title: sortseq_1_unsorted_highinput

extract_protocol:
Genomic DNA was extracted from 9.3M cells using QuickExtract (Lucigen).
In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.

value: Sort-seq INSERT-seq


title: WT [HON082820_006]

status: Public on Apr 06 2022

type: SRA

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

description: wild-type mouse heart

library_source: transcriptomic

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: quant_counts.txt: Tab-delimited text table.

molecule: total RNA

organism: Mus musculus

source_name: WT

extract_protocol:
Maxwell® RSC simplyRNA Tissue Kit (Promega PN AS1340).
Universal Plus mRNA-Seq Library Preparation Kit with NuQuant (Tecan PN 0520-A01).
PolyA capture based library construction.

treatment_protocol: Hv1 gene knockout.

tag: tissue

value: Heart

tag: genotype

value: WT


title: SJRHB010928_X1_barcode

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: barcode dialout PCR

data_processing:
Library strategy: tagged amplicon
Single cell or nucleus RNA-seq reads from tumors or O-PDXs were aligned using the 10x Genomics Cell ranger Pipeline (v3.0.2) to the hg19 reference data v3.0.0 (for tumors) or hg19-and-mm10 v3.0.0 (for O-PDXs). In the case of single-nucleus datasets, a custom pre-mRNA reference was used to include intronic reads into expression matrices
Genome_build: hg19 or hg19-and-mm10
Supplementary_files_format_and_content: Cell Ranger output

organism: Homo sapiens

source_name: Orthotopic patient-derived xenograft

extract_protocol:
barcode dialout PCR
Tagged amplicon PCR of 10x gene expression libraries using primers targeted to the lineage barcode
Tagged amplicon PCR

value: xenograft

tag: protocol

value: Barcode dialout PCR


title: sir2Δrpd3Δ_rep3 (Total)

city: Los Angeles

first: Yiwei

last: He

state: CA

address: 1050 Childs Way RRI 203

department: Molecular Biology

institute: University of Southern California

description: Sample 12

library_source: genomic

data_processing:
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome of S288C from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: R64
Supplementary files format and content: binned.bed files
Library strategy: BrdU-IP-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: 10–20 mL of cells were grown per sample to OD ~ 0.5 in YEPD at 23 °C

extract_protocol:
Cells were resuspend in 500 μL genomic lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extractracion and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

treatment_protocol: Cells were arrested with α-factor (~5 nM ) and incubated for ~4 h at 23 °C then released in fresh YEPD containing 400 μg/mL BrdU, 200 μg/mL Pronase and 200 mM hydroxyurea. Harvested cells after 60/90min of incubation.

tag: strain

tag: antibody

tag: treatment

value: hydroxyurea


title: sir2Δrpd3Δ_rep2 (Total)

description: Sample 11


title: KO [HON082820_001]

description: Hv1 null mouse heart

source_name: KO

value: Hv1 null


title: KO [HON082820_002]

description: Hv1 null mouse heart


title: sortseq_1_unsorted_lowerinput

city: Boston

first: Hanneke

last: Vlaming

state: MA

address: 45 Shattuck St

department: Department of Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

source_name: Mouse embryonic stem cells

growth_protocol: mESCs were cultured in KO-DMEM media (Gibco) supplemented with 15% KO Serum replacement (Gibco), GlutaMAX, penicillin-streptomycin, non-essential amino acids, beta-mercaptoethanol, 1000 U/ml LIF (Cell Guidance Systems), 1µM MEK inhibitor (PD0325901; Stemgent), and 3µM GSK3 inhibitor (CHIR99021; Stemgent). Cells were passaged onto new gelatin-coated plates every other day, and received fresh media on other days.

extract_protocol:
Genomic DNA was extracted from 2.5M cells using QuickExtract (Lucigen).
In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.

tag: cell line

value: F121-9 mESCs with at the 129 allele of Pou5f1:mKate2  uaTSS +172, TagBFP2  Oct4 C terminus

tag: library integration location

value: Pou5f1 uaTSS + 157 (129 allele, upstream of mKate2 reporter)

tag: assay

tag: condition

value: Untreated


title: rpd3Δ_rDNA20_rep2 (Total)

description: Sample 16

value: rpd3{delta} rDNA20


title: sir2Δ_rep3 (Total)

description: Sample 9


title: sir2Δ_rep2 (Total)

description: Sample 8


title: sortseq_1_bin3

extract_protocol:
Genomic DNA was extracted from sorted cells using QuickExtract (Lucigen).
In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.


title: sortseq_1_bin5


title: WT mESC PRO-seq Rep 4

description: Nascent RNAs from WT mESCs (biotin enrichent)

data_processing:
Library strategy: PRO-seq
Reads were trimmed to 40nt, and adapter sequences, reads with low quality 3'end information and reads shorter than 20nt were removed using cutadapt 1.14.
Reads were first mapped to dm6 using bowite. Reads that failed to map to dm6 were next mapped to mm10 using bowtie.
Strand-specific and single nucleotide resolution bedGraphs reporting the 3'end read position (Reflecting the biotinylated nascent RNA 3'end) were generated. As described in Mahat et al., 2016, the stranded bedgraph file names were flipped due to the "forward/reverse" orientation of illumnia paired-end sequencing. For each strand, bedgraph files from all four replicates were merged together.
Genome_build: mm10
Supplementary_files_format_and_content: "mm10_mESC_PROseq_mESC_N4_F/R.bedGraph.gz" is a compressed bedgraph file with combined data from four PRO-seq replicates (strand speciifc)

growth_protocol: mESCs were cultured in Serum-Free Embryonic Stem Cell Media (SFES). SFES was composed of 50/50 NeuroBasal Media (Gibco) and DMEM/F12 Media (Gibco), supplemented with 0.5x B-27 (Gibco), 0.5x N-2 (Gibco), 2 mM L-Glutamine (Gibco), 0.05% Bovine Albumin Fraction V (Gibco) and 1.5x10-4 M Monothioglycerol (Sigma), 1000 U/ml LIF (Cell Guidance Systems), 1µM MEK inhibitor (PD0325901; Stemgent), and 3µM GSK3 inhibitor (CHIR99021; Stemgent). Cells were passaged using accutase and plated onto new gelatin-coated plates every other day, and received fresh media on other days.

extract_protocol:
mESCs were washed with PBS, brought into a single cell suspension with accutase, permeabilized and flash frozen. 1 million mESCs were subject to a nuclear run-on reaction containing only biotin-NTPs for 5 mins at 37C. Following the nuclear run-on, RNA was extracted by the Norgen Biotek Corp Total RNA Purification Kit (following manufacturer instructions) and fragmented by base hydrolysis. Nascent RNAs were enriched using prepared Dynabeads™ MyOne™ Streptavidin C1 (ThermoFisher) and trizol extracted.
Following extraction, Isolated nascent RNAs underwent 3'end adapter ligation, biotin enrichment, 5'end decapping, 5'hydroxyl repair, on-bead reverse transcription, bead elution, and PCR amplifcation to 9-11 cycles

value: F121-9 wt mESCs

tag: cell type

value: Mouse embryonic stem cells

value: PRO-seq

value: WT, Untreated


title: sortseq_1_bin4


title: tumor pericytes, vector, con313_2

city: ChangSha

first: Ke

last: Gong

address: 139 Renmin Middle road

department: cardiovascular surgery

country: China

institute: The Second Xiangya Hospital of Central South University

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text file includes raw counts and FPKM values for each Sample

source_name: Tumor tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

tag: disease state

value: non-metastatic colorectal cancer (CRC)

value: Tumor tissue

value: tumor pericytes

value: control


title: tumor pericytes, vector, con313_3


title: sortseq_1_bin2

value: Sort-seq INSERT-seq


title: WT mESC PRO-seq Rep 3


title: tumor pericytes,TCF21-overexpressing, TCF21_3

value: TCF21 overexpressing


title: tumor pericytes, vector, con313_1


title: lupus lesional skin spatial sample

first: Feiyang

last: Ma

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

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced on an Illumina Nova-Seq (Illumina, San Diego, CA) as 150bp paired end reads and were converted from bcl files to fastq files using bcl2fastq.
After sequencing, the reads were aligned to the human genome (hg38), and the expression matrix was extracted using the spaceranger pipeline.
Seurat was then used to analyze the expression matrix. Specifically, the SCTransform function was used to scale the data and find variable genes with default parameters. PCA was applied for dimensional reduction. The FindTransferAnchors function was used to Find a set of anchors between the spatial-seq data and scRNA-seq data, which were then transferred from the scRNA-seq to the saptial-seq data using the TransferData function.  The predicted cell type composition for each spot was then used to cluster the spots by the k-means algorithm. The clusters were annotated based the average cell type prediction score across all the spots in the cluster.
Assembly: hg38
Supplementary files format and content: h5 file containing raw  counts for every gene in every spot
Supplementary files format and content: image.png: H&E staining image

