title: poolC-56


title: GBM28_OncoD-0J1 3

status: Public on Dec 05 2025

type: SRA

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

country: USA

institute: Augusta University

description: Library name: GBM28.15

library_source: transcriptomic

data_processing:
cutadapt (for adapter trimming and quality filtering)
Alignment using STAR aligner
Normalization, quality control, and differential gene expression analysis were performed in R using DESeq2.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Count matrix in CSV format with rows as genes and columns as samples, values represent raw read counts.

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: Primary GBM cells GBM12 and GBM28 were maintained in 150 mm TC-treated Culture Dishes with 2%FBS DMEM.

extract_protocol:
Total RNA was isolated using the Rneasy Plus kit from Qiagen and samples were submitted for bulk RNA sequencing
Library preparation was performed with the SMARTer® Stranded Total RNA Sample Prep Kit (Takara Bio USA, Inc., cat# 634878). This process incorporated RiboGone™ and SMART® (Switching Mechanism at the 5' end of RNA Template) technologies, along with PCR amplification, to generate Illumina-compatible libraries without adapter ligation. RiboGone efficiently depleted rRNA from total RNA before library construction. Library quality was assessed using the TapeStation 2000 (Agilent Technologies), and concentrations were measured with Qubit (Thermo Fisher Scientific) before sequencing. Dual-indexed i5/i7 paired-end libraries were sequenced on the NovaSeq 6000 system (Illumina) with a minimum coverage of 50-60 million reads per sample.

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: glioblastoma


title: L12 TDT- Kupffer Cells mWD-CH-WD

city: OKC

first: Sarah

middle: Jane

last: Miller

state: OK

address: 940 Stanton L. Young Blvd

institute: University of Oklahoma Health Sciences Center

description: Library name: L12_TDT-KC_S36

data_processing:
Generated Fastq files were subjected to a data cleaning step involving trimming to remove low quality bases, eliminating short/low-quality reads and polyA/G tails, and trimming adapters using the FastP tool.
We used multiQC as a means to confirm alignment with GENCODE reference genome GRCm39/M34 using the STAR software package. Following alignment, differential expression was then applied to the count files using DESeq2.
Assembly: GRCm39/M34
Supplementary files format and content: raw counts

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was isolated using a standard TRIzol extraction protocol.
Libraries were generated using QuantSeq protocol on an Ilumina NovaSeq 6000 system.

value: Liver

value: Macrophages

tag: genotype

value: Ms4a3 (Cre/WT) Rosa26TdT (T/WT)

tag: treatment

value: mWD-CH-WD

tag: cell subtype

value: TDT- Kupffer cells


title: GBM12_OncoD-0J1 4

description: Library name: GBM12.16


title: poolC-42

city: Essen

first: Florian

last: Rambow

department: IKIM

country: Germany

institute: University Hospital Essen

library_source: transcriptomic single cell

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4). Reads were then mapped to the mouse genome (mm10) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2).
The merged gene expression matrix (raw counts) containing all samples was analyzed with the Seurat3 package in R. Cells were filtered by nFeature_RNA (genes detected) >3000 and <7000, percent.mt (percentage of mitochondria genes) < 10. This resulted in n=306 valid cells for downstream analysis. After filtering cells, log-normalization was performed using the default NormalizeData function in Seurat. The scaled data was regressed for cell cycle phases (S.Score and G2M.Score) and number of genes per cell (nFeature_RNA) before performing UMAP based dimension reduction (dims=1:20, resolution =0.4).
Assembly: mm10
Supplementary files format and content: csv

molecule: polyA RNA

source_name: tumor

extract_protocol:
Single cells were sorted (BD FACSAriaIII) in 96 well plates (VWR) containing 2μL of PBS including 0.2% Triton X-100 and 4U of RNase inhibitor (Takara) per well. Plates were properly sealed and spun down at 2000g for 1min before storing at −80°C. Whole transcriptome amplification was performed with a modified SMART-seq2 protocol as described previously, using 20 instead of 18 cycles of cDNA amplification. PCR purification was realized with a 0.8:1 ratio (ampureXP beads:DNA). Amplified cDNA quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent)
SMART-seq2 based scRNA-seq; Sequencing libraries were performed using the Nextera XT kit (Illumina) as described previously, using 1/4th of the recommended reagent volumes and 1/5th of input DNA with a tagmentation time of 9min. Library quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent). Indexing was performed with the Nextera XT index Kit V2 (A-D).

value: tumor


title: poolC-55


title: L12 Ly6C Hi mWD-CH-WD

description: Library name: L12_Ly6CHi_S34

value: Ly6C Hi Monocytes


title: poolC-43


title: poolC-58


title: GBM12_OncoD-0J1 3

description: Library name: GBM12.15


title: GBM28_OncoD 4

description: Library name: GBM28.8


title: poolC-53


title: poolC-51


title: GBM28_OncoD 2

description: Library name: GBM28.6


title: poolC-50


title: GBM28_OncoD 1

description: Library name: GBM28.5


title: poolC-40


title: L11 TDT+ Kupffer cells mWD-CH-WD

description: Library name: L11_TDT+_KC_S32

value: TDT+ Kupffer cells


title: poolC-37


title: poolC-47


title: GBM12_OncoD 4

description: Library name: GBM12.8


title: poolC-45


title: GBM28_PBS 1

description: Library name: GBM28.1


title: L10 TDT- Kupffer cells mWD-CH-CH

description: Library name: L10_TDT-KC_S30

value: mWD-CH-CH


title: poolC-41


title: poolC-44


title: poolC-32


title: poolC-31


title: GBM12_OncoD-0J1 2

description: Library name: GBM12.14


title: GBM12_OncoD 1

description: Library name: GBM12.5


title: poolC-29


title: L9 TDT- Kupffer cells mWD-CH-CH

description: Library name: L9_TDT-KC_S27


title: poolC-39


title: L11 TDT- Kupffer Cells mWD-CH-WD

description: Library name: L11_TDT-KC_S33


title: poolC-38


title: GBM12_OncoD-0J1 1

description: Library name: GBM12.13


title: L12 TDT+ Kupffer cells mWD-CH-WD

description: Library name: L12_TDT+_KC_S35


title: GBM12_OncoD 3

description: Library name: GBM12.7


title: poolC-36


title: poolC-25


title: L9 TDT+ Kupffer cells mWD-CH-CH

description: Library name: L9_TDT+_KC_S26


title: poolC-34


title: poolC-35


title: L11 Ly6C Hi mWD-CH-WD

description: Library name: L11_Ly6CHi_S31


title: poolC-33


title: poolC-22


title: L10 TDT+ Kupffer cells mWD-CH-CH

description: Library name: L10_TDT+_KC_S29


title: GBM12_OncoD 2

description: Library name: GBM12.6


title: GBM12_PBS 1

description: Library name: GBM12.1


title: poolC-30


title: poolC-20


title: L8 TDT+ Kupffer cells mWD-CH-WD

description: Library name: L8_TDT+_KC_S23


title: L10 Ly6C Hi mWD-CH-CH

description: Library name: L10_Ly6CHi_S28


title: poolC-19


title: poolC-28


title: THP1-sgCASP1-2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: Sample 4
CASP1 KO THP1 cells

data_processing:
FastQC (v0.11.2) was used to test read quality.
Paired-end reads were aligned against mm10 genome using HISAT (v2.0.5). Stranded (RF)
Gene counts were summarized using featureCounts (v1.5.2)
Assembly: hg38
Supplementary files format and content: rawCounts.tsv
Supplementary files format and content: Tab-delimted raw gene counts

source_name: blood

growth_protocol: THP1 cells were cultured in RPMI with 10% FBS and 1% P/S

extract_protocol:
The cells were collected, and RNA was extracted using ZYMO RESEARCH Quick-RNA Miniprep kit (#R1055).
After the confirmation of the RNA quality using Agilent 2100 Bioanalyzer, the libraries were prepared with polyA selection using the Truseq RNA Library Prep Kit, and the libraries were sequenced at an average depth of 30M paired-end 100bp nucleotide reads. After the quality of reads was examined using FastQC (v0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc), paired-end reads were aligned against mouse mm10 genome (iGenome,https://support.illumina.com/sequencing/sequencing_software/igenome.html) using HISAT2 (v2.0.5,http://daehwankimlab.github.io/hisat2).

treatment_protocol: Lentiviral CRISPR/Cas9 can infect a broad variety of mammalian cells by co-expressing a mammalian codon-optimized Cas9 nuclease along with a single guide RNA (sgRNA) to facilitate genome editing. To generate Pro-CAPS1 KO cells through lentiviral transduction of sgRNAs, WT THP1 cells were first transduced with dCas9-GFP and sorted on GFP+ expression to obtain pure populations. Then, dCas9-GFP+ expressing cells were subsequently transduced with BFP lentiviral vectors expressing sgRNA targeting either 1) safe harbor gene AAVS1 (WT) or 2)  CASP1 (KO) . sgCASP1-BFP and sgAAVS1-BFP transduced into Cas9-GFP-expressing THP1 cells. THP1 cells subsequently sorted on both BFP X GFP expression to obtain pure populations. This strategy allowed us to independently monitor Cas9 and sgRNA expression due to their separate plasmids.

value: blood

value: AML blasts

value: KO


title: GBM12_PBS 4

description: Library name: GBM12.4


title: 5065_Female WD4

city: Shreveport

first: Sandeep

last: Das

state: LA

address: 1501 Kings Highway

institute: LSU Health Shreveport

data_processing:
Gene level quantification was performed using HTSeq-counts v0.6.0 based on the GRCm38.90 genome annotations. The R package DESeq2 v1.42.1 was then used to identify significant differentially expressed genes (DEGs). Genes with adjusted p value <0.05 were considered as significant DEGs. The upregulated and downregulated DEGs were analyzed for significantly enriched KEGG pathways using the clusterProfiler v4.10.1 package. The significance of the enrichment was determined by the right-tailed Fisher’s exact test followed by Benjamini-Hochberg multiple testing adjustment.
Assembly: GRCm38.90
Supplementary files format and content: .csv format

growth_protocol: Mice were fed with different diets during the growth

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen)
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions.
The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End configuration. Image analysis and base calling were conducted by the Control Software.

treatment_protocol: Mice were fed with different diets

value: Female

value: Ldlr-/-

value: Dietary

value: WD


title: poolC-27


title: L8 Ly6C Hi mWD-CH-WD

description: Library name: L8_Ly6CHi_S22


title: poolC-24


title: poolC-26


title: poolC-23


title: L9 Ly6C Hi mWD-CH-CH

description: Library name: L9_Ly6CHi_S25


title: 4409_Female mCDHFD4

value: mCDHFD


title: L7 TDT+ Kupffer cells mWD-CH-WD

description: Library name: L7_TDT+_KC_S20

value: Liver


title: L8 TDT- Kupffer Cells mWD-CH-WD

description: Library name: L8_TDT-KC_S24

value: Macrophages


title: GBM12_PBS 2

description: Library name: GBM12.2

value: cell line

value: glioblastoma


title: poolC-21


title: L7 Ly6C Hi mWD-CH-WD

description: Library name: L7_Ly6CHi_S19

value: Ms4a3 (Cre/WT) Rosa26TdT (T/WT)

value: mWD-CH-WD


title: MDSL-CASP1KOC2-2

description:
Library name: Sample 6
CASP1 KO MDSL cells

growth_protocol: MDSL cells were cultured in RPMI with 10% FBS, 1%P/S, and human IL-3

treatment_protocol: To generate Pro-CASP1KO clones through Neon transfecting sgRNAs MDS-L WT cells were suspended in buffer R with Cas9-NLS and three concomitant modified synthetic gRNAs targeting exon 3 of CASP1 and electroporated (1700 mV x 20 ms x 1 pulse) using the Neon Transfection system (Invitrogen). Transfected cells were recovered for 48 hours in antibiotic-free RPMI-1640 with 1% FBS. Following recovery, transfected cells were plated in 96 well plates at a target density of 0.25 cells/well to isolate single clones. Clones were expanded and screened for CASP1 deletion by immunoblotting. Deletion was confirmed by PCR amplification of the PAM site for Sanger sequencing.

