title: Male main olfactory epithelium replicate 3

data_processing:
The sequencing reads were processed using the DolphinNext Single Cell-10X Genomics pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=420, default settings except STAR v2.6.1 was used for alignment).
The OR_deconvolution script (https://github.com/elisadonnard/ORdeconvolution) was used to correct mis-mapped olfactory receptor reads.
All the downstring analysis were processed with Seurat, the scripts can be found at https://github.com/Greerlab/OSN_2021_paper
Genome_build: mm10
Supplementary_files_format_and_content: Seruat object containing the raw and normalized count, cell type assignment, PCA, UMAP, clustering information.

source_name: Main olfactory epithelium

extract_protocol:
RNA was extracted with an RNeasy micro kit (QIAGEN).
Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) following the manufacturer’s guidelines
scRNA-seq

treatment_protocol: Mice were euthanized according to IACUC protocol, and then main olfactory epithelia were dissected and quickly immersed in ice-cold HBSS (Worthington). Olfactory epithelia were separated from the bone under a dissection microscope and then were minced into small pieces using forceps.  Each epithelium was then washed once with HBSS and resuspended in 2 ml of EBSS containing papain (20 U/mL, Worthington) and DNase I (2000 U/mL, Worthington). After 40 minutes of incubation with gentle agitation at 37°C, the suspension was washed with 5 ml of PBS + 0.02% BSA twice and passed through a 30 μm cell strainer (Miltenyi Biotec).

value: Main olfactory epithelium


title: control TERT WT mouse #4 physiological regeneration

status: Public on Jan 31 2022

type: SRA

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

library_source: transcriptomic

data_processing:
Paired-end sequencing (2x100bp) was performed by BGI Global services.
Quality of raw reads was assessed with FastQC. Clipping adaptor sequences were carried out using Trimmomatic and the trimmed reads were aligned to the mouse genome reference (mm10) downloaded from ENSEMBL using the STAR read aligner.
Differentially expressed genes (DEGs) were identified using the Bioconductor package DESeq2. DEGs were considered statistically significant at an adjusted p-value (Padj) < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: whole kidney

growth_protocol: All mice were treated in accordance with the Institutional Animal Care and Use Committee approved guidelines at the Université Côte d’Azur (UCA, Nice, France) (CIEPAL-AZUR Agreements NCE/2012-32, NCE/2015-237#05225.03, APAFIS#2590-2015102215087555v3, APAFIS#16319-2018071917443610v2, and APAFIS#15232-2018051116515863-M20210803)

extract_protocol:
Total RNA was extracted from whole kidney using RNeasy Micro Kit with DNase treatment (Qiagen, Ref# 74004). RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Only samples with RNA Integrity Number (RIN) >7 were further submitted to high throughput sequencing.
Libraries were prepared by BGI Global services.

treatment_protocol:
Mouse model of ADR-induced podocyte injury. A single dose of 12 mg/kg of Adriamycin (ADR, Doxorubicin Hydrochloride, Sigma, Ref# D1515) or saline (NaCl 0.9%) was injected in tail vein of 2-3 months old BALB/c mice or TERT knockout mice backcrossed for 10 generations with BALB/c mice (N10 BALB/c mice). For TERTKO/KO experiment, TERTWT/WT littermates were used as controls. For RNA-seq analysis, kidneys of TERTKO/KO and TERTWT/WT mice were collected 18 days after intravenous injection of ADR or saline (NaCl). All mice were weighed twice a week in the time course of the experiments, and urine was collected for each individual mouse twice a week. BALB/c mice were obtained from Janvier Lab (strain BALB/cJRj).
Transient TERTci overexpression in i-TERTci mice. Double transgenic i-TERTci mice encompass both actin-rtTA+ and tetOp-TERTci+ transgenes, allowing doxycycline-regulated and ubiquitous expression of TERTci in those mice. Those mice are maintained at a heterozygous status for each transgene. In order to induce TERTci overexpression in adult i-TERTci mice, doxycycline (2 mg/ml in 5% sucrose) (Doxycycline Hyclate, Sigma, Ref# D9891) was administered in drinking water in light-protected bottles and changed biweekly. The actin-rtTA+ control mice followed the same treatment than i-TERTci mice. High proteinuria levels (above 10mg/mL) were observed in i-TERTci mice at about 15 days of doxycycline treatment (D15). At that time point, the doxycycline treatment was stopped (R0), and both i-TERTci and actin-rtTA+ control mice entered a reversal period during which proteinuria gradually regressed in i-TERTci mice. Only residual proteinuria persisted after 15 to 30 days of reversal (R15-30). For RNA-seq analysis, kidneys of i-TERTci and actin-rtTA+ control mice were collected 8 days after doxycycline withdrawal (reversal day 8, R8). All mice were weighed twice a week in the time course of the experiments, and urine was collected for each individual mouse twice a week.

tag: strain

value: Balb/c background

tag: gender

value: Female

tag: treatment

value: IV injection NaCl at day 0

tag: age

value: 2 months

tag: genotype

value: TERT WT/WT


title: control TERT WT mouse #3 physiological regeneration


title: control TERT WT mouse #2 physiological regeneration


title: GFP_Control_Experiment_5 [LIB2_3]

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

description: processed data file: Library_2.xlsx

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Genome_build: hg19
Supplementary_files_format_and_content: Excel Spreadsheet containing raw counts for miRNA, including isoforms

organism: Homo sapiens

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_GFP_empty

growth_protocol: DMEM + 10% FBS

extract_protocol:
Total RNA, including microRNAs, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

treatment_protocol: Transfection by Lipofectamine 3000 of PCDNA 3.1 vectors containing indicated MDEs

tag: cell line

value: HeLa

tag: library

tag: experiment

tag: tdmd construct

tag: miRNA family

value: negative control

tag: time point

value: 72 hours after transfection of TDMD constuct

tag: molecule subtype

value: small RNA


title: Male main olfactory epithelium replicate 2

city: Worcester

first: I-Hao

last: Wang

state: MA

address: 370 Sunderland Rd, Unit D24

department: PMM

country: USA

institute: UMMS

molecule: polyA RNA

tag: tissue

value: wild type

value: male


title: control TERT WT mouse #1 physiological regeneration


title: experimental TERT WT mouse #3 physiological regeneration

value: IV injection adriamycin at day 0


title: Male main olfactory epithelium replicate 1


title: experimental TERT WT mouse #2 physiological regeneration


title: GFP_Control_rep1_Experiment_3 [LIB2_1]

description: processed data file: Library_2.xlsx


title: Female main olfactory epithelium replicate 3

value: female


title: TMEM_rep1_Experiment_4 [LIB2_8]

description: processed data file: Library_2.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_TMEM196


title: Scrambled_Control_rep1_Experiment_2 [LIB1_12]

description: processed data file: Library_1.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Scrambled_SERPINE_Control


title: Dd2_KO

city: Braga

first: Nuno

middle: S.

last: Osório

address: Campus de Gualtar

country: Portugal

institute: ICVS

data_processing:
Transcriptome datasets for both 3D7 and Dd2 were mapped against the 3D7 v3 (Böhme, U. et al., Wellcome Open Res., 2019) reference sequence using HISAT2 2-2.0.0-beta (Kim, D. et al., Nat.Biotechnol, 2019) (--rna-strandness RF --max-intronlen 5000).
Read counts were determined using HTSEQ v0.6.0 (Anders, S. et al., Oxf. Engl., 2015) (-r pos -s no). Deconvolution analysis was performed as described previously in Aunin, E. et al., PLOS Pathogens, 2020.
Differentially expressed genes were determined using edgeR (Robinson, M.D. et al.,  Bioinforma, 2010), with genes expressed at <=3 counts per million (cpm) excluded.
Because there were no biological replicates for any condition, we used the exact test with dispersion set to 0.01, as suggested for data concerning genetically identical model organisms (https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf).
We used a false discovery rate (FDR) cut off of 0.01 and a fold change cut off of 2 to call differentially expressed genes.
Genome_build: 3D7 v3 reference sequence (Böhme, U. et al., Wellcome Open Res., 2019)
Supplementary_files_format_and_content: Table with genes up or down in KO relative to WT  with FDR <= 0.01 and fold change > 2. Direction of up or downregulation, gene ID, false discovery rate (FDR), log counts per million (logCPM), log fold change (logFC), and gene description (Desc).

organism: Plasmodium falciparum Dd2

source_name: Red blood cells infected P. falciparum

growth_protocol: P. falciparum 3D7 and Dd2 strains (MRA-120 and MRA-156, MR4-Malaria Resources) were maintained at 4% hematocrit in RBCs with RPMI-1640 (Gibco) supplemented with 2 g/L sodium bicarbonate, 2 mM L-glutamine, 25 mM HEPES (Gibco), 25 µg/mL gentamycin (Gibco), 100 µM hypoxanthine (Sigma-Aldrich) and 0.25% (w/v) AlbuMAXII (Gibco) with daily medium changes. Parasites were maintained at 37 °C in an airtight environment with 3% O2, 5% CO2 and 92% of N2.

extract_protocol:
RNA was extracted from trophozoite stages, estimated between 28 to 32 hours old, using a RNeasy Mini Kit (Qiagen)
Libraries and sequencing were outsourced (Macrogen Inc), using TruSeq RNA Illumina Library v2 construction (nonstranded polyA enrichment) and HiSeq2500 Illumina 2x100bp 2Gb (20M pair-end reads) throughput-based sequencing.

treatment_protocol: Parasites were tightly synchronized with 5% sorbitol in intervals of 20 hours for 3 consecutive life cycles.

value: 28-32h after cycle initiation

value: knock-out of PfMRP1 transporter


title: Female main olfactory epithelium replicate 2


title: Main olfactory bulb replicate 1 slide 4

data_processing:
Library strategy: Slide-seq V2
The data processing were performed as previously described (PMID: 33288904)
All the downstring analysis were processed with Seurat, the scripts can be found at https://github.com/Greerlab/OSN_2021_paper
Genome_build: mm10
Supplementary_files_format_and_content: Seruat object containing the raw and normalized count, PCA, UMAP, spatial coordinates

source_name: Main olfactory bulb

extract_protocol: The extraction and library protocol were performed as previously described (PMID: 33288904)

treatment_protocol: Male mice were euthanized according to our IACUC protocol. The anterior part of the brain containing the olfactory bulb was dissected and placed in a plastic mold filled with OCT (Sakura Finetek from VWR), The molds were then frozen with dry ice pre-chilled 2-methylbutane (Fisher Scientific). The samples were incubated in -80°C overnight prior to cryosectioning. 20 OB sections were obtained with equal spacing (130 μm) along the anterior-posterior axis. In total, two sets of 20 slides were obtained from different animals.