molecule: polyA RNA

source_name: lupus patient skin lesion

extract_protocol:
Skin samples were frozen in OCT medium and stored at -80°C until sectioning.
Optimization of tissue permeabilization was performed on 20-μm-thick sections using Visium Spatial Tissue Optimization Reagents Kit (10X Genomics, Pleasanton, CA, USA), which established an optimal permeabilization time to be 6 minutes. Samples were mounted onto a Gene Expression slide (10X Genomics), fixed in ice-cold methanol, stained with hematoxylin and eosin, and scanned under a microscope (Keyence, Itasca, IL, USA). Tissue permeabilization was performed to release the poly-A mRNA for capture by the poly(dT) primers that are precoated on the slide and include an Illumina TruSeq Read, spatial barcode, and unique molecular identifier (UMI). Visium Spatial Gene Expression Reagent Kit (10X Genomics) was used for reverse transcription to produce spatially barcoded full-length cDNA and for second strand synthesis followed by denaturation to allow a transfer of the cDNA from the slide into a tube for amplification and library construction. Visium Spatial Single Cell 3ʹ Gene Expression libraries consisting of Illumina paired-end sequences flanked with P5/P7 were constructed after enzymatic fragmentation, size selection, end repair, A-tailing, adaptor ligation, and PCR. Dual Index Kit TT Set A (10X Genomics) was used to add unique i7 and i5 sample indexes and generate TruSeq Read 1 for sequencing the spatial barcode and UMI and TruSeq Read 2 for sequencing the cDNA insert, respectively.

tag: disease

value: lupus lesional

value: skin lesion


title: WT mESC PRO-seq Rep 2


title: 312246716_FRA102220-002

description:
library type: single-cell (10x Genomics)
Cells were grown in PRF-RPMI 1640 media supplemented with 17β-Estradiol (E2) in 10nM concentration.

data_processing:
Raw R2 reads were mapped to the reference transcriptome (hg38 Ensembl gene sequences, exonic only) using BWA MEM. Cell barcodes and UMIs were extracted from R1 using a custom pipeline following OneCellBio adapter design for inDrop. Unique UMI counts were summed for each gene and each unique cell barcode. Only cell barcodes with >500 counts included in the final counts table. For 10X Genomics, cellRanger (v3.0.0) was run on the raw data to align hg38 Ensembl gene sequences.
Assembly: hg38 Ensembl gene sequences (exonic only)
Supplementary files format and content: Cell list: Tab-delimited text of cell name (matches columns in scRNA-seq counts tables), barcode, number of genes expressed, and UMI counts. All cell barcodes are listed in this file, including those below the 500 count minimum.
Supplementary files format and content: For 10X Genomics, processed data includes matrix.mtx.gz, barecode.tsv.gz, features.tsv.gz files.

source_name: MCF-7 cell line

growth_protocol: Before treatments, cells were routinely cultured in RPMI 1640 containing 10% fetal bovine serum, 1% penicillin–streptomycin, 1% nonessential amino acids, 2 mmol/L L-glutamine, and 0.5 µg/ml puromycin, or for untreated cells PRF-RPMI 1640 containing 5% CD-FBS supplemented with E2 10nM.

extract_protocol:
Single cell encapsulation was performed using inDrop system from 1CellBio, followed by transfer to 1CellBio UV Cleavage Device to release oligo linkers from the hydrogel beads and RT reaction. For control sample cells were incapsulated and processed using 10x Genomics system, according to manufacturer's protocol.
Sequencing was performed using the Illumina NextSeq 500 with the High Output Kit 75 cycles. Read format was as follows: Read1 50b, Read2 36b. Total cDNA reads output approximately 400Mb. For 10X Genomics, libraries were pooled and sequenced on NovaSeq 6000 and S4 lane with 28x150nt reads and produced over 5.4 billion reads.

treatment_protocol: Cell were seeded in 6 well plate 1000 cells/well and treated with 4-Hydroxytamoxifen for next 2 weeks. Treatment was refreshed each 3-4 days. Control untreated cells were grown in media supplemented with E2 in concentration 10nM.

value: Breast


title: tumor pericytes,TCF21-overexpressing, TCF21_2


title: rpd3Δ_rep3 (Total)

description: Sample 6

value: hydroxyurea


title: sir2Δ_rep1 (Total)

description: Sample 7


title: tumor pericytes,TCF21-overexpressing, TCF21_1


title: 2122-IRE3_S6

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

country: Spain

institute: Centro de Investigación del Cáncer de Salamanca

data_processing:
Illumina 3' adapters and low quality bases (Phred Score < 20 ) were trimmed using cutadapt version 1.12
FASTQ files were aligned to the Homo sapiens genome hg19 from Ensembl using the STAR aligner, version 2.5.3a
Gene counts were obtained using the HTSeq algorithm version 0.6.1p1 in the intersection-strict mode.
Gene count normalization was carried out using edgeR version 3.24.3
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene count values for each sample. Supplementary files: tab-delimited matrix that includes edgeR normalized gene expression values (TMM method) for each sample

source_name: NCI-H929 cell line

growth_protocol: NCI-H929 cell line was cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and antibiotics (Gibco Life Technologies, Grand Island, NY, USA).

extract_protocol:
RNA was extracted using the RNeasy Plus Mini kit (Qiagen). The RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were constructed using approximately (0.7- 1.0 u g) of total RNA from each sample, and the TruSeq stranded mRNA Sample Preparation Kit version 1.0 (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Total RNA (5ug) was incubated for 1 hour at 37 °C in cleavage buffer (20mM HEPES, pH 7.5, 50 mM NaCl, 1 mM DTT, and 2 mM ATP) in the presence or in the absence of 2ug of recombinant human ERN1/IRE1a (aa 467–977) (Sino biological Inc). The reaction was inactivated at 95°C for 5 minutes. RNA cleanup for these samples was performed using RNeasy MinElute Cleanup Kit according to the manufacturer's instructions, (Qiagen, Valencia, USA).

tag: cleavage assay

value: IRE1 cleavage

value: multiple myeloma


title: sortseq_1_bin6

value: F121-9 mESCs with at the 129 allele of Pou5f1:mKate2  uaTSS +172, TagBFP2  Oct4 C terminus

value: Pou5f1 uaTSS + 157 (129 allele, upstream of mKate2 reporter)

value: Untreated


title: G2

city: Suzhou

first: Wenjing

last: Zhou

state: 江苏

address: SuZhou JiangSu

institute: Soochow University

data_processing:
Illumina Casava 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the whole Mus musculus reference genome GRCm39 using HISAT2 (v2.0.5)
Fragments Per Kilobase of transcripts per Million fragment mapped (FPKM) was used in calculating the expression level of genes or transcripts.
Differential expression analysis between the two tissues was performed using the DESeq2 R package. Genes with an adjusted P-value < 0.05, and fold change (FC) >=2 (|log2 (fold change)| >= 1) identified by DESeq2 were assigned as differentially expressed.
Genome_build: GRCm39
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Mus heart

extract_protocol:
Ischemic myocardium from GlcN/E or saline hearts on Day 3 post-MI  were collected in TRIzol reagent for RNA-seq (Novogene). Briefly, mRNA was puriﬁed from total RNA using poly-T oligo-attached magnetic beads and subjected to library preparation using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB).
The library preparations were sequenced on an Illumina NovaSeq 6000 sequencer.