value: MDSL

value: MDS-L blasts


title: L6 TDT- Kupffer Cells mWD-CH-WD

description: Library name: L6_TDT-KC_S18

value: TDT- Kupffer cells


title: poolC-15

value: tumor


title: GBM12_PBS 3

description: Library name: GBM12.3


title: THP1-sgCASP1-1

description:
Library name: Sample 3
CASP1 KO THP1 cells

value: blood

value: AML blasts


title: 4418_Female mMASHD4

value: Female

value: mMASHD


title: poolC-17


title: THP1-sgAAVS1-2

description:
Library name: Sample 2
WT THP1 cells

value: WT


title: L7 TDT- Kupffer Cells mWD-CH-WD

description: Library name: L7_TDT-KC_S21


title: poolC-16


title: 4127_Female SD4

value: Ldlr-/-

value: Dietary

value: SD


title: poolC-12


title: MDSL-CASP1KOC1-1

description:
Library name: Sample 3
CASP1 KO MDSL cells


title: 4408_Female mCDHFD3

value: Liver

value: mCDHFD


title: THP1-sgAAVS1-1

description:
Library name: Sample 1
WT THP1 cells


title: 4192_Female mCDHFD2


title: 4059_Female mMASHD3


title: poolC-18


title: L6 TDT+ Kupffer cells mWD-CH-WD

description: Library name: L6_TDT+_KC_S17

value: Macrophages

value: TDT+ Kupffer cells


title: 4129_Male WD4

value: male

value: WD


title: L5 TDT- Kupffer cells mCH-CH-WD

description: Library name: L5_TDT-KC_S15

value: Ms4a3 (Cre/WT) Rosa26TdT (T/WT)

value: mCH-CH-WD


title: MDSL-CASP1KOC1-2

description:
Library name: Sample 4
CASP1 KO MDSL cells

value: MDSL

value: MDS-L blasts


title: poolC-13

value: tumor


title: L5 TDT+ Kupffer cells mCH-CH-WD

description: Library name: L5_TDT+_KC_S14


title: MDSL-WT-2

description:
Library name: Sample 2
WT MDSL cells

value: blood


title: 4056_Male SD4


title: MDSL-WT-1

description:
Library name: Sample 1
WT MDSL cells


title: MDSL-CASP1KOC2-1

description:
Library name: Sample 5
CASP1 KO MDSL cells


title: poolC-14


title: poolC-10


title: poolC-09


title: NativeSkin, IL-22, 24h, biol rep 3

city: Davos Wolfgang

first: Yasutaka

last: Mitamura

state: Graubünden

address: Herman-Bruchard-Strasse 9

department: Immunology

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research

description:
Library name: IL22_3
Column name in raw_exon_counts_all.txt.gz: IL22_3_24h_mg17_19

data_processing:
Sequence reads were shortened to a length of 101 bp from the end, adapter and low-quality sequences were trimmed off, as well as dark cycles appearing as high-quality G bases using Cutadapt (v 2.5).
Processed reads were aligned to the CRCh38 human genome assembly and annotated with the GRCh38.109 gtf file using STAR (v 2.7.9a).
Exons were counted using the featureCounts read summarization program from the Subread package (v 2.0.1).
Assembly: GRCh38 (hg38) human genome assembly
Supplementary files format and content: Tab-delimited text file includes raw exon counts for each sample.

source_name: skin

growth_protocol: Upon arrival, NativeSkin samples were incubated with Genoskin xeno-free medium at 37°C and 5% CO2 overnight for an equilibration period.

extract_protocol:
One-eighth of the 15 mm diameter ex-vivo human skin was minced and digested in Trizol and processed with Precellys devices (Precellys 24 homogenizer) at 4°C to extract RNA from the tissue. The RNA was then purified using an RNAeasy Plus Micro Kit (Qiagen) following the manufacturer’s guidelines.
For sequencing_batch 1: Illumina Stranded mRNA Prep kit following the manufacturer’s protocol. For sequencing_batch 2: Illumina TruSeq Stranded mRNA kit following the manufacturer’s protocol.

treatment_protocol: After equilibration time, NativeSkin samples were treated with IL4 (100 ng/mL), IL-13 (100 ng/mL), IL-4+IL-13 (100 ng/mL each), IL-22 (100 ng/mL), or PBS with 0.1% BSA. The stimulation media was exchanged after 12 hours of stimulation and samples were collected after a total stimulation time of 24 hours.

value: skin

tag: time

tag: donor

tag: experiment batch

tag: rna extraction_batch

tag: sequencing batch


title: L4 TDT- Kupffer cells mCH-CH-CH

description: Library name: L4_TDT-KC_S12

value: mCH-CH-CH

value: TDT- Kupffer cells


title: L5 Ly6C Hi mCH-CH-WD

description: Library name: L5_Ly6c_Hi_S13

value: Ly6C Hi Monocytes


title: 4055_Male SD3

value: Ldlr-/-

value: Dietary

value: SD


title: NativeSkin, IL-4 + IL-13, 24h, biol rep 3

description:
Library name: IL4_IL13_3
Column name in raw_exon_counts_all.txt.gz: IL4_IL13_3_24h_mg17_17


title: NativeSkin, IL-13, 24h, biol rep 3

description:
Library name: IL13_3
Column name in raw_exon_counts_all.txt.gz: IL13_3_24h_mg17_15


title: L6 Ly6C Hi mWD-CH-WD

description: Library name: L6_Ly6c_Hi_S16

value: Liver

value: Macrophages

value: mWD-CH-WD


title: 4001_Female mCDHFD1

value: Female

value: mCDHFD


title: poolC-08


title: poolC-11


title: L4 TDT+ Kupffer cells mCH-CH-CH

description: Library name: L4_TDT+_KC_S11

value: Ms4a3 (Cre/WT) Rosa26TdT (T/WT)

value: TDT+ Kupffer cells


title: poolC-07


title: 3946_Male mCDHFD3

value: male


title: NativeSkin, Control, 24h, biol rep 3

description:
Library name: CTRL_3
Column name in raw_exon_counts_all.txt.gz: CTRL_3_24h_mg17_11

value: PBS with 0.1% BSA


title: L3 TDT+ Kupffer cells mCH-CH-WD

description: Library name: L3_TDT+_KC_S8

value: mCH-CH-WD


title: poolC-04

value: tumor


title: 4058_Female mMASHD2

value: mMASHD


title: L4 Ly6C Hi mCH-CH-CH

description: Library name: L4_Ly6c_Hi_S10

value: mCH-CH-CH


title: poolC-06


title: 3991_Male mMASHD 4


title: poolC-03


title: L3 TDT- Kupffer cells mCH-CH-WD

description: Library name: L3_TDT-KC_S9

value: TDT- Kupffer cells


title: NativeSkin, IL-4, 24h, biol rep 3

description:
Library name: IL4_3
Column name in raw_exon_counts_all.txt.gz: IL4_3_24h_mg17_13

value: skin


title: NativeSkin, IL-4 + IL-13, 24h, biol rep 2

description:
Library name: IL4_IL13_2
Column name in raw_exon_counts_all.txt.gz: IL4_IL13_2_24h_mg15_8


title: 3947_Male mCDHFD4

value: Ldlr-/-

value: Dietary


title: poolC-05


title: 3940_Female SD3

value: Liver

value: SD


title: NativeSkin, IL-22, 24h, biol rep 2

description:
Library name: IL22_2
Column name in raw_exon_counts_all.txt.gz: IL22_2_24h_mg15_10


title: NativeSkin, IL-13, 24h, biol rep 2

description:
Library name: IL13_2
Column name in raw_exon_counts_all.txt.gz: IL13_2_24h_mg15_6


title: poolC-02


title: L3 Ly6C Hi mCH-CH-WD

description: Library name: L3_Ly6c_Hi_S7

value: Macrophages

value: Ly6C Hi Monocytes


title: L2 TDT+ Kupffer cells mCH-CH-CH

description: Library name: L2_TDT+_KC_S5


title: NativeSkin, IL-4, 24h, biol rep 2

description:
Library name: IL4_2
Column name in raw_exon_counts_all.txt.gz: IL4_2_24h_mg15_4


title: 3937_Male WD3

value: WD


title: 3925_Female mMASHD1

value: Female


title: poolB-96


title: L2 TDT- Kupffer cells mCH-CH-CH

description: Library name: L2_TDT-KC_S6

value: Ms4a3 (Cre/WT) Rosa26TdT (T/WT)


title: 3792_Male mCDHFD2

value: male

value: mCDHFD


title: poolC-01


title: NativeSkin, IL-22, 24h, biol rep 1

description:
Library name: IL22_1
Column name in raw_exon_counts_all.txt.gz: IL22_1_24h_mg13_10


title: poolB-95


title: 3787_Female WD3


title: poolB-94


title: NativeSkin, Control, 24h, biol rep 2

description:
Library name: CTRL_2
Column name in raw_exon_counts_all.txt.gz: CTRL_2_24h_mg15_2

value: PBS with 0.1% BSA


title: 3750_Female WD2


title: poolB-93

value: tumor


title: NativeSkin, IL-4 + IL-13, 24h, biol rep 1

description:
Library name: IL4_IL13_1
Column name in raw_exon_counts_all.txt.gz: IL4_IL13_1_24h_mg13_8


title: 3747_Female WD1


title: Baf3_ERH_KO_sgRNA_2_3

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

description:
Library name: Baf3_ERH_KO_sgRNA_2_3
2198_3F

data_processing:
For data analysis, BAM files were converted into FASTQ files using Samtools, and adaptor trimming, mapping against a reference of all mature miRNAs and read counting were done using miRDeep2. For spike-in control RNA read counts, FASTQ files were mapped against a reference file using bbmap/bbduk.
Assembly: In the course of data analysis, reads were mapped against the latest annotation of murine miRNAs in mirbase.org (release 22.1).
Supplementary files format and content: tab-delimited text file containing raw read counts including reference spike-in controls for each sample

source_name: Baf3 (DSMZ no. ACC300)

growth_protocol: Baf3 cells were cultured in RPMI medium containing 7.5% FCS, 100 U/ml penicillin and 100 U/ml streptomycin, supplemented with recombinant IL-3 in excess, in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using TRIZOL, and 400 ng of total RNA were spiked with a defined mix of the following reference small RNAs: spike-in 1 pNNNNACGATCGGCTCTANNNN; spike-in 2 pNNNNTGAACGTCCGTACNNNN; spike-in 3 pNNNNTCTCGCGCGCGTTNNNN; spike-in 4 pNNNNCGAGTAATGAACGNNNN. 100 ng of this total RNA + spike-in mix was then used for library preparation.
Libraries were constructed with the QIAGEN QIAseq miRNA Library Kit according to the manufacturers recommendation.

