccRCC70

type: RNA

city: Singapore

first: Abner

last: Lim

address: 30 Hospital Boulevard

department: Division of Medical Oncology

country: Singapore

institute: National Cancer Center Singapore

description:
Tissue sample from ccRCC patient
total RNA from ccRCC was extracted from FFPE and profiled from Nanostring PanCancer IO360 Panel

scan_protocol: nCounter Analysis Platform

data_processing: nCounter Analysis Platform

label: No Labelling

source_name: Renal Cell Caccinoma - Tumor

extract_protocol: The samples was extracted from FFPE samples using Norgen RNA/DNA purification kit

tag: condition

value: ccRCC


title: WT_BAP_D7-A_S22_L003

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (GRCh38) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified by using FeatureCount (Version 2.0.1) with mouse genome as a reference and were adjusted to provide CPM (Counts per million mapped reads). Principal component analysis (PCA) and cluster analysis were performed by using R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) was identified by using edgeR in R. The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology (GO) and KEGG pathways in R.
Assembly: GRCh38
Supplementary files format and content: txt, normalized read counts

source_name: hESC BAPD7

extract_protocol:
RNA isolation from cultured cells was used Trizol reagent.
RNA-seq libraries were prepared using the NEBNext RNA Library Prep Kit (New England Biolabs, NEB) .

treatment_protocol: TSC lines CT27 (female) and CT-29 (male) were obtained from the RIKEN Cell Engineering Division (https://cell.brc.riken.jp/en/) and cultured as previously described (Okae). In brief, stem-state CTB cells were plated on plates pre-coated with 5 μg/mL collagen IV (Corning, cat # 354277) and maintained in stem state medium containing DMEM/F12 with 0.3 % w/v bovine serum albumin (BSA, FisherSci, BP9704100), 1X insulin, transferrin, selenium- ethanolamine supplement ( ITS-X, ThermoFisher, cat # 51500056), 0.2 % v/v fetal bovine serum (FBS, ThermoFisher, cat # 16141061), 0.1 mM 2-mercaptoethanol, 50 ng/mL epidermal growth factor, 1.5 μg/mL L-ascorbic acid, 0.8 mM valproic acid, 5 μM Y27632 (ReproCell, cat #04-0012), 2 μM CHIR99021 (ReproCell, cat #04-0004), 0.5 μM A83-01 (ReproCell, cat #04-0004), and 1 μM SB431542 (ReproCell, cat #04-0010). Monolayers were rinsed with phosphate-buffered saline, dispersed to single cells with TrypLE Express for approximately 15 min, and passaged at 75% confluence. Undifferentiated TSC were collected for as CTB for downstream analysis.  To induce STB differentiation in TSC, cells were passaged to a plate coated with 2.5 μg/mL collagen IV and seeded at 1 x 105 cells per 35 mm well of a 6 well plate. Cells were differentiated over the course of 6 ds in medium containing DMEM/F12 with 0.3% w/v BSA, 1X ITS-X, 0.1 mM 2-mercaptoethanol, 2.5 μM Y27632, 2 μM Forskolin, and 4% v/v Knockout Serum Replacement (KSR) with medium changes every other day.  To induce EVTB/MTB differentiation in TSC, cells were passaged to a plate coated with 1 μg/mL collagen IV and seeded at 1 x 105 cells per 35 mm well of a 6 well plate. Cells were differentiated over the course of 6 d in medium containing DMEM/F12 with 0.3 % w/v BSA, 1X ITS-X, 0.1 mM 2-mercaptoethanol, 2.5 μM Y27632, 7.5 μM A83-01, 100 ng/mL NRG1, 2% Matrigel, and 4 % v/v KSR with medium changes every other day. On d 3 of differentiation, medium was exchanged with the above recipe without NRG1. On d 6, medium was exchanged with the above recipe without NRG1 and KSR and cells were passaged a final time to enhance EVTB differentiation.   Human embryonic stem cell (hESC) lines H1 (WA01, male, XY) and H9 (WA09, female, XX) were obtained from the WiCell Research in Madison, WI (Thomson et al.) Cells were seeded at a density of 50,000 cells/well onto Matrigel (Corning)-coated 6-well plates in mTESR1 medium (Stem Cell Technologies). Cells were then cultured in basal DMEM/F12 with 20 % v/v KOSR, non-essential amino acids, 2mM L-glutamine, and FGF2 (4 ng/mL)  for 24 h. The trophoblast phenotype was initiated using an established protocol (Amita). Medium was exchanged with the same recipe without FGF2, and additional supplementation of BMP4 (10 ng/mL), A83-01 (1 µm), and PD173074 (0.1 µm) (BAP) each day over the course of 8 days. Upon completion of BAP treatment, cells were dispersed and passed through a cell strainer to separate small, CTB-like cells (<40 μm) and large, STB-like cells (>70 μm) (Yabe; {Yabe, 2016 #8777}. After separation, cells were centrifuged and snap frozen for downstream assays. All cell culture was completed at 37 °C in a humidified incubator at 5% CO2 and atmospheric oxygen.

