title: Hematopoietic stem cell (HSC) 84

extract_protocol:
Whole bone marrow cells were isolated by crushing long bones with mortar and pestle using PBS/2% FCS/2 mM EDTA and filtered through a 100 µm mesh. After erythrocyte lysis in hypotonic NH4Cl-buffer, cells were filtered through a 40 µm mesh. Hematopoietic lineage+ cells were removed with the lineage cell depletion kit (Miltenyi Biotec). Cells were incubated with antibodies in PBS / 2% FCS for 30 min, washed twice with PBS / 2% FCS. Single BM HSPC cells were sorted on an BD ARIA II SORP flow cytometer. Single hematopoietic stem and progenitor cells were index-sorted into 384 well plates containing 0.5 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. After thawing, 0.5 µl of a primer mix were added (5 mM dNTP (Invitrogen), 0.5 µM dT-primer (C6 aminolinkerAAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), 1 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription (RT) was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG), 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 µM UP-primer (AAGCAGTGGTATCAACGCAGAGT) under following cycling conditions: initial denaturation at 98°C for 3 min, 23 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA was eluted in 12 µl nuclease free water and the concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium).
For library preparation up to 700 pg cDNA was desiccated and rehydrated in 1 µl Tagmentation mix (1x TruePrep Tagment Buffer L, 0.1 µl TruePrep Tagment Enzyme V50; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme) and tagmented at 55°C for 5 min. Subsequently, Illumina indices are added during PCR (72°C 3 min, 98°C 30 sec, 13 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina 50 bp paired-end sequencing on a Novaseq6000 aiming at an average sequencing depth of 0.5 mio reads per cell.

value: rtTA/rtTA

value: induced


title: BJ-LC-08_S8

status: Public on Apr 28 2022

type: SRA

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
RNA-seq libraries were sequenced with single-end 50bp reads on an Illumina HiSeq4000.
FastQC (v0.11.5)
Single end Illumina reads were checked for quality using FastQC (v0.11.5) and they were trimmed for quality and adapters using Cutadapt (v1.12).
Each sample was mapped to the Mouse Ensembl reference genome GRCh38 using the fast alignment tool HISAT2 v2.1.0 with default settings and library type set to RF (1).
Genes in GRCm38 were quantified used HTSeq v0.9.0 using default settings  library type set to reverse.
edgeR, an R Bioconductor package, with R version 4.0, was used for differential gene analysis comparing various sample groups
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: liver, untreated, Tet2fl/fl vav cre+ symptom free

extract_protocol:
A piece of the left liver lobe (~3x3mm) was incubated in RNAlaterTM (Qiagen) at 4 °C for 48 h and stored at -80 °C until further analysis. For RNA extraction a Tissue-Tearor Homogenizer (Biospec) was used. RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using Total RNA-seq Prep Kit following manufacturer's protocols.

tag: tissue

value: liver

tag: genotype

value: Tet2fl/fl vav cre+

tag: treatment

value: untreated

tag: age

value: 20 weeks

tag: phenotype

value: asymptomatic


title: Human_Explant_Macula_Right_Targeted

city: Pittsburgh

first: Leah

last: Byrne

address: 3501 Fifth Avenue

department: Ophthalmology

description:
10X targeted enrichment, targeting GFP and marker genes
aav_barcode_key.txt

data_processing:
scRNA-seq data was aligned and cells were demultiplexed using STARsolo (v2.7).
Empty droplets were removed using DropletUtils (v1.4.3, lower.prop=0.05). Doublets were removed using SCDS (v1.0.0), with a hybrid score cutoff of 1.3. Gene expression was normalized using Scran (v1.12.1) and imputation was achieved using ALRA (v1.0) to improve the sparsity of the scRNA-seq datasets. The analysis of scRNA-seq datasets and cell type identification was  performed with Scanpy (v1.4.4.post1). Specifically, the top 50 principal  components of the gene expression matrix were calculated and used to  compute the Euclidean distance between cells. Cells were embedded into a  neighborhood graph for visualization using the UMAP algorithm, and Leiden  clustering was performed on this graph to identify cell populations. Cell types were identified using a hypergeometric test using a list of known retinal cell type  marker genes compiled from multiple sources. P-values were corrected for multiple hypothesis testing using the Bonferroni method and the cell type for  each cluster was chosen based on the most significant marker gene intersection p-value (< 0.05). Clusters that did not meet the significance threshold for cell type identification were analyzed and annotated manually using the known gene markers.
AAV variants were identified using a unique 25 bp barcode at the end of the GFP gene for each variant. GFP was identified  from these samples using two datasets: (1) whole transcriptome scRNA-seq data and (2) 10x targeted enrichment against GFP and other marker genes.  Salmon (v0.9.1) was used for GFP transcript quantification and in-house scripts were used to identify the AAV barcode and map these reads back to  their respective cells as previously described in our scAAVengr eLife paper.
Due to ethical concerns, raw fastq files were processed with BAMboozle to remove any donor-specific genetic variants before being submitted to GEO.
Assembly: GRCh38 (GCA_000001405.15) fasta with its associated NCBI RefSeq annotation file
Supplementary files format and content: Matrix tables with raw gene expression counts for every cell; Cell-by-GFP tables with raw GFP-barcode expression counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Retina explant macula region

growth_protocol: Eyes from postmortem donors/ rhesus were dissected within 30 minutes after surgical removal. The anterior segment was removed and eye cups were flat mounted. Around 5mm wide macular (central), mid-peripheral and peripheral retina was dissected and retinal tissue was carefully separated from RPE/choroid/sclera and immediately transferred to cell culture inserts with 0.40 μm pore size, with the photoreceptor side attached to the membrane. Culture wells contained 3 retinal explants; macular (central), mid-peripheral and peripheral retina. The retinal explants were cultured in Neurobasal Plus Medium supplemented with 2% B-27, 5 μg/ml Plasmocin prophylactic and Penicillin-streptomycin at 37 °C, 5% CO2. In order to keep the retinal explant attached to the transmembrane, a volume of 1.3 mL of medium was added into each culture well, which is a sufficient volume for wetting the transmembrane but not enough to submerge the explant.

extract_protocol:
On the 8th day of AAV incubation, the 1mm edges of each explant, which had the highest level of GFP expression, were collected and underwent single-cell dissociation, FACS, and scRNA-seq. The 1mm edge of each retinal explant was placed in Hibernate solution after dissection, and was then dissociated with an enzymatic and mechanical method using a  MACS Neural Tissue Dissociation Kit for postnatal neurons according to manufacturer’s recommendations. The macular,  mid-peripheral and peripheral region from the temporal quadrant retina of  human donor#2 was dissected, and the same anatomical regions from left and  right eye were combined and immediately dissociated using the same method.  The retinal single cells were resuspended in D-PBS with 0.1% BSA and  processed immediately for scRNA-seq or FACS. The GFP-positive cells in the  retinal explant cell suspensions were enriched using a MACS Tyto sorter. GFP-positive cells were resuspended in D-PBS with 0.1% BSA and processed immediately for scRNA-seq.
Following the manufacture’s protocol, using the Chromium Single Cell 3’ v3 kit (10x Genomics), single retinal cells were partitioned into Gel Beads in Emulsion (GEMs), mRNA was reverse transcribed to cDNA and barcoded with unique molecular identifiers (UMIs). The GEM emulsions were then broken and the cDNA was purified using DynaBeads. After PCR amplification, the cDNA was cleaned and further purified with SPRIselect reagent The final indexed library was constructed following fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR steps. The libraries were sequenced on Illumina S1 flow cells at the UPMC Genome Center. GFP transcripts with unique AAV barcodes were further enriched using a custom Targeted Gene Expression kit (10x Genomics) and the resulting library was sequenced with an Illumina MiSeq reagent nano kit v2 (300 cycles).

treatment_protocol: Fresh medium was replaced at the second day of incubation and 10μl of AAV capsid library was applied dropwise onto the surface of each explant (30μl per culture well). Every second day, medium was completely replaced and AAV application was performed. A total of 120 μl of AAV suspension was applied per culture well during 8 days of AAV incubation. GFP expression in the retina was monitored using an ECHO Revolve fluorescence microscope.

value: Retina explant

tag: sorting strategy

value: unsorted


title: Human_Explant_Macula_Right

description:
10x processed whole transcriptome
barcodes.tsv
genes.tsv
aav_barcode_key.txt


title: KO_t2

city: Changchun

first: Boqi

last: Zhang

state: Jilin

address: 5333 Xian Road

country: China

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

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

tag: strain background

value: testis

value: Aanat-/-


title: BJ-LC-05_S5


title: Human_Explant_FACS_Left

source_name: Retina explant all regions FACS

value: FACS-sorted


title: KO_t1


title: Hematopoietic stem cell (HSC) 82

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

country: Germany

institute: Medical Faculty TU Dresden

description:
raw_counts+metadata.csv
counts_filtered.csv
counts_filtered_normalized_log.csv
cell_metadata_filtered.csv

data_processing:
Alignment of the samples with GSNAP (version 2018–07-04) to the mm10 reference, and using Ensembl 87 for the support of splicesite detection
featureCounts (version1.6.2) was used to assign the reads to genes with the help of Ensembl 87 annotation
Genome_build: mm10

source_name: bone marrow

tag: col1a1 genotype

tag: rosa26 genotype

tag: doxycyclin induction


title: KO_St3

value: stomach


title: Hematopoietic stem cell (HSC) 81


title: sYW-2-RNHinput

city: Boston

first: Catherine

middle: LW

last: Miller

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard

description: S. pombe spike-in

library_source: genomic

data_processing:
Briefly, data was aligned to a combined S. cerevisiae + S. pombe genome using Bowtie2 (Langmead and Salzberg, 2012). Sequences were trimmed with cutadapt and processed using samtools (Li et al., 2009), bedtools, and deeptools (Ramírez et al., 2016) to generate genome coverage tracks.
Assembly: combined: S. cerevisiae R64-2-1, S. pombe ASM294v2
Library strategy: S1-DRIP-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells with S. pombe spike-in

growth_protocol: All S. cerevisiae strains used in this study are in the S288C background. All S. cerevisiae liquid cultures were grown in YPD (1% yeast extract, 2% peptone, 2% glucose) at 30°C . For spike-in normalization, S. pombe liquid cultures were grown in YES (0.5% yeast extract, 3% glucose, 225 mg/l each of adenine, histidine, leucine, uracil, and lysine) at 32°C.

extract_protocol:
For DRIP-seq, genomic DNA was isolated using Qiagen Tip kit according to manufacturer’s protocol with the exception that RNase was not added to buffer G2. Genomic DNA was first treated with S1 nuclease for 30 minutes at 50°C (as described in (Wahba et al., 2016b)). Samples were then fragmented by sonication to ~300 bp. For qPCR analysis, genomic DNA was isolated by phenol:chromoform extract followed by a brief treatment with RNaseA/T1 in 300 mM NaCl. DNA was fragmented by overnight digestion at 37°C with restriction enzymes (AccI, EcoRV, NcoI, HaeIII, BsrG1) in cutsmart buffer in the presence or absence of 20 U RNaseH. For DRIP-seq and DRIP-qPCR, following fragmentation, samples were purified by phenol:chloroform extraction then ethanol precipitated. Samples were resuspended in 1XFA buffer (1% TritonX-100, 0.1% sodium deoxycholate, 0.1% SDS, 50 mM HEPES, 150 mM NaCl, 1 mM EDTA). Antibody S9.6 (25µg) was pre-bound to 100 µL Protein A Dynabeads for 1 hour at 4°C in 1XFA buffer. 100 µg fragmented DNA was incubated with the S9.6-protein A beads for 2 hours at 4°C. Beads were washed in 5 successive washes: 1XFA, 1XFA with 0.5M NaCl, LiCl wash buffer (0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl), twice with TE buffer. DNA was eluted in 300 µL elution buffer (1%SDS, 0.1M NaHCO3) for 2 hr at 65°C. Samples were then treated with 1 µL Proteinase K (20 mg/mL) for 1 hour at 42°C, extracted with phenol:chloroform, and then ethanol precipitated. The final DNA pellet was resuspended in 50 µL TE buffer.
Libraries were prepared with Qiagen GeneRead Kit according to manufacturers instructions.

