title: 9425-3-UNT

value: kochia meristem tissue


title: CaOV3 GFP, biological rep3

status: Public on Dec 08 2023

type: RNA

city: Boston

first: Alex

last: Miranda Rodriguez

state: Massachusetts

address: 55 Fruit St.

department: Massachusetts General Hospital

country: USA

institute: Harvard Medical School

description: Gene expression data from a human ovarian cell line with TET-On inducible expression of the MYCN oncogene.

hyb_protocol: Performed by Genome Quebec

scan_protocol: Performed by Genome Quebec

data_processing:
Data was preprocessed using the R package OLIGO and limma to identify differentially expressed genes.
RMA based normalized intensity summarized at gene level

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CaOV3 GFP TET-On cells, control 72 hours

label_protocol: Performed by Genome Quebec

growth_protocol: 2x105 CaOV3 TET-On MYCN-GFP and GFP control cells were cultured in triplicate in wells of a 6-well plate during 72 hours.

extract_protocol: Total RNA was isolated using the RNeasy plus kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured in the presence or absence of 1 ug/ml of Doxycycline (DOX) for 3 days.

tag: tissue

value: High grade ovarian serous carcinoma cell line


title: CaOV3 GFP, biological rep2


title: MEEC+OP9-Dll4_6h.1

type: SRA

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

library_source: genomic

data_processing:
Fastq files were pre-processed using FastQC and Cutadapt, to remove Illumina and Nextera adapter contamination.
Resulting reads were then mapped against reference genome GRCm38/MM10 with bowtie2 as aligner, Piccard to mark duplicate alignments, and samtools   to eliminate duplicate, chimeric and sub-optimally multi-mapped alignments, keeping only properly paired and mapped reads. Alignments against the mitochondrial genome and chromosome Y were also removed.
Once filtered alignments had been obtained, peaks (accessible DNA regions) were called with MACS2 using parameters "--nomodel --shift -100 –extsize  200", and "-q 0.05" as the false discovery rate cut-off.
Assembly: GRCm38/MM10
Supplementary files format and content: ATAC-Seq peaks called with MACS2, in narrowPeak (XLS) format.

molecule: genomic DNA

organism: Mus musculus

source_name: MEEC

growth_protocol: MEECs were cultured on 0.1% gelatin-coated dishes and maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. GFP-, Jag1- or Dll4-expressing OP9 cells were cultured on 0.1% gelatin-coated dishes and maintained in MEM Alpha (1X) supplemented with 20% FBS and 1% penicillin/streptomycin. Cultures were incubated at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
50,000 cells were lysated with cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% IGEPAL CA-630) spinning for 15 at 500g (4C), and DNA tagmentated with Nextera DNA Library Prep Kit (Illumina)
ATAC-seq libraries were prepared using the NEB Next High-Fidelity 2x PCR Mastermix (New England BioLabs). Libraries were size selected using Agencourt AMPure XP beads from Beckman Coulter.

treatment_protocol: Co-culture with OP9 cells: To define the effect of Dll4- and Jag1-mediated cell-to-cell signaling, MEECs were co-cultured for 6h (50% confluency) and 24h (25% confluency) over GFP-, Jag1- or Dll4-expressing OP9 cells at 90% confluence. To define the effect of NICD nuclear translocation inhibition, MEECS were cultured with DMSO (vehicle) or 20 μM of the γ-secretase inhibitor RO4929097 for 24 h. Next, MEECs were co-cultured for 6h (50% confluency) over GFP-expressing OP9 cells at 90% confluence.

tag: cell line

value: MEEC

tag: cell type

value: Mouse embryonic endocardial cells

tag: chip antibody

value: ATAC-seq


title: Wildtype E16.5 Sample 2 [WT_ATF4_E16_5_12_S96]

city: Newark

first: Melinda

last: Duncan

state: DE

address: 105 The Green

department: Biological Sciences

institute: University of Delaware

library_source: transcriptomic

data_processing:
Aggregate individual lane files (4 per sample) into a single file for each sample
Trim reads using trimgalore
Remove reads aligning to the Rn45s prespliced transcript using HISAT2
Align "non-ribosomal" reads using HISAT2 (-fr --rna-strandness RF --dta)
Quantify genes using htseq-count
Normalize counts using TMM using edgeR
Test for differential expression using edgeR's Exact test
Assembly: GRCm39 / Ensembl v104
Supplementary files format and content: Gene level counts for each sample in text file
Supplementary files format and content: Gene level counts and Differential Expression analysis in excel spreadsheet

source_name: whole lens

extract_protocol:
mirVana mirRNA Isolation Kit, with phenol
Takara SMARTer Stranded Pico v2

value: whole lens

value: Mouse embryonic lens cells

tag: genotype

value: WT

tag: time


title: Wildtype E16.5 Sample 1 [WT_ATF4_E16_5_11_S99]


title: RWPE1, Contol-sh S9.6 Rep1

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

data_processing:
150bp paired-end reads for the CUT&Tag-seq were trimmed for adapters using the Trimmomatic tool and aligned to the hg38 genome through local Bowtie2 (version 2.4.5) with these parameters for pair-end mapping: --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. The bam files were sorted and indexed using the samtools (version 1.9) sort and the samtools index. Merging of multiple replicates was performed using samtools merge.
The sorted bam files were used to generate bed, bedgraph and bigwig formats for individual modifications. Sorted bam files were subjected to bigwig generation via deepTools (version 3.5.1) bamCoverage tool with --binSize 20 --scaleFactor=1.0 --smoothLength 60 --extendReads 150 --centerReads options. The corresponding bigwig files were normalized by factoring in the reads mapped to E. coli in Control-sh and PSIP1-sh.
Peak-calling and analyses  The reads were extracted from the bam to bed by the bedtools bamtobed option. Further reads were processed as mentioned in the SEACR (version 1.3) manual to get the bedgraph. These bedgraph files were subjected to peak calling through SEACR keeping IgG as a background with the norm and relaxed options for individual replicates. Peaks consistenet in both replicates were reatins and the coordinates were merged.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: RWPE-1 cells were grown on 100 mm culture dishes (Corning Falcon product number: 353003 ) in keratinocytes serum-free medium (Gibco, 10724-011) supplemented with 100 U/ml penicillin-streptomycin (Gibco, 15140122) and 10% FBS (Sigma, F7524). The cells were passaged every 3-4 days. All the cell lines were tested for Mycoplasma contamination using EZ-PCR Kit (Geneflow, K1-0210).

extract_protocol:
CUT&Tag was performed according to the protocol of Kaya-Okur et al (1) with modifications to tissue processing as described below. ~100,000 cells were pelleted by centrifugation for 3 min at 600 x g at room temperature and resuspended in 500μl of ice-cold NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 1% Triton X-100, and 20 % glycerol and cOmplete EDTA free protease inhibitor tablet) and was let to sit for 10 min on ice. Nuclei were pelleted by centrifugation for 4 min at 1300 x g at 4°C, resuspended in 500μl of wash buffer and held on ice until beads were ready. Required amount of BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences, Inc) were transferred into binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2), washed once in the same buffer, each time placing them on a magnetic rack to allow the beads to separate from the buffer and resuspended in binding buffer. 10 μl of beads was then added to each tube containing cells and rotated on an end-to-end rotator for 10 minutes. After a quick spin to remove liquid from the cap, tubes were placed on a magnet stand to clear, the liquid was withdrawn and 800μl of antibody buffer containing 1μg of primary antibodies: normal rabbit IgG (Santa Cruz Cat no sc-2027), H3K27ac (Abcam, ab4729), H4K16ac (Abcam, ab109463), H3K122ac (Abcam, ab33309), H3K4me1(Abcam, ab8895), H3K36me3 (Abcam, ab9050)) H3K4me3 (Millipore, 07-473),  H3K27me3 (Abcam, ab192985) and H3K9me3 (Abcam, ab176916)) was added and incubated at 4ºC overnight in a nutator. Secondary antibodies (guinea pig α-rabbit antibody, Antibodies online, ABIN101961) were added 1:100 in Dig-wash buffer (5% digitonin in wash buffer) and 100 µL was squirted in per sample while gently vortexing to allow the solution to dislodge the beads from the sides and incubated for 60 min on a nutator. Unbound antibodies were washed in 1 ml of Dig-wash buffer three times. 100 μl of (1:250 diluted) protein-A-Tn5 loaded with adapters in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine with Roche cOmplete EDTA free protease inhibitor) was added to the samples, placed on nutator for 1 hour and washed three times in 1 ml of Dig-300 buffer to remove unbound pA-Tn5. 300 µL Tagmentation buffer (Dig-300 buffer + 5 mM MgCl2) was added while gentle vortexing and samples were incubated at 37ºC for 1 hr on an incubator. Tagmentation was stopped by adding 10 µL 0.5M EDTA, 3 µL 10% SDS and 2.5 µL 20 mg/mL Proteinase K to each sample. Samples were mixed by full speed vortexing for ~2 seconds and incubated for 1 hr at 55ºC to digest proteins. DNA was purified by phenol: chloroform extraction using phase-lock tubes (Quanta Bio) followed by ethanol precipitation.
Libraries were prepared using NEBNext HiFi 2x PCR Master mix (M0541S) with a 72ºC gap-filling step followed by 13 cycles of PCR with 10-second combined annealing and extension for the enrichment of short DNA fragments. Libraries were sequenced in Novaseq 6000 (Novogene) with 150bp paired-end reads.

treatment_protocol: Cells were transduced with either control shRNA or PSIP1 shRNA and grown in a medium containing 2ug/ml puromycin

value: Human Prostate Epithelial cells

tag: antibody


title: MEEC+OP9-GFP_6h.4


title: CaOV3 GFP, biological rep1


title: MEEC+OP9-GFP_6h.3


title: CaOV3 MYCN-GFP + DOX, biological rep3

source_name: CaOV3 MYCN-GFP TET-On cells, Doxycycline (1ug/ml) 72 hours


title: RWPE1, PSIP1-sh PSIP1 Rep2

value: PSIP1(Abcam, ab4729)


title: RWPE1, PSIP1-sh PSIP1 Rep1


title: ATF4 Knockout E16.5 Sample 4 [Homo_ATF4_E16_5_3_S91]

value: ATF4 knockout


title: RWPE1, Contol-sh YH2AX Rep1

value: YH2AX(Abcam, ab8895)


title: ATF4 Knockout E16.5 Sample 3 [E_16_5_ATF4_30_S93]


title: RWPE1, Contol-sh PSIP1 Rep2


title: CaOV3 MYCN-GFP + DOX, biological rep2


title: CaOV3 MYCN-GFP + DOX, biological rep1


title: CaOV3 MYCN-GFP, biological rep3

source_name: CaOV3 MYCN-GFP TET-On cells, control 72 hours


title: cihPod cells, levamisole 1 µM 24 hours, control, biol rep 3

city: Nijmegen

first: Susan

last: Veissi

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

data_processing:
low-quality ﬁltering and adapter trimming was performed using Trim Galore! v0.4.5 (Babraham Bioinformatics), a wrapper tool around the tools Cutadapt v1.18 and FastQC v0.11.8 (Babraham Bioinformatics)
Reads were mapped to a human reference genome (GRCh38.95, Ensembl) with Star v2.7.5a, resulting in BAM ﬁles. BAM ﬁles were counted (number of reads mapped to a feature, e.g. a gene) with HTSeq (HTSeq-count tool v0.11.0) with default parameters using a complementary gtf ﬁle, containing an annotation for GRCh38.95 (Ensembl). MultiQC (quality control) was used to combine results and quality checks of all the samples.
Diﬀerential gene expression analysis was carried out with DESeq2 v1.22.0 in R v3.5.3, with internal statistical and normalization method (i.e. correction for multiple testing with the Benjamini–Hochberg procedure) using a cutoﬀ value of at least 5 reads per sample per gene.
Pathway and GO term enrichment were performed with selected genes based on p-value < 0.05.
Assembly: GRCh38.95 (Ensembl).
Supplementary files format and content: CSV files with P-value and P-adjusted value

growth_protocol: Conditonally immortalized human podocytes (AB 8/13) were cultured in RPMI- 1640 medium, supplemented with 10% fetal bovine serum (FBS), 1% insulin-transferrin-sodium selenite (ITS), and 1% penicillin-streptomycin at 33°C with 5% CO2 under growth-permissive conditions

extract_protocol:
RNA was harvested using standard TRIzol method. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Truseq small RNA primers

treatment_protocol:
For experiments, podocytes were cultured at 37°C with 5% CO2 under growth-restrictive conditions for 7 to 10 days in the same medium in order to differentiate.
Podocytes were cultured in medium without FBS (24 houra) for control condition or treated with 1 µM levamisole in serum free medium for 24 hours.