value: Trophoblasts

value: BAP


title: OPA1+/- cornea, 6 months, replicate #2

description:
M62_S13
M62_S13


title: Tissue sample from ccRCC patient ccRCC63


title: Hipocamppus_009

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

hyb_protocol: GeneChip Hybridization, Wash and Stain kit was used for hybridization in a GeneChip Hybridization oven 640 and in a GeneChip Fluidics Station 450 using the protocol FS450-0007, as explained in the protocol provided by Affymetrix.

scan_protocol: Arrays were scanned in a GeneChip 7G scanner and analysed in Affymetrix GeneChip Command Console Scan Control v4.0.0.1567.

data_processing: Transcriptome Analysis Console 4.0 software was used for normalization, detection and summarization purposes, applying Gene Level - SST-RMA algorithm.

label: biotin

source_name: brain hippocampus

label_protocol: Biotinylated single-stranded cDNA were prepared using GeneChip Pico kit according to the Affymetrix protocol from 5 ng total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Human brain hippocampi were isolated and kept frozen until used for RNA isolation.


title: Hipocamppus_80


title: WT_BAP_D3-C_S12_L002

source_name: hESC BAPD3


title: Tissue sample from ccRCC patient ccRCC69


title: Tissue sample from ccRCC patient ccRCC62


title: Hipocamppus_007


title: Hipocamppus_77


title: Tissue sample from ccRCC patient ccRCC67


title: Tissue sample from ccRCC patient ccRCC52


title: WT rep1


title: WT_BAP_D7-C_S24_L003


title: WT_BAP_D3-A_S10_L002


title: Tissue sample from ccRCC patient ccRCC51


title: Hipocamppus_82


title: WT_BAP_D7-B_S23_L003


title: WT_Ctrl-C_S9_L002

source_name: hESC CTRL

value: Embryonic stem cells

value: Control


title: Tissue sample from ccRCC patient ccRCC64


title: Tissue sample from ccRCC patient ccRCC50


title: OPA1+/- cornea, 3 months, replicate #4

description:
M34_S8
M34_S8

value: 3 months


title: Tissue sample from ccRCC patient ccRCC65


title: Tissue sample from ccRCC patient ccRCC48


title: Hipocamppus_322


title: WT_Ctrl-A_S7_L002


title: Hipocamppus_004


title: Hipocamppus_003


title: Hippocampus_152


title: T9C_CKDL220007706-1a-N701-N503_HN2WWDSX3_L4

value: Differentiated


title: Hipocamppus_229


title: OPA1+/- cornea, 3 months, replicate #3

description:
M33_S7
M33_S7


title: WT_BAP_D3-B_S11_L002


title: Tissue sample from ccRCC patient ccRCC47


title: OPA1+/- cornea, 3 months, replicate #2

description:
M32_S6
M32_S6


title: T8C_CKDL220007706-1a-N710-N502_HN2WWDSX3_L4


title: OPA1+/- cornea, 3 months, replicate #1

description:
M31_S5
M31_S5


title: Hipocamppus_002


title: OPA1+/+ cornea, 3 months, replicate #4

description:
C34_S4
C34_S4


title: Hippocampus_008


title: OPA1+/+ cornea, 3 months, replicate #2

description:
C32_S2
C32_S2


title: OPA1+/+ cornea, 3 months, replicate #3

description:
C33_S3
C33_S3


title: WT_Ctrl-B_S8_L002


title: Tissue sample from ccRCC patient ccRCC39


title: Hipocamppus_005


title: CAR T CD45 scRNAs

city: Chapel Hill

first: Mark

last: Woodcock

state: NC

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

description: 10x Genomics

data_processing:
Sequencing reads were mapped to mm10, and unique molecular identifier (UMI) counts were collapsed based on the 10x Genomics Cell Ranger software (version 6.1.2). Resulting datasets were analyzed via the Seurat package (v4.0.4) in R (v4.1.1).
Assembly: Sequencing reads were mapped to mm10,
Supplementary files format and content: Tap-separated values files and matrix files

