title: pif4 pif5_Heat_bio2

first: Lei

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

description: fpkm.txt

data_processing:
150 nt paired-end high throughput sequencing was performed on an Illumina Hiseq X ten.
Low quality sequencing reads were removed. Clean reads were mapped to the Arabidopsis reference genome (TAIR10, www.arabidopsis.org) with Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml) software, and differential expressed genes (DEGs) was identified using edgeR in the R package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) if FoldChange > 2 and FDR < 0.05 between case group sample and control group sample. GO and KEGG pathway enrichment analysis was performed using TopGO in the R package (http://bioconductor.org/).
Genome_build: TAIR10
Supplementary_files_format_and_content: fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: 3rd and 4th rosette leaves

growth_protocol: The Arabidopsis thaliana plants material grown on soil for 3 weeks under 22°C condition.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion) and treated with DNase I (Thermo Fisher).
Sequencing libraries were prepared following the protocol of the Directional RNA library Prep Kit (NEB).

treatment_protocol: The materials were treated at 42°C for 5 hours, and after 3 days of recovery growth, the 3rd and 4th rosette leaves were collected.

tag: ecotype/background

value: 3 weeks

value: 3rd and 4th rosette leaves

value: Heat (42C for 5 hours)

tag: medium

value: Soil


title: CAPTURE-3C-seq_HUDEP2_beta3

status: Public on Jul 30 2021

type: SRA

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

description:
3C DNA
The combined sample represents all three beta samples. In our study, all the replicates (beta1,2,3) were combined for downstream data analysis, so only the processed data files for the combined datasets have been provided. However, all sample files were uploaded to make them available to the research community.

library_source: genomic

data_processing:
Sequencing reads were aligned to human genome assembly hg19 using Bowtie2 v2.2.8 with default parameters. The reads with low mapping quality and duplicate reads were removed after the alignment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (https://eg.readthedocs.io/en/latest/text.html#longrange).
Genome_build: hg19
Supplementary_files_format_and_content: Pairwise Interaction Format

molecule: genomic DNA

organism: Homo sapiens

source_name: HUDEP2 cells

growth_protocol: HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies) with 50 ng/ml SCF, 3 IU/ml EPO, 10-6 M dexamethasone, 1 ug/ml doxycycline, and passaged every three days.

extract_protocol:
10 ng of 3C DNA was processed for library generation using the NEBNext Ultra II DNA Library prep kit following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.
CAPTURE-3C-seq

tag: cell line

tag: genotype

value: wild-type (WT)


title: FH-Piwi-IP_1_3

city: Bethesda

first: Pavol

last: Genzor

state: MD

address: 6720A Rockledge Drive, Suite 100

department: ACESO

institute: Henry M Jackson Foundation

description:
Piwi-associated RNA (piRNA)
size-selected piRNAs with 10 UMIs

library_source: transcriptomic

data_processing:
Fastq files were trimmed using cutadapt (v2.3) to remove the 5` and 3` adapters and keep 10 unique molecular identifiers (UMI) - 8N's at 5` end and 2N's at 3` end.
Fastq files were processed in R using custom script where sequences were collapsed by UMI to remove PCR duplicates, UMI's were trimmed,  and sequences shorter than 18-nt in length were removed. To reduce the file size while retaining all the information, the sequences were collapsed and individual sequence abundance was recorded in fasta header. Fasta header is comprised of sample name that is followed by a unique alphanumeric string containing sequence ID number (S) and abundance count (M) and have following structure: SAMPLE_XY - S[UniqueSequenceID]M[SequenceAbundance]. Fasta header "FH-Piwi-IP_1_1-S32M12" can be split into sample name ("FH-Piwi-IP_1_1") and unique string ("S32M12")  that can be further split into unique sequence ID ("S32") and abundance count of this particular sequence ("M12"). Please see UNIQSEQS.fa processed files. These files are deposited for the convenient, fast download and analysis.
UNIQSEQS.fasta files were aligned to genome comprised of the structural RNAs (tRNA, rRNA, snRNA, snoRNA) using STAR (v2.5.2b), the unmapped sequences were collected and mapped to the dm6 genome using the same aligner. The obtained .bam files were analyzed in R using custom scripts.
piRNA quantification was performed by determining the number of cells per sample (S1-S8) using molecular counts of the callibrator oligoes in the UNIQSEQS.fasta files. MiRNAs were quantified by mapping to miR Base (Release 22.1). PiRNAs were quantified by considering seqeunces in 24 - 29-nt size range.
Genome_build: dm6 (Drosophila melanogaster)
Supplementary_files_format_and_content: xlsx: piRNA_quantification; fasta: custom trimmed and filtered unique sequence files

molecule: total RNA

organism: Drosophila melanogaster

source_name: OSC cell line

growth_protocol: OSC cell culture was grown as described in protocols described here: https://dgrc.bio.indiana.edu/product/View?product=288

extract_protocol:
piRNAs: RNA was extracted from the OSC cell lysate by immunoprecipitating PIWI proteins using anti-Flag antibody beads or custom made fly anti-Piwi antibodies. Total small RNAs: RNA was extracted from the cells usign PureLink miRNA Isolation kit (Thermo Fisher Scientific, K157001)
piRNA libraries: Imunoprecipitated RNA was ligated to 3` adapter containing unique indexes and two random bases (2N), and ligation products in 48 to 58-nt size range (equivalent to 19 - 29-nt long initial fragments) were recovered from Urea PAGE gel. Purified fragments were then ligated to 5` adapter containing eight random bases (8N) and purified on Urea PAGE gel again by selecting fragments in 82 - 92-nt size range. Final fragments were PCR amplified to add sequencing adapters. Total small RNAs libraries: A pellet of one million cells was used to purifiy small RNAs using PureLink miRNA Isolation kit (Thermo Fisher Scientific, K157001) and were spiked with a mix of 26 nt-long synthetic RNA callibrator sequences. RNA was ligated to 3` adapter containing unique indexes and two random bases (2N), and ligation products in 48 to 58-nt size range (equivalent to 19 - 29-nt long initial fragments) were recovered from Urea PAGE gel. Purified fragments were then ligated to 5` adapter containing eight random bases (8N) and PCR ampliffied to add sequencing adapters.

value: ovarian somatic sheet cells (OSC)

value: 3xFH-Piwi / WT

tag: ip antibody

value: anti-Flag M2 magnetic beads, Millipore Sigma, M8823

value: GTTCAGAGTTCTACAGTCCGACGATCNNNNNNNN

value: NNGCGATATGGAATTCTCGGGTGCCAAGG


title: FH-Piwi-IP_1_1


title: ChIP-Rx CPSF73 dTAG7 2h Rep 2

city: Innsbruck

first: Univ.-Prof. Dr. Andreas

last: Mayer

address: Innrain 80/82

department: Institute for Genomics and RNomics

country: Austria

institute: Biocenter, Medical University Innsbruck

data_processing:
For ChIP-Rx, we aligned the sequencing reads to a joined reference genome which we assembled from human (hg38/GRCh38) and the spiked-in mouse (mm10/GRCm38)
reference genomes using Bowtie2 v2.3.5.1 (Langmead and Salzberg, 2012) in paired-end mode with '-k 1'.
We extracted the raw density from human for the protein of interest using bedtools (Quinlan and Hall, 2010) in the 'genomecov -bg' mode.
Genome_build: Human (hg38/GRCh38) and the spiked-in mouse (mm10/GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using ‘bedGraphToBigWig’; Scores represent Reads per Million (RPM) or the fold-enrichment 'FE' signal over the matched input control.

source_name: bone marrow, CML

growth_protocol: K562 dTAG-BRD4 cells were cultured in RPMI containing 10% FBS, 5% penicillin-streptomycin. NIH3T3 cells, which were used as spike-ins, were grown in DMEM containing 10% FBS , 5% penicillin-streptomycin. K562 dTAG-BRD4 cells were plated at 5 x 10^5 cells/ml, NIH3T3 were plated at 2 x 10^6 cells/T75 flask every two days.

extract_protocol:
K562 dTAG-BRD4 cells were crosslinked with 1% formaldehyde for 5 min at room temperature, NIH3T3 cells were crosslinked for 8 min. After combining NIH3T3 and K562 dTAG-BRD4 cells in a ratio of 1:5, cells were lysed as described by Baluapuri et al. (2019), followed by sonication using a Covaris E220evolution at intensity 4, duty cycle 5%, 200 cycles per burst for 20 min. Lysates were pre-cleared by centrifugation. Lysates and antibodies coupled to Dynabeads Protein G (Thermo Fisher Scientific) were incubated at 4°C overnight with rotation. Afterwards, the beads were washed with buffers prepared according to Baluapuri et al. (2019). DNA fragments were purified using the ChIP DNA Clean & Concentrator kit (Zymo).
Libraries were constructed from 6 to 30 ng DNA using the NEBNext Ultra II DNA kit (NEB) according to the manufacturer's instructions. After purifying the amplified libraries with AMPure XP beads (Beckman Coulter), fragments of 200 to 500 bp were extracted from an 8% TBE gel. Library quality and quantity were assessed using BioAnalyzer HS DNA (Agilent) and Qubit dsDNA HS (Thermo Fisher) assays, respectively.

treatment_protocol: K562 dTAG-BRD4 cells at a concentration of 1 x 10^6/ml were treated with 500 nM dTAG7 or DMSO for 2 h.

value: K562 dTAG-BRD4

tag: treatment

value: BRD4 degradation

tag: antibody

value: CPSF73, Bethyl, A301-091A, 10 µg

tag: matched input

value: ChIP-Rx Input R7


title: s11-CD3posCD45RAneg-TR3

city: Graz

first: Silvia

last: Fibi-Smetana

state: Styria

address: Stremayrgasse 16

department: Biomedical Informatics

institute: Graz University of Technology

description: hospitalized patient s11, technical replicate 3

data_processing:
RNA-Seq data was processed using published Drop-seq pipeline (v1.0) to obtain the count table
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
Blood sampling 2 weeks after positive SARS-CoV-2-RNA results, stained samples were sorted for CD3+ CD45RA- population (memory T cells), RNA-isolation via TCL-lysis buffer and 2-mercaptoethanol
Library preparation according to Parekh et. Al 2016, Nature Scientific Reports

tag: diagnosis

tag: cell type

value: memory T cell

tag: group

value: hospitalized

tag: sample name as in counts.txt.gz

value: GTACCG


title: m42-CD3posCD45RAneg-TR3

description: not hospitalized patient m42, technical replicate 3

value: not hospitalized

value: ATTTCA


title: ChIP-Rx CPSF73 DMSO 2h Rep 1

value: control

value: ChIP-Rx Input R6


title: ChIP-Rx FIP1 dTAG7 2h Rep 2

value: FIP1, Bethyl, A301-461A, 8 µg

value: ChIP-Rx Input R5


title: pif4 pif5_Heat_bio1

city: Beijing

last: Wang

country: China

description: fpkm.txt

tag: age

value: 3 weeks

tag: tissue

value: 3rd and 4th rosette leaves

value: Heat (42C for 5 hours)

value: Soil


title: pif4 pif5_Mock_bio2

description: fpkm.txt

value: Mock


title: m29-CD3posCD45RAneg-TR3

description: not hospitalized patient m29, technical replicate 3

value: AATCTT


title: s10-CD3posCD45RAneg-TR2

description: hospitalized patient s10, technical replicate 2

value: TTGAAA


title: pif4 pif5_Mock_bio1

description: fpkm.txt


title: Col_0_Heat_bio2

description: fpkm.txt

value: Wild type


title: 21P: Vβ11+ Bcl6KO-R-par #3 bulkRNA-seq

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

data_processing:
Processing of sequencing data was performed with the cellranger pipeline v3.0.2 (10X Genomics) according to the manufacturer’s instructions. Briefly, subsequent read alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters. The cellranger aggr pipeline was employed to aggregate samples with mapping normalization to leave each sample with similar sequencing depth per cell.
A reverse-complement modification of read2 data was done by using the SeqKit v0.11.0. We also replaced the cell barcode white list of the 5’ VDJ kit with the cell barcodes white list of 10x 3’ v3 kit: In the folder of “/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/”, we unzipped the file “3M-february-2018.txt.gz”, renamed it as “737K-august-2016.txt” and replaced the same name file in the same folder. Processing of modified sequencing data was performed with the modified cellranger VDJ pipeline v3.1.0 (10X Genomics) according to the manufacturer’s instructions with default settings.
 The cellranger aggr pipeline was employed, to generate a single cell-barcode matrix containing all the samples with normalization.
Counted files were normalized and analyzed by R language package DESeq2 v1.28.1. Genes with expression count below 5 in all samples were filtered out. Differential Expression genes were calculated by DESeq2 v 1.28.1 with Wald test.
Genome_build: mm10
Supplementary_files_format_and_content: Standard cellranger output format

