title: WT_1

city: Tianjin

first: Zeyun

last: Mi

address: Qi Xiang Tai Road

institute: Tianjin Medical University

data_processing:
Low quality reads was filtered using internal software SOAPnuke
Clean reads were mapped to reference using Bowtie2. Only unique mapped reads were used in further analysis.
DEGs (differential expressed genes) between samples were generated by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Normal kidney

growth_protocol: The culture condition of Pkd1fl/fl; Cre/Esr1+ mice is specific pathogen free (SPF) level.

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen) from whole kidney (WT and ADPKD). Total RNAs from kidney tissues were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

treatment_protocol: Tamoxifen was injected at P10 (10 mg/kg) to generate the early-onset ADPKD mouse model

value: Kidney

tag: genotype

value: wildtype


title: CoRest-C_light1

status: Public on May 16 2020

type: SRA

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

library_source: genomic

data_processing:
The adaptors were trimmed via Trimommatic, followed by mapping to the Drosophila reference genome, dm6 from UCSC using STAR.
The reads with low mapping quality below 8 and the non-primary mapped reads were eliminated.
MACS was used for peak calling in ChIP-seq on Strand NGS software, using a default setting except for the following parameters; 10-4 as a P-value cutoff, and 3 as a enrichment factor.
The binding sites were determined when the peaks were overlapped in at least 2 out of 3 biological replicates.
For RNA-seq, the filtered reads were analyzed with HTSeq-count to obtain numbers of the reads mapped on exons, which was further analyzed on R using DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include statistical results and fold enrichment comparing to naive samples

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: mushroom body

growth_protocol: Flies were raised under a 12 h:12 h, light:dark cycle, at 25℃ and 60% humidity.

extract_protocol:
Heads were collected and homogenized in crosslinking buffer. The nuclei were dissolved in extraction buffer, sonicated to dissociate the individual nuclei, and precipitated with ANTI-FLAG M2 Affinity Gel. The precipitates were rinsed 4 times in extraction buffer, with 5 min nutation at 4℃ between washes, and subjected to ChIP analysis or RNA extraction for RNA-seq.
The library for ChIP-seq was prepared by NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs inc. Ipswich, MA, USA), and that for nuclear RNA-seq was prepared by Oligo d(T)25 Magnetic Beads (New England Biolabs inc. Ipswich, MA, USA), and NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs inc. Ipswich, MA, USA), according to the manufacturer’s instructions.

treatment_protocol: Flies were subjected to optogenetic activation by expressing CsChrimson with red-light illumination.

tag: line

tag: tissue

value: mushroom body

tag: treatment

value: 5-min optogenetic activation

tag: chip antibody

value: anti-myc (2278, Cell Signaling Technology, lot 5)


title: HIC039_DN_Thy_rep1

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

country: USA

institute: Ohio State University

description: DNA - Hi-C DNA seq

data_processing:
HI-C Reads were processed using Juicer pipeline
Genome_build: mm9
Supplementary_files_format_and_content: hic files as produced by Juicer. The files are inter_30.hic.

organism: Mus musculus

source_name: Double Negative (DN) thymocyte

extract_protocol:
5x10^6 formaldehyde-cross-linked cells were lysed on ice for 15 minutes with 250 μl of ice-cold Hi-C lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630) containing protease inhibitors (Roche). Chromatin was digested using DpnII (100 U) at 37°C for 6 hours. The digested DNA ends were then filled and marked with biotin using Klenow, followed by ligation with T4 DNA ligase. After reversing the cross-links, DNA was fragmented using a Covaris E220 Evolution Sonicator followed by size-selection for 300-500bp using AMPure XP Beads (Beckman Coulter).
DNA end-repair was performed using NEBNext Ultra II DNA Library Prep Kit according to the manufacturer’s instructions using 1μg of the Hi-C DNA. Adaptor-ligated DNA was then selected for 300-400bp using AMPure XP beads and the biotinylated DNA fragments were pulled down using MyOne Streptavidin T1 beads (Life Technologies). The final Hi-C library was generated with 5 PCR cycles using the NEBNext Ultra II DNA Library Prep Kit and NEBNext Dual Index primers (NEB) for Illumina sequencing.
Paired end using NEBNext Ultra II DNA Library Prep Kit and NEBNext Dual Index primers (NEB)

tag: tissue source

value: Thymus

tag: protocol

value: Hi-C

tag: rnp


title: SC_RNA-seq_D21_38F_HDF1

city: Melbourne

first: Fernando

last: Rossello

state: VIC

address: L 10, 305 Grattan Street

country: Australia

institute: The University of Melbourne

library_source: transcriptomic

data_processing:
Cellranger mkref (v2.1.0) was run to create a reference using the modified GTF annotation file and the  hg19 genome (GRCh37, CellRanger reference version 1.2.0, genome build GRCh37.p13, which contained the Sendai virus KLF4, MYC and SeV sequences as extra chromosomes, also accounted for as extra annotations on the annotation file).
Sequencing single cell samples were aligned to the created custom reference and UMI counting were performed using cellranger count (v2.10, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.0/what-is-cell-ranger).
Genome_build: hg19
Supplementary_files_format_and_content: Gene/cell read counts matrices are contained in compressed Market Exchange Format (MEX) for sparse matrices. Feature, in this case genes, and cell barcodes  are gzipped TSV files, corresponding to row and column indices of count matrices respectively. For more information, please refer to: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

molecule: total RNA

organism: Homo sapiens

source_name: human fibroblasts

growth_protocol: To generate the intermediates used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=5, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter.  On day 7, for d21 fibroblast intermediates, the cells were kept in fibroblast media till day 21 with media change every other day. For d21 naive and trophoblast intermediates, cells were seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to naive or TSC media. ~21 days after transduction, cells were collected for scRNA-seq.

extract_protocol:
The collected cells were isolated, encapsulated and library constructed as described in the Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).
Libraries were constructed as described on the Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).

tag: cell type

value: day 21 fibroblast intermediates

tag: passages

value: day 21


title: WT_2

country: China


title: CoRest-C_naive3

value: naïve


title: CoRest-C_naive1


title: HIC075_6312_rep1

description: DNA - Hi-C DNA seq

value: cell line - 63-12 pre B cell


title: BC-DM6

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

data_processing:
Sequencing reads were trimmed using StringTie software.
Clean reads were mapped to human genome database (GRCh37) using the Hisat2 software.
Differential expression and normalized reads counts (FPKM, Fragments Per Kilobase of gene/transcript model per Million mapped fragments) were calculated using the Ballgown software.
Genome_build: GRCh37
Supplementary_files_format_and_content: Differential expression and normalized reads counts

source_name: Breast cancer with diabetes

extract_protocol:
Total RNA was extracted from tissues using the TRIzol Reagent.
RNA-seq libraries were prepared using the Illumina KAPA Stranded RNA-Seq Library Prep Kit.Sequencing was performed on an Illumina NovaSeq 6000.

tag: subject status

value: Breast cancer patient with diabetes

value: Breast cancer


title: BC-DM7


title: ADPKD_2

source_name: ADPKD kidney

value: Pkd1fl/fl; Cre/Esr1+


title: SC_RNA-seq_D21_38F_TSC

value: day 21 TSC intermediates


title: Rpd3_light3

value: anti-Rpd3 (lab made antibodies)


title: BC-DM5


title: null_THZ1_2

source_name: epithelial cells

growth_protocol: pkd1 and null cells were cultured in DMEM-F12 medium supplemented with 3% fetal bovine serum (FBS) and 1% penicillin/streptomycin,1% Insulin-Transferrin-Selenium, IFNγ,  Nystatin suspension and T3.

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from cultured cells were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

treatment_protocol: pkd1  cells and null cells were treated with 50 nM THZ1 for 6 h

value: Pkd1-/- Null

tag: cell line

value: null(PN)


title: BC-DM4


title: null_THZ1_1

value: Kidney


title: SC_RNA-seq_D21_38F_Naive

value: day 21 naive intermediates


title: ADPKD_1


title: Rpd3_light1

value: mushroom body

value: 5-min optogenetic activation


title: Rpd3_light2


title: BC-DM3


title: nRNAseq_5minLight3


title: BC-DM2


title: null_DMSO_2


title: CoRest-C_naive2

value: anti-myc (2278, Cell Signaling Technology, lot 5)


title: null_DMSO_1


title: Rpd3_naive3


title: BC-DM1


title: Rpd3_naive2


title: glioma stem-like cell line h676

city: Madrid

first: Massimo

last: Squatrito

address: Calle Melchor Fernandez Almagro 3

country: Spain

institute: Spanish National Research Center (CNIO)

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of BCL files to FASTQ format was performed with Local Run Manager Generate FASTQ Analysis Module (Illumina).
Nextpresso pipeline
Supplementary_files_format_and_content: FPKM at gene level
Supplementary_files_format_and_content: FPKM at isoforms level

source_name: glioma stem-like cells

growth_protocol: Human NeuroCult basal medium, supplemented with Proliferation supplement (Stem Cell Technologies #05701), 20 ng/mL recombinant human EGF (Gibco #PHG0313), 10 ng/mL basic-FGF (Millipore #GF003-AF), 2 µg/mL Heparin (Stem Cell Technologies #07980) and L-glutamine (2mM, Hyclone #SH3003401)

extract_protocol:
Trizol
Total RNA samples (1000ng) were used as provided by the user. Sample RNA Integrity numbers were 9.2 on average (range 8.9-9.6) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760) as recommended by the kit manufacturer. Briefly, polyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated library was completed by PCR with Illumina PE primers. {This kit generates directional libraries stranded in the antisense orientation [the read1 (the only read in single read format) has the antisense orientation (--library-type fr-firststrand in TopHat, --stranded=reverse in HTSeq]} The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's protocols.

value: brain

tag: tumor

value: GBM


title: BC-control6

source_name: Breast cancer without diabetes

value: Breast cancer patient without diabetes


title: glioma stem-like cell line h561


title: glioma stem-like cell line h543


title: CBP_light3

value: anti-CBP (lab made antibodies)


title: Rpd3_naive1

value: naïve


title: CBP_light2


title: pkd1_THZ1_2

value: Pkd1+/- Heterozygous


title: pkd1_DMSO_1


title: pkd1_THZ1_1


title: null_H3K27ac

data_processing:
ChIP-seq data were mapped to mus musculus genome (mm10) by SOAPaligner/SOAP2
ChIP-Seq peaks were generated using peak finding algorithm MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2)
Reads mapped only once at locus were allowed for peak calling.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated by MACS-1.4.2.

