title: TT4_H3K27me3

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

institute: CHU de Québec - Université Laval

data_processing:
For ChIP-seq, sequencing data were processed using the Illumina analysis pipeline
The quality of the sequence data was assessed using FastQC (Version 0.11.5).
Adaptors were trimmed using Trim Galore (Version 0.0.4).
FastQ format reads were aligned to the mm10 mouse reference using the Bowtie alignment algorithm. Bowtie version 2.1.0 was used with the pre-set sensitive parameter to align ChIP sequencing reads.
The MACS version 2.0.10 (model based analysis of ChIPseq) peak finding algorithm was used to identify regions of ChIP-Seq enrichment over background. Default parameters were used for H3K4me3, and broad peak parameters were used for H3K27me3 and H3K36me3 data.
Multicov command from Bedtools v2.17.0 was used to obtain raw read counts within each histone mark peak identified by MACS and input reads within these peaks. The number of reads per kilobase of peak per million reads (RPKM) was calculated for each peak and the corresponding input levels of that peak. The RPKM values for the histone mark peak were then subtracted by those of the input RPKM values to obtain a final and background-adjusted RPKM value, as modified from Hawkins et al. (https://doi.org/10.1016/j.stem.2010.03.018). Peak calls with background-adjusted RPKM values less than or equal to 0 were excluded from further analysis. The background adjusted RPKM values were averaged across -2 kb to +3 kb of a gene transcription start site (TSS), for downstream data analysis and visualization. Read densities and enrichment scores per locus, where defined, were normalized to the total number of million uniquely mapped reads producing values in units of reads per million mapped reads (RPM).
For long-read DNAseq, raw fast5 files were basecalled using the Guppy v.4.2.2 software, with the guppy_basecaller command and the dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg configuration file. GPU basecalling mode was employed with the following arguments: --num_callers 6 --gpu_runners_per_device 6 --chunks_per_runner 1000 --chunk_size 1000. Output fast5 files were generated with the --fast5_out argument.
The resulting FASTQ reads were concatenated and then indexed with Nanopolish version 0.13.2, using the nanopolish index command.
Reads were aligned to the mm10 mouse reference with Minimap2 version 2.17-r941 using the following parameters: -a -x map-ont.
BAM files were generated with SAMtools version 1.3.1.
CpG methylation was called using the call-methylation function of Nanopolish.
Methylation frequency for CpGs was analyzed using the calculate_methylation_frequency.py script from Nanopolish and fraction of methylated CpGs at gene TSS was calculated with a sliding window approach of 300 bp, sliding every 30 bp. Analysis was confined to -1 kb to +1 kb region of TSS as we found this to be the region frequently spanning hypomethylation for key genes in pluripotent stem cells.
To correct for sample-to-sample differences in CpG methylation percentages, values for fraction methylated CpGs were first subtracted to distribution means in each separate samples, and then averaged for two independent animal replicates.
Genome_build: mm10
Supplementary_files_format_and_content: DNAmethyl.CpG.TSS.table.txt
Supplementary_files_format_and_content: HistoneMarks_peak_gene.ids.rpkm.mean.txt

source_name: Induced pluripotent stem cells (iPSCs) derived from TTFs

extract_protocol:
Chromatin immunoprecipitation was performed on two PTC iPSC lines and two TTF iPSC lines following the protocol outlined in the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technologies, 9003). Briefly, 30-60 million cells were fixed in 1% methanol-free formaldehyde (Thermo Fisher, 28906) at room temperature (RT) for 10 min. Glycine was added to the fixed cells at a final concentration of 0.125 M for 5 min at RT. Cells were centrifuged at 500 g, 4℃, 5 min, and washed twice with ice cold phosphate buffered saline (PBS). Chromatin was digested with micrococcal nuclease at a concentration of 0.1 µl/million cells for 30 min at 37℃. Cells were then sonicated using the Sonics VibraCell (VCX130) with 3 mm probe at 40% amplitude and 5 sets of 20 s pulses. Approximately 10 µg of digested, cross-linked chromatin was incubated with 10 µg of anti-H3K4me3 (Abcam, AB8580, lot #GR3175719-3), anti-H3K27me3 (Millipore, 07-449, lot #3018864), or anti-H3K36me3 (Abcam, AB9050, lot #GR3210077-1) antibody overnight at 4℃. ChIP-grade protein G magnetic beads were added to each immunoprecipitation reaction and incubated for 2 h at 4℃. Magnetic beads were pelleted using a magnetic separation rack (Cell Signaling Technologies, 7017) and washed in a sequence of low salt and high salt washes. Finally, chromatin was eluted from the magnetic beads and DNA was reverse cross-linked from the histone. DNA was cleaned up using the Qiaquick PCR Purification Kit (Qiagen). Enrichment was validated using qPCR with Pax2 primers (Active Motif, #71020) and Actb2 primers (Active Motif, #71017).
Libraries were prepared according to the manufacturer's instructions, by the Centre for Applied Genomics (Toronto, ON) on the Illumina HiSeq 2500 and 50 million reads were acquired for each sample.

value: iPSCs

tag: chip antibody


title: single protoplasts transfected with a pool of bHLHs; protoplast #94

status: Public on Nov 21 2022

type: SRA

city: Wuhan

first: Junpeng

last: Zhan

state: Hubei

address: 1 Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

library_source: transcriptomic single cell

data_processing:
The raw CEL-seq2 reads were demultiplexed based on cell-specific barcodes using Fastq-Multx. The UMI sequences from read 1 were added to the read 2 sequence names and then filtered and trimmed with Fastp (parameters: -y -x -3 -f 6). The clean reads were mapped to B73 RefGen_v3 with Hisat2, and the UMIs quantified with SAMtools and UMI-tools. The counts of UMIs mapped to each gene/locus/construct were normalized to transcripts per million.
Assembly: B73 RefGen_v3
Supplementary files format and content: tab-delimited text file including TPM values for each gene

molecule: polyA RNA

organism: Zea mays

source_name: leaf protoplasts

growth_protocol: Seeds of the B73 maize were germinated and grown in constant darkness at 25oC and 50–70% humidity. Leaves were collected from more than 10 etiolated seedlings 10 to 12 days after germination for each protoplast isolation.

extract_protocol:
CEL-seq2
CEL-seq2

tag: cell type

value: leaf protoplasts

tag: genotype


title: single protoplasts transfected with a pool of bHLHs; protoplast #92


title: single protoplasts transfected with a pool of bHLHs; protoplast #91


title: single protoplasts transfected with a pool of bHLHs; protoplast #95


title: single protoplasts transfected with a pool of bHLHs; protoplast #96


title: single protoplasts transfected with a pool of bHLHs; protoplast #93


title: i706_i516

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: Mouse hypothalamus Rxfp4-EYFP, sample 91

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adapter sequence using cutadapt, mapped to the primary mouse genome (GRCm38) using STAR, and raw counts generated with featureCounts.
Gene expression modelling and normalised counts per million were generated using Seurat (v4.0.2).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes raw count values for all samples.

molecule: total RNA

organism: Mus musculus

source_name: Hypothalamus

extract_protocol:
Cells were sorted directly into individual wells of 96-well plates containing lysis buffer using an Influx Cell Sorter, sorting for EYFP-positive and DraQ5-negative. 384 YFP-positive cells were isolated and processed using a Smart-Seq2 protocol.
The library was constructed using the Nextera XT DNA preparation kit and Nextera XT 96-Index kit.

treatment_protocol: Mice were sacrificed by cervical dislocation and the hypothalamus dissected into Hibernate-A medium supplemented with 0.25% GlutaMAX and 2% B27. Tissue digested in Hibernate-A medium without calcium containing 20 U/mL Papain and 1% GlutaMAX for 30 min at 37oC under agitation (Thermomixer, 500 rpm). After digestion, tissue was triturated in Hibernate-A medium with 3.5 U/mL DNase I. The trituration supernatant was loaded on a BSA gradient prepared in Hibernate-A medium, spun for 5 min at 300 rcf, and the pellet resuspended in Hibernate-A medium + 1% BSA. The cell suspension was filtered through a 70 µm cell strainer into a fresh tube.

tag: tissue

value: Hypothalamus

tag: expression


title: TT1_H3K27me3

country: Canada

library_source: genomic

molecule: genomic DNA


title: single protoplasts transfected with a pool of bHLHs; protoplast #90


title: single protoplasts transfected with a pool of bHLHs; protoplast #89


title: single protoplasts transfected with a pool of bHLHs; protoplast #88


title: i706_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 90


title: IAV-specific CD8 T cells Replicate 3

type: RNA

city: Baltimore

first: Nan-Ping

last: Weng

address: 251 Bayview Blvd

department: LMBI

country: USA

institute: NIA

description: Biological replicate 3 of 4.  IAV-specific CD8 T cells

hyb_protocol: 750 ng of labeled sample probes mixed with equal amount of universal reference probes in 500 µl of hybridization solution onto Agilent SurePrint G3 Human Gene Expression 8x60 K microarrays chip (Agilent) at 60 °C for 17 hours according to manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2600D scanner

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and LOWESS normalization. The data were further processed with ExAtlas. See https://lgsun.irp.nia.nih.gov/exatlas/ for details

organism: Homo sapiens

source_name: IAV-specific CD8 T cells

label_protocol: 400 ng of total RNA was used for cRNA synthesis using LowInput QuickAmp labeling kit (Agilent).