organism: Mus musculus

source_name: bulk-RNA seq data of Bcl6KO-Th17 cells from SC parenchyma of AT-EAE recipient

extract_protocol: After fluorescent labeling of blood leukocytes, peak of disease AT-EAE recipient mice (of either wt-Th17 or Bcl6KO-Th17 donor cells) were anesthetized and intracardially perfused, and spinal cord (SC) meninges and parenchyma were extracted separately. Parenchymal tissue was flushed out from the spinal canal with hydrostatic pressure. SC meninges remained attached to the vertebrae and were peeled of under the binocular. Parenchymal tissue was digested with collagenase D/DNase I and cells were isolated via 70%/37% percoll gradient as described before. Meningeal cell were extracted using collagenase D for digestion. Isolated cells were sorted either for CD45highCD45iv- cells or Vß11+CD4+CD45highCD45iv- cells. In vitro differentiated Th17 cultures were sorted for Vß11+CD4+ cells. Single cell suspensions of CD45highCD45iv- cells (5 µl each) were manually counted in a Fuchs-Rosenthal chamber and the cell concentration was adjusted to achieve a cell recovery of approx. 5’000-6’000 cells. In total, 5 wt-R AT-EAE mice vs. 5 Bcl6KO-R AT-EAE mice were used to generate single cell RNA sequencing data from SC meningeal vs. parenchymal tissues. Per tissue, an average of 4,017 ± 132 SEM cells were used for analysis. 57,846 ± 1,060 SEM reads per cell were sequenced and this resulted in 2136 ± 176 SEM median genes detected per cell. In addition, we did bulk RNA sequencing on sorted Vß11+CD4+CD45highCD45iv- cells of SC meninges (5 wt-R AT-EAE mice vs. 5 Bcl6KO-R AT-EAE mice) or parenchyma (4 wt-R AT-EAE mice vs. 4 Bcl6KO-R AT-EAE mice) or on sorted Vß11+CD4+ of in vitro differentiated Th17 cells (5 wt-Th17 vs. 5 Bcl6KO-Th17 in vitro cultures). On average, 15,19 ± 0,65 SEM M reads were sequenced and used for bulk-seq analysis.

value: Bcl6KO-R SC parenchyma-derived sorted VBeta11+ CD4+ T cells

tag: strain

value: 2D2tg CD4cre Bcl6flox (=Bcl6KO)

tag: condition

value: adoptive transfer experimental autoimmune encephalomyelitis

tag: type of library

value: RNA expression


title: 24P: Vβ11+ Bcl6KO-R-par #4 bulkRNA-seq


title: ChIP-Rx FIP1 DMSO 2h Rep 1

value: K562 dTAG-BRD4

value: ChIP-Rx Input R4


title: ChIP-Rx FIP1 DMSO 2h Rep 2

value: control


title: m43-CD3posCD45RAneg-TR2

description: not hospitalized patient m43, technical replicate 2

value: memory T cell

value: not hospitalized

value: TACTAT


title: 20P: Vβ11+ Bcl6KO-R-par #2 bulkRNA-seq


title: 18P: Vβ11+ Bcl6KO-R-par #1 bulkRNA-seq


title: Col_0_Heat_bio1

description: fpkm.txt

tag: ecotype/background

value: 3 weeks

value: 3rd and 4th rosette leaves


title: ChIP-Rx PAF1 dTAG7 2h Rep 2

value: BRD4 degradation

value: PAF1, abcam, Ab20662, 10 µg

value: ChIP-Rx Input R2


title: Col_0_Mock_bio2

description: fpkm.txt

value: Mock

tag: medium

value: Soil


title: m42-CD3posCD45RAneg-TR2

description: not hospitalized patient m42, technical replicate 2

value: ATTCTA


title: ChIP-Rx PAF1 dTAG7 2h Rep 1

tag: cell line

value: ChIP-Rx Input R3


title: m29-CD3posCD45RAneg-TR2

description: not hospitalized patient m29, technical replicate 2

value: AATACA


title: Col_0_Mock_bio1

description: fpkm.txt

tag: genotype

value: Wild type


title: 16P: Vβ11+ wt-R-par #4 bulkRNA-seq

source_name: bulk-RNA seq data of wt-Th17 cells from SC parenchyma of AT-EAE recipient

value: wt-R SC parenchyma-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg (=wt)

value: adoptive transfer experimental autoimmune encephalomyelitis

value: RNA expression


title: 11P: Vβ11+ wt-R-par #3 bulkRNA-seq


title: ChIP-Rx PAF1 DMSO 2h Rep 2

value: K562 dTAG-BRD4

value: control


title: s11-CD3posCD45RAneg-TR2

description: hospitalized patient s11, technical replicate 2

value: memory T cell

value: hospitalized

value: CCAACC


title: 9P: Vβ11+ wt-R-par #2 bulkRNA-seq


title: 3P: Vβ11+ wt-R-par #1 bulkRNA-seq


title: pifq_hypocotyl_Bio3

data_processing:
150-nucleotide paired-end high-throughput sequencing was performed on an Illumina Hiseq platform
Then low quality sequencing reads were removed. The obtained clean data were aligned against the Arabidopsis thaliana reference genome sequence (TAIR10 Genome Release) with HISAT2. DESeq2 was used for differential gene expression analysis. Genes with q≤0.05 and |log2_ratio|≥1 were identified as differentially expressed genes (DEGs).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Arabidopsis hypocotyl

growth_protocol: Plants were grown under continuous darkness conditions at 22ºC for 4 days.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion) and treated with DNase I (Thermo Fisher).
sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following manufacturer’s instructions.

value: hypocotyl

tag: time point

value: Continuous darkness

value: MS+3percent sucrose

value: pif1pif3pif4pif5 -/-/-/-

value: 4 d

tag: ecotype


title: pifq_hypocotyl_Bio2


title: ChIP-Rx PAF1 DMSO 2h Rep 1

tag: treatment

tag: antibody

value: PAF1, abcam, Ab20662, 10 µg

value: ChIP-Rx Input R3


title: ChIP-Rx SPT5 dTAG7 2h Rep 2

value: BRD4 degradation

tag: matched input

value: ChIP-Rx Input R2


title: 24M: Vβ11+ Bcl6KO-R-men #5 bulkRNA-seq

source_name: bulk-RNA seq data of Bcl6KO-Th17 cells from SC meninges of AT-EAE recipient

value: Bcl6KO-R SC meninges-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg CD4cre Bcl6flox (=Bcl6KO)


title: pifq_hypocotyl_Bio1


title: m43-CD3posCD45RAneg-TR1

description: not hospitalized patient m43, technical replicate 1

tag: diagnosis

tag: cell type

value: not hospitalized

value: TAATGA


title: ChIP-Rx SPT5 dTAG7 2h Rep 1

value: K562 dTAG-BRD4

value: ChIP-Rx Input R1


title: pifq_hook_Bio3

source_name: Arabidopsis apical hook

value: apical hook


title: ChIP-Rx SPT5 DMSO 2h Rep 2

value: control


title: 23M: Vβ11+ Bcl6KO-R-men #4 bulkRNA-seq

value: adoptive transfer experimental autoimmune encephalomyelitis

value: RNA expression


title: m42-CD3posCD45RAneg-TR1

description: not hospitalized patient m42, technical replicate 1

value: memory T cell

tag: group

tag: sample name as in counts.txt.gz

value: ATTACT


title: pifq_hook_Bio2

tag: tissue

value: Continuous darkness

value: MS+3percent sucrose

value: pif1pif3pif4pif5 -/-/-/-

tag: age

value: 4 d


title: 22M: Vβ11+ Bcl6KO-R-men #3 bulkRNA-seq

tag: strain

tag: condition


title: ChIP-Rx SPT5 DMSO 2h Rep 1


title: pifq_hook_Bio1


title: 21M: Vβ11+ Bcl6KO-R-men #2 bulkRNA-seq

tag: type of library


title: ChIP-Rx Pol II dTAG7 2h Rep 2

value: BRD4 degradation

value: Pol II RPB2, GeneTex, TX102535, 5 µg


title: s10-CD3posCD45RAneg-TR1

description: hospitalized patient s10, technical replicate 1

value: hospitalized

value: TTATTG


title: P016_00d

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

data_processing:
Illumina Casava1.7 software used for basecalling.
Single end reads were adapter and quality trimmed by Trimmomatic v0.39, aligned to Ensembl v96 human transcriptome by Kallisto v0.46, and collapsed to gene level annotations by Biomart.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Nasopharyngeal Swab

extract_protocol:
RNA was isolated from NP swabs in viral transport media using the Roche MagNAPure or Qiagen BioRobot
First strand cDNA was synthesized by SuperScriptIV/Random hexamers, second strand by Sequenase v2.0, and libraries constructed by Nextera XT Kit

tag: patient

value: Nasopharyngeal Swab

value: Unknown

tag: collection

value: day after initial positive test:0

value: initial or repeat:initial


title: 20M: Vβ11+ Bcl6KO-R-men #1 bulkRNA-seq

value: Bcl6KO-R SC meninges-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg CD4cre Bcl6flox (=Bcl6KO)


title: s11-CD3posCD45RAneg-TR1

description: hospitalized patient s11, technical replicate 1

value: TCTGCA


title: P009_17d

value: day after initial positive test:17


title: 18M: Vβ11+ wt-R-men #5 bulkRNA-seq

source_name: bulk-RNA seq data of wt-Th17 cells from SC meninges of AT-EAE recipient

value: wt-R SC meninges-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg (=wt)

value: adoptive transfer experimental autoimmune encephalomyelitis

value: RNA expression


title: pifq_cotyledon_Bio3

source_name: Arabidopsis cotyledon

value: cotyledon

value: Continuous darkness

tag: medium

value: MS+3percent sucrose

tag: genotype

value: pif1pif3pif4pif5 -/-/-/-

value: 4 d


title: ChIP-Rx Pol II DMSO 2h Rep 2

tag: cell line

value: K562 dTAG-BRD4

value: control

value: Pol II RPB2, GeneTex, TX102535, 5 µg


title: pifq_cotyledon_Bio2

tag: time point

tag: ecotype


title: m29-CD3posCD45RAneg-TR1

description: not hospitalized patient m29, technical replicate 1

value: memory T cell

value: not hospitalized

value: AAGATT


title: 16M: Vβ11+ wt-R-men #4 bulkRNA-seq


title: P008_00d

value: Nasopharyngeal Swab

value: day after initial positive test:0

value: initial or repeat:initial


title: 14M: Vβ11+ wt-R-men #3 bulkRNA-seq

value: wt-R SC meninges-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg (=wt)


title: P004_00d


title: ChIP-Rx Pol II DMSO 2h Rep 1

tag: treatment

tag: antibody

tag: matched input


title: SI-NET-seq K562 dBET6 50min R2

description: 10 nt random molecular barcodes

data_processing:
Library strategy: NET-seq
Data processing of SI-NET-seq data sets was performed similar as described in Mayer et al., 2015.
Pre-processing: The six or ten 5’ end nucleotides corresponding to the molecular barcode, are trimmed from the reads, but remain associated with the read using a custom python script.
Mapping: Reads are aligned using the STAR aligner (v2.5.3a) (Dobin et al., 2013) with the following parameters : --clip3pAdapterSeq ATCTCGTATGCCGTCTTCTGCTTG --clip3pAdapterMMp 0.21 --clip3pAfterAdapterNbases 1 –outFilterMultimapNmax 1000000000 –outSJfilterOverhangMin 3 1 1 1 –outSJfilterDistToOtherSJmin 0 0 0 0 –alignIntronMin 11 –alignEndsType EndToEnd. The reference genome consisted of a joined reference genome which we assembled from human (GRCh38.p12) and mouse (GRCm38.p6) reference genomes, with additional sequences containing the rDNA sequences (genBank U13369.1, genBank U67616.1), and the sequence of processed tRNA (with the additional CCA at their end, and intron removed, when present). The alignment was performed with the GENCODE annotation v28.
Filtering: We separated reads mapping to the mouse genome for normalization. We removed putative contaminations such as reverse transcription mispriming events (barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read), PCR duplicates (reads that align to the same genomic position and contain identical barcode) and splicing intermediates (exact single bp 3’ ends of introns and exons).
Normalization: We extracted the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, using the HTSeq package (Anders et al., 2014). The Reference-adjusted Reads Per Million (RRPM) were calculated as described by (Orlando et al., 2014) using the number of reads mapping to the mouse genome as reference.
Genome_build: Human (hg38/GRCh38) and the spiked-in mouse (mm10/GRCm38)
Supplementary_files_format_and_content: Bedgraph files; Scores represent Reference-adjusted Reads Per Million (RRPM).