extract_protocol:
pkd1 and null cells were cross-linked with 1% formaldehyde for 10 min at RT. The crosslink was stopped by adding 1/20 volume of 2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed with H3K27ac antibody (Abcam cat# ab4729). After elution and reversal cross-linking, DNA was purified and sequenced on BGISEQ-500.
Construction of ChIP-seq library was completed by BGI company (Shenzhen,China).

value: H3K27ac (Abcam cat# ab4729)


title: pkd1_DMSO_2


title: glioma stem-like cell line h516


title: glioma stem-like cell line BTSC380


title: null_input


title: CBP_naive2


title: CBP_naive1


title: CBP_light1


title: NKR cells, Uninfected

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v2.1.1 mkfastq pipline (10x Genomics) and bcl2fastq2 v 2.20.0 (Illumina)
Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v2.1.1 count pipeline (10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, mtx files generated by CellRanger v2.1.1

molecule: polyA RNA

source_name: Cell line

extract_protocol:
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics) according to the manufacture's protocol (User guide RevC)
Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol (User guide RevC). In short, sequencing libraries were generated by  1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: Cultured CEM.NKR.DC-SIGN cells were washed with RPMI media supplemented with 10% fetal calf serum prior to analysis. Populations of interest (total viable cells or surface DENV1 NS1 positive cells) were isolated by flow cytometric sorting using a BD FACSAria Fusion instrument. Post-sort population purity was assessed prior to downstream analysis. Sorted cells were washed in PBS supplemented with 2% fetal calf serum prior to scRNAseq library generation.

tag: infection

value: Uninfected

tag: primer

value: Oligo(dT)


title: BC-control5

value: Breast cancer


title: CBP_naive3


title: glioma stem-like cell line BTSC349


title: 48_u22-2

status: Public on May 15 2020

city: Cambridge

first: Peter

middle: W

last: Reddien

state: MA

address: 9 Cambridge Center

department: MIT Biology

institute: Whitehead Institute for Biomedical Research

data_processing:
Basecalling was performed by Illumina CASAVA 1.9
Sequenced reads from all three lanes were concatenated and quality trimmed using cutadapt v1.8 with parameteres -m 20 -q 30,30 and mapped to the ddv4 transcriptome using Bowtie v1.2 with parameter --best.
Raw read counts were generated with Samtools v1.6 idxstats and transcripts from different isoforms were summed (sum of counts for dd_v6_Smed_XXX_Y_Z for all Z)
Differential expression was determined with DESeq
Dresden S. mediterranea Transcriptome Assembly (ddv6, Rozanskii et al, Nucleic Acids Res 2019, http://planmine.mpi-cbg.de/planmine/report.do?id=2000001#ad-image-0)
Genome_build: Tab-separated text files
Supplementary_files_format_and_content: readcounts and DESeq output

organism: Schmidtea mediterranea

source_name: post pharyngeal fragment (posterior-facing wound)

growth_protocol: Standard planarian culture conditions

extract_protocol:
Total RNA extracted from tail fragments with TriZOL reagent with 5 wounds per replicate. Tissue was homogenized with TissueLyser II at 30.0 Hz for 30 sec and an extra 1:1 chloroform extractation was performed to removed excess phenol. RNA was quantified by Qubit and Agilent Bioanalyser.
Kapa Stranded mRNA-Seq Kit Illumina Platform (KapaBiosystems)

treatment_protocol: Animals fed IVT-produced dsRNA 4 times over 14 dayys day. Cut 7 days after 4th feeding

value: post pharyngeal fragment

tag: strain

tag: hours post amputation (hpa)

value: 48 hpa

tag: RNAi

tag: RNAi feedings

tag: wound orientation

value: posterior-facing wound


title: 48_a2-3

tag: tissue


title: BC-control2


title: BC-control3


title: pkd1_input

value: Kidney

tag: chip antibody


title: 48_a2-1


title: 48_u22-3


title: 24_u22-2

value: 24 hpa


title: 24_u22-3


title: 48_u22-1


title: BC-control4


title: 24_a2-3


title: BC-control1


title: 48_a2-2


title: 24_u22-1


title: 24_a2-2


title: 18_P_u222

value: 18 hpa


title: pkd1_H3K27ac


title: 18_P_u223


title: 201557510031_R07C01

type: genomic

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using iSCAN BeadArray reader

data_processing: R library minfi

label: Cy5, Cy3

source_name: Adrenocortial tumor C2

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

value: Adrenocortial tumor


title: 18_P_a22


title: 18_P_a24


title: 18_A_u222

source_name: post pharyngeal fragment (anterior-facing wound)

value: anterior-facing wound


title: 18_P_a23


title: 18_P_u221


title: 18_A_u224


title: 18_A_u223


title: 18_A_u221


title: 18_A_a23


title: 18_A_a24


title: 18_A_a22


title: 06_u22-2

value: 6 hpa


title: 06_u22-1


title: 06_a2-3


title: 06_u22-3


title: 00_u22-3

source_name: post pharyngeal fragment

value: 0 hpa


title: 18_A_a21


title: 18_P_a21


title: 24_a2-1


title: 06_a2-1


title: 06_a2-2


title: 18_P_u224


title: 00_u22-2


title: 00_u22-1


title: 00_a2-2


title: 00_a2-3


title: Sample_279_CF

city: Philadelphia

first: Paul

middle: Zhiping

last: Wang

state: pa

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

description:
Sample_279_CF
read_counts.txt

data_processing:
The quality of fastq files were checked by FastQC-0.11.2.
The alignment was done over assembly hg19 using STAR_2.4.0i with option "--alignMatesGapMax 2000". The mapped reads were filtered with Samtools-1.1 with options "-h -F 4 -q 1".
The read count was performed by FeatureCounts v1.5.1 with options "-T 5 -C -M -t exon".

source_name: amniocyte

growth_protocol: Amniocyte cells were collected from expectant mothers during the 16-17th week of their pregnancies at the University of Pennsylvania.  Cells were incubated at 37C with 5% CO2 overnight in AmnioMax II Complete (Thermo Fisher) with gentamicin and L-glutamine.  Cells were grown until 80% confluence and then harvested with 0.25% trypsin EDTA quenched with AmnioMax II.  Cells were pelleted centrifugation and frozen at 80C in DMSO freezing media.

extract_protocol:
After flash thaw, pellet was washed with AmnioMaxII and RNA was extracted with PicoPure RNA Isolation Kit (Thermo Fisher).
Libraries were generated lwith the Illumina TruSeq stranded total RNA kit.

treatment_protocol: GDM status was obtained from outcome questionnaire completed by mothers 1 month after delivery.  GDM status confirmed by measuring c-peptide concentration in second trimester amniocit fluid samples by ELISA (Mercodia).

tag: exposure group (gdm or control)

value: control

tag: sex  (f /m)

value: F

tag: gestational age of amniocentesis (weeks)

tag: maternal age

tag: gestational age birth


title: Sample_763_DM

description:
Sample_763_DM
read_counts.txt

value: GDM

value: M


title: Sample_323_DM

description:
Sample_323_DM
read_counts.txt


title: Sample_665_CF

description:
Sample_665_CF
read_counts.txt


title: Sample_511_CM

description:
Sample_511_CM
read_counts.txt


title: Sample_487_CM

description:
Sample_487_CM
read_counts.txt


title: Sample_812_CF

description:
Sample_812_CF
read_counts.txt


title: Sample_324_DF

description:
Sample_324_DF
read_counts.txt


title: Sample_566_DF

description:
Sample_566_DF
read_counts.txt


title: Sample_620_CM

description:
Sample_620_CM
read_counts.txt


title: Sample_223_CM

description:
Sample_223_CM
read_counts.txt


title: Sample_571_CF

description:
Sample_571_CF
read_counts.txt


title: Sample_252_DM

description:
Sample_252_DM
read_counts.txt


title: Sample_338_DF

description:
Sample_338_DF
read_counts.txt


title: PC9 01

city: Kanazawa

first: Eishu

last: Hirata

state: Ishikawa

address: Kakuma-machi

country: Japan

institute: Kanazawa University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trim Galore! v0.5.0, then mapped to GRCh38 whole genome using TopHat2 v2.0.9 with --library-type=fr-firststrand.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.1.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Human lung cancer cells

growth_protocol: WM266.4 human melanoma cells or PC9 human lung cancer cells expressing EGFP and firefly luciferase were injected into the left ventricle of anesthetized nude mice. The mouse brains were cut out ~33 days after intra-cardiac injection and dissociated into single cells by using gentleMACS Dissociator (Miltenyi Biotec). The dispersed cells were cultured on a plastic dish with appropriate antibiotics to select cancer cells and BrM1 cells were established. BrM2, BrM3 and BrM4 cells were established by the repetition of the intra-cardiac injection and cancer cell collection. All the cells were maintained in DMEM with 10% FBS / 1% PenStrep (GIBCO)

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and the integrity was examined with the TapeStation (Agilent Technologies).
cDNA was prepared from polyA-selected RNA by using an NEBNext Ultra Directional RNA Library Prep kit (New England BioLabs) and was subjected to next-generation sequencing from both ends with the HiSeq 2500 platform (Illumina).

tag: cell types

value: PC9 cells stably expressing EGFP and firefly luciferase (PC9-Luc-EGFP)

tag: experiment

value: parental cell

tag: culture media

value: DEMD supplemented with 10% FBS and 1% PenStrep (GIBCO)

tag: genotype


title: WM266.4 02

source_name: Human melanoma cells

value: WM266.4 cells stably expressing EGFP and firefly luciferase (WM266.4-Luc-EGFP)

value: BRAF.V600E, PTEN hemizugous deletion


title: PC9 02


title: WM266.4-BrM3 01

value: WM266.4 cells stably expressing EGFP and firefly luciferase, with enhanced brain tropism (WM266.4-Luc-EGFP-BrM3)

value: Repetition of intra-cardiac injection and collection of WM266.4-Luc-EGFP cells for 3 times.


title: WM266.4-BrM3 02


title: PC9-BrM4 02

value: PC9 cells stably expressing EGFP and firefly luciferase, with enhanced brain tropism            (PC9-Luc-EGFP-BrM3)

value: Repetition of intra-cardiac injection and collection of PC9-Luc-EGFP cells for 4 times.


