title: Renal Allograft Biopsy_P_30

value: Australian Chronic Allograft Dysfunction


title: Renal Allograft Biopsy_P_25

status: Public on Apr 05 2024

type: SRA

city: Westmead

first: Harry

last: Robertson

state: NSW

address: 176 Hawkesbury Rd

department: Centre for Transplant and Renal Research

country: Australia

institute: Westmead Institute for Medical Research

library_source: transcriptomic

data_processing:
Raw RNA-Seq reads were quality controlled and trimmed using FastQC and Trimmomatic. Alignment to the GRCh38 human reference genome was performed using STAR, followed by quantification of gene-level expression with featureCounts.
Assembly: GRCh37-hg19
Supplementary files format and content: A comma-seperated text file includes raw counts per sample

molecule: total RNA

organism: Homo sapiens

source_name: Kidney

extract_protocol:
Kidney biopsy specimens were left in RNAlater (Sigma-Aldrich) overnight at 4°C before removal and storage at -80°C until RNA extraction. Specimens were chemically and physically lysed by using 2-Mercaptoethanol (Sigma-Aldrich) and TissueLyser II (Qiagen, Germany), follow by RNA extraction using AllPrep DNA/RNA/microRNA and MiniElute clean- up kits (Qiagen, Germany).
All RNA samples were frozen and stored at -80°C and then sent in bulk to the Australian Genome Research Facility (AGRF, Melbourne, Australia). Sample QC and library preparation were performed in-house, and the resultant libraries sequenced using the NovaSeq 6000 platform (Illumina)

tag: tissue

value: Kidney

tag: protocol

value: Renal Allograft Biopsy

tag: disease

tag: treatment

value: Immediate


title: S00-28974

type: RNA

city: Toronto

first: Shivani

middle: Nainesh

last: Kamdar

state: ON

address: 60 Murray Street

department: Cancer Biology

country: Canada

institute: Sinai Health System (LTRI)

hyb_protocol: The miRtagged miRNA was then hybridized to a probe pair where the Reporter Probe carried the signal and the Capture Probe allowed the complex to be immobilized for data collection.

data_processing: miRNA abundance was normalized using the R package NanoStringNorm (v1.1.21). It examined the signal intensities of housekeeping genes, positive genes and negative genes by changing optimization options (such as SampleContent, CodeCount, and Background) and normalizes abundance values to show high abundance of housekeeping genes and positive genes but low abundance for negative controls. We used seven metrics for SampleContent, three metrics for CodeCount, four metrics for Background and three other optimization options to correct scale of abundance values. In total, 252 parameter combinations were tested. To find the best parameter combinations, we adopted a new strategy to use control sample. Control sample is composed of miRNAs that are extracted from the mix of four prostate cancer cell lines (DU-145, PC-3, C42, and LNCaP). They were equally mixed together and loaded to each batch. We measured the similarity of abundance profiles between control samples in batches and the similarity of entire miRNA profiles across batches. Also, we counted the fraction of misinterpreted samples that are erroneously normalized in the parameter settings. Additionally, we examined whether miRNAs showing significant abundance changes in TCGA data set also show differential abundances in our miRNA profiles. Finally, we identified the best parameter combination that minimizes batch effect, the variability of control samples across the two batches and misinterpreted samples, and maximize concordance of abundance changes between TCGA data set and our miRNA profiles. Similarity between control samples is measured using Spearman’s correlation coefficient (ρ). Batch effect is measured using standard deviation between batches that is estimated from linear mixed effect-model. Misinterpreted samples occur when positive controls (ratio of average abundance of positive controls and abundance of each positive control was either < 0.3 or > 3), negative controls (Z-score > 5), and housekeeping genes (Z-score > 5) are not expressed or show high abundance variation as well as the fraction of detected miRNAs (normalized transcript count > 0) in a sample is less than 10% of total endogenous miRNAs. To combine all criteria, rank product was calculated and the best optimal parameter combination was selected. In results, the data was normalized using geometric means of genes showing low coefficient of variation (low.cv.geo.mean). Quantile normalization was performed based on pegging each sample to an empirically derived distribution. The distribution is simply the mean abundance across all samples for each gene rank. Normalized miRNA abundances were log2 transformed.

label: miRtag

source_name: Macrodissected tissue

label_protocol: DNA sequences called miRtags were ligated to the mature miRNAs through base complementarity. Excess tags were removed via enzymatic digestion.

extract_protocol: Areas with ≥80% neoplastic cellularity were marked on the matched H&E slides for tumour macrodissection as described previously. RNA was extracted using mirVana miRNA Isolation Kit (Thermo-Fisher). The quality (260/230, 260/280 ratios), and concentrations of each sample were assessed using NanoDrop 1000 spectrophotometer (Thermo Scientific). Samples were stored at -80°C. RNA was eluted to a final concentration of 35 ng/uL and a total of 100 ng of RNA was analyzed on NanoString's nCounter® platform.

tag: cell type

value: prostate cancer

tag: biochemical recurrence

value: TRUE

tag: time to last event

tag: age

tag: pt

tag: preoperative psa

tag: pathological gleason score

tag: metastasis

value: FALSE


title: egr3 mutants 2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 104) with STAR 2.7.10a
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2) and batch corrected using CountClust (each biological replicate = one batch) (Dey K et al., Visualizing the structure of RNA-seq expression data using grade of membership models).
Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
Assembly: danRer11
Supplementary files format and content: libryr size notmalize amd batch corrected counts

organism: Danio rerio

source_name: Heart

extract_protocol:
Total RNA was isolated using the miRNeasy micro Kit (Qiagen 217084), followed by on-column DNase digestion (DNase-Free DNase Set, Qiagen 79254), and final elution was performed in 12μl of RNase-free water
10ng total RNA was used for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio).

value: Heart

tag: genotype


title: S99-10839


title: S01-13385


title: S01-4414


title: S98-31351


title: Renal Allograft Biopsy_P_24


title: egr3 mutants 1


title: Renal Allograft Biopsy_P_27

value: Delayed


title: Renal Allograft Biopsy_P_23


title: K75-2-FMFC

city: Houston

first: Yuan

last: Pan

state: TX

address: 6565 MD Anderson Blvd. Suite Z8.5000

country: USA

institute: UT MD Anderson Cancer Center

description: Fresh frozen Visium Spatial transcriptome sequencing

data_processing:
Raw data processed through 10x Genomics Space Ranger pipeline
Sequences aligned to mm10. Space Ranger default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange format
Supplementary files format and content: tif : image of tissue
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Mus musculus

source_name: brain

extract_protocol:
OCT embedded fresh frozen tissue. 10 um sections on a Cryostat.
10x Genomics Visium Fresh Frozen Spatial Gene Expression Library prep protocol (CG000239, 10x Genomics)
Visium Fresh Frozen

value: brain


title: Renal Allograft Biopsy_P_21


title: Renal Allograft Biopsy_P_20


title: S99-4582


title: S99-29540


title: S01-23434


title: S00-522


title: K75-1-FMFC


title: S01-7225


title: S01-23518


title: K73-8-FMFC


title: Renal Allograft Biopsy_P_19


title: S00-1882


title: M9_TU_Tpex, replicate 2, Tcf1 Cut&Tag

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool, in order to remove potential adapters and quality trim 3’ end of reads with cutadapt program, followed by FastQC analysis. A quality score cutoff of Q20 was used. Next, reads were mapped to mouse reference genome (mm10; GRCm38.p6) with bwa aln, followed by bwa samse with -K flag set to 10000000, and the output was converted to BAM format with samtools. Afterward, duplicated reads were marked by biobambam2.
Assembly: mm10
Supplementary files format and content: bigWig files normalized by total reads
Library strategy: Tcf1 CUT&Tag

molecule: genomic DNA

source_name: tumor

extract_protocol:
0.6-1x100,000 naïve P14 CD8 T cells, FACS-sorted CD44+CD90.1+CD8+ cells (from tdLN of M9 group) and PD1+Tim3- CD90.1+CD8+ (from tumors of M9 groups) were washed with PBS before nuclei extraction.
Library construction was performed following the Epicypher CUTANA Direct-to-PCR CUT&TAG protocol with slight modifications and all the buffer used were freshly prepared.

value: tumor

value: CD8 T cells

tag: cell subset

tag: antibody

tag: gp33 status

value: High Affinity GP33


title: S98-31488


title: S99-15887


title: S01-24267


title: S01-8543


title: Renal Allograft Biopsy_P_22


title: Renal Allograft Biopsy_P_17


title: S00-22157


title: S99-26217


title: S01-16461


title: M9_LN, replicate 2, Tcf1 Cut&Tag

source_name: lymph node

value: lymph node


title: Renal Allograft Biopsy_P_16


title: S99-29898


title: S01-11902


title: M9_LN, replicate 1, Tcf1 Cut&Tag


title: Renal Allograft Biopsy_P_18


title: Renal Allograft Biopsy_P_15


title: M9_TU_Tpex, replicate 1, Tcf1 Cut&Tag


title: S00-5466


title: LN_C6M9 Day 8, replicate 3, WGBS

data_processing:
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the HG19 genome using the BSMAP v.2.90 software
CpG methylation levels were determined by methratio.py script from BSMAP
Assembly: mm10
Supplementary files format and content: txt files with columns of chr, loc, cov, meth

extract_protocol:
DNA was extracted from the sorted cells and then bisulfite treated using an EZ DNA Methylation-Direct kit (Zymo Research).
Bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicentre) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina NovaSeq 6000 systems

value: Low Affinity GP33


title: S99-15417


title: Naive, replicate 2, Tcf1 Cut&Tag

source_name: spleen

value: spleen


title: K73-6-FMFC


title: Renal Allograft Biopsy_P_13


title: S98-30964


title: S00-12187


title: S01-4446


title: Renal Allograft Biopsy_P_11


title: S00-1458


title: LN_M9 Day 8, replicate 3, WGBS


title: S00-11516


title: LN_C6M9 Day 8, replicate 2, WGBS


title: S99-1858


title: S01-7594


title: S01-22540


title: LN_M9 Day 8, replicate 2, WGBS


title: Naive, replicate 1, Tcf1 Cut&Tag


title: S01-15301


title: S99-5427


title: Renal Allograft Biopsy_P_12


title: Renal Allograft Biopsy_P_9


title: Renal Allograft Biopsy_P_10


title: Renal Allograft Biopsy_P_14


title: Renal Allograft Biopsy_P_7


title: S01-12253


title: TU_M9_TIM3+ Day 8, WGBS


title: S99-25426


title: S98-29184


title: TU_C6M9_TIM3+ Day 8, WGBS


title: Renal Allograft Biopsy_P_6


title: Renal Allograft Biopsy_P_8


title: S99-3417


title: S99-13757


title: S00-8871


title: S01-9677


title: S01-25823


title: TU_M9_TIM3- Day 8, WGBS


title: S01-7078


title: Renal Allograft Biopsy_P_5


title: LN_C6M9 Day 8, replicate 1, WGBS


title: S99-29330


title: S01-7551


title: Renal Allograft Biopsy_P_4


title: LN_M9 Day 8, replicate 1, WGBS


title: TU_C6M9_TIM3- Day 8, WGBS


title: Renal Allograft Biopsy_P_3


title: TU_C6M9 Day 12, WGBS


title: TU_M9 Day 12, WGBS


title: Renal Allograft Biopsy_P_2


title: S99-1657


title: S99-13814


title: S01-14747


title: Renal Allograft Biopsy_P_1


title: S01-10726


title: S01-30091


title: S01-7748


title: iNK-3

city: Changsha

first: Yuxuan

last: Zhang

state: Hunan

address: 110 Xiangya Road

department: School of Life Sciences

country: China

institute: Central South University

data_processing:
The raw data from Illumina NovaSeq 6000 was handled by Skewer v0.2.2.
Data quality was checked by FastQC v0.11.2.The read length was 2×150 bp.
Clean reads were aligned to the human genome (GRCh38) from ensmble using STAR, with one mismatch allowed.
StringTie (v1.3.1c) was used to generate gene expression data.
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt:tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: gene_sample_FPKM.txt:tab-delimited text file includes FPKM values for each Sample

source_name: Human iPSCs

growth_protocol: Human iPSCs (hiPSCs) were cultured in mTeSR Plus medium (STEMCELL Technologies) in humidified atmosphere with 5% CO2 at 37℃. hiPSCs were seeded onto the Aggrewell™800 (STEMCELL Technologies). After a 10-day half-medium change with EB formation medium, EBs were transferred to gelatin-coated dishes, and half-medium changes were made twice a week after the first week.