growth_protocol: Antigen-specific cells were sorted

extract_protocol: Total RNA extracted using RNeasy Mini kit (Qiagen) following manufacturer's instructions

value: CD8 T cells

tag: age

value: day 0

tag: antigen

value: IAV

source_name: Universal Human reference RNA

tag: sample type

value: Reference RNA


title: CMV-specific CD8 T cells Replicate 1

description: Biological replicate 1 of 4. CMV-specific CD8 T cells

source_name: CMV-specific CD8 T cells

value: CMV


title: IAV-specific CD8 T cells Replicate 1

description: Biological replicate 1 of 4.  IAV-specific CD8 T cells


title: CMV-specific CD8 T cells Replicate 2

description: Biological replicate 2 of 4. CMV-specific CD8 T cells


title: single protoplasts transfected with a pool of bHLHs; protoplast #87


title: i706_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 89


title: CMV-specific CD8 T cells Replicate 3

description: Biological replicate 3 of 4. CMV-specific CD8 T cells


title: IAV-specific CD8 T cells Replicate 2

description: Biological replicate 2 of 4.  IAV-specific CD8 T cells


title: PTC11_2_H3K27me3

source_name: Induced pluripotent stem cells (iPSCs) derived from PTCs


title: CMV-specific CD8 T cells Replicate 4

description: Biological replicate 4 of 4. CMV-specific CD8 T cells


title: single protoplasts transfected with a pool of bHLHs; protoplast #86


title: PTC11_1_H3K27me3


title: single protoplasts transfected with a pool of bHLHs; protoplast #84


title: i706_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 88


title: single protoplasts transfected with a pool of bHLHs; protoplast #85


title: i706_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 86


title: i706_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 87


title: single protoplasts transfected with a pool of bHLHs; protoplast #83


title: i706_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 85


title: TT1_H3K36me3


title: TT4_H3K36me3


title: single protoplasts transfected with a pool of bHLHs; protoplast #78


title: single protoplasts transfected with a pool of bHLHs; protoplast #81


title: single protoplasts transfected with a pool of bHLHs; protoplast #79


title: single protoplasts transfected with a pool of bHLHs; protoplast #82


title: single protoplasts transfected with a pool of bHLHs; protoplast #80


title: PTC11_H3K36me3


title: single protoplasts transfected with a pool of bHLHs; protoplast #75


title: i706_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 83


title: TT4_H3K4me3


title: single protoplasts transfected with a pool of bHLHs; protoplast #74


title: single protoplasts transfected with a pool of bHLHs; protoplast #73


title: i706_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 84


title: i706_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 82


title: single protoplasts transfected with a pool of bHLHs; protoplast #77


title: TT1_H3K4me3


title: single protoplasts transfected with a pool of bHLHs; protoplast #72


title: single protoplasts transfected with a pool of bHLHs; protoplast #76


title: i710_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 119


title: i706_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 81


title: single protoplasts transfected with a pool of bHLHs; protoplast #71


title: PTC12_H3K36me3


title: PTC12_H3K4me3


title: IAV-specific CD8 T cells Replicate 4

description: Biological replicate 4 of 4.  IAV-specific CD8 T cells


title: single protoplasts transfected with a pool of bHLHs; protoplast #69


title: PTC11_H3K4me3


title: i705_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 80


title: single protoplasts transfected with a pool of bHLHs; protoplast #68


title: single protoplasts transfected with a pool of bHLHs; protoplast #67


title: i705_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 79


title: 4hr_control_3D_replicate2_18

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins Dr

institute: NIBR

data_processing:
Reads were generated from by a HiSeq 1000 instrument with bcl2fastq from Illumina, v 2.20.0.422-2 and were aligned to a mouse reference based on ensembl version 100 with STAR aligner v2.7.3a (23).
Gene counts were assessed with RSEM v1.3 (24).
Differential gene expression was assessed with DESeq2 v.1.28.0, in R version 4.0 (25)
Assembly: ensembl version 101
Supplementary files format and content: a single Excel file includes DESEQ2-derived expression values for each Sample

source_name: RPTEC

growth_protocol: From 24-well TC dishes, human RPTEC (in monolayer, or 3D in 50% matrigel) were lysed directly on the plate,

extract_protocol:
Samples were homogenized using QiaShredder, and then RNA was extracted from the cells using a Zymo DirectZol kit with the elution step done in water.
RNA libraries for RNA-seq were prepared using Lexogen RNA Library Prep Kit following manufacturer's protocols.

