title: ATAC_CRISPR_i_sgHIV_1G2_Rep1

value: Jurkat Cm6


title: HMDM_Donor-3_LPS+NAM

status: Public on May 01 2023

type: RNA

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

country: USA

institute: nih

hyb_protocol: Protocols were followed for the GeneChip hybridization Wash and Stain kit (ThermoFisher #900720)

scan_protocol: GeneChip Scanner 3000 7G with a carousel, two Fluidics Station 450, one Hybridization Oven 640, and a computer workstation with dual Xeon processors loaded with Affymetrix GeneChip Command Console (AGCC) and GTYPE

data_processing:
Microarray signal intensity values were assessed using ThermoFisher Transcriptome Analysis Console (Version 4.0.1.36) and they were normalized and log2 transformed using the Robust Multiarray Average (RMA) method. Probe set IDs were annotated using PrimeView Human Gene Expression Array annotation file version 36 (release date 03/30/16).
Data are log2 transformed using the Robust Multiarray Average (RMA) method

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human elutriated monocytes Donor 3

label_protocol: Biotin-labeled cRNA was generated with the GeneChip 3” IVT Plus Reagent kit (ThermoFisher  #902416)

growth_protocol: Human elutriated monocytes from 4 male donors were differentiated 6 days with 30ng/ml macrophage colony-stimulating factor (M-CSF) in IMDM (Iscove's Modified Dulbecco's Medium) supplemented with 10% heat-inactivated fetal bovine serum (media). Human monocyte-derived macrophages (HMDMs) were lifted by treating with 0.25% trypsin (0.5mL) for 3m, quenching with 0.5mL media and scraping with a cell scraper. HMDMs were resuspended at 1x10^6 cells/2mL media in 6-well plates and allowed to adhere 24h.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) with processing through QIAshredder columns (Qiagen)

treatment_protocol: HMDMs were treated with vehicle control (media), 10ng/ml lipopolysaccharide (LPS), or 10mM nicotinamide (NAM) for 4h.

tag: subject id

value: Donor 3

tag: gender

value: Male

tag: age

value: 54 years old

tag: cell type

value: human monocyte-derived macrophages (HMDMs)

tag: treatment

value: LPS+NAM


title: valvular interstitial cells OIM induced calcification rep1 [OIM_1]

type: SRA

city: shanghai

first: YUAN

last: GAO

address: No. 168, Changhai Road, Yangpu District, Shanghai

department: Cardiovascular surgery

country: China

institute: Changhai Hospital

library_source: transcriptomic

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences.
In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered.
Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
Using hisat2  to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Using the Stringtie software to assemble the reads, the new transcript was spliced. Then the candidate lncRNA transcripts were selected by comparing the gene annotation information of the reference sequence produced by Cuffcompare  software. Finally, transcripts with coding potential were screened out by CPC , CNCI , Pfam and PLEK to obtain lncRNA predicted sequences.
Assembly: sscrofa11.1
Supplementary files format and content: tab-delimited text files include counts values for each Sample

organism: Sus scrofa

source_name: aortic valve

growth_protocol: Porcine aortic VICs were harvested and isolated from pigs aged 4–5 months (Wufeng, Shanghai). The porcine hearts were collected in an icebox after sacrifice and immediately taken back to the laboratory. Aortic valve leaflets were cut and immersed in precooled phosphate- buffered saline (PBS) solution. The valve leaflets were digested in 2 mg/mL type II collagenase for 15 min and the valve endothelial cells on the surface were gently scraped off with a sterile cotton swab. The valve leaflets were cut into pieces and then digested in type II collagenase for another 2 hours. Undigested tissue was removed by a filtrating screen. The harvested VICs were collected by centrifugation and then seeded on culture dish in DMEM containing 10% fetal bovine serum, and the medium was changed every 2–3 days.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.
Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 ) and 150 bp/125bp paired-end reads were generated

treatment_protocol: The porcine valvular interstitial cells (PVIC) as the model. We used OIM differentiation medium containing 2 mmol/L sodium dihydrogen phosphate, 50 µg/mL ascorbic acid, and 10−7mol/L insulin to induce calcification as well as bFGF  (50 ng/ml, peprotech) treatment to inhibit the calcification for 3 days.

tag: tissue

value: aortic valve

value: valvular interstitial cell

tag: genotype

value: wild type

value: OIM induce calcification for three days


title: 58491

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
ChIP-Seq:  Reads were aligned against the Mus musculus genome version of July 2007 (NCBI37/mm9) with the Bowtie program version 0.12.5. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously.
total RNA-Seq: Reads were aligned with STAR version 2.4.2 to the Mus musculus genome version of July 2007 (NCBI37/mm9). Read coverages were calculated with the BEDTool program, were normalized to reads per millions (RPM) using the SAMTools as well as the KentTools.
Assembly: mm9 (total RNA-Seq, RNA-Seq,ChIP-Seq), mm10 (VDJ-Seq)
Supplementary files format and content: tab-delimited text files include RPM values for each VDJ-Seq sample and TPM values for RNA-Seq samples. bigWig files include read coverage for total RNA-Seq and ChIP-Seq samples.

molecule: polyA RNA

organism: Mus musculus

source_name: mRNA-Seq IgMb immature B cell Igh(P4V/P4V)

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit

value: bone marrow

tag: chip antibody

value: IgMb immature B cell

value: Ex-vivo FACS sorted from bone marrow


title: Control_A2Cdh5_Cre

city: Boston

first: Thomas

last: Michel

state: MA

address: 75 Francis Street

institute: BWH/HMS

data_processing:
Reads (Fastq files) obtained from paired-end sequencing were aligned were to the mouse genome (GRCm38 - mm10) using hisat2(v2.0.5)
Quality control was performed on raw reads and alignment results using fastQC and Qualimap, respectively. Sample clustering was visualized using principal component analysis.
Differential expression analysis was performed using DESeq2 (v1.20.0) using standard parameters, comparing DAAO mouse with their controls
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: DRGs

extract_protocol:
DRGs were removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA quantification and sample integrity were then analyzed using a Nanodrop spectrophotometer and an Agilent 2100 bioanalyzer, respectively.
Library preparation and sequencing were performed by Novogene (Sacramento, CA) using an Illumina Platform PE150.

tag: strain

value: DRGs

value: D-Alanine


title: 2881-6-liverWT  rep2

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
Quality control checks on raw sequencing reads using FastQC (0.11.5)
Sequence reads were trimmed for adaptor sequence using Trim Galore (0.6.5)
alignment and gene count by STAR (2.6.0b)
gene annotation using GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (4.0.2) using Bioconductor package DESeq2
Assembly: GRCm38
Supplementary files format and content: gene raw count matrix
Supplementary files format and content: tab-delimited text file

source_name: embryonic liver

extract_protocol:
Embryonic livers, lungs and brains were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: embryonic liver

value: WT


title: valvular interstitial cells rep2 [NC_2]

value: DMEM cultivation for three days


title: 58489

source_name: mRNA-Seq IgMb immature B cell Igh(_delta_890/+)


title: Control_A1Cdh5_Cre


title: 58490


title: ATAC_8B10_Rep3

city: New Haven

first: Ya-Chi

last: Ho

state: Connecticut

address: 295 Congress Avenue,BCMM 354E

institute: Yale University

library_source: genomic

data_processing:
Raw reads were timmed of the Nextera adpter using cutadapt (version 3.5), mapped using Bowtie2 (version 2.4.4), and used to call peaks with Genrich (version 0.6.1) with options -j -y -r -e chrM -v.
Peaks from all samples were appended, sorted, and merged with bedtools (verison 2.30.0).
DeepTools (version 3.5.1) was used to make bigwig files with bamCoverage (options --binSize 10 --normalizeUsing CPM --ignoreDuplicates)
Assembly: Hg38 + NL4-3
Supplementary files format and content: .bw, bigwig files of genome tracks for ATAC-seq signal from a given sample, resolution of 10bp

molecule: genomic DNA

source_name: Blood

growth_protocol: Jurkat T cells were grown in R10 (RPMI + 10% FBS) at high viability, passaged 1:10 twice weekly.

extract_protocol:
DNA was isolated using a MinElute PCR cleanup kit (Qiagen #28004) and eluted in 10 L twice. The resulting
The resulting DNA was amplified using NEBNext ULTRA II Q5 master mix (New England Biolabs #M0544X) and Nextera indexing primers for 72°C for 5 minutes, then 98°C for 1 minute, followed by 5 cycles of 98°C for 15 seconds, 63°C for 30 seconds, and 72°C for 1 minute, with a final extension at 72°C for 5 minutes. Additional cycles were added based on qPCR measurements of library amplification for a total of 8–20 cycles per library.

treatment_protocol: cells were lysed on ice for 3 minutes in 50 L ATAC-lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% NP40, 0.01% digitonin) before the addition of 1mL of ATAC-wash buffer (10 mM Tris-HCl pH 7.4, 10  mM NaCl, 3 mM MgCl2, 0.1% Tween-20). Cells were pelleted at 4°C and then transposed with ATAC-transposition mix (1X TD buffer with 33% PBS, 0.1% Tween-20, 0.01% digitonin, 2.5 L TDE1) at 37°C for 30 minutes.

value: Blood

tag: cell line

value: Jurkat Cm6

value: CD4 T cell lymphoma


title: 58488


title: ATAC_8B10_Rep2


title: ESC, Usp28 KO, rep2

city: Chongqing, China

first: jiangjun

last: wang

address: Chongqing, China

department: Depart of Histology and Embryology

institute: Cell Biology Department

description: Usp28 KO ESCs cultured in 2i/LIF medium

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2.
featureCount software was used to calculate gene expression from aligned bam files
R statistical package DESeq2 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: raw reads counts

growth_protocol: Mouse ESCs were cultured on 0.2% gelatin-coated plates in the indicated medium. 2i/LIF culture:  N2B27 medium was supplemented with 1 μM  PD0325901, 3 μM CHIR99021 (Selleck), and 10 ng/ml LIF

extract_protocol:
Total RNA was extracted from the cells using TRIzol Reagent according the manufacturer’s instructions(Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.
RNA-seq transcriptome libraries were prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA), using 1μg of total RNA. Shortly, messenger RNA was isolated with polyA selection by oligo(dT) beads and fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol.

treatment_protocol: Mouse ESCs were cultured on 0.2% gelatin-coated plates in the 2i/LIF medium.