tag: cell type

tag: background strain

tag: antibody


title: sYW-2-input

description: S. pombe spike-in

value: Saccharomyces cerevisiae cells with S. pombe spike-in


title: sYW-2-RNH

description: S. pombe spike-in


title: Megakaryocyte Progenitor (MkP) 45


title: KO_St2


title: sYW-2-IP

description: S. pombe spike-in


title: KO_St1


title: Megakaryocyte Progenitor (MkP) 44


title: KO_Sp2

value: spleen


title: Human_Explant_Periphery_Right

source_name: Retina explant periphery region


title: KO_Sp1


title: Megakaryocyte Progenitor (MkP) 46


title: KO_Sp3


title: Megakaryocyte Progenitor (MkP) 43


title: sYW-1-RNH

description: S. pombe spike-in


title: Megakaryocyte Progenitor (MkP) 42


title: KO_SM3

source_name: skeletal muscle_Aanat-/-

value: skeletal muscle


title: WT-2-RNHinput

description: S. pombe spike-in

value: WT


title: Hematopoietic stem cell (HSC) 83

value: rtTA/rtTA


title: Megakaryocyte Progenitor (MkP) 41

value: induced


title: Megakaryocyte Progenitor (MkP) 40


title: WT-2-input

description: S. pombe spike-in


title: WT-2-RNH

description: S. pombe spike-in


title: Megakaryocyte Progenitor (MkP) 39


title: KO_Lu3

value: lung


title: Megakaryocyte Progenitor (MkP) 47


title: WT-1-RNH

description: S. pombe spike-in


title: KO_SK1

value: skin


title: KO_SK2


title: WT-1-RNHinput

description: S. pombe spike-in


title: KO_SK3


title: Megakaryocyte Progenitor (MkP) 37


title: Megakaryocyte Progenitor (MkP) 38


title: Megakaryocyte Progenitor (MkP) 34


title: WT-1-IP

description: S. pombe spike-in


title: sYW-1-input

description: S. pombe spike-in


title: KO_Lu1


title: sYW-1-RNHinput

description: S. pombe spike-in


title: Megakaryocyte Progenitor (MkP) 36


title: Megakaryocyte Progenitor (MkP) 35


title: KO_Lu2


title: sYW-1-IP

description: S. pombe spike-in


title: WT-1-input

description: S. pombe spike-in


title: Megakaryocyte Progenitor (MkP) 33


title: Megakaryocyte Progenitor (MkP) 32


title: KO_L3

value: liver


title: KO_L2


title: KO_SM1


title: WT-2-IP

description: S. pombe spike-in


title: KO_L1


title: Hematopoietic stem cell (HSC) 79


title: Hematopoietic stem cell (HSC) 78


title: Hematopoietic stem cell (HSC) 87


title: KO_K3

value: kidney


title: KO_K2


title: Hematopoietic stem cell (HSC) 76


title: Hematopoietic stem cell (HSC) 77


title: KO_H3

value: heart


title: Yak 4 +240d mammary gland tissue

type: RNA

city: Chengdu

first: Yu

last: Wang

state: Sichuan

address: #16, South Section, 1st Ring Road

institute: Southwest Minzu University

description: Gene expression of Yak mammary gland at 9 time points ralatead to parturition

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray.Array hybridization was performed in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: The cleaned chip was scanned by Agilent chip scanner (g2565ca) to obtain the hybridization image.

data_processing: Agilent feature extraction (v10.7) software was used to analyze the hybrid images and extract the data. Thwn genespring software V12 (Agilent)  for data analysis.

organism: Bos grunniens

source_name: Yak 4 mammary gland tissue

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method with subsequent enzymatic reaction. In detail, double-stranded cDNA (containing the T7 RNA polymerase promoter sequence) was synthesized from 100 ng total RNA using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer’s protocol (Capitalbio) with the T7 Oligo (dT). Germany).  The Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase.  Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (Macherey-Nagel, Düren, Germany) and resuspended in elution buffer.

extract_protocol: Total RNA containing small RNA was extracted from yak mammry gland tissue by using  the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol.

treatment_protocol: Biopsy of the mammary gland was performed by a veterinarian. Approximately 1 g of tissue was obtained alternatively at each time point from the left and right rear quarter on the mammary gland. Briefly, to obtain mammary parenchyma, the mammary capsule was incised and blunt dissection was performed. Fat and connective tissue were dissected, and clean mammary parenchyma subsequently washed with diethyl pyro carbonate-treated water. Tissue was cut into small pieces and immediately stored in liquid nitrogen for total RNA extraction.

value: mammary gland

tag: gender

value: female

tag: days relative to parturition


title: Yak 3 +240d mammary gland tissue

source_name: Yak 3 mammary gland tissue


title: KO_H2


title: KO_SM2


title: KO_K1


title: Yak 2 +240d mammary gland tissue

source_name: Yak 2 mammary gland tissue


title: Yak 3  +180d mammary gland tissue


title: Yak 1 +240d mammary gland tissue

source_name: Yak 1 mammary gland tissue


title: Yak 4  +180d mammary gland tissue


title: Hematopoietic stem cell (HSC) 75


title: KO_H1


title: Hematopoietic stem cell (HSC) 74


title: Hematopoietic stem cell (HSC) 73


title: KO_ew3

value: EWAT


title: Yak 2  +180d mammary gland tissue


title: Hematopoietic stem cell (HSC) 72


title: KO_ew2

value: Aanat-/-


title: Hematopoietic stem cell (HSC) 80


title: Hematopoietic stem cell (HSC) 71


title: Hematopoietic stem cell (HSC) 70


title: KO_ew1


title: KO_B3

value: brain


title: Yak 1 +180d mammary gland tissue


title: Yak 4 +120d mammary gland tissue


title: Yak 3 +120d mammary gland tissue


title: Hematopoietic stem cell (HSC) 68


title: Hematopoietic stem cell (HSC) 69


title: KO_B1


title: Yak 4 +60d mammary gland tissue


title: Hematopoietic stem cell (HSC) 67


title: Yak 2 +120dmammary gland tissue


title: Yak 1 +120d mammary gland tissue


title: Yak 3 +60d mammary gland tissue


title: Cont_t3

source_name: testis_wild type

value: testis

value: wild type


title: Hematopoietic stem cell (HSC) 66


title: Cont_t2


title: E34 Hematopoietic Stem Cell (E34 HSC) 32


title: Hematopoietic stem cell (HSC) 65


title: Cont_t1


title: Cont_St3

source_name: stomach_wild type

value: stomach


title: Cont_St2


title: Cont_St1


title: Yak 1 +60d mammary gland tissue


title: Yak 3 +30d mammary gland tissue


title: Yak 2 +60d mammary gland tissue


title: Yak 2 +30d mammary gland tissue


title: Yak 4 +30d mammary gland tissue


title: Yak 4 +15d mammary gland tissue


title: Cont_Sp3

source_name: spleen_wild type

value: spleen


title: Yak 1 +30d mammary gland tissue


title: E34 Hematopoietic Stem Cell (E34 HSC) 29


title: E34 Hematopoietic Stem Cell (E34 HSC) 28


title: KO_B2


title: Cont_Sp2


title: E34 Hematopoietic Stem Cell (E34 HSC) 27


title: E34 Hematopoietic Stem Cell (E34 HSC) 26


title: Cont_Sp1


title: Yak 3 +15d mammary gland tissue


title: Cont_SM3

source_name: skeletal muscle_wild type

value: skeletal muscle


title: E34 Hematopoietic Stem Cell (E34 HSC) 24

value: rtTA/rtTA


title: Cont_SM2


title: Yak 2 +15d mammary gland tissue


title: Yak 4 +1d mammary gland tissue


title: Yak 3 +1d mammary gland tissue


title: Cont_SM1


title: E34 Hematopoietic Stem Cell (E34 HSC) 31

value: induced


title: E34 Hematopoietic Stem Cell (E34 HSC) 23


title: Yak 1 +15d mammary gland tissue


title: Cont_SK3

source_name: skin_wild type


title: Yak 2 +1d mammary gland tissue


title: E34 Hematopoietic Stem Cell (E34 HSC) 25


title: E34 Hematopoietic Stem Cell (E34 HSC) 30


title: E34 Hematopoietic Stem Cell (E34 HSC) 20


title: Cont_SK2


title: Yak 1 +1d mammary gland tissue


title: Cont_SK1


title: E34 Hematopoietic Stem Cell (E34 HSC) 21


title: Cont_Lu3

source_name: lung_wild type

value: lung


title: Yak 4 -15d mammary gland tissue


title: Cont_Lu2


title: E34 Hematopoietic Stem Cell (E34 HSC) 18


title: Yak 3 -15d mammary gland tissue


title: E34 Hematopoietic Stem Cell (E34 HSC) 19


title: Cont_Lu1


title: Restricted hematopoietic progenitor 1 (HPC-1) 64


title: Yak 2 -15d mammary gland tissue


title: E34 Hematopoietic Stem Cell (E34 HSC) 17


title: Cont_L3

source_name: liver_wild type


title: Yak 1 -15d mammary gland tissue


title: Restricted hematopoietic progenitor 1 (HPC-1) 63


title: Yak 2 -30d mammary gland tissue


title: Cont_L1


title: Yak 4 -30d mammary gland tissue


title: Yak 3 -30d mammary gland tissue


title: Cont_L2


title: Restricted hematopoietic progenitor 1 (HPC-1) 62


title: Restricted hematopoietic progenitor 1 (HPC-1) 61


title: E34 Hematopoietic Stem Cell (E34 HSC) 22


title: Restricted hematopoietic progenitor 1 (HPC-1) 60


title: Cont_K1

source_name: kidney_wild type


title: Cont_K3


title: Yak 1 -30d mammary gland tissue


title: Restricted hematopoietic progenitor 1 (HPC-1) 59


title: Cont_K2


title: Restricted hematopoietic progenitor 1 (HPC-1) 58


title: Cont_H3

source_name: heart_wild type


title: Cont_H2


title: Restricted hematopoietic progenitor 1 (HPC-1) 57

source_name: bone marrow


title: Cont_H1


title: Cont_ew3

source_name: EWAT_wild type


title: Cont_ew2


title: Restricted hematopoietic progenitor 1 (HPC-1) 55


title: Restricted hematopoietic progenitor 1 (HPC-1) 54


title: Cont_B3

source_name: brain_wild type


title: Restricted hematopoietic progenitor 1 (HPC-1) 52


title: Cont_ew1


title: Restricted hematopoietic progenitor 1 (HPC-1) 53


title: Cont_B2


title: Restricted hematopoietic progenitor 1 (HPC-1) 49


title: Multipotent Progenitor (MPP) 79


title: Multipotent Progenitor (MPP) 78


title: Multipotent Progenitor (MPP) 77


title: TB836

city: Milwaukee

first: Stephanie

last: Olivier Van-Stichelen

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted and given in the counts.txt file.
Assembly: GRCh38

source_name: pituitary adenomas

extract_protocol:
mRNA was isolated with the PureLink RNA Mini Kit (#12183018A, Thermo Fisher Scientific) following the kit instruction.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).
Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR.