growth_protocol: K562 dTAG-BRD4 and MOLT4 cells were cultured in RPMI containing 10% FBS, 5% penicillin-streptomycin. NIH3T3 cells, which were used as spike-ins, were grown in DMEM containing 10% FBS , 5% penicillin-streptomycin. K562 dTAG-BRD4 and MOLT4 cells were seeded at 5 x 10^5 cells/ml, NIH/3T3 were seeded at 2 x 10^6 cells/T75 flask every two days.

extract_protocol:
Nascent RNA was extracted as described by Mayer and Churchman (2016) with the following modification: After treatment of MOLT4 or K562 dTAG-BRD4, NIH3T3 cells were added in a ratio of 1:6.
Libraries were constructed as described by Mayer and Churchman (2016). In case of the libraries on K562 dTAG-BRD4,  the following modifications were implemented: After purification of the nascent RNA, a DNA linker containing a random decamer sequence was ligated to the 3'-end of the transcripts. Ligated RNA was fragmented by incubation with NEBNext RNA fragmentation solution at 95°C for 10 min. To improve read mapping and take the increased linker length into account, all size selection steps were adapted.

treatment_protocol: K562 dTAG-BRD4 cells at a concentration of 1 x 10^6/ml were treated with 100 nM dBET6, 500 nM dTAG7 or DMSO for 40, 50, 60 or 120 min.

value: pan-BET degradation

tag: treatment time

value: 50 min

tag: molecule subtype

value: nascent RNA


title: P007_06d

tag: tissue

value: day after initial positive test:6

value: initial or repeat:repeat


title: Col-0_hypocotyl_Bio3

value: hypocotyl

value: Continuous darkness

value: MS+3percent sucrose

value: Wild type

tag: age

value: 4 d


title: Col-0_hypocotyl_Bio2


title: P003_05d

value: day after initial positive test:5


title: SI-NET-seq K562 dBET6 50min R1

description: 10 nt random molecular barcodes

value: K562 dTAG-BRD4


title: ChIP-Rx Pol II dTAG7 2h Rep 1

value: BRD4 degradation

value: Pol II RPB2, GeneTex, TX102535, 5 µg


title: Col-0_hypocotyl_Bio1


title: 11M: Vβ11+ wt-R-men #2 bulkRNA-seq

tag: strain

value: adoptive transfer experimental autoimmune encephalomyelitis

value: RNA expression


title: Col-0_hook_Bio3

value: apical hook


title: 3M: Vβ11+ wt-R-men #1 bulkRNA-seq

value: wt-R SC meninges-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg (=wt)

tag: condition


title: P015_00d

value: Nasopharyngeal Swab

value: Unknown

value: day after initial positive test:0

value: initial or repeat:initial


title: KO756: Vβ11+ Bcl6KO-Th17 #4 bulkRNA-seq

source_name: bulk-RNA seq data of in vitro differentiated Bcl6KO-Th17 cells

value: in vitro Th17-Bcl6KO culture-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg CD4cre Bcl6flox (=Bcl6KO)

value: in vitro Th17 differentiation (pre-AT-EAE transfer)

tag: type of library


title: KO758: Vβ11+ Bcl6KO-Th17 #5 bulkRNA-seq


title: P003_00d

tag: patient


title: Col-0_hook_Bio2

value: Continuous darkness

value: MS+3percent sucrose

value: Wild type

value: 4 d


title: SI-NET-seq K562 dBET6 40min R1

description: 10 nt random molecular barcodes

value: K562 dTAG-BRD4

value: pan-BET degradation

value: 40 min

value: nascent RNA


title: P002_00d

tag: collection


title: pifq_cotyledon_Bio1

value: cotyledon

tag: medium

value: pif1pif3pif4pif5 -/-/-/-


title: SI-NET-seq K562 DMSO 60min R2

description: 10 nt random molecular barcodes; control experiment for SI-NET-seq K562 dBET6 50min R2

value: control

value: 60 min


title: P001_05d

value: Nasopharyngeal Swab

value: day after initial positive test:5

value: initial or repeat:repeat


title: Col-0_hook_Bio1

value: apical hook

tag: genotype


title: SI-NET-seq K562 DMSO 60min R1

description: 10 nt random molecular barcodes; control experiment for SI-NET-seq K562 dBET6 50min R1

tag: cell line


title: SI-NET-seq MOLT4 dBET6 2h R2

description: 6 nt random molecular barcodes

source_name: T lymphoblast, ALL


title: SI-NET-seq K562 dBET6 40min R2

description: 10 nt random molecular barcodes


title: KO755: Vβ11+ Bcl6KO-Th17 #3 bulkRNA-seq

value: in vitro Th17-Bcl6KO culture-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg CD4cre Bcl6flox (=Bcl6KO)

value: in vitro Th17 differentiation (pre-AT-EAE transfer)

value: RNA expression


title: KO21: Vβ11+ Bcl6KO-Th17 #2 bulkRNA-seq


title: Col-0_cotyledon_Bio3

tag: time point

value: Continuous darkness

value: MS+3percent sucrose

value: Wild type

value: 4 d


title: SI-NET-seq MOLT4 dBET6 2h R1

description: 6 nt random molecular barcodes

value: pan-BET degradation

value: nascent RNA


title: SI-NET-seq K562 DMSO 50min R2

description: 10 nt random molecular barcodes

value: K562 dTAG-BRD4

value: 50 min


title: SI-NET-seq K562 DMSO 50min R1

description: 10 nt random molecular barcodes

value: control

value: 40 min


title: SI-NET-seq MOLT4 DMSO 2h R2

description: 6 nt random molecular barcodes


title: Col-0_cotyledon_Bio1

value: cotyledon

tag: ecotype


title: wt4110: Vβ11+ wt-Th17 #5 bulkRNA-seq

source_name: bulk-RNA seq data of in vitro differentiated wt-Th17 cells

value: in vitro Th17-wt culture-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg (=wt)


title: MPRA_RNA_day-6_rep-4

city: Stanford

first: Daniel

middle: Sunwook

last: Kim

state: CA

address: 269 Campus Drive, CCSR 2150

institute: Stanford School of Medicine

description: Demultiplexed file which does not contain the UMI sequence as the UMI conflicts with the standard demultiplexing algorithm. Provided to give the demultiplexed read ids.

data_processing:
library strategy: Massively parallel reporter assays (MPRA)
MPRA read strategy: single ended reads where UMI is in read name and barcode is on the read (the 20 bps after the first 17 bps)
Reads are trimmed and UMI is associated to matching read such that downstream analysis proceeds with reads as just the barcodes
Reads (barcodes) are matched to original barcodes with BWA alignment with default params to get reads per MPRA fragment
UMIs are used to get unique reads per fragment
Counts are normalized according to the plasmid fractions and then run through DESeq2 rlog transformation for a normalized signal matrix
Genome_build: hg19
Supplementary_files_format_and_content: Master file of all tested fragments with relevant metadata, FASTA file of tested fragments, read counts for each fragment in the plasmid library, MPRA RNA read counts for each fragment per sample

growth_protocol: Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiate for 6 days as previously describe (Zarnegar 2012)

extract_protocol:
At each timepoint, total RNA was isolated using Qiagen's Rneasy Plus kit
cDNA was synthesized using SuperScript IV using primers containing UMIs, cDNA synthesis reactions were cleaned up witih SPRIselect beads and amplified with PrimeSTAR Max DNA Polymerase, sequennce indices were added, then libraries were ge purified and pooled.

treatment_protocol: Keratinocyes were infected with lentiviral MPRA library, selected for infected cells 24 hours later with puromycin, then induced to differentiate 24 hours later (Zarnegar 2012) for up to 6 days, harvested at days 0, 3, and 6

tag: cell type

value: Primary foreskin keratinocytes

tag: timepoint

tag: replicate


title: ChIP-Rx FIP1 dTAG7 2h Rep 1

tag: treatment

value: BRD4 degradation

tag: antibody

value: FIP1, Bethyl, A301-461A, 8 µg

tag: matched input

value: ChIP-Rx Input R4


title: SUDHL4_INPUT

city: New York

first: David

last: Dominguez-Sola

state: NY

address: One Gustave L. Levy Place, Box 1044A

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: SUDHL4 cells

data_processing:
Sequencing data were acquired through the default Illumina pipeline using bcl2fastq pipeline
Reads were aligned to the UCSC hg19 human genome using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads were removed with samtools v0.1.19 rmdup option.
Peaks were called over the input using MACS2 peakcall function at a q (minimum FDR) value cutoff of 0.05
Bam files were converted to bigwig files for viewing in the UCSC genome browser by using DeepTools v3.0.0 bamCoverage with arguments --binSize=10 --extendReads=100 --normalizeUsing RPKM
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing normalized read density for viewing in the UCSC genome browser

source_name: SUDHL4 cell line

growth_protocol: Cells were maintained in log growth phase in IMDM medium supplemented with 10% FBS and 1% Penicillin/Streptomicin at 37C and 5% CO2. Cells were washed twice in 1X Hanks Buffered Saline Solution (HBSS), then  resuspended in 1X HBSS + 0.1% IMDM with no serum for 3 hours at 37C, 5% CO2

extract_protocol:
Nuclei were isolated by resuspending cell pellet in a buffer containing 10mM Tris pH 8.0, 10 mM NaCl, and 0.2% NP-40 and leaving on ice for 30 minutes. Nuclei were pelleted by centrifugation at 7400 rpm, 4C for 30 seconds, and pellet was resuspended in a buffer containing 50 mM Tris pH 8.0, 10 mM EDTA, and 1% SDS and left on ice for 30 minutes with vortexing every 5 minutes. Sample was transferred to a thin-walled 1.5 mL sonication tube and sonicated at low-power setting until chromatin was on average 200-600 basepairs. 250 ug of chromatin was diluted in a 1:4 ratio with IP dilution buffer containing 20 mM Tris pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, and 0.01% SDS, and precleared with IgG coated protein A+G dynabeads for 3 hours at 4C. The diluted chromatin was then separated from the beads and 5 ug of FOXO1 ChIP-seq grade antibody (abcam) was added to the sample for rotation overnight at 4C. The next morning, protein A+G beads were added and sample was rotated for an additional 3 hours at 4C. Beads were then washed with increasing stringency, then resuspended in DNA elution buffer containing SDS and NaHCO3, and were allowed to shake for 1 hour at 65C. DNA-containing supernatant was removed from the beads into a new tube and DNA crosslinks were reversed overnight at 65C in the presence of NaCl and RNase.
Libraries for next-generation sequencing were generated using the NEBNext NGS DNA Library Preparation kit (E7645 and E7500)

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 15 min at room temperature while rotating, then quenched by the addition of glycine to a final concentration of 0.125 M

value: DLBCL cell

value: SUDHL4 cell line

value: wildtype


title: wt760: Vβ11+ wt-Th17 #3 bulkRNA-seq

tag: tissue

value: in vitro Th17 differentiation (pre-AT-EAE transfer)

value: RNA expression


title: FOXO1_M1L47_SUDHL4

description: CRISPR-Cas9 was used to introduce bi-allelic point mutations to introduce an M1L amino acid change in the FOXO1 locus in SUDHL4 cells. Single clones were isolated and verified

source_name: SUDHL4 cell line bi-allelic M1L point mutation in FOXO1 locus

value: anti-FOXO1 (abcam 39670)


title: wt4098: Vβ11+ wt-Th17 #4 bulkRNA-seq

tag: strain


title: wt21: Vβ11+ wt-Th17 #2 bulkRNA-seq

tag: condition


title: MPRA_RNA_day-6_rep-2


title: MPRA_RNA_day-6_rep-3


title: dIF1-2-1h

city: Freiburg

first: Ute

middle: A.

