title: T_d_15

city: Helsinki

first: Jouni

last: Kvist

address: Haartmaninkatu 8

institute: University of Helsinki

data_processing:
Sample de-multiplexing, alignment, filtering, and UMI counting was performed with 10x Genomics Cell Ranger (v3.1) pipeline.
The raw data were mapped to the same customized human reference genome (GRCh38.99 + pCXLE-gw) using Cell Ranger (10x Genomics, v.3.1.0).
Empty droplets were removed with DropletUtils (Lun et al., 2019). The remaining droplets were filtered to exclude cells with less than 2000 detected genes, and cells with high mitochondrial fraction (>50 %). Transcripts that were detected in less than 10 cells were also excluded. The UMI counts were analyzed with R (R Core Team, 2019) using Seurat (version 3.1.4) (Stuart et al., 2018).
The data were normalized and the 1000 most variable features were identified per sample (using FindVariableFeatures). The data were scaled (using ScaleData), and the top 50 principal components were extracted. The PCA matrix was "harmonized" using Harmony (Korsunsky et al., 2018) to reduce sample specific biases, with sample id as the main variable, theta-value set to 2, using 50 clusters and maximum iterations for clusters set to 40 and 15 for the entire harmony series. The harmonized PCA values were then used as input for a 2D and 3D UMAP.
Cell clusters were identified with Seurat functions (FindNeighbors, FindClusters and BuildClusterTree) with resolution set to 0.04 and the rest of the settings set to default.
For pseudotime analysis we used monocle 3 (v0.2.2) (Trapnell et al., 2014) in combination with tradeSeq (Van den Berge et al., 2020), as well as diffusion maps using destiny (v3.0.1) (Angerer et al., 2016). Diffusion pseudotime of all the 32,758 analyzed cells was calculated with the DPT function.
Expression scores of pluripotency genes were calculated using the AddModuleScore function of Seurat.
Differential gene expression analysis between different conditions was performed with the FindMarkers function of Seurat with default settings, and genes with Bonferroni adjusted p-value < 0.01 (Wilcoxon rank-sum test) were considered as differentially expressed.
Pearson correlation coefficients between cells were calculated using the normalized expression values of 2,000 most variable genes among the mid-reprogramming samples.
Annotation of cell identity for the mid-reprogramming samples was performed using SingleR (v1.0.6) (Aran et al., 2019) with Human Primary Cell Atlas (Mabbot et al. 2013) as the reference.
Genome_build: GRCh38.99 + pCXLE-gw
Supplementary_files_format_and_content: single cell read count matrix (mtx), cell barcode (tsv), gene names (tsv)

source_name: IPSC, mid-reprogramming

growth_protocol: LCL cells were cultured in LCL medium (RPMI 1640 with GlutaMAX (Thermo Fisher Scientific) supplemented with 15% fetal bovine serum (FBS) (Life Technologies) and 1 µM sodium pyruvate). Human induced pluripotent stem cells (iPSC) were cultured in plates coated with Matrigel (Corning) in E8 (Gibco) or E8 Flex (Gibco) medium. The medium was changed every other day. All cells were kept in an incubator at 37 °C and 5% CO2 and were routinely tested for mycoplasma contamination.

extract_protocol:
Cells were dissociated with Accutase at 37 °C for 5 min, resuspended in PBS + 0.04% BSA on ice and passed through a Flowmi tip strainer (Fisher Scientific) to yield a single-cell suspension. The quality of the samples was assessed using a Luna cell counter (Logos Biosystems). Single cell RNA sequencing (scRNA-seq) was performed using the 10x Genomics Chromium Single Cell 3’RNA-seq platform at Institute of Molecular Medicine Finland (FIMM).
10x Genomics Chromium Single Cell 3’RNAseq platform using the Chromium Next GEM Single Cell 3' Gene Expression (version 3.1 chemistry)