source_name: Melanoma tumor

extract_protocol:
Mice bearing B16-OVA-hCD19 tumors received non-transduced T cells, CAR.CD19 T cells or CAR.CD19 NKTs and 16 days later, CD45+ cells were sorted from multiple pooled tumors from each group and processed for single-cell RNA sequencing analysis.
Barcoding and library preparation were performed following manufacture instructions with the 10x Genomics Chromium Next GEM Single Cell 3’ kit v3.1.

value: Melanoma tumor

value: Immune cells in the Melanoma

value: Wild type

value: CAR T


title: Hipocamppus_001


title: ChIP-seq H3K27me2me3 ∆rlp1 (∆NCU09007) strain: N8186

first: Hideki

last: Tanizawa

address: Kita 15, Nishi 7, Kita-ku

institute: Hokkaido University

data_processing:
Sequence reads were aligned to the neurospora crassa genome (OR74A) using Bowtie2 (version 2.3.3) with default option.
Reads with low mapping quality (MapQ < 10) and from repetitive seuqnces were discarded.
Pileup score were calculated using Homer software (version 4.10.1).
ChIP-seq scores correspond to the total number of mapped tags after normalizing to 10 million reads.
Assembly: neurospora crassa genome (OR74A)
Supplementary files format and content: bigwig of pileup graph

extract_protocol:
Lysates were cleared by centrifugation and 1/20th input was saved. H3K27me2/3 antibody (Active Motif, 2uL), H3K9ac antibody (Diagenode, 2 uL), or H3K14ac antibody (Millipore, 2 uL) was added and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl wash buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the Qiagen MinElute PCR purification kit and eluted in 30 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions. AMPure XP beads (Beckman Coulter A63881) were used for size selection of ~200-800 bp fragments. Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

value: [delta]rlp1 ([delta]NCU09007)


title: T5C_CKDL220007706-1a-N705-N502_HN2WWDSX3_L4

value: undifferentiated


title: Tissue sample from ccRCC patient ccRCC35


title: OPA1+/+ cornea, 3 months, replicate #1

description:
C31_S1
C31_S1


title: Tissue sample from ccRCC patient ccRCC46


title: ChIP-seq H3K27me2me3 ∆rlp1 (∆NCU09007) strain: N8185


title: Tissue sample from ccRCC patient ccRCC43


title: Hippocampus_85


title: CAR NKT CD45 scRNAs

description: 10x Genomics

value: CAR NKT


title: ChIP-seq H3K27me2me3 ∆rlp2 (∆NCU02898) strain: N6708

value: [delta]rlp2 ([delta]NCU02898)


title: T7C_CKDL220007706-1a-N707-N502_HN2WWDSX3_L4


title: Hipocamppus_006


title: NT NKT CD45 scRNAs

description: 10x Genomics

value: NT NKT


title: pCas13d alone, 4hpf, rep2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description:
pCas13d_rep2
G4 sequencer from Singular Genomics
znf281b_KD_TPMs.csv

data_processing:
Raw reads from zebrafish oocytes (stages I-IV) and embryos (0-, 2-, 4-, and 6-hours post fertilization) were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl-convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner (version 2.7.3a), using Ensembl 106 gene models. Counts were converted to TPM values using RSEM (version v1.3.0) and all subsequent analysis was done using TPM.
Assembly: danRer11 Ensembl 106 gene models
Supplementary files format and content: comma-separated files with TPMs from all replicates