value: embryonic stem cells

value: Usp28 KO


title: ATAC_8B10_Rep1


title: ESC, Usp28 KO, rep1

description: Usp28 KO ESCs cultured in 2i/LIF medium


title: ESC, CTL, rep2

description: Control ESCs cultured in 2i/LIF medium


title: Wildtype liver, scRNAseq

city: Cincinnati

first: Yunguan

last: Wang

state: oh

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
10x scRNA-seq data was preprocessed using the Cell Ranger software (5.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: HDF5 format matrix files

source_name: Perfused liver

extract_protocol:
Primary hepatocytes were isolated by the 2-step collagenase perfusion through the inferior vena cava. Mice were perfused with Liver Perfusion Medium (Gibco #17701038) followed by Liver Digest Medium (Gibco #17703034). The liver cell suspension was filtered through a 70 μM strainer. Equal amounts of Hepatocyte Wash Medium (Gibco #17704024) was added to the liver cell suspension and centrifuged at 50 g for 5 minutes to collect hepatocytes. After washes, primary hepatocytes were resuspended in GBSS (Sigma Aldrich #G9779) with 0.7% CHAPS  (Sigma Aldrich #C5070) and 0.2U/μL RNase inhibitor (Roche Diagnostics #3335399001), and kept on ice for 5 min. The samples were centrifuged at 500g for 5 minutes and further washed twice using PBS with 1% BSA and 0.2U/μL RNase inhibitor. The nuclear extraction efficiency was determined with trypan blue under a microscope. The isolated nuclei were resuspended in the wash buffer to around 1x106 nuclei/mL.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: hepatocytes

value: Perfused liver

value: 8 weeks old

value: ad libitum feeding


title: Fasted liver, scRNAseq

description: 10x Genomics

value: fasting 24 hours


title: Lung KP CD45+MHCII-CD4+ (CD4 T cell) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

city: New York

first: Dana

last: Pe'er

state: NY

address: 417 E 68th St

department: Computational and Systems Biology

institute: Memorial Sloan Kettering Cancer Center

description: project 08233

data_processing:
Cell by gene count matrices were constructed using the Sequence Quality Control (SEQC) package (Azizi Cell 2018).
The cell barcodes are contained in the dense.csv files. It is the      first column (which is followed by CLUSTER and then genes). The      cell barcodes are stored as numerals instead of basepair sequence for      legacy and memory issues, and is hard-wired in the pre-processing software      we use (SEQC: https://github.com/dpeerlab/seqc). However, to make the cell      barcodes accessible in basepair sequence format, we have provided a Python      code that converts the cell barcodes from numerals to basepair sequences.
Assembly: GRCm38
Supplementary files format and content: csv files

source_name: lung

extract_protocol:
For isolation of immune and stromal cells, lungs were perfused, placed into 5 ml Eppendorf tubes containing 400ml of cold serum-free RPMI and chopped with scissors (1-2 mm). Lung fragments were placed in 2-3 ml of pre-warmed digestion medium (RPMI 1640, 10 mM HEPES buffer, 1% penicillin–streptomycin, 1% L-glutamine, liberase (Sigma-Aldrich #05401020001) and 1 U/ml DNase I (Sigma-Aldrich #10104159001)) (2-3 ml) and incubated for 30 min at 37°C. After digestion supernatant was collected and cells were resuspended in ice-cold RPMI1640 containing 5% FCS (ThermoFisher #35010CV), 1mM HEPES (Corning #MT25060CI), 1% penicillin–streptomycin (Corning #MT30002CI) and 200mM L-glutamine (Corning #MT25005CI). After additional digestion for 1 hr of the remaining tissue, both digested cell fractions passed through a 100um strainer (Corning #07-201-432), washed and FACS sorted.
Bulk RNA seq - Cell populations were sorted straight into Trizol (ThermoFisher #15596018), RNA was precipitated with isopropanol and linear acrylamide, washed with 75% ethanol, and resuspended in RNase-free water. After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.4-2.0ng total RNA with RNA integrity numbers ranging from 1.0 to 9.9 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech #63488), with 12 cycles of amplification. Subsequently, 1.5-10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems #KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or HiSeq 2500 in Rapid Mode in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit or HiSeq Rapid SBS Kit v2 (Illumina).  An average of 32 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 62% to 88%. scRNAseq- Single-cell RNA-Seq was performed on FACS sorted mouse lung KP cells or patient LuAd samples, on the Chromium instrument (10X genomics) following the user guide manual (CG00052 Rev E) for 3′ v2 and v3 as previously described46.  Briefly, sorted cells were washed once with PBS containing 0.04% bovine serum albumin (BSA) and resuspended in PBS containing 0.04% BSA to a final concentration of 700–1,200 cells per μl. Viability of cells was confirmed to be above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Then samples were encapsulated in microfluidic droplets at a dilution of ∼70 cells/μl (doublet rate ∼3.9%.). Encapsulated cells were subjected to reverse transcription (RT) reaction at 53°C for 60 min. After RT, the emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads MyOne SILANE, followed by 14-cycles of PCR-amplification (98°C for 180 s; [98°C for 15 s, 67°C for 20 s, 72°C for 60 s] x 12-cycles; 72°C for 60 s). 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, the DNA library was ligated to the sequencing adaptor followed by indexing PCR (98°C for 45 s; [98°C for 20 s, 54°C for 30 s, 72°C for 20 s] x 10 cycles; 72°C for 60 s). An average of 5,000 cells were targeted for each tumor sample. The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NovaSeq platform (R1 – 26 cycles (KP) 28 cycles (LuAd), i7 – 8 cycles, R2 – 96 cycles (KP), 90 cycles (LuAd)) resulting in 184.5-186.1 million reads per sample (average reads per single-cell being 42,000 and average reads per transcript 4.40-7.14) (KP)
Bulk RNA seq, scRNA-seq

value: CD4 T cell

value: lung

value: 21-25 weeks


title: ESC, CTL, rep1

description: Control ESCs cultured in 2i/LIF medium


title: ATAC_5F9_Rep2


title: Lung KP CD45+MHCII-CD4+ (CD4 T cell) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08233


title: ATAC_5F9_Rep1


title: Lung KP CD45+MHCII-CD4+ (CD4 T cell) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08233


title: TFR cells, HDM-4

city: Indianapolis

first: Qiang

last: Chen

state: IN

address: 332/333 RESEARCH II, 950 W Walnut Street

department: Microbiology and Immunology

institute: Indiana University School of Medicine

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats (from ngsutilsj v.0.4.17). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -p –countReadPairs -Q 10”.
The data were normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.38.4) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: Excel table including fold change, log2 fold change, p-values, FDR, log2CPM, and raw counts

source_name: mediastinal lymph nodes

extract_protocol:
Total RNA isolated using RNeasy Plus Micro Kit
Total RNA samples were first evaluated for their quantity and quality using Agilent Bioanalyzer 2100. All samples had good quality with RIN (RNA Integrity Number) greater than 9. One nanograms of total RNA was used for library preparation with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Mountain View, CA) following the manufacturer’s protocol. Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and Agilent TapeStation, and multiple libraries were pooled in equal molarity. The pooled libraries were sequenced with 2×100bp paired-end configuration on an Illumina NovaSeq 6000 sequencer using the v1.5 reagent kit.

treatment_protocol: PCT group: Mice were sensitized with peanut plus cholera toxin (i.g.) at day 1 and day 8, then TFR cells were sorted from mesenteric lymph node.  HDM group: Mice were treated with house dust mite (i.n.) for two weeks (every two days), then TFR cells were sorted  from mediastinal lymph node.  Naive group: As control, TFR cells were sorted from spleen of naive mice.

value: mediastinal lymph nodes

value: TFR cells

value: HDM


title: ATAC_Jurkat_Rep1


title: ipRGC, P1, rep192

city: Baltimore

first: Alex

last: Kolodkin

state: Maryland

address: 725 N Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

description:
SmartSeq2
P1_191

data_processing:
FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 version 2.1.0.
The resulting SAM files were converted to BAM files using SAMtools version 1.9.
Transcript abundance was estimated using Cuffquant and normalization was performed using Cuffnorm in Cufflinks version 2.2.1.
All analyses were performed using Seurat in R version 3.6.2.
Assembly: mm10
Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell
Supplementary files format and content: Cuffnorm matrix containing annotations for each gene
Supplementary files format and content: Cuffnorm matrix containing annotations for each sample

source_name: Retina

extract_protocol:
Retinas were dissected in cold Hibernate A medium lacking Ca2+, Mg2+, and phenol red (BrainBits). Retinas were then dissociated in papain (Worthington Biochemical, LS003126), 5.5 mM Cysteine-HCl, and 1.1 mM EDTA dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) for seven minutes at 37°C. Cell suspension was passed through a 40 μm cell strainer (Falcon, 352340) and incubated for 30 minutes on ice with Brilliant Violet (BV)-421 anti-mouse CD90.2 antibody (BioLegend, 105341, 1:300), which binds to RGCs and provides an additional selection marker during FACS. The cells were then centrifuged and resuspended in 0.4% bovine serum albumin dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red). Cells were again centrifuged and resuspended in 2000 U/ml DNase I (New England Biolabs, M0303S) in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) prior to cell sorting. Individual GFP+, BV-421+ cells were sorted into a lysis solution consisting of 3500 U/ml RNase inhibitor (New England Biolabs, M0314S), 140 U/ml DNase I, and 0.17% v/v Triton X-100 in water using a MoFlo Legacy cell sorter (Beckman Coulter).
Single-cell DNA libraries were prepared according to the Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014) and sequenced using an Illumina NextSeq 500 sequencer (75 bp paired-end reads, 400 million total reads).

value: Retina

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: TFR cells, HDM-3


title: ipRGC, P1, rep191

description:
SmartSeq2
P1_190


title: valvular interstitial cells rep1 [NC_1]

value: aortic valve

value: valvular interstitial cell

value: wild type

value: DMEM cultivation for three days


title: Lung KP CD45+MHCII-CD4+ (CD4 T cell) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08233


title: ATAC_1G2_Rep1

value: Blood

value: Jurkat Cm6

value: CD4 T cell lymphoma


title: Lung KP CD45+MHCII-CD4+ (CD4 T cell) control (PBS 48 hr) sample #4 bulk RNAseq

description: project 08233


title: ipRGC, P1, rep189

description:
SmartSeq2
P1_188


title: TFR cells, HDM-2


title: ATAC_1G2_Rep2


title: ATAC_1D7_Rep3


title: ipRGC, P1, rep188

description:
SmartSeq2
P1_187


title: Lung KP CD45+MHCII-CD4+ (CD4 T cell) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08233


title: TFR cells, HDM-1


title: Lung KP CD45+MHCII-CD4+ (CD4 T cell) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08233


title: ATAC_1D7_Rep2


title: ipRGC, P1, rep187

description:
SmartSeq2
P1_186


title: ipRGC, P1, rep186

description:
SmartSeq2
P1_185


title: ATAC_1D7_Rep1


title: TFR cells, PCT-3

source_name: mesenteric lymph nodes

value: mesenteric lymph nodes

value: PCT


title: ipRGC, P1, rep185

description:
SmartSeq2
P1_184


title: Lung KP CD45+MHCII-CD8+ (CD8 T cell) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08233

value: CD8 T cell

value: lung


title: Lung KP CD45+MHCII-CD8+ (CD8 T cell) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08233

value: 21-25 weeks


title: TFR cells, PCT-2

value: TFR cells


title: Lung KP CD45+MHCII-CD8+ (CD8 T cell) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08233


title: 4C_Jurkat_Rep1

data_processing:
Reads were trimmed using Cutadatp (Version 3.5) in paired end mode to remove primer sequences from the 5’ end of reads associated with the target window (Read 1 – NTTCTCTCTCAGGGTCATCCATTCCATG, Read 2 – GAGGGGCGGCGACTGGTGAGTACGCCAAAAATT) and filtered to select only reads with the correct primer sequence using the cutadapt option “--discard-untrimmed”.
Trimmed reads were mapped using Bowtie2 (Version 2.4.4)
Fragement coverage was  quatified across samples using bedtools (version 2.30.0), resuling count file was filtered to remove any row with 0 fragments across all samples.
Bigwig files were generated using DeepTools bamCoverate (version 3.5.1), bin size 10 and otherwise default parameters
Assembly: Hg38 + NL4-3
Supplementary files format and content: 4C_counts.csv - bed file followed by results of bedtools coverage for each sample, .bw - bigwig files of genome tracks for given sample
Library strategy: 4C-Seq

extract_protocol:
DNA was isolated by ehtnol precipitation (1.4mL of 3M sodium acetate and 36mL 100% ethanol were added to 14 mL ligation mixture, frozen at -20 for 4 hours, spun at max speed, wahed twice with 80% ethanol, dired and then resuspended in TE).
1ug of DNA was used to make 8 PCR reactions with NEBNEXT Ultra II Q5 Master Mix and primers targetting the HIV-1 LTR with appended Nextera adapters, program of 98°C for 2 minutes, followed by 30 cycles for 98°C for 10 seconds, 68°C for 30 seconds, 72°C for 1 minute, reducing the annealing temperature by 1°C per cycle until 63°C was reached, with a final extension time of 5 minutes at 72°C. Rections were pooled and then barcoded.