treatment_protocol: Cells were stably transduced with vectors encoding Cas9 and the following sgRNAs (provided is only the spacer sequence): control_sgRNA_1 CATGGCAGAATTCCGTCGGG; control_sgRNA_2 TGCGACGGTCCCGTCTCGCG; SAFB1+2_sgRNA_1 CCCAGGCCACGAGTAGCGTG; SAFB1+2_sgRNA_2 GGAGCTGGTGCGAGCGCCCA; ERH_sgRNA_1 AGATCTACGTGCTCCTCCGT; ERH_sgRNA_2 CAGCCTGTTGGGCCTGCCGA.Transduced cells were selected with puromycin (1 µg/ml) for up to 5 days, and cells that had lost the capacity to perform cluster assistance were sorted out based on de-repression of the dsRed-based fluorescent reporter monitoring miR-15a activity. Sorted polyclonal populations were regrown and subjected to total RNA preparation.

value: Baf3 (DSMZ no. ACC300)

value: pro B cell

value: Erh KO

value: untreated

tag: batch


title: NativeSkin, IL-13, 24h, biol rep 1

description:
Library name: IL13_1
Column name in raw_exon_counts_all.txt.gz: IL13_1_24h_mg13_6

value: skin


title: poolB-92


title: NativeSkin, IL-4, 24h, biol rep 1

description:
Library name: IL4_1
Column name in raw_exon_counts_all.txt.gz: IL4_1_24h_mg13_4


title: 3699_Male mMASHD 3

value: Ldlr-/-

value: Dietary

value: mMASHD


title: L1 TDT+ Kupffer cells mWD-CH-CH

description: Library name: L1_TDT+_KC_S2

value: Liver

value: Macrophages

value: mWD-CH-CH

value: TDT+ Kupffer cells


title: L1 Ly6C Hi mWD-CH-CH

description: Library name: L1_Ly6c_Hi_S1

value: Ms4a3 (Cre/WT) Rosa26TdT (T/WT)

value: Ly6C Hi Monocytes


title: poolB-91


title: 3935_Male WD2

value: male

value: WD


title: Baf3_ERH_KO_sgRNA_2_1

description:
Library name: Baf3_ERH_KO_sgRNA_2_1
2198_1F


title: L2 Ly6C Hi mCH-CH-CH

description: Library name: L2_Ly6c_Hi_S4

value: mCH-CH-CH


title: Baf3_ERH_KO_sgRNA_2_2

description:
Library name: Baf3_ERH_KO_sgRNA_2_2
2198_2F

value: Baf3 (DSMZ no. ACC300)


title: 3659_Female SD2

value: Female

value: SD


title: 3658_Female SD1


title: TET1 OE-Sealseq

city: Hangzhou

first: Jun

last: Lu

state: Zhejiang

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

description: Library name: Sample 2

library_source: genomic

data_processing:
Basecalls performed using Illumina Novaseq
Illunima Casava v1.8 was used to indentify bases
5hmC reads were deeper filtered with Trimmomatic and were mapped to Ensembl GRCh37 human reference genome using Burrows Wheeler Aligner.
PePr software (with a threshold of q value < 1e-5) was used to complete the differential enrichment peak calling analysis between the two groups of samples.PePr was used to statistically analyzed the number, width and distribution of differential enrichment.
5hmC-seq reads were aligned to the hg19 genome assembly using Integrative Genomics Viewer
Assembly: hg19
Supplementary files format and content: wig
Supplementary files format and content: xls files include differential peaks
Library strategy: 5hmC-Seal

molecule: genomic DNA

growth_protocol: THP1 cells were cultured in RPMI-1640 medium (Gibco, Grand Island, NY, USA), supplemented with 10% FBS (Gibco) and penicillin-streptomycin.

extract_protocol:
Genomic DNA was obtained from 5x106 cells with Cell/Tissue DNA Isolation Mini Kit (Vazyme)
50 ng genomic DNA were fragmented in Tagmentation buffer at 55 °C. Fragmented DNA was purified with Zymo DNA Clean and Concentration Kit (Zymo). Then, the selective 5hmC chemical labeling was performed. The above fragmented DNA was added to glucosylation buffer (50 mM HEPES buffer, 25 mM MgCl2, pH 8.0) containing β-GT and N3-UDP-Glc, and incubated at 37°C for 2 hours. T After DNA purification, DBCO-PEG4-Biotin (Click Chemistry Tools) was added into the DNA and incubated at 37°C for 2 hours. The biotin-labeled DNA was pulled down by C1 Streptavidin beads (Life Technologies) for 15 min at room temperature. Next, the captured DNA fragments were subjected to PCR amplification using Nextera DNA sample preparation kit (Illumina). The amplified PCR products were purified by 1.0x AMPure XP beads (Acegen). The input library was prepared from fragmented DNA through direct PCR, without chemical labeling or capture. The libraries were quantified with a Qubit fluorometer (Life Technologies) and sequenced on Illumina Novaseq with 150-bp paired-end reads.

value: AML cell line


title: poolB-90

value: tumor


title: NativeSkin, Control, 24h, biol rep 1

description:
Library name: CTRL_1
Column name in raw_exon_counts_all.txt.gz: CTRL_1_24h_mg13_2

value: skin

value: PBS with 0.1% BSA


title: poolB-89


title: L1 TDT- Kupffer cells mWD-CH-CH

description: Library name: L1_TDT-KC_S3

value: TDT- Kupffer cells


title: Ctrl-Sealseq

description: Library name: Sample 1


title: 3656_Male SD2

value: Liver

value: Ldlr-/-

value: Dietary


title: Baf3_ERH_KO_sgRNA_1_3

description:
Library name: Baf3_ERH_KO_sgRNA_1_3
2197_3F

value: pro B cell

value: Erh KO

value: untreated


title: Baf3_ERH_KO_sgRNA_1_2

description:
Library name: Baf3_ERH_KO_sgRNA_1_2
2197_2F


title: poolB-88


title: 3652_Male mMASHD 2

value: male

value: mMASHD


title: TET1 OE-RNAseq

description: Library name: Sample 2

data_processing:
illumina Novaseq™ 6000 sequence platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Using HISAT packagealigned reads of sample to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome , which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.
Assembly: hg19
Supplementary files format and content: xls file includes RPKM values for each sample

extract_protocol:
The total RNA was extracted from cells with Trizol.
RNA libraries were prepared for sequencing using standard Illumina RNA libraries were prepared for sequencing using standard Illumina protocols.


title: poolB-87


title: Baf3_ERH_KO_sgRNA_1_1

description:
Library name: Baf3_ERH_KO_sgRNA_1_1
2197_1F


title: Baf3_SAFB1+2_KO_sgRNA_2_3

description:
Library name: Baf3_SAFB1+2_KO_sgRNA_2_3
1527_3F

value: Safb1 KO, Safb2 KO


title: poolB-86


title: OSA9_Long_Treat_PM_T2_D1t3

first: Bala S. C.

last: Koritala

address: 3333 Burnet Avenue

department: Division of Pediatric Otolaryngology

description: Library name: T2_D1t3

data_processing:
Each sample was processed with kallisto to quantify expression levels. The human reference transcriptome, GRCh38, was indexed using kallisto. Transcript abundances were determined from paired-end reads via the pseudoalignment method. Differential gene expression analysis was conducted using the DESeq2 R package.
Assembly: GRCh38
Supplementary files format and content: CVS file including normalized counts of all samples

source_name: Blood

extract_protocol:
RNA was extracted from PBMCs using miRCURY RNA Isolation kit – Cell and Plant (#300110, Exiqon), following the manufacturer's instructions.
The library was created by Novogene, utilizing poly A enrichment and paired-end sequencing to ensure a minimum of 50 million reads per sample.

value: Blood

value: Peripheral Blood Mononuclear Cells

tag: disease

value: OSA

value: long-term CPAP


title: poolB-85

value: tumor


title: OSA8_Long_Treat_PM_T2_D25t3

description: Library name: T2_D25t3


title: Baf3_SAFB1+2_KO_sgRNA_2_1

description:
Library name: Baf3_SAFB1+2_KO_sgRNA_2_1
1527_1F

value: Baf3 (DSMZ no. ACC300)


title: 3499_Male SD1

value: SD


title: OSA7_Long_Treat_PM_T2_D18t3

description: Library name: T2_D18t3


title: 3494_Male WD1

value: WD


title: poolB-83


title: OSA6_Long_Treat_PM_T2_D15t3

description: Library name: T2_D15t3


title: Baf3_SAFB1+2_KO_sgRNA_1_3

description:
Library name: Baf3_SAFB1+2_KO_sgRNA_1_3
1526_3F


title: poolB-84


title: OSA5_Long_Treat_PM_T2_D11t3

description: Library name: T2_D11t3


title: poolB-82


title: shTET1_TET1

data_processing:
Peak calling was performed with STAR (version 2.5.3a) with default parameters.
ChIP-seq sequencing was paired-end.ChIP-seq reads shorter than 15bp were filtered out.
Peaks were annotated with UCSC human genome GRCh38 by use of Bedtools (version 2.25.0), HOMER (Hypergeometric Optimization of Motif EnRichment) (version 4.10).
RSeQC (version 2.6) was used for peak distribution analysis. Data visualization was performed with the Integrative Genomics Viewer.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: Kasumi-1 cells were cultured in RPMI-1640 medium (Gibco, Grand Island, NY, USA), supplemented with 10% FBS (Gibco) and penicillin-streptomycin.

extract_protocol:
ChIP assays were performed with SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling)
For library construction, DNA was mixed with end repair mix and incubated at 20℃ for 30 minutes. The end-repaired DNA was purified using the QIAquick PCR Purification Kit (Qiagen). Then A-tailing mix was added and the mixture was incubated at 37℃ for 30 minutes. The purified DNA, adapter and ligation mix was incubated at 20℃ for 15 minutes, and the adapter-ligated DNA was purified with the QIAquick PCR Purification Kit. After PCR amplification, the PCR products (about 100-300 bp) were separated through agarose gel running, and purified with QIAquick Gel Extraction kit (QIAGEN). The library was qualified with Qubit ssDNA kit. Sequencing was conducted by Beijing Genomics Institution (BGI, Shenzhen, China) and was implemented on the platform of Illumina Hiseq2500.