value: human kidney podocytes

tag: treatment

value: Levamisole 1 µM 24 hours

value: 24 hours


title: RWPE1, Contol-sh PSIP1 Rep1


title: RWPE1, Contol-sh S9.6 Rep2


title: CaOV3 MYCN-GFP, biological rep2


title: cihPod cells, levamisole 1 µM 24 hours, control, biol rep 2


title: ATF4 Knockout E16.5 Sample 1 [ATF4_E16_5_24_Homo_S94]


title: BMDM_2B

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

data_processing:
Reads were trimmed for adapters, length and quality using the bbduk tool from the BBMap Suite (v. 38.05) with arguments ‘ref=adapters.fa ktrim=r qtrim=10 k=23 mink=11 hdist=1 ftr=36 maq=10 minlen=20’.
Trimmed reads were mapped to the mouse genome (mm10; downloaded from http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Mus_musculus/UCSC/mm10/Mus_musculus_UCSC_mm10.tar.gz on December 21, 2021, with corresponding hisat2 index files) using hisat2 (v. 2.1.0) in ‘--very-sensitive’ mode.
Resulting SAM files were converted to sorted BAM files using samtools (v. 1.3.1) and then passed to MarkDuplicates (Picard v. 2.6.0) with setting ‘REMOVE_DUPLICATES=true’ to remove PCR and sequencing duplicates.
Deduplicated BAM files were converted to bedGraph format and sorted using genomeCoverageBed and sortBed, respectively, from the BEDTools suite (v. 2.25.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BedGraph files are non-normalized coverage files.

source_name: primary bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMDM) were generated in vitro by flushing bone marrow from mouse tibias and femurs. Progenitor cell suspensions were cultured for 7 days in DMEM containing 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin and 20 ng/ml M-CSF (Peprotech). Macrophage differentiation was confirmed by flow cytometry (>95% positive for F4/80 and CD11b).

extract_protocol:
Cells were washed twice with 1X PBS and collected by scraping and pelleting prior to counting. Approximately 50K cells were pelleted and processed in duplicate as described in the Omni-ATAC-seq protocol published by Corces et al. (Nature Methods, 2017).
Uniquely indexed sequencing adapters from the Nextera DNA CD Indexes Kit were added to both ends of transposed fragment libraries by PCR. Following final purification and size selection for 100-1000 bp fragments, libraries were pooled and sequenced on an Illumina NovaSeq 6000 instrument using 150 bp paired-end reads.

treatment_protocol: ATAC-seq was performed on untreated BMDM harvested from WT and FABP5-deficient mice.

tag: strain

value: Primary bone marrow-derived macrophages


title: cihPod cells, levamisole 1 µM 24 hours, control, biol rep 1


title: CaOV3 MYCN-GFP, biological rep1


title: RWPE1, PSIP1-sh IgG Rep1

value: IgG(Abcam, ab4729)


title: RWPE1, Contol-sh IgG Rep2


title: Diestrus

city: Karnal

first: Suneel

middle: Kumar

last: Onteru

state: HARYANA

address: Lab No 154, Animal Biochemistry Division, NDRI, Karnal

department: Animal Biochemistry

country: India

institute: NDRI

description: cell free total RNA

data_processing:
poor quality reads with with QC score ≤ 20 were removed from raw data to get high-quality reads.
Tophat software having bowtie aligner was used to align high quality raw reads to Bos taurus (UMD 3.1) reference genome.
BAM and SAM files were processed using cufflinks software to estimate reads abundance.
cufflinks output *.gtf files obtained from each RNA samples were merged using Cuffmerge to get the transcriptome assembly of the entire data.
Cuffquant tool software was used to quantify aligned reads, that takes BAM files of individual samples and the transcriptome assembly of the entire data were given as input.
Cuffquant output *.cxb file was used to determine the differential gene expression using Cuffdiff.
Statistical significance and differential gene expression data visualization was done using the CummeRbund R package
Genome_build: Bos taurus (UMD 3.1)
Supplementary_files_format_and_content: Excel file that include FPKM values for each Sample

organism: Bubalus bubalis

source_name: Saliva

growth_protocol: Not Applicable

extract_protocol:
Protocol established by Pandit, Cooper-White, and Punyadeera 2013
Illumina® TruSeq® RNA Sample Preparation Kit v2 as per manufacturer protocol

treatment_protocol: Not Applicable

tag: breed

value: Murrah

tag: oestrous stage

value: Diestrus


title: cihPod cells, serum free 24 hours, control, biol rep 3

value: Serum free 24 hours


title: MEEC+OP9-GFP_6h.2

value: MEEC

value: Mouse embryonic endocardial cells


title: MEEC+OP9-GFP_6h.1

value: ATAC-seq


title: RWPE1, Contol-sh IgG Rep1


title: Estrus

description: cell free total RNA

value: Estrus


title: cihPod cells, serum free 24 hours, control, biol rep 1


title: BMDM_1A

value: WT


title: cihPod cells, serum free 24 hours, control, biol rep 2


title: BMDM_2A


title: ATF4 Knockout E16.5 Sample 2 [E_16_5_ATF4_27_S92]

value: whole lens

value: Mouse embryonic lens cells


title: Ah20mirS3_AGO1-IP

status: Public on Dec 07 2023

city: Villeneuve d'Ascq

first: Vincent

last: Castric

address: Batiment SN2, bureau 207

country: France

institute: CNRS / Universite de Lille - Sciences et Technologies

description: small RNAs from IP experiment - AGO1-bound fraction

library_source: other

data_processing:
read trimming: trim_galore --fastqc --length 18 --max_length 25
mapping to TAIR10 genome: ShortStack --bowtie_cores 4 --mismatches 1 --bowtie_m 50 --mmap u
mapping to S locus: ShortStack --bowtie_cores 2 --mismatches 1 --bowtie_m 50 --mmap u
only reads that mapped only to S locus and not to TAIR10 were kept for further analysis
reads from different samples of the same genotype were poooled to generate a smallRNA dabase for that genotype (see processed data file)
Assembly: for all libraries: TAIR10; for libraries AVBR-14, AVBR-5 and AVBR-6: Ah04 S locus (GenBank ID: KJ461484); for libraries AVBR-15, AVBR-8 and AVBR-9: Ah20 S locus (GenBank ID KJ772400)
Supplementary files format and content: smallRNA database columns: sRNA_chr/sRNA_start/sRNA_end/sRNA_id/sRNA_size /sRNA_strand/sRNA_seq/mir_of_origin/allele_of_origin/sample_of_origin

molecule: other

organism: Arabidopsis thaliana

source_name: immature floral buds

growth_protocol: Arabidopsis thaliana plants used in this study were grown in a greenhouse, using standard growth conditions (16 h light/8 h dark; 110 μmol/s/m2; 21°C; 70% humidity)

extract_protocol:
AGO1 and AGO4 immunoprecipitation (IP) assays were performed on immature buds of plants carrying an homozygous Ah04mir1887 or Ah20mirS3 transgene, using a protocol adapted from (Schott et al., 2012), with the following modifications: IPs were performed on 1.4 g of finely ground powder of frozen immature buds. The anti-AGO1 (AS09 527, Agrisera) and anti-AGO4 (AS09 617, Agrisera) antibodies were added at a 1/500 dilution for the incubation step and their immobilization was performed using Dynabeads Protein G (Invitrogen). The IP products were washed six times with PBS prior to sRNA extraction using the Trizol reagent (Ambion). In parallel, an aliquot of each input extract was used for total sRNA isolation using the Trizol LS reagent (Invitrogen), according to the supplier instructions. For each genotype three sRNA fractions were obtained: AGO1-IP, AGO4-IP and input. These three sRNA fractions were subjected to an acrylamide gel-based size selection for sRNAS.
TruSeq Small RNA library kit (Illumina)

value: immature floral buds

value: C24 Ah20mirS3

value: AGO1-IP fraction

value: anti-AGO1 (AS09 527, Agrisera)


title: Ah20mirS3_AGO4-IP

description: small RNAs from IP experiment - AGO4-bound fraction

value: AGO4-IP fraction

value: anti-AGO4 (AS09 617, Agrisera)


title: RWPE1, PSIP1-sh IgG Rep2

value: Human Prostate Epithelial cells

value: IgG(Abcam, ab4729)


title: Ah04mir1887_AGO1-IP


title: Ah04mir1887_AGO4-IP


title: Ah04mir1887_Input

description: small RNAs from IP experiment - input fraction

value: input fraction


title: retina, 40 hr apf, w[*] sev[14], rep 3

city: Austin

first: John

middle: Calvin

last: Aldrich

state: TX

address: 1601 Trinity St. Bldg B

department: Neurology

institute: University of Texas at Austin, Dell Medical School

data_processing:
Raw paired-end reads were examined with FastQC (v0.11.4) and adapters were trimmed with cutadapt (v1.9.1) resulting in an average read length of 135 nt.
The trimmed reads were then aligned to the dm6 genome using HISAT2 (v2.0.3) and quantified to the Ensembl (BDGP6 release 89) transcriptome with RSEM (v1.2.31).
The R package DESeq2 (ver. 1.32.0) was used to fit a negative binomial model. To determine genes that are differential expressed between strain a Likelihood Ratio Test (LRT) was fit with the full model includes the predictor of strain and the null model is an intercept only model. To account for multiple testing the Benjamini and Hochberg False Discovery Rate (FDR) was used. Genes with zero counts across all sample have NA values or those with one or more extreme outliers (detected by Cook’s distance) were automatically excluded from significance testing by DESeq2.
Assembly: dm6
Supplementary files format and content: comma-seperated (csv) file with a) DESeq2-normalized counts for each sample, b) gene details  (FlyBase ID, gene symbol, chromosome location and strand, and gene type), and c) differential gene expression results from DESeq2 (log2-transformed fold change sev vs. control, LRT statistic, p-value, and FDR). Genes with zero counts across all sample have NA values for fold change and LRT results while those with one or more extreme outliers (detected by Cook’s distance) are excluded from significance testing.