value: pituitary adenomas

value: Non functioning

value: Tpit -


title: Restricted hematopoietic progenitor 1 (HPC-1) 56


title: Multipotent Progenitor (MPP) 76


title: Restricted hematopoietic progenitor 1 (HPC-1) 51


title: TB846

value: ACTH secreting

value: Tpit +


title: Multipotent Progenitor (MPP) 75


title: TB841


title: TB847


title: TB842


title: TB789


title: Multipotent Progenitor (MPP) 73


title: TB833


title: TB835


title: Multipotent Progenitor (MPP) 74


title: TB788


title: Multipotent Progenitor (MPP) 72


title: Multipotent Progenitor (MPP) 70


title: TB779


title: TB763


title: Multipotent Progenitor (MPP) 71


title: TB784


title: Multipotent Progenitor (MPP) 69


title: TB738


title: TB737


title: Multipotent Progenitor (MPP) 68


title: Restricted hematopoietic progenitor 1 (HPC-1) 50


title: Multipotent Progenitor (MPP) 66


title: Cont_B1


title: TB675


title: TB660


title: Multipotent Progenitor (MPP) 65


title: Multipotent Progenitor (MPP) 64


title: TB614


title: TB596


title: TB599


title: Hematopoietic stem cell (HSC) 64


title: Hematopoietic stem cell (HSC) 63


title: Hematopoietic stem cell (HSC) 60


title: Hematopoietic stem cell (HSC) 62


title: TB594


title: TB512


title: Hematopoietic stem cell (HSC) 59


title: TB101


title: TB055


title: Hematopoietic stem cell (HSC) 57


title: Hematopoietic stem cell (HSC) 58


title: TB644


title: Hematopoietic stem cell (HSC) 55


title: B001-A-501, Dounce, scATACseq

city: Stanford

first: Winston

last: Becker

state: CA

address: 1291 Welch Road, B259 Beckman Center

institute: Stanford University

description: 10x genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcode processing, alignment, and fragments file generation was performed using Cell Ranger ATAC v1.2.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: hg38
Supplementary files format and content: Fragments files and tabix index of fragments files

source_name: Colon

extract_protocol:
The isolation of nuclei was accomplished using the OmniATAC protocol (Corces*, Granja* et al. Science 362, 2018). Dissociation of nuclei was carried out entirely on wet ice. 40-60mg of flash-frozen tissue was placed into 2ml dounce tissue grinders containing 1ml HB (Lysis) Buffer (1.0341x HB Stable solution, 1M DTT, 500 mM Spermidine, 150mM Spermine, 10% NP40, cOmplete Protease Inhibitor, Ribolock), gently triturated, then allowed to thaw for 5 minutes in the solution. After 5 minutes, tissue was dounced 10 times with pestle A and 20 times with pestle B, or until there was no resistance from either pestle. Sample was filtered through a 40um cell strainer (Falcon; 352340) and resulting homogenate transferred to a pre-chilled 2ml LoBind tube. Samples were spun in a 4°C fixed angle centrifuge for 5 minutes at 350 RCF to pellet nuclei. After spinning, all but 50ul of supernatant was removed. 350ul HB was added to the nuclei pellet for a total volume of 400ul. Nuclei were gently resuspended with a wide bore pipet. One volume of 50% Iodixanol (60% OptiPrep [Sigma Aldrich; D1556], Diluent Buffer [2M KCl, 1M MgCl2, 0.75M Tricine-KOH pH 7.8], Water) was added and gently triturated. Next, 600ul of 30% Iodixanol was carefully layered under the 25% mixture. Finally, 600ul of 40% Iodixanol was layered under the 30% mixture. Sample was then spun in a 4°C swinging bucket centrifuge for 20 min at 3,000 RCF. Upon completion of the spin, a band of nuclei was visible. Supernatant was aspirated down to within 200-300ul of the nuclei band. The nuclei band was then collected at 200ul and transferred to a fresh 1.5ml tube. Sample was diluted with one volume (200ul) Resuspension Buffer (1x PBS, 1% BSA, 0.2u/uL Ribolock). Nuclei concentration was determined using the Countess II FL Automated Cell Counter (ThermoFisher; AMQAF1000). In addition to isolating nuclei with the omni-ATAC dounce method, we used the Singulator from S2 Genomics to isolate nuclei for 4 samples (2 normal and 2 polyp) from patient A002. The same buffers (lysis, wash, resuspension) were used for both the manual omni-ATAC dounce and S2 Singulator methods. HB buffer was prepared following the OmniATAC protocol, with the addition of 15ul Ribolock per 1mL HB buffer to help maintain RNA integrity. Approximately 50-70mg tissue in small chunks were placed into the Nuclei Isolation Cartridge. We ran the Extended Nuclei Isolation Singulator program which includes disruption, 5 minute incubation, disruption, filtration (150um and 40um filters) and buffer rinse of the cartridge. Following dissociation, nuclei were spun at 300g for 5 minutes. Supernatant was removed and nuclei were resuspended in Resuspension Buffer (noted above). Nuclei were counted using the Countess Automated Cell Counter (ThermoFisher). The total dissociation time for 4 samples was approximately 1 hour, as one sample can be run at a time on the S2 Singulator.
scATAC-seq targeting 9,000 cells per sample was performed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10x Genomics, 1000175) and Chromium Next GEM Chip H (10x Genomics, 1000161).

value: Colon

tag: disease state

value: Normal

tag: familial adenomatous_polyposis

value: N

tag: Sex

value: F


title: Hematopoietic stem cell (HSC) 54


title: B001-A-406, Dounce, scATACseq

description: 10x genomics

tag: tissue


title: Multipotent Progenitor (MPP) 67


title: Hematopoietic stem cell (HSC) 53


title: Hematopoietic stem cell (HSC) 52


title: TBJ360_DP2

city: London

first: Charles

middle: R. M.

last: Bangham

address: Norfolk Place

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

data_processing:
Raw fastq files for the same sample from different sequencing lanes were concatenate.
Trim-galore with parameteres –paired –length 30 –stringency 3 was used.
STAR aligner was used with to create genome index with custom gtf and genome, which included the Timer construct sequence and HTLV-1 genome (GenBank: AB513134).
STAR aligner was used to align fastq files. Important parameters: --outSAMtype BAM SortedByCoordinate –quantMode TranscriptomeSam Genecounts
RSEM was used to quantify transcript abundances. Parameters: -p 30 –paired-end –forward-prob 0 –calc-pme
Genome_build: GRCh38/hg38;GenBank: AB513134
Supplementary_files_format_and_content: Tab-delimited text files of RSEM output including expected raw readcounts, TPM, FPKM.

source_name: Blood

growth_protocol: Two naturally infected T-cell clones isolated from non-malignant HTLV-1 positive individuals were stably transduced with a Tax-responsive fluorescent timer protein reporter cassette.  Transduced cells were cultured in T75 flasks at 1-2 million cells per millilitre in RPMI-1640 and 20% fetal bovine serum supplemented twice weekly with 100 IU/ml human interleukin 2, 10 µM Raltegravir and 1 µg/ml Puromycin Dihydrochloride.

extract_protocol:
RNA was extracted from flow cytometry sorted cells using Qiagen RNeasy Micro Kit (Catalogue number 74034).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
150 bp poly-A enriched stranded RNA-seq. All samples were sequenced in two lanes.

treatment_protocol: Sub-populations (DN, Blue, DP and Red) of timer protein-expressing cells were flow cytometry sorted.

value: CD4 T-cell

tag: timer phase

value: DP

tag: clone


title: TBJ360_Red2

value: Red


title: Hematopoietic stem cell (HSC) 51


title: TBJ360_Blue2

value: Blue


title: B001-A-401, Dounce, scATACseq

description: 10x genomics


title: B001-A-302, Dounce, scATACseq

description: 10x genomics


title: Hematopoietic stem cell (HSC) 50


title: TBJ360_DN2

value: DN


title: Restricted hematopoietic progenitor 1 (HPC-1) 48

value: rtTA/rtTA


title: Hematopoietic stem cell (HSC) 61

value: induced


title: TBJ360_Red1


title: TB586

tag: genotype


title: Restricted hematopoietic progenitor 1 (HPC-1) 47


title: TBJ360_DP1


title: TBJ360_Blue1


title: Hematopoietic stem cell (HSC) 49


title: TBJ360_DN1


title: TBX4B_Red2


title: Restricted hematopoietic progenitor 1 (HPC-1) 44


title: Restricted hematopoietic progenitor 1 (HPC-1) 46


title: Restricted hematopoietic progenitor 1 (HPC-1) 45


title: Hematopoietic stem cell (HSC) 56


title: sample SCD-A067

city: Nanjing

first: Shuwen

last: Cheng

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

data_processing:
trimmed and filtered by fastp
aligned to hg38 by STAR
check bam file quality by RSeQC
quantification by Stringtie
circRNAs are identified by CIRCexplorer2
Assembly: hg38
Supplementary files format and content: mRNA_Gene_Differential_Expression_Summary.xlsx, containing gene name ,  geen expression and differentail analysis result
Supplementary files format and content: lncRNA_Gene_Differential_Expression_Summary.xlsx, containing gene name ,  geen expression and differentail analysis result
Supplementary files format and content: circRNA_Gene_Differential_Expression_Summary.xlsx, containing gene name ,  geen expression, differentail analysis result and standard ID

source_name: whole blood

extract_protocol:
Total RNA was extracted using a PAXgene blood RNA kit (Qiagen)  under standardized conditions using a QIAcube (Qiagen) automated  processor in accordance with the manufacturer’s instructions
rRNA depletion 1st-stranded (dUTP)

value: whole blood

tag: group

value: SCD

value: RNA

tag: treatment

value: No treatment


title: sample SCD-A040


title: TBX4B_Blue2


title: TBX4B_DP2


title: sample SCD-A038


title: Restricted hematopoietic progenitor 1 (HPC-1) 43

tag: col1a1 genotype


title: sample SCD-A031


title: TBX4B_Red1


title: Restricted hematopoietic progenitor 1 (HPC-1) 40

tag: rosa26 genotype


title: Restricted hematopoietic progenitor 1 (HPC-1) 41

tag: doxycyclin induction


title: TBX4B_DP1

tag: cell type


title: sample SCD-A022


title: TBX4B_Blue1


title: sample SCD-A020


title: Restricted hematopoietic progenitor 1 (HPC-1) 38


title: sample SCD-A012


title: HEK293T Bin1

city: Hong Kong

first: John

middle: Hoi Chun

last: Fong

address: Laboratory Block, 21 Sassoon Road, Hong Kong

department: School of Biomedical Sciences, LKS Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Using software from PacBio (SMRT Link version 8.0.0), reads were assigned into individual samples with a bq >= 26 (bq: barcode quality). Conversion of subreads into consensus sequences was done by using ccs v4.2.0 with default parameters.
Library reference was used to map the 5' UTR sequence in the concensus reads by Bowtie 2 after trimming.  Only reads with more than 70nt matches to a reference 5’ UTR would be further analysed. 5' UTR counts were then combined across sequencing file via in-house R script.
Supplementary files format and content: CSV file including each 5' UTR sequence mapped, their nature, and their correponding read counts.
Library strategy: SMRT-seq

source_name: Human embryonic kidney

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA was extracted by DNeasy Blood and Tissue kit (Qiagen). PCR was done by using Kapa HiFi Hotstart Ready-mix (Kapa Biosystems) with the following primers: 5'- GTTAATTAAGGCCTGGGAGACG-3’ and 5’-GTGACTCGAACTCGCTTCCG-3’. Amplified fragments were gel purified by QIAquick Gel Extraction Kit (Qiagen).
SMRTbell® Libraries were prepared by using PacBio® Barcoded Overhang Adapters for Multiplexing Amplicons #101-791-700 Version 06 (January 2021), constructed by SMRTbell™ Express Template Prep Kit 2.0 (# 100-938-900), bined and cleaned up by Sequel Binding and Internal Ctrl Kit 3.0 (#101-626-000) following manufacturer's protocols.