value: AML cell line

tag: chip antibody

value: TET1(GeneTex, #GTX627420)


title: shTET1_input


title: Baf3_SAFB1+2_KO_sgRNA_1_1

description:
Library name: Baf3_SAFB1+2_KO_sgRNA_1_1
1526_1F


title: Baf3_SAFB1+2_KO_sgRNA_1_2

description:
Library name: Baf3_SAFB1+2_KO_sgRNA_1_2
1526_2F


title: Ctrl-RNAseq

description: Library name: Sample 1


title: OSA4_Long_Treat_PM_T2_D8t3

description: Library name: T2_D8t3


title: Baf3_control_sgRNA_2_3

description:
Library name: Baf3_control_sgRNA_2_3
2056_3F


title: 3651_Male mMASHD 1

value: Liver

value: Ldlr-/-

value: Dietary


title: OSA3_Long_Treat_PM_T2_D6t3

description: Library name: T2_D6t3


title: 3647_Male mCDHFD1

value: mCDHFD


title: shNC_input


title: Baf3_SAFB1+2_KO_sgRNA_2_2

description:
Library name: Baf3_SAFB1+2_KO_sgRNA_2_2
1527_2F

value: pro B cell

value: untreated


title: OSA2_Long_Treat_PM_T2_D5t3

description: Library name: T2_D5t3


title: poolB-79


title: Baf3_control_sgRNA_2_2

description:
Library name: Baf3_control_sgRNA_2_2
2056_2F


title: Baf3_control_sgRNA_2_1

description:
Library name: Baf3_control_sgRNA_2_1
2056_1F


title: Rep3 for wild type mammary gland

city: Houston

first: Bin

last: Liu

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

description: Library name: Sample_MG_WT03

data_processing:
Raw reads were mapped to GRCm38 with Tophat  v2.1.1 and bowtie2
Assembly: GRCm38 - mm10
Supplementary files format and content: text file for count file

source_name: Mammary gland

extract_protocol:
Qiagen total RNA purification
TruSeq® Stranded Total RNA

value: Mammary gland

value: Wild Type


title: poolB-78


title: OSA1_Long_Treat_PM_T2_D4t3

description: Library name: T2_D4t3

value: Blood

value: Peripheral Blood Mononuclear Cells


title: poolB-77


title: Rep2 for wild type mammary gland

description: Library name: Sample_MG_WT01


title: poolB-81


title: Baf3_control_sgRNA_1_2

description:
Library name: Baf3_control_sgRNA_1_2
2055_2F


title: OSA9_Long_Treat_AM_T2_D1t1

description: Library name: T2_D1t1

value: OSA

value: long-term CPAP


title: poolB-76

value: tumor


title: Rep4 for tumor with mutant p53 in fibroblasts

description: Library name: Sample_16-T400

source_name: Tumor

value: Tumor


title: shNC_TET1


title: poolB-75


title: Baf3_control_sgRNA_1_1

description:
Library name: Baf3_control_sgRNA_1_1
2055_1F

value: Baf3 (DSMZ no. ACC300)


title: Rep3 for tumor with mutant p53 in fibroblasts

description: Library name: Sample_15-T290


title: OSA7_Long_Treat_AM_T2_D18t1

description: Library name: T2_D18t1


title: 3T3-L1, IL4IL13 + Inf, 3

city: San Diego

first: Tomofumi

last: Numata

state: CA

address: 9452 Medical Center Drive, Department of Dermatology

department: Dermatology

institute: university of california, SD

description: Library name: IL-4-13_TNFa_IL-17A_IL-1b_3_S70

data_processing:
Alignment to reference genome using STAR
Raw counts table generated using FeatureCounts
Assembly: GRCm39
Supplementary files format and content: CSV files with raw counts values for each sample

extract_protocol:
ThermoFisher PureLink RNA Kit
Illumina stranded mRNA

value: Fibroblast

value: Wild type

value: IL4/13 + TNFa + IL-17A + IL-1b


title: poolB-74


title: poolB-80


title: Rep2 for tumor with mutant p53 in fibroblasts

description: Library name: Sample_14-T183-2


title: poolB-73


title: OSA5_Long_Treat_AM_T2_D11t1

description: Library name: T2_D11t1


title: OSA6_Long_Treat_AM_T2_D15t1

description: Library name: T2_D15t1


title: Rep1 for tumor with mutant p53 in fibroblasts

description: Library name: Sample_13-T183


title: 3T3-L1, IL4IL13 + Inf, 2

description: Library name: IL-4-13_TNFa_IL-17A_IL-1b_2_S69


title: OSA4_Long_Treat_AM_T2_D8t1

description: Library name: T2_D8t1


title: 3T3-L1, IL4IL13 + Inf, 1

description: Library name: IL-4-13_TNFa_IL-17A_IL-1b_1_S68


title: poolB-71


title: poolB-72


title: Rep4 for tumor with wild type p53 in fibroblasts

description: Library name: Sample_12-T251

value: MMTV-neu;Fsp-Cre


title: 3T3-L1, Inf, 3

description: Library name: TNFa_IL-17A_IL-1b_3_S67

value: TNFa + IL-17A + IL-1b


title: OSA3_Long_Treat_AM_T2_D6t1

description: Library name: T2_D6t1


title: Rep1 for wild type mammary gland

description: Library name: Sample_MG_WT02


title: Rep3 for tumor with wild type p53 in fibroblasts

description: Library name: Sample_11-T201


title: OSA8_Long_Treat_AM_T2_D25t1

description: Library name: T2_D25t1


title: poolB-70


title: 3T3-L1, Inf, 2

description: Library name: TNFa_IL-17A_IL-1b_2_S66


title: OSA2_Long_Treat_AM_T2_D5t1

description: Library name: T2_D5t1


title: Rep2 for tumor with wild type p53 in fibroblasts

description: Library name: Sample_10-T191-2


title: OSA1_Long_Treat_AM_T2_D4t1

description: Library name: T2_D4t1


title: 3T3-L1, Inf, 1

description: Library name: TNFa_IL-17A_IL-1b_1_S65


title: poolB-69


title: poolB-68


title: 3T3-L1, IL4IL13, 3

description: Library name: IL-4-13_3_S64


title: Rep4 for mammary gland with mutant p53 in fibroblasts

description: Library name: Sample_8-MG259


title: OSA9_Short_Treat_PM_T1_D1t3

description: Library name: T1_D1t3

value: short-term CPAP


title: poolB-67


title: Baf3_control_sgRNA_1_3

description:
Library name: Baf3_control_sgRNA_1_3
2055_3F

value: pro B cell


title: 3T3-L1, IL4IL13, 2

description: Library name: IL-4-13_2_S63


title: 3T3-L1, IL4IL13, 1

description: Library name: IL-4-13_1_S62


title: OSA7_Short_Treat_PM_T1_D18t3

description: Library name: T1_D18t3


title: Rep3 for mammary gland with mutant p53 in fibroblasts

description: Library name: Sample_7-MG53


title: poolB-66


title: 3T3-L1, control, 3

description: Library name: Untreated_3_S61

value: Vehicle


title: OSA8_Short_Treat_PM_T1_D25t3

description: Library name: T1_D25t3


title: poolB-65


title: OSA6_Short_Treat_PM_T1_D15t3

description: Library name: T1_D15t3


title: Rep1 for mammary gland with mutant p53 in fibroblasts

description: Library name: Sample_5-MG44

value: Mammary gland


title: OSA5_Short_Treat_PM_T1_D11t3

description: Library name: T1_D11t3


title: 3T3-L1, control, 1

description: Library name: Untreated_1_S59


title: Rep4 for mammary gland with wild type p53 in fibroblasts

description: Library name: Sample_4-MG322


title: poolB-63


title: OSA4_Short_Treat_PM_T1_D8t3

description: Library name: T1_D8t3


title: 3T3-L1, control, 2

description: Library name: Untreated_2_S60


title: poolB-64


title: Rep2 for mammary gland with wild type p53 in fibroblasts

description: Library name: Sample_2-MG244


title: poolB-61


title: poolB-60


title: OSA2_Short_Treat_PM_T1_D5t3

description: Library name: T1_D5t3


title: MAFL-2

city: Shanghai

first: Xu

last: Xu

address: 宜山路600号 科研综合楼13楼

institute: 上海市第六人民医院

description:
Library name: Sample2
Fresh frozen Spatial Transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger’s default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger’s default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Exchange Format
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh livers from MAFL and MASH mouse livers were embedded in tissue-Tek (OCT) and snap-frozen using dry ice. Tissues were processed for 10 x Visium ST.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacture’s construction

value: Liver

tag: model

value: MAFL

value: WD fed for 8 weeks


title: MP3_R3

city: London

first: Emad

last: Moeendarbary

state: -- Please select --

address: Torrington Place, Roberts Engineering Building,

country: United Kingdom

institute: University College London

description:
Library name: Sample 6
Fresh frozen transcriptomic sequencing

data_processing:
Sequencing reads were evaluated for quality, trimmed, mapped to the Rattus norvegicus Rnor6.0 reference genome using the STAR aligner v.2.5.2b and Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: Rnor6.0
Supplementary files format and content: Text files include raw counts for each sample
Supplementary files format and content: csv file include rlog transformed values for each sample

organism: Rattus norvegicus

source_name: Oligodendrocyte progenitor cells

extract_protocol:
Total RNA were extracted using the zymo extraction kit (R2060)
Poly(A)+ mRNA was enriched from total RNA using oligo-dT beads, then fragmented and reverse transcribed using random hexamer priming. First- and second-strand cDNA was synthesized, followed by end repair, 5' phosphorylation, and dA-tailing. Indexed sequencing adapters were ligated, and the libraries were PCR-enriched and quality-checked before sequencing.

value: Oligodendrocyte progenitor cells

value: Wild-type

value: Cultured on micropillar hydrogel


title: poolB-59

value: tumor


title: Rep1 for tumor with wild type p53 in fibroblasts

description: Library name: Sample_9-T102

value: Tumor


title: Rep3 for mammary gland with wild type p53 in fibroblasts

description: Library name: Sample_3-MG260


title: MAFL-1

address: 宜山路600号 科研综合楼13楼

description:
Library name: Sample1
Fresh frozen Spatial Transcriptome sequencing


title: MASH-2

address: 宜山路600号 科研综合楼13楼

description:
Library name: Sample4
Fresh frozen Spatial Transcriptome sequencing

value: MASH

value: WD fed for 16 weeks


title: OSA3_Short_Treat_PM_T1_D6t3

description: Library name: T1_D6t3

value: Blood

value: Peripheral Blood Mononuclear Cells

value: OSA


title: MP1_R1

description:
Library name: Sample 4
Fresh frozen transcriptomic sequencing


title: MASH-1

address: 宜山路600号 科研综合楼13楼

description:
Library name: Sample3
Fresh frozen Spatial Transcriptome sequencing


title: Rep1 for mammary gland with wild type p53 in fibroblasts

description: Library name: Sample_1-MG46

value: MMTV-neu;Fsp-Cre


title: Flat3_R3

description:
Library name: Sample 3
Fresh frozen transcriptomic sequencing

value: Cultured on flat hydrogel


title: T12_IgG

first: Diego

last: Pedroza

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: T12_IgG
cellranger demultiplexed

data_processing:
We utilized the cellranger pipeline for processing the multiplexed raw data. In each dataset and for every patient, we generated multiplexing and count assays based on CellRanger outputs, with all subsequent steps performed using Seurat packages.
Assembly: mm10
Supplementary files format and content: tab-seperarated values files and matrix files

source_name: mammary tumor

extract_protocol:
all mice received the final doses 24h prior to euthanasia. Single cell suspensions were processed as previously described and pooled from 3 mice per treatment. Only viable cells were used for single cell analysis as such, isolated single cell suspensions were first stained with Ghost Dye UV 450 (Tonbo Biosciences, 13-0868) for 10 min and sorted via FACS to isolate viable cells. Briefly, primary tumor cells were harvested and resuspended in RBC Lysis Buffer (BioLegend, Inc., 420301) and passed through a 70- µm strainer. Viable single cell suspensions were tagged with 3’ CellPlex barcoding oligos (10X Genomics, PN-1000262) and were quickly subjected for scRNA-seq library preparation by the Single Cell Genomics Core at BCM.
Single-cell libraries were prepared following the Chromium Single Cell Gene Expression 3’ v3.1 kit encompassing the multiplex capture CMO barcoding kit (10x Genomics, PN-1000262).

