title: Intermediate progenitors - Dam-only_Rep3

description:
pTa1_iDam.bedgraph
pTa1_iDam.bedgraph.bw
pTa1_Notch_unlog.bedgraph
pTa1_RBPJ_unlog.bedgraph


title: CRC00704

status: Public on Jan 07 2022

type: SRA

city: Tao-Yuan

first: Ian Yi-Feng

last: Chang

state: Type below ...

address: 259 Wen-Hwa 1st Road, Kwei-Shan

department: Molecular Medicine Research Center

country: Taiwan

institute: CHANG GUNG UNIVERSITY

library_source: transcriptomic

data_processing:
Raw fastq data were submitted to irweb.irepertoire.com for data analysis.
1) separate reads based on barcode (5'-NNN-BARCODE(6bp)-READS-3') in Read 1 (de-multiplex-script.zip provided by irpertoire.com)
2) map reads to TRA/TRB VDJ sequences
3) assign TRA/TRB reads to correct patients
Genome_build: N/A
Supplementary_files_format_and_content: Text file in comma-separated values (csv) format. The identified sequence and frequencies of TCRA or TCRB sequences. The patient ID are included in the file names.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated following the standard procedure, and total RNA from PBMCs was extracted using TRIzol reagent
A multiplex PCR amplification reaction was used to amplify the TCR immune repertoire. Human TCRα and TCRβ libraries were prepared using the HTAI-M and HTBI-M Kits (iRepertoire, Inc.) according to the manufacturer’s instructions and sequenced on the Illumina MiSeq platform.
Equal concentrations of each library with different barcodes were pooled and sequenced using the Illumina Paired-End Sequencing Kit (MiSeq, Illumina).

tag: disease

value: colon cancer

tag: age

tag: Sex

value: female

tag: tcra

tag: tcrb

tag: run

tag: tissue

value: blood


title: PCC6803_WT_2h_rep2

type: RNA

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture, at 4% NaCl for 2h

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis sp. 6803 substrain PCC-M (Trautmann et al., 2012) was used for the experiment. Axenic cells were grown photoautotrophically at 29°C in glass tubes containing liquid BG11 medium (Rippka et al., 1979, TES-buffered at pH 8). If not stated differently, cultures were aerated with CO2-enriched air (5% CO2 [v/v]) and kept under continuous illumination of 150 µmol photons m-2 s-1 (warm light, Osram L58 W32/3).

extract_protocol: Synechocystis 6803 cells were collected by rapid filtration on hydrophilic polyethersulfone filters (Pall Supor 800 Filter, 0.8 µm). Filters covered with cells were dissolved in 1 ml PGTX (Pinto et al., 2009; BMC Mol Biol 10: 79) and RNA was extracted as described (Hein et al., 2013; RNA Biol 10: 852–864).

treatment_protocol: Control cells were cultured in NaCl-free BG11 medium. Short-term salt shock experiments were performed by adding crystalline NaCl to a final concentration of 4% into the suspension of control cultures at time point zero. Subsequently, cells were harvested at defined time points.

tag: genotype

value: WT

tag: treatment


title: CRC00607

value: male


title: PCC6803_WT_0h_rep2

source_name: cells from liquid culture, control conditions (0% NaCl)


title: PCC6803_WT_0.5h_rep1

source_name: cells from liquid culture, at 4% NaCl for 0.5h


title: PCC6803_WT_0.5h_rep2

value: cells from liquid culture, at 4% NaCl for 0.5h


title: Intermediate progenitors - Dam-only_Rep4

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

country: United Kingdom

institute: The Gurdon Institute

library_source: genomic

data_processing:
Fastq-files were processed with the damidseq_pipeline (Marshall and Brand, Bioinformatics, 2015), with bins=300, RPM normalization and otherwise default parameters.
For transcripton factor data, each Dam-fusion sample was normalized to each Dam-only sample from the same cell-type, resulting in a matrix of n1 Dam-fusion x n2 Dam-only. All normalizations were then averaged and backtransformed ("unlog") to generate a final average .bedgraph file.
For chromatin accessibility data, Dam-only files from a each experimental condition were averaged and provided as .bedgraph files.
Peaks were called using MACS2 (broad peaks), and only peaks present in all replicates at FDR<10^-5 were considered.
Peaks from all samples were merged and then k-means clustered to generate pHespTa1_NotchRbpj_clus8_FDR5.allPeak.bed
Genome_build: mm10
Supplementary_files_format_and_content: .bedgraph files are tracks at gatc-fragment resolution, of averaged transcription factor or chromatin accessibility DamID. Scores represent normalised fold enrichment of transcription factor DamID vs Dam-only; for chromatin accessibility scores represent read density.
Supplementary_files_format_and_content: .bw files are browser-readable versions of the .bedgraph files
Supplementary_files_format_and_content: .bed files contain peak coordinates

molecule: genomic DNA

organism: Mus musculus

source_name: Intermediate progenitors E13-14

extract_protocol:
After dissection of electroporated cortex, gDNA was extracted using the QiAmp DNA Micro kit. The gDNA was digested with DpnI, adaptors were ligated and then digested with DpnII and amplified by PCR (Marshall et al, Nat Protoc, 2016).
After gDNA extraction and DamID, DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed with AlwI digestion. Sonicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified (see Marshall et al., Nat Protoc, 2016).
DamID-seq

value: mouse embryonic cortex

tag: stage of electroporation-dissection

tag: dam-fusion protein

value: Dam-only

tag: cell type

value: IPC


title: CRC00606


title: PCC6803_WT_0h_rep1

value: cells from liquid culture, control conditions (0% NaCl)


title: Neurons - Dam-only_Rep1

description:
pND1_floxDam.bedgraph
pND1_floxDam.bedgraph.bw

source_name: Neurons E13-16

value: Neurons


title: CRC00701


title: 662

city: College Station

first: Dustin

middle: A

last: Therrien

state: Texas

address: 474 Olsen Blvd

department: Animal Science

country: USA

institute: Texas A&M University

data_processing:
RNA was sequenced using the Illumina NextSeq 500 platform (SE 1 x 75 bp).
Sequence quality was assessed via the FastQC program, and low-quality sequence data (Phred score < 20) and the adapter sequences were removed with Trimmomatic v0.32 genomic trimming program (Andrew, 2010; Bolger et al., 2014).
Following this, the hairpin.bta.fa and mature.bta.fa files were extracted from the miRNA sequence database, miRBase (v.22.1), and uploaded onto the TIGSS HPCC where they would be incorporated within further analyses (Kozomara et al., 2019). These FASTA files contain the sequence data for all the precursor hairpins and mature (miRNA hairpins = 1064 and mature miRNAs = 1030) miRNAs that have been currently identified and associated with the Bos taurus species.
The remaining filtered sequence reads that passed the initial quality control were then mapped to these acquired precursor hairpins and mature miRNAs, and then quantified via the mirDeep2 software package (Friedlander et al., 2012). This process generated a miRNA expression profile in the form of a .csv file for each sample and contained all the identified mature miRNAs along with their respective read counts.
The individual .csv files were then concatenated into a singular numerical matrix, which was then screened for duplicated miRNAs that appeared in multiple rows with either identical or slightly differing read counts.
The 78 samples along with their respective miRNA read counts were then organized within the matrix and separated into two groups, non-DFD (n = 53) and DFD (n = 25).
DESeq2 (v.1.34.0) software package was utilized to determine differential expression of the miRNAs between the two groups ( Love et al., 2014).
Genome_build: miRBase (v.22.1): hairpin.bta.fa and mature.bta.fa files
Supplementary_files_format_and_content: matrix.csv / csv file / miRDeep2 count matrix
Supplementary_files_format_and_content: DESEQ2.csv / csv file / DESeq2 output file

organism: Bos indicus x Bos taurus

source_name: Muscle biopsy

extract_protocol:
A modified version of the Molecular Research Center Inc. (MRC; Cincinnati, OH, USA) TRI reagent RNA extraction protocol was used to extract total RNA from each of the frozen L. lumborum skeletal muscle biopsies (n = 78). During RNA extraction, each muscle sample was removed from the -80ºC freezer and placed within dry ice to prevent them from thawing. Approximately 100-200 mg of biopsied skeletal muscle tissue was used from each sample for RNA extraction and were all homogenized in liquid nitrogen using a ceramic mortar and pestle as described within the protocol.
Sample libraries were prepared with the NEXTflex Small RNA-Seq kit v3 (BIOO SCIENTIFIC, Austin, TX) library kit. The quality of all sample libraries was evaluated via the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA) prior to sequencing, as recommended by the library preparation kit’s protocol.

value: Longissimus lumborum muscle

tag: phenotype

value: Dark-cutter (2/3)


title: 608

value: Dark-cutter (3/4)


title: 601


title: blood_285 [SampleGSM5058703]

type: genomic

city: Davis

first: Anita

last: Oberbauer

state: CA

address: One Shields Ave.

department: Animal Science Department

institute: University of California, Davis

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

hyb_protocol: Hybridization was performed according to the Infinium HD Super Assay documentation using the automated protocol.

scan_protocol: Scanning was performed according to the Infinium HD Super Assay documentation using the automated protocol.

data_processing:
The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.

label: C-Bio, G-Bio, A-DNP, T-DNP

organism: Bos taurus

source_name: blood from coccygeal vein in the tail

label_protocol: According to the Infinium HD Super Assay documentation (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-hd-super-assay/infinium-hd-super-assay-reference-guide-11322427-03.pdf), labels were added during allele-specific base extension.