organism: Drosophila melanogaster

source_name: retina

growth_protocol: Stocks were maintained in 12:12 hr light:dark cycling, humidified incubators at 25°C on cornmeal media based on the Bloomington Drosophila Stock Center recipe. White pre-pupae were collected and aged 40 hours at 25°C. Retinas were dissected in cold 1X PBS and transferred to a microcentrifuge tube containing RNAlater (Invitrogen, AM7020). 10-20 retinas were prepared for each genotype.

extract_protocol:
RNAlater was removed from samples prior to homogenization with a plastic pestle. Total RNA was isolated using the PureLink RNA purification kit (Invitrogen, 12183020) according to the manufacturer’s instructions along with on-column PureLink DNase treatment (Invitrogen, 12185010).
Library construction (from polyA-selected RNA) and sequencing was performed by the Genomic Sequencing and Analysis Facility at UT Austin, Center for Biomedical Research Support (RRID# SCR_021713) using the Illumnia MiSeq  v3 Reagent Kit (paired-end, 150 cycles; MS-102-3001) and platform.

value: retina

value: 40 hrs apf

tag: Sex

value: female


title: Ah20mirS3_Input


title: retina, 40 hr apf, w[*] sev[14], rep 4


title: retina, 40 hr apf, w[*] sev[14], rep 1


title: retina, 40 hr apf, w[1118], rep 3


title: retina, 40 hr apf, w[1118], rep 4


title: retina, 40 hr apf, w[1118], rep 1


title: retina, 40 hr apf, w[*] sev[14], rep 2


title: retina, 40 hr apf, w[1118], rep 2


title: BMDM_1B

value: Primary bone marrow-derived macrophages


title: hMSC-TERT20,LINC01114KD,DAY21,rep3

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore v 0.6.10
Trimmed sequence reads were mapped to STAR index hg38cannon with Gencode v36 annotation using STAR 2.7.10b in "QuantMode" using the following parameters (-outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic)
Assembly: hg38canon/ Gencode v36 annotation
Supplementary files format and content: hMSC-hTERT20_LINC01114kd_LINC01638kd_raw_counts.txt

source_name: mesenchymal stromal cells

growth_protocol: Human immortalized MSCs (hMSC-hTERT20) were infected with pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP to induce LINC01638 or LINC01114 knockdown. Cells were then induced to osteogenesis using 280 μM ascorbic acid, 10 mM beta-glycerophosphate, 10nM dexamethasone. Cells were grown in ascorbic acid-free alpha-MEM  supplemented with 16.5% fetal bovine serum, 2 mM L-glutamine, 100 U/ml of penicillin and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was isolated from Trizol with DNaseI treatment following manufacturers protocol (Invitrogen) or using the Direct-zol RNA mini-prep kit (Zymo Research #R2050).
RNA libraries were prepared for sequencing with the SMARTer® Stranded Total RNA Sample  Prep Kit - HI Mammalian kit  (Takara) using standard protocols.
Barcoded libraries (SMARTer Stranded ) were loaded onto an Illumina HiSeq 1500 and single-end 75-base (SE75) sequencing was performed at the The Vermont Integrative Genomics Resource (VIGR). Illumina HiSeq 1500

treatment_protocol: Cells were seeded at 1x106 cells per 100 mm dish and grown to 90% confluence.  To induce osteogenic differentiation, complete alpha-MEM was supplemented with 280 μM ascorbic acid, 10 mM beta-glycerophosphate, 10nM dexamethasone and 100ng/ BMP2. Cells were harvested at defined time points (0, 7, 14 days) and stored at -80C in TRIzol.

value: mesenchymal stromal cells

value: LINC01114KD (CRISPRi)

value: osteogenic differentiation

value: day 21


title: hMSC-TERT20,LINC01114KD,DAY21,rep2


title: hMSC-TERT20,LINC01114KD,DAY14,rep1

value: day 14


title: hMSC-TERT20,LINC01114KD,DAY14,rep3


title: hMSC-TERT20,LINC01114KD,DAY7,rep3

value: day 7


title: hMSC-TERT20,LINC01114KD,DAY21,rep1


title: hMSC-TERT20,LINC01114KD,DAY0,rep3

value: day 0


title: hMSC-TERT20,LINC01114KD,DAY14,rep2


title: hMSC-TERT20,LINC01114KD,DAY7,rep2


title: hMSC-TERT20,LINC01114KD,DAY7,rep1


title: hMSC-TERT20,LINC01638KD,DAY21,rep2

value: LINC01638KD (CRISPRi)


title: hMSC-TERT20,LINC01114KD,DAY0,rep2


title: hMSC-TERT20,LINC01638KD,DAY7,rep3


title: hMSC-TERT20,LINC01638KD,DAY21,rep1


title: hMSC-TERT20,LINC01638KD,DAY14,rep2


title: hMSC-TERT20,LINC01638KD,DAY7,rep2


title: hMSC-TERT20,LINC01638KD,DAY0,rep3


title: hMSC-TERT20,LINC01638KD,DAY0,rep2


title: hMSC-TERT20,LINC01638KD,DAY14,rep3


title: hMSC-TERT20,LINC01638KD,DAY7,rep1


title: hMSC_8013_Day14

data_processing:
The reads were aligned to hg38 with STAR (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation v37.
Differential gene expression was calculated by using the Deseq2 version 1.8.1 package in R studio.
Genome_build: hg38 (human)
Supplementary_files_format_and_content: hMSCdonor_normalized_counts.txt (HTSeq_normalized_count file)

source_name: MSCs from young, healthy male donor

growth_protocol: Human MSCs were maintained in ascorbic acid-free alpha-MEM (Hyclone) supplemented with 10% fetal bovine serum (Hyclone), 2 mM L-glutamine, 100 U/ml of penicillin and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was isolated from Trizol with DNaseI treatment following manufacturers protocol (Invitrogen) or using the Direct-zol RNA mini-prep kit (Zymo Research #R2050).
RNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA with Ribo-Zero Gold kit using standard Illumina protocols with the exception that library amplifcation was performed using KAPA HiFi™ Real-Time PCR Library Amplification Kit (Kapa Biosystems #KK2701).
Barcoded libraries (Illumina TruSeq) were loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1.5x10e6 cells per 100 mm dish and grown to 80% confluence.  Osteogenic differentiation was induced in complete alpha-MEM supplemented with 280 μM ascorbic acid, 10 mM beta-glycerophosphate, 10nM dexamethasone and 100ng/ml BMP2. Cells were harvested at defined time points (0, 7, 14 days) and stored at -80C in TRIzol.

value: marrow stromal cell

tag: donor

value: Texas A&M IRM Donor ID 8013


title: hMSC_8004_Day14

value: Texas A&M IRM Donor ID 8004


title: hMSC_7083_Day14

value: Texas A&M IRM Donor ID 7083


title: hMSC_7043_Day14

value: Texas A&M IRM Donor ID 7043


title: hMSC-TERT20,LINC01638KD,DAY0,rep1


title: hMSC_8013_Day7


title: hMSC_7078_Day14

value: Texas A&M IRM Donor ID 7078


title: hMSC_8004_Day7


title: hMSC-TERT20,LINC01638KD,DAY21,rep3


title: hMSC-TERT20,LINC01114KD,DAY0,rep1


title: hMSC_7083_Day7


title: hMSC_8013_Day0


title: hMSC_7078_Day7


title: hMSC-TERT20,LINC01638KD,DAY14,rep1


title: hMSC_7043_Day7


title: hMSC_7083_Day0


title: hMSC_8004_Day0


title: hMSC_7043_Day0


title: Idiopathic Pulmonary Fibrosis 1

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6.0 except for ipf1 which uses v4.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 74 yo Male

extract_protocol:
Briefly, around 10,000 cells were targeted per sample and loaded onto each well of a Chromium Single Cell G Chip to generate single cell emulsions primed for reverse transcription.  After breaking the emulsion, the single cell specific barcoded DNAs were subjected to cDNA amplification and QC on the Agilent 4200 TapeStation Instrument, using the Agilent D5000 kit.  Each sample cDNA was used to prepare indexed libraries that were pooled prior to sequencing.  A quality control run was performed on the Illumina Miseq using the nano 300 cycle kit (1.4 Million reads/run), to estimate the number of targeted cells per sample. The cell estimate enabled the core to re-balance the pooled sample prior to deep sequencing.
The generation of single cell indexed libraries, from the thawed COVID PF and IPF PBMCs, was performed by the School of Medicine Genome Analysis and Technology Core, RRID:SCR_018883, using the 10X Genomics chromium controller platform and the Chromium Single Cell 5′ Library & Gel Bead Kit v1.1 reagent.  Deep sequencing was performed on either the NGS Illumina NextSeq 500 using the 150 cycle kit or NextSeq 2000 using the P3-100 cycle kit.  Control samples were sequenced on the MGISEQ-2000.

value: blood

value: peripheral blood mononuclear cells

tag: phenotype

value: Idiopathic Pulmonary Fibrosis


title: hMSC_7078_Day0


title: HeLa sh GFP rep 3

city: Napoli

first: Danilo

last: Swann Matassa

address: Via Sergio Pansini 5

department: Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Naples “Federico II”

description: replicate 3

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scanning protocol using HiScan system

data_processing: The data were normalised using neqc() quantile normalization with limma in R

source_name: T-REx™-HeLa Cell Line

label_protocol: Standard Illumina label protocol

growth_protocol: HeLa cells were grown on 10-cm dishes until were approximately 85% confluent

extract_protocol: Total RNA from HeLa cells was extracted using a standard acid guanidinium thiocyanate-phenol-chloroform extraction protocol

treatment_protocol: Cells were treated with Tetracycline (1 ug/mL) for 24 hrs to induce the expression of GFP-fusion proteins

value: T-REx-HeLa Cell Line

tag: genotype/variation

value: sh GFP


title: HeLa sh TRAP1 rep 5

description: replicate 5

value: sh TRAP1


title: HeLa sh TRAP1 rep 2

description: replicate 2


title: HeLa sh TRAP1 rep 6

description: replicate 6


title: HeLa sh GFP rep 1

description: replicate 1


title: Neg_3

city: St. Louis

first: Brian

last: Laidlaw

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

data_processing:
Sequences reported as fastq files
Fastq files alligned to mm10 genome with STAR
Mappable reads counted with HTseq and imported into RStudio
DESeq2 used  to analyze differential expression
Assembly: mm10
Supplementary files format and content: CSV sheet with normalized count for all samples

source_name: Spleen

extract_protocol:
Cells were isolated by sorting using an Aria sorter and total RNA purified using the RNeasy Micro kit (Qiagen).
Barcoded sequencing libraries were generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).Paired-end sequencing was performed on an IlluminaHiSeq2x150bp or Illumina NovaSeq X Plus.