title: PC9-BrM4 01

value: PC9 cells stably expressing EGFP and firefly luciferase, with enhanced brain tropism                (PC9-Luc-EGFP-BrM3)


title: WM266.4 siCtrl 03

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trim Galore! v0.5.0, then mapped to hg19 whole genome using TopHat2 v2.0.9 with --library-type=fr-firststrand.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: WM266.4 human melanoma cells stably expressing EGFP and firefly luciferase were maintained in DMEM with 10% FBS / 1% PenStrep (GIBCO)

treatment_protocol: Cells were prepared on 6-well plate the day before, and control siRNA (ON-TARGET plus Non-targeting Pool, Dharmacon) or siRNA against DNMT1 (ON-TARGET plus Human DNMT1 siRNA SMARTpool, Dharmacon) were transfected with lipofectamine RNAiMax (Invitorgen) according to the manufacture’s protocol on day 0. The cells were subcultured to 9 cm dish on day 2 and siRNAs were transfected again on day 3. The cells were further expanded and sent for the following experiments on day 7.

value: WM266.4 cells stably expressing EGFP and firefly luciferase

value: Treated with control siRNA for 7 days (transfected at day 0 and 3)


title: WM266.4 siDNMT1 03

value: Treated with siRNA against human DNMT1 for 7 days  (transfected at day 0 and 3)


title: WM266.4 siDNMT1 02


title: WM266.4 siCtrl 02


title: WM266.4 siDNMT1 01


title: WM266.4 siCtrl 01


title: WM266.4 01


title: 00_a2-1

value: post pharyngeal fragment

value: 0 hpa


title: Sample_CVFR3-96

description: Brain metastatic WM266.4 cells

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to GRCh38 whole genome using TopHat2 v2.0.9 with --library-type=fr-firststrand.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cuffquant v2.1.1 and Cuffnorm v2.2.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: WM266.4 human melanoma cells stably expressing EGFP and firefly luciferase were injected into the left ventricle of anesthetized nude mice (1e6 cells in PBS). Successful injection was confirmed by intraperitoneal injection of D-Luciferin (150 mg/kg) and bioluminescence imaging. Progression of brain metastasis was confirmed by follow up bioluminescence imaging. Mice were euthanized at day 20 and brain metastatic WM266.4 cells were collected. Mouse brains were surgically extracted and dissociated into single cells by gentleMACS Dissociator (Miltenyi Biotec). The dispersed cells were seeded onto a plastic dish and cultured for 1 hours, then the cells attached on the bottom of the plate were collected.

extract_protocol:
The cells were applied to the C1 Single-Cell Auto Prep System (Fluidigm) and confirmed that the Fluidigm C1 ICF contains a single WM266.4 cell by real-time imaging with its size and appearance. Then, we underwent on-chip RNA preparation and whole-transcriptome amplification with SMART-Seq v4 Ultra kit for 96 individual cells. The products were then converted to Illumina sequencing libraries using Nextera XT (Illumina)
single cell RNA-seq

value: Cells were collected from the brain of nude mice 20 days after intra-cardiac injection


title: Sample_CVFR3-90

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-91

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-94

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-92

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-84

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-83

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-89

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-93

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-85

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-81

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-76

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-95

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-82

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-73

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-77

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-74

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-79

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-78

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-72

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-71

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-86

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-70

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-68

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-69

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-67

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-87

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-66

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-88

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-80

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-75

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-65

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-64

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-60

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-61

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-63

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-58

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-59

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-52

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-54

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-50

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-53

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-51

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-56

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-48

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-45

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-47

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-42

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-43

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-41

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-40

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-39

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-37

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-36

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-57

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-55

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-62

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-49

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-44

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-35

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-33

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-46

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-30

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-28

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-29

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-32

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-31

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-25

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-24

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-27

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-21

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-34

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-26

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-13

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-17

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-19

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-14

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-18

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-16

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-12

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-11

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-09

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-15

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-23

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-08

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-10

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-22

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-20

description: Brain metastatic WM266.4 cells


title: Hela_NT_Input_F

city: Baltimore

first: Marina

middle: A

last: Bellani

state: Maryland

address: 251 Bayview Blvd

department: LMB

institute: NIA

data_processing:
ChIP-seq reads were aligned to the human genome assembly hg38 using BWA [version 0.7.17] using the following parameters
Picard [version 2.20.8] SamFormatConverter was used to convert SAM to BAM, SortSAM was used to sort the resulting BAM file [VALIDATION_STRINGENCY=Lenient], MarkDuplicates was used to mark duplicates
Deeptools [version 3.3.0] bamCoverage was used to generate BigWig files with the following parameters [-bs 150 -e  --normalizeUsing RPKM --ignoreDuplicates]
Deeptools [version 3.3.0] bigwigCompare was used to calculate log2 ratios between bigwig files from each ChIP-seq and the corresponding Input [parameters: --skipZeroOverZero --operation log2 --skipNonCoveredRegions --outFileFormat bigwig --blackListFileName]
Genome_build: hg38
Supplementary_files_format_and_content: bigwig, bedgraph

source_name: Input DNA

growth_protocol: GFP-DONSON expressing HeLa cells 30 were cultured with L-Glutamine (Gibco), 200 ug/ml Hygromycin B (Invitrogen), and 5 ug/ml Blasticidin (Gibco). To induce GFP-DONSON expression, cells were incubated with 1 μg/ml Doxycycline for 48 hr.

extract_protocol:
Cells were crosslinked with 1% formaldehyde in culture media for 8 min, followed by quenching the formaldehyde with 0.1 M glycine. Cells were washed with PBS, harvested by scraping, then suspended in lysis buffer (0.5% SDS, 10 mM EDTA, 50 mM Tris-HCL pH 8.0) supplemented with protease and phosphatase inhibitors. Lysates were sonicated in a 4 ⁰C water bath ultrasonicator (Bioruptor, Diagenode). The time of sonication was adjusted to yield short DNA fragments <500 bp (total 8 minutes, 30 seconds sonication, then cool 30 seconds). In some experiments the time was adjusted to yield longer DNA fragments of 500-5000 bp (2 x 30 seconds with a 30 second cooling period). Diluted lysates were incubated overnight at 4 °C with antibodies as indicated. Immunoprecipitations were performed using Protein G magnetic beads (Pierce, 10% v/v), or GFP Trap (Chromotek, gta-20). Bead bound complexes were washed with low salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), high salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), LiCl immune complex buffer (0.25 M LiCl, 1% NP-40, 1% mM EDTA, 10 mM Tris-HCl pH 8.0) and TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0). DNA was eluted in elution buffer (1% SDS, 0.2 M NaCl) with Proteinase K (100 µg/ml) overnight at 65 °C. Eluted DNA was purified with DNA Clean & Concentrator PCR purification Kit (ZYMO Research, D4033) according to the manufacturer instructions.
Illumina sequencing adapters with a T-overhang were ligated to the precipitated ChIP DNA fragments or the input DNA, with a corresponding A-overhang, to construct a sequencing library according to the manufacturer’s protocol (Illumina, San Diego, CA). The fragments were purified using a magnetic bead protocol and eighteen cycles of PCR amplification were performed to enrich for fragments with an adapter on both ends. The products were purified again with size selection (approximately 200–600 bases) using a dual bead selection protocol with SPRIselect Beads (Beckman Coulter, Brea, CA). These libraries were sequenced on an Illumina Hi-Seq 2500 sequencer using on-board cluster generation on a rapid run paired end flow cell for 75 X 75 cycles (DONSON) and single end of 75 bp for 75 cycles (FANCM). Real-time analysis was performed using RTA v1.18.66.3 and base-calling was performed using bcl2fastq v2.18.0.12.

treatment_protocol: Non-treated cells

tag: cell line

value: Hela/GFP-DONSON cells


title: Hela_NT_Input_D


title: Hela_NT_GFP-DONSON_ChIP

source_name: GFP-DONSON ChIP-Seq

value: Chromotek  gta-20, GFP-Trap®_Agarose


title: Sample_CVFR3-05

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-07

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-04

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-03

description: Brain metastatic WM266.4 cells


title: BeWo_new_2_3'READS

first: Bin

last: Tian

state: PA

address: 3601 Spruce Street

department: Program in Gene Expression and Regulation; Center for Systems and Computational Biology

institute: Wistar Institute

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to hg19 or mm9 using bowtie2
reads with a mapping quality score (MAPQ) ≥10 were kept for further analysis. Reads with ≥2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for each pAs

source_name: BeWo

extract_protocol:
TRIzol
3'READS: The 3’READS procedure has been described in (Hoque et al, 2013; Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer.

tag: cell type

value: trophoblast

tag: treatment

value: Untreated

tag: protocol

tag: molecule subtype

value: newly made RNA


title: Sample_CVFR3-38

description: Brain metastatic WM266.4 cells

value: BRAF.V600E, PTEN hemizugous deletion


title: BeWo_steady_2_3'READS

value: steady state RNA


title: Sample_CVFR3-01

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-02

description: Brain metastatic WM266.4 cells


title: Sample_CVFR3-06

description: Brain metastatic WM266.4 cells


title: BeWo_new_3'READS

description: newly made RNA


title: BeWo_steady_3'READS

description: steady state RNA


title: Pro_Organoid_Week_12

city: Belfast

first: Rebecca

middle: Elizabeth

last: Steele

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Resulting RNA-Seq fastq reads were aligned to Hg19 (GRCh37) using STAR
Mapped to genes using HTSeq counts
Normalized count and differential expression analysis data was generated using DESeq2
Gene Set Enrichment Analysis (GSEA) was performed on normalized RNA-seq count data and calculated by permuting genes 1000 times in the GSEA software.
Genome_build: Hg19 (GRCh37)
Supplementary_files_format_and_content: Normalized counts

extract_protocol:
Total RNA was extracted from cells using Ribozol™ RNA Extraction Reagent (Amresco) following manufacturer’s instructions
RNA-Seq library construction and sequencing was performed at Otogenetics Corporation (Atlanta, USA) according to standard protocols

value: Pro Organoid Week 12


title: Luminal_DLK_Replicate2

value: Luminal


title: Basal_DLK_Replicate1

value: Basal


title: Basal_DLK_Replicate2


title: Pro_IPSC

value: IPSC


title: Luminal_DLK_Replicate1


title: Hela_NT_FANCM_ChIP

source_name: FANCM ChIP-Seq

value: Bethyl A302-637A, Rabbit anti FANCM


title: Definitive_Endoderm

value: Definitive Endoderm


title: Clodronate_18

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

data_processing:
Illumina HiSeq Control Software 3.4.0 used for basecalling.
STAR 2.5.3a used for alignment.
STAR 2.5.3a used for normalized abundance measurement.
Genome_build: GRCm38 GencodeM15
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include CPM values for each Sample.