extract_protocol:
Total RNA was extracted from iPSCs-derived NK cells with the Universal RNA Extraction CZ Kit (RNC643, ONREW) according to the manufacturer’s instructions.1.5 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-0, Vazyme), followed sequencing using the Illumina NovaSeq 6000 platform with the 150 paired-end sequencing strategy.

treatment_protocol: Biotinylated IL-21 (Acro Biosystems) and biotinylated 4-1BBL (Acro Biosystems) bound Streptavidin magnetic beads (Invitrogen) were employed to stimulate the expansion of NK cells. Beads were added into NK cells at a ratio of 1:1. Medium was replaced every 2-3 days with NK cell expansion medium freshly added with 500 IU/ml IL-2 and 10 ng/ml IL-15.

tag: cell line

value: Human iPSCs

value: iPSCs-derived NK cells

value: Wild type

value: NK cells differentiation


title: C6M9_TU_Tpex, replicate 4, ATAC

description: ATACseq

data_processing:
Raw ATACseq FASTQ files were mapped to mm10 by Bowtie2 v2.2.9 using the following parameters: -k 1 -X2000 -t --quiet –mm. PCR duplicates were marked using Picard before the removal of unmapped, unpaired, mitochondrial reads and ENCODE blacklist regions.
Assembly: mm10
Supplementary files format and content: bigWig files normalized by total reads

extract_protocol:
CD44+CD90.1+CD8+ cells (from tdLN) and indicated CD90.1+CD8+ 564 subsets (from tumors) were FACS purified from 3-5 (M9 group, per sample) and 20-30 (C6M9 group, per sample) C57BL/6 mice on day 14 post tumor implantation, into 1.5 mL Lo-Bind Eppendorf tubes containing RPMI-1640 and 10% FBS.
5000 - 20000 cells were collected per sample and subjected to library construction according to the optimized Omni-ATAC protocol with slight modification of the library cleanup step. Double-sided size selection (0.6X and 1.2X) was performed with SPRIselect (Beckman Coulter) to enrich sequenceable fragments in the final library.

tag: tissue


title: C6M9_LN, replicate 4, ATAC

description: ATACseq


title: S01-26136


title: S01-28516


title: iNK-2


title: S00-17946


title: S01-8963


title: S01-14412


title: S01-13432


title: S01-9003


title: C6M9_TU_Tpex, replicate 3, ATAC

description: ATACseq


title: S99-11503


title: S99-10987


title: LV-CAR19-iNK-3


title: M9_TU_Tpex, replicate 5, ATAC

description: ATACseq


title: S00-24532


title: S00-12169


title: C6M9_TU_Tpex, replicate 5, ATAC

description: ATACseq


title: LV-CAR19-iNK-2


title: CPCG-490


title: C6M9_TU_Tex, replicate 2, ATAC

description: ATACseq


title: CPCG-539


title: C6M9_TU_Tpex, replicate 2, ATAC

description: ATACseq


title: LV-CAR19-iNK-1


title: CAR19-iNK-3


title: M9_TU_Tex, replicate 2, ATAC

description: ATACseq


title: CPCG-592


title: CPCG-591


title: CPCG-601


title: CAR19-iNK-2


title: iNK-1


title: M9_TU_Tpex, replicate 4, ATAC

description: ATACseq


title: C6M9_LN, replicate 3, ATAC

description: ATACseq


title: CAR19-iNK-1


title: CAR19-IL24-iNK-3


title: CPCG-437


title: CPCG-600


title: M9_LN, replicate 4, ATAC

description: ATACseq


title: CAR19-IL24-iNK-2


title: CPCG-603


title: C6M9_TU_Tex, replicate 1, ATAC

description: ATACseq


title: CAR19-IL24-iNK-1


title: CPCG-593


title: CPCG-604


title: CPCG-597


title: C6M9_TU_Tpex, replicate 1, ATAC

description: ATACseq


title: CPCG-594


title: CPCG-433


title: CPCG-590


title: CPCG-607


title: CPCG-598


title: M9_TU_Tex, replicate 1, ATAC

description: ATACseq


title: CPCG-599


title: M9_TU_Tpex, replicate 3, ATAC

description: ATACseq


title: CPCG-606


title: AML38_dn_refractory

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, gene counting, barcode processing we made using Cell Ranger software provided by 10X Genomics (Cell Ranger 6.0.2, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger )
Assembly: GRCh38
Supplementary files format and content: tab-separated value and matrix files

source_name: Human AML

extract_protocol:
Cells were FACS purified by 7AAD exclusion from de novo sources and hCD45/CD33 7AAD exclusion from xenograft sources. In AML2-3 PDXs, staining with labelling oligonucleotides from a cell multiplexing kit (10X Genomics, part no: 1000262)
Library construction was performed according to manufactures recommendations (10X Genomics, Part No: 1000078, Part No: 1000094)

value: Human AML

tag: number of_multiplexed_samples

value: AraC

tag: timepoint


title: BM2

description: 10X Genomics

source_name: Bone Marrow

value: Bone Marrow

tag: treatment


title: C6M9_LN, replicate 2, ATAC

description: ATACseq

tag: cell type


title: CPCG-432

value: prostate cancer

tag: biochemical recurrence

value: FALSE


title: CPCG-587

tag: time to last event


title: M9_LN, replicate 3, ATAC

description: ATACseq


title: AML38_dn_dx

description: 10X Genomics


title: M9_TU_Tpex, replicate 2, ATAC

description: ATACseq


title: CPCG-0395

tag: age


title: AML3_dn

description: 10X Genomics


title: CPCG-0346

tag: pt


title: CPCG-0467

tag: preoperative psa


title: CPCG-0465

value: TRUE

tag: pathological gleason score


title: CPCG-588

tag: metastasis


title: AML2_dn

description: 10X Genomics


title: BM1

description: 10X Genomics


title: CPCG-0391


title: M9_TU_Tpex, replicate 1, ATAC

description: ATACseq


title: M9_LN, replicate 2, ATAC

description: ATACseq


title: CPCG-0514


title: CPCG-0452


title: AML1_dn

description: 10X Genomics


title: CPCG-0445


title: CPCG-0365


title: CB_PDX_d17

description: 10X Genomics

source_name: BM from Cord Blood PDXs

value: BM from Cord Blood PDXs

value: Day 17


title: C6M9_LN, replicate 1, ATAC

description: ATACseq

value: CD8 T cells


title: CPCG-0331


title: CPCG-0508


title: M9_LN, replicate 1, ATAC

description: ATACseq

value: High Affinity GP33


title: CPCG-0408


title: CPCG-0397


title: Naive, replicate 2, ATAC

description: ATACseq


title: AML3PDX_endpoint1-3_pooled, GEX

description: 10X Genomics

source_name: BM from AML PDXs

value: BM from AML PDXs

value: Endpoint


title: CPCG-0251


title: CPCG-0369


title: Naive, replicate 1, ATAC

description: ATACseq

value: spleen


title: CB_PDX_untreated

description: 10X Genomics

value: Saline

value: Untreated


title: Liver, AF1 peptide, biol rep 4

city: College station

first: Shaodong

last: Guo

state: Texas

address: Rm135 Cater-Mattil Hall 2253 TAMU

department: Nutrition

institute: Texas A&M University

data_processing:
Reads were trimmed for adapters and low-quality bases with TrimGalore v0.6.7 with default settings
Trimmed reads were aligned to the domestic mouse genome using HiSat2.2.1
Alignment files were sorted and indexed with SAMtools v1.17
Read counts were generated with the R package GenomicAlignments v11.34.1
Assembly: mm39
Supplementary files format and content: csv file of normalized read counts

source_name: Liver

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). 1 ug of total RNA was used for the constrution of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina Stranded mRNA Prep Kit.

value: Liver

tag: genotype

value: db/db

value: AF1 peptide


title: Liver, AF1 peptide, biol rep 3


title: AML3PDX_d14_1-3, CMO

description: 10X Genomics

value: AraC

value: Day 14


title: AML3PDX_d14_1-3, GEX

description: 10X Genomics


title: CPCG-0366

value: prostate cancer


title: CPCG-0191

value: FALSE


title: AML3PDX_d10_1-3, CMO

description: 10X Genomics

value: Day 10


title: CPCG-0482


title: CPCG-0248

value: TRUE


title: Liver, AF1 peptide, biol rep 2


title: CPCG-0411


title: CB_PDX_d14

description: 10X Genomics

value: BM from Cord Blood PDXs


title: CPCG-0344


title: CPCG-0565


title: CPCG-0522


title: AML3PDX_d10_1-3, GEX

description: 10X Genomics


title: Liver, AF1 peptide, biol rep 1


title: CPCG-0372


title: CPCG-0415


title: CPCG-0573


title: AML3PDX_untreated1-2, CMO

description: 10X Genomics


title: Liver, control, biol rep 4

value: control


title: AML3PDX_untreated1-2, GEX

description: 10X Genomics


title: CPCG-0434


title: Liver, control, biol rep 3


title: CPCG-0184


title: Liver, control, biol rep 2


title: AML2PDX_endpoint1-2, CMO

description: 10X Genomics


title: Liver, control, biol rep 1


title: CPCG-0354


title: AML2PDX_d14_1-3, CMO

description: 10X Genomics


title: CPCG-0569


title: CPCG-0336


title: LN_C6M9, replicate 2, scRNAseq

description: 10x Gernomics 3' kit

data_processing:
The demultiplexing, barcoded processing, mapping, counting and aggregation were done by Cell Ranger 6.0.0 software.
Assembly: mm10
Supplementary files format and content: Tab separated files of genes
Supplementary files format and content: Tab separated files of cell barcodes
Supplementary files format and content: MEX file of gene-barcode matrix

extract_protocol:
CD44+CD90.1+CD8+ cells were FACS-purified from tdLN of 10 (M9 group with biological duplicate) - 35 (C6M9 group with biological duplicate) C57BL/6 mice on day 14 post tumor implantation into 1.5 mL Lo-Bind Eppendorf tubes containing RPMI-1640 and 10% FBS. 10000-20000 cells were washed with PBS and 0.04% BSA before loading into a Chromium Next GEM Chip G (10X Genomics).
GEM generation, cDNA amplification and library construction were performed following the protocol of Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index, 10X Genomics) with target recovery of 5000-10000 cells per library/sample

value: lymph node

tag: cells loaded

value: CD8 T cells

tag: cell subset

value: Low Affinity GP33


title: CPCG-0462


title: LN_M9, replicate 2, scRNAseq

description: 10x Gernomics 3' kit

tag: gp33 status

value: High Affinity GP33


title: CPCG-0246


title: CPCG-0371


title: AML2PDX_endpoint1-2, GEX

description: 10X Genomics

value: BM from AML PDXs

value: Endpoint


title: CPCG-0453


title: CPCG-0387


title: LN_C6M9, replicate 1, scRNAseq

description: 10x Gernomics 3' kit


title: AML2PDX_d10_1-3, CMO

description: 10X Genomics


title: AML2PDX_d14_1-3, GEX

description: 10X Genomics


title: AML2PDX_d10_1-3, GEX

description: 10X Genomics


title: LN_M9, replicate 1, scRNAseq

description: 10x Gernomics 3' kit


title: CPCG-0352


title: CPCG-0241


title: CPCG-0435


title: CPCG-0468


title: AML2PDX_d7_1-3, CMO

description: 10X Genomics

value: Day 7


title: CPCG-0208


title: CPCG-0439


title: wild type mose, replicate 6

city: Shanghai

first: hu

last: xiaolin

state: Shanghai

address: south congqing road 227#

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Adapter sequences, low-quality reads (≥20% of bases with Phred score <15), and reads containing >5% ambiguous bases were trimmed using Trim Galore (v0.6.4)
The cleaned reads were then aligned to the reference genome using STAR (v2.7.10b) with default parameters. Read counts were derived from the alignments and quantified at the gene level.