treatment_protocol: LCL were passaged the day before reprogramming. On the day of reprogramming (day 0), LCL were dissociated into single cells by trituration and washed in PBS (Thermo Fisher Scientific). Cells were electroporated with the Neon transfection system (Invitrogen) using R buffer. A total of 106 cells and 6 µg of plasmid mixture, containing 1.5 µg of dCas9-activator plasmid (Addgene #69535) and 4.5 µg of guide plasmids, were electroporated in a 100 µl tip using 1300 V, 10 ms and 3x pulses conditions. For conventional reprogramming, plasmid mixture containing 2 µg of each ectopic expression plasmids (Addgene #27077, #27078, #27080) (Okita et al. 2011) was transfected with the same electroporation conditions as CRISPRa. Electroporated LCL were then plated onto cell culture dishes in LCL growth medium supplemented with 0.25 mM sodium butyrate (NaB). The GFP expression from the episomal dCas9 activator-plasmid was visualized on the next day to verify a successful electroporation. After 3 days, the cells were passaged onto Matrigel coated plates. On day 4 after the transfections, the medium was changed to hES medium (DMEM/F12 with GlutaMAX (Life Technologies) supplemented with 20% KnockOut Serum Replacement (Life technologies), 0.0915 mM 2-mercaptoethanol (Life Technologies), 1x Non-Essential Amino Acids (Life Technologies) and 6 ng/mL bFGF (Sigma or Life Technologies)) supplemented with 0.25 mM NaB. The cell growth medium was changed to E8 medium at day 10 of reprogramming, and the unattached LCL were removed at this point. The cells were cultured until day 21, when the colonies were large enough so that they could be picked manually and plated on Matrigel coated wells in E8 medium. Media was changed every other day.

tag: reprogramming method

value: Transgene

tag: reprogramming stage

tag: label

value: TG d15

tag: sequencing batch


title: RNA_12h_rep2

status: Public on Dec 23 2021

type: SRA

city: Wuhan

first: Baibai

last: Gao

address: 1 Shizishan Street, Hongshan District

country: China

institute: National Key Laboratory of Crop Genetic Improvement

library_source: transcriptomic

data_processing:
Trimmomatic fitered the raw reads.
The cleaned reads were mapped to the MH63 reference genome using TopHat.
gene expression was quantified using Cufflinks v2.2.5
Genome_build: MH63
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

molecule: total RNA

organism: Oryza sativa

source_name: MH63 mature leaf

growth_protocol: Rice [Oryza sativa L. ssp. indica cv. Minghui 63 (MH63)] seeds were sown on May 19, 2017 in a paddy field. At 20 days after germination, the seedlings were transplanted into a paddy field of Huazhong Agricultural University at Wuhan, China, and grown under normal agricultural conditions. In the paddy field, the plants were transplanted at a density of one plant per 15 × 30 cm area.

extract_protocol:
Total RNA was isolated from mature leaves at 12:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.

treatment_protocol: Samples for RNA isolation were immediately frozen in liquid nitrogen and stored at -80°C until use.

tag: tissue

value: mature leaf

tag: age

value: mature leaves were flag leaf at floral induction phase

tag: cultivar

value: Minghui 63

tag: time point


title: RNAPII_ChIP_4h_rep2

library_source: genomic

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the duplication reads
peaks were called using MACS.2.2.1 with narrow parameters
Genome_build: MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 20 min and quenched with 0.2 M glycine at room temperature.

tag: development stage

value: mature leaves harvested at 4:00 at floral induction stage

tag: chip antibody

value: RNAPII


title: Lens WT rep2

city: GaungZhou

first: Minglei

last: Zhao

address: 7#, Jinsui Road

institute: Sun yat sen 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 (RPKM) 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.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Lens

extract_protocol:
Lens were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lens

tag: strain

tag: genotype

value: WT


title: WT Dura CD45- RNA

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description: CD45- cells

data_processing:
Raw data bcl files were first demultiplexed using Cellranger mkfastq
Demultiplexed data was then processed using the Cellranger count pipeline
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: h5 files including raw counts (output CellRanger Count) and annotation metadata with information per cell

source_name: CD45- cells

extract_protocol: All methods listed in Scheyltjens et al. Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues. Nat. Protoc, 2022

value: dura CD45- cells

tag: platform

value: 10x Genomics


title: Lens WT rep1


title: circPOLR2A_Ana NAI rep1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: cDNA

data_processing:
Library strategy: SHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Analyses by CIRCshapemapper.
Genome_build: Target RNA sequence
Supplementary_files_format_and_content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