treatment_protocol: 5' UTR-driving GFP was delivered to the cell by lentivirus. Cells were isolated by FACS on Day 7 post transduction.

value: Human embryonic kidney

tag: cell line


title: Female Control2

city: Cologne

first: Muhammad Sajid

last: Hussain

address: Weyertal 115b

department: Cologne Center for Genomics

institute: University of Cologne

data_processing:
Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline  version 1.2.7, based on Ensembl 87
Sequenced reads mapped to Homo sapiens
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: Ensembl version 87 ( Homo sapiens )
Supplementary_files_format_and_content: Text file include FPKM values for each Sample

growth_protocol: We generated LCLs from blood by getting pelleted lymphocytes which were immortalized by transfection of Epstein-Barr-virus. Cells were grown RPMI 1640 Medium supplemented with fetal bovine serum, L-glutamine and antibiotics (Penicillin/Streptomycin)

extract_protocol:
No extra protocole was followed
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Control LCLs

value: Blood

value: Wild type

value: Female


title: sample SCD-A008


title: M3 HLF, TGF-β1, Polysome mRNA

city: College Station

first: Richard

middle: H

last: Gomer

state: TX

address: 301 Old Main Drive

department: Biology

institute: Texas A&M University

description:
Polysome mRNA
Monosome_Polysome mRNA_Control_TGF-beta1.xlsx

data_processing:
RNA sequencing data was analyzed using the QuantSeq Data Analysis Pipeline on the BlueBee Genomic Platform.
Read QC, FASTQC report of raw reads; Trimming, Bbduk from the bbmap suite trimming: low quality tails, poly(A)read-through, adapter contamination; Read QC, FASTQC report of trimmed reads; Alignment, STAR Aligner with modified ENCODE settings.
Alignment output, Aligned BAM fille for download; Mapping QC, RSEQC report of the distribution of the reads on the annotation features; Gene read counting, HTSeq-count with kit-specific options (FWD); Differential expression, DESeq2 Pipeline (http://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: Homo sapiens - human (GRCh38)
Supplementary files format and content: Total_RNA_Control_TGF-beta1.xlsx: Excel file includes RPKM values for each Sample.
Supplementary files format and content: Monosome_Polysome_mRNA_Control_TGF-beta1.xlsx: Excel file includes RPKM values for each Sample.

source_name: HLF

growth_protocol: HLF cells were cultured in DMEM supplemented with 10% bovine calf serum (BCS), 100 U/ml penicillin, 100 μg/ml streptomycin, and 2 mM glutamine in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNAs or mRNAs from monosome & polysome fractions of HLF cells were extracted and purified with TRIzol reagents, chloroform and isopropanol. 2 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-Seq FWD library prep kits for Illumina.

treatment_protocol: 5 × 10^5 HLF were cultured in 100 mm tissue culture dishes for 24-48 hours. When the cell density reached ∼60% confluence, the supernatant was removed and cells were gently rinsed with prewarmed PBS 3 times. The medium was changed to prewarmed 10 ml DMEM supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, and 2 mM glutamine (no BCS) with or without 10 ng/ml TGF-β1. Cells were cultured in the new medium for 48 hours.

value: HLF

value: Human lung fibroblasts


title: F5 HLF, TGF-β1, Polysome mRNA


title: Restricted hematopoietic progenitor 1 (HPC-1) 36


title: Female Control1


title: sample SCD-A005


title: Restricted hematopoietic progenitor 1 (HPC-1) 35


title: F2 HLF, TGF-β1, Polysome mRNA


title: sample VCI-A065

value: VCI


title: M3 HLF, Control, Polysome mRNA


title: TBX4B_DN2

value: CD4 T-cell


title: sample VCI-A044


title: M2 HLF, Control, Polysome mRNA


title: Restricted hematopoietic progenitor 1 (HPC-1) 42


title: FP2

value: Patient derived LCLs

value: Mutant


title: sample SCD-A029


title: Restricted hematopoietic progenitor 1 (HPC-1) 33

value: rtTA/rtTA


title: sample VCI-A041


title: TBX4B_DN1

value: DN


title: Restricted hematopoietic progenitor 1 (HPC-1) 39

value: induced


title: Multipotent Progenitor (MPP) 63


title: Restricted hematopoietic progenitor 1 (HPC-1) 37


title: sample VCI-A034

value: whole blood


title: M3 HLF, TGF-β1, Monosome mRNA

description:
Monosome mRNA
Monosome_Polysome mRNA_Control_TGF-beta1.xlsx


title: Multipotent Progenitor (MPP) 62


title: M2 HLF, TGF-β1, Polysome mRNA


title: sample VCI-A032

value: RNA


title: Multipotent Progenitor (MPP) 61


title: M2 HLF, TGF-β1, Monosome mRNA


title: Multipotent Progenitor (MPP) 60


title: sample VCI-A025

value: No treatment


title: MUT1


title: sample VCI-A023


title: sample VCI-A021


title: Multipotent Progenitor (MPP) 59


title: F5 HLF, TGF-β1, Monosome mRNA


title: Multipotent Progenitor (MPP) 58


title: F2 HLF, TGF-β1, Monosome mRNA


title: Restricted hematopoietic progenitor 1 (HPC-1) 34


title: sample VCI-A013


title: M3 HLF, Control, Monosome mRNA


title: F5 HLF, Control, Polysome mRNA


title: RS8

city: New Delhi

first: Ankita

last: Ray

state: Delhi

address: Safdarjung hospital campus

country: India

institute: ICMR-National Institute of Pathology

description: non-heparanized blood

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to an Agilent Human Gene Expression Microarray 8X60K.Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: The microarray slide was scanned on a G2600D scanner (Agilent Technologies).

data_processing: Data extraction from Images was done using Feature Extraction software v 11.5.1.1 of Agilent.

label_protocol: Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step.

extract_protocol: Total RNA was extracted using Trizol(Ambion). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn blood from recurrent spontaneous aborters and controls were collected. Serum was seaparated and stored for further use.

value: Ct-negative control

value: serum

value: female

tag: age


title: H1975

city: Kurume

first: Yuichi

last: Murakami

address: Tsubukuhonmachi 422

country: Japan

institute: St Mary's Institute of Health Sciences

description: Gene expression data from NCI-H1975 cells.

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Cells were maintained in RPMI medium supplemented with 10% fetal bovine serum and incubated in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: OR1 and OR2 cells were established from NCI-H1975 cells by step-wise increasing doses of osimertinib up to 2 μmol/L over a period of four months.

tag: parental cell line

value: non-small cell lung cancer cell line

tag: phenotype

value: osimertinib sensitive


title: F2 HLF, Control, Polysome mRNA

value: HLF


title: RS7

description: non-heparanized blood

tag: gender


title: sample VCI-A003


title: RS6

description: non-heparanized blood

value: Ct-negative spontaneous abortion


title: OR2

description: Gene expression data from OR2 cells.

source_name: osimertinib resistant cells derived from NCI-H1975

value: osimertinib resistant


title: OR1

description: Gene expression data from OR1 cells.


title: Multipotent Progenitor (MPP) 56


title: F5 HLF, Control, Monosome mRNA

value: Human lung fibroblasts


title: SCD-A067

data_processing:
raw fastq files were trimmed by fastp
map to miRBase by miRDeep2
predict novel miRNA by miRDeep2
Assembly: miRBase
Supplementary files format and content: miRNA_Gene_Differential_Expression_Summary.xlsx, containing miRNA name ,  gmiRNA expression and differentail analysis result

extract_protocol:
Total RNA was extracted using a PAXgene blood RNA kit (Qiagen)  under standardized conditions using a QIAcube (Qiagen) automated  processor in accordance with the manufacturer’s instructions
3' and 5' adapters were ligated by T4 RNA ligase 2 and amplified by PCR

value: SCD


title: RS5

description: non-heparanized blood


title: F2 HLF, Control, Monosome mRNA


title: RS4

description: non-heparanized blood


title: SCD-A038


title: SCD-A031


title: Multipotent Progenitor (MPP) 54


title: spt650-2-HU-input

description: his3D200 lys2-128d ura3-52 leu2D0 hENT::AUR1C GDP-TK::URA3 spt6-50 bar1D::KanMX

data_processing:
Briefly, data was aligned to a combined S. cerevisiae + S. pombe genome using Bowtie2 (Langmead and Salzberg, 2012). Sequences were trimmed with cutadapt and processed using samtools (Li et al., 2009), bedtools, and deeptools (Ramírez et al., 2016) to generate genome coverage tracks.
Assembly: combined S. cerevisiae R64-2-1 and S. pombe ASM294v2
Library strategy: BrdU-IP-seq

source_name: Saccharomyces cerevisiae cells with S. pombe spike-in

extract_protocol:
Cell pellets were resuspended in lysis buffer (2% SDS, 2% Triton-X100, 100 mM NaCl, 10 mM Tris pH 8.0, 1 mM EDTA) and 500 µL acid washed glass beads were added. Cells were lysed by vortexing for a total of 30 minutes at 4°C. Genomic DNA was isolated by phenol-chloroform isolation followed by ethanol precipitation with NaCl salt. DNA pellet was washed once with 70% ethanol and then resuspended in sterile water. DNA was treated with RNaseA/T1 for 30 minutes at 37°C followed by Proteinase K for 30 minutes at 50°C. Genomic DNA (gDNA) was column purified by a PCR purification kit. gDNA was fragmented by sonication to ~300 bp. Sonication efficiency was confirmed by gel electrophoresis. DNA concentration was measured by nanodrop and an equal amount of sonicated S. pombe genomic DNA was added to each sample. Input samples were removed immediately following spike-in addition. For next-generation sequencing experiments, libraries were prepared with the Qiagen GeneRead kit according to manufacturer’s instructions prior to IP. For the IP, gDNA was boiled for 5 minutes at 95°C. Samples were incubated on ice for 3 minutes. 50 µL of gDNA (50-500 ng in EB) was combined with 50 µL anti-BrdU (1:250 in 2X IP buffer (2XPBS, 0.001% Triton-X100)) and incubated on a rotisserie for 2 hours at 4°C. 15 µL of washed Protein G Dynabeads was added. Samples were incubated on a rotisserie for 1 hour at 4°C. Samples were washed thrice in 1XIP buffer. Sample was eluted by the addition of TES and incubating for 10 min at 65°C.
Libraries were prepared with Qiagen GeneRead Kit according to manufacturers instructions.

treatment_protocol: Yeast strains were grown to an OD~0.2 and then synchronized by treatment with alpha factor for 2 hours. Visual inspection confirmed >90% of cells had shmoo-like morphology. Cells were then washed three times with YPD media lacking glucose supplemented with fresh 50 µg/mL pronase. Cells were released into indicated media and harvested. Following alpha-factor arrest (see above), cells were released into fresh YPD supplemented with 50 µg/mL pronase and 400 µg/mL BrdU. For HU-treated samples, hydroxyurea was added to a final concentration of 0.2M HU. Cells were harvested after 30 minutes (untreated) or 60 minutes (HU treatment) by the addition of sodium azide to a final concentration of 0.1%.