treatment_protocol: Cells were fixed in 2% EM grade PFA for 10 minutes at room temperature with shaking, quenced with 2M glycine to a final concentration of 0.125M, lysed in HiC lysis buffer on ice for 30 minutes, washed twice with HiC lysis buffer, resuspended in an SDS containing buffer. Remaining nuclei were treate with NLAIII restriction digest over night, followed by ligation at room temperature. Nuclei then underwet reverse crosslinking with protinase K at 55C for one hour with 500 rpm shaking, them incubated at 68C overnight. DNA was then phenol-chloroform extracted and and ethanol precipitated before being digested with MluC1 for 4 hours, followed by fresh restriction enzyme and overnight incubation. DNA was then ethnol precipitate and then ligated in dlute conditions to produce circular DNA.


title: ipRGC, P1, rep190

description:
SmartSeq2
P1_189


title: 4C_8B10_Rep2


title: ipRGC, P1, rep183

description:
SmartSeq2
P1_182


title: Lung KP CD45+MHCII-CD8+ (CD8 T cell) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08233


title: TFR cells, PCT-1


title: ipRGC, P1, rep182

description:
SmartSeq2
P1_181


title: Lung KP CD45+MHCII-CD8+ (CD8 T cell) control (PBS 48 hr) sample #4 bulk RNAseq

description: project 08233


title: ipRGC, P1, rep184

description:
SmartSeq2
P1_183


title: TFR cells, Naïve-4

value: Naïve, no treatment


title: 4C_8B10_Rep1


title: ATAC_CRISPR_i_sgHIV_1D7_Rep1


title: TFR cells, PCT-4


title: TFR cells, Naïve-2


title: Lung KP CD45+MHCII-CD8+ (CD8 T cell) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08233


title: 4C_5F9_Rep2


title: ipRGC, P1, rep180

description:
SmartSeq2
P1_179

value: Retina


title: 4C_Jurkat_Rep2


title: Lung KP CD31+GP38- (Vascular endothelial) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08233

value: Vascular endothelial


title: TFR cells, Naïve-1


title: 4C_1G2_Rep2


title: ipRGC, P1, rep179

description:
SmartSeq2
P1_178

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: Lung KP CD31+GP38- (Vascular endothelial)DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08233


title: 4C_1G2_Rep1


title: ipRGC, P1, rep178

description:
SmartSeq2
P1_177


title: PU1+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer KO, Rep2

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

data_processing:
FASTQ files were mapped to the mouse mm10 genome using Bowtie2 with default parameters (Langmead and Salzberg, 2012). After mapping, tag directories were created using the HOMER command makeTagDirectory (Heinz et la., 2010). To quantify the TF binding and chromatin accessibility between conditions, raw and normalized tag counts at merged IDR peaks identified by HOMER’s mergePeaks were identified using HOMER’s annotatePeaks with “-noadj,” “-size 500” for TF ChIP-seq peaks and “-size 1000” for ATAC peaks annotated with H3K27ac reads. DESeq2 was used to identify differentially bound TF binding distal sites or differential distal chromatin accessibility (p-adj. < 0.05 and FC >2 or <-2).  Super-enhancers were defined using the HOMER ‘findPeaks -style super’ command.
Supplementary files format and content: Tab delimited text file containing IDR peaks for P300, SALL1 and SMAD4
Supplementary files format and content: Tab delimited text file containing Microglia H3K27ac peaks centered on ATAC peaks
Supplementary files format and content: Tab delimited text file containing peak files for H3K27ac for NeuN, PU1, and Olig2 nuclei

source_name: Brain

extract_protocol:
Mouse brains were homogenized as previously described (Gosselin et al. 2014)  by gentle mechanical dissociation. Cells were then incubated in staining buffer on ice with anti-CD16/32 blocking antibody (BioLegend 101319) for 15 minutes, and then with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006) for 25 minutes. Cell preparations for H3K27ac ChIP-seq were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for 5 minutes after staining, and subsequently washed three times. Cells were washed once and filtered through a 40 M cell strainer. Sorting was performed on a Sony MA900 or MoFlo Astrios EQ cell sorter. Microglia were defined as events that were DAPI negative, singlets, and CD11b+CD45lowCX3CR1+. Sorted microglia were pelleted at 800xg for 5 minutes, pellets were then snap frozen and stored at -80°C prior to library preparation. Brain nuclei were isolated as previously described (Nott et al., 2019), with initial homogenization performed with either 1% formaldehyde in Dulbecco’s phosphate buffered saline or 2mM DSG (Proteochem) in Dulbecco’s phosphate buffered saline. Nuclei were stained overnight with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099) or SALL1 AF647 (Thermo, clone NRNSTNX 51-9279-82) or NEUN-AF488 (Millipore MAB 377X). Nuclei were washed the following day with 4 mL FACs buffer, passed through a 40 uM strainer, and stained with 0.5 ug/mL DAPI. Nuclei for each cell type were sorted with a Beckman Coulter MoFlo Astrio EQ cell sorter and pelleted at 1600xg for 5 minutes at 4°C in FACs buffer. Nuclei pellets were snap frozen and stored at -80°C prior to library preparation.
Chromatin immunoprecipitation was performed as previously described (Heinz et al., 2018). For H3K27ac ChIP, 500,000-1,000,000 fixed sorted cells or nuclei were thawed on ice and resuspended in ice-cold LB3 (10mM Tris-HCl pH 7.5, 100mM NaCl, 1 mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine), 1x protease inhibitor cocktail (Sigma). Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microtube Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles with the following setting: time 60 seconds, duty cycle 5.0, PIP 175, cycles, 200, amplitude 0.0, velocity 0.0, dwell 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The supernatant was then diluted 1.1-fold with ice-cold 10% Triton X-100. One percent of the lysate was kept as ChIP input. 25 uL of Dynabeads Protein A were added per sample, in addition to 1ug of a specific antibody for H3K27ac (Active Motif 39685). The samples were rotated overnight at 4°C and were washed as follows the next day: 3x with Wash Buffer I (20mM Tris-HCl pH 7.5, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100) + protease inhibitor cocktail, 3x with Wash Buffer III (10mM Tris-HCl pH 7.5, 250 mM LiCl, 1% Triton X-100, 1mM EDTA, 0.7% Sodium Deoxycholate)+ protease inhibitor cocktail, 2x with TET (0.2% Tween-20/TE) + 1/3 protease inhibitor cocktail, 1x with TE-NaCl (50mM NaCl + TE), and 1x with IDTET (0.2% Tween-20, 10mM Tris pH8, 0,1mM EDTA). Samples were finally resuspended in TT buffer (10mM Tris pH 8 + 0.05% Tween 20) prior to on-bead library preparation. For SALL1, SMAD4, and P300 ChIPs, 500,0000-2million nuclei were thawed on ice and resuspended in ice-cold RLNR1 buffer (20mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 1% NP-40, 0,1% SDS, 0.5mM DTT) + 1x protease inhibitor cocktail/PMSF. Samples were sonicated in a 96 Place microtube Rack (Covaris cat#500282) using a Covaris E220 for 20 cycles with the following setting: time 60 seconds, duty cycle 5.0, PIP 175, cycles, 200, amplitude 0.0, velocity 0.0, dwell 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. One percent of the lysate was kept as ChIP input. 10 uL of Dynabead Protein A and 10 uL of Dynabead Protein G beads per sample were coupled to either 4 ug of SALL1 antibody (Abcam, ab41974), SMAD4 antibody (1 μg each of Cell Signaling technology 46535 and 38454), or P300 antibody (1 ug each of EMD Millipore RW128  and Diagenode C15200211). Beads/antibody was added to each sample, which were then rotated overnight at 4°C. The samples were washed with the following buffers: 3x RLNR1 + PIC/PMSF/DTT, 6x LWB-RCNR1 (10mM Tris HCl pH 7.5, 1mM EDTA, 0.7% sodium deoxycholate, 1% NP-40, 250mM LiCl)+ PIC/PMSF, 3x TET, 2x IDTET, and then resuspended in TT for on-bead library preparation. Libraries for ChIP and input samples were prepared with NEBNext Ultra II DNA library prep kit (NEB) reagents according to the manufacturer’s protocol on the beads suspended in 25 μL TT (10mM Tris/HCl pH7.5, 0.05% Tween-20), with reagent volumes reduced by half. DNA was eluted and crosslinks reversed by adding 4 μl 10% SDS, 4.5 μl 5 M NaCl, 3 μl EDTA, 4 μl EGTA, 1 μl proteinase K (20 mg/ml), 16 μl water, incubating for 1 h at 55°C, then 30 minutes to overnight at 65°C. DNA was purified using 2 μL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 1.5M NaCl to final of 12% PEG, eluted with 25 μl TT.  DNA contained in the eluate was then amplified for 12-14 cycles in 25 μl PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. Resulting libraries were size selected by gel excision to 200-500 bp, purified, and single-end sequenced using a HiSeq 4000 or paired end on a NovaSeq 6000.

value: Brain

value: PU1+ nuclei

value: Sall1 Enhancer Knockout

tag: antibody

value: Input


title: PU1+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer KO, Rep1


title: Lung KP CD45+MHCII-CD8+ (CD8 T cell) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08233


title: Lung KP CD31+GP38- (Vascular endothelial) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08233


title: 4C_1D7_Rep2

value: Blood

value: Jurkat Cm6


title: ipRGC, P1, rep177

description:
SmartSeq2
P1_176


title: Olig2+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer KO, Rep2

value: Olig2+ nuclei


title: ipRGC, P1, rep181

description:
SmartSeq2
P1_180


title: Donor_9_tail

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

data_processing:
Samples were run using 50-cycle paired-end reads on the NovaSeq 6000 (Illumina) to a depth of 100,000 reads.  Cell Ranger count version 6.0 was used with default settings, with an initial expected cell count of 10,000.  The GCH38 refererence genome was used for aligment.Ambient RNA correction was done for each sample independently using SoupX. Briefly, SoupX estimates the ambient RNA profile from the cell-free RNA, then it estimates the cell-specific contamination fraction using a set of user-specified negative markers. Then, we used Seurat’s recommended workflow for scRNASeq data processing and integration. Briefly, we removed low-quality cells with more than a 15% fraction of mitochondrial genes expression or less than 200 features (genes) detected.
Assembly: GRCH38

source_name: Pancreas tail

extract_protocol:
Briefly, the donor pancreas was dissected by a clinically-trained pancreatobiliary surgeon. The organ was dissected into head, body, and tail, with portions of each placed into DMEM media with 1%BSA/10μM Y27632.  Tissue was minced into 1mm3 pieces, then digested with 1 mg/mL collagenase P for 20-30 min at 37°C with gentle agitation.  Digested tissue was rinsed three times with DMEM/1%BSA/10μM Y27632, then filtered through a 40μm mesh.  Resulting cells were submitted to the University of Michigan Advanced Genomics Core for single cell sequencing using the 10x Genomics Platform.
Single-cell complementary DNA libraries were prepared and sequenced at the University of Michigan Sequencing Core using the 10× Genomics Platform.