organism: synthetic construct

source_name: circPOLR2A_Ana NAI

extract_protocol:
For in vitro SHAPE-MaP, RNA are purified. About 50-100 μg of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for linear or circular RNAs (5S rRNA was used as a spike-in control). Mn2+ was removed using G-25 micro-spin columns (GE Healthcare) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase and nested PCR was performed to further improve DNA yield.
circSHAPE-MaP libraries were prepared from 1 ng of DNAs for circular (circSHAPE-MaP) RNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina X Ten at CAS-MPG Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For in vitro circSHAPE-MaP, circular RNAs were refolded in 3.3× folding buffer (333 mM HEPES, pH 8.0; 333 mM NaCl; 33 mM MgCl2). After refolding, RNAs were incubated with10x SHAPE Chemical in DMSO with the final concentration of NAI (EMD Millipore) at 100 mM for 10 minutes at 37°C.

tag: sample type

value: in vitro

tag: treatment

value: circPOLR2A_Ana NAI samples modified by NAI in DMSO


title: RNA_12h_rep1


title: WT Dura CD45- ADT

description: CD45- cells


title: RNA_8h_rep2

extract_protocol:
Total RNA was isolated from mature leaves at 8:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.


title: PTG WT ZT4 rep1 [#1 ctrl 10:30]

city: Copenhagen

first: Søren

last: Egstrand

address: Blegdamsvej 9

department: Depart. of Nephrology

country: Denmark

institute: Rigshospitalet

data_processing:
NovaSeq System Software generated base calls
Sequenced reads were alligned to the mm10 genome using STAR (version 2.7.8a+galaxy0)
Unambigously alligned reads were counted by featureCounts (version 2.0.1+galaxy1)
Genes with less then 10 counts in total were excluded
Counts were then normalized for sequencing depth and RNA composition using the median of ratios method employed in DESeq2 (version 1.30.1).
Counts were transformed using the rlog transformation function employed in DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Parathyroid glands

growth_protocol: Mice with parathyroid gland-specific deletion of Bmal1 (Arntl) was generated using the Cre-LoxP recombination system by crossing B6.129S4(Cg)-Arntltm1Weit/J mice in which LoxP sequences are inserted into the flanking regions of exon 8 of the Bmal1 gene (Bmal1flox/flox) with 129;FVB-Tg(PTH-cre)4167Slib/J (PTHcre). This novel genotype: PTHcre;Bmal1flox/flox is the "Knockout" which have human PTH promoter controlled Cre-recombinase activity, resulting in excision of the Bmal1 exon 8, restricted to the parathyroid glands. The Bmal1flox/flox littermates without recombinase activity constitutes the "Wildtype".

extract_protocol:
Parathyroid glands were harvested, flash frozen in liquid nitrogen and store at -80 degrees. Samples are pooled from two male mice. Total RNA was isolated using Allprep DNA/RNA minikit (Qiagen, Hilden, Germany) and purified using Qiagen RNase-Free DNase Set (Qiagen, Hilden, Germany) on a QIAcube Connect (Qiagen, Hilden, Germany). RNA quality was examined using an Agilent Technologies 2100 Bioanalyzer. Library preparation was done using a TruSeq Stranded Total RNA Gold kit with dual adaptor indexing strategy; IDT for Illumina – TruSeq RNA UD Indexes (Illumina, San Diego, USA). The library was diluted and pooled to a concentration of 2 nM according to the procedure of “Denature and Dilute Libraries Guide of Illumina Novaseq 6000” and final loading concentration was 400 pM.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples from each genotype was harvested at 4-hour interval over 24h as indicated.

value: Bma1 Wildtype

tag: zeitgebertime

tag: Sex

value: Male

value: 11 weeks

value: Parathyroid glands


title: circPOLR2A_Ana NAI rep2

description: cDNA


title: HEL_206_late

middle: Antero

state: Uusimaa

department: Research Program for Molecular Neurology

country: Finland

molecule: polyA RNA

organism: Homo sapiens

source_name: iPSC, final point

tag: reprogramming method

value: Transgene

value: late

value: TG late


title: Lens heterozygous rep3

value: Lss mutant heterozygous


title: circPOLR2A_TD DMSO

description: cDNA

source_name: circPOLR2A_TD DMSO

value: circPOLR2A_TD DMSO samples only treated with DMSO


title: RNA_8h_rep1

value: mature leaf

value: mature leaves were flag leaf at floral induction phase

value: Minghui 63


title: Lens heterozygous rep2

value: Lens


title: circPOLR2A_TD DC

description: cDNA

source_name: circPOLR2A_TD DC

value: circPOLR2A_TD DC samples denatured by formamide at 95C


title: RNA_4h_rep2

extract_protocol:
Total RNA was isolated from mature leaves at 4:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.