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.

tag: mastitis

tag: metritis

tag: milk fever

tag: farm

value: A


title: blood_283 [SampleGSM5058701]


title: CRC00605

tag: disease


title: blood_286 [SampleGSM5058704]


title: Intermediate progenitors - Dam-only_Rep1


title: 289


title: 691


title: blood_284 [SampleGSM5058702]


title: CRC00604

tag: age


title: Intermediate progenitors - Dam-only_Rep2


title: blood_282 [SampleGSM5058700]

tag: Sex


title: blood_287 [SampleGSM5058705]


title: 771

value: Dark-cutter (1/2)


title: blood_281 [SampleGSM5058699]


title: Radial glia cells - Dam-only_Rep3

description:
pHes5_iDam.bedgraph
pHes5_iDam.bedgraph.bw
pHes5_Notch_unlog.bedgraph
pHes5_RBPJ_unlog.bedgraph

source_name: Radial glia cells E13-14

value: RGC


title: CRC00603

value: colon cancer

tag: tcra


title: blood_280 [SampleGSM5058698]

value: female


title: Radial glia cells - Dam-only_Rep4

description:
pHes5_iDam.bedgraph
pHes5_iDam.bedgraph.bw


title: Radial glia cells - Dam-only_Rep2


title: 427


title: blood_279 [SampleGSM5058697]


title: CRC00602

tag: tcrb

value: blood


title: CRC00601

tag: run


title: 703

tag: tissue


title: 692

value: Dark-cutter (1/3)


title: Radial glia cells - Dam-only_Rep1


title: blood_278 [SampleGSM5058696]


title: 682

value: male


title: blood_277 [SampleGSM5058695]


title: CRC00506


title: CRC00507


title: Ubiquitous - Dam-only_Rep7

description:
pCAG_iDam.bedgraph
pCAG_iDam.bedgraph.bw

source_name: RGCs and progeny E13-17

value: RGC-IPC-neurons


title: 674


title: Ubiquitous - Dam-only_Rep6

value: mouse embryonic cortex


title: blood_276 [SampleGSM5058694]


title: Radial glia cells - Dam-only_Rep5

value: Dam-only


title: 671


title: Ubiquitous - Dam-only_Rep5


title: blood_275 [SampleGSM5058693]


title: CRC00505


title: CRC00504


title: 631


title: 651


title: blood_273 [SampleGSM5058691]


title: blood_274 [SampleGSM5058692]


title: 209


title: CRC00501


title: Ubiquitous - Dam-only_Rep2


title: CRC00502


title: Ubiquitous - Dam-only_Rep1


title: 177


title: blood_271 [SampleGSM5058689]


title: 140


title: blood_270 [SampleGSM5058688]


title: CRC00401


title: 684

value: Dark-cutter (1/4)


title: Intermediate progenitors - RBPJ_Rep3

description:
pTa1_RBPJ_unlog.bedgraph
pTa1_RBPJ_unlog.bedgraph.bw
pTa1_RBPJ_FDR5.allPeak.bed
pHes5pTa1_NotchRbpj_clus8_FDR5.allPeak.bed

value: human RBPJ1

value: IPC


title: CRC00308


title: Intermediate progenitors - RBPJ_Rep1


title: 669

value: Longissimus lumborum muscle


title: blood_268 [SampleGSM5058686]


title: CRC00307


title: CRC00503


title: 650


title: CRC00306


title: Ubiquitous - Dam-only_Rep3


title: Intermediate progenitors - RBPJ_Rep2


title: blood_267 [SampleGSM5058685]


title: Ubiquitous - Dam-only_Rep4


title: Intermediate progenitors - Notch_Rep3

description:
pTa1_Notch_unlog.bedgraph
pTa1_Notch_unlog.bedgraph.bw
pTa1_Notch_FDR5.allPeak.bed
pHes5pTa1_NotchRbpj_clus8_FDR5.allPeak.bed

value: mouse NICD


title: CRC00305


title: Intermediate progenitors - Notch_Rep2


title: 635


title: 648


title: 263


title: blood_272 [SampleGSM5058690]


title: CRC00304


title: 130


title: blood_264 [SampleGSM5058682]

value: B


title: blood_265 [SampleGSM5058683]


title: 57


title: blood_262 [SampleGSM5058680]


title: Intermediate progenitors - Notch_Rep4


title: blood_269 [SampleGSM5058687]

value: A


title: Radial glia cells - RBPJ_Rep3

description:
pHes5_RBPJ_unlog.bedgraph
pHes5_RBPJ_unlog.bedgraph.bw
pHes5_RBPJ_FDR5.allPeak.bed
pHes5pTa1_NotchRbpj_clus8_FDR5.allPeak.bed


title: blood_263 [SampleGSM5058681]


title: 713

value: Normal


title: blood_266 [SampleGSM5058684]


title: CRC00301


title: Radial glia cells - RBPJ_Rep2

value: RGC


title: CRC00202

value: colon cancer


title: CRC00204


title: 716


title: 704


title: Radial glia cells - RBPJ_Rep1


title: 701


title: CRC00201


title: blood_259 [SampleGSM5058677]

value: female


title: Intermediate progenitors - Notch_Rep1


title: CRC00203

value: blood


title: Radial glia cells - Notch_Rep2

description:
pHes5_Notch_unlog.bedgraph
pHes5_Notch_unlog.bedgraph.bw
pHes5_Notch_FDR5.allPeak.bed
pHes5pTa1_NotchRbpj_clus8_FDR5.allPeak.bed

value: mouse NdECD


title: blood_261 [SampleGSM5058679]


title: CRC00303


title: Radial glia cells - Notch_Rep4


title: Radial glia cells - Notch_Rep3


title: blood_258 [SampleGSM5058676]


title: CRC00302


title: 695

value: male


title: Radial glia cells - Notch_Rep1


title: CRC00106


title: 694


title: blood_257 [SampleGSM5058675]


title: CRC00105


title: blood_260 [SampleGSM5058678]


title: 693


title: blood_253 [SampleGSM5058671]


title: 687


title: 689


title: 688


title: blood_254 [SampleGSM5058672]


title: blood_255 [SampleGSM5058673]


title: CRC00102


title: 680


title: blood_252 [SampleGSM5058670]

value: D


title: CRC00103


title: CRC00104


title: blood_251 [SampleGSM5058669]


title: K562-biological, rep4

city: Kunming

first: Shen

last: Zhenglei

state: Yunnan

address: No.519, Kunzhou Road, Xishan District

country: China

institute: The third Affiliated Hospital of Kunming Medical University

description: Gene expression data from control cell lines

hyb_protocol: Following fragmentation, cRNA were hybridized for 16-18 hr at 45 ℃ on GeneChip PrimeView Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The gene expression profile was preprocessed using Limma package in Bioconductor and Affymetrix annotation files. The background correction, quantile normalization and probe summarization of the microarray data were performed using the Robust Multiarray average algorithm to obtain the gene expression matrix. The cut-off for the background correction was 20%, and the coefficient of variation was 25%. The Benjamini-Hochberg method was used to correct the significant difference level (FDR). The screening criteria for significantly different genes were: |Fold Change|>1.5 and FDR<0.05.

label: biotin

source_name: HUVEC cell line & K562

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50-500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cell lines were maintained using Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The cell lines were infected by RNAi lentiviral vectors of shDIDO1 and shCtrl; K562 and HUVEC cultivated cells

tag: cell line

value: HUVEC and K562

tag: genotype/variation


title: blood_250 [SampleGSM5058668]


title: 675


title: CRC00107


title: blood_256 [SampleGSM5058674]


title: blood_249 [SampleGSM5058667]


title: 667


title: 666


title: blood_248 [SampleGSM5058666]


title: K562-biological, rep3


title: blood_247 [SampleGSM5058665]


title: blood_246 [SampleGSM5058664]


title: K562-biological, rep1


title: HUVEC-biological, rep1

source_name: HUVEC

value: HUVEC

value: wild type


title: HUVEC-biological, rep3


title: HUVEC-biological, rep2


title: K562-biological, rep2


title: CRC00101


title: RCC_AJ204: Renal cell carcinoma 8

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).

scan_protocol: The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).

source_name: A/J mouse normal kidney

label_protocol: The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

treatment_protocol: The treated mice were intraperitoneally injected with ferric nitrilotriacetate 5 times a week for 12 weeks. The administration was started at a dose of 5 mg iron/mouse kg weight for the first two weeks. The dose was increased to 7 mg iron/mouse kg weight for the next 10 weeks. The mice were euthanized when they were dying.

tag: genotype

value: A/J wild type

value: normal kidney

tag: treatment

value: Fe-NTA, 3 months

value: renal cell carcinoma


title: 659

value: Longissimus lumborum muscle


title: RCC_AJ203: Renal cell carcinoma 7


title: shCtrl-biological,rep2

value: shCtrl


title: 656

value: Normal


title: shCtrl-biological,rep3


title: HUVEC-biological, rep4


title: 654


title: blood_245 [SampleGSM5058663]


title: RCC_AJ201: Renal cell carcinoma 5


title: RCC_AJ199: Renal cell carcinoma 4


title: 653


title: 652


title: B6_AIRE_KO_MTECHI

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

data_processing:
The paired-end sequencing (2x100bp) was performed on the Illumina HiSeq2000 sequencer
The fastq files were mapped to the mm10 genome using TopHat 2.
Genome_build: mm10
Supplementary_files_format_and_content: WT vs Aire-KO differential expression (gene and transcript levels) is computed using Cuffdiff

source_name: medullary thymic epithelial cells

extract_protocol:
Total RNA was extracted by Trizol
TruSeq Stranded mRNA Library Prep (Illumina)

treatment_protocol: WT and Aire-KO MHC-II high mTECs were isolated from a pool of B6 mice using a BD FACS Aria III cell sorter, following the typical isolation procedure

tag: strain

value: thymus

tag: type

value: MHCII high medullary epithelial cells

value: Aire-/-


title: blood_243 [SampleGSM5058661]

tag: mastitis

value: female


title: B6_MTECHI

value: WT


title: blood_242 [SampleGSM5058660]

tag: metritis


title: shDIDO1-biological,rep3

description: Gene expression data from shDIDO1 lines


title: shDIDO1-biological,rep2

description: Gene expression data from shDIDO1 lines


title: wdr72ko4

city: San Francisco

first: Yan

last: Zhang

address: 513 Parnassus Avenue

department: Orofacial Sciences

institute: UCSF

data_processing:
Files provided in BAM format--a standard file format that contains mapping results–indicate the information of the corresponding referenced genome and gene annotations for some species. The Integrative Genomics Viewer (IGV) is a recommended software for visualizing data from BAM files.
Basecalls performed using CASAVA
the details of Illumina Sequencing identifier are as follows: (1) HWI-ST1276:71 HWI-ST1276, Instrument - unique identifier of the sequencer; 71, run number - Run number on instrument; (2) C1162ACXX:1:1101:1208:2458 means the coordinate of read on C1162ACXX (Flowcell ID) flowcell, line 1, 1101 tile is(x=1208, y=2458); (3) 1:N:0:CGATGT the first number is 1 or 2, 1 refers to single reads or the first read of paired ends, 2 refers to the second of paired ends; the second letter means whether reads is adjusted(Y means yes, N means no); the third number represent the number of Control Bits in sequence; six bases on the fourth place is Illumina index sequence. The sequencing reads/raw reads often contain low quality reads or reads with adaptors, which will affect the quality of downstream analysis. To avoid this, it is necessary to filter the raw reads and obtain the clean reads. Mapping clean reads to the reference genome or the transcriptome is the basis for the next following analysis. For human and mice, the species with completed annotation, when only differential expression gene(quantification) analysis is needed, the raw data can map reads to the transcriptome directly. However, in studies on transcript structural variation, such as alternative splicing, variation, the fusion gene, the alignment should be carried out at the genomic level.
Mapped regions can be classified as exons, introns, or intergenic regions. Exon-mapped reads should be the most abundant type of read when the reference genome is well-annotated. Intron-reads may be derived from pre-mRNA contamination or intron-retention from alternative splicing. Reads mapped to intergenic regions are mainly attributed to weak annotation of the reference genome. The distribution of sequencing reads of all samples in the genomic region is shown in the figure below.
Genome_build: mm39
Supplementary_files_format_and_content: Wdr72-readcount with genename copy.txt

source_name: P12 first molar enamel organ cells

growth_protocol: Wdr72-/- colony was purchased from UC Davis Mouse Biology Center. C57BL/6 wild type and Wdr72-/- has been maintained in UCSF Laboratory Animal Resource Center (LARC).