value: Pancreas tail


title: 4C_5F9_Rep1

value: CD4 T cell lymphoma


title: NeuN+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer KO, Rep2

value: NeuN+ nuclei


title: Lung KP CD31+GP38- (Vascular endothelial) control (PBS 48 hr) sample #4 bulk RNAseq

description: project 08233

value: lung

value: 21-25 weeks


title: ipRGC, P1, rep175

description:
SmartSeq2
P1_174


title: ipRGC, P1, rep174

description:
SmartSeq2
P1_173


title: Donor_9_head

source_name: Pancreas head

value: Pancreas head


title: NeuN+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer KO, Rep1


title: Donor_8_tail


title: Lung KP CD31+GP38- (Vascular endothelial) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08233


title: PU1+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer WT, Rep2

value: Wild type


title: ipRGC, P1, rep173

description:
SmartSeq2
P1_172

value: Retina


title: Donor_8_head


title: ipRGC, P1, rep172

description:
SmartSeq2
P1_171

value: ipRGC


title: PU1+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer WT, Rep1


title: Lung KP CD45+MHCII+ CD11b+Gr1- (Macrophage) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08233

value: Macrophage


title: Donor_6_tail


title: PU1+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer WT, Rep2

value: Brain


title: Olig2+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer KO, Rep1


title: Donor_6_head


title: ipRGC, P1, rep176

description:
SmartSeq2
P1_175

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P1, rep171

description:
SmartSeq2
P1_170


title: Lung KP CD45+MHCII+ CD11b+Gr1- (Macrophage) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08233


title: Lung KP CD31+GP38- (Vascular endothelial) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08233

value: Vascular endothelial


title: Lung KP CD31+GP38- (Vascular endothelial) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08233


title: Lung KP CD45+MHCII+ CD11b+Gr1- (Macrophage) control (PBS 48 hr) sample #4 bulk RNAseq

description: project 08233


title: Olig2+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer WT, Rep2

value: Input


title: Lung KP CD45+MHCII+ CD11b+Gr1- (Macrophage) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08233


title: Olig2+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer WT, Rep1


title: ipRGC, P1, rep169

description:
SmartSeq2
P1_168


title: Donor_5_tail


title: Donor_5_head


title: ipRGC, P1, rep168

description:
SmartSeq2
P1_167


title: Olig2+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer WT, Rep2


title: Lung KP CD45+MHCII+ CD11b+Gr1- (Macrophage) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08233


title: Donor_4_tail


title: Donor_4_head


title: NeuN+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer WT, Rep2


title: ipRGC, P1, rep166

description:
SmartSeq2
P1_165


title: NeuN+ nuclei, H3K27ac Input ChIPseq, SALL1 Enhancer WT, Rep1


title: ipRGC, P1, rep167

description:
SmartSeq2
P1_166


title: Lung KP CD45+MHCII+ CD11b+Gr1- (Macrophage) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08233


title: Lung KP CD31+GP38+ (Lymphatic endothelial) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08233

value: Lymphatic endothelial


title: ipRGC, P1, rep165

description:
SmartSeq2
P1_164


title: Donor_2_tail


title: NeuN+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer WT, Rep2


title: 4C_1D7_Rep1

value: Blood

value: Jurkat Cm6


title: Donor_2_head


title: Microglia, HiC, SALL1 Enhancer KO, Rep4

data_processing:
Hi-C fastq files were trimmed at DpnII recognition sites (GATC) and then mapped to using Bowtie2 (Langmead & Salzberg, et a;., 2012). Hi-C interaction matrices were generated using juicertools (Durand et al., 2016)  and were visualized using juicebox (Durand et al., 2016). PC1 values for each sample were calculated using HOMER’s runHiCpca.pl with -res 50000 30and were visualized using the UCSC genome browser. Differential PC1 compartments were determined using the command ‘getHiCCorrDiff.pl”. TADs and loops were called using HOMER’s findTADsAndLoops.pl find with parameters -res 3000 and -window 15000. To compare TADs and loops between groups, TADs and loops were merged using merge2Dbed.pl -tad and -loop, respectively. Differential enrichment of these features was then calculated using Homer’s getDiffExpression.pl.
H3K4me3 ChIP-seqs from purified ex-vivo microglia were performed in duplicate with input controls. Alignment, QC and peak calling were performed with the official ENCODE-ChIP-seq pipeline as previously described (Nott et al., 2019). PLAC-seq fastq-files were processed with MAPS 33 at 5000-bp resolution as previously described (Nott et al., 2019); the H3K4me3-ChIP-seq peak files from the ENCODE pipeline were used as a template.
Assembly: mm10

extract_protocol:
Mouse brains were homogenized as previously described (Gosselin et al. 2014)  by gentle mechanical dissociation. Cells were then incubated in staining buffer on ice with anti-CD16/32 blocking antibody (BioLegend 101319) for 15 minutes, and then with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006) for 25 minutes. Cell preparations for H3K27ac ChIP-seq were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for 5 minutes after staining, and subsequently washed three times. Cells were washed once and filtered through a 40 M cell strainer. Sorting was performed on a Sony MA900 or MoFlo Astrios EQ cell sorter. Microglia were defined as events that were DAPI negative, singlets, and CD11b+CD45lowCX3CR1+. Sorted microglia were pelleted at 800xg for 5 minutes, pellets were then snap frozen and stored at -80°C prior to library preparation. Brain nuclei were isolated as previously described (Nott et al., 2019), with initial homogenization performed with either 1% formaldehyde in Dulbecco’s phosphate buffered saline or 2mM DSG (Proteochem) in Dulbecco’s phosphate buffered saline. Nuclei were stained overnight with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099) or SALL1 AF647 (Thermo, clone NRNSTNX 51-9279-82) or NEUN-AF488 (Millipore MAB 377X). Nuclei were washed the following day with 4 mL FACs buffer, passed through a 40 uM strainer, and stained with 0.5 ug/mL DAPI. Nuclei for each cell type were sorted with a Beckman Coulter MoFlo Astrio EQ cell sorter and pelleted at 1600xg for 5 minutes at 4°C in FACs buffer. Nuclei pellets were snap frozen and stored at -80°C prior to library preparation.
PLAC-seq libraries were prepared for ex vivo microglia as previously described with minor modifications (Nott et al., 2019; Fang et al., 2016). In situ Hi-C was performed as described previously, with minor modifications (Heinz et al., 2018).

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

value: Sall1 Enhancer Knockout


title: Lung KP CD31+GP38+ (Lymphatic endothelial) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08233


title: Donor_1_head_and_tail

source_name: Pancreas head and tail

value: Pancreas head and tail


title: ipRGC, P1, rep164

description:
SmartSeq2
P1_163


title: Lung KP CD31+GP38+ (Lymphatic endothelial) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08233

value: lung


title: Lung KP CD31+GP38+ (Lymphatic endothelial) control (PBS 48 hr) sample #4 bulk RNAseq

description: project 08233

value: 21-25 weeks


title: Microglia, HiC, SALL1 Enhancer KO, Rep3


title: ipRGC, P1, rep163

description:
SmartSeq2
P1_162


title: Lung KP CD31+GP38+ (Lymphatic endothelial) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08233


title: Microglia, HiC, SALL1 Enhancer WT, Rep2


title: ipRGC, P1, rep162

description:
SmartSeq2
P1_161


title: 4_4221CSMC_KURAMOCHI

city: San Antonio

first: Kate

last: Lawrenson

address: 7703 Floyd Curl Dr.

institute: Cedars Sinai Medical Center

data_processing:
BWA 0.7.17-r1188
Juicer 1.6
HICCUPS
Assembly: hg38

source_name: KURAMOCHI

extract_protocol:
Cells were trypsinized, pelleted and snap frozen and submitted to Active Motif for their end-to-end HiC service
Active Motif

value: KURAMOCHI

value: High-grade serous "ovary" cancer


title: 3_4221CSMC_OVCAR4


title: ipRGC, P1, rep161

description:
SmartSeq2
P1_160

value: Retina


title: ipRGC, P1, rep160

description:
SmartSeq2
P1_159

value: ipRGC


title: 2_4221CSMC_FT282

value: Fallopian Tube Secretory Epithelium


title: Lung KP CD31+GP38+ (Lymphatic endothelial) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08233


title: Microglia, HiC, SALL1 Enhancer WT, Rep1

value: Brain

value: Wild type


title: ipRGC, P1, rep159

description:
SmartSeq2
P1_158

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: 1_4221CSMC_FT246


title: ipRGC, P1, rep158

description:
SmartSeq2
P1_157


title: HOCL 4

city: Suresnes

first: Perrine

last: Soret

address: 52 rue Carnot

country: France

institute: Servier

data_processing:
Raw readsquality was assessed using FastQC tools.
Reads were trimmed for adaptors using Cutadapt and trimmed reads were aligned to mouse mm39 reference genome using the STAR aligner
Aligned data was evaluated for quality using several quality metrics (e.g., mapping rate, %rRNA, %mRNA) using Samtools and Picard tools.
Aligned reads per gene were quantified using FeatureCount
Read count were normalized by the variance stabilizing transformation vst function from DESeq2 R package
Assembly: mm39
Supplementary files format and content: tab-delimited text files include Count and count vst normalized values for each Sample

source_name: whole blood

extract_protocol:
Total RNA was extracted from whole blood collected in RNA protect tubes (Qiagen) and were proceeded for extraction using the RNeasy Protect Animal blood kit with the optional on-column DNAse I digestion
At least 250 ng of purified RNA samples were used as input for the TruSeq Strand-specific RNA-seq (poly A selection and globin depletion) according to the manufacturer’s instructions (Illumina)
Following the preparation of libraries, samples matching the requested criteria were sequenced on a NovaSeq 6000 sequencer (Illumina).

