title: Brain, Flu, rep3

city: Urbana

first: Andrew

middle: J

last: Steelman

state: IL

address: 1201 West Gregory

institute: University of Illinois

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger (v1.1) pipeline to generate FASTQ files
Sequences were aligned to a custom combined reference of NCBI's GRCm39 genome, Annotation Release 109 plus Influenza A virus (A/Puerto Rico/8/1934(H1N1)) genome assembly ViralMultiSegProj15521 (GCF_000865725.1) and gene expressison quantified using default settings of spaceranger count (SpaceRanger v1.3, 10X Genomics)
Assembly: NCBI  GRCm39 + GCF_000865725.1
Supplementary files format and content: *_aligned_fiducials.jpg - aligned fiducials of the tissue image
Supplementary files format and content: *_detected_tissue_image.jpg - image of tissue and spots
Supplementary files format and content: *_scalefactors_json.json - scale factors in json format
Supplementary files format and content: *_tissue_hires_image.png - hi-res image of tissue
Supplementary files format and content: *_tissue_lowres_image.png - low res image of tissue
Supplementary files format and content: *_tissue_positions_list.csv
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 UMI count data in Matrix Market Exchange format
Library strategy: Spatial Transcriptomics

source_name: Brain

growth_protocol: Eight week old C57BL/6J mice were obtained from Jackson Laboratories (No. 000664). Animals were group-housed under constant 12-h light/dark cycles and constant temperature and fed ad libitum

extract_protocol:
At 5 weeks and 5.5 weeks post-cuprizone, corresponding to peak demyelination and partial remyelination, respectively, brains were harvested, bisected sagitally, trimmed rostral to the fornix and caudal to the splenium of the CC, immediately frozen in a bed of finely crushed dry ice, and then embedded in Tissue-Tek® O.C.T. Compound (Sakura #4583) in a dry ice-ethanol slurry. Sagittal sections were cut on a cryostat microtome (Leica CM 1950) at 10 µm thickness and within 0-0.5 mm from the midline. Fresh, frozen sections were placed on slides (one replicate of each treatment per slide) containing spatially-barcoded oligonucleotide probes in a 6.5 x 6.5 mm area
cDNA libraries were constructed according to manufacturer’s instructions (Visium Spatial Gene Expression kit V1, 10x Genomics). Briefly, tissues were fixed, stained, and permeabilized on the slide and cDNA libraries were synthesized from captured RNA. They were pooled and sequenced on two S4 2x150nt lane in a NovaSeq 6000.  Read1 is 28nt in length, Read2 is 150nt in length and  indexes are 10nt in length

treatment_protocol: Mice were fed 0.2% (w/w) cuprizone-laced diet (Teklad 140800) for 5 weeks to induce demyelination, followed by 0.5 weeks of standard rodent chow (Teklad 2918). Cuprizone diet was refreshed every other day. Non-cuprizone control animals were maintained on standard rodent chow throughout the experiment. At 4.5 weeks post-cuprizone, mice were anesthetized with 3% isoflurane and then inoculated with sterile phosphate-buffered saline (PBS) or 100 plaque-forming-units (PFU) of mouse-adapted human influenza A virus (A/Puerto Rico/8/1934 H1N1) diluted in sterile PBS.

value: Brain

tag: age

value: 13.5 weeks

tag: diet

value: 0.2% cuprizone chow

tag: time on_cuprizone_diet

value: 5 weeks

value: 5.5 weeks

value: Influenza virus inoculated


title: 19278X29 CM10

status: Public on Aug 14 2024

type: SRA

city: Salt Lake City

first: Dekker

last: Deacon

state: Utah

address: 2000 Circle of Hope Dr #1950

department: Dermatology

country: USA

institute: University of Utah

library_source: other

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 104 and a reference database was created using STAR version 2.7.9a
A custom Perl script (smallRNA_pe_umi_extractor.pl from https://github.com/HuntsmanCancerInstitute/UMIScripts) was used to trim adapters and extract the Unique Molecular Index (UMI) from the second read of a paired-end Qiagen small RNA library.
The trimmed reads were aligned to the reference database using STAR options optimized for shorter miRNA reads (>=16 bases matched to the genome, number of mismatches <= 5% of mapped length, splicing switched off).
A second Perl script (bam_umi_dedup.pl) removed duplicates from the aligned BAM file
Mapped reads were assigned to annotated miRNAs in miRbase release 22.1 using featureCounts version 1.6.3.
Assembly: GRCh38
Supplementary files format and content: featureCount output files combined into a single tab-delimited matrix

molecule: other

organism: Homo sapiens

source_name: Primary human skin, FFPE

extract_protocol:
RNA was extracted from whole unstained sections of FFPE blocks using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE, after CitriSolv de-parrafinization.
small RNA library prep
RNA libraries were constructed using the Qiagen QIAseq miRNA Library Prep

tag: tissue

value: Primary human skin, FFPE

tag: sample type

value: Cutaneous Melanoma

tag: years in_ffpe

tag: gender

value: F

tag: rna concentration_(ng/ul)

tag: biopsy type

value: shave

tag: % melanocytic_estimate


title: 19278X27 AM02

value: Acral Melanoma

value: M

value: EXCISION


title: Brain, Flu, rep1

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: Sex

tag: treatment


title: Ileum, male, control, rep4

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

data_processing:
Aligned to mm10 with STAR
Tabulated to gene regions using htseq count
ANOVA like analysis in edgeR
Assembly: mm10
Supplementary files format and content: Excel file R results

source_name: Ileum

extract_protocol:
Total RNA was harvested from ileum samples from male mice via the phenol-chloroform method using TRI Reagent. The RNA purity and quantity were measured using a spectrophotometer. 1 ug of total RNA was used for the construction of sequencing libraries.
Lexogen QuantSeq 3' mRNAseq

treatment_protocol: Male and female B6.129S7-Ldlrtm1Her/J mice (Ldlr-/-) mice were fed an atherogenic diet (Clinton/Cybulsky low fat diet, 0.15% cholesterol) for one week prior to the beginning of PFAS exposure, then continued on the atherogenic diet for the remainder of the study. Mice were exposed to either control water or water containging a mixture of 5 PFAS (PFOA, PFOS, PFNA, PFHxS, and GenX) each at a concentration of 2mg/L for 7 weeks.

value: Ileum

tag: genotype

value: LDLR KO

value: Control Water


title: Brain, Saline, rep3

value: PBS inoculated


title: 19278X26 CN17

value: Cutaneous Nevus

value: PUNCH


title: Ileum, male, control, rep1


title: Brain, Flu, rep2

value: Brain

value: 13.5 weeks

value: 0.2% cuprizone chow


title: 19278X25 CN02


title: Brain, Saline, rep1

value: 5 weeks

value: 5.5 weeks


title: Brain, Saline, rep2


title: 19278X23 CN11

value: Primary human skin, FFPE

value: SHAVE


title: 19278X21 CN19

value: F


title: Brain, Demyelinated, rep3

value: 13 weeks


title: 19278X22 CN10


title: Brain, Demyelinated, rep2

value: M


title: 19278X20 CN07


title: Brain, Demyelinated, rep1


title: Brain, Normal, rep3

value: Standard rodent chow


title: 19278X19 CM17

value: Cutaneous Melanoma


title: 19278X30 CM01


title: Brain, Normal, rep2


title: 19278X17 CM03

value: EXCISION


title: C_CRE_DX3

city: Beijing

first: Runping

last: Liu

state: Beijing

address: 11 Beisanhuandonglu

country: China

institute: Beijing University of Chinese Medicine

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, 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 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

molecule: polyA RNA

source_name: bone marrow-derived dendritic cells

extract_protocol:
Total RNA was isolated using TRIzol (Vazyme, Nanjing, China) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: cell type

value: bone marrow-derived dendritic cells

value: CRE

value: DX


title: C_CRE_CT3

value: CT


title: 19278X18 CM08


title: 19278X24 CN09

value: Cutaneous Nevus


title: 19278X16 CM20


title: Brain, Normal, rep1

value: Brain

value: PBS inoculated


title: C_WT_DX3

value: WT


title: 19278X15 CM16


title: C_CRE_DX2


title: 19278X14 CM13


title: 19278X13 CM02


title: C_CRE_CT2


title: 19278X12 AN22

value: Acral Nevus


title: C_WT_DX2


title: 19278X10 AN17

value: Primary human skin, FFPE


title: 19278X9 AN09

value: SHAVE


title: 19278X8 AN07

value: F

value: PUNCH


title: C_CRE_DX1


title: 19278X7 AN05

value: M


title: C_WT_DX1


title: C_WT_CT2


title: 19278X6 AN4


title: C_WT_CT1


title: 19278X5 AM17

value: Acral Melanoma


title: M_CRE_DX3

source_name: bone marrow-derived macrophages

value: bone marrow-derived macrophages


title: 19278X4 AM15

value: EXCISION


title: C_WT_CT3

value: bone marrow-derived dendritic cells


title: 19278X3 AM11


title: 19278X2 AM09


title: M_CRE_CT3

value: CRE


title: M_WT_CT3


title: M_WT_DX3

value: DX


title: M_CRE_DX2


title: 19278X1 AM05


title: 19137X5 CN16


title: 19137X6 AN21


title: M_WT_DX2


title: 19137X3 AN13


title: 19137X2 AM08


title: M_CRE_CT2

value: CT


title: M_WT_CT2


title: C_CRE_CT1


title: M_CRE_DX1


title: DSS_CRE_5

source_name: colon

extract_protocol:
Total RNA was isolated using TRIzol (Vazyme, Nanjing, China) according to the manufacturer’s instructions and then and purified by lithium chloride (Sigma, Missouri, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: colon

value: DSS


title: M_WT_CT1


title: M_WT_DX1


title: VCap_9069_12h

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

data_processing:
Reads were aligned to homan genome using STAR with default setting. Reads mapped to genes were quantified with featureCounts.
Assembly: hg38
Supplementary files format and content: bigWig file for each library
Supplementary files format and content: raw cound matrix in tsv file

source_name: prostate

growth_protocol: VCaP cells were seeded at a density of 2 × 107 cells per 10 cm dish 24 hours prior to treatment.

