title: Cultured SVF cells, eWAT, scRNA seq

description: 10x Genomics


title: Cultured DFAT cells, eWAT, scRNA seq

status: Public on Mar 05 2025

type: SRA

city: Beijing

first: Meng

last: Xie

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw fastq sequencing data were processed using Cell Ranger 7.0.0 with the "--include-introns" option enabled to include reads mapping to the introns annotated in Ensembl, and the mm10 mouse reference genome was utilized to quantify gene expression levels.
Assembly: mm10
Supplementary files format and content: *barcodes.tsv.gz: gzipped tab-separated values (TSV) file containing unique cell barcodes. *DFAT_features.tsv.gz: gzipped tab-separated values (TSV) file containing feature (gene) information, including gene names and identifiers. *DFAT_matrix.mtx.gz: gzipped Matrix Market (MTX) file containing the sparse expression matrix with gene counts per cell, indexed by cell barcodes and features.

molecule: total RNA

organism: Mus musculus

source_name: Adipose tissue

extract_protocol:
Adherent cells were gently washed 3 times with PBSto remove residual culture medium and debris. An appropriate amount of 0.25% Trypsin-EDTA(Gibco, Cat#25200-056) was added to ensure complete coverage of the cells, which were then incubated at 37°C for 3-5 minutes. Cell morphology changes were observed under a microscope, and when the cells became round and began to detach from the culture plate, the plate was gently shaken to facilitate cell detachment. Complete culture medium containing serum was added to terminate the dissociation process. Complete culture medium containing serum was added to terminate the dissociation process. The cell suspension was centrifuged at 450g for 10 minutes to obtain a cell pellet, which was then resuspended in sorting buffer supplemented with 2% FBS.
Isolated cells were stained with 7-AAD at a concentration of 5 μg/mL and subjected to FACS sorting. Number of cells were quantified with a Countstar Rigel S5 Automated Cell Counter. Approximately 20,000 cells were applied to the Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10x Chromium Controller using the Single-Cell 3′ Reagent Kit v3.1 (10x Genomics). The following program was used for GEM-Reverse Transcription: 53℃ for 45 min, 85℃ for 5 min, and held at 4℃. The resulting emulsions were lysed for cDNA isolation and purification with the Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Scientific) and amplified with PCR. cDNA quality was assessed with an Agilent 2100 Bioanalyzer. cDNA amplicon size was optimized by enzymatic fragmentation and size selection. P5, P7, i7, and i5 sample indexes and TruSeq Read 2 (read 2 primer sequence) were added by end repair, A-tailing, adaptor ligation, and PCR, respectively. Final libraries containing the P5 and P7 primers were sequenced by an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads, aiming for a coverage of approximately 50,000 raw reads per cell.

tag: tissue

value: Adipose tissue

tag: cell line

value: Primary cultured cells

tag: cell type

value: DFAT cells


title: Al1-29_ZT13_20-3

city: St. Paul

first: kathleen

last: Greenham

state: MN

address: 1445 Gortner Avenue

country: USA

institute: University of Minnesota

library_source: transcriptomic

data_processing:
Raw reads were mapped to a concatenated reference consisting of B. rapa R500 v1.2 (Lou et al., 2020) and B. olerarcea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77)  genomes.
The reads were trimmed and filtered by quality using Trimmomatic v0.33, and alignment was performed using HISAT2 2.1.0.
Raw counts were normalized using the R package edgeR
Genes with no variance in expression across the time series were removed and are referred to as 'Processed Genes' which are available on the GreenhamLab GitHub.
We further filtered out lowly expressed genes by retaining those with a mean log2 FPKM greater than zero in at least one time point.
Gene expression for any missing replicate (See MetaData table) was imputed as the median of the two remaining replicates for that time point.
Assembly: We used a concatenated genome consisting of B. rapa R500 v1.2 (Lou, P. et al. (2020). Genetic and genomic resources to study natural variation in Brassica rapa. Plant Direct 4: e00285) and B. oleracea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77.) genomes.
Supplementary files format and content: Raw counts for each gene (rows) at every timepoint and treatment (columns). ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.
Supplementary files format and content: Normalized counts for each gene (rows) at every timepoint and treatment (columns). We require at least one sample (where a sample is a full time course for a single plant) to have mean FPKM greater than zero to be kept as a "processed gene". ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.

organism: Brassica napus

source_name: leaf

growth_protocol: Seeds were inbibed on wet whatman paper for five days before sowing into 4inch wide pots filled with MetroMix360. Growth conditions were 28C/22C day/night temperatures, 14 hour day lengths with 400 umol/m2/s light intensity and 40% relative humidity for the duration of the four week experiment.

extract_protocol:
Leaf tissue from the apex of the youngest leaf from three individual plants was collected at_ZT (Zeitgeber; hours after dawn) 1, 7, 13, and 19. RNA was isolated using the MagMAX Plant RNA Isolation Kit (Thermo Fisher Scientific, Waltham MA).
Illumina TruSeq Stranded mRNA HT

treatment_protocol: Plants were equally separated into two treatments for the duration of the experiment: 100% watering (well-watered) and 20% watering (water limited). The target watering weights were determined as described in Fahlgren et al. (Fahlgren et al., 2015). All pots were watered once to 100% capacity on the first day of the experiment, and then weighed twice per day to maintain a target water weight through day seven on the Bellwether phenotyping platform. Starting on day eight, water limited plants were allowed to dry down to 20% capacity and maintained at 20% capacity until day 14 (seven days after water limitation treatment began). At this point all watering amounts were increased by 10% for the rest of the experiment.

value: leaf

tag: temperature

tag: photoperiod

tag: timepoint (zt_=_hours_after_dawn)

tag: genotype

tag: treatment

value: Water limited, 20% full capacity


title: Al1-29_ZT7_20-3


title: Al1-29_ZT19_100-2

value: Well watered, 100% full capacity


title: Al1-29_ZT7_100-3


title: Al1-29_ZT13_100-3


title: mouse_3mth_FMC_ON

city: Saint Louis

first: David

middle: H.

last: Gutmann

state: MO

address: 1 Childrens Place Suit 2130

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using the cellranger pipline v7.2.0 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
genome build: mm10-2020-A for mus musculus
single cell data were processed using Partek® Flow® (Version 11.0) https://www.partek.com/partek-flow/.
Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read, followed by CPM (counts per million) normalization. To account for library chemistry, and other possible unknown differences between experiments, cells were integrated using the Seurat3 integration method to produce batch-corrected data. PCA analysis followed by graph-based clustering using Louvain algorithm, and t-SNE/ UMAP generation employing Euclidean distance, were conducted on the first 20 principal components of the integrated expression data. Differential analyses were performed using Hurdle model(MAST).
Assembly: mm10-2020-A for mus musculus
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

source_name: optic nerve

extract_protocol:
Nf1-OPG optic nerves and meningeal duras were collected separately from ten 12-week old mice, and pooled to prepare a single-cell suspension. Optic nerves were collected and dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) followed by debris (Miltenyi Biotec, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. Single cell supensions from meningeal duras were prepared as described above, stained with 7-AAD, and sorted using MoFlo.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: optic nerve

value: single cell

value: Control


title: blood, Alzheimer's disease, 79y.o., female [DK22119_03]

city: Toon

first: Junichi

last: Iga

state: Ehime

address: Shitsukawa 454

department: Neuropsychiatry

country: Japan

institute: Ehime University

data_processing: The sequencing was done using the NextSeq 500/550 High Output Kit v2.5 (75 cycles) (Illumina, Sun Diego, CA, USA) on a NextSeq500 (Illumina) according to the manufacturer’s instructions. A p-value of 0.05 was set as the threshold for significantly differentially expressed genes (DEGs). Data analysis was conducted using CLC Genomics Workbench (QIAGEN, Germantown, MD, USA).

organism: Homo sapiens

source_name: blood

extract_protocol:
Blood was collected into PaxGene Blood RNA Systems tubes (BD, Tokyo, Japan), and RNA was isolated according to the manufacturer’s protocol.
RNA-seq library preparation was performed using 145 ng total RNA from each sample. An RNA-seq library of each sample was prepared with the QuantiSeq 3’mRNA-Seq Library Prep Kit for Illumina (LEXOGEN, Greenland, NH, USA), and globin mRNA was removed using the Globin Block Modules for QuantSeq (LEXOGEN) according to the manufacturer’s protocol.

value: blood

tag: disease state

value: Alzheimer's disease

tag: age

tag: Sex

value: female


title: BM NK/T, elderly Healthy Donor, HD80

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description:
scRNA-seq
nkt_scrna_expr.rds

data_processing:
Sequencing analysis was performed using 10x Genomics’ CellRanger software (version 7.2.0). Fastq files were generated using the CellRanger MkFastq pipeline (version 7.2.0). Raw reads were mapped to the human reference genome (refdata-cellranger-GRCh38-3.0.0) using the CellRanger Count pipeline. The digital expression matrix was analyzed with the R package Seurat (version 5.1.0)
Assembly: hg38
Supplementary files format and content: raw count expression matrix

source_name: Bone Marrow

extract_protocol:
FACS-purified live BM MNCs or NK/T cells were sequenced at the Advanced Technology Genomics Core facility at MDACC. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (ThermoFisher Scientific) and manual counting.
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented for library preparation. Pooled libraries were sequenced on a NovaSeq6000 SP 100-cycle flow cell (Illumina, San Diego, CA).

value: Bone Marrow

value: NK/T cells


title: blood, Alzheimer's disease, 81y.o., male [DK22119_01 ]

value: male


title: Al1-29_ZT1_100-2


title: CB2 DNMT3A KO

description:
Sample6
bulk RNA-seq
bulk_expr.csv

source_name: Cord Blood

value: Cord Blood

value: NK cells


title: CB1 TET2 KO

description:
Sample2
bulk RNA-seq
bulk_expr.csv


title: CB1 Cas9

description:
Sample1
bulk RNA-seq
bulk_expr.csv


title: mouse_Vanco

description: 10x Genomics

value: Vancomycin


title: human choroid plexus endothelial cells, immortalized, passage 50, rep3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
Fragmented RNA underwent reverse transcription using barcoded oligo(dT) primers containing TrueQuant unique molecular identifiers, followed by template switching. PCR amplified libraries were purified
Unprocessed sequencing reads were adapter-trimmed and quality-trimmed using Cutadapt (version 3.4)
Processed sequencing reads were mapped with a reference genome using Bowtie2 (version 2.4.4). Quantification of mapped reads to each gene was performed using HTSeq (version 2.0.2).
Raw counts were geometric-mean-normalized using DESeq2 (version 1.38) and TPM-normalized by dividing each count with the sum of all counts for each sample multiplied by one million.
Assembly: hg38, release 102
Supplementary files format and content: TPM abundance estimates and raw counts.

source_name: choroid plexus

growth_protocol: Primary HCPEnC and iHCPEnC (Muranyi et al., 2022) were cultured in 25 cm2 cell culture flasks with Complete Classic MediumTM (Cell Systems, Kirkland, USA) supplemented with CultureBoostTM (Cell Systems, Kirkland, USA) at 37°C and 5% CO2.

extract_protocol:
The RNeasy Micro Kit from Qiagen was used for subsequent isolation and purification of RNA.
Rapid MACE-seq was used to prepare 3' RNA sequencing libraries. Samples of 100 ng of DNA-depleted RNA were used for library preparation, using the Rapid MACE-Seq kit (GenXPro GmbH, Germany).