value: Spleen

value: B220+IgDloGL7-CD38+S1pr2-Tomato+ CD62L-

value: LCMV Armstrong day 40


title: Neg_2


title: Pos_3

value: B220+IgDloGL7-CD38+S1pr2-Tomato+ CD62L+


title: Pos_2


title: HeLa sh GFP rep 2

description: replicate 2


title: Pos_1


title: HeLa hyper TRAP1 rep 4

description: replicate 4

value: hyper TRAP1


title: Neg_1


title: HeLa sh TRAP1 rep 4

description: replicate 4


title: HeLa sh GFP rep 5

description: replicate 5


title: HeLa hyper TRAP1 rep 6

description: replicate 6


title: HeLa sh TRAP1 rep 1

description: replicate 1


title: HeLa hyper GFP rep 3

description: replicate 3

value: hyper GFP


title: HeLa sh GFP rep 6

description: replicate 6


title: HeLa sh GFP rep 4

description: replicate 4


title: HeLa hyper GFP rep 4

description: replicate 4


title: HeLa hyper TRAP1 rep 2

description: replicate 2


title: HeLa hyper GFP rep 2

description: replicate 2


title: HeLa hyper TRAP1 rep 1

description: replicate 1


title: HeLa sh TRAP1 rep 3

description: replicate 3


title: HeLa hyper GFP rep 5

description: replicate 5


title: HeLa hyper TRAP1 rep 5

description: replicate 5


title: DP_3

value: LCMV Armstrong day 15


title: HeLa hyper GFP rep 6

description: replicate 6


title: DP_2


title: HeLa hyper TRAP1 rep 3

description: replicate 3


title: SP_3


title: SP_2


title: HeLa hyper GFP rep 1

description: replicate 1


title: DP_1


title: DN_1


title: DN_3


title: SP_1


title: KO3_129_064_S29

city: Orange

first: Nabil

middle: E.

last: Boutagy

state: CT

address: 419 Butternut Court

department: Pharmacology

institute: Yale

data_processing:
Reads aligned to hg19 build of human genome with STAR
Quantified to hg19 RefSeq annotation model through Partek E/M
Genes were normalized as counts per million
Assembly: hg19
Supplementary files format and content: tab-delimited text file include cpm values for each Sample

source_name: mLECs

growth_protocol: mouse lung endothelial cells were harvested from control (ATGL f/f) and ATGL ECKO (endothelial specific knockout) mice. Cells were immortalized by the middle T antigen after immunoselection with CD31.    Cells were cultured in EGM-2 media (Lonza) with 20% fetal bovine serum (FBS), penicillin/streptomycin and glutamine (2.8 mM) in a 37°C incubator with 5% CO2 supply

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated from control cells using TrueSeq Small RNA Library preparation (Illumina)

treatment_protocol: No treatment

value: mLECs

value: Immortalized Endothlelial Cell

value: endothelial specific  ATGL knock out mice (ATGL ECKO)

value: No Treatment


title: Control 3

source_name: 73 yo Male

value: blood

value: non-diseased control


title: KO2_141_052_S28


title: KO1_153_040_S27


title: WT3_165_028_S26

value: control (ATGL f/f)


title: WT1_189_004_S24


title: Control 2

source_name: 60 yo Male

value: peripheral blood mononuclear cells


title: WT2_177_016_S25


title: Control 1


title: NST8_Treg

city: San Francisco

first: Margaret

last: Lowe

state: CA

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

data_processing:
Fastq files were analyzed with Cell Ranger Version 3.0.2
Assembly: GRCh38
Supplementary files format and content: filtered feature bc matrices

molecule: polyA RNA

source_name: skin from healthy donor

extract_protocol:
Cells were purified as live, CD45+, CD3+, CD4+CD8-,CD25+CD27+ (Treg) or CD25-CD27- (CD4Teff) from skin that was enzymatically digested overnight with collagenase IV in the presence of DNAse.
sRNASeq was performed using the 10x Single Cell 5’ Chemistry

value: skin from healthy donor

value: CD4 Treg (CD25+CD27+)


title: NST8_CD4Teff

value: CD4 Teffector (CD25-CD27-)


title: NST9_Treg_CD4Teff

value: 1:1 Ratio of CD4 Treg (CD25+CD27+) and CD4 Teffector (CD25-CD27-)


title: NST10_Treg_CD4Teff


title: NST7_Treg_CD4Teff


title: NST5_Treg_CD4Teff


title: DN_2

value: Spleen


title: HS10x5_Treg

source_name: skin from HS lesion

value: skin from HS lesion


title: HS10x6_CD4Teff


title: HS10x6_Treg


title: HS10x5_CD4Teff


title: HS10x4_Treg


title: HS10x2_TregCD4Teff


title: HS419_Treg_CD4Teff


title: HS10x4_CD4Teff


title: NST10_CD45Neg

extract_protocol:
Cells were purified as live, CD45- from skin enzymatically digested overnight with collagenase IV in the presence of DNAse.
sRNASeq was performed using the 10x Single Cell 5’ Chemistry

value: Live CD45 negative cells


title: NST29_CD45Neg


title: NST8_CD45Neg


title: NST9_CD45Neg


title: NST22_CD45Neg


title: NST11_CD45Neg


title: HS10x2_CD45Neg


title: HS10x4_CD45Neg


title: HS10x6_CD45Neg


title: New CMML according to WHO2022 only, sample 9

city: Munich

first: Stephan

last: Hutter

address: Max-Lebsche-Platz 31

country: Germany

institute: MLL Munich Leukemia Laboratory

data_processing:
Data processing was performed within Illumina's BaseSpace plattform using the RNA-seq Alignment app (v2.0.1)
Reads were mapped with STAR aligner (v2.5.0a) to the human reference genome hg19 (RefSeq annotation)
Gene specific read abundance was calculated with Cufflinks (v2.2.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text files contain gene specific read count values for each sample

source_name: Bone marrow aspirate

extract_protocol:
Total RNA was extracted using the MagNA Pure 96 Instrument and the MagNA Pure 96 Cellular RNA LV Kit (Roche LifeScience, Mannheim, Germany)
The TruSeq Total Stranded RNA kit was used, starting with 250ng of total RNA, to generate RNA libraries following the manufacturer’s recommendations (Illumina, San Diego, CA, USA)

value: Bone marrow aspirate

tag: disease state

value: New CMML


title: New CMML according to WHO2022 only, sample 8


title: New CMML according to WHO2022 only, sample 4


title: New CMML according to WHO2022 only, sample 6


title: New CMML according to WHO2022 only, sample 5


title: New CMML according to WHO2022 only, sample 7


title: New CMML according to WHO2022 only, sample 11


title: New CMML according to WHO2022 only, sample 2


title: New CMML according to WHO2022 only, sample 10


title: New CMML according to WHO2022 only, sample 3


title: New CMML according to WHO2022 only, sample 1


title: New CMML according to WHO2022 and ICC2022, sample 8


title: New CMML according to WHO2022 and ICC2022, sample 6


title: New CMML according to WHO2022 and ICC2022, sample 4


title: New CMML according to WHO2022 and ICC2022, sample 7


title: New CMML according to WHO2022 and ICC2022, sample 9


title: New CMML according to WHO2022 and ICC2022, sample 22


title: New CMML according to WHO2022 and ICC2022, sample 21


title: New CMML according to WHO2022 and ICC2022, sample 2


title: New CMML according to WHO2022 and ICC2022, sample 3


title: New CMML according to WHO2022 and ICC2022, sample 20


title: New CMML according to WHO2022 and ICC2022, sample 17


title: New CMML according to WHO2022 and ICC2022, sample 18


title: New CMML according to WHO2022 and ICC2022, sample 19


title: New CMML according to WHO2022 and ICC2022, sample 5


title: New CMML according to WHO2022 and ICC2022, sample 13


title: New CMML according to WHO2022 and ICC2022, sample 16


title: New CMML according to WHO2022 and ICC2022, sample 12


title: Established myeloproliferative CMML, sample 93

value: myeloproliferative CMML


title: New CMML according to WHO2022 and ICC2022, sample 1


title: New CMML according to WHO2022 and ICC2022, sample 10


title: New CMML according to WHO2022 and ICC2022, sample 11


title: Established myeloproliferative CMML, sample 91


title: AKPS_Smad4_4b_A3474

city: Rochester

first: Aram

middle: F.

last: Hezel

state: New York

address: 601 Elmwood Ave, Box 704

institute: Wilmot Cancer Institute

data_processing:
RRBS sequencing data were aligned to the mouse mg38 genome using the Bismark pipeline with special attention to RRBS specific issues, as noted in the Bismark User Guide and the Bismark RRBS Guide.
CpGs were then further parsed and analyzed using Bismark output tables in R. Briefly, only CpGs with read coverage greater than 8 across all samples were considered scoreable for downstream analysis.
CpGs were then grouped into regions when they occurred within 50 bp of one another. Regions with more than 5% absolute change in methylation relative to control samples were classified as differentially methylated.
RRBS regions were annotated using Homer AnnotatePeaks function, and the output of Homer was then used to assess CpG density, and proximity to nearest transcription start site.
Assembly: mm9
Supplementary files format and content: bedGraph file format

source_name: liver

growth_protocol: All cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Genomic DNA was extracted from cell lines using the DNeasy Blood & Tissue Kit (Qiagen).
Purified DNA samples were fragmented by restriction digestion with MspI. Following digestion, Klenow Fragment was utilized to create 3’A overhangs. DNAs were subsequently column purified, and then ligated to Methylated Illumina PE Adapters. Ampure SPRI beads were then used to purify products prior to Sodium Bisulfite Converted and amplification to generate libraries.

treatment_protocol: AKPS cancer cells were infected with lentivirus containing EV or Smad4 plasmid over 3 rounds with polybrene (8 μg/ml), each lasting 2 hours. In experiments in which EV- and Smad4-expressing AKPS cancer cells were treated with TGFβ1, it was provided at 20 ng/ml in DMEM with 1% FBS. 16 hours prior to treatment cells were changed to low FBS media. Genomic DNA was harvested 48 hours after treatment.

