title: 138_XT

city: Parma

first: Marco

last: Morselli

state: Parma

address: Parco Area delle Scienze, 23/A

country: Italy

institute: University of Parma

description:
Xen-capture16
Targeted Bisulfite Sequencing (TBSeq)

data_processing:
Demultiplexed Fastq files were subject to QC (FastQC - Babraham Bioinformatics) and trimming with cutadapt v2.10 (Martin 2011) (options: -u -10 -U 10 -q 20 -m 50).
Alignment to the Xenopus tropicalis genome (version XENTR_10.0) with BSBolt Align (Farrell et al. 2021) (default options).
PCR duplicates were removed with samtools markdup (option -r) v1.15 (Danecek et al. 2021).
DNA methylation was called using BSBolt CallMethylation v1.3.0 (options: -BQ 10 -MQ 20 -IO) resulting in CGmap files.
The matrices of common CpG sites (with at least 100x coverage) were produced using BSBolt AggregateMatrix.
Assembly: Xenopus tropicalis genome (version XENTR_10.0)
Supplementary files format and content: Xen-CGmatrix_TBSeqPilot_100x_100.txt: Tab-delimited text file, CGmatrix. First column = chromosome:position; from the second column = methylation value of common cytosines (CpG context) covered by at least 3 reads. One column for each sample.
Library strategy: TBSeq

organism: Xenopus tropicalis

source_name: hindlimb webbing

growth_protocol: Sixteen adult Xenopus tropicalis were housed at the National Xenopus Resource (RRID:SCR_013731) in two multi-rack recirculating aquatic systems with established diet and water parameters (conductivity, pH, and temperature) as previously defined.

extract_protocol:
Disposable biopsy punches were used to collect tissue (VWR 21909–140) from the hindlimb webbing of the frogs. DNA extraction was performed from web punches (4 mm in diameter except 6-months old for which we did 2mm), according to Xu Y. et al. (Xu et al. 2020) with minor modifications. Briefly, tissue chunks were digested o/n in a 1.5 ml tube containing 200 µl of lysis buffer (100 mM Tris-HCl pH 8; 200 mM NaCl; 0.20% SDS; 5 mM EDTA) + 4 µl of Proteinase K (20 mg/ml, NEB) at 55°C (300 rpm continuous shaking in a thermomixer). After centrifugation for 15 min at 16'000g (room temperature), the supernatant was transferred into a new tube avoiding the debris. The centrifugation step was repeated after the addition and mixing of the same volume of isopropanol. The resulting pellet was then washed twice with 500 µl of EtOH 70% (centrifugation at 16'000g for 10 min, RT). The remaining ethanol was then carefully removed and the pellet air dried for 5-10 minutes at 55°C (open caps). The dried pellet was then resuspended with 55 µl of EB buffer (10 mM Tris-HCl pH 8) at 55°C for 1 h at 1400 rpm in a thermomixer, before being quantified (Qubit dsDNA BR - Life Technologies) and quality checked (Agilent 4200 TapeStation - Genomic Assay).
500 ng of purified DNA was sonicated using the Bioruptor Pico (Diagenode) for 15 cycles of 30 second ON / 90 seconds OFF. Libraries were prepared according to Morselli et al. (Morselli et al. 2022) with minor modifications. Briefly, NEB Next Ultra II DNA kit was used for end-repair, A-tailing and ligation of pre-methylated unique-dual indexed adapters (Morselli et al., Methods 2021). Hybridization capture was performed as described in Morselli et al., Epigenetics 2022). Bisulfite conversion was performed with EZ DNA Methylation-Gold (Zymo Research) according to the manufacturer's instructions. The final amplification was performed with KAPA HiFi U+ (Roche Sequencing), IDT xGen Primers (20 µM - Integrated DNA Technologies), and 12 PCR cycles. Library QC was performed using the D1000 Assay on a 4200 Agilent TapeStation, and its concentration measured with the Qubit dsDNA BR Assay (Life Technologies). Libraries were sequenced on a NovaSeq6000 (SP lane) as paired-end 150 bases.

treatment_protocol: Frogs were kept in tanks with constant temperature of 25°C and 12/12 hour light cycle.

value: hindlimb webbing

value: CMV MEM GFP

tag: dob


title: Naïve Old B4

status: Public on Apr 28 2023

type: SRA

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

country: USA

institute: Washington University in Saint Louis

description: RNA was isolated from 5 mice

library_source: transcriptomic single cell

data_processing:
Demultiplexing with custom Python and perl script
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Assembly: mm10
Supplementary files format and content: raw gene counts for all cells

molecule: total RNA

organism: Mus musculus

source_name: Spinal cord meninges

extract_protocol:
For the contusion injury, mice were anesthetized with ketamine (100 mg/kg)-xylazine (10 mg/kg) mixture. A 15-mm midline skin incision was made, and the connective tissue and muscles were bluntly dissected to expose T6-T13. Laminectomy was performed at T9 to expose the dorsal spinal cord, and the vertebral column was stabilized with angled clamps attached to the T7 and T12 transverse processes. The contusion injury was delivered using an Infinite Horizon Impactor (IH-0400 Impactor) with a force of 90 dynes. After injury, the muscles and skin were sutured separately. Mice were humanely euthanized with an intraperitoneal injection of a lethal dose of Euthasol® (10% v/v), followed by transcardiac perfusion of PBS with 5 U/mL of Heparin. Vertebral columns were obtained. The ventral bone of the vertebrae was cut laterally and was removed to expose the spinal cord. Nervous tissue was carefully dissected from the bone using fine forceps to release the dorsal root ganglia surrounded by the meninges. The meninges was cut along the ventral side and peeled from the spinal cord. Spinal cord meninges was enzymatically digested in RPMI containing 1 mg/mL collagenase VIII, 0.5 mg/mL DNase I, and 2% FBS for 30 minutes at 37°C with shaking. Samples were passed through a 70 µm filter to obtain single-cell suspensions, washed with FACS buffer, and pelleted at 380 xg for 5 minutes. Cells were resuspended in FACS buffer with 1:100 CD16/32 Fc block. They were stained with CD31, CD45, Podoplanin and Lyve1, washed, and resuspended in DAPI-containing FACS buffer. Single meningeal lymphatic endothelial cells were sorted as Live (DAPI-) CD45- CD31+ PDPN+ Lyve1+ cells using a FACS Aria II. Individual cells were sorted into 96-well plates containing 2 µL of 10X RNA lysis buffer (Takara) and 5% RNAse out (Takara) and rapidly frozen over dry ice.
Library preparation was performed with 2 µL of single cell lysates arrayed in 96-well PCR plates. ds-cDNA was prepared using a protocol adapted from the Takara-Clontech SMARTer methods. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified using a standard Illumina i7 primer to introduce an index sequence and FACSseq Lib PCR 1.0 specific to fragments containing the cell barcode added during cDNA synthesis. Fragments were sequenced on an Illumina NovaSeq.

tag: tissue

value: Spinal cord meninges

tag: age

value: 24 months

tag: cell type

value: Lymphatic endothelial cells

tag: genotype

tag: Sex

value: female

tag: sample group

value: Naïve


title: Brother RNA-seq repB

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

library_source: transcriptomic

data_processing:
Overall Summary: The fastq files were trimmed and mapped to the GRCh38/hg38 reference genome and prepared for analysis and visualization through our in-house pipEfathernes.
fastq read files were first trimmed using bbduk (version 38.05) to remove adapter sequences, as well as short or low quality reads.
Reads were mapped with HISAT2 (version 2.1.0), and resulting SAM files converted to BAM files with Samtools (version 1.8).
Multimapped reads were filtered from these files using Samtools.
Annotations were downloaded from RefSeq (release number 109, downloaded August 14, 2019 from UCSC genome browser). For featureCounts, BED6 region files were converted to SAF format with the following command: awk -F "\textbackslash t" -v OFS="\textbackslash t" `print\{\$4, \$1, \$2, \$3, \$6\}' region.bed > region.saf.
Assembly: Gene counts were generated using featureCounts (version 1.6.2) from the R Subread package (version 1.6.0), counting over the gene body region (+150 from transcription start site to annotated transcription end site) to avoid the 5$^\prime$ peak seen in GRO-seq. This method was also used for this RNA-seq feature counts so the data from the two methods would match.
Supplementary files format and content: featurecounts_rna_rmsked.sense.txt which contains read counts for each transcript for each sample

organism: Homo sapiens

source_name: blood

growth_protocol: The lymphoblastoid cell lines of 4 individuals were obtained from the Translational Nexus Biobank (COMIRB 08-1276), University of Colorado School of Medicine, JFK Partners. Lymphoblastoid cell lines (LCLs) were seeded in upright T-25 suspension flasks with 10 ml RPMI (10\% FBS, 1X L-Glutamine, 1X Penicillin/Streptamycin). These were passaged approximately every 2 to 3 days by pelleting the cells via centrifugation (300 x g, 5 min) and resuspension. Cells were grown to an approximate density of 1 million cells per ml, before being harvested for subsequent experiments.  The three RNA-seq replicates per sample were based on three separate growths of cells.

extract_protocol:
RNA was isolated from the cells via Trizol extraction.
NEBNext rRNA Depletion kit was used to remove rRNA. NEBNext Ultra II RNA was used to transform the  RNA into an RNA-seq library. The product was amplified 15 plus or minus 3 cycles and products >150 bp (insert > 70 bp) were size selected with 1X AMPure XP beads (Beckman) before being sequenced.

treatment_protocol: cells were not treated

value: M

value: blood

tag: cell line

value: EBV transformed Lymphbastiods

value: Disomic chr 21

tag: treatment


title: T21 RNA-seq repA

value: Trisomic chr 21


title: T21 RNA-seq repB


title: Brother RNA-seq repC


title: Mother RNA-seq repC

value: F


title: Brother RNA-seq repA


title: Naïve Old B3

description: RNA was isolated from 5 mice


title: 134_XT

description:
Xen-capture14
Targeted Bisulfite Sequencing (TBSeq)

library_source: genomic

molecule: genomic DNA

tag: strain


title: T21 RNA-seq repC


title: 108_XT

description:
Xen-capture13
Targeted Bisulfite Sequencing (TBSeq)


title: 137_XT

description:
Xen-capture15
Targeted Bisulfite Sequencing (TBSeq)


title: TRIBE-ID_2hr_rapamycin_NaAsO2_rep1

city: Princeton

first: Ralph

middle: E

last: Kleiner

state: NJ

address: Frick Laboratory on Washington Rd

department: Chemistry

institute: Princeton University

data_processing:
Alignment with STAR (v.2.7.0f)
Nucleotide frequency at each position in the transcriptome was uploaded to MySQL database.
A-to-I mutations were detected by comparing the nucleotide frequencies in each sample with the background control.
Differential expression with DESeq2 (v.2.11.40.6)
Assembly: CRCh38
Supplementary files format and content: For bedgraph files, first three columns denote genomic coordinates of edit sites. The fourth column represents the editing percentages of edit sites.
Supplementary files format and content: Tabular files are output of DESeq2.