organism: Danio rerio

source_name: Whole embryo

extract_protocol:
Isolated oocytes were snap-frozen and RNA was extracted with TRIzol (Invitrogen #15596026) following manufacturer’s protocols. 0-, 2-, 4- and 6-hpf zebrafish embryo RNA was extracted with Direct-zol RNA MicroPrep kit (Zymo Research #R2062) following manufacturer’s protocols.
Zebrafish embryos (0-, 2-, 4-, and 6-hours post fertilization) total RNA sequencing libraries were generated from 500ng of high-quality total RNA, as assessed using Bioanalyzer (Agilent). Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold (Illumina #20020598), and TruSeq RNA Single Indexes Sets A and B (Illumina #20020492 and #20020493). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Life Technologies). Libraries were pooled, quantified, and sequenced as 75bp single reads on a high-output flow cell using the Illumina NextSeq500 instrument. Following sequencing, Illumina Primary Analysis (version RTA 2.11.3.0) and bcl-convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes (stages I-IV) total RNA-Seq libraries were generated from 100 ng of high-quality total RNA, as assessed by a Bioanalyzer (Agilent Technologies). Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, Cat. No. 20020598), and TruSeq RNA Single Indexes; Sets A and B (Illumina Cat. No. 20020492 and 20020493). Resulting short-fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer (Life Technologies). Libraries were normalized, pooled, and sequenced on a NextSeq 500 instrument (Illumina), as 75 bp single-end reads on a high-output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing, Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent), with the Watchmaker mRNA Library Prep Kit (Watchmaker, Cat. No. 7BK0001) at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification, 2 µL of IDT indexed primers (using xGen™ Stubby Adapter-UDI Primers, 96 reactions, Cat No. 10005921) was added to 3 µL of library, and 5 µL of Equinox Amplification Master Mix (2x). These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect (Beckman Coulter, Cat. No. B23318) bead ratio was used during the Post-Amplification Cleanup, and post amplification libraries were eluted in 10 µL of Qiagen EB (Qiagen, Cat. No. 19086). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer (Life Technologies). Equal molar libraries were pooled, quantified, and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit, following the “Adapting Libraries for the G4 – Retaining Original Indices” protocol. The converted pool was sequenced on an F2 flow cell (Cat. No. 700104) on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit (Cat. No. 700141), using Instrument Control Software G4-23.08.1-1 with the following read length: 8 bp Index1, 50 bp Read1, and 8 bp Index2, 50 bp Read 2. Following sequencing, sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.

value: Whole embryo

value: AB, TF and TLF


title: ChIP-seq H3K27me2me3 ∆sds3 (∆NCU01599) strain: N8194

city: Sapporo

value: [delta]sds3 ([delta]NCU01599)


title: T6C_CKDL220007706-1a-N706-N502_HN2WWDSX3_L4

value: Trophoblasts


title: Tissue sample from ccRCC patient ccRCC37

value: ccRCC


title: T41C_CKDL220007706-1a-N707-N505_HN2WWDSX3_L4


title: NT T CD45 scRNAs

description: 10x Genomics

value: NT T


title: RNA-seq ∆rlp1 (∆NCU09007) strain: N8185

data_processing:
Sequence reads were aligned to the Neurospora crassa genome (OR74A) using STAR program (version 2.7.3a)
Total aligned reads per Neurospora gene were calculated using RSEM software (version 1.3.1) and normalized using DESeq2 software (version 1.24.0)
Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNaseI, amplification grade (Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
Assembly: Neurospora crassa genome (OR74A)
Supplementary files format and content: Excel file with average read count, log2FC, P-value, FDR and category (Up & Down)

extract_protocol:
Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNaseI, amplification grade (Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq kit (KAPA Biosystems).


title: Tissue sample from ccRCC patient ccRCC23


title: Tissue sample from mRCC patient with ICB treatment RCC2

description:
Tissue sample from mRCC patient with ICB treatment
total RNA from mRCC was extracted from FFPE and profiled with Nanostring PanCancer IO360 Panel

source_name: Renal Cell Carcinoma - Tumor

value: mRCC


title: T40C_CKDL220007706-1a-N706-N505_HN2WWDSX3_L4

value: Differentiated


title: T54C_CKDL220007706-1a-N705-N508_HN2WWDSX3_L4

value: BAP


title: znf281b KD, 4hpf, rep1

description:
znf281b_KD_rep1
G4 sequencer from Singular Genomics
znf281b_KD_TPMs.csv