value: Main olfactory bulb


title: experimental TERT WT mouse #1 physiological regeneration


title: Scrambled_Control_rep1_Experiment_1 [LIB1_11]

description: processed data file: Library_1.xlsx


title: control TERT KO mouse #3 physiological regeneration

value: TERT KO/KO


title: Female main olfactory epithelium replicate 1

value: Main olfactory epithelium


title: ZFYVE26_rep2_Experiment_2 [LIB1_10]

description: processed data file: Library_1.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_ZFYVE26


title: 296XXF

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

description: rRNA depleted

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (Agilent).
Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 6bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Reads were filtered based on the mapping status and only those reads that aligned normally (in the appropriate direction) were retained. Normalization was performed with the DESeq algorithm.
Transcripts with an average read count value >20 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue. Those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
Genome_build: mm10 (RefSeq Genes and Transcripts (2013.04.01))
Supplementary_files_format_and_content: matrix of all expressed genes (txt)

source_name: hippocampus

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Alabama at Birmingham (UAB) under protocol 21506. Four Core Genotypes mice on a C57Bl/6J background were obtained from the Jackson Laboratory where they were revitalized from frozen embryo stocks. Breeder pairs were set up with a XX female and a XY male. Pups were weaned into sex specific cages of 4-5 animals based on visual inspection of genitalia. Animals were maintained in an AAALAC approved UAB animal facility at 21°C on a 12/12 light/dark cycle (lights on at 6:00am). Animals were provided ad libitum water and standard mouse chow (NIH31) until time of tissue collection, ~12 months of age for both males and females. Euthanasia prior to tissue harvesting was carried out by cervical dislocation followed by rapid decapitation.

extract_protocol:
Hippocampi were dissected from XXF, XXM, XYF, and XYM FCG mice (n=5-6/group), snap frozen in microfuge tubes with liquid nitrogen, and stored at -80ºC prior to DNA isolation. Nucleic acids (DNA/RNA) were isolated from flash-frozen tissues using the All Prep DNA/RNA Mini Kit (Qiagen, Germantown, MD).
Illumina’s TruSeq Stranded mRNA Library Prep Kit (#20020594, Illumina) was used on 500 ng of total RNA for the preparation of strand-specific sequencing libraries according to manufacturer’s guidelines. As previously described, rRNA depletion was performed prior to library construction.

tag: animal number

tag: sex chromosome

value: XX

tag: gonad

value: ovaries

value: hippocampus


title: 295XYF

description: rRNA depleted

value: XY


title: LPS_circDYM3

city: Nanjing

first: Xiaoyu

last: Yu

state: Jiangsu

address: Dingjiaqiao 87

country: China

institute: Southeast univeristy

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of mouse was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the UCSC (http://genome.ucsc.edu/) C57BL_6NJ mouse reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: primary mouse microglia

growth_protocol: primary mouse microglia were obtained from brain of postnatal C57BL/6J mice (postnatal 1-2 d).

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012), and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq TM 6000 following the vendor's recommended protocol.

treatment_protocol: Cells were transfected with the circDYM lentivirus or circCon lentivirus.

value: brain

value: post natal day 2

tag: group

value: LPS + circDYM


title: control TERT KO mouse #1 physiological regeneration

tag: strain

value: Balb/c background

value: Female

value: IV injection NaCl at day 0

value: 2 months


title: ZFYVE26_rep1_Experiment_2 [LIB1_9]

description: processed data file: Library_1.xlsx

value: HeLa

value: 72 hours after transfection of TDMD constuct

value: small RNA


title: 292XYM

description: rRNA depleted

value: testes


title: GIGYF1_rep2_Experiment_1 [LIB1_7]

description: processed data file: Library_1.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_GIGYF1


title: LPS_circDYM1


title: experimental TERT KO mouse #3 physiological regeneration

tag: gender

value: IV injection adriamycin at day 0

value: TERT KO/KO


title: experimental TERT KO mouse #2 physiological regeneration

tag: treatment


title: LPS_circCon3

tag: age

value: LPS + circCon group


title: GIGYF1_rep3_Experiment_1 [LIB1_8]

description: processed data file: Library_1.xlsx


title: GFP_Control_rep1_Experiment_4 [LIB2_2]

description: processed data file: Library_2.xlsx

value: negative control


title: LPS_circCon2


title: SERPINE1_rep2_Experiment_1 [LIB1_5]

description: processed data file: Library_1.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_SERPINE1


title: experimental TERT KO mouse #1 physiological regeneration

tag: genotype


title: GIGYF1_rep1_Experiment_1 [LIB1_6]

description: processed data file: Library_1.xlsx

tag: cell line


title: experimental mouse #3 telomerase-induced regeneration

value: mixed background

value: doxycycline 15 days then reversed 8 days

value: actin-rtTA+;tetOp-TERTci+


title: LPS_circCon1

value: brain

value: post natal day 2


title: SERPINE1_rep1_Experiment_1 [LIB1_4]

description: processed data file: Library_1.xlsx

tag: library


title: Con_circDYM3

value: Con + circDYM


title: GFP_Control_rep1_Experiment_2 [LIB1_3]

description: processed data file: Library_1.xlsx

tag: experiment


title: experimental mouse #2 telomerase-induced regeneration

value: Female


title: Con_circDYM2


title: experimental mouse #1 telomerase-induced regeneration


title: Con_circDYM1


title: control mouse #4 telomerase-induced regeneration

value: actin-rtTA+


title: GFP_Control_rep1_Experiment_1 [LIB1_1]

description: processed data file: Library_1.xlsx

tag: tdmd construct


title: control mouse #3 telomerase-induced regeneration

value: 2 months


title: control TERT KO mouse #2 physiological regeneration

value: Balb/c background

value: IV injection NaCl at day 0


title: control mouse #2 telomerase-induced regeneration


title: Con_circCon2

value: Con + circCon


title: control mouse #1 telomerase-induced regeneration


title: Con_circCon1


title: LPS_circDYM2

value: LPS + circDYM


title: 645_DMSO rep3

status: Public on Jan 30 2022

city: PISA

first: antonino

last: cattaneo

address: piazza dei calieri, 7

institute: Scuola Normale Superiore

data_processing:
total RNA was quantified using Agilent 2100 Bioanalyzer Instrument (Agilent RNA 6000 Pico). Libraries were prepared from 1000 ng of input material using TruSeq Stranded mRNA (manufacturer's instructions) and subsequently quantified and quality checked using Agilent 2100 Bioanalyzer Instrument (DNA 7500 kit). Libraries were pooled and sequenced in one lane of HiSeq 2500 System running in 51 cycle/single-end/high output mode. Sequence information was converted to FASTQ format using bcl2fastq v1.8.4
Data were released as FASTQ files and then processed using Linux-based software tools. An initial quality check of the raw sequence data was performed using FASTQC. Trimming was performed with the cutadapt tool. Using the 3rd version (April 2011) S. cerevisiae genome as reference genome, the mapping procedure was carried out with the segemehl software. The number of mapped reads within the coding regions of each gene was calculated with the bamutils software tool (NGSutils suite).
The raw counts statistical analysis (i.e., PCA and hierarchical clustering), the differential expression analysis with the DESeq2 package, as well as the subsequent statistical analysis (i.e., MA plots and heatmaps), were all performed in R
Genome_build: Sacer3, 3rd version (April 211) S.cerevisiae genome
Supplementary_files_format_and_content: normalized abundance measurements, e.g., output from Deseq, complete data with values for all features

organism: Saccharomyces cerevisiae

source_name: strain: L40

extract_protocol:
An aliquot of the same samples, of the  five experimental conditions described above, used for yeast protein extract was used for total RNA isolation. Briefly, after the one hour of growth, the yeast cultures were centrifuged (5 min at 3000 rpm) and the RNA extraction was performed using the Yeast Ribopure® kit (Ambion, Invitrogen #AM1926), following manufacturer instructions.  The integrity of RNA was assessed by agarose electrophoresis.  The fifteen RNA samples have been delivered to the Leibniz Institute on Aging (FLI) in Jena where library preparation and sequencing steps have been performe
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype of host strain

value: mat-a his{delta}200trp1-901 leu2-3,112 ade2 LYS2::(lexAop)4-  HIS3 URA3::(lexAop)8-lacZ Gal4

value: Transformed with pL220-scFv645. Growth in SD-L medium


title: 645_DMSO rep2


title: 58F_DMSO rep1

value: Transformed with pL220-ScFv58F and  Growth in SD-L medium


title: 58F_DMSO rep2


title: 58F_DMSO rep3


title: 645_DMSO rep1


title: pL220_CPTH2 rep3

value: GROWTH with  CPTH2 (400 µM) in SD-L media for 1 hour


title: pL220_CPTH2 rep1


title: pL220_CUR rep3

value: with  Curcumin (200 µM)  in SD-L media for 1 hour


title: pL220_CPTH2 rep2


title: pL220_CUR rep2


title: pL220_DMSO rep2

value: Transformed with pL220 empty vector solely. Growth in SD-L medium


title: pL220_CUR rep1


title: pL220_DMSO rep3


title: pL220_DMSO rep1


title: GFP_Control_rep2_Experiment_1 [LIB1_2]

description: processed data file: Library_1.xlsx

value: HeLa

tag: miRNA family

value: negative control

tag: time point

value: 72 hours after transfection of TDMD constuct

value: small RNA


title: tsRNA glh-1K391A rep1

first: Siyuan

last: Dai

address: 368 Plantation St.

department: RTI

institute: UMass Chan Medical School

data_processing:
cutadapt, trim 3' linkers
Bowtie2, mapping to C. elegans genome and transcriptome
Python, extract information from SAM files to csv files
WBcel235
Genome_build: WS262

organism: Caenorhabditis elegans

source_name: C. elegans yound adults

growth_protocol: C. elegans were grown on NGM plates with OP50 E. coli

extract_protocol:
Total RNAs were Trizol and isopropanol precipitation, small RNAs were enriched using mirVana miRNA isolation kit.
Purified small-RNAs were pre-treated with PIR-1 and ligated with 3' and 5' linkers. cDNA were generated by reverse transcribed and further amplified by PCR. A size selection procedure on native PAGE were carried out.