value: Ischemic myocardium

value: GlcN


title: WT mESC PRO-seq Rep 1

value: F121-9 wt mESCs

value: Mouse embryonic stem cells

value: PRO-seq

value: WT, Untreated


title: sir2Δrpd3Δ_rep1 (Total)

description: Sample 10


title: G3


title: G1


title: 2121-IRE2_S5


title: tumor pericytes, TCF21-overexpressing, TCF21 IP

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
ChIP-seq reads were mapped to the GRCh38.101 genome using STAR software (version 2.5.3a) with default parameters.
The MACS2 software（Version 2.1.1）was used for peak calling.
The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The Homer（version 4.10）was used for motifs analysis. the R package edgeR（version 1.0.0） was used for analysis of diffpeak and gene.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
The tumor pericytes was fixed in 1% formaldehyde for 10 min at room temperature , after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The tumor pericytes was then collected and frozen in liquid nitrogen, it was treated with cell lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: non-metastatic colorectal cancer (CRC)

value: Tumor tissue

value: tumor pericytes

tag: chip antibody


title: tumor pericytes, TCF21-overexpressing, TCF21 Input

value: TCF21 overexpressing


title: 2120-IRE1_S4


title: rpd3Δ_rep1 (Total)

description: Sample 4


title: S2

value: saline


title: S3


title: sortseq_1_bin1

value: Sort-seq INSERT-seq


title: 2118-C2_S2

value: Control


title: WT_rep1 (Total)

description: Sample 1

value: WT

value: hydroxyurea


title: HEK293T, Cut&Tag, siDot1L, OGT, rep2

city: Wuhan

first: Bo

last: Xu

address: East Lake South Road

department: College of Life Sciences

institute: Wuhan University

data_processing:
Library strategy: Cut&Tag
Basecalls performed using CASAVA version 1.4
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches.
Alignment results f were further filtered by Bedtools veresion 2.30.0.
CUT&Tag peaks were called using SEACR version 1.3.
Visulaization with Deeptools and Intergrative Genomics Viewer platform.
Assembly: hg38
Supplementary files format and content: bigWig, bed

growth_protocol: HEK293T cells were cultured with Dulbecco’s modified Eagle’s media supplemented with 10% fetal bovine serum and 1x penicillin-streptomycin at 5% CO2 at 37°C. Mycoplasma was detected in all cell lines.

extract_protocol:
HEK293T cells were harvested and washed three times by PBS
Cut&Tag experiments were performed with Hieff In-Situ DNA Binding Profiling Library Prep Kit (Yeasen, 12598ES48) following manufacturer’s protocols. Briefly, for each sample, 5x104 cells were harvested and washed three times by PBS, resuspend the cells with cell wash buffer gently, and incubate with the concanavalin A coated magnetic beads previously washed by ConA bind buffer. Then concanavalin A beads coupled cells were collected and incubated with primary antibody Rabbit IgG (Abcam) or Dot1L(CST) or OGT(Proteintech) at 4 °C overnight. Incubate the secondary antibody with the concanavalin A beads coupled cells at room temperature 1 h. Collecting the ConA beads coupled cells and the pA/G-Transposome Mix was added. And standard tagmentation and amplification were performed. Amplified DNA libraries were purified and shipped for next-generation sequencing (NGS) sequencing.

treatment_protocol: treated with siRNA 72h

value: treated with siRNA targeted Dot1L72h

value: Human embryonic kidney

value: OGT(Proteintech, Cat #11576-2-AP)


title: fkh1Δfkh2-dsm rpd3Δ_rep1 (IP)

description: Sample 23

value: anti-BrdU

value: fkh1{delta} fkh2-dsm rpd3{delta}


title: HEK293T, Cut&Tag, siDot1L, OGT, rep1


title: HEK293T, Cut&Tag, siNC, OGT, rep2

value: treated with negative siRNA 72h


title: S1

value: Ischemic myocardium


title: rpd3Δ_rep2 (Total)

description: Sample 5


title: 2117-C1_S1

value: multiple myeloma


title: WT_rep3 (Total)

description: Sample 3


title: fkh1Δfkh2-dsm rpd3Δ_rep2 (IP)

description: Sample 24


title: 2119-C3_S3


title: HEK293T, Cut&Tag, Dot1L, rep1

value: untreated

value: Dot1L(CST, Cat#77087)


title: Sample_42_Bcl2Setd2het_lymphNodeTumor_RNAseq_repl3

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
RNAseq reads were aligned using STAR and annotated to RefSeq annotation using Rsubread
Cut&Run reads were aligned using BWA-MEM and peaks were called using SICER2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited TPM or SICER2 peak

growth_protocol: not applicable

extract_protocol:
Total RNA was extracted using Trizol (LifeTechnologies) and RNeasy isolation Kit (Qiagen).
CUT&RUN was performed following CUTANA protocol v1.5.2 (Epicypher).  Enriched DNA was purified using Monarch DNA cleanup kit (NEB; T1030S).

value: Rosa26-Bcl2-GFP Setd2WT/-

tag: tissue/cell type

value: Lymph node

tag: isolation strategy

value: DAPI-, GFP+


title: rpd3Δ_90min_rep2 (IP)

description: Sample 22


title: Sample_38_Bcl2Setd2het_splenicTumor_RNAseq_repl3

value: Spleen


title: CD31Neg Non-myo, replicate 1, scRNAseq

city: San Antonio

first: Brian

last: Iskra

state: Texas

address: 8403 Floyd Curl Dr

institute: GCCRI

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
The heart was removed by cutting the heart below the atrium and residual atrial tissue was trimmed off after removal. In order to remove residual blood, ventricular tissue was washed in HBSS  (without calcium or magnesium) several times, then cut into large pieces in ice cold HBSS, and placed into ice cold HBSS for up to 15 minutes. Once harvest of ventricular tissue was completed, the tissue was removed from HBSS, wet with a digestion buffer, and minced into fine particles with a scalpel. Digestion buffer consisted of collagenase IV and dispase II at a concentration of 2 mg/mL and 1.2 U/mL. Tissue was collected and each heart was placed into a 3 mL digestion buffer, where it was then incubated in 15 mL conical tubes in a 37 degree water bath. Following 15 minutes of digestion, the digestate was triturated with a 1000 uL pipette tip, and then digested for another 15 minutes. The digestion was kept at 30 to 45 minutes, depending on particle size and completeness of digestion. After digestion, cells were strained, and the strainer was washed with ice cold HBSS with 2% FBS, until a final volume of 10 mL was obtained. This suspension was washed one more time with ice cold HBSS, and then incubated in 5 mL of ACK lysis buffer for 5 minutes at room temperature to induce lysis in remaining erythrocytes. The reaction was quenched by adding an equal volume of ice cold HBSS with 2% FBS, washed once more with HBSS with 2% FBS and then a MACS depletion or debris removal step was performed.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: Heart

value: Non-myocytes


title: HEK293T, Cut&Tag, siNC, OGT, rep1


title: chr-RNA #3

description:
Chromatin-associated RNA
chr-RNA #3

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences plus spliced versions of these inserts as called by STAR. STAR v2.7.0 was run on replicates 2-4 using flags --outSJfilterOverhangMin 10 4 4 4 --peOverlapNbasesMin 10 --peOverlapMMp 0.08 --alignEndsType EndToEnd --outFilterMismatchNmax 5 --scoreDelOpen -10 --scoreInsOpen -10. The detected splice junctions were filtered down to only junctions on the + strand with >10 read counts and >25% of the maximum counts for other junctions detected in the same insert. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "HV20220110_normalized_WTscreens.txt" is a tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.

extract_protocol:
Chromatin-associated RNA (Chr-RNA) was isolated from ~20M cells as published previously (Henriques et al, Mol Cell 2013), but 0.1% Triton-X-100 was added after pellets were resuspended in buffer B. Incubations were all performed on ice, 8 minutes in buffer A and two incubations in buffer B for 15 minutes. The washed chromatin pellets were resuspended in Trizol, RNA was extracted using Direct-zol RNA miniprep columns (Zymo Research), treated with RQ1 DNase (Promega), then cleaned up again using a total RNA purification kit (Norgen Biotek Corp).
First, RNA was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer in mKate2 annealed 221nt downstream of the variable regions. cDNA was RNase-treated and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through 17-20 PCR cycles using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).

value: F121-9 mESCs with at the 129 allele of Pou5f1:mKate2 @ uaTSS +172, TagBFP2 @ Oct4 C terminus

value: Pou5f1 uaTSS + 157 (129 allele, upstream of mKate2 reporter)

value: RNA-based INSERT-seq

value: Untreated


title: Sample_41_Bcl2Setd2het_lymphNodeTumor_RNAseq_repl2

tag: genotype


title: chr-RNA #2

description:
Chromatin-associated RNA
chr-RNA #2


title: HEK293T, Cut&Tag, OGT, rep1

value: Human embryonic kidney

value: OGT(Proteintech, Cat #11576-2-AP)


title: HEK293T, Cut&Tag, Dot1L, rep2


title: fkh1Δfkh2-dsm_rep1 (IP)

description: Sample 19

value: anti-BrdU

value: fkh1{delta} fkh2-dsm

value: hydroxyurea


title: rpd3Δ_90min_rep1 (IP)

description: Sample 21


title: Sample_40_Bcl2Setd2het_lymphNodeTumor_RNAseq_repl1


title: WT_rep2 (Total)

description: Sample 2

value: WT


title: Sample_39_Bcl2Setd2het_splenicTumor_RNAseq_repl4


title: fkh1Δfkh2-dsm_rep2 (IP)

description: Sample 20


title: AL4938 [OSKM 2 (i4F 2)]