source_name: lung

extract_protocol:
Total RNA was extracted using TRIzol reagent (Magen, China) following the manufacturer's instructions.
For each sample, 1 μg of total RNA was used to enrich and purify polyadenylated mRNAs using oligo(dT) beads. The purified mRNAs were then reverse transcribed into cDNA using reverse Rnase H and DNA polymerase I.

value: lung

value: Control


title: AML2PDX_d7_1-3, GEX

description: 10X Genomics

value: AraC


title: wild type mose, replicate 5


title: CPCG-0340


title: CPCG-0368


title: AML2PDX_untreated1-3, CMO

description: 10X Genomics

value: Saline

value: Untreated


title: wild type mose, replicate 4


title: AML1PDX_endpoint_1-2pooled

description: 10X Genomics


title: AML2PDX_untreated1-3, GEX

description: 10X Genomics


title: CPCG-0398

value: prostate cancer

value: FALSE


title: CPCG-0448-F1-R

value: TRUE


title: CPCG-0183


title: CPCG-0381


title: wild type mose, replicate 1


title: CPCG-0527


title: mouse model for HALI, replicate 6

treatment_protocol: Six mice were randomly selected and housed in a hyperoxic chamber maintained at 25-27°C and 50-70% relative humidity. Oxygen flow into the chamber was regulated to keep oxygen levels at ≥90% saturation. Sodium lime was placed inside the chamber to absorb carbon dioxide exhaled by the mice and maintain CO2 levels below 0.5%. Mice were exposed to hyperoxia for 23.5 hours per day. The chamber was opened for 0.5 hours daily at scheduled times to provide food, water, and clean bedding.

value: HALI


title: AML1PDX_d10_1-3pooled

description: 10X Genomics

value: Day 10


title: AML1PDX_d14_1-3pooled

description: 10X Genomics

value: Day 14


title: CPCG-0388-F1-R


title: CPCG-0350-F1-R


title: CPCG-0373-F1-R


title: AML1PDX_d7_1-3pooled

description: 10X Genomics


title: CPCG-0407-F1-R


title: CPCG-0356-F1-R


title: mouse model for HALI, replicate 5


title: AML1PDX_untreated_1-3pooled

description: 10X Genomics


title: CPCG-0271-F1-R


title: mouse model for HALI, replicate 4


title: CPCG-0525-F1-R


title: CPCG-0339-F1-R


title: wild type mose, replicate 3


title: wild type mose, replicate 2


title: CPCG-0349-F1-R


title: mouse model for HALI, replicate 3


title: CPCG-0341-F1-R


title: mouse model for HALI, replicate 2


title: BM3

data_processing:
FASTQ data was processed and aligned using 10X Genomics Space Ranger Software (v1.3.1) default settings to generate processed data
Assembly: GRCh38
Supplementary files format and content: barcode.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz list of gene IDs
Supplementary files format and content: matrix.mtx.gz matrix file of gene expression counts
Supplementary files format and content: aligned_fiducials.jpg aligned fudicials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: scalefactors_json.json scalefactors in json format
Supplementary files format and content: tissue_hires_image.png hi res image of tissue
Supplementary files format and content: tissue_lowres_image.png low res image of tissue
Supplementary files format and content: tissue_positions_list.csv list of spatial barcodes and associated coordinates specifying spots
Library strategy: Spatial Transciptomics

source_name: Trephine BM Biopsy

extract_protocol:
Prior to performing spatial transcriptomics experiment, DV200 assessment was done on all the samples with a minimum criterion set at 30%. RNA was extracted from paraffin curls (4 curls at 10µm per tissue) using Qiagen’s RNeasy Mini Kit (Cat#74104). All working space and instruments were treated with RNase zap (Invitrogen, Cat#AM9780) prior to RNA extraction, and gentle scoring was performed around the tissue to minimize excess paraffin during curl collection
Spatial transcriptomics experiment was performed using Visium Spatial Transcriptomics (10X genomics, Cat#1000185), following materials and methods according to the manufacturer’s website (User Guide, CG000407).

value: Trephine BM Biopsy

tag: disease state

value: Healthy


title: CPCG-0487-F1-R


title: CPCG-0374-F1-R


title: AML12

tag: tissue

value: AML


title: mouse model for HALI, replicate 1


title: KO+WD-4

city: Oklahoma City

first: Tiangang

last: Li

state: OK

address: 975 NE 10th St

institute: University of Oklahoma Health Sciences Center

data_processing:
Derived sequences were analyzed by applying a custom computational pipeline consisting of the open-source gSNAP, Cufflinks, and R forsequence alignmentand ascertainment ofdifferential gene expression.
reads generated were mapped to the mouse genome (mm10) by gSNAP,54expression (FPKM) was derived by Cufflinks
Assembly: mm10
Supplementary files format and content: excel

source_name: liver

growth_protocol: Mice were fed CD or WD for 13 weeks

extract_protocol:
Trizol was used to extract total liver RNA
Stranded RNA sequencing (RNAseq) libraries were constructed using Lexogen’s QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina and the established protocols. The library construction was done using 500 ng of total RNA. Each of the libraries was indexed during library construction to multiplex for sequencing. Samples were normalized, and the libraries were pooled and run on Illumina’s NovaSeq Platform

treatment_protocol: AAV-Null or AAV-TBG-cre was injected via tail vein, then mice were maintained on the same diet for additional 5 weeks

value: liver

tag: strain background

value: Liver Cullin 3 KO

value: WD


title: CPCG-0459-F1-R


title: CPCG-0335-F1-R


title: KO+WD-3


title: Siha74_7

city: Brussels

first: Camille

last: Lefevre

state: Belgium

address: Avenue Emmanuelle Mounier 73 (bte B1.73.11)

department: Louvain Drug Research Institute (LDRI)

country: Belgium

institute: UClouvain

data_processing:
De-multiplexed using Illumina's bcl2fastq 2.20 software
Quality-controlled and trimming using FastQC tool and Trimmomatic Version 0.38
Read alignment using STAR Version 2.6.1d
Count matrices were generated from reads aligned to the reference genome (BAM files) using the function summarizeOverlaps from the R package GenomicAlignments and then tested for differential expression and normalized using the R package DESeq2 Version 1.22.2
Assembly: Homo_sapiens.GRCh37.75
Supplementary files format and content: Normalized_counts_Acidosis.csv
Supplementary files format and content: Normalized count table in csv format (generated in .R, DESeq2 object)

source_name: Cervix

growth_protocol: Human colon HCT-116, hypopharyngeal FaDu and cervix SiHa cell lines  were maintained in DMEM (Sigma, D5030), 10% fetal bovine serum (FBS, Biowest, South America, S181B-050), 10 mM D-glucose, 2 mM L-glutamine, 100 Units/ml penicillin, 100 µg/ml streptomycin, buffered with 25 mM HEPES and 25 mM PIPES with pH adjusted to 7.4 or 6.5. Cells were maintained at 37°C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA). Excess DNA was removed by DNase I treatment (Qiagen) and RNA hydrolysis was protected with RNAsin (Promega).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: pH adjusted at pH6.5 or pH7.4

value: Cervix

tag: cell line

value: SiHa

value: Cancer cells


title: CPCG-0375-F1-R


title: CPCG-0392-F1-R


title: CPCG-0263-F1-R


title: Siha74_6

tag: treatment


title: CPCG-0457-F1-R

tag: cell type


title: KO+WD-2


title: Siha74_5


title: CPCG-0418-F1-R

tag: biochemical recurrence


title: BM4


title: S00-25707

tag: time to last event


title: KO+WD-1


title: S01-21099

tag: age


title: CPCG-0401-F1-R

tag: pt


title: Siha74_4


title: AML11


title: Siha74_1


title: WT+WD-4

value: WT


title: S01-6020

tag: preoperative psa


title: WT+WD-3


title: S01-31238

tag: pathological gleason score


title: S99-10552

tag: metastasis


title: CPCG-0509-F1-R


title: Siha65_7


title: S01-5357


title: WT+WD-2

tag: genotype


title: S99-25371


title: Siha65_6


title: Siha65_5


title: S01-14504


title: S99-13976


title: WT+WD-1


title: KO+CD-3

value: CD


title: S01-17632

value: prostate cancer


title: S99-10300

value: FALSE


title: CPCG-0499-F1


title: Siha65_4


title: KO+CD-2


title: Siha65_1


title: CPCG-0382-F1

value: TRUE


title: CPCG-0428-F1


title: CPCG-0236-F1


title: KO+CD-1


title: CPCG-0410-F1


title: WT+CD-4


title: CPCG-0402-F1


title: CPCG-0493-F1


title: HCT74_6

source_name: Colon

value: Colon

value: HCT


title: WT+CD-3


title: HCT74_5


title: WT+CD-1


title: HCT74_3


title: CPCG-0249-F1

source_name: Macrodissected tissue


title: CPCG-0414


title: CPCG-0463-F1


title: CISKO, rep2

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.  Reference genome and annotation files were downloaded from Ensembl, and RNA-seq data were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CISKO

extract_protocol:
Total RNA was isolated from ileal or colonic mucosa per mouse using the RNeasy mini kit (Qiagen, Valencia, CA).
NEBNext Ultra II RNA Library Prep Kit (NEB #E7775).
An RNA integrity number (RIN) > 7.2 was considered the minimum requirement for library preparation. RNA was reverse transcribed into cDNA using the oligo-dT primer. An insert size of 250–300 bp was used for cDNA library preparation.