extract_protocol:
Total RNA was extracted from VCaP cells using the RNeasy Mini Kit (Qiagen, 74104) following the manufacturer’s protocol. For Nascent RNA-seq, 5 μg of the total RNA was diluted and incubated in a Click-iT reaction cocktail for 30 minutes with gentle vortexing. Chilled 100% ethanol was added, and the samples were incubated at -80 °C overnight. Following this, the tubes were centrifuged, and the RNA pellets were dried at room temperature and then resuspended in 50 μl of RNase-free distilled water. For each sample, 1 μg of total biotinylated RNA was isolated, and three different spike-in controls (100 pg each) were added. The prepared RNA binding reaction mix was then introduced to the samples. This was followed by co-heating at 68 °C for 5 minutes. The bead suspension was added, and the samples were incubated at room temperature for 30 minutes with gentle vortexing. After washing, the RNA captured on the beads was processed for cDNA synthesis using the KAPA RNA Hyper Kit (Roche Cat#: 08098107702)
Ribosomal RNA was removed by enzymatic digestion from 800 ng total RNA, following with cDNA and double strand cDNA synthesis, end repair, A-tailing, and ligation with NEB adapter. cDNA fragments with the size between 250-300 bp were separated using double AMPure beads and PCR amplified using 2x KAPA HiFi HotStart mix and NEB dual indexes (Roche Cat#: E6440L).
Nascent RNA-seq

treatment_protocol: The cells were treated in triplicate with YJ9069 at a concentration of 500 nM. 5-ethynyl Uridine (EU, Thermo Fisher Scientific, C10365) was added to a final concentration of 0.5 mM.  After incubation for additional one hour, the cells were harvested

value: prostate

tag: cell line

value: VCaP

value: Epithelial


title: VCap_9069_8h


title: VCap_9069_6h


title: DSS_CRE_1


title: VCap_9069_4h


title: DSS_CRE_2


title: VCap_9069_2h


title: DSS_WT_3

value: WT


title: VCap_Ctl

value: Ctl


title: DSS_WT_1


title: 19137X4 CM04

value: Primary human skin, FFPE

value: Cutaneous Melanoma

value: F

value: SHAVE


title: Control_CRE_3

value: Control


title: DSS_WT_2


title: VCaP 9069_12hr-R2

data_processing:
Transcripts were quantified by kallisto with mouse reference genome (hg38) and then summarized to obtain gene level counts and TPM.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts of each sample
Supplementary files format and content: tab-delimited text file includes TPM of each sample

extract_protocol:
Total RNA was extracted from VCaP cells using the RNeasy Mini Kit (Qiagen, 74104) following the manufacturer’s protocol.
RNA-seq libraries were prepared using KAPA RNA Hyper+RiboErase HMR (Roche Cat#: 08098140702). Ribosomal RNA was removed by enzymatic digestion from 800 ng total RNA, following with cDNA and double strand cDNA synthesis, end repair, A-tailing, and ligation with NEB adapter. cDNA fragments with the size between 250-300 bp were separated using double AMPure beads and PCR amplified using 2x KAPA HiFi HotStart mix and NEB dual indexes (Roche Cat#: E6440L).


title: VCaP 9069_12hr-R1


title: M_CRE_CT1

value: bone marrow-derived macrophages


title: VCaP 9069_12hr-R3


title: Control_CRE_2


title: Control_CRE_1


title: Control_WT_2


title: Subject4, Dopaminergic organoid, with microglia, LEO2

city: New York

first: Scott

middle: Allen

last: Noggle

state: NY

address: 619 West 54th Street

institute: NYSCF

data_processing:
Raw FASTQ data were filtered for adapters with fastp v0.23.0 software.
Initial quality control suggested mouse sequence contamination in some raw FASTQ sample files.  Sequence reads were next separately aligned to human genome using STAR v 2.7.10a with indexes generated from the Homo sapiens GRCh38 primary assembly with the GRCh38.107 gtf build ensemble annotations and to the Mus musculus GRCm39 primary assembly with the Mus musculus GRCm39.107 gtf build ensemble annotations. The XenofilteR R-package software (Kluin, R. J. C. et al. 2018) was then used to generate human .bam files filtered for mouse sequence contamination.
The featureCounts v2.0.3 software was used to generate a counts matrix for differential expression analysis
Assembly: Homo_sapiens GRCh38 primary assembly
Supplementary files format and content: all_counts.txt contains the final counts matrix generated by featureCounts v2.0.3 software.

growth_protocol: iPSC line 051121-01-MR-017 and AK003-01-MR-008 were differentiated into cortical neural precursors using established protocols (Yao, Z et al., 2017) and iPSC line HDF410iPS504 and iPSC line UEC741iPS517 were differentiated into dopaminergic neural precursors (Hills et al., 2023). Twenty-five days after differentiation was initiated, both cortical and dopaminergic precursors were dissociated and cryopreserved. Isogenic microglia were derived from all of the cell lines. A week before the estimated launch date, cryopreserved neural precursors were thawed, washed in DMEM/F12. Cell pellets were resuspended in cortical neuron medium or dopaminergic neuron medium and were plated onto ultra-low attachment 96-well V-bottom plates and allowed to aggregate overnight into organoids. For half of the samples, isogenic iPSC-derived microglia (Douvaras, P.  et al., 2017) were added to the neural organoids after 24 hours, and a medium exchange was performed, adding IL-34 and GM-CSF to promote microglia maturation. Cultures were then incubated for an additional 24 hours before being shipped at 4°C to the Kennedy Space Center for payload preparation and launch.

extract_protocol:
Individual organoids cultured in LEO and from ground control, both with and without added microglia, were snap-frozen and stored at -80°C. RNA was extracted using the Qiagen RNeasy Micro kit (QIAGEN) and eluted into 12μL of ultrapure DI water. RNA quality and concentration was assessed on Bioanalyzer Pico with RIN reported.
The RNA was sequenced by Novogene using an ultra-low input preparation of samples with a minimum of 10ng of RNA. A pilot subset of samples were cDNA amplified before sequencing with the Clontech SMART kit employing Clontech SMART CDS Primer IIA. Remaining samples used Nextera library preparation. All samples were then sequenced using the Illumina NovaSeq Platform for high-throughput PE150 sequencing.

treatment_protocol: For payload preparation and launch to culture organoids in microgravity on the ISS, organoids were individually transferred into a cryovial  containing 1 mL of cortical or dopaminergic medium with the addition of IL-34 (100ng/mL) and GM-CSF (10ng/mL) in DMEM/F-12 medium buffered with 15mM HEPES. The cryovials were closed and sealed with parafilm and loaded into a CubeLab, a miniaturized incubator that maintains a stable temperature of 37 ̊C. The CubeLab was then transferred to the rocket and after two days, launched into low-Earth orbit onboard the SpaceX 19th Commercial Resupply Services mission (SpX CRS-19) to the ISS for a 30-day stay in microgravity. Under similar conditions, ground control samples were kept at the Kennedy Space Center. After 30 days, the Dragon capsule carrying the organoids back to Earth splashed down in the Pacific Ocean, and the CubeLab was opened six days post undock from the ISS and transferred to the lab for RNA extraction.

value: iPSC-derived dopaminergic organoid with microglia

value: 38 days microgravity exposure


title: Control_WT_3


title: VCaP_DMSO-R2

value: DMSO


title: Control_WT_1


title: 19137X1 AM16

value: Acral Melanoma

value: M

value: EXCISION


title: Subject4, Dopaminergic organoid,  with microglia , LEO1


title: Subject4, Dopaminergic organoid, without microglia, LEO4

value: iPSC-derived dopaminergic organoid without microglia


title: AOM_CRE_2

source_name: tumor

value: tumor

value: CRE

value: AOM/DSS induction


title: Subject4, Dopaminergic organoid, without microglia, LEO3


title: AOM_CRE_1


title: AOM_CRE_3


title: Subject4, Dopaminergic organoid, without microglia, LEO1


title: Subject4, Dopaminergic organoid, without microglia, LEO2


title: AOM_WT_3

value: WT


title: AOM_WT_2


title: Subject3, Dopaminergic organoid, with microglia, LEO2


title: AOM_WT_1


title: Subject3, Dopaminergic organoid, with microglia, LEO1


title: VCaP_DMSO-R3

value: prostate

value: VCaP

value: Epithelial


title: Subject3, Dopaminergic organoid, without microglia, LEO3


title: WT_D6

city: Chicago

first: Timothy

middle: Jon

last: Koh

address: 1919 W Taylor Room 650

institute: University of Illinois at Chicago

library_source: genomic

data_processing:
Peak calling and demultiplexing was performed using cellranger-atac v2.0.0.
Assembly: mm10
Supplementary files format and content: *_barcodes.tsv: Cell barcodes corresponding to cell indices in *_matrix.mtx.gz files
Supplementary files format and content: *_peaks.bed: Peak coordinates corresponding to feature IDs in *_matrix.mtx.gz files
Supplementary files format and content: *_matrix.mtx.gz: Read counts per nuclei per peak matrix in MatrixMarket sparse format
Supplementary files format and content: *_fragments.tsv.gz: Coordinates of aligned fragments.

molecule: genomic DNA

source_name: Skin wound

extract_protocol:
Monocytes and macrophages isolated from skin wounds on male C57BL6/J mice on day 3 and 6 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per time point. Nuclei were processed using the 10x Chromium platform. Libraries sequenced on NovaSeq 6000 with paired-end reads. Fastq files were generated and demultiplexed into single cells using Cell Ranger software.
10x User Guide CG000338
single-nuclei ATAC-seq

value: Skin wound

tag: time point

value: Day 6


title: Subject3, Dopaminergic organoid, without microglia, LEO1


title: VCaP_DMSO-R1


title: Subject3, Dopaminergic organoid, without microglia, LEO2


title: control CUT&TAG Tcf4-tag rep1

city: Shanghai

first: Yunli

last: Xie

address: 131 Dong`an Road

department: Institutes of Brain Science

institute: Fudan University

data_processing:
trim adptors using trim_galore
mapping using bowtie2
remove duplicates using samtools
peaks calles by MACS2
diffrential accessible peaks were analyzed using R package diffbind2
Assembly: mm10
Supplementary files format and content:final differential accessible peaks with annotation
Supplementary files format and content:motif activity in WT and Tcf4 cKO
Library strategy: CUT&TAG

source_name: brain

extract_protocol: not provided

value: brain

value: Nkx2.1 lineage cells

value: mouse brain cells

value: Tcf4-tag mouse


title: control CUT&TAG Tcf4-tag rep2


title: WT_D3

value: Day 3


title: mutant CUT&TAG  H3K27me3 rep2

value: Tcf4 cKO


title: Subject4, Dopaminergic organoid, with microglia, Ground3

value: iPSC-derived dopaminergic organoid with microglia

value: ground control, no microgravity exposure


title: mutant CUT&TAG  H3K27me3 rep1


title: control CUT&TAG  H3K27me3 rep2


title: Subject4, Dopaminergic organoid, without microglia, Ground4

value: iPSC-derived dopaminergic organoid without microglia


title: control CUT&TAG  H3K27me3 rep1


title: Subject4, Dopaminergic organoid, without microglia, Ground3


title: Subject4, Dopaminergic organoid, without microglia, Ground2


title: mutant CUT&TAG  H3K27ac rep1


title: Subject4, Dopaminergic organoid, with microglia, Ground1


title: Subject4, Dopaminergic organoid, without microglia, Ground1


title: mutant CUT&TAG  H3K4me1 rep2


title: mutant CUT&TAG  H3K4me1 rep1


title: Subject3, Dopaminergic organoid, without microglia, Ground2


title: control CUT&TAG  H3K4me1 rep2


title: Subject3, Dopaminergic organoid, without microglia, Ground1


title: control CUT&TAG  H3K4me1 rep1


title: mutant ATACseq rep1

data_processing:
trim adptors using trim_galore
mapping using bowtie2
remove duplicates using samtools
peaks calles by MACS2
diffrential accessible peaks were analyzed using R package diffbind2
Assembly: mm10
Supplementary files format and content:final differential accessible peaks with annotation
Supplementary files format and content:motif activity in WT and Tcf4 cKO


title: Subject2, Cortical organoid, with microglia, LEO1

value: iPSC-derived cortical organoid with microglia

value: 38 days microgravity exposure


title: Subject2, Cortical organoid, with microglia, LEO2


title: mutant ATACseq rep2


title: control ATACseq rep2

value: WT


title: mutant CUT&TAG  H3K27ac rep2


title: Subject2, Cortical organoid, without microglia, LEO2

value: iPSC-derived cortical organoid without microglia


title: control ATACseq rep1


title: Subject1, Cortical organoid, with microglia, LEO3


title: mutant scRNAseq

library_source: transcriptomic single cell

data_processing:
matrix retrieved using  cellranger
downstream analysis were performed using R package Seurat


title: Subject2, Cortical organoid, without microglia, LEO1


title: control CUT&TAG  H3K27ac rep2


title: Subject3, Dopaminergic organoid, with microglia, Ground3


title: S209A_2 24h Fast light polysome

city: San Francisco

first: Haojun

last: Yang

state: CA

address: 1450 3rd Street

institute: UCSF

data_processing:
Galaxy server at the University of Manchester (https://centaurus.itservices.manchester.ac.uk/)
Sequence reads were trimmed with Trimmomatic.
Trimmed reads were aligned to the mouse genome (Version mm10) using HISAT2
Counts were calculated using Stringtie and annotated using GENCODE.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

growth_protocol: Wild type or eIF4E S209A/S209A C57BL/6 mice were were maintained under pathogen-free conditions and all experiments were performed in compliance with guidelines approved by the Institutional Animal Care and Use Committee of UCSF.