molecule: polyA RNA

source_name: FlpIn 293 Trex

growth_protocol: All cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1x penicillin-streptomycin, and 2mM L-glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with TRIzol reagent (Thermo Fisher), and poly-A RNA was isolated using oligo-(dT) beads (NEB).
All libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

value: FlpIn 293 Trex

value: Embryonic kidney cells

value: Stable expression of G3BP1-FRB and FKBP-ADAR

value: Tetracycline induction, rapamycin and sodium arsenite treatment

tag: condition

value: 1ug/mL tetracycline, 100 nM rapamycin, 200 uM sodium arsenite

tag: time

value: 24 hour for tetracycline, 2 hour for rapamycin and sodium arsenite


title: Naïve Old B6

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: Mother RNA-seq repA


title: TRIBE-ID_inhibitors_PDS_rep1

value: Tetracycline induction, rapamycin and PDS treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 20 uM PDS

value: 24 hour for tetracycline, 2 hour for rapamycin and PDS


title: Mother RNA-seq repB


title: 100_XT

description:
Xen-capture12
Targeted Bisulfite Sequencing (TBSeq)

value: hindlimb webbing


title: TRIBE-ID_8hr_rapamycin_rep1

value: Tetracycline induction, rapamycin treatment

value: 1ug/mL tetracycline, 100 nM rapamycin

value: 24 hour for tetracycline, 8 hour for rapamycin


title: TRIBE-ID_4hr_rapamycin_NaAsO2_rep2

value: 24 hour for tetracycline, 4 hour for rapamycin and sodium arsenite


title: 61_XT

description:
Xen-capture11
Targeted Bisulfite Sequencing (TBSeq)


title: Naïve Old A12

description: RNA was isolated from 5 mice

value: 24 months

value: Lymphatic endothelial cells

value: female

value: Naïve


title: TRIBE-ID_4hr_rapamycin_rep2

value: FlpIn 293 Trex

value: Embryonic kidney cells

value: Stable expression of G3BP1-FRB and FKBP-ADAR

value: 24 hour for tetracycline, 4 hour for rapamycin


title: TRIBE-ID_2hr_rapamycin_NaAsO2_rep2

value: Tetracycline induction, rapamycin and sodium arsenite treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 200 uM sodium arsenite

value: 24 hour for tetracycline, 2 hour for rapamycin and sodium arsenite


title: Father RNA-seq repC

value: M

value: blood

value: EBV transformed Lymphbastiods

value: Disomic chr 21


title: 59_XT

description:
Xen-capture10
Targeted Bisulfite Sequencing (TBSeq)

value: hindlimb webbing


title: Naïve Old A11

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: Naïve Old A10

description: RNA was isolated from 5 mice

value: 24 months


title: Father RNA-seq repA


title: 43_XT

description:
Xen-capture8
Targeted Bisulfite Sequencing (TBSeq)


title: TRIBE-ID_4hr_rapamycin_rep1

value: Tetracycline induction, rapamycin treatment

value: 1ug/mL tetracycline, 100 nM rapamycin


title: TRIBE-ID_8hr_rapamycin_rep2

value: 24 hour for tetracycline, 8 hour for rapamycin


title: TRIBE-ID_2hr_rapamycin_rep1

value: FlpIn 293 Trex

value: 24 hour for tetracycline, 2 hour for rapamycin


title: Father RNA-seq repB


title: Naïve Old B1

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells

value: female

value: Naïve


title: 44_XT

description:
Xen-capture9
Targeted Bisulfite Sequencing (TBSeq)


title: T21 GRO-seq repC

library_source: other

data_processing:
Overall Summary: The fastq files were trimmed and mapped to the GRCh38/hg38 reference genome and prepared for analysis and visualization through our in-house pipEfathernes.
fastq read files were first trimmed using bbduk (version 38.05) to remove adapter sequences, as well as short or low quality reads.
Reads were mapped with HISAT2 (version 2.1.0), and resulting SAM files converted to BAM files with Samtools (version 1.8).
Multimapped reads were filtered from these files using Samtools.
Annotations were downloaded from RefSeq (release number 109, downloaded August 14, 2019 from UCSC genome browser). For featureCounts, BED6 region files were converted to SAF format with the following command: awk -F "\textbackslash t" -v OFS="\textbackslash t" `print\{\$4, \$1, \$2, \$3, \$6\}' region.bed > region.saf.
Assembly: Gene counts were generated using featureCounts (version 1.6.2) from the R Subread package (version 1.6.0), counting over the gene body region (+150 from transcription start site to annotated transcription end site) to avoid the 5$^\prime$ peak seen in GRO-seq.
Supplementary files format and content: featurecounts_gro_noproms_nomultis.sense.txt which contains read counts for each transcript for each sample
Library strategy: GRO-seq

molecule: other

growth_protocol: The lymphoblastoid cell lines of 4 individuals were obtained from the Translational Nexus Biobank (COMIRB 08-1276), University of Colorado School of Medicine, JFK Partners. Lymphoblastoid cell lines (LCLs) were seeded in upright T-25 suspension flasks with 10 ml RPMI (10\% FBS, 1X L-Glutamine, 1X Penicillin/Streptamycin). These were passaged approximately every 2 to 3 days by pelleting the cells via centrifugation (300 x g, 5 min) and resuspension. Cells were grown to an approximate density of 1 million cells per ml, before being harvested for subsequent experiments.  The three GRO-seq replicates per sample were based on three separate growths of cells. Nuclei were isolated from the cells.

extract_protocol:
Nuclie were preped from the cells.  RNA was isolated from the cells via Trizol extraction.    Wash solutions for Anti-BrdU-beads were prepared ahead of time;  Binding buffer (0.25X SSPE, 37.5 mM NaCl, 0.05\% Tween, 1mM EDTA pH 8, 0.2\% SuperRNAseIN), Low Salt Wash Buffer (0.25X SSPE, 0.05\% Tween, 1mM EDTA pH 8, 0.2\% SuperRNAseIN), High Salt Wash Buffer(0.25X SSPE, 137.5mM NaCl, 0.05\% Tween, 1 mM EDTA pH 8, 0.2\% SuperRNAseIN), TET Buffer(10 mM Tris-Cl pH 8.0,  0.05\% Tween, 1 mM EDTA pH 8.0, 0.2\% SuperRNAseIN), Elution Buffer (150 mM NaCl, 50 mM Tris-Cl pH 7.5, 20 mM DTT, 0.1\% SDS, 1 mM EDTA,  0.2\% SuperRNAseIN).      Anti-BrdU beads (Santa Cruz, sc-32323-ac) were prepared by washing and blocking. Per sample, 60µl were washed twice in 500 $\mu$l binding buffer. beads were blocked in 500 $\mu$l blocking buffer(1X binding buffer, 0.1\% PVP, 1 $\mu$g/mL BSA UltraPure, 0.002 more superRNAseIN). Beads were then resuspended in 450 $\mu$l binding buffer.    Run-on reactions were performed as in \cite{Core2008}. In brief, ice-cold isolated nuclei (100 $\mu$L) were added to 37$^\circ$C 100 $\mu$L reaction buffer (Final Concentration: 5 mM Tris-Cl pH 8.0, 2.5 mM MgCl$_2$, 0.5 mM DTT, 150 mM KCl, 10 units of SUPERase In, 0.5\% sarkosyl, 500 $\mu$M rATP, rGTP, and Bromo-UTP, 2 $\mu$M rCTP). The reaction was allowed to proceed for 10 min at 37$^\circ$C, followed by the addition of 1 $\mu$L of Trizol. RNA was extracted once with phenol-chloroform, washed once with chloroform, and precipitated with 3 volumes of ice-cold Etrisomy21ol and 1-2 $\mu$L GlycoBlue. The pellet was washed in 75\% Etrisomy21ol before resuspending in 18 $\mu$L of DEPC-treated water.    Libraries were prepared similar to \cite{Hunter2022}. In brief, RNA was treated with 2 $\mu$l NEB Fragmentation Buffer at 94 degrees for 5 min.  The RNA was then buffer exchanged via BioRad P-30 (or a G-25) column per the manufacturer’s protocol. Next, 2 $\mu$l DNaseI and 5 $\mu$l of 10X RQ1 DNase buffer and water were added to create a 1X final concentration of the buffer. After incubation at 37$^\circ$C for 10min, 5 $\mu$l DNAse stop solution was added, and the reaction was placed at 65$^\circ$C for 5 min. As prepared above, the beads in 450 $\mu$l binding buffer was immediately added to this mixture.     Fragmented nascent RNA was purified using Anti-BrdU beads via washing with 500 $\mu$l for 1 min with each solution (binding buffer, low salt buffer, high salt buffer, TET buffer). Between washes, beads were spun down per manufacturer instructions. RNA was eluted from the bead via soaking the beads in 125 $\mu$l  elution buffer at 42$^\circ$C, 10 min 2 times. The beads were then added to acid phenol-chloroform, as was the elute. The RNA was washed with chloroform and precipitated with 5M NaCl and 3x the Etrisomy21ol column.  The second round of Anti-BrdU bead binding and extraction enriched BrdU-labeled products was completed as above.
NEBNext Ultra II RNA was used to transform the nascent RNA into an RNA-seq library. The product was amplified 15 $\pm$ three cycles and products >150 bp (insert > 70 bp) were size selected with 1X AMPure XP beads (Beckman) before being sequenced.

value: Trisomic chr 21


title: 40_XT

description:
Xen-capture7
Targeted Bisulfite Sequencing (TBSeq)


title: Naïve Old A8

description: RNA was isolated from 5 mice


title: Naïve Old A9

description: RNA was isolated from 5 mice


title: TRIBE-ID_2hr_rapamycin_rep2

value: Embryonic kidney cells

value: Stable expression of G3BP1-FRB and FKBP-ADAR


title: T21 GRO-seq repBss  (repB technical rep)

value: M

value: blood


title: Naïve Old B2

description: RNA was isolated from 5 mice


title: TRIBE-ID_0hr_rep2

value: Tetracycline induction

value: 1ug/mL tetracycline

value: 24 hour for tetracycline


title: Naïve Old A7

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: 24 months


title: 30_XT

description:
Xen-capture5
Targeted Bisulfite Sequencing (TBSeq)

value: hindlimb webbing


title: 38_XT

description:
Xen-capture6
Targeted Bisulfite Sequencing (TBSeq)


title: TRIBE-ID_0hr_rep1


title: T21 GRO-seq repB

value: EBV transformed Lymphbastiods


title: Naïve Old A6

description: RNA was isolated from 5 mice


title: T21 GRO-seq repA


title: TRIBE_No_transfection_rep2

value: WT


title: 26_XT

description:
Xen-capture4
Targeted Bisulfite Sequencing (TBSeq)

value: gtpbp2 F1 KO


title: Naïve Old A5

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells


title: Brother GRO-seq repC

value: Disomic chr 21


title: TRIBE_No_transfection_rep1


title: 16_XT

description:
Xen-capture3
Targeted Bisulfite Sequencing (TBSeq)


title: 14_XT

description:
Xen-capture2
Targeted Bisulfite Sequencing (TBSeq)


title: Naïve Old A4

description: RNA was isolated from 5 mice

value: female

value: Naïve


title: Brother GRO-seq repBss  (repB technical rep)


title: TRIBE_G3BP1-hADAR_E488Q_T375G_rep2

value: Embryonic kidney cells

value: Transient transfection

value: Lipofectamine transfection of G3BP1-ADAR transgene

value: 24 hour post-transfection


title: Naïve Old A3

description: RNA was isolated from 5 mice


title: 10_XT

description:
Xen-capture1
Targeted Bisulfite Sequencing (TBSeq)