tag: background strain

tag: brdu antibody

value: none (input)

value: his3delta200 lys2-128delta ura3-52 leu2delta0 hENT::AUR1C GdeltaP-TK::URA3 spt6-50 bar1delta::KanMX

value: 0.2M HU, 60 min


title: Multipotent Progenitor (MPP) 57

extract_protocol:
Whole bone marrow cells were isolated by crushing long bones with mortar and pestle using PBS/2% FCS/2 mM EDTA and filtered through a 100 µm mesh. After erythrocyte lysis in hypotonic NH4Cl-buffer, cells were filtered through a 40 µm mesh. Hematopoietic lineage+ cells were removed with the lineage cell depletion kit (Miltenyi Biotec). Cells were incubated with antibodies in PBS / 2% FCS for 30 min, washed twice with PBS / 2% FCS. Single BM HSPC cells were sorted on an BD ARIA II SORP flow cytometer. Single hematopoietic stem and progenitor cells were index-sorted into 384 well plates containing 0.5 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. After thawing, 0.5 µl of a primer mix were added (5 mM dNTP (Invitrogen), 0.5 µM dT-primer (C6 aminolinkerAAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), 1 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription (RT) was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG), 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 µM UP-primer (AAGCAGTGGTATCAACGCAGAGT) under following cycling conditions: initial denaturation at 98°C for 3 min, 23 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA was eluted in 12 µl nuclease free water and the concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium).
For library preparation up to 700 pg cDNA was desiccated and rehydrated in 1 µl Tagmentation mix (1x TruePrep Tagment Buffer L, 0.1 µl TruePrep Tagment Enzyme V50; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme) and tagmented at 55°C for 5 min. Subsequently, Illumina indices are added during PCR (72°C 3 min, 98°C 30 sec, 13 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina 50 bp paired-end sequencing on a Novaseq6000 aiming at an average sequencing depth of 0.5 mio reads per cell.

value: rtTA/rtTA

value: induced


title: RS3

description: non-heparanized blood

value: Ct-positive spontaneous abortion

tag: tissue


title: M3 HLF, TGF-β1, Total RNA

description: Total RNA_Control_TGF-beta1.xlsx


title: RS2

description: non-heparanized blood


title: M2 HLF, TGF-β1, Total RNA

description: Total RNA_Control_TGF-beta1.xlsx


title: spt650-1-HU-input

description: his3D200 lys2-128d ura3-52 leu2D0 hENT::AUR1C GDP-TK::URA3 spt6-YW bar1D::KanMX

value: Saccharomyces cerevisiae cells with S. pombe spike-in

value: his3delta200 lys2-128delta ura3-52 leu2delta0 hENT::AUR1C GdeltaP-TK::URA3 spt6-YW bar1delta::KanMX


title: RS1

description: non-heparanized blood

value: serum


title: SCD-A022

value: whole blood


title: M3 HLF, Control, Total RNA

description: Total RNA_Control_TGF-beta1.xlsx


title: M2 HLF, Control, Monosome mRNA


title: Multipotent Progenitor (MPP) 52


title: spt6YW-2-HU-input


title: spt650-2-30-input

value: untreated, 30 min


title: F5 HLF, TGF-β1, Total RNA

description: Total RNA_Control_TGF-beta1.xlsx


title: Multipotent Progenitor (MPP) 53


title: Multipotent Progenitor (MPP) 55


title: F2 HLF, TGF-β1, Total RNA

description: Total RNA_Control_TGF-beta1.xlsx


title: Multipotent Progenitor (MPP) 50


title: Multipotent Progenitor (MPP) 51


title: SCD-A040


title: SCD-A008


title: F5 HLF, Control, Total RNA

description: Total RNA_Control_TGF-beta1.xlsx


title: SCD-A012


title: spt6YW-1-HU-input


title: M2 HLF, Control, Total RNA

description: Total RNA_Control_TGF-beta1.xlsx


title: Multipotent Progenitor (MPP) 48


title: spt6YW-2-30-input


title: Multipotent Progenitor (MPP) 47


title: spt650-1-30-input


title: SCD-A005


title: F2 HLF, Control, Total RNA

description: Total RNA_Control_TGF-beta1.xlsx


title: Multipotent Progenitor (MPP) 49


title: A673 BARD1 rep3

first: Kelly

middle: M

last: Bailey

address: Rangos Research Building 4401 Penn Ave

department: Pediatrics

data_processing:
FastQC v0.11.5 was used to perform QC of fastq files
fastp v0.20.0 was used for adapter and quality trimming,  --qualified_quality_phred 15       --length_required 20
transcript quantification was performed using salmon v0.13.1,  --validateMappings --rangeFactorizationBins 4       --gcBias --seqBias
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing counts and transcripts per million

source_name: A673 cell line

growth_protocol: cells cultured in RPMI with 10%FBS at 37C and 5% CO2

extract_protocol:
Quagen RNeasy PLUS mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 30nM BARD1siRNA SMART pool (Dharmacon) or non-targeting control siRNA (Dharmacon) was transfected into cells using Lipofectamine RNAiMAX and optiMEM media. RNA was extracted at hour 72 post-transfection.

value: BARD1 siRNA

tag: replicate


title: Multipotent Progenitor (MPP) 46


title: SCD-A029


title: VCI-A044

value: VCI


title: Multipotent Progenitor (MPP) 45


title: spt6YW-1-30-input


title: WT-2-30-input

description: his3D200 lys2-128d ura3-52 leu2D0 hENT::AUR1C GDP-TK::URA3 bar1D::KanMX

value: his3delta200 lys2-128delta ura3-52 leu2delta0 hENT::AUR1C GdeltaP-TK::URA3 bar1delta::KanMX


title: VCI-A065


title: SCD-A020


title: A673 BARD1 rep1


title: A673 BARD1 rep2


title: A673 ctrl rep3

value: ctrl


title: WT-2-HU-input


title: WT-1-HU-input


title: Multipotent Progenitor (MPP) 44


title: Multipotent Progenitor (MPP) 42


title: VCI-A041


title: Multipotent Progenitor (MPP) 43


title: VCI-A034


title: Multipotent Progenitor (MPP) 41


title: spt650-2-HU-IP

value: BD Pharmingen 555627


title: VCI-A025


title: PDO-1 late

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
Raw base call (BCL) files were demultiplexed and converted to FASTQ files, which were subsequently used to generate feature-barcode matrices using Cell Ranger RNA v3.1 (10x Genomics). cellranger-atac version 1.2.0 was used to convert Illumina bcls to FASTQ files and align samples to reference genome for snATACseq data.
Initial single-cell analysis was performed using Seurat v3.1.0. Cells containing less than 200 genes were removed, and log-normalized expression of 2,000 variable genes were used to reduce the data into two-dimensional space. For snATACseq analysis, Seurat v3.1.0 and Signac v 1.0.0 were used.
Cells from all samples were combined using merge functions. Cell identities were manually assigned using highly expressed genes. To retain the highest number of cells for subsequent analyses, no additional filters were initially applied.
Genome_build: GrCh38

source_name: Liver

growth_protocol:
Organoids were maintained in growth factor-reduced matrigel and grow in progenitor tumor organoid media (PaTOM)
Cell lines were maintained in cell line media as proscribed by the ATCC

extract_protocol: Single-cell transcriptomic amplification and library preparation were performed using 10x Genomics Single Cell 3' Reagent kits; for snATACseq, nuclei were isolated and libraries were prepared using the 10x Genomics Single Cell Atac Kit v1.

value: Patient derived organoid 1 late passage

value: Liver


title: VCI-A032


title: WT-1-30-input

value: none (input)


title: A673 ctrl rep2


title: VCI-A021


title: PDO-1 early

value: Patient derived organoid 1 early passage


title: A673 ctrl rep1


title: VCI-A023


title: Multipotent Progenitor (MPP) 40

value: rtTA/rtTA


title: Multipotent Progenitor (MPP) 39

value: induced


title: VCI-A013


title: spt650-2-30-IP

value: his3delta200 lys2-128delta ura3-52 leu2delta0 hENT::AUR1C GdeltaP-TK::URA3 spt6-50 bar1delta::KanMX


title: spt650-1-HU-IP

value: Saccharomyces cerevisiae cells with S. pombe spike-in

value: 0.2M HU, 60 min


title: spt650-1-30-IP


title: Multipotent Progenitor (MPP) 37


title: Multipotent Progenitor (MPP) 38


title: MP2B

source_name: Pancreas

value: Pancreatic cancer cell line

value: Pancreas


title: MP2C


title: spt6YW-2-HU-IP


title: spt6YW-1-HU-IP

value: his3delta200 lys2-128delta ura3-52 leu2delta0 hENT::AUR1C GdeltaP-TK::URA3 spt6-YW bar1delta::KanMX


title: Multipotent Progenitor (MPP) 36


title: VCI-A003

value: whole blood


title: spt6YW-2-30-IP

value: untreated, 30 min


title: Multipotent Progenitor (MPP) 34


title: MP2A


title: Multipotent Progenitor (MPP) 35


title: HPDE

value: Normal pancreas control cell line

value: HPDE


title: CT treated 24hr

city: Seoul

first: Hyeon-Cheol

last: Lee

address: 136, Changgyeonggung-ro,Jongro-gu

department: Research center

country: South Korea

institute: BPgene Co., Ltd.

description:
24hr-CT
data3_24hr-CT_vs_6hr-CON_fc2_&_raw.p

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling and quality check using FastQC v0.11.7
Sequenced reads were trimmed for adaptor sequence using Trimmomatic 0.38, and mapped to hg38 whole genome using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Transcript assembly and abundance estimation using StringTie v2.1.3b
Statistical significance of the differential expression data was determined using DESeq2
Gene-enrichment and functional annotation analysis and pathway analysis for significant gene list were performed based on gProfiler
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values
Supplementary files format and content: Matrix table with raw gene counts

growth_protocol: Human triple-negative breast cancer cell lines (MDA-MB-231)  were cultured in Plasmax™ cell culture medium (Xymbio) supplemented with 2.5% dialyzed FBS (Gibco) and 1X Penicillin-Streptomycin (Gibco). Cells were maintained at 37 °C under 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was isolated from cells using TRIzol solution. After RNA extraction, it was quantified at a concentration of 1 μg.
Libraries were prepared according to TruSeq Stranded mRNA Sample Preparation Guide, Part #  15031047 Rev. E accompanying the TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Cells were plated 24 h before transfection in a 6-well plate at 5x105 cells/well. Cells were transfected 1.25 µg of mRNA complexed with Lipofectamine® MessengerMAX (Invitrogen) diluted in Opti-MEM medium (Gibco) to obtain a total volume of 200 µl. The transfection mix was added to the cells and cells were incubated at 37 °C, 5% of CO2 incubator during a time period depending on the experiment.