title: HEL_206

source_name: iPSC, early clones

tag: reprogramming stage

value: early

value: TG early


title: Lens heterozygous rep1


title: RNA_4h_rep1


title: OM_d15

value: CRISPRa+miR

tag: label

value: CRISPRa+M d15


title: RNA_0h_rep2

extract_protocol:
Total RNA was isolated from mature leaves at 0:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.


title: circPOLR2A_TD NAI rep2

description: cDNA

source_name: circPOLR2A_TD NAI

value: in vitro

value: circPOLR2A_TD NAI samples modified by NAI in DMSO


title: HEL219_early

value: CRISPRa+M early

tag: sequencing batch


title: MC3T3 Sp7Mut FLAG-IP 2

city: Bethesda

first: James

last: Iben

state: MD

address: 10 CENTER DR

department: NICHD

country: USA

institute: NIH

data_processing:
Sequenced on a NovaSeq 6000
Reads adapter and quality (Q20) trimmed by cutadapt.  Aligned by Bowtie2 to mm10 (Gencode).  Peak Calling was performed by macs2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files in BED format

growth_protocol: MC3T3 were maintained in alpha-MEM with 10% FBS and 1% P/S

extract_protocol:
Cells were lysed as previously described (PMID: 33315202) and sonicated for 16 strokes of 30s (then 60s off) using Misonix 3000 sonicator
Takara Bio DNA SMART ChIP-Seq Kit

treatment_protocol: cells were transfected with pcDNA3.1-myc-DLX5 and pcDNA3.1-FLAG-Sp7(WT) or (Mut) with lipofectamine 2000

tag: tissue

tag: antibody

value: Sigma anti-FLAG M2

value: transfected:myc-DLX5, FLAG-SP7(Mut)


title: miR302_d15

value: CRISPRa+miR+EEA

value: CRISPRa+ME d15


title: HEL215_early

value: CRISPRa+ME early


title: circPOLR2A_Lig DC

description: cDNA

source_name: circPOLR2A_Lig DC

value: circPOLR2A_Lig DC samples denatured by formamide at 95C


title: MC3T3 Sp7Mut FLAG-IP 1


title: circPOLR2A_Lig DMSO

description: cDNA

source_name: circPOLR2A_Lig DMSO

value: circPOLR2A_Lig DMSO samples only treated with DMSO


title: RNA_0h_rep1

value: mature leaf

tag: age

value: mature leaves were flag leaf at floral induction phase

tag: cultivar

value: Minghui 63


title: circPOLR2A_Lig+RIG-I NAI rep2

description: cDNA

source_name: circPOLR2A_Lig+RIG-I NAI

value: circPOLR2A_Lig interact with RIG-I samples modified by NAI in DMSO


title: MC3T3 Sp7Mut Input1


title: circPOLR2A_TD NAI rep1

description: cDNA


title: CRISPRa_d15

value: CRISPRa+EEA

value: CRISPRa+E d15


title: circPOLR2A_Lig+RIG-I NAI rep1

description: cDNA


title: HEL_207

value: early

value: CRISPRa+E early


title: MC3T3 Sp7WT FLAG-IP 1

value: transfected:myc-DLX5, FLAG-SP7(WT)


title: circPOLR2A_Lig+PKR NAI rep2

description: cDNA

source_name: circPOLR2A_Lig+PKR NAI

value: in vitro

value: circPOLR2A_Lig interact with PKR samples modified by NAI in DMSO


title: LCL

source_name: Blood cells

value: LCL


title: MC3T3 Sp7Mut Input2

value: transfected:myc-DLX5, FLAG-SP7(Mut)


title: MC3T3 Sp7WT FLAG-IP 2

value: Sigma anti-FLAG M2


title: dUTP strand-specific RNA-seq log-phase cells of Schizosaccharomyces japonicus grown in BMW