value: mammary tumor

value: breast cancer

value: IgG


title: poolB-56


title: poolB-62


title: OSA1_Short_Treat_PM_T1_D4t3

description: Library name: T1_D4t3

value: short-term CPAP


title: OSA9_Short_Treat_AM_T1_D1t1

description: Library name: T1_D1t1


title: T12_CTX

description:
Library name: T12_CTX
cellranger demultiplexed

value: CTX


title: MP2_R2

description:
Library name: Sample 5
Fresh frozen transcriptomic sequencing

value: Oligodendrocyte progenitor cells


title: poolB-55


title: T12_SNDX_ms6352

description:
Library name: T12_SNDX_ms6352
cellranger demultiplexed


title: Flat1_R1

description:
Library name: Sample 1
Fresh frozen transcriptomic sequencing

value: Wild-type


title: OSA8_Short_Treat_AM_T1_D25t1

description: Library name: T1_D25t1


title: OSA4_Short_Treat_AM_T1_D8t1

description: Library name: T1_D8t1


title: poolB-58


title: OSA7_Short_Treat_AM_T1_D18t1

description: Library name: T1_D18t1


title: poolB-57


title: T12_CTX_SNDX_ms6352

description:
Library name: T12_CTX_SNDX_ms6352
cellranger demultiplexed


title: 2151R_SNDX_ms6352

description:
Library name: 2151R_SNDX_ms6352
cellranger demultiplexed


title: K562_gDNA_input

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

description:
Library name: sample15
non-captured input gDNA

data_processing:
FAST5/POD5 files containing raw Oxford Nanopore (ONT) data were basecalled using a Tesla A100 GPU cluster (UT Southwestern BioHPC) via the Guppy software (v6.5.7) running on “super accuracy” mode with the following parameters: -c dna_r10.4.1_e8.2_260bps_sup.cfg --chunks_per_runner 512 --compress_fastq --device cuda:all
Basecalled FASTQ files per sample were processed using the Pore-C Nextflow pipeline (wf-pore-c v1.0.0, https://github.com/epi2me-labs/wf-pore-c).
Assembly: hg38
Supplementary files format and content: pairs and bigwig format

extract_protocol:
Cell preparation: Adherent cells were cultured to 80% confluency in 10-cm plates (10-20 million cells). Suspension cells were cultured in T-25 flasks. For ASO experiments, cells were seeded at 40% confluency within 6-well plates (2 wells for SCR ASO and 4 wells for LINE-1 ASOs due to impaired growth) and treated with 8 μM ASOs for 5 days. Cells from all wells were combined per condition to achieve 5 million cells. On the day of harvest, adherent cells were trypsinized, washed once with 10 mL 1X PBS, and spun down at 800xg for 3 min at 4°C. Cell pellets were resuspended in 10 mL 1% v/v formaldehyde in 1X PBS and crosslinked at RT with gentle rocking for 10 min. Crosslinking was quenched with 500 µL of 2.5 M glycine for 5 min at RT and spun down at 800xg for 3 min at 4°C. Cell pellets were resuspended in 10 mL 1X PBS, spun down again to wash, resuspended in 1 mL 1X PBS, transferred to 1.5 mL DNA LoBind tubes (Eppendorf), and spun down at 800xg for 3 min at 4°C. The supernatant was aspirated, naked cell pellets were flash frozen in liquid nitrogen and stored at -80°C until ready for use. Chromatin preparation: Frozen cell pellets were lysed in KCl cell lysis buffer (10 mM Tris-HCl pH 7.0, 10 mM EDTA, 85 mM KCl) and rotated at 4°C for 30 min. Lysed cells were spun down at 800xg for 5 min at 4°C, resuspended in 600 µL ice-cold 1X DpnII reaction buffer, and spun down at 800xg for 5 min at 4°C. Cell pellets were resuspended in 100 µL 0.5% SDS and incubated at 62°C for 10 min to lyse nuclei. Excess SDS was quenched by diluting with 324 µL nuclease-free water and adding 60 µL 10% Triton X-100 followed by 30 min incubation at 37°C. Lysed nuclei were spun down at 1200xg for 5 min at 4°C, resuspended in 1 mL 1X PBS, and spun down again to remove residual SDS which can inhibit subsequent enzymatic steps. The supernatant was aspirated and pellets were resuspended in 600 µL 1X DpnII reaction buffer; 10 µL was taken aside to quality check genomic DNA integrity and the remaining samples were treated with 300 U DpnII (New England Biolabs, R0543M) overnight at 37°C with shaking at 2000 rpm. After the overnight digestion period, another 10 µL was taken aside to quality check digestion efficiency (non-digested and digested chromatin aliquots were diluted to 100 µL with cell lysis buffer and treated with 1 µL 10 mg/mL RNase A and 5 µL of 20 mg/mL proteinase K at 56 C for 45 min followed by purification through a standard PCR spin column and gel electrophoresis in a 2% agarose gel. Completely digested chromatin should have peak band intensity around 500-1000 bp). After complete digestion, DpnII reactions were heat inactivated at 62°C for 20 min then chilled on ice for 2 min. Heat inactivated samples were spun down at 1200xg for 3 min at 4°C and washed once with 1 mL 1X PBS to remove residual DpnII. Digested chromatin was resuspended in 3 mL T4 DNA ligation reaction buffer: 300 µL 10X T4 DNA ligation reaction buffer with 10 mM ATP, 240 µL 10% Triton X-100, 15 µL 400 U/µL T4 DNA ligase (New England Biolabs, M0202L), and topped off with nuclease-free water; 300 µL 10 mM ATP can be supplemented to ensure complete ligation efficiency. T4 ligation reactions were split across three 1.5 mL Eppendorf tubes per sample. Proximity ligation was performed at RT with rotation for 2 h. Ligation efficiency was quality checked with another 10 µL aliquot extracted as described earlier (complete ligation should produce an upward shifted smear on a 2% agarose gel with the strongest band intensity at 15-45 kb). Chimeric ligation DNA was purified by resuspending the chromatin pellet in 300 µL DNA elution buffer (10 mM Tris-HCl pH 7.0, 2% SDS) and treatment with 5 µL 10 mg/mL RNase A for 30 min at 37°C followed by overnight shaking at 2000 rpm at 65°C with 5 µL 20 mg/mL proteinase K to reverse crosslinks. De-crosslinked DNA was purified by phenol/chloroform/isoamyl alcohol extraction. The concentration of the purified high-molecular weight (HMW) chimeric DNA product was measured by Qubit 4. Pre-capture DNA library prep: The HMW DNA sample was diluted to 150 µL in 1X TE and transferred to a miniTUBE Red 5.0 kb (Covaris, PN 520066). The DNA was sheared to 3-5 kb using a Covaris ME220 fitted with the red ME220 Waveguide 4 (PN 500534) following the manufacturer’s shearing program. Shearing efficiency was checked using a Genomic DNA Screen Tape (Agilent, 5067-5365) ran on an Agilent Tape Station 4150 instrument. Sheared DNA samples were converted into DNA libraries using the NEBNext® Ultra II DNA library prep kit but substituting the PCR step with LongAmp® Taq 2X master mix (New England Biolabs, M0287L) and using custom primers specific for the 3’ end of the NEBNext Illumina adaptor (see Supplemental Table S2). The purified PCR products were size-selected to deplete fragments <2 kb using a custom “>3 kb” magnetic beads formulation (see Supplemental Table S3) and amplified further to yield at least 1 µg purified DNA. Hybridization capture: Two rounds of hybridization capture was performed using the Roche KAPA HyperCapture kit reagents (Fischer Scientific, NC1876492) following manufacturer’s protocol with the following modifications: 1 µg pre-capture DNA library was combined with 20 µL human Cot DNA and dehydrated using a SpeedVac vacuum concentrator. Each hybridization reaction was performed with 20 pmol 120-bp L1HS DpnII 3C ssDNA oligo probe (see Supplemental Table S2), incubated at 95°C for 10 min to denature double-stranded DNA followed by 16 h at 55°C. 16 cycles of post-capture PCR was performed with the same primer pair as pre-capture amplification; 4 cycles were done for second round of hybridization capture. Captured DNA was size-selected using 1 vol of custom >3 kb magnetic beads to deplete <2 kb fragments and size distribution was checked with a Genomic DNA Screen Tape. Additional PCR cycles were performed to yield 1 µg DNA.
Nanopore library prep: Captured DNA libraries were ligated with ONT sequencing adaptors using LSK114 native ligation kit (Oxford Nanopore Technologies) and sequenced using a PromethION R10.4.1 flow cell ran on a P2 Solo device for 72 h.

value: cell line

value: erythroblast cells

value: wild-type


title: 2151R_IgG

description:
Library name: 2151R_IgG
cellranger demultiplexed


title: poolB-53

value: tumor


title: Flat2_R2

description:
Library name: Sample 2
Fresh frozen transcriptomic sequencing


title: K562_gDNA_hybrid_capture

description:
Library name: sample14
hybridization captured gDNA


title: MCF7_Rogi2_EV_nodox_rep2_L1CaP-C

description:
Library name: sample13
L1CaP-C

value: human breast cancer cell line

value: stably expressing a transgenic "empty vector" TagBFP at the "Rogi2" safe harbor locus at chr3:22,746,757


title: OSA6_Short_Treat_AM_T1_D15t1

description: Library name: T1_D15t1

value: Blood

value: Peripheral Blood Mononuclear Cells


title: OSA1_Short_Treat_AM_T1_D4t1

description: Library name: T1_D4t1

value: OSA


title: poolB-54


title: poolB-52


title: OSA2_Short_Treat_AM_T1_D5t1

description: Library name: T1_D5t1


title: 2151R_CTX_SNDX_ms6352

description:
Library name: 2151R_CTX_SNDX_ms6352
cellranger demultiplexed


title: poolB-51


title: germ-free mouse replicate 3

city: Birmingham

first: Craig

middle: L

last: Maynard

state: AL

address: 1825 University Blvd, SHEL 613

institute: University of Alabama at Birmingham

description: Library name: GF_3_H2O

data_processing:
TrimGalore 0.4.4 (paired sequences, --phred33)
STAR 2.5.2 (default settings)
HTSeq-Count 0.6.1p1 (stranded = no)
EdgeR 4.4.1 for differential expression analysis
Assembly: GRCm39
Supplementary files format and content: htSeq-Count text files

source_name: Large Intestine

growth_protocol: Colon cleared of visible luminal contents was cut open longitudinally then cut into 1cm pieces and collected into cold H2 media (HBSS with 2% fetal bovine serum). Tissue were gently rotated for 20 minutes in H2/DTT/EDTA buffer at 37°C to remove epithelial fraction. Released cells were collected, tissue was washed and the procedure was repeated. Cells from both rotations were combined, washed, pelleted, and resuspended in RNALater before total RNA was isolated.

extract_protocol:
RNA was extracted from total epithelial fraction using TRI Reagent (Zymo Research, R2050-1-200) according to the manufacturer’s instructions.
RNA libraries were prepared using the NEBNext Ultra II Directional RNA-Seq kit using standard techniques (NEB, Ipswich MA). All libraries were prepared by the Genomics Core Lab of the Heflin Center for Genomic Sciences at the University of Alabama at Birmingham.