extract_protocol:
The remaining molars were placed into TRIzol solution and homogenized, the total RNA from the enamel organ cells were purified by using Zymo quick RNA purification kit.
Total RNA went through polyA capture to remove rRNA removal), RNA was fragmented, and reverse transcription was performed to generate cDNA library.

treatment_protocol: P13 pups were genotyped and the first molars were microdissected from wild type and wdr72 deficient pups. The pulp tissues were removed from molars.

tag: cell type

value: epithelially derived ameloblasts


title: wdrko5


title: blood_241 [SampleGSM5058659]

tag: milk fever

tag: farm

value: D


title: mTEClo Input serie 2

data_processing:
Illumina HiSeq 2000 machine
paired-end 75bp reads
Alignment to the mm10 genome was done using Bowtie 2. Duplicate alignments were removed using samtools and the command ligne: "samtools view -S -hf 0x2 alignments.sam | grep -v "XS:i:" | foo.py > filtered.alignments.sam" the foo.py script been available online: "https://www.biostars.org/p/95929/".
Peak calling for a sample (in comparison to the inputs) was done using macs2 callpeak and the options -f BAMPE, --SPMR and --broad
Enrichment for a sample compared to the inputs, was calculated using macs2 bdgcmp and the option -m FE
Ceas was used to calculate the average entrichment within the gene body and its upstream and downstream regions
Genome_build: mm10
Supplementary_files_format_and_content: wig and peak files were generated using macs2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Nano-ChIP-seq libraries were prepared with the TruSeq ChIP Sample Preparation Kit (Illumina).

treatment_protocol: mTEClo were isolated from individual B6 mice using a BD FACS Aria III cell sorter, following the typical isolation procedure

value: mTEClo medullary epithelial cells

tag: chip antibody


title: 646

tag: phenotype

tag: Sex

value: male


title: 642


title: RCC_AJ198: Renal cell carcinoma 3


title: shDIDO1-biological,rep1

description: Gene expression data from shDIDO1 lines

data_processing: The gene expression profile was preprocessed using Limma package in Bioconductor and Affymetrix annotation files. The background correction, quantile normalization and probe summarization of the microarray data were performed using the Robust Multiarray average algorithm to obtain the gene expression matrix. The cut-off for the background correction was 20%, and the coefficient of variation was 25%. The Benjamini-Hochberg method was used to correct the significant difference level (FDR). The screening criteria for significantly different genes were: |Fold Change|>1.5 and FDR<0.05.. The background correction, quantile normalization and probe summarization of the microarray data were performed using the Robust Multiarray average algorithm to obtain the gene expression matrix. The cut-off for the background correction was 20%, and the coefficient of variation was 25%. The Benjamini-Hochberg method was used to correct the significant difference level (FDR). The screening criteria for significantly different genes were: |Fold Change|>1.5 and FDR<0.05.

value: HUVEC


title: RCC_AJ194: Renal cell carcinoma 2

value: A/J wild type


title: RCC_AJ193: Renal cell carcinoma 1

value: normal kidney


title: 641


title: mTEClo H3K36me3 serie 2

value: H3K36me3 (Abcam, ab9050)


title: wdr72ko1

tag: age


title: blood_239 [SampleGSM5058657]


title: 636


title: mTEClo Input serie 1 replicate


title: P12wt5

value: wild type


title: 634

value: Longissimus lumborum muscle


title: P12wt4


title: mTEClo Input serie 1


title: blood_237 [SampleGSM5058655]


title: RCC_AJ202: Renal cell carcinoma 6

value: Fe-NTA, 3 months

value: renal cell carcinoma


title: wdr72ko3


title: blood_240 [SampleGSM5058658]


title: 633

value: Normal


title: mTEClo H3K36me3 serie 1

value: thymus


title: P12wt3


title: YPDA-PINK3

city: Shanghai

first: LI

last: TAO

state: Shanghai

address: Yangpu district Songhu Road

institute: Fudan University

data_processing:
The library products were sequenced using an Illumina NovaSeq platform.
The clean reads were aligned to the reference sequence (C.haemulonii genomic sequence data from the NCBI database, GCA_002926055.1) via the sofeware HiSat2 v2.0.5 with default parameters.
FPKM method is used in calculated expression level, the formula is shown as follows, and the formula is shown as follows: FPKM=106C/(NL/103). Given to be the expression of gene A , C to be number of fragments that are uniquely aligned to gene A , N to be total number of fragments that are uniquely aligned to all genes, and L to be number of bases on gene A.
Genome_build: C.haemulonii genomic sequence data from the NCBI database, GCA_002926055.1
Supplementary_files_format_and_content: text files containing FPKM values for each Sample

organism: Candidozyma haemuli

source_name: pink cells

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 630


title: P12wt2


title: blood_238 [SampleGSM5058656]


title: YPDA-PINK2


title: blood_235 [SampleGSM5058653]


title: CD49b_pool3

city: Hamburg

first: Jan-Eric

last: Turner

state: Hamburg

address: Martinistraße 52

department: III. Department of Medicine

institute: University Medical Center Hamburg-Eppendorf

description:
expression_matrix.xlsx
CD49b5

data_processing:
trimming the reads using Trimmomatic (Version 0.38)
data was aligned on the Mus_musculus.GRCm38.95 reference genome using STAR aligner (version 2.6.1)
A transcript database was generated by using the same reference genome and counting reads per gene with the summarizeOverlaps function from GenomicAlignments package (Bioconductor Version 3.12) (25) in R (version 4.03). Genes with less than 5 reads in total were filtered out and differential expression analysis was performed by using the DESeq function of R package DEseq2 (version 1.30.0)
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: expression matrix

source_name: kidney

extract_protocol:
Leukocytes were isolated from kidneys by digestion, percoll gradient, erythrocyte lysis and CD45 enrichment using CD45-microbeads (Miltenyi). After sorting of CD49bhiNK1.1+NKp46+CD3- and CD49a+CD49blow/intNK1.1+NKp46+CD3- cells, total RNA was extracted using RNAeasy MicroKit (Qiagen).
250-300 bp cDNA insert library, 6G raw data/sample on average

value: kidney

value: Leukocytes

tag: cell type (sorted)

value: cNK cell


title: blood_234 [SampleGSM5058652]

value: female


title: 624

tag: tissue


title: YPDA-PINK1

value: WT


title: YPDA-WHITE3

source_name: white cells


title: CD49a_pool3

description:
expression_matrix.xlsx
CD49a4


title: shCtrl-biological,rep1

tag: cell line

value: shCtrl


title: blood_232 [SampleGSM5058650]

value: D


title: CD49b_pool2

description:
expression_matrix.xlsx
CD49b3


title: YPDA-WHITE2


title: blood_233 [SampleGSM5058651]


title: 622

value: male


title: blood_231 [SampleGSM5058649]


title: blood_236 [SampleGSM5058654]


title: 623


title: 621


title: YPDA-WHITE1


title: blood_230 [SampleGSM5058648]


title: CD49b_pool1

description:
expression_matrix.xlsx
CD49b


title: 606


title: CD49a_pool1

description:
expression_matrix.xlsx
CD49a


title: blood_229 [SampleGSM5058647]


title: 626


title: COVID patient 10

city: Lausanne

first: Jeremy

last: Di Domizio

address: Av Boveresses 155

country: Switzerland

institute: CHUV

description: internal positive and negative controls were used

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Data were normalized and analysed using either nSolver® 4.0 (Nanostring Technologies) or ROSALIND® (ROSALIND, Inc., San Diego, CA). Basically, housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: NanoString indexing

source_name: skin biopsy

label_protocol: standard protocol

extract_protocol: mRNA expression of 600 targets was analysed with the nCounter Human Immunology V2 panel including 20 customized probes (Nanostring Technologies, Seattle, WA, USA) on the nCounter® platform (Nanostring Technologies) using 100 ng of RNA per skin sample.

tag: gender

value: M

tag: diagnosis

value: COVID-19-associated skin lesion

value: skin biopsy


title: 664


title: Pool-2, RNA, S6

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

description:
Pool-2, RNA, S6, L001
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Library strategy: CITE-Seq
The pipeline employed for data analysis included FastQC for quality control, Cutadapt for adapter trimming and excluding low-quality reads, STAR for genome indices creation and alignment of reads to the GRCm38 mouse genome, HTSeq to assign reads to genes, and DESeq2 to detect differentially expressed genes.
Cite-seq data were processed by Cell Ranger 6.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The scRNA-seq data was mapped to mm10 genome and the expression status of protein markers were separately computed by using Cite-Seq Count (https://github.com/Hoohm/CITE-seq-Count). In total, 30603 cells having matched RNA-seq and antibody profiles were identified.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, barcode.csv (Barcode information)

source_name: CD45 positive cells

growth_protocol: C57Bl/6J mice (CD45.2), Tet2-deﬁcient mice (Tet2-/-, CD45.2) (13), competitor Boy/J (CD45.1) mice, and recipient B6xBoy/J F1 (F1; dual CD45.2/CD45.1) mice were used for BM collection and transplantation studies. C57Bl/6J, Boy/J and B6xBoy/J F1 mice were obtained from the In Vivo Therapeutics core facility at the Indiana University School of Medicine. Mice husbandry and care were performed under 21-24°C temperature- and 12-hour light,12-hour dark cycle); group-housed according to age, sex, and genotype; and fed ad libitum. C57Bl/6J and Tet2-/- mice were 3 - 4 months of age when utilized. Boy/J (CD45.1), and B6xBoy/J F1 (F1; dual CD45.2/CD45.1) mice were 8-10 weeks of age when used for experiments. Both male and female mice were used as donors, competitors, and recipients for experiments. All experiments were matched for age and sex for each experiment. We did not observe any difference in function or phenotypes between males and females.

extract_protocol:
LSK cells were enriched and processed as described above. Dead and apoptotic cells were removed using dead cell removal kit. Cells were blocked with TruStain FcX™ PLUS (anti-mouse CD16/32). Cell multiplexing and labeling was performed according to the manufacturer’s instructions. Surface protein fixation was done by treating the cells with freshly prepared cell membrane crosslinker (DTSSP, 3,3'- dithiobis(sulfosuccinimidyl propionate). All samples were pooled in equal numbers into two groups (ambient air (~21% O2) and physioxia (3% O2)). Labeled cells were loaded to a 10X Genomics Chromium Next GEM chip G for reverse transcription and complementary DNA inside gel bead-in-emulsion. Full-length cDNA was amplified, and sequencing libraries were normalized for sequencing. The constructed library was sequenced on Illumina instrument.
Library preparation was performed using New England Biolabs Single Cell/Low Input RNA Library Prep Kit for Illumina. Paired-end RNA-sequencing (RNA-seq) was performed on Illumina instrument by IU School of Medicine Medical Genomics core. Each group/condition consists of four matched biological replicates and ~30 million reads were obtained per sample.