value: MDA-MB-231 breast cancer cell

tag: time point

value: treated with CT mRNA


title: NT5M mRNA treated 24hr

description:
24hr-NT5M
data3_24hr-NT5M_vs_6hr-CON_fc2_&_raw.p

value: treated with NT5M mRNA


title: HPNE

value: HPNE


title: spt6YW-1-30-IP

value: BD Pharmingen 555627

tag: genotype


title: CT treated 12hr

description:
12hr-CT
data3_12hr-CT_vs_6hr-CON_fc2_&_raw.p


title: cdN mRNA treated 24hr

description:
24hr-cdN
data3_24hr-cdN_vs_6hr-CON_fc2_&_raw.p

value: treated with cdN mRNA


title: Multipotent Progenitor (MPP) 33

data_processing:
Alignment of the samples with GSNAP (version 2018–07-04) to the mm10 reference, and using Ensembl 87 for the support of splicesite detection
featureCounts (version1.6.2) was used to assign the reads to genes with the help of Ensembl 87 annotation
Genome_build: mm10

value: rtTA/rtTA

value: induced


title: untreated 12hr

description:
12hr-CON
data3_12hr-CON_vs_6hr-CON_fc2_&_raw.p

value: untreated


title: Restricted hematopoietic progenitor 1 (HPC-1) 29


title: PANC1_3D_snATAC

value: nuclei isolated from cultured spheroid cell line


title: WT-2-HU-IP

value: Saccharomyces cerevisiae cells with S. pombe spike-in

value: 0.2M HU, 60 min


title: untreated 24hr

description:
24hr-CON
data3_24hr-CON_vs_6hr-CON_fc2_&_raw.p


title: Multipotent Progenitor (MPP) 32


title: HEK-293T cells, HA-Dicer/Flag-Gag (isotype control)

city: Montreal

first: Anne

last: Gatignol

state: Quebec

address: Lady Davis Institute, Jewish General Hospital

department: Medicine

country: Canada

institute: McGill University

description: Small RNA

data_processing:
Reads were trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters were removed from the reads, and all reads <16 nt were filtered out. Trimming and clipping were performed using Trimmomatic (Bolger, Lohse, and Usadel 2014).
The filtered reads were aligned to Homo sapiens assembly GRCh37 using STAR (Dobin et al. 2012). Reads in the library were not size selected and several are expected to be miRNA species, multi-mapping reads were allowed in the output, with a maximum of 1000 multi-mapping sites (--outFilterMultimapNmax 1000). Then, all readset BAM files from the same conditions were merged into single global BAM files using Picard. All control samples (the three HA/Gag-Flag and the isotype antibody sample) were merged into a single file as well to use with peak-calling software.
Peaks are called using MACSv2 software (Zhang et al. 2008).
Assembly: GRCh37
Supplementary files format and content: annotated peak file, text

source_name: kidney; Embryo

extract_protocol:
HEK 293T cells were transfected with HA-Dicer/pFlag, HA-Dicer/Flag-Gag, HA/Flag-Gag (negative control). After 48 h, cells were washed once with PBS and lysed with RNA extraction buffer (150 mM NaCl, 50 mM Tris, pH 7.5, 5 mM EDTA, 0.5% Nonidet P-40, 0.5% of RNaseOUT (Invitrogen), 0.2% of Vanadyl (NEB), 100mM of DTT (Invitrogen) protease and phosphatase inhibitor cocktail (Roche)). 30 µl of agarose protein A beads (Millipore) washed with RNA extraction buffer were added to 1 mg of protein lysate for a 1.5 h incubation at 4 ℃ on a rocking platform. After centrifugation, the supernatant was incubated with 50 µl of 1% BSA blocked Pierce anti-HA magnetic beads (Thermo Fisher) or 1% BSA blocked Pierce NHS-activated magnetic beads (Thermo Fisher) conjugated with a mouse monoclonal IgG1 isotype antibody (Thermo fisher)   overnight at 4 ℃  in constant rotation. Next day, samples were magnetically separated and the flow through was discarded. The magnetic beads were washed 3 times with RNA extraction buffer and separated in two samples for protein and RNA analysis. For protein analysis, 30 µl of Laemmli sample buffer was added to the beads and incubated 5 min at 95 °C. RNA extraction was performed on the second sample of the beads after adding Trizol reagent and purified with miRNeasy mini kit (QIAGEN). An RNase-free DNase (QIAGEN) was used according to kit protocols in the miRNeasy columns to eliminate possible DNA contamination.
Libraries were synthesized from 300 ng of total RNA with the New England BioLabs NEBNext® Small RNA Library Prep Kit for Illumina®. Libraries were run in an Illumina HiSeq2500 SR50 sequencing lane at Genome Quebec, Canada.
RIP-seq-small RNAs

value: kidney

tag: encoded plasmids

value: pCMV2-HA-Dicer /pCI-Neo-Flag-Gag

tag: rip antibody

value: IgG1 isotype antibody (Invitrogen 02-6100)


title: BXPC3

value: Pancreatic cancer cell line

value: Pancreas


title: CT treated 6hr

description:
6hr-CT
data3_6hr-CT_vs_6hr-CON_fc2_&_raw.p

value: MDA-MB-231 breast cancer cell

tag: treatment


title: WT-2-30-IP

value: his3delta200 lys2-128delta ura3-52 leu2delta0 hENT::AUR1C GdeltaP-TK::URA3 bar1delta::KanMX

value: untreated, 30 min


title: NT5M mRNA treated 6hr

description:
6hr-NT5M
data3_6hr-NT5M_vs_6hr-CON_fc2_&_raw.p

value: treated with NT5M mRNA


title: NT5M mRNA treated 12hr

description:
12hr-NT5M
data3_12hr-NT5M_vs_6hr-CON_fc2_&_raw.p


title: PANC1_3D_scRNA

value: Pancreatic cancer cell line cultured in spheroid matrigel


title: Restricted hematopoietic progenitor 1 (HPC-1) 32

description:
raw_counts+metadata.csv
counts_filtered.csv
counts_filtered_normalized_log.csv
cell_metadata_filtered.csv

tag: col1a1 genotype

tag: rosa26 genotype


title: Restricted hematopoietic progenitor 1 (HPC-1) 27

tag: doxycyclin induction


title: cdN mRNA treated 12hr

description:
12hr-cdN
data3_12hr-cdN_vs_6hr-CON_fc2_&_raw.p

tag: cell line

value: treated with cdN mRNA


title: WT-1-30-IP

tag: cell type

value: BD Pharmingen 555627


title: Restricted hematopoietic progenitor 1 (HPC-1) 30

value: rtTA/rtTA

value: induced


title: Restricted hematopoietic progenitor 1 (HPC-1) 26


title: Restricted hematopoietic progenitor 1 (HPC-1) 28


title: PANC1_2D_scRNA

value: Pancreatic cancer cell line cultured in monolayer


title: PANC1_2D_snATAC

value: nuclei isolated from cultured monolayer cell line


title: Restricted hematopoietic progenitor 1 (HPC-1) 31


title: HEK-293T cells, HA-Dicer/Flag-Gag 2

description:
Small RNA
Pooled_Dicer-FlagGag_peaks.narrowPeak.annot.txt

value: anti-HA (Sigma H6908)


title: HEK-293T cells, HA/Flag-Gag 2 (control)

description: Small RNA

value: kidney

value: pCMV2-HA /pCI-Neo-Flag-Gag


title: Restricted hematopoietic progenitor 1 (HPC-1) 25


title: HPAF2


title: 1h stressed plus 3h recovered

first: Wolfram

middle: Christian

last: Poller

address: One Gustave L. Levy Place

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic single cell

data_processing:
CellRanger (v4.0.0) was used for sequences alignment and generate read counts per gene in each cell.
Downstream analysis was performed using the Seurat 3.2.3 package (Butler et al, 2018)
Exclude cells with <200 expressed genes, genes expressed in <3 cells and cells with mitochondrial transcripts > 10%
Assembly: mm10
Supplementary files format and content: count text files

source_name: Blood neutrophils

extract_protocol: Blood was collected and RBC lysis buffer (Biolegend) was used twice to lyse the red blood cells. Staining of single-cell suspensions was performed in FACS buffer (0.5% BSA and 2mM EDTA in PBS) containing the fluorophore-coupled antibodies at a concentration of 1:700 at 4 °C for 15 min. To differentiate between live and dead cells, the cell-suspensions were stained with Zombie Aqua (BioLegend) at a concentration of 1:1,000 in PBS at 4 °C for 15 min. After cell surface marker staining, neutrophils were sorted on a FACS Aria II sorter (BD Biosciences). Neutrophils were identified as CD45+;LIN-;CD11b+;Ly-6G+

tag: strain

value: restraint stressed for 1 hour followed by recovery for 3 hours


title: 1h stressed plus 3h recovered replicate 3

data_processing:
Sequencing was performed on Illumina HiSeq 2500 instrument
Sequencing reads were mapped in a splice-aware fashion to the Ensembl annotation of the mouse GRCm37/mm9 transcriptome using STAR (Dobin et al., 2013).
Read counts over transcripts were calculated using HTSeq (Anders et al., 2015)
Assembly: GRCm37/mm9
Supplementary files format and content: tab-delimited text file of raw gene expression values for each sample

extract_protocol: Blood was collected (pooled from 3 mice per sample) and RBC lysis buffer (Biolegend) was used twice to lyse the red blood cells. Staining of single-cell suspensions was performed in FACS buffer (0.5% BSA and 2mM EDTA in PBS) containing the fluorophore-coupled antibodies at a concentration of 1:700 at 4 °C for 15 min. To differentiate between live and dead cells, the cell-suspensions were stained with Zombie Aqua (BioLegend) at a concentration of 1:1,000 in PBS at 4 °C for 15 min. After cell surface marker staining, neutrophils were sorted on a FACS Aria II sorter (BD Biosciences). Neutrophils were identified as CD45+;LIN-;CD11b+;Ly-6G+


title: Restricted hematopoietic progenitor 1 (HPC-1) 23

first: Alexander

last: Gerbaulet

address: Fetscherstr. 74


title: WT-1-HU-IP

first: Catherine

last: Miller

address: 77 Avenue Louis Pasteur

value: Saccharomyces cerevisiae cells with S. pombe spike-in

value: 0.2M HU, 60 min


title: 1h stressed

value: restraint stressed for 1 hour


title: HEK-293T cells, HA/Flag-Gag 1 (control)

description: Small RNA


title: HEK-293T cells, HA-Dicer/Flag-Gag 3

value: pCMV2-HA-Dicer /pCI-Neo-Flag-Gag


title: B004-A-008, snRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, alignment, and gene counting were done using Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The expression matricies produced from Cell Ranger are included as processed data.
Assembly: hg38
Supplementary files format and content: Expression matricies divided into matrix, barcode, and feature files.

extract_protocol:
The isolation of nuclei was accomplished using the OmniATAC protocol (Corces*, Granja* et al. Science 362, 2018). Dissociation of nuclei was carried out entirely on wet ice. 40-60mg of flash-frozen tissue was placed into 2ml dounce tissue grinders containing 1ml HB (Lysis) Buffer (1.0341x HB Stable solution, 1M DTT, 500 mM Spermidine, 150mM Spermine, 10% NP40, cOmplete Protease Inhibitor, Ribolock), gently triturated, then allowed to thaw for 5 minutes in the solution. After 5 minutes, tissue was dounced 10 times with pestle A and 20 times with pestle B, or until there was no resistance from either pestle. Sample was filtered through a 40um cell strainer (Falcon; 352340) and resulting homogenate transferred to a pre-chilled 2ml LoBind tube. Samples were spun in a 4°C fixed angle centrifuge for 5 minutes at 350 RCF to pellet nuclei. After spinning, all but 50ul of supernatant was removed. 350ul HB was added to the nuclei pellet for a total volume of 400ul. Nuclei were gently resuspended with a wide bore pipet. One volume of 50% Iodixanol (60% OptiPrep [Sigma Aldrich; D1556], Diluent Buffer [2M KCl, 1M MgCl2, 0.75M Tricine-KOH pH 7.8], Water) was added and gently triturated. Next, 600ul of 30% Iodixanol was carefully layered under the 25% mixture. Finally, 600ul of 40% Iodixanol was layered under the 30% mixture. Sample was then spun in a 4°C swinging bucket centrifuge for 20 min at 3,000 RCF. Upon completion of the spin, a band of nuclei was visible. Supernatant was aspirated down to within 200-300ul of the nuclei band. The nuclei band was then collected at 200ul and transferred to a fresh 1.5ml tube. Sample was diluted with one volume (200ul) Resuspension Buffer (1x PBS, 1% BSA, 0.2u/uL Ribolock). Nuclei concentration was determined using the Countess II FL Automated Cell Counter (ThermoFisher; AMQAF1000). In addition to isolating nuclei with the omni-ATAC dounce method, we used the Singulator from S2 Genomics to isolate nuclei for 4 samples (2 normal and 2 polyp) from patient A002. The same buffers (lysis, wash, resuspension) were used for both the manual omni-ATAC dounce and S2 Singulator methods. HB buffer was prepared following the OmniATAC protocol, with the addition of 15ul Ribolock per 1mL HB buffer to help maintain RNA integrity. Approximately 50-70mg tissue in small chunks were placed into the Nuclei Isolation Cartridge. We ran the Extended Nuclei Isolation Singulator program which includes disruption, 5 minute incubation, disruption, filtration (150um and 40um filters) and buffer rinse of the cartridge. Following dissociation, nuclei were spun at 300g for 5 minutes. Supernatant was removed and nuclei were resuspended in Resuspension Buffer (noted above). Nuclei were counted using the Countess Automated Cell Counter (ThermoFisher). The total dissociation time for 4 samples was approximately 1 hour, as one sample can be run at a time on the S2 Singulator.
snRNA-seq targeting 9,000 cells per sample was performed using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, 1000121) and Chromium Next GEM Chip G Single Cell Kit (10x Genomics, 1000120).