title: RNA-seq ∆rlp2 (∆NCU02898) strain: N6707


title: Tissue sample from ccRCC patient ccRCC33


title: T53C_CKDL220007706-1a-N704-N508_HN2WWDSX3_L4


title: RNA-seq ∆rlp2 (∆NCU02898) strain: N6706


title: Zebrafish Oocyte, Stage IV, rep2

source_name: Oocyte

extract_protocol:
Isolated oocytes were snap-frozen and RNA was extracted with TRIzol (Invitrogen #15596026) following manufacturer’s protocols. 0-, 2-, 4- and 6-hpf zebrafish embryo RNA was extracted with Direct-zol RNA MicroPrep kit (Zymo Research #R2062) following manufacturer’s protocols.
Ribo-dep Stranded RNA-Seq
Zebrafish embryos (0-, 2-, 4-, and 6-hours post fertilization) total RNA sequencing libraries were generated from 500ng of high-quality total RNA, as assessed using Bioanalyzer (Agilent). Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold (Illumina #20020598), and TruSeq RNA Single Indexes Sets A and B (Illumina #20020492 and #20020493). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Life Technologies). Libraries were pooled, quantified, and sequenced as 75bp single reads on a high-output flow cell using the Illumina NextSeq500 instrument. Following sequencing, Illumina Primary Analysis (version RTA 2.11.3.0) and bcl-convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes (stages I-IV) total RNA-Seq libraries were generated from 100 ng of high-quality total RNA, as assessed by a Bioanalyzer (Agilent Technologies). Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, Cat. No. 20020598), and TruSeq RNA Single Indexes; Sets A and B (Illumina Cat. No. 20020492 and 20020493). Resulting short-fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer (Life Technologies). Libraries were normalized, pooled, and sequenced on a NextSeq 500 instrument (Illumina), as 75 bp single-end reads on a high-output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing, Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.

value: Oocyte

value: Stage IV


title: Hypothalamus, 180 day, M6-5

city: Tai'an

first: Qing

last: Li

address: Tai’an, Shandong Province, P.R. China

institute: College of Animal Science and Veterinary Medicine

data_processing:
Clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNAs. miRBase20.0 was used as the reference, and the modified software mirdeep2 and sRNA-tools-cli were used to obtain the potential miRNA and draw the secondary structures. The software miREvo and mirdeep2 were integrated to predict novel miRNAs.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Assembly: ARS1.2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

organism: Capra hircus

source_name: hypothalamus

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: hypothalamus

value: 180 day


title: Tissue sample from ccRCC patient ccRCC31


title: T39C_CKDL220007706-1a-N705-N505_HN2WWDSX3_L4


title: ChIP-seq H3K27me2me3 ∆rlp2 (∆NCU02898) strain: N6706


title: RNA-seq ∆rlp1 (∆NCU09007) strain: N8186

value: [delta]rlp1 ([delta]NCU09007)


title: Zebrafish Oocyte, Stage IV, rep1


title: Tissue sample from ccRCC patient ccRCC29


title: T4C_CKDL220007706-1a-N704-N502_HN2WWDSX3_L4

value: undifferentiated


title: Hypothalamus, 180 day, M6-3


title: pCas13d alone, 4hpf, rep1

description:
pCas13d_rep1
G4 sequencer from Singular Genomics
znf281b_KD_TPMs.csv


title: Tissue sample from ccRCC patient ccRCC25


title: RNA-seq ∆sds3 (∆NCU01599) strain: N8194


title: T42C_CKDL220007706-1a-N710-N506_HN2WWDSX3_L4


title: Retina_18w_S02

city: Leuven

first: Lieve

last: Moons

address: Naamsestraat 61

department: Biology

institute: KU Leuven

description: 10x Genomics 3' scRNA-seq

data_processing:
Sequencing reads were mapped to the custom build transcriptome using CellRanger (v7.0.1)
Mapped scRNA-seq data was processed in Monocle 3 (monocle3_1.2.9)
Assembly: PRJEB5837
Supplementary files format and content: Comma-separated value files and matrix files

organism: Nothobranchius furzeri

source_name: Neural Retina

growth_protocol: Killifish of the GRZ-AD inbred strain were housed in a standarised system maintaining constant pH (7.0), conducitivty (600µs) and temperature (28,0°C).

extract_protocol:
Fish were euthanized using 0.1% tris buffered tricaine. Retinas were collected in complete L15 (Leibovitz 15 medium complemented with 2% Penicilin-Streptomycin, 0.5% Gentamycin, 2% heat-inactivated Fetal Bovin Serum, 1% Glutamax, 2% MEM Essential Amino Acids, 2% B27, 25 mM D-Glucose, 25 mM HEPES and brought to pH7.4) after retinal pigment epitheluim removal. Retinas were rinsed three times with complete L15 before enzymetic digesting using papain (16 U/ml) for 30 min at 28°C.  Before mechinal tritruation in sterile PBS with 1% bovine serum albumine (fraction V), digested retinas were rinsed three times with complete L15. Cell clumps were removed using a 40 µm cell strainer.
scRNA-seq was performed using standard 10x Genomics v3 3' sequencing protocol.