value: Large Intestine

value: Epithelial Cells

value: WT C57BL/6

tag: replicate


title: 2151R_CTX

description:
Library name: 2151R_CTX
cellranger demultiplexed

value: mammary tumor

value: breast cancer


title: poolB-50


title: OSA5_Short_Treat_AM_T1_D11t1

description: Library name: T1_D11t1

value: short-term CPAP


title: OSA9_PM_D1t1

description: Library name: D1t1


title: germ-free mouse replicate 2

description: Library name: GF_2_H2O


title: OSA8_PM_D25t1

description: Library name: D25t1


title: poolB-49


title: MCF7_Rogi2_EV_dox_rep2_L1CaP-C

description:
Library name: sample11
L1CaP-C


title: MCF7_Rogi2_EV_dox_rep1_L1CaP-C

description:
Library name: sample10
L1CaP-C


title: MCF7_Rogi2_5UTR-LRE3_nodox_rep2_L1CaP-C

description:
Library name: sample9
L1CaP-C

value: stably expressing a transgenic LINE-1 element at the "Rogi2" safe harbor locus at chr3:22,746,757


title: poolB-48


title: OSA7_PM_D18t1

description: Library name: D18t1


title: OSA3_Short_Treat_AM_T1_D6t1

description: Library name: T1_D6t1


title: gnotobiotic G2 mouse replicate 2

description: Library name: G2_2_H2O


title: germ-free mouse replicate 1

description: Library name: GF_1_H2O


title: OSA6_PM_D15t1

description: Library name: D15t1


title: MCF7_Rogi2_5UTR-LRE3_dox_rep2_L1CaP-C

description:
Library name: sample7
L1CaP-C


title: MCF7_Rogi2_5UTR-LRE3_nodox_rep1_L1CaP-C

description:
Library name: sample8
L1CaP-C


title: gnotobiotic G2 mouse replicate 1

description: Library name: G2_1_H2O


title: poolB-46


title: poolB-47


title: OSA5_PM_D11t1

description: Library name: D11t1


title: gnotobiotic G1 mouse replicate 3

description: Library name: G1_3_H2O


title: MCF7_Rogi2_5UTR-LRE3_dox_rep1_L1CaP-C

description:
Library name: sample6
L1CaP-C


title: OSA3_PM_D6t1

description: Library name: D6t1


title: MCF7_Rogi2_EV_nodox_rep1_L1CaP-C

description:
Library name: sample12
L1CaP-C


title: poolB-43


title: poolB-44


title: gnotobiotic G1 mouse replicate 2

description: Library name: G1_2_H2O


title: OSA4_PM_D8t1

description: Library name: D8t1


title: poolB-42


title: MCF7_SCR_ASO_L1CaP-C

description:
Library name: sample4
L1CaP-C

value: Scrambled ASO


title: gnotobiotic G2 mouse replicate 3

description: Library name: G2_3_H2O


title: MCF7_LINE1_ASO_L1CaP-C

description:
Library name: sample5
L1CaP-C

value: cell line

value: LINE-1 targeting ASO


title: OSA1_PM_D4t1

description: Library name: D4t1


title: T47D_L1CaP-C

description:
Library name: sample3
L1CaP-C

value: epithelial cells

value: wild-type


title: OSA8_AM_D25t3

description: Library name: D25t3


title: Batch4

city: Mainz

first: Wolfram

last: Ruf

address: Langenbeckstrasse 1

institute: CTH Mainz

description:
Library name: Multiplexed_Library_4
See Demultiplex file

data_processing:
The Rhapsody pipeline and seven bridges genomics was used to map the fastq files and generate count matrixes
Assembly: GRCm39.primary_assembly.genome / GRCm39.primary_assembly.genome
Supplementary files format and content: The Comma Seperated Value (.csv) files contain the count matrixes per sample

source_name: Intestine

extract_protocol:
The protocol for immune cells isolation from the laminar propria is derived from the IECs isolation protocol with some modifications. The Peyer’s patches from the intestine were removed, prior to the longitudinal dissection of the intestinal segments. Tissue digestion was performed using Lamina Propria Dissociation Kit from Miltenyi as briefly described here. The intestine pieces (1-2 cm long) were subjected to dissociation twice in 50 ml tube with each time 20 ml of fresh prepared pre-digestion buffer (containing 10 mM HEPES, 5% FCS, 2 mM ETDA, 1 mM DTT in 1X HBSS without Ca2+/Mg2+) in a shaker at 37°C, 60 rpm for 20 mins. After each 20 mins of incubation, the supernatant containing IECs, and intestine were strained using 100µm filter and supernatant was discarded. Next, the intestine pieces were washed with washing buffer (containing 1X HBSS without Ca2+/Mg2+ with 10 mM HEPES) in a shaker at 37°C, 60 rpm for 20 mins followed by passing the supernatants through 100µm filter. Afterwards, the pieces were transferred into the C-tube with 8-10 ml of digestion buffer (10mM HEPES, 5% FCS in 1X HBSS with Ca2+/Mg2+ + Enzymes D, R, and A) and tissue was digested using 37C_m_LPDK_1 program in the miltenyi octo dissociator. Later, the digest was centrifuged (1200g, 2 mins at 37°C) and strained by passing through the different meshed sized filter (in ascending order: 100, 70, 40 µm) with spinning steps in between to get rid of tissue fat content and enrich the cells suspension with intestinal immune cells that was used for downstream single cell RNA-sequencing analysis.
Library construction and quality control were done according to the Rhapsody pipeline

value: Intestine

value: CD45+ selected cells


title: K562_L1CaP-C

description:
Library name: sample2
L1CaP-C

value: erythroblast cells


title: poolB-41

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4). Reads were then mapped to the mouse genome (mm10) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2).
The merged gene expression matrix (raw counts) containing all samples was analyzed with the Seurat3 package in R. Cells were filtered by nFeature_RNA (genes detected) >3000 and <7000, percent.mt (percentage of mitochondria genes) < 10. This resulted in n=306 valid cells for downstream analysis. After filtering cells, log-normalization was performed using the default NormalizeData function in Seurat. The scaled data was regressed for cell cycle phases (S.Score and G2M.Score) and number of genes per cell (nFeature_RNA) before performing UMAP based dimension reduction (dims=1:20, resolution =0.4).
Assembly: mm10
Supplementary files format and content: csv

extract_protocol:
Single cells were sorted (BD FACSAriaIII) in 96 well plates (VWR) containing 2μL of PBS including 0.2% Triton X-100 and 4U of RNase inhibitor (Takara) per well. Plates were properly sealed and spun down at 2000g for 1min before storing at −80°C. Whole transcriptome amplification was performed with a modified SMART-seq2 protocol as described previously, using 20 instead of 18 cycles of cDNA amplification. PCR purification was realized with a 0.8:1 ratio (ampureXP beads:DNA). Amplified cDNA quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent)
SMART-seq2 based scRNA-seq; Sequencing libraries were performed using the Nextera XT kit (Illumina) as described previously, using 1/4th of the recommended reagent volumes and 1/5th of input DNA with a tagmentation time of 9min. Library quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent). Indexing was performed with the Nextera XT index Kit V2 (A-D).

value: tumor


title: Batch3

description:
Library name: Multiplexed_Library_3
See Demultiplex file


title: poolB-45


title: poolB-40


title: OSA6_AM_D15t3

description: Library name: D15t3

value: Blood

value: Peripheral Blood Mononuclear Cells

value: OSA


title: Batch2

description:
Library name: Multiplexed_Library_2
See Demultiplex file


title: OSA7_AM_D18t3

description: Library name: D18t3


title: poolB-39


title: si-KRT7 transfected rep3

city: Wuhan

first: Minghe

last: Zhang

state: Hubei

address: Donghu Road

institute: WuHan University

description: Library name: Sample6

data_processing:
Raw data with adapter sequences or low-quality sequences were filtered using SOAPnuke developed by BGI with the following parameters: ”-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --polyX 50 --minReadLen 150”. Filtering steps included removing reads matching over 25.0% of adapter sequences, reads shorter than 150 bp, reads with over 0.1% N content, reads with polyX lengths exceeding 50 bp, and reads with over 40.0% of bases having a quality value below 20. Clean reads were obtained with the quality value system set to Phred+33.
The high quality clean reads were aligned to the reference genome with STAR software (v2.7.11b)
Raw read counts were extracted from the second column of the STAR output file 'ReadsPerGene.out.tab', which contained the unstranded RNA-seq read counts.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: PAAD CFPAC1 celles

extract_protocol:
Total RNA samples were obtained and mRNAs with poly(A) tails were enriched using oligo(dT) beads. The mRNA was then fragmented, and first- and second-strand cDNA were synthesized using random primers.
The cDNA underwent end-repair, 3' adenylation, and adaptor ligation, followed by PCR amplification and purification. Library quality was assessed, circularized, and amplified to form DNA nanoballs (DNBs). Sequencing was performed on the DNBSEQ platform using DNBSEQ Technology.

value: PAAD CFPAC1 celles


title: MCF7_L1CaP-C

description:
Library name: sample1
L1CaP-C

value: human breast cancer cell line


title: poolB-37


title: Normal_D009

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

description:
Library name: Normal_D009
10X Chromium Single Cell Gene Expression assay with v3 chemistry was used to constuct single-cell cDNA libraries

data_processing:
Read were aligned using CellRanger v7.1.0
Assembly: Sus scrofa (Sscrofa11.1) (GTF V109)
Supplementary files format and content: Raw and filtered count matrix in hierarchical data (H5) format.

organism: Sus scrofa

source_name: Kidney

extract_protocol:
This process was performed following the 10x guidelines of Chromium Nuclei Isolation Kit (Sample Prep User Guide, CG000505). Briefly, frozen tissue (3-50 mg) from a harvested kidney from each pig was minced and transferred to sample dissociation tubes in wet ice. Then, 200 µl of lysis buffer was added to each sample dissociation tube. Kidney tissue was dissociated with a plastic pestle until homogeneous, 300 µl of lysis buffer was added and sample incubated on ice for 10 min. Next, all liquid from the dissociation tube was transferred to the nuclei isolation column to avoid nuclei loss; samples were centrifuged at 16,000 relative centrifuge force (RCF) for 20 sec at 4°C, followed by 10-sec Vortex mixing at 3,200 rpm or max speed to resuspend nuclei. The pellets were resuspended in 500 µl of debris removal buffer, mixed until no pellets were visualized, and then centrifuged again at 700 RCF for 10 minutes at 4°C. The pellets were then resuspended again in 1 ml of wash and resuspension buffer and centrifuged again at 500 RCF for 10 minutes at 4°C to discard the supernatant. The nuclei pellets were resuspended again in 1 ml of wash and resuspension buffer, centrifuged again at 500 RCF for 10 minutes at 4°C, and the supernatant was again discarded. The nuclei pellet was resuspended in 50-500 µl of wash and resuspension buffer, gently mixed with pipette, and vortexed for 3 sec at 3,200 revolutions per minute (RPM). The nuclei concentration was determined using AOPI or Ethidium Homodimer-1 fluorescent staining dyes, re-vortexed for 3 sec at 3,200 RPM, and samples (kept on ice) subsequently transferred for sequencing.
Chromium Next GEM (V3) Single nuclei 3’ RNA-Seq reagents. Samples were sequenced with the NovaSeq 6000 S4-PE100 flow cell.