value: sox3 F0


title: Brother GRO-seq repB

value: M

value: blood


title: Naïve Old A2

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: TRIBE_G3BP1-hADAR_E488Q_rep2


title: TRIBE_G3BP1-hADAR_E488Q_rep1


title: Mother GRO-seq repC

value: F


title: Xen-9_YOUNG3

data_processing:
Demultiplexed Fastq files were subject to QC (FastQC - Babraham Bioinformatics) and trimming with cutadapt v2.10 (Martin 2011) (options: -u -10 -U 10 -q 20 -m 50)
alignment to the  Xenopus tropicalis genome (version XENTR_10.0) with BSBolt Align (Farrell et al. 2021) (default options)
PCR duplicates were removed with samtools markdup (option -r) v1.15 (Danecek et al. 2021).
DNA methylation was called using BSBolt CallMethylation v1.3.0 (options: -BQ 10 -MQ 20 -IO) resulting in CGmap files.
The matrices of common CpG sites (with at least 3x or 5x coverage) were produced using BSBolt AggregateMatrix.
Assembly: Xenopus tropicalis genome (version XENTR_10.0)
Supplementary files format and content: Xen-CGmatrix_WGBS_3x_100.txt (text file, CGmatrix. First column = chromosome:position; from the second column = methylation value of common cytosines (CpG context) covered by at least 3 reads. One column for each sample.)
Supplementary files format and content: Xen-CGmatrix_WGBS_5x_100.txt (text file, CGmatrix. First column = chromosome:position; from the second column = methylation value of common cytosines (CpG context) covered by at least 5 reads. One column for each sample.)
Supplementary files format and content: Xen-CGmatrix_WGBS_combined_10x_100.txt (text file, CGmatrix. First column = chromosome:position; from the second column = methylation value of common cytosines (CpG context) covered by at least 3 reads. One column for each sample. Conversely  to the previous ones, this CGmatrix derives from the combined bam files of all the samples from the same age group)

growth_protocol: Nine sampled adult Xenopus tropicalis were housed at the National Xenopus Resource (RRID:SCR_013731) in two multi-rack recirculating aquatic systems with established diet and water parameters (conductivity, pH, and temperature) as previously defined.

extract_protocol:
Disposable biopsy punches were used to collect tissue (VWR 21909–140) from the hindlimb webbing of mutant, transgenic, and wild type X. tropicalis with Nigerian St.549 background (RRID_NXR_1018). DNA extraction was performed from web punches (4 mm in diameter except 6-months old for which we did 2mm), according to Xu Y. et al. (Xu et al. 2020) with minor modifications. Briefly, tissue chunks were digested o/n in a 1.5 ml tube containing 200 µl of lysis buffer (100 mM Tris-HCl pH 8; 200 mM NaCl; 0.20% SDS; 5 mM EDTA) + 4 µl of Proteinase K (20 mg/ml, NEB) at 55°C (300 rpm continuous shaking in a thermomixer). After centrifugation for  15 min at 16'000g (room temperature), the supernatant was transferred into a new tube avoiding the debris. The centrifugation step was repeated after the addition and mixing of the same volume of isopropanol. The resulting pellet was then washed twice with 500 µl of EtOH 70% (centrifugation at 16'000g for 10 min, RT). The remaining ethanol was then carefully removed and the pellet air dried for 5-10 minutes at 55°C (open caps). The dried pellet was then resuspended with 55 µl of EB buffer (10 mM Tris-HCl pH 8) at 55°C for 1 h at 1400 rpm in a thermomixer, before being quantified (Qubit dsDNA BR - LifeTechnologies) and quality checked (Agilent 4200 TapeStation - Genomic Assay).
1 µg of purified DNA was sonicated using the Bioruptor Pico (Diagenode) for 15 cycles of 30 second ON / 90 seconds OFF. Libraries were prepared according to Morselli et al. (Morselli et al. 2022) with minor modifications. Briefly, NEB Next Ultra II DNA kit was used for end-repair, A-tailing and ligation of pre-methylated unique-dual indexed adapters (Morselli et al. 2021). Bisulfite conversion was performed with EZ DNA Methylation-Gold (Zymo Research) according to the manufacturer's instructions. The final amplification was performed with KAPA HiFi U+ (Roche Sequencing), IDT xGen Primers (20 µM - Integrated DNA Technologies), and 12 PCR cycles.
Library QC was performed using the D1000 Assay on a 4200 Agilent TapeStation, and its concentration measured with the Qubit dsDNA BR Assay (LifeTechnologies). Libraries were sequenced on a NovaSeq6000 (S4 lane) as paired-end 150 bases.
Bisulfite-seq (WGBS)

value: hindlimb webbing

value: wt Nigerian St.549

tag: developmental stage

value: YOUNG


title: Brother GRO-seq repA

value: EBV transformed Lymphbastiods


title: TRIBE_G3BP1-hADAR_E488Q_T375G_rep1

value: WT


title: Xen-8_YOUNG2


title: Naïve Old A1

description: RNA was isolated from 5 mice

value: 24 months

value: Lymphatic endothelial cells


title: Prop_4

city: Nanjing

first: Xinghua

last: Gao

state: Jiangsu

address: #639 Longmian Dadao

country: China

institute: China Pharmaceutical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads.
Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome.
The gene alignment and FPKM were calculated using featureCounts v1.6.2 / StringTie v1.3.4d.
DESeq2 v1.22.1 / edgeR v3.24.3 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression.
Assembly: GRCm39.104
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: CT26 subcutaneous tumors

extract_protocol:
CT26 subcutaneous tumors were removed, flash frozen on dry ice, and total RNA was extracted using Trizol (Takara, Japan) and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The mouse colorectal cancer model was established with male BABL/C mice injected subcutaneously mouse CT26 cells. Animals were administered propranolol once a day by intraperitoneal injection (i.p.) when tumors reached 70-100 mm3. When

value: CT26 subcutaneous tumors

value: colon cancer cell

value: Propranolol treatment


title: Xen-7_YOUNG1


title: Mother GRO-seq repB

value: Disomic chr 21


title: TRIBE_G3BP1-dADAR_E488Q_rep1

value: Embryonic kidney cells

value: Transient transfection

value: Lipofectamine transfection of G3BP1-ADAR transgene

value: 24 hour post-transfection


title: Mother GRO-seq repBss  (repB technical rep)

value: blood


title: Xen-6_MID3

value: MID


title: TRIBE_G3BP1-dADAR_E488Q_rep2


title: Prop_3


title: Prop_2


title: Prop_1


title: TRIBE_hADAR_E488Q_T375G_rep1

value: Lipofectamine transfection of ADAR transgene


title: TRIBE_hADAR_E488Q_T375G_rep2


title: TRIBE_hADAR_E488Q_rep2


title: Xen-4_MID1

value: hindlimb webbing

value: no privacy; Xtr.hps6n Grngr


title: Mother GRO-seq repA

value: F

value: EBV transformed Lymphbastiods


title: Xen-3_OLD3

value: OLD


title: Con_3

value: WT

value: PBS treatment


title: Father GRO-seq repC

value: M


title: TRIBE_dADAR_E488Q_rep2


title: TRIBE_hADAR_E488Q_rep1


title: Xen-2_OLD2


title: Con_2

value: CT26 subcutaneous tumors

value: colon cancer cell


title: Father GRO-seq repB

value: Disomic chr 21


title: Father GRO-seq repA


title: Con_1


title: Blood, IR, HTO-derived cDNA

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
RRW-04-barcodes.tsv.gz
RRW-04-features.tsv.gz
RRW-04-matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing and gene counting were made using 10X Genomics Cell Ranger (v6.0.1).
Further processing was done with Seurat (v4.0.6) (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Blood

growth_protocol: CD45+CD11b+Ly6Chi were sorted from MC38 tumors or blood of MC38 tumor-bearing mice

extract_protocol:
first use totalseq B for hashtagging, then use a Takara iCell 8 and a MissionBio Tapestri
The libraries were performed using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1
CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

treatment_protocol: MC38 tumors were received irradition (20 Gy, one dose), three days after IR, cells were collected

value: Blood

value: CD11b+ myeloid cells

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD45 + Anti MHC classI :WT--/TotalSeq-HTO-B0301 ; Ythdf2 cKO--/TotalSeq-HTO-B0302

value: Irradiation


title: H9 osteoblasts, shCORIN-2

city: Houston

first: Mo-Fan

last: Huang

state: TX

address: 6431 Fannin Street

department: Integrative Biology and Pharmacology

institute: University of Texas Health science center

data_processing:
The first tool of this workflow is FastQC and file was trimmed using Cutadapt. This tool trimmed the sequence with high uncertainty (i.e. low quality bases) at the reads ends.
 After groomed and trimmed, the reads were assembled using RNA STAR with human reference genome (hg19).
The output of RNA STAR was BAM file containing information for all our reads which can be inspected by the Integrative Genomics Viewer(IGV).
The aligned reads from RNA STAR output were assembled by featureCounts to count reads per genes. This process produced tabular files showing table with the counts, i.e. the number of reads mapped to each gene (in rows, with their ID in the first column) in the provided annotation.
The expression level of each transcript was stated in term of Fragments Per Kilobase of exon per Million fragments (FPKM).
Analysis of the differential gene expression was performed by DESeq2.
Assembly: hg19
Supplementary files format and content: Excel files reporting readcounts or FPKMs

growth_protocol: The MSCs were maintained in aMEM medium. Then the MSCs were cultured in ostegenic differentiation medium (ODM) for osteoblast differentiation.

extract_protocol:
Whole RNA extraction using Trizol.
Libraries were prepared according to Illumina's instructions.

treatment_protocol:
(S1-S44) MSCs were cultured in osteogenic differentiation medium. Cells were collected for whole RNA extraction at different differentiation stages.
(S45-S48) We prepared lentivirus expressing system to overexpress SDC1 in H9 MSCs. And cultured the H9 MSCs in osteogenic differentiation medium. After 24 days, cells were collected for whole RNA extraction.
(S49-S52) We prepared lentivirus expressing system to knockout CEBPD in H9 MSCs. And cultured the H9 MSCs in osteogenic differentiation medium. After 24 days, cells were collected for whole RNA extraction.
(S53-S56) We prepared lentivirus expressing system to knockout IL1R1 in H9 MSCs. And cultured the H9 MSCs in osteogenic differentiation medium. After 24 days, cells were collected for whole RNA extraction.
(S55-S58) We prepared lentivirus expressing system to knockdown CORIN in H9 MSCs. And cultured the H9 MSCs in osteogenic differentiation medium. After 24 days, cells were collected for whole RNA extraction.