value: choroid plexus

value: iHCPEnC

tag: passages


title: U19

city: Oslo

first: Frode

middle: Amador

last: Norheim

address: Sognsvannsveien 9

department: Faculty of Medicine

country: Norway

institute: University of Oslo

data_processing:
50 bp paired-end reads were sequenced on an Illumina Novaseq 6000 instrument
BBDuk (BBMap v38.86) was used to remove/trim low-quality reads and adapter sequences
Assembly: Reads were mapped to the Mus musculus reference genome (ENSEMBL release 108) using HiSat2 v.2.1.1 Read counting was done with FeatureCounts v2.0.1
Supplementary files format and content: Supplementary files format and content: Ubiad1MaleHFDHetvsWT.csv and Ubiad1FemaleHFDHetvsWT.csv  is csv files that containes unnormalized and normalized counts (TPM), for all samples, annotated to ensembl, generated in HiSat2 v.2.1.1

source_name: Liver

growth_protocol: Male and Female week old Ubiad1+/+ and Ubiad1+/- mice on C57BL/6N background fed High fat diet.

extract_protocol:
RNA was isolated with a NucleoSpin RNA mini kit (Machery-Nagel), according to the manufacturer’s instructions.
Strand-Specific TruSeqTM mRNA-seq library preparation

value: Liver

tag: gender

value: Ubiad1 +/-

value: High fat diet


title: BM NK/T, CCUS, CUS-1

description:
scRNA-seq
nkt_scrna_expr.rds


title: Al1-29_ZT19_20-3

value: leaf

value: Water limited, 20% full capacity


title: Al1-29_ZT13_100-1

value: Well watered, 100% full capacity


title: CB1 DNMT3A KO

description:
Sample3
bulk RNA-seq
bulk_expr.csv


title: BM NK/T, young Healthy Donor, YHD658

description:
scRNA-seq
nkt_scrna_expr.rds


title: U18


title: human choroid plexus endothelial cells, immortalized, passage 50, rep1


title: U17


title: BM NK/T, elderly Healthy Donor, HD16

description:
scRNA-seq
nkt_scrna_expr.rds


title: Al1-29_ZT1_20-2


title: U16


title: BM NK/T, young Healthy Donor, YHD636

description:
scRNA-seq
nkt_scrna_expr.rds


title: U15


title: Al1-29_ZT7_100-1


title: BM NK/T, CCUS, CUS-50

description:
scRNA-seq
nkt_scrna_expr.rds

value: Bone Marrow Mononuclear cells


title: human choroid plexus endothelial cells, immortalized, passage 20, rep2


title: Al1-29_ZT13_100-2


title: human choroid plexus endothelial cells, immortalized, passage 20, rep1


title: human choroid plexus endothelial cells, immortalized, passage 20, rep3


title: BM NK/T, CCUS, CUS-53

description:
scRNA-seq
nkt_scrna_expr.rds


title: U14


title: human choroid plexus endothelial cells, primary, passage 6, rep3

value: Primary HCPEnC


title: U13

value: female


title: BM MNCs, elderly Healthy Donor, HD3

description:
scRNA-seq
bm_scrna_expr.rds

value: Bone Marrow


title: Al1-29_ZT13_20-2


title: human choroid plexus endothelial cells, primary, passage 6, rep2


title: human choroid plexus endothelial cells, immortalized, passage 50, rep2


title: Al1-29_ZT19_20-2


title: Al1-29_ZT19_100-1


title: human choroid plexus endothelial cells, primary, passage 6, rep1


title: BM MNCs, young Healthy Donor, YHD658

description:
scRNA-seq
bm_scrna_expr.rds


title: Al1-29_ZT7_20-1


title: BM MNCs, young Healthy Donor, YHD636

description:
scRNA-seq
bm_scrna_expr.rds


title: U12


title: U8

value: Ubiad1 +/+


title: Al1-29_ZT1_100-1


title: U7


title: ATAC-Sample_15

city: Oxford

first: Charlotte

last: Brierley

address: University of Oxford, Headley Way

country: United Kingdom

institute: MRC WIMM

library_source: genomic

data_processing:
BCL files were demultiplexed using bcl2fastq v2.20.0.422 and trimmed using TrimGalore v0.6.5
Trimmed reads were mapped to hg19 using Bowtie2 v.2.4.2. Duplicate reads were removed using MarkDuplicates module from Pica v.2.3.2 and mitochondrial reads remoded using Samtools v.1.9
ATAC-seq QC was performed with ATACseqQC R package, and coordinates shifted to account for the 5' overhang created by tagmentation of Tn5 transposases
BAM files were merged and peak calling performed with MACS2 v 2.2.7.1. Peaks were annotated with the ChIPseeker and TxDb.Hsapiens R packages.
Peak quantification was performed using the countOverlaps function from the GenomicRanges packahe
Assembly: hg19
Supplementary files format and content: Tab separated matrix file: columns are the peak coordinates, rows the sample and values the raw read count.
Supplementary files format and content: For each sample, the raw counts were normalised by the corresponding sample’s library size (total raw counts) and then multiplied by 1,000,000 to obtain the peak expression values in counts per million (CPM) unit.

molecule: genomic DNA

source_name: hematopoietic

extract_protocol:
ATAC-seq was performed on 1000 CD34+ lineage negative cells. Primary patient cells were sorted directly into 11.25 uL of lysis buffer mix containing 0.25uL 1% digitonin (Promega G9441), 0.25uL 10% Tween-20 (Sigma), 8.25uL of 1X nuclease free PBS (Thermo Fisher AM9625) and 2.5uL nuclease free water (Thermo Fisher 10977049) aliquoted into a well of a 96 well PCR (Thermo Fisher segmented semi-skirted Cat #AB-0900) plate on ice. After sorting, 12.5uL of 2X TD buffer and 1.25uL of Tn5 transposase (Illumina 20034198) were added prior to incubation at 37°C for 30 min. The reaction was stopped using MinElute Reaction Cleanup kit (Qiagen 28204) and the samples eluted in 10uL warmed EB (10mM Tris-HCL, pH8).
Samples were then amplified and indexed using NEBNext High-fidelity 2X Mastermix (NEB M0541L) and customised HPLC-purified Nextera indexed primers (IDT) using the following PCR programme: 72°C 5 min, 98°C 30 s, 13 cycles of 98°C 10 s, 63°C 30s, 72°C 1min. Library quality was assessed using High-Sensitivity DNA Kit in a Bioanalyzer instrument (Agilent 5067-4626) and quantitated by qPCR using the NEBNext library quantitation kit (NEB E7630L). Libraries were pooled at 4nM and sequenced on the NextSeq 500 platform (Illumina) using a NextSeq 500/550 High Output v2.5 (75 cycle) sequencing kit (Illumina 20024906), generating 40-bp pair-end reads.

value: hematopoietic

value: Peripheral blood

value: Lin- CD34+ cells

value: control


title: BM MNCs, CCUS, CUS-53

description:
scRNA-seq
bm_scrna_expr.rds


title: U6


title: ATAC-Sample_14


title: ATAC-Sample_13

value: non-chr21amp BPMPN


title: Al1-29_ZT7_20-2


title: CRISPR_screen_low_fluorescence_intensity

city: GuangZhou

first: meijun

last: ye

state: -- Please Select --

address: Room 418, Science and Technology Building, North Campus, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, Guangdong, China.

institute: SUN YAT-SEN UNIVERSITY

library_source: other

data_processing:
Raw reads were trimmed using Cutadapt to remove the constant flanking sequences of sgRNA sequences.
Read counts of the sgRNAs were calculated by the count command of MAGeC.
The sgRNAs with MAGeCK normalized read counts of high-VENUS-signal or low-VENUS-signal samples < 200 were removed for further analysis. The test command of MAGeCK was used to calculate the p values for the comparison between two samples of sgRNAs.
The Genes with p-value < 0.01 and fold change (high-VENUS-signal/low-VENUS-signal) > 1.5 were identified as the gene enriched in high-VENUS-signal populations. Meanwhile, genes with p-value < 0.01 and fold change (low-VENUS-signal/high-VENUS-signal) > 1.5 were identified as genes enriched in low-VENUS-signal populations.
Finally, GO and GSEA analyses for enriched genes were performed using Clusterprofile.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: other

growth_protocol: A549 cells were grown in Ham's F-12K (Kaighn's) medium (21127030, Gibco) with 10% fetal bovine serum (F0193-500ML, Sigma), and were cultured in a humidified incubator at 37 ℃ under an atmosphere containing 5% CO2.

extract_protocol:
At 5 d post puromycin selection, cells were treated with doxycycline for 48 h. Next, 1.5 × 108 cells were sorted by flow cytometry sorting and collected 5% in high-VENUS-signal cells and low-VENUS-signal cells. Genomic DNA was isolated using a Quick-gDNA MidiPrep (Zymo Research, USA).
sgRNA after PCR amplification was sent to the GENEWIZ (Suzhou, China) to be sequenced on Illumina HiSeq 4000 platform on PE150 mode.

treatment_protocol: A549 cells with stably expressed TETon-BIFC reporter (1.2 × 108) were transduced with a genome-wide gRNA library Brunello in lentiCRISPRv2 (73179, Addgene, USA) at a multiplicity of infection of 0.3. Cells with stably transduced genome-wide gRNA library were selected with 5 μg/ml puromycin, and 4.5 × 107 cells were passaged every 48-72 h at a density of 5 × 106 cells per 15 cm dish in Ham's F-12K (Kaighn's) medium for the duration of the screen.

value: Human Non-Small Cell Lung Cancer Cells

value: Doxycycline was used to treat A549 cells for 48 h with 2 ug/ml (Sigma)


title: ATAC-Sample_11


title: U5

value: Liver


title: Al1-29_ZT1_20-3


title: ATAC-Sample_12


title: BM MNCs, CCUS, CUS-50

description:
scRNA-seq
bm_scrna_expr.rds


title: CRISPR_screen_high_fluorescence_intensity


title: Ab4-28_ZT7_100-3

value: Aburamasari


title: BM MNCs, elderly Healthy Donor, HD2

description:
scRNA-seq
bm_scrna_expr.rds


title: U4

value: High fat diet


title: Ab4-28_ZT13_20-3

value: leaf

value: Water limited, 20% full capacity


title: ATAC-Sample_10

value: chr21amp BPMPN


title: hSC 3

city: Shenzhen

first: haohui

last: Lin

state: Guangdong

address: 1066 Xueyuan avenue

department: Medical School

institute: Shenzhen university

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0) software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
Assembly: GRCh37
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

source_name: Schwann cell

growth_protocol: For hBMSC-dSCs and hSCs, these cells were cultured in the medium consisting of  glutamine-free α-MEM (Gibco) and Neurobasal medium (1:1, v/v) (Invitrogen) supplemented with 1 % B27 (v/v)  (Invitrogen), 5 % FBS (Hyclone) and antibiotics (1 % penicillin G and 1 % streptomycin). For hBMSCs, maintained in DMEM (Gibco) medium containing 10 % FBS and antibiotics (1 % penicillin G and 1 % streptomycin). All cells were incubated at 37℃ with 5%CO2 and medium was changed every two days.