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

data_processing:
Cell Ranger software
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrices and cell metadata

source_name: pancreas

extract_protocol:
To isolate all pancreatic cell types, tissue was digested using 1 mg/ml Collagenase P (Sigma, 11213865001), 2 U/ml Dispase II (Life Technologies, 17105041), 0.1 mg/ml Soybean Trypsin Inhibitor (Life Technologies, 17075-029) and 0.1 mg/ml DNase I (Sigma, D4513) in HBSS with Ca2+/Mg2+ (Life Technologies, 14025050). Tissue dissociation was performed using the gentle MACSTM Octo Dissociator (Miltenyi Biotech) at 37°C for 40 min. The tissue was further digested with 0.05% Trypsin-EDTA (Life Technologies, 25300062) for 5 min at 37°C and erythrocytes were removed with red blood cell lysis buffer (Biolegend, 420301).
Cells were loaded onto a 10x Chromium Single Cell Controller chip B (10x Genomics) as described in the manufacturer’s protocol (Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, PN-1000075). Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean up, cDNA amplification, and library construction were performed following the manufacturer’s recommendations.

treatment_protocol: Doxycycline hyclate was administered in the drinking water (1 mg/ml) supplemented with 7.5% sucrose for 7 days. Mild acute pancreatitis was induced by 7 intraperitoneal injections, given once per hour, of a pancreatic secretagogue cholecystokinin (CCK) analogue called caerulein at 100 μg/kg for 2 consecutive days.

tag: age

value: 2 months

value: Pancreas

value: Doxycycline


title: WT_90min_rep1 (IP)

description: Sample 17

tag: strain


title: Sample_34_Bcl2_splenicTtumor_RNAseq_repl3

value: DAPI-, GFP+


title: AML2

city: Beijing

first: Tong

last: Xing

address: No. 11 Xizhimen South Street

institute: Peking University People’s Hospital

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reads mapping to the reference genome: hg38
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BM EPC

growth_protocol: BMMNCs(5×106 per well)  were cultured in fibronectin-precoated(Sigma, St. Louis, MO, USA) 6-well culture plates with EGM-2-MV-SingleQuots(Lonza, Walkersville, MD, USA) and 10% foetal bovine serum(FBS, Gibco, MA, USA) at 37°C in a humidified incubator with 5% CO2 for 7 days until collecting.

extract_protocol:
RNA was harvested using Trizol reagent. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease status

value: acute myloid leukemia(AML)

value: Bone Marrow Endothelial Progenitor Cells

tag: iPSs-r

value: No


title: HEK293T, Cut&Tag, IgG, rep2

tag: cell line

tag: treatment

value: untreated

tag: antibody

value: IgG(Abcam, Cat#ab6702)


title: AML3


title: Sample_36_Bcl2Setd2het_splenicTumor_RNAseq_repl1

value: Rosa26-Bcl2-GFP Setd2WT/-

value: Spleen


title: WT_90min_rep2 (IP)

description: Sample 18


title: rpd3Δ_rDNA20_rep1 (IP)

description: Sample 15

value: rpd3{delta} rDNA20


title: Sample_33_Bcl2_splenicTumor_RNAseq_repl2


title: HEK293T, Cut&Tag, OGT, rep2

value: Human embryonic kidney

value: OGT(Proteintech, Cat #11576-2-AP)


title: Sample_35_Bcl2_splenicTumor_RNAseq_repl4


title: AM4989 [CERULEIN 1]

value: Wild type

value: cerulein


title: Sample_37_Bcl2Setd2het_splenicTumor_RNAseq_repl2


title: AM4990 [CERULEIN 2]


title: H-MDS3

value: Myelodysplastic syndromes(MDS)

value: higher-risk


title: AM4988 [WT 2]

value: 2 months

value: Pancreas


title: WT_rDNA20_rep2 (IP)

description: Sample 14

value: anti-BrdU

value: WT rDNA20

value: hydroxyurea


title: AML1

value: acute myloid leukemia(AML)

value: Bone Marrow Endothelial Progenitor Cells

value: No


title: WT_rDNA20_rep1 (IP)

description: Sample 13


title: AL4939 [OSKM 3 (i4F 3)]

value: Doxycycline


title: AL4937 [OSKM 1 (i4F 1)]


title: AL4936 [WT 1]


title: H-MDS2


title: H3K4me3 ChIP-seq 2 run2

description:
H3K4me3 ChIP-seq
mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw

data_processing:
Data was mapped to mm10 (GRCm38) using Bowtie v1.2.2. The following Bowtie parameters were used: -k1 -v2 -X1000 –best
Bedgraphs mapping the midpoints of deduplicated fragments in 50 bp bins were generated using custom scripts.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

extract_protocol:
mESCs were cross-linked for 5 minutes with 1% formaldehyde and quenched with 0.25μM glycine. Chromatin fragmentation was performed in sonication buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5mM EGTA, 0.5% SDS, 0.5mM PMSF) with a Qsonica Q800R bath sonicator at 70% amplitude pulsing with 15 second “ON” and 45 seconds “OFF” cycles for 30 minutes total sonication time. Fragment sizes were checked by agarose gel. Fragmented chromatin from 7.5M mESCs was used as input for immunoprecipitation. ChIP material was diluted with 1mL of IP buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5% Triton X-100, 150mM NaCl, 10% Glycerol, 5% BSA) and pre-cleared with 10μL DynaBeads Protein A (ThermoFisher) for 1 hr at 4°C. The supernatant was then further diluted with 250μL IP buffer and incubated with 16 μL H3K4me3 antibody (EpiCypher Cat#13-0028) overnight at 4°C. Bound chromatin was isolated with 150 μL of pre-blocked DynaBeads Protein A for 2 hrs at 4°C. Beads were washed 1x in low salt (20mM Tris pH 8.0, 2mM EDTA, 1% Triton X-100, 150mM NaCl, 0.1% SDS), 3x in high salt (20mM Tris pH 8.0, 2mM EDTA, 1% Triton X-100, 500mM NaCl, 0.1% SDS), 1x in LiCl (20mM Tris pH 8.0, 2mM EDTA, 250mM LiCl, 1% IGEPAL, 1%[w/v] sodium deoxycholate), and 2x in TE (10mM Tris pH 8.0, 0.1mM EDTA) prior to elution with 2x 250uL of elution buffer (10% SDS, 100mM sodium bicarbonate). Crosslinks were reversed by the addition of 0.2M NaCl and incubation at 65°C overnight. The IP mixture was treated with Proteinase K (Invitrogen) for 1 hr at 50°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Kit (New England Biolabs) as per the manufacturer’s protocol.

value: F121-9 wt mESCs

tag: assay

value: ChIP-seq

tag: condition

value: Untreated


title: m3-ipsi

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0.422, Illumina), allowing no mismatches in the index read. After the quality and polyA trimming by BBDuk and alignment by HISAT2 (version 2.1.0), read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCm38.78). DESeq2 R package was used to determine differentially expressed genes by taking into account a paired design where each mouse individual was compared between ipsi and contra. Significance was defined to be those with adjusted p-value < 0.1 calculated by the Benjamini-Hochberg method to control the false discovery rate (FDR).
Genome_build: GRCm38.78
Supplementary_files_format_and_content: raw read counts are provided in a csv ifle

source_name: olfactory bulb

growth_protocol: Eight-week-old C57BL/6J (The Jackson Laboratory; stock # 000664) were deeply anesthetized with isoflurane and intranasally administered 10μL of lipopolysaccharide (LPS) from Escherichia coli (Sigma; product #L2880; lot #025M4040V) in physiologic saline (1 mg/ml; Sigma). LPS administrations took place three times per week for 4 weeks and were carried out unilaterally to the left naris of each mouse, with the right side serving as an internal control. The OB ipsilateral to the side of the injected naris is referred to as ipsilateral (ipsi), and the opposite OB (control) as contralateral (contra).