source_name: left 4th mammary tissue

growth_protocol: EO771 cells expressing firefly luciferase were cultured in RPMI-1640 with L-glutamine (Cellgro-Corning, Inc., #10-040-CV), supplemented with 10% FBS (Atlanta Biologicals, #S11550H), at 37oC, in a 5% CO2 atmosphere. After harvesting, tumor cells (1 × 10e5) were injected into the left fourth mammary fat pad.

extract_protocol:
Mammary tissues were dissected, flash frozen, and stored at -80 C until being dissociated in RLT lysis buffer (supplemented with beta-mercaptoethanol) with a bead mill (Qiagen TissueLyser LT). Lysates were then processed with Qiagen RNeasy Mini Kit, utilizing qiashredder tubes for homogenization and on-column DNase.
Lexogen QuantSeq 3' FWD.

treatment_protocol: Mice were given access to the wheel-hub for two weeks prior to tumor engraftment; liposome injections were performed 24 hours before tumor engraftment and again at the time of tumor engraftment.

value: Mammary tissue with engrafted EO771 cells

tag: activity

value: Control

value: Clodronate liposomes

tag: experiment #

tag: replicate

tag: reagent

value: Hub Shelter (Bio-Serve, #K3328) +  Clodronate Liposome (Cedarlane, #CP-005-005)


title: Clodronate_16

tag: tissue


title: WheelClodronate_22

value: Wheel

value: Fast-Trac Wheel (Bio-Serve, #K3250) +  Clodronate Liposome (Cedarlane, #CP-005-005)


title: WheelClodronate_24


title: WheelClodronate_21


title: Clodronate_13


title: Clodronate_15


title: Clodronate_14


title: Wheel_12

value: PBS liposomes

value: Fast-Trac Wheel (Bio-Serve, #K3250) +  PBS Liposome (Cedarlane, #CP-005-005)


title: Wheel_8


title: WheelClodronate_20


title: Wheel_10


title: Control_6

value: Hub Shelter (Bio-Serve, #K3328) +  PBS Liposome (Cedarlane, #CP-005-005)


title: Wheel_9


title: Wheel_7


title: Control_5


title: Control_3


title: Wheel_11


title: Control_2


title: WheelClodronate_19


title: MSMO6

city: chapel hill

first: Seth

last: Weir

address: 115 mason farm rd

institute: UNC Chapel Hill

description:
single-cell sequencing
MSMO_Working.rds

data_processing:
Raw sequence data were processed in a Linux environment using Drop-seq Tools V1.13. (https://github.com/broadinstitute/Drop-seq/releases) to generate a digital expression (DGE) matrix
alignment: Star aligner was used version 2.5.4a
DGE creation: We first convert Fastq to BAM/SAM format and merge samples that were sequenced across multiple lanes.
full downstream pipeline code: https://github.com/malawsky/Gershon_single-cell
Genome_build: mm10 genome
Supplementary_files_format_and_content: digital expression matrix

source_name: Medulloblastoma model

extract_protocol:
Brains were cut in half sagittally and drop-fixed in 4% paraformaldehyde for IHC, and half cerebellum or tumor collected for Drop-Seq.Cells were dissociated using the Papain Dissociation System (Worthington Biochemical) according to the manufacturer’s protocol, as in our prior studies. https://www.nature.com/articles/s41467-019-13657-6#Sec18
Drop-Seq libraries were prepared according to the Drop-seq protocol V3.1 (ref. 32), with full details available online (http://mccarrolllab.com/dropseq/). Cell and bead concentrations were both set to between 95 and 110/μL.
to high-throughput sequencing facility that does their own QC before running samples.
RNA libraries were prepared for sequencing using standard Illumina protocols (Multiplexed samples using nextera indexes so that libraries could be pooled)

value: Cerebellum

tag: age

value: Postnatal age 15


title: MSMO9

description:
single-cell sequencing
MSMO_Working.rds


title: MSMO7

description:
single-cell sequencing
MSMO_Working.rds


title: MSMO11

description:
single-cell sequencing
MSMO_Working.rds


title: bmErythroidPreCFU_vehicle_R3

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

data_processing:
Sequence reads were aligned to the mouse genome with Hisat2 (version 2.1.0) [1] using a “genome” index built from the GRCm38 release of the mouse genome and known splice sites extracted from Ensembl version 91 annotations (using the hisat2_extract_splice_sites.py tool). A two-pass mapping strategy was used to discover novel splice sites (with the additional parameters: --dta and --score-min L,0.0,-0.2).
Mapped reads were counted using featureCounts (Subread version 1.6.3; Ensembl version 91 annotations; default parameters).
TPMs were estimated with salmon (version 0.9.1); using a quasi-index (built with Ensembl version 91 annotations and k=31) and gc bias correction (parameter “--gcBias”)
Genome_build: GRCm38
Supplementary_files_format_and_content: (1) "featureCounts_raw_counts_pre.txt" is a tab-delimited text file containing the table of gene-by-sample read counts computed with the featureCounts algorithm. (2) "salmon_tpms_pre.txt" is a tab-delimited text file containing the table of gene-by-sample raw TPMs computed with salmon.

source_name: Bone marrow progenitors

growth_protocol: Bone marrow flushed from the femurs and tibiae of SKG mice, then depleted of lineage+ cells using biotin/streptavidin kit.  Pre-CFU-E sorted by FACS using following definition: Live, Lineage-, cKit+, Sca1-, CD41-, CD16/32-, CD105+, CD150+

extract_protocol:
RNA was extracted using the RNEasy Micro kit, according to the manufacturer’s instructions
The mRNA fraction was selected from the total RNA provided before conversion to cDNA. The cDNA was end-repaired, A-tailed and adapter-ligated. The prepared libraries were size selected, multiplexed and QC’ed before paired end sequencing.  Data will be aligned to the reference and quality checked.

treatment_protocol: Cells re-suspended in serum-free expansion medium with EPO (2 U/ml) and SCF (100 ng/ml), with or without IL-33 (10 ng/ml) for 6 hours, as indicated in SAMPLES

value: Incubated with EPO (2 U/ml) and SCF (100 ng/ml) for 6 hours

value: Pre colony forming unit (CFU) erythroid cells

tag: cell phenotype


title: MSMO8

description:
single-cell sequencing
MSMO_Working.rds


title: bmErythroidPreCFU_vehicle_R1


title: bmErythroidPreCFU_vehicle_R2


title: Control_4


title: bmErythroidPreCFU_IL33_R3

value: Incubated with IL-33 (10 ng/ml), EPO (2 U/ml) and SCF (100 ng/ml) for 6 hours


title: bmErythroidPreCFU_IL33_R2


title: D60_Gut_scRNA

city: La Jolla

first: John

last: Chang

address: 9500 Gilman Drive

department: School of Medicine

institute: UCSD

description: 3' Transcriptome sequencing (10X genomics V2)

data_processing:
data were processed by cellranger 2.1.0 with default parameter, using mm10 as reference.
Raw cell-reads were then loaded to R using the cellrangerRkit package. The scRNA-seq dataset was then further filtered based on gene numbers and mitochondria gene counts total counts ratio. Only cells with > 400 genes,UMI > 0,and 0.5% ~ 20% of their UMIs mappingto mitochondria genes were kept for downstream analysis.
For the scRNA-seq, the first 16 bp of R1 is the cell barcode and the next 10bp (17-26bp) is the UMI.
Genome_build: mm10
Supplementary_files_format_and_content: cell-gene UMI table: UMI table with each row represent a cell and each column represent a gene.

source_name: Gut CD8+ T cell

growth_protocol: No growth procedure was required.

extract_protocol:
For isolation of CD8+ T cells from spleen, spleens were collected and dissociated to yield a cell suspension prior to lysis of red blood cells. For isolation of CD8+ T cells from the small intestinal epithelium, Peyer’s patches were removed and the tissue was cut longitudinally and washed of luminal contents. The tissue was then cut into 1cm pieces that were incubated while shaking in DTE buffer (1ug/ml dithioerythritolin 10% HBSS and 10% HEPES bicarbonate) at 37°C for 30 minutes. Cells within the supernatant were collected and passed through a 44/67% Percoll density gradient to enrich for lymphocytes.
Single cell libraries were prepared according to the protocol for 10X Genomics for 3’ Gene Expression. Approximately 10,000 sorted CD45.1+ Va2+ CD8+ CD44+ cells were loaded and partitioned into Gel Bead In-Emulsions (GEM). scRNA libraries were sequenced on a HiSeq4000 (Illumina).

treatment_protocol: These details are included in extraction protocol.

tag: time point

value: gut

tag: cell type surface markers

value: CD8 T cells


title: D90_Gut_scRNA


title: bmErythroidPreCFU_IL33_R1


title: D32_Gut_scRNA_2


title: D21_Gut_scRNA


title: D32_Gut_scRNA


title: D32_Spleen_scRNA

source_name: Spleen CD8+ T cell

value: spleen


title: D10_Spleen_scRNA_2


title: D14_Gut_scRNA


title: D90_Spleen_scRNA


title: D21_Spleen_scRNA_2


title: Control_1

value: Mammary tissue with engrafted EO771 cells


title: D10_Gut_scRNA


title: D14_Spleen_scRNA_2


title: D10_Spleen_scRNA


title: D7_Gut_scRNA


title: D4_Gut_scRNA


title: D7_Spleen_scRNA


title: D5_Spleen_scRNA


title: D6_Spleen_scRNA


title: D7_Spleen_scRNA_2


title: D3_Spleen_scRNA


title: D4_Spleen_scRNA


title: D60_Spleen_scRNA


title: Naïve_Spleen_scRNA

value: Naïve


title: Serum exosomes, N5

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The reads were aligned to the reference genome (UCSC HG19) with STAR software and circRNAs were detected and annotated with DCC software.
circBase database and circ2Trait disease database were used to annotate the identified circRNAs.
The junction read counts were normalized and differentially expressed circRNAs were determined using edgeR package of R software
Genome_build: UCSC HG19
Supplementary_files_format_and_content: Excel file reporting number of raw junction reads, logCPMs

source_name: Serum exosomes

growth_protocol: All samples were collected at The Second Hospital of Shandong University between 2017 and 2019. Patients with CRC were diagnosed by histopathology or histobiopsy, and samples were collected prior to any therapies.

extract_protocol:
Total RNA was extracted from serum exosomes,and 5 μg total RNA were pretreated to enrich circRNA using CircRNA Enrichment Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To thoroughly remove cell debris, about 5 mL of venous blood obtained from each participant was centrifuged at 3,000 rpm for 10 min at 4℃, then 10,000 rpm for 10min, within 2 hours of collection. The supernatant (serum) was then stored at -80℃ before using.