extract_protocol:
Total RNA was extracted from cell using Trizol RNA Extraction Kit (Invitrogen).RNA quality and quantity was measured by using NanoDrop ND-1000 (Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit (Roche) according to the manufacture‘s instruction

value: Schwann cell


title: Ab4-28_ZT7_100-2

value: Well watered, 100% full capacity


title: U2

value: female


title: ATAC-Sample_9


title: hSC 2


title: ATAC-Sample_8


title: U1

value: Ubiad1 +/+


title: Ab4-28_ZT13_100-3


title: hSC 1


title: UM20

value: male

value: Ubiad1 +/-


title: hBMSC 3

source_name: Mesenchymal stem cell

value: Mesenchymal stem cell


title: Ab4-28_ZT13_100-1


title: Ab4-28_ZT13_20-2


title: ATAC-Sample_6

value: hematopoietic

value: Peripheral blood

value: Lin- CD34+ cells

value: control


title: ATAC-Sample_7


title: Ab4-28_ZT1_100-2


title: UM19

value: Liver


title: UM18


title: Ab4-28_ZT19_20-2

value: Aburamasari


title: U3

value: High fat diet


title: hBMSC 2


title: ATAC-Sample_5


title: Ab4-28_ZT19_20-3

value: leaf


title: hBMSC-dSC 3


title: ATAC-Sample_3

value: non-chr21amp BPMPN


title: ATAC-Sample_2

value: chr21amp BPMPN


title: UM16


title: ATAC-Sample_1


title: hBMSC-dSC 1

value: Schwann cell


title: Ab4-28_ZT7_100-1

value: Well watered, 100% full capacity


title: hBMSC-dSC 2


title: UM14


title: Sample_15

data_processing:
BCL files were demultiplexed using bcl2fastq v2.20.0.422 and trimmed using TrimGalore v0.6.5
Trimmed reads were mapped to hg19 using STAR v2.6.1d
Mapped reads were quantified by featureCounts of the Subread package suite
Assembly: hg19

molecule: polyA RNA

extract_protocol:
200 CD34+ lineage negative cells were isolated by FACS and sorted directly into 8 uL of lysis buffer (0.2% Triton X-100, Sigma) containing oligo-dT primers (2.5 uM, Integrated DNA Technologies UK Ltd, Cat #51-01-15-01), dNTP mix (2.5 uM, Life Technologies, Cat#19155) and RNase inhibitor (10 U/ul, Takara (Clontech), Cat# 2313A) aliquoted into 96 well PCR plate (Thermo Fisher segmented semi-skirted Cat #AB-0900) on ice.
Cell lysis, RT and PCR amplification (20 cycles) was performed using the Smart-Seq 2 kit (SMARTScribe, Takara(Clontech) #639537).
Libraries were pooled and sequenced on a on the NextSeq 500 platform (Illumina) using a NextSeq 500/550 High Output v2.5 (75 cycle) sequencing kit (Illumina 20024906), generating 75-bp single-end reads.


title: Ab4-28_ZT13_100-2


title: Ab4-28_ZT19_100-2


title: UM15


title: Sample_14


title: hBMSC 1


title: UM13


title: MV4-11-ETV6

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description: CUT&Tag DNA

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS2 (v2.0.10)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: WT


title: Ab4-28_ZT19_100-1


title: Sample_13


title: UM10

value: Ubiad1 +/+


title: Ab4-28_ZT1_100-3


title: sh-IRF1-1

description: MV4-11 sample with IRF1 knockdown

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: IRF1 knockdown


title: UM7

value: male


title: UM17

value: Ubiad1 +/-


title: sh-IRF1-2

description: MV4-11 sample with IRF1 knockdown


title: Ab4-28_ZT19_20-1

value: Water limited, 20% full capacity


title: Sample_11

value: hematopoietic

value: Peripheral blood


title: UM8


title: NC-2

description: MV4-11 sample with no treatment


title: Ab4-28_ZT1_100-1


title: Sample_12

value: Lin- CD34+ cells


title: Sample_10


title: UM5

value: Liver


title: UM4


title: Sample_9


title: NC-1

description: MV4-11 sample with no treatment


title: T47D treated with romidepsin repeat 2

city: taipei

first: Jiun-I

last: Lai

state: State...

address: no 155, linong street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming Chiao-Tung University

description:
T47D treated with romidepsin repeat 2
T47D_romi_002

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to H.  sapiens, GRCh38 using HISAT2 software (v 2.1.0) (parameters- default)
Read count extraction  were performed using FeatureCounts (v 2.0.0 )
Normalization were performed using DEGseq (v 1.40.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: breast

growth_protocol: T47D and MCF7 were treated with RPMI, DMEM/F12 medium, repectively, each supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Total RNA Isolate Kit (NovelGene). 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer's protocols.

treatment_protocol: cells were treated with DMSO or romidepsin 50nM

value: breast

value: romidepsin


title: Ab4-28_ZT1_20-3

value: leaf

value: Aburamasari


title: Ab4-28_ZT1_20-1


title: UM2

value: High fat diet


title: UM1


title: MV4-11-IRF1

description: CUT&Tag DNA


title: Sample_8

value: chr21amp BPMPN


title: T47D treated with DMSO repeat 1

description:
T47D treated with DMSO repeat 1
T47D_DMSO_001

value: DMSO


title: T47D treated with DMSO repeat 2

description:
T47D treated with DMSO repeat 2
T47D_DMSO_002


title: T47D treated with romidepsin repeat 1

description:
T47D treated with romidepsin repeat 1
T47D_romi_001


title: Sample_7

value: control


title: Ab4-28_ZT7_20-1


title: Sample_5


title: MCF7 treated with romidepsin repeat 2

description:
MCF7 treated with romidepsin repeat 2
MCF7_romi_002


title: Sample_3

value: non-chr21amp BPMPN


title: IEL_KO_HTO

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

description: Hashtag-derived oligonucleotide (HTO)

data_processing:
The Cell Ranger pipeline (10x Genomics, version 5.0.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene expression, cell surface and hashing protein libraries. Read 2 of the gene expression libraries was mapped to the mouse reference genome (GRCm38.99).
Subsequent barcode processing, unique molecular identifiers filtering and gene counting was performed using the Cell Ranger suite. CITE-seq reads were quantified using the feature-barcoding functionality.
Assembly: GRCm38.99
Supplementary files format and content: h5 matrices and fastq files
Library strategy: CITE-seq

molecule: protein

source_name: IEL cells

extract_protocol:
Single cells were prepared from the small intestine. The cells were subsequently stained with fluorochrome-conjugated monoclonal antibodies recognizing CD45 (eBioscience, clone 30-F11), DAPI for cell viability, TruStain FcX Block (BioLegend, cat 101320), the mouse cell surface protein antibody panel containing 165 oligo-conjugated antibodies and 9 TotalSeq-A isotype controls (TotalSeq-A, BioLegend) and a unique TotalSeq-A cell hashing antibody (BioLegend). 70000 CD45+ and 30000 CD45- were sorted of each sample using FACSAria™ II and FACSAria™ III cell sorters (BD Biosciences) and afterwards combined to ensure enough of both CD45+ and CD45- cells would be available for sequencing.
Three biological replicates were multiplexed per lane using TotalSeq-A cell hashing antibodies. Sorted IET single-cell suspensions were resuspended at an estimated final concentration of 1000 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library kit, version 3.1 (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primers (3nM each, 5’CCTTGGCACCCGAGAATT*C*C - 5’GTGACTGGAGTTCAGACGTGTGC*T*C) during cDNA amplification to enrich the TotalSeq-A cell surface and hashing protein oligos respectively. Size selection with SPRIselect Reagent Kit (Beckman Coulter, B23318) was used to separate amplified cDNA molecules for 3’ gene expression and cell surface protein construction. TotalSeq-A protein library construction including sample index PCR using Illumina’s Truseq Small RNA primer sets and SPRIselect size selection was performed according to the manufacturer’s instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in a 70:20:10 ratio for the combined 3’ gene expression, cell surface and hashing protein samples, respectively.

value: IEL cells


title: IEL_KO_ADT

description: Antibody-derived tag (ADT)


title: MCF7 treated with romidepsin repeat 1

description:
MCF7 treated with romidepsin repeat 1
MCF7_romi_001


title: Ab4-28_ZT1_20-2


title: IEL_KO_cDNA

description: polyA RNA


title: experiment: mRNA, plate_number: 8, Untreated

city: Boston

first: Silvi

last: Rouskin

state: MA

address: 77 avenue louis pasteur

institute: Harvard Medical School

description: mRNA.fasta

data_processing:
Data processing: the sequencing files were aligned with Bowtie2. On each position, we count how many reads were aligned and how many of them were mutated. This gives us a mutation fraction signal for each sequence. Only the AC bases were considered, GU bases being set to -1000. We normalize these signals by computing its 95th percentile, dividing the data by this value, then clipping the data to [0,1]. We used the code available on github.com/rouskinlab/seismic-rna. Data filtering: we filter out sequences for which we aligned less than 3,000 reads. We filter out sequences for which the Pearson score between replicateson AC bases is below 0.8.
Assembly: No Genome Assembly
Supplementary files format and content: The processed data is stored under a json format. The first level of the json is the names of the construct defined in the fasta files. The second level is a set of attributes per construct, such as the sequence, the normalized DMS signal and the predicted structure using Dr. Mathew's RNAstructure with the normalized DMS signal as an argument. The DMS signals with less than 3,000 reads are filtered out. The data is filtered by quality using the AUROC method: we compute the AUROC between the normalized DMS signal and the structure on AC bases, using unpaired bases as 1 and paired bases as 0. We only keep AUROC scores above 0.8.
Supplementary files format and content: json format. The first level of the json is the names of the sequences as defined in the fasta file. The second level a set of attributes such as the dms signal, the sequence and the structure predicted using Mathew's RNAstructure wusing DMS as constrains