treatment_protocol: glh-1 DQAD worms were treated with auxin and taken away from it

value: untreated


title: tsRNA glh-1K391A rep2


title: tsRNA glh-1DQAD rep2

value: cultured with 500mM IAA and remove from auxin


title: tsRNA glh-1DQAD rep1


title: tsRNA glh-1null rep1


title: tsRNA WT rep2

value: wild-type


title: tsRNA glh-1null rep2


title: tsRNA WT rep1


title: Con_circCon3

tag: tissue

value: brain

value: post natal day 2


title: Cardiac NCCs, KO

city: New Haven

first: Arya

last: Mani

state: CT

address: 300 George Street

department: Internal Medicine

institute: Yale University

data_processing:
Basecalls performed by CellRanger software v 1.3.1
Reads were aligned to the mm10 genome assembly and unique molecular identifiers were quantified using CellRanger software v 1.3.1
Cells with less than that 200 and more than 6000 raw unique molecular identifiers (UMI) were removed. Genes expressed in fewer than 3 cells were removed. Cells that expressed fewer than 200 genes were removed. Mitochondrial and ribosomal genes were removed.
Counts in each cell were normalized to their library size. Normalized counts were then square-root transformed.
Batch effect correction using Scanpy’s (version 1.4.6) approximate batch-balanced kNN graph for manifold learning.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts in each sample for every gene and every cell

source_name: E9.5 embryos from the mid otic placode to the posterior edge of the 4th somite

growth_protocol: E9.5 embryos

extract_protocol:
E9.5 embryos were harvested and briefly placed ion ice-cold DPBS and then placed on a plastic petri dish resting on ice. Using insulin needles, the cardiac neural crest is dissected out from the mid otic placode to the posterior edge of the 4th somite. The tissues were removed and placed in a 1.5mL conical snap cap plastic tube on ice and 1x enzyme digestion buffer containing 100 μL of B. licheniformis stock (100mg/ml, Sigma P5380), 895 μL of DPBS and 5 μL of 0.5 M EDTA was added. The tube was quickly shaken thoroughly to mix and resuspend, incubated in ice water bath, and triturated using a cut-down 1ml pipet tip for 15s every 2 min. Cells were filtered through a 40 μm strainer, rinsed with 10 mL of ice-cold PBS/BSA, weighed and subsequently 300 g of the cells were transferred to 15 mL conical tube and centrifuged at 300X for 5 min at 4°C and the supernatant was discarded. The pelleted cells were then resuspended in 100 μL of ice-cold DPBS and counted on a Countess II (ThermoFisher Scientific). Cell count and viability was determined using trypan blue dye exclusion
10X Single Cell 3' v3 lib prep protocol
ScRNA-Seq

treatment_protocol: no treatment

value: Prdm6f/f; Wnt1-Cre2; ZsGreen1

tag: cell type

value: Cardiac neural crest cells (CNCCs)


title: NKO mice_CUT&Tag_NKO_Ab

city: Beijing

first: Qing-Feng

last: Wu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

data_processing:
library strategy: CUT&RUN
CellRanger Mkfatsq/Count Analysis
For scRNA-seq or snRNA-seq, the matrix files arising from different batches of experiments were subsequently integrated and analyzed using Seurat v3 software. For quality control, cells or nuclei with more than 10% mitochondrial gene counts were removed. In addition, cells with less than 600 genes or 500 UMIs were filtered out from the analysis, while nuclei were filtered on the basis of gene detection between 800 and 8,000.
CUT&Tag data were mapped to mouse (mm9) reference genome using Bowtie2 software. Only paired-end reads with both ends mapped correctly were kept for further analysis. All multimapped reads were removed using SAMtools for further analysis and duplicate reads were removed using Sambamba software. Peak calling was performed using peak calling algorithm MACS2.
Genome_build: mm10 for RNA-seq, mm9 for CUT&Tag
Supplementary_files_format_and_content: Lineage tracing experiment: A_TA lineage tracing_total cells_9224.rds; Tbx3 knockout experiment: B_NKO mice scRNA-seq_total cells_45406.rds, C_NKO mice snRNA-seq_neurons_50872.rds. RDS files are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with `readRDS(“A_TA lineage tracing_total cells_9224.rds”)`. It contains the gene counts, sample metadata, and feature metadata for single cell / nucleus that passed quality control.
Supplementary_files_format_and_content: CUT&Tag experiment: D_02_89-Ab-WT_peak_summits.motif.bed, D_03_89-Ab-WT_peak_summits.motif.bed. BED is used to save genomic data and linked annotations in a text format. BED files can be read and modified using bedtools, Integrative Genomics Viewer (IGV) and UCSC genome browser.

source_name: Hypothalamus

extract_protocol:
Lineage tracing experiment: Hypothalamus were dissected from Tbx3-CreER::Ai14 mice (E9 > P12). Then Tbx3-derived cells were isolated by FACS and sequenced by scRNA-seq. Tbx3 knockout experiment: Tuberal and mammillary zones of hypothalamus were dissected from NKO mice and its littermate control. Then tissue were dissociated into single cell for scRNA-seq, or were ground to power to extract the nuclei for snRNA-seq. CUT&Tag experiment: Hypothalamus were dissected from NKO mice and its littermate control and ground to power to extract the nuclei for CUT&Tag.
We took advantage of DNBSEQTM technology platforms (BGI Genomics, China) and DNBelab C4 Single-Cell Library Prep Set (MGI, #1000021082) for single-nucleus RNA library preparation. And we followed the manufacturer’s recommendations for the 10x Genomics 3’ Gene Expression v3 chemistry to prepare single-cell RNA library. For CUT&Tag library, DNA samples were processed with TruePrep DNA Library Prep kit (Vazyme; #TD501-01) according to manufacturer’s instructions.

tag: strain background

value: Brain

value: Postnatal day 0

value: NKO

value: Hypothalamus

tag: antibody

value: Tbx3 (Abcam, ab154828)


title: Cardiac NCCs, WT

value: Prdm6+/+; Wnt1-Cre2; ZsGreen1


title: NKO mice_CUT&Tag_WT_input

value: Wildtype

value: Normal Rabbit IgG Control (R&D SYSTEMS, AB-105-C)


title: NKO mice_CUT&Tag_WT_Ab rep1


title: NKO mice_CUT&Tag_WT_Ab rep2


title: scRNA-seq of Homo sapiens: 368-20 d201 lymph node ELAB-WU368-20-20_FNA_d201_GEX_2

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

data_processing:
Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v6.0.1
Single cell feature counts for multiple libraries were pooled by subsampling to the same effective sequencing depth using `cellranger aggr` from Cell Ranger v6.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary_files_format_and_content: features.tsv.gz contains feature information that corresponds to the row index of matrix.mtx.gz
Supplementary_files_format_and_content: barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz. The trailing dash and number (e.g. -12) indicate the sample from which the cell originated and correspond to the row number for that sample in aggregation.csv.
Supplementary_files_format_and_content: aggregation.csv contains sample information. The order of the samples represented as rows in aggregation.csv corresponds to the numbers after the dash (e.g. -12) in barcodes.tsv.gz.

source_name: lymph node

extract_protocol:
PBMCs were isolated from blood. Fine-needle aspiration was performed on draining ipsilateral axillary lymph nodes.
Libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 5' gene expression workflow

value: lymph node

tag: isolate

tag: lymph node number

tag: biological replicate

value: various


title: NKO mice_scRNA-seq_NKO rep1

data_processing:
CellRanger Mkfatsq/Count Analysis
For scRNA-seq or snRNA-seq, the matrix files arising from different batches of experiments were subsequently integrated and analyzed using Seurat v3 software. For quality control, cells or nuclei with more than 10% mitochondrial gene counts were removed. In addition, cells with less than 600 genes or 500 UMIs were filtered out from the analysis, while nuclei were filtered on the basis of gene detection between 800 and 8,000.
CUT&Tag data were mapped to mouse (mm9) reference genome using Bowtie2 software. Only paired-end reads with both ends mapped correctly were kept for further analysis. All multimapped reads were removed using SAMtools for further analysis and duplicate reads were removed using Sambamba software. Peak calling was performed using peak calling algorithm MACS2.
Genome_build: mm10 for RNA-seq, mm9 for CUT&Tag
Supplementary_files_format_and_content: Lineage tracing experiment: A_TA lineage tracing_total cells_9224.rds; Tbx3 knockout experiment: B_NKO mice scRNA-seq_total cells_45406.rds, C_NKO mice snRNA-seq_neurons_50872.rds. RDS files are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with `readRDS(“A_TA lineage tracing_total cells_9224.rds”)`. It contains the gene counts, sample metadata, and feature metadata for single cell / nucleus that passed quality control.
Supplementary_files_format_and_content: CUT&Tag experiment: D_02_89-Ab-WT_peak_summits.motif.bed, D_03_89-Ab-WT_peak_summits.motif.bed. BED is used to save genomic data and linked annotations in a text format. BED files can be read and modified using bedtools, Integrative Genomics Viewer (IGV) and UCSC genome browser.

source_name: Hypothalamus (Tuberal and Mammillary zones)

value: Postnatal day 14


title: NKO mice_scRNA-seq_NKO rep2

description: B_NKO mice scRNA-seq_total cells_45406.rds

value: Hypothalamus (Tuberal and Mammillary zones)


title: scRNA-seq of Homo sapiens: 368-20 d201 lymph node ELAB-WU368-20-20_FNA_d201_GEX_1


title: NKO mice_scRNA-seq_WT rep1


title: NKO mice_scRNA-seq_WT rep2


title: D3_mRNA_LC

city: Stanford

first: Madeleine

last: Scott

state: CA

address: 729 Lagunita Dr

institute: Stanford

description: mRNA

data_processing:
Cellranger 3.1.0
Seurat 3.6.3 used for all downstream processing
Genome_build: mm10
Supplementary_files_format_and_content: gene expression matrices (mtx)
Supplementary_files_format_and_content: raw counts for genes
Supplementary_files_format_and_content: cell barcodes
Supplementary_files_format_and_content: gene names
Supplementary_files_format_and_content: phenotypic information for all cells

extract_protocol:
Lymph node harvest and single-cell suspension at baseline or 1, 3, or 7 days after treatment with yellow fever vaccine  or the mRNA covid vaccine
10x Single Cell 3' v3

tag: strain

tag: day

tag: agent

value: Pfizer BioNTech mRNA COVID vaccine (mRNA)

value: LC


title: D7_mRNA_LC

description: mRNA


title: HepaRG cells pre-treated with nVE and OA [nVE_OA 3]

type: RNA

city: Sansepolcro

first: Jacopo

last: Lucci

state: Arezzo

address: Loc. Aboca, 20

institute: Bios-Therapy, Physiological Systems For Health S.p.A

hyb_protocol: Fragmented and labeled cDNA was prepared according to the manufacturer's instructions and hybridized to a Human Clariom Go Screen 384-array plate for 17 h at 45°C on a GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific). Arrays were washed and stained on a GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Arrays were scanned using the GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific). Affymetrix GeneChip Command Console Software (AGCC, ThermoFisher Scientific) was used for GeneTitan MC Instrument control.