treatment_protocol: BM cell collection was conducted in a hypoxia chamber, maintained at 3% O2, 5% CO2, and N2 balance. All reagents and supplies were equilibrated in the hypoxia chamber for at least 18 hours before cell harvest (4). BM harvest was performed by flushing femurs, tibia and pelvis and crushing spinal bones with ice cold PBS. Flow cytometry staining, and fixation, HPC colony assays, and i.v. injections for in vivo transplantation were conducted in the hypoxia chamber for the 3% O2 physiological oxygen (physioxia) groups. For ambient air control groups, half of the cells were immediately removed from the hypoxia chamber to acclimate in ambient air (~21% O2) for one to six hours before applying equivalent techniques. Colony-forming cell assays cells were incubated at 5% O2, 5% CO2 for both physioxia and ambient air collected groups, as this enhances the detection of optimal growth of HPCs (granulocyte macrophage (CFU-GM), erythroid (BFU-E), and multipotential (CFU-GEMM) type colonies

tag: genotype

value: Mixture of WT and TET2 cells

tag: molecule

value: scRNA-seq

tag: stress

value: normoxia

value: bone marrow

value: CD45 positive cells


title: COVID patient 9


title: 602

value: Longissimus lumborum muscle

value: Normal


title: CD49a_pool2

description:
expression_matrix.xlsx
CD49a2

value: kidney

tag: strain

value: Leukocytes


title: Pool-2, HTO, S8

description:
Pool-2, HTO, S8, L001
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

molecule: protein

value: Barcodes of samples. See details in barcode.csv


title: 507


title: 458


title: blood_227 [SampleGSM5058645]

tag: mastitis

tag: metritis

value: female


title: Pool-2, ADT, S7

description:
Pool-2, ADT, S7, L001
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

value: Surface Antibody. See details in barcode.csv

tag: cell type


title: 446


title: Pool-1, RNA, S3

description:
Pool-1, RNA, S3, L001
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

value: physioxia


title: blood_226 [SampleGSM5058644]

tag: milk fever

tag: farm

value: D


title: blood_224 [SampleGSM5058642]


title: 382

tag: phenotype

value: male


title: blood_225 [SampleGSM5058643]

tag: Sex


title: COVID patient 6

value: M

tag: age

value: COVID-19-associated skin lesion


title: COVID patient 7

value: skin biopsy


title: COVID patient 5

value: F


title: blood_223 [SampleGSM5058641]


title: Pool-1, HTO, S5

description:
Pool-1, HTO, S5, L001
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

value: Mixture of WT and TET2 cells


title: 379


title: 604


title: Pool-1, ADT, S4

description:
Pool-1, ADT, S4, L001
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

value: bone marrow


title: COVID patient 4


title: blood_228 [SampleGSM5058646]


title: H8, TET2KO-Hypoxia, 004, S54

data_processing:
The pipeline employed for data analysis included FastQC for quality control, Cutadapt for adapter trimming and excluding low-quality reads, STAR for genome indices creation and alignment of reads to the GRCm38 mouse genome, HTSeq to assign reads to genes, and DESeq2 to detect differentially expressed genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2_normalized_counts.csv

source_name: CD45 positve cells

extract_protocol:
(Lin-Ckit+Sca1+) cells were enriched inside the hypoxia chamber using mouse lineage cell depletion kit , EasySep™ release mouse biotin positive selection kit and EasySep™ mouse SCA1 positive selection kit consecutively. LSK enriched cells were divided into two groups; group 1 was incubated inside the hypoxia chamber for RNA extraction, and group 2 was equilibrated in ambient air for 6 hours before RNA extraction. Total RNA was extracted using Qiagen RNeasy Plus Micro Kit. RNA with Agilent Bioanalyzer RIN of > 7 were selected for library preparation.
Library preparation was performed using New England Biolabs Single Cell/Low Input RNA Library Prep Kit for Illumina. Paired-end RNA-sequencing (RNA-seq) was performed on Illumina instrument by IU School of Medicine Medical Genomics core. Each group/condition consists of four matched biological replicates and ~30 million reads were obtained per sample.

value: CD45 positive cells


title: 378

value: Longissimus lumborum muscle


title: COVID patient 8


title: COVID patient 3


title: blood_221 [SampleGSM4820766]

value: A


title: COVID patient 1


title: 346

value: Normal


title: 345


title: blood_220 [SampleGSM4820765]

value: B


title: H5, TET2KO-Hypoxia, 001, S51


title: blood_219 [SampleGSM4820764]


title: H3, WT-Hypoxia, 003, S49

value: Wild Type


title: blood_218 [SampleGSM4820763]

value: female


title: CLE patient 10

value: cutaneous lupus erythematosus


title: CLE patient 11


title: blood_217 [SampleGSM4820762]


title: H2, WT-Hypoxia, 002, S48

value: physioxia


title: 328


title: H4, WT-Hypoxia, 004, S50


title: blood_222 [SampleGSM4820767]


title: 327


title: blood_216 [SampleGSM4820761]

value: D


title: 249

value: male


title: CLE patient 9


title: COVID patient 2


title: CLE patient 8

value: M


title: 176


title: CLE patient 7


title: H1, WT-Hypoxia, 001, S47


title: 139


title: H6, TET2KO-Hypoxia, 002, S52


title: blood_244 [SampleGSM5058662]


title: H7, TET2KO-Hypoxia, 003, S53


title: blood_215 [SampleGSM4820760]


title: blood_214 [SampleGSM4820759]


title: CLE patient 6


title: 138


title: CLE patient 5


title: blood_213 [SampleGSM4820758]


title: A6, TET2KO-Air, 002, S44

value: normoxia


title: 136


title: blood_212 [SampleGSM4820757]


title: 93


title: A5, TET2KO-Air, 001, S43


title: blood_211 [SampleGSM4820756]


title: CLE patient 3

value: skin biopsy


title: blood_210 [SampleGSM4820755]


title: A4, WT-Air, 004, S42


title: 66


title: 32


title: A3, WT-Air, 003, S41


title: CLE patient 1

value: F


title: CLE patient 4


title: blood_209 [SampleGSM4820754]


title: CLE patient 2


title: A1, WT-Air, 001, S39


title: A8, TET2KO-Air, 004, S46


title: healthy donor 4

value: healthy donor


title: blood_207 [SampleGSM4820752]


title: A7, TET2KO-Air, 003, S45

value: bone marrow


title: healthy donor 3


title: hESCs-Exosomes-3D-3

city: Guangzhou

first: Ning

last: Wang

address: No.382 Waihuan East Road, Guangzhou 510006, P.R. China.

department: School of Biomedical Sciences and Engineering

institute: South China University of Technology

description: Gene expression for 3D-hESCs-exosomes

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 Blocking Agent and 2.2 μl of 25 Fragmentation Buffer, then heated at 60 C for 30 min, and finally 55 μl 2 GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65 C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number G2505C).

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v14.9 software package (Agilent Technologies).

source_name: hESCs-exosomes, 3D, replicate 1

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase. The labeled cRNA over the procession of inspissation and desiccation and then redissolved with water.

extract_protocol: Lyse samples in TRIzol Reagent by repetitive pipetting. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent.Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol.RNA quantity and quality were measured by NanoDrop ND-1000.

treatment_protocol: Freshly exosomes from 2D cultured hESCs and 3D cultured hESCs were collected and suquenced

tag: cell

value: Human embryonic stem cells

tag: sample

value: Exosome


title: healthy donor 2

tag: tissue


title: hESCs-Exosomes-3D-2

description: Gene expression for 3D-hESCs-exosomes


title: blood_206 [SampleGSM4820751]


title: vagusRC4

city: New Haven

first: Le

state: CT

address: 300 George Street

department: Neurology

institute: Yale University

description: single cell RNA sequencing

data_processing:
A custom mouse genome reference with additional foreign sequence information for organ-barcodes (Projection-seq) was generated by 10x Cell Ranger (10x Genomics).
Single cell RNA sequencing data were aligned to a custom mouse genome reference based on mm10 mouse genome reference with additional foreign sequence information of organ projection barcodes (Projection-seq) using 10x Cell Ranger software version 3.1.0 (10x Genomics).
Genome_build: mm10 mouse genome reference; Projection-seq mouse genome reference
Supplementary_files_format_and_content: Filtered gene expression matrix

source_name: vagus

extract_protocol:
For each sample, vagal ganglia were acutely harvested from 10 age and gender-matched mice. Fibers were trimmed off with a micro scissors in ice cold Medium A (L-15 medium (Gibco, 11415064)), the ganglia were then digested in 0.25% Trypsin solution (Gibco, 25200056) for 10 min at 37C, followed by 1 mg/mL  collagenase I (MP Biomedicals, 0219510901) / 3 mg/mL Dispase II (Roche, 04942078001) HBSS solution for 30 min at 37C. Cells were centrifuged at 200 g for 5 min at 4C, washed twice with Medium B (L-15 medium containing 10% Fetal Bovine Serum (Gibco, 16000044)), then carefully triturated with 3 glass Pasteur pipettes with decreasing openings. Cells were pelleted, resuspended with 1 mL Medium B, and loaded onto a Percoll gradient (Sigma-Aldrich, P1644), constituted with 30% Percoll/HBSS solution in the upper layer, and 60% Percoll/L-15 solution in the lower layer. After centrifugation (800 g, 20 min, 4C), the enriched neurons at the interface of the two Percoll layers were gently collected and transferred into Medium B, and centrifuged at 200 g for 10 min at 4C. Cell pellet was resuspended in 10-15 L 0.04% BSA (Thermo Fisher, AM2616)/HBSS solution, immediately, 1 L cell solution was aliquoted for cell counting and viability assay with 0.4% trypan blue (Thermo Fisher, T10282). After that, the cell solution was subjected to 10x Gemonics for single cell RNA sequencing. Approximately 5,000-10,000 VSNs were loaded in each channel of the 10x Chromium microfluidic device to target for 3,000-6,000 cells as an output of one sample.
Single cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer’s instructions and sequenced using an Illumina NovaSeq S4 sequencer at 300 million reads to achieve a fine sequencing depth of 30,000-50,000 reads per cell.
Single cell RNA sequencing, Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics).

treatment_protocol: For each sample of Projection-seq, 10 age and gender-matched wildtype mice were first injected with different Projection-seq AAVs into thoracic and abdominal organs. Vagal ganglia were harvested 7 days later.