value: H9 osteoblasts

value: H9 cells infected with lentivirus expressing sgCORIN


title: TRIBE_dADAR_E488Q_rep1

value: Embryonic kidney cells

value: Transient transfection

value: Lipofectamine transfection of ADAR transgene

value: 24 hour post-transfection


title: Xen-1_OLD1

value: hindlimb webbing

value: OLD


title: Blood, IR, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
RRW-04-barcodes.tsv.gz
RRW-04-features.tsv.gz
RRW-04-matrix.mtx.gz

value: mRNA


title: HPC7, ATAC-seq, rep6

city: College Station

first: Masako

last: Suzuki

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

data_processing:
The obtained sequences were adapter trimmed and aligned to the mouse reference genome (mm10 including small contigs) using the BWA-MEM software (arXiv:1303.3997v1).
We selected and used only uniquely aligned reads for the analysis. Reads aligned to mitochondrial DNA and PCR duplicate reads were eliminated from further analysis.
We performed peak calling using MACS2 .
Assembly: mm10
Supplementary files format and content: narrowPeak

growth_protocol: HPC-7 cells were maintained at density of 2-10 x10^5/ml in Iscove’s modified Dulbecco’s medium (Invitrogen) supplemented with 50 ng/ml of mouse stem cell factor (Gemini Bio-Products), 1 mM Sodium Pyruvate, 6.9 ng/mL α-Monothioglycerol (SIGMA-Aldrich), 5% of bovine calf serum and Penicillin-Streptomycin.

extract_protocol:
We lysed pelleted cells with lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin (Invitrogen, cat# BN2006)) for 3 minutes on ice, then we washed nuclei with wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20).
ATAC-seq libraries were prepared according to Buenrostro et al. 2013 (PMID:24097267) with some modifications.

value: Hematopoietic progenitor cell


title: Xen-5_MID2

value: MID


title: H9 osteoblasts, shCORIN-1


title: HPC7, ATAC-seq, rep8


title: HPC7, ATAC-seq, rep7


title: Con_4

value: CT26 subcutaneous tumors

value: colon cancer cell

value: WT

value: PBS treatment


title: Father GRO-seq repBss  (repB technical rep)

value: M

value: blood

value: EBV transformed Lymphbastiods

value: Disomic chr 21


title: pHALO_tom_vv_rep2

city: Paterna

first: José Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: Institute for Integrative Systems Biology

data_processing:
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Raw reads were trimmed using fastp version 0.21.0 with the following parameters: " -w 16 --n_base_limit 5 cut_front_window_size 1 cut_front_mean_quality 30 --cut_front cut_tail_window_size 1 cut_tail_mean_quality 30 --cut_tail -l 20 -i "
Trimmed reads were aligned by bowtie2 version 2.0-beta7  against the Vitis vinifera genome assembly PN40024_12X.2 with default parameters, and additionally filter for alignments with MAPQ score of at least 30.
Peaks were called using GEM peak caller version 3.4 with the default version 3.4 read distribution, PN40024_12X.2 genome sequences, in multi-replicate mode and with the Pix-halo samples as control, and parameters “–q 1 –t 1 –k_min 6 –kmax 20 –k seqs 600 –k_neg_dinu_shuffle”, limited to nuclear chromosomes.
Peak summits called by GEM were associated with the closest gene model in the V1 transposed on the 12X.v2 assembly annotation file using the BioConductor package ChIPpeakAnno with default parameters (i.e., NearestLocation).
Supplementary files format and content: Peak regions in narrowPeak format were created by GEM analysis.
Library strategy: DAP-Seq

organism: Vitis vinifera

source_name: young leaf

extract_protocol:
Genomic DNA (gDNA) was purified from young grapevine leaves of cv. ‘Pinot Noir’ (clone PN-94) according to Chin et al. (2016). gDNA library construction, DAP-Seq, peak calling, and motif analysis were performed as described in (Orduña et al., 2022)
The bound DNA resulting from the DAP-Seq experiment was eluted and sequencing libraries were generated by PCR amplification.

treatment_protocol: Leaf material was collected and flash frozen with liquid nitrogen prior gDNA isolation.

tag: cultivar

value: Pinot Noir

tag: protein

value: pIX-HALO

tag: protein affinity tag

value: HALO

tag: expression system

value: rabbit reticulocyte lysate

tag: dna source

tag: replicate


title: pHALO_tom_vv_rep1

growth_protocol: Genomic DNA (gDNA) was purified from young grapevine leaves of cv. ‘Pinot Noir’


title: MYBPA1-2_S26_.R2

tag: gene id vcost

tag: gene id v1

tag: protein family

value: MYB

tag: protein source

value: Vitis vinifera


title: Blood, Control, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
RRW-03-barcodes.tsv.gz
RRW-03-features.tsv.gz
RRW-03-matrix.mtx.gz

tag: tissue

value: Blood

tag: cell type

value: CD11b+ myeloid cells

value: HTO

value: Anti CD45 + Anti MHC classI :WT--/TotalSeq-HTO-B0301 ; Ythdf2 cKO--/TotalSeq-HTO-B0302

tag: treatment

value: Control


title: H9 osteoblasts, shCtrl-2

tag: cell line

value: H9 osteoblasts

value: H9 cells infected with lentivirus expressing sgCtrl RNA as control


title: MYBPA1-1_S25_.R1


title: HPC7, ATAC-seq, rep5

value: Hematopoietic progenitor cell


title: Blood, Control, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
RRW-03-barcodes.tsv.gz
RRW-03-features.tsv.gz
RRW-03-matrix.mtx.gz

value: mRNA


title: H9 osteoblasts, shCtrl-1


title: PoxKu70-3

city: Nanning

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

data_processing:
Raw reads or raw data of the original sequencing sequence in FASTQ (fq) format are obtained after base calling and Bcl2 Fastq conversion.
The raw sequencing data contains linker information、low-quality bases、and undetected bases (represented by N). These information will cause great interference to subsequent information analysis. Clean reads will be obtained after analyzing by SOAPnuke software (v2.1.0).
The clean reads mapped onto the genome of Penicillium oxalicum strain HP7-1 to functional annotation, using the software HISAT2
FPKM, representing gene expression levels, was calculated with the software RSEM.
Assembly: GenBank database under accession number  JRVD02000000
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

organism: Penicillium oxalicum

growth_protocol: Fresh spores of the delta ku70 and mutant delta POX03070、delta PoxCxrA were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 4 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 10^8 spores per milliliter. The inoculated MMM containing glucose (1.0% w/v) with a final concentration of 1 × 10^6 spore/mL was pre-grown for 24 h at 28°C. The mycelia (~ 1.0 g) were collected and then transferred into fresh 100 mL liquid MMM containing 2% Avicel for 24 h.

extract_protocol:
Total RNA were extracted using TRIzol RNA Kit
The total RNA is enriched, the RNA fragments are reverse transcribed with random N6 primers, and the cDNA obtained to synthesize double-stranded DNA. A sticky end of "A" is connected with a linker, the ligated product is amplified by PCR with specific primers, the PCR product is heat denatured to form a single-stranded DNA, and the single-stranded DNA is obtained by a bridge primer to obtain a single-stranded circularization library.

value: Mycelium

tag: genotype

value: WT

value: Transfer from glucose medium to Avicel,and then culture for 24h


title: HPC7, ATAC-seq, rep2


title: Tumor, IR, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
RRW-02-barcodes.tsv.gz
RRW-02-features.tsv.gz
RRW-02-matrix.mtx.gz

source_name: Tumor

value: Tumor

tag: library type

value: Irradiation


title: HPC7, ATAC-seq, rep4


title: H9 osteoblasts, sgIL1R1-2

value: H9 cells infected with lentivirus expressing sgIL1R1


title: PoxKu70-2


title: HPC7, ATAC-seq, rep1


title: H9 osteoblasts, sgIL1R1-1


title: PoxKu70-1


title: Tumor, IR, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
RRW-02-barcodes.tsv.gz
RRW-02-features.tsv.gz
RRW-02-matrix.mtx.gz

tag: antibodies/tags


title: Tumor, Control, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
RRW-01-barcodes.tsv.gz
RRW-01-features.tsv.gz
RRW-01-matrix.mtx.gz


title: H9 osteoblasts, sgCEBPD-2

value: H9 cells infected with lentivirus expressing sgCEBPD


title: H9 osteoblasts, sgCEBPD-1


title: PoxCxrA-2

value: PoxCxrA knockout


title: WT, IR, YTHDF2 IP, r3, RIP-seq

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Reads on each GENCODE annotated gene were counted using HTSeq
Differentially expressed genes were called using DESeq2 package in R requiring at least 10 read counts in at least three samples with adjusted p-value < 0.05
YTHDF2 target genes were identified as differentially up-regulated genes comparing YTHDF2 IP sample with the corresponding Input samples
Assembly: mm10
Supplementary files format and content: text files include read counts for each Sample

source_name: MC38 tumors

growth_protocol: CD11b+ myeloid cells were sorted from MC38 tumors or blood of MC38 tumor-bearing mice

extract_protocol:
total RNA was harvested using Rneasy mini plus kit (Qiagen), followed by mRNA isolation using Dynabeads™ mRNA Purification Kit,then RIP for YTHDF2 was performed
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit (TaKaRa)

value: MC38 tumors

tag: antibody

value: anti-mouse YTHDF2 antibody (Abcam, ab220163)


title: H9 osteoblasts, sgCtrl-2


title: Spheroid2_RelB

city: BETHESDA

first: Christina

last: Annunziata

state: Maryland (MD)

address: 10 center drive, Building 10, room 12N226

institute: National Cancer Institute

data_processing:
Cutadapt: Adapter trimming
miRDeep2: Alignment and counts
edgeR GLM-LRT: Normalization and differential expression
Assembly: miRBase v22 (GRCh38)
Supplementary files format and content: Tab-separated text file with CPM values for each sample

source_name: ovarian carcinoma

growth_protocol: Adherent OV90 cells were grown in RPMI 1640 medium supplemented with Tetracycline-free Fetal Calf Serum (10%) and 1% penicillin/streptomycin. Spheroids were grown in in ultra-low attachment plates or flasks in DMEM-F12 media supplemented with 1% KnockOut serum replacement, 1% penicillin/streptomycin, 0.1% insulin-transferrin-selenium, and 0.4% bovine serum albumin and growth factors EGF 20 ng/mL and FGF 10 ng/mL.

extract_protocol:
Total RNA was collected from cells according to the manufacturer's instructions using the RNeasy Mini Kit (Qiagen 74104)
miRNA sequencing libraries were prepared by using the QIAseq miRNA Library Kit (Qiagen 331502)

treatment_protocol: 72 hours exposure to 1ug/ml doxycycline to induce shRNA silencing of indicated targets.