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

data_processing:
For each of the 11 Ascomycota yeast species described above, the reads were merged and assembled using Trinity (Grabherr et al., 2011) (version ‘trinityrnaseq_r2012-05-18’) and mapped onto the assemblies to the respective genomes using GMAP (Wu and Watanabe, 2005). The Jaccard coefficient was used to join adjacent assemblies given enough connecting reads (a Jaccard cutoff of 0.35, the default in Trinity was used). Finally, upon mapping all of the reads to all of the merged assemblies, the Jaccard coefficient was used to clip assemblies which did not have enough support over a certain region. For each of the species, the reads were mapped to the genome sequence (Wapinski et al., 2007) using BLAT (Kent, 2002).
The RPKM used in the analysis described below were calculated for each transcript using RSEM (Li and Dewey, 2011), and only reads mapping to the sense mRNA strand were considered. Orthology between genes in different species was used as determined previously (Wapinski et al., 2007).
Genome_build: Various (from Wapinski et al, 2007, Nature)
Supplementary_files_format_and_content: tab delimited text containing all RPKM values for genes with S. cerevisiae orthologs

organism: Schizosaccharomyces japonicus

source_name: log-phase cells

growth_protocol: We conducted RNA-seq on the following 11 Ascomycota yeast species: Candida albicans, Candida glabrata, Kluyveromyces lactis, Kluyveromyces waltii, Saccharomyces bayanus, Naumovozyma castellii, Saccharomyces cerevisiae, Schizosaccharomyces japonicus, Schizosaccharomyces octosporus, Schizosaccharomyces pombe, Yarrowia lipolytica. Each of the 11 species was grown in BMW medium, chosen to minimize cross-species growth differences, as previously described (Thompson et al., 2013). N. castellii was grown at 25℃ while the rest of the species were grown at 30℃.

extract_protocol:
RNeasy Midi or Mini Kits (Qiagen, Valencia, CA) were used to isolate total RNA from log-phase cells by mechanical lysis using the manufacturer instructions as previously described (Thompson et al., 2013).
dUTP strand-specific RNA-seq libraries were constructed as previously described (Yassour et al., 2010) with the following modifications. (1) The polyA+-selected RNA was fragmented in a 40 µl reaction containing 1x Fragmentation Buffer (Affymetrix) by heating at 80℃ for 4 minutes followed by cleanup via ethanol precipitation for all libraries (except Y. lipolytica, S. pombe, S. japonicus, and S. octosporus; for these species, the conditions described previously were used (Yassour et al., 2010)), followed by cleanup via 1.8x RNAClean XP beads (Beckman Coulter Genomics). (2) For C. glabrata, K. lactis, S. bayanus, S. pombe, S. japonicus, and S. octosporus libraries, the adapter ligation was performed overnight at 16℃. For the rest, this was done at 16 degrees for 2 hours as described previously (Yassour et al., 2010). (3) Normalization was carried out based on the cDNA input and pooling of selected Illumina barcoded-adaptor-ligated cDNA products followed by gel size selection occurred as follows: range of 275 to 575 bp for pooled C. albicans, K. polysporus, K. waltii, and N. castellii libraries, and 375 to 575 bp for C. glabrata, K. lactis, and S. bayanus libraries. For the other libraries, no pooling was performed before gel size-selection – range of 310 to 510 bp for Y. lipolytica and 350 to 550 bp for S. pombe, S. japonicus, and S. octosporus. (4) The final PCR product was purified by 1.8x AMPure XP beads (Beckman Coulter Genomics) followed by a second gel size-selection for the range of 300 to 575 bp for C. albicans, K. polysporus, K. waltii, and S. castellii libraries, but no gel size-selection was performed for the other libraries. The pooled final library was sequenced on one to four lanes of HiSeq2000 (Illumina) with 68 base (Y. lipolytica had 76 base) paired-end reads and 8 base index reads.