extract_protocol:
Samples were seperated using sucrose gradient, and fractions 2-7, and 8-13 were pulled together, same amout of ERCC was added to each pool, PureLink™ RNA Mini Kit (ThermoFisher). 10ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian following manufacturer's protocols.

treatment_protocol: For studying fasting, food was removed from mice for 24h. Fed mice were available to food all the time.

value: Liver

value: Male

value: eIF4E S209A/S209A

value: Fast

tag: time


title: Subject3, Dopaminergic organoid, with microglia, Ground2


title: control scRNAseq

value: brain


title: Subject1, Cortical organoid, with microglia, LEO1


title: S209A_2 24h Fast heavy polysome


title: Subject1, Cortical organoid, without microglia, LEO2


title: S209A_1 24h Fast light polysome


title: Subject2, Cortical organoid, with microglia, Ground2


title: S209A_1 24h Fast heavy polysome


title: WT_2 24h Fast light polysome


title: Subject2, Cortical organoid, with microglia, Ground1


title: Subject4, Dopaminergic organoid, with microglia, Ground2


title: Subject2, Cortical organoid, without microglia, Ground1


title: WT_2 24h Fast heavy polysome


title: Subject1, Cortical organoid, with microglia, Ground3


title: WT_2 Fed heavy polysome

value: Fed


title: Subject1, Cortical organoid, with microglia, Ground1


title: WT_1 24h Fast light polysome


title: control CUT&TAG  H3K27ac rep1

value: Nkx2.1 lineage cells

value: mouse brain cells


title: Subject2, Cortical organoid, without microglia, Ground2


title: Subject1, Cortical organoid, without microglia, Ground2


title: WT_2 Fed light polysome


title: WT_1 Fed heavy polysome


title: WT_1 Fed light polysome


title: RNA: splenocytes_IL4KO

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

data_processing:
We used Cell Ranger v5.0.0 (10X Genomics) pipeline for FASTQ file generation from raw sequencing data.
raw BCL files from Illumina HiSeqXten were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’.
raw FASTQ files were analyzed using ‘cellranger count’.
The ‘cellranger count’ step includes mapping to the mouse reference genome (mm10), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis. Count can take input from multiple sequencing runs on the same library.
The final dataset was built by aggregating multiple independent samples using ‘cellranger aggr’.
Raw count matrices resulting by Cell Ranger ‘aggr’ were imported to Seurat 4.3.0.
Assembly: mm10
Supplementary files format and content: The lists of cell barcode in tsv format, filtered gene matrix table with raw gene counts in mtx and HDF5 format.

source_name: spleen

extract_protocol:
Splenocytes for single-cell RNA-seq were obtained from 6- to 8-week-old male IL-4-/- (B6.129P2-Il4tm1Cgn/J) mice and wild-type (WT) (C57BL/6) mice. Spleen tissues from WT and IL-4 KO mice were minced into a single-cell suspension using a 70-μm filter. And CD8+ splenocytes were subsequently sorted using mouse CD8 MicroBeads.
Libraries were prepared using the Chromium Controller according to the 10x Chromium Next GEM Single Cell 3’ v3.1 protocol (CG000315).

value: spleen


title: Subject1, Cortical organoid, without microglia, Ground3


title: breast cancer MCF7TR replicate 1 [Hi-C]

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

description: untreated

data_processing:
The raw reads of Hi-C were first aligned to human HG19 genome, then filtered by HiC-Pro to get the valid pairs.
Genome_build: HG19
Supplementary_files_format_and_content: Headers of allValidPairs files: read_name, chromosome of first locus, read position of first locus (currently middle of the reads), strand of first locus, chromosome of second locus, read position of second locus, strand of second locus, DNA fragment length, name of first restriction fragment, name of second restiction fragment, mapping quality of first read, mapping quality of second read, allele-specific analysis (0-0 = first read from genome1 and second read from genome1, 1-0 = first read from genome2 and second read from genome1, 0-1 = first read from genome1 and second read from genome2, 1-1 = first read from genome2 and second read from genome2), please refer to: https://groups.google.com/g/hic-pro/c/qhHNbQVJfYY

growth_protocol: Routine cell media for all cell lines, respectively.

extract_protocol:
Extraction of cell nucleus and DNA were performed as described (Rao et al. 2014).
Hi-C was performed as described (Rao et al. 2014).

treatment_protocol: Untreated

tag: cell types

value: immortalized breast epithelial cell

tag: analysis

value: Hi-C


title: Subject1, Cortical organoid, with microglia, Ground2

value: ground control, no microgravity exposure


title: breast cancer MCF7M1 replicate 2 [Hi-C]

description: untreated


title: Subject1, Cortical organoid, without microglia, LEO1


title: Subject1, Cortical organoid, without microglia, Ground1


title: breast cancer MCF7M1 replicate 1 [Hi-C]

description: untreated


title: breast cancer MCF7 replicate 2 [Hi-C]

description: untreated


title: breast cancer MCF7TR replicate 1

description: untreated

data_processing:
The raw reads of scRNA-seq were first aligned to human HG19 genome and then feature-barcode matrices were generated with software Cell Ranger developed by 10X Genomics.
Genome_build: HG19
Supplementary_files_format_and_content: *barcodes.tsv.gz: Barcode sequences correspond to column indices. *features.tsv.gz: Features correspond to row indices. For each feature, its feature ID and name are stored in the first and second column of the (unzipped) features.tsv.gz file, respectively. The third column identifies the type of feature, which will be one of Gene Expression, Antibody Capture, CRISPR, or CUSTOM, depending on the feature type. *matrix.mtx.gz: Matrices of features to barcodes. First column: feature indices; second column : barcode indices; third column: counts.

extract_protocol:
Single cells were picked up by 10X Genomics Chromium System.
Single-cell RNA-seq protocol was run according to the technical manual of 10X Genomics Chromium System.

value: single cell RNA-seq


title: breast cancer MCF7TR replicate 2

description: untreated


title: breast cancer MCF7 replicate 1 [Hi-C]

description: untreated


title: breast cancer MCF7M1 replicate 2

description: untreated


title: WT_1 24h Fast heavy polysome

tag: tissue


title: breast cancer MCF7M1 replicate 1

description: untreated


title: RNA: splenocytes_ctrl

value: ctrl


title: breast cancer MCF7 replicate 2

description: untreated


title: breast cancer MCF7 replicate 1

description: untreated


title: Subject3, Dopaminergic organoid, with microglia, Ground1

value: iPSC-derived dopaminergic organoid with microglia


title: breast cancer single cell A288

data_processing:
The raw reads of scHi-C were first aligned to human HG19 genome, then filtered by HiC-Pro to get the valid pairs.
Genome_build: HG19
Supplementary_files_format_and_content: the column headers of *allValidPairs are:
read_name, chromosome of first locus, read position of first locus (currently middle of the reads), strand of first locus, chromosome of second locus, read position of second locus, strand of second locus, DNA fragment length, name of first restriction fragment, name of second restiction fragment, mapping quality of first read, mapping quality of second read, allele-specific analysis

extract_protocol:
Extraction of cell nucleus and DNA were performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).
single-cell Hi-C was performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).

value: immortalized breast epithelial cell line

value: untreated

value: single-cell Hi-C


title: breast cancer MCF7TR replicate 2 [Hi-C]

description: untreated


title: breast cancer single cell A286


title: breast cancer single cell A289


title: breast cancer single cell A285


title: breast cancer single cell A292


title: breast cancer single cell A291


title: breast cancer single cell A290


title: breast cancer single cell A287


title: Subject1, Cortical organoid, with microglia, LEO2

value: iPSC-derived cortical organoid with microglia

value: 38 days microgravity exposure


title: breast cancer single cell A282


title: breast cancer single cell A279


title: breast cancer single cell A281


title: breast cancer single cell A284


title: breast cancer single cell A275


title: breast cancer single cell A278


title: breast cancer single cell A277


title: breast cancer single cell A276


title: YSINT26

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

institute: Ajou University School of Medicine

data_processing:
The low quality sequence reads with less than 30 PHRED score and adapter sequence reads were trimmed using a Trim Galore tool
Sequence reads were mapped to the human reference genome (hg38) using TopHat2 with default parametes
RNA abundance was estimated by as the FPKM values according to GENCODE database (version 33) using Cufflinks tool
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include log2(FPKM+1) values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Intermediate cell carcinoma

extract_protocol:
Total RNA was extracted from each sample using the RNeasy total RNA extraction kit (Qiagen) according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: batch


title: breast cancer single cell A293


title: breast cancer single cell A272


title: breast cancer single cell A274


title: YSINT25


title: YSINT22

source_name: Intrahepatic cholangiocarcinoma


title: YSINT24

source_name: Non-tumor


title: breast cancer single cell A273


title: breast cancer single cell A280


title: YSINT21


title: breast cancer single cell A271


title: YSINT20


title: YSINT23


title: breast cancer single cell A268


title: breast cancer single cell A267


title: YSINT18


title: breast cancer single cell A270


title: breast cancer single cell A269


title: breast cancer single cell A265


title: YSINT16

source_name: Hepatocellular carcinoma


title: breast cancer single cell A283


title: breast cancer single cell A266


title: YSINT17


title: YSINT15


title: breast cancer single cell A264


title: breast cancer single cell A263


title: breast cancer single cell A262


title: YSINT13


title: YSINT11


title: breast cancer single cell A260


title: YSINT9


title: breast cancer single cell A259


title: YSINT12


title: YSINT10


title: YSINT19


title: YSINT7


title: breast cancer single cell A256


title: breast cancer single cell A254


title: breast cancer single cell A257


title: YSINT6


title: YSINT4


title: YSINT14


title: YSINT5


title: breast cancer single cell A255


title: breast cancer single cell A251


title: breast cancer single cell A250


title: YSINT2


title: breast cancer single cell A261


title: breast cancer single cell A248


title: YSINT3


title: breast cancer single cell A253


title: Panc89_paraclone_rep2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

data_processing:
Raw sequencing data was pseudo-aligned against the human transcriptome (Ensembl GRCh38.106) using kallisto (v0.46.1) with 30 bootstraps. Gene expression was summarized from the scaledTPM values of the transcripts using tximport (v1.26).
Assembly: Ensembl GRCh38 version 106
Supplementary files format and content: comma delimited text file with scaled TPM values summarized to gene expression using tximport

growth_protocol: The human cell line Panc89 (kindly provided by Prof. T. Okabe, University of Tokyo, JP) originating from a lymph node metastasis of PDAC was used as a model for epithelial PDAC cells. As a model for mesenchymal PDAC cells, the human cell line Panc1 was used (purchased from ATCC, Manassas, Virginia US) originating from a primary tumor of a PDAC patient. Single cell cloning of Panc1 cells to isolate Panc1 Holo- and Paraclone cells, respectively, is described in Knaack et. al., Oncotarget 2018. To isolate Holo- and Paraclone cells from Panc89 cells, the parental cells were pre-diluted to a cell count of 1000 cells per ml Panc-medium. From this cell suspension, 100 µl (corre-sponding to 100 cells) were added to 20 ml of Panc-medium to obtain a concentration of one cell per 200 µl of cell medium, which were filled in each well of a flat 96-well plate. The plate was centrifuged and the first screening was performed directly after centrifuga-tion by imaging the plate in the brightfield channel of a NYONE® Scientific Imager (Synen-Tec GmbH, Elmshorn, DE) and with the brightfield channel of EVOS microscope (AMG, Bothell, US). Only wells containing exactly one cell were considered for further monitoring and expansion. The microscopical screening was performed twice a week. After 12-20 days, the colony shape was determined and the colonies monitored until a cell confluence of about 80%. Cell clones with a stable colony morphology were detached from one well and transferred to one well of a 6-well plate. The morphology of expanded cell clones was con-tinued to be checked regularly. Only clones with a clear CSC- or non-CSC morphology and stable phenotype were further cultivated, expanded and used for phenotypic and functional characterization. Phenotypes were regularly checked by marker analysis via qPCR.