tag: strain


title: CPCG-0258-F1


title: CISKO, rep3


title: CPCG-0348


title: CISKO, rep1


title: CPCG-0256


title: CPCG-0523


title: HCT65_6


title: HCT74_7


title: CPCG-0474


title: CWT, rep3

source_name: CWT


title: HCT65_5


title: CPCG-0357-F1


title: CWT, rep2


title: CPCG-0265


title: HCT65_3


title: CPCG-0267


title: CPCG-0255


title: CPCG-0423


title: CWT, rep1


title: CPCG-0537


title: HCT74_1


title: ILISKO, rep3

source_name: ILISKO

value: Ileum


title: CPCG-0333


title: CPCG-0262


title: CPCG-0519


title: ILISKO, rep2


title: Fadu74_5

source_name: Pharynx

value: Pharynx

value: FaDu


title: HCT65_7


title: Fadu74_4


title: CPCG-0378


title: CPCG-0566


title: CPCG-0235


title: Fadu74_3


title: Fadu74_2


title: HCT65_1


title: ILWT, rep2

source_name: ILWT


title: Fadu74_1


title: Fadu65_5


title: CPCG-0502


title: CPCG-0529


title: tcr_Sample 4b [WT Low TCR Rep 2]

city: San Francisco

first: Yang

last: Sun

state: CA

address: 513 Parnassus Ave

department: Rheumatology

institute: UCSF

data_processing:
Bulk RNA Seq: The raw fastq files were clipped and filtered using fastq-mcf v.1.04.636 to remove low quality reads and bases, homopolymers, and adapter sequences. The filtered reads were aligned using the STAR v.2.4 with the default settings to the mm10 transcriptome to produce count matrices for each sample.
Single cell RNA seq: The raw fastq files were aligned using CellRanger v3.0.1 and 3.0.2 software with the default settings to the mm10 transcriptome with the addition of the sequence for the eGFP transcript and the vdj GRCm38 v 3.1.0 reference for the GEX and TCR fastqs, respectively.
We filtered out 721 cells with less than 100 or more than 3000 genes detected and filtered out 14,388 genes detected in less than 3 cells. We also filtered out 1,066 cells with more than 10% of total counts (UMIs) mapping to mitochondrial genes and 1008 cells determined to be contaminating B cells based on CD19 expression.
The raw counts were normalized to 10,000 counts, log1p-normalized and scaled.
For technical and batch correction, we regressed out total UMI counts and % counts mapping to mitochondrial genes and used combat for batch correction with each sample as a batch.
We identified 1119 highly variable genes (excluding all Trav and Trbv genes to avoid clustering cells based on expression of those genes) which were used with the default settings in scanpy v.1.4.3 for PCA analysis followed by leiden clustering after nearest neighbor detection and UMAP projection. This analysis identified 13 clusters which we collapsed into 9 cell sub-types based on differential gene analysis.
For each 10x well alignment output from cellranger, we used velocyto v.0.17.17 to create a loom file with the spliced, unspliced, and ambiguous counts with the Dec. 2011 GRCm38/mm10 repeat masking gtf file from the UCSC genome browser 70, 71. The loom files across all wells were merged and then subsetted to all cells in the T.4NNr4a1 cluster.
The resulting object was used to run the dynamical model from scvelo v.0.2.1 with the default settings to uncover the RNA velocity to predict the latent time for each cell.
We used we used a Gaussian mixture model with the GaussianMixture tool from sklearn v.0.23.1  to deconvolute four underlying individual Gaussian distributions from the latent time distribution for cells from the T.4NNr4a1 cluster.
For trajectory inference between the four distributions (“Stage 1” – “Stage 4”), we used the graph-based tool PAGA within scvelo to predict velocity-inferred transitions among the clusters.
Genome_build: mm10
Genome_build: vdj GRCm38 v 3.1.0
Supplementary_files_format_and_content: comma separated text file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: h5ad file with filtered, processed, and cluster annotated data from all eight combined single cell RNA seq libraries
Supplementary_files_format_and_content: h5ad file with cells from T.4 Nr4a1 cluster from single cell RNA seq data post trajectory analysis with scvelo
Supplementary_files_format_and_content: comma separated text file with clonotype and TCR chain assignment for each cell barcode in the indicated library

source_name: naive CD4 T cells

extract_protocol:
Negatively selected CD4 T cells from the lymph node and spleen were sorted for CD62LhiCD44loCD25- and the 10% lowest (GFPlo)  expressing T cells. Droplet-based paired single-cell RNA and TCR library preparation was performed using the 10x single cell 5’+V(D)J v.1 kit.
VDJ RNA libraries were prepared for sequencing using standard 10x protocols

value: Balb/c

value: lymph node and spleen

value: wild type

tag: subgroup

value: naive CD4 T cells


title: tcr_Sample 4a [WT High TCR Rep 2]

extract_protocol:
Negatively selected CD4 T cells from the lymph node and spleen were sorted for CD62LhiCD44loCD25- and the 10% highest (GFPhi)  expressing T cells. Droplet-based paired single-cell RNA and TCR library preparation was performed using the 10x single cell 5’+V(D)J v.1 kit.
VDJ RNA libraries were prepared for sequencing using standard 10x protocols


title: CPCG-0353

extract_protocol: Areas with ≥80% neoplastic cellularity were marked on the matched H&E slides for tumour macrodissection as described previously. RNA was extracted using mirVana miRNA Isolation Kit (Thermo-Fisher). The quality (260/230, 260/280 ratios), and concentrations of each sample were assessed using NanoDrop 1000 spectrophotometer (Thermo Scientific). Samples were stored at -80°C. RNA was eluted to a final concentration of 35 ng/uL and a total of 100 ng of RNA was analyzed on NanoString's nCounter® platform.


title: ILISKO, rep1


title: CPCG-0567


title: CPCG-0406


title: CPCG-0489


title: Fadu65_4


title: CPCG-0500


title: Fadu65_3


title: CPCG-0466


title: CPCG-0266


title: CPCG-0572


title: tcr_Sample 3b [SKG Low TCR Rep 2]

value: SKG


title: CPCG-0456


title: Fadu65_2


title: ILWT, rep1


title: W4 cells infected with retro-vial vector for RASSF1A re-expression-1

city: Setagaya-ku

first: NOBUTAKA

last: KIYOKAWA

state: Tokyo

department: Pediatric Hematology & Oncology Research

country: Japan

institute: National Research Institute for Child Health & Development

description: Gene expression data from RTK cells infected with retro-vial vector for RASSF1A re-expression

hyb_protocol: The labeled probes were hybridized to Human Genome U133 Plus 2.0 Arrays (Affymetrix).  The experiments were performed in triplicate.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000.

data_processing: The data were analyzed using GENECHIP OPERATING Software 1.2 (Affymetrix) and GENESPRING GX 14.9 software (Agilent Technologies, Santa Clara, CA, USA).

label: biotin

label_protocol: The cRNAs were amplified and labeled using the GeneChip® 3' IVT Express Kit (Affymetrix, Santa Clara, CA, USA), as instructed by the manufacturer.

growth_protocol: Not adapted

extract_protocol: Total RNA was extracted from cells using ISOGEN, according to the manufacturers’ protocols.  Total RNA was treated with rDNase and purified with NucleoSpin® RNA Clean-up XS.  The concentration of RNA was assessed with an absorption spectrometer.

treatment_protocol: RTK cell were infected with a retro-viral vector for RASSF1A re-expression or an empty retro-viral vector as control were cultured and harvested.

value: RTK cells

value: absence of SMARCB1


title: W4 cells infected with retro-vial vector for RASSF1A re-expression-3

value: Philadelphia chromosome-positive


title: W4 cells infected with retro-vial vector for RASSF1A re-expression-2


title: W4 cells infected with empty retro-vial vectors-3

description: Gene expression data from RTK cells infected with empty retro-vial vectors


title: W4 cells infected with empty retro-vial vectors-2


title: CPCG-0363

data_processing: miRNA abundance was normalized using the R package NanoStringNorm (v1.1.21). It examined the signal intensities of housekeeping genes, positive genes and negative genes by changing optimization options (such as SampleContent, CodeCount, and Background) and normalizes abundance values to show high abundance of housekeeping genes and positive genes but low abundance for negative controls. We used seven metrics for SampleContent, three metrics for CodeCount, four metrics for Background and three other optimization options to correct scale of abundance values. In total, 252 parameter combinations were tested. To find the best parameter combinations, we adopted a new strategy to use control sample. Control sample is composed of miRNAs that are extracted from the mix of four prostate cancer cell lines (DU-145, PC-3, C42, and LNCaP). They were equally mixed together and loaded to each batch. We measured the similarity of abundance profiles between control samples in batches and the similarity of entire miRNA profiles across batches. Also, we counted the fraction of misinterpreted samples that are erroneously normalized in the parameter settings. Additionally, we examined whether miRNAs showing significant abundance changes in TCGA data set also show differential abundances in our miRNA profiles. Finally, we identified the best parameter combination that minimizes batch effect, the variability of control samples across the two batches and misinterpreted samples, and maximize concordance of abundance changes between TCGA data set and our miRNA profiles. Similarity between control samples is measured using Spearman’s correlation coefficient (ρ). Batch effect is measured using standard deviation between batches that is estimated from linear mixed effect-model. Misinterpreted samples occur when positive controls (ratio of average abundance of positive controls and abundance of each positive control was either < 0.3 or > 3), negative controls (Z-score > 5), and housekeeping genes (Z-score > 5) are not expressed or show high abundance variation as well as the fraction of detected miRNAs (normalized transcript count > 0) in a sample is less than 10% of total endogenous miRNAs. To combine all criteria, rank product was calculated and the best optimal parameter combination was selected. In results, the data was normalized using geometric means of genes showing low coefficient of variation (low.cv.geo.mean). Quantile normalization was performed based on pegging each sample to an empirically derived distribution. The distribution is simply the mean abundance across all samples for each gene rank. Normalized miRNA abundances were log2 transformed.


title: Midbrain, R3AC+Vehicle, mouse3

city: Piscataway

first: Brian

last: Daniels

state: NJ

address: 604 Allison Road

department: Cell Biology and Neuroscience

institute: Rutgers, The State University of New Jersey

data_processing:
Raw data quality was evaluated by FastQC.
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 Mus musculus GRCm38 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.
the gene hit counts table was used for downstream differential expression analysis via DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes unique gene hit counts for each sample

source_name: Midbrain

extract_protocol:
Total RNA from midbrain tissue was harvested using Zymo Direct-zol RNA Miniprep kit following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols

treatment_protocol:
All animals were treated for five days with 60 mg/kg tamoxifen in sunflower oil (i.p.) at least one week prior to further experimentation.
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was administered at 20 mg kg-1 (i.p.) once per day for five days. Saline were used for the control animals.

value: Midbrain

value: Ripk3fl/fl Aldh1l1Cre+

value: tamoxifen, Saline


title: Fadu65_1

value: Cancer cells


title: P_69

data_processing:
Raw RNA-Seq reads were quality controlled and trimmed using FastQC and Trimmomatic. Alignment to the GRCh38 human reference genome was performed using STAR, followed by quantification of gene-level expression with featureCounts.
Assembly: GRCh37-hg19
Supplementary files format and content: A comma-seperated text file includes raw counts per sample

source_name: Whole Blood

extract_protocol:
Peripheral blood was collected into PAXgene Blood RNA tubes (Qiagen, Germany), left at room temperature for 5 hours, and stored at -80°C until RNA extraction. RNA was extracted by using PAXgene Blood miRNA kit (Qiagen, Germany). RNA samples were frozen and stored at -80°C.
Frozen RNA samples were then sent to Australian Genome Research Facility (AGRF), Melbourne, Australia. Sample QC and library preparation were performed in-house by AGRF, and the resultant libraries sequenced using the NovaSeq 6000 platform (Illumina) with 100bp  read length.