title: blood_205 [SampleGSM4820750]


title: vagusRC3

description: single cell RNA sequencing


title: Experiment_2_sample_2_VDJ

city: Munich

first: Sebastian

last: Jarosch

state: Bavaria

address: Trogerstr. 30

department: Institute for Medical Microbiology, Immunology and Hygiene

institute: TU Munich

description:
TCR sequences
scRNAseq

data_processing:
Experiment_1: Cell Ranger (version 3.0.2; 10x Genomics) was used for demultiplexing and alignment using default parameters
Experiment_2: Cell Ranger (version 5.0.0; 10x Genomics) was used for demultiplexing and alignment using default parameters
Python software package SCANPY (version 1.4.3) was used for downstream analysis
Experiment_1: cells filtered out that express < 200 and >7000 genes, >50000 counts,  > 20% mitochondrial genes. Genes were filtered out that were present in < 3 cells.
Experiment_2: cells filtered out that express < 200 and >6000 genes, >40000 counts,  > 20% mitochondrial genes. Genes were filtered out that were present in < 3 cells.
Gene counts were per-cell normalized and (log+1)-transformed
Cell cycle, percent mito, n_genes and n_counts were regressed out
Genome_build: Experiment_1: human reference genome GRCh38 (Ensembl 93)
Genome_build: Experiment_2: human reference genome GRCh38 (Ensembl 98)
Supplementary_files_format_and_content: Output of the Cell Ranger count Analysis Pipeline (mtx and tsv files; unfiltered and unnormalized)
Supplementary_files_format_and_content: Output of the Cell Ranger VDJ Analysis Pipeline (json file for clonotype annotation)

source_name: peripheral blood

extract_protocol:
Chromium Next GEM Single Cell 5' GEM, Library & Gel Bead Kit v1.1 (10x genomics)
Chromium Next GEM Single Cell 5' Library Kit v1.1 (10x genomics)   Chromium Single Cell V(D)J EnrichmentKit, Human T Cell (10x genomics)  Chromium Single Cell 5' Feature Barcode Library Kit (10x genomics)
Paired-end, single indexing

treatment_protocol: PBMCs from mild COVID-19 donors were in vitro expanded via stimulation with SARS-CoV-2 peptides for 10-12 days, and freshly re-stimulated with individual SARS-CoV-2 peptides for 4 h prior to sorting. For the second experiment, cells were stained with TotalSeq-C anti-human Hashtag Antibodies (Biolegend, Clone: LNH-94; 2M2) prior to sorting of individual donors to ensure a good demultiplexing of individual donors.

value: CD8+ T cells IFNG +

value: blood


title: blood_204 [SampleGSM4820749]

source_name: blood from coccygeal vein in the tail


title: healthy donor 1

tag: gender


title: Experiment_2_sample_2_GEX

description:
total mRNA
scRNAseq


title: blood_203 [SampleGSM4820748]


title: hESCs-Exosomes-3D-1

description: Gene expression for 3D-hESCs-exosomes


title: vagus010419

description: single cell RNA sequencing


title: vagus051818

description: single cell RNA sequencing


title: blood_208 [SampleGSM4820753]


title: Experiment_2_sample_1_VDJ

description:
TCR sequences
scRNAseq


title: vagus071819V2

description: single cell RNA sequencing


title: Experiment_2_sample_1_GEX

description:
total mRNA
scRNAseq


title: blood_202 [SampleGSM4820747]


title: blood_201 [SampleGSM4820746]


title: A2, WT-Air, 002, S40

value: CD45 positive cells


title: hESCs-Exosomes-2D-2

description: Gene expression for 2D-hESCs-exosomes

source_name: hESCs-exosomes, 2D, replicate 1


title: hESCs-Exosomes-2D-1

description: Gene expression for 2D-hESCs-exosomes


title: sgKrt19s8

city: Cold Spring Harbor

first: Zhikai

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Base-calling
Alignment
Filtering
Peak-calling
Normalization
Genome_build: mm10
Supplementary_files_format_and_content: txt

molecule: polyA RNA

source_name: Subcutaneous PDA tumor

growth_protocol: Subcutaneous tumors

extract_protocol:
Qiagen RNAeasy Kit
Illumina TrueSeq
10nM cDNA, 12 cycles for cDNA amplification

treatment_protocol: No treatment

tag: tumor stage

value: 2 weeks after inoculation

tag: cancer cell type

value: 1242 KPC cell

tag: mouse strain

tag: condition

value: Krt19 knockout tumor


title: sgKrt19s5


title: sgKrt19s6


title: vagus070519V2

description: single cell RNA sequencing

tag: strain


title: vagus071819V1

description: single cell RNA sequencing


title: Experiment_1_donor_32_33_A1_ORF3a_FTS_VDJ

description:
TCR sequences
scRNAseq

value: CD8+ T cells IFNG + and -


title: vagus070519V1

description: single cell RNA sequencing


title: blood_199 [SampleGSM4820744]

tag: mastitis

value: D

value: female


title: Experiment_1_donor_24_34_A3_ORF1_VTN_VDJ

description:
TCR sequences
scRNAseq


title: blood_198 [SampleGSM4820743]

tag: metritis


title: hESCs-Exosomes-2D-3

description: Gene expression for 2D-hESCs-exosomes


title: sgScramble3

value: Control tumor


title: Experiment_1_donor_24_34_A3_ORF1_VTN_GEX

description:
total mRNA
scRNAseq

tag: cell type


title: sgScramble2


title: sgScramble1


title: LG72-NY-142

city: New York

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

data_processing:
Gene counts were obtained by aligning reads to the mm10 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with unique gene counts over 9,000 or less than 300, and cells with high fraction of mitochondrial reads (> 5%).
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
Seurat v3.0 (Butler et al., 2018) R package used for analysis.
Genome_build: mm10 genome

source_name: single nuclei from mouse hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

tag: r47h genotype

tag: mutation

value: P301S mutation

tag: mk-2206 treatment

value: hippocampus


title: LG72-NY-130


title: blood_197 [SampleGSM4820742]

data_processing:
The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.

tag: milk fever

tag: farm

tag: Sex


title: Gan_66

description: mRNA expression in human frontal cortical brain cells

data_processing:
Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
Seurat v3.0 (Butler et al., 2018) R package used for analysis.
Genome_build: hg38 genome
Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)

source_name: single nuclei from frozen postmortem human tissue

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2073
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

tag: age

value: M

tag: diagnosis

value: Normal

value: frontal cortical brain cells


title: LG72-NY-112

tag: tissue


title: blood_196 [SampleGSM4820741]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.


title: Gan_65

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2072
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: Setd2 knockdown mTEC sh2

description:
primary mTEC in a 3D organotypic co-culture system infected by a lentivius to express an anti-Setd2 shRNA (sh2) and GFP as reporter of lentiplasmid integration
Setd2_KD_mTEC_sh2

data_processing:
Illumina NextSeq 500 sequencer
Paired-end reads (2x75bp)
Nextera adapter sequences were removed using trimmomatic-0.39
The fastq files were mapped to the mm10 genome using TopHat 2
gene and isoform quantification were performed using Cufflinks 2 and processed to assess the inclusion of alternative splicing events (ASEs) using the process that we documented in (https://github.com/TeamGiraud/TEC_splicing_2021)
Genome_build: mm10
Supplementary_files_format_and_content: csv text files include inclusion frequency of each annotated ASE retrieved from Refseq annotations for each gene

extract_protocol:
Total RNA was extracted using the Single Cell RNA Purification Kit (Norgen Biotek)
SMART-seq v4 Ultra Low Input RNA kit (Takara) combined with the Nextera XT DNA Library Preparation Kit (Illumina) was used for library preparation

treatment_protocol: Infected mTECs (DAPI- I-A/E+ GFP+) were isolated using a BD FACS Aria III cell sorter

value: thymus

tag: type

value: medullary epithelial cells

tag: genotype

value: Setd2 knockdown (sh2)


title: blood_195 [SampleGSM4820740]


title: blood_200 [SampleGSM4820745]


title: blood_194 [SampleGSM4820739]


title: Setd2 knockdown mTEC sh1

description:
primary mTEC in a 3D organotypic co-culture system infected by a lentivius to express an anti-Setd2 shRNA (sh1) and GFP as reporter of lentiplasmid integration
Setd2_KD_mTEC_sh1

value: Setd2 knockdown (sh1)


title: Gan_64

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2071
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: Gan_63

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2070
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: LG72-NY-105


title: Experiment_1_donor_32_33_A1_ORF3a_FTS_GEX

description:
total mRNA
scRNAseq

value: blood


title: blood_193 [SampleGSM4820738]


title: Raver2 knockdown mTEC sh2

description:
primary mTEC in a 3D organotypic co-culture system infected by a lentivius to express an anti-Raver2 shRNA (sh2) and GFP as reporter of lentiplasmid integration
Raver2_KD_mTEC_sh2

value: Raver2 knockdown (sh2)


title: LG72-NY-111


title: Raver2 knockdown mTEC sh1

description:
primary mTEC in a 3D organotypic co-culture system infected by a lentivius to express an anti-Raver2 shRNA (sh1) and GFP as reporter of lentiplasmid integration
Raver2_KD_mTEC_sh1

value: Raver2 knockdown (sh1)


title: Ctr knockdown (LacZ) mTEC replicate

description:
primary mTEC in a 3D organotypic co-culture system infected by a lentivius to express an anti-LacZ shRNA (Ctr) and GFP as reporter of lentiplasmid integration
Ctr_KD_mTEC_replicate

value: LacZ knockdown (Ctr)


title: blood_192 [SampleGSM4820737]


title: blood_191 [SampleGSM4820736]


title: Gan_60

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2067
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: F


title: Ctr knockdown (LacZ) mTEC

description:
primary mTEC in a 3D organotypic co-culture system infected by a lentivius to express an anti-LacZ shRNA (Ctr) and GFP as reporter of lentiplasmid integration
Ctr_KD_mTEC


title: Gan_61

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2068
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: blood_190 [SampleGSM4820735]

value: D


title: scRNAseq in ES(iZfp131-HA Zfp131KO and Wildtype H2B-GFP)

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
R1 is cell barcode (16bp) followed by UMI (10bp)  R2 is the RNA read (98bp)  I1 is the sample index (8bp)
Fastq files were generated by using 10X Genomics CellRanger (version 4.0.0) with default settings. New fasta and annotation files were created using mkref in mm10 for detection of H2B-GFP sequence (Addgene #11680).
CellRanger count function was used to assign reads to genomic features. 7510 cells were estimated for Zbtb11KO and H2B-GFP population whereas 6982 cells were estimated for Zfp131KO and H2B-GFP population. Seurat R package (version 3.0) was used for differential gene expression analysis and for data visualization (UMI plots, violin plots, gene-specific UMI plots)(Stuart et al. 2019).
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 format  gene expression matrix from 10X Genomics cellranger count.

source_name: Mutant ESCs with Zfp131 knockout and Wildtype ESCs with H2B::GFP

growth_protocol: ESCs were cultured on 0.1% gelatin (Milipore) coated dishes at 37 °C, 8% CO2 in ESC medium (Advanced DMEM/F12: Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% mESC-grade fetal bovine serum (Corning), 1x N2 (Gibco), 1x B27 (Gibco), 2 mM L-glutamine (Gibco), 0.1 mM ß-mercaptoethanol (Gibco)) supplemented with LIF (leukemia inhibitory factor, 1,000 U ml–1  (Millipore)) and 2-inhibitor cocktail (3 mM CHIR (BioVision) and 1 mM PD0325901 (Sigma)) unless stated otherwise.