tag: cell line

value: RPTEC

value: proximal tubule epithelial cells

tag: treatment

tag: time


title: single protoplasts transfected with a pool of bHLHs; protoplast #65


title: 4hr_control_3D_replicate3_24


title: single protoplasts transfected with a pool of bHLHs; protoplast #66


title: single protoplasts transfected with a pool of bHLHs; protoplast #64


title: i705_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 78


title: 4hr_control_3D_replicate1_12


title: single protoplasts transfected with a pool of bHLHs; protoplast #62


title: i705_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 77


title: i705_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 76


title: 4hr_control_2D_replicate3_21


title: single protoplasts transfected with a pool of bHLHs; protoplast #61


title: 4hr_control_2D_replicate2_15


title: single protoplasts transfected with a pool of bHLHs; protoplast #60


title: i705_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 75


title: single protoplasts transfected with a pool of bHLHs; protoplast #70


title: 4hr_control_2D_replicate1_9


title: single protoplasts transfected with a pool of bHLHs; protoplast #57


title: single protoplasts transfected with a pool of bHLHs; protoplast #56


title: single protoplasts transfected with a pool of bHLHs; protoplast #53


title: single protoplasts transfected with a pool of bHLHs; protoplast #52


title: single protoplasts transfected with a pool of bHLHs; protoplast #54


title: single protoplasts transfected with a pool of bHLHs; protoplast #51


title: 4hr_cisplatin_3D_replicate1_13


title: i705_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 71


title: single protoplasts transfected with a pool of bHLHs; protoplast #59


title: 4hr_cisplatin_2D_replicate3_22


title: single protoplasts transfected with a pool of bHLHs; protoplast #49


title: single protoplasts transfected with a pool of bHLHs; protoplast #48


title: single protoplasts transfected with a pool of bHLHs; protoplast #58


title: 4hr_cisplatin_2D_replicate2_16


title: i705_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 70


title: 4hr_cisplatin_2D_replicate1_10


title: single protoplasts transfected with a pool of bHLHs; protoplast #46


title: i705_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 74


title: single protoplasts transfected with a pool of bHLHs; protoplast #45


title: 4hr_cisplatin_3D_replicate3_25


title: single protoplasts transfected with a pool of bHLHs; protoplast #44


title: i705_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 68


title: single protoplasts transfected with a pool of bHLHs; protoplast #55


title: i705_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 73


title: 4hr_cadmium_3D_replicate3_26


title: i705_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 72


title: 4hr_cisplatin_3D_replicate2_19


title: single protoplasts transfected with a pool of bHLHs; protoplast #47


title: single protoplasts transfected with a pool of bHLHs; protoplast #43


title: i705_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 67


title: 4hr_cadmium_3D_replicate2_20


title: single protoplasts transfected with a pool of bHLHs; protoplast #41


title: i705_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 66


title: 4hr_cadmium_3D_replicate1_14


title: single protoplasts transfected with a pool of bHLHs; protoplast #40


title: i705_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 65


title: single protoplasts transfected with a pool of bHLHs; protoplast #38


title: i705_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 69


title: single protoplasts transfected with a pool of bHLHs; protoplast #37


title: 4hr_cadmium_2D_replicate3_23


title: i704_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 64


title: single protoplasts transfected with a pool of bHLHs; protoplast #36


title: single protoplasts transfected with a pool of bHLHs; protoplast #35


title: single protoplasts transfected with a pool of bHLHs; protoplast #34


title: i704_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 63


title: 4hr_cadmium_2D_replicate1_11


title: single protoplasts transfected with a pool of bHLHs; protoplast #33


title: i704_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 62


title: i704_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 61


title: single protoplasts transfected with a pool of bHLHs; protoplast #42


title: single protoplasts transfected with a pool of bHLHs; protoplast #30


title: single protoplasts transfected with a pool of bHLHs; protoplast #32


title: single protoplasts transfected with a pool of bHLHs; protoplast #29


title: 48hr_control_3D_replicate3_60


title: i704_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 60


title: single protoplasts transfected with a pool of bHLHs; protoplast #28


title: 48hr_control_3D_replicate1_48


title: 48hr_control_3D_replicate2_54


title: i704_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 59


title: single protoplasts transfected with a pool of bHLHs; protoplast #39


title: single protoplasts transfected with a pool of bHLHs; protoplast #27


title: single protoplasts transfected with a pool of bHLHs; protoplast #26


title: single protoplasts transfected with a pool of bHLHs; protoplast #25


title: 48hr_control_2D_replicate2_51


title: i704_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 58


title: 4hr_cadmium_2D_replicate2_17


title: single protoplasts transfected with a pool of bHLHs; protoplast #24


title: single protoplasts transfected with a pool of bHLHs; protoplast #23


title: i704_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 57


title: 48hr_control_2D_replicate1_45


title: single protoplasts transfected with a pool of bHLHs; protoplast #22


title: single protoplasts transfected with a pool of bHLHs; protoplast #21


title: single protoplasts transfected with a pool of bHLHs; protoplast #31


title: single protoplasts transfected with a pool of bHLHs; protoplast #20


title: i704_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 56


title: 48hr_cisplatin_3D_replicate3_61


title: single protoplasts transfected with a pool of bHLHs; protoplast #18


title: single protoplasts transfected with a pool of bHLHs; protoplast #19


title: single protoplasts transfected with a pool of bHLHs; protoplast #17


title: single protoplasts transfected with a pool of bHLHs; protoplast #16


title: i704_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 54


title: 48hr_cisplatin_3D_replicate2_55


title: 48hr_control_2D_replicate3_57


title: i704_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 53


title: i704_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 55


title: single protoplasts transfected with a pool of bHLHs; protoplast #14


title: 48hr_cisplatin_2D_replicate3_58


title: single protoplasts transfected with a pool of bHLHs; protoplast #13


title: single protoplasts transfected with a pool of bHLHs; protoplast #12


title: single protoplasts transfected with a pool of bHLHs; protoplast #15


title: i704_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 52


title: single protoplasts transfected with a pool of bHLHs; protoplast #50


title: single protoplasts transfected with a pool of bHLHs; protoplast #11


title: 48hr_cisplatin_2D_replicate2_52


title: i704_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 51


title: i704_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 50


title: 48hr_cisplatin_2D_replicate1_46


title: single protoplasts transfected with a pool of bHLHs; protoplast #10


title: single protoplasts transfected with a pool of bHLHs; protoplast #8


title: single protoplasts transfected with a pool of bHLHs; protoplast #7


title: 48hr_cadmium_3D_replicate3_62


title: single protoplasts transfected with a pool of bHLHs; protoplast #9


title: i704_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 49


title: 48hr_cadmium_3D_replicate2_56


title: single protoplasts transfected with a pool of bHLHs; protoplast #5


title: 48hr_cisplatin_3D_replicate1_49


title: single protoplasts transfected with a pool of bHLHs; protoplast #6


title: i703_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 48


title: single protoplasts transfected with a pool of bHLHs; protoplast #3


title: i703_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 47


title: 48hr_cadmium_2D_replicate3_59


title: single protoplasts transfected with a pool of bHLHs; protoplast #2


title: single protoplasts transfected with a pool of bHLHs; protoplast #1


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #96


title: i703_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 46


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #95


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #94


title: i703_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 45


title: 48hr_cadmium_2D_replicate1_47


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #93


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #92


title: i703_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 44


title: 0hr_control_3D_replicate4_8


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #91


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #89


title: 48hr_cadmium_3D_replicate1_50


title: 0hr_control_3D_replicate3_7


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #90


title: i703_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 43


title: i703_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 42


title: single protoplasts transfected with a pool of bHLHs; protoplast #4


title: f5_PTS1_c, small-sample RNA-seq, female

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 94). Transcript per million (TPM) and expected counts were generated by RSEM. All samples are of high percentage of uniquely mapped reads (> 80%) and are included for downstream analysis. Unless otherwise specified, the computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
ATAC-seq data was processed using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). In brief, The illumina adapters (-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT) were removed using cutadapt. Trimmed pair-ended reads were mapped mm10 (iGenomes) using BOWTIE2. Duplicated reads were marked by Picard and removed by Samtools (-F1804, -q 30). Peak calling was performed using MACS2 after the reads were shifted. Peaks falling into the blacklist regions were removed based on mm10-blacklist
Assembly: Ensemble release 94 and mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Kidney

growth_protocol: All animal work was conducted in accordance with NIH animal protocol (H-0047R4). 6- to 8-week-old male and female C57BL/6 mice from Taconic were used throughout the study.

extract_protocol:
2-5 tubules were collected for either RNA extraction (Direct-zol RNA MicroPrep kit, Zymo Research) or ATAC-seq.
Trizol-extracted RNA was eluted in 10 µl water and immediately proceeded to cDNA generation using the SMARTer V4 Ultra Low RNA Kit (Takara Bio). cDNA was generated with 10-12 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform.

tag: Sex

value: female

value: Kidney

value: Proximal tubule cells


title: 0hr_control_3D_replicate2_6


title: 0hr_control_3D_replicate1_5


title: 48hr_cadmium_2D_replicate2_53


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #87


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #88


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #86


title: f5_PTS1_b, small-sample RNA-seq, female


title: i703_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 40


title: f5_PTS1_a, small-sample RNA-seq, female


title: 0hr_control_2D_replicate4_4


title: i703_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 41


title: f4_PTS1_c, small-sample RNA-seq, female


title: i703_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 38


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #85


title: f4_PTS1_b, small-sample RNA-seq, female


title: 0hr_control_2D_replicate2_2


title: i703_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 37


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #84


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #83


title: 0hr_control_2D_replicate1_1


title: i703_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 36


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #82


title: f5_PTS3_b, small-sample RNA-seq, female


title: f4_PTS1_a, small-sample RNA-seq, female


title: i703_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 35


title: i703_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 39


title: f5_PTS3_a, small-sample RNA-seq, female


title: PILLAR-3

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

data_processing:
Illumina base call (BCL) files were converted in fastq files through bcl2fastq
Sequence reads were trimmed using cutadapt to remove adaptor sequences, poly-A tails and low-quality end bases
Alignment was performed by using RSEM 1.3 with STAR 2.7
Genes without identifiers in the current NCBI annotation or if not expressed at a count-per-million (CPM) higher than 0.5 in at least 3 samples of at least one condition (flat or micropillared PDMS) were filtered out
Data were normalized using the trimmed mean of M-values normalization method (TMM) implemented in edgeR package (version 3.34.1) within Bioconductor (version 3.13) in R (version 4.1.1).
Genome_build: Human genome GRCh38.p13 (database version 103)
Supplementary_files_format_and_content: Matrix table with counts per million (CPM) for every gene and every sample

source_name: SaOs-2 cells cultured on micro-pillared substrate

growth_protocol: SaOs-2 cell line has been obtained from Chinese Academy of Sciences cell bank and maintained in DMEM (cat#11965, ThermoScientific) supplemented with 10% FBS (ThermoScientific). Cells were maintained on culture-ware coated with Matrigel growth-factor reduced (MGFR 50 μg/ml, cat# 354230, Corning) and passaged by 0.25% trypsin digestion (ThermoScientific) before reaching confluence.

extract_protocol:
Cell lysis was carried out using TRIzol (ThermoScientific) followed by RNA purification from the aqueous phase with RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing by Genewiz using standard Illumina protocols

treatment_protocol: Cells were cultured for 48 h on flat or micropillared PDMS substrates. Prior to cell seeding, PDMS substrates were coated with 50 μg/ml MGFR at 4°C for at least 3 hours and equilibrated in cell incubator for 3 hours. Soft-edge cell scrapers were employed for homogenous MGFR distribution in inter-pillar spaces and bubble displacement prior to 4°C incubation.

value: SaOs-2 cell

value: primary osteogenic sarcoma

tag: passage


title: 0hr_control_2D_replicate3_3


title: PILLAR-2


title: f4_PTS3_b, small-sample RNA-seq, female


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #81


title: i703_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 33


title: i703_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 34


title: f4_PTS3_a, small-sample RNA-seq, female


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #79


title: i702_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 32


title: f3_PTS3_b, small-sample RNA-seq, female


title: FLAT-4

source_name: SaOs-2 cells cultured on flat substrate


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #78


title: i702_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 31


title: f3_PTS3_a, small-sample RNA-seq, female


title: PILLAR-1


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #77


title: PILLAR-4


title: i702_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 30


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #76


title: FLAT-2


title: FLAT-3


title: i702_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 29


title: FLAT-1


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #75


title: i702_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 28


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #80


title: i702_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 27


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #74


title: i702_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 26


title: f3_PTS2_a, small-sample RNA-seq, female


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #73


title: f2_PTS2_a, small-sample RNA-seq, female


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #72


title: i702_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 25


title: f1_PTS2_b, small-sample RNA-seq, female


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #71


title: single protoplasts transfected with a pool of bHLHs; protoplast #63


title: f1_PTS2_a, small-sample RNA-seq, female


title: f2_PTS3_a, small-sample RNA-seq, female


title: f3_PTS2_b, small-sample RNA-seq, female


title: RNAseq human LEC

city: Adelaide

first: Natasha

last: Harvey

state: SA

address: UniSA CRI Building, North Terrace

country: Australia

institute: Centre for Cancer Biology

data_processing:
Reads were mapped against the human reference genome (hg19) using Tophat version 2.1.1 with passed read pair distance arguments
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file of gene expression

source_name: Human lymphatic endothelial cells

extract_protocol:
Refer to Kazenwadel et al, JCI, 2015
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human lymphatic endothelial cells

tag: passages

value: HMVEC-dLyAd (Lonza)


title: ChIP-Seq FOXC2

description: Control Input 5

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.7.9a-r786, allowing at most 3 alignments
Peak calling was done by MACS version 1.4
Genome_build: hg19
Supplementary_files_format_and_content: peak files were generates using MACS1.4

extract_protocol:
Refer to Kazenwadel et al, JCI, 2015
Single read – Illumina

value: 3 and 4

value: HMVEC-dLyAd

value: goat anti-FOXC2 (Abcam, ab5060)


title: ChIP-Seq input 5

value: none (input)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #70

value: leaf protoplasts


title: RNAseq human BEC

source_name: Human blood vascular endothelial cells

value: Human blood vascular endothelial cells

value: HMVEC-dBlAd (Lonza)


title: i702_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 23

value: Hypothalamus


title: i702_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 22


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #69


title: ChIP-Seq NFATC1

description: Control Input 5

value: rabbit anti-NFATC1 (Santa Cruz, sc13033X)