value: ovarian carcinoma

tag: cell type_growth_condition

value: Spheroid

value: RELB shRNA knockdown


title: Spheroid3_RelB


title: Spheroid4_RelB


title: PoxCxrA-1


title: Spheroid1_RelB


title: WT, IR, YTHDF2 IP, r2, RIP-seq

value: CD11b+ myeloid cells


title: POX03070-3

value: POX03070 knockout


title: H9 osteoblasts, sgCtrl-1

value: H9 osteoblasts

value: H9 cells infected with lentivirus expressing sgCtrl RNA as control


title: Spheroid4_RelA

value: RELA shRNA knockdown


title: Spheroid3_RelA


title: POX03070-2

value: Mycelium


title: WT, Control, YTHDF2 IP, r3, RIP-seq

value: WT

value: Control


title: Spheroid2_RelA


title: WT, Control, YTHDF2 IP, r2, RIP-seq


title: Tumor, Control, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
RRW-01-barcodes.tsv.gz
RRW-01-features.tsv.gz
RRW-01-matrix.mtx.gz

value: Tumor

value: mRNA


title: POX03070-1

value: Transfer from glucose medium to Avicel,and then culture for 24h


title: PoxCxrA-3

value: PoxCxrA knockout


title: H9 osteoblasts, SDC1-2 Ctrl

value: H9 cells infected with lentivirus expressing GFP as control


title: H9 osteoblasts, SDC1-1 Ctrl


title: WT, Control, YTHDF2 IP, r1, RIP-seq

value: MC38 tumors

value: anti-mouse YTHDF2 antibody (Abcam, ab220163)


title: Spheroid1_RelA

value: ovarian carcinoma

value: Spheroid


title: Nucleus accumbens, LR vehicle 5

city: Nuthetal

first: Andre

last: Kleinridders

state: Brandenburg

address: Arthur-Scheunert-Allee 155

department: Molecular and Experimental Nutritional Medicine

country: Germany

institute: University of Potsdam

data_processing:
BGI Bioinformatic analysis workflow
After sequencing, raw reads were filtered. Data filtering included removing adaptor sequences, contamination and low-quality reads from raw reads using SOAPnuke software developed by BGI (DOI: 10.1093/gigascience/gix120).
Filtered sequences were mapped to GrCM38/mm10 using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) Version: v2.0.4 (Parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000 --rna-strandness RF)
Clean reads were mapped to reference using Bowtie2 Version: v2.2.5 (Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --nomixed  --no-discordant -p 1 -k 200).
Gene expression level were calculated using RSEM Version: v1.2.12 (Parameters: default).
DEGs were detected with DEseq2 (Parameters: Fold Change >= 2.00 and Adjusted Pvalue <= 0.05).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples (AllSamples.GeneExpression.FPKM.xls)
Supplementary files format and content: tab-delimited text files includes DEG analyses (DEseq2_Method.GeneDiffExp.xls)

source_name: nucleus accumbens

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library

value: nucleus accumbens

tag: strain

tag: gender

value: male

value: wildtype

value: high fat diet/ LR


title: Nucleus accumbens, LR vehicle 6


title: WT, IR, Input, r3, RIP-seq

value: CD11b+ myeloid cells

value: Irradiation


title: Nucleus accumbens, LR vehicle 4


title: WT, IR, YTHDF2 IP, r1, RIP-seq

value: WT


title: Spheroid3_Neg

value: Wildtype


title: Spheroid2_Neg


title: WT, IR, Input, r1, RIP-seq


title: WT, IR, Input, r2, RIP-seq


title: H9 osteoblasts, SDC1-2

value: H9 osteoblasts

value: H9 cells infected with lentivirus expressing SDC1


title: Nucleus accumbens, LR vehicle 2


title: WT, Control, Input, r3, RIP-seq

value: Control


title: H9 osteoblasts, SDC1-1


title: Nucleus accumbens, LR vehicle 1


title: AD4_RelB

value: Adherent

value: RELB shRNA knockdown


title: WT, Control, Input, r1, RIP-seq

value: MC38 tumors


title: WT, Control, Input, r2, RIP-seq


title: Spheroid4_Neg


title: Nucleus accumbens, HFD vehicle 5

value: high fat diet/ vehicle


title: Nucleus accumbens, HFD vehicle 6


title: Nucleus accumbens, LR vehicle 3


title: RasV12cdc42- tumor at Day10, biological rep4

type: RNA

city: new haven

first: Tian

last: Xu

state: CONNECTICUT

address: 295 congress ave

department: Genetics

institute: Yale school of medicine

hyb_protocol: Reference and tumor mRNAs were hybridized to custom-made slides using a solution of TE, SSC, SDS and poly-A as a blocking agent. Hybridization was performed in chambers (DIE-TECH) for 10 min at 42°C, then approximately 15 hours at 64°C. Slides were washed three times with increasingly dilute concentrations of SSC, then dried.

scan_protocol: Images were scanned on an Axon 4000B scanner and analyzed using GenePix Pro 3.0 software (Axon Instruments).

data_processing: The raw measurements produced were the median fluorescence of each spot for the wavelength of the reference and tumor sample, as well as the ratio of Medians. These data were further lowess normalized and analyzed using GeneSpring software (Silicon Genetics).

organism: Drosophila melanogaster

source_name: Drosophila tumors from third instar larvae

label_protocol: mRNA amplification and labeling were performed with random hexamers as previously reported (Baugh et al., 2001). Wild-type reference mRNAs were labeled with dUTP-Cy5 and tumor mRNAs with dUTP-Cy3.

growth_protocol: Flies were raised on standard Drosophila media at 25°C.

extract_protocol: Approximately 30-40 discs were dissected from third instar larvae (wild-type, day 5-6 AEL; tumors, day 10 AEL) and placed in 300 μl TRIzol (Invitrogen) to isolate total RNAs.

value: eye-antennal discs at 3rd instar larval stage (Day 10)

source_name: Drosophila wild-type reference from third instar larvae

tag: tissues

value: eye-antennal discs at 3rd instar stage (Day5-6)


title: RasV12cdc42- tumor at Day10, biological rep2

description: dye-swap


title: AD2_RelB

value: ovarian carcinoma


title: IR, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using 10X Genomics Cell Ranger (v6.0.1).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: CD45+ cells were sorted from MC38 tumors of MC38 tumor-bearing mice

extract_protocol:
use a Takara iCell 8 and a MissionBio Tapestri
The libraries were performed using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

treatment_protocol: MC38 tumors were received irradition (20 Gy, one dose), four days after IR, cells were collected by flow sorting


title: Nucleus accumbens, HFD vehicle 4

value: nucleus accumbens

value: male


title: RasV12cdc42- tumor at Day10, biological rep1

description: dye-swap


title: RasV12cdc42- tumor at Day10, biological rep3


title: Control, scRNAseq

description: 10x Genomics


title: AD1_RelB


title: Nucleus accumbens, HFD vehicle 3

value: wildtype


title: AD4_RelA

value: RELA shRNA knockdown


title: Young 14 dpi

description: RNA was isolated from the brains of 5 mice.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 5.0.0. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Spinal Cord Meninges

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

treatment_protocol: see sample description

value: Spinal Cord Meninges

tag: age

value: 4 months

tag: Sex

value: female

tag: condition

value: 14 dpi


title: Nucleus accumbens, HFD vehicle 2


title: Young 7 dpi

value: 7 dpi


title: RasV12baz- tumor at Day10, biological rep4


title: AD3_RelA


title: Spheroid1_Neg

value: Spheroid

value: Wildtype


title: AD3_RelB

value: Adherent

value: RELB shRNA knockdown


title: Nucleus accumbens, HFD vehicle 1

value: high fat diet/ vehicle


title: Young 3 dpi

value: 3 dpi


title: AD2_RelA


title: RasV12baz- tumor at Day10, biological rep3

value: eye-antennal discs at 3rd instar larval stage (Day 10)

value: eye-antennal discs at 3rd instar stage (Day5-6)


title: RafGOFscirb- tumor at Day10, biological rep4


title: Young Naïve

value: naive


title: AD1_RelA

value: ovarian carcinoma


title: Nucleus accumbens, LFD vehicle 5

value: nucleus accumbens

value: male

value: wildtype

value: low fat diet/ vehicle


title: Nucleus accumbens, LFD vehicle 4


title: Aged 7 dpi

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

value: Spinal Cord Meninges

value: 22 months

value: female


title: AD3_Neg


title: Aged 14 dpi

value: 14 dpi


title: Nucleus accumbens, LFD vehicle 3


title: AD2_Neg

value: Wildtype


title: Aged 3 dpi


title: RasV12baz- tumor at Day10, biological rep1


title: Nucleus accumbens, LFD vehicle 2


title: Aged Naïve


title: RasV12baz- tumor at Day10, biological rep2


title: AD1_Neg

value: Adherent


title: RafGOFscirb- tumor at Day10, biological rep1


title: RafGOFscirb- tumor at Day10, biological rep2


title: Nucleus accumbens, LFD vehicle 1


title: RasV12scrib- tumor at Day10, biological rep3

description: dye-swap


title: Nucleus accumbens, LFD vehicle 6


title: RafGOFscirb- tumor at Day10, biological rep3


title: WGBS Dppa3 KO FGO rep2

status: Public on Apr 27 2023

city: Fukuoka

first: Wan Kin

last: Au Yeung

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

data_processing:
WGBS data was mapped to mouse genome mm10 using Bismark v0.20.0.
Assembly: mm10/GRCm38
Supplementary files format and content: The CG coverage files are tab-delimited, 1-based genomic coordinates for every covered CG site in the experiment and are in the following format: <chromosome> <start position> <end position> <methylation level> <methylated cytosine> <unmethylated cytosine>.

source_name: fully grown oocyte (FGO)

growth_protocol: All animal experiments were performed under the ethical guidelines of Kyushu University, the Institutional Animal Care and Use Committee at Harvard Medical School. All mice used in this manuscript were euthanized by CO2 asphyxiation.

extract_protocol: WGBS (PBAT) libraries were constructed as previously described (Miura et al., 2012; Au Yeung et al., 2019).

tag: Stage

value: fully grown oocyte (FGO)


title: WGBS control FGO rep2

value: Stella+/-


title: WGBS Dppa3 KO FGO rep1


title: WGBS control FGO rep1


title: RasV12scrib- tumor at Day10, biological rep4


title: ‘Tarocco’ Blood orange juice sac, 90 days after storege, Biol rep 3

city: Changsha

first: Ling

last: Sheng

address: Donghu

institute: Hunan Agricultural 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, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.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 .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: http://citrus.hzau.edu.cn/orange/（Citrus sinensis v1.0)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Citrus sinensis

source_name: fruit

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fruit

value: postharvest stage

value: fruit juice sac

value: Tarocco' Blood orange

value: postharvest storage

tag: time

value: 90 days after storege


title: ‘Tarocco’ Blood orange juice sac, 90 days after storege, Biol rep 2

tag: tissue


title: RasV12scrib- tumor at Day10, biological rep1

description: dye-swap

value: eye-antennal discs at 3rd instar larval stage (Day 10)

value: eye-antennal discs at 3rd instar stage (Day5-6)