value: Colon

tag: disease stage

value: Normal

tag: familial adenomatous_polyposis

value: N

tag: Sex

value: M


title: 1h stressed plus 3h recovered replicate 2


title: Relaxed

value: relaxed


title: untreated 6hr

value: MDA-MB-231 breast cancer cell

value: untreated


title: 1h stressed plus 3h recovered replicate 4


title: B004-A-204, snRNAseq

description: 10x Genomics


title: HEK-293T cells, HA/Flag-Gag 3 (control)

description: Small RNA


title: HEK-293T cells, HA-Dicer/pFlag 2

description:
Small RNA
Pooled_Dicer-Flag_peaks.narrowPeak.annot.txt

value: pCMV2-HA-Dicer /pCI-Neo-Flag


title: 1h stressed plus 3h recovered replicate 1


title: Restricted hematopoietic progenitor 1 (HPC-1) 21

value: rtTA/rtTA

value: induced


title: cdN mRNA treated 6hr

description:
6hr-cdN
data3_6hr-cdN_vs_6hr-CON_fc2_&_raw.p

value: treated with cdN mRNA


title: B001-A-501, snRNAseq

description: 10x Genomics

value: F


title: Restricted hematopoietic progenitor 1 (HPC-1) 20


title: Restricted hematopoietic progenitor 1 (HPC-1) 24


title: HEK-293T cells, HA-Dicer/Flag-Gag 1

value: kidney

value: anti-HA (Sigma H6908)


title: B004-A-104, snRNAseq

description: 10x Genomics


title: Restricted hematopoietic progenitor 1 (HPC-1) 22


title: HEK-293T cells, HA-Dicer/pFlag 3


title: B001-A-406, snRNAseq

description: 10x Genomics


title: HEK-293T cells, HA-Dicer/pFlag 1


title: Restricted hematopoietic progenitor 1 (HPC-1) 19


title: 1h stressed replicate 3


title: LCRP, 3

city: New Haven

first: Stuart

middle: G

last: Campbell

state: CT

address: 55 Prospect Street, Malone 301

department: Biomedical Engineering

institute: Yale University

data_processing:
Data processed in Partek flow software. Prior to processing, pre-alignment QA/QC was performed using Partek Flow's algorithm.
Alignment performed using STAR 2.7.8a using default parameters in Partek Flow
Post alignment QA/QC was performed in Partek Flow
Quantified to annotation model using default parameters: hg38_ensembl_release104_v2 in Partek Flow
Filter: Exclude features where maximum <= 90.0 in Partek Flow
Assembly: hg38
Supplementary files format and content: CSV file containing Features (genes) on rows. The corresponding annotations (chromosomes, start, stop,gene, strand, gene symbol, gene biotype, gene name, gene version) and sample names are on columns. The values show raw gene counts in each sample for each gene.

source_name: Engineered Heart Tissue (EHT)

growth_protocol: hiPSC-CMs differentiation followed commonly used protocol (Lian et al., 2013). Healthy control  hiPSC line PGP1 (GM23338, Coriell Institute) was differentiated with 15 μM CHIR99021 on day 0 for  24 h and 5 μM IWP4 on day 3 for 48 h. On day 12, 4-day treatment with 4 mM lactate was used to purify hiPSC-CMs before cells were seeded on day 18. A second healthy control line was generated from monocytes in a peripheral blood sample of a healthy adult male and differentiated with 17.5 μM CHIR99021 on day 0. The same differentiation protocol was followed after day 0 to day 14, after which   the cells were expanded (Maas et al., 2021) with 2.4 μM CHIR99021 on day 1, 3, and 5 post-expansion. Media was switched back to RPMI + B27 Plus on day 6 with media change every other day until seeding on day 10.    Cells were seeded onto decellularized poricne scaffold. For seeding, one million cells of 90% hiPSC-CMs and 10% adult human cardiac fibroblasts (PromoCell 306-05A) were used per tissue in the seeding media (10% FBS, 1% P/S, 1% NEAA, 1% L-glutamine, and 1% sodium pyruvate in DMEM).

extract_protocol:
Tissues were flash frozen on dry ice and stored in -80C. Aqueous phase   was collected after TRIzol (Ambion) phase separation, and the RNA pellets were precipitated for total RNA extraction. Samples were treated with DNAse and cleaned with Qiagen RNeasy columns.
mRNA was purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352). Following first-strand synthesis with random primers, second strand  synthesis and A-tailing were performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs were ligated to library insert fragments. Library amplification amplified fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP were not amplified. Indexed libraries were quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp were used for sequencing.

treatment_protocol: The tissues were maintained in low calcium groups (LCRP and LCNP) with RPMI and in high calcium groups (HCRP and HCNP) with DMEM. A custom bioreactor was used to electrically stimulate tissues in Ramp Paced groups (HCRP and LCRP) while the No Pacing groups (HCNP and LCNP) received no electrical stimulation. These treatments were continued for 14 days prior to extraction.

value: Engineered Heart Tissue (EHT)

value: GM23338, Coriell Institute

value: iPSC derived cardiomyocyte

value: WT

value: Low Calcium, Ramp Pacing

tag: biomaterial provider


title: LCRP, 2

tag: tissue


title: 1h stressed replicate 4

value: restraint stressed for 1 hour


title: 1h stressed replicate 2


title: B004-A-004, snRNAseq

description: 10x Genomics

value: Colon

value: Normal

value: N

value: M


title: B001-A-301, snRNAseq

description: 10x Genomics


title: B001-A-401, snRNAseq

description: 10x Genomics


title: Restricted hematopoietic progenitor 1 (HPC-1) 18

institute: Medical Faculty TU Dresden

source_name: bone marrow


title: Restricted hematopoietic progenitor 1 (HPC-1) 17


title: 1h stressed replicate 1


title: LCRP, 1


title: LCNP, 5

value: Low Calcium, No Pacing


title: Relaxed replicate 4

value: relaxed


title: F091, snRNAseq

description: 10x Genomics

value: Polyp

value: Y


title: Hematopoietic stem cell (HSC) 48

value: rtTA/rtTA

value: induced


title: Hematopoietic stem cell (HSC) 47


title: F072B, snRNAseq

description: 10x Genomics


title: LCNP, 2


title: LCNP, 4


title: Relaxed replicate 3


title: F034, snRNAseq

description: 10x Genomics


title: Relaxed replicate 2


title: Hematopoietic stem cell (HSC) 46


title: LCNP, 1


title: F007, snRNAseq

description: 10x Genomics


title: HCRP, 5

value: High Calcium, Ramp Pacing


title: Relaxed replicate 1


title: Hematopoietic stem cell (HSC) 45


title: CRC3_11773, snRNAseq

description: 10x Genomics

value: CRC

value: F


title: Hematopoietic stem cell (HSC) 44


title: CRC2_15564, snRNAseq

description: 10x Genomics


title: Hematopoietic stem cell (HSC) 43


title: CRC1_8810, snRNAseq

description: 10x Genomics


title: Hematopoietic stem cell (HSC) 42


title: A022-E-002, snRNAseq

description: 10x Genomics


title: HCRP, 1

value: Engineered Heart Tissue (EHT)

value: GM23338, Coriell Institute

value: iPSC derived cardiomyocyte


title: HCRP, 2

value: WT


title: Hematopoietic stem cell (HSC) 41


title: HCNP, 3

value: High Calcium, No Pacing


title: Hematopoietic stem cell (HSC) 40


title: A018-E-020, snRNAseq

description: 10x Genomics

value: Colon


title: A018-E-013, snRNAseq

description: 10x Genomics


title: HCNP, 2


title: mESCs, mch, input

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

institute: HHMI Janelia

data_processing:
RNA-seq: RNA-seq raw reads were quality trimmed using Cutadapt (v3.4) with “-m 10 -j 8 -q 20,20 parameters” (Martin, 2011). Reads were mapped to GRCm38 using STAR (v2.7.8a) with default parameters to generate sorted BAM files (Dobin et al., 2013). BAM files were counted by HTSeq (v0.11.4) with “-m intersection-strict -f bam -s no” parameters (Anders et al., 2015). Count files were used for differential analysis with DESeq2 to obtain differentially expressed genes (Love et al., 2014).
ChIP-seq: Original ChIP-seq fastq files were aligned to GRCm38 using Bowtie2 (v2.4.4) (Langmead and Salzberg, 2012). Generated SAM files were converted to BAM files, sorted, and filtered for uniquely mapping reads using Sambamba (v0.8.1)(Tarasov et al., 2015). Peaks were called using MACS2 (v2.2.7.1) (Zhang et al., 2008), and the anti-IgG sample and anti-mCherry of mCherry transfected samples used as controls, respectively. Each biological replicate was processed individually to obtain peaks. Consensus peaks were generated using BEDtools (v2.30.0) (Quinlan and Hall, 2010).
Assembly: mm10
Supplementary files format and content: RNA-seq: count files
Supplementary files format and content: ChIP-seq: peak files

source_name: derived mESCs

growth_protocol: Mouse pre-implantation embryos were cultured in KSOM at 37 ºC with 5% CO2. Derived mESCs were cultured in SF001 (Sigma) medium.

extract_protocol:
RNA-seq: single embryo RNA-seq was performed using GT-seq as described previously (Macaulay et al., 2016). Briefly, embryos were collected individually into RLT buffer at E2.5 and E2.75. ERCC spike-in (1:100,000) was added to each sample. RNA was separated by oligo-dT conjugated beads, and the remaining genomic DNA was used for genotyping of each embryo. || ChIP-seq: Cells were dissociated by Accutase and collected into lobind tubes 48 hr after transfection. ChIP-seq libraries were prepared using True MicroChIP & MicroPlex Library Preparation™ Package (C01010131) according to the manufacturer’s instructions. Briefly, cells were washed with PBS and fixed by 1% formaldehyde (15 min, room temperature). Crosslink was stopped by adding glycine (115 ul per 1 ml reaction) and incubated for 5 min at room temperature. Cells were washed twice with HBSS, collected, and for frozen overnight at -80 ºC. On the second day, cells were lysed and sonicated using the Bioruptor for 10 cycles. Sheared DNA was purified using phenol/chloroform/isoamyl alcohol (25:24:1) (Sigma-Aldrich P2069). 20 ul from each sample was removed as the input sample and held at -80 ºC. 1 ug of the anti-mCherry antibody or rabbit IgG was added into each sample. Samples were incubated overnight at 4 ºC. On the next day, magnetic beads were pre-treated and added into each sample and incubated for 2 hr at 4 ºC. Samples were washed, de-crosslinked and purified using phenol/chloroform/isoamyl alcohol (25:24:1).
RNA-seq: RNA was reverse transcribed through template switch and Superscript II reverse transcriptase. cDNA was amplified for 18 cycles and purified with Agencourt AMPure beads (A63881). Purified cDNA was evaluated with Agilent Bioanalyzer and constructed into sequencing libraries using the Nextera XT Sample Preparation Kit. || ChIP-seq: ChIP-seq libraries were prepared using True MicroChIP & MicroPlex Library Preparation™ Package (C01010131) according to the manufacturer’s instructions. Quality of the samples was evaluated by Bioanalyzer 2100. Samples were used for library preparation following the MicroPlex Library Preparation manual, purified with Agencourt AMPure XP beads and pooled for sequencing.