title: f2_PTS2_b, small-sample RNA-seq, female


title: placenta RNA-seq, e9.5, rep6

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

data_processing:
The quality and adapter content were assessed using FastQC (v0.11.7). Low quality reads and adapters were trimmed with Trimmomatic (version 0.39).
Technical replicates were then merged, and the reads were pseudo-aligned and quantified (in TPM) using Kallisto (version 0.43.1; l = 200, s = 30; b = 100).
Transcript sequences on autosomal and sex chromosomes of the mouse genome (GRCm38.p6) from Ensembl release 98 were used to build the Kallisto index.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited file with estimated raw counts on transcript level obtained with Kallisto

source_name: fetal placenta

extract_protocol:
Placenta tissue was collected from timed pregnant mice following the guidelines and protocol approved by Iowa State University Institutional Animal Care and Use Committee (IACUC), protocol number 18–350.
Placenta samples were collected at e7.5, e8.5, e9.5 following the same protocol in Tuteja et al., 2016.
Placenta tissue was collected for a total of 6 biological replicates for each timepoint. For e7.5, 12 ectoplacental cones (EPCs) were collected per replicate. For e8.5, five placentas were collected per replicate, and for e9.5, one placenta was collected per replicate.
Tissues were processed immediately after collection for RNA isolation using the Purelink RNA micro scale kit (Thermofisher, 12183016). RNA concentration and RIN values were measured using The RNA 6000 Nano assay kit on the Agilent 2100 Bioanalyzer (GTF facility, ISU), and all samples had a RIN score ≥ 7.7
Libraries were sequenced using the Illumina HiSeq 3000 with single-end 50 base pair reads. The pooled library sample was run over two sequencing lanes (technical replicates for each sample).

value: fetal placenta

value: wild type, CD1 mice


title: placenta RNA-seq, e9.5, rep5


title: ChIP-Seq PROX1

description: Control Input 3.5

value: goat anti-PROX1 (AF2727; R&D Systems)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #68


title: placenta RNA-seq, e9.5, rep4


title: i702_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 21


title: ChIP-Seq input 3.5


title: i702_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 20


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #67


title: i702_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 24


title: placenta RNA-seq, e9.5, rep3


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #66


title: i702_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 19


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #65


title: i702_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 18


title: placenta RNA-seq, e9.5, rep2


title: placenta RNA-seq, e9.5, rep1


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #64


title: placenta RNA-seq, e8.5, rep6


title: i702_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 17


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #63


title: young-22

city: Philadelphia

first: Kelly

middle: A

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

description: inDrop

data_processing:
FASTQ files from the sequencing run were downloaded from Illumina’s BaseSpace sequence hub. To resolve the mapping of cellular barcodes and Unique Molecular Identifiers (UMIs), UMI-tools (v1.0.0) was used to whitelist and extract the barcodes. Likely barcodes were found using the whitelist function of UMI-tools, which searches for the inDrop regular expression pattern of "(?P<cell_1>.(7))(?P<discard_1>GAGTGATTGCTTGTGACGCCTT){s<=2}(?P<cell_2>.{8})(?P<umi_1>.{6})T(42).*" in the R2 of the read pairs. Using a whitelist of likely barcodes, the extract function relocated both the cell barcode and the unique molecular identifier found in the same read to the read name in the FASTQ files. The extraction retains the information of unique cellular barcodes while enabling correct read mapping of genes without the attached cell and transcript identifiers. Reads were then mapped using the aligner STAR (v2.7.3). First, the murine genome index was made using the M23 GRCm38 genomic sequence from GENCODE. Using the index, all read pairs were aligned to the genome for an output of BAM files. To limit the variance of amplification on the length of transcripts, the UMI-tools dedup tool was used to deduplicate the reads, which deduplicates UMIs that match to a single transcript. The resulting deduplicated alignments were then mapped to the murine gene transfer file (GTF) from GENCODE using featureCounts to count the number of reads mapping to each gene in the genome. Finally, the UMI-Tools count function was used to summarize the gene counts in each cell in each sample to give an output of a matrix with gene names and cell barcodes.
Assembly: GRCm38
Supplementary files format and content: Matrix files in comma-separated values

source_name: Esophageal epithelium

extract_protocol:
Esophageal epithelium-enriched tissue layer was peeled from muscle then incubated in 1 ml 1X Dispase I (354235; Corning; Bedford, MA, USA) diluted 1:4 in Hank’s Balanced Salt Solution (HBSS; 14025-076; Gibco; Grand Island, NY, USA) for 10 minutes at 37 °C with shaking at 1000 RPM (5384; Eppendorf F1.5 Thermomixer; Hamburg, Germany). Following removal from Dispase I, esophageal epithelium was minced with sharp scissors then incubated in 1 ml of 0.25% Trypsin-EDTA (25-053-CI; Corning; Manassas, VA, USA) for 10 min at 37 °C with shaking at 1000 RPM. Trypsin and tissue pieces were forced through 70 μm cell strainer into 50 ml conical tube containing 4 ml soybean trypsin inhibitor (STI; 9035-81-8; Grand Island, NY, USA). Cells were pelleted at 1300 RPM for 3 min then resuspended in 500 μl complete mouse keratinocyte–serum-free medium (37010022; Gibco; Carlsbad, CA, USA). Cell number and viability were measured using Automated Cell Count (AMQAX1000, Invitrogen Countess II, Bothell, WA, USA) by mixing 5 μl cell suspension with 5 μl 0.4% trypan blue solution (T10282; Invitrogen; Eugene, OR, USA).
Library was performed according to the manufacter’s instructions (Illumina inDrop). In brief, single epithelial cells were isolated into droplets and lysed. Droplets were fused with hydrogel microsphere containing cell-specific barcodes and underwent reverse transcription, with barcodes serving as primers. cDNA was purified from droplets and ligated to adapters, where they were amplified, annealed to indexed primers, and further amplified prior to sequencing.

treatment_protocol:
EoE-like inflammation was induced over a period of 32 days. For 12 days, ears of mice were scraped with a scalpel blade then 20  ul MC903 (10  M dissolved in 100% ethanol) was applied to each ear followed by 10  ul ovalbumin (OVA) (10  M in PBS). From days 15-32, mice were subjected to oral gavage with 100  ul OVA (500 mg/ml in water) every other day and provided ad libitum access to drinking water supplemented with OVA (15 g/L). Mice were euthanized at day 32 and esophagi were dissected for scRNA-Seq analysis.
To induce ESCC, mice were administered 4NQO (100  g/mL in 2% propylene glycol) for 16 weeks via drinking water. 4NQO was then withdrawn for a period of 8 weeks. At the end of this 24-week protocol, mice were euthanized, and esophagi were dissected for scRNA-Seq analysis.

value: Squamous cells

value: Esophageal epithelium

tag: disease state

value: control

tag: strain

value: 3-4 months


title: young-21

description: inDrop


title: i701_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 16


title: i701_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 15


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #62


title: placenta RNA-seq, e8.5, rep5


title: young-62

description: inDrop


title: old-52

description: inDrop

value: 18-20 months


title: young-61

description: inDrop


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #61


title: placenta RNA-seq, e8.5, rep3


title: i701_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 14


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #60


title: old-51

description: inDrop


title: i701_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 13


title: old-42

description: inDrop


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #59


title: i701_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 12


title: placenta RNA-seq, e8.5, rep4


title: placenta RNA-seq, e8.5, rep1


title: young-11

description: inDrop


title: old-41

description: inDrop


title: i701_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 11


title: placenta RNA-seq, e7.5, rep6


title: old-32

description: inDrop


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #57


title: i701_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 10


title: young-12

description: inDrop


title: placenta RNA-seq, e7.5, rep5


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #56


title: i701_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 9


title: old-31

description: inDrop


title: i701_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 8


title: placenta RNA-seq, e7.5, rep4


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #55


title: i701_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 7


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #54


title: 17M-4NQO-16W2

description: inDrop

value: induced with ESCC

value: 8-10 months


title: placenta RNA-seq, e7.5, rep3


title: 17M-4NQO-16W1

description: inDrop


title: placenta RNA-seq, e7.5, rep2


title: 17F-4NQO-16W2

description: inDrop


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #53


title: placenta RNA-seq, e7.5, rep1


title: i701_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 6


title: 17F-4NQO-16W1

description: inDrop


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #58


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #52


title: i701_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 5


title: 12oldEoE

description: inDrop

value: induced with EoE

value: 19-20 months


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #51

value: leaf protoplasts


title: i701_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 4


title: 11oldEoE

description: inDrop


title: i701_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 3


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #49


title: 10youngEoE

description: inDrop

value: 6-8 weeks old


title: i701_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 2


title: i701_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 1


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #46


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #48


title: 9youngEoE

description: inDrop


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #47


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #45


title: 8M-4NQO-16W1

description: inDrop


title: CUTRUN_State3_IgG

first: Sofia

last: Hu

email: sofiahu@mit.edu, xsu@cpdr.org

state: MA

address: 500 Main Street

institute: MIT

description: CUT&RUN for IgG in State 3

data_processing:
CUT&RUN reads were trimmed using cutadapt (v1.16) (-m 10 -q 10). Paired-end reads were aligned to the mm10 reference genome and the E.coli MG1655 using bowtie2 with default parameters. The normalization factor for each replicate was calculated as 1/((unique E.coli reads⁄unique mouse reads)× 100%). Normalized bigWig files were generated for each replicate using the bamCoverage function in the deeptools package by inputting the normalization factor as the --scaleFactor parameter. Replicates were further normalized to IgG negative control using the bigwigCompare function with the parameter --operation log.
Assembly: mm10
Supplementary files format and content: CUT&RUN: bigWig format
Library strategy: CUT&RUN

source_name: State3, IgG

growth_protocol: V6.5 mouse embryonic stem cells (mESC) were cultured on tissue culture-treated 10cm plates pre-coated with 0.2% gelatin in phosphate-buffered saline (PBS). ESC were cultured in Dulbecco’s Modified Eagle Medium (Fisher), plus 10% fetal bovine serum, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x β-mercaptoethanol, and 1000 U ml-1 leukemia inhibitor factor. All cells were grown at 37C and 5% CO2 and passaged every two days to maintain 10-70% confluency.