organism: synthetic construct

source_name: in vitro

extract_protocol:
For the in vitro transcription of the human mRNA library, all the designed amplicons were amplified via PCR, adding a T7 promoter sequence at the forward primer (5′ TAATACGACTCACTATAG 3′ ) using a 2X PCR PreMix (Syd Labs, Cat. MB067-EQ2N), human cDNA (ZYAGEN, Cat. HD-UR-40) and an INTEGRA VIAFLO384 channel pipette. For each 384 plate, 5 µl of each individual reaction were pooled together and purified using a Zymo DNA clean up kit (Cat. D4003). The PCR product pool was used as template for the in vitro transcription, using the T7 MEGAscript kit (Thermo Fisher, Cat. AMB13345) according to the manufacturer’s instructions. After DNase treatment, the transcribed RNAs were purified using a Zymo RNA clean up kit (Cat. R1017). 10 µg of the purified RNAs were diluted in 10 µl of nuclease free water, denatured for 1 minute at 95 degrees and placed on ice for 2 minutes. 88.5 µl of the refolding buffer (sodium cacodylate 397.5 mM and MgCl2 6 mM final) were added and the RNAs were left refolding at 20 minutes at 37ºC. After, 1.5 µl of DMS (dimethyl sulfate) was added to obtain a 1.5% final concentration, for 5 minutes at 37ºC, while shaking at 600 RPM. The reaction was stopped by adding 60 µl of β-mercaptoethanol, followed by Zymo RNA clean up.    Libraries were generated as previously described and the indexed samples were sequenced in a Illumina NextSeq 2000.    For the pri-miRNA library, in vitro transcription templates were prepared via 8 cycles of PCR using 2x Q5 Master Mix (New England Biolabs, Cat. M0492S) with a T7 promoter containing forward primer as previously described. Following column clean up (Zymo Research, Cat. D4013), 100 ng of template DNA was used in a 2 hour in vitro transcription reaction using the HiScribe T7 High Yield RNA (New England Biolabs, Cat. E2040S) kit according to the manufacturer's instructions. Following DNase digestion (Invitrogen, Cat. AM2238) and column clean up (Zymo Research, Cat. R1017), 1 ug of RNA from each library was DMS treated separately as described above, substituting a 1.5% final DMS concentration for 2.5%. Following DMS treatment, the samples were reverse transcribed with Induro Reverse Transcriptase (New England Biolabs, Cat. M0681L) for 30 minutes at 55°C using the appropriate reverse primer for each library according to the manufacturer protocol. After alkaline hydrolysis with 1 ul of 4M NaOH, cDNA was cleaned and concentrated using Zymo Oligo Clean and Concentrator (Zymo Research, D4060). Sub-library specific primers were then used to amplify 1 ul of cDNA template for 24 cycles using Advantage 2 PCR Mix (Takara Bio, Cat. 639206). Finally, library indexing was carried out with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Cat. E7645S) and sequenced on a NextSeq 1000 P2 cartridge (Illumina, Cat. 20046813)  in accordance with the manufacturer's instructions.
To generate the human mRNA library, all human protein-coding transcripts were downloaded from GENCODE Release 43 [CITE GENCODE]. Every transcript with a non-AUG start codon or without an annotated 5’ UTR, CDS, and 3’ UTR was discarded. To focus on 3’ UTRs and maximize the likelihood of successful RT-PCRs, for each gene, the longest common suffix (i.e. subsequence beginning at the 3’ end) among all isoforms was selected. Each gene was discarded if it had no annotated name, if its longest common suffix was shorter than 253 nt, or (to minimize mispriming and misalignment) if its longest common suffix contained any 41-mers that were present in the longest common suffix of any other gene. To verify that alignment to the wrong gene would be minimal, a simulated FASTQ file containing every 128 nt segment in 64 nt increments from every gene’s longest common suffix was aligned to all longest common suffixes with Bowtie2 v2.5.1 [CITE Bowtie2].  Primers for human mRNAs were designed against the longest common suffixes of all remaining genes using Primer3 v2.6.1 [CITE Primer3] with the parameters PRIMER_TASK=generic, PRIMER_PICK_LEFT_PRIMER=1, PRIMER_PICK_INTERNAL_OLIGO=0, PRIMER_PICK_RIGHT_PRIMER=1, PRIMER_PRODUCT_SIZE_RANGE=253-1021, PRIMER_OPT_SIZE=28, PRIMER_MIN_SIZE=20, PRIMER_MAX_SIZE=36, PRIMER_WT_SIZE_LT=0.0, PRIMER_WT_SIZE_GT=0.0, PRIMER_MIN_TM=65.0, PRIMER_OPT_TM=75.0, PRIMER_MAX_TM=80.0, PRIMER_PAIR_MAX_DIFF_TM=10.0, PRIMER_GC_CLAMP=0, PRIMER_MAX_NS_ACCEPTED=0, P3_FILE_FLAG=0, PRIMER_EXPLAIN_FLAG=1, SEQUENCE_OVERHANG_LEFT=TAATACGACTCACTATAGGG. A T7 promoter ending in three G bases was prepended to every forward primer. Genes that received no primer pairs were discarded; for those that received more than one pair, the pair that would produce the longest amplicon was selected. The sequences of the amplicons (including only the last 3 Gs of the T7 promoter) were used as the reference sequences in the subsequent analysis.  To select amplicons for verification in HEK 293T cells, four microarray datasets of gene expression in HEK 293T cells from two studies [CITE Alla et al. and Abramson et al.] were downloaded from the National Center for Biotechnology Information’s Gene Expression Omnibus [CITE NCBI GEO] (accession numbers GSM389756, GSM389757, GSM609202, and GSM609205). Microarray probe IDs were converted to gene names using DAVID [CITE DAVID]. The amplicons of at most 600 nt (the maximum paired-end read length on Illumina sequencers) were ranked by the minimum expression level of their genes among the four datasets (to be conservative); the 96 highest-ranked amplicons were chosen for mutational profiling in HEK 293T cells.  To generate the pri-miRNA library, human genome annotations were downloaded from miRBase (mirbase.org, Kozomara A, Birgaoanu M, Griffiths-Jones S Nucleic Acids Res (2019) 47:D155-D162; Kozomara A, Griffiths-Jones S Nucleic Acids Res (2014) 42:D68-D73; Kozomara A, Griffiths-Jones S Nucleic Acids Res (2011) 39:D152-D157; Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ Nucleic Acids Res (2008) 36:D154-D158; Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ Nucleic Acids Res (2006) 34:D140-D144, Griffiths-Jones S Nucleic Acids Res (2004) 32:D109-D111). After removing redundant sequences, 1292 miRBase hairpins were selected for downstream library creation. The miRBase hairpins were then padded with their flanking genomic sequence to a total of 192 nt using Biopython’s Entrez interface [CITE Biopython, NCBI Entrez]. These 1292 sequences were then separated into 3 sub-libraries to reduce jackpotting during library processing. To each construct, a sub-library specific pair of 19 nt universal primer binding regions were added to minimize primer associated PCR and reverse transcription bias, bringing the full length library size to 230 nt. The final sequences were then synthesized as an oligo pool (Agilent Technologies).

value: in vitro


title: Ab4-28_ZT19_100-3

value: Well watered, 100% full capacity


title: MCF7 treated with DMSO repeat 2

description:
MCF7 treated with DMSO repeat 2
MCF7_DMSO_002


title: experiment: mRNA, plate_number: 7, Untreated

description: mRNA.fasta


title: LPL_KO_HTO

description: Hashtag-derived oligonucleotide (HTO)

source_name: LPL cells

value: LPL cells


title: UM3

value: male

value: Ubiad1 +/+


title: MCF7 treated with DMSO repeat 1

description:
MCF7 treated with DMSO repeat 1
MCF7_DMSO_001


title: Ab4-28_ZT13_20-1

value: Water limited, 20% full capacity


title: Sample_1

value: hematopoietic

value: Peripheral blood

value: Lin- CD34+ cells


title: Sample_6


title: LPL_KO_ADT

description: Antibody-derived tag (ADT)


title: experiment: mRNA, plate_number: 6, Untreated

description: mRNA.fasta


title: ad-selm-3

city: Xi'an

first: Yitong

last: Zhao

state: Shaanxi

address: West Yanta Street No.76

department: Department of Biochemistry and Molecular Biology

institute: Xi'an Jiaotong University School of Basic Medical Sciences

data_processing:
Sequencing data quality of the samples was visually assessed using FastQC. Data processing using Trimmomatic to get Clean data. Utilizing the reference genome as a template, align the quality-controlled sequencing reads with the reference genome using HISAT2, followed by employing RSeQC to assess the alignment results.
Assembly: hg38
Supplementary files format and content: TXT type files includes raw counts for each sample
Supplementary files format and content: TXT type files includes TPM values for each sample

source_name: knee cartilage

growth_protocol: The primary chondrocytes were suspended in complete DMEM/F12 medium and incubated in a cell culture incubator at 37℃ with 5% CO2. The medium was changed every two days during the incubation period.

extract_protocol:
Chondrocytes were lysed and total RNA was extracted by the TRIZOL method
Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® (YEASEN, 12301ES96)  and Hieff NGS® DNA Selection Beads (YEASEN, 12601ES56) were used for cDNA synthesis and library construction.

treatment_protocol: The siRNAs utilized for knockdown experiments were specifically designed and synthesized by Genepharma (Shanghai, China) with transfection facilitated by Lipofectamine 2000 (Thermo Fisher, 11668-019). For high-expression experiments, adenovirus was synthesized by Hanbio (Shanghai, China). The experiments were conducted on primary chondrocyte monolayers with a fusion rate of 70-80%.

value: knee cartilage

value: primary chondrocyte

value: chondrocyte

value: nomal

value: adenovirus infection


title: ad-selm-2


title: LPL_KO_cDNA

description: polyA RNA


title: experiment: mRNA, (plate_number: 5, Untreated) and  (plate_number: 12, [DMS]:1.5%, replicate: B)

description: mRNA.fasta


title: experiment: mRNA, plate_number: 3, Untreated

description: mRNA.fasta


title: LPL_WT_HTO

description: Hashtag-derived oligonucleotide (HTO)


title: ad-selm-1


title: ad-gfp-3


title: LPL_WT_ADT

description: Antibody-derived tag (ADT)


title: LPL_WT_cDNA

description: polyA RNA


title: experiment: mRNA, plate_number: 2, Untreated

description: mRNA.fasta


title: experiment: mRNA, plate_number: 4, Untreated

description: mRNA.fasta


title: Sample_2

value: chr21amp BPMPN


title: ad-gfp-2


title: IEL_WT_HTO

description: Hashtag-derived oligonucleotide (HTO)


title: KO_Allo

type: RNA

city: seoul

first: Tomoyo

last: AGURA

address: 103, Daehak-ro, Jongno-gu, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University College of Medicine

description: RMA expression value derived from Affymetrix® Power Tool

hyb_protocol: Samples were hybridized with the Affymetrix GeneChip® Mouse Gene 2.0 ST arrays.

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix).

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT). We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis. Statistical significance of the expression data was determined using fold change. For a DEG set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity. Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using Gene Ontology (http://geneontology.org) and KEGG(http://kegg.jp). All data analysis and visualization of differentially expressed genes was conducted using R 3.3.2 (www.r-project.org).

label: biotin

source_name: B6.Cg-Il22ra1tm1.1Koll/J male

label_protocol: Single-stranded cDNA was generated from the amplified cRNA and then fragmented and labeled with the GeneChip™ WT Sense Target Labeling and Control Reagents.

growth_protocol: Psoriasis induction - IMQ (a topical dose of 83.3 mg Aldara cream (5% IMQ) was applied to the dorsal area and ear daily starting from day 1 up to day 7.

extract_protocol: Total RNA was extracted from the dorsal skin using TRIzol (Invitrogen). 100 nanograms of each RNA sample was subjected to the Affymetrix analytical procedure.

treatment_protocol: Treatment group mice were administered either vehicle cream or alloferon cream every day, 6 hours after IMQ application.

value: skin tissue


title: ad-gfp-1


title: experiment: mRNA, plate_number: 12, Untreated

description: mRNA.fasta


title: KO_IMQ_B


title: experiment: mRNA, plate_number: 11, Untreated

description: mRNA.fasta


title: si-selm-2

value: sirna transfection


title: Mixed_tissue_ADT

city: SAINT PAUL

first: Sara

last: Hamilton Hart

state: Minnesota

address: 1898 Eustis St.

description: 10x Genomics

data_processing:
*library strategy: CITE-seq
10X Genomics Cell Ranger (scRNAseq) software was used to generate fastq files.
Gene level quantification was completed using cellranger count software (ver. 6.0.0) using a custom GTF from cellranger. HTO counts were generated by cellranger count using the specific antibody-oligo tags sequences used in this experiment. All 12 sample groups were classified using HTO counts respectivley via Seurat's HTOdemux function.
Raw counts data was imported into R (ver 4.1.1) for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc. primarily using the Seurat R package (ver. 4.0.4. Although ADT data were generated they were not used in this analysis.
Seurat (v 4.3.0) was used to process and cluster cells, and to create UMAP images and gene expression feature plots
Assembly: mm10
Supplementary files format and content: plain text files with raw gene expression counts (GEX_counts), hashtag oligo matrix (HTO_matrix), raw protein counts (ADT_counts) and the metadata needed to connect cell barcode IDs to sample ID (SeuratObject_metadata)

source_name: spleen, lymph nodes, small intestine and kidney

extract_protocol:
Tissue was harvested from mice using a collagenase digestion and P14 cells were FACS sorted. After sorting cells were hashtagged and pooled for library construction using the 10X chromium controller.
10x Genomics Chromium Single Cell 3′ (v 3.1) reagent kits and protocol were followed to generate independent gene expression and feature barcode libraries.