value: whole blood

value: HOCL


title: HOCL + E07 3


title: VTP_3

city: Mainz

first: Johanna

last: Rausch

address: Langenbeckstraße 1

department: Department of Hematology and Medical Oncology

country: Germany

institute: University Medical Center, Johannes Gutenberg-University Mainz

data_processing:
Sequencing of mRNA (150 base pair paired-end reading) was performed on an Illumina NovaSeq 6000 Sequencing System
mRNA was purified from RNA using poly-T-oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by second strand cDNA synthesis. The library was ready after end-repair, A-tailing, adapter ligation, size selection, amplification and purifiication
Reads were normalized to MRC
Differentially expressed genes between the treatment groups were calculated using DESeq version 2
the normalized expression counts were formatted as gct file
Assembly: For gene expression analysis, reads were mapped to the human genome Hg38
Supplementary files format and content: Differential_Expression__DESeq2__compare_2_groups__on_MOLM13_KO_MRC_vs_MOLM13_DMSO_MRC.norm, GCT format
Supplementary files format and content: Differential_Expression__DESeq2__compare_2_groups__on_MV411_KO_MRC_vs_MV411_DMSO_MRC.norm, GCT format
Supplementary files format and content: Differential_Expression__DESeq2__compare_2_groups__on_OCI3_KO_vs_DMSO_MRC.norm, GCT format
Supplementary files format and content: Differential_Expression__DESeq2__compare_2_groups__on_OCI3__VTP_MRC_vs_DMSO_MRC.norm, GCT format

growth_protocol: MV411, MOLM13 and OCI-AML3 were grown in liquid cell culture inRPMI-1640 supplemented with 10% FBS, 1% L-Glutamin, 1% penicillin/streptomycin

extract_protocol:
1x10e6 cells were harvested and 2µL of 1:100 ERCC RNA Spike in mix (Thermo Fisher) were added to each sample for normalization. RNA was isolated using the Rneasy Kit (Qiagen) including on-column DNAse digestion. RNA libraries were prepared for sequencing using standard Illumina protocols. RNA-seq, paired-end sequencing, 150 base pair
poly A enrichment, RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 150nM ziftomenib (KO-539) or DMSO for 4 days (OCI-AML3 and MOLM13)  or 3 days (MV411) respectively. Independently, OCI-AML3 were treated with 100nM VTP-50469 or DMSO for 4 days. All experiments were performed in triplicates.

value: AML cell line

value: WT


title: Lung KP CD31-GP38+  (Fibroblast) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08233

value: Fibroblast


title: HOCL + D06 9


title: Lung KP CD31-GP38+  (Fibroblast) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08233


title: Lung KP CD31-GP38+  (Fibroblast) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08233


title: VTP_2

description: Differential_Expression__DESeq2__compare_2_groups__on_OCI3__VTP_MRC_vs_DMSO_MRC.norm


title: ipRGC, P1, rep156

description:
SmartSeq2
P1_155


title: Lung KP CD31-GP38+  (Fibroblast) control (PBS 48 hr) sample #4 bulk RNAseq

description: project 08233


title: DMSO_3

value: DMSO


title: HOCL + D06 8


title: VTP_1


title: Lung KP CD31+GP38+ (Lymphatic endothelial) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08233

value: Lymphatic endothelial


title: ipRGC, P1, rep155

description:
SmartSeq2
P1_154


title: HOCL + D11 6


title: HOCL 9


title: DMSO_2


title: HOCL + BPR21 6


title: ipRGC, P1, rep154

description:
SmartSeq2
P1_153


title: ipRGC, P1, rep170

description:
SmartSeq2
P1_169


title: DMSO_1


title: ipRGC, P1, rep157

description:
SmartSeq2
P1_156


title: ipRGC, P1, rep153

description:
SmartSeq2
P1_152


title: OCI-AML3_KO_3

description: Differential_Expression__DESeq2__compare_2_groups__on_OCI3_KO_vs_DMSO_MRC.norm


title: Lung KP CD31-GP38+  (Fibroblast) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08233

value: lung


title: OCI-AML3_KO_2


title: HOCL + D11 11


title: ipRGC, P1, rep152

description:
SmartSeq2
P1_151


title: ipRGC, P1, rep151

description:
SmartSeq2
P1_150


title: Lung KP normal Epcam+ DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08820

value: normal epithelial

value: 21-25 weeks


title: OCI-AML3_KO_1


title: Normal lung CD45+MHCII-CD8+ (CD8 T cell) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08820

value: CD8 T cell


title: Lung KP normal Epcam+ DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08820


title: Lung KP CD31-GP38+ (Fibroblast) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08233


title: Lung KP CD31-GP38+  (Fibroblast) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08233


title: CTRL 7


title: OCI-AML3_DMSO_3


title: HOCL + BPR21 8


title: OCI-AML3_DMSO_2


title: HOCL + D06 7


title: Lung KP normal Epcam+ DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08820


title: HOCL + D11 2


title: ipRGC, P1, rep149

description:
SmartSeq2
P1_148

value: Retina


title: Normal lung CD45+MHCII-CD8+ (CD8 T cell) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08820


title: HOCL + BPR21 1


title: Normal lung CD45+MHCII-CD4+ (CD4 T cell) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08820

value: CD4 T cell


title: MOLM13_KO_3

description: Differential_Expression__DESeq2__compare_2_groups__on_MOLM13_KO_MRC_vs_MOLM13_DMSO_MRC.norm


title: ipRGC, P1, rep146

description:
SmartSeq2
P1_145

value: ipRGC


title: ipRGC, P1, rep147

description:
SmartSeq2
P1_146


title: HOCL + D11 9


title: HOCL + D11 3


title: ipRGC, P1, rep150

description:
SmartSeq2
P1_149


title: ipRGC, P1, rep145

description:
SmartSeq2
P1_144


title: Normal lung CD45+MHCII-CD4+ (CD4 T cell) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08820


title: HOCL + D11 7


title: MOLM13_KO_2


title: ipRGC, P5, rep192

description:
SmartSeq2
P5_191


title: MOLM13_DMSO3


title: MOLM13_KO_1


title: HOCL + E07 2


title: CTRL 9


title: ipRGC, P1, rep148

description:
SmartSeq2
P1_147


title: Normal lung CD45+MHCII- CD11b+ GR1+ (Neutrophil) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08820

value: Neutrophil


title: Normal lung CD45+MHCII-CD4+ (CD4 T cell) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08820


title: MOLM13_DMSO2


title: CTRL 12


title: ipRGC, P5, rep190

description:
SmartSeq2
P5_189


title: OCI-AML3_DMSO_1


title: ipRGC, P5, rep189

description:
SmartSeq2
P5_188


title: MOLM13_DMSO1


title: ipRGC, P5, rep188

description:
SmartSeq2
P5_187


title: CTRL 8


title: HOCL + D11 8


title: MV411_KO_2

description: Differential_Expression__DESeq2__compare_2_groups__on_MV411_KO_MRC_vs_MV411_DMSO_MRC.norm


title: ipRGC, P5, rep187

description:
SmartSeq2
P5_186


title: HOCL + E07 11


title: Normal lung CD45+MHCII+ CD11b+Gr1- (Macrophage) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08820

value: Macrophage


title: Normal lung CD45+MHCII- CD11b+ GR1+ (Neutrophil) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08820


title: ipRGC, P5, rep186

description:
SmartSeq2
P5_185

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P5, rep191

description:
SmartSeq2
P5_190


title: Normal lung CD45+MHCII+ CD11b+Gr1- (Macrophage) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08820


title: Normal lung CD45+MHCII+ CD11b+Gr1- (Macrophage) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08820


title: CTRL 4

value: whole blood


title: MV411_DMSO_3


title: Normal lung CD31+GP38+ (Lymphatic endothelial) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08820


title: MV411_KO_1


title: Normal lung CD45+MHCII- CD11b+ GR1+ (Neutrophil) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08820


title: Lung KP CD45+MHCII+ CD11b+Gr1- (Macrophage) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08233


title: TFR cells, Naïve-3

value: mesenteric lymph nodes

value: TFR cells

value: Naïve, no treatment


title: ipRGC, P5, rep185

description:
SmartSeq2
P5_184


title: CTRL 2

value: HOCL


title: Normal lung CD31+GP38+ (Lymphatic endothelial) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08820


title: ipRGC, P5, rep184

description:
SmartSeq2
P5_183


title: CTRL 1


title: Normal lung CD31+GP38+ (Lymphatic endothelial) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08820


title: MV411_DMSO_1

value: AML cell line

value: WT

value: DMSO


title: HOCL + E07 1


title: MV411_KO_3


title: ipRGC, P5, rep183

description:
SmartSeq2
P5_182


title: LN229_NDV_3

city: Hangzhou China

first: Zecheng

last: Yu

address: 481 Binwen Road, Binjiang District, Hangzhou City, Zhejiang Province, China

institute: Hangzhou Medical College

data_processing:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
Synthesize double-stranded cDNA.
Select cDNA fragments of preferentially 370~420 bp in length by using AMPure XP system. Then PCR amplification, the PCR product was purified by  AMPure XP beads, and the library was finally obtained.
The library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by  Agilent 2100 bioanalyzer. Then qRT-PCR is used to accurately quantify the effective concentration of the library.
The different libraries are pooling and being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is  generated.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain/right frontal parieto-occipital cortex

growth_protocol: LN229 cells were cultured in DMEM containing 10% FBS and 1% antibiotics. Virus incubated with LN229 cells was maintained at 37°C and 5% CO2 for 30 min.

extract_protocol:
The infectious virus was propagated in embryonated chicken eggs and stored at -80°C after detection of viral titers. Virus infection was initiated by incubating with LN229 cells.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: DMEM＋10% FBS＋1% P/S，37℃，5%CO2,  30min

value: Human glioma cells

value: rLa Sota-GFP


title: ipRGC, P5, rep182

description:
SmartSeq2
P5_181


title: LN229_NDV_2

value: brain/right frontal parieto-occipital cortex


title: ipRGC, P5, rep181

description:
SmartSeq2
P5_180

value: Retina


title: LN229_NDV_1


title: ipRGC, P5, rep180

description:
SmartSeq2
P5_179


title: HOCL 12


title: HOCL + E07 8


title: HOCL + D11 5


title: Normal lung CD31-GP38+ (Fibroblast) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08820

value: Fibroblast

value: lung

value: 21-25 weeks


title: MV411_DMSO2


title: Normal lung CD31-GP38+ (Fibroblast) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08820


title: Normal lung CD31+GP38- (Vascular endothelial) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08820

value: Vascular endothelial)


title: HOCL + D06 6


title: LN229_2


title: Normal lung CD31+GP38- (Vascular endothelial) DT (Diphteria Toxin 48 hr) sample #2 bulk RNAseq

description: project 08820


title: Normal lung CD31+GP38- (Vascular endothelial) DT (Diphteria Toxin 48 hr) sample #1 bulk RNAseq

description: project 08820


title: HOCL + D06 12


title: LN229_1


title: LN229_3


title: HOCL + E07 7


title: HOCL + D06 2


title: Normal lung CD45+MHCII-CD8+ (CD8 T cell) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08820

value: CD8 T cell


title: NTC3_NTC2; Replicate 2; RNAPolII CUT&Tag; MDAMB231

first: Brenton

last: Munson

address: 9500 Gilman Drive, MC 0688

department: Bioengineering

institute: University of California San Diego

description:
NTC3_NTC2
Cut&Tag

data_processing:
Adapter triming with Trim Galore (version 0.6.8dev)
Read Alignment with bowtie2 (version 2.4.5)
Sorting and duplicate removal with Picard Tools (version 2.17.11)
Read coverage deepTools (version 3.5.1)
Assembly: GRCh38
Supplementary files format and content: Bigwig coverage track for each sample of paired-end sequencing data
Library strategy: CUT&Tag

source_name: Breast; Mammary gland

extract_protocol: CUT&Tag library preparation following the manufacturer's recommendations

value: Triple Negative Breast Cancer

value: Breast; Mammary gland

tag: replicate

value: RNAPII (ActiveMotif # 91152)


title: Normal lung CD31-GP38+ (Fibroblast) DT (Diphteria Toxin 48 hr) sample #3 bulk RNAseq