extract_protocol:
Olfafctory bulb tissues were microdissected from fixed and cryopreserved whole mouse brains. Approximately 5mg of the frozen tissue was incubated with proteinase K (500 μg/ml) in 500 ul of 10 mM NaCl, 500 mM Tris (pH 8.0), 20 mM EDTA, and 1% SDS at 55 ˚C for 3 hrs until the sections are completely dissolved (Korbler et al., 2003).  The acid phenol-chloroform method was applied for RNA extraction using Direct-zol™ RNA Micro prep Kit (Zymo Research). RNA quality and quantity were determined by RNA Pico BioAnalyzer (Agilent technologies).
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) as per the manufacturer’s instructions. Briefly, total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment close to the 3’ end gets captured for later indexed adapter ligation and PCR amplification. The processed libraries were assessed for their size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The denatured libraries were loaded onto an SP flow cell on an Illumina NovaSeq 6000 and run for 53-101 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: Each mouse was then housed in polycarbonate cages and had ad lib access to irradiated rodent chow and water. The animal facility was programmed with a 12:12-h light: dark cycle. All experiments were conducted in accordance with institutional guidelines, the Guide for the Care and Use of Laboratory Animals (Institute for Laboratory Animal Research, 2011), and approved by the Penn State College of Medicine Institutional Animal Care and Use Committee.

tag: mouse individuals

value: ipsi (LPS-treated side)

tag: Sex

value: M


title: Sample_32_Bcl2_splenicTumor_RNAseq_repl1

value: Spleen

value: DAPI-, GFP+


title: m3-contra

value: contra (non-treated side)


title: rpd3Δ_rDNA20_rep2 (IP)

description: Sample 16

data_processing:
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome of S288C from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: R64
Supplementary files format and content: binned.bed files
Library strategy: BrdU-IP-seq

extract_protocol:
Cells were resuspend in 500 μL genomic lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extractracion and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

value: rpd3{delta} rDNA20


title: HEK293T, Cut&Tag, IgG, rep1

value: untreated

tag: cell type

value: Human embryonic kidney

value: IgG(Abcam, Cat#ab6702)


title: sir2Δrpd3Δ_rep2 (IP)

description: Sample 11

value: anti-BrdU

value: hydroxyurea


title: L-MDS3

value: Myelodysplastic syndromes(MDS)

value: Bone Marrow Endothelial Progenitor Cells

value: lower-risk


title: H-MDS1

value: higher-risk


title: m2-ipsi


title: H3K4me3 ChIP-seq 2 run1

value: F121-9 wt mESCs

value: ChIP-seq


title: sir2Δrpd3Δ_rep1 (IP)

description: Sample 10


title: sir2Δrpd3Δ_rep3 (IP)

description: Sample 12


title: H3K4me3 ChIP-seq 1 run1

description:
H3K4me3 ChIP-seq repl1, run 1 and run 2 samples were sequenced from the same sample and data was combined before processing
mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw

value: Untreated


title: H3K4me3 ChIP-seq 1 run2


title: sir2Δ_rep3 (IP)

description: Sample 9


title: L-MDS2


title: L-MDS1


title: sir2Δ_rep2 (IP)

description: Sample 8


title: HD3

value: healthy

value: No


title: 20-minute TT-seq 2 lane2

description:
20-minute TT-seq repl2, lane 1 and lane 2 samples were sequenced from the same sample in parallel and data was combined before processing
200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F.bw
200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_R.bw

data_processing:
Library strategy: TT-seq
Reads were trimmed for a minimum quality score of 20 using a custom script (https://github.com/AdelmanLab/NIH_scripts/tree/main/trim_and_filter_PE), adapter sequences were removed using cutadapt version 1.14.
Reads were first mapped to dm6 using bowtie16, before aligning to mm10 using STAR (version 2.7.3a).
Strand-specific bedgraphs were generated from deduplicated BAM files using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

extract_protocol:
Cells were counted and collected in Trizol, to which was added 5% S2 cells, labelled with 4sU for 2 hours. RNA was chloroform extracted, DNase-treated, and chloroform extracted. To 60 μg total RNA was added 2X fragmentation buffer (final concentration: 75 mM Tris Cl, pH 8.3, 112.5 mM KCl, and 4.5 mM MgCl2) and heated to 95 C for 5 minutes. Fragmentation was stopped by adding EDTA to 50 mM and placing samples on ice. RNA was ethanol precipitated and resuspended in H2O. Fragment sizes were checked on the TapeStation (peak size of ~800 nt). Biotinylation reaction was performed with 0.025 mg/mL MTSEA-Biotin XX (Biotum) in reaction buffer (20% N,N-Dimethylformamide, 1mM EDTA, 10 mM HEPES pH 8) for 45 minutes in the dark. Labelled RNA was chloroform extracted and ethanol precipitated, and resuspended in 90 μL H2O. 75 μL DynabeadsTM M-280 Streptavidin (ThermoFisher) were pre-washed with decon solution (0.1M NaOH + 50mM NaCl), 2X 100mM NaCl, 2X High Salt buffer (100mM Tris Cl pH 7.4, 10mM EDTA pH 8, 1M NaCl, 0.05% (v/v) Tween 20), and resuspended in High salt buffer. Labelled RNA was denatured by heating to 65 C for 5 minutes and placing on ice for 2 minutes. 10 μL High salt buffer was added to labelled RNA. Prewashed beads were placed on magnet, supernatant discarded, and then beads were resuspended in the labelled RNA. Beads and RNA were rotated for 30 minutes in the dark. Beads were then washed 4X for 1 minute with high salt buffer. Labelled RNA was eluted 2X with 100 mM DTT (1,4-Dithiothreitol). RNA was cleaned up with microelute columns (Norgen).
Sequencing libraries were prepared from 250 ng of labelled RNA using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion, shortening the fragmentation step to 3 minutes and using 8 cycles of PCR amplification.

treatment_protocol: 1 day after plating, media was changed to that containing 0.03% DMSO and cells collected in Trizol after an additional 4 hours before 20' labelling with 500µM 4sU

value: TT-seq


title: m1-ipsi

value: ipsi (LPS-treated side)

value: M


title: gDNA corresponding to total-RNA #3

description: gDNA corresponding to total-RNA #3

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

extract_protocol:
Genomic DNA was extracted from >6M cells using QuickExtract (Lucigen).
In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.

value: F121-9 mESCs with at the 129 allele of Pou5f1:mKate2  uaTSS +172, TagBFP2  Oct4 C terminus

tag: library integration location

value: Pou5f1 uaTSS + 157 (129 allele, upstream of mKate2 reporter)

value: RNA-based INSERT-seq


title: sir2Δ_rep1 (IP)

description: Sample 7

value: anti-BrdU


title: gDNA corresponding to total-RNA #2

description: gDNA corresponding to total-RNA #2


title: m2-contra

value: contra (non-treated side)


title: m1-contra


title: rpd3Δ_rep3 (IP)

description: Sample 6

value: hydroxyurea


title: HD2

value: Bone Marrow Endothelial Progenitor Cells


title: 20-minute TT-seq 2 lane1


title: total-RNA #3

description: total-RNA #3

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences plus spliced versions of these inserts as called by STAR. STAR v2.7.0 was run on replicates 2-4 using flags --outSJfilterOverhangMin 10 4 4 4 --peOverlapNbasesMin 10 --peOverlapMMp 0.08 --alignEndsType EndToEnd --outFilterMismatchNmax 5 --scoreDelOpen -10 --scoreInsOpen -10. The detected splice junctions were filtered down to only junctions on the + strand with >10 read counts and >25% of the maximum counts for other junctions detected in the same insert. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

extract_protocol:
For total-RNA, >5M library-containing cells was pelleted and resuspended in Trizol (Ambion). RNA was cleaned up using Direct-zol RNA miniprep columns (Zymo Research), treated with RQ1 DNase (Promega), then cleaned up again using a total RNA purification kit (Norgen Biotek Corp).
First, RNA was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer in mKate2 annealed 221nt downstream of the variable regions. cDNA was RNase-treated and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through 17-20 PCR cycles using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).


title: 20-minute TT-seq 1 lane2

description:
20-minute TT-seq repl1, lane 1 and lane 2 samples were sequenced from the same sample in parallel and data was combined before processing
200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F.bw
200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_R.bw


title: US7_OE3

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
RNA-seq results were aligned to hg38.
UCSC Genome assembly GRCh38.p13 (GCA_000001405.28) genome annotation files (around 19,862 mainly protein-encoding genes but not including IGHM).
Reads were quality-checked and processed using the nf-core/rnaseq analysis workflow v1.3 pipeline consisting of Nextflow v19.04.1, FastQC v0.11.8 Cutadapt v2.4, Trim Galore! v0.5.0, STAR vSTAR_2.6.1d, HISAT2 v2.1.0, Picard MarkDuplicates v2.18.27, Samtools v1.9, featureCounts v1.6.4, StringTie v1.3.5, Preseq v2.0.3, deepTools, v3.2.0, RSeQC v3.0.0, MultiQCv1.7 software.
Raw count results were analyzed using edgeR (RNA-seq differential expression analysis, two groups) against hg38 to determine significantly regulated genes (criteria: fold change ≥2; p<0.05; low expression filter rpkm <1.0).
Genome_build: GRCh38.p13

source_name: US7 transduced with pLV411G-ST6GAL1

growth_protocol: Leukemia cells were co-cultured on mitomycin-C inactivated OP9 stromal cells in alpha-MEM media supplemented with 20% FBS, 1% L-glutamine and 100 μg/ml penicillin/streptomycin

extract_protocol:
RNA was extracted from frozen cell pellets using Trizol (ThermO-Fisher 315596026) and further purified using an RNEasy Mini kit (Qiagen #74104). Quality control analysis was done using Bioanalyzer RNA Nano and D1000Chips. Nucleic acid concentrations were determined by Qubit.
RNAseq was performed by Novogene using an unstranded high throughput TruSeq stranded mRNA prep kit.