extract_protocol:
Pooled ESCs (mix1 (Zbtb11KO and H2B::GFP) and mix2 (Zfp131KO and H2B::GFP)) were washed with 1X PBS with 0.04 mg/ml BSA (Thermo Fisher Sci AM2616). Cells were strained with CellTrics 30 µM (Cat #04-004-2326) to remove cell clumps. Knockout and wildtype cells were mixed 9:1 ratio to have 1000 cells/µL.
10X Genomics Chromium Single Cell 3’ library kit was used to generate the single-cell library with a cell recovery rate of 10.000 cells (120262 Chromium™ i7 Multiplex Kit, 120236 Chromium™ Single Cell 3’ Chip Kit v2, 120237 Chromium™ Single Cell 3’ Library & Gel Bead Kit v2). Agilent High Sensitivity DNA D1000 Screentape (5067– 5585) was used to detect fragment length distribution of the library.  KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing. Libraries were sequenced on Illumina NovaSeq 6000 using SP chemistry (100 cycles, 26x98 bp) at the Genomics Core Facility at NYU.

treatment_protocol: iZbtb11-HA Zbtb11KO and iZfp131-HA Zfp131KO cells were grown in -2i +LIF media in the absence of doxycycline and mixed with H2B-GFP expressing wt cells.

value: Ainv15(iZfp131-HA Zbtb11KO) and Ainv15(H2B::GFP)

tag: treatment

value: 3 days with media minus 2i plus LIF  (-2i + LIF) without doxycycline

value: Embryonic Stem Cells


title: blood_189 [SampleGSM4820734]

value: female


title: LG72-NY-146

value: control

value: hippocampus


title: Gan_59

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2066
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: Normal

value: frontal cortical brain cells


title: LG72-NY-136

value: P301S mutation


title: Gan_56

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2065
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: M

value: AD


title: scRNAseq in ES(iZbtb11-HA Zbtb11KO and Wildtype H2B-GFP)

source_name: Mutant ESCs with Zbtb11 knockout and Wildtype ESCs with H2B::GFP

value: Ainv15(iZbtb11-HA Zbtb11KO) and Ainv15(H2B::GFP)


title: Gan_55

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2064
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: LG72-NY-95


title: Gan_62

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2069
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: RNAseq in Zfp131KO ES grown in -2i+LIF replicate 2

description: ES(iZfp131-HA Zfp131KO)_RNAseq_minus2iplusLIF_rep2

data_processing:
RNA-seq fastq files were aligned to the mouse genome (version mm10) using Hisat2 (version 2.1.0)(D. Kim, Langmead, and Salzberg 2015)
FeatureCounts R package was used to assign reads to genomic features (Liao, Smyth, and Shi 2014).
The DESeq2 package was used for differential gene expression analysis and for data visualization (volcano plots, heatmaps, PCA plots)(Love, Huber, and Anders 2014). A q-value cutoff of < 0.01 was used for significantly misregulated genes.
PANTHER (version 14) (http://geneontology.org) was used to perform Gene Ontology term enrichment analysis (Mi et al. 2019).
Genome_build: mm10
Supplementary_files_format_and_content: TXT: tab-delimited text file containing output of featurecounts for Refseq genes.

source_name: Embryonic stem cells

extract_protocol:
RNA-seq: 500K cells were collected and RNA was extracted by resuspending in Trizol reagent (Invitrogen, 15596026) followed by purification using Qiagen RNeasy mini kit (Qiagen, 74106).
TruSeq Stranded mRNA Library Preparation kit (Illumina, 20020594) was used to prepare RNA-seq libraries. High Sensitivity DNA ScreenTape (Agilent, 5067-5584) was used to verify library sizes. A KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing.

treatment_protocol: Wildtype, iZbtb10-HA Zbtb10KO, iZbtb11-HA Zbtb11KO and iZfp131-HA Zfp131KO cells were grown in the absence of doxycycline in +2i+LIF or -2i +LIF media for 3 days.

tag: growth

value: grown in -2i+LIF

value: Ainv15(iZfp131-HA Zfp131KO)

value: No treatment

value: Embryonic stem cells


title: blood_187 [SampleGSM4820732]

value: D


title: Gan_54

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2063
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: RNAseq in Zfp131KO ES grown in -2i+LIF replicate 1

description: ES(iZfp131-HA Zfp131KO)_RNAseq_minus2iplusLIF_rep1


title: LG72-NY-78


title: LG72-NY-132


title: blood_186 [SampleGSM4820731]


title: sgScramble4

extract_protocol:
Qiagen RNAeasy Kit
Illumina TrueSeq
10nM cDNA, 12 cycles for cDNA amplification

tag: tumor stage

value: 2 weeks after inoculation

tag: cancer cell type

value: 1242 KPC cell

tag: mouse strain

tag: condition

value: Control tumor


title: LG72-NY-79

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

tag: r47h genotype


title: LG72-NY-70

tag: mutation


title: LG72-NY-149

tag: mk-2206 treatment


title: LG72-NY-102


title: blood_185 [SampleGSM4820730]

tag: mastitis

tag: metritis

tag: milk fever

value: female


title: Gan_51

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2061
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

tag: age

tag: Sex

value: F

tag: cell type


title: RNAseq in Zfp131KO ES grown in +2i+LIF replicate 1

description: ES(iZfp131-HA Zfp131KO)_RNAseq_plus2iplusLIF_rep1

value: grown in +2i+LIF


title: blood_184 [SampleGSM4820729]

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.

tag: farm


title: LG72-NY-71

value: control

tag: tissue

value: hippocampus


title: Gan_50

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2060
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: WT

tag: diagnosis

value: frontal cortical brain cells


title: RNAseq in Zbtb11KO ES grown in -2i+LIF replicate 2

description: ES(iZbtb11-HA Zbtb11KO)_RNAseq_minus2iplusLIF_rep2

tag: growth

tag: genotype

value: Ainv15(iZbtb11-HA Zbtb11KO)

tag: treatment


title: Gan_49

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2059
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: M

value: AD


title: blood_188 [SampleGSM4820733]


title: RNAseq in Zbtb11KO ES grown in -2i+LIF replicate 1

description: ES(iZbtb11-HA Zbtb11KO)_RNAseq_minus2iplusLIF_rep1

value: grown in -2i+LIF


title: LG72-NY-135


title: LG72-NY-127


title: blood_182 [SampleGSM4820727]

value: C


title: RNAseq in Zbtb11KO ES grown in +2i+LIF replicate 2

description: ES(iZbtb11-HA Zbtb11KO)_RNAseq_plus2iplusLIF_rep2

value: No treatment

value: Embryonic stem cells


title: Gan_52

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2062
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: AD/ALS


title: blood_181 [SampleGSM4820726]


title: Gan_48

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2058
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: LG72-NY-120


title: LG72-NY-119


title: RNAseq in Zbtb11KO ES grown in +2i+LIF replicate 1

description: ES(iZbtb11-HA Zbtb11KO)_RNAseq_plus2iplusLIF_rep1


title: blood_180 [SampleGSM4820725]


title: Gan_47

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2057
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: B16-Tbx2-3xHA clone09_input_rep2

city: Oxford

first: Sizhu

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research, Oxford branch

data_processing:
Adapter contamination were removed using cutadapt (v.2.8)
Sequences were mapped to the mouse reference genome (mm10) with bowtie2 (v.2.3.5)
Peak calling was performed using MACS2 (v.2.1.2) taking a q-value of 0.01 as threshold
Bowtie2 generated SAM files were compressed to BAM files, then indexed using SAMtools (v.1.9), and sequentially converted to bigWig files using uscstools (v.373) and uploaded to the UCSC Genome Browser for visualisation. Input and ChIP bigWigs were overlayed in the same track for a more intuitive presentation for peak quality
HOMER (v.4.8) was used to perform known motif enrichment and de novo motif identification, taking given peak size as input as we have paired-end data
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: melanoma cells

extract_protocol: ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody


title: RNAseq in Zbtb10KO ES grown in -2i+LIF replicate 2

description: ES(iZbtb10-HA Zbtb10KO)_RNAseq_minus2iplusLIF_rep2

value: Ainv15(iZbtb10-HA Zbtb10KO)


title: RNAseq in Zfp131KO ES grown in +2i+LIF replicate 2

description: ES(iZfp131-HA Zfp131KO)_RNAseq_plus2iplusLIF_rep2

value: Ainv15(iZfp131-HA Zfp131KO)


title: Gan_46

description: mRNA expression in human frontal cortical brain cells

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2056
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: blood_179 [SampleGSM4820724]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

value: female


title: Gan_44

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2054
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: F


title: blood_178 [SampleGSM4820723]


title: RNAseq in Zbtb10KO ES grown in -2i+LIF replicate 1

description: ES(iZbtb10-HA Zbtb10KO)_RNAseq_minus2iplusLIF_rep1


title: B16-Tbx2-3xHA clone09_input_rep1


title: B16-Tbx2-3xHA clone09_HA_rep2


title: blood_183 [SampleGSM4820728]


title: RNAseq in Zbtb10KO ES grown in +2i+LIF replicate 2

description: ES(iZbtb10-HA Zbtb10KO)_RNAseq_plus2iplusLIF_rep2

value: grown in +2i+LIF


title: Gan_45

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2055
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: RNAseq in Zbtb10KO ES grown in +2i+LIF replicate 1

description: ES(iZbtb10-HA Zbtb10KO)_RNAseq_plus2iplusLIF_rep1


title: blood_176 [SampleGSM4820721]


title: B16-Tbx2-3xHA clone09_HA_rep1


title: RNAseq in Wildtype ES grown in -2i+LIF replicate 2


title: Gan_43

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2053
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: blood_175 [SampleGSM4820720]


title: B16-Tbx2-3xHA clone02_input_rep2


title: B16-Tbx2-3xHA clone02_HA_rep2


title: Gan_39

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2051
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: AD/CAA/BLBD


title: Gan_38

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2050
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: blood_173 [SampleGSM4820718]


title: RNAseq in Wildtype ES grown in +2i+LIF replicate 2

extract_protocol:
RNA-seq: 500K cells were collected and RNA was extracted by resuspending in Trizol reagent (Invitrogen, 15596026) followed by purification using Qiagen RNeasy mini kit (Qiagen, 74106).
TruSeq Stranded mRNA Library Preparation kit (Illumina, 20020594) was used to prepare RNA-seq libraries. High Sensitivity DNA ScreenTape (Agilent, 5067-5584) was used to verify library sizes. A KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing.


title: RNAseq in Wildtype ES grown in -2i+LIF replicate 1


title: B16-Tbx2-3xHA clone02_input_rep1


title: Gan_37

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2049
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: AD/CAA


title: RNAseq in Wildtype ES grown in +2i+LIF replicate 1


title: B16-Tbx2-3xHA clone02_HA_rep1


title: blood_172 [SampleGSM4820717]


title: Gan_35

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2048
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: ChIPseq HA in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 2