extract_protocol: CUT&RUN was performed using CUTANA ChIC/CUT&Run Kit (Epicypher 14-1048) following manufacturer’s instruction in User Manual Version 2.1 or User Manual Version 3. Three technical replicates per antibody were performed. For sorted state populations, cells were harvested using versene, and 8x105 cells per replicate were isolated by flow cytometry. Harvested cells were permeabilized using 0.005% digitonin. Additionally, 1 ug of antibody per sample was added (Klf4 Abcam ab12947, Zfp281 Abcam ab10131), with Rabbit IgG antibody (CUTANA 13-0042) used as the negative control. E.coli spike-in DNA was also added to each sample.

value: embryonic stem cell line

tag: cut&run antibody

value: IgG (CUTANA 13-0042)

value: WT


title: Rat,PH,C2-3

city: Nanjing

first: Liu

last: Xu

address: No.138,Xianlin Avenue,Qixia District,Nanjing City

institute: Nanjing University of Chinese medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Differential expression analysis was performed using the DESeq2 . P value < 0.05 and foldchange > 1.5 or foldchange < 0.67 was set as the threshold for significantly differential expression gene (DEGs) .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Rattus norvegicus

source_name: tibia

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min.  B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube.  C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase.  D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through.  E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.  F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min.  G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.  H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3.  I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
1. Purify and Fragment mRNA  a. Add 50 μL RNA Purification Beads to each well with 50 μL total RNA (4μg) and mix thoroughly.  b. Incubate at 65°C for 5 min, remove at 4°C, and then place at room temperature for 5 min.  c. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.  d. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly.  e. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.  f. Add 50 μL of Elution Buffer in each well and mix thoroughly.  g. Incubate at 80°C for 2 min, remove at 25°C, and then place at room temperature.  h. Add 50 μL of Beads Binding Buffer in each well and mix thoroughly. The mixture was placed at room temperature for 5 min.  i. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.  j. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly.  k. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.  l. Remove the magnetic stand, add 19.5 μL of Elute, Primer,Fragment Mix in each well and mix thoroughly.  m. Incubate at 94°C for 8 min, remove at 4°C, and then centrifuge.  2. Synthesize First Strand cDNA  a. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well and mix thoroughly.  b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C.  3. Synthesize Second Strand cDNA  a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL Resuspension Buffer) in each well.  b. Add 20 μL Second Strand Marking Master Mix and mix thoroughly. The mixture was incubated at 16°C for 60 min.  3.1 Purification  a. Add 90 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.  b. Place it on the magnetic stand at room temperature for 5 min.  c. Remove and discard all of the supernatant from each well.  d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.  e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.  f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.  g. Add 17.5 μL Resuspension Buffer and mix thoroughly.  h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min.  i. Transfer 15 μL the supernatant from each well into the new PCR plate.  4. Adenylate 3’Ends  a. Add 2.5 μL diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL Resuspension Buffer) in each well.  b. Add 12.5 μL A-Tailing Mix and mix thoroughly.  c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C.  5. Ligate Adapters  a. Add 2.5 μL diluted Ligation Control (1 μL Ligation Control + 99 μL Resuspension Buffer) in each well.  b. Add 2.5 μL Ligation Mix.  c. Add 2.5 μL RNA Adapter Index and mix thoroughly.  d. The mixture was incubated at 30°C for 10 min.  e. Add 5 μL Stop Ligation Buffer in each well and mix thoroughly.  5.1 Purification  a. Add 42 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.  b. Place it on the magnetic stand at room temperature for 15 min.  c. Remove and discard 79.5 μL of the supernatant from each well.  d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.  e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.  f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.  g. Add 52.5 μL Resuspension Buffer and mix thoroughly.  h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min.  i. Transfer 50 μL the supernatant from each well into the new PCR plate.  j. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.  k. Place it on the magnetic stand at room temperature for 15 min.  l. Remove and discard 95 μL of the supernatant from each well.  m. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.  n. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.  o. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.  p. Add 22.5 μL Resuspension Buffer and mix thoroughly.  q. Incubate the mixture at room temperature for 2 min. Place it on the magnetic  stand at room temperature for 5 min.  r. Transfer 20 μL the supernatant from each well into the new PCR plate.  6. Enrich DNA Fragments  a. Add 5 μL PCR Primer Cocktail.  b. Add 25 μL PCR Master Mix and mix thoroughly.  c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 sec; 15  cycles 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; 1 cycle 72°C for 5 min; hold at 10°C.  7. Purification  a. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.  b. Place it on the magnetic stand at room temperature for 15 min.  c. Remove and discard 95 μL of the supernatant from each well.  d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.  e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.  f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.  g. Add 32.5 μL Resuspension Buffer and mix thoroughly.  h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic  stand at room temperature for 5 min.  i. Transfer 30 μL the supernatant from each well into the new PCR plate.  8. Validate library  a. Load 1 μL sample on an Agilent 2100 Bioanalyzer.  b. Check the size and purity of the library.

value: Sprague Dawley

value: 10 weeks old

value: Male

value: peptide hydrogel treatment group

value: tibia


title: Rat,PH,C2-4


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #50


title: Rat,PH,C2-2


title: Embryonic mouse lymphatic endothelial cells at E18.5, biological replicate 2

last: Toubia

address: Frome Rd

hyb_protocol: Standard protocols for Affymetrix GeneChip Mouse Gene 1.0 ST Array

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: The data were processed using the R package Oligo (version 1.54.1) using the RMA method for background correction and normalization.

label: Biotin

source_name: Lymphatic endothelial cells

extract_protocol: As published in Kazenwadel J, Michael MZ, Harvey NL. Prox1 expression is negatively regulated by miR-181 in endothelial cells. Blood. 2010 Sep 30;116(13):2395-401. doi: 10.1182/blood-2009-12-256297.

value: Embryonic

value: Lymphatic endothelial cells

value: Embryonic day 18.5


title: Embryonic mouse lymphatic endothelial cells at E18.5, biological replicate 1

label_protocol: Standard protocols for Affymetrix GeneChip Mouse Gene 1.0 ST Array


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #44

source_name: leaf protoplasts


title: Embryonic mouse lymphatic endothelial cells at E18.5, biological replicate 3


title: Embryonic mouse lymphatic endothelial cells at E14.5, biological replicate 3

value: Embryonic day 14.5


title: Embryonic mouse lymphatic endothelial cells at E16.5, biological replicate 2

value: Embryonic day 16.5


title: Embryonic mouse lymphatic endothelial cells at E16.5, biological replicate 3


title: Embryonic mouse lymphatic endothelial cells at E16.5, biological replicate 1


title: 8M-4NQO-16W2

description: inDrop

value: Squamous cells

value: Esophageal epithelium

value: induced with ESCC

value: 8-10 months


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #43

value: leaf protoplasts


title: CUTRUN_State1_IgG

description: CUT&RUN for IgG in State 1

source_name: State1, IgG

value: embryonic stem cell line

value: IgG (CUTANA 13-0042)


title: ANFX6013

city: Ljubljana

first: Ales

last: Maver

address: Slajmerjeva 3

country: Slovenia

institute: Clinical institute of medical genetics Ljubljana Slovenia

data_processing:
Demultiplexing and adaptor trimming was performed using the Illumina BCL2Fastq software
Alignments to the human reference genome (hg19) were performed  using bowtie and tophat algorithms
Transcript abundances were then estimated using read counts function in Subread package for R, followed by intersample normalization by variance modelling at the observational level (voom) approach implemented in limma Bioconductor package.
Differences in gene expression were estimated using linear modelling and significance estimation procedures in limma.
Assembly: hg19, mm10

source_name: Peripheral blood

extract_protocol:
Whole blood samples were collected into Tempus™ Blood RNA tubes (Thermo Fisher Scientific, Waltham, MA, USA) or PAXgene blood tubes (Qiagen, Hilden, Germany) containing RNA stabilizing reagent. Total RNA was isolated using QuickGene blood cell kit (RB-S) and Fujifilm QuickGene-810 automated system (Fujifilm Life Sciences, Tokyo, Japan) or PAXgene Blood miRNA Kit and fully automated QIAcube system (Qiagen), according to manufacturer’s isolation protocol. The purity of isolated RNA was assessed using the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific) and integrity was determined on Agilent 2100 Bioan+alyzer using RNA 6000 Nano LabChip kit (Agilent Technologies, Santa Clara, CA, USA). All samples used for library preparation had RNA integrity values greater than 7.0. Extracted RNA samples were stored at -80ºC before further processing.
We performed library preparation using the TrueSeq stranded total RNA sample preparation kit (Illumina, San Diego, CA, USA), according to the manufacturer’s protocol. After Ribo-Zero rRNA depletion, the remaining RNA was purified, fragmented, and primed for first strand cDNA synthesis with reverse transcriptase (SuperScript II) and random primers, followed by second strand cDNA synthesis performed in the presence of dUTP. Blunt ended double strand DNA was 3’ adenylated and multiple indexing adapters (T-tailed) were ligated to the ends of the ds cDNA. Fragments with adapter molecules on both ends were selectively enriched with 15 cycles of PCR reaction. 44 libraries were normalized to the final concentration of 10 nM and then pooled in equimolar concentrations. Sequencing was performed on the Illumina Hiseq 2000 sequencing system in 2×100 sequencing cycles using pair-end sequencing mode.