value: Neural Retina

value: Wildtype

value: 18 weeks


title: znf281b KD, 4hpf, rep2

description:
znf281b_KD_rep2
G4 sequencer from Singular Genomics
znf281b_KD_TPMs.csv

value: Whole embryo

value: AB, TF and TLF


title: Zebrafish Oocyte, Stage II, rep2

value: Stage II


title: T35C_CKDL220007706-1a-N702-N508_HN2WWDSX3_L4

value: Trophoblasts


title: Zebrafish Oocyte, Stage II, rep1


title: Retina_12w_S02

description: 10x Genomics 3' scRNA-seq

value: 12 weeks


title: Hypothalamus, 120 day, M4-5

value: 120 day


title: pCas13d alone, 4hpf, rep3

description:
pCas13d_rep3
G4 sequencer from Singular Genomics
znf281b_KD_TPMs.csv


title: Zebrafish Oocyte, Stage I, rep2

value: Stage I


title: T3C_CKDL220007706-1a-N703-N502_HN2WWDSX3_L4


title: znf281b KD, 4hpf, rep3

description:
znf281b_KD_rep3
G4 sequencer from Singular Genomics
znf281b_KD_TPMs.csv


title: Tissue sample from mRCC patient with ICB treatment RCC1

value: mRCC


title: T37C_CKDL220007706-1a-N703-N505_HN2WWDSX3_L4

value: Differentiated


title: Retina_12w_S01

description: 10x Genomics 3' scRNA-seq


title: T33C_CKDL220007706-1a-N703-N506_HN2WWDSX3_L4

value: BAP


title: Retina_06w_S01

description: 10x Genomics 3' scRNA-seq

value: 6 weeks


title: Hypothalamus, 180 day, M6-4

value: hypothalamus

value: 180 day


title: RNA-seq WT strain: N3753

value: WT


title: T38C_CKDL220007706-1a-N704-N505_HN2WWDSX3_L4


title: Zebrafish Oocyte, Stage III, rep2

value: Oocyte

value: Stage III


title: T2C_CKDL220007706-1a-N702-N502_HN2WWDSX3_L4

value: undifferentiated


title: Zebrafish Embryo, 4hpf, rep3

value: Whole embryo


title: Zebrafish Oocyte, Stage III, rep1

value: AB, TF and TLF


title: RNA-seq WT strain: N3752


title: Hypothalamus, 180 day, M6-2


title: PATZ1_KO_ESCs

city: Miami

first: Danny

last: Reinberg

address: 1501 NW 10th Ave

institute: University of Miami

description:
Patz1 KO ESCs
microc_hiccompare_WT_v_KO_ESC.results_related_to_Fig_S12E.txt

data_processing:
The raw data was processed by Dovetail pipeline into the processed files.
Assembly: mm10
Supplementary files format and content: hic
Library strategy: Micro-C sequencing

source_name: Embryonic stem cells

extract_protocol:
Cells were processed according to the Dovetail Micro-C kit instructions. Briefly, they were trypsinized, counted, washed with 1X PBS and frozen in the recommended numbers at -80 C. They were then processed with the Dovetail Micro-C kit.
Libraries were prepared according to manufacturer’s instructions (Dovetail Micro-C kit compatible with Illumina sequencing) as described in STAR Methods.

value: Embryonic stem cells


title: Hypothalamus, 180 day, M6-1


title: Retina_18w_S01

description: 10x Genomics 3' scRNA-seq

value: Neural Retina

value: Wildtype

value: 18 weeks


title: Hypothalamus, 60 day, M2-4

value: 60 day


title: T34C_CKDL220007706-1a-N704-N506_HN2WWDSX3_L4

value: Trophoblasts


title: T27C_CKDL220007706-1a-N707-N503_HN2WWDSX3_L4


title: T36C_CKDL220007706-1a-N703-N508_HN2WWDSX3_L4


title: T29C_CKDL220007706-1a-N701-N505_HN2WWDSX3_L4


title: Hypothalamus, 120 day, M4-4

value: 120 day


title: Zebrafish Embryo, 2hpf, rep3