value: Primary

value: T cells; LLEC, TCM, TEM

value: LCMV Memory


title: IEL_WT_ADT

description: Antibody-derived tag (ADT)

value: IEL cells


title: si-selm-3


title: M2 macrophages, vehicle treated (EtOH), day10 [M2_C10_E]

city: Solna

first: Ivan

last: Nalvarte

address: Visionsgatan 4, J9:20

department: NVS

country: Sweden

institute: Karolinska Institute

description:
Library name: M2_C10_E
M2_C10_E

data_processing:
Clean reads of FASTQ format were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. Paired-end clean reads were then mapped to GRCh38/hg19 human reference genome using HISAT2 software (v2.0.5). The Cufflinks Reference Annotation Based Transcript (RABT) assembly method was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. Read numbers were counted using HTSeq, followed by RPKM (reads per kilobase exon model) calculation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw counts and FPKM values for each sample

source_name: Blood

growth_protocol: Cells were differentiated to macrophages using media supplemented phorbol 12-myrisate 13-acetate (100 nM, PMA) for 6 days, followed by 2 day polarization to M1 or M2 macrophages with interferon-gamma (IFNγ, 20 ng/ml) and Lipopolysaccharides from E. Coli (LPS, 100 ng/ml), or IL(interleukin)-4 (20 ng/ml) and IL-10 (20 ng/ml), respectively.

extract_protocol:
Total RNA from cells was isolated using RNeasy Mini kit as recommended by the manufacturer (Qiagen).
Library was constructed using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Cells were incubated with DEX (100µM) for 8 days during macrophage differentiation and M1 polarization, or for 2 days of fully M1 polarized macrophages.

value: Blood

value: Monocyte

value: WT

value: Vehicle

tag: time point

value: Day 10


title: experiment: mRNA, plate_number: 9, Untreated

description: mRNA.fasta

value: in vitro


title: experiment: mRNA, plate_number: 1, Untreated

description: mRNA.fasta


title: M2 macrophages, vehicle treated (EtOH), day10 [M2_B10_E]

description:
Library name: M2_B10_E
M2_B10_E


title: KO_CTRL


title: IEL_WT_cDNA

description: polyA RNA


title: M2 macrophages, vehicle treated (EtOH), day10 [M2_A10_E]

description:
Library name: M2_A10_E
M2_A10_E


title: experiment: mRNA, (plate_number: 10, Untreated) and (plate_number: 3, [DMS]:1.5%, replicate: B)

description: mRNA.fasta


title: Mixed_tissue_HTO

description: 10x Genomics

value: spleen, lymph nodes, small intestine and kidney


title: experiment: mRNA, plate_number: 8, [DMS]:1.5%, replicate: A

description: mRNA.fasta


title: si-nc-3

value: knee cartilage

value: primary chondrocyte

value: chondrocyte


title: Mixed_tissue_GEX

description: 10x Genomics


title: si-nc-2

value: nomal


title: experiment: mRNA, plate_number: 7, [DMS]:1.5%, replicate: A

description: mRNA.fasta


title: ABT_F

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Aortic cells pooled from three HFD ABT treated mice

data_processing:
Pre-processing of sequencing results and generation of count matrices was performed using the Cell Ranger version 6.1.1 (10x Genomics) with prebuilt annotation platform mm10-2020-A.
Further processing was done with Seurat v 4.1.0
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Aorta

extract_protocol:
The whole aorta was collected after left ventricular perfusion with 10 ml of PBS and quickly transferred to cold PBS. To prepare a single-cell suspension, perivascular adipose tissue was removed and whole aortas from three mice were cut into ~1-mm pieces and digested with an enzyme solution consisting of 10 mg/ml Collagenase II (Gibco) and 1 mg/ml elastase (Worthington) for 15 min at 37 °C.  The cell suspension was strained through a 40-μm filter and centrifuged at 500 x g for 5 min.  Cells were stained with 2 μg/ml of propidium iodide (PI) for 5 min to assess cell viability and single, viable cells were collected for 10x Genomics library preparation.
The single-cell libraries were prepared with Chromium Next GEM Single Cell 3' Kit v3.11 (10x Genomics) with Chromium Next GEM Chip G Single Cell Kit (10x Genomics) according to manufacturer’s protocol with Chromium Controller (10x Genomics).

value: 9 mo

value: Female

tag: strain

value: Aorta

value: Aortic cells

value: HFD + ABT


title: ABT_M

value: Male


title: KO_CTRL-B

value: skin tissue


title: KO_IMQ_Allo


title: KO_IMQ


title: WT_IMQ

source_name: C57BL/6 male


title: si-nc-1

value: sirna transfection


title: si-selm-1


title: M1 macrophages, DEX treated, day10 [M1_C10_D]

description:
Library name: M1_C10_D
M1_C10_D

value: Blood

value: Monocyte

value: WT

value: Dex


title: WT_CTRL


title: miR_1271_3

city: Moncton

first: Eric

middle: P

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

country: Canada

institute: Vitalité Health Network

data_processing:
Alignment with bwa. Parameters: bwa mem -M -t 16 -R @RG
Read counts generated with featureCounts for R. Parameters: isGTFAnnotationFile = TRUE, GTF.featureType = "exon", GTF.attrType = "gene_id", isPairedEnd = TRUE
Assembly: hg38 / GRCh38
Supplementary files format and content: text file, raw counts matrix

source_name: Kidney

growth_protocol: 786-0 cells were maintained in DMEM/High glucose supplemented with 10% Fetal bovine serum (FBS), 2mM L-glutamine and 1mM sodium pyruvate in a humidifed incubator with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent and Monarch Total RNA Miniprep Kit (New England BioLabs). RNA was further concentrated using RNA clean & concentrator-5 (Zymo Research)
RNA libraries for RNA-seq were prepared using Takara SMARTer kit (TaKaRa) following manufacturer's protocols

value: Kidney

value: epithelial


title: experiment: mRNA, plate_number: 9, [DMS]:1.5%, replicate: A

description: mRNA.fasta

value: in vitro


title: miR_1271_2


title: M1 macrophages, DEX treated, day10 [M1_B10_D]

description:
Library name: M1_B10_D
M1_B10_D

value: Day 10


title: experiment: mRNA, plate_number: 5, [DMS]:1.5%, replicate: A

description: mRNA.fasta


title: HFD_F

description: Aortic cells pooled from three HFD vehicle treated mice

value: HFD + Vehicle


title: miR_1271_1


title: experiment: mRNA,( plate_number: 5, [DMS]:1.5%, replicate: B) and  (plate_number: 6, [DMS]:1.5%, replicate: B)

description: mRNA.fasta


title: HFD_M

value: 9 mo


title: M1 macrophages, vehicle treated (EtOH), day10 [M1_C10_E]

description:
Library name: M1_C10_E
M1_C10_E

value: Vehicle


title: Ctrl_F

description: Aortic cells pooled from three normal diet untreated mice

value: Female

value: Aorta

value: ND


title: M1 macrophages, vehicle treated (EtOH), day10 [M1_F10_E]

description:
Library name: M1_F10_E
M1_F10_E


title: M1 macrophages, DEX treated, day10 [M1_F10_D]

description:
Library name: M1_F10_D
M1_F10_D


title: miR_2355_2


title: experiment: pri-miRNA, plate_number: 3, [DMS]:1.5%, replicate: A


title: M1 macrophages, vehicle treated (EtOH), day10 [M1_B10_E]

description:
Library name: M1_B10_E
M1_B10_E


title: miR_2355_1


title: experiment: mRNA, plate_number: 3, [DMS]:1.5%, replicate: A

description: mRNA.fasta


title: M2 macrophages, vehicle treated (EtOH), day8 [M2_C8_E]

description:
Library name: M2_C8_E
M2_C8_E

value: Day 8


title: Control_miR_3


title: experiment: mRNA, plate_number: 2, [DMS]:1.5%, replicate: B

description: mRNA.fasta


title: f2 scRNAseq

city: changsha

first: Hui

last: Xie

state: hunan

address: #87 Xiangya Road

department: Orthopedics

institute: Central South University

data_processing:
Reads from single-cell RNA-seq were aligned to mm10 and collapsed into unique molecular identifier (UMI) counts using the 10x Genomics Cell Ranger software (version 4.0.0) with default parameters.
Further analyses were performed using Seurat 3.0 in the R Statistical language.
Cells with more than 20% mitochondrial gene expression were removed.
Doublets were removed using the ScDblFinder package. This package finds doublets in single cell data by creating artificial doublets and looking at their prevalence in the neighborhood of each cell.
hematopoietic clusters and small groups of cell without clear ASC or preadipocyte characteristics were removed, then cells were annotated as ASC1, ASC2 or preadipocyte group according to literature.
Genome_build: mm10
Supplementary_files_format_and_content: TAR (of barcodes.tsv, features.tsv,matrix.mtx)

source_name: 12-week-old mice (n = 1)

extract_protocol:
IWAT and GWAT were collected from 12-week-old mice (n = 1 for sample f2, n = 2 for sample f5), digested in alphaMEM medium containing 2% FBS, 1 mg/mL type II collagenase (17101015, Gibco), 1 mg/mL Dispase II (04942078001, Sigma-Alderich) and 1 mg/mL DNase (10104159001, Roche), shaken at 120 r.p.m. at 37 °C for 45 minutes with mixing of tissues by serological pipets every 15 minutes. Following digestion, samples were filtered through 70-μm cell strainers and spun at 300 × g for 5 minutes. The pellet was sorted by FACS for live single Lin/CD45/CD71 negative cells. If the cell viability was higher than 85%, the cell concentration was adjusted to 700-1200 /L. The prepared cell suspension was carried out using microflow control chip, and the bead and cells with cell Barcode sequence (cell Barcode) were wrapped in the droplets, where the cells burst, and the released mRNA are connected with the cell tag sequence on the Gel beads to form single-cell GEMs structures (Gel Bead in Emulsions). Cell mRNAs undergo a reverse transcriptional reaction in the droplet to form cDNA, followed by demulsification and cDNA library construction.
single cell mRNA libraries were prepared for sequencing using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1(#1000121)

value: inguinal and gonadal adipose tissue

value: 12 weeks


title: f5 scRNAseq

source_name: 12-week-old mice (n = 2)


title: experiment: pri-miRNA, plate_number: 2, [DMS]:1.5%, replicate: B


title: M2 macrophages, vehicle treated (EtOH), day8 [M2_B8_E]

description:
Library name: M2_B8_E
M2_B8_E

value: Blood


title: Control_miR_1


title: M2 macrophages, vehicle treated (EtOH), day8 [M2_A8_E]

description:
Library name: M2_A8_E
M2_A8_E

value: Monocyte


title: experiment: pri-miRNA, plate_number: 3, [DMS]:1.5%, replicate: B


title: M1 macrophages, DEX treated, day8 [M1_C8_D]