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_HA_rep2
Zfp131_2iPLUS.events.gz

data_processing:
Fastq files were aligned to the mouse genome (mm10) using Bowtie (v1.0.1) with options “-q–best–strata -m 1–chunkmbs 1024”.
MultiGPS (v.0.74) was used to call peaks after alignment on all transcription factors. A q-value cutoff of <0.01 was used to identify significant binding events. Histone modification and ATAC-seq peaks were called using the DomainFinder module in SeqCode (https://github.com/seqcode/seqcode-core/blob/master/src/org/seqcode/projects/seed/DomainFinder.java). Contiguous 50-bp genomic bins with significantly higher read enrichment compared with normalized input were identified (binomial test, p <0.05).
Differential binding and modification analyses were done using DESeq2 (v1.28.1) with an adjusted p-value cutoff of <0.05 and all default options. To create the count matrix for DESeq2, peaks were first called independently in the wildtype and knockout ChIP-seq datasets. Overlapping peak regions were merged between the wt and KO. Peak regions found exclusively in either file were also included. The final count matrix was created using Bedtools coverage with the “-counts” option separating each replicate into its own count column. Before running DESeq2 on the matrix, counts were normalized by the length of the corresponding region for histone modifications (domains have differing lengths).
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location

extract_protocol:
Wildtype and mutant cells were collected after being grown for 3d in +2i or -2i conditions in the presence or absence of 3 ng/uL doxycycline. 1 mM DSG (ProteoChem) was used for crosslinking at RT for 15min. 1% Formaldehyde (vol/vol) was added for an additional 15min until quenched with glycine (Sigma). Cells were separated into aliquots of 25x106 and centrifuged to freeze pellets at -80°C. Thawed cells were lysed in 5mL of 50 mM HEPES-KOH pH 7.5 (Gibco), 140 mM NaCl (Thermo Fisher), 1 mM EDTA pH 8.0, 10% glycerol (vol/vol) (Thermo Fisher), 0.5% Igepal (vol/vol) (Sigma), 0.25% Triton X-100 (vol/vol) with 1×protease inhibitors (Roche) for 10min at 4°C. Cells were centrifuged for 5min at 1100 rpm and resuspended in 5mL of 10 mM Tris-HCl pH 8.0 (Boston BioProducts), 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 (Boston BioProducts) with 1×protease inhibitors, and incubated for an additional 10 min at 4°C on a rotating platform. Cells were centrifuged for 5min at 1100 rpm and resuspended in 2mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1×protease inhibitors). Sonication was performed in two Bioruptor tubes per sample with 0.45 g sonication beads. Bioruptor Pico (Diagenode) was used for 18 cycles of 30 sec on and 30 sec off to sonicate to an average size of approximately 200 bp. To immunoprecipitate, Dynabeads protein-G (Thermo Fisher) and antibodies (HA, H3K4me3, H3K27me3, H3K27ac, SIN3A, CHD4) were incubated with sonicated chromatin for 16h at 4°C on a rotating platform. After the immunoprecipitation, the sample was washed with sonication buffer, high salt sonication buffer (500 mM NaCl, LiCl wash buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl (Sigma), 0.5% Igepal (vol/vol), 0.5% sodium deoxycholate (wt/vol)), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8). The sample was eluted in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS (vol/vol)) by incubating for 45min at 65°C. Crosslinks were reversed by incubating the sample for 16h at 65°C. RNA was removed by 0.2 mg/mL RNAse A (Sigma) in 200 μL of TE for 2h at 37°C. To remove protein, 0.2 mg/mL Proteinase K (Invitrogen) and CaCl2 (Sigma) were added and the sample incubated at 55°C for 30min. DNA was first purified with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) and then by performing salt-ethanol precipitation. DNA pellets were resuspended in 50 uL H2O.
Illumina DNA sequencing libraries were prepared with half of the ChIP sample and a 1:100 dilution of the input sample in H2O. Library preparation was performed with end repair, A-tailing and ligating multiplexed adapters (Illumina-compatible Bioo Scientific). Agencourt AmpureXP beads (Beckman Coulter) were used to remove unligated adapters. Libraries were then amplified by PCR with TruSeq primers (Sigma) and Phusion polymerase (New England Biolabs). Libraries with sizes ranging between 250-550bp were gel purified (Qiagen). KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing. Libraries were sequenced on Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75bp) at the Genomics Core Facility at NYU.

tag: chip target

value: HA

value: anti-HA (Abcam ab9110)

value: 3d with doxycycline in +2i+LIF


title: blood_171 [SampleGSM4820716]

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.


title: Notch2-mKO-Diabetes rep4

city: Kumamoto

first: Shin

last: Fujimaki

address: Honjo 2-2-1

department: IMEG

institute: Kumamoto University

description:
KO_DB4
processed data file: N2-mKO Control-Diabetes.txt

data_processing:
StrandNGS software 3.4 (by Tomy digital biology) was used for base-calling.
Sequenced reads were trimmed for low-quality sequences and then mapped to UCSC mm10 mouse reference transcript and genome.
TPM (transcripts per million) was used as a normalization procedure to quantify the gene expressions in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Text files including raw read counts and TPM-normalized values for each sample.

extract_protocol:
Gastrocnemius muscles were collected and immediatelly frozen by liquid nitrogen. Total RNA was extracted using ISOGEN and RNeasy kit.
Library preparation was commercially commisioned to Novogene.

treatment_protocol: Mechanical unloading was caused by hindlimb suspension. Diabetes mellitus was induced by a single intraperitoneal injection of storeptozotocin (STZ) at a dose of 150 mg/kg body weight.

tag: strain

value: 14 days after STZ injection

value: Gastrocnemius muscle


title: ChIPseq HA in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 1

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_HA_rep1
Zfp131_2iPLUS.events.gz


title: blood_170 [SampleGSM4820715]

city: Davis

first: Anita

address: One Shields Ave.

institute: University of California, Davis


title: Gan_33

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2047
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

tag: r47h genotype

value: AD/DLBD

value: frontal cortical brain cells


title: Gan_40

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2052
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: WT


title: Notch2-mKO-Diabetes rep2

description:
KO_DB2
processed data file: N2-mKO Control-Diabetes.txt


title: Notch2-mKO-Diabetes rep3

description:
KO_DB3
processed data file: N2-mKO Control-Diabetes.txt


title: Gan_31

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2046
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: AD/TLBD


title: ChIPseq HA in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 2

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_HA_rep2
Zbtb11_2iPLUS.events.gz

value: Ainv15(iZbtb11-HA Zbtb11KO)

value: Embryonic stem cells


title: blood_174 [SampleGSM4820719]

value: C


title: blood_169 [SampleGSM4820714]

value: female


title: Notch2-mKO-Diabetes rep1

description:
KO_DB1
processed data file: N2-mKO Control-Diabetes.txt


title: blood_168 [SampleGSM4820713]


title: Gan_30

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2045
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: M


title: Notch2-mKO-Unloading rep4

description:
KO_HU4
processed data file: N2-mKO Control-Unloading.txt

value: 7-days hindlimb suspension


title: ChIPseq HA in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 1

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_HA_rep1
Zbtb11_2iPLUS.events.gz


title: Gan_29

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2044
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: blood_167 [SampleGSM4820712]


title: Gan_27

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2043
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: F

value: AD


title: ChIPseq H3K27me3 in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 1

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_H3K27me3_rep1
H3K27me3_2iMINUS_Zfp131KO.domains.gz
H3K27me3_Zfp131_deseq.txt.gz

value: Ainv15(iZfp131-HA Zfp131KO)

value: anti-H3K27me3 (ActiveMotif 39155)

value: 3d without doxycycline in -2i+LIF


title: ChIPseq H3K27me3 in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 2

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_H3K27me3_rep2
H3K27me3_2iMINUS_Zfp131KO.domains.gz
H3K27me3_Zfp131_deseq.txt.gz


title: Notch2-mKO-Unloading rep2

description:
KO_HU2
processed data file: N2-mKO Control-Unloading.txt


title: Notch2-mKO-Unloading rep3

description:
KO_HU3
processed data file: N2-mKO Control-Unloading.txt


title: blood_166 [SampleGSM4820711]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)


title: Gan_26

description: mRNA expression in human frontal cortical brain cells

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2042
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: ChIPseq H3K27me3 in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 2

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_H3K27me3_rep2
H3K27me3_2iMINUS_Zbtb11KO.domains.gz
H3K27me3_Zbtb11_deseq.txt.gz


title: blood_165 [SampleGSM4820710]


title: Gan_25

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2041
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: Notch2-mKO-Unloading rep1

description:
KO_HU1
processed data file: N2-mKO Control-Unloading.txt


title: blood_177 [SampleGSM4820722]


title: Notch2-mKO-Control rep4

description:
KO_CT4
processed data file: N2-mKO Control-Unloading.txt

source_name: Notch2-mKO-Control_gastrocnemius muscle

value: Control


title: Notch2-mKO-Control rep3

description:
KO_CT3
processed data file: N2-mKO Control-Unloading.txt

value: Gastrocnemius muscle


title: blood_162 [SampleGSM4820707]


title: Gan_22

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2038
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: blood_163 [SampleGSM4820708]


title: blood_164 [SampleGSM4820709]


title: ChIPseq H3K27me3 in wildtype ES cells (iCre) replicate 2

description:
ES(iCre)_ChIPseq_H3K27me3_rep2
H3K27me3_2iMINUS_WT.domains.gz


title: blood_161 [SampleGSM4820706]


title: Notch2-mKO-Control rep2

description:
KO_CT2
processed data file: N2-mKO Control-Unloading.txt


title: ChIPseq H3K27ac in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 2

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_H3K27ac_rep2
H3K27ac_2iMINUS_Zfp131KO.domains.gz
H3K27ac_Zfp131_deseq.txt.gz

value: anti-H3K27ac (Abcam ab4729)


title: ChIPseq H3K27ac in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 1

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_H3K27ac_rep1
H3K27ac_2iMINUS_Zfp131KO.domains.gz
H3K27ac_Zfp131_deseq.txt.gz


title: ChIPseq H3K27me3 in wildtype ES cells (iCre) replicate 1

description:
ES(iCre)_ChIPseq_H3K27me3_rep1
H3K27me3_2iMINUS_WT.domains.gz


title: Notch2-mKO-Control rep1

description:
KO_CT1
processed data file: N2-mKO Control-Unloading.txt


title: Gan_21

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2037
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: frontal cortical brain cells


title: blood_160 [SampleGSM4820705]


title: ChIPseq H3K27ac in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 2

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_H3K27ac_rep2
H3K27ac_2iMINUS_Zbtb11KO.domains.gz
H3K27ac_Zbtb11_deseq.txt.gz


title: WT-Diabetes rep4

description:
WT_DB4
processed data file: WT Control-Diabetes.txt

source_name: WT-Diabetes_gastrocnemius muscle

value: 14 days after STZ injection


title: Gan_20

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2036
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: WT


title: WT-Diabetes rep3

description:
WT_DB3
processed data file: WT Control-Diabetes.txt


title: ChIPseq H3K27ac in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 1

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_H3K27ac_rep1
H3K27ac_2iMINUS_Zbtb11KO.domains.gz
H3K27ac_Zbtb11_deseq.txt.gz

value: Ainv15(iZbtb11-HA Zbtb11KO)


title: blood_158 [SampleGSM4820703]


title: Gan_24

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2040
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: ChIPseq H3K27ac in wildtype ES cells (iCre) replicate 2

description:
ES(iCre)_ChIPseq_H3K27ac_rep2
H3K27ac_2iMINUS_WT.domains.gz

value: Embryonic stem cells


title: WT-Diabetes rep2

description:
WT_DB2
processed data file: WT Control-Diabetes.txt


title: Gan_18

description: mRNA expression in human frontal cortical brain cells

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2034
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: AD/VaD


title: ChIPseq H3K27me3 in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 1