extract_protocol:
Total high-purity RNA of all cell variants was isolated using the total RNA kit peqGOLD (PeqLab, Erlangen, DE) with an additional DNase digestion step according to manufacturer's specifications.
RNA-triplicates (3 biological replicates) of each cell line were placed in a 96-well plate in a concentration of at least 150 ng/15 µl RNase-free water. Input total RNA was quantified using the Quant-it RNA Assay (Thermo Fisher, Waltham, USA) and RIN scores were determined using the Agilent Tape Station (Agilent, Santa Clara, USA). All RIN scores were > 8. 200 ng input total RNA were processed using the Illumina stranded mRNA kit (Illumina, San Diego, USA).

value: cancer cell line

tag: clone

value: para clone

tag: replicate

value: replicate 2


title: Panc89_paraclone_rep3

value: replicate 3


title: Panc89_paraclone_rep1

value: replicate 1


title: Panc89_holoclone_rep2

value: holo clone


title: Panc89_holoclone_rep3


title: breast cancer single cell A245


title: Panc89_holoclone_rep1


title: breast cancer single cell A252


title: breast cancer single cell A244


title: breast cancer single cell A247


title: breast cancer single cell A246


title: YSINT8


title: breast cancer single cell A249


title: Panc89_parental_rep3

value: parental


title: Panc89_parental_rep2


title: breast cancer single cell A243


title: Panc89_parental_rep1


title: breast cancer single cell A242


title: breast cancer single cell A241


title: breast cancer single cell A258


title: Panc1_paraclone_rep3


title: breast cancer single cell A240


title: Panc1_holoclone_rep3


title: Panc1_paraclone_rep1


title: breast cancer single cell A238


title: breast cancer single cell A239


title: Panc1_holoclone_rep1


title: breast cancer single cell A237


title: breast cancer single cell A236


title: breast cancer single cell A235


title: breast cancer single cell A234


title: Panc1_parental_rep2


title: Panc1_holoclone_rep2


title: breast cancer single cell CL6_20

data_processing:
mapped to HG19 with BWA
copy number variation was called by SCCNV
Assembly: HG19
Supplementary files format and content: chr, pos1, pos2, Mappability, AT, GC, N and copy number of each cell
Library strategy: scDNA-seq

source_name: breast cancer

extract_protocol:
single cell was isolated and total genomic DNA was extracted
ResolveDNA Whole Genome Amplification Kit (Catalog # 100136, BioSkryb Genomics) was used for amplification of genomic DNA. ResolveDNA Library Preparation Kit (Catalog # 100080, BioSkryb Genomics) was used for library preparation.

value: breast cancer


title: breast cancer single cell A230


title: Panc1_parental_rep1


title: breast cancer single cell A233


title: breast cancer single cell CL6_21


title: breast cancer single cell CL6_17


title: Panc1_paraclone_rep2


title: breast cancer single cell A229


title: breast cancer single cell A228


title: breast cancer single cell A226


title: breast cancer single cell CL6_13


title: breast cancer single cell CL6_14


title: breast cancer single cell CL6_16


title: breast cancer single cell A227


title: breast cancer single cell A224


title: breast cancer single cell CL6_11


title: Panc1_parental_rep3


title: breast cancer single cell CL6_05


title: breast cancer single cell A221


title: breast cancer single cell A220


title: breast cancer single cell CL6_03


title: breast cancer single cell CL6_12


title: breast cancer single cell A217


title: breast cancer single cell CL6_02


title: breast cancer single cell A232


title: breast cancer single cell CL6_01


title: breast cancer single cell A231


title: breast cancer single cell CL5_17


title: breast cancer single cell A215


title: breast cancer single cell CL6_10


title: breast cancer single cell A223


title: breast cancer single cell CL5_16


title: breast cancer single cell CL6_09


title: breast cancer single cell A218


title: breast cancer single cell A214


title: breast cancer single cell A213


title: breast cancer single cell A219


title: breast cancer single cell CL5_15


title: breast cancer single cell A222


title: breast cancer single cell CL6_15


title: breast cancer single cell CL5_19


title: breast cancer single cell CL5_20


title: breast cancer single cell A216


title: breast cancer single cell A211


title: breast cancer single cell CL5_13


title: breast cancer single cell A225


title: breast cancer single cell A212


title: breast cancer single cell A209


title: breast cancer single cell CL5_11


title: breast cancer single cell CL5_12


title: breast cancer single cell A207


title: breast cancer single cell CL5_09


title: breast cancer single cell A210


title: breast cancer single cell A208


title: breast cancer single cell A206


title: breast cancer single cell CL5_14


title: breast cancer single cell CL5_10


title: breast cancer single cell A204


title: breast cancer single cell CL5_05


title: breast cancer single cell CL5_08


title: breast cancer single cell A205


title: breast cancer single cell CL5_06


title: breast cancer single cell CL5_03


title: breast cancer single cell A202


title: breast cancer single cell CL5_07


title: breast cancer single cell CL5_02


title: breast cancer single cell A203


title: breast cancer single cell CL5_01


title: breast cancer single cell A201


title: breast cancer single cell CL4_20


title: breast cancer single cell CL4_21


title: breast cancer single cell CL4_18


title: breast cancer single cell A200


title: breast cancer single cell A199


title: breast cancer single cell A195


title: breast cancer single cell A198


title: breast cancer single cell A197


title: breast cancer single cell A192


title: breast cancer single cell CL4_19


title: breast cancer single cell CL4_14


title: breast cancer single cell A194


title: breast cancer single cell A190


title: breast cancer single cell A189


title: breast cancer single cell A193


title: breast cancer single cell CL4_11


title: breast cancer single cell A188


title: breast cancer single cell CL4_12


title: breast cancer single cell A187


title: breast cancer single cell CL4_10


title: breast cancer single cell A196


title: breast cancer single cell CL4_16


title: breast cancer single cell A185


title: breast cancer single cell CL4_15


title: breast cancer single cell CL4_17


title: breast cancer single cell A191


title: breast cancer single cell CL4_13


title: breast cancer single cell CL4_05


title: breast cancer single cell A183


title: breast cancer single cell CL5_04


title: breast cancer single cell A186


title: breast cancer single cell CL4_09


title: breast cancer single cell CL4_08


title: breast cancer single cell A179


title: breast cancer single cell A177


title: breast cancer single cell A176


title: breast cancer single cell A181


title: breast cancer single cell A175


title: breast cancer single cell A182


title: breast cancer single cell A184


title: breast cancer single cell A174


title: breast cancer single cell CL4_06


title: breast cancer single cell CL4_07


title: breast cancer single cell A180


title: breast cancer single cell CL3_14


title: breast cancer single cell A172


title: breast cancer single cell A173


title: breast cancer single cell CL4_04


title: breast cancer single cell CL3_12


title: breast cancer single cell CL3_17


title: breast cancer single cell A171


title: breast cancer single cell CL4_02


title: breast cancer single cell CL4_03


title: breast cancer single cell CL3_15


title: breast cancer single cell CL3_10


title: breast cancer single cell CL3_11


title: breast cancer single cell CL3_13


title: breast cancer single cell CL3_09


title: breast cancer single cell CL3_16


title: breast cancer single cell A178


title: breast cancer single cell A168


title: breast cancer single cell A169


title: breast cancer single cell CL3_06


title: breast cancer single cell CL3_07


title: breast cancer single cell A165


title: breast cancer single cell CL3_08


title: breast cancer single cell CL4_01


title: breast cancer single cell A170


title: breast cancer single cell A166


title: breast cancer single cell A163


title: breast cancer single cell CL3_05


title: cciT replicate 2

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
CLC Genomic Workbench 20
Raw read files were imported with paired reads option with a minimum distance of 1 and a maximum distance of 1000. Failed reads where remove using NCBI/Sanger or Illumna Pipeline 1.8 and later setting
Reads were mapped to Caluobacter Crescentus genome CP001340 with the following parameters: Mismatch cost 2, Insertion cost: 3, Deletion cost: 3,  Length fraction: 0.8, Similarity fraction 0.8, Select Auto-detect paired distances, and Maximum number of hits for a read: 10
Read counts were extracted and normalized in CLC Genomic Workbench
Assembly: CP001340
Supplementary files format and content: comma-delimited files containing RAW, RPKM, TPM, and CPM counts for each sample.

organism: Caulobacter vibrioides

growth_protocol: CB15 cells were grown in M2X broth. Growth in M2X with 10 μM FeCl3.

extract_protocol:
Cells were harvested by centrifugation and stored at -80˚C until RNA extraction.  RNA was extracted using TRIzol (Invitrogen) as previously described
RNA-sequencing libraries were prepared utilizing the Illumina TruSeq Stranded RNA Kit and sequenced on the Illumina NextSeq 500 platform at SeqCoast Genomics (Portsmouth, NH).

treatment_protocol: Wildtype CB15, ΔcciO (CCNA_00027) and ΔcciT (CCNA_00028) (strains) were grown overnight in 2 mL of M2X medium containing the standard 10 µM Fe•EDTA chelate.  These cultures were used to inoculate 10 mL of M2X to an OD660 of 0.001, which was then incubated overnight. After the OD660 exceeded 0.1, cells were collected by centrifugation, rinsed with iron-free M2X medium, and resuspended in 10 mL of M2X medium containing 10 µM FeCl3. The suspension was adjusted to an OD660 of 0.1 before incubation at 30˚C, shaken at 200 RPM for 2.5 hours.

value: {delta}cciT


title: breast cancer single cell A162


title: breast cancer single cell A164


title: cciO replicate 1

value: {delta}cciO


title: breast cancer single cell CL3_03


title: cciT replicate 1


title: cciT replicate 3


title: breast cancer single cell CL3_01


title: cciO replicate 2


title: breast cancer single cell CL3_04


title: WT replicate 3

value: WT


title: cciO replicate 3


title: WT replicate 1


title: breast cancer single cell CL3_02

value: immortalized breast epithelial cell line


title: breast cancer single cell A161

value: untreated


title: breast cancer single cell A167

value: single-cell Hi-C


title: WT replicate 2


title: breast cancer single cell A159


title: breast cancer single cell A158


title: breast cancer single cell CL2_21


title: breast cancer single cell A160


title: breast cancer single cell CL2_19


title: Subject Z21-visit 2-Null stim

type: RNA

city: Cottingham

first: Simon

last: Hart

state: East Yorkshire

address: Castle Hill Hospital

department: Respiratory Research Group

country: United Kingdom

institute: Hull York Medical School/ University of Hull

hyb_protocol: 100 ng of the resulting RNA was then hybridised to probes from the nCounter XT autoimmune profiling panel (NS_Hs_AI_Pro_v1.1, NanoString Technologies, 770 genes involved in 35 pathways and processes), according to the manufacturer’s guidelines using an 18-hour hybridisation.