tag: media

value: BMW

tag: growth temperature (celcius)

tag: growth phase

value: log phase


title: circPOLR2A_Lig+PKR NAI rep1

description: cDNA


title: MC3T3 Sp7WT Input2

tag: genotype


title: dUTP strand-specific RNA-seq log-phase cells of Kluyveromyces waltii grown in BMW

organism: Lachancea waltii


title: dUTP strand-specific RNA-seq log-phase cells of Candida glabrata grown in BMW

organism: Nakaseomyces glabratus


title: circPOLR2A_Lig NAI rep1

description: cDNA

source_name: circPOLR2A_Lig NAI

value: circPOLR2A_Lig NAI samples modified by NAI in DMSO


title: Nevi_rep2

type: RNA

city: Xi'an

first: Jingjing

last: Ma

address: No. 127 Changlexi Road

institute: Fourth Military Medical University

description: lncRNA expression

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

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

data_processing:
The scanned images were extracted with Agilent Feature Extraction (v10.7) and analyzed with Agilent GeneSpring.
Normalization: Percentile 75 in GeneSpring GX software.
DEG_AM_vs_NS_lncRNA.xls: The red rows indicate the expression of lncRNAs significantly up-regulated in primary melanoma, the green rows indicate the expression of lncRNAs significantly down-regulated in primary melanoma, and the black rows indicate the expression of lncRNAs not significantly changed in primary melanoma, compared with nevus.

source_name: Nevi tissue, replicate2

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

extract_protocol: Total RNA was extracted from 3 pairs of primary melanoma and nevus tissues using Trizol reagent (Life Technologies, Carlsbad, CA) according to manufacturer’s protocol.

value: Nevi

tag: gender

value: Female


title: MC3T3 Sp7WT Input1


title: HEL_207_late

value: late

value: CRISPRa+E late


title: circPOLR2A_Lig NAI rep2

description: cDNA

tag: sample type


title: ev566L_DMSO_for_dualtherapy

status: Public on Dec 22 2021

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: Raw count data were normalized by linear normaliztion uisng R statistical language (www.r-project.org).

label: biotin

source_name: snap-frozen surgical liver tissue

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Precision-cut liver slice (PCLS, 300-micron-thick) sections were generated from fresh surgical tissue, and cultured with various candidate anti-fibrotic agents desolved in DMSO for 24h at 80% O2 and 5% CO2. PCLSs were snap-frozen in RNAlater for storage until RNA isolation.

value: liver

tag: diagnosis

value: HCV-infected, F2 fibrosis

tag: treatment group

value: Control for dual-therapy

tag: agent


title: ev566L_DMSO_for_mono_therapy

scan_protocol: Refer to the NanoString nCounter Assay System Manual

value: Control for mono-therapy


title: ev566L_EGCG_MG132

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: Dual-therapy

value: EGCG + MG132


title: Nevi_rep3

description: lncRNA expression

source_name: Nevi tissue, replicate3

value: Male


title: ev566L_EGCG_Metformin

value: EGCG + Metformin


title: Primary melanoma_rep3

description: lncRNA expression

source_name: Primary melanoma tissue, replicate3

value: Primary melanoma

tag: tumor stage

value: IIC


title: ev566L_EGCG_Bortezomib

value: EGCG + Bortezomib


title: ev566L_MG132

value: Mono-therapy


title: ev566L_EGCG

value: EGCG


title: Primary melanoma_rep1

description: lncRNA expression

source_name: Primary melanoma tissue, replicate1

value: IIB


title: ev566L_Metformin

value: Metformin


title: RT-2

city: BOTHELL

first: Hailing

last: Lu

state: WA

institute: Seattle Genetics

hyb_protocol: Labeling and hybridization was done in the Fred Hutchinson Cancer Center Genomic core following standard protocol

scan_protocol: Scanning was done in the Fred Hutchinson Cancer Center Genomic core following standard protocol on the nCounter platform

data_processing: Data processing was done in the Fred Hutchinson Cancer Center Genomic core following standard protocol on the nCounter platform. Raw values were used in the analysis.

source_name: implanted A20 tumor_RT

growth_protocol: A20 tumor cells were grown in RPMI medium with 10% FBS before the cells were harvested and injected subcutaneously to the mice for tumor implantation.

extract_protocol: RNA was extracted using the Qigen DNA/RNA Allprep kit.

treatment_protocol: Female Balb/c mice received A20 tumor cell injection.  After the tumor was established (about 3x3mm), the mice were randomized into four different treatment groups.  The mice received intratumoral injection of GLA or control PBS.  Mice in the radiation group received X-ray radiation alone or radiation plus GLA.  After the last injection of GLA, the tumors were collected for RNA extraction.  Total RNA (200ng) was used for nanostring gene expression analysis.