tag: disease state

value: healthy control

value: blood

tag: sample type

value: Serum exosomes


title: Serum exosomes, N4

institute: The Second Hospital of Shandong University


title: D14_Spleen_scRNA


title: Serum exosomes, N3


title: Serum exosomes, N1


title: Serum exosomes, C5

value: colorectal cancer (CRC)


title: Serum exosomes, C2


title: Serum exosomes, C1


title: Serum exosomes, C4


title: Serum exosomes, C3


title: dmso_rep2

city: Frederick

first: George

last: Pavlakis

state: MD

address: 535 Sultan St

department: Vaccine Branch

institute: NCI

data_processing:
Library strategy: Ribo-seq
Adapter trimming with cutadapt (v2.4)
read pairing with PANDASeq (v2.11)
Demultiplexed libraries with perl
rRNA and tRNA alignment with bowtie (v.1.2.3)
Genomic alignment with HISAT2 (v2.1.0)
host derived primer extraction with perl
Genome_build: hg38
Supplementary_files_format_and_content: Extracted influenza primer junction sequences in text format

growth_protocol: A549 human lung epithelial cells  were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% foetal bovine serum, and maintained at 37C and 5% CO2

extract_protocol: RNaseI footprinting, pelleting of ribosomes, RNA-extraction with TRIzol reagent, linker ligation onto footprints, reverse-transcription,cDNA circularization, rRNA depletion, PCR amplification

treatment_protocol: Cells were infected with A/Puerto Rico/8/1934 (H1N1) at an MOI of 3

tag: innoculum

value: A/Puerto Rico/8/1934 (H1N1)

value: dmso


title: dmso+B73_rep1


title: UC47rN28

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

data_processing:
The reads were trimmed for quality and length using custom scripts. The trimmed reads were aligned to the hg38 (UCSC genome) with Gencode annotation for the same version of the genome using HiSAT2. The alignments were processed with StringTie to generate gene specific count matrix for all the samples.
The count matrices were then processed using DESeq2 in R to determine significantly differentially expressed genes.
The results were visualized using R
Genome_build: hg38
Supplementary_files_format_and_content: tpm matrix file where each row is the gene, and each column is the sample.

source_name: Resting CD4+ T cells following ex vivo PMA/ionomycin activation, Sortseq

growth_protocol: Resting CD4+ T cells were isolated from ART-treated, virally suppressed, HIV-1-infected individuals using magnetic negative selection.

extract_protocol:
Resting CD4+ T cells were sorted by HIV-1 RNA SortSeq into single cells into RNA preserving buffer. RNA was reverse crosslinked with proteinase K and SDS under 50°C for 1 hour. RNA was extracted by Quick-RNA Microprep (Zymo Research) with a built-in on-column DNase treatment step.
Total RNA from single cells was extracted followed by a ribosomal RNA depletion step using the SMARTer Stranded Total RNA-Seq Kit Pico Input Mammalian v2.
Samples with different barcodes were pooled into one Hiseq4000 2x150 platform, targeting an estimated reads of 20-40 million per sample.

treatment_protocol: Cells were treated with PMA (1 µg/ml) and ionomycin (1 µM) for 16-18 hours in the presence of enfurvitide to induce HIV-1 RNA expression without causing new rounds of infection in vitro.

value: Resting CD4+ T cells

value: PMAionomycine for 16 hours under enfuvirtide

tag: individual


title: UC47rN29

tag: cell type


title: UC47rN24

tag: treatment


title: not1 rep2 (small RNA-seq)

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were  mapped to TAIR10  genome using bowtie v1.1.1 with parameters -a -p 4 -f -S -v 0
The TAIR10 genome was split into 500kb windows and the number of reads in every window were counted by the total number of clean reads that mapped to the nuclear genome .
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include reads count for each sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 23ºC

extract_protocol:
Total RNA was extracted from two-week-old seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for small RNA-seq

tag: seedlings

value: Arabidopsis seedlings

tag: strain

tag: genotype


title: har_rep2

value: harringtonine


title: UC47rN23


title: WT rep2 (small RNA-seq)

source_name: wild type (C24)

value: wild type (C24)


title: nrpd1 rep2 (small RNA-seq)


title: nrpd1 rep1 (small RNA-seq)


title: Serum exosomes, N2


title: harr_rep1


title: WT rep1 (small RNA-seq)


title: ex vivo BMRC biological rep4

type: RNA

city: Albuquerque

first: Dario

last: Marchetti

state: NM

address: 1 University of New Mexico

department: Internal Medicine

institute: University of New Mexico

description: Gene expression data from CTC-derived model of metastatic dormancy

data_processing:
Affymetrix User Manual: GeneChip WT plus Reagent Kit for Whole Transcript Expression Assay, P/N 703174 Rev 1
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: BrPt91 xenograft bone marrow

growth_protocol: NSG mice were injected with CTC-enriched cells obtained from metastatic breast cancer patients. After 4-8 months of in vivo selection, mice were euthanized and ex vivo BMRC/CTCs were isolated by FACS. Only samples from mice that did not develop overt metastasis (confirmed by gross and microscopic examination) were included in this study.

extract_protocol: Sorted cells were collected directly into a pre-chilled tube maintained at 4oC containing RNA lysis buffer and total RNA was collected according to the manufacturer’s protocol (Macherey-Nagel, Inc.).

treatment_protocol: Ex vivo CTCs and BMRCs were isolated using a BD FACSAriaII (BD Biosciences) housed inside a BSL-2 facility allowing for collection of cells in sterile conditions. The flow cell was cleaned and sterilized before and after running each sample.

tag: subject status

value: metastatic breast cancer patient

tag: subject/sample id

tag: gender

value: female

tag: primary tumor subtype

tag: host strain

value: NGS

tag: tissue/cell type

value: xenograft bone marrow-resident cells (BMRCs)


title: ex vivo BMRC biological rep5

hyb_protocol: Affymetrix User Manual: GeneChip WT plus Reagent Kit for Whole Transcript Expression Assay, P/N 703174 Rev 1

source_name: BrPt67 xenograft bone marrow

value: TNBC


title: UC47rN20


title: UC47rN19


title: UC47rN21


title: ex vivo CTC biological rep5

scan_protocol: Affymetrix User Manual: GeneChip WT plus Reagent Kit for Whole Transcript Expression Assay, P/N 703174 Rev 1

source_name: BrPt67 xenograft blood

value: xenograft blood


title: ex vivo BMRC biological rep2

source_name: BrPt92 xenograft bone marrow

label_protocol: Affymetrix User Manual: GeneChip WT plus Reagent Kit for Whole Transcript Expression Assay, P/N 703174 Rev 1

value: ER+/PR+


title: cFOS_Pos_DNA_p3_G1 snRRBS

city: New York

first: Miklos

last: Toth

state: NY

address: 1300 York Ave, W506

department: Pharmacology

institute: Weill Cornell Medicine

description: single nuclei DNA

data_processing:
UCSC mm9 was prepared and indexed
alignment and methylation calling using Bismark (v17)
Differential methylation and statistical analysis were performed using the MethylKit package in R at default setting.  Differentially methylated sites were defined as sites where the sliding linear model (SLIM)-corrected p-values (q) were ≤0.01
Supplementary_files_format_and_content: xlsx files with genome coordinates along with methlyation % per site

source_name: dorsal dentate gyrus granule cell

extract_protocol:
Following sacrafice, dentate gryus were microdissected, nuclei isolated, stained, and FACS sorted by PROX+/FOS+ and /FOS- populations into 96-well plates
For single nuclei RRBS, bisulfite converted DNA was amplified using primers containing an Illumina i7 index. A different i7 index was used for every 24-nuclei pool, allowing multiplexing of 96 nuclei for paired-end sequencing on one Illumina HiSeq 2500 lane.

treatment_protocol: animals were exposed to a novel environment for 15minutes.

tag: tissue

value: dentate gryus granule cell

tag: age

value: adult

value: CTL FOS POS sorted


title: 25rN5


title: ex vivo BMRC biological rep6

source_name: BrPt73 xenograft bone marrow


title: ex vivo CTC biological rep4

source_name: BrPt91 xenograft blood


title: ex vivo CTC biological rep2

source_name: BrPt92 xenograft blood


title: ex vivo BMRC biological rep3

source_name: BrPt75 xenograft bone marrow


title: ex vivo CTC biological rep6

source_name: BrPt73 xenograft blood


title: cFOS_Pos_DNA_p3_C1 snRRBS

description: single nuclei DNA


title: not1 rep1 (small RNA-seq)


title: cFOS_Pos_DNA_p3_E1 snRRBS

description: single nuclei DNA


title: 25rN4


title: ex vivo CTC biological rep1

source_name: BrPt62 xenograft blood


title: ex vivo CTC biological rep3

source_name: BrPt75 xenograft blood


title: ex vivo BMRC biological rep1

source_name: BrPt62 xenograft bone marrow


title: 25rN2


title: cFOS_Pos_DNA_p3_A1 snRRBS

description: single nuclei DNA


title: UC47rN22


title: cFOS_Pos_DNA_p2_G1 snRRBS

description: single nuclei DNA


title: 02rN5


title: 22rN3


title: cFOS_Pos_DNA_p2_E1 snRRBS

description: single nuclei DNA


title: 02rN4


title: cFOS_Pos_DNA_p2_C1 snRRBS

description: single nuclei DNA


title: 25rN1


title: 02rN3


title: 02rN1


title: cFOS_Pos_DNA_p1_G1 snRRBS

description: single nuclei DNA


title: 02rN2


title: cFOS_Pos_DNA_p2_A1 snRRBS

description: single nuclei DNA


title: cFOS_Pos_DNA_p1_E1 snRRBS

description: single nuclei DNA


title: PN241_passage_10_A

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

institute: University of Liverpool

description:
Sample_18-PN241_p10_a
RNAseq_counts.Sample_18.PN241_p10_a.BAM.sorted.bam.COUNT.txt.Count

data_processing:
Raw fastq files were trimmed using Cutadapt 1.2.1 and Sickle 1.2 with a minimum window quality score of 20. Reads < 10nt were removed.
QC was performed using Fastqc and Multiqc.
Sequence data was mapped to human genome GRCh38 using Bowtie2 1.1.2.
Gene level count data was estimated using htseq-count 0.9.0 using the standard GTF file accompanying GRCh38.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene level counts produced by htseq-count.