last: Hoffmann

address: Schänzlestr. 1

department: Institute of Biology III

institute: University of Freiburg

description: rne(Ts) 1h replicate 2

data_processing:
Basecalls were performed online during the sequencing procedure with Real-Time Analysis (RTA) software v2.4.11 and System Suite v2.1.2.1. bcl2fastq script v2.18.0.12 was used for coversion of bcl2 files to de-multiplexed gzipped fastq files
Transcript, TSS and PSS data sets were demultiplexing using BBDuk
Sequenced reads were trimmed for adaptor sequences and low-quality base calls using cutadapt (Galaxy v1.16.5), then aligned using bowtie2 (Galaxy v2.3.4.3+galaxy0) –very-sensitive
PCR duplicates were removed using UMI-tools deduplicate (Galaxy v0.5.3.0) with parameters --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --subset 1.0
Reads were filtered for a minimum mapping quality of 20 using bamtools filter (Galaxy v2.4.1)
Transcript pattern reads were assigned to annotated regions using htseq-count (Galaxy v0.9.1+galaxy1)
Transcript coverage files and 5’ end counts of PSS and TSS reads were created using bedtools Genome coverage (Galaxy v2.29.2)
DESeq2 (v1.30.1) was used  to classify PSS and TSS positions
TSS positions with a TSS-reads/transcript coverage ratio < 0.02 and > 2.00 were excluded. Furthermore, only TSS-positions with a maximum distance of 20nt to TSS identified by Kopf et al., 2014, were used in further analyses.
DESeq2 (v1.30.1) was used to evaluate differential expression at newly determined PSS and TSS positions and for htseq-count files
Genome_build: GCF_000009725.1
Supplementary_files_format_and_content: gff file with PSS and TSS positions determined as part of this analysis
Supplementary_files_format_and_content: Comma-delimited matrix tables with normalized read counts for RNA features (for transcript data), PSS or TSS (PSS, TSS data set, respectively)

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture

growth_protocol: Synechocystis sp. PCC 6803 strains rne(WT) and rne(Ts) were grown in BG-11 (Rippka et al., 1979) medium supplemented with 0.3% (w/v) sodium thiosulphate and 10mM (w/v) TES pH 8.0 at constant shaking (135 rpm) and 30 µm mol photons m-2 s-1 white light illumination

extract_protocol:
20 ml culture were collected by vacuum filtration through 0.8 µm polyethersulphone filter disks (Pall, Germany). Filters were immediately transferred to 1.6 ml PGTX solution (Pinto et al., 2009), vortexed, frozen in liquid nitrogen and stored at -80°C. RNA was extracted according to Pinto et al. (2009) with modifications as described in Wallner et al. (2020).
For RNA Sequencing, biological triplicates were used of each strain at each condition. Residual DNA was removed from samples containing each 10 µg RNA by three subsequent incubation steps with Ambion TURBO DNase (Thermo Fisher Scientific, Germany). For each step, 2 U TurboDNase was added, followed by 20 min incubation at 37°C. RNA was recovered using RNA Clean & Concentrator kits (Zymo Research, USA). RNA integrity was controlled for on a Fragment Analyzer using the High Sensitivity RNA Analysis Kit (Advanced Analytical Technologies, Germany). cDNA libraries were constructed and sequenced as a service provided by vertis Biotechnologie AG (Germany) according to the tagRNA-Seq protocol (Innocenti et al., 2015), including unique molecular identifiers (UMIs) (Smith et al., 2017). Ribosomal RNAs were depleted using in-house depletion probes. 5‘-P RNA fragments were ligated to the 5‘ Illumina TruSeq sequencing adapter carrying the sequence tag CTGAAGCT. After incubation with 5‘-phosphate-dependent exoribonuclease XRN-1 (New England BioLabs, Inc., USA), samples were treated with RNA 5‘ Polyphosphatase (5‘PP, Lucigen). The 5‘ Illumina TruSeq sequencing adapter carrying sequence tag TAATGCGC was ligated to newly formed 5‘-P RNA ends. RNA was fragmented and an oligonucleotide adapter was ligated to the resulting 3‘ ends. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3‘ adapter as primer. First-strand cDNA was purified and the 5‘ Illumina TruSeq sequencing adapter was ligated to the 3‘ end of the antisense cDNA. This was followed by PCR amplification to about 10-20 ng/µl using a high fidelity DNA polymerase. cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). Samples were pooled in approximately equimolar amounts and the cDNA pool in the size range of 200 – 600 bp was eluted from a preparative agarose gel.

treatment_protocol: The set temperature of the used incubator shaker (Multitron Pro, Infors AG, Switzerland) was changed to 39°C. Samples were taken exactly 60min thereafter.

value: rne(Ts)

value: 1h incubation 39°C

value: cells from liquid culture


title: MPRA_RNA_day-6_rep-1


title: dIF1-1-1h

description: rne(Ts) 1h replicate 1


title: dIF3-1-1h

description: rne(Ts) 1h replicate 3


title: FOXO1_M1L39_SUDHL4

value: CRISPR-Cas9 was used to introduce bi-allelic point mutations to introduce an M1L amino acid change in the FOXO1 locus


title: wt20: Vβ11+ wt-Th17 #1 bulkRNA-seq

tag: type of library


title: Col-0_cotyledon_Bio2

value: cotyledon

value: Continuous darkness

value: MS+3percent sucrose

value: Wild type

tag: age

value: 4 d


title: dWT3-1h

description: rne(WT) 1h replicate 3

value: rne(WT)


title: MPRA_RNA_day-3_rep-4

value: Primary foreskin keratinocytes


title: FOXO1_SUDHL4

description: SUDHL4 cells

value: DLBCL cell


title: KO19: Vβ11+ Bcl6KO-Th17 #1 bulkRNA-seq

value: in vitro Th17-Bcl6KO culture-derived sorted VBeta11+ CD4+ T cells

value: 2D2tg CD4cre Bcl6flox (=Bcl6KO)


title: MPRA_RNA_day-3_rep-3


title: SI-NET-seq MOLT4 DMSO 2h R1

description: 6 nt random molecular barcodes

value: control

tag: treatment time

tag: molecule subtype

value: nascent RNA


title: dWT2-1h

description: rne(WT) 1h replicate 2


title: dWT1-1-1h

description: rne(WT) 1h replicate 1


title: MPRA_RNA_day-3_rep-2


title: S22P29

description: SUDHL4 cells edited by CRISPR-Cas9 to introduce an S22P point mutation in a single FOXO1 allele

data_processing:
Sequencing data were acquired through the default Illumina pipeline using bcl2fastq pipeline
reads were aligned to human genome reference hg19 using TopHat with options –read-mismatches 2 –read-edit-dist 2 –max-multihits 10
Htseq-count was used to generate gene counts
Genome_build: grch37
Supplementary_files_format_and_content: Tab delimited text file of raw gene counts

growth_protocol: Cells were maintained in log-phase growth in a 37C incubator with 5% CO2 in growth media (IMDM, 10% FBS, 1% Penicillin/Strepromycin)

extract_protocol:
Total RNA was isolated using the PureLink RNA Extraction kit (Qiagen), according to the manufacturer's instructions.
Libraries were prepared using the Nugen Universal Plus mRNA-seq kit (Nugen).

tag: genotype


title: WPRTCR: wt-R-par TCR TCR-seq

description: This sample was sequenced both by Illumina NextSeq 500 (shallow-seq) and NovaSeq 6000 (deep-seq).

data_processing:
Library strategy: TCR-seq
Processing of sequencing data was performed with the cellranger pipeline v3.0.2 (10X Genomics) according to the manufacturer’s instructions. Briefly, subsequent read alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters. The cellranger aggr pipeline was employed to aggregate samples with mapping normalization to leave each sample with similar sequencing depth per cell.
A reverse-complement modification of read2 data was done by using the SeqKit v0.11.0. We also replaced the cell barcode white list of the 5’ VDJ kit with the cell barcodes white list of 10x 3’ v3 kit: In the folder of “/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/”, we unzipped the file “3M-february-2018.txt.gz”, renamed it as “737K-august-2016.txt” and replaced the same name file in the same folder. Processing of modified sequencing data was performed with the modified cellranger VDJ pipeline v3.1.0 (10X Genomics) according to the manufacturer’s instructions with default settings.
 The cellranger aggr pipeline was employed, to generate a single cell-barcode matrix containing all the samples with normalization.
Counted files were normalized and analyzed by R language package DESeq2 v1.28.1. Genes with expression count below 5 in all samples were filtered out. Differential Expression genes were calculated by DESeq2 v 1.28.1 with Wald test.
Genome_build: mm10
Supplementary_files_format_and_content: Standard cellranger output format

source_name: TCR seq data of SC parenchyma of AT-EAE recipients of wt-Th17 cells

value: wt-R SC parenchyma-derived leukocytes

value: donor:2D2tg (=wt), recipient:C57BL/6

value: adoptive transfer experimental autoimmune encephalomyelitis

value: RNA expression


title: dIF3-1-0h

description: rne(Ts) 0h replicate 3

value: rne(Ts)

value: untreated

value: cells from liquid culture


title: KMRTCR: Bcl6KO-R-men TCR TCR-seq

source_name: TCR seq data of SC meninges of AT-EAE recipients of Bcl6KO-Th17 cells

value: Bcl6KO-R SC meninges-derived leukocytes

value: donor:2D2tg CD4cre Bcl6flox (=Bcl6KO), recipient:C57BL/6


title: MPRA_RNA_day-3_rep-1


title: dIF1-2-0h

description: rne(Ts) 0h replicate 2


title: S22P10

tag: cell line

value: CRISPR-Cas9 to introduce an S22P point mutation in a single FOXO1 allele


title: KPR: Bcl6KO-R-par scRNA-seq

source_name: single-cell RNA seq data of SC parenchyma of AT-EAE recipients of Bcl6KO-Th17 cells

value: Bcl6KO-R SC parenchmya-derived leukocytes


title: MPRA_RNA_day-0_rep-3

value: Primary foreskin keratinocytes


title: MPRA_RNA_day-0_rep-2


title: KPRTCR: Bcl6KO-R-par TCR TCR-seq

source_name: TCR seq data of SC parenchyma of AT-EAE recipients of Bcl6KO-Th17 cells


title: M1L39

description: SUDHL4 cells edited by CRISPR-Cas9 to introduce bi-allelic M1L point mutations in the FOXO1 locus

value: DLBCL cell


title: WT2

description: SUDHL4 Cells

value: Wildtype


title: dIF1-1-0h

description: rne(Ts) 0h replicate 1


title: WMRTCR: wt-R-men TCR TCR-seq

source_name: TCR seq data of SC meninges of AT-EAE recipients of wt-Th17 cells

value: wt-R SC meninges-derived leukocytes


title: WPR: wt-R-par scRNA-seq

source_name: single-cell RNA seq data of SC parenchyma of AT-EAE recipients of wt-Th17 cells


title: MPRA_RNA_day-0_rep-1


title: dWT2-0h

description: rne(WT) 0h replicate 2

value: rne(WT)


title: S22P43


title: WMR: wt-R-men scRNA-seq

source_name: single-cell RNA seq data of SC meninges of AT-EAE recipients of wt-Th17 cells


title: M1L47

value: CRISPR-Cas9 to introduce bi-allelic M1L point mutations in the FOXO1 locus


title: WT1

description: SUDHL4 Cells


title: MPRA_RNA_non_demultiplexed

description: UMI is the last 12 bp at the end of the read name, barcode is the 20 bps after the first 17 bps in the read. This file is important because it maintains the UMI sequences

value: all


title: dWT1-1-0h

description: rne(WT) 0h replicate 1


title: KMR: Bcl6KO-R-men scRNA-seq

source_name: single-cell RNA seq data of SC meninges of AT-EAE recipients of Bcl6KO-Th17 cells


title: MPRA_RNA_day-0_rep-4


title: dWT3-0h

description: rne(WT) 0h replicate 3


title: Rep161_H3.3G34V_ATAC_Rep2

status: Public on Jul 29 2021

city: Frederick

first: GuoJun

last: Yu

address: 560 CHANDLER STREET

department: Cell Biology

institute: National Institutes of Health

data_processing:
Adaptors and low-quality reads were filtered out using Trim Galore (version 0.3.7)
For whole genome analysis, clean reads were aligned to the human genome from GENCODE (GRCh38 v30) with STAR (v 2.7.6a, --alignIntronMax 1 --seedSearchStartLmax 25 --outFilterMultimapNmax 2 --outFilterMismatchNmax 1).
Samtools was used to remove the reads mapped to mitochondria and duplicated reads were filtered out using Picard.
Macs2 (v2.2.7.1) was adopted to call peaks for all the samples and the differential peaks were determined using featureCounts and DEseq2 with threshold: foldchange >=2 and Padj <= 005.
bamCoverage was used to generate the bigwig files and the ATAC-seq profile for each sample was plotted using computeMatrix and plotProfile command from deeptools.
The genomic track of ATAC-seq for Ig locus was plotted using pyGenomeTracks program.
Genome_build: GRCh38 v30
Supplementary_files_format_and_content: genome browser track

source_name: human B cell line Ramos-Rep161-H3.3G34V

growth_protocol: The cells were cultured with Iscove’s modified Dulbecco’s medium (BioWhittaker) supplemented with 10% (vol/vol) FBS (Atlanta Biologicals) and 100 U/mL penicillin-streptomycin (Mediatech).