value: liver

value: AKPS tumor cell line

value: mouse liver cancer cells

value: Smad4-expressing AKPS

value: TGFβ treated


title: Established myeloproliferative CMML, sample 90


title: Established myeloproliferative CMML, sample 9


title: AKPS_Smad4_4_A3474


title: AKPS_EV_3b_A3474

value: EV-expressing AKPS


title: AKPS_EV_3_A3474


title: Established myeloproliferative CMML, sample 88


title: AKPS_Smad4_2b_A3723


title: AKPS_Smad4_2_A3723


title: Established myeloproliferative CMML, sample 87


title: Established myeloproliferative CMML, sample 85


title: New CMML according to WHO2022 and ICC2022, sample 14


title: AKPS_EV_1b_A3723


title: AKPS_EV_1_A3723


title: New CMML according to WHO2022 and ICC2022, sample 15


title: Established myeloproliferative CMML, sample 84


title: Established myeloproliferative CMML, sample 83


title: Established myeloproliferative CMML, sample 92


title: PLA, implanted with PLA, 6 weeks, rep1

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

country: China

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads.2.Raw reads were processed using fastp and the low quality reads were removed to obtain the clean reads.3.Then, the clean reads were mapped to the mRatBN7.2 using HISAT2.4.FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.5.Differential expression analysis was performed using the DeSeq.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: cranium

extract_protocol:
Nascent tissue from the suture-bony composite defects implanted with GelMA, CTS, PLA or without scaffold (NC) for 6 weeks were harvested and digested in type 1 collagenase (3.5 mg·mL-1) at 37°C for 1 hour. Flow cytometry was used to isolate Cd45- cells from digested tissue for RNA-seq.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instruction

value: cranium

value: Sprague Dawley rat

tag: age

value: 4 months

value: Cd45- digested cells

value: calvarial suture-bony composite defects implanted with PLA for 6 weeks


title: Established myeloproliferative CMML, sample 81

tag: tissue


title: CTS, implanted with CTS, 6 weeks, rep2

value: calvarial suture-bony composite defects implanted with CTS for 6 weeks


title: CTS, implanted with CTS, 6 weeks, rep3


title: CTS, implanted with CTS, 6 weeks, rep1


title: Established myeloproliferative CMML, sample 82


title: GelMA, implanted with GelMA, 6 weeks, rep3

value: calvarial suture-bony composite defects implanted with GelMA for 6 weeks


title: Established myeloproliferative CMML, sample 80


title: GelMA, implanted with GelMA, 6 weeks, rep1


title: Established myeloproliferative CMML, sample 89


title: Established myeloproliferative CMML, sample 78


title: GelMA, implanted with GelMA, 6 weeks, rep2


title: Established myeloproliferative CMML, sample 8


title: Established myeloproliferative CMML, sample 77


title: Established myeloproliferative CMML, sample 86


title: PLA, implanted with PLA, 6 weeks, rep2


title: Established myeloproliferative CMML, sample 76


title: NC, without scaffold implantation, 6 weeks, rep1

value: calvarial suture-bony composite defects without scaffold implantation


title: Established myeloproliferative CMML, sample 74

value: Bone marrow aspirate


title: Established myeloproliferative CMML, sample 73


title: Established myeloproliferative CMML, sample 75


title: Established myeloproliferative CMML, sample 72


title: S4-28D

city: Beijing

first: Songming

last: Liu

address: Xueyuan Road No 38,Haidian District

institute: Peking University

data_processing:
Fastp (version 0.19.7)
Fastp was used to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows:(1) Discard a paired read if either one read contains adapter contamination;(2) Discard a paired read if more than 10% of bases are uncertain in either one read;(3) Discard a paired read if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Trimmed sequence reads were mapped to GCF_015227675.2_mRatBN7.2 using STAR (parameters:runThreadN 20; alignIntronMin 20;alignIntronMax 50000; outSAMtype BAM SortedByCoordinate; sjdbOverhang 149)
Read count extraction and normalization were performed using FeatureCounts(v2.0.1)
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: SD Male Rat ,Sorafenib,28 Days

extract_protocol:
RNA was harvested using trizol (ambion) and purified using Illumina Ribo-Zero plus rRNA Depletion Kit to romove rRNA.1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: 180-200 g SD male rats were given 50 mg/kg sorafenib or the same volume of deionized water once a day for 14 or 28 days.

value: Heart

value: SD

value: male

value: WT

value: Sorafenib 50mg/kg

value: 28 days


title: S3-28D


title: Established myeloproliferative CMML, sample 71

value: myeloproliferative CMML


title: S2-28D


title: C4-28D

source_name: SD Male Rat ,Control,28 Days

value: Deionized Water


title: C2-28D


title: Established myeloproliferative CMML, sample 79


title: Established myeloproliferative CMML, sample 7


title: ITK7_3

city: Philadelphia

first: Raghavendra

last: Basavaraja

address: 380 south, University ave

department: Biomedical Sceinces

institute: Univeristy of Pennsylvania

data_processing:
The raw fastq files were aligned to the mouse genome GRcm 39 (mm39) by salmon 10.1 with standardized parameter
Normalization and differential expression (DE) analysis was conducted by DESeq2 v. 1.28.1
Significantly DE genes were defined as those with BonferroniadjustedP-value < 0.05 and log2(fold change) > 0.58 or <-0.58.
Significantly enriched pathways (P-value< 0.05) weredetermined through gene set enrichment analysis integrated in the R/Bioconductor packages clusterProfiler v. 3.14.3 and GseaVis in R
Assembly: mm39
Supplementary files format and content: tab- delimted includes raw counts for each samples

source_name: Tumor

extract_protocol:
Total RNA was then extracted with RNeasy Plus Mini Kit (QIAGEN) according to manufactures instructions
RNA libraries were prepred with Illumina® Stranded mRNA Prep based on manufacturer instructions

treatment_protocol: MC38 tumor bearing mice recived either DMSO or ITK7 as treatment

value: Tumor

tag: cell line

value: Mouse adenocarcinoma epithelial cells.


title: Established myeloproliferative CMML, sample 68


title: S6-14D

source_name: SD Male Rat ,Sorafenib,14 Days

value: 14 days


title: C3-28D


title: S7-14D


title: Established myeloproliferative CMML, sample 69


title: Established myeloproliferative CMML, sample 67


title: ITK7 _1

tag: cell type


title: NC, without scaffold implantation, 6 weeks, rep3

value: cranium

value: Sprague Dawley rat

value: 4 months

value: Cd45- digested cells


title: Established myeloproliferative CMML, sample 66


title: Established myeloproliferative CMML, sample 65


title: NC, without scaffold implantation, 6 weeks, rep2

value: calvarial suture-bony composite defects without scaffold implantation


title: DMSO_3

value: DMSO


title: C7-14D

source_name: SD Male Rat ,Control,14 Days

value: Heart


title: C3-14D

value: SD


title: Established myeloproliferative CMML, sample 61

value: Bone marrow aspirate


title: Established myeloproliferative CMML, sample 64


title: C2-14D

value: male

value: WT


title: Established myeloproliferative CMML, sample 6


title: Established myeloproliferative CMML, sample 70


title: Established myeloproliferative CMML, sample 63


title: Established myeloproliferative CMML, sample 60


title: DMSO_1


title: KPN-Romidepsin-CD45,scRNAseq

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

description: 10x Genomics

data_processing:
Raw sequencing reads from single cells were aligned against the mm10 mouse transcriptome and processed using count module of Cell Ranger  (v6.0, 10X Genomics).. Gene-barcodes matrices containing only barcodes with UMI counts passing threshold were imported to Seurat 115 for further analysis. Genes detected in less than 3 cells were excluded; cells with less than 200 genes detected or greater than 10% mitochondrial UMIs were also filtered out. Doublets were detected using Scrublet 116, DoubletFinder 117, scDblFinder 118, and doubletCells implemented in scran 119, assuming 0.08% doublet rate for every 1,000 sequenced cells. Cells identified as doublets by at least two algorithms were removed from further analysis. Raw UMI counts were log normalized and the top 5000 variable genes were identified using “vst” method implemented in the FindVaribleFeatures function in Seurat. T cell receptor and immunoglobulin genes were removed from the variable genes to prevent clustering based on V(D)J transcripts. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring function.
To further remove batch effects, individual samples were integrated using FindIntegrationAnchors and IntegrateData functions 120 with 8000 anchor genes and 40 dimensions of canonical correlation analysis (CCA). Briefly, dimension reduction was performed on each sample using diagonalized CCA and L2-normalization was applied to the canonical correlation vectors to project all samples into a shared space. The mutual nearest neighbors (MNS) across cells from different datasets were used as “anchors” to encode the cellular relationship between samples. Samples were integrated based on correction vectors for sample calculated form anchors.
Integrated data were further scaled using ScaleData function by regressing against total reads count, % of mitochondrial UMIs, and cell cycle phase scores (S and G2/M). A shared nearest neighbor (SNN) based graph was constructed using top 40 principal components, and clusters were identified using the Louvain algorithm using FindCluster function at resolution=1 (33 clusters). Uniform Manifold Approximation and Projection (UMAP) were generated by RunUMAP function and used for visualization.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files

extract_protocol:
RNA was isolated using NucleoSpin RNA II kit.
Library was performed using Chromium Single Cell 3’ Reagent Kits (v2) per user guideline (CG00052, Rev D). Sequencing was performed on a Nextseq 2000 platform (Illumina) aiming for a minimum of 50,000 reads/cells.

value: KRAS-G12D TP53-null (KP) lung tumor model (KPN1) cell-line

value: KRAS-G12D TP53-null

value: Romidepsin


title: Established myeloproliferative CMML, sample 59

value: myeloproliferative CMML


title: S5-14D

value: Sorafenib 50mg/kg


title: Established myeloproliferative CMML, sample 57


title: KPN-PD1-CD45,scRNAseq

description: 10x Genomics

value: Tumor


title: KPN-CTRL-CD45,scRNAseq

description: 10x Genomics

value: Control


title: Established myeloproliferative CMML, sample 53


title: Established myeloproliferative CMML, sample 58


title: Established myeloproliferative CMML, sample 54


title: Established myeloproliferative CMML, sample 56


title: BBX_1DL

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper TopHat 2.1.1 (Kim et al., 2013) set for Forward Read (FR) unstranded libraries and adjusting the maximum intron length to 5000 bp.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Assembly: TAIR10
Supplementary files format and content: tab-delimited file includes DESeq2 normalized values for each sample

growth_protocol: Seeds were surface-sterilized in 10 % bleach and 0.01% Triton-X-100 for 10 min, they were plated on sucrose-free agar (Sigma-Aldrich/Merck, Darmstadt, Germany) plates containing 0.5X Murashige and Skoog (MS) medium followed by stratification at 4°C in dark for 3 days. Then, seeds were exposed to 2 h of white light (100 µmol photons m-2 sec-1) after stratification, and seedlings were grown for 3 days in darkness.