value: Peripheral blood

tag: anaphylaxis stage/severity

tag: individual


title: CUTRUN_bulk_IgG

description: CUT&RUN for IgG in unsorted cells

source_name: bulk, IgG

tag: cell type

tag: genotype

value: WT


title: ANFX6008

tag: tissue


title: CUTRUN_bulk_Zfp281_BR3

description: CUT&RUN for Zfp281 in unsorted cells

source_name: bulk, Zfp281

value: Zfp281 (Abcam ab10131)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #42


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #41


title: ANFX6009


title: Embryonic mouse lymphatic endothelial cells at E14.5, biological replicate 1

tag: age


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #40


title: CUTRUN_bulk_Zfp281_BR2

description: CUT&RUN for Zfp281 in unsorted cells


title: Embryonic mouse blood vascular endothelial cells at E18.5, biological replicate 3

source_name: Blood vascular endothelial cells

value: Blood vascular endothelial cells


title: CUTRUN_bulk_Zfp281_BR1

description: CUT&RUN for Zfp281 in unsorted cells


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #39


title: ANFX6007


title: CUTRUN_State3_Zfp281_BR3

description: CUT&RUN for Zfp281 in State 3

source_name: State3, Zfp281


title: ANFX6006


title: Embryonic mouse blood vascular endothelial cells at E18.5, biological replicate 2


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #38


title: ANFX6004


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #37


title: Embryonic mouse blood vascular endothelial cells at E16.5, biological replicate 3


title: CUTRUN_State3_Zfp281_BR1

description: CUT&RUN for Zfp281 in State 3


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #36


title: ANFX6328


title: Embryonic mouse lymphatic endothelial cells at E14.5, biological replicate 2


title: Embryonic mouse blood vascular endothelial cells at E16.5, biological replicate 1


title: Embryonic mouse blood vascular endothelial cells at E14.5, biological replicate 3


title: CUTRUN_State2_Zfp281_BR3

description: CUT&RUN for Zfp281 in State 2

source_name: State2, Zfp281


title: Embryonic mouse blood vascular endothelial cells at E18.5, biological replicate 1


title: ANFX6318


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #35


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #34


title: ANFX6314


title: ANFX6005


title: placenta RNA-seq, e8.5, rep2

value: fetal placenta

value: wild type, CD1 mice


title: CUTRUN_State2_Zfp281_BR1

description: CUT&RUN for Zfp281 in State 2


title: CUTRUN_State3_Zfp281_BR2

description: CUT&RUN for Zfp281 in State 3


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #32


title: CUTRUN_State1_Zfp281_BR3

description: CUT&RUN for Zfp281 in State 1

source_name: State1, Zfp281


title: CUTRUN_State1_Zfp281_BR2

description: CUT&RUN for Zfp281 in State 1


title: ANFX6323


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #31


title: Embryonic mouse blood vascular endothelial cells at E14.5, biological replicate 1

value: Embryonic


title: Embryonic mouse blood vascular endothelial cells at E16.5, biological replicate 2


title: Embryonic mouse blood vascular endothelial cells at E14.5, biological replicate 2


title: A3

city: Ningbo

first: yichen

last: chen

address: NO.46 Yangshan Road，Ningbo

institute: Ningbo Institute of Medical Science

description: No pain

data_processing:
Cellranger standard processing
**Cell filter**  Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells:  1.gene counts 500-Inf per cell.  2.UMI counts  3. the percentage of mitochondrial genes < 25% %(customized).  4.DoubletFinder for detecting doublets.
**Cell clustering**  Cell clustering contains the following steps:  1)Normalizing the data  After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression.
PCA(Principal component analysis): To overcome the extensive technical noise in any single gene for scRNA-seq data, Seurat clusters cells based on their PCA scores, with each PC essentially representing a ‘metagene’ that combines information across a correlated gene set.
t-SNE (t-distributed Stochastic Neighbor Embedding) visualization: Seurat continues to use t-SNE as a powerful tool to visualize and explore these datasets. The tSNE aims to place cells with similar local neighborhoods in high-dimensional space together in low-dimensional space.
Assembly: Homo_sapiens_GRCh38_96
Supplementary files format and content: barcodes.tsv.gz,genes.tsv.gz,matrix.mtx.gz,fastq.gz

source_name: Uterine muscle layer

extract_protocol:
Uterine muscle layer tissue was dissected into five segments and the single cell suspension was obtained by enzymatic digestion. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 8000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single Cell 3'  Reagent Kits（v3）.The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system

value: Uterine muscle layer

value: Adenomyosis tissue1(Painfree)


title: A4

description: No pain

value: Adenomyosis tissue2(Painfree)


title: A1

description: VAS score greater than or equal to 4

value: Adenomyosis tissue1(Pain)


title: ANFX6337


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #30


title: CUTRUN_State2_Zfp281_BR2

description: CUT&RUN for Zfp281 in State 2


title: ANFX6335


title: CUTRUN_State1_Zfp281_BR1

description: CUT&RUN for Zfp281 in State 1


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #33


title: CUTRUN_bulk_Klf4_BR3

description: CUT&RUN for Klf4 in unsorted cells

source_name: bulk, Klf4

value: Klf4 (Abcam ab12947)


title: A2

description: VAS score greater than or equal to 4

value: Adenomyosis tissue2(Pain)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #28


title: ANFX6307


title: CUTRUN_bulk_Klf4_BR2

description: CUT&RUN for Klf4 in unsorted cells


title: ANFX6332


title: PAE2_72_Lapatinib

city: Palo Alto

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Assembly: hg38
Supplementary files format and content: Raw read counts from featureCounts

source_name: Endothelial cells

extract_protocol:
miRNeasy Micro Kit  (Qiagen)
Library construted by Novogene
bulk RNA-seq

value: Primary aorta endothelial cells

value: ATCC:Human Aortic EC

value: Lapatinib (1 uM)

value: 72 hours


title: PAE2_72_Doxorubicin

value: Doxorubicin (0.05 uM)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #29

value: leaf protoplasts


title: ANFX6339

value: Peripheral blood


title: PAE2_72_dmso

value: DMSO


title: PAE2_72_Sunitinib

value: Sunitinib (0.1 uM)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #26


title: ANFX6303


title: CUTRUN_bulk_Klf4_BR1

description: CUT&RUN for Klf4 in unsorted cells

value: embryonic stem cell line

value: WT


title: CUTRUN_State3_Klf4_BR3

description: CUT&RUN for Klf4 in State 3

source_name: State3, Klf4


title: PAE2_72_Cyclophosphamide

value: Cyclophosphamide (100 uM)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #22


title: PAE2_72_Bortezomib

value: Bortezomib (0.002 uM)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #25


title: ANFX6301


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #24


title: CUTRUN_State3_Klf4_BR2

description: CUT&RUN for Klf4 in State 3


title: PAE2_72_Chloroquine

value: Chloroquine (1 uM)


title: ANFX6299


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #23


title: PAE2_72_Carfilzomib

value: Carfilzomib (0.025 uM)


title: ANFX6298


title: CUTRUN_State3_Klf4_BR1

description: CUT&RUN for Klf4 in State 3

value: Klf4 (Abcam ab12947)


title: PAE2_72_Aspirin

value: Aspirin (1 uM)

value: 24 hours


title: PAE2_24_Sunitinib

value: Primary aorta endothelial cells

value: ATCC:Human Aortic EC


title: CUTRUN_State2_Klf4_BR1

description: CUT&RUN for Klf4 in State 2

source_name: State2, Klf4


title: ANFX6297


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #27


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #21


title: CUTRUN_State1_Klf4_BR3

description: CUT&RUN for Klf4 in State 1

source_name: State1, Klf4


title: ANFX6305


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #20


title: PAE2_24_Lapatinib

value: Lapatinib (1 uM)


title: CUTRUN_State1_Klf4_BR2

description: CUT&RUN for Klf4 in State 1


title: ANFX6042


title: PAE2_24_Doxorubicin

value: Doxorubicin (0.05 uM)


title: PAE2_24_Cyclophosphamide


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #17

value: leaf protoplasts


title: CUTRUN_State1_Klf4_BR1

description: CUT&RUN for Klf4 in State 1


title: ChIPseq_Zfp281KO_Klf4

description: ChIPseq for Klf4 in Zfp281KO mESC

data_processing:
scRNAseq: Cellranger (v.3.1.0) mkfastq and count pipelines were used for: demultiplexing, converting to fastq format, combining sequencing results, alignment to GRCm38 (mm10) genome assembly and gene annotation, barcode processing, and UMI counting.
ChIPseq: Reads were aligned to the mm10 reference genome using BWA-MEM (v.0.7.16a) with default parameters. Reads per genomic content (RPGC)-normalized bigWig files were generated for each IP using the bamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads --extendReads 150. Background signal was subtracted from each sample ChIP using the bigwigCompare function with the parameter –operation subtract (ex. Klf4 ChIP signal in Klf4-/- cells was subtracted from Klf4 ChIP signal in WT cells and from Klf4 ChIP signal in Zfp281-/- cells).
V6.5 mouse embryonic stem cells (mESC) were cultured on tissue culture-treated 10cm plates pre-coated with 0.2% gelatin in phosphate-buffered saline (PBS+B39). ESC were cultured in Dulbecco’s Modified Eagle Medium (Fisher), plus 10% fetal bovine serum, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x β-mercaptoethanol, and 1000 U ml-1 leukemia inhibitor factor. All cells were grown at 37C and 5% CO2 and passaged every two days to maintain 10-70% confluency.
Assembly: mm10
Supplementary files format and content: scRNAseq: filtered feature-barcode matrix in MEX format
Supplementary files format and content: ChIPseq: bigWig format

source_name: mouse embryonic stem cell

extract_protocol:
scRNAseq: Single-cell suspension of V6.5 mESC was made by treatment with 0.25% trypsin followed by inactivation in complete medium. Single-cell isolation and library preparation was done using a 10x Genomics Chromium machine in 3’ RNA digital gene expression mode.
ChIP-seq: Cells were crosslinked in 1% formaldehyde on a rocker at room temperature for 10 minutes. Crosslinking was quenched with 250 mM glycine on a rocker at room temperature for 5 minutes. After cell lysis, chromatin was Maase-treated and sonicated using a Covaris220 evolution solicitor. ChIPseq libraries were prepared using NEB UltraII kit from 6-10 ng of DNA. Libraries were prepared by the MIT BioMicro Center.