source_name: Mesenchymal Stem Cells_P10

extract_protocol:
RNA was extracted from cells using the Rneasy Plus Mini Kit (Qiagen) according to manufacturers instructions.
Ribosomal RNA depletion was performed using Ribo-Zero Kit (New England Biolabs). RNA-seq libraries were prepared using the NEB Next Ultra Directional RNA Library Kit (New England Biolabs).

tag: cell line

value: Mesenchymal Stem Cells

tag: passage


title: cFOS_Pos_DNA_p1_C1 snRRBS

description: single nuclei DNA


title: PN264_passage_15

description:
Sample_16-PN264_p15
RNAseq_counts.Sample_16.PN264_p15.BAM.sorted.bam.COUNT.txt.Count

source_name: Mesenchymal Stem Cells_P15


title: PN251_passage_15_A

description:
Sample_17-PN251_p15_a
RNAseq_counts.Sample_17.PN251_p15_a.BAM.sorted.bam.COUNT.txt.Count


title: cFOS_Neg_DNA_p3_G1 snRRBS

description: single nuclei DNA

value: CTL FOS NEG sorted


title: PN264_passage_10

description:
Sample_15-PN264_p10
RNAseq_counts.Sample_15.PN264_p10.BAM.sorted.bam.COUNT.txt.Count


title: PN264_passage_5

description:
Sample_14-PN264_p5
RNAseq_counts.Sample_14.PN264_p5.BAM.sorted.bam.COUNT.txt.Count

source_name: Mesenchymal Stem Cells_P5


title: cFOS_Pos_DNA_p1_A1 snRRBS

description: single nuclei DNA


title: cFOS_Neg_DNA_p3_C1 snRRBS

description: single nuclei DNA


title: PN251_passage_15

description:
Sample_12-PN251_p15
RNAseq_counts.Sample_12.PN251_p15.BAM.sorted.bam.COUNT.txt.Count


title: cFOS_Neg_DNA_p3_A1 snRRBS

description: single nuclei DNA


title: cFOS_Neg_DNA_p3_E1 snRRBS

description: single nuclei DNA


title: cFOS_Neg_DNA_p2_G1 snRRBS

description: single nuclei DNA


title: PN264_passage_1

description:
Sample_13-PN264_p1
RNAseq_counts.Sample_13.PN264_p1.BAM.sorted.bam.COUNT.txt.Count

source_name: Mesenchymal Stem Cells_P1


title: PN251_passage_5

description:
Sample_10-PN251_p5
RNAseq_counts.Sample_10.PN251_p5.BAM.sorted.bam.COUNT.txt.Count


title: PN251_passage_1

description:
Sample_9-PN251_p1
RNAseq_counts.Sample_9.PN251_p1.BAM.sorted.bam.COUNT.txt.Count


title: cFOS_Neg_DNA_p2_E1 snRRBS

description: single nuclei DNA


title: cFOS_Neg_DNA_p2_C1 snRRBS

description: single nuclei DNA


title: PN251_passage_10

description:
Sample_11-PN251_p10
RNAseq_counts.Sample_11.PN251_p10.BAM.sorted.bam.COUNT.txt.Count


title: cFOS_Neg_DNA_p2_A1 snRRBS

description: single nuclei DNA


title: PN242_passage_15

description:
Sample_8-PN242_p15
RNAseq_counts.Sample_8.PN242_p15.BAM.sorted.bam.COUNT.txt.Count


title: scRNA Mouse Spleen Untreated

city: Bethesda

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description:
mouse_spl_untreated
WT Mouse
Exp ID: 190822_0270_E1
Lab data ID: SWT4
mRNA
read1_26/i7index_8/read2_98

data_processing:
Raw sequencing data were processed with Cell Ranger software (version 3.0.2). Cell Ranger output files were loaded into R for analysis using the Seurat package. Low quality cells were removed based on % mitochondrial gene expression. Data were integrated, normalized, and transformed for downstream analysis. Clustering was performed using the UMAP algorithm. Cell clusters were annotated using the SingleR algorithm. Unclassified cells were removed from downstream analysis. Gene expression was subsequently determined in each cluster. Data were visualized using ggplot2.
Genome_build: Mouse: mm10 (GRCm38); Human: GRCh38
Supplementary_files_format_and_content: barcodes.tsv: Cell Ranger count raw_feature_bc_matrix barcodes.
Supplementary_files_format_and_content: features.tsv: Cell Ranger count raw_feature_bc_matrix features.
Supplementary_files_format_and_content: matrix.mtx: Cell Ranger count raw_feature_bc_matrix matrix.

source_name: Spleen

extract_protocol:
Spleens were isolated and smashed through a 70uM sterile filter to obtain single cell suspensions. Red blood cells (RBCs) were lysed using ACK lysing buffer. Cells were resuspended in RPMI supplemented with 10% FBS and 1% Pen/Strep. For human samples, cells were isolated from whole blood of healthy volunteers using ErythroClear RBC depletion kit (STEMCELL). Cells were resuspended in RPMI supplemented with 10% FBS and 1% Pen/Strep. Cells were treated with recombinant interferon for 4 hours as indicated.
Isolated cells were encapsulated using microfluidics technology, and barcoded using a unique molecular identifier (UMI).
scRNAseq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.

value: WT

value: Spleen

value: Immune cells

value: Untreated


title: PN242_passage_10

description:
Sample_7-PN242_p10
RNAseq_counts.Sample_7.PN242_p10.BAM.sorted.bam.COUNT.txt.Count


title: scRNA Mouse Spleen IFN lambda

description:
mouse_spl_ifnlambda
WT Mouse
Exp ID: 190822_0270_E2
Lab data ID: SWTL
mRNA
read1_26/i7index_8/read2_98

value: IFN lambda


title: cFOS_Neg_DNA_p1_G1 snRRBS

description: single nuclei DNA


title: cFOS_Neg_DNA_p1_E1 snRRBS

description: single nuclei DNA


title: cFOS_Neg_DNA_p1_C1 snRRBS

description: single nuclei DNA


title: PN242_passage_5

description:
Sample_6-PN242_p5
RNAseq_counts.Sample_6.PN242_p5.BAM.sorted.bam.COUNT.txt.Count


title: mac1 sterile anthers, 1.5 mm, rep 2

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
All reads from RNA-seq libraries were trimmed to remove adapter sequences using a Perl script. After trimming off adapters, small RNA reads with the length between 18 and 34 were kept; PARE reads that are longer than 21-nt are discarded, and 21-nt PARE reads are chopped to 20-nt by removing the last nucleotide. Small RNA and PARE reads were mapped to the reference genome using bowtie, and RNA-seq reads were mapped using Tophat. We developed three websites and databases (for sRNA, PARE and RNA-seq, respectively) using the Maize AGPv2 genome, to store and analyze all libraries; we used these visualization tools extensively for this analysis. These Web sites are available at http://mpss.udel.edu/maize_sRNA2/ , http://mpss.udel.edu/maize_RNAseq2/ and http://mpss.udel.edu/maize_pare/
Genome_build: MAIZE_AGPv4_genome
Supplementary_files_format_and_content: tag count

organism: Zea mays

source_name: dissected maize whole anthers

growth_protocol: Fertile anthers of the W23 inbred line and mac1-Y211  introgressed five times into W23, and ocl4 in the A188 inbred were grown in Stanford, CA under greenhouse conditions.

extract_protocol:
Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA).
RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). All libraries were sequenced on an Illumina Hi-Seq 2000 instrument at the Delaware Biotechnology Institute, Newark, DE.

value: anther

tag: Sex

value: male

tag: genotype/variation

value: mac1 sterile


title: mac1 sterile anthers, 2.0 mm, rep 1


title: cFOS_Neg_DNA_p1_A1 snRRBS

description: single nuclei DNA


title: D21_Spleen_scRNA

description: 3' Transcriptome sequencing (10X genomics V2)

source_name: Spleen CD8+ T cell

tag: time point

value: spleen

tag: cell type surface markers

tag: cell type

value: CD8 T cells


title: PN242_passage_1

description:
Sample_5-PN242_p1
RNAseq_counts.Sample_5.PN242_p1.BAM.sorted.bam.COUNT.txt.Count


title: PN241_passage_15

description:
Sample_4-PN241_p15
RNAseq_counts.Sample_4.PN241_p15.BAM.sorted.bam.COUNT.txt.Count


title: mac1 sterile anthers, 1.0 mm, rep 1


title: PN241_passage_10

description:
Sample_3-PN241_p10
RNAseq_counts.Sample_3.PN241_p10.BAM.sorted.bam.COUNT.txt.Count


title: mac1 sterile anthers, 2.0 mm, rep 2


title: cFOS_Neg_RNA_1 snRNA-Seq

description: single nuclei RNA

extract_protocol:
Following sacrafice, dentate gryus were microdissected, nuclei isolated, stained, and FACS sorted by PROX+/FOS+ and /FOS- populations into 96-well plates
For single nuclei RNA profiling, standard 10x Genomics Chromium 3′ libraries (v3) were prepared according to the manufacturer’s recommendations. The FOS+ and FOS- 10x libraries were sequenced together on a HiSeq 2500 Illumina machine.

tag: strain

tag: treatment


title: ocl4 sterile anthers, 1.5 mm, rep 2

value: ocl4 sterile


title: ocl4 sterile anthers, 2.0 mm, rep 1


title: mac1 sterile anthers, 1.0 mm, rep 2


title: PN241_passage_5

description:
Sample_2-PN241_p5
RNAseq_counts.Sample_2.PN241_p5.BAM.sorted.bam.COUNT.txt.Count


title: PN241_passage_1

description:
Sample_1-PN241_p1
RNAseq_counts.Sample_1.PN241_p1.BAM.sorted.bam.COUNT.txt.Count


title: ocl4 sterile anthers, 2.0 mm, rep 2


title: scRNA Mouse Spleen IFN alpha

description:
mouse_spl_ifnalpha
WT Mouse
Exp ID: 190822_0270_E3
Lab data ID: SWTA
mRNA
read1_26/i7index_8/read2_98

tag: genotype

value: IFN alpha


title: CTL_dDG_2 RRoxBS

description: RRoxBS treated

extract_protocol:
Following sacrifice, brains from adult WT and virus injected mice were collected, quick frozen on dry ice and sectioned (200 μM) in cryostat. The dentate gyrus was microdissected from the sections. DNA was isolated using the QIAamp DNA Micro Kit according to manufacturer instructions (Qiagen)
For RRoxBS, the libraries were normalized and pooled according to the desired plexity, clustered at 6.5pM on single read flow cells and sequenced for 50 cycles on an Illumina HiSeq 2500

treatment_protocol: CTL

value: dentate gryus granule cell

value: CTL


title: ocl4 sterile anthers, 1.5 mm, rep 1


title: Marmoset_Stomach_H3K27ac_2

city: Utrecht

first: Menno

middle: P

last: Creyghton

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
Genome_build: Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac bigwig files are in .bw

organism: Callithrix jacchus

extract_protocol: TruSeq DNA sample preparation kit (Illumina)

value: Stomach

tag: chip antibody


title: CTL_dDG_3 RRoxBS

description: RRoxBS treated

value: adult


title: mac1 sterile anthers, 1.5 mm, rep 1


title: Marmoset_Stomach_H3K27ac_1


title: UC47rN17

data_processing:
The reads were trimmed for quality and length using custom scripts.  The trimmed reads were aligned to the hg38 (UCSC genome) with Gencode annotation for the same version of the genome using HiSAT2.  The alignments were processed with StringTie to generate gene specific count matrix for all the samples.
The count matrices were then processed using DESeq2 in R to determine significantly differentially expressed genes.
The results were visualized using R
Genome_build: hg38
Supplementary_files_format_and_content: tpm matrix file where each row is the gene, and each column is the sample.