treatment_protocol: Leukemia cells in the culture supernatant were harvested. Cultures were actively growing.

value: US7 cell line

value: B-cell precursor acute lymphoblastic leukemia


title: HD1


title: sortseq_2_unsorted

extract_protocol:
Genomic DNA was extracted from 9.3M cells using QuickExtract (Lucigen).
In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.

value: Sort-seq INSERT-seq


title: total-RNA #2

description: total-RNA #2


title: US7_OE2


title: rpd3Δ_rep1 (IP)

description: Sample 4


title: 20-minute TT-seq 1 lane1

value: F121-9 wt mESCs


title: WT_rep3 (IP)

description: Sample 3

value: WT


title: sortseq_2_bin6

extract_protocol:
Genomic DNA was extracted from sorted cells using QuickExtract (Lucigen).
In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.

value: Untreated


title: gDNA siRRP40 C

description: gDNA siRRP40 C

treatment_protocol: 48 hours prior to harvesting, cells were transfected with 40 nM siRNAs, using the RNAiMAX reagent (Invitrogen) in a suspension transfection. A mix of four siGENOME siRNAs against EXOSC3 was used (Catalog ID MQ-064537-01-0002, Horizon Discovery).

value: siRNA pool against EXOSC3 (RRP40)


title: US7_EV3

source_name: US7 transduced with pLV411G empty vector


title: sortseq_2_bin5


title: US7_OE1


title: WT_rep1 (IP)

description: Sample 1


title: WT_rep2 (IP)

description: Sample 2


title: gDNA RRP40 B

description: gDNA RRP40 B


title: rpd3Δ_rep2 (IP)

description: Sample 5


title: T5_PDGFR_pos

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads are trimmed for adapters and poly(A/T) tails, and then filtered by sequencing Phred quality (>= Q15) using fastp
Aligned to mm39 using STAR with two-pass option
Counts per genomic feature are calculated with featureCounts, where multi-mapping reads are counted as fractions
We filtered out genes that do note have counts per million (CPM) more than 1 in at least 3 samples
Normalized counts by weighted trimmed mean of M-values (TMM) and apply voom to calculate log2 of CPM
Genome_build: mm39
Supplementary_files_format_and_content: logCPM has log2 of CPM per genomic feature per sample

source_name: EGFR+ GBM from mouse brains

extract_protocol:
Libraries were prepared using SMARTer Stranded Total RNAseq v3 Pico Input Mammalian sample preparation kits from 1ng of purified total RNA according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

value: mixed (C57Bl/6J, 129S4, FVBN/J, Balb/cJ)

value: flow sorted PDGFR+


title: gDNA siRRP40 A

description: gDNA siRRP40 A


title: sortseq_2_bin4


title: gDNA siNT C

description: gDNA siNT C

treatment_protocol: 48 hours prior to harvesting, cells were transfected with 40 nM siRNAs, using the RNAiMAX reagent (Invitrogen) in a suspension transfection. The siGENOME Non-Targeting Control siRNA #2 was used.

value: Non-targeting siRNA control


title: T5_PDGFR_neg

value: flow sorted PDGFR-


title: gDNA siNT B

description: gDNA siNT B

value: F121-9 mESCs with at the 129 allele of Pou5f1:mKate2  uaTSS +172, TagBFP2  Oct4 C terminus

value: Pou5f1 uaTSS + 157 (129 allele, upstream of mKate2 reporter)


title: US7_EV1


title: gDNA siNT A

description: gDNA siNT A

value: RNA-based INSERT-seq


title: sortseq_2_bin3


title: sortseq_2_bin2


title: T5_Gal1_pos

value: flow sorted Gal1+


title: SJRHB00026_X1_treat_day28

description: single nucleus RNA-sequence

data_processing:
Single cell or nucleus RNA-seq reads from tumors or O-PDXs were aligned using the 10x Genomics Cell ranger Pipeline (v3.0.2) to the hg19 reference data v3.0.0 (for tumors) or hg19-and-mm10 v3.0.0 (for O-PDXs). In the case of single-nucleus datasets, a custom pre-mRNA reference was used to include intronic reads into expression matrices
Genome_build: hg19 or hg19-and-mm10
Supplementary_files_format_and_content: Cell Ranger output

extract_protocol:
single nucleus extraction
Nuclei were isolated from frozen tissue samples using a combination of detergent and mechanical separation in TST buffer. A detailed protocol is available on protocols.io at https://dx.doi.org/10.17504/protocols.io.bhbcj2iw
10x Genomics 3' single-cell gene expression kit

value: xenograft

tag: protocol

value: 10x genomics 3' snRNA-seq


title: total-RNA siRRP40 C

description: total-RNA siRRP40 C

extract_protocol:
Genomic DNA was extracted from >6M cells using QuickExtract (Lucigen).
First, RNA was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer in mKate2 annealed 221nt downstream of the variable regions. cDNA was RNase-treated and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through 17-20 PCR cycles using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).


title: glioblastoma tumor_3

data_processing:
Raw sequencing data were demultiplexed, aligned to the mouse genome mm10  using bcbio-nextgen single-cell RNA-seq pipeline (https://bcbio-nextgen.readthedocs.io/en/latest/).
We select cells by removeing small outliers of library size and feature number, and large outliers of mitochondrial genes using a median absolute deviation (MAD)-based threshold of 2, 3 and 4 respectively.
Genome_build: mm10
Supplementary_files_format_and_content: counts, metadata provided for each barcoded sample.

source_name: EGFR WT driven glioblastoma

extract_protocol:
Mice were perfused with 10ml PBS, brain was harvested, and cerebellum removed. Brain was minced and resuspended in 1.5mg/ml Collagenase in HBSS with calcium and magnesium. Mixture was incubated rotating at 37°C for 30 minutes, with gentle dissociation using a P1000 pipette halfway through to break apart large pieces. Dissociated cell mixture is filtered through a 100μm filter and diluted with HBSS. All washes are pelleted at 400g for 5min. Mixture is resuspended in 30% Percoll in PBS for myelin removal at 700g for 15min with brake on low. Myelin layer is removed, and mixture is diluted and pelleted at 400g for 5min. Red blood cells are lysed using Biolegend RBC lysis buffer according to manufacturer protocol. sample was stained with CD45 and Zombie Yellow fixable viability dye. Cells were washed with RNAse free PBS with 0.1% BSA and immediately sorted on a FACs Aria Cell Sorter for viable CD45+ and CD45- populations into ice cold RNAse free PBS with 0.1% BSA. A minimum of 1 million CD45+ and CD45- cells were harvested when possible to account for the low capture rate of InDrop system. If fewer cells were available, then two samples were pooled, this occurred on samples 1 and 2 (S1+S2).
Cells were then filtered through a 70um filter before being given to the Harvard Medical School Single Cell Sequencing core where they were run on the InDrop system with the goal of encapsulating 10k cells per sample. Following encapsulation, the reverse transcription reaction was performed, and libraries were made, full protocol has been described previously. As per core recommendation, 4 libraries per 10k cells were made. Following harvest of all three samples, libraries were sequenced using the NextSeq system with 16 libraries per sequencing run, so that the depth of sequencing was calculated to be 25,000 genes per cell.