description: project 08820


title: NTC3_NTC2; Replicate 1; RNAPolII CUT&Tag; MDAMB231

description:
NTC3_NTC2
Cut&Tag


title: ipRGC, P5, rep175

description:
SmartSeq2
P5_174

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: NTC3_PRMT5; Replicate 2; RNAPolII CUT&Tag; MDAMB231

description:
NTC3_PRMT5
Cut&Tag


title: HOCL + BPR21 2

value: whole blood

value: HOCL


title: ipRGC, P5, rep179

description:
SmartSeq2
P5_178


title: Normal lung CD45+MHCII-CD8+ (CD8 T cell) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820


title: NTC3_PRMT5; Replicate 1; RNAPolII CUT&Tag; MDAMB231

description:
NTC3_PRMT5
Cut&Tag


title: Normal lung CD45+MHCII-CD8+ (CD8 T cell) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820


title: Normal lung CD45+MHCII-CD4+ (CD4 T cell) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820

value: CD4 T cell


title: ipRGC, P5, rep177

description:
SmartSeq2
P5_176


title: CTRL 6


title: Normal lung CD45+MHCII-CD4+ (CD4 T cell) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820


title: ipRGC, P5, rep178

description:
SmartSeq2
P5_177


title: ipRGC, P5, rep176

description:
SmartSeq2
P5_175


title: HOCL 7


title: CDK9_PRMT5; Replicate 2; RNAPolII CUT&Tag; MDAMB231

description:
CDK9_PRMT5
Cut&Tag


title: Normal lung CD45+MHCII- CD11b+ GR1+ (Neutrophil) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820

value: Neutrophil


title: ipRGC, P5, rep173

description:
SmartSeq2
P5_172


title: HOCL + BPR21 9


title: CDK9_PRMT5; Replicate 1; RNAPolII CUT&Tag; MDAMB231

description:
CDK9_PRMT5
Cut&Tag


title: HOCL + E07 4


title: CDK12_PRMT5; Replicate 2; RNAPolII CUT&Tag; MDAMB231

description:
CDK12_PRMT5
Cut&Tag


title: Normal lung CD45+MHCII-CD4+ (CD4 T cell) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08820


title: ipRGC, P5, rep172

description:
SmartSeq2
P5_171


title: CDK12_PRMT5; Replicate 1; RNAPolII CUT&Tag; MDAMB231

description:
CDK12_PRMT5
Cut&Tag


title: CDK7_PRMT5; Replicate 2; RNAPolII CUT&Tag; MDAMB231

description:
CDK7_PRMT5
Cut&Tag


title: ipRGC, P5, rep171

description:
SmartSeq2
P5_170


title: Normal lung CD45+MHCII+ CD11b+Gr1- (Macrophage) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820

value: Macrophages


title: HOCL + E07 6


title: CDK12_NTC2; Replicate 2; RNAPolII CUT&Tag; MDAMB231

description:
CDK12_NTC2
Cut&Tag


title: HOCL 1


title: HOCL + D06 1


title: Normal lung CD45+MHCII- CD11b+ GR1+ (Neutrophil) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08820


title: Normal lung CD45+MHCII- CD11b+ GR1+ (Neutrophil) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820


title: CTRL 5


title: ipRGC, P5, rep170

description:
SmartSeq2
P5_169


title: ipRGC, P5, rep167

description:
SmartSeq2
P5_166


title: ipRGC, P5, rep168

description:
SmartSeq2
P5_167


title: ipRGC, P5, rep166

description:
SmartSeq2
P5_165


title: Normal lung CD45+MHCII+ CD11b+Gr1- (Macrophage) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08820


title: ipRGC, P5, rep174

description:
SmartSeq2
P5_173


title: CDK9_NTC2; Replicate 2; RNAPolII CUT&Tag; MDAMB231

description:
CDK9_NTC2
Cut&Tag


title: ipRGC, P5, rep165

description:
SmartSeq2
P5_164


title: CDK9_NTC2; Replicate 1; RNAPolII CUT&Tag; MDAMB231

description:
CDK9_NTC2
Cut&Tag


title: HOCL 6


title: ipRGC, P5, rep163

description:
SmartSeq2
P5_162


title: Normal lung CD45+MHCII+ CD11b+Gr1- (Macrophage) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820


title: HOCL + BPR21 4


title: HOCL + D11 1


title: CDK12_NTC2; Replicate 1; RNAPolII CUT&Tag; MDAMB231

description:
CDK12_NTC2
Cut&Tag


title: ipRGC, P5, rep169

description:
SmartSeq2
P5_168


title: HOCL + BPR21 5


title: ipRGC, P5, rep162

description:
SmartSeq2
P5_161


title: ipRGC, P5, rep164

description:
SmartSeq2
P5_163


title: Normal lung CD31+GP38+ (Lymphatic endothelial) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820

value: Lymphatic endothelial


title: Normal lung CD31+GP38+ (Lymphatic endothelial) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08820


title: Normal lung CD31+GP38+ (Lymphatic endothelial) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820


title: CDK7_NTC2; Replicate 1; RNAPolII CUT&Tag; MDAMB231

description:
CDK7_NTC2
Cut&Tag


title: CDK7_NTC2; Replicate 2; RNAPolII CUT&Tag; MDAMB231

description:
CDK7_NTC2
Cut&Tag


title: CTRL 11


title: Normal lung CD31-GP38+ (Fibroblast) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820


title: ipRGC, P5, rep161

description:
SmartSeq2
P5_160

value: Retina


title: CTRL 10


title: CDK7_PRMT5; Replicate 1; RNAPolII CUT&Tag; MDAMB231

description:
CDK7_PRMT5
Cut&Tag


title: Normal lung CD31-GP38+ (Fibroblast) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08820

value: Fibroblast


title: HOCL + D06 4


title: ipRGC, P5, rep160

description:
SmartSeq2
P5_159


title: HOCL + BPR21 3


title: WT, NC2

city: Shanghai

first: jing

last: zhang

address: South Chongqing road 280

institute: Shanghai Jiaotong university school of medicine

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

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

value: breast cancer cell

value: NC1 treated

tag: time

value: Day 0


title: WT, NC3


title: WT, ctrl2

value: untreated


title: WT, NC1


title: ipRGC, P5, rep157

description:
SmartSeq2
P5_156


title: Normal lung CD31-GP38+ (Fibroblast) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820

value: lung

value: 21-25 weeks


title: HOCL + E07 12


title: ipRGC, P5, rep159

description:
SmartSeq2
P5_158


title: WT, ctrl3


title: ipRGC, P5, rep156

description:
SmartSeq2
P5_155


title: Lung KP normal Epcam+ DT (Diphteria ToxinPBS 48 hr) sample #3 bulk RNAseq

description: project 08820

value: normal epithelial


title: Normal lung CD31+GP38- (Vascular endothelial) control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08820

value: Vascular endothelial


title: Normal lung CD31+GP38- (Vascular endothelial) control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820


title: ipRGC, P5, rep155

description:
SmartSeq2
P5_154

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: HOCL + D06 11

value: whole blood

value: HOCL


title: HOCL + D11 12


title: HOCL + BPR21 10


title: ipRGC, P5, rep158

description:
SmartSeq2
P5_157


title: HOCL + D06 5


title: HOCL 3


title: Lung KP normal Epcam+ DT (Diphteria ToxinPBS 48 hr) sample #2 bulk RNAseq

description: project 08820


title: Lung KP normal Epcam+ DT (Diphteria ToxinPBS 48 hr) sample #1 bulk RNAseq

description: project 08820


title: TGF+AS2 3

first: Xiaolong

last: Zhu

address: 300 George

data_processing:
Novaseq sequencing with 25 million reads per sample was performed to detect the whole transcriptome. RNA-seq data was aligned to the human reference genome (human genome build 38GRCh38) using the short reads aligner STAR.
Read counts were normalized using the trimmed mean of M-values (TMM) method and differentially expressed genes were identified (edgeR R package). Differentially expressed genes with a false discovery corrected P ≤ 0.05 were used for further analysis (heatmaps and functional enrichment).
Assembly: human genome build 38GRCh38

source_name: Human umbilical artery endothelial cells

growth_protocol: HUAECs cells were maintained in complete EGM-2 supplemented with 5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HUAECs were incubated in the complete EGM-2 media (Control group or cells were transfected with scramble siRNA) or EndMT-induction media (TGFβ2 group) for 5 days. For siRNA treatment, siRNAs were incubated with RNAimax and added into the medium with final concentration 15 nM. And total RNA was isolated from cell lysates using the RNeasy Plus Mini Kit (Qiagen).

value: HUAECs

value: ACSS2 siRNA +TGFbeta

value: 6 days


title: TGF+AS2 2

value: Human umbilical artery endothelial cells


title: TGF+AS2 1


title: ipRGC, P5, rep153

description:
SmartSeq2
P5_152

value: Retina


title: ipRGC, P5, rep154

description:
SmartSeq2
P5_153


title: ipRGC, P5, rep152

description:
SmartSeq2
P5_151


title: HOCL 8


title: Normal lung CD31+GP38- (Vascular endothelial) control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820


title: Lung KP tumor Epcam+ control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820

value: KP adenocarcinoma


title: HOCL + E07 5


title: ipRGC, P5, rep150

description:
SmartSeq2
P5_149


title: Lung KP tumor Epcam+ control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820


title: WT, ctrl1

value: breast cancer cell


title: ipRGC, P5, rep151

description:
SmartSeq2
P5_150


title: TGF+NC 2

value: Scramble siRNA + TGFbeta


title: HOCL 10


title: Lung KP normal Epcam+ control (PBS 48 hr) sample #3 bulk RNAseq

description: project 08820


title: ipRGC, P5, rep149

description:
SmartSeq2
P5_148


title: TGF+NC 1


title: NC 3

value: Scramble siRNA


title: ipRGC, P5, rep148

description:
SmartSeq2
P5_147


title: Lung KP normal Epcam+ control (PBS 48 hr) sample #1 bulk RNAseq

description: project 08820

value: lung


title: HOCL + D11 10


title: NC 2


title: AKT1.MYC (F3)

city: Nanjing

first: Binghua

last: Li

state: Jiangsu

address: Zhongshan road 321, Nanjing, Jiangsu, China

department: Department of Hepatobiliary Surgery

institute: the Affiliated Drum Tower Hospital, Medical School of Nanjing University

description: AKT1.MYC (F3)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mouse HCC tissue

extract_protocol:
Tumor tissues were resected from the livers of NRAS.MYC.ND and AKT1. MYC mouse model, sliced into small pieces and put into a gentleMACS C Tube (Miltenyi Biotec) containing enzymatic digestion solution and automatically digested using gentleMACS dissociator. The resulting cell suspension was passed through a 70 μm cells strainer (Miltenyi Biotec; 130-098-462), washed with 1xPBS buffer containing 0.2% FBS. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific). The live cells were enriched using a Dead Cell Removal kit (Miltenyi Biotec; 130-090-101), following the manufacturer’s instructions. Enriched live cells were washed and counted using a hemocytometer with trypan blue.
Cell capture and cDNA synthesis were carried out using 10x Chromium system (10xGenomics) following the recommended protocol for the Chromium Single Cell 30 Reagent Kit (v2 Chemistry).