value: Whole Blood

value: Rej


title: W4 cells infected with empty retro-vial vectors-1


title: tcr_Sample 1a [SKG High TCR Rep 1]


title: tcr_Sample 2b [WT Low TCR Rep 1]


title: P_67

value: Nill


title: Midbrain, R3AC-Vehicle, mouse2

value: Ripk3fl/fl Aldh1l1Cre-


title: P_70


title: Midbrain, R3AC+Vehicle, mouse2


title: tcr_Sample 2a [WT High TCR Rep 1]


title: tcr_Sample 3a [SKG High TCR Rep 2]


title: tcr_Sample 1b [SKG Low TCR Rep 1]


title: CPCG-0269

value: prostate cancer

value: FALSE


title: Midbrain, R3AC-Vehicle, mouse3


title: P_66


title: Midbrain, R3AC+Vehicle, mouse1


title: P_68


title: sc_Sample 4b [WT Low single cell Rep 2]

extract_protocol:
Negatively selected CD4 T cells from the lymph node and spleen were sorted for CD62LhiCD44loCD25- and the 10% lowest (GFPlo)  expressing T cells. Droplet-based paired single-cell RNA and TCR library preparation was performed using the 10x single cell 5’+V(D)J v.1 kit.
RNA libraries were prepared for sequencing using standard 10x protocols

value: Balb/c

value: lymph node and spleen


title: CPCG-0379

value: TRUE


title: CPCG-0571


title: Midbrain, R3AC-Vehicle, mouse1


title: sc_Sample 4a [WT High single cell Rep 2]

extract_protocol:
Negatively selected CD4 T cells from the lymph node and spleen were sorted for CD62LhiCD44loCD25- and the 10% highest (GFPhi)  expressing T cells. Droplet-based paired single-cell RNA and TCR library preparation was performed using the 10x single cell 5’+V(D)J v.1 kit.
RNA libraries were prepared for sequencing using standard 10x protocols

value: wild type

value: naive CD4 T cells


title: CPCG-0504


title: CPCG-0416


title: P_65


title: sc_Sample 3b [SKG Low single cell Rep 2]

value: SKG


title: Midbrain, R3AC+MPTP, mouse3

value: tamoxifen, MPTP


title: P_64


title: sc_Sample 3a [SKG High single cell Rep 2]


title: P_63


title: Midbrain, R3AC+MPTP, mouse2

value: Midbrain


title: Midbrain, R3AC+MPTP, mouse1

value: Ripk3fl/fl Aldh1l1Cre+


title: P_61


title: P_60


title: CPCG-0471


title: sc_Sample 2a [WT High single cell Rep 1]


title: sc_Sample 1b [SKG Low single cell Rep 1]


title: sc_Sample 1a [SKG High single cell Rep 1]


title: CPCG-0324


title: Midbrain, R3AC-MPTP, mouse3


title: P_59


title: CPCG-0409


title: CPCG-0404


title: Midbrain, R3AC+MPTP, mouse4


title: R.315_Contraction_CARNeg_VDJ

city: Boston

first: Jim

last: Kaminski

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description:
10x Genomics
Initial_NHPs.hdf5
Initial_NHP_scVI_model.pt

data_processing:
Paired GEX and VDJ libraries were aligned using the ‘Cellranger multi’ pipeline (v7.0.0) with 32 CPU’s and 128 GB of RAM, with VDJ libraries listed as “vdj-t” to indicate T cell libraries. Samples were aggregated with the ‘Cellranger aggr’ pipeline (v7.0.0) with arguments ‘--normalize=none --nosecondary’. Our reference transcriptome was created with the Cellranger makeref command, and used genome assembly Mmul_10 as the reference genome and Ensembl v107 as the reference set of genomic annotations for the NHP samples, with CAR sequences added. For the scTCR-Seq libraries, we used the reference VDJ set created in (Gerdemann et al 2021) for NHPs
The “filtered_feature_bc_matrix.h5” file and “filtered_contig_annotations.csv” output files from Cellranger were combined into an AnnData object and loaded into scanpy. scTCR-Seq for R.301-R.304 was removed due to low quality. Since the libraries for R.315 and the libraries for R.301-R.304 were generated under different conditions, we decided to keep the two datasets separate rather than attempt to integrate them.
For the Initial NHP dataset, we retained cells that met the following criteria: <10% of the transcripts mapped to the mtDNA, genes detected > 900, and total transcripts between 2,500 and 25,000. For the validation dataset, we retained cells that met the following criteria: <10% of the transcripts mapped to the mtDNA, genes detected > 200, and total transcripts between 1000 and 25,000.
We then identified the 7,500 most variable genes in each of the two datasets and filtered the datasets to these genes along with CD3E, TRAC, CD4, CD8A, and the two CAR transcripts. We then applied PCA, and the neighbors, Leiden (clustering), and UMAP commands from Scanpy with default parameters on each dataset and retained clusters enriched for CD3E and TRAC, and removed those enriched for monocyte and other non-T cell markers.
We then used scvi-tools (v0.19.0) to fit a variational autoencoder (VAE) to each of the datasets. For each dataset, we trained the variational autoencoder on our raw transcript counts using the parameters n_layers=2, n_latent=30, gene_likelihood="nb". We found a small monocyte cluster in the initial NHP dataset, removed these cells, and fit a new VAE to the data.
We used the “get_latent_representation” function from scVI to get the latent space from the VAE for each dataset. We then applied the neighbors, UMAP, and Leiden functions from Scanpy with default settings to obtain clusters and the UMAP dimensionality reduction for the two datasets. We used the “get_normalized_expression” function from scVI with library size set to 10,000 to obtain normalized counts for the cells.
Assembly: Mmul10
Supplementary files format and content: “*.hdf5” files of filtered single-cell data that can be loaded into scanpy, “*.pt” files containing parameters for scVI VAEs .

organism: Macaca mulatta

source_name: peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated from adult NHP peripheral blood by Ficoll-PaquePLUS (GE Healthcare Bio-Sciences) or SepMate-50 (Stemcell). Total T cells were isolated from PBMCs using a T cell isolation kit per manufacturer’s instructions (Miltenyi Biotech). Polyclonal T cells were activated with Miltenyi NHP T cell Activation/Expansion kit (Miltenyi Biotec) in NHP media (X-Vivo 15 medium (Lonza) supplemented with 10% FBS (HyClone/Gibco), and recombinant human IL-2 (rhIL2,50 U/mL; R&D Systems/CellGenix)) with or without 1% penicillin/streptomycin/l-glutamine (Invitrogen), with or without 50 pmol/L p-mercaptoethanol (Sigma). Lentiviral transduction with spinoculation was performed 24-48 hours post stimulation. At the end of the stimulation cycle, stimulation beads were removed using Miltenyi LS columns (Miltenyi Biotec) and cryopreserved. Cryopreserved NHP cells were thawed, stained with fixable Live/Dead stain (Invitrogen), CD4 (BD bioscience, Cat# 563914, RRID:AB_2738485), CD8 (BD bioscience Cat# 563795, RRID:AB_2722501), CD20 (BD Bioscience, Cat# 566988, RRID:AB_2869992) and CD14 (Biolegend, Cat# 301834, RRID:AB_11126983) antibodies. The CAR was detected by staining with an anti-rituximab conjugated flow antibody (GeneTex, Cat# GTX43347, RRID:AB_11166924) in animal R.315 and with an anti-EGFR antibody (R&D systems, Cat# FAB9577G-100) for animals R.301-304. CD3 flow cytometric antibodies were not utilized, to avoid in vitro stimulation, which can result in alteration of the transcriptional profile. Live CARpos and CARneg, CD4/CD8pos and CD20/CD14neg cells were flow cytometrically sorted and immediately processed for single cell sequencing.
All products used in the preparation of these samples, excluding the NHP TCR specific custom primer set, are available from 10x Genomics. Samples in this publication were prepared using the Next GEM 5’ v2 Gel Beads with the i7 Multiplex Plate (Single Index) or the Next GEM Single Cell 5’ v2 Sample Index Plate TT (Dual Index). GEMs were generated using v2 Gel Beads and the v1 Target Enrichment kit utilizing the off-the-shelf human/mouse T Cell Mix 1 and 2 premixed primers for the human samples and substituting the provided primers with custom designed primers as previously described in (Gerdemann et al 2021) for NHP samples.

treatment_protocol: NHP CD20 CAR-T cells were transduced and expanded as previously described in (Taraseviciute et al 2018).

tag: car

value: CARNeg

tag: day

tag: timepoint

value: Contraction

tag: library type

value: VDJ

tag: nhp

value: peripheral blood


title: Midbrain, R3AC-MPTP, mouse2

tag: tissue

tag: treatment


title: CPCG-0458

tag: cell type

tag: biochemical recurrence


title: CPCG-0532

tag: time to last event

tag: age


title: Midbrain, R3AC-MPTP, mouse1


title: sc_Sample 2b [WT Low single cell Rep 1]


title: DOZI_KO_ga_R3

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

data_processing:
Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained.
Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2
Differentially expressed genes are determined by DESeq2  with Padj < 0.01 and absolute log2 fold change higher than 1.
The transcriptional profiles are normalized by TPM for multi-time points or condition comparisons.
Genome_build: pf3D7_V3.0.fasta
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Plasmodium falciparum

source_name: Plasmodium parasite

growth_protocol: 3D7 strains of P. falciparum were cultured in type O+ human RBCs at 5% hematocrit in RPMI 1640 medium supplemented with 25 mM HEPES, 50mg/L hypoxanthine, 25 mM NaHCO3, 0.5% Albumax II and 40 mg/ml gentamicin sulfate. The culture was maintained at 37°C in a gas mixture of 5% CO2, 3% O2 and 92% N2.

extract_protocol:
Parasites of designated developmental stages were harvested after lysis of the RBC membrane with 0.1% (v/v) saponin in PBS. Total RNA was isolated from the purified parasites using Quick-RNA MiniPrep kit (Zymo Research). The RNA was treated with the ezDNaseTM Enzyme (Invitrogen) to remove contaminating genomic DNA. RNA pellets were dissolved in 50 µL RNase-free water, and the RNA integrity was checked using the Agilent Bioanalyzer.
RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. RNA was fragmented by heating at 94 °C for 8 min, and cDNA was synthesized using reverse transcriptase with random primers. Afterward, 3’ dTMP adapters were ligated to the 3’ dAMP library fragments. The quality of the barcoded libraries was validated using the Agilent Bioanalyzer. The DNA 1000 Reagents were used to quantify the library sizes and confirm the absence of primer dimers. Libraries were quantified using a KAPA Universal Library Quantification Kit (Roche), and library concentrations were adjusted for library size. Libraries were sequenced on an Illumina HiSeq 2500 in the Rapid Run mode using 100 nt single read sequencing.

treatment_protocol: To generate stressed schizonts, ring-stage PfDOZI::GFP parasites were synchronized twice in two successive IDCs by 5% D-sorbitol treatment. The synchronized trophozoites were then used to set up culture at 2.0–2.5% parasitemia and 3% hematocrit. On the following day, when the parasitemia reached 10–12%, two-third of the medium was replaced by the fresh medium to generate stressed schizonts.