description:
Library name: M1_C8_D
M1_C8_D

value: WT

value: DEX


title: experiment: mRNA, plate_number: 2, [DMS]:1.5%, replicate: A

description: mRNA.fasta


title: experiment: pri-miRNA, plate_number: 2, [DMS]:1.5%, replicate: A


title: SKOV3-OE rep3

city: Yantai

first: Huachang

last: zhang

state: Shandong

address: 346 Guanhai Road, Laishan District

institute: Binzou medical university

data_processing:
Reads were compared to the reference genome using Subjunc v2.0 and then quantified using featureCounts v2.0.3.
Assembly: Homo_sapiens.GRCh38.84
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include the raw count of each sample's protein-encoding mRNA

source_name: cell line

extract_protocol:
Total RNA was extracted with Trizol, 1.0 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit following manufacturer'sprotocols

value: cell line

value: OE


title: M1 macrophages, DEX treated, day8 [M1_B8_D]

description:
Library name: M1_B8_D
M1_B8_D


title: SKOV3-OE rep2


title: 204, 20 Gy + TLY012

city: Providence

first: Wafik

middle: S

last: El-Deiry

state: Rhode Island

address: 70 Ship Street

department: Pathology and Laboratory Medicine

institute: Brown University

hyb_protocol: Hybridization is 18 h at 65 C with heated lid

scan_protocol: After hybridization each sample was injected in a different lane of the analysis cartridge and visualized on the nCounter SPRINT ™ Profiler using the built-in software

data_processing: The data file generated by the nCounter sprint profiler contains the absolute counts detected for each of the probes and combined with the panel library information

label: NanoString’s nCounter TagSet

source_name: primary lung tissue

label_protocol: The reporter and capture probes bind to the target sequence in the mRNA, 150 ng for FFPE derived RNA and 50 ng for fresh frozen RNA per reaction.

extract_protocol: 1 mL of 2 mg/mL EDTA in PBS was injected through the right ventricle to perfuse the lungs, after which the lungs were excised, washed further in PBS, submerged in RNAlater (Sigma-Aldrich, #R0901, Missouri, USA), and flash frozen in liquid nitrogen.    Frozen lung tissue was stored long-term at -80ºC. Thawing was performed over 16 hours at 4ºC. Tissue homogenization was performed with Precellys Lysing Kit (Cayman Chemical Company, #16859, Michigan, USA) and a Bulley Blender Homogenizer (Next Advance, #G14-G15) prior to RNA extraction with QIAgen RNeasy kit (Qiagen, #74104, Hilden, Germany) and cleaned up with QIAgen RNeasy MinElute Cleanup kit (Qiagen, #74204, Hilden, Germany). Quality and concentration were verified by Nanodrop.

value: primary lung tissue

value: male


title: M1 macrophages, DEX treated, day8 [M1_A8_D]

description:
Library name: M1_A8_D
M1_A8_D


title: 194, 20 Gy

value: female

value: 20 Gy


title: Ctrl_M

value: 9 mo

value: Male

value: Aortic cells


title: 190, 20 Gy + TLY012


title: experiment: mRNA, plate_number: 1, [DMS]:1.5%, replicate: B

description: mRNA.fasta

value: in vitro


title: SKOV3-OE rep1


title: experiment: pri-miRNA, plate_number: 1, [DMS]:1.5%, replicate: B


title: M1 macrophages, vehicle treated (EtOH), day8 [M1_C8_E]

description:
Library name: M1_C8_E
M1_C8_E

value: Vehicle

value: Day 8


title: SKOV3-NC rep3

value: NC


title: 207, 20 Gy


title: Control_miR_2

value: Kidney

value: epithelial


title: M1 macrophages, vehicle treated (EtOH), day8 [M1_B8_E]

description:
Library name: M1_B8_E
M1_B8_E

value: Blood

value: Monocyte

value: WT


title: experiment: mRNA, plate_number: 1, [DMS]:1.5%, replicate: A

description: mRNA.fasta


title: SKOV3-NC rep2

value: cell line


title: M1 macrophages, vehicle treated (EtOH), day8 [M1_A8_E]

description:
Library name: M1_A8_E
M1_A8_E


title: SKOV3-NC rep1


title: 196, 20 Gy + TLY012

value: primary lung tissue


title: 191, 20 Gy + TLY012


title: M0 THP-1 cells, untreated, day0 [M0_F0_U]

description:
Library name: M0_F0_U
M0_F0_U

value: Untreated

value: Day 0


title: experiment: mRNA, plate_number: 12, [DMS]:1.5%, replicate: A

description: mRNA.fasta


title: experiment: mRNA, plate_number: 11, [DMS]:1.5%, replicate: B

description: mRNA.fasta


title: S_4_H358_DNA_2

city: Aarhus C

first: martin

middle: R

last: Jakobsen

address: Høegh-Guldbergs Gade 10, Bygn. 1115

department: Biomedicine

country: Denmark

institute: Aarhus University

description: Library name: S_4

data_processing:
The output fastq files were analyzed with R version 4.4.1 or the CLC Genomics Workbench 12 (QIAGEN) software. Using R or the RNA-seq module of the CLC Genomics Workbench 12, all reads were trimmed and mapped to the Genome Reference Consortium Human Build 38 (GRCh38/hg38). Expression values of each gene were normalized to transcripts per million (TPM).
Assembly: Genome Reference Consortium Human Build 38 (GRCh38/hg38)
Supplementary files format and content: All processed data is located in one csv file. Sheet 1 contains sample 1-12 and sheet 2 contains samle S_1, S_2, S_3, and S_4. Gene names are in the first clumn followed by samples in the next columns. Expression level is transcripts per million (TPM).

extract_protocol: RNA was purified using RNeasy mini kit (Qiagen, Cat#: 74106) or NucleoSpin RNA kit (Macherey-nagel, Cat#: 740955) and eluted in 30-40uL RNase-free water.

value: non-small cell lung cancer

value: DNA


title: experiment: mRNA, plate_number: 11, [DMS]:1.5%, replicate: A

description: mRNA.fasta


title: S_3_H358_DNA_1

description: Library name: S_3


title: 200, 20 Gy

value: male

value: 20 Gy


title: 202, 20 Gy + TLY012


title: S_2_H358_UT_2

description: Library name: S_2


title: M0 THP-1 cells, untreated, day0 [M0_B0_U]

description:
Library name: M0_B0_U
M0_B0_U


title: experiment: mRNA, (plate_number: 10, [DMS]:1.5%, replicate: B) and (plate_number: 6, [DMS]:1.5%, replicate: A)

description:
pri-miRNA.json
mRNA.fasta

value: in vitro


title: S_1_H358_UT_1

description: Library name: S_1


title: experiment: mRNA, (plate_number: 10, [DMS]:1.5%, replicate: A) and (plate_number: 4, [DMS]:1.5%, replicate: B)

description:
mRNA.json
mRNA.fasta


title: 193, 20 Gy

value: female


title: experiment: pri-miRNA, plate_number: 1, [DMS]:1.5%, replicate: A


title: CHIPSEQ_P65_CXCL-EC1_E1_REP_2

status: Public on Mar 04 2025

city: Cambridge

first: Charles

last: O'Donnell

address: 140 First Street, Suite 501

institute: Omega Therapeutics

description: Library name: CHIPSEQ_P65_CXCL-EC1_E1_REP_2

data_processing:
Each library was sequenced targeting a depth of 30M raw reads/fragments. Illumina sequencing data in FASTQ format was collected and QCed using FASTQC. Illumina sequencing adaptors were trimmed using Trimmomatic to eliminate technical sources of ChIP-Seq bias. Trimmed reads were aligned to human genome hg19 using Bowtie2. Mapped reads in the BAM files were sorted and filtered to remove duplicate reads in the generated duplicated BAM files using Picard. was applied on filtered BAM files of individual ChIP samples to call ChIP peaks using FDR <0.05 against input control.
Assembly: hg19/GRCh37
Supplementary files format and content: Processed data represent MACS2 peaks in BED format filtered by q val < 0.05 relative to input control

source_name: lung

extract_protocol:
DNeasy Blood & Tissue Kit (69516; Qiagen)
500,000 cells were cross-linked in 1% formaldehyde for 15 minutes and quenched with 275 mM glycine prior to flash freezing and storage at -80C. Fixed cells were thawed in Cell Lysis Buffer (50 mM Tris HCl, 10 mM EDTA, 0.5% SDS) and HALT Protease Inhibitor (Thermo Fisher Scientific, Cat# 87786) and then processed via multi-modal shearing using a probe-based sonicator (QSonica) followed by the PIXUL acoustic Sonicator (Active Motif).  An input fraction was reserved, and cell lysates were transferred onto pre-loaded antibody-bead conjugates for immunoprecipitation overnight, rotating at 4oC. Beads were washed prior to on-bead tagmentation of chromatin using Tagment DNA Enzyme 1 (Illumina, Cat# 20034197). Samples were washed and PCR amplified for 12 cycles using HiFi MasterMix (New England Biolabs, Cat# M0541) and combinatorial i5/i7 primers derived from Mezger A, et al. The PCR protocol included an initial 5-minute 72 oC incubation for gap-filling and a 5-minute incubation at 95 oC, sufficient for cross-linking reversal. Final libraries were purified using SPRI beads (1X SPRISelect, Beckman Coulter, Cat# B23318), pooled at equimolar ratios, and sequenced on a NextSeq 2000 Sequencing System (Illumina) using a 2x50 PE strategy.

value: lung

value: fibroblast

tag: batch


title: CHIPSEQ_P65_Stimulated_CXCL-EC1_REP_1

description: Library name: CHIPSEQ_P65_Stimulated_CXCL-EC1_REP_1


title: CHIPSEQ_HA_CXCL-EC1_REP_2

description: Library name: CHIPSEQ_HA_CXCL-EC1_REP_2


title: 199, 20 Gy


title: M0 THP-1 cells, untreated, day0 [M0_A0_U]

description:
Library name: M0_A0_U
M0_A0_U


title: CHIPSEQ_HA_CXCL-EC1_REP_1

description: Library name: CHIPSEQ_HA_CXCL-EC1_REP_1


title: M0 THP-1 cells, untreated, day0 [M0_C0_U]

description:
Library name: M0_C0_U
M0_C0_U


title: K562_WholeCell_RNAseq_n2_(231128,240318_NK_hs_2101)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: RNA-sequencing on RNA isolated from K562 cells, replicate 2

data_processing:
1. Adapter trimming of 100bp single-end reads was performed using Trim Galore 0.6.4_dev with parameters "-q 20 --length 20."
2. Trimmed reads were mapped to the Homo sapiens reference genome (hg19, UCSC) using HISAT2 2.1.0 with the parameter "--max-intronlen 30000."
3. Aligned reads were sorted using SAMtools 1.19.2 using samtools sort. Sorted reads were then indexed using using SAMtools 1.19.2 using samtools index.
4. BigWig files were generated using deepTools 3.3.1 bedCoverage with the parameter "--normalizeUsing CPM" (Supplementary file .bw).
Assembly: hg19
Supplementary files format and content: bigwig (.bw)

extract_protocol:
RNA was extracted from whole cell K562 cells using Qiagen RNeasy Plus Mini Kit (Cat#74134) as per the manufacturer's instructions.
First-strand synthesis was performed using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) with the oligo(dT)-ME-B fusion oligonucleotide as the primer. Tagmentation was carried out using 100 ng of RNA-cDNA hybrids, ME-A loaded pAG-Tn5, and tagmentation buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 10 mM MgCl2) for 1 hour at 37°C. The tagmented RNA-cDNA hybrids were purified using the HighPrep PCR Cleanup System (MagBio) at a 1x ratio following the manufacturer's instructions. Sequencing libraries were amplified using the NEBNext Master Mix (NEB) under the following PCR conditions: 58°C for 5 minutes, 72°C for 5 minutes, 98°C for 30 seconds, followed by 12 cycles of 98°C for 10 seconds and 60°C for 15 seconds, then 72°C for 2 minutes, and held at 4°C. Libraries were further purified using the HighPrep PCR Cleanup System (MagBio) at a 0.8x ratio according to the manufacturer's instructions. Sequencing was performed using single-end 100 base pair sequencing.