scan_protocol: Sample slides were prepared, and absolute counts generated using the nCounter FLEX analysis system.

data_processing: Data were normalized and analysed using nSolver 4.0 (NanoString®).

source_name: Sarcoidosis

extract_protocol: RNA was extracted from 2 mls sample using the RiboPure™ RNA Purification Kit, blood (Invitrogen; Thermo Fisher Scientific). Samples were spun at 800 x g for 10 minutes, the supernatant removed, and loose blood cell pellet was carried forward into the protocol and continued according to the manufacturer’s instructions. Samples were eluted from the columns into 100 µl EB. 80 µl eluted RNA was then cleaned and concentrated using RNAClean XP (Beckman Coulter); briefly, 1.8 volumes RNAClean XP solution was added to the sample, and incubated at room temperature for 10 minutes, prior to magnetic separation. The supernatant was removed, and pellet washed twice with 70 % ethanol, briefly air dried, then RNA eluted into 10 ul nuclease free water.

treatment_protocol: Blood (1ml) from patients with sarcoidosis at baseline and 1 month were drawn into tubes (TruCulture®, Myriad-RBM) containing 100 ng/ml LPS or null control (no stimulant). After stimulation for 24h at 37°C, samples were separated into supernatants (aliquoted and stored at -70°C for later cytokine analysis) and cell pellets (mixed with 3ml RNAlater® (Ambion) and stored at -70°C).

tag: disease state

value: Sarcoidosis

tag: treatment group

value: 1 month Post-treatment with azithromycin

value: whole blood


title: Subject Z21-visit 2-LPS stim


title: Subject Z17-visit 2-Null stim


title: Subject Z21-visit 1-LPS stim

value: Pre-treatment


title: breast cancer single cell CL2_18


title: breast cancer single cell A157


title: breast cancer single cell CL2_17


title: Subject Z17-visit 1-Null stim


title: breast cancer single cell A156


title: breast cancer single cell CL2_20


title: Subject Z17-visit 2-LPS stim


title: Subject Z17-visit 1-LPS stim


title: breast cancer single cell CL2_16


title: Subject Z16-visit 2-LPS stim


title: Subject Z16-visit 2-Null stim


title: breast cancer single cell CL2_15


title: breast cancer single cell A154


title: breast cancer single cell A155


title: Subject Z21-visit 1-Null stim


title: breast cancer single cell A153


title: Subject Z14-visit 2-Null stim


title: Subject Z16-visit 1-Null stim


title: Subject Z16-visit 1-LPS stim


title: breast cancer single cell CL2_14


title: breast cancer single cell A152


title: breast cancer single cell CL2_13


title: breast cancer single cell CL2_12


title: Subject Z14-visit 1-Null stim


title: Subject Z12-visit 2-Null stim


title: breast cancer single cell A150


title: Subject Z12-visit 2-LPS stim


title: Subject Z12-visit 1-Null stim


title: Subject Z14-visit 2-LPS stim


title: breast cancer single cell CL2_09


title: breast cancer single cell A149


title: breast cancer single cell CL2_10


title: breast cancer single cell A147


title: Subject Z11-visit 2-LPS stim


title: Subject Z12-visit 1-LPS stim


title: Subject Z11-visit 1-Null stim


title: Subject Z11-visit 2-Null stim


title: Subject Z10-visit 2-Null stim


title: breast cancer single cell CL2_07


title: breast cancer single cell A148


title: breast cancer single cell CL2_08


title: breast cancer single cell A151


title: Subject Z10-visit 2-LPS stim


title: Subject Z10-visit 1-LPS stim


title: breast cancer single cell A146


title: Subject Z14-visit 1-LPS stim


title: breast cancer single cell A145


title: Subject Z10-visit 1-Null stim


title: breast cancer single cell CL2_06


title: breast cancer single cell A144


title: Subject Z09-visit 2-LPS stim


title: Subject Z09-visit 2-Null stim


title: Subject Z09-visit 1-Null stim


title: breast cancer single cell CL2_11


title: Subject Z09-visit 1-LPS stim


title: Subject Z11-visit 1-LPS stim


title: breast cancer single cell A143


title: Hep2

city: Birmingham

first: Jillian

last: Richter

state: AL

address: 1900 University Blvd

department: Surgery

institute: University of Alabama at Birmingham

data_processing:
Basecalls were performed using bcl2fastq version 2.18.0.12 to create raw sequence FASTQ files
STAR (version 2.7.7a) was used to align raw sequence reads to genome using parameters --outReadsUnmapped FastX --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances from alignments were calculated using HTSeq-count (version 0.11.1) using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: GRCh38 p13 Release36
Supplementary files format and content: tab-delimited Excel file containing transcript abundances for each sample for each Ensembl ID#

source_name: lung

growth_protocol: Primary human lung microvascular ECs (HLMVEC) (S540-05a, Cell Applications, San Diego, CA, United States) were maintained in complete growth media. All experiments were performed with passage 4-6 HLMVEC.

extract_protocol:
Total RNA was isolated from cell lysate using an RNAspin mini RNA isolation kit (25-0500-72, Cytiva, Marlborough, MA, United States)
RNA libraries were developed using the NEBNext Ultra II Directional RNA-Seq library prep kit (E7760S, New England Biolabs, Inc., Ipswich, MA, United States). The resulting libraries were quantitated using the KapaBiosystems qPCR quantitation kit (MilleporeSigma, Burlington, MA, United States)

treatment_protocol: HLMVEC were conditioned under shear stress (15 dynes/cm2) for 48 hours prior to a 6-hour treatment with vehicle (PBS) or 500mU/mL heparin lyase III (P0737L, New England BioLabs, Ipswich, MA, United States).

value: lung

value: primary

value: microvascular endothelial cell

value: heparin lyase


title: C4_Ischemia 6 h + Lactate_rep4

city: Chengdu

first: Xiao-Yi

last: Xiong

address: 37 Shierqiao Road, 610075, Chengdu, China

institute: Chengdu University of Traditional Chinese Medicine

data_processing:
Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp.
full-length, non-chemiric (FLNC) transcripts were determined by  searching for primer at both ends of reads.
Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: gene expression of all sample

source_name: Ischemia 6 h + Lactate_brain tissue

extract_protocol:
Brains were removed, flash frozen on dry ice, and total RNA was  extracted using TRIzol reagent (Takara, Kyoto,  Japan) according to the manufacturer’s instructions
cDNA libraries were constructed from 1 μg of total RNA by using a cDNA-PCR Sequencing Kit (SQK-PCS109) according to the protocol.

treatment_protocol: Cerebral ischemic mice were preconditiong treated with lactate or vehicle.

value: brain

tag: age

value: 8 wks

value: cerebral ischemia

value: Lactate


title: Hep1


title: breast cancer single cell CL2_05

value: breast cancer


title: breast cancer single cell A142


title: breast cancer single cell CL2_04


title: C2_Ischemia 6 h + Lactate_rep2

tag: strain


title: C3_Ischemia 6 h + Lactate_rep3


title: breast cancer single cell A141


title: breast cancer single cell CL2_02


title: breast cancer single cell A140


title: breast cancer single cell CL1_21


title: B4_Ischemia 6 h + Veh_rep4

source_name: Ischemia 6 h + Veh_brain tissue

value: Vehicle


title: C1_Ischemia 6 h + Lactate_rep1


title: breast cancer single cell CL1_20

value: immortalized breast epithelial cell line


title: FC1

value: WT

value: untreated


title: breast cancer single cell A139

value: single-cell Hi-C


title: B3_Ischemia 6 h + Veh_rep3


title: breast cancer single cell CL1_18


title: B16F10 cell, Ozonated olive oil, 6h_1

city: Sapporo-shi

first: Seong-jin

last: An

state: Hokkaido

address: Kita 12 nishi 6, kita-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Hokkaido university

data_processing:
RNA-seq reads were preprocessed with bcl2fastq and FastQC software (v. 0.11.7) and aligned to mm10 reference genome with HISAT2 (v. 2.1.0)
StringTie algorithm (v.1.3.4d) was then used with default parameter settings to assemble RNA-Seq alignments into annotated transcripts to estimate their expression using the UCSC annotated human genome (mm10) assembly files.
Transcript expression was normalized using the transcripts per million (TPM) algorithms. For differential expression analysis, we used the R package (edgeR).
For analysis and interpretation, we used SAMtools (v.1.9), BEDTools (v.2.27.1), Seqkit (version 0.13.2), RSeQC (v.3.0.1), and Ngsplot (v.2.6.3).
Assembly: mm10
Supplementary files format and content: Text files include TPM values for each Sample

source_name: Skin

growth_protocol: B16F10 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Sigma-aldrich) contained 10% fetal bovine serum (FBS; cosmobio) at 37℃ in humidified 5% CO2/95% air atmosphere.

extract_protocol:
Total mRNA was extracted by using Tri reagent (Trizol; Sigma-aldrich) according to manufacturer's protocol
RNA libraries for RNA-seq were constructed by using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer's manual. After which library quality was further assessed using the TapeStation 4200 with High sensitivity D1000 Screen Tape (Agilent Technologies).

treatment_protocol: Cells were cultured in presence of 0.01% ozonated olive oil or olive oil for 6h.

value: Skin

value: Melanoma

value: ozonated olive oil-treated for 6h


title: B2_Ischemia 6 h + Veh_rep2


title: FC2

value: lung


title: breast cancer single cell CL1_13


title: breast cancer single cell A137


title: breast cancer single cell CL1_15


title: B1_Ischemia 6 h + Veh_rep1


title: breast cancer single cell A136


title: breast cancer single cell CL1_12


title: A4_Sham_rep 4

source_name: Sham_brain tissue

value: sham


title: Mouse, BIO300-High, TBI, Day 1_60

city: Minneapolis

first: Artur

last: Serebrenik

state: MN

address: 7760 France Ave S, Suite 920

institute: Humanetics Corporation

description:
9vs10_raw_counts.csv
9vs10_Differential_expression_analysis_table.csv

data_processing:
Following evaluation of sequencing quality and trimming of poor-quality reads using Trimmomatic v.0.36, the reads were mapped to the Mus musculus GRCm38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated using the Subread package v.1.5.2 and differential expression analysis was performed using DESeq2. A Wald test was used to determine p-values for log2 fold change in expression for pre-specified comparisons.
Assembly: GRCm38
Supplementary files format and content: CSV file with raw counts for each sample
Supplementary files format and content: CSV file with differential gene expression (fold change, statistics) for each sample

source_name: Whole Blood

extract_protocol:
Total RNA was isolated from whole blood following the manufacturer’s protocol for the PAXgene Blood RNA Kit (PreAnalytiX, Switzerland) and quantified by fluorometry using Qubit 4 fluorometer (Invitrogen, Carlsbad, CA). The quality of RNA was analyzed on a Bioanalyzer Eukaryote Total RNA Pico Chip (Agilent 2100, Agilent, CA). The average RNA Integrity Number (RIN) score across all samples was above the recommended minimum RIN of 7. Total RNA samples were stored at -80 °C until use.
RNA was shipped frozen to Genewiz, an Azenta Life Sciences company (South Plainfield, New Jersey), for library preparation, RNA sequencing, and differential gene expression analysis. Sequencing was conducted via polyA selection on an Illumina NextSeq 500.