data_processing: Data analysis were performed using Transcriptomic Analysis Console Software (TAC, ThermoFisher Scientific) that provides quality control analysis, performs normalization and summarization, based on the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) analysis algorithm, and provides a list of differentially expressed genes (Limma Bioconductor package, pvalue<0,05) from the biological duplicates for WGO-VE_OA or triplicates of the other condition.

label: biotin

source_name: Treated with William E complete medium with oleic acid [200 µM]+ naturally occurring RRR-α-Tocopherol [25nM]

label_protocol: Biotinylated cRNA was prepared according to the standard ThermoFisher Scientific protocol from 6 ug total RNA (GeneChip™ 3’ IVT Pico Kit Manual Workflow).

growth_protocol: Cells were seeded at a density of 10,000 cells/well and kept at 37˚C in a humidified 5% CO2 cell culture incubator.

extract_protocol: Total RNA was extracted from cells lysates using an QIAsymphony RNA Kit (Qiagen,) with the QIAsymphony SP instrument (Qiagen) according to the manufacturer's instructions.

treatment_protocol: At 70% confluence, HepaRG cells were incubated for 24 hrs with either the vehicle or the three different sources of Vitamin E at final concentration of α-Tocopherol in the colture medium of 25 nM. Subsequently HepaRG were incubated with OA at  the final concentration in the colture medium of 200 µM. Cell treatments with this OA lasted for 48 hrs.

tag: cell line

value: hepatic cell line

value: Immortalized hepatic cell line terminally differentiated

tag: age

value: Adult

tag: treatment

value: pre-treated with nVE and OA


title: HepaRG cells pre-treated with nVE and OA [nVE_OA 2]


title: HepaRG cells treated with sVE and OA [sVE_OA 3]

source_name: Treated with William E complete medium with oleic acid [200 µM]+ synthetic all-rac-α-Tocopherol [25nM]

value: treated with sVE and OA


title: HepaRG cells pre-treated with nVE and OA [nVE_OA 1 ]


title: scRNA-seq of Homo sapiens: 368-10 d201 lymph node ELAB-WU368-10-2-10-2_FNA_d201_GEX_1


title: HepaRG cells pre-treated with WGO-VE and  with OA [WGO-VE_OA 1]

source_name: Treated with William E complete medium with oleic acid [200 µM]+ wheat germ oil (at final concentration of α-Tocopherol in the colture medium of 25 nM)

value: pre-treated with WGO-VE and  with OA


title: HepaRG cells pre-treated with WGO-VE and  with OA [WGO-VE_OA 2]


title: HepaRG cells untreated  [DMSO 3]

source_name: Treated with William’s E complete medium with DMSO [0.001%]

value: untreated


title: HepaRG cells treated with sVE and OA [sVE_OA 2]


title: HepaRG cells treated only with oleic acid [OA 1]

source_name: Treated with William E complete medium with oleic acid [200 µM]

value: treated only with oleic acid


title: HepaRG cells treated only with oleic acid [OA 2]


title: HepaRG cells untreated  [DMSO 2]


title: HepaRG cells treated with sVE and OA [sVE_OA 1]


title: HepaRG cells untreated  [DMSO 1]


title: D1_mRNA_LC

description: mRNA


title: scRNA-seq of Homo sapiens: 368-07 d201 lymph node ELAB-WU368-07-07_FNA_d201_GEX_2


title: D7_naive_LC

description: naive

value: naive


title: scRNA-seq of Homo sapiens: 368-10 d201 lymph node ELAB-WU368-10-1-10-1_FNA_d201_GEX_1


title: D3_naive_LC

description: naive


title: HepaRG cells treated only with oleic acid [OA 3]


title: scRNA-seq of Homo sapiens: 368-07 d201 lymph node ELAB-WU368-07-07_FNA_d201_GEX_1


title: D1_naive_LC

description: naive


title: scRNA-seq of Homo sapiens: 368-01a d201 lymph node ELAB-WU368-01-01_FNA_d201_GEX_2


title: D3_YFV_LN

description: YFV

value: yellow fever vaccine (YFV)

value: LN


title: D7_YFV_LN

description: YFV


title: D1_YFV_LN

description: YFV


title: scRNA-seq of Homo sapiens: 368-10 d110 lymph node ELAB-WU368-10-2-10-2_FNA_d110_GEX_2

value: lymph node


title: scRNA-seq of Homo sapiens: 368-10 d110 lymph node ELAB-WU368-10-2-10-2_FNA_d110_GEX_1

value: various


title: scRNA-seq of Homo sapiens: 368-01a d201 lymph node ELAB-WU368-01-01_FNA_d201_GEX_1


title: scRNA-seq of Homo sapiens: 368-10 d201 lymph node ELAB-WU368-10-2-10-2_FNA_d201_GEX_2


title: D7_naive_LN

description: naive


title: D3_naive_LN

description: naive


title: scRNA-seq of Homo sapiens: 368-10 d60 lymph node ELAB-WU368-10-2-10-2_FNA_d60_GEX_1


title: D1_naive_LN

description: naive


title: scRNA-seq of Homo sapiens: 368-10 d110 lymph node ELAB-WU368-10-1-10-1_FNA_d110_GEX_2


title: Org_M_3

city: Seoul

first: Suran

last: Kim

address: Yonsei-ro 50

department: Department of Biotechnology

country: South Korea

institute: Yonsei University

data_processing:
For data processing, base calling software bcl2fastq2 (Version 2.20) with ASCII Q-score (offset 33) were used.
Reads for each sample were mapped to the reference genome by Tophat(v2.0.13). The aligned results were added to Cuffdiff(v2.2.1) to report differentially expressed genes.
Differentially expressed genes were selected with the following parameters: fold change > 2, p value < 0.05, and FDR < 0.1.
Functional annotation for gene ontology enrichment analysis was conducted based on the DAVID program (https://david.ncifcrf.gov).
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited excel file contains the FPKM values for each sample.
Supplementary_files_format_and_content: The lists of differentially expressed genes and ontology data are also included in tab-delimited excel files.

source_name: gastric organoids grown in Matrigel

growth_protocol: gastric organoid and intestinal organoids cultured in the same basal medium, which was composed of advanced DMEM/F12 (Dulbeccos Modified Eagle Medium/Hams F-12) supplemented with 10 mM HEPES (N-2-hydroxyethylpiperazine-N-2-ethane sulfonic acid), 2 mM GlutaMax, and 100 U/ml P/S (all from Thermo Fisher Scientific). Mouse gastric organoid culture medium was composed of the basal medium supplemented with 50% (v/v) Wnt3a-conditioned medium, 10% (v/v) R-spondin1-conditioned medium, 1× B27 (Thermo Fisher Scientific), 100 ng ml-1 mouse Noggin (Peprotech, Rocky Hill, NJ, USA), 100 ng ml-1 human fibroblast growth factor-10 (FGF10, Peprotech), 50 ng ml-1 mouse epidermal growth factor (EGF, Thermo Fisher Scientific), 10 nM [Leu15]-Gastrin I (Sigma), 1 mM N-acetyl cysteine (Sigma), and 10 nM Y-27632 (initial 3 days only; BioGems International, Inc., Westlake Village, CA, USA). Mouse intestinal organoid culture medium was composed of the basal medium supplemented with 10% (v/v) R-spondin1-conditioned medium, 1× N2 (Thermo Fisher Scientific), 1× B27 (Thermo Fisher Scientific), 100 ng ml-1 mouse Noggin (Peprotech), 50 ng ml-1 mouse EGF (Thermo Fisher Scientific), 1 mM N‐acetyl cysteine (Sigma), and 10 nM Y-27632 (initial 2 days only; BioGems International, Inc.).

extract_protocol:
RNA samples were extracted from organoids and tissues using the TaKaRa MiniBEST Universal RNA Extraction Kit (TaKaRa).
The Novaseq 6000 platform was used for sequencing, and the Illumina Truseq stranded mRNA kit (Illumina, San Diego, CA, USA) was used to prepare the sequencing libraries.

value: gastric organoids


title: Org_M_2


title: Asthma_rep4 [X15]

city: Shanghai

first: Shiyuan

state: Shanghai

address: 12 Middle Urumqi Road

department: Department of Integrative Medicine

institute: Huashan Hospital, Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using TopHat(version:2.0.9).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample ...

source_name: Peripheral whole blood

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: patient with asthma

tag: Sex

value: Female

tag: bmi

value: Peripheral whole blood


title: Org_M_1


title: scRNA-seq of Homo sapiens: 368-10 d60 lymph node ELAB-WU368-10-1-10-1_FNA_d60_GEX_2

tag: time point


title: scRNA-seq of Homo sapiens: 368-10 d110 lymph node ELAB-WU368-10-1-10-1_FNA_d110_GEX_1

tag: tissue


title: Asthma_rep2 [X12]


title: Asthma_rep3 [X13]

value: Male


title: Asthma_rep1 [X5]


title: Healthy_rep3 [X45]

value: healthy


title: Org_D_3

source_name: gastric organoids grown in decellularized gastric ECM hydrogel

tag: cell type


title: scRNA-seq of Homo sapiens: 368-10 d60 lymph node ELAB-WU368-10-1-10-1_FNA_d60_GEX_1


title: scRNA-seq of Homo sapiens: 368-02a d60 lymph node ELAB-WU368-02-2-02-2_FNA_d60_GEX_2


title: Org_D_2


title: Healthy_rep2 [X42]


title: Healthy_rep1 [X7]


title: scRNA-seq of Homo sapiens: 368-02a d60 lymph node ELAB-WU368-02-2-02-2_FNA_d60_GEX_1


title: Org_D_1


title: Pat29-A

city: GOYANG

first: JIHYUN

last: KIM

address: 323 ILSAN-RO

institute: National cancer center

data_processing:
Single-cell RNA sequencing data were quantified using the 10X software package cellranger to map sequencing data to version 1.2.0 of the build of the hg19 reference genome supplied by 10X Genomics
Gene count matrix was generated from unique molecular identifiers (UMIs) that produced from cellranger count.
We filtered out cells that if any cells meet one of the following thresholds: 1) cells that lower variation than average variation with all genes; 2) cells that have zero UMI count 90% of all genes; 3) cells that greater than 10% expression originating from mitochondrial or hemoglobin genes; 4) cells that have UMIs lower than 100 or larger than 20000.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI count values for each Sample