title: AD4_Neg

value: ovarian carcinoma


title: ‘Tarocco’ Blood orange juice sac, 90 days after storege, Biol rep 1

tag: cell type


title: ‘Tarocco’ Blood orange juice sac, 60 days after storege, Biol rep 2

tag: treatment

value: 60 days after storege


title: ‘Tarocco’ Blood orange juice sac, 60 days after storege, Biol rep 3

tag: cell line


title: ‘Bingtangcheng' fruit juice sac, 90 days after storege, Biol rep 1

tag: genotype

value: Bingtangcheng' sweet orange


title: ‘Bingtangcheng' fruit juice sac, 90 days after storege, Biol rep 3


title: RasV12scrib- tumor at Day10, biological rep2


title: ‘Tarocco’ Blood orange juice sac, 30 days after storege, Biol rep 1

value: 30 days after storege


title: ‘Tarocco’ Blood orange juice sac, 30 days after storege, Biol rep 2


title: ‘Bingtangcheng' fruit juice sac, 30 days after storege, Biol rep 2


title: ‘Tarocco’ Blood orange juice sac, 15 days after storege, Biol rep 3

value: 15 days after storege


title: ‘Tarocco’ Blood orange juice sac, 15 days after storege, Biol rep 2


title: ‘Bingtangcheng' fruit juice sac, 30 days after storege, Biol rep 1


title: ‘Tarocco’ Blood orange juice sac, 15 days after storege, Biol rep 1


title: ‘Bingtangcheng' fruit juice sac, 30 days after storege, Biol rep 3


title: ‘Tarocco’ Blood orange juice sac, 30 days after storege, Biol rep 3


title: ‘Bingtangcheng' fruit juice sac, 60 days after storege, Biol rep 1


title: ‘Tarocco’ Blood orange juice sac, 60 days after storege, Biol rep 1


title: ‘Bingtangcheng' fruit juice sac, 60 days after storege, Biol rep 3


title: ‘Bingtangcheng' fruit juice sac, 60 days after storege, Biol rep 2


title: ‘Tarocco’ Blood orange juice sac, 0 days after storege, Biol rep 2

value: 0 days after storege


title: ‘Bingtangcheng' fruit juice sac, 15 days after storege, Biol rep 3


title: ‘Bingtangcheng' fruit juice sac, 0 days after storege, Biol rep 3


title: ‘Tarocco’ Blood orange juice sac, 0 days after storege, Biol rep 1


title: ‘Bingtangcheng' fruit juice sac, 0 days after storege, Biol rep 2


title: ‘Bingtangcheng' fruit juice sac, 90 days after storege, Biol rep 2


title: ‘Bingtangcheng' fruit juice sac, 0 days after storege, Biol rep 1


title: ‘Tarocco’ Blood orange juice sac, 0 days after storege, Biol rep 3


title: CITE-seq-4wks-cDNA

city: Bordeaux

first: Stephania

last: Contreras Castillo

address: 2, Docteur Hoffman Martinot

country: France

institute: Université de Bordeaux

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
wk4_barcodes.tsv.gz
wk4_features.tsv.gz
wk4_matrix.mtx.gz
wk4_raw_barcodes.tsv.gz
wk4_raw_features.tsv.gz
wk4_raw_matrix.mtx.gz

data_processing:
Fastq files were processed with 10x Genomics Cell Ranger 6.0 software using "count" pipeline with --feature-ref parameter to include the surface protein barcodes (ADT and HTO). Reads were aligned to the mouse reference genome mm10 (GENCODE vM23/Ensembl98).
Further processing was done with Seurat v4.1.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Bone marrow

extract_protocol:
Total bone marrow was obtained by crushing femur, tibia, humerus and pelvis bones. Cells were lineage depleted using Streptavidin Microbead Kit (Miltenti) using two different cocktails of biotinylated antibodies according to each time point. For the 4-weeks timepoint we used Gr-1, CD19, TCRb, Ter119, CD11b and NK1.1 and for the 8-weeks timepoint we used Gr-1, CD19, TCRb and Ter119. After lineage depletion, cells were stained with Zombie Aqua (Biolegend), followed by incubation with 25 different TotalSeq-A antibodies (Biolegend) listed in Supplementary Table 2. Lin-ckit+Tom+ cells (4-weeks time point) and Lin-Flt3+Tom+ (8-weeks time point) were sorted using flow cytometry. From each mice, 6000 cells were collected and loaded into a Chromium Controller (10X Genomics).
Library was prepared using Chromium Next GEM Single Cell 3' Reagens Kits v3.1 with Feature Barcoding technology for surface protein protocol (Revision D, (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR and with specific primers amplifying the antibody-derived tags, following Biolegend protocol for TotalSeq-A antibodies. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions. For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-ADT-seq library: amplification was performed at 98°C for 2’ followed by 16 cycles at 98°C for or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with Small RNA RPI3 and RPI4 primer as i7 primer (Illumina) for 4- and 8-weeks time points, respectevely.
-Hashtag-seq library: amplification was performed at 98°C for 2’ followed by 16 cycles 98°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with TruSeq D703_long and D704_long primer as i7 primer (Illumina) for 4- and 8-weeks time points, respectevely.
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC*T*C-3’ SI-PCR primer as i5 primer (Illumina) was used for both ADT- and Hashtag- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% hashtag library before sequencing.
scRNA-seq coupled to CITE-seq

value: Bone marrow

value: Lin-cKit+Tom+

value: Pdzk1ip1-CreER R26Tom/Tom

value: Female

tag: timepoint

tag: developmental stage

value: old and young


title: CITE-seq-4wks-ADT

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
wk4_barcodes.tsv.gz
wk4_features.tsv.gz
wk4_matrix.mtx.gz
wk4_raw_barcodes.tsv.gz
wk4_raw_features.tsv.gz
wk4_raw_matrix.mtx.gz


title: CITE-seq-8wks-Hashtag

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
HTO1: young1; HTO2: young2; HTO3: young3; HTO4: old1; HTO5: old2; HTO6: old3
wk8_barcodes.tsv.gz
wk8_features.tsv.gz
wk8_matrix.mtx.gz
wk8_raw_barcodes.tsv.gz
wk8_raw_features.tsv.gz
wk8_raw_matrix.mtx.gz


title: CITE-seq-8wks-ADT

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
wk8_barcodes.tsv.gz
wk8_features.tsv.gz
wk8_matrix.mtx.gz
wk8_raw_barcodes.tsv.gz
wk8_raw_features.tsv.gz
wk8_raw_matrix.mtx.gz


title: CITE-seq-4wks-Hashtag

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
HTO1: young1; HTO2: young2; HTO3: young3; HTO4: old1; HTO5: old2; HTO6: old3
wk4_barcodes.tsv.gz
wk4_features.tsv.gz
wk4_matrix.mtx.gz
wk4_raw_barcodes.tsv.gz
wk4_raw_features.tsv.gz
wk4_raw_matrix.mtx.gz


title: ‘Bingtangcheng' fruit juice sac, 15 days after storege, Biol rep 2

value: fruit

value: postharvest stage

value: fruit juice sac


title: ‘Bingtangcheng' fruit juice sac, 15 days after storege, Biol rep 1

value: postharvest storage


title: 91

city: Boston

first: James

middle: M.

last: Billingsley

state: MA

address: Landmark Center, 3rd Floor East, 401 Park Drive

institute: harvard T.H. Chan school of public health

data_processing:
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Quality control and initial data exploration was conducted using the GeoMx DSP Analysis Suite.  Sequencing quality per AOI was examined and an under-sequenced area (B_04) with zero deduplicated reads was excluded.  Expression of each transcript was measured by 5 or more probes; outlier probes (geomean probe in all AOI/geomean of all probes for a transcript = <0.1; or probe failure in the Grubbs outlier test in over 20% AOIs) were excluded and the remaining probes combined to generate a single (post “biological probe QC”) expression value per gene target per AOI.
The expression matrix was quantile normalised and corrected for batch effects using the Limm "removeBatchEffect" function.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.
Library strategy: GeoMx-Seq

source_name: femur

growth_protocol: 3-month and 18-month old wild type mice

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: femur

value: 18 months


title: 87


title: 94


title: 83


title: 85


title: 90


title: 88


title: 86


title: 84


title: 89


title: 81


title: Old_ATAC-seq, sample5

library_source: genomic single cell

data_processing:
Fastq files were processed with 10x Genomics Cell Ranger arc 2.0.0 software using "count" pipeline; reads aligned to mm10 reference genome (cellranger version 2020, bulild A, based on GRCm38)
QC; dimensionality reduction; normalization and scaling were performed with Seurat v.4.3.0 and Signac version 1.9.0.
Assembly: mm10
Supplementary files format and content: .h5 format, readable easily in R or python; contains the RNA and ATAC count data slots (only ATAC used for analysis, as RNA failed) generated by cellranger; these are the starting point for analysis

extract_protocol:
Bone marrow cells were harvested by flushing the femur, tibia, humerus, and pelvis bones. Lineage negative (Lin-) compartment was enriched by using Streptavidin Microbeads with biotinylated antibodies (B220, TCRβ, NK1.1, CD11b, Gr-1, and Ter119). Collected Lin- cells were stained with c-Kit, Sca-1, CD150, and CD48 to define and sort HSCs. ~33,000 Lin -Sca-1 +c-Kit +CD150 +CD48 -HSCs were sorted and pooled, and nuclei isolation was performed according to Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol (10x Genomics).
scRNA-seq and scATAC-Seq libraries were constructed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit (10x Genomics, PN-10000285) according to the manufacturer’s protocol. Briefly, 5-7K nuclei in 1x nuclei buffer were loaded with a target output of∼4,000. Single nuclei were encapsulated into emulsion droplets using Chromium Controller (10x Genomics). Transposition, reverse transcription and library preparation were performed on C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). Amplified cDNA was evaluated on a Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies, PN5067-4626) and final libraries on a Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies,PN5067-5584). Individual libraries were normalized to 2nM and pooled for sequencing. Pools were sequenced with 200 cycle run kits (50bp Read1, 10bp Index1 24bp Index2 and 90bp Read2) on the NovaSeq 6000 Sequencing System (Illumina) and analyzed using CellRanger software.

value: Male

value: old


title: Old_ATAC-seq, sample6


title: Old_ATAC-seq, sample8


title: 78


title: 80


title: Old_ATAC-seq, sample7


title: 75


title: 79


title: 82


title: CITE-seq-8wks-cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
wk8_barcodes.tsv.gz
wk8_features.tsv.gz
wk8_matrix.mtx.gz
wk8_raw_barcodes.tsv.gz
wk8_raw_features.tsv.gz
wk8_raw_matrix.mtx.gz


title: 76


title: 73


title: 72


title: 69


title: 68


title: 71


title: 77


title: 70


title: 66


title: 59


title: 60


title: 63


title: 64


title: 58


title: 65


title: 56


title: 53


title: 51


title: 50


title: 49


title: 48


title: 52


title: 42

value: 3 months


title: 44


title: 40


title: 41


title: 37


title: 38


title: 33


title: 36


title: 35


title: 39


title: 67


title: 34


title: 57


title: 61


title: 32


title: 55


title: 31


title: 29


title: 30


title: 28


title: 27


title: 25


title: 43


title: 24


title: 23


title: 21


title: 18


title: 19


title: 15


title: 16


title: 14


title: 13


title: 10


title: 9


title: 11


title: 26


title: 1


title: MFS Vehicle, scRNAseq

city: Palo Alto

first: Alex

last: Dalal

state: California

address: CT Surgery, 870 Quarry Rd Ext

department: Cardiothoracic Surgery

institute: Stanford University

description: 10x Genomics

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite 3.1.0’. Raw base-call files from NovaSeq 6000 sequencer were demultiplexed to first generate FASTQ files using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (mm10-3.0.0) genome, cell barcodes and unique molecular identifiers were filtered and corrected using the cellranger count pipeline
The final output filtered expression matrices were imported into the Seurat package in R and built into Seurat objects using the CreateSeuratObject function.
Standard quality control measures were then taken to exclude outliers representing doublets/clumps and free RNA. Cells with greater than 5% mitochondrial gene content were excluded  Data normalization, scaling and regression by mitochondrial content were then performed using the SCTransform command in Seurat.
Assembly: mm10
Supplementary files format and content: Processed data files(.csv format) are exported expression matrices from the SCT assay within the Seurat package in R. Columns represent individual cell barcodes, rows represent features (genes) and numerical values represent the normalized expression data.