treatment_protocol: Mouse liver tumors were induced by hydrodynamic tail vein injection (HTVi) of oncogenes together with the sleeping beauty transposase. To generate the Nras-driven HCC model, two expression constructs for human N-Ras (19 μg/mouse) and human c-Myc (1 μg/mouse), together with a plasmid expressing Sleeping Beauty transposase (SB) (2 μg/mouse) were co-transfected. To generate the AKT1.MYC model, two expression constructs for Akt1 (10 μg/mouse) and human c-Myc (10 μg/mouse), together with a plasmid expressing Sleeping Beauty transposase (SB) (5 μg/mouse) were co-injected. All plasmid DNAs were diluted in phosphate-buffered saline (PBS) and injected at a final volume of 10% of the mouse’s body weight through the tail vein in less than 8 seconds.

value: Mouse HCC tissue

value: hydrodynamic tail vein injection (HTVi)


title: NC 1


title: HOCL + D06 10


title: ipRGC, P5, rep147

description:
SmartSeq2
P5_146


title: ipRGC, P5, rep146

description:
SmartSeq2
P5_145


title: TGF+NC 3


title: HOCL 5


title: NRAS.MYC.ND (F1)

description: NRAS.MYC.ND (F1)


title: Lung KP tumor Epcam+ control (PBS 48 hr) sample #2 bulk RNAseq

description: project 08820

value: 21-25 weeks


title: HOCL + BPR21 7


title: HOCL 11


title: ipRGC, P5, rep145

description:
SmartSeq2
P5_144

value: ipRGC


title: TGFbeta 3

value: TGFbeta

value: 5 days


title: TGFbeta 2


title: ipRGC, P1, rep144

description:
SmartSeq2
P1_143

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: HOCL + D06 3

value: whole blood

value: HOCL


title: TGFbeta 4

value: HUAECs


title: Wounded TM Day 14

city: San Francisco

first: Sonia

last: Scaria

address: 513 Parnassus Avenue, HSE 740

department: Otolaryngology-Head and Neck Surgery

institute: University of California, San Francisco

data_processing:
10x Genomics Cell Ranger pipeline
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include barcodes and genes for every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tympanic Membrane

extract_protocol:
TMs were removed and kept in cold PBS; The epithelial and fibrous layers were separated using dispase and separately digested using TryplE (epithelial) and Collagenase + DNAse (fibrous), filtered, and dead cells removed. Cells were loaded onto the Chromium Controller from 10x Genomcis for single cell capture.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: tympanic membrane

value: post natal week 8

value: wild type


title: ipRGC, P1, rep143

description:
SmartSeq2
P1_142

value: Retina


title: Wounded TM Day 3


title: TGFbeta 1

value: Human umbilical artery endothelial cells


title: HOCL + E07 10


title: Wounded TM Day 1


title: ipRGC, P1, rep142

description:
SmartSeq2
P1_141


title: Unwounded TM Pars Flaccida


title: Control 4

value: BSA


title: Control 3


title: ipRGC, P1, rep140

description:
SmartSeq2
P1_139


title: ipRGC, P1, rep141

description:
SmartSeq2
P1_140


title: HOCL + BPR21 12


title: HOCL 2


title: Unwounded TM Pars Tensa


title: Control 2


title: Wounded TM Day 7


title: HOCL + BPR21 11


title: KO-antiPD1&LGG rep3

city: Beijing

first: Liangliang

address: #30 Shuangqing Road

institute: Tsinghua University

data_processing:
The short sequence reads were aligned to mouse mm10 reference genome using STAR (2.4.0
The aligned sequence reads were assembled and quantified by HTSeq (0.6.1) with Gencode M8 as annotation
DESeq2 was used for differential gene expression analysis among subgroups.
Hierarchical clustering and principal component analysis were plotted applying FactoMineR and gplots libraries in R. log2 [FPKM] was calculated for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized_log2-gene-counts

source_name: MLN in MC38 tumor bearing Myd88 knockout mice

growth_protocol: Six-eight week old C57BL/6 female mice (WT or Myd88 knockout mice) were subcutaneously injected in the right flank with 1×10^6 MC38 cells. Mice were pooled and randomly divided into different groups with comparable average tumor size 100 mm3, 7-10 days after tumor cells injection.

extract_protocol:
The CD11c+ dendritic cells were purified from MLN of MC38 tumor bearing mice using  CD11c MicroBeads (Miltenyi Biotec). The RNA extraction, and reverse transcription were then performed.
cDNA library construction were performed also following the bulk-seq protocols.

treatment_protocol: Oral administration of live LGG (2 x 109 CFU/per time) was administered twice each week and anit-PD-1 antibody or IgG control antibody (200 μg per mouse) were injected intraperitoneally twice each week. Total four treatment groups were IgG, anti-PD-1, LGG and anti-PD-1&LGG. The mice were treated for two-three weeks.

value: Myd88 knockout

value: CD11c+ dendritic cells

value: anti-PD-1 antibody plus live LGG


title: KO-antiPD1&LGG rep2


title: ipRGC, P1, rep139

description:
SmartSeq2
P1_138

value: ipRGC


title: Control 1

institute: Yale University


title: ipRGC, P1, rep135

description:
SmartSeq2
P1_134


title: KO-antiPD1&LGG rep1


title: A375 cells, TFCP2 KO, biol rep 3

city: Athens

first: Ryan

middle: Joseph

last: Weiss

state: GA

address: 315 Riverbend Road

department: Biochemistry and Molecular Biology

institute: University of Georgia

data_processing:
Qiagen RNA-seq Analysis Portal v3.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GRCh38.103 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38 (GRCh38.103)
Supplementary files format and content: Excel file includes RPKM values for each Sample

growth_protocol: A375 cells (ATCC® CRL-1619™) were grown in DMEM (Gibco) supplemented with 10% FBS and 1% Penicillin/Streptomycin (10,000 U/mL, gibco) at 37˚C with 5% CO2.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: malignant melanoma cells

value: TFCP2 knockout


title: KO-LGG rep3

value: oral administration of live LGG


title: KO-533

city: Guangzhou

first: Xinyu

state: Guangdong

address: Zhongshan 2nd Road

department: Department of Immunology

institute: Sun-yat sen University

data_processing:
Hisat2 v2.1.0,Stringtie-1.3.5
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality, and then trimmed sequence reads were mapped to GrCM38 using Hisat2 with default parameters
Read count extraction and normalization were performed using stringtie and the DEseq2 package
Assembly: GRCM38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Tumor

extract_protocol:
Total RNA was extracted from tumor tissue with TRIzol reagent (Sigma-Aldrich) according to the manufacturer’s instructions. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: The tumor-bearing mice were euthanized, and the tumor tissues were harvested at day 21 after tumor inoculation.

value: Tumor

value: CD43 KO

value: C57BL/6J mouse model bearing CD43 KO-MC38 tumors


title: A375 cells, TFCP2 KO, biol rep 1


title: HOCL + D11 4

value: whole blood

value: HOCL


title: KO-535


title: KO-LGG rep1


title: ipRGC, P1, rep138

description:
SmartSeq2
P1_137

data_processing:
FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 version 2.1.0.
The resulting SAM files were converted to BAM files using SAMtools version 1.9.
Transcript abundance was estimated using Cuffquant and normalization was performed using Cuffnorm in Cufflinks version 2.2.1.
All analyses were performed using Seurat in R version 3.6.2.
Assembly: mm10
Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell
Supplementary files format and content: Cuffnorm matrix containing annotations for each gene
Supplementary files format and content: Cuffnorm matrix containing annotations for each sample

extract_protocol:
Retinas were dissected in cold Hibernate A medium lacking Ca2+, Mg2+, and phenol red (BrainBits). Retinas were then dissociated in papain (Worthington Biochemical, LS003126), 5.5 mM Cysteine-HCl, and 1.1 mM EDTA dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) for seven minutes at 37°C. Cell suspension was passed through a 40 μm cell strainer (Falcon, 352340) and incubated for 30 minutes on ice with Brilliant Violet (BV)-421 anti-mouse CD90.2 antibody (BioLegend, 105341, 1:300), which binds to RGCs and provides an additional selection marker during FACS. The cells were then centrifuged and resuspended in 0.4% bovine serum albumin dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red). Cells were again centrifuged and resuspended in 2000 U/ml DNase I (New England Biolabs, M0303S) in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) prior to cell sorting. Individual GFP+, BV-421+ cells were sorted into a lysis solution consisting of 3500 U/ml RNase inhibitor (New England Biolabs, M0314S), 140 U/ml DNase I, and 0.17% v/v Triton X-100 in water using a MoFlo Legacy cell sorter (Beckman Coulter).
Single-cell DNA libraries were prepared according to the Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014) and sequenced using an Illumina NextSeq 500 sequencer (75 bp paired-end reads, 400 million total reads).

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P1, rep137

description:
SmartSeq2
P1_136


title: KO-antiPD1 rep3

value: anti-PD-1 antibody


title: KO-antiPD1 rep2


title: ipRGC, P1, rep134

description:
SmartSeq2
P1_133

value: Retina


title: HOCL + E07 9


title: A375 cells, Wildtype, biol rep 1

value: WT


title: ipRGC, P1, rep133

description:
SmartSeq2
P1_132


title: A375 cells, TFCP2 KO, biol rep 2


title: WT-551

value: C57BL/6J mouse model bearing Vec-MC38 tumors


title: KO-529


title: KO-532


title: A375 cells, Wildtype, biol rep 3


title: A375 cells, Wildtype, biol rep 2


title: KO-antiPD1 rep1

value: Myd88 knockout


title: ipRGC, P1, rep132

description:
SmartSeq2
P1_131


title: ipRGC, P1, rep131

description:
SmartSeq2
P1_130


title: KO-LGG rep2

value: CD11c+ dendritic cells


title: HEK393 cells, control, rep2

first: Yibo

last: Lu

address: No.1678, Dongfang Road, Shanghai

department: Shanghai Children's Medical Center

institute: Shanghai Jiao Tong University

data_processing:
Illumina Stranded mRNA Prep was used for base calling.
The quality of raw sequence datas were checked using FastQC(v0.11.9). Low quality sequences were removed with Trim Galore!(v0.6.6) and rRNA sequences were removed with SortMeRNA(v4.3.2).
STAR-aligner(v2.7.9a) was used for aligning RNA-seq data to genomes.
featureCounts(v2.0.1) outputs numbers of reads assigned to features.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include featurecounts for each sample

extract_protocol:
RNA was harvested using NovaSeq 6000 Reagent Kit. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard NovaSeq stranded mRNA prep protocols

value: human embryonic kidney cells


title: KO-534

last: Wang


title: ipRGC, P1, rep136

description:
SmartSeq2
P1_135

value: ipRGC


title: KO-IgG rep3

value: IgG control antibody


title: WT-550


title: HEK393 cells, control, rep3


title: KO-IgG rep2


title: HEK393 cells, control, rep1


title: ipRGC, P1, rep130

description:
SmartSeq2
P1_129


title: WT-548


title: ipRGC, P1, rep127

description:
SmartSeq2
P1_126


title: ipRGC, P1, rep128

description:
SmartSeq2
P1_127


title: HEK393 cells, HSALNG0134318 knockdown, rep1

value: HSALNG0134318 knockdown


title: HEK393 cells, HSALNG0134318 knockdown, rep3


title: HEK393 cells, HSALNG0134318 knockdown, rep2


title: ipRGC, P1, rep126

description:
SmartSeq2
P1_125


title: WT-antiPD1&LGG rep2

source_name: MLN in MC38 tumor bearing WT mice

value: anti-PD-1 antibody plus live LGG


title: ipRGC, P1, rep125

description:
SmartSeq2
P1_124


title: KO-IgG rep1


title: ipRGC, P1, rep129

description:
SmartSeq2
P1_128


title: WT-antiPD1&LGG rep1


title: E15.5, vMB, snapCREST, biol rep 3b,CREST_sc, library 3

first: Yuejun

state: Shanghai

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

data_processing:
Cellranger (7.0.0) was used to process scRNA-seq datasets. LinTind (https://bioconductor.org/packages/devel/bioc/html/LinTInd.html) was used to recover CREST barcodes for individual cells from bulk (identified by UMIs) or scRNA-seq (identified by 10X cell barcodes [CBs]) datasets.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ventral midbrain