source_name: Control

extract_protocol:
Human stomach tissues were cut into approximately 1 mm3 pieces and add the 5 ml of dispase in Hanks’ Balanced Salt Solution (STEMCELL Cat# 07913) and 5 mg collagenase type IV (Sigma Cat# C5138) and incubate at 37 °C for 2 h with gently shaking. After the sample was passed through a 100 m cell strainer (Falcon), the suspended cells in PBS (with1 mM EDTA) were centrifuged at 720 g for 5 min. To remove RBC in the sample, cell pellets were re-suspended PBS (with1 mM EDTA) and centrifuged through a discontinuous 50% Percoll® (Sigma Cat# P4937) gradient, at 470 g for 20 min, with minimum acceleration and no deceleration. The sample between layers PBS and 50% Percoll® was collected re-suspended in PBS for scRNA-seq.
10x signle cell 3' v2 kit
scRNA-seq

value: normal stomach


title: Pat28-A


title: scRNA-seq of Homo sapiens: 368-02a d35 lymph node ELAB-WU368-02-2-02-2_FNA_d35_GEX_2


title: Pat26-A


title: Adult_T_3

source_name: gastric tissue

value: gastric tissue


title: Pat27-A


title: Adult_T_2


title: scRNA-seq of Homo sapiens: 368-02a d35 lymph node ELAB-WU368-02-2-02-2_FNA_d35_GEX_1


title: scRNA-seq of Homo sapiens: 368-02a d60 lymph node ELAB-WU368-02-1-02-1_FNA_d60_GEX_2


title: scRNA-seq of Homo sapiens: 368-10 d60 lymph node ELAB-WU368-10-2-10-2_FNA_d60_GEX_2


title: Pat25-A


title: scRNA-seq of Homo sapiens: 368-02a d35 lymph node ELAB-WU368-02-1-02-1_FNA_d35_GEX_1


title: M_or_3

source_name: small intestinal organoids grown in Matrigel

value: small intestinal organoids


title: Adult_T_1


title: scRNA-seq of Homo sapiens: 368-13 d110 lymph node ELAB-WU368-13-13_FNA_d110_GEX_1


title: D_or_3

source_name: small intestinal organoids grown in decellularized intestinal ECM hydrogel


title: scRNA-seq of Homo sapiens: 368-02a d35 lymph node ELAB-WU368-02-1-02-1_FNA_d35_GEX_2


title: scRNA-seq of Homo sapiens: 368-13 d60 lymph node ELAB-WU368-13-13_FNA_d60_GEX_1


title: scRNA-seq of Homo sapiens: 368-07 d110 lymph node ELAB-WU368-07-07_FNA_d110_GEX_2


title: D_or_1


title: M_or_1


title: T_ad_3

source_name: small intestinal tissue

value: small intestinal tissue


title: T_ad_2


title: scRNA-seq of Homo sapiens: 368-07 d110 lymph node ELAB-WU368-07-07_FNA_d110_GEX_1


title: scRNA-seq of Homo sapiens: 368-07 d60 lymph node ELAB-WU368-07-07_FNA_d60_GEX_2


title: T_ad_1


title: scRNA-seq of Homo sapiens: 368-07 d60 lymph node ELAB-WU368-07-07_FNA_d60_GEX_1


title: scRNA-seq of Homo sapiens: 368-20 d110 lymph node ELAB-WU368-20-20_2FNA_d110_GEX_2


title: GA Muscle 231 EV5 [EV231_5]

city: La Jolla

first: Shizhen

address: 9500 Gilman Dr

institute: UCSD

data_processing:
RNA-seq and data processing were performed by Novogene Co., Ltd. Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene's wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet including FPKM values or raw gene counts for each sample

source_name: GA Muscle 231 EV

growth_protocol: Female NOD scid gamma (NSG) mice were maintained in a standard mouse facility in sterile conditions.

extract_protocol:
Homogenized GA tissue (~20 mg) was used to extract RNA by using 1 ml of Trizol reagent (Invitrogen). The RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Co., Ltd.
mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer.

treatment_protocol: Mice received tail-vein injections of EVs twice a week for 5 weeks (~10 ug EV per injection). Two days after the last injection, GA muscle was collected for immediate RNA extraction.

value: NSG

tag: genotype

value: Wild Type

value: week 12

value: MDA-MB-231 EV

value: gastrocnemius (GA) muscle


title: GA Muscle 231 EV4 [EV231_4]


title: scRNA-seq of Homo sapiens: 368-20 d110 lymph node ELAB-WU368-20-20_2FNA_d110_GEX_1

value: lymph node


title: scRNA-seq of Homo sapiens: 368-20 d60 lymph node ELAB-WU368-20-20_2FNA_d60_GEX_2

value: various


title: scRNA-seq of Homo sapiens: 368-20 d60 lymph node ELAB-WU368-20-20_2FNA_d60_GEX_1


title: GA Muscle 231 EV2 [EV231_2]


title: GA Muscle 231 EV1 [EV231_1]


title: GA Muscle 231 EV3 [EV231_3]


title: GA Muscle 10A EV3 [BABEVms3]

source_name: GA Muscle 10A EV

value: MCF-10A EV


title: scRNA-seq of Homo sapiens: 368-04 d60 lymph node ELAB-WU368-04-04_FNA_d60_GEX_1

source_name: lymph node


title: GA Muscle 10A EV4 [BABEVms4]


title: M_or_2


title: scRNA-seq of Homo sapiens: 368-02a d60 lymph node ELAB-WU368-02-1-02-1_FNA_d60_GEX_1


title: scRNA-seq of Homo sapiens: 368-04 d28 lymph node ELAB-WU368-04-04_FNA_d28_GEX_2


title: GA Muscle 10A EV2 [BABEVms2]


title: GA Muscle 10A EV1 [BABEVms1]


title: scRNA-seq of Homo sapiens: 368-22 d110 lymph node ELAB-WU368-22-22_FNA_d110_GEX_2


title: D_or_2


title: scRNA-seq of Homo sapiens: 368-13 d60 lymph node ELAB-WU368-13-13_FNA_d60_GEX_2


title: scRNA-seq of Homo sapiens: 368-22 d110 lymph node ELAB-WU368-22-22_FNA_d110_GEX_1


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_72hpi_rep4

city: Sydney

first: Jonathan

middle: Michael

last: Plett

state: New South Wales

address: 50 Bourke street

department: Soil Biology and Genomics

country: Australia

institute: Western Sydney University

description: Cicer arietinum variety 'Sonali' and Phytophthora medicaginis isolate 7831

data_processing:
Raw RNA-sequencing reads were trimmed with default parameters, and then aligned to the primary transcripts of the Cicer arietinum Desi genome (Jain et al., 2013) using CLC Genomics Workbench 10. For the alignment, the minimum length fraction was set to 0.9, the minimum similarity fraction 0.9 and the maximum number of hits per read was 10 while all other parameters were set to default.
Total gene reads were calculated using CLC Genomics Workbench 10.
Genome_build: Cicer arietinum Desi genome primary transcripts (Jain, M., Misra, G., Patel, R. K., Priya, P., Jhanwar, S., Khan, A. W., Shah, N., Singh, V. K., Garg, R., Jeena, G., Yadav, M., Kant, C., Sharma, P., Yadav, G., Bhatia, S., Tyagi, A. K. & Chattopadhyay, D. 2013. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). The Plant Journal, 74, 715-729.)
Supplementary_files_format_and_content: Matrix table of the raw gene counts for every Cicer arietinum gene and every sample

organism:
Cicer arietinum
Phytophthora medicaginis

source_name: Cicer arietinum roots inoculated with Phytophthora medicaginis mycellium

growth_protocol: Chickpea var. 'Sonali' seeds were surface sterilised (4% NaOCl solution for 15 min, 70% EtOH for ten minutes and sterile ddH2O rinse three times) before sowing on modified full strength Murashige and Skoog agar plates (4.4% MS; 3% CaCO3, pH 7, 1.1% bacto agar) supplemented with Gamborg’s vitamins. Seedlings were grown in controlled growth chambers with 15 h light/ 9 h dark cycle at 18˚C, 70% relative humidity and 500 μmol m-2 s-1 light intensity. Fifteen-day old seedlings were used for inoculation. P. medicaginis isolate TR7831 was maintained on V8 juice agar plates (containing 200 mL L-1 V8TM bottled juice; 3.0 g L-1 CaCO3, 15.0 g L-1 agar) supplemented with ampicillin (100 μg mL-1) at 25˚C in the dark. Prior to inoculations, P. medicaginis was passaged through the host to ensure pathogenicity, and after reisolating on V8 juice agar plates supplemented with ampicillin (100 ug mL-1), the 2rd generation of P. medicaginis was used to prepare inoculum. P. medicaginis inoculum (3rd generation) was prepared one day before inoculations by aseptically transferring mycelial agar blocks taken from the edge of an actively growing culture onto 0.5 x 0.5 mm2 sterile membranes overlaid on V8 juice agar plates.

extract_protocol:
Root samples flash frozen with liquen nitrogen; RNA was extracted using the Bioline Plant II RNA extraction kit according to the manufacturer’s guidelines.
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration

treatment_protocol: Roots were inoculated with P. medicaginis mycellial agar blocks 1 cm from the root tip and harvested at 12, 24 and 72 hpi. P. medicaginis axenically growing on V8 juice media were transferred to full strength MS media for 12 hours before harvesting mycellium.

value: Root and mycellium

value: 72 hours post inoculation

tag: diseased state

value: diseased


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_72hpi_rep3


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_72hpi_rep2


title: scRNA-seq of Homo sapiens: 368-22 d60 lymph node ELAB-WU368-22-22_FNA_d60_GEX_2

tag: isolate


title: scRNA-seq of Homo sapiens: 368-22 d60 lymph node ELAB-WU368-22-22_FNA_d60_GEX_1

tag: lymph node number


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_72hpi_rep1


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_24hpi_rep3

value: 24 hours post inoculation

value: Onset of disease


title: scRNA-seq of Homo sapiens: 368-01a d60 lymph node ELAB-WU368-01-01_FNA_d60_GEX_2

tag: biological replicate


title: scRNA-seq of Homo sapiens: 368-01a d110 lymph node ELAB-WU368-01-01_FNA_d110_GEX_2


title: scRNA-seq of Homo sapiens: 368-01a d110 lymph node ELAB-WU368-01-01_FNA_d110_GEX_1


title: scRNA-seq of Homo sapiens: 368-01a d60 lymph node ELAB-WU368-01-01_FNA_d60_GEX_1


title: scRNA-seq of Homo sapiens: 368-04 d60 lymph node ELAB-WU368-04-04_FNA_d60_GEX_2