value: deltapfdozi

tag: Stage

value: gametocyte

value: no treatment


title: P_62

city: Westmead

first: Harry

last: Robertson

institute: Westmead Institute for Medical Research

value: Whole Blood

value: Rej


title: CPCG-0259

city: Toronto

first: Shivani

last: Kamdar

institute: Sinai Health System (LTRI)

value: prostate cancer

value: FALSE

tag: pt

tag: preoperative psa

tag: pathological gleason score


title: R.315_Contraction_CARPos_VDJ

value: CARPos


title: DOZI_KO_ga_R2

tag: genotype


title: R.315_PeakExp_CARNeg_VDJ

value: PeakExp


title: CPCG-0413

tag: metastasis


title: P_57

value: Nill


title: P_56


title: R.315_PeakExp_CARPos_VDJ

tag: car


title: P_55


title: P_58


title: X3D7_ga_R3

value: wildtype


title: CPCG-0454


title: CPCG-0345


title: R.315_Product_CARNeg_VDJ

tag: day

value: Product


title: CPCG-0588


title: R.315_Product_CARPos_VDJ

tag: timepoint


title: X3D7_ga_R2


title: CPCG-0531


title: P_53


title: P_52


title: R.315_Pre_CARNeg_VDJ

value: Pre

tag: library type


title: R.315_Contraction_CARNeg_GEX

value: CARNeg

value: GEX

tag: nhp


title: CPCG-0570


title: X3D7_ga_R1


title: DoziKo_R3_40h

value: schizont


title: P_51

tag: tissue


title: CPCG-0470


title: P_50

tag: treatment


title: DoziKo_R2_40h


title: R.315_Contraction_CARPos_GEX

value: Contraction

value: peripheral blood


title: DoziKo_R1_40h

value: deltapfdozi


title: CPCG-0250

tag: cell type


title: R.315_PeakExp_CARNeg_GEX


title: P_49


title: X3D7_R3_40h

value: no treatment


title: P_54

value: Whole Blood


title: CPCG-0455

tag: biochemical recurrence


title: R.315_PeakExp_CARPos_GEX


title: P_48


title: X3D7_R2_40h


title: R.315_Product_CARNeg_GEX


title: P_47


title: CPCG-0524

tag: time to last event


title: CPCG-0483

tag: age


title: P_46


title: R.315_Product_CARPos_GEX


title: DoziKo_R3_30h

tag: Stage

value: late-trophozoite


title: R.315_Pre_CARNeg_GEX


title: P_45


title: CPCG-0472

value: prostate cancer

value: TRUE

tag: pt


title: R.304_Product_CARNeg_GEX

description:
10x Genomics
Remaining_NHPs.hdf5
Remaining_NHPs_scVI_model.pt


title: DoziKo_R2_30h


title: CPCG-0412

value: FALSE

tag: preoperative psa


title: DoziKo_R1_30h


title: P_44


title: CPCG-0528

tag: pathological gleason score


title: R.304_Product_CARPos_GEX

value: CARPos


title: X3D7_R3_30h

tag: genotype


title: P_43

value: Rej


title: R.304_Pre_CARNeg_GEX


title: P_42

value: Nill


title: CPCG-0396

tag: metastasis


title: CPCG-0342


title: R.304_PeakExp_CARNeg_GEX

tag: car

value: PeakExp


title: DOZI_KO_ga_R1

value: gametocyte


title: CPCG-0464


title: P_41


title: X3D7_R1_40h

value: wildtype


title: X3D7_R1_30h


title: X3D7_R2_30h


title: ILWT, rep3

tag: strain

value: Ileum


title: R.304_PeakExp_CARPos_GEX

tag: day

tag: timepoint

value: GEX


title: CPCG-0268


title: P_40


title: R.303_Pre_CARNeg_GEX

value: CARNeg

value: Pre

tag: library type

tag: nhp


title: DoziKo_R3_20h

value: deltapfdozi

value: early-trophozoite

tag: treatment


title: P_39

tag: tissue

value: Whole Blood


title: P_38


title: S01-5046

tag: cell type

tag: biochemical recurrence


title: R.303_PeakExp_CARNeg_GEX

value: peripheral blood


title: DoziKo_R2_20h

value: no treatment


title: DoziKo_R1_20h


title: CPCG-0521

value: prostate cancer

value: TRUE

tag: time to last event

tag: age


title: R.303_PeakExp_CARPos_GEX

value: CARPos


title: P_37


title: S01-20390

tag: pt

value: FALSE


title: X3D7_R3_20h

tag: Stage


title: R.303_Contraction_CARNeg_GEX

value: Contraction


title: S00-10059

tag: preoperative psa

tag: pathological gleason score


title: P_36

value: Nill


title: X3D7_R2_20h

tag: genotype


title: R.303_Contraction_CARPos_GEX

tag: car


title: S01-26545

tag: metastasis


title: P_35


title: P_34


title: X3D7_R1_20h


title: R.301_Pre_CARNeg_GEX

tag: day


title: DoziKo_R3_10h

value: Ring


title: R.301_PeakExp_CARNeg_GEX

tag: timepoint

value: PeakExp


title: P_33


title: S98-28609


title: S01-23163


title: P_32


title: R.301_PeakExp_CARPos_GEX

tag: library type


title: S01-12770


title: S99-14702


title: DoziKo_R1_10h


title: R.301_Day28_CARNeg_GEX

tag: nhp


title: P_31

tag: treatment


title: R.301_Day28_CARPos_GEX

tag: tissue


title: P_30

value: Rej


title: X3D7_R3_10h

value: wildtype


title: X3D7_R2_10h


title: R.301_Day22_CARNeg_GEX

value: CARNeg

value: GEX


title: CPCG-589

tag: cell type


title: CPCG-605

tag: biochemical recurrence


title: X3D7_R1_10h


title: enriched-NIK3x-BS2 (nucleolar)-transfected and AC-2 treated-biol rep 2 [G2]

city: Chicago

first: Bryan

last: Dickinson

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

description:
enriched RNA
Table1_Filtered_TMM_normalized_cpm_reads_all_samples

data_processing:
The RNA-seq library generated were mapped to the Homo sapiens GRCh38 reference genome using STAR, version 2.7.9a. ligned reads were quantified using Salmon, version 1.4.0
Annotation data from Gencode V34 was used to summarize data from transcript-level to gene-level. Filtering was carried out to remove particular gene biotypes or genes with low expression and selected the following gene biotypes of interest: protein coding, lncRNA, Mt_rRNA, Mt_tRNA, rRNA, snRNA, scRNA, snoRNA.
To identify differentially expressed genes, precision weights were applied to TMM-normalized gene counts based on within-group sample-level variance and gene-level mean-variance trends using VOOM. The count data was fitted to a gene-wise linear model with group status as a coefficient, and contrasts were specified for comparisons of interest. The Limma empirical Bayes method was used to estimate the posterior odds of differential expression (|logFC| > 0) after adjusting for gene-level posterior residual standard deviations.
Assembly: GRCh38
Supplementary files format and content: Filtered and TMM normalized log2cpm reads for all samples.

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM (GlutaMAX™, high glucose, sodium pyruvate, phenol red) supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin/streptomycin. Cells were maintained in a water-saturated, 5% CO2-containing, 37°C incubator.

extract_protocol:
RNA was extracted with QIAGEN Rneasy Plus Mini Kit, followed by Click reaction with biotin and enrichment of biotinylated RNA.
The enriched RNAs for all the samples were subjected to polyA capture and subsequently the DNA library with dual-index adapters was generated and amplified using the mRNA Hyper Prep Kit (Kapa Biosystems, KK8581) following manufacturer’s protocol

treatment_protocol: BS2 plasmid with different subcellular localization tags was transfected at 70% confluency using Lipofectamine 3000. 24 hr post-transfection, cells were treated with 50µM AC-2 for 3 min at 37°C, quenched with 1mM PMSF solution, washed twice with DPBS, and then RNA was harvested.

tag: cell line

value: HEK293T cells

value: human embryonic kidney 293 cells

value: Transient expression of BS2 in the nucleolus

value: AC-2 treatment for 3 min


title: R.301_Day22_CARPos_GEX

value: peripheral blood


title: P_28

address: 176 Hawkesbury Rd

value: Whole Blood


title: ulcerative colitis colon biopsy, rep 16

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

data_processing:
Fastq files were processed with trimmomatic (v. 0.39) to remove adaptor contamination and poor-quality bases.
The resulting read files were mapped to the GRCh38 assembly of the human genome using Hisat2 (v. 2.2.1) with default parameters.
The number of reads mapping uniquely and concordantly to the genomic features annotated in Ensembl with a MAPQ score higher than or equal to 10 was calculated for all samples using htseq-count (v. 0.11.3) with default parameters.
Assembly: GRCh38
Supplementary files format and content: file in comma-separated value format reporting the number of read counts mapped to each gene in each sample

source_name: colon

extract_protocol:
Total RNA was isolated from whole tissue biopsies using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. On-column DNase digestion was performed to remove any residual genomic DNA (Qiagen). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with hairpin loop structure were ligated. The library fragments were then purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: colon

tag: condition

value: active ulcerative colitis


title: CPCG-596

address: 60 Murray Street

value: prostate cancer

value: FALSE

tag: time to last event

tag: age

tag: pt


title: R.302_Pre_CARNeg_GEX

value: Pre


title: enriched-NIK3x-BS2 (nucleolar)-transfected and AC-2 treated-biol rep 1 [G1]


title: P_27

value: Nill


title: P_26


title: ulcerative colitis colon biopsy, rep 14


title: R.302_PeakExp_CARPos_GEX

value: CARPos

value: PeakExp


title: R.302_PeakExp_CARNeg_GEX


title: enriched-mitochondrial-BS2-transfected and AC-2 treated-biol rep 2 [E2]

value: Transient expression of BS2 in the mitochondria


title: P_25


title: ulcerative colitis colon biopsy, rep 13


title: DoziKo_R2_10h

value: deltapfdozi

tag: Stage

value: Ring

value: no treatment


title: enriched-nuclear-BS2-transfected and AC-2 treated-biol rep 3 [C3]

value: HEK293T cells

value: human embryonic kidney 293 cells

tag: genotype

value: Transient expression of BS2 in nucleus


title: P_29

value: Rej


title: ulcerative colitis colon biopsy, rep 12


title: P_24

value: Whole Blood


title: enriched-nuclear-BS2-transfected and AC-2 treated-biol rep 2 [C2]

value: AC-2 treatment for 3 min


title: ulcerative colitis colon biopsy, rep 11

value: colon

value: active ulcerative colitis


title: P_23


title: C2C12 cells, siNr2f6.4, Day 3

city: Campinas

first: Dimitrius Santiago

middle: Passos Simoes Froes

last: Guimaraes

state: Sao Paulo

address: Carl von Linneaus

department: BFM

country: Brazil

institute: Unicamp

data_processing:
Quality control with Trimmomatic, Alignment with RNAstar 2.7 and Differential expression by EdgeR
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (Headcrop = 10, AvgQual = 20, MinLEn = 20)
Assembly: mm10
Supplementary files format and content: Excel file containing normalized counts data (CPM) and differential expression statistics.

growth_protocol: C2C12 myoblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), antibiotics and pyruvatei in humidified atmosphere with 5% CO2 at 37C. After confluency FBS was in the media was switched to 2% HS.

extract_protocol:
Cells were harvested in TriZOL and RNA purified in RNAsy collumns.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA LT Sample Prep Kit (Human  Mouse Rat) following manufacturer's protocols (TruSeq Stranded Total RNA Sample Prep Guide, Part #  15031048 Rev. E)

treatment_protocol: 200 nM siScr or siNr2f6 transfected with Lipofectamine RNAiMax at Day 0 and collected 72 hours later.