value: Whole Blood

value: BIO 300 High Dose

tag: day

tag: animal numbers_in_group

value: Animals #55-60

tag: animal number


title: B16F10 cell, Ozonated olive oil, 6h_2

tag: cell type

tag: genotype

tag: treatment


title: A3_Sham_rep 3

value: brain

value: 8 wks


title: breast cancer single cell A135

tag: cell line


title: A2_Sham_rep 2


title: breast cancer single cell CL1_11


title: breast cancer single cell CL1_10


title: Mouse, BIO300-High, TBI, Day 1_58


title: breast cancer single cell A134


title: breast cancer single cell A133


title: breast cancer single cell CL1_09


title: Mouse, BIO300-High, TBI, Day 1_59


title: breast cancer single cell A132


title: breast cancer single cell A131


title: breast cancer single cell CL1_08


title: Mouse, BIO300-High, TBI, Day 1_57


title: breast cancer single cell A138


title: NPM1-CCDC28A-2

city: Minato-ku

first: Yuko

last: Shimosato

state: Tokyo

address: 4-6-1 Shirokanedai

department: Molecular Oncology

institute: Tokyo university

description: NPM1-CCDC28A 2

data_processing:
Pair‐end sequencing FASTQ files were aligned to the mouse reference genome (mm10) using HISAT2 30 on the Galaxy platform (https://usegalaxy.org). Raw gene counts were obtained from the read alignments using Subread 31 (v2.4.3) and converted to counts per million (CPM) by edgeR 32 (v3.32.1)
Assembly: mm10
Supplementary files format and content: tab-declimited text file including raw counts

source_name: Bone marrow

extract_protocol:
Total RNA was extracted from GFP+ cells using the RNeasy Mini kit (QIAGEN, 74004)
mRNA was purified from total RNA using poly‐T oligo‐attached magnetic beads.

value: Bone marrow


title: NPM1-CCDC28A-3

description: NPM1-CCDC28A 3


title: breast cancer single cell A130


title: Mouse, BIO300-High, TBI, Day 1_56


title: breast cancer single cell CL1_04

value: breast cancer


title: B16F10 cell, Olive oil, 6h_2

value: olive oil-treated for 6h


title: Mouse, BIO300-High, TBI, Day 1_55


title: B16F10 cell, Olive oil, 6h_1


title: Mouse, Vehicle, TBI, Day1_53

description:
3vs9_raw_counts.csv
5vs9_raw_counts.csv
9vs10_raw_counts.csv
3vs9_Differential_expression_analysis_table.csv
5vs9_Differential_expression_analysis_table.csv
9vs10_Differential_expression_analysis_table.csv

value: Vehicle

value: Animals #49-54


title: NPM1-MLF1-2

description: NPM1-MLF1 2


title: Mouse, Vehicle, TBI, Day1_52


title: breast cancer single cell A128

value: immortalized breast epithelial cell line

value: untreated


title: NPM1-CCDC28A-1

description: NPM1-CCDC28A 1


title: Mouse, Vehicle, TBI, Day1_51


title: breast cancer single cell CL1_07


title: Mouse, Vehicle, TBI, Day1_54


title: NPM1-MLF1-3

description: NPM1-MLF1 3


title: A1_Sham_rep 1

value: Sham


title: breast cancer single cell A129

value: single-cell Hi-C


title: Mouse, Vehicle, TBI, Day1_50


title: Super-enhancer 78 replicate 1

city: Chapel Hill

first: Hector

middle: L

last: Franco

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Lineberger Cancer Center

description:
HF78R1
RNA-seq

data_processing:
Merge multiple FASTQs together
Map the data with STAR 2.7.6a
Quantify the expression with Salmon 1.4.0
Perform QC by running Picard 2.22.4 CollectRnaSeqMetrics, and FastQC 0.11.9
Assembly: hg38
Supplementary files format and content: salmon_gene.matrix

growth_protocol: MDA-MB-436 TNBC cells expressing dCas9-KRAB were routinely grown and replated in T75 flasks in Dulbecco's modified eagle media supplemented with 10% fetal bovine serum and 1% pen-strep

extract_protocol:
RNA was extracted and purified from cells 48 hrs post-transfection using the Zymo RNA miniprep kit (Cat# R1054). Transfection replicates 1, 3, and 4 were used to construct RNA-seq libraries for experimental samples. Four replicates were used for positive controls (both CSF1 gene promoter and CSF1 enhancer). Three replicates were used for each of two scrambled negative controls for six total negative control replicates.
RNA-seq libraries were constructed by Novogene. 250~300 bp insert cDNA library,PolyA selected, non-strand specific

treatment_protocol: Cells were seeded into 6-well plates and transiently transfected via Fugene 6 (Promega) with unique guide RNA plasmids to target dCas9-KRAB to the region of interest.

value: Triple-negative breast cancer

value: dCas9-KRAB expressing

tag: sgrna pool_target


title: breast cancer single cell CL1_02


title: Wild type2

description: Vector 2


title: breast cancer single cell A125

tag: analysis


title: Super-enhancer 78 replicate 3

description:
HF78R3
RNA-seq


title: breast cancer single cell CL1_01

tag: tissue


title: Wild type1

description: Vector 1


title: breast cancer single cell A127


title: Positive control CSF1 gene promoter replicate 4

description:
HFG1R4
RNA-seq

value: Positive control CSF1 gene promoter


title: NPM1-MLF1-1

description: NPM1-MLF1 1


title: Negative control scramble 2 replicate 1

description:
HFN2R1
RNA-seq

value: Negative control scramble 2


title: Super-enhancer 78 replicate 4

description:
HF78R4
RNA-seq


title: Wild type3

description: Vector 3


title: D92_WTAP_ctrl

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

data_processing:
ATAC-seq results were analyzed using the ENCODE ATAC-seq pipeline
Assembly: hg38
Supplementary files format and content: ATAC-seq results were analyzed using the ENCODE ATAC-seq pipeline

source_name: Normal

extract_protocol:
Fifty thousand cells were washed with PBS and centrifuged at 350 × g for 5 min at 4 °C. Cell pellets were resuspended in 100 μl of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1 % BSA, 0.1% Tween-10, 0.1% NP40, 0.01% Digitonin, 1mM DTT, RNase inhibitor 1 U/µl). After 3 min incubation on ice chilled wash buffer was added (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1 % BSA, 0.1% Tween-10, 1 mM DTT, Rnase Inhibitor 1 U/µl)) and centrifuged at 500 g for 10 min at 4 °C. The cell pellet was resuspended in the transposase reaction mix (5 μL Tn5 transposase (Genentech) and 25 μL TAPS buffer). The transposition reaction was carried out for 30 min at 37 °C. The reaction was stopped through addition of 70 µl of Qiagen ERC buffer and purified by 1 x SPRI bead clean up.
Library fragments were amplified using NEBNext HiFi 2 x PCR master mix and 10 µM of Nextera PCR primers, using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling (for 13 – 16 cycles) at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. The libraries were purified 1 x SPRI bead clean up and were subjected to high-throughput sequencing using the Illumina HiSeq 2500 Sequencer.

value: Normal

value: monocyte-derived macrophages


title: Negative control scramble 2 replicate 3

description:
HFN2R3
RNA-seq


title: breast cancer single cell A121


title: Mouse, BIO300-High, Day1_45

description:
5vs8_raw_counts.csv
5vs8_Differential_expression_analysis_table.csv

value: Whole Blood

value: BIO 300 High Dose

value: Animals #43-48


title: Mouse, Vehicle, TBI, Day1_49


title: Negative control scramble 2 replicate 4

description:
HFN2R4
RNA-seq


title: Mouse, BIO300-High, Day1_48


title: breast cancer single cell A123


title: D92_ZC3H13_ctrl


title: breast cancer single cell A124


title: breast cancer single cell A126


title: Mouse, BIO300-High, Day1_47


title: Super-enhancer 45 replicate 4

description:
HF45R4
RNA-seq


title: breast cancer single cell A122


title: Mouse, BIO300-High, Day1_46


title: breast cancer single cell A119


title: breast cancer single cell A118


title: D92_WTAP_IFNg


title: Super-enhancer 45 replicate 1

description:
HF45R1
RNA-seq


title: Mouse, BIO300-Med, Day1_42

description:
5vs7_raw_counts.csv
5vs7_Differential_expression_analysis_table.csv

value: BIO 300 Med Dose

value: Animals #37-42


title: Mouse, BIO300-High, Day1_44


title: Super-enhancer 74 replicate 3

description:
HFFGR3
RNA-seq


title: breast cancer single cell A117


title: D92_NTC_TNF_IFNg


title: D91_WTAP_ctrl


title: D91_WTAP_IFNg


title: Mouse, BIO300-Med, Day1_41


title: breast cancer single cell A116


title: breast cancer single cell A115


title: Super-enhancer 45 replicate 3

description:
HF45R3
RNA-seq


title: D92_ZC3H13_IFNg


title: Super-enhancer 74 replicate 1

description:
HFFGR1
RNA-seq


title: breast cancer single cell A120


title: D91_ZC3H13_IFNg


title: breast cancer single cell A114


title: D92_NTC_TNF


title: Mouse, BIO300-Med, Day1_39


title: Mouse, BIO300-High, Day1_43


title: Super-enhancer 43 replicate 1

description:
HF43R1
RNA-seq


title: Super-enhancer 74 replicate 4

description:
HFFGR4
RNA-seq


title: breast cancer single cell A113


title: Mouse, BIO300-Med, Day1_38


title: Super-enhancer 43 replicate 3

description:
HF43R3
RNA-seq


title: Super-enhancer 42 replicate 4

description:
HF42R4
RNA-seq


title: breast cancer single cell A112


title: D91_NTC_TNF


title: Mouse, BIO300-Low, Day1_36

description:
5vs6_raw_counts.csv
5vs6_Differential_expression_analysis_table.csv

value: BIO 300 Low Dose

value: Animals #31-36


title: Mouse, BIO300-Med, Day1_40


title: breast cancer single cell A111

value: immortalized breast epithelial cell line


title: Super-enhancer 42 replicate 3

description:
HF42R3
RNA-seq


title: Mouse, BIO300-Low, Day1_35


title: D37_WTAP_IFNg


title: D37_WTAP_ctrl


title: Mouse, BIO300-Low, Day1_34


title: Super-enhancer 43 replicate 4

description:
HF43R4
RNA-seq


title: Super-enhancer 42 replicate 1

description:
HF42R1
RNA-seq


title: D37_ZC3H13_IFNg


title: Mouse, BIO300-Med, Day1_37


title: D37_ZC3H13_ctrl


title: breast cancer single cell A108

value: untreated


title: breast cancer single cell A109


title: Mouse, BIO300-Low, Day1_33


title: breast cancer single cell A107


title: Super-enhancer 2 replicate 4

description:
HF2R4
RNA-seq


title: Mouse, BIO300-Low, Day1_32


title: breast cancer single cell A106


title: Mouse, BIO300-Low, Day1_31


title: D91_NTC_TNF_IFNg


title: Super-enhancer 2 replicate 1

description:
HF2R1
RNA-seq


title: Super-enhancer 2 replicate 3

description:
HF2R3
RNA-seq


title: breast cancer single cell A105


title: D37_NTC_TNF


title: breast cancer single cell A110


title: D91_ZC3H13_ctrl


title: Mouse, BIO300-High, Day0_24

description:
3vs4_raw_counts.csv
3vs4_Differential_expression_analysis_table.csv

value: Animals #19-24


title: Mouse, BIO300-High, Day0_23


title: mec-7(u278); mbl-1(tm1563); uIs115, L4

city: HK

first: Chaogu

last: Zheng

address: The University of Hong Kong, Pokfulam Road

department: School of Biological Science

country: Hong Kong

institute: University of Hong Kong

data_processing:
The trimmed sequencing reads were mapped to C. elegans reference genome (WB235) using STAR (2.7.10) with the option --quantMode geneCounts. The counts were then normalized and the differentially expressed genes were then identified using the standard pipeline of DESeq2 in R.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files contain the read count generated by STAR