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_24hpi_rep2


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_24hpi_rep1


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_12hpi_rep4

value: 12 hours post inoculation

value: Non-diseased


title: scRNA-seq of Homo sapiens: 368-13 d28+d35 blood plasmablast ELAB-WU368-13-13_PB_d28-35_GEX

source_name: PBMC

value: blood

value: plasmablast


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_12hpi_rep3


title: scRNA-seq of Homo sapiens: 368-07 d28 blood plasmablast ELAB-WU368-07-07_PB_d28_GEX


title: vehicle control treated CD16+ monocytes - replicate 1

city: Philadelphia

first: Steven

middle: D

last: Douglas

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: The Children's Hospital of Philadelphia

data_processing:
Illumina HiSeq software was used to create sequencing files
STAR software was used to align sequencing data to the  Ensembl hg38 genome with parameters  --runMode alignReads --runThreadN 20 --readFilesCommand zcat --twopassMode Basic
HTSeq was used to count reads with the htseq-count command using the folowing parameters   -f sam -r name -s no -a 10 -i gene_id -m intersection-strict sorted.sam
Genome_build: hg38
Supplementary_files_format_and_content: .out.txt count files for each sample

source_name: primary monocytes

extract_protocol:
RNA was purified from sorted monocytes with the Qiagen RNeasy Mini Kit. For each sample 200 ng of RNA was used to construct libraries with he Illumina TruSeq stranded total RNA library Prep kit
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For SP treatment, monocytes were incubated for 3 hours at 37°C with 10 µM SP. For vehicle control treatment, monocytes were incubated for 3 hours at 37°C with or 50 µM acetic acid.

tag: cell subset

value: CD16+ monocytes

tag: donor sex

value: Female

tag: donor age

tag: cell treatment

value: vehicle control treatment


title: vehicle control treated CD16- monocytes - replicate 2

value: CD16- monocytes


title: vehicle control treated CD16+ monocytes - replicate 2


title: scRNA-seq of Homo sapiens: 368-04 d28 lymph node ELAB-WU368-04-04_FNA_d28_GEX_1


title: scRNA-seq of Homo sapiens: 368-04 d28 blood plasmablast ELAB-WU368-04-04_PB_d28_GEX


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_mock-inoculated and axenic_rep4

source_name: Cicer arietinum roots and Phytophthora medicaginis mycellium

value: Mock-inoculated root tissue and mycellium grown axenically

value: No interaction


title: scRNA-seq of Homo sapiens: 368-01a d28 blood plasmablast ELAB-WU368-01-01_PB_d28_GEX


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_12hpi_rep2


title: scRNA-seq of Homo sapiens: 368-22 d28 blood plasmablast ELAB-WU368-22-22_PB_d28_GEX


title: SP treated CD16- monocytes - replicate 2

value: SP treatment


title: vehicle control treated CD16- monocytes - replicate 1


title: scRNA-seq of Homo sapiens: 368-10 d28 blood plasmablast ELAB-WU368-10-PB_d28_GEX


title: scRNA-seq of Homo sapiens: 368-20 d28 blood plasmablast ELAB-WU368-20-PB_d28_GEX


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_mock-inoculated and axenic_rep3


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_mock-inoculated and axenic_rep2


title: SP treated CD16- monocytes - replicate 1


title: scRNA-seq of Homo sapiens: 368-02a d28 blood plasmablast ELAB-WU368-02-PB_d28_GEX


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_24hpi_rep4


title: ES8P71_5d

city: shanghai

first: Liu

last: Yujie

address: South Chongqing Road

institute: Shanghai Jiao Tong Univeraity School of Medicine

data_processing:
Sanger / Illumina 1.9 software used for basecalling.
Sequenced fragments were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated .
DEGs between the two groups were identified using the R 3.1.0 software package DESeq2 1.4.5.
Genome_build: hg19

source_name: Human embryonic stem cells

growth_protocol: SHhES8 were grown in mTeSR1 medium.

extract_protocol:
Human ESCs were collected and  RNA was harvested using Trizol reagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were  incubated at 37°C in 5% CO2 and plated with dispase digested pellets. Dox was added to induce OGDH knockdown on the second day after plating, and the RNAs of the untreated group and the treated groups with Dox added for 4 days and 5 days were collected respectively.

tag: cell line

value: SHhES8 hESC line

value: Human embryonic stem cells

tag: culture medium


title: ES8P71_4d


title: untreated CD16+ monocytes - replicate 3

value: no treatment


title: 428_Wang_input_AtWX181_ATGN_250uMIPTG4h

city: Bloomington

first: Xindan

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

library_source: genomic

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
[Hi-C]
For Hi-C, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.
The two resulting SAM files were then merged together. Unaligned reads were discarded.
The A. tumefaciens C58 genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
The genomes of A. tumefaciens C58 was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle: mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
[ChIP-seq]
For ChIP-seq, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) using CLC genomics workbench 8.0, and exported .csv file.
Genome_build: GCA_000092025.1
Supplementary_files_format_and_content: *.matrix.txt: Tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Columns: 10kb bins of A. tumefaciens genome, values: normalized Hi-C interaction scores.
Supplementary_files_format_and_content: *.csv: Comma-separated values files of ChIP-seq results. Columns: Genome position, values: number of reads at each genome position.

molecule: genomic DNA

organism: Agrobacterium tumefaciens

source_name: Agrobacterium tumefaciens C58

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al., 2013, PMID: 24158908; Wang et al. 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-GFP, anti-ParB1 and anti-RepBCh2 antibodies according to previous publication (Graham et al. 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq550 sequencing platforms. Illumina TruSeq indexes were used.

treatment_protocol:
Cells were growing in ATGN at 30˚C, IPTG was added to 0.25mM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature.
None

tag: strain

tag: treatment

value: ATGN, 30C, 0.25mM IPTG for 4h

tag: restriction enzyme

tag: chip antibody


title: 427_Wang_ChIP_antiGFP_AtWX181_ATGN_250uMIPTG4h

description: ChIP using anti-GFP antibodies.

value: anti-GFP


title: SP treated CD16+ monocytes - replicate 1

tag: tissue


title: ES8P70_5d

tag: cell type


title: ES8P70_4d


title: untreated CD16- monocytes - replicate 2


title: 425_Wang_HiC_AtWX193_LB_AHL_Theo_rep2

treatment_protocol:
Cells were growing in LB at 30˚C, AHL was added to 1uM final concentration for 4h and theophylline was added to 2mM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature.
None

value: LB, 30C, 1uM AHL and 2mM Theophylline


title: untreated CD16+ monocytes - replicate 2


title: 424_Wang_HiC_AtWX193_ATGN

treatment_protocol:
Cells were growing in ATGN at 30˚C for 30h, fixed by 3% formaldehyde for 30min at room temperature.
None

value: ATGN, 30C


title: untreated CD16+ monocytes - replicate 1

value: Male


title: untreated CD16- monocytes - replicate 3

value: blood


title: ES8P69_5d


title: untreated CD16- monocytes - replicate 1


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_12hpi_rep1

value: Root and mycellium

value: 12 hours post inoculation

value: Non-diseased


title: 426_Wang_HiC_AtWX193_LB

treatment_protocol:
Cells were growing in LB at 30˚C for 30h, fixed by 3% formaldehyde for 30min at room temperature.
None

value: LB, 30C


title: 423_Wang_HiC_AtWX193_ATGN_AHL_Theo

treatment_protocol:
Cells were growing in ATGN at 30˚C, AHL was added to 1uM final concentration for 4h and theophylline was added to 2mM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature.
None

value: ATGN, 30C, 1uM AHL and 2mM Theophylline


title: ES8P69_4d


title: 422_Wang_HiC_AtWX192_ATGN

value: HindIII


title: NDEA + CFT-1 rep3

city: Fuzhou

first: Sufeng

last: Liao

state: Fujian

address: No.15 Shangxiadian Road, Cang Shan Distrit,

institute: Fujian Agriculture and Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to Rnor whole genome using hisat2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated according to the previous method  (Trapnell, Cole, et al., 2010).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: NDEA + CFT-1_liver

growth_protocol: Male Wistar rats (N = 48, 140–160 g) were housed (4 per 43 × 27 × 15 cm cage), in a specific pathogen-free animal room and maintained under standard experimental conditions: temperature 22 ± 1 °C, relative humidity 50 ± 10% with a 12 h light/dark cycle China (Experimental Animal Food Standard, GB 14924.3-2001).

extract_protocol:
Three liver samples from each group were collected and stored at -80℃ for RNA sequencing. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 1 week quarantine, the rats were randomized into 4 groups (N = 12/group):  control group, model controls group, CFT-1-treated group, FYT-treated group.

value: Wistar

tag: Sex

value: male

value: NDEA + CFT-1

value: liver

tag: time point

value: 20 weeks-post-treatment


title: 421_Wang_HiC_AtWX192_ATGN_AHL_Theo

last: Wang


title: NDEA + CFT-1 rep2


title: ES8P69_0

value: SHhES8 hESC line

value: Human embryonic stem cells


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_mock-inoculated and axenic_rep1

value: Mock-inoculated root tissue and mycellium grown axenically

tag: diseased state

value: No interaction


title: 420_Wang_HiC_AtWX063_ATGN_AHL_Theo


title: NDEA + FYT rep3

source_name: NDEA + FYT_liver

value: NDEA + FYT


title: 419_Wang_HiC_AtWX063_ATGN_Theo

treatment_protocol:
Cells were growing in ATGN at 30˚C, theophylline was added to 2mM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature.
None

value: ATGN, 30C, 2mM Theophylline


title: NDEA + CFT-1 rep1


title: 418_Wang_HiC_AtWX063_ATGN_AHL

treatment_protocol:
Cells were growing in ATGN at 30˚C, AHL was added to 1uM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature.
None

value: ATGN, 30C, 1uM AHL


title: ES8P71_0


title: BC1 iBMEC 3D+TFNa 2 [T24]

city: BALTIMORE

first: Peter

middle: C

last: Searson

state: MD

address: 3400 North Charles Street

institute: Johns Hopkins University

data_processing:
Alignment and quantification to reference genome (GRCh38) was performed using Rsubread (v2.0.1)
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) values were computed according to Trapnell et al., Nature Biotechnology, 2010. For every gene, one meta-transcript was created by merging the exons from all isoforms of that gene. Next, for each sample, the total number of unique paired-end reads mapped to each meta-transcript was tallied and normalized by the size of the meta-transcript, as well as by the size of the library.
Normalization, visualization, and differential analysis was performed using DESeq2 (v1.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: abundance measurements