value: myogenic

value: Nr2f6 knockdown

value: myogenic differentiation

tag: time

value: Day 3


title: ulcerative colitis colon biopsy, rep 15


title: ulcerative colitis colon biopsy, rep 10


title: enriched-nuclear-BS2-transfected and AC-2 treated-biol rep 1 [C1]


title: enriched-cytoplasmic-BS2-transfected and AC-2 treated-biol rep 2 [B3]

value: Transient expression of BS2 in cytosol


title: P_22

state: NSW

value: Nill


title: healthy colon biopsy, rep 6

value: healthy


title: enriched-mitochondrial-BS2-transfected and AC-2 treated-biol rep 1 [E1]

value: Transient expression of BS2 in the mitochondria


title: P_21


title: C2C12 cells, siNr2f6.1, Day 3


title: P_20


title: healthy colon biopsy, rep 5


title: C2C12 cells, siNr2f6.2, Day 3


title: R.302_Contraction_CARPosAndCARNeg_GEX

tag: car

value: CARPosAndCARNeg

value: Contraction

value: GEX

value: peripheral blood


title: enriched-cytoplasmic-BS2-transfected and AC-2 treated-biol rep 1 [B2]

value: HEK293T cells

value: human embryonic kidney 293 cells


title: enriched-non-transfected and AC-2 treated-biol rep 3 [A3]

value: WT

value: AC-2 treatment for 3 min


title: P_19

value: Whole Blood

value: Rej


title: C2C12 cells, siScr4, Day 3

value: myogenic


title: P_18


title: healthy colon biopsy, rep 4

value: colon


title: ulcerative colitis colon biopsy, rep 9

value: active ulcerative colitis


title: C2C12 cells, siNr2f6.5, Day 3

value: Nr2f6 knockdown

value: myogenic differentiation

value: Day 3


title: enriched-non-transfected and AC-2 treated-biol rep 2 [A2]


title: C2C12 cells, siScr3, Day 3


title: ulcerative colitis colon biopsy, rep 8


title: input-mitochondrial-BS2-transfected and AC-2 treated [EE1]

description: Table1_Filtered_TMM_normalized_cpm_reads_all_samples

value: Transient expression of BS2 in the mitochondria


title: P_16

value: Nill


title: C2C12 cells, siNr2f6.3, Day 3


title: C2C12 cells, siScr2, Day 3


title: enriched-non-transfected and AC-2 treated-biol rep 1 [A1]


title: ulcerative colitis colon biopsy, rep 7


title: P_15


title: ulcerative colitis colon biopsy, rep 6


title: C2C12 cells, siScr1, Day 3


title: input-nuclear-BS2-transfected and AC-2 treated [CC1]

value: Transient expression of BS2 in nucleus


title: normalized_DOZI_Ga_IP2

value: GFP tagging

value: gametocyte

value: no treatment


title: P_14


title: input-cytoplasmic-BS2-transfected and AC-2 treated [BB1]

value: HEK293T cells

value: human embryonic kidney 293 cells

value: Transient expression of BS2 in cytosol


title: ulcerative colitis colon biopsy, rep 5


title: ulcerative colitis colon biopsy, rep 4


title: P_13

value: Whole Blood


title: input-non-transfected and AC-2 treated [AA1]

value: WT

value: AC-2 treatment for 3 min


title: P_12


title: normalized_DOZI_Ga_Input2


title: SMC from mosue skeletal muscle vasculature-iSM-G5C-KO1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38.p5) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm10
Supplementary files format and content: library size normalized counts

source_name: C57BL6J, Gprc5c-floxed, male, age 8-24 weeks, skeletal muscle

extract_protocol:
For RNA sequencing, EGFP-expressing SMC were isolated from skeletal muscle vasculature of tamoxifen-induced control and iSM-G5C-KOs carrying the mTmG reporter strain. To do so, freshly isolated mouse skeletal muscles were chopped on ice into small pieces using surgical scissors,  digested with 0.2 mg/ml collagenase II (Worthington Biochemical Corporation, 4174) and 0.2 mg/ml dispase II (ThermoFischer, 17105041) in HBSS at 37°C for 30 min with 300 rpm shaking. By the end of the digestion procedure, cell suspensions were immediately filtered through 100 µm cell strainers, centrifuged at 1000 x g for 4 min at 4°C. Cell pellets were then suspended in cold HBSS containing 1% BSA, incubated with APC conjugated anti-CD31 (eBioscience, 17-0311), anti-CD45 (eBioscience, 17-0451-82) and anti-Ter119 (eBioscience, 17-5921) antibodies (dilution 1:100) for 15 min at 4°C to enable non-SMC depletion using anti-APC beads (Miltenyi Biotec, 130-090-855) following instructions of AutoMACS Pro Separator (Miltenyi Biotec). The negative AutoMACS fractions were centrifuged at 1000 x g for 4 min at 4°C and resulting cell pellets were suspended in 1 ml cold DMEM. With the DAPI based live/dead gating strategy, viable EGFP-positive cells were sorted into 1.5 ml reaction tubes containing cold DMEM/PBS (v/v 1:1) using BD FACSAria III or BD FACSMelody and spun down at 600 x g for 5 min at 4°C. Supernatants were removed and RNA were isolated as described above.
5ng total RNA was used as input for SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian Kit (Takara Bio).

value: vascular smooth muscle cells


title: normalized_DOZI_Schi_IP2

value: schizont


title: healthy colon biopsy, rep 3

value: colon

value: healthy


title: SMC from mosue skeletal muscle vasculature-iSM-G5C-KO2

value: C57BL6J, Gprc5c-floxed, male, age 8-24 weeks, skeletal muscle


title: healthy colon biopsy, rep 2


title: P_11


title: healthy colon biopsy, rep 1


title: normalized_DOZI_Ga_IP1


title: P_9


title: SMC from mosue skeletal muscle vasculature-iSM-G5C-KO3


title: normalized_DOZI_Ga_Input1


title: SMC from mosue skeletal muscle vasculature-Ctrl3

value: wild type


title: normalized_DOZI_Schi_IP1


title: ulcerative colitis colon biopsy, rep 3

value: active ulcerative colitis


title: P_17

value: Rej


title: normalized_DOZI_Schi_Input2

value: GFP tagging


title: P_8


title: P_10

value: Nill


title: SMC from mosue skeletal muscle vasculature-Ctrl1


title: ulcerative colitis colon biopsy, rep 2


title: SMC from mosue skeletal muscle vasculature-Ctrl2


title: ulcerative colitis colon biopsy, rep 1


title: DOZ.KO_Stress_Schi_3

value: deltapfdozi

value: nutrient starvation


title: mTEC-Org, DM+RR, double-neg, scRNA-seq

city: Utrecht

first: Sangho

last: Lim

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the mouse reference genome (GRCm38, ENSEMBL release 98). For DM+RR differentiated organoids sequencing, which contain Aire-P2A-tdTomato reporter, tdTomato sequence was added to detect Aire-P2A-tdTomato expression.
Assembly: GRCm38
Supplementary files format and content: h5Seurat

source_name: Thymus

extract_protocol:
Live cells were sorted into 384-well hard shell plates (Bio-rad) with vapor-lock (Qiagen) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4 bp random molecular barcode (UMI), a cell-specific barcode, the 5'-Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to -80°C. Before starting with SORT-seq protocol, cells were lysed 5 min at 65°C.
After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT). Following amplification, library preparation was performed following the CEL-Seq2 protocol (Hashimshony et al., 2016) to prepare a cDNA library for sequencing using TrueSeq small RNA primers (Illumina).  The DNA library was paired-end sequenced on an Illumina Nextseq 500, high output, with a 1 x 75 bp illumina kit.

value: Thymus

value: organoid

value: epithelial cell

value: DM+RR


title: P_7

value: Whole Blood


title: P_6


title: DOZ.KO_Stress_Schi_2


title: scc, scRNA-seq

city: changsha

first: Liqing

last: Ding

address: xiangya street

institute: Central South University

description:
BD Biosciences
cell status used in BD210207002_Sample_Tag_Calls.csv:CA

data_processing:
Data analysis was performed with the R package Seurat V4.1.0 13 and R V4.1.3. Cells were filtered for greater than 300 genes, more than 500 unique molecular identifiers (UMI), log10 of the ratio of genes over UMI per cell more than 0.75, and less than 50 percent mitochondrial genes. Sctransform was used for data normalization, and canonical correlation analysis (CCA) and mutual nearest neighbor (MNN) analyses were used to integrate data from all samples.
Assembly: hg18
Supplementary files format and content: matrix files

source_name: skin

extract_protocol:
We obtained broad bean-sized tissues at the sites diagnosed as BP and cSCC respectively during the operation. Among them, cSCC was differentiated according to the paracancerous and cancerous center, and NS was obtained as the control. All the tissues were embedded in wax, stained with HE, and built a single-cell library.
In order to the origin of labeled cells, every antibody-oligo in the BD Human Single-Cell Multiplexing Kit referred to as a sample tag has a unique sample oligo barcode conjugated to a human universal antibody. Single-cell capture and cDNA synthesis were performed on the BD Rhapsody Single-Cell Analysis System (BD Biosciences). Then, the single-cell library was generated and sent to sequencing on the Illumina platform. The single-cell sequencing data were aligned and quantified using the BD Rhapsody whole transcriptome analysis local bioinformatics pipeline.

value: skin

value: Stromal cells and immune cells

tag: disease state

value: squamous cell carcinoma

value: enzyme digestion


title: mTEC-Org, DM+RR, clover-pos, scRNA-seq


title: P_5


title: P_4


title: X3D7_Stress_Schi_3

value: wildtype

value: schizont


title: mTEC-Org, DM, replicate 2, scRNA-seq

value: wild-type

value: DM


title: hpv, scRNA-seq

description:
BD Biosciences
cell status used in BD210207002_Sample_Tag_Calls.csv:HPV


title: nc, scRNA-seq

description:
BD Biosciences
cell status used in BD210207002_Sample_Tag_Calls.csv: NC

value: normal skin


title: normalized_DOZI_Schi_Input1

value: GFP tagging

value: no treatment


title: X3D7_Stress_Schi_2

value: nutrient starvation


title: P_2

value: Nill


title: X3D7_Stress_Schi_1


title: mTEC-Org, DM, replicate 1, scRNA-seq

value: Thymus

value: organoid


title: mTEC-Org, EM, scRNA-seq

value: epithelial cell

value: EM


title: Amygdala, Rhesus Monkeys and Humans

city: Davis

first: Andrew

last: Fox

address: 1 Shields Ave

institute: University of California, Davis Davis, CA

data_processing:
Alignment and count matrix generation was performed using the parse biosciences pipeline. Preprocessing, visualization and clustering was performed on the generated count matrix using scanpy (version 1.8.2) and anndata (version 0.7.8).
Sequenced reads from Human and Rhesus FASTQ files were aligned to the GRCH38 and RheMac10 genome assemblies. Rhesus reference genome was built using annotations created by the Comparative Annotation Toolkit (CAT). Human samples were annotated using the latest Ensembl annotation (Ensembl release 106).
Assembly: GRCH38 and RheMac10
Supplementary files format and content: .h5ad

organism:
Macaca mulatta
Homo sapiens

source_name: Brain

extract_protocol:
Single nuclei suspensions were made following minor modifications to 10x genomics demonstrated protocol: Nuclei Isolation from Cell Suspensions and Tissue for Single Cell RNA Sequencing. (CG000124 revE). Briefly, 1 ml of lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Nonidet P40 substitute, in nuclease free water) was added to each sample, homogenized 20x, and incubated on ice for 5 minutes. Samples were centrifuged at 850 RCF for 5 minutes at 4C. The resulting pellet was rinsed 3 times by resuspending in 1.5% BSA in PBS and centrifuged at 850 RCF for 5 minutes at 4C. Finally, the pellet was resuspended in 250ul 1.5% BSA in PBS and passed through 40µm Flowmi Cell strainer (Bel-art, H13680-0040).
All barcoding and library preparation was performed by the UC Davis Genomics Core using the Single Cell Whole Transcriptome Kit (W01030, V1.3.1 Parse Biosciences) with strict adherence to manufacturer’s instructions
Libraries were prepared by the UC Davis Genomics Core and sequenced on a NovaSeq S4 300 150 bp pair-ended reads (PE150)

value: Brain

tag: tissue region

value: amygdala

tag: amygdala region

value: mixed sample (ce, lat)

tag: subject id


title: F1 ram Sperm, OVER, rep3

status: Public on Apr 04 2024

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
The raw reads pre-process, map and annotate to the sheep genome were performed using the software SPORTS1.0 with default settings.
Specific small RNA composition from treatment groups were established and differential expression of small RNA were revealed using a R package edgeR with cutoff set as FDR <0.05 and fold change >2 after normalization of reads per million (RPM)
Assembly: Oar_v4.0/oviAri4
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Ovis aries

source_name: Semen

extract_protocol:
the sperm were treated with somatic cell lysis buffer (0.1 % SDS, 0.5 % Triton X in DEPC H2O) for 40 min on ice to eliminate somatic cell contamination, followed by centrifugation at 600g for 5 minutes. The sperm pellet was washed and used for RNA extraction using TRIzol reagent.
Small RNA libraries were constructed according to the NEBNext Small RNA Library Prep Kit protocol, employing 15 to 50 nt small RNA pre-size selection, followed by the standard cDNA library construction using NEBNext Small RNA Library Prep Kit and sequencing with Illumina NovaSeq 6000 platform.