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: The animals were bleached to obtain eggs, which were hatched in M9 overnight. The next day, L1s were seeded onto NGM plates with OP50 bacteria and grown until L4 stage before being harvested.

extract_protocol:
The L4 animals were washed with water and the worm pellet was extracted using TRIzol reagent (Invitrogen).
The library was constructed by BGI using the standard DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing service (P_Stranded Library & PE100 Seq).

value: Whole worm

tag: developmental stage


title: mbl-1(tm1563); uIs115, L4


title: Super-enhancer 40 replicate 4

description:
HF40R4
RNA-seq

value: Triple-negative breast cancer


title: breast cancer single cell A103

value: single-cell Hi-C


title: Super-enhancer 40 replicate 3

description:
HF40R3
RNA-seq

value: dCas9-KRAB expressing


title: Mouse, BIO300-High, Day0_20


title: breast cancer single cell A104


title: Super-enhancer 87 replicate 4

description:
HFALR4
RNA-seq


title: Super-enhancer 87 replicate 3

description:
HFALR3
RNA-seq


title: breast cancer single cell A100


title: Super-enhancer 40 replicate 1

description:
HF40R1
RNA-seq


title: Mouse, BIO300-Med, Day0_12

description:
3vs2_raw_counts.csv
3vs2_Differential_expression_analysis_table.csv

value: Animals #7-12


title: Positive control CSF1 gene promoter replicate 2

description:
HFG2R3
RNA-seq

value: Positive control CSF1 gene promoter


title: Mouse, BIO300-High, Day0_21


title: mec-7(u278); uIs115, L4


title: breast cancer single cell A102


title: WT, uIs115, L4


title: D37_NTC_IFNg_TNF

value: Normal

value: monocyte-derived macrophages


title: mec-3(u184); uIs134, L4


title: mbl-1(tm1563); mec-3(unk206); uIs115, L4


title: Super-enhancer 81 replicate 4

description:
HF81R4
RNA-seq


title: breast cancer single cell A097


title: Mouse, BIO300-High, Day0_19

value: Whole Blood

value: BIO 300 High Dose


title: PCL_siSlu7_3

city: Pamplona

first: Carmen

last: Berasain

state: Navarra

address: Avda. Pio XII 55

country: Spain

institute: CIMA

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
Trimming of the reads with Trimmomatic v.0.38
Pseudoalignment against the human reference genome (GRCh38) and the quantification of the transcript abundances were performed using kallisto v.0.46.1 and Gencode v37
Sleuth v0.30.0 R package was used for the differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include transcript counts obtained with kallisto for each sample.

growth_protocol: Human hepatocellular carcinoma cell line PLC/PRF/5 was grown in DMEM (Gibco-Life Technology, Madrid, Spain) supplemented with 10% FBS, glutamine and antibiotics.

extract_protocol:
Cells transfected with siGL  or siSLU7 in triplicates were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions.
Libraries for sequencing were prepared using “ScriptSeq mRNA-Seq Library Preparation kit” (Cat. No. SS10906, Epicentre Biotechnologies) following manufacturer´s instructions.


title: breast cancer single cell A101


title: mec-3(unk206); uIs115, L4


title: mec-3(syb8382); uIs134, L4


title: breast cancer single cell A099


title: Super-enhancer 87 replicate 1

description:
HFALR1
RNA-seq


title: Mouse, BIO300-Med, Day0_8

value: BIO 300 Med Dose


title: Mouse, BIO300-Med, Day0_11


title: Super-enhancer 83 replicate 4

description:
HF83R4
RNA-seq


title: breast cancer single cell A095


title: Mouse, BIO300-High, Day0_22


title: breast cancer single cell A096


title: breast cancer single cell A098


title: Mouse, BIO300-Low, Day0_6

description:
3vs1_raw_counts.csv
3vs1_Differential_expression_analysis_table.csv

value: Animals #1-6


title: PCL_siGL_3


title: Mouse, BIO300-Med, Day0_10


title: Mouse, BIO300-Low, Day0_5

value: BIO 300 Low Dose


title: Super-enhancer 85 replicate 1

description:
HF85R1
RNA-seq


title: Super-enhancer 81 replicate 3

description:
HF81R3
RNA-seq


title: Mouse, BIO300-Low, Day0_4


title: PCL_siSlu7_2


title: Super-enhancer 85 replicate 3

description:
HF85R3
RNA-seq


title: Mouse, BIO300-Med, Day0_9


title: breast cancer single cell A091


title: Super-enhancer 85 replicate 4

description:
HF85R4
RNA-seq


title: PCL_siGL_1


title: breast cancer single cell A093


title: Mouse, BIO300-Med, Day0_7


title: Super-enhancer 81 replicate 1

description:
HF81R1
RNA-seq


title: PCL_siGL_2


title: Super-enhancer 18 replicate 3

description:
HF18R3
RNA-seq


title: Immunoprecipitated RNA, replication 1

city: London

first: Chi

last: Zhang

address: 15 Cotswold Road

department: Division of Cancer Therapeutics

institute: The Institute of Cancer Research

description: Immunoprecipitated RNA, replication 1

data_processing:
Data was processed using the protocol described in ENCODE. In addition, the resultant sequencing read alignment file was subjected to cluster identification using PureCLIP programme
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel file,listing the results for cluster calling by PureCLIP.

source_name: mammary gland

growth_protocol: T-47D (ATCC HTB-133) cells were obtained from ATCC, and maintained in RPMI-1640 medium supplemented with 10% v/v FBS (PAA), 0.2 Units/ml bovine insulin (Sigma) and 0.5% v/v pen/strep (Gibco). Cells were transduced with lentiviral inducible 3×Flag-A3B-P2A-hUGI-HA cassette, which was maintained with 1 µg/ml puromycin (Gibco

extract_protocol:
T-47D cells transduced with lentiviral inducible A3B were treated with 1 µg/mL doxycycline for 48 hours in petri dishes, followed by aspiration of culture medium and expose to 254 nm UV as previously described in a Stratalinker instrument. The cells were scraped, frozen, and submitted EclipseBio for further extraction.
eCLIP-seq experiment and analysis were performs with two biological repeats, with anti-flag M2 monoclonal antibody (Sigma). Library was constructed using ENCODE standard eCLIP protocol.

value: mammary gland

value: cell line

value: 1 ug/ml doxycycline-treated


title: breast cancer single cell A090

value: immortalized breast epithelial cell line

value: untreated


title: Size-matched input RNA, replication 2

description: Size-matched input RNA, replication 2


title: Super-enhancer 18 replicate 1

description:
HF18R1
RNA-seq

value: Triple-negative breast cancer


title: PCL_siSlu7_1


title: Mouse, BIO300-Low, Day0_3


title: Mouse, BIO300-Low, Day0_1


title: breast cancer single cell A094

value: single-cell Hi-C


title: breast cancer single cell A092


title: Immunoprecipitated RNA, replication 2

description: Immunoprecipitated RNA, replication 2


title: Mouse, BIO300-Low, Day0_2


title: breast cancer single cell A089


title: Super-enhancer 47 replicate 3

description:
HF47R3
RNA-seq

value: dCas9-KRAB expressing


title: Size-matched input RNA, replication 1

description: Size-matched input RNA, replication 1


title: breast cancer single cell A087


title: breast cancer single cell A086


title: 5W_Control_6

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

data_processing:
Sequenced reads were mapped to the mouse genome mm10 using STAR.
EdgeR was used to find the differential expression of genes at both the 8 day and 5 week time points.
Count data was transformed to CPM using EdgeR's cpm conversion, after excluding lowly filtered genes
Assembly: mm10
Supplementary files format and content: Processed datafiles contain the CPM expression values for each gene.

source_name: Retina

growth_protocol: Male C57BL/6J mice (The Jackson Laboratory) were maintained in a regular diurnal lighting cycle (12 light: 12 dark) with ad libitum access to food and water

extract_protocol:
Mice were euthanized by cervical dislocation, and eyes enucleated and immersed in RNAlater solution. Retinas were dissected rapidly in RNAlater,and stored in RNAlater solution. Lysis was performed with the TissueLyser LT (Qiagen Gmbh, Hilden, Germany) bead mill, using one steel ball at 50 Hz for 5 min on ice. For the 5-week timepoint, total RNA was extracted using the RNeasy Mini Kit (Qiagen Gmbh, Hilden, Germany) and for the 1-week timepoint it was extracted using the RNeasy Plus Mini Kit (Qiagen Gmbh, Hilden, Germany), following the manufacturer’s instructions.
500 ng of DNase I-treated total RNA was used to enrich for polyA-containing transcripts, using oligo(dT) primers bound to beads. The enriched RNA pool was fragmented and converted to cDNAs, which were ligated to sequencing adaptors containing index sequences using the Illumina TruSeq stranded mRNA sample preparation kit (Cat. #RS-122-2101, Illumina, Inc., San Diego, CA). Pools were sequenced on the Illumina HiSeq 4000 genome sequencer using 75 bp paired-end SBS chemistry.

treatment_protocol: Mice were exposed to a blast-wave in an enclosed chamber.

value: Retina

tag: Sex

value: male

value: Retinal ganglion cell

value: Control

tag: time

value: 5 weeks


title: Super-enhancer 18 replicate 4

description:
HF18R4
RNA-seq


title: Super-enhancer 47 replicate 1

description:
HF47R1
RNA-seq


title: 5W_Control_5


title: Super-enhancer 47 replicate 4

description:
HF47R4
RNA-seq


title: Mouse, Vehicle, Day1_29

description:
3vs5_raw_counts.csv
5vs6_raw_counts.csv
5vs7_raw_counts.csv
5vs8_raw_counts.csv
5vs9_raw_counts.csv
3vs5_Differential_expression_analysis_table.csv
5vs6_Differential_expression_analysis_table.csv
5vs7_Differential_expression_analysis_table.csv
5vs8_Differential_expression_analysis_table.csv
5vs9_Differential_expression_analysis_table.csv

value: Whole Blood

value: Vehicle

value: Animals #25-30


title: Mouse, Vehicle, Day1_28


title: 5W_Control_4


title: breast cancer single cell A085

data_processing:
The raw reads of scHi-C were first aligned to human HG19 genome, then filtered by HiC-Pro to get the valid pairs.
Genome_build: HG19
Supplementary_files_format_and_content: the column headers of *allValidPairs are:
read_name, chromosome of first locus, read position of first locus (currently middle of the reads), strand of first locus, chromosome of second locus, read position of second locus, strand of second locus, DNA fragment length, name of first restriction fragment, name of second restiction fragment, mapping quality of first read, mapping quality of second read, allele-specific analysis

extract_protocol:
Extraction of cell nucleus and DNA were performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).
single-cell Hi-C was performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).