title: K562_WholeCell_RNAseq_n1_(231128,240318_NK_hs_2100)

description: RNA-sequencing on RNA isolated from K562 cells, replicate 1


title: K562_2hrPladB_IgG_RTTag_n2_(240518,240521_NK_hs_2194)

description: IgG-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 2hours, replicate 2

data_processing:
1. Adapter trimming of 100bp single-end reads was performed using Trim Galore 0.6.4_dev with parameters "-q 20 --length 20."
2. Trimmed reads were mapped to the Homo sapiens reference genome (hg19, UCSC) using HISAT2 2.1.0 with the parameter "--max-intronlen 30000."
4. BigWig files were generated using deepTools 3.3.1 bedCoverage with the parameter "--normalizeUsing CPM" (Supplementary file .bw).
Assembly: hg19
Supplementary files format and content: bigwig (.bw)
Library strategy: SLAMRT&Tag

extract_protocol:
The detailed RT&Tag protocol can be found here: dx.doi.org/10.17504/protocols.io.x54v9jyjqg3e/v1.
Sequencing libraries were then amplified by mixing the nuclei suspension with 15 μL of 0.67% Triton X-100, 2 μL of 10 mM i7 primer, 2 μL of 10 mM i5 primer, and 25 μL of 2x NEBNext Master Mix (NEB). The following PCR conditions were used: 1) 58°C for 5 minutes, 2) 72°C for 5 minutes, 3) 98°C for 30 seconds, 4) 98°C for 10 seconds, 5) 60°C for 15 seconds, 6) Repeat steps 4-5 13 times, 7) 72°C for 2 minutes, 8) Hold at 4°C. The sequencing libraries were then purified using 0.8x HighPrep PCR Cleanup System (MagBio) beads according to the manufacturer's instructions. Sequencing was performed using single-end 100 bp reads.

tag: group

value: 2hr PladB treatment

tag: antibody

value: IgG (Abcam ab172730)


title: 203, 20 Gy + TLY012

tag: tissue


title: K562_4hrPladB_IgG_RTTag_n2_(240518,240521_NK_hs_2196)

description: IgG-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 4hours, replicate 2

tag: cell type

value: 4hr PladB treatment


title: K562_DMSO_SC35_RTTag_n2_(240518,240521_NK_hs_2191)

description: SC35-targeted RT&Tag performed on K562 cells treated with DMSO, replicate 2

value: DMSO treated

value: SC35 (Abcam ab11826)


title: CHIPSEQ_P65_BASELINE_REP_2

description: Library name: CHIPSEQ_P65_BASELINE_REP_2

tag: cell line


title: K562_DMSO_IgG_RTTag_n2_(240518,240521_NK_hs_2190)

description: IgG-targeted RT&Tag performed on K562 cells treated with DMSO, replicate 2


title: 198, 20 Gy


title: K562_4hrPladB_IgG_RTTag_n1_(240518,240521_NK_hs_2174)

description: IgG-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 4hours, replicate 1


title: K562_4hrPladB_SC35_RTTag_n1_(240518,240521_NK_hs_2175)

description: SC35-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 4hours, replicate 1


title: K562_2hrPladB_SC35_RTTag_n1_(240518,240521_NK_hs_2173)

description: SC35-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 2hours, replicate 1


title: K562_2hrPladB_SC35_RTTag_n2_(240518,240521_NK_hs_2195)

description: SC35-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 2hours, replicate 2


title: K562_30minPladB_IgG_RTTag_n2_(240518,240521_NK_hs_2192)

description: IgG-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 30minutes, replicate 2

value: 30min PladB treatment


title: K562_30minPladB_SC35_RTTag_n2_(240518,240521_NK_hs_2193)

description: SC35-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 30minutes, replicate 2


title: K562_WholeCell_RNAseq_n3_(231128,240318_NK_hs_2102)

description: RNA-sequencing on RNA isolated from K562 cells, replicate 3


title: CHIPSEQ_P65_BASELINE_REP_1

description: Library name: CHIPSEQ_P65_BASELINE_REP_1


title: K562_30minPladB_SC35_RTTag_n1_(240518,240521_NK_hs_2171)

description: SC35-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 30minutes, replicate 1


title: K562_30minPladB_IgG_RTTag_n1_(240518,240521_NK_hs_2170)

description: IgG-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 30minutes, replicate 1


title: K562_2hrPladB_IgG_RTTag_n1_(240518,240521_NK_hs_2172)

description: IgG-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 2hours, replicate 1


title: K562_DMSO_SC35_RTTag_n1_(240518,240521_NK_hs_2169)

description: SC35-targeted RT&Tag performed on K562 cells treated with DMSO, replicate 1


title: K562_DMSO_IgG_RTTag_n1_(240518,240521_NK_hs_2168)

description: IgG-targeted RT&Tag performed on K562 cells treated with DMSO, replicate 1


title: K562_4hrPladB_SC35_RTTag_n2_(240518,240521_NK_hs_2197)

description: SC35-targeted RT&Tag performed on K562 cells treated with 100nM Pladienolide B for 4hours, replicate 2


title: HEK293T_H3K27me3_RTTag_n3_(231128_NK_hs_2031)

description: H3K27me3-targeted RT&Tag performed on HEK293T cells, replicate 3

value: H3K27me3 (Cell Signaling Technology CST9733)


title: HEK293T_SC35_RTTag_n2_(230802_NK_hs_2006)

description: SC35-targeted RT&Tag performed on HEK293T cells, replicate 2


title: HEK293T_SC35_RTTag_n3_(231128_NK_hs_2032)

description: SC35-targeted RT&Tag performed on HEK293T cells, replicate 3


title: HEK293T_IgG_RTTag_n3_(231128_NK_hs_2030)

description: IgG-targeted RT&Tag performed on HEK293T cells, replicate 3


title: HEK293T_H3K27me3_RTTag_n2_(230802_NK_hs_2005)

description: H3K27me3-targeted RT&Tag performed on HEK293T cells, replicate 2


title: HEK293T_IgG_RTTag_n2_(230802_NK_hs_2004)

description: IgG-targeted RT&Tag performed on HEK293T cells, replicate 2


title: HEK293T_SC35_RTTag_n1_(230802_NK_hs_1985)

description: SC35-targeted RT&Tag performed on HEK293T cells, replicate 1


title: HEK293T_H3K27me3_RTTag_n1_(230802_NK_hs_1984)

description: H3K27me3-targeted RT&Tag performed on HEK293T cells, replicate 1


title: K562_SC35_compartment_comparison_RTTag_n3_(230703_NK_hs_1944)

description: SC35-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison, replicate 3


title: K562_IgG_compartment_comparison_RTTag_n3_(230703_NK_hs_1942)

description: IgG-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison, replicate 3


title: HEK293T_IgG_RTTag_n1_(230802_NK_hs_1983)

description: IgG-targeted RT&Tag performed on HEK293T cells, replicate 1


title: K562_K27me3_RTTag_n3_(230802_NK_hs_1972)

description: H3K27me3-targeted RT&Tag performed on K562 cells, replicate 3


title: K562_H3K27me3_compartment_comparison_RTTag_n3_(230703_NK_hs_1943)

description: H3K27me3-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison, replicate 3


title: K562_IgG_forH3K27me3_RTTag_n3_(230802_NK_hs_1971)

description: IgG-targeted RT&Tag performed on K562 cells, replicate 3


title: HGC27_WT_H3K27acHiChIP_rep2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
Hi-C reads were processed using HiC-Pro
Assembly: hg19
Supplementary files format and content: .hic

source_name: Gastric cancer cell line

growth_protocol: These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.

extract_protocol: Hi-C experiment were conducted in biological replicates using MboI, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).

value: uninfected control cell

value: H3K27ac_ChIP (Active Motif, 91193, lot 22420004)


title: K562_IgG_forSC35_RTTag_n2_(230703,231128_NK_hs_1918)

description: IgG-targeted RT&Tag performed on K562 cells, replicate 2


title: K562_H3K27me3_compartment_comparison_RTTag_n2_(230703,231128_NK_hs_1887)

description: H3K27me3-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison, replicate 2


title: HGC27_WT_H3K4me1_rep2

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie1.0.1.
Duplication reads were removed from aligned file by using picard-tools-1.119.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

value: Gastric cancer cell line

tag: ChIP

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: K562_SC35_compartment_comparison_RTTag_n2_(230703,231128_NK_hs_1888)

description: SC35-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison, replicate 2


title: K562_IgG_forSC35_RTTag_n3_(231128_NK_hs_2084)


title: HGC27_WT_H3K4me1_rep1


title: K562_IgG_compartment_comparison_RTTag_n2_(230703,231128_NK_hs_1886)

description: IgG-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison, replicate 2


title: K562_SC35_RTTag_n3_(231128_NK_hs_2085)

description: SC35-targeted RT&Tag performed on K562 cells, replicate 3


title: HGC27_RUNX3KO_H3K4me3_rep2

value: H3K4me3_ChIP (Active Motif, 39159, lot 25817005)


title: K562_SC35_compartment_comparison_RTTag_n1_(230703_NK_hs_1879)

description: SC35-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison, replicate 1


title: HGC27_RUNX3KO_H3K27ac_rep2


title: K562_IgG_compartment_comparison_RTTag_n1_(230703_NK_hs_1876)

description: IgG-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison, replicate 1


title: K562_H3K27me3_compartment_comparisonl_RTTag_n1_(230703_NK_hs_1877)

description: H3K27me3-targeted RT&Tag performed on K562 cells, Polycomb domain vs nuclear speckle comparison,replicate 1


title: HGC27_WT_H3K4me3_rep2


title: HGC27_WT_H3K27ac_rep2


title: K562_K27me3_RTTag_n2_(221109_NK_hs_1510)

description: H3K27me3-targeted RT&Tag performed on K562 cells, replicate 2


title: K562_IgG_forH3K27me3_RTTag_n2_(221109_NK_hs_1509)


title: HGC27_WT_RUNX3_rep2

value: RUNX3 ChIP (MBL, D235-3, lot 010 )


title: K562_SC35_RTTag_n2_(230703,231128_NK_hs_1920)

description: SC35-targeted RT&Tag performed on K562 cells, replicate 2


title: HGC27_RUNX3KO_H3K4me1_rep2


title: HGC27_RUNX3KO_H3K4me1_rep1


title: CHIPSEQ_P65_CXCL-EC2-Stimulated_REP_1

description: Library name: CHIPSEQ_P65_CXCL-EC2-Stimulated_REP_1


title: CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC1_REP_2

description: Library name: CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC1_REP_2


title: CHIPSEQ_P65_CXCL-Stimulated_REP_1

description: Library name: CHIPSEQ_P65_CXCL-Stimulated_REP_1


title: K562_IgG_forH3K27me3_RTTag_n1_(221109_NK_hs_1480)