value: implanted A20 tumor

tag: treatment

value: RT


title: GLA+RT-3

source_name: implanted A20 tumor_GLA+RT

label_protocol: Labeling and hybridization was done in the Fred Hutchinson Cancer Center Genomic core following standard protocol

value: GLA+RT


title: RT-3


title: GLA-3

source_name: implanted A20 tumor_GLA

value: GLA


title: GLA-2


title: RT-1


title: GLA+RT-1


title: GLA-1


title: ev566L_Bortezomib

value: liver

value: HCV-infected, F2 fibrosis

value: Bortezomib


title: PBS-3

source_name: implanted A20 tumor_PBS

value: PBS


title: Primary melanoma_rep2

description: lncRNA expression

source_name: Primary melanoma tissue, replicate2

value: Female


title: VeroE6_SARS-CoV2 infected replicate 4

city: Zurich

first: Moritz

last: Schaefer

address: Otto-Stern-Weg 7

department: Biology

country: Switzerland

institute: ETH Zurich

description: replicate 4

data_processing:
Library strategy: CRISPR screen
FastQ files were obtained as provided by the sequencing facility
The MAGeCK-VISPR pipeline (v0.5.6) was employed to map R1-reads to sgRNA-library and for all downstream analyses
Genome_build: Custom-made CRISPR KO library for Chlorocebus sabaeus (provided in publication’s supplementary data)

organism: Chlorocebus sabaeus

source_name: Vero E6 cells

extract_protocol:
SARS-CoV2: Quick-DNA Midiprep Plus Kit (Zymo Research) OC43 and controls: DNA STAT-60
Genomic DNA was extracted from each sample (detailed extraction methods are described in supplemental methods). The sgRNA regions were then amplified and indexed for Illumina sequencing using a one-step PCR method and primers specific to the LentiCRISPRv2-based Vervet libraries. Primers and indices used for the generation of amplicon libraries are listed in Table S1.  Vervet DNA samples were amplified in ten 100 µl reactions using the NEBNext High-Fidelity 2X Master Mix Kit (New England Biolabs), 0.5 µM of forward and reverse primers and 10 µg of DNA template per reaction with the following program: initial denaturation at 98°C for 3 min, 24 cycles of denaturation at 98°C for 10 s, annealing 60°C for 15 s and extension 72°C for 25 s, and final extension at 72°C for 2 min. 256 bp amplicons were quantified on a 2% agarose gel stained with SYBR Safe (Invitrogen), using the Gel Doc quantification software (Bio-Rad).
Amplicons were first pooled in an equimolar fashion and then the pools were gel-extracted using the PureLink Quick Gel Extraction Kit (Thermo Fisher Scientific). The sequencing was carried out at the Interdisciplinary Center for Biotechnology Research (ICBR; University of Florida) using a NovaSeq 6000 sequencer (Illumina). The Brunello amplicons were sequenced using the S4 2X150 cycles Kit (Illumina)

treatment_protocol: Vero E6 cells  were transduced with the custom Vervet sgRNA library. For each screen, 1.2x108 cells were transduced with lentivirus-packaged sgRNA library at MOI 0.3 in the presence of 8 μg/ml polybrene (Sigma) to achieve ~500-fold overrepresentation of each sgRNA. After 48 h, 0.6 µg/ml puromycin (Gibco) was added to eliminate non-transduced cells and cultures were expanded in (Corning) T300 flasks. Control replicates were collected at this time to determine input library composition and additional replicates were infected with SARS-CoV-2 or OC43 at the indicated MOIs. Cells surviving initial infections were collected when they had expanded to confluency. A portion of each replicate was stored in DNA/RNA Shield (Zymo Research) at -80°C for genomic DNA extraction and the remaining cells were reseeded and reinfected at the indicated MOIs.