extract_protocol:
The nuclei from each group were treated with Tn5 transposase and the accessible DNA regions were collected and amplified.
Liabries were prepared under the standard Omni-ATAC protocol using Illumina Tagment DNA Enzyme and Buffer Small Kit.

treatment_protocol: The HIRA was knocked out using CRISPR-Cas9 and positive clones were screend by western blotting. For the H3.3 WT and H3.3 G34V mutant transfection, 3rd generation of lenti virus was used and the stable pool was selected by treating the transfected cells with 0.8 mg/ml G418.

tag: aid level

value: endogenous AID is undectable

tag: aid-er

value: Ectopic AID-ER is stably transfected

value: Stable expression of ectopic H3.3G34V mutant and endogenous wild type H3.3 is still there.


title: Rep161_H3.3WT_ATAC_Rep1

source_name: human B cell line Ramos-Rep161-H3.3-WT

value: Stable expression of ectopic H3.3 WT and endogenous wild type H3.3 is still there.


title: Rep161_H3.3G34V_ATAC_Rep1


title: Luchuan rep2_ATAC

city: Nanning

last: Zhou

state: Guangxi

address: Daxuedong Road, Xixiangtang District

department: College of Animal Science and Technology

institute: Guangxi university

description:
180-day-old male pigs were fed under the same feeding conditions for 180 days
ATAC_Peaks

data_processing:
ATAC-seq: MACS2 software was used for peak detection to obtain an overview of the open chromatin regions of the whole genome of each sample.
RNA-seq: We used Bowtie2 to align clean reads to the reference sequence, and then we used RSEM to calculate the gene and transcriptome expression.
Genome_build: Genome_build: Sus scrofa 11.1 (ATAC-seq)& Sus scrofa 10.2 (RNA-seq)
Supplementary_files_format_and_content: ATAC-seq: Luchuan peaks& Duroc peaks& Common peaks
Supplementary_files_format_and_content: RNA-seq: FPKM& log2Ratio

organism: Sus scrofa

growth_protocol: 180-day-old male pigs were fed under the same feeding conditions for 180 days.

extract_protocol:
ATAC-seq: The original Illumina high-throughput sequencing image data files were converted into original sequences after base group recognition by bcl2fastq software. The results were stored in FASTQ file format. Trimmomatic (v0.36) software was used to filter the original sequences to obtain high quality clean reads, and Bowtie2 software was used to compare the sequencing sequences with the reference genome (Sus scrofa 11.1).  RNA-seq: Transcriptome data were assembled using Stringtie and compared with the reference genome (Sus scrofa 10.2) using CuffCompare.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Longissimus dorsi muscle

value: Luchuan

tag: Sex

value: male

value: post natal day 180


title: Duroc rep2_mRNA

description:
180-day-old male pigs were fed under the same feeding conditions for 180 days
mRNA_FPKM&log2Ratio

value: Duroc


title: Duroc rep1_mRNA


title: Duroc rep2_ATAC


title: Luchuan rep3_ATAC


title: Luchuan rep1_mRNA


title: Luchuan rep3_mRNA


title: Duroc rep3_mRNA


title: Duroc rep1_ATAC


title: Rep161_HIRA_KO_ATAC_Rep1

source_name: human B cell line Ramos-Rep161-HIRA_KO

value: HIRA KO by CRISPR/Cas9


title: Duroc rep3_ATAC


title: Rep161 WT_ATAC_Rep2

source_name: human B cell line Ramos-Rep161-WT

value: WT


title: Luchuan rep1_ATAC


title: Rep161_HIRA_KO_ATAC_Rep2


title: Luchuan rep2_mRNA


title: Rep161 WT_ATAC_Rep1


title: Rep161_H3.3WT_ATAC_Rep2


title: HH2_treated_repl3

city: Nijmegen

first: Nael

last: Nadif Kasri

address: Geert Grooteplein Zuid 10

department: Department of Human Genetics

country: Netherlands

institute: Radboudumc

data_processing:
Base calls were converted to fastq format and demultiplexed using Illumina's bcl2fastq conversion software (v2.16.0.10) tolerating one mismatch per library barcode.
Reads were filtered for unique molecular identifier (UMI) and sample barcode, tolerating one mismatch per barcode
Trimming of adapter sequences and over-represented sequences was performed using Trimmomatic (version 0.33)
Trimmed reads were mapped to a combined human (GRCh38.p12) and rat (Rnor_6.0) reference genome to separate reads belonging to the human iNeurons from reads origniating from rat astrocytes using STAR (version 2.5.1b)
Uniquely mapped reads (mapping quality of 255) were extracted and read duplicates were removed using the UMI-tools software package
Count matrices were generated with HTSeq (version 0.9.1) using a combined human (GRCh38.p12) and rat (Rnor_6.0) reference transcriptome
Genome_build: GRCh38.p12 and Rnor_6.0
Supplementary_files_format_and_content: count table (text file)

source_name: iNeurons (co-cultured with rat astrocytes)

growth_protocol: rtTA/Ngn2-positive iPS cells were plated as single cells at DIV0 onto multi-electrode arrays (Multichannel Systems, MCS GmbH, Reutlingen, Germany) coated with 50µg/mL poly-L-ornithine hydrobromide (PLO; Sigma-Aldrich #P3655-10MG) and 5 µg/mL human recombinant laminin 521 (BioLamina #LN521-02) in E8 basal medium (Gibco #A1517001) supplemented with 1% Penicillin/Streptomycin (Pen/Strep; Sigma-Aldrich P4333), 1% RevitaCell (Thermo-Fisher #A2644501), and 4 µg/mL doxycycline (Sigma-Aldrich #D9891-5G) to drive Ngn2 expression. These were incubated at 37°C/5%CO2, at 20,000 cells per well (24 well plate) for the LH- lines, and 30,000 cells per well (24 well plate) for HH lines, to ensure similar mature neuron cell density. At DIV1, medium was changed to DMEM/F12 (Gibco #11320-074) supplemented with 1% Pen/Strep, 4 µg/mL doxycycline, 1% N-2 supplement (Gibco #17502-048), 1% MEM non-essential amino acid solution (NEAA; Sigma-Aldrich #M7145), 10 ng/mL human recombinant BDNF (Promokine #C66212), 10 ng/mL human recombinant NT-3 (Promokine #C66425). To support the neuronal culture, freshly prepared primary cortical rat astrocytes (Frega et al., 2017) were added on DIV2, in a 1:1 ratio. At DIV3, the medium was changed to Neurobasal (Gibco #21103-049), supplemented with 20 μg/mL B-27 (Gibco #0080085SA), 1% GlutaMAX (Gibco), 1% Pen/Strep, 4 µg/mL doxycycline, 10 ng/mL human recombinant NT3, 10 ng/mL human recombinant BDNF. At DIV3 only, 2 µM Cytosine β-D-arabinofuranoside (Ara-C; Sigma-Aldrich C1768-100MG) was added to remove any proliferating cells. From DIV5-DIV9 50% of the medium was refreshed every 2 days. From DIV 9-23 onwards the medium was supplemented with 2.5% Fetal Bovine Serum (FBS; Sigma-Aldrich #F2442-500ML) to support astrocyte viability.

extract_protocol:
RNA was isolated with the Quick-RNA Microprep kit (Zymo Research, R1051)
Tagmentation was performed per pool by adding 5.5 µL double-stranded cDNA sample to 5.0 µL Nextera TD buffer (Illumina, 15027866), and 1.5 µL TDE1 Enzyme (Illumina, 15027865), incubated at 55°C for 5 min. Samples were directly placed on ice for at least 3 min. The reaction was terminated by adding 12 µL Buffer PB (QiaQuick, 19066) and incubating for 5 min at room temperature. Samples were purified using 48 µL Ampure XP beads and eluted in 10 µL NF H2O. Next, each sample was mixed with 2 µL P5 primer (10 µM), (5ʹ-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3ʹ; IDT),  2 µL P7 primer (10 µM) (5ʹ-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3ʹ; IDT), 6 µL NF H2O, and 20 µL NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541). Amplification was performed using the following program: 72°C for 5 min, 98°C for 30 sec, 15 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final step at 72°C for 5 min. Samples were purified using 32 µL Ampure XP beads and eluted in 14 µL NF H2O. Libraries were visualized by electrophoresis on a 1% agarose and 1X TAE gel containing 0.3 µg/mL ethidium bromide (Invitrogen, 15585011). Gel extraction was performed to select products between 200 – 1000 bp using the Nucleospin Gel and PCR Clean-up kit (Macherey-Nagel, 740609). Samples were eluted in 15 µL NF H2O. cDNA concentrations were measured by Qubit dsDNA HS Assay kit (Invitrogen, Q32854). Product size distributions were visualized using Agilent’s Tapestation system (D5000 ScreenTape and Reagents, 5067-5588/9).

treatment_protocol: HH1 and HH2 were treated with sonlicromanol from DIV3

tag: cell type

value: iPSC-derived neurons

value: sonlicromanol from DIV3

value: high (66%) m.3243A>G heteroplasmy (HH)

tag: disease state

value: MELAS


title: HH2_treated_repl2

tag: treatment


title: 10 mg/kg RE-administered with TST group 2

type: RNA

city: Tsukuba

first: Kazunori

last: Sasaki

address: 1-1-1 Tennodai

country: Japan

institute: AIST

description: Gene expression data from mice hippocampus

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Thermo Fisher Science, Japan).

data_processing: The raw CEL data were normalized using the transcriptome analysis console (TAC) software ver.4.0.1 following the robust multichip average (RMA) algorithm (Thermo Fisher Scientific, Japan).

label: biotin

source_name: Mice limbic system administered with 10 mg/kg RE with TST group 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: Male ICR mice aged eight weeks were purchased from Charles River, Japan. The animals were housed in individual cages and kept under controlled environmental conditions of constant room temperature at 21–23 °C, a 12 h light-dark cycle, humidity 50–55%, and ad libitum access to food and water. After one week of acclimatization to the laboratory condition, mice were subjected to experiments. Animal care and experimental procedures used in this study were approved by the Ethics Animal Care and Use Committee of the University of Tsukuba (19-364).

extract_protocol: Total RNA was extracted from the limbic system using the ISOGEN kit (Nippon Gene Co. Ltd., Tokyo, Japan), following the manufacturer’s instructions. Total RNA concentration was determined using NanoDrop 2000 spectrophotometer (Thermo SCIENTIFIC, Wilmington, DE, USA).