value: Kidney

value: Tissue

value: Renal arteries

value: WT

value: Normal

value: nuclear RNA


title: Normal_D010

description:
Library name: Normal_D010
10X Chromium Single Cell Gene Expression assay with v3 chemistry was used to constuct single-cell cDNA libraries


title: Normal_D011

description:
Library name: Normal_D011
10X Chromium Single Cell Gene Expression assay with v3 chemistry was used to constuct single-cell cDNA libraries


title: OSA3_AM_D6t3

description: Library name: D6t3


title: Batch1

description:
Library name: Multiplexed_Library_1
See Demultiplex file


title: poolB-38

first: Florian


title: poolB-36


title: OSA2_PM_D5t1

description: Library name: D5t1


title: OSA5_AM_D11t3

description: Library name: D11t3


title: poolB-35


title: si-Control transfected rep3

description: Library name: Sample3

value: si-Control


title: gnotobiotic G1 mouse replicate 1

description: Library name: G1_1_H2O

value: Large Intestine

value: Epithelial Cells

value: WT C57BL/6


title: OSA4_AM_D8t3

description: Library name: D8t3


title: si-Control transfected rep2

description: Library name: Sample2


title: Healthy10_PM_C12t1

description: Library name: C12t1

value: Healthy


title: si-KRT7 transfected rep2

description: Library name: Sample5


title: CKD_D005

description:
Library name: CKD_D005
10X Chromium Single Cell Gene Expression assay with v3 chemistry was used to constuct single-cell cDNA libraries

value: CKD


title: limited_male_dms_cort_rep3

city: Philadelphia

first: Keegan

middle: Scott

last: Krick

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: limited_male_dms_cort_rep3

data_processing:
Raw reads had adapters trimmed using BBDuk and were then aligned to the mm39 genome and quantified using kallisto.
Assembly: mm39
Supplementary files format and content: Matrix of TPM abundances for each sample

source_name: brain

growth_protocol: 8-week-old male and female C57BL/6J mice housed under a 12-hour light-dark cycle at 23 ºC.

extract_protocol:
Bilateral 2mm-diameter biopsy punches of dorsal medial striatum (DMS) and dorsal lateral striatum (DLS) were taken from two coronal slices (4 total punches per region per animal). Tissue samples were processed for RNA and chromatin using single sample sequencing (S3EQ) as described in Xu and Heller 2018 (PMID: 30031009)
Libraries were prepared from polyA-selected RNA for Illumina sequencing by Azenta Life Sciences (Plainfield, NJ).

treatment_protocol: Vehicle-treated groups received 1% ethanol in their drinking water. Mice had ad libitum access to water, which was weighed and replaced with fresh solutions every two days. A CORT concentration of 50µg/mL was used for mice undergoing operant behavior. Water bottle weights and mouse body weights per cage were used to calculate the average CORT dose per cage of ~7mg/kg/day. Mice underwent two weeks of water administration before beginning behavior, and water administration continued throughout the duration of behavior.

value: brain

tag: brain region

value: dms

tag: behavior paradigm

value: limited

tag: Sex

value: male

value: cort


title: limited_male_dls_cort_rep3

description: Library name: limited_male_dls_cort_rep3

tag: tissue

value: dls


title: si-KRT7 transfected rep1

description: Library name: Sample4

tag: cell line

value: PAAD CFPAC1 celles


title: OSA2_AM_D5t3

description: Library name: D5t3

value: Blood

tag: cell type

value: Peripheral Blood Mononuclear Cells

value: OSA

tag: treatment


title: Healthy8_PM_AMC4t3

description: Library name: AMC4t3


title: CKD_D004

description:
Library name: CKD_D004
10X Chromium Single Cell Gene Expression assay with v3 chemistry was used to constuct single-cell cDNA libraries

value: Kidney

value: Tissue

value: Renal arteries

tag: genotype

value: WT

value: nuclear RNA


title: poolB-30

last: Rambow

institute: University Hospital Essen

value: tumor


title: Healthy7_PM_CB16t3

institute: Cincinnati Children's Hospital Medical Center

description: Library name: CB16t3

value: Healthy


title: iWATirHFD_1

city: BROOKLINE

first: Mu

last: A

state: MA

address: 77 Pond Ave, Apt 1003

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Library name: iWATirHFD_1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: xls files include FKPM values for each sample

source_name: iWAT

extract_protocol:
Total RNA was isolated from inguinal fat or epididymal fat tissues using TRIzol reagent (Invitrogen, 15596018) and RNeasy Mini purification kit (Qiagen, 74104) according the manufacture’s protocol. Tissues were homogenized in TRIzol reagent using a bead homogenizer for 20 min at max speed (Qiagen, TissueLyser II). DNA was digested on column using RNase-Free DNase Set (Qiagen, 79254).
For adipose tissue RNAseq, RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, and then the second strand cDNA synthesis was either the same way as the first strand (for non strand specific library) or was synthesized using dUTP, instead of dTTP to generate the directional library (for strand specific library). The library was ready after end repair, A-tailing adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, then subjected to Illumina sequencing

value: iWAT


title: poolB-34

city: Essen


title: OSA1_AM_D4t3

city: Cincinnati

description: Library name: D4t3


title: iWATirCHW_3

description: Library name: iWATirCHW_3


title: CKD_D002

description:
Library name: CKD_D002
10X Chromium Single Cell Gene Expression assay with v3 chemistry was used to constuct single-cell cDNA libraries

value: CKD


title: Healthy5_PM_CB7t3

description: Library name: CB7t3


title: poolB-33


title: poolB-32


title: si-Control transfected rep1

description: Library name: Sample1

value: si-Control


title: Healthy4_PM_F2D12t3

description: Library name: F2D12t3


title: Healthy9_PM_AMC7t3

description: Library name: AMC7t3


title: poolB-31


title: iWATirHFD_2

description: Library name: iWATirHFD_2


title: limited_female_dms_cort_rep3

description: Library name: limited_female_dms_cort_rep3

value: brain

value: dms

value: limited

value: female


title: Healthy3_PM_C22t1

description: Library name: C22t1

value: Blood


title: Healthy6_PM_CB14t3

description: Library name: CB14t3

value: Peripheral Blood Mononuclear Cells


title: limited_female_dls_cort_rep3

description: Library name: limited_female_dls_cort_rep3

value: dls

value: cort


title: poolB-29


title: poolB-25


title: iWATgfpHFD_3

description: Library name: iWATgfpHFD_3


title: Healthy2_PM_C16t1

description: Library name: C16t1


title: limited_male_dls_cort_rep2

description: Library name: limited_male_dls_cort_rep2

value: male


title: poolB-28


title: iWATgfpHFD_2

description: Library name: iWATgfpHFD_2


title: limited_male_dls_cort_rep1

description: Library name: limited_male_dls_cort_rep1


title: iWATirCHW_2

description: Library name: iWATirCHW_2


title: iWATgfpHFD_1

description: Library name: iWATgfpHFD_1


title: Rep2 for mammary gland with mutant p53 in fibroblasts

description: Library name: Sample_6-MG48

value: Mammary gland


title: poolB-23


title: poolB-27


title: limited_female_dls_cort_rep1

description: Library name: limited_female_dls_cort_rep1


title: iWATirHFD_3

description: Library name: iWATirHFD_3


title: limited_female_dls_cort_rep2

description: Library name: limited_female_dls_cort_rep2


title: poolB-26


title: iWATirCHW_1

description: Library name: iWATirCHW_1


title: limited_female_dms_cort_rep2

description: Library name: limited_female_dms_cort_rep2


title: limited_male_dms_cort_rep2

description: Library name: limited_male_dms_cort_rep2


title: poolB-24


title: poolB-21


title: limited_male_dms_cort_rep1

description: Library name: limited_male_dms_cort_rep1


title: Healthy9_AM_AMC7t1

description: Library name: AMC7t1


title: poolB-20


title: Healthy5_AM_CB7t1

description: Library name: CB7t1


title: extended_male_dms_vehicle_rep3

description: Library name: extended_male_dms_vehicle_rep3

value: extended

value: vehicle


title: limited_female_dms_cort_rep1

description: Library name: limited_female_dms_cort_rep1


title: iWATgfpCHW_1

description: Library name: iWATgfpCHW_1


title: poolB-22

value: tumor


title: iWATgfpCHW_3

description: Library name: iWATgfpCHW_3


title: Healthy7_AM_CB16t1

description: Library name: CB16t1

value: Healthy


title: Healthy6_AM_CB14t1

description: Library name: CB14t1


title: Healthy3_AM_C22t3

description: Library name: C22t3


title: extended_male_dls_vehicle_rep2

description: Library name: extended_male_dls_vehicle_rep2


title: eWATirCHW_3

description: Library name: eWATirCHW_3

source_name: eWAT

value: eWAT


title: eWATirHFD_3

description: Library name: eWATirHFD_3


title: extended_male_dls_vehicle_rep3

description: Library name: extended_male_dls_vehicle_rep3


title: poolB-19


title: Healthy4_AM_F2D12t1

description: Library name: F2D12t1


title: eWATirHFD_2

description: Library name: eWATirHFD_2


title: extended_female_dls_vehicle_rep3

description: Library name: extended_female_dls_vehicle_rep3


title: poolB-18


title: extended_female_dms_vehicle_rep3

description: Library name: extended_female_dms_vehicle_rep3


title: extended_female_dls_vehicle_rep2

description: Library name: extended_female_dls_vehicle_rep2


title: Untreated 3D system mimicking bone marrow and containing CD117+ MSC, HMEC1 and primary CD34+ selected MNCs, scRNASeq

city: Lyon

first: Kevin

last: Geistlich

address: 28 rue Laennec

country: France

institute: CRCL

description: 10X Genomics

data_processing:
Data were demultiplexed and aligned to the human genome, 10X and cellplex barcodes were assigned for each cell, and genes were counted by unique molecular.identifier (UMI) counts, using cellranger multi pipeline (v6.0)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
3D culture was performed in inserts with a membrane of 3 μm pores placed in a 6-well plate. Sterilized ceramic biphasic calcium phosphate particles (BCP) were immersed in PBS and loaded into the insert. BCP particles were incubated for 2 days in PBS with 10% FBS. Cells (1.4x106 of primary pAML MSCs and 0.7x106 HMEC-1) were resuspended in a 50/50 combination of osteoblastic differentiation medium (DMEM, 10% FBS, 1% penicillin-streptomycin, 0.1 M dexamethasone, 10 mM β-glycerophosphate, 250 µM ascorbic acid) and HMEC-1 medium (MCDB-131, 10% FBS, 1% penicillin-streptomycin, 1% glutamax 100X, 1 mg/L hydrocortisone, 10 μg/L epidermal growth factor) and added to the insert. Medium was changed twice a week for 3 weeks. Then, 1x106 of healthy pediatric BM mononuclear cells, positively-selected for CD34 (EasySepTMHuman CD34 Positive Selection Kit II following the manufacturer’s instructions), were added. The medium was replaced by a mix of HMEC-1 medium and IMDM with 10% FBS, 1% penicillin-streptomycin, and 1% glutamax 100×. The next day, 1 µM of aracytidine was added or not. Medium was changed twice a week for 1 week. Disks formed in the insert were washed twice with PBS, and then retrieved by cutting the membrane of the insert. Disks were incubated for 10 min at 37°C in 5 mL of IMDM medium with 10% FBS, 1% penicillin–streptomycin, and collagenase (0.4 mg/mL), centrifuged, resuspended in 5 mL PBS and recentrifuged. The disks were then incubated 1 min in 300 μL of trypsin (in EDTA 0.05%) at 37°C. The remaining clots were finally dislocated by flushing. The reaction was stopped with 1 mL FBS. After centrifugation, cells were resuspended in 3 mL PBS containing 10% FBS and filtered through a 35 µm nylon mesh incorporated into the cap of a Falcon flow cytometry tube, and then centrifuged. Cells were resuspended in 50 µL PBS with 2% FBS. 35 µL were used for single-cell isolation.
Gene expression and cellplex libraries were generated with the Chromium Single Cell 3′ v3.1 assay with feature barcoding (10X Genomics) and sequenced on the NovaSeq 6000 platform (Illumina, SP flow cell) to obtain around 100,000 reads per cell for gene expression and 5,000 reads per cell for cellplex