extract_protocol:
Tissues, organoids and cultured cells were dissociated using papain (Worthington), Accutase (Gibco) or Trypsin-EDTA accordingly, and then pipetted into single-cell suspensions in collection medium [Neurobasal Medium, supplemented with 5% FBS]. Cells were filtered (Falcon 5mL Round Bottom Polyst) and then sorted by FACS to collect EGFP+/BFP+ cells for genomic DNA extraction (Vazyme) for bulk amplification or for single-cell RNA sequencing (10x Chromium System V3 or V3.1).
Single-cell RNA sequencing library were performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). CREST barcode libraries were amplified from the single-cell cDNA libraries generated in step 2.3 of the 10X Chromium single cell 3’ protocol with two rounds of PCR. Briefly, CREST_sc_1st_F and CREST_sc_1st_R primers were first used to enrich CREST barcodes tagged with 10X cell barcodes and UMIs. PCR products were purified using a 2-step bead purification process (0.5x then 1.1x) and then used as templates for a second round of PCR to attach sequencing adaptors and indices with CREST_sc_2nd_F and CREST_sc_2nd_R1/2 primers. The second-round PCR products (single-cell CREST libraries) were purified using a gel purification kit (Vazyme) and DNA of the targeted size collected.  For bulk amplification of CREST barcodes, both V1 and V2 CREST barcodes were enriched together from genomic DNA using three rounds of PCR amplification. Specifically, UMI-indexing PCR was first performed to identify CREST DNA from individual cells using the CREST_bulk_1st_F primer (containing 39 bp of partial Illumina sequencing adaptor, 12 bp of random UMI, and 20 bp of BFP binding sequence [10 bp upstream from CREST barcode]). Up to 500 ng of gDNA was used as template for UMI-indexing PCR for each library (for samples yielding less than 500 ng of gDNA, entire volumes were used as templates). The indexed CREST barcodes were purified using 1.6x VAHTS DNA Clean Beads (Vazyme) and amplified via a second round of PCR (using primers REST_bulk_2nd_F and CREST_bulk_2nd_R). Amplified CREST barcodes were selected and purified using a 2-step bead purification process (0.55x, then 1.45x) according to the manufacturer’s recommendations (Vazyme). Finally, sequencing adaptors and sample indices were attached to each library via a third round of PCR (using primers CREST_bulk_3rd_F and CREST_bulk_3rd_R1-8 [containing 8 bp indices]). PCR products were purified using 1.6x VAHTS DNA Clean Beads.

value: ventral midbrain

value: FACS sort, EGFP+/BFP+ cells


title: WT-antiPD1&LGG rep3


title: E15.5, vMB, snapCREST, biol rep 3a,CREST_sc, library 3


title: E15.5, vMB, snapCREST, biol rep 3b,CREST_sc, library 2


title: E15.5, vMB, snapCREST, biol rep 3b,CREST_sc, library 1


title: WT-LGG rep3

value: oral administration of live LGG


title: E15.5, vMB, snapCREST, biol rep 3a,CREST_sc, library 2


title: WT-549

value: Tumor


title: WT-LGG rep2


title: MG63, Vehicle, 48 hours, rep 1

city: Coral Gables

first: Thomas

last: Lisse

state: Florida

address: 1801 Memorial Drive

department: Biology

institute: University of Miami

data_processing:
HISAT2 was performed for sample alignment to the human genome (Ensembl 87: GRCh38.p7 human transcriptome) to generate BAM files .
HTseq-count was performed to generate non-normalized gene counts for each sample. Normalization of RNAseq gene counts (counts per million [CPM]), and differential gene expression and visualization analyses were performed with iDEP
Assembly: hg19
Supplementary files format and content: tab-delimited files with gene count cpm

growth_protocol: MG63 cells were maintained in EMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
PureLink™ RNA Mini Kit
Illumina TruSeq, Stranded Total RNA with RiboZero Gold rRNA depletion

treatment_protocol: 1,25(OH)2D in ethanol was applied to the cell culture.

value: osteosarcoma

value: Vdr+, p53 low

value: Vehicle


title: MG63, Vehicle, 48 hours, rep 2


title: MG63, Vit D, 48 hours, rep 2


title: MG63, Vit D, 48 hours, rep 1


title: E15.5, vMB, snapCREST, biol rep 3a,CREST_sc, library 1

last: Chen


title: ipRGC, P1, rep122

first: Alex

last: Kolodkin

address: 725 N Wolfe St

institute: Johns Hopkins University School of Medicine

description:
SmartSeq2
P1_121

source_name: Retina

value: Retina

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: MG63, Vit D, 24 hours, rep 2


title: E15.5, vMB, snapCREST, biol rep 2b,CREST_sc, library 2


title: ipRGC, P1, rep120

description:
SmartSeq2
P1_119


title: ipRGC, P1, rep123

description:
SmartSeq2
P1_122


title: E15.5, vMB, snapCREST, biol rep 2b,CREST_sc, library 3


title: WT-IgG rep3

value: WT


title: E15.5, vMB, snapCREST, biol rep 2a,CREST_sc, library 3


title: WT-antiPD1 rep2

value: anti-PD-1 antibody


title: MG63, Vit D, 24 hours, rep 1


title: MG63, Vehicle, 24 hours, rep 2


title: ipRGC, P1, rep124

description:
SmartSeq2
P1_123


title: E15.5, vMB, snapCREST, biol rep 2a,CREST_sc, library 2


title: E15.5, vMB, snapCREST, biol rep 2b,CREST_sc, library 1


title: WT-IgG rep2

value: CD11c+ dendritic cells


title: WT-antiPD1 rep3


title: ipRGC, P1, rep121

description:
SmartSeq2
P1_120


title: WT-antiPD1 rep1


title: WT-LGG rep1


title: ipRGC, P1, rep117

description:
SmartSeq2
P1_116


title: E15.5, vMB, snapCREST, biol rep 2a,CREST_sc, library 1


title: MG63, Vehicle, 24 hours, rep 1


title: ipRGC, P1, rep116

description:
SmartSeq2
P1_115


title: NKTs, BTG1 overexpression, sample 5

city: HOUSTON

first: Leonid

last: Metelitsa

address: 3639 Skyline Dr1102 Bates Ave., Ste. 1570

department: Pediatrics

institute: BAYLOR COLLEGE OF MEDICINE/Texas Children's Hospital

data_processing:
QC by FastQC (version 0.11.2)
Mapping and alignment by HISAT2 software (v2.1.0)
transcripts assembly by StringTie software (v1.3.5)
Generates raw read counts by prepDE.py (under stringtie software)
extracts coding genes by custom python scripts
Assembly: GRCh38.p13 assembly
Supplementary files format and content: gtf files including FPKM and TPM matrices for each sample

source_name: Peripheral blood

growth_protocol: Peripheral blood of healthy donors was purchased from Gulf Coast Regional Blood Center. PBMCs were isolated from buffy coats by density gradient centrifugation. NKTs were purified using anti-iNKT microbeads (Miltenyi Biotec), and the negative PBMC fraction was irradiated (40 Gy) and aliquoted. Enriched NKTs were stimulated with an aliquot of autologous PBMCs pulsed with αGalCer (100 ng/mL; Kyowa Hakko Kirin). The culture was supplemented every other day with recombinant IL2 and IL21 (NCI, 200U/mL and CellGenix, 10ng/mL, respectively) in complete RPMI (RPMI 1640, 10% heat-inactivated FBS, 2 mM GlutaMAX-1). NKTs were expanded for 6 to 7 days and transduced with retroviral particles encoding the GFP.BTG1 or GFP.FFLuc construct in RetroNectin-coated plates (Takara Bio) for 48 hours then washed, replated, and cultured for continued expansion. NKT number was determined by trypan blue (Life Technologies) counting. At day 14 after NKT isolation, transduced NKTs were FACS sorted according to GFP expression.

extract_protocol:
RNA was harvested using the Rneasy Mini Plus kit.
RNA libraries were generated through polyA capture and reverse transcription of cDNA. Illumina PE150 technology was employed to sequence the sample (Novogene).

value: Peripheral blood

value: Primary human NKTs

value: NKTs

value: BTG1 OE


title: NKTs, BTG1 overexpression, sample 4


title: E15.5, vMB, snapCREST, biol rep 1b,CREST_sc, library 3


title: ipRGC, P1, rep119

description:
SmartSeq2
P1_118

value: ipRGC


title: NKTs, BTG1 overexpression, sample 3


title: Mock_PR8-5

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Adapters were trimmed using Trimmomatic-0.39
reads were aligned to mm10 genome using STAR2.7.1a
reads were summarized at the gene-level using featureCounts-1.4.6
gene expression was quantified using Cufflinks v2.2.1
Differential expression analysis was done using DESeq2v1.24
Genome_build: mm10
Supplementary_files_format_and_content: depth-normalized read counts and FPKM

source_name: Lung

extract_protocol: Single cells were produced from whole lungs from PR8-infected mice. The single cells were then enriched for monocytes using Miltenyi Biotech's monocyte sorting kit. Briefly, single cells were incubated with antibodies against non-monocyte markers and subsequently incuabted with beads that bind the primary antibodies. Using LS columns, the non-monocyte cells were captured and retained within the column while the unbound monocytes eluted through and were collected for RNA-sequencing. The purity and viability of the monocytes was assessed via flow cytometry post-sorting.

value: Mock

value: Monocyte

value: lung


title: ipRGC, P1, rep118

description:
SmartSeq2
P1_117


title: ipRGC, P1, rep115

description:
SmartSeq2
P1_114


title: Mock_PR8-4


title: E15.5, vMB, snapCREST, biol rep 1b,CREST_sc, library 2

value: ventral midbrain

value: FACS sort, EGFP+/BFP+ cells


title: NKTs, BTG1 overexpression, sample 2


title: NKTs, BTG1 overexpression, sample 1


title: Mock_PR8-3


title: E15.5, vMB, snapCREST, biol rep 1b,CREST_sc, library 1


title: IFNg_K0-5

value: IFN-g KO


title: E15.5, vMB, snapCREST, biol rep 1a,CREST_sc, library 2


title: Mock_PR8-2


title: ipRGC, P1, rep112

description:
SmartSeq2
P1_111


title: ipRGC, P1, rep113

description:
SmartSeq2
P1_112


title: ipRGC, P1, rep111

description:
SmartSeq2
P1_110


title: NKTs, wild-type, sample 4


title: E15.5, vMB, snapCREST, biol rep 1a,CREST_sc, library 1


title: WT-IgG rep1

value: IgG control antibody


title: Mock_PR8-1


title: NKTs, wild-type, sample 3


title: E11.5, vMB, snapCREST, biol rep 3,CREST_sc, library 3