treatment_protocol: Dis3 null allele was constructed using Crispr/Cas9 method. Embryos were collected from Dis3 heterozygous matings. mESCs were transfected with mcherry or Pou6f1-mcherry.

value: derived mESCs

value: mch

tag: chip antibody

value: input


title: mESCs, mch, anti-mCh

value: anti-mCh


title: mESCs, pou6f1mch, input, rep1


title: Hematopoietic stem cell (HSC) 39

city: Dresden


title: mESCs, pou6f1mch, input, rep2


title: mESCs, pou6f1mch, anti-mCh, rep2


title: mESCs, pou6f1mch, anti-mCh, rep1


title: HCNP, 1


title: A015-C-208, snRNAseq

first: Winston

last: Becker

address: 1291 Welch Road, B259 Beckman Center

description: 10x Genomics

value: Unaffected


title: mESCs, pou6f1mch, anti-IGG

value: anti-IGG


title: Hematopoietic stem cell (HSC) 38

value: rtTA/rtTA


title: A015-C-204, snRNAseq

description: 10x Genomics

value: Polyp

value: Y


title: Hematopoietic stem cell (HSC) 37

value: induced


title: E2.75 mouse embryos, Null, rep3

description: with ERCC spike in

source_name: single pre-implantation embryo

value: single pre-implantation embryo

tag: developmental stage


title: HCRP, 4

value: Engineered Heart Tissue (EHT)

tag: genotype

value: High Calcium, Ramp Pacing


title: A015-C-203, snRNAseq

description: 10x Genomics

value: F


title: E2.75 mouse embryos, Null, rep2

description: with ERCC spike in


title: 635

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to Ensembl transcriptome of GRCm38
DESeq2 for differential gene expression
Assembly: GRCm38
Supplementary files format and content: A .csv file including TPM of each gene for all 12 samples

source_name: skeletal muscle from NIA aging colony

growth_protocol: Mice were individually housed and fed ad libitum.

extract_protocol:
Skeletal muscle was homogenized with QIAzol using MP Bio FastPrep-24 (5G) disruptor. Qiagen RNeasy Mini kit was used for the following RNA extraction
Illumina TruSeq Stranded Total RNA Library Prep Kit was used with polyA pull-down strategy

treatment_protocol: Mice had 8 weeks of volitional running wheel exercise in their home cages. Laparotomy was conducted in experimental mice.

value: laparotomy

tag: condition

value: high functioning


title: 622


title: Hematopoietic stem cell (HSC) 36


title: Hematopoietic stem cell (HSC) 35


title: E2.75 mouse embryos, Null, rep1

description: with ERCC spike in


title: 644

value: control


title: E2.75 mouse embryos, Het, rep5

description: with ERCC spike in

value: Het


title: A015-C-109, snRNAseq

description: 10x Genomics

source_name: Colon

value: Colon


title: 613


title: Hematopoietic stem cell (HSC) 34


title: A015-C-202, snRNAseq

description: 10x Genomics


title: 634


title: Hematopoietic stem cell (HSC) 33


title: E2.75 mouse embryos, Het, rep3

description: with ERCC spike in


title: A015-C-106, snRNAseq

description: 10x Genomics


title: Multipotent Progenitor (MPP) 31


title: 615


title: E2.75 mouse embryos, Het, rep4

description: with ERCC spike in


title: A015-C-104, snRNAseq

description: 10x Genomics


title: A015-C-010, snRNAseq

description: 10x Genomics


title: A015-C-008, snRNAseq

description: 10x Genomics


title: Multipotent Progenitor (MPP) 30


title: E2.75 mouse embryos, Het, rep2

description: with ERCC spike in


title: Multipotent Progenitor (MPP) 29


title: 623

value: low functioning


title: A015-C-006, snRNAseq

description: 10x Genomics


title: Multipotent Progenitor (MPP) 28


title: 633


title: E2.75 mouse embryos, Het, rep1

description: with ERCC spike in


title: Multipotent Progenitor (MPP) 27


title: A015-C-005, snRNAseq

description: 10x Genomics


title: 624


title: A015-C-002, snRNAseq

description: 10x Genomics


title: 631


title: Multipotent Progenitor (MPP) 26


title: A015-C-001, snRNAseq

description: 10x Genomics

value: CRC


title: 614


title: Multipotent Progenitor (MPP) 25


title: E2.75 mouse embryos, WT, rep3

description: with ERCC spike in

value: WT


title: A014-C-201, snRNAseq

description: 10x Genomics

value: Unaffected


title: E2.75 mouse embryos, WT, rep1

description: with ERCC spike in


title: E2.75 mouse embryos, WT, rep2

description: with ERCC spike in


title: Multipotent Progenitor (MPP) 24

value: rtTA/rtTA


title: E2.5 mouse embryos, Null, rep3

description: with ERCC spike in


title: E2.5 mouse embryos, Null, rep4

description: with ERCC spike in


title: 625


title: A014-C-114, snRNAseq

description: 10x Genomics


title: E2.5 mouse embryos, WT, rep6

description: with ERCC spike in


title: mouse-90-PBS-TH

city: Winnipeg

first: Jessy

middle: Andrew

last: Slota

state: Manitoba

address: 1015 Arlington St.

department: One Health Division

institute: National Microbiology Laboratory; Public Health Agency of Canada

data_processing:
raw sequecing reads were trimmed using trimmomatic (sliding window trimming quality > 20, drop reads average quality < 25 and drop reads length < 20)
rRNA reads were removed using Bowtie2 by writing unaligned reads to fastq files
reads were mapped to the mm10 reference genome with HISAT2 with default parameters
raw read counts were counted for each transcript using FeatureCounts with default parameters
Assembly: mm10
Supplementary files format and content: Raw read counts are provided in CSV format for each sample

source_name: thalamus

extract_protocol:
Total RNA was isolated from microdissected CA1 or thalamus tissues using the RNAqueous–Micro Kit (Life Technologies Inc.)
Sequencing libraries were prepared from total RNA using the Smart-Seq v4 Ultra Low Input RNA Kit (TakaraBio)

treatment_protocol: Mice were intraperitoneally inoculated with either 2% RML scrapie brain homogenate (RML) or non-infectious brain homogenate (Mock)

value: thalamus

value: Mock

tag: days post_infection


title: mouse-90-PBS-CA1

tag: treatment


title: mouse-88-PBS-TH


title: Multipotent Progenitor (MPP) 22

tag: col1a1 genotype

value: induced


title: E2.5 mouse embryos, WT, rep5

description: with ERCC spike in

value: single pre-implantation embryo


title: mouse-88-PBS-CA1


title: A014-C-108, snRNAseq

institute: Stanford University

description: 10x Genomics

value: Polyp

value: Y


title: Multipotent Progenitor (MPP) 21

tag: rosa26 genotype


title: mouse-87-PBS-TH


title: mouse-87-PBS-CA1


title: mouse-72-PBS-TH


title: A014-C-101, snRNAseq

description: 10x Genomics

value: F


title: E2.5 mouse embryos, Null, rep2

description: with ERCC spike in


title: Multipotent Progenitor (MPP) 19

tag: doxycyclin induction


title: E2.5 mouse embryos, WT, rep4

description: with ERCC spike in


title: E2.5 mouse embryos, Het, rep2

description: with ERCC spike in


title: Multipotent Progenitor (MPP) 23


title: A014-C-052, snRNAseq

description: 10x Genomics


title: A014-C-054, snRNAseq

description: 10x Genomics


title: mouse-71-PBS-TH


title: A014-C-043, snRNAseq

description: 10x Genomics


title: Multipotent Progenitor (MPP) 17


title: A014-C-111, snRNAseq

description: 10x Genomics


title: mouse-71-PBS-CA1


title: Multipotent Progenitor (MPP) 16


title: A014-C-008, snRNAseq

description: 10x Genomics


title: E2.5 mouse embryos, WT, rep2

description: with ERCC spike in


title: E2.5 mouse embryos, WT, rep3

description: with ERCC spike in


title: A014-C-040, snRNAseq

description: 10x Genomics


title: mouse-69-PBS-TH


title: Restricted hematopoietic progenitor 1 (HPC-1) 15


title: E2.5 mouse embryos, Null, rep1

description: with ERCC spike in


title: E2.5 mouse embryos, WT, rep1

description: with ERCC spike in


title: A014-C-001, snRNAseq

description: 10x Genomics


title: Multipotent Progenitor (MPP) 20


title: Restricted hematopoietic progenitor 1 (HPC-1) 16


title: mouse-72-PBS-CA1


title: Multipotent Progenitor (MPP) 18


title: Restricted hematopoietic progenitor 1 (HPC-1) 14


title: mouse-69-PBS-CA1


title: A010-E-023, snRNAseq

description: 10x Genomics

value: M


title: mouse-41-PBS-TH


title: E2.5 mouse embryos, Het, rep1

description: with ERCC spike in


title: A010-E-018, snRNAseq

description: 10x Genomics


title: HUVEC cells, P3, siRELA 10hr TNF, Biol Rep 3

first: Joseph Wayne

middle: Montano

last: Fowler

address: 10 Amistad St.

department: Pharmacology

data_processing:
Reads aligned to hg19 build of human genome with STAR
Quantified to hr19 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 includes cpm values for each Sample

source_name: HUVEC

growth_protocol: HUVECs were obtained from the Yale School of Medicine, Vascular Biology and Therapeutics Core facility. Cells were cultured in EGM-2 media (Lonza) with 10% 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: HUVEC were treated with 20nM of indicated siRNA for 10 hours and refed with fresh media. 48hrs later, HUVEC were treated with 10ng/mL TNF for indicated time.

tag: cell line

value: HUVEC

value: Primary Endothlelial Cell

value: RELA Knockdown

value: 10ng/mL TNF, 10hr


title: mouse-41-PBS-CA1


title: HUVEC cells, P3, siRELA 10hr TNF, Biol Rep 1

tag: cell type


title: Restricted hematopoietic progenitor 1 (HPC-1) 13


title: Restricted hematopoietic progenitor 1 (HPC-1) 12


title: A008-E-008, snRNAseq

description: 10x Genomics

value: Colon


title: mouse-38-PBS-TH


title: A002-C-212, snRNAseq

description: 10x Genomics


title: HUVEC cells, P3, siRELA 4hr TNF, Biol Rep 3

value: 10ng/mL TNF, 4hr


title: HUVEC cells, P3, siRELA 4hr TNF, Biol Rep 2


title: HUVEC cells, P3, siRELA 4hr TNF, Biol Rep 1


title: A002-C-204, snRNAseq

description: 10x Genomics


title: mouse-37-PBS-CA1


title: HUVEC cells, P3, siRELA 0hr TNF, Biol Rep 3

value: Vehicle


title: HUVEC cells, P3, siRELA 10hr TNF, Biol Rep 2


title: A002-C-201, snRNAseq

description: 10x Genomics