value: multiplexed sample (mixture of CD45- and CD45+)

tag: tumor stage

value: multiplexed sample (mixture of early, medium, and large)

tag: run

tag: date


title: sortseq_2_bin1

value: Sort-seq INSERT-seq


title: SJRHB00026_X1_treat_day0

description: single nucleus RNA-sequence

source_name: Orthotopic patient-derived xenograft

tag: tissue


title: T5_Gal1_neg

value: flow sorted Gal1-


title: T4_PDGFR_pos


title: SJRHB00026_X1_treat_day3

description: single nucleus RNA-sequence


title: US7_EV2

value: US7 cell line

value: B-cell precursor acute lymphoblastic leukemia


title: glioblastoma tumors_pool_2


title: SJRHB030680_X1_organoid

description: single cell RNA-sequence

source_name: Organoid

extract_protocol:
single cell dissociation
Tumor and xenograft samples were dissociated using an enzymatic tumor dissociation with papain. A detailed protocol is available on protocols.io at https://dx.doi.org/10.17504/protocols.io.98ah9se
10x Genomics 3' single-cell gene expression kit

value: organoid

value: 10x genomics 3' scRNA-seq


title: total-RNA RRP40 B

description: total-RNA RRP40 B

value: siRNA pool against EXOSC3 (RRP40)


title: glioblastoma tumors_pool_1


title: T4_PDGFR_neg

value: mixed (C57Bl/6J, 129S4, FVBN/J, Balb/cJ)


title: T4_Gal1_pos


title: Tbx20 KD [Tbx20-c]

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description:
Transfected with 2 guide RNAs targeting Tbx20
Tbx20-c_GT18-10894_AGTACTCC-AACAGGTT_S3
18-furtado-001_gene_counts.txt

data_processing:
Single-end reads were mapped to the UCSC mouse transcriptome by Bowtie, allowing up to two mismatches, and expression levels of all UCSC genes were estimated by RSEM with default parameters.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: 18-furtado-001_gene_counts.txt: Tab-delimited count matrix.

source_name: Murine adult cardiac fibroblasts

extract_protocol:
Total RNA was isolated from fibroblasts using the RNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. Sample concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico LabChip assay (Agilent Technologies). Libraries were constructed using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions. Libraries were pooled and sequenced 75 bp single-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2 reagents (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Adult cardiac fibroblasts isolated from 8-10 weeks old RosaCas9-EGFP, were cultured for 3 days, then FACS sorted for CD45-CD31-CD90+ and re-plated at 10,000cells/cm2. After 6 days, when reaching 80-90% confluency, cells were transfected with guide RNAs (scrambled for control samples, or targeted towards Gata4 or Tbx20), using Lipofectamine MessengerMAX (ThermoFisher) according to manufacturer’s instructions.

value: primary cardiac fibroblasts

tag: genotype

value: C57BL/6 background Cas9GFP

tag: age

value: adult

tag: grna

value: targeting Tbx20


title: T4_Gal1_neg


title: total-RNA siNT C

description: total-RNA siNT C

source_name: Mouse embryonic stem cells

tag: cell line

value: F121-9 mESCs with at the 129 allele of Pou5f1:mKate2  uaTSS +172, TagBFP2  Oct4 C terminus

value: Pou5f1 uaTSS + 157 (129 allele, upstream of mKate2 reporter)

value: RNA-based INSERT-seq

value: Non-targeting siRNA control


title: Tbx20 KD [Tbx20-b]

description:
Transfected with 2 guide RNAs targeting Tbx20
Tbx20-b_GT18-10893_TGGCCGGT-GCGCTCTA_S8
18-furtado-001_gene_counts.txt


title: T3_PDGFR_pos

value: flow sorted PDGFR+


title: total-RNA siNT B

description: total-RNA siNT B


title: total-RNA siNT A

description: total-RNA siNT A


title: SJRHB013758_X2_scATAC

description: single cell ATAC-sequence

extract_protocol:
single nucleus extraction for scATAC-seq
Nuclei were isolated from frozen tissue samples using a combination of detergent and mechanical separation in TST buffer. A detailed protocol is available on protocols.io at https://dx.doi.org/10.17504/protocols.io.bhbcj2iw
10x Genomics single-cell ATAC kit

value: xenograft

value: 10x genomics scATAC-seq


title: T3_Gal1_pos

value: flow sorted Gal1+


title: T3_PDGFR_neg

value: flow sorted PDGFR-


title: SJRHB013758_X1_scATAC

description: single cell ATAC-sequence


title: SJRHB010928_X1_scATAC

description: single cell ATAC-sequence


title: total-RNA siRRP40 A

description: total-RNA siRRP40 A


title: Tbx20 KD [Tbx20-a]

description:
Transfected with 2 guide RNAs targeting Tbx20
Tbx20-a_GT18-10892_CAATTAAC-ATATCTCG_S6
18-furtado-001_gene_counts.txt


title: Gata4 KD [Gata4-c]

description:
Transfected with 2 guide RNAs targeting Gata4
Gata4-c_GT18-10897_CATAGAGT-TGGTGGCA_S12
18-furtado-001_gene_counts.txt

value: targeting Gata4


title: T3_Gal1_neg

value: flow sorted Gal1-


title: Ifitm_3

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
after the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Genome_build: hg18
Supplementary_files_format_and_content: processed data files format is in xlsx, and content the fpkm of all the samples.

source_name: retina

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: treatment

value: ifitm3 knockdown


title: SJRHB046156_X1_scATAC

first: Michael

last: Dyer

address: 262 Danny Thomas Pl MS 324

institute: St. Jude Children's Research Hospital

description: single cell ATAC-sequence


title: Ifitm_2


title: SJRHB013759_X15_scATAC

description: single cell ATAC-sequence


title: Gata4 KD [Gata4-b]

description:
Transfected with 2 guide RNAs targeting Gata4
Gata4-b_GT18-10896_TGCGAGAC-CAACAATG_S10
18-furtado-001_gene_counts.txt


title: Gata4 KD [Gata4-a]

description:
Transfected with 2 guide RNAs targeting Gata4
Gata4-a_GT18-10895_GACGTCTT-GGTGAACC_S4
18-furtado-001_gene_counts.txt


title: SJRHB010927_X1_scATAC

description: single cell ATAC-sequence


title: SJRHB010468_X1_scATAC

description: single cell ATAC-sequence


title: SJRHB046156_X1_barcode

description: barcode dialout PCR

data_processing:
Library strategy: tagged amplicon
Single cell or nucleus RNA-seq reads from tumors or O-PDXs were aligned using the 10x Genomics Cell ranger Pipeline (v3.0.2) to the hg19 reference data v3.0.0 (for tumors) or hg19-and-mm10 v3.0.0 (for O-PDXs). In the case of single-nucleus datasets, a custom pre-mRNA reference was used to include intronic reads into expression matrices
Genome_build: hg19 or hg19-and-mm10
Supplementary_files_format_and_content: Cell Ranger output

extract_protocol:
barcode dialout PCR
Tagged amplicon PCR of 10x gene expression libraries using primers targeted to the lineage barcode
Tagged amplicon PCR

value: Barcode dialout PCR


title: CS_seedling_GRO_seq_v2_rep3

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
Library strategy: GRO-seq
Sequencing reads were cleaned with Trim Galore (version 0.6.4) and cutadapt (version 1.16) programs to remove sequencing adapters, low quality bases (< 20), short reads and the 4 bases in 5’end and 3’end of R1 and R2 which were randomly introduced.
Clean reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0) with the bowtie2 (version 2.3.5.1) program and only keep the reads with one best unique alignment. We also used SortMeRNA (version 2.1b) program to remove the reads originating from chloroplast, mitochondria and rRNA.
For GRO-seq, the 5′ coordinate of R1 reads was considered the position of the engaged polymerase for future analyses. Each site density of GRO-seq was then calculated in plus and minus strands and normalized by the count of unique mapped reads. For pNET-seq,  the 5′ coordinate of R2 reads with the directionality indicated by R1 reads was considered the position of the engaged polymerase.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: GRO-seq and pNET-seq signal in each site were provided in bedgraph file.

organism: Triticum aestivum

source_name: Triticum aestivum 12-days-old seedlings

growth_protocol: The bread wheat (Triticum aestivum) cultivar “Chinese Spring” were grown under long day condition.

extract_protocol:
Leaf tissue of 12-day-old seedlings were collected by flash freezing with liquid nitrogen and followed by nuclei isolation.
For GRO-seq, nuclei were isolated by the Percoll gradient procedure as previously described except that the concentration of Triton X-100 was reduced to 0.5%. In vitro run-on, and nascent RNA purification were performed as previously reported20. The obtained nascent RNA was treated with T4 PNK (NEB), followed by TRIzol purification and subject to small RNA library construction using NEXTflex™ Small RNA-Seq Kit v3 (PerkinElmer) according to the manufacturer manual. The cDNA libraries were sequenced on the Illumina NovaSeq platform.For the second time (v2_rep1, v2_rep2, and v2_rep3), to obtain a deeper sequencing coverage at a reasonable sequencing cost, we added a rRNA removal step after nucleus RNA isolation and before the affinity purification of nascent RNA using riboPOOL kit (siTOOLs BIOTECH) . For pNET-seq, nuclei were isolated by a lysis-and-wash procedure as previously described except that the concentration of Triton X-100 was reduced to 0.5%. The RNA Pol II associated RNA were immunoprecipitated using Pol II antibody (Abcam, ab817) and followed by small RNA cDNA library construction. The size selection of nascent RNA was omitted. The cDNA libraries were sequenced on the Illumina NovaSeq platform.