source_name: Resting CD4+ T cells following ex vivo PMA/ionomycin activation, Sortseq

extract_protocol:
Resting CD4+ T cells were sorted by HIV-1 RNA SortSeq into  single cells into RNA preserving buffer. RNA was reverse crosslinked with proteinase K and SDS under 50°C for 1 hour. RNA was extracted by Quick-RNA Microprep (Zymo Research) with a built-in on-column DNase treatment step.
Total RNA from single cells was extracted followed by a ribosomal RNA depletion step using the SMARTer Stranded Total RNA-Seq Kit Pico Input Mammalian v2. Samples with different barcodes were pooled into one Hiseq4000 2x150 platform, targeting an estimated reads of 20-40 million per sample.

value: Resting CD4+ T cells

value: PMAionomycine for 16 hours under enfuvirtide

tag: individual


title: ocl4 sterile anthers, 1.0 mm, rep 1


title: Marmoset_Spleen_H3K4me3_2

value: Spleen


title: ocl4 sterile anthers, 1.0 mm, rep 2


title: Marmoset_Spleen_H3K27ac_2


title: cFOS_Pos_RNA_1 snRNA-Seq

description: single nuclei RNA

source_name: dorsal dentate gyrus granule cell

value: CTL FOS POS sorted


title: CTL_dDG_1 RRoxBS

description: RRoxBS treated


title: W23 fertile pollen (control), rep 1

value: pollen


title: UC47noP9

source_name: Non-resting CD4+ T cells following ex vivo PMA/ionomycin activation, Sortseq

value: Non-resting CD4+ T cells


title: OE_dDG_ADULT_8 RRBS

description: RRBS treated

extract_protocol:
Following sacrifice, brains from adult WT and virus injected mice were collected, quick frozen on dry ice and sectioned (200 μM) in cryostat. The dentate gyrus was microdissected from the sections. DNA was isolated using the QIAamp DNA Micro Kit according to manufacturer instructions (Qiagen)
For bulk RRBS single end 50 bp RRBS sequencing was performed using Illumina HiSeq2000 and 2500 machines according to the manufacturer's instructions.

treatment_protocol: OE and CTL mice for bulk RRBS were bilaterally injected with eitherAAV-DJ-Syn-Dnmt3a-T2a-GFP (1.2E+07 IU./mL), or control virus, AAV-DJ-Syn-GFP.

value: injected with OE DNMT3A virus


title: Marmoset_Spleen_H3K27ac_1


title: OE_dDG_ADULT_9 RRBS

description: RRBS treated


title: UC47noP8


title: Marmoset_SkeletalMuscle_H3K4me3_2

value: SkeletalMuscle


title: W23 anthers, 5.0 mm, rep 1

value: anther

value: male


title: UC47noP7


title: UC47rN18


title: UC47noP6


title: W23 anthers, 4.0 mm, rep 2


title: OE_dDG_ADULT_4 RRBS

description: RRBS treated


title: OE_dDG_ADULT_5 RRBS

description: RRBS treated


title: OE_dDG_ADULT_3 RRBS

description: RRBS treated


title: Marmoset_SkeletalMuscle_H3K27ac_2


title: W23 anthers, 4.0 mm, rep 1


title: Marmoset_Pancreas_H3K4me3_2

value: Pancreas


title: UC47noP3


title: CTL_dDG_ADULT_10 RRBS

description: RRBS treated

value: injected with CTL virus


title: UC47rP27


title: Marmoset_Stomach_H3K4me3_2


title: W23 anthers, 3.0 mm, rep 2


title: Marmoset_Pancreas_H3K27ac_2


title: W23 anthers, 3.0 mm, rep 1


title: CTL_dDG_ADULT_7 RRBS

description: RRBS treated


title: W23 anthers, 5.0 mm, rep 2


title: CTL_dDG_ADULT_6 RRBS

description: RRBS treated


title: Marmoset_Pancreas_H3K27ac_1


title: UC47rP26


title: UC47rP25


title: Marmoset_Liver_H3K4me3_2

value: Liver


title: CTL_dDG_ADULT_2 RRBS

description: RRBS treated

value: dentate gryus granule cell


title: Marmoset_SkeletalMuscle_H3K27ac_1


title: Marmoset_Liver_H3K27ac_2


title: CTL_dDG_ADULT_1 RRBS

description: RRBS treated


title: W23 anthers, 2.0 mm, rep 2


title: W23 anthers, 2.5 mm, rep 1


title: W23 anthers, 2.0 mm, rep 1


title: Marmoset_Liver_H3K27ac_1


title: UC47rP24


title: UC47rP21


title: UC47rP23


title: Marmoset_Kidney_H3K4me3_2

value: Kidney


title: E14.5 mouse fetal liver bulk RNA sequencing

first: Siyuan

last: Wang

address: 333 Cedar Street

department: Department of Genetics and Department of Cell Biology

institute: Yale University

data_processing:
Default base calling software from Illumina HiSeq 2500 was used to generate final FASTQ files
Tophat aligns RNA-seq reads to the mm10 genome using Bowtie2.
Cufflinks assembles the mapped reads into possible transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: Estimated isoform-level and gene-level expression values in the generic FPKM tracking format.

source_name: Mouse E14.5 fetal liver

extract_protocol:
Total RNA was extracted and purified from E14.5 fetal liver using the Qiagen RNeasy Mini Kit (Qiagen, 74104) according to manufacturer’s instructions. Polyadenylated messenger RNA (mRNA) was selectively enriched using Invitrogen Dynabead mRNA Purification Kit (Invitrogen, 61006).
A sequencing library was constructed with NEBNext Ultr II RNA Library Prep Kit (NEB, E7770S) and amplified with NEBNext Multiplex Oligos (NEB, E7335S). Paired-end reads were obtained with Illumina HiSeq2500. Paired-end reads were aligned to the mouse genome (Gencode vM14) with Tophat and transcripts were assembled with Cufflinks.

value: fetal liver

tag: developmental stage

value: Embryonic day 14.5


title: W23 anthers, 1.5 mm, rep 2


title: Irg1KO+ITA_rep3

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 41bpX11bp pair-end sequencing on two lanes. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outReadsUnmapped Fastx --outSAMstrandField All. Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file that includes raw count data for each sample and tab delimited file with barcode annotations

source_name: BMDM

extract_protocol: mRNA was isolated directly from cell pellets with oligo-dT beads (Dynabeads mRNA DIRECT Kit, Invitrogen) and cDNA synthesized using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). Samples were pooled based on Actb qPCR values, RNA-DNA hybrids degraded with acid-alkali treatment and a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB). After SPRI-beads clean-up (Agencourt AMPure XP, BeckmanCoulter). the mixture was PCR-enriched (12 cycles) and SPRI-purified yielding final strand-specific RNA-seq libraries.

tag: hour post stimulation

tag: stimulation

value: LPS + 1 mM itaconate


title: Irg1KO+ITA_rep2


title: W23 anthers, 2.5 mm, rep 2

tag: tissue


title: W23 anthers, 1.5 mm, rep 1


title: UC47rP16

value: Resting CD4+ T cells

value: PMAionomycine for 16 hours under enfuvirtide


title: Marmoset_Kidney_H3K27ac_2


title: Marmoset_Kidney_H3K27ac_1


title: Irg1KO_rep3

value: LPS


title: Marmoset_Heart_H3K4me3_2

value: Heart


title: UC47rP17


title: W23 anthers, 1.0 mm, rep 1


title: UC47rP15


title: Irg1KO_rep2


title: UC47rP4


title: Marmoset_Heart_H3K27ac_2


title: W23 anthers, 0.7 mm, rep 2


title: UC47rP1


title: UC06N5


title: WT_rep3

value: wildtype


title: Irg1KO_rep1


title: W23 anthers, 0.2 mm, rep 2


title: Marmoset_Colon_H3K4me3_2

value: Colon


title: Marmoset_Colon_H3K27ac_2


title: W23 anthers, 0.4 mm, rep 2


title: Marmoset_Heart_H3K27ac_1


title: W23 anthers, 1.0 mm, rep 2


title: W23 anthers, 0.2 mm, rep 1


title: Irg1KO+ITA_rep1


title: UC06N4


title: UC06N3


title: Marmoset_Colon_H3K27ac_1


title: WT_rep1


title: UC06N2


title: Sevoflurane rep2

city: Heidelberg

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

country: Germany

institute: Heidelberg University Hospital

data_processing:
Sequenced reads were depleted from ribosomal reads using SortMeRNA v2.1b and trimmed for adaptor sequences and low-quality reads by Trimmomatic v0.36. Remaining reads were then mapped to Gencode Release M17 primary assembly reference genome utilizing STAR v2.6.0c considering read strand specificity.
After conversion to sorted binary alignment format (BAM) by SAMtools v1.8.3, sample-wise count tables were generated by htseq-count v0.9.1 with the “-s yes” option set.
Genome_build: Gencode Release M17 (GRCm38.p6)
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files include raw count values for each gene.