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Firstly, ribosomal RNA was removed by rRNA removal kit, and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA and performing procedures as follows. Briefly, after fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized and dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: 3d dark growth, 1 d light

value: Day 4


title: BBX_3DL


title: Established myeloproliferative CMML, sample 52


title: BBX_2DL


title: Duxbl-sgko-WT/Het_22

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: 2-cell mouse embryo

extract_protocol:
Single embryos were separated into tubes.
SMART-Seq stranded Kit (Takara Bio) was used following manufacture’s protocol without RNA extraction. Sequencing was performed on NextSeq2000 instrument (Illumina) using P3 flowcell with 2x61bp paired end setup.

value: 2-cell mouse embryo

value: Duxbl-WT/Het


title: Established myeloproliferative CMML, sample 62


title: Col_3DL


title: Established myeloproliferative CMML, sample 51


title: KPN-COMBO-CD45,scRNAseq

description: 10x Genomics


title: Duxbl-sgko-WT/Het_21


title: Col_2DL


title: Established myeloproliferative CMML, sample 50


title: Established myeloproliferative CMML, sample 5


title: Duxbl-sgko-WT/Het_20


title: Established myeloproliferative CMML, sample 49


title: Col_1DL


title: Established myeloproliferative CMML, sample 55


title: Duxbl-sgko-WT/Het_18


title: CD34+_APOBECYTH_STM2457 rep3

city: New York

first: Michael

middle: G.

last: Kharas

state: NY

address: 417 East 68th Street

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Adapter trimmer of the fastq files was performed using Cutadapt (v1.13) with option -m 50.
Aligment to human (hg38) genomes using HISAT3N78 (v2.2.1-3n) with –base-change C,T and –no-repeat-index as parameters.
Bullseye pipeline (https://github.com/mflamand/Bullseye) was employed to identify C-to-T mutations in each RNA-seq library. A minimal coverage of 10 reads and duplicate removal were required to construct the variant quantification matrices using the parseBAM.pl script, provided by the Bullseye pipeline. The Bullseye/Find_edit_site.pl was applied with parameters --ControlMinCoverage 10, --EditMinCoverage 10, --minEdit 2.5, --maxEdit 95, --editFoldThreshold 1, --bedt, --intron, and --extUTR. Additionally, --minEditSites 1 was used to account for edited sites that may appear as single positions instead of clusters.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read variant values per position.

source_name: cord blood

growth_protocol: Human CD34+ HSPCs were purified from at least 6 mixed CB units (each unit from one healthy donor). Freshly purified CD34+ cells were cultured overnight in X-Vivo 10 media containing 1% BSA, 100ng/ml hSCF, 100ng/ml hFlt3L, 50ng/ml hTPO, and 10ng/ml hIL7, PeproTec.

extract_protocol:
After PicoGreen quantification and quality control by Agilent BioAnalyzer, library preparation is performed using  the SMART-Seq v4 Ultra Low Input RNA Kit
After PicoGreen quantification and quality control by Agilent BioAnalyzer, library preparation is performed using  the SMART-Seq v4 Ultra Low Input RNA Kit

treatment_protocol:
Cells were infected with virus expressing APOBEC-YTH retrovirus or empty vector. 24hr post infection, CD34+ cells were treated with STM2457 at a concentration of 20µM for 2 days. GFP+ cells were sorted .
Sorted cells were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform

value: cord blood

value: primary cells

tag: cell lineage

value: hematopoietic stem cell

tag: construct

value: APOBEC-YTH OE


title: Established myeloproliferative CMML, sample 48

value: Bone marrow aspirate


title: CD34+_APOBECYTH_STM2457 rep2


title: Established myeloproliferative CMML, sample 46


title: Established myeloproliferative CMML, sample 44


title: Established myeloproliferative CMML, sample 45


title: CD34+_APOBECYTH_STM2457 rep1


title: Established myeloproliferative CMML, sample 43


title: Established myeloproliferative CMML, sample 42


title: CD34+_MIG_DMSO rep3

value: empty vector

value: DMSO


title: Duxbl-sgko-WT/Het_15

tag: genotype


title: Established myeloproliferative CMML, sample 41


title: Duxbl-sgko-WT/Het_14


title: Established myeloproliferative CMML, sample 40


title: CD34+_MIG_DMSO rep2


title: Established myeloproliferative CMML, sample 39


title: CD34+_MIG_DMSO rep1


title: Established myeloproliferative CMML, sample 4


title: Established myeloproliferative CMML, sample 38


title: Duxbl-sgko-WT/Het_19


title: Duxbl-sgko-WT/Het_13


title: CD34+_APOBECYTH_DMSO rep3


title: Established myeloproliferative CMML, sample 37


title: Established myeloproliferative CMML, sample 36


title: Established myeloproliferative CMML, sample 47


title: Established myeloproliferative CMML, sample 35


title: Duxbl-sgko-WT/Het_12


title: Established myeloproliferative CMML, sample 34


title: Duxbl-sgko-WT/Het_11


title: Established myeloproliferative CMML, sample 33


title: CD34+_APOBECYTH_DMSO rep1


title: Established myeloproliferative CMML, sample 32


title: Duxbl-sgko-WT/Het_16


title: NB7.sisiGGGGGC.ATA.R3 (DISE-067)

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after).  This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Supplementary files format and content: Tab-delimited text file with read, seed (bp 2-7), cell viability based on seed, raw read counts for each sample, and putative source based on blast

source_name: NB7 Neuroblastoma cell line

extract_protocol:
Cell lysates were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: RNA was isolated from NB7 cells transfected either with 1 nM siNT1 or siGGGGGC with and without ATA treatment

value: NB7 Neuroblastoma cell line

value: Transfected with 1 nM siGGGGGC +ATA for 24 hrs

tag: fraction

value: Ago bound RNA


title: Duxbl-sgko-WT/Het_9


title: Established myeloproliferative CMML, sample 31

value: myeloproliferative CMML


title: Duxbl-sgko-WT/Het_8


title: Established myeloproliferative CMML, sample 30


title: Established myeloproliferative CMML, sample 28


title: NB7.sisiGGGGGC.ATA.R1 (DISE-067)

tag: treatment


title: Established myeloproliferative CMML, sample 27


title: NB7.sisiGGGGGC.ATA.R2 (DISE-067)


title: Established myeloproliferative CMML, sample 26


title: Duxbl-sgko-WT/Het_7

tag: strain


title: Duxbl-sgko-WT/Het_17


title: NB7.siGGGGGC.R3 (DISE-067)

value: Transfected with 1 nM siGGGGGC for 24 hrs


title: Duxbl-sgko-WT/Het_6


title: Established myeloproliferative CMML, sample 23


title: CD34+_APOBECYTH_DMSO rep2


title: NB7.siGGGGGC.R2 (DISE-067)


title: Established myeloproliferative CMML, sample 24


title: Established myeloproliferative CMML, sample 25


title: Duxbl-sgko-WT/Het_5


title: Established myeloproliferative CMML, sample 22


title: NB7.siGGGGGC.R1 (DISE-067)


title: Duxbl-sgko-WT/Het_10


title: Established myeloproliferative CMML, sample 20


title: Established myeloproliferative CMML, sample 2


title: Duxbl-sgko-WT/Het_4


title: Established myeloproliferative CMML, sample 29


title: Established myeloproliferative CMML, sample 3


title: Duxbl-sgko-WT/Het_3


title: Established myeloproliferative CMML, sample 19


title: NB7.siNT1.R2 (DISE-067)

value: Transfected with 1 nM siNT1 for 24 hrs


title: Established myeloproliferative CMML, sample 18


title: Established myeloproliferative CMML, sample 17


title: Duxbl-sgko-WT/Het_2


title: NB7.siNT1.R1 (DISE-067)


title: Duxbl-sgko-WT/Het_1


title: Established myeloproliferative CMML, sample 16


title: Abeta42.6h.rep2 (DISE-062)

source_name: SH-SY5Y 7 days differentiated with RA/BDNF

growth_protocol: 7 days differentiated with RA/BDNF

treatment_protocol: RNA was isolated from cells treated with either Aβ-40 or Aβ-42 for either 2, 4 or 6 hrs.

value: 20 uM Aβ-42 for 6 hrs


title: Established myeloproliferative CMML, sample 15


title: Established myeloproliferative CMML, sample 11


title: Established myeloproliferative CMML, sample 1


title: NB7.siNT1.R3 (DISE-067)


title: Established myeloproliferative CMML, sample 12


title: Established myeloproliferative CMML, sample 10


title: Abeta40.6h.rep2 (DISE-062)

value: 20 uM Aβ-40 for 6 hrs


title: Established myeloproliferative CMML, sample 21


title: Duxbl-sgko-KO_5

value: 2-cell mouse embryo

value: Duxbl-KO


title: Established myeloproliferative CMML, sample 13


title: Abeta40.6h.rep1 (DISE-062)


title: Abeta42.4h.rep2 (DISE-062)

value: 20 uM Aβ-42 for 4 hrs


title: Abeta42.6h.rep1 (DISE-062)


title: Established myelodysplastic CMML, sample 99

value: myelodysplastic CMML


title: Established myelodysplastic CMML, sample 96


title: Duxbl-sgko-KO_2


title: Established myelodysplastic CMML, sample 97


title: Abeta42.4h.rep1 (DISE-062)


title: Established myelodysplastic CMML, sample 95


title: Established myeloproliferative CMML, sample 14


title: Established myelodysplastic CMML, sample 94


title: Abeta40.4h.rep2 (DISE-062)

value: 20 uM Aβ-40 for 4 hrs


title: Duxbl-sgko-KO_3


title: wt-l2c_6

value: WT


title: Established myelodysplastic CMML, sample 93

value: Bone marrow aspirate


title: wt-l2c_5


title: Established myelodysplastic CMML, sample 92


title: Established myelodysplastic CMML, sample 91


title: Established myelodysplastic CMML, sample 90


title: wt-l2c_4


title: Established myelodysplastic CMML, sample 9


title: Established myelodysplastic CMML, sample 89


title: Abeta42.2h.rep1 (DISE-062)

value: 20 uM Aβ-42 for 2 hrs


title: Established myelodysplastic CMML, sample 98


title: Abeta42.2h.rep2 (DISE-062)


title: Duxbl-sgko-KO_1


title: Abeta40.2h.rep2 (DISE-062)

value: 20 uM Aβ-40 for 2 hrs


title: Established myelodysplastic CMML, sample 88


title: Established myelodysplastic CMML, sample 86


title: Established myelodysplastic CMML, sample 87


title: wt-l2c_1


title: wt-l2c_2


title: Established myelodysplastic CMML, sample 85


title: Abeta40.2h.rep1 (DISE-062)


title: Established myelodysplastic CMML, sample 82


title: NB7.DroshaKO.A3-11 (DISE-035)

source_name: Neuroblastoma cell line

treatment_protocol: RNA was isolated from 250 mg of cortex combined

value: NB7 neuroblastoma cell line

value: DroshaKO


title: Established myelodysplastic CMML, sample 80


title: wt-e2c_8


title: NB7.DroshaKO.A3-3 (DISE-035)

value: Ago bound RNA


title: Established myelodysplastic CMML, sample 83


title: Established myelodysplastic CMML, sample 81


title: wt-e2c_6


title: Abeta40.4h.rep1 (DISE-062)


title: wt-l2c_3


title: wt-e2c_7


title: Established myelodysplastic CMML, sample 8


title: Established myelodysplastic CMML, sample 79


title: NB7 (DISE-035)

value: control


title: Established myelodysplastic CMML, sample 78


title: wt-e2c_5


title: NCIcontrol.rep3 (DISE-035)

source_name: Brain cortex, CN patient #A17-60(1862)

value: Brain cortex

value: CN


title: Established myelodysplastic CMML, sample 76


title: Established myelodysplastic CMML, sample 77


title: wt-e2c_4


title: NCIcontrol.rep2 (DISE-035)

source_name: Brain cortex, CN patient #A14-139(1114)


title: wt-e2c_3


title: Established myelodysplastic CMML, sample 84


title: Established myelodysplastic CMML, sample 74


title: wt-e2c_2


title: Established myelodysplastic CMML, sample 75


title: Established myelodysplastic CMML, sample 73


title: NCIcontrol.rep1 (DISE-035)

source_name: Brain cortex, CN patient #A13-04(1725)


title: Established myelodysplastic CMML, sample 72


title: Established myelodysplastic CMML, sample 70


title: SuperAgers.rep3 (DISE-035)

source_name: Brain cortex, SA patient #A20-29(1919)

value: SA


title: Dux-Duxbl_3

extract_protocol:
RNA was isolated with the Direct-zolTM RNA MiniPrep Plus Kit (Zymo Research, R2072) according to the manufacturer’s protocol.
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). 1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).