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_H3K27me3_rep1
H3K27me3_2iMINUS_Zbtb11KO.domains.gz
H3K27me3_Zbtb11_deseq.txt.gz


title: Gan_23

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2039
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: Gan_16

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2033
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: ChIPseq H3K27ac in wildtype ES cells (iCre) replicate 1

description:
ES(iCre)_ChIPseq_H3K27ac_rep1
H3K27ac_2iMINUS_WT.domains.gz

extract_protocol:
Wildtype and mutant cells were collected after being grown for 3d in +2i or -2i conditions in the presence or absence of 3 ng/uL doxycycline. 1 mM DSG (ProteoChem) was used for crosslinking at RT for 15min. 1% Formaldehyde (vol/vol) was added for an additional 15min until quenched with glycine (Sigma). Cells were separated into aliquots of 25x106 and centrifuged to freeze pellets at -80°C. Thawed cells were lysed in 5mL of 50 mM HEPES-KOH pH 7.5 (Gibco), 140 mM NaCl (Thermo Fisher), 1 mM EDTA pH 8.0, 10% glycerol (vol/vol) (Thermo Fisher), 0.5% Igepal (vol/vol) (Sigma), 0.25% Triton X-100 (vol/vol) with 1×protease inhibitors (Roche) for 10min at 4°C. Cells were centrifuged for 5min at 1100 rpm and resuspended in 5mL of 10 mM Tris-HCl pH 8.0 (Boston BioProducts), 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 (Boston BioProducts) with 1×protease inhibitors, and incubated for an additional 10 min at 4°C on a rotating platform. Cells were centrifuged for 5min at 1100 rpm and resuspended in 2mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1×protease inhibitors). Sonication was performed in two Bioruptor tubes per sample with 0.45 g sonication beads. Bioruptor Pico (Diagenode) was used for 18 cycles of 30 sec on and 30 sec off to sonicate to an average size of approximately 200 bp. To immunoprecipitate, Dynabeads protein-G (Thermo Fisher) and antibodies (HA, H3K4me3, H3K27me3, H3K27ac, SIN3A, CHD4) were incubated with sonicated chromatin for 16h at 4°C on a rotating platform. After the immunoprecipitation, the sample was washed with sonication buffer, high salt sonication buffer (500 mM NaCl, LiCl wash buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl (Sigma), 0.5% Igepal (vol/vol), 0.5% sodium deoxycholate (wt/vol)), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8). The sample was eluted in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS (vol/vol)) by incubating for 45min at 65°C. Crosslinks were reversed by incubating the sample for 16h at 65°C. RNA was removed by 0.2 mg/mL RNAse A (Sigma) in 200 μL of TE for 2h at 37°C. To remove protein, 0.2 mg/mL Proteinase K (Invitrogen) and CaCl2 (Sigma) were added and the sample incubated at 55°C for 30min. DNA was first purified with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) and then by performing salt-ethanol precipitation. DNA pellets were resuspended in 50 uL H2O.
Illumina DNA sequencing libraries were prepared with half of the ChIP sample and a 1:100 dilution of the input sample in H2O. Library preparation was performed with end repair, A-tailing and ligating multiplexed adapters (Illumina-compatible Bioo Scientific). Agencourt AmpureXP beads (Beckman Coulter) were used to remove unligated adapters. Libraries were then amplified by PCR with TruSeq primers (Sigma) and Phusion polymerase (New England Biolabs). Libraries with sizes ranging between 250-550bp were gel purified (Qiagen). KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing. Libraries were sequenced on Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75bp) at the Genomics Core Facility at NYU.


title: blood_156 [SampleGSM4820701]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.

value: C

value: female


title: Gan_15

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2032
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: blood_155 [SampleGSM4820700]


title: WT-Unloading rep3

description:
WT_HU3
processed data file: WT Control-Unloading.txt

source_name: WT-Unloading_gastrocnemius muscle

extract_protocol:
Gastrocnemius muscles were collected and immediatelly frozen by liquid nitrogen. Total RNA was extracted using ISOGEN and RNeasy kit.
Library preparation was commercially commisioned to Novogene.

value: 7-days hindlimb suspension


title: WT-Diabetes rep1

description:
WT_DB1
processed data file: WT Control-Diabetes.txt


title: blood_154 [SampleGSM4820699]


title: Gan_19

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2035
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: M


title: WT-Unloading rep4

description:
WT_HU4
processed data file: WT Control-Unloading.txt


title: blood_159 [SampleGSM4820704]


title: ChIPseq H3K4me3 in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 1

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_H3K4me3_rep1
H3K4me3_2iMINUS_Zfp131KO.domains.gz
H3K4me3_Zfp131_deseq.txt.gz

value: anti-H3K4me3 (ActiveMotif 39159)


title: ChIPseq H3K4me3 in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 2

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_H3K4me3_rep2
H3K4me3_2iMINUS_Zbtb11KO.domains.gz
H3K4me3_Zbtb11_deseq.txt.gz


title: WT-Unloading rep2

description:
WT_HU2
processed data file: WT Control-Unloading.txt


title: blood_153 [SampleGSM4820698]

value: B


title: Gan_13

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2030
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: F


title: WT-Unloading rep1

description:
WT_HU1
processed data file: WT Control-Unloading.txt


title: ChIPseq H3K4me3 in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 1

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_H3K4me3_rep1
H3K4me3_2iMINUS_Zbtb11KO.domains.gz
H3K4me3_Zbtb11_deseq.txt.gz

value: 3d without doxycycline in -2i+LIF


title: Gan_11

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2029
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: AD/ALB


title: blood_152 [SampleGSM4820697]


title: ChIPseq H3K4me3 in wildtype ES cells (iCre) replicate 2

description:
ES(iCre)_ChIPseq_H3K4me3_rep2
H3K4me3_2iMINUS_WT.domains.gz


title: Gan_10

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2028
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: AD/DLBD


title: blood_151 [SampleGSM4820696]


title: Gan_9

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2027
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: WT-Control rep3

description:
WT_CT3
processed data file: WT Control-Unloading.txt

source_name: WT-Control_gastrocnemius muscle

value: Control

value: Gastrocnemius muscle


title: ChIPseq H3K4me3 in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 2

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_H3K4me3_rep2
H3K4me3_2iMINUS_Zfp131KO.domains.gz
H3K4me3_Zfp131_deseq.txt.gz

value: Ainv15(iZfp131-HA Zfp131KO)


title: ChIPseq H3K4me3 in wildtype ES cells (iCre) replicate 1

description:
ES(iCre)_ChIPseq_H3K4me3_rep1
H3K4me3_2iMINUS_WT.domains.gz


title: blood_150 [SampleGSM4820695]


title: Gan_14

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2031
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: WT

value: frontal cortical brain cells


title: Gan_8

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2026
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: AD


title: ChIPseq SIN3A in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 2

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_SIN3A_rep2
SIN3A_2iMINUS_Zfp131KO.events.gz
SIN3A_Zfp131_deseq.txt.gz

value: anti-SIN3A (Abcam ab3479)

value: Embryonic stem cells


title: WT-Control rep2

description:
WT_CT2
processed data file: WT Control-Unloading.txt


title: blood_157 [SampleGSM4820702]

value: C

value: female


title: WT-Control rep1

description:
WT_CT1
processed data file: WT Control-Unloading.txt


title: Gan_6

description: mRNA expression in human frontal cortical brain cells

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2024
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: M

value: AD/CAA


title: blood_148 [SampleGSM4820693]

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

value: B


title: ChIPseq SIN3A in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 1

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_SIN3A_rep1
SIN3A_2iMINUS_Zfp131KO.events.gz
SIN3A_Zfp131_deseq.txt.gz


title: ChIPseq SIN3A in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 2

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_SIN3A_rep2
SIN3A_2iMINUS_Zbtb11KO.events.gz
SIN3A_Zbtb11_deseq.txt.gz

value: Ainv15(iZbtb11-HA Zbtb11KO)


title: Gan_5

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2023
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: ChIPseq POL2 5SP in wildtype ES cells (iCre) replicate 1

description:
ES(iCre)_ChIPseq_POL2_5SP_rep1
POL2S5P_2iMINUS_WT.domains.gz

value: POL2 5SP

value: anti-POL2 5SP (Abcam ab5131)

value: 3d without doxycycline in -2i+LIF


title: blood_146 [SampleGSM4820691]


title: ChIPseq SIN3A in wildtype ES cells (iCre) replicate 2

description:
ES(iCre)_ChIPseq_SIN3A_rep2
SIN3A_2iMINUS_WT.events.gz


title: WT-Control rep4

description:
WT_CT4
processed data file: WT Control-Unloading.txt

value: Control


title: ChIPseq POL2 5SP in wildtype ES cells (iCre) replicate 2

description:
ES(iCre)_ChIPseq_POL2_5SP_rep2
POL2S5P_2iMINUS_WT.domains.gz


title: blood_147 [SampleGSM4820692]


title: Gan_4

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2022
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: F

value: AD/DLBD


title: Gan_3

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2021
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: ChIPseq SIN3A in wildtype ES cells (iCre) replicate 1

description:
ES(iCre)_ChIPseq_SIN3A_rep1
SIN3A_2iMINUS_WT.events.gz


title: ChIPseq NELF in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 2

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_NELF_rep2
NELF_2iMINUS_Zfp131KO.events.gz
NELF_Zfp131_deseq.txt.gz

value: Ainv15(iZfp131-HA Zfp131KO)

value: NELF

value: anti-NELF (Sigma HPA007187)


title: 6mA_DIP-seq_Av

city: Woods Hole

first: Irina

last: Arkhipova

state: MA

address: 7 MBL St

department: Josephine Bay Paul Center

institute: Marine Biological Laboratory

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence (cutadapt v1.9.2), and masked for short sequences (<15nt) or low-quality scores (<20), then mapped to reference genome using Bowtie, with default parameters and -n 1 -l 30
Aligned sequence reads processed with MACS using nomodel nolambda parameters
BigWig files were generated with deepTools2 using bamCoverage function
Supplementary_files_format_and_content: bed files with peak, BigWig files

organism: Adineta vaga

source_name: whole animal

extract_protocol:
Genomic DNA extraction with Dneasy Tissue Kit (Qiagen). Sonication (Covaris S220) to obtain 200-400 bp range.
DNA library construction with NuGen Ovation Ultra Low System v2

value: MBL

value: whole animal

tag: medip antibody

value: N6-methyl-A (NEB)


title: 4mC_DIP-seq_Av

value: N4-methyl-C (NEB)