source_name: BC1 iPSCs

growth_protocol:
Differentiation protocol (iBMECs): Cell culture was conducted at 5% CO2 and 37 °C. WTC and BC1 iPSCs were routinely passed onto Matrigel-coated plates at 10,000 cells/cm^2 and grown for three days in mTESR1 (WTC) or two days in TeSR-E8 (BC1) with daily media switches. iBMECs were differentiated as previously published (PMID: 30391800) using sequential treatment of iPSC colonies with unconditioned media without bFGF (for six days) and endothelial media (for two days). Unconditioned media without bFGF: DMEM/F12 supplemented with 20% knockout serum replacement, 1% non-essential amino acids, 0.5% GlutaMAX, and 0.836 μM beta-mercaptoethanol. Endothelial media: human endothelial cell serum-free medium supplemented with 1% human platelet poor derived serum, 2 ng/mL bFGF, and 10 μM all-trans retinoic acid. iBMECs were subcultured at the end of the differentiaiton on tissue-culture treated six-well plates coated with 50 μg/mL human placental collagen IV and 25 μg/mL fibronectin from human plasma in endothelial media supplemented with 1% penicillin-streptomycin and 10 μM ROCK inhibitor Y27632.  After one hour, media was switched for an additional 24 hours in the same media, before switching to human endothelial serum free media supplemented with 1% penicillin-streptomycin and 10 μM ROCK inhibitor after another 24 hours.
Differentiation protocol (iECs): iPSC-derived endothelial cells (iECs) were differentiated using ETV2 modRNA following published protocols (PMID: 32832668). The iECs were cultured in endothelial cell growth medium 2 kit supplemented into basal media (except hydrocortisone, Lonza) with 1x GlutaMax (ThermoFisher) and 10 μM SB431542 (Selleckchem), and routinely passed using Accutase at 1:3 splitting ratios on tissue-culture treated surfaces.
Differentiation protocol (iPCs): iPSC-derived brain pericyte-like cells (iPCs) were derived through a neural crest intermediate using published protocols (PMID: 30891496).  The iPCs were cultured in E6 media (StemCell Technologies) supplemented with 10% FBS and routinely passed using Accutase at 1:5 splitting ratios on tissue-cultured treated surfaces.
Primary endothelial cell culture: Primary neonatal human dermal microvascular endothelial cells (HDMECs: Lonza) were cultured in MCDB-131 (Caisson Labs, Carlsbad, CA) supplemented with 10% heat inactivated fetal bovine serum (Sigma), 25 mg/mL endothelial mitogen (Biomedical Technologies), 2 U/mL heparin (Sigma), 1 μg/mL hydrocortisone (Sigma), 0.2 mM ascorbic acid 2-phosphate (49752, Sigma), and 1% penicillin-streptomycin-glutamine (ThermoFisher).  Cells were routinely passed using 0.25% Trypsin-EDTA at 1:5 splitting ratios on tissue-culture treated surfaces.

extract_protocol:
3D experiments: iBMECs subcultured for one hour were detached using Accutase and then seeded into 150 μm diameter channels patterned in 7 mg/mL genipin-crosslinked type I collagen (Corning) as previously reported (PMID: 30391800). 3D microvessels comprised of BC1 iBMECs were cultured for two days, and then treated with and without 5 ng/mL human recombinant TNF-alpha (R&D Systems) for 24 hours.
RNA was collected at the following time points: three days after passing for WTC iPSCs, two days after subculture or seeding into 3D microvessels for WTC iBMECs in 2D and 3D, two days after passing following differentiation for WTC iPCs and iECs, three days after subculture or seeding into 3D microvessels for BC1 iBMECs in 2D and 3D, and two days after passing for HDMECs. Cells were washed with 1xPBS and lysed using RLT buffer supplemented with β-mercaptoethanol, before isolating RNA using a RNeasy Mini Kit (Qiagen) with DNase I digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols conducted by Novogene.

tag: differentiation

value: iBMEC

tag: ibmec differentiation media volume

value: 2 mL

tag: microenvironment

tag: cytokine exposure

value: TNF-a


title: BC1 iBMEC 3D+TNFa 1 [T18]


title: BC1 iBMEC 3D 2 [T23]


title: 417_Wang_HiC_IBJun138_LB

treatment_protocol:
Cells were growing in LB at 28˚C, fixed by 3% formaldehyde for 30min at room temperature.
None

value: LB, 28C


title: NDEA + FYT rep2


title: 416_Wang_HiC_IB124_LB

value: HindIII


title: BC1 iBMEC 3D 1 [T17]


title: 415_Wang_HiC_AtWX050_LB


title: ES8P70_0


title: 414_Wang_HiC_AtWX063_LB_rep2

treatment_protocol:
Cells were growing in LB at 30˚C, fixed by 3% formaldehyde for 30min at room temperature.
None

value: LB, 30C


title: BC1 iBMEC 2D 2 [T25]


title: BC1 iBMEC 2D 1 [T19]


title: NDEA rep2

value: Wistar

value: male

value: Model


title: WTC iEC 2 [E3]

source_name: WTC iPSC

value: iEC


title: NDEA rep1

value: liver

value: 20 weeks-post-treatment


title: 413_Wang_HiC_IBE13A_virulence

treatment_protocol:
Cells were growing in virulence inducing medium at 28˚C, fixed by 3% formaldehyde for 30min at room temperature.
None

value: Virulence inducing medium, 28C


title: 412_Wang_HiC_IB124_virulence


title: 411_Wang_HiC_AtWX050_virulence


title: Control rep2

value: Control


title: HDMEC 2 [T11]

source_name: primary human dermal microvascular endothelial cells


title: Control rep1


title: HDMEC 1 [T5]


title: CTRL8d_R3

city: Dresden

first: Maximina

last: Yun

state: Saxony

address: Fetscherstrasse 105

department: CRTD

country: Germany

institute: TUD

data_processing:
Basecalls were done with Illumina bcl2fastq version 2.19.1.
Sequence and gene annotation of the axolotl nuclear genome assembly AmexG_v6.0-DD were downloaded from https://www.axolotl-omics.org. The gene models for the HoxA and HoxD genes were replaced with manual curated gene models (personal communication with Sergej Nowoshilow, axolotl-omics.org). Sequence and gene annotation of the mitochondrial genome assembly (NCBI GenBank, AY659991.1) and RNA spike-in control sequences (ERCC, Ambion; for quality control) were included as well.
Reads were aligned to the axolotl reference genome  AmexG_v6.0-DD using the aligner STAR (v2.7.6a) with AmexG_v6.0-DD splice sites as support (parameters:--outSAMmultNmax 1).
Uniquely mapped fragments were compared based on their overlap to AmexG_v6.0-DD gene annotations using featureCounts (v2.0.1) to create a table of counts per gene and cell (parameters:  -a AmexG_v6_DD/AmexG_v6_DD.gtf -s 0 -o genecount/bfx1392.AmexG_v6_DD.eAmexG_v6_DD.txt -Q 1).
Genome_build: AmexG_v6.0-DD
Supplementary_files_format_and_content: bfx1392.AmexG_v6_DD.eAmexG_v6_DD.txt.gz is a tab separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the samples.

organism: Ambystoma mexicanum

source_name: Blastema cells

extract_protocol:
Samples were collecte, dissociated with LiberaseTM and immediated isolated by FACs sorting based on double positive (Ch+GFP+) or single channel fluorescence (CH+). cDNA library preparation was performed using 300 cells per sample.
RNAseq was based on Smart-seq2 sensitive full-length transcriptome profiling and modified from Picelli et. al., 2013 (Picelli et al., 2013).

treatment_protocol: Forelimb were amputated and electroporated with Tig1-t2A-GFP  or Tig1P155Amut-t2A-GFP constructs-containing plasmids when the hoxa13:Cherry+ domain was visible; Blastema tissue was collected at 3 or 8 days post-electroporation.

tag: animal line

value: Hoxa13:Cherry  transgenic line

value: Non-transfected cells

tag: isolation

value: Dissociation and FACS isolation at 8 days post- transfection


title: 410_Wang_HiC_AtWX050_ATGN

treatment_protocol:
Cells were growing in ATGN at 28˚C, fixed by 3% formaldehyde for 30min at room temperature.
None

value: ATGN, 28C


title: 409_Wang_WGS_AtWX063_ATGN_rep1

treatment_protocol:
Cells were growing in ATGN at 30˚C, fixed by 3% formaldehyde for 30min at room temperature.
None

value: ATGN, 30C


title: T1Mut8d_DP_R3

value: Cells transfected with Tig1P155Amut construct


title: WTC iPC 2 [P3]

value: iPC


title: NDEA + FYT rep1

value: NDEA + FYT


title: WTC iPC 1 [P2]


title: 408_Wang_HIC_AtWX089_ATGN

value: HindIII


title: T1Wt8d_DP_R3

value: Cells transfected with Tig1wt construct


title: WTC iBMEC 3D 2 [A40]

value: iBMEC

value: 1 mL


title: 406_Wang_HiC_AtWX192_LB_AHL_Theo

treatment_protocol:
Cells were growing in LB at 30˚C, AHL was added to 1uM final concentration and theophylline was added to 2mM final concentration, fixed by 3% formaldehyde for 30min at room temperature.
None

value: LB, 30C, 1uM AHL and 2mM Theophylline


title: WTC iBMEC 3D 3 [A41]


title: CTRL8d_R2


title: T1Mut8d_DP_R2


title: NDEA rep3

value: Wistar

value: male

value: Model

value: liver


title: 407_Wang_HiC_AtWX192_LB

value: LB, 30C


title: T1Wt8d_DP_R2

value: Hoxa13:Cherry  transgenic line


title: WTC iBMEC 3D 1 [A8]


title: Control rep3

value: Control

value: 20 weeks-post-treatment


title: WTC iBMEC 2D 2 mL 3 [A35]

value: 2 mL


title: 404_Wang_ChIP_anti_AtParB_AtWX063_ATGN

description: ChIP using anti-AtParB1 antibodies.

value: ATGN, 30C


title: WTC iEC 1 [E2]

value: iEC


title: WTC iBMEC 2D 2 mL 2 [A7]


title: T1Mut3d_DP_R3

value: Cells transfected with Tig1P155Amut construct

value: Dissociation and FACS isolation at 3 days post- transfection


title: CTRL3d_R3

value: Non-transfected cells


title: WTC iBMEC 2D 2 mL 1 [A3]

value: iBMEC


title: 402_Wang_HiC_AtWX108_ATGN

value: HindIII


title: T1Wt3d_DP_R3

value: Cells transfected with Tig1wt construct


title: WTC iBMEC 2D 1 mL 3 [A36]

value: 1 mL


title: 401_Wang_HiC_AtWX063_ATGN


title: ductus arteriosus, KO2

data_processing:
Raw reads were trimmed to remove the low-quality bases and reads with 45+ bases were keep for later analysis
Trimmed reads were aligned to the mouse reference genome mm10 using TopHat2
The alignment data was converted to per-gene counts using cufflinks
Data visualization was done using R.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file; FPKM values generated from cufflinks

source_name: ductus arteriosus, KO

growth_protocol: E17.5 ductus arteriosus of wild type and Prdm6f/f; SM22-Cre mice.