source_name: tumor

extract_protocol:
For isolation of tumor RNA, small pieces of tissue were put into 1ml of TRIzol® reagent (Thermo Fisher Scientific, Waltham, USA) together with CK18 ceramic beads (1.4mm), followed by disruption in a Precellys® bead mill (Bertin Instruments, Montigny-le-Bretonneux, France) for up to 5 cycles of 20sec each with 5.000rpm. For RNA isolation, RNeasy Mini Kit (Qiagen, Hilden, Germany) was used. Purity and quantity were evaluated in a Nanodrop™ photometer (Thermo Fisher Scientific, Waltham, USA), integrity on a Bioanalyzer system with RNA 6000 Nano Kit (both Agilent Technologies, Santa Clara, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: wild type

value: Melanoma

value: Monocytes

value: Sevoflurane priming


title: RNA-seq_t2iLGoY-D21_rep2

city: Melbourne

first: Fernando

last: Rossello

address: L 10, 305 Grattan Street

institute: The University of Melbourne

data_processing:
Cellranger mkref (v2.1.0) was run to create a reference using the modified GTF annotation file and the  hg19 genome (GRCh37, CellRanger reference version 1.2.0, genome build GRCh37.p13, which contained the Sendai virus KLF4, MYC and SeV sequences as extra chromosomes, also accounted for as extra annotations on the annotation file).
Low quality sequencing reads and were filtered and trimmed with Trimmomatic (v 0.36, Phred score of 6 consecutive bases below 15, minimum read length of 36nt) and mapped to a custom version of hg19 human genome (with modifications described above with STAR (v 2.4.2a).
Gene read counting was performed with featureCounts (v1.5.2, unstranded) against the custom version of Ensembl’s GRCh37 annotation with modifications described above.
Genome_build: hg19
Supplementary_files_format_and_content: Each sample gene (rows) read counts matrices

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to primed and a few types of naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time.

extract_protocol:
Reprogramming intermediates and hiPSCs were isolated by FACS (Supplementary Table 4) and RNA extraction was performed using the RNeasy micro kit (Qiagen, Cat#74004) from ∼2–20 × 10^4 cells with QIAcube (Qiagen). The concentrations of RNA were measured by a Qubit RNA HS Assay Kit (ThermoFisher, Cat#Q32855) on a Qubit 2.0 Fluorometer (ThermoFisher).
~25 ng of RNA was used for library construction with the SPIA kit (NuGen) and subsequently sequenced by HiSeq 1500 or HiSeq 3000 sequencer (Illumina). Sequencing libraries were single-end with 50 nt length and a targeted number of reads of 20-30 million.

tag: source cell type

value: human fibroblasts

value: reprogramming intermeidates or hiPSCs

tag: cell subtype/time point


title: RNA-seq_t2iLGoY-D13_rep3


title: UC06N6


title: Sevoflurane rep1


title: UC06rP2


title: RNA-seq_Primed-P3_rep3


title: Control rep3

value: Control


title: WT_rep2


title: RNA-seq_Primed-P3_rep4


title: UC06P1


title: 29rN6


title: RNA-seq_Primed-P10_rep2


title: Sevoflurane rep3


title: Control rep1


title: RNA-seq_t2iLGoY-D21_rep1


title: 29rN5


title: UC06N1


title: RNA-seq_Primed-P10_rep1


title: RNA-seq_5iLAF-D13_rep1


title: KD_GFP_N55

city: Seoul

first: Youngkyung

last: Cho

department: Biological Science

country: South Korea

institute: Seoul National University

data_processing:
Filtering: Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Sequence alingment: Filtered reads were mapped to GRCm38 (ensembl) using the aligner STAR v.2.4.0b. Reads were aligned with Tophat (v2.1.1) and Fragments per kilobase of exon per million reads (FPKMs) were calculated using Cufflinks (v2.1.1). Cuffdiff (v2.1.1) was used for normalization.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: 427.1.86 thymoma cells

growth_protocol: DMEM with 10% FBS

extract_protocol:
Total RNA was prepared using TRIzol reagent (Invitrogen) according to manufacturer's instructions. The quality of the RNA was assessed by a Agilent 2100 BioAnalyzer. Then mRNA was enriched using Oligo dT magnetic beads for library preparation.  Libraries were prepared for 100bp paired-end sequencing using TruSeq RNA Library Preparation kit (Illumina, CA, USA) according to manufacturer's instructions.
mRNA molecules were purified and fragmented from 2μg of total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. After sequential process of end repair, A-tailing and adapter ligation, cDNA libraries were amplified with PCR (Polymerase Chain Reaction). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×100bp) using Illumina HiSeq2500 (Illumina, CA, USA).

treatment_protocol: 427.1.86 cells which are stably transfected with pSUPER vector were deprived serum for 2 h and then treated DMSO (CONT) or 1 µM of PMA (CONT+PMA) for 2 h to compare the conditions increased EICD upon the PMA-induced shedding. 427.1.86-SPPL2b knockdown cells (KD) were treated with 1 µM of PMA for 2 h after serum deprivation for 2 h to exclude the other effect of PMA. 427.1.86-SPPL2b knockdown cells were transfected with GFP vector alone (KD/GFP) or GFP vector and Flag-N55 (KD/GFP+N55) and GFP-positive cells were sorted using FACS. Using KD/GFP and KD/GFP+N55, we analyzed the direct effect of EICD.

value: SPPL2b KD

tag: passage

tag: treated with

value: SPPL2b siRNA and GFP vector/Flag-EICD


title: KD_GFP

value: SPPL2b siRNA and GFP vector


title: 29rN4


title: Arthritic mouse 2

city: Chicago

first: Tibor

middle: T

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

description: Gene expression after 10 days of 3rd PG-injection

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using Direct-Zol™ RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA) treated with Turbo™ DNase (ThermoFisher Scientific, Waltham, MA, USA) and purified with RNA Clean and Concentrator™-5 kit (Zymo).

treatment_protocol: BALB/c mice were immunized with human PG three times, and after the third treatment B cells were affinity purified from spleens collected from the sacrificed mice.

value: BALB/c

value: spleen

value: B cell

tag: gender

value: female


title: Non-arthritic mouse 3

description: Gene expression after 10 days of adjuvant-injection


title: RNA-seq_RSeT-D21_rep2

state: VIC


title: Arthritic mouse 3


title: Arthritic mouse 1


title: KD_PMA

value: SPPL2b siRNA and PMA


title: 29rN3

value: Resting CD4+ T cells

value: PMAionomycine for 16 hours under enfuvirtide


title: RNA-seq_RSeT-D21_rep1


title: Control rep2

value: wild type


title: VC_ttcA_24h

city: Boston

first: Satoshi

last: Kimura

state: Massachusetts

address: 181 Longwood Avenue

institute: Brigham and Women's Hospital

description: total tRNA

data_processing:
3’ linker sequences and one nucleotide at the 5’ end was trimmed
Bowtie v. 1.2.2 with default settings was used for mapping reads to reference tRNA sequences retrieved from tRNAdb (http://trnadb.bioinf.uni-leipzig.de/DataOutput/Search)
Two sequences in V. cholerae (tdbD00003706, tdbD00008082) and three sequences in E. coli (tdbD00007320, tdbD00010329, and tdbD00011810) were eliminated from the reference sequences due to extremely low coverage.
Mpileup files were made using the samtools mpileup command without any filtration (option, -A –ff 4 -x -B -q 0 -d 10000000 -f).
The frequency of misincorporation was calculated in each mpileup file. 5’ end termini of the mapped reads were piled up using the bedtools genomecov command (-d -5 -ibam).
To calculate the termination frequency, the number of 5’ termini at any given position was divided by the total number of mapped termini at the given position along with all upstream positions (5’ side).
genome build: Sequencing data of Vibrio cholerae and Escherichia coli are mapped to VCtRNA.fa and ECtRNAs.fa, respectively. These reference files are available at https://drive.google.com/open?id=1EsilghrGGcKp2cwND6Q1oPLk_cI2cWww
processed data files format and content: Tab-delimited text files containing frequencies of RT-signatures (misincorporation and termination) observed in tRNAs. Each row and column represents species and positions of tRNAs, respectively.

organism: Vibrio cholerae

extract_protocol:
Bacterial cells in a culture medium or cecal fluid were harvested by centrifugation. Total RNA was immediately extracted from cell pellets with Trizol according to the manufacture’s instruction.
The tRNA fraction was cut out from 10% TBE-Urea gels and recovered by isopropanol precipitation. tRNA fraction (250 ng) was deacylated in 500 ul of 100 mM Tris-HCl pH 9.0 at 37 °C for 1 hr and recovered by isopropanol precipitation. After dephosphorylation with alkaline phosphatase from calf intestine (New England Biolabs), tRNAs were ligated to 100 pmol of 5’ adenylated and 3’ end-blocked DNA oligo (3’ linker) using truncated T4 RNA ligase at 25 °C for 2.5 hr in 25% PEG 8000. The ligated product was purified on a 10 % TBE-Urea polyacrylamide gel (Thermo Fisher Scientific) as above. Half of the recovered ligated tRNAs were reverse transcribed with 5 pmol TGIRT-III (InGex) in 100 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 450 mM NaCl, 5 mM MgCl2, 5 mM DTT, 1 mM dNTPs, and 1.25 pmol primer (ocj485) at 60 °C for 1 hr. After the elimination of template RNAs by alkali treatment, cDNA was purified on a 10 % TBE-Urea polyacrylamide gel. The single stranded cDNA was then circularized using 50 U of CircLigase II(Epicenter) at 60 °C for 1 hr, followed by addition of another 50 U of CircLigase II for an additional 1 hr at 60 °C. cDNA was amplified using Phusion DNA polymerase (New England Biolabs) with o231 primer and index primers. After 12-18 rounds of PCR amplification, the product was gel purified from an 8 % TBE-Urea polyacrylamide gel (Thermo Fisher Scientific).

tag: growth phase

value: stationary phase

value: DttcA


title: VC_miaA_24h

description: total tRNA

value: DmiaA


title: Non-arthritic mouse 2


title: Non-arthritic mouse 1


title: 29rN2


title: RNA-seq_RSeT-D13_rep1

value: human fibroblasts


title: KD

value: SPPL2b siRNA and DMSO


title: VC_thiI_24h

description: total tRNA

value: DthiI


title: 29rN1


title: VC_trmK_24h

description: total tRNA

value: DtrmK


title: CONT_PMA

value: pSUPER vector and PMA


title: RNA-seq_RSeT-D13_rep2

value: reprogramming intermeidates or hiPSCs


title: 29rP3


title: 29rP1


title: RNA-seq_t2iLGoY-D13_rep2


title: VC_WT_CF_1

description: total tRNA

value: cecal fluid

value: WT


title: VC_WT_CF_2

description: total tRNA