value: mouse embryonic stem cell line

value: transfected with plasmid encoding Dux and plasmid encoding Duxbl


title: Established myelodysplastic CMML, sample 71

source_name: Bone marrow aspirate


title: SuperAgers.rep2 (DISE-035)

source_name: Brain cortex, SA cpatient #A20-22(1719)


title: Duxbl-sgko-KO_4

value: 2-cell mouse embryo

value: Duxbl-KO


title: wt-e2c_1


title: Established myelodysplastic CMML, sample 7

value: myelodysplastic CMML


title: SuperAgers.rep1 (DISE-035)

source_name: Brain cortex, SA patient #A18-148(421)


title: Dux-Duxbl_2


title: Established myelodysplastic CMML, sample 68


title: Established myelodysplastic CMML, sample 67


title: Established myelodysplastic CMML, sample 66


title: iPSCs.5month (DISE-034)

source_name: iPSC derived neurons, 5 months old

treatment_protocol: RNA was isolated from cells

value: iPSC derived neurons

value: 5 months old


title: Established myelodysplastic CMML, sample 65

value: Bone marrow aspirate


title: Dux-Duxbl_1


title: iPSCs.1month (DISE-034)

source_name: iPSC derived neurons, 1 month old

value: 1 month old


title: Established myelodysplastic CMML, sample 64


title: Duxbl_3

value: transfected with plasmid encoding Duxbl


title: Established myelodysplastic CMML, sample 63


title: iPSCs.AD.rep2 (DISE-024)

source_name: iPSC derived neurons, AD patient derived, AD2: AG5810

value: AD


title: Established myelodysplastic CMML, sample 62


title: Duxbl_2


title: iPSCs.AD.rep1 (DISE-024)

source_name: iPSC derived neurons, AD patient derived, AD1: AG11414


title: Established myelodysplastic CMML, sample 60


title: Established myelodysplastic CMML, sample 61


title: Duxbl_1


title: Established myelodysplastic CMML, sample 6


title: Dux_3

value: transfected with plasmid encoding Dux


title: Established myelodysplastic CMML, sample 59


title: iPSCs.Control.rep2 (DISE-024)

source_name: iPSC derived neurons, control 2: NUAD0635

value: Ago bound RNA


title: Established myelodysplastic CMML, sample 69


title: iPSCs.Control.rep1 (DISE-024)

source_name: iPSC derived neurons, control 1: AG02261

value: control


title: Established myelodysplastic CMML, sample 57


title: Established myelodysplastic CMML, sample 58


title: control7

city: Hangzhou

first: Zhenjie

address: No. 88, Jiefang Road

department: Vascular Surgery

institute: Second Affiliated Hospital of Zhejiang University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data were calculated.
All the downstream analyses were based on the clean data with high quality.
Genome_build: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary_files_format_and_content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.

source_name: normal abdominal aorta

extract_protocol:
AAA and control samples were collected, RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: female

tag: smoking status

value: no


title: Dux_2


title: Established myelodysplastic CMML, sample 56


title: Established myelodysplastic CMML, sample 55


title: Dux_1


title: CTRL_3

value: transfected with control plasmid


title: Established myelodysplastic CMML, sample 53


title: Established myelodysplastic CMML, sample 54


title: Established myelodysplastic CMML, sample 52


title: control5

value: male

value: yes


title: control6


title: Established myelodysplastic CMML, sample 49


title: Established myelodysplastic CMML, sample 5


title: CTRL_2

value: mouse embryonic stem cell line


title: Established myelodysplastic CMML, sample 48


title: Duxb1-200_5

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: 2-cell mouse embryo

value: 2-cell mouse embryo

value: WT

value: injected with 200 ng/ul Duxbl-5-2A-NLS-mCherry mRNA


title: control4


title: Established myelodysplastic CMML, sample 51

value: myelodysplastic CMML


title: Duxb1-200_4


title: Established myelodysplastic CMML, sample 46

value: Bone marrow aspirate


title: Established myelodysplastic CMML, sample 47


title: control1


title: Established myelodysplastic CMML, sample 45


title: CTRL_1


title: Established myelodysplastic CMML, sample 43


title: Established myelodysplastic CMML, sample 44


title: control3


title: Duxb1-200_2


title: AAA7

source_name: abdominal aortic aneurysm


title: Duxb1-200_3


title: SPT16 GAL1pr-FLO8-sfGFP grown at 28C in galactose

city: Vancouver

first: LeAnn

last: Howe

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry and Molecular Biology

country: Canada

institute: University Of British Columbia

data_processing:
FASTQ files were mapped to custom Saccer3 genomes with the FLO8::sfGFP alleles using BWA-MEM.
Mapped reads were filtered for MAPQ score >10, sorted, and reads mapping to chrV extracted using Samtools view.
BAM files were converted to strand-specific wig files using the BAM to Wiggle tool in Galaxy (Version 5.0.1+galaxy2), and normalized to reads per genome coverage using the Java Genomics Toolkit. (https://github.com/timpalpant/java-genomics-toolkit) wigmath.Scale.
Assembly: saccer3_FLO8_crypTSS_sfGFP.fa (YLH1086 and YLH1088) and saccer3_GAL1pr_FLO8_crypTSS_sfGFP.fa (YLH2036)
Supplementary files format and content: wig files with reads from chrV and normalized to reads per genome coverage

organism: Saccharomyces cerevisiae S288C

source_name: Mata his3200 leu21 lys2-128 ura3-52 trp163 NAT:GAL1pr-FLO8-sfGFP-HpH

growth_protocol: Cells were grown in yeast extract, peptone media to mid-log phase.

extract_protocol:
Total RNA was isolated using hot acid phenol from 10 OD600 units of cells.
rRNA depletion and library preparation was performed by Azenta Life Sciences .

treatment_protocol: Cells were grown in either dextrose or galactose at 28 or 37C for one hour.

value: grown at 28C in galactose


title: Established myelodysplastic CMML, sample 42


title: control2


title: AAA6


title: Duxb1-200_1


title: Established myelodysplastic CMML, sample 50


title: Established myelodysplastic CMML, sample 41


title: AAA5


title: spt16-197 FLO8-sfGFP grown at 37C in dextrose

source_name: Mata his3200 leu21 lys2-128 ura3-52 trp163 FLO8-sfGFP-HpH spt16-197

value: grown at 37C in dextrose


title: AAA4


title: Established myelodysplastic CMML, sample 40


title: SPT16 FLO8-sfGFP grown at 37C in dextrose


title: mCherry_4

value: injected with 200 ng/ul NLS-mCherry mRNA


title: Established myelodysplastic CMML, sample 4


title: AAA3


title: spt16-197 FLO8-sfGFP grown at 28C in dextrose

source_name: Mata his3200 leu21 lys2-128 ura3-52 trp163 FLO8-sfGFP-HpH

value: grown at 28C in dextrose


title: mCherry_3


title: AAA2


title: SPT16 FLO8-sfGFP grown at 28C in dextrose


title: mCherry_2


title: Established myelodysplastic CMML, sample 39


title: Established myelodysplastic CMML, sample 38


title: AAA1


title: mCherry_1


title: SPT16 GAL1pr-FLO8-sfGFP grown at 28C in dextrose


title: ILC3_C, biological replicate 3

city: London

first: Joana

middle: F

last: Neves

state: County

address: Guy’s Hospital, St Thomas Street

department: Host Microbiome Interactions

institute: King's College London

description: excluded from the final analysis

data_processing:
Library preparation and sequencing was performed at the Wellcome Trust Oxford Genomics Core, where basic alignment (GRCm38.ERCC (2011)) and QC was also performed.
Acceptable data were trimmed by Trimmomatic 0.39 to remove poor quality reads and adapter sequences.
Processed transcripts were indexed and aligned to GRCm38.p6 v98 from Ensembl using Salmon 0.14.1 to quantify transcript-level read counts, which were summarised to gene-level counts by tximport 1.13.16.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Small intestinal organoid

extract_protocol:
RNA was harvested using RNeasy MicroRNA isolation kit (QIAGEN)
SMARTSeq2

value: Small intestinal organoid

value: 6-8 weeks

tag: Sex

value: Female

value: Co-cultured with type-3 innate lymphoid cells


title: MSK1, Kp, aCD3, 24h, 2

city: Genève

first: Clément

last: David

state: Canton de Genève

address: Rue Michel-Servet 1

department: PATIM

country: Switzerland

institute: Université de Genève

data_processing:
Raw sequence reads were filtered using Trimmomatic (v.0.39).
Raw sequence reads were sequentially aligned to the mouse genome to remove mouse-derived sequences and then to the Kp genome using bowtie2
BAM files obtained were analysed using R (v.4.0.3): Reads were assigned to genes using Rsubread package (v.2.4.2)
Reads were then analysed using ‘DeSeq2’ package (v.1.30.0)
GSEA was performed using the package ‘clusterProfiler’ (v.4.6.0)
Assembly: mm10 and
Supplementary files format and content: tab-delimited tables include raw counts affiliated to each sample
Supplementary files format and content: tab-delimited tables include DESeq2 statistical output for each experiment

organism: Klebsiella pneumoniae

source_name: bacteria

growth_protocol: CR-Kp ST-258 contained in feces samples was frozen at-80°C until RNA extraction. Murine cecal tissues were put at -20°C in RNAlater.

extract_protocol:
CR-Kp ST-258 RNA and murine RNA were isolated from faecal pellets or caecal contents using the RNeasy PowerMicrobiome Kit (Qiagen).
CR-KP ST-258 RNA sample libraries and murine RNA sample libraries  were prepared using the Illumina Stranded Total RNA Prep kit with the Ribo-zero Plus, and they were sequenced using the Illumina NovaSeq 6000 with single read 100bp.

value: bacteria

value: Klebsiella pneumoniae ST258

value: gram-negative bacteria

tag: agent

tag: time point


title: Established myelodysplastic CMML, sample 36

source_name: Bone marrow aspirate


title: WT Female

city: Sydney

first: Hani Jieun

last: Kim

state: NSW

address: Camperdown

country: Australia

institute: The University of Sydney

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: h5 matrix file

source_name: Whole Brain

extract_protocol:
Brain dissociation and endothelial cell isolation was performed using the adult brain dissociation kit and CD31 magnetic beads from Miltenyi Biotec. Briefly, meninges were removed mechanically and brain cortex from 9-month old APP/PS1 transgenic and WT mice were collected into ice-cold PBS. After magnetic bead separation, the flow through containing endothelial cells was subjected to single-cell RNA sequencing (scRNA seq) using 10X Chromium.
Single cell RNA libraries were prepared using 10X Genomics Chromium Single Cell 3' Reagent Kits following manufacturer's protocol.