value: mouse embryonic stem cell

tag: chip antibody

value: Zfp281 KO


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #19

data_processing:
The raw CEL-seq2 reads were demultiplexed based on cell-specific barcodes using Fastq-Multx. The UMI sequences from read 1 were added to the read 2 sequence names and then filtered and trimmed with Fastp (parameters: -y -x -3 -f 6). The clean reads were mapped to B73 RefGen_v3 with Hisat2, and the UMIs quantified with SAMtools and UMI-tools. The counts of UMIs mapped to each gene/locus/construct were normalized to transcripts per million.
Assembly: B73 RefGen_v3
Supplementary files format and content: tab-delimited text file including TPM values for each gene

extract_protocol:
CEL-seq2
CEL-seq2


title: ANFX6036

value: Peripheral blood


title: ANFX6041


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #18


title: ANFX6039


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #15


title: ANFX6034


title: PAE2_24_DMSO

value: DMSO


title: ChIPseq_Zfp281KO_Zfp281

description: ChIPseq for Zfp281KO in Zfp281KO mESC

value: embryonic stem cell line

value: Zfp281 (Abcam ab10131)


title: PAE2_24_Chloroquine


title: ChIPseq_WT_Zfp281

description: ChIPseq for Zfp281 in WT mESC

value: WT


title: ChIPseq_Klf4KO_Zfp281

description: ChIPseq for Zfp281 in Klf4KO mESC

value: Klf4 KO


title: PAE2_24_Carfilzomib

value: Carfilzomib (0.025 uM)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #16


title: ANFX6032


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #14


title: ChIPseq_Klf4KO_Klf4

description: ChIPseq for Klf4 in Klf4KO mESC


title: ANFX6033


title: PAE2_24_Bortezomib

value: Bortezomib (0.002 uM)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #13


title: PAE1_72_Sunitinib

value: PromoCell:Human Aortic EC

value: Sunitinib (0.1 uM)

value: 72 hours


title: ANFX6029


title: PAE1_72_Lapatinib

value: Primary aorta endothelial cells


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #11


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #10


title: Homozygous mutant pre-OP9 cultured

data_processing:
Illumina bcl2fastq Conversion Software v2.20 used for basecalling
Reads were mapped against the mouse reference genome (mm10) using the STAR spliced alignment algorithm version 2.5.3a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts
Duplicate reads were removed using the markdup function of Sambamba version 0.6.7
Deduplicated raw read counts for all annotated genes were tabulated using the htseq-count function of HTSeq version 0.11.2
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file of gene expression

source_name: Lymphatic endothelial cells

growth_protocol: Single cell suspensions from the dorso-anterior regions of an entire litter of embryos of each genotype were FACS sorted. CD45 neg, LYVE1+, VECAD/CD144+ cells were isolated  from each sample and half of these were placed in Trizol.

extract_protocol:
Trizol and Direct-zol RNA microprep kit (ZymoResearch)
RNA was sequenced with a Smart-Seq Stranded Kit (Takara Bio). Single replicate total RNA-seq libraries were multiplexed and sequenced on the Illumina NextSeq 500 platform using the stranded, paired end protocol with a read length of 75.

treatment_protocol: The remaining half of each cell sample was cultured for 7d on OP9 feeder cells (~70% confluent) in 10% MEM-alpha containing cytokines FLT3L, IL3 and SCF (Peprotech) at a concentration of 100 ng/ml each, followed by FACS sorting of LYVE1+,VECAD/CD144+ cells into Trizol.

value: Embryonic

value: Lymphatic endothelial cells

value: pre natal day 14.5

value: Homozygous mutant

tag: culture


title: ANFX6037


title: ChIPseq_WT_Klf4

description: ChIPseq for Klf4 in WT mESC

value: mouse embryonic stem cell

tag: cell line


title: ANFX6030

value: Peripheral blood


title: Homozygous mutant  post-OP9 cultured


title: ANFX6028


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #12

source_name: leaf protoplasts

value: leaf protoplasts


title: Wildtype post-OP9 cultured

value: Wild type


title: PAE1_72_Doxorubicin

tag: treatment

value: Doxorubicin (0.05 uM)


title: ANFX6014


title: CUTRUN_State2_IgG

description: CUT&RUN for IgG in State 2

source_name: State2, IgG

value: embryonic stem cell line

value: IgG (CUTANA 13-0042)

value: WT


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #8


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #7


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #9


title: ANFX6027

source_name: Peripheral blood


title: PAE2_24_Aspirin

value: ATCC:Human Aortic EC

value: Aspirin (1 uM)

tag: time

value: 24 hours


title: PAE1_72_DMSO

value: PromoCell:Human Aortic EC

value: DMSO

value: 72 hours


title: ANFX6023


title: Wildtype pre-OP9 cultured

value: Embryonic

value: Lymphatic endothelial cells


title: ANFX6025


title: PAE1_72_Cyclophosphamide

value: Primary aorta endothelial cells

value: Cyclophosphamide (100 uM)


title: ANFX6020

value: Peripheral blood


title: mPROseq_ESC_unsorted_BR3

description:
mPROseq
nascent RNA

data_processing:
Library strategy: PRO-Seq
scRNAseq: Cellranger (v.3.1.0) mkfastq and count pipelines were used for: demultiplexing, converting to fastq format, combining sequencing results, alignment to GRCm38 (mm10) genome assembly and gene annotation, barcode processing, and UMI counting.
scATACseq: Cellranger ATAC (v.1.1.0) mkfastq and count pipelines were used for demultiplexing sequencing results and converting to fastq format, as well as alignment to GENCODE vM17 basic genome annotation, barcode processing, and UMI counting.
mPROseq: Raw reads were processed using fastxtoolkit (v.0.0.13). Fastq files were converted to fasta format using the fastq_to_fasta command with parameter -n. Adapter sequence was removed using fastx_clipper with parameters -n -a ATCTCGTATGCCGTCTTCTGCTTG -l 14. PCR duplicates were removed using fastx_collapser with default parameters. The 6bp unique molecular identifier (UMI) was removed using fastx_trimmer (-f 7). Then, libraries were demultiplexed using fastx_barcode_splitter with parameters --mismatches 2 --partial 1. Library barcodes were trimmed using fastx_trimmer (-f 10). The reverse complement of trimmed sequences were obtained using fastx_reverse_complement and aligned to the mm10 reference genome using Bowtie2 (v.2.3.5.1) with parameter --sensitive-local -f. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads -e 150.
ATACseq: Reads were trimmed for adapter sequences using TrimGalore (v.0.6.5) (--paired --nextera). Paired-end reads were aligned to the mm10 reference genome using Bowtie2 (v.2.3.5.1) (--very-sensitive -k 10) and filtered for autosomal, properly-paired, mapped read pairs with mapping quality >= 30 using samtools (v.1.10) view (-b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30). Peak calling was performed separately for each sample using Genrich (-a 10 -j -r -e chrM,chrY), excluding ENCODE blacklisted regions (ENCFF547MET.bed, downloaded from https://www.encodeproject.org/files/ENCFF547MET/). Peaks called in each sample were collated, and overlapping peaks were merged to generate a consensus list of peaks using bedtools merge. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads.
RNAseq: Reads were trimmed for adapter sequences using TrimGalore (--paired --illumina --length 20). Sequences were trimmed for read quality using fastq_quality_filter in fastxtoolkit (-Q33 -q 30 -p 90). Paired-end reads were aligned to the mm10 reference genome using hisat2 (v.2.2.0) (--rna-strandness FR). Aligned reads were counted to GENCODE vM15 genomic transcripts using featureCounts in the subread package (v.1.6.2) using default parameters. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .tar archives include barcodes.tsv, features.tsv, and matrix.mtx files.
Supplementary_files_format_and_content: bigWig coverage files

source_name: mouse embryonic stem cell V6.5

growth_protocol: V6.5 mouse embryonic stem cells (ESC) were cultured on tissue culture-treated 10cm plates pre-coated with 0.2% gelatin in phosphate-buffered saline (PBS). ESC were cultured in Dulbecco’s Modified Eagle Medium (Fisher), plus 10% fetal bovine serum, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x β-mercaptoethanol, and 1000 U ml-1 leukemia inhibitor factor. All cells were grown at 37C and 5% CO2 and passaged every two days to maintain 10-70% confluency.