description: IgG-targeted RT&Tag performed on K562 cells, replicate 1


title: K562_splicinginhibition_4hs4U_2hFlavo_SLAMRTTag_SC35_n2_(240518,240521_NK_hs_2211)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Flavopiridol for 2 hours, replicate 2

data_processing:
1)Reads were aligned using SLAM-DUNK v0.4.3 to the UCSC hg19 genome using the default slamdunk all pipeline. Overall T>C conversion rate was calculated using SLAM-DUNK 'alleyoop rates -o summary' option.
2)Aligned reads were sorted using SAMtools 1.19.2 using samtools 'sort -n -o' option.
3)Sorted aligned reads were then processed using the bam2bakR pipeline. Processing was performed to the UCSC hg19 genome and used the GENCODE GRCh37.p13 v19 gene annotation. Default bam2bakR pipeline was used to generate tdf browser tracks and cB files for differential kinetic analysis.
Assembly: hg19
Supplementary files format and content: bigwig (.bw)
Supplementary files format and content: tar of tdf files
Library strategy: SLAMRT&Tag

extract_protocol:
K562 cells were cultured until they reached approximately 70% confluency. For RNA metabolic labeling, 100 µM s4U was added to the cell media for 4 hours. Cells were then collected by centrifugation at 300 g for 5 minutes and washed with 1x PBS. Nuclei were isolated by resuspending the cell pellets in NE1 buffer (10 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine, Roche Complete Protease Inhibitor Cocktail, 1 U/μL RNasin Ribonuclease Inhibitor) and incubating on ice for 10 minutes. The nuclei were centrifuged at 500 g for 8 minutes and resuspended in Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, Roche Complete Protease Inhibitor Cocktail, 1 U/μL RNasin Ribonuclease Inhibitor).  Next, 200,000 K562 nuclei were bound to 5 μL of ConA beads (Bangs Laboratories) for 10 minutes at room temperature. After removing the Wash Buffer, the nuclei were treated with 10 mM iodoacetamide in Wash Buffer and incubated for 1 hour at 37°C. The nuclei were then washed twice with Wash Buffer.  Subsequently, standard RT&Tag steps were followed starting from primary antibody incubation overnight. The detailed RT&Tag protocol can be found here: dx.doi.org/10.17504/protocols.io.x54v9jyjqg3e/v1.
Sequencing libraries were then amplified by mixing the nuclei suspension with 15 μL of 0.67% Triton X-100, 2 μL of 10 mM i7 primer, 2 μL of 10 mM i5 primer, and 25 μL of 2x NEBNext Master Mix (NEB). The following PCR conditions were used: 1) 58°C for 5 minutes, 2) 72°C for 5 minutes, 3) 98°C for 30 seconds, 4) 98°C for 10 seconds, 5) 60°C for 15 seconds, 6) Repeat steps 4-5 13 times, 7) 72°C for 2 minutes, 8) Hold at 4°C. The sequencing libraries were then purified using 0.8x HighPrep PCR Cleanup System (MagBio) beads according to the manufacturer’s instructions. Sequencing was performed using single-end 100 bp reads.

value: 4.25h s4U + 2h Flavo treatment


title: CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC1_REP_1

description: Library name: CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC1_REP_1


title: CHIPSEQ_H3K9ME3_CXCL-EC1_REP_2

description: Library name: CHIPSEQ_H3K9ME3_CXCL-EC1_REP_2


title: K562_splicinginhibition_4hs4U_4hPladB_SLAMRTTag_SC35_n2_(240518,240521_NK_hs_2209)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 4 hours, replicate 2

value: 4.25h s4U + 4h PladB treatment


title: K562_splicinginhibition_4hs4U_4hPladB_SLAMRTTag_IgG_n2_(240518,240521_NK_hs_2208)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 4 hours, replicate 2


title: CHIPSEQ_H3K9ME3_CXCL-EC1_REP_1

description: Library name: CHIPSEQ_H3K9ME3_CXCL-EC1_REP_1

value: lung


title: CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC2_REP_2

description: Library name: CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC2_REP_2

value: fibroblast


title: K562_splicinginhibition_4hs4U_2hPladB_SLAMRTTag_SC35_n2_(240518,240521_NK_hs_2207)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 2 hours, replicate 2

value: 4.25h s4U + 2h PladB treatment


title: CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC2_REP_1

description: Library name: CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC2_REP_1


title: K562_splicinginhibition_4hs4U_2hPladB_SLAMRTTag_IgG_n2_(240518,240521_NK_hs_2206)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 2 hours, replicate 2

value: IgG (Abcam ab172730)


title: CHIPSEQ_H3K9ME3_CXCL-EC2_REP_2

description: Library name: CHIPSEQ_H3K9ME3_CXCL-EC2_REP_2


title: CHIPSEQ_H3K9ME3_CXCL-EC2_REP_1

description: Library name: CHIPSEQ_H3K9ME3_CXCL-EC2_REP_1


title: K562_splicinginhibition_4hs4U_30minPladB_SLAMRTTag_IgG_n2_(240518,240521_NK_hs_2204)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 30 minutes, replicate 2

value: 4.25h s4U + 30min PladB treatment


title: CHIPSEQ_HA_CXCL-EC2_REP_2

description: Library name: CHIPSEQ_HA_CXCL-EC2_REP_2


title: K562_splicinginhibition_4hs4U_DMSO_SLAMRTTag_SC35_n2_(240518,240521_NK_hs_2203)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and DMSO for 4 hours, replicate 2

value: 4.25h s4U + 4h DMSO treatment


title: K562_splicinginhibition_4hs4U_DMSO_SLAMRTTag_IgG_n2_(240518,240521_NK_hs_2202)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and DMSO for 4 hours, replicate 2


title: CHIPSEQ_HA_CXCL-EC2_REP_1

description: Library name: CHIPSEQ_HA_CXCL-EC2_REP_1


title: K562_splicinginhibition_untx_SLAMRTTag_SC35_n2_(240518,240521_NK_hs_2201)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 2

value: untreated

value: SC35 (Abcam ab11826)


title: K562_splicinginhibition_untx_SLAMRTTag_IgG_n2_(240518,240521_NK_hs_2200)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 2


title: K562_splicinginhibition_4hs4U_2hFlavo_SLAMRTTag_IgG_n1_(240518,240521_NK_hs_2188)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Flavopiridol for 2 hours, replicate 1


title: K562_splicinginhibition_4hs4U_2hFlavo_SLAMRTTag_IgG_n2_(240518,240521_NK_hs_2210)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Flavopiridol for 2 hours, replicate 2


title: K562_splicinginhibition_4hs4U_2hFlavo_SLAMRTTag_SC35_n1_(240518,240521_NK_hs_2189)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Flavopiridol for 2 hours, replicate 1


title: K562_splicinginhibition_4hs4U_4hPladB_SLAMRTTag_SC35_n1_(240518,240521_NK_hs_2187)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 4 hours, replicate 1


title: K562_K27me3_RTTag_n1_(221109_NK_hs_1481)

description: H3K27me3-targeted RT&Tag performed on K562 cells, replicate 1

value: H3K27me3 (Cell Signaling Technology CST9733)


title: K562_splicinginhibition_4hs4U_30minPladB_SLAMRTTag_SC35_n1_(240518,240521_NK_hs_2183)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 30 minutes, replicate 1


title: K562_splicinginhibition_4hs4U_2hPladB_SLAMRTTag_IgG_n1_(240518,240521_NK_hs_2184)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 2 hours, replicate 1


title: K562_splicinginhibition_4hs4U_2hPladB_SLAMRTTag_SC35_n1_(240518,240521_NK_hs_2185)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 2 hours, replicate 1


title: K562_splicinginhibition_4hs4U_4hPladB_SLAMRTTag_IgG_n1_(240518,240521_NK_hs_2186)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 4 hours, replicate 1


title: K562_splicinginhibition_4hs4U_30minPladB_SLAMRTTag_IgG_n1_(240518,240521_NK_hs_2182)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 30 minutes, replicate 1


title: K562_splicinginhibition_4hs4U_DMSO_SLAMRTTag_SC35_n1_(240518,240521_NK_hs_2181)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and DMSO for 4 hours, replicate 1


title: K562_splicinginhibition_untx_SLAMRTTag_SC35_n1_(240518,240521_NK_hs_2179)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 1


title: K562_splicinginhibition_untx_SLAMRTTag_IgG_n1_(240318_NK_hs_2178)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 1


title: K562_timecourse_4hs4U_SLAMRTTag_SC35_n4_(240318_NK_hs_2124)

description: Optimization of s4U labeling time. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 4

value: 4h s4U treatment


title: K562_timecourse_8hs4U_SLAMRTTag_H3K27me_n4_(240318_NK_hs_2119)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 8 hours, replicate 4

value: 8h s4U treatment


title: K562_splicinginhibition_4hs4U_DMSO_SLAMRTTag_IgG_n1_(240518,240521_NK_hs_2180)

description: Splicing inhibition assay. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and DMSO for 4 hours, replicate 1


title: K562_timecourse_4hs4U_SLAMRTTag_H3K27me_n4_(240318_NK_hs_2117)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 4


title: K562_splicinginhibition_4hs4U_30minPladB_SLAMRTTag_SC35_n2_(240518,240521_NK_hs_2205)

description: Splicing inhibition assay. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with s4U for 4 hours & 15 minutes and Pladienolide B for 30 minutes, replicate 2


title: K562_timecourse_24hs4U_SLAMRTTag_H3K27me_n4_(240318_NK_hs_2121)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 24 hours, replicate 4

value: 24h s4U treatment


title: K562_timecourse_2hs4U_SLAMRTTag_H3K27me_n4_(240318_NK_hs_2115)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 2 hours, replicate 4

value: 2h s4U treatment


title: K562_timecourse_untx_SLAMRTTag_IgG_n4_(231128,240318_NK_hs_2112)

description: Optimization of s4U labeling time. IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 4


title: K562_timecourse_untx_SLAMRTTag_H3K27me_n4_(240318_NK_hs_2113)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 4


title: K562_timecourse_4hs4U_SLAMRTTag_IgG_n4_(240318_NK_hs_2116)

description: Optimization of s4U labeling time. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 4


title: K562_4hs4U_SC35_SLAMRTTag_n3_(240318_NK_hs_2099)

description: SC35-targeted RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 3


title: K562_4hs4U_IgG_forSC35_SLAMRTTag_n3_(231128_NK_hs_2098)

description: IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 3


title: K562_timecourse_4hs4U_SLAMRTTag_SC35_n3_(240318_NK_hs_2096)

description: Optimization of s4U labeling time. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 3


title: K562_untx_SC35_SLAMRTTag_n3_(231128_NK_hs_2097)

description: SC35-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 3


title: K562_untx_IgG_forSC35_SLAMRTTag_n3_(231128_NK_hs_2096)

description: IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 3


title: K562_4hs4U_IgG_forSC35_SLAMRTTag_n2_(231128,240318_NK_hs_2094)

description: IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 2


title: K562_untx_SC35_SLAMRTTag_n2_(231128_NK_hs_2093)

description: SC35-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 2


title: K562_timecourse_24hs4U_SLAMRTTag_H3K27me_n3_(240318_NK_hs_2093)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 24 hours, replicate 3


title: K562_4hs4U_SC35_SLAMRTTag_n2_(231128,240318_NK_hs_2095)

description: SC35-targeted RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 2