treatment_protocol: For the TST model, mice were randomly assigned to four groups with seven mice in each group: control, negative control, low-dose RE, and high-dose RE groups. RE was dissolved in drinking water and orally administered to the animals. Low and high dosage RE groups were administered with 10 mg/kg and 100 mg/kg RE, respectively. The remaining groups (control and negative control groups) were administered with the same amount of drinking water. The negative control group was subjected to TST. The duration of the treatment was seven days.

value: ICR

value: Brain (limbic system)

tag: agent

value: Low dose RE treatment


title: 10 mg/kg RE-administered with TST group 1

source_name: Mice limbic system administered with 10 mg/kg RE with TST group 1


title: water-administered with TST group 1

source_name: Mice limbic system administered with water with TST group 1

value: Negative control


title: water-administered without TST group 2

source_name: Mice limbic system administered with water without TST group 2

value: Positive Control


title: 100 mg/kg-administered with TST group 1

source_name: Mice limbic system administered with 50 mg/kg RE with TST group 1

value: High dose RE treatment


title: water-administered without TST group 1

source_name: Mice limbic system administered with water without TST group 1


title: water-administered with TST group 2

source_name: Mice limbic system administered with water with TST group 2


title: 100 mg/kg-administered with TST group 2

source_name: Mice limbic system administered with 50 mg/kg RE with TST group 2


title: HH1_repl2

value: untreated

value: high (61%) m.3243A>G heteroplasmy (HH)


title: LH1_repl2

value: low (0%) m.3243A>G heteroplasmy (LH)

value: healthy


title: HH2_treated_repl1


title: HH1_treated_repl3


title: HH2_repl2


title: LH2_repl3


title: LH2_repl1


title: HH1_treated_repl2


title: LH1_repl1


title: HH1_repl1


title: HH1_treated_repl1


title: LH1_repl3


title: LH2_repl2


title: HH2_repl1


title: HiC_iXEN_48hr

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

data_processing:
Data was processed using the Hi-Cpro pipeline to produce a list of valid interactions pairs. This list was converted into cool and mcool files for visualization with higlass.
For CaptureC, the make_viewpoints Hicpro script was used to obtain individual Capture-C bigwig files for each replicate of each viewpoint with 1kb-sized bins.
Supplementary_files_format_and_content: bigWig, mcool files

source_name: Embryonic stem cell line

growth_protocol: Cells were maintained at a density of 1 million cells per 10cm gelatinized plates at 37ºC x% O2, x% CO2 in 2i media (50% DMEM/F12, 50% Neurobasal, Penicillin-Streptomycin, GlutaMAX, 2-Mercaptoethanol, N2, B27, 0.3nM PD0325901, 0.1nM CHIR9902, and 2x10^5units/mL LIF).

extract_protocol:
1 million cells per sample were trypsinized, washed in growth media and fixed for 10 minutes at room temperature while rotating with 1% formaldehyde (Thermo: 28908) in 1ml of HBSS media. To stop fixation, Glycine was added at final concentration of 0.13M and incubated for 5 minutes at RT and 15 minutes on ice. Cells were then washed once in cold PBS, centrifuged at 2500g 4oC for 5 mins (these centrifugation conditions were used for all washes following fixation) and pellets frozen at -80oC. Thawed cell pellets were incubated in 1ml lysis buffer (10mM Tris-HCL pH8, 10mM NaCl, 0.2% Igepal CA-630, Roche Complete EDTA-free Sigma #11836170001). Following lysis, cells were dounced for a total of 40 strokes with the “tight pestle” and then washed in cold PBS. For DpnII digest, cells were resuspended in 50µl 0.5% SDS and incubated at 62oC for 10 minutes. Then 150µl of 1.5% Triton-X was added and cells incubated for 15 minutes at 37oC while shaking at 900rpm. 25µl of 10X DpnII restriction buffer (NEB) was added, and cells further incubated for 15 minutes while shaling. 200U of DpnII (NEB R0543M) were then added and incubated for 2hours, then 200U more and incubated overnight. Next morning 200U more were added and incubated for 3h (total 600U of DpnII). DpnII was inactivated at 62oC for 20 minutes. Biotin fill-in was done by incubating cells with a mixture of 4.5 µl dCTP dTTP and dGTP at 3.3 mM, 8µl klenow polymerase (NEB M0210L) and 37.5µl Biotin-14-dATP (Thermo 19524016) for 4h at RT while shaking at 900rpm for 10 seconds every 5 minutes. Ligation was done overnight at 16oC also rotating at 900rpm for 10 seconds every 5 minutes by adding 120µl of 10X ligation buffer (NEB), 664µl water, 100µl 10% Triton-X, 6µl BSA 20mg/ml, and 2µl T4 ligase (NEB cat #M0202M). For Capture-C, biotin fill-in step was skipped and 50µl more of water was added to the ligation mix. Crosslink removal was done overnight with 50µl of proteinase K in 300µl of following buffer (10mM Tris-HCl pH8.0, 0.5M NaCl, 1%SDS) while shaking at 1400rpm at 65oC. Following Sodium Acetate and 100% Ethanol -80oC precipitation, DNA was resuspended in 50µl 10mM Tris HlL for Hi-C or 130µl for Capture-C. Sonication for Hi-C was done using Covaris onetube-10 AFA strips using the following parameters for a 300bp fragment size (Duration: 10secs, repeat for 12 times, total time 120 secs, peak power-20W, duty factor 40%, CPB-50). Sonication for Capture-C was done using Covaris AFA microtubes 130 with following settings for a fragment size of 200bp fragments (Duration: 225Secs, peak power-75W, duty factor 25%, Cycles per Burst-1000). Sonications were performed in a Covaris ME220 sonicator. Sonicated material was then size selected using SPRI beads with the following ratios: 0.55X and 1X for Capture-C and 0.55X and 0.75X for Hi-C. Hi-C material was then bound, washed and recovered to 150µl Streptavidin C1 beads (Thermo 65002) per sample following manufacturer's recommendations. Bead-bound DNA was resuspended in 50µl 10mM Tris HCl.
Library preparation was done using Kapa Hyper Prep KK8502 kit. 10µl of End-repair buffer and enzyme mix were added to resuspended beads and incubated for 30 minutes at RT and then 30 minutes at 65oC. 1µl of 15mM annealed-Illumina adaptors, containing an universal p5 and an indexed p7 oligo, were then incubated with a mixture containing 40µl of ligase and ligation buffer at RT for 60 minutes. Libraries were then amplified using 4 reactions per sample for a total of 200µl and 10 cycles, as recommended by manufacturer. For Capture-C, following sonication and size selection, 1µg of template material was resuspended in 50µl of 10mM Tris and used for library prep with 10µl of End-Repair reaction. 5µl of 15mM annealed -Illumina adaptors were ligated to the Capture-C material. Using a total volume of 100µl, library was amplified by PCR using 6 cycles. For capture, 1µg of Capture-C library per sample was mixed with mouse COT1 DNA and universal as well as index-specific blocking oligos from SeqCap EZ HE-oligo (Roche). 4.5µl pool of biotinylated probes (xGen Lockdown Probe Pools from IDT), with each probe at 0.4fmol/µl targeting the promoters of our loci of interested were added to this mixture and incubated for 3 days at 47oC. Following binding to Streptavidin C1 beads, material was washed as recommended by the SeqCap EZ Hybridization and Wash Kits. Following washes material was amplified by PCR using Kapa polymerase and 14 cycles. Material from different samples was then combined and 1µg of pooled libraries was recaptured in a single reaction and amplified with 8 cycles.
Paired-end 50.

treatment_protocol: Differentiation into primitive endoderm was induced in serum containing ESS media (Knockout DMEM, 15% FBS,1% GlutaMAX, 1% Penicillin-Streptomycin, 1% 2-Mercaptoethanol, 1% Sodium Pyruvate, 1% MEM NEAA, 2x10^5units/mL LIF) containing doxycycline (1ug/mL) for 2 to 12 hours. For time points greater than 12 hours, mES cells were induced in serum media containing doxycycline for 12 hours and switched to serum media in the absence of doxycycline for the remaining time.

value: Embryonic stem cells

tag: time point

value: 48 hour post doxycycline

tag: trangene

value: Stem cells have TRE:GATA6-DSREd2

tag: assay

value: Hi-C


title: HiC_iXEN_0hr

value: 0 hour no doxycycline

tag: strain


title: CaptureC_ixen_0h_rep2

description: Baits: Cdx2-promoter, Cobl-promoter, Col4a1-promoter, Dppa2-promoter, Dppa4-promoter, Fgf3-promoter, Fgf4-promoter, Fgfr2-promoter, Foxa2-promoter, Gata4-promoter, Gata6-promoter, Igfbp2-promoter, Klf4-promoter, Lamb1-promoter, Morc1-promoter, Nanog-promoter, Pax5-promoter, Pdgfra-promoter, Podxl-promoter, Pou5f1-promoter, Prdm14-promoter, Shh-promoter, Sox17-promoter, Sox2-promoter, Sox7-promoter.

value: Capture-C


title: CaptureC_ixen_16h_rep1

value: 16 hour post doxycycline


title: CaptureC_ixen_16h_rep2


title: CaptureC_ixen_48h_rep2


title: CaptureC_ixen_48h_rep1


title: CaptureC_ixen_0h_rep1


title: JT_506_0h_ixen_merged_Input

description: Input

data_processing:
Mapping to genome using bowtie2 with the following options (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that mapped to ENCODE mm10 blacklist regions were removed using Samtools (Li et al., 2009). Piccard (broadinstitute.github.io/picard/) was then used to identify non-duplicated reads. Duplicate reads were removed for libraries generated from blastocysts but kept for all others.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

extract_protocol:
30 million cells were fixed by resuspending them in 1% formaldehyde in HBSS (1ml/million cells). Cells were incubated for 10 mins at room temperature, protected from light, on a nutator. After 10 mins, 1.42M glycine (100µl/ml of fixative) was added and cells were mixed by inversion and incubated for 5 mins at room temperature to quench PFA. Cells were then pelleted at 2000g, at 40C for 5 mins and washed twice in 1X TBS (50 mM Tris-Cl, pH 7.5, 150 mM NaCl). Cell pellets were then flash frozen and stored at -800C. To perform ChIP, pellets were thawed on ice for 10 mins and lysed in Farnham lysis buffer (5mM PIPES PH 8.0, 85mM KCl, 0.5% NP-40, supplemented with protease inhibitors). To lyse cells, pellets were reconstituted in 1ml buffer/ 10 million cells and incubated on ice for 10 mins, following which they were dounced and then centrifuged at 2000g, at 40C for 5 mins. The pelleted nuclei were then resuspended in 500µl RIPA (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA pH8, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS, supplemented with ROCHE Complete protease inhibitor tablets (no EDTA), mixed gently by pipetting, and incubated on ice for 10 mins to achieve complete lysis. Extracted chromatin was then sonicated using Bioruptor (10 cycles of 30’ on and 30’, paused on ice for 5mins, repeated 10 cycles of 30’ on and 30’). Sonicated material was then spun down at 20000g, at 40C for 15 mins. Supernatant was collected in fresh tubes and chromatin was quantified using Qubit high sensitivity DNA kit. 10µg of chromatin was used for each ChIP reactions, in a total reaction volume of 1ml, adjusted with RIPA. For each sample, 30 µl of Protein A/G beads preconjugated to 2 µg antibody (by incubation of antibody with washed beads resuspended in 500µl RIPA for 3h) was added to the reaction and chromatin was capture by overnight incubation at 40C, on a rotating platform. The next day, captured chromatin was washed successively as follows: once in low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), twice in lithium chloride wash buffer (250mM LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and twice in 1X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Bound chromatin was then eluted in 200 µl freshly prepared direct elution buffer (10mM Tris-HCl pH8, 0.3M NaCl, 5mM EDTA pH8, 0.5% SDS) supplemented with 2 µl RNase A (10 mg/ml), by incubating on a thermomixer at 650C, at 800 rpm, overnight. The next day, the beads were discarded, and the supernatant was incubated with 3 µl of Proteinase K (20mg/ml) at 550C, 1200rpm, for 2h to reverse crosslinks.
DNA was using the Zymo DNA Clean and Concentrator kit. For each sample, double stranded DNA (10µl), Template Preparation D Buffer (2µl), and Template Preparation D Enzyme (1µl) were combined and End Repair and A-tailing was performed in a Thermocycler with a heated lid (22ºC, 25 min; 55ºC, 20 min). Library Synthesis D Buffer (1µl) and Library Synthesis D Enzyme (1µl) were subsequently added, and library synthesis was performed (22ºC, 40min). Immediately after, Library Amplification D Buffer (25µl), Library Amplification D Enzyme (1µl), Nuclease-free water (4µl), and a unique Illumina-compatible indexed primer (5µl) were added. Library amplification was performed using the following cycling conditions: 72ºC for 3 min; 85ºC for 2 min; 98ºC for 2 min (denaturation); 4 cycles of 98ºC for 20 s, 67ºC for 20 s, 72ºC for 10 s (addition of indexes); 14 cycles of 98ºC for 20 s, 72ºC for 10 s (library amplification). Post-PCR clean-up was performed on amplified libraries with a SPRIselect bead 0.6X left/1x right double size selection then washed twice gently in 80% ethanol and eluted in 10-12µl 10 mM Tris pH 8.0.
PE50

tag: transgene

tag: chip antibody


title: JT_507_2h_ixen_Nanog_ChIP_merged_rep1

value: 2 hour post doxycycline

value: NANOG


title: JT_508_2h_ixen_Nanog_ChIP_merged_rep2


title: JT_511_2h_ixen_merged_Input

description: Input


title: JT_505_0h_ixen_IgG_ChIP_merged_rep1

value: IgG


title: scRNA-Seq_SX682_mixed cells.1.2.3  (3 replicates)