extract_protocol:
Ductus arteriosus were removed, flash frozen on dry ice, and RNA was harvested using miRNeasy Micro Kit(Mat. No. 1071023).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: age

tag: genotype

value: Prdm6f/f; SM22-Cre

value: ductus arteriosus


title: T1Mut3d_DP_R2


title: WTC iBMEC 2D 1 mL 1 [A2]


title: WTC iBMEC 2D 1 mL 2 [A6]


title: T1Wt3d_DP_R2


title: ductus arteriosus, KO1

tag: strain


title: WTC iPSC 3 [A34]


title: ductus arteriosus, WT2

source_name: ductus arteriosus, WT

value: wild type


title: T1Mut8d_DP_R1

tag: treatment

value: Dissociation and FACS isolation at 8 days post- transfection


title: 405_Wang_ChIP_anti_AtRepBCh2_AtWX063_ATGN

description: ChIP using anti-AtParB1 antibodies.

tag: restriction enzyme


title: WTC iPSC 2 [A5]


title: WTC iPSC 1 [A1]


title: ductus arteriosus, WT0


title: CTRL8d_R1

value: Hoxa13:Cherry  transgenic line


title: CTRL3d_R1


title: ductus arteriosus, WT1


title: ChIP-PP2R1A_dTAG-3h_PAF1-fkbp-DLD1_Batch12

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

data_processing:
ChIP-Rx: paired raw reads were quality checked with FastQC v0.11.9 (Babraham-Institute) and trimmed by Trim Galore v0.6.6 (Babraham-Institute) with the parameter “-q 25” to remove adaptors and low-quality reads. Then the remaining reads were aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 (Langmead and Salzberg, 2012). Duplicates and low mapping quality reads were removed using Picard v2.23.3 (Broad-Institute) and SAMtools v1.9 (Li et al., 2009). The number of spike-in mm10 reads was counted with SAMtools v1.9 and used to generate normalization factor alpha = 1e6/mm10_count for coverage profiles (Li et al., 2009). Normalized bigwig files were generated with deepTools v3.5.0 (Ramirez et al., 2016) and peaks were called using MACS 2.1.0 (Zhang et al., 2008). The called peaks overlapped with ENCODE Blacklist regions (Amemiya et al., 2019) were further removed by BEDTools v2.29.2 (Quinlan and Hall, 2010).
PRO-seq: The PRO-seq raw reads were processed with Trim Galore v0.6.6 (Babraham-Institute) and reads shorter than 15 bp after clipping were discarded. Ribosomal RNA reads were removed by Bowtie v2.3.5.1 with “--un-conc-gz” (Langmead and Salzberg, 2012). Then the remaining reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with the parameter “--very-sensitive-local” (Langmead and Salzberg, 2012). PCR duplicate and low-quality reads were removed. The normalization factor was calculated the same as described in ChIP-Rx. Strand-specific normalized bigwig files were generated with deepTools v3.5.0 (Ramirez et al., 2016).
TT-seq: The TT-seq raw reads were trimmed with Trim Galore v0.6.6 (Babraham-Institute)  and then aligned to hg19 or mm10 genome using STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate” (Langmead and Salzberg, 2012). We removed duplicates and low-quality reads and kept only properly paired reads for the downstream analyses. The number of spike-in mm10 reads was counted to generate the normalization factor. Strand-specific normalized bigwigs were generated with deepTools v3.5.0 (Ramirez et al., 2016).
RNA-seq: Raw reads were first trimmed by Trim Galore v0.6.6 (Babraham-Institute), followed by mapping to hg19 or mm10 genome using STAR v2.7.5c with parameters “--outSAMtype BAM SortedByCoordinate –twopassMode Basic --outFilterMismatchNmax 2” (Langmead and Salzberg, 2012). Duplicates and low-quality reads were removed, and reads mapped in proper pairs were isolated using SAMtools v1.9 with parameter “-f 2” (Li et al., 2009). The normalization factor was calculated the same as described in ChIP-Rx. Strand-specific Normalized bigwigs were generated.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: PAF1-dTAG DLD1

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
ChIP-seq: Lysates were clarified from sonicated cells and protein was isolated with antibody.  TT-seq/PRO-seq/RNA-seq: RNA was isolated with TRIzol.
ChIP-seq: Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.  TT-seq/PRO-seq/RNA-seq:  Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: The cell was  treated with dTAG13

value: colorectal adenocarcinoma cell lines

tag: chip antibody

value: treated with dTAG-13


title: ChIP-PP2R1A_DMSO_PAF1-fkbp-DLD1_Batch12

value: untreated


title: 403_Wang_input_AtWX063_ATGN_rep2

value: ATGN, 30C


title: 3_T-N1G_1.0µM_MG132

city: Aoba-ku, Sendai

first: Fumiki

last: Katsuoka

state: Miyagi

address: 2-1 Seiryo-cho

country: Japan

institute: Tohoku University

data_processing:
Illumina bcl2fastq v2.16.0.10 was used for basecalling.
Reads were mapped against mouse (mm9) genome using the TopHat v2.0.8b.
Differential gene analaysis was performed using Cuffdiff v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genotype were generated using Cuffdiff.

source_name: embryonic fibroblast

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was prepared by using RNeasy Mini Kit (QIAGEN).
Isolation of poly(A)-tailed RNA and library construction were performed using SureSelect Strand Specific RNA Sample Prep Kit (Agilent Technologies).

treatment_protocol: Cells were treated with Vehcle, 0.3 µM or 1.0 µM  Proteasome Inhibitor (MG132)  for 12hr.

value: embryonic fibroblast

value: 1.0 microM_MG132


title: ChIP-input_dTAG-3h_PAF1-fkbp-DLD1_Batch12

value: input


title: 3_T-N1G_0.3µM_MG132

value: 0.3 microM_MG132


title: T1Wt3d_DP_R1

value: Dissociation and FACS isolation at 3 days post- transfection


title: ChIP-input_DMSO_PAF1-fkbp-DLD1_Batch12


title: 442_Wang_HiC_AtWX295_ATGN

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the A. tumefaciens C58 genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of A. tumefaciens C58 was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: GCA_000092025.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices; column information (10kb bins of A. tumefaciens genome); matrix value (normalized Hi-C interaction scores).
Supplementary_files_format_and_content: Files inside the .zip files containing multiple  .csv files which are comma-separated values files of ChIP-seq results; column information (genome position; reads), matrix value (number of reads at each genome position).

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-GFP, anti-ParB1 and anti-RepBCh2 antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq550 sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in ATGN at 30˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: ATGN, 30˚C

value: HindIII


title: CTRL3d_R2

value: Non-transfected cells


title: 3_Mock_1.0µM_MG132


title: 441_Wang_HiC_AtWX278_ATGN


title: RNA-seq_dTAG-24h_PAF1-fkbp-DLD1_rep2_Batch11


title: RNA-seq_dTAG-24h_PAF1-fkbp-DLD1_rep1_Batch11


title: 3_Mock_0.3µM_MG132


title: ductus arteriosus, KO0

city: New Haven

first: Arya

address: 300 George Street

institute: Yale University

value: Prdm6f/f; SM22-Cre

tag: tissue


title: T1Wt8d_DP_R1

value: Cells transfected with Tig1wt construct


title: RNA-seq_DMSO-24h_PAF1-fkbp-DLD1_rep2_Batch11

tag: cell type


title: 3_Mock_Vehicle

value: Vehicle


title: 2_T-N1G_1.0µM_MG132


title: 2_T-N1G_0.3µM_MG132


title: PRO_dTAG-3h_PAF1-fkbp_DLD1_Batch9

data_processing:
Library strategy: PRO-seq
ChIP-Rx: paired raw reads were quality checked with FastQC v0.11.9 (Babraham-Institute) and trimmed by Trim Galore v0.6.6 (Babraham-Institute) with the parameter “-q 25” to remove adaptors and low-quality reads. Then the remaining reads were aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 (Langmead and Salzberg, 2012). Duplicates and low mapping quality reads were removed using Picard v2.23.3 (Broad-Institute) and SAMtools v1.9 (Li et al., 2009). The number of spike-in mm10 reads was counted with SAMtools v1.9 and used to generate normalization factor alpha = 1e6/mm10_count for coverage profiles (Li et al., 2009). Normalized bigwig files were generated with deepTools v3.5.0 (Ramirez et al., 2016) and peaks were called using MACS 2.1.0 (Zhang et al., 2008). The called peaks overlapped with ENCODE Blacklist regions (Amemiya et al., 2019) were further removed by BEDTools v2.29.2 (Quinlan and Hall, 2010).
PRO-seq: The PRO-seq raw reads were processed with Trim Galore v0.6.6 (Babraham-Institute) and reads shorter than 15 bp after clipping were discarded. Ribosomal RNA reads were removed by Bowtie v2.3.5.1 with “--un-conc-gz” (Langmead and Salzberg, 2012). Then the remaining reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with the parameter “--very-sensitive-local” (Langmead and Salzberg, 2012). PCR duplicate and low-quality reads were removed. The normalization factor was calculated the same as described in ChIP-Rx. Strand-specific normalized bigwig files were generated with deepTools v3.5.0 (Ramirez et al., 2016).
TT-seq: The TT-seq raw reads were trimmed with Trim Galore v0.6.6 (Babraham-Institute)  and then aligned to hg19 or mm10 genome using STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate” (Langmead and Salzberg, 2012). We removed duplicates and low-quality reads and kept only properly paired reads for the downstream analyses. The number of spike-in mm10 reads was counted to generate the normalization factor. Strand-specific normalized bigwigs were generated with deepTools v3.5.0 (Ramirez et al., 2016).
RNA-seq: Raw reads were first trimmed by Trim Galore v0.6.6 (Babraham-Institute), followed by mapping to hg19 or mm10 genome using STAR v2.7.5c with parameters “--outSAMtype BAM SortedByCoordinate –twopassMode Basic --outFilterMismatchNmax 2” (Langmead and Salzberg, 2012). Duplicates and low-quality reads were removed, and reads mapped in proper pairs were isolated using SAMtools v1.9 with parameter “-f 2” (Li et al., 2009). The normalization factor was calculated the same as described in ChIP-Rx. Strand-specific Normalized bigwigs were generated.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig


title: RNA-seq_DMSO-24h_PAF1-fkbp-DLD1_rep1_Batch11