value: Bone marrow

value: Primary cells

value: Mix of endothelial, stromal and hematopoietic cells

value: Untreated


title: eWATirHFD_1

description: Library name: eWATirHFD_1


title: poolB-17

source_name: tumor


title: Healthy2_AM_C16t3

description: Library name: C16t3


title: poolB-14


title: poolB-13


title: eWATgfpHFD_3

description: Library name: eWATgfpHFD_3


title: Healthy8_AM_AMC4t1

description: Library name: AMC4t1


title: Healthy1_AM_AMC6t1

description: Library name: AMC6t1


title: extended_male_dms_vehicle_rep2

description: Library name: extended_male_dms_vehicle_rep2

value: brain

value: dms


title: poolB-16


title: eWATgfpHFD_2

description: Library name: eWATgfpHFD_2


title: eWATirCHW_2

description: Library name: eWATirCHW_2


title: Kasumi-1_input-Sealseq

description: Kasumi-1-input_treat_afterfiting_all.wig

data_processing:
library strategy: 5hmC-Seal
Basecalls performed using Illumina Novaseq
Illunima Casava v1.8 was used to indentify bases
5hmC reads were deeper filtered with Trimmomatic and were mapped to Ensembl GRCh37 human reference genome using Burrows Wheeler Aligner.
PePr software (with a threshold of q value < 1e-5) was used to complete the differential enrichment peak calling analysis between the two groups of samples.PePr was used to statistically analyzed the number, width and distribution of differential enrichment.
5hmC-seq reads were aligned to the hg19 genome assembly using Integrative Genomics Viewer
Assembly: hg19
Supplementary files format and content: wig
Supplementary files format and content: xls files include differential peaks

growth_protocol: Kasumi-1 and MV4;11 cells were cultured in RPMI-1640 medium (Gibco, Grand Island, NY, USA), supplemented with 10% FBS (Gibco) and penicillin-streptomycin.

extract_protocol:
Genomic DNA was obtained from 5x106 cells with Cell/Tissue DNA Isolation Mini Kit (Vazyme)
50 ng genomic DNA were fragmented in Tagmentation buffer at 55 °C. Fragmented DNA was purified with Zymo DNA Clean and Concentration Kit (Zymo). Then, the selective 5hmC chemical labeling was performed. The above fragmented DNA was added to glucosylation buffer (50 mM HEPES buffer, 25 mM MgCl2, pH 8.0) containing β-GT and N3-UDP-Glc, and incubated at 37°C for 2 hours. T After DNA purification, DBCO-PEG4-Biotin (Click Chemistry Tools) was added into the DNA and incubated at 37°C for 2 hours. The biotin-labeled DNA was pulled down by C1 Streptavidin beads (Life Technologies) for 15 min at room temperature. Next, the captured DNA fragments were subjected to PCR amplification using Nextera DNA sample preparation kit (Illumina). The amplified PCR products were purified by 1.0x AMPure XP beads (Acegen). The input library was prepared from fragmented DNA through direct PCR, without chemical labeling or capture. The libraries were quantified with a Qubit fluorometer (Life Technologies) and sequenced on Illumina Novaseq with 150-bp paired-end reads.

value: AML cell line


title: iWATgfpCHW_2

description: Library name: iWATgfpCHW_2

value: iWAT


title: poolB-12


title: poolB-11


title: eWATirCHW_1

description: Library name: eWATirCHW_1


title: Kasumi-1-Sealseq


title: extended_female_dms_vehicle_rep2

description: Library name: extended_female_dms_vehicle_rep2

value: female


title: poolB-15


title: MV4;11-Sealseq


title: MV4;11_input-Sealseq


title: extended_female_dms_vehicle_rep1

description: Library name: extended_female_dms_vehicle_rep1


title: poolB-10


title: extended_male_dms_vehicle_rep1

description: Library name: extended_male_dms_vehicle_rep1


title: poolB-09


title: limited_male_dls_vehicle_rep3

description: Library name: limited_male_dls_vehicle_rep3

value: dls

value: limited


title: eWATgfpCHW_1

description: Library name: eWATgfpCHW_1


title: meRIP seq of MOLM13:RBM15B-NC rep3

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

data_processing:
Trim-galore (v0.6.10) was used to trim adapters and filter for sequences, remaining reads were then aligned to the Hg19  using Bowtie2 (v2.5.0) Hisat2 aligner (v2.1.0)
m6A peaks were identified using exomePeak2 R package (v1.6.1) under parameters: “FRAGMENT_LENGTH=140,p_cutoff = 1e-05,paired_end = TRUE” ; for epz_meRIP data , called peaks under parameters:"FRAGMENT_LENGTH=140, log2FC_cutoff = 1,p_cutoff = 1e-05,paired_end = TRUE" for shRBM15B_meRIP data.
CUT&Tag peaks were  identified using MACS2 (v2.2.7.1) under parameters:"-f BAMPE -g hs --keep-dup all -B -q 0.05 -m 5 50"
Assembly: Hg19
Supplementary files format and content: bed, narrowPeak (except for lnput sample)
Library strategy: m6A-RIP-seq

source_name: Bone Marrow

extract_protocol:
For Cut&Tag, 5 × 104 MOLM13 cells were sorted and washed once in 0.5 mL wash buffer (20 mM Hepes (pH 7.5); 150 mM NaCl; 0.5 mM spermidine; and 1 × protease inhibitors) and were incubated with 10 μL pre-washed concanavalin A–coated magnetic beads in a 1.5 mL microtube at 25 °C for 10 min. Cells were resuspended in 80 μL ice-cold antibody incubation buffer with 1 μg RBM15B antibody per sample (22249-1-AP, proteintech) and then rotated end-over-end at 4 °C overnight. The cells were resuspended in 100 μL of dig-wash buffer [20 mM Hepes (pH 7.5); 150 mM NaCl; 0.5 mM spermidine; 1 × protease inhibitors; 0.025% digitonin) with rabbit anti-mouse IgG (1:100 dilution, Ab6709; ThermoFisher) and rotated end-over-end at 25 °C for 1 h. After washing, home-made pA-Tn5 adapter complexes in dig-300 buffer (20 mM Hepes pH 7.5; 300 mM NaCl; 0.5 mM spermidine; 1 × protease inhibitors; 0.01% digitonin) were added to the samples at a final concentration of 1:100 and then rotated end-over-end at 25 °C for 1 h. After washing, the cells were resuspended in 300 μL fragmentation buffer (dig-300 buffer with 10 mM MgCl2) and incubated at 37 °C for 1 h. After extraction with phenol–chloroform and ethanol precipitation, the libraries were amplified by PCR.  For m6A-RIP, Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). 10μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The fragmented RNA was incubated with anti-m6A monoclonal antibody (abcam,ab208577) for 3 h at 4℃ and then with protein A/G magnetic beads (Invitrogen, 8880210002D/10004D) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was purified using TRIzol™ Reagent (Invitrogen, 15596018).
For Cut&Tag sequencing, the barcoded libraries were pooled and sequenced on the Illumina HiSeq X™ Ten platform to generate 150 bp paired-end reads. For m6A-RIP sequencing, the library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: For Cut&Tag sequencing, the MOLM-13 cells treated by 1uM epz5676 or DMSO(negative control)  for 72 hours.

value: Bone Marrow

value: acute myeloid leukemia cells

value: epz5676, 1uM for 72 hours


title: TPTN-3

city: Chongqing

first: Chen

last: yan

address: 30 Gaotanyan Main Street

institute: Third Military Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, 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 research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
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.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of pval below 0.05 and absolute fold change ≥ 1.5 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus_musculus.GRCm38 v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were 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 librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: strain

value: Heart

tag: age

value: 8–12 weeks old

value: Wildtype

value: TPTN


title: eWATgfpHFD_1

description: Library name: eWATgfpHFD_1

value: eWAT


title: extended_female_dls_vehicle_rep1

description: Library name: extended_female_dls_vehicle_rep1

value: extended

value: vehicle


title: MV4;11-RNAseq

city: Hangzhou

first: Jun

last: Lu

institute: Zhejiang University

data_processing:
illumina Novaseq™ 6000 sequence platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Using HISAT packagealigned reads of sample to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome , which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.
Assembly: hg19
Supplementary files format and content: xlsx file includes RPKM values for each sample

extract_protocol:
The total RNA was extracted from cells with Trizol.
RNA libraries were prepared for sequencing using standard Illumina RNA libraries were prepared for sequencing using standard Illumina protocols.

value: WT


title: poolB-07

value: tumor


title: extended_male_dls_vehicle_rep1

description: Library name: extended_male_dls_vehicle_rep1

value: brain

value: male


title: Kasumi-1-RNAseq

value: AML cell line


title: TPTN-2


title: limited_female_dms_vehicle_rep3

description: Library name: limited_female_dms_vehicle_rep3

value: dms

value: female


title: eWATgfpCHW_3

description: Library name: eWATgfpCHW_3


title: poolB-08


title: eWATgfpCHW_2

description: Library name: eWATgfpCHW_2


title: meRIP seq Input of MOLM13:RBM15B-NC rep2

description: NC-2 input

value: Bone Marrow

value: Negative control


title: limited_male_dms_vehicle_rep2

description: Library name: limited_male_dms_vehicle_rep2

value: limited


title: poolB-03


title: meRIP seq Input of MOLM13:RBM15B-NC rep3

description: NC-3 input

value: acute myeloid leukemia cells


title: limited_male_dms_vehicle_rep3

description: Library name: limited_male_dms_vehicle_rep3


title: limited_female_dls_vehicle_rep3

description: Library name: limited_female_dls_vehicle_rep3

value: dls


title: meRIP seq of MOLM13:RBM15B-NC rep2

value: epz5676, 1uM for 72 hours


title: poolB-06


title: poolB-02


title: Control-3

value: Heart

value: 8–12 weeks old

value: Wildtype

value: Control


title: TPTN-1

value: TPTN


title: poolB-05

value: tumor


title: poolB-04


title: meRIP seq Input of MOLM13:RBM15B-knockdown rep3

description: B-3 input


title: Control-2


title: limited_male_dls_vehicle_rep2

description: Library name: limited_male_dls_vehicle_rep2

value: brain

value: vehicle


title: DOX-2

value: DOX


title: limited_female_dls_vehicle_rep2

description: Library name: limited_female_dls_vehicle_rep2


title: meRIP seq Input of MOLM13:RBM15B-NC rep1

description: NC-1 input


title: Control-1


title: DOX-1


title: poolA-95


title: meRIP seq of MOLM13:RBM15B-knockdown rep2


title: meRIP seq of MOLM13:RBM15B-knockdown rep3


title: poolB-01


title: poolA-94


title: limited_female_dms_vehicle_rep2

description: Library name: limited_female_dms_vehicle_rep2

value: dms


title: limited_female_dls_vehicle_rep1

description: Library name: limited_female_dls_vehicle_rep1

value: female


title: limited_male_dls_vehicle_rep1

description: Library name: limited_male_dls_vehicle_rep1

value: male


title: limited_male_dms_vehicle_rep1

description: Library name: limited_male_dms_vehicle_rep1


title: no-behavior_male_dls_cort_rep3

description: Library name: no-behavior_male_dls_cort_rep3

value: no-behavior

value: cort


title: poolA-96