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description:
Sample 9
scRNA-Seq_raw_all_samples_matrix.mtx.gz
scRNA-Seq_raw_all_samples_barcodes.tsv.gz
scRNA-Seq_raw_all_samples_genes.tsv.gz
scRNA-Seq_metadata_all_samples.tsv.gz
scRNA-Seq_metadata_Neutrophil.tsv.gz
scRNA-Seq_metadata_Tcells.tsv.gz

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
For sc-RNA-Seq additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files, count tables, matrix, barcodes and gene name files

growth_protocol:
Sample 1-6: KP cells were injected I.V. into syngeneic mouse to form orthotopic lung tumor, tumor formation was confirmed by MRI
Sample 7-10: KP cells were injected I.V. into syngeneic mouse to form orthotopic lung tumor, tumor formation was confirmed by MRI

extract_protocol:
Sample 1-6: Tumor nodules were harvested from the treated mice, and dissociated into single cell suspensions. Epcam+ tumor cells were sorted out, total RNA were extracted
Sample 1-6: Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit and sequenced on an Illumina NovaSeq 6000 machine using 150bp paired end reads.
Sample 1-6: Bulk RNA-Seq
Sample 7-10: Tumor nodules were harvested from the treated mice, and dissociated into single cell suspensions. Magnetic bead based live cell enrichment was performed on the single cell suspension. Cell suspensions from different mice within each treatment code were hashtagged and pooled.
Sample 7-10: Libraries were prepared using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1
Sample 7-10: 10X scRNA-Seq

treatment_protocol:
Sample 1-6: Tumor-bearing mice were treated with respective treatments for 11 days
Sample 7-10: Tumor-bearing mice were treated with respective treatments for 11 days

tag: hto

value: Hashtag Oligo demultiplexing with 3 replicates

value: mixed samples (live single cells, including neutrophils and Tcells, from dissociated tumors)


title: scRNA-Seq_Vehicle_mixed cells.1.2.3  (3 replicates)

description:
Sample 10
scRNA-Seq_raw_all_samples_matrix.mtx.gz
scRNA-Seq_raw_all_samples_barcodes.tsv.gz
scRNA-Seq_raw_all_samples_genes.tsv.gz
scRNA-Seq_metadata_all_samples.tsv.gz
scRNA-Seq_metadata_Neutrophil.tsv.gz
scRNA-Seq_metadata_Tcells.tsv.gz

value: Vehicle


title: JT_499_0h_ixen_Nanog_ChIP_merged_rep1


title: FL_35s_ctrl_rep1_RNA

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

data_processing:
Single-end reads were aligned to the mm9 reference genome and to the Mus Musculus transcriptome (iGenome refGene GTF) using TopHat v2.0.13 (PMID: 23618408). The option --no-coverage-search was specified. Only uniquely mapped reads were considered for the analyses.
Gene-wise counts were computed using htseq-count from the HTSeq package (PMID: 25260700) with -s set to no. Genes on chromosomes X, Y and M were excluded.
Genome_build: mm9 (NCBI Build 37), transcripts from iGenome
Supplementary_files_format_and_content: *.counts.txt, HTseq quantifications

source_name: Smad4+/+ PrxCreT/+, embryonic forelimb bud

growth_protocol: The Smad4 loss of function allele was generated by crossing Smad4flox/flox (PMID: 11857783) females with Smad4∆/+ PrxCreT/+ males (PMID: 12112875). The day the vaginal plug was observed was considered as embryonic day 0.5 (E0.5). Mice and embryos were genotyped by PCR using genomic DNA extracted from ear biopsies and yolk sacs, respectively.

extract_protocol:
Dissected WT and Smad4Δ/Δc forelimbs from E10.0 embryos (30 somites) and 10.5 embryos (35 somites) were collected in RNAlater, incubated overnight at 4°C and then stored at -80°C. Both forelimbs of an embryo were pooled for one replicate. After genotyping, 4 age-matched replicates of Smad4Δ/Δc and 3 replicates of WT forelimb buds per stage were sequenced. RNA was extracted using the Qiagen RNeasy micro kit
For each replicate, the quality of total RNA was analysed using the RNA 6000 Pico kit (Agilent 2100 bioanalyzer), which was followed by polyA RNA library preparation. Sequencing was done on the HiSeq 2500 machine using the single-read 50 cycles protocol

value: NMRI

value: Smad4+/+ PrxCreT/+

tag: developmental stage

value: 35 somites

tag: age

value: gestational day e10.5

tag: tissue

value: forelimb buds

tag: library type

value: Unstranded


title: FL_35s_Smad4ddc_rep5_RNA

source_name: Smad4∆/∆c PrxCreT/+, embryonic forelimb bud

tag: genotype

value: Smad4{delta}/{delta}c PrxCreT/+


title: FL_35s_ctrl_rep3_RNA


title: FL_30s_ctrl_rep3_RNA

value: 30 somites

value: gestational day e10.0


title: FL_30s_ctrl_rep2_RNA


title: FL_35s_Smad4ddc_rep4_RNA


title: FL_30s_Smad4ddc_rep5_RNA


title: FL_30s_ctrl_rep1_RNA


title: FL_35s_Smad4ddc_rep1_RNA


title: Adult_svf

city: St. Louis

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Adult adipose SVF

data_processing:
Demultiplexing, barcode processing, single-cell 3' counting was performed with Cell Ranger Single-Cell Software Suite v2.1.1
Alignment was performed using Cell Ranger
See detailed methods in Goldberg et al., Cell Metabolism 2019
Genome_build: mm10-2.1.0
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

source_name: total SVF of visceral adipose tissue

extract_protocol:
Total RNA was extracted with RLT buffer
Single-cell libraries were prepared using standard 10x Genomics protocols.

value: wt

value: adult

value: visceral adipose tissue (VAT)

value: total SVF of visceral adipose tissue


title: Old_cd45

description: Old adipose immune cells

source_name: tissue resident CD45+ cells from visceral adipose tissue

value: old

value: visceral adipose tissue-resident CD45+


title: JT_500_0h_ixen_Nanog_ChIP_merged_rep2

tag: cell line

value: Embryonic stem cells

value: 0 hour no doxycycline

value: Stem cells have TRE:GATA6-DSREd2

value: NANOG


title: FL_30s_Smad4ddc_rep3_RNA

value: NMRI


title: scRNA-Seq_SHP099_mixed cells.1.2.3 (3 replicates)

description:
Sample 8
scRNA-Seq_raw_all_samples_matrix.mtx.gz
scRNA-Seq_raw_all_samples_barcodes.tsv.gz
scRNA-Seq_raw_all_samples_genes.tsv.gz
scRNA-Seq_metadata_all_samples.tsv.gz
scRNA-Seq_metadata_Neutrophil.tsv.gz
scRNA-Seq_metadata_Tcells.tsv.gz

value: Hashtag Oligo demultiplexing with 3 replicates

tag: cell type

value: mixed samples (live single cells, including neutrophils and Tcells, from dissociated tumors)


title: scRNA-Seq_Combo_mixed cells.1.2.3 (3 replicates)

description:
Sample 7
scRNA-Seq_raw_all_samples_matrix.mtx.gz
scRNA-Seq_raw_all_samples_barcodes.tsv.gz
scRNA-Seq_raw_all_samples_genes.tsv.gz
scRNA-Seq_metadata_all_samples.tsv.gz
scRNA-Seq_metadata_Neutrophil.tsv.gz
scRNA-Seq_metadata_Tcells.tsv.gz


title: FL_35s_Smad4ddc_rep2_RNA

value: 35 somites

value: gestational day e10.5

value: forelimb buds

value: Unstranded


title: FL_35s_ctrl_rep2_RNA

value: Smad4+/+ PrxCreT/+


title: FL_30s_Smad4ddc_rep1_RNA

value: Smad4{delta}/{delta}c PrxCreT/+

value: 30 somites

value: gestational day e10.0


title: JT234_RNA_8hr_rep4

data_processing:
RNA-seq analysis was performed using LCDB workflow (github.com/lcdb/lcdb-wf). Briefly, the data was first assessed for quality control using fastQC v0.11.8 (bioinformatics.babraham.ac.uk/projects/fastqc/) to look for sequencing quality issues and trimmed for quality using cutadapt v2.7. The RNA-Seq data was then mapped to the mouse genome version GRCm38.p6 using HISAT2 v2.1.0.
Expression levels were estimated at gene-level with featureCounts (subread v1.6.4) (Liao et al., 2014) using the GENCODE version m18 annotation.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: norm_cns_per_timepoint.tsv

extract_protocol:
Cells were harvested using accutase and RNA from four replicates at each time point was isolated using Trizol.
After confirming that the RNA integration number for each sample was above 8, libraries were prepared using TruSeq Stranded mRNA prep kit with PolyA purification.
SE50

value: 8 hour post doxycycline


title: Transwell iRPE

last: McGaughey

address: 10 Center Dr

department: NEI

institute: NIH

data_processing:
kallisto 0.46.2
Genome_build: gencode.v35.annotation.gtf.gz
Supplementary_files_format_and_content: csv

source_name: Transwell iRPE

growth_protocol: iPSCs were cultured on mouse embryonic fibroblasts (MEFs) for 4 days before using for differentiation

extract_protocol:
Total RNA was isolated using NucleoSpin RNA (#740955, Machery-Nagel) per manufacturer’s protocol.
10xv2 chemistry
scRNA-seq

treatment_protocol: After collagenase was aspirated, NEIM (DMEM/F12, KOSR, supplemented with N2, B27, LDN-193189 10uM, SB431452 10 nM, CKI-7 hydrochloride 0.5 uM, and IGF-1 1ng/ml) was added to the wells (1ml/well) and cell scarper was used to scrape the colonies. Cell aggregates were grown in 10 cm2 low attachment corning dishes in NEIM medium for 48 hrs. After 48 hours, floating cell aggregates were collected and seeded in matrigel coated plates in RPEIM (DMEM/F12, KOSR, supplemented with N2, B27, LDN-193189 100uM, SB431452 100 nM, CKI-7 hydrochloride 5 uM, and IGF-1 10ng/ml, PD0325901 1uM) and cultured for 3 weeks. After 3 weeks in RPEIM, cells were moved to RPECM (DMEM/F12, KOSR, supplemented with N2, B27, Nicotinamde 10mM and Activin A 100ng/ml) for 3 more weeks with regular medium change. Pigmented patches of immature RPE cells were collected through differential trypsinization and seeded on to transwells RPEGM (MEM, Sigma; 1% N2 supplement, ThermoFisher; 1% Glutamine, ThermoFisher; 1% non-essential amino acids, ThermoFisher; 125 mg Taurine (Sigma)/500 ml; 10 ug Hydrocortisone (Sigma)/500 ml; 0.0065 ug Triiodo-thyronin (Sigma)/500 ml; 5% FBS, Sigma) (32)