value: Whole Brain

value: Endothelial Cells

value: 10 months


title: ILC3_B, biological replicate 2

description: included within the final analysis


title: MSK1, Kp, aCD3, 24h, 1


title: Established myelodysplastic CMML, sample 35


title: MSK1, Kp, aCD3, 6h, 4


title: WT Male

description: 10X Genomics

value: WT

value: Male

value: 7 Months


title: mCherry_5

value: 2-cell mouse embryo


title: ILC3_A, biological replicate 1

description: included within the final analysis


title: Established myelodysplastic CMML, sample 34

value: Bone marrow aspirate

value: myelodysplastic CMML


title: MPP4 APOBEC-YTH rep2

data_processing:
Alignment to mouse (mm10) genome using STAR aligner.
GATK workflow for calling variants in RNA-seq to identify all the mutations in each RNA-seq library.
We then restricted to the mutations within annotated mRNA transcripts, as well as restricting to C-to-T mutations in transcripts encoded by the forward strand and G-to-A mutations in transcripts encoded by the reverse strand. We also filtered out mutations found in the dbSNP database since they are most likely DNA-level mutations. We then combined the filtered sets of RNA editing events from all RNA-seq libraries of the same experiment and counted the number of reads containing reference (C/G) and alternative (T/A) alleles from each library at each site.
Gene expression levels from the bam files were quantified using featureCounts v2.0.3
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene read count values for each Sample

source_name: bone marrow

growth_protocol: B6 mice were used to harvest bone marrow. HSC and MPP1-4 cells were FACS sorted and placed in SFEM media supplemented with cytokines (50 ng/ml SCF, 10 ng/ml IL-3, and 10 ng/ml IL-6, 10ng/ml TPO and 20 ng/ml FLT3L)

extract_protocol: After PicoGreen quantification and quality control by Agilent BioAnalyzer, library preparation is performed using  the SMART-Seq v4 Ultra Low Input RNA Kit

treatment_protocol:
Cells were infected with virus expressing APOBEC-YTH retrovirus or empty vector and sorted for GFP+ expression 48hrs post transduction.
Sorted cells were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform

value: bone marrow

value: primary cells

value: APOBEC-YTH OE


title: AKPS_Smad4_20_A3474

data_processing:
Sequence reads were cleaned and adapter trimmed using trimmomatic-0.36 before mapping each sample individually to the mouse reference genome (GRCm38.p6, primary assembly + GENCODE M17 annotation) with STAR2.6.0c.
Raw read counts were obtained using featurecounts from the subread1.6.1 package and GENCODE M17 mouse gene annotations using only uniquely aligned reads (default) and including multi-mapping reads (-M).
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05 on each set of raw expression measures.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: liver

extract_protocol:
RNA was extracted from cell lines using the RNeasy Mini Kit (Qiagen).
mRNA sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit with 200 ng total RNA following the manufacturer’s specifications.

treatment_protocol: AKPS cancer cells were infected with lentivirus containing EV or Smad4 plasmid over 3 rounds with polybrene (8 μg/ml), each lasting 2 hours. In experiments in which EV- and Smad4-expressing AKPS cancer cells were treated with TGFβ1, it was provided at 20 ng/ml in DMEM with 1% FBS. 16 hours prior to treatment cells were changed to low FBS media. RNA was harvested 48 hours after treatment.

value: liver

value: AKPS tumor cell line

value: mouse liver cancer cells

value: Smad4-expressing AKPS

value: TGFβ treated


title: AKPS_EV_19_A3474

value: EV-expressing AKPS


title: Established myelodysplastic CMML, sample 33

data_processing:
Data processing was performed within Illumina's BaseSpace plattform using the RNA-seq Alignment app (v2.0.1)
Reads were mapped with STAR aligner (v2.5.0a) to the human reference genome hg19 (RefSeq annotation)
Gene specific read abundance was calculated with Cufflinks (v2.2.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text files contain gene specific read count values for each sample

extract_protocol:
Total RNA was extracted using the MagNA Pure 96 Instrument and the MagNA Pure 96 Cellular RNA LV Kit (Roche LifeScience, Mannheim, Germany)
The TruSeq Total Stranded RNA kit was used, starting with 250ng of total RNA, to generate RNA libraries following the manufacturer’s recommendations (Illumina, San Diego, CA, USA)


title: APP/PS1 Female

description: 10X Genomics

value: Whole Brain

value: Endothelial Cells

value: Female


title: Established myelodysplastic CMML, sample 32


title: MPP4 MIG rep3

value: empty vector


title: MPP4 APOBEC-YTH rep1


title: AKPS_Smad4_16_A3723


title: Established myelodysplastic CMML, sample 31


title: MSK1, Kp, aCD3, 6h, 1

value: bacteria

value: Klebsiella pneumoniae ST258

value: gram-negative bacteria


title: MPP4 MIG rep2


title: AKPS_EV_15_A3723


title: APP/PS1 Male

description: 10X Genomics

value: Male

value: 7 months


title: Established myelodysplastic CMML, sample 37

value: Bone marrow aspirate

value: myelodysplastic CMML


title: MSK1, Kp, 0h, 3


title: MPP4 MIG rep1

value: bone marrow

value: primary cells


title: Established myelodysplastic CMML, sample 30


title: MPP2 APOBEC-YTH rep3

value: APOBEC-YTH OE


title: duxbl-late-2C_7

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

extract_protocol:
Five embryos were pooled and dispensed into tubes.
SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio) was used following manufacturer’s protocol without RNA extraction and the Nextera XT kit with v2 Full Set indexes (N7-S5) was used for library preparation.Sequencingwas performed on a Nova-seq instrument (Illumina) with2x75bp paired end setup.

value: 2-cell mouse embryo

value: WT

value: injected with 200 ng/µl Duxbl-V5-2A-NLS-mCherry mRNA


title: duxbl-late-2C_6


title: MSK1, Kp, 0h, 1


title: Established myelodysplastic CMML, sample 29


title: MPP2 APOBEC-YTH rep2


title: duxbl-late-2C_4


title: MSK2, Kp, 24h, 2


title: MSK1, Kp, aCD3, 6h, 2


title: Established myelodysplastic CMML, sample 28


title: MPP2 APOBEC-YTH rep1


title: MSK1, Kp, aCD3, 6h, 3


title: duxbl-late-2C_3


title: Established myelodysplastic CMML, sample 27


title: MSK2, Kp, 24h, 1


title: MPP2 MIG rep3


title: Established myelodysplastic CMML, sample 26


title: MSK2, Kp, 6h, 2


title: duxbl-late-2C_1


title: Established myelodysplastic CMML, sample 25


title: MSK1, Kp, 0h, 2


title: MPP2 MIG rep1


title: MSK2, Kp, 0h, 2


title: duxbl-early-2C_6


title: Established myelodysplastic CMML, sample 3


title: MPP1 APOBEC-YTH rep3


title: Established myelodysplastic CMML, sample 24


title: duxbl-early-2C_5


title: MSK2, Kp, 0h, 1


title: CMU1, aCD3, 24h, 4

description:
CD32_Kpn_Counts.txt
CD32_mouse_counts.txt

source_name: cecum/bacteria

value: cecum/bacteria

value: Klebsiella pneumoniae ST258/intestinal cells

value: gram-negative bacteria/murine cells


title: MPP1 APOBEC-YTH rep2


title: Established myelodysplastic CMML, sample 23


title: duxbl-early-2C_3


title: MPP1 APOBEC-YTH rep1


title: Established myelodysplastic CMML, sample 22


title: Established myelodysplastic CMML, sample 21


title: MPP2 MIG rep2

value: empty vector


title: CMU1, aCD3, 24h, 3


title: MSK2, Kp, 6h, 1

value: bacteria


title: CMU1, aCD3, 24h, 2


title: duxbl-early-2C_7


title: Established myelodysplastic CMML, sample 20


title: duxbl-late-1C_6

source_name: 1-cell mouse embryo

value: 1-cell mouse embryo


title: MPP1 MIG rep3


title: Established myelodysplastic CMML, sample 2


title: MPP1 MIG rep2


title: duxbl-late-1C_7


title: duxbl-late-1C_5


title: CMU1, aCD3, 24h, 1


title: CMU1, PBS 24h, 4

value: PBS


title: Established myelodysplastic CMML, sample 19


title: MPP1 MIG rep1


title: HSC APOBEC-YTH rep3

value: hematopoietic stem cells


title: duxbl-late-1C_4


title: duxbl-early-2C_4


title: mcherry-late-2C_7

value: injected with 200 ng/µl NLS-mCherry mRNA


title: Established myelodysplastic CMML, sample 18

value: Bone marrow aspirate


title: HSC APOBEC-YTH rep2


title: CMU1, PBS 24h, 3


title: CMU1, PBS 24h, 2


title: HSC APOBEC-YTH rep1


title: Established myelodysplastic CMML, sample 17

value: myelodysplastic CMML


title: Established myelodysplastic CMML, sample 16


title: mcherry-late-2C_6


title: HSC MIG rep3

value: bone marrow


title: mcherry-late-2C_5


title: Idiopathic Pulmonary Fibrosis 4

city: Charlottesville

first: Anwaruddin

last: Mohammad

address: Pinn Hall

institute: University of Virginia

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6.0 except for ipf1 which uses v4.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 66 yo Male

extract_protocol:
Briefly, around 10,000 cells were targeted per sample and loaded onto each well of a Chromium Single Cell G Chip to generate single cell emulsions primed for reverse transcription.  After breaking the emulsion, the single cell specific barcoded DNAs were subjected to cDNA amplification and QC on the Agilent 4200 TapeStation Instrument, using the Agilent D5000 kit.  Each sample cDNA was used to prepare indexed libraries that were pooled prior to sequencing.  A quality control run was performed on the Illumina Miseq using the nano 300 cycle kit (1.4 Million reads/run), to estimate the number of targeted cells per sample. The cell estimate enabled the core to re-balance the pooled sample prior to deep sequencing.
The generation of single cell indexed libraries, from the thawed COVID PF and IPF PBMCs, was performed by the School of Medicine Genome Analysis and Technology Core, RRID:SCR_018883, using the 10X Genomics chromium controller platform and the Chromium Single Cell 5′ Library & Gel Bead Kit v1.1 reagent.  Deep sequencing was performed on either the NGS Illumina NextSeq 500 using the 150 cycle kit or NextSeq 2000 using the P3-100 cycle kit.  Control samples were sequenced on the MGISEQ-2000.

value: blood

value: peripheral blood mononuclear cells

tag: phenotype

value: Idiopathic Pulmonary Fibrosis


title: Established myelodysplastic CMML, sample 15

tag: disease state


title: Early-Resolving COVID associated Pulmonary Fibrosis 7

source_name: 43 yo Male


title: HSC MIG rep2

value: primary cells


title: mcherry-late-2C_4

value: 2-cell mouse embryo

value: WT


title: mcherry-late-2C_3


title: Established myelodysplastic CMML, sample 14


title: HSC MIG rep1


title: Late-Resolving COVID associated Pulmonary Fibrosis 7

source_name: 70 yo Female


title: Late-Resolving COVID associated Pulmonary Fibrosis 6

source_name: 59 yo Female


title: Established myelodysplastic CMML, sample 12