title: Positive control CSF1 gene promoter replicate 3

description:
HFG1R3
RNA-seq

value: Positive control CSF1 gene promoter


title: Mouse, Vehicle, Day1_27


title: 5W_Treated_6

value: TBI


title: breast cancer single cell A084


title: Mouse, Vehicle, Day1_26


title: Super-enhancer 16 replicate 1

description:
HF16R1
RNA-seq


title: breast cancer single cell A088


title: 5W_Treated_5


title: breast cancer single cell A082


title: Mouse, Vehicle, Day1_25


title: breast cancer single cell A083


title: 5W_Treated_4


title: Super-enhancer 16 replicate 3

description:
HF16R3
RNA-seq


title: Mouse, Vehicle, Day1_30


title: 5W_Control_3


title: breast cancer single cell A081


title: Mouse, Vehicle, Day0_18

description:
3vs5_raw_counts.csv
3vs1_raw_counts.csv
3vs2_raw_counts.csv
3vs4_raw_counts.csv
3vs9_raw_counts.csv
3vs5_Differential_expression_analysis_table.csv
3vs1_Differential_expression_analysis_table.csv
3vs2_Differential_expression_analysis_table.csv
3vs4_Differential_expression_analysis_table.csv
3vs9_Differential_expression_analysis_table.csv

value: Animals #13-18


title: Super-enhancer 44 replicate 1

description:
HF44R1
RNA-seq


title: Super-enhancer 16 replicate 4

description:
HF16R4
RNA-seq


title: breast cancer single cell A080


title: Mouse, Vehicle, Day0_17


title: Mouse, Vehicle, Day0_16


title: Super-enhancer 44 replicate 4

description:
HF44R4
RNA-seq


title: 5W_Treated_2


title: breast cancer single cell A079


title: 5W_Treated_1


title: breast cancer single cell A078


title: breast cancer single cell A077


title: Positive control CSF1 enhancer replicate 2

description:
HFE2R3
RNA-seq

value: Positive control CSF1 enhancer


title: 5W_Control_2


title: 5W_Control_1


title: Mouse, Vehicle, Day0_13


title: breast cancer single cell A076

value: immortalized breast epithelial cell line


title: Super-enhancer 63 replicate 1

description:
HF63R1
RNA-seq


title: Super-enhancer 63 replicate 4

description:
HF63R4
RNA-seq


title: ChIPSeq_H3K4me3_iMEF2_KO_HOT_minus

city: Aachen

first: Ivan

middle: G.

last: Costa

state: NRW

address: Pauwelsstr. 19

department: RWTH Aachen Medical Faculty

institute: Institute for Computational Genomics

data_processing:
Illumina RTA 2.0 for basecalling
Alignment by BWA 0.7.13 with default parameters
Count table is generated by bedtools multicov
bigWig files are generated by Deeptools 3.5.0 bamCoverage
Genome_build: mm9

growth_protocol: For the generation of immoralized fibroblast cultures (iMEF) the cells were infected with a retrovirus encoding an shRNA against p19Arf and a Blasticidin resistance gene used for the initial selection of infected cells (10 µg/ml Blasticidin, Invivogen, ant-bl). MEF cells were cultivated in DMEM (ThermoFisher Scientific, 61965059) supplemented with 10% heat-inactivated fetal bovine serum (FBS, ThermoFisher Scientific, 10270106) and 1% penicillin/streptomycin (ThermoFisher Scientific, 15070063).

extract_protocol:
iMEF cells were treated with HOT or vehicle for 5 days and cross-linked with 1% formaldehyde in cell culture medium on a shaking platform for 10 min at room temperature (RT). The cross-linking reaction was quenched by adding glycine to 125 mM and incubation for another 5 min at RT. Adherent cells were washed with PBS twice and collected in PBS by scraping the cells from the dish. Cells were centrifuged at 380 x g for 5 min at 4°C and resuspended in 1 ml Lysis Buffer B (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 0.25% (v/v) Triton X-100) per 2 x 107 cells and centrifuged. To the pellet 1 ml Lysis Buffer C (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 200 mM NaCl) was added per 2 x 107 cells, followed by an incubation on ice for 10 min. After a further centrifugation step, disruption of the pelleted nuclei was performed in 200 μl lysis buffer D (50 mM Tris pH 8, 10 mM EDTA, 1% (w/v) SDS, protease inhibitor cocktail (1xPIC, Merck, P8340) per 5 x 106 MEF cells for 30 min at 15°C.  200 μl aliquots were sonicated for a minimum of 10 cycles using a Bioruptor Pico (Diagenode) with 30-second on-off-cycles to achieve DNA fragment lengths of about 800 bp or 300 bp for ChIP-qPCR or ChIP-seq, respectively. The size distribution of the resulting DNA fragments was assessed by agarose gel electrophoresis. To remove cell debris, lysates were centrifuged for 10 min at 10,000 x g (15°C), the supernatants pooled, and DNA concentrations were measured using a NanoDrop 1000 device (Peqlab). ChIP assays were performed using the OneDay ChIP Kit from Diagenode (C01010080) according to the manufacturer’s instructions. To capture protein-DNA complexes, 42 μl of Protein A beads per sample were pre-incubated in 1 x ChIP buffer for 2 hours at 4 °C with 2 μg of specific antibody or rabbit IgG (provided by the kit). The sheared chromatin (10 – 100 µg) was diluted 4.7-fold with 1 x ChIP buffer, setting aside 1/10 of the diluted chromatin for the input control, and mixed with the pre-incubated beads for 30 min at 4°C. Subsequently, the chromatin-antibody-bead complexes were washed three times with 1 x ChIP buffer and taken up in DNA purifying slurry. The diluted input control chromatin was precipitated by the addition of 5 volumes 100% ethanol and centrifuged at 16,000 x g, 4°C for 10 min. The dried pellets were resuspended in RNase-free H2O and mixed with DNA purifying slurry. The DNA of all samples was reverse crosslinked and further purified according to the manual.
The libraries were prepared using the Next Ultra II kit (New England BioLabs) and the sequencing was performed as single reads for 75 cycles with a NextSeq 500/550 High Output kit v2 (Illumina) according to the manufacturers recommendations.

treatment_protocol: At day 0 cells were treated with 5 nM 4-Hydroxytamoxifen (+HOT) (Tocris, 3412) or with vehicle (-HOT, 100% ethanol). Thereafter cells were passaged when needed to maintain subconfluency or solely supplied with new medium with the addition of HOT or vehicle as before.

tag: chip antibody

value: HOT minus


title: breast cancer single cell A075

city: San Antonio

first: Yufan

last: Zhou

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

value: untreated


title: Super-enhancer 63 replicate 3

description:
HF63R3
RNA-seq

value: Triple-negative breast cancer


title: Super-enhancer 80 replicate 1

description:
HF80R1
RNA-seq

value: dCas9-KRAB expressing


title: 8D_Control_5

value: Retina

value: 8 days


title: 8D_Control_6

value: male

value: Retinal ganglion cell


title: ChIPSeq_H3K4me3_iMEF2_KO_HOT_plus

value: HOT plus


title: Super-enhancer 44 replicate 3

description:
HF44R3
RNA-seq


title: Mouse, Vehicle, Day0_15

value: Whole Blood


title: 5W_Treated_3

value: 5 weeks


title: breast cancer single cell A073

value: single-cell Hi-C


title: ChIPSeq_H3K4me3_iMEF2_WT_HOT_minus


title: 8D_Treated_6


title: Super-enhancer 80 replicate 3

description:
HF80R3
RNA-seq


title: 8D_Control_4

value: Control


title: breast cancer single cell A072


title: Mouse, Vehicle, Day0_14

value: Vehicle


title: ChIPSeq_H3K4me3_iMEF2_WT_HOT_plus


title: Super-enhancer 80 replicate 4

description:
HF80R4
RNA-seq


title: ChIPSeq_H3K4me3_iMEF2_input


title: breast cancer single cell A071


title: Super-enhancer 6 replicate 1

description:
HF6R1
RNA-seq


title: 8D_Treated_5

value: TBI


title: breast cancer single cell A070


title: breast cancer single cell A074


title: Super-enhancer 6 replicate 3

description:
HF6R3
RNA-seq


title: ChIPSeq_H3K4me3_iMEF1_KO_HOT_plus


title: 8D_Control_2


title: 8D_Control_3


title: ChIPSeq_H3K4me3_iMEF1_KO_HOT_minus


title: breast cancer single cell A069


title: Negative control scramble 1 replicate 4

description:
HFN1R4
RNA-seq

value: Negative control scramble 1


title: Super-enhancer 6 replicate 4

description:
HF6R4
RNA-seq


title: 8D_Treated_4


title: Negative control scramble 1 replicate 3

description:
HFN1R3
RNA-seq


title: ChIPSeq_H3K4me3_iMEF1_WT_HOT_plus


title: 8D_Treated_3


title: breast cancer single cell A067

value: immortalized breast epithelial cell line


title: ChIPSeq_H3K4me3_iMEF1_input


title: Negative control scramble 1 replicate 1

description:
HFN1R1
RNA-seq


title: ChIPSeq_H3K4me1_iMEF2_KO_HOT_minus

value: HOT minus


title: 8D_Control_1


title: 8D_Treated_2


title: Super-enhancer 71 replicate 1

description:
HF71R1
RNA-seq


title: ChIPSeq_H3K4me1_iMEF2_KO_HOT_plus


title: 8D_Treated_1


title: ChIPSeq_H3K4me1_iMEF2_WT_HOT_minus


title: Super-enhancer 71 replicate 3

description:
HF71R3
RNA-seq


title: breast cancer single cell A064

value: untreated


title: Super-enhancer 71 replicate 4

description:
HF71R4
RNA-seq

value: Triple-negative breast cancer


title: ChIPSeq_H3K4me1_iMEF2_WT_HOT_plus


title: db4 MeRIP-m6A

city: Shanghai

first: Yunchen

last: Luo

address: shanghai hongkou

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10) by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts.
Assembly: MM10
Supplementary files format and content: Methylated_RNA_sites.mRNA.xlsx: methylation sites and enrichment information of all samples.
Library strategy: MeRIP-m6A

source_name: liver

growth_protocol: All mice were raised under Specific Pathogen Free conditions with a 12-hour dark/light cycle, 20–22 °C and 45–65% humidity with water and food provided ad libitum.

extract_protocol:
Total RNAs were obtained from db/db mice and lean control mice using TRIzol reagent (catalog T9108, Takara) according to the manufacturer's protocol.
Fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.

value: liver

value: db/db


title: breast cancer single cell A068


title: db4 Input

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10) by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts.
Assembly: MM10
Supplementary files format and content: Methylated_RNA_sites.mRNA.xlsx: methylation sites and enrichment information of all samples.


title: ChIPSeq_H3K4me3_iMEF1_WT_HOT_minus


title: Super-enhancer 69 replicate 4

description:
HF69R4
RNA-seq

value: dCas9-KRAB expressing


title: breast cancer single cell A061


title: breast cancer single cell A063


title: breast cancer single cell A062


title: Super-enhancer 69 replicate 3

description:
HF69R3
RNA-seq


title: db3 Input

value: male


title: breast cancer single cell A060


title: db3 MeRIP-m6A


title: Super-enhancer 69 replicate 1

description:
HF69R1
RNA-seq


title: ChIPSeq_H3K4me1_iMEF1_KO_HOT_minus


title: breast cancer single cell A066


title: breast cancer single cell A065


title: breast cancer single cell A059


title: db2 Input


title: ChIPSeq_H3K4me1_iMEF2_input


title: Super-enhancer 9 replicate 3

description:
HF9R3
RNA-seq


title: ChIPSeq_H3K4me1_iMEF1_WT_HOT_minus


title: db2 MeRIP-m6A


title: Super-enhancer 9 replicate 1

description:
HF9R1
RNA-seq


title: ChIPSeq_H3K4me1_iMEF1_KO_HOT_plus


title: breast cancer single cell A058


title: ChIPSeq_H3K4me1_iMEF1_WT_HOT_plus


title: breast cancer single cell A057


title: db1 Input


title: Positive control CSF1 gene promoter replicate 1

description:
HFG1R1
RNA-seq

value: Positive control CSF1 gene promoter


title: ChIPSeq_H3K4me1_iMEF1_input


title: breast cancer single cell A055


title: db1 MeRIP-m6A


title: Super-enhancer 9 replicate 4

description:
HF9R4
RNA-seq


title: Super-enhancer 66 replicate 4

description:
HF66R4
RNA-seq