extract_protocol: scRNAseq: Single-cell suspension of V6.5 mESC was made by treatment with 0.25% trypsin followed by inactivation in complete medium. Single-cell isolation and library preparation was done using a 10x Genomics Chromium machine in 3’ RNA digital gene expression mode. scATACseq: Single-nuclei suspension of V6.5 mESC was isolated following the 10x Genomics nuclei isolation protocol (CG000169 Rev D). mPROseq: The PROseq protocol established in Mahat et al. 2016 was modified to enable small cell input and performed. ATACseq: Library preparation was performed according to protocol established in Buenrostro et al. 2013 (PMID 24097267), Buenrostro et al. 2015 (PMID 25559105). RNAseq: RNA was extracted by standard Trizol protocol. rRNA-depleted RNA sequencing libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche 08098140702) to manufacturer’s instructions.

tag: subpopulation

value: unsorted

tag: biological replicate


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #3

value: leaf protoplasts


title: mPROseq_ESC_State3_BR2

description:
mPROseq
nascent RNA

value: late pseudotime


title: PAE1_72_Chloroquine

value: Chloroquine (1 uM)


title: ANFX6024


title: mPROseq_ESC_unsorted_BR2

description:
mPROseq
nascent RNA

value: embryonic stem cell line


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #6


title: ANFX6019


title: mPROseq_ESC_State3_BR1

description:
mPROseq
nascent RNA

value: WT


title: mPROseq_ESC_unsorted_BR1

description:
mPROseq
nascent RNA


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #5


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #1


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #4


title: mPROseq_ESC_State3_BR3

description:
mPROseq
nascent RNA


title: PAE1_72_Aspirin


title: PAE1_24_Sunitinib

value: Sunitinib (0.1 uM)


title: ANFX6017


title: PAE1_24_Lapatinib

value: Lapatinib (1 uM)


title: ANFX6021


title: mPROseq_ESC_State2_BR3

description:
mPROseq
nascent RNA

value: middle pseudotime


title: PAE1_72_Bortezomib

value: PromoCell:Human Aortic EC

value: Bortezomib (0.002 uM)


title: single protoplasts transfected with a pool of pre-meiotic TFs; protoplast #2


title: ANFX6016


title: p35S-GFP-EREB69; protoplast prep #2

data_processing:
RNA-seq reads were mapped to the maize reference genomeusing Hisat v2.1.0. Reads mapped to each gene/locus were counted using the featureCounts program of the Subread package (v1.6.3). Read counts were normalized using edgeR v3.20.9.
Assembly: B73 RefGen_v3
Supplementary files format and content: tab-delimited text file including RPKM values

extract_protocol:
RNA was extracted using the TRI reagent (Sigma-Aldrich).
RNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) following the manufacturer’s protocol for use with the NEBNext Poly(A) mRNA magnetic isolation module.

tag: tf


title: PAE1_72_Carfilzomib

value: Carfilzomib (0.025 uM)

value: 72 hours


title: PAE1_24_Cyclophosphamide

value: 24 hours


title: ANFX6012


title: PAE1_24_Doxorubicin

value: Primary aorta endothelial cells

value: Doxorubicin (0.05 uM)


title: mPROseq_ESC_State2_BR2

description:
mPROseq
nascent RNA


title: mPROseq_ESC_State2_BR1

description:
mPROseq
nascent RNA


title: PAE1_24_Chloroquine


title: PAE1_24_DMSO

value: DMSO


title: CUTRUN_State2_Klf4_BR2

description: CUT&RUN for Klf4 in State 2

value: Klf4 (Abcam ab12947)


title: mPROseq_ESC_State1_BR2

description:
mPROseq
nascent RNA

value: early pseudotime


title: mPROseq_ESC_State1_BR3

description:
mPROseq
nascent RNA


title: p35S-GFP-ZFL1; protoplast prep #4

value: leaf protoplasts


title: ANFX6011

value: Peripheral blood


title: ANFX6010


title: p35S-GFP-ZFL1; protoplast prep #2


title: PAE1_24_Carfilzomib


title: mPROseq_ESC_State1_BR1

description:
mPROseq
nascent RNA

value: embryonic stem cell line


title: PAE1_24_Bortezomib


title: p35S-GFP-NAC25; protoplast prep #4


title: ANFX2420


title: scATACseq_ESC

description: scATACseq

data_processing:
scRNAseq: Cellranger (v.3.1.0) mkfastq and count pipelines were used for: demultiplexing, converting to fastq format, combining sequencing results, alignment to GRCm38 (mm10) genome assembly and gene annotation, barcode processing, and UMI counting.
scATACseq: Cellranger ATAC (v.1.1.0) mkfastq and count pipelines were used for demultiplexing sequencing results and converting to fastq format, as well as alignment to GENCODE vM17 basic genome annotation, barcode processing, and UMI counting.
mPROseq: Raw reads were processed using fastxtoolkit (v.0.0.13). Fastq files were converted to fasta format using the fastq_to_fasta command with parameter -n. Adapter sequence was removed using fastx_clipper with parameters -n -a ATCTCGTATGCCGTCTTCTGCTTG -l 14. PCR duplicates were removed using fastx_collapser with default parameters. The 6bp unique molecular identifier (UMI) was removed using fastx_trimmer (-f 7). Then, libraries were demultiplexed using fastx_barcode_splitter with parameters --mismatches 2 --partial 1. Library barcodes were trimmed using fastx_trimmer (-f 10). The reverse complement of trimmed sequences were obtained using fastx_reverse_complement and aligned to the mm10 reference genome using Bowtie2 (v.2.3.5.1) with parameter --sensitive-local -f. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads -e 150.
ATACseq: Reads were trimmed for adapter sequences using TrimGalore (v.0.6.5) (--paired --nextera). Paired-end reads were aligned to the mm10 reference genome using Bowtie2 (v.2.3.5.1) (--very-sensitive -k 10) and filtered for autosomal, properly-paired, mapped read pairs with mapping quality >= 30 using samtools (v.1.10) view (-b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30). Peak calling was performed separately for each sample using Genrich (-a 10 -j -r -e chrM,chrY), excluding ENCODE blacklisted regions (ENCFF547MET.bed, downloaded from https://www.encodeproject.org/files/ENCFF547MET/). Peaks called in each sample were collated, and overlapping peaks were merged to generate a consensus list of peaks using bedtools merge. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads.
RNAseq: Reads were trimmed for adapter sequences using TrimGalore (--paired --illumina --length 20). Sequences were trimmed for read quality using fastq_quality_filter in fastxtoolkit (-Q33 -q 30 -p 90). Paired-end reads were aligned to the mm10 reference genome using hisat2 (v.2.2.0) (--rna-strandness FR). Aligned reads were counted to GENCODE vM15 genomic transcripts using featureCounts in the subread package (v.1.6.2) using default parameters. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .tar archives include barcodes.tsv, features.tsv, and matrix.mtx files.
Supplementary_files_format_and_content: bigWig coverage files

value: unsorted

value: WT


title: ANFX2300


title: ANFX6015


title: Tim-3 deficient Treg-3

city: Pittsburgh

first: Binfeng

last: Lu

address: 200 Lothrop St

department: Immunology

institute: University of Pittsburgh

data_processing:
RNA-seq data were aligned to mouse reference genome GRCm38 using STAR
Gene expression level was quantified and count expression matrices were generated using RSEM from aligned reads. Count per million (TPM) was used for further analysis.
Package limma in R was used to identify differentially expressed genes (DEGs).
DEGs with Benjamini-Hochberg adjusted P value <0.05 and absolute log2(fold change) (log2FC)>=0.5 were selected for further analysis.
The signal-to-noise ratio was used for gene ranking and javaGSEA was used to run GSEA with 1000 permutations to estimate P values
Genome_build: mm10
Supplementary_files_format_and_content: Comma seperated values file includes TPM values for each sample

source_name: tumoral Treg cells

growth_protocol: MC38 tumors (~8mm in diameter) were isolated from Tim-3 sufficient and Tim-3 deficient in Treg mice.

extract_protocol:
Treg cells were sorted from tumors directly into lysis buffer containing 96-well plate
libraries were generated using the Nextera XT DNA Library Preparation kit (Illumina).Libraries were normalized, diluted and heat-denatured and then loaded for sequencing. Cluster generation and 75bp paired-end dual-indexed sequencing was performed using the NextSeq® 500/550 High Output Kit v2 on the NextSeq 500 Sequencing System (Illumina)

value: tumoral Tregs

tag: tumor type


title: ANFX2190


title: iPSC-EC2_72_Sunitinib

value: iPSC-derived endothelial cells

value: Sunitinib (0.1 uM)


title: p35S-GFP-MYB131; protoplast prep #2


title: Tim-3 deficient Treg-2

tag: strain


title: p35S-GFP-MYB131; protoplast prep #4


title: ANFX2410


title: ANFX2260


title: p35S-GFP-DOF7; protoplast prep #4


title: iPSC-EC2_72_Doxorubicin


title: p35S-GFP-DOF7; protoplast prep #2


title: Tim-3 deficient Treg-1


title: Tim-3 sufficient Treg-3


title: Tim-3 sufficient Treg-2


title: p35S-GFP-NAC25; protoplast prep #2


title: ANFX2330


title: p35S-GFP-WRKY81; protoplast prep #4


title: PAE1_24_Aspirin

value: PromoCell:Human Aortic EC

value: Aspirin (1 uM)


title: Tim-3 sufficient Treg-1


title: iPSC-EC2_72_Cyclophosphamide

value: Cyclophosphamide (100 uM)

value: 72 hours


title: ANFX2140


title: p35S-GFP-WRKY81; protoplast prep #2


title: p35S-GFP-ZHD4; protoplast prep #4