source_name: Thoracic aorta

extract_protocol:
The aortic root was dissected completely and divided below the aortic valve. The ascending aorta was divided at the takeoff of the brachiocephalic artery. Aortas were transferred to a separate dish and rinsed in HBSS. Specimens were combined into groups with age and genotype-matched animals as biologic replicates with equal numbers of male and female samples. The aortas were then digested in enzymatic solution containing 2U/mL Liberase TM (Roche #05401127001) and 2U/mL elastase (Worthington #LS002279) in Hanks buffered saline solution (HBSS) for one hour. The cell suspension was filtered through a 70uM strainer, centrifuged and resuspended in cold HBSS. Suspensions were processed with FACS to exclude debris. Samples were then processed using a 10x Genomics microfluidics chip to generate barcoded Gel Bead-In Emulsions (GEMs) according to manufacturer protocols.
Individual sample libraries were generated from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

value: Thoracic aorta

value: pooled male and female

value: control

value: 16 weeks


title: 3


title: 4


title: 2


title: MFS GLPG, scRNAseq

description: 10x Genomics


title: 22


title: Tail, 3 week infection, Imatinib, rep5

city: Atlanta

first: Daniel

last: Kalman

state: GA

address: 144 Whitehead Bldg., 615 Michael St.

department: Pathology

institute: Emory University

data_processing:
Quality control was performed on the raw reads using FastQC.
Adaptors were trimmed from the ends of reads using QuasR.
Hisat2 was used for alignment of the reads to the mouse genome with 66-80% of reads mapped to a single gene. 6-25% of the mapped reads were successfully assigned to gene alignments resulting in 5.5 million-14million assigned alignments per sample. Genes with low expression levels were filtered out.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

source_name: Tail

extract_protocol:
3-5mm sections of tail were cut fresh from the tail from areas containing granulomatous lesions and immediately placed in Trizol (Invitrogen). Tissue was cut with sterile scissors and then homogenized in the Bullet Blender Tissue homogenizer (Next Advance, Troy, NY). RNA extraction was performed in accordance with manufacture instructions.
RNA libraries for RNA-seq were prepared using Clontech SmartER Stranded Total RNA-seq Kit- Pico Input Mammalian + rRNA depletion following manufacturer's protocols.

treatment_protocol: 7 day Osmotic pumps containing either water or 100mg/kg/day imatinib were installed in the no infection C57BL6/J mice. 7 days later mice were sacrificed and 3-5 mm of whole tail tissue was removed  1-2cm  from the base of the tail, and imidiatelty placed in Trizol. For 1 week infection- 7 day osmotic pumps containing either water or 100mg/kg/day imatinib were installed 1 day prior to   infection via the tail vein with 2x10^6 CFU M. marinum in  sterile PBS. Mice were scarificed and tissue collected at day 6 post infection. For 3 week infection- Mice were infected via the tail vein with 2x10^6 CFU M. marinum in  sterile PBS and infection developed for 14 days. 7 day osmotice pump containing either water or 100mg/kg/day imatinib was installed on day 14 of infection. . Mice were scarificed and tissue collected at day 21 post infection.

value: Tail

tag: infection length

value: 3 weeks

value: Gleevec


title: 5


title: Tail, 3 week infection, Imatinib, rep3


title: Tail, 3 week infection, Imatinib, rep2


title: Tail, 3 week infection, Imatinib, rep4


title: 17


title: 12


title: 6


title: Tail, 3 week infection, no treatment, rep5


title: Tail, 3 week infection, no treatment, rep4


title: Tail, 3 week infection, no treatment, rep3


title: Tail, 3 week infection, no treatment, rep2


title: MGD1551F

city: Los Angeles

first: Valerie

last: Arboleda

address: 615 Charles E. Young Drive South

institute: UCLA

data_processing:
Arboleda Lab Pipeline
Samples were demultiplexed after sequencing.
Raw reads were then aligned against the Gencode human genome version hg38 (GR38) version 31 using STAR 2.7.0e with default parameters.
Gene counts from raw reads were generated using featureCounts 1.6.5 from the Subread package. Only reads that uniquely mapped to exons of a gene were counted per gene. Differential expression analysis was completed using DESeq2 v1.24.0, adjusting for sample gender.
Assembly: GR38
Supplementary files format and content: Text files include raw count values for each sample, csv files include DESeq normalized counts per sample

source_name: Patient-Derived

growth_protocol: Patient- derived fibroblast cell lines were grown in DMEM (Gibco™, #11-995-073), 10% FBS, 1% Non-essential Amino Acid (100X, Gibco™, 11140-050) and 1% PenStrep at 37℃ in 5% CO2 incubators.

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen, #74136). 1ug of. NA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QIAseq FastSelect −rRNA HMR (Qiagen, #334386) and lllumina Truseq® Stranded Total RNA Library Prep Gold (Illumina, 20020599)

value: Patient-Derived

value: Fibroblast

value: Control


title: MGD1614F


title: MGD1615F


title: MGD1560F


title: MGD1613F


title: MGD1616F


title: MGD1558F


title: MGD1557F


title: Tail, 3 week infection, no treatment, rep1


title: MGD1550F


title: 1551-Input

description:
fibroblast_CUTnRUN-H3K27me3_rawCounts.txt
fibroblast_CUTnRUN-H3K4me3_rawCounts.txt

data_processing:
Samples were analyzed using the established NF-Core CUT&RUN analysis pipeline.
Assembly: GR38
Supplementary files format and content: Text files with raw peak counts normalized to IgG peak counts
Library strategy: CUT&RUN

source_name: Control-Derived

extract_protocol:
100,000 cells per line per antibody / condition was washed with 1X Wash Buffer three times, before resuspension in 100 µl of 1X Wash Buffer (+ spermidine + PIC), according to protocol.
CUT&RUN (Cleavage Under Targets & Release Using Nuclease) libraries were prepared with the established CUT&RUN Assay Kit (Cell Signaling, #86652S). CUT&RUN libraries were prepared using the SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina (Cell Signaling, #56795S) with SimpleChIP ChIP-seq Multiplex Oligos for Illumina (Cell Signaling, #47538S) according to manufacturer guidelines, with modifications for CUT&RUN as noted in the CUT&RUN Assay Kit (Cell Signaling, #86652S). All libraries were quantified on the Qubit 4.0 and library quality assessed using Agilent High Sensitivity DNA Tapestation (Agilent, 5067-5584) before multiplexing and sequencing on a Nextseq 550 Mid Output Kit (150 cycles) with 1% PhiX for a minimum of 5 million paired-end reads per sample with 50bp read length.

value: Control-Derived

tag: chip antibody


title: MGD1549F


title: Tail, 1 week infection, Imatinib, rep5

tag: strain

value: 1 week


title: 1551-IgG

value: IgG


title: MGD1548F


title: 1550-Input


title: Tail, 3 week infection, Imatinib, rep1


title: 1551-H3K27me3

description: fibroblast_CUTnRUN-H3K27me3_rawCounts.txt


title: 1551-H3K4me3

description: fibroblast_CUTnRUN-H3K4me3_rawCounts.txt


title: 1550-IgG


title: Tail, 1 week infection, Imatinib, rep4


title: Tail, 1 week infection, Imatinib, rep3


title: MGD1547F


title: Tail, 1 week infection, Imatinib, rep2


title: MGD1546F


title: 1550-H3K4me3


title: 1545-IgG


title: Tail, 1 week infection, Imatinib, rep1


title: 1545-Input


title: Tail, 1 week infection, no treatment, rep5


title: 1545-H3K27me3


title: MGD1734B

extract_protocol:
Whole blood samples were collected and purified using MagMAX for Stabilized Blood Tubes RNA Isolation Kit (Qiagen, #3341894) with DNase treatment. 1ug of total RNA was used to construct libraries.
RNA libraries for RNA-seq were prepared using QIAseq FastSelect −rRNA HMR (Qiagen, #334386) and lllumina Truseq® Stranded Total RNA Library Prep Gold (Illumina, 20020599)

value: Whole Blood


title: Tail, 1 week infection, no treatment, rep3


title: 1545-H3K4me3


title: 1544-IgG


title: 1544-Input


title: MGD1544F


title: 1544-H3K27me3


title: Tail, 1 week infection, no treatment, rep2


title: 1544-H3K4me3


title: Tail, 1 week infection, no treatment, rep4


title: MGD1732B


title: MS_ZKW.17.2345

data_processing:
Quality of reads were assessed using FastQC.
Raw reads were then aligned to GENCODE Human genome version hg38 (GR38) version 31 using BWA-MEM.
BAM files were then sorted, indexed, filtered against chrX, chrY, and MT reads using SAMtools. Picard tools were then used to generate insert size histograms and remove duplicates from BAM files.
Narrow peaks from each sample were called using MACS2 callpeak; any peak that overlapped by at least one base was then merged using BEDtools merge. Reads overlapping merged peaks were counted using featureCounts.
Reads overlapping merged peaks were counted using featureCounts. Peaks were annotated using annotatePeaks.pl from HOMER to the nearest gene or regulatory element, including exon, intron, promoter, 5’ untranslated region (UTR), 3’ UTR, and other genomic features.
DESeq2 was used to identify differentially open peaks between disease and control samples, adjusting for sample gender. Peaks with p-adjusted value (Benjamini-Hochberg) less than 0.05 were classified as significantly differentially open (Wald’s test), and fold changes were shrunk using approximate posterior estimation for GLM coefficients.
Assembly: GR38
Supplementary files format and content: Text files include raw peak count values for each sample, csv files include DESeq normalized peak counts per sample

extract_protocol:
50,000 freshly isolated cells per line were treated with Tn5 transposase.
ATAC-seq libraries were prepared according to established protocol (Corces, 2017). 50,000 freshly isoated cells per fibroblast line was used as input. After purification and PCR amplification for library generation, the libraries were double-sided bead purified using AMPure XP beads (Beckman, A63881) to remove contaminating primer dimers. All libraries were quantified on the Qubit 4.0 and library quality was assessed using Agilent High Sensitivity DNA Tapestation (Agilent, 5067-5584) before multiplexing and sequencing on a Nextseq 550 for Libraries  to a minimum of 40 million paired-end reads per sample with 75bp length.


title: MGD1731B


title: MS_MGD_1551


title: MGD1727B


title: Tail, no infection, Imatinib, rep5


title: MS_GMO1651


title: MS_ZKW.17.2343


title: MGD1724B


title: MS_GMO0323


title: MGD1733B


title: 1550-H3K27me3


title: MGD1723B


title: Tail, no infection, Imatinib, rep4


title: Tail, no infection, Imatinib, rep3


title: MGD1613


title: MGD1616


title: MGD1560


title: Tail, no infection, Imatinib, rep2


title: MGD1551


title: MGD1557


title: MGD1722B


title: Tail, 1 week infection, no treatment, rep1


title: MGD1550


title: Tail, no infection, Imatinib, rep1


title: Tail, no infection, no treatment, rep5


title: MGD1715B


title: GMO1651


title: MGD1714B


title: GMO0323


title: MGD1547


title: Tail, no infection, no treatment, rep4


title: Tail, no infection, no treatment, rep3


title: DHEP Input

city: Bronx

first: Julio

middle: A

last: Aguirre-Ghiso

state: NY

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
fastQC
bowtie/1.1.2: bowtie -p 12 -k 1 -m 1 --best -S -n 2 -l 50 -q --chunkmbs 500 -q /sc/orga/projects/bernse03a/bowtieIndexes/hg19
macs/2.1.0
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: DHEP.enriched.H3K27ac.TE.txt: Differential enhancer.
Supplementary_files_format_and_content: THEP.enriched.H3K27ac.TE.txt: Differential enhancer.