value: Semen

value: Sperm

value: WT

tag: treatment

value: Over feeding


title: F1 ram Sperm, OVER, rep2

tag: tissue


title: F1 ram Sperm, RES, rep1

tag: cell type

value: Restricted feeding


title: F1 ram Sperm, OVER, rep1


title: F1 ram Sperm, CON, rep2

value: Standard feeding


title: F1 ram Sperm, CON, rep1


title: pc-scc, scRNA-seq

description:
BD Biosciences
cell status used in BD210207002_Sample_Tag_Calls.csv:CJ

value: skin

value: Stromal cells and immune cells

value: paracancerous squamous cell carcinoma

value: enzyme digestion


title: F1 ram Sperm, CON, rep3


title: F1 ram sperm, RES, rep5

data_processing:
The sequencing adapters were removed by TrimGalore-0.4.3
The reads were removed if they had a quality score lower than 20, length less than 36 and a total number of 15 Ns or more. FastQC
The first 12 bp at the 5′ end of both pairs were found to be of low quality and removed. Trimmed sequences were mapped to the bovine genome UMD3.1.1 using Bismark - v.0.18.1
Assembly: Oar_v4.0/oviAri4

source_name: semen

extract_protocol:
the sperm were treated with somatic cell lysis buffer (0.1 % SDS, 0.5 % Triton X in DEPC H2O) for 40 min on ice to eliminate somatic cell contamination, followed by centrifugation at 600g for 5 minutes. The sperm pellet was washed and used for DNA extraction using TRIzol reagent.
DNA extraction, MspI digestion, end-repair, dA-tailing, adaptor ligation, and bisulfite conversion were conducted in a single tube to minimize DNA loss. Amplified DNA fragments of 200 to 500 bp were size selected using a 2% agarose gel.

value: semen

value: sperm


title: F1 ram sperm, RES, rep4


title: F1 ram sperm, RES, rep3


title: DOZ.KO_Stress_Schi_1

value: deltapfdozi

value: schizont

value: nutrient starvation


title: F1 ram sperm, RES, rep2


title: P_3

value: Whole Blood

value: Nill


title: mTEC-Org, DM+RR, tdTomato-pos, scRNA-seq

value: Thymus

value: organoid

value: epithelial cell

value: DM+RR


title: F1 ram sperm, RES, rep1

value: WT

value: Restricted feeding


title: F1 ram sperm, OVER, rep3

value: Over feeding


title: F1 ram sperm, OVER, rep5


title: F1 ram sperm, OVER, rep4


title: P_1


title: F1 ram sperm, OVER, rep2


title: F1 ram sperm, OVER, rep1


title: F1 ram Sperm, RES, rep3

value: Semen

value: Sperm


title: F1 ram sperm, CON, rep1

value: Standard feeding


title: MCF7  cells, LY2603618 treated

city: Columbus

first: Chandra

middle: Bhushan

last: Prasad

state: OH

address: 460 W. 12th Ave. Biomedical Research Tower, Room 460G

department: radiation Oncology

institute: OSU Wexner Medical Center

data_processing:
TrimGalore was used for trimming and quality evaluation of the sequences from the shRNA samples. Sequences that passed the quality filters were aligned to the shRNA library sequences provided by Dharmacon (GE). The R package DESeq was used to determine whether there was differential expression.
Assembly: hg38
Supplementary files format and content: Output excel file includes raw count for each samples.
Library strategy: DNA-seq

source_name: Breast

growth_protocol: H1299 and MCF7 cells were mainteined in DMEM supplemented with 10% FBS and antibiotic in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Genomic DNA was extracted using DNesy kit (Qiagen).  1μg of total DNA was used for library preparation.
PCR amplification of shRNA, and PCR product purification were performed according to the manufacture's (RHS6083) protocol. Purified amplicons from different samples were pooled and analyzed with a Bioanalyzer (Agilent).

treatment_protocol: Cell were trasfected with shRNA lentivirus pool and puromycin selection was done for 5 days. After puromycin selection cell were treaed with 1uM CHK1 inhibitor LY2603618.

value: Breast

value: Epithelial cells

value: LY2603618 treated


title: F1 ram Sperm, RES, rep2


title: F1 ram sperm, CON, rep2

value: semen

value: sperm


title: H1299 Cells, LY2603618 treated

source_name: Lung

value: Lung


title: H1299 cells, Untreated

value: Untreated


title: DamID_DamControl_K562_LBRLMNAKO_r2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-LMNA-KO
K562_r8_LMNALBR_14_LMNB1-25kb.bw

data_processing:
1. DamID: the full protocol is described in the corresponding manuscript; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts; remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17; reads overlapping GATC fragments were counted in 50 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of the target protein over the Dam control using custom R scripts.
2. RNA-seq: the full protocol is described in the corresponding manuscript; adapter sequences and low quality reads were removed with fastp 0.12.2; reads were aligned to hg38 and counted in gencode v24 genes with STAR 2.5.4a; STAR was also used to create BigWig tracks of uniquely mapped reads; DESeq2 was used to call differentially expressed genes and compute FPKM values.
3. Repli-seq: adapter sequences and low quality reads were removed with fastp 0.12.2; reads were processed as described for DamID, except that duplicated reads were removed and reads were not required to overlap with GATC fragments.
Assembly: hg38
Supplementary files format and content: 1. DamID: BigWig files of log2-normalized pADamID scores for 25 kb genomic bins; 2. RNA-seq: BigWig files of read coverage, tsv file with read counts; 3. Repli-seq: BigWig tracks of quantile-normalized early/late log2-ratios (linked to the corresponding *early sample records).

growth_protocol: K562 cells (from ATCC) were cultured according to their ATCC guidelines.

extract_protocol:
1. DamID: Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit; 2. RNA-seq: RNA was isolated using the Qiagen RNeasy column purification kit; 3. Repli-Seq: cells were harvested by centrifugation and immediately fixed in ice-cold ethanol.
1. DamID: the full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at m6A-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified and further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; 2: RNA-seq: sequencing libraries were prepared using the Illumina TruSeq polyA stranded RNA kit; 3: replicated DNA was enriched for with a BrdU IP, before libraries were prepared as described in Marchal, 2018.
1. OTHER: DamID; 2. RNA-seq; 3. OTHER: Repli-seq

treatment_protocol: 1. DamID: cells were transduced with lentivirus containing Dam constructs. Three days after transduction, genomic DNA was isolated.; 2. Repli-seq: BrdU was added to a final concentration of 100 uM and cells were incubated at 37 °C for another 2 h.

value: LBR/LMNA DKO


title: DamID_DamControl_K562_LBRLMNAKO_r1

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-LMNA-KO
K562_r7_LMNALBR_14_LMNB1-25kb.bw


title: DamID_DamControl_K562_LMNAKO_r1

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LMNA-KO
K562_r7_LMNA_14_LMNB1-25kb.bw

value: LMNA KO


title: DamID_DamControl_K562_LBRKO_r2

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-KO
K562_r2_LBRKO_LMNB1-25kb.bw

value: LBR KO


title: DamID_DamControl_K562_LBRKO_r3

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-KO
K562_r8_LBR_1_LMNB1-25kb.bw


title: DamID_LMNB1_K562_LBRLMNAKO_r2

description:
Lamin B1 DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
K562_LMNALBR_LMNB1_14-25kb-combined.bw


title: DamID_DamControl_K562_wt_r2

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
K562_r2_17_LMNB1-25kb.bw


title: DamID_LMNB1_K562_LBRLMNAKO_r1


title: DamID_DamControl_K562_wt_r1

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
K562_r1_17_LMNB1-25kb.bw


title: DamID_LMNB1_K562_LMNAKO_r2

description:
Lamin B1 DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
K562_LMNA_LMNB1_14-25kb-combined.bw


title: DamID_LMNB1_K562_LMNAKO_r1


title: DamID_LMNB1_K562_LBRKO_r3

description:
Lamin B1 DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
K562_LBRKO_LMNB1-25kb-combined.bw


title: DamID_LMNB1_K562_LBRKO_r2


title: DamID_LMNB1_K562_wt_r3

description:
Lamin B1 DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
K562_17_LMNB1-25kb-combined.bw


title: F1 ram sperm, CON, rep3


title: DamID_LMNB1_K562_wt_r1


title: RNAseq_K562_LBRLMNAKO_r1

description:
5822_4_4_GATCAGA_S57
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-LMNA-KO
rna_seq_count_table.tsv


title: F1 ram sperm, CON, rep4


title: RNAseq_K562_LMNAKO_r2

description:
5822_8_8_CGATGTA_S60
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LMNA-KO
rna_seq_count_table.tsv


title: DamID_LMNB1_K562_LBRKO_r1


title: RNAseq_K562_LBRLMNAKO_r2

description:
5822_10_10_ACAGTGA_S62
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-LMNA-KO
rna_seq_count_table.tsv


title: DamID_LMNB1_K562_wt_r2


title: RNAseq_K562_LMNAKO_r1

description:
5822_2_2_ACTGATA_S55
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LMNA-KO
rna_seq_count_table.tsv


title: RNAseq_K562_LBRKO_r3

description:
5287_12_K562_17_LBRKO_19_r3_CTTGTAA_S48
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-KO
rna_seq_count_table.tsv


title: DamID_DamControl_K562_LMNAKO_r2

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LMNA-KO
K562_r8_LMNA_14_LMNB1-25kb.bw


title: RNAseq_K562_LBRKO_r2

description:
5287_11_K562_17_LBRKO_19_r2_GGCTACA_S47
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-KO
rna_seq_count_table.tsv


title: MCF7 cells, Untreated


title: RNAseq_K562_wt_r2

description:
5287_2_K562_17_r2_CGATGTA_S39
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
rna_seq_count_table.tsv


title: RNAseq_K562_LBRKO_r1

description:
5287_10_K562_17_LBRKO_19_r1_TAGCTTA_S46
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-KO
rna_seq_count_table.tsv


title: DamID_DamControl_K562_LBRKO_r1

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-KO
K562_r1_LBRKO_LMNB1-25kb.bw


title: RNAseq_K562_wt_r3

description:
5287_3_K562_17_r3_TTAGGCA_S40
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
rna_seq_count_table.tsv


title: DamID_DamControl_K562_wt_r3

description:
Dam control DamID on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
K562_r8_WT_1_LMNB1-25kb.bw