value: 12-days-old seedlings

tag: cultivar

value: Chinses Spring


title: Control_3

value: control


title: CS_seedling_GRO_seq_v2_rep2


title: Control [cont-b]

description:
Transfected with scrambled guide RNAs
cont-b_GT18-10902_CTGCTTCC-GATCTATC_S1
18-furtado-001_gene_counts.txt

value: primary cardiac fibroblasts

value: C57BL/6 background Cas9GFP

value: adult

value: srambled control


title: Control_2


title: SJRHB031320_X1

description: single cell RNA-sequence

value: 10x genomics 3' scRNA-seq


title: Control_1


title: CS_seedling_GRO_seq_v2_rep1


title: CS_seedling_pNET_seq_rep4

data_processing:
Library strategy: pNET-seq
Sequencing reads were cleaned with Trim Galore (version 0.6.4) and cutadapt (version 1.16) programs to remove sequencing adapters, low quality bases (< 20), short reads and the 4 bases in 5’end and 3’end of R1 and R2 which were randomly introduced.
Clean reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0) with the bowtie2 (version 2.3.5.1) program and only keep the reads with one best unique alignment. We also used SortMeRNA (version 2.1b) program to remove the reads originating from chloroplast, mitochondria and rRNA.
For GRO-seq, the 5′ coordinate of R1 reads was considered the position of the engaged polymerase for future analyses. Each site density of GRO-seq was then calculated in plus and minus strands and normalized by the count of unique mapped reads. For pNET-seq,  the 5′ coordinate of R2 reads with the directionality indicated by R1 reads was considered the position of the engaged polymerase.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: GRO-seq and pNET-seq signal in each site were provided in bedgraph file.

extract_protocol:
Leaf tissue of 12-day-old seedlings were collected by flash freezing with liquid nitrogen and followed by nuclei isolation.
For GRO-seq, nuclei were isolated by the Percoll gradient procedure as previously described except that the concentration of Triton X-100 was reduced to 0.5%. In vitro run-on, and nascent RNA purification were performed as previously reported20. The obtained nascent RNA was treated with T4 PNK (NEB), followed by TRIzol purification and subject to small RNA library construction using NEXTflex™ Small RNA-Seq Kit v3 (PerkinElmer) according to the manufacturer manual. The cDNA libraries were sequenced on the Illumina NovaSeq platform. For pNET-seq, nuclei were isolated by a lysis-and-wash procedure as previously described except that the concentration of Triton X-100 was reduced to 0.5%. The RNA Pol II associated RNA were immunoprecipitated using Pol II antibody (Abcam, ab817) and followed by small RNA cDNA library construction. The size selection of nascent RNA was omitted. The cDNA libraries were sequenced on the Illumina NovaSeq platform.

treatment_protocol: No treatment applied


title: Control [cont-a]

description:
Transfected with scrambled guide RNAs
cont-a_GT18-10901_GGTCACGA-CATAATAC_S5
18-furtado-001_gene_counts.txt


title: SJRHB046156_X1

description: single cell RNA-sequence


title: Ifitm_1


title: DC907 cold treat 3 day and recover 3 day rep3

city: Nanning

first: Zhichi Zeng

last: Zhichi Zeng

address: Nanning

institute: Guangxi University

data_processing:
Illumina Casava1.8 software used for basecalling.
Use fastq software to evaluate the quality of the row data. Use NGS QC toolkit software to filter the row data.
Clean reads were compared to the reference genome of rice cultivar 9311 using hisat2
The genome mapping results of all sequenced reads data were put together, assembled with cufflinks, and then compared with known gene models with cuffcompare
Differential expression analysis was performed using DEseq  package in R. We define Padj < 0.05 as differential gene, where Padj is the p value corrected by multi hypothesis test
Genome_build: 9311
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa Indica Group

source_name: stems and leaves

growth_protocol: 9311 and DC07 were hydroponically cultured in plastic barrels with Hogland nutrient solution and grew to four leaf stage at room temperature

extract_protocol:
The aboveground samples of rice were collected, quenched in liquid nitrogen, and RNA was collected with Trizol reagent. Illumina truseq RNA sample preparation kit was used to construct sequencing library together with 1 ug total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In this study, rice seedlings were treated with cold stress at 8 ℃± 0.5 ℃ for 1 or 3 days, and then recovered at room temperature for 1 or 3 days

tag: developmental stage

value: four-leaf stage

value: recovered 3 day after cold treatment for 3 day


title: KF-cultured [K3c]

description:
Control kept additional 3 days in culture
K3c-RNA_GT20-13852_TCTCGCGC-GCCTCTAT_S18
20-rosenthal-001_gene_counts.txt

data_processing:
Single-end reads were mapped to the UCSC mouse transcriptome by Bowtie, allowing up to two mismatches, and expression levels of all UCSC genes were estimated by RSEM with default parameters.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: 20-rosenthal-001_gene_counts.txt: Tab-delimited count matrix.

source_name: Murine adult kidney fibroblasts

extract_protocol:
RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico assay (Agilent Technologies). Libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2-Pico (Takara), according to the manufacturer’s protocol. Libraries were pooled and sequenced 75 bp single-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2.5 reagents (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Adult fibroblasts from heart, tail and kidney were isolated from 10 weeks old Rosa mT/mG male mice. After ten days cells were collected, counted and 4-5x10^5 cells were transferred in individual 1.5ml Eppendorf tubes (one per each kidney transplant), resuspended in 15-20ul of saline solution and kept on ice, until ready for the surgery. Fragments of fragments of sterile absorbable gelatin foam (Surgifoam, Ethicon), about 1mm long, were soaked in a drop of cell suspension and transplanted in the further end of a pocket created in the subcapsular space of the kidney of syngeneic 10-11 weeks old C57bl6/j mice. The full surgical procedure is described in the paper. The remaining cells were re-plated (5x10^4/well of a mw6 plate) for the cultured cells controls.

value: primary kidney fibroblasts

value: C57BL/6 background Rosa mT/mG

tag: condition

value: Cultured


title: CS_seedling_pNET_seq_rep3


title: SJRHB013759_X15

city: Memphis

description: single cell RNA-sequence

value: xenograft


title: KF-cultured [K2c]

description:
Control kept additional 3 days in culture
K2c-RNA_GT20-13851_TCCGCGAA-GCCTCTAT_S9
20-rosenthal-001_gene_counts.txt


title: SJRHB013759_X14

description: single cell RNA-sequence


title: DC907 cold treat 3 day and recover 3 day rep2


title: KF-cultured [K1c]

description:
Control kept additional 3 days in culture
K1c-RNA_GT20-13850_CGGCTATG-GCCTCTAT_S14
20-rosenthal-001_gene_counts.txt


title: Control [cont-c]

description:
Transfected with scrambled guide RNAs
cont-c_GT18-10903_TCATCCTT-AGCTCGCT_S2
18-furtado-001_gene_counts.txt


title: KF- transplanted [K3]

description:
Transplanted under the kidney capsule for 3 days
Kidney-Fibros_GT20-13843_TCCGCGAA-ACGTCCTG_S5
20-rosenthal-001_gene_counts.txt

value: Transplanted


title: DC907 cold treat 3 day and recover 1 day rep3

value: recovered 1 day after cold treatment for 3 day


title: SJRHB013757_X1

description: single cell RNA-sequence


title: CS_seedling_pNET_seq_rep1


title: CS_seedling_GRO_seq_rep2


title: SJRHB010468_X1

description: single cell RNA-sequence


title: CS_seedling_GRO_seq_rep1


title: DC907 cold treat 3 day and recover 1 day rep2


title: DC907 cold treat 3 day and recover 1 day rep1


title: SJRHB049189_X1

description: single cell RNA-sequence


title: KF- transplanted [K1]

description:
Transplanted under the kidney capsule for 3 days
K1-RNA_GT20-13841_TAATGCGC-GTCAGTAC_S8
20-rosenthal-001_gene_counts.txt


title: DC907 cold treat 3 day rep3

value: cold stress treatment for 3 day