tag: celltype

value: iRPE

tag: Stage

value: transwell


title: FL_30s_Smad4ddc_rep4_RNA


title: JT236_RNA_96hr_rep2

value: Embryonic stem cells

value: 96 hour post doxycycline


title: JT233_RNA_8hr_rep3

value: Stem cells have TRE:GATA6-DSREd2


title: shKLF7_I_scRNA-Seq

city: Singapore

first: Kiyofumi

last: Hamashima

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB)

description: Sample 28

data_processing:
Sample demultiplexing was carried out with the mkfastq function from Cell Ranger software (version 2.1.1, 10X Genomics)
Sample alignment was carried out with the count function from Cell Ranger software (>version 2.1.1, 10X Genomics). We used the “--force-cells 6000” option for donor 75 retina and ‘--expect-cells=6000’ for the others
The reference genome index of hg19 (or hg38 for donor 72/73 cornea, donor 73/74 iris, RGC differentiation series), suscr11 and GRCz11 was used for human, pig and zebrafish, respectively
Supplementary_files_format_and_content: Csv files including gene expression matrix from each human/pig/zebrafish
Genome_build: hg19 (or hg38), susScr11 and GRCz11
Supplementary_files_format_and_content: Count matrix was generated using the count function from Cell Ranger

source_name: Retinal ganglion cells (RGCs)

extract_protocol:
All samples were treated with trypsin for 30 minutes at 37C. The samples were passed through nylon membrane to remove clumps. After it, cells were either subject to 10X genomics single cell RNA protocol or frozen down to store the celltypes. For cells in cell culture, cells were dissociated with Accutase or RELSR for 5 minutes. The cells are then called through nylon membrane to separate clumps. After centrifuging, cells are resuspended in PBS. The cells are then processed for 10x Genomics scRNA cdna preparation and library generation protocol.
10x single cell RNA seq library preparation V2(samples GSM4451262-GSM4451279, GSM5360357) and V3(GSM5360358-GSM5360366)

value: ES-derived retinal ganglion cells


title: shEV_II_scRNA-Seq

description: Sample 27

value: shEV


title: shKLF7_II_scRNA-Seq

description: Sample 29


title: JT232_RNA_8hr_rep2

city: Bethesda


title: JT238_RNA_96hr_rep4


title: JT237_RNA_96hr_rep3


title: OE-KLF7_scRNA-Seq

description: Sample 25


title: JT230_RNA_4hr_rep4

value: 4 hour post doxycycline


title: JT231_RNA_8hr_rep1


title: JT235_RNA_96hr_rep1


title: shEV_I_scRNA-Seq

description: Sample 26


title: JT228_RNA_4hr_rep2


title: JT227_RNA_4hr_rep1


title: OE-EV_scRNA-Seq

description: Sample 24

value: OE-EV


title: Iris74_scRNA-Seq

description: Sample 23

source_name: Iris

value: Iris

tag: donor


title: Cornea72_scRNA-Seq

description: Sample 20

source_name: Cornea

value: Cornea


title: Iris73_scRNA-Seq

description: Sample 22


title: JT226_RNA_48hr_rep4

tag: time point

value: 48 hour post doxycycline


title: Cornea73_scRNA-Seq

description: Sample 21


title: JT225_RNA_48hr_rep3


title: JT224_RNA_48hr_rep2


title: JT223_RNA_48hr_rep1


title: pRPE_scRNA-Seq

source_name: RPE

value: RPE


title: 253J_siFTO_5

city: Fuzhou

first: Zhihua

address: 312 Xihong Road

institute: Menchao Hepatobiliary Hospital of Fujian Medical University

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

source_name: human 253J cells

growth_protocol: The human 253J were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of 253J bladder cancer cells with different treatment was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The 253J bladder cancer cells were transfected with control siRNA or FTO siRNA.

value: bladder cancer

tag: passage


title: C24

first: Yilin

last: Lin

address: 38 Xueyuan Road

institute: peking university

data_processing:
Hisat2, samtools, htseq-count packages were used to align 150 bp paired-end reads with hg38. The expression of genes and transcripts were quantified by using cufflinks tools.
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: gastric cancer

extract_protocol:
Liquid nitrogen quickly grinds gastric cancer tissue, and uses Trizol reagent to harvest RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) is used together with 1 ug of total RNA to construct a sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: gastric cancer

value: stomach


title: 253J_control_3


title: 253J_siFTO_4


title: pRetina_scRNA-Seq

source_name: Retina

value: Retina


title: JT221_RNA_2hr_rep3

value: 2 hour post doxycycline

tag: strain


title: C23


title: JT229_RNA_4hr_rep3

tag: transgene


title: pIris_scRNA-Seq


title: 253J_control_2


title: 253J_siFTO_6


title: C22


title: JT220_RNA_2hr_rep2


title: C20


title: C21


title: 253J_control_1


title: JT219_RNA_2hr_rep1


title: C17


title: Retina75_scRNA-Seq


title: C16


title: JT218_RNA_24hr_rep4

value: 24 hour post doxycycline


title: C15


title: C10


title: Retina74_scRNA-Seq


title: JT222_RNA_2hr_rep4

value: Embryonic stem cells


title: C31


title: C9


title: IrisStroma75_scRNA-Seq

source_name: IrisStroma

value: IrisStroma


title: JT217_RNA_24hr_rep3

value: Stem cells have TRE:GATA6-DSREd2


title: C5


title: C6


title: IrisPE75_scRNA-Seq

source_name: IrisPE

value: IrisPE


title: JT216_RNA_24hr_rep2


title: JT215_RNA_24hr_rep1


title: RPE78_scRNA-Seq


title: C4


title: B8


title: JT214_RNA_16hr_rep4

value: 16 hour post doxycycline


title: C2


title: B7


title: JT213_RNA_16hr_rep3


title: B4


title: B3


title: B2


title: JT212_RNA_16hr_rep2


title: JT211_RNA_16hr_rep1


title: Retina76_scRNA-Seq


title: B6


title: Retina78_scRNA-Seq


title: C7


title: A27


title: A16


title: A39


title: IrisStroma76_scRNA-Seq


title: JT210_RNA_0hr_rep4

value: 0 hour no doxycycline


title: JT209_RNA_0hr_rep3


title: IrisPE76_scRNA-Seq


title: JT208_RNA_0hr_rep2


title: A11


title: A6


title: Sclera75_scRNA-Seq

source_name: Sclera

value: Sclera


title: IrisMuscle76_scRNA-Seq

source_name: IrisMuscle

value: IrisMuscle


title: A1


title: RPE76_scRNA-Seq


title: Cornea76_scRNA-Seq

value: Cornea


title: JT207_RNA_0hr_rep1

source_name: Embryonic stem cell line


title: Choroid75_scRNA-Seq

source_name: Choroid

value: Choroid


title: A15


title: IL33KO_SEV_D12

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: 660 S. Euclid Avenue

department: Department of Developmental Biology, Washington University School of Medicine

institute: Washington University in St Louis

data_processing:
Next-generation sequencing (NGS) data was processed with the Cell Ranger set of analysis pipelines (version 2.1.0, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines) as follows: FASTQ files were generated for each sample by demultiplexing the sequencer’s base call files. Then, single-cell gene count matrices were generated by running “cellranger count” with mm10 transcript reference per sample, and all sample data was aggregated with “cellranger aggr”. In this process, sequence depth was normalized by subsampling reads from higher-depth data.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-seq gene expression count matrix in 10x Genomics cellranger format

source_name: Day 12 after mouse was inoculated with Sendai virus strain 52

extract_protocol:
CD31–CD45–EpCAM+ cells were isolated from mouse lungs at 12 and 21 after SeV infection or control PBS challenge, and cellular mRNA was purified and subjected to scRNAseq using the 10x Genomics platform.
Library construction was done according to 10x Genomics 3' scRNA-seq protocol.

treatment_protocol: Mice were inoculated intranasally with Sendai virus (SeV strain 52) or an equivalent amount of UV-inactivated virus (SeV-UV) or PBS as controls

tag: treatment

value: lung


title: WT

data_processing:
Fastq files were processed with the Cell Ranger ATAC pipelines (Cell Ranger ATAC version 1.0.0 from 10x Genomics) to generate bam files. Bam files were subjected to the preprocessing pipeline with Snap tools (version 1.2.6). Snap files were created for each sample condition according to the developer’s instructions as described at: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac and https://github.com/r3fang/SnapATAC/wiki/FAQs#10X_snap, respectively).
Genome_build: mm10
Supplementary_files_format_and_content: snap ATAC data format

extract_protocol:
CD31–CD45–EpCAM+ cells were isolated from mouse lungs at 12 day after SeV infection, and subjected to scATAC-seq using the 10x Genomics platform.
Library construction was done according to 10x Genomics scATAC-seq protocol.

treatment_protocol: Mice were inoculated intranasally with Sendai virus (SeV strain 52)

value: wild type

value: CD31-CD45-EpCAM+ cells


title: IL33KO_SEV_D21

source_name: Day 21 after mouse was inoculated with Sendai virus strain 52


title: IL33KO_PBS

source_name: inoculated with PBS

value: PBS


title: WT_SEV_D21


title: SS-12

first: Hongen

last: Yin

address: 10 Center Dr. Bldg10, Rm1A21

institute: NIDCR

description: The normalized gene expression data was used to analyze the correlation with clinical data.

hyb_protocol: 1 ug of each labeled cRNA was fragmented by adding 5 uL 10 x Blocking Agent and 1 uL of 25 x Fragmentation Buffer, then heated the mixture at 60C for 30 min, finally 25 uL 2 x GE Hybridization buffer was added to dilute the labeled cRNA. 50 uL of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: The microarrays were scanned with an Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.
The raw data values are scanner intensity values. The normalized values in the Matrix data  are log2 transformed normalized intensities.
547 genes were  detected by the microarray scanner (signals significantly above the background and passed the QC).

source_name: labial salivary gland

label_protocol: Each sample was reverse transcribed by random priming and linearly amplified into Cy3 fluorescent cRNA along the entire length of the transcripts by Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000

extract_protocol: Total RNA was extracted from FFPE samples.

value: labial salivary gland

tag: patient diagnosis

value: Sjogren's syndrome

tag: microscopic category by sicca

value: FLS


title: SS-20

value: SCS


title: A5

city: Beijing

value: gastric cancer

value: stomach


title: SS-18


title: SS-16


title: SS-13


title: SS-19


title: SS-17


title: SS-14


title: SS-15


title: WT_SEV_D12


title: SS-10

value: FLS/SCS


title: SS-11


title: SS-9


title: IL33KO


title: SS-7


title: SS-8


title: SS-6


title: WT_PBS


title: Animal 240

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from progressor animal 240.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.61.0), using R version 3.6.0 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: lung homogenate

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Female DO (generations 15, 16, 21, 22, 34) and C57BL/6J mice were purchased from The Jackson Laboratory (Bar Harbor, ME) and housed in sterile BSL3 conditions at the New England Regional Biosafety Laboratory (Tufts University, Cummings School of Veterinary Medicine, North Grafton, MA).

extract_protocol: One lung lobe from each mouse was homogenized in TRIzol™ and stored at -80C until RNA extraction using Pure Link mini-kits (Life Technologies, Carlsbad, CA).

treatment_protocol: At 8-10-weeks old, mice were infected with aerosolized Mtb strain Erdman bacilli (~100 in experiments 1 and 2; ~25 in experiments 3, 4, 5) using a CH Technologies nose-only exposure system. All mice were weighed at least twice per week, and examined daily for lethargy, respiratory distress, and body condition.

tag: class

value: progressor


title: Animal 239

description: Gene expression data from progressor animal 239.


title: Animal 231

description: Gene expression data from progressor animal 231.


title: SS-5

tag: tissue

value: NSCS


title: SS-4


title: Animal 216

description: Gene expression data from progressor animal 216.


title: Animal 221

description: Gene expression data from progressor animal 221.


title: SS-3


title: SS-1


title: SS-2


title: Animal 212

description: Gene expression data from progressor animal 212.


title: Animal 210

description: Gene expression data from progressor animal 210.


title: Animal 203

description: Gene expression data from progressor animal 203.