source_name: DHEP Input

growth_protocol: T-HEp3 tumor grown on chicken CAM were extracted and dissociated with collagenase. Single cell suspension of T-HEp3 were grown on dish, and D-HEp3 cells grown on dish (passage >P130 cells) were used to isolate nuclei and perform ChIP-seq experiment.

extract_protocol: Alonso A, Bernstein E, Hasson D. Histone Native Chromatin Immunoprecipitation. Methods Mol Biol. 2018;1832:77-104. doi: 10.1007/978-1-4939-8663-7_5. PMID: 30073523.

value: DHEP

value: head and neck squamous cell carcinoma

tag: passage


title: MGD1711B


title: Tail, no infection, no treatment, rep2


title: THEP Control_H3K27ac_1

description: THEP_CTL_AA_merged_q1e-2_peaks_bl_AllEnhancers.table.xlsx

data_processing:
ChIP-seq reads were trimmed with Trim Galore! V0.6.6 with default parameters
ChIP-seq reads were aligned to the UCSC hg38 genome using bowtie2  with flags -end-to-end, --sensitive, -X 2000
Mitochodrial  and pseudo chromosomes were filtered out from the aligned reads, followed with removal of duplicated reads using picard v2.2.4 Markduplicates with  flags REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using deepTools 3.2.1 bamCoverage with flags --outFileFormat bigwig  --binSize=10  --normalizeUsing RPKM --extendReads=200
Assembly: hg38
Supplementary files format and content: THEP_CTL_AA_merged_q1e-2_peaks_bl_AllEnhancers.table

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated.
Sequencing libraries were generated and barcoded for multiplexing according to Illumina recommendations with minor modifications. Briefly, 2–8 ng Input or ChIP DNA was end- repaired and A-tailed. Illumina Truseq adaptors were ligated, and libraries were PCR-amplified using KAPA HiFi DNA Polymerase with no more than 12-15 cycles. Libraries were size-selected to exclude polynucleosomes using AMpure Beads. All steps in library preparation were carried out using NEB enzymes (Hasson et al., 2013). Libraries were sequenced on Illumina NextSeq500 (75bp single-end reads).

treatment_protocol: Cells were treated with 5 nM Azacytidine for 48 hrs followed by atRA 1 uM for 48 hrs. For control, PBS and DMSO were used.

value: Epicypher antibody, cat # 13-0045


title: MGD1710B


title: THEP Input

source_name: THEP Input

value: THEP


title: THEP H3K27me3

data_processing:
fastQC
bowtie/1.1.2: bowtie -p 12 -k 1 -m 1 --best -S -n 2 -l 50 -q --chunkmbs 500 -q /sc/orga/projects/bernse03a/bowtieIndexes/hg19
macs/2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: THEP H3K27me3


title: DHEP H3K27me3

source_name: DHEP H3K27me3


title: THEP H3K27ac

source_name: THEP H3K27ac


title: MGD1712B


title: THEP Aza Atra_H3K27ac_1

value: AZA (5 nM)+atRA (1uM)


title: DHEP H3K27ac

source_name: DHEP H3K27ac


title: Tail, no infection, no treatment, rep1


title: MGD1616B


title: GST rep 3

city: Dresden

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

institute: MPI-CBG

data_processing:
Basecalling was performed with bcl2fastq v2.19.1
Reads were mapped using STAR v2.5.2b (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Abundance estimation was performed with STAR (--quantMode GeneCounts)
Genome_build: GRCh38.p13, Ensembl_v99
Supplementary_files_format_and_content: Raw counts

source_name: HEK 293

growth_protocol: HEK 293 cell were grown in suspension culture to a density of 4 million cells/ml.

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacterers protocol
mRNA was treated using the NEBNext rRNA depletion Kit (human, mouse, rat) from New England Biolabs (NEB) according to the manufacturer’s instructions to remove ribosomal RNA. Subsequently, the samples were subjected to the workflow for strand specific RNA-Seq library preparation (NEBNext Ultra II Directional RNA Library Prep, NEB).

treatment_protocol:
Lysate preparation: HEK cells were suspended in lysate buffer (50 mM HEPES (pH 7.5), 100 mM NaCl, 5 mM MgCl2, 1 mM DTT, 0.1% Tween 20) in the presence of a protease inhibitor cocktail, frozen, thawed and lysed using a microfluidizer (LM-20, microfluidics).
GST pulldown: Proteins were incubated with GSH resin to allow binding. After washing the resin, it was incubated with freshly prepared HEK 293 lysate for 1.5 h. Prior elution the resin was extensively washed to remove unspecific binding partners.

value: HEK 293

value: HEK 293 suspension cells

tag: bait

value: GST


title: GST rep 2


title: MGD1615B


title: RNAseq E10.5 PA3 delta-E3  3

city: Basel

first: Filippo

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
HiSeq 2500: Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
NovaSeq 6000: Illumina RTA 3.4.4 and bcl2fastq2 v2.20 was used for basecalling and demultiplexing.
Reads of single-end and paired-end datasets were aligned to the reference genome using the QuasR Bioconductor package (REF: PMID: 25417205, version 1.34.0) by the qAlign function with parameters aligner="Rhisat2" (REF: PMID: 25751142, version 1.12.0) and splicedAlignment=TRUE.
Alignments overlapping genes from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.4.7) were quantified using the qCount function from the QuasR Bioconductor package (REF: PMID: 25417205, version 1.34.0) with parameter orientation = "opposite".
Assembly: mm10/ GRCm38
Supplementary files format and content: Comma-seperated text files with gene annotation (ENTREZID, number of exonic bases, ENSEMBL gene ID, gene symbol) and raw alignment counts for each gene and sample.

source_name: Cranial neural crest cells

extract_protocol:
Embryonic tissues were micro-dissected at E10.5, E12.5 or E14.5. Dissected tissue from E10.5 and E12.5 embryos was kept in 1× PBS on ice, then treated with 0.5% trypsin/1× EDTA at 37 °C for 10 minutes and immediately put on ice. Dissected tissue from E14.5 embryos was kept in 1× PBS on ice, then treated with papain digestion mix (10 mg ml−1 papain, 2.5 mM cysteine, 10 mM HEPES (pH 7.4), 0.5 mM EDTA and 0.9× DMEM) for 7 min at 37 °C and immediately put on ice. The tissue was rinsed once in ice-cold 1× DMEM/10% FBS, followed by two washes in ice-cold 1× DMEM. Tissue was dissociated by pipetting. Cranial NCCs from embryos with genotype Wnt1::Cre;ROSARFP were filtered and collected by FACS. After sorting, cranial NCCs were pelleted by centrifugation for 5 minutes, 1000 rpm at 4°C. Total RNA was extracted using the Single Cell RNA Purification Kit (NORGEN, 51800) with genomic DNA digestion using an RNase-Free DNase I Kit (NORGEN, 25710) according to the manufacturers’ protocol. For each sample, three independent biological replicates were prepared.  For sequencing of total RNA, unstranded RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 according to manufacturers’ instructions. Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single-end)  or an Illumina NovaSeq machine (50bp read length, paired-end).
IlluminaTruSeqTotalRNA

value: Cranial neural crest cells

tag: location


title: GST-Ferry rep 3

value: GST-Ferry complex


title: MGD1713B

value: Patient-Derived


title: GST rep 1


title: GST-Ferry rep 1


title: RNAseq E10.5 PA3 delta-E3  1


title: MGD1569B


title: GST-Ferry rep 2


title: CD57+ CD8+_rep 3

city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

country: Australia

institute: JCSMR

data_processing:
The RNA sequencing data of all 12 samples were assessed by FastQC, and aligned to human genome GRCh38 using HISAT2 (version 2.1.0) and sorted with SAMtools, and mapped reads were assigned and counted based on gene annotations by FeatureCount.
Lowly expressed genes were excluded for the downstream analysis, the genes with at least 0.5 count per million reads in more than 3 samples were selected.
Counts were normalized by trimmed mean of M values (TMM) method and transformed by voom with sample quality adjustment, then the data was fitted in a linear model and moderated t-statistics with empirical Bayes method, and the different expression genes were determined by Benjamini-Hochberg adjusted P value < 0.05, and visualized with glimma.
Supplementary_files_format_and_content: text format of raw exon level count for all samples

source_name: PBMCs

growth_protocol: No growth protocol. Fresh FACS-isolated cells from PBMCs of healthy donors

extract_protocol:
Different indicated T cell subsets are FACS-purified from PBMCs of three healthy donors with >95% purity. Cells are immediated submmited to GenElute Total RNA isolation kit (Sigma) for total RNA extraction according to the instruction, and the quality and integrity of RNA samples are validated by Bioanalyzer (Agilent) with RIN values > 8.0.
The mRNA library is prepared by ACRF Biomolecular Resource Facility at ANU using Illumina TruSeq Stranded mRNA Library Prep kit and sequenced in one high-output flow cell with 75 bp single-end reads by NextSeq500 sequencer (Illumina), each sample was covered with at least 25 million reads.

treatment_protocol: No treatment protocol. Fresh FACS-isolated cells from PBMCs of healthy donors

tag: marker

value: Viability Dye eFluo 780- CD4- CD8+ CD57+

tag: sample type


title: CD57+ CD8+_rep 2

value: Fresh FACS-isolated cells from PBMCs of healthy donors


title: CD57+ CD8+_rep 1


title: CD57- CD4+ TEM_rep 1

value: Viability Dye eFluo 780- CD4+ CD8- CD57- CD45RA- CCR7-


title: CD57- CD4+ TEM_rep 2


title: CD57+ CD4+ TEM_rep 3

value: Viability Dye eFluo 780- CD4+ CD8- CD57+ CD45RA- CCR7-


title: RNAseq E10.5 PA2 delta-E3  2


title: CD57+ CD4+ TEMRA_rep 2

value: Viability Dye eFluo 780- CD4+ CD8- CD57+ CD45RA+ CCR7-


title: RNAseq E10.5 PA2 delta-E3  3


title: RNAseq E10.5 PA2 delta-E3  1


title: fy-5 KO 2

data_processing:
Basecalling was performed with bcl2fastq
Reads were mapped using STAR v2.7.3a (--outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 3 1 1 1)
Abundance estimation was performed with STAR v2.7.3a (--quantMode GeneCounts)
Assembly: GRCh38.p10, Ensembl_v88
Supplementary files format and content: Raw counts

source_name: HeLa Kyoto

growth_protocol: Adherent grown HeLa cells were allowed to reach 1-2 million cells

extract_protocol:
RNA was extracted using the RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacterers protocol
mRNA was treated using the NEBNext rRNA depletion Kit (human, mouse, rat) from New England Biolabs (NEB) according to the manufacturer’s instructions to remove ribosomal RNA. Subsequently, the samples were subjected to the workflow for strand specific RNA-Seq library preparation (NEBNext Ultra II Directional RNA Library Prep, NEB).

treatment_protocol: After detachment cells were pelleted by centrifugation (2000 x g, 5 min, 4 °C), washed twice with PBS and lysed by adding Trizol reagent

value: HeLa Kyoto

value: fy-5 knock-out


title: fy-5 KO 1