tag: cell line

value: Vero E6

tag: virus

tag: single or double infected

value: double-infected

tag: moi


title: PBS-1

tag: tissue


title: VeroE6_SARS-CoV2 infected replicate 1

description: replicate 1


title: VeroE6_SARS-CoV2 infected replicate 2

description: replicate 2


title: Nevi_rep1

description: lncRNA expression

source_name: Nevi tissue, replicate1

value: Nevi


title: PBS-2


title: GLA+RT-2


title: VeroE6_OC43 double-infected replicate 2

description: replicate 2

value: MOI 0.1


title: VeroE6_OC43 single-infected replicate 4

description: replicate 4

value: single-infected


title: VeroE6_OC43 double-infected replicate 1

description: replicate 1


title: VeroE6_Day 0 replicate 2

description: replicate 2

value: uninfected


title: VeroE6_OC43 single-infected replicate 3

description: replicate 3


title: VeroE6_OC43 double-infected replicate 3

description: replicate 3


title: VeroE6_OC43 single-infected replicate 1

description: replicate 1


title: VeroE6_SARS-CoV2 infected replicate 3

description: replicate 3


title: KP tumour cell line 1_FOSL1_ChIP_rep2

city: Durham

first: Preetish

last: Kadur Lakshminarasimha Murthy

state: NC

address: 101 Science Dr

institute: Duke University

data_processing:
FASTQ files were processed and aligned to the mm10 genome as described in (Kobayashi et al., 2020) using this pipeline: https://github.com/jianhong/MintChIP. Signal tracks were calculated using deepTools bamCoverage() command and visualised on Integrative Genomics Viewer (Ramírez et al., 2014; Robinson et al., 2011).
Genome_build: mm10

source_name: lung

extract_protocol:
Mouse KP cell lines were cultured in DMEM (Thermo Fisher) with 10% FBS and 1% Antibiotic-Antimycotic. Cultured cells were trypsinised and filtered through a 70 µm filter to obtain a single cell suspension. To obtain primary SK tumour cells, mice were anaesthetised using Avertin. Skin and muscular layers were cut to expose the abdominal and thoracic cavities. Descending aorta was cut to exsanguinate and euthanise the animal. Cold PBS was perfused through the cardiac right ventricle to flush the blood out of the lungs. Lungs were inflated with lung/tumour dissociation buffer (Miltenyi Biotec), cut into small pieces and incubated at 370C for 45 minutes. A single cell suspension was obtained by mechanically dissociating using gentleMACS (Miltenyi Biotec) dissociator and passing the samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). tdTomato+ tumour cells were sorted using Sony SH800 sorter.
Approximately 500,000 cells were used from each sample. FOSL1 binding sites were identified using the Mint-ChIP assay (Kobayashi et al., 2020; van Galen et al., 2016). Updated version of the Mint-ChIP protocol (version 3) was used (https://tinyurl.com/udqksct). Cells were lysed on ice for one hour followed by digestion with 300 units of MNase for 10 minutes at 370C. T7 adapters were then ligated, and samples were incubated with anti-FOSL1 antibody overnight at 40C. Chromatin fragments bound to antibody were isolated using protein A/G Dynabeads and digested with proteinase K for one hour at 630C. DNA was purified using 1x SPRI bead clean-up. In vitro transcription was performed using T7 RNA polymerase (New England BioLabs). RNA was purified using silane beads followed by reverse transcription using Superscript III enzyme (Thermo Fisher). cDNA was purified using SPRI beads and used for library preparation PCR using Terra DNA polymerase (Takara). Size selection of libraries was performed using SPRI beads. Libraries were sequenced using NovaSeq S4 flow cell in 150 bp PE configuration.
Mint-ChIP

tag: strain

value: mixed


title: 4w SK tumour_FOSL1_ChIP


title: KP tumour cell line 1_input_control_rep2


title: KP tumour cell line 2_input_control_rep2


title: KP tumour cell line 2_FOSL1_ChIP_rep2


title: 4w SK tumour_input_control


title: KP tumour cell line 2_FOSL1_ChIP_rep1


title: KP tumour cell line 1_input_control_rep1


title: KP tumour cell line 1_FOSL1_ChIP_rep1


title: VeroE6_OC43 single-infected replicate 2

description: replicate 2


title: VeroE6_OC43 double-infected replicate 4

description: replicate 4


title: VeroE6_Day 0 replicate 3

description: replicate 3


title: VeroE6_Day 0 replicate 1

description: replicate 1


title: RNA-GW3

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

description:
RNA-GW3
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.

data_processing:
For ribo-seq, reads were first aligned to rRNA followed by mapping to the rest of the mm10 reference genome using STAR aligner. Hg38 was used for human cell lines.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: text file, featureCounts

growth_protocol: HEK293T cells and PPP1R15A uORF mutant cells were cultured in Dulbecco’s Modified Eagle Medium with 10% fetal bovine serum and 100 U/mL penicillin and 100 µg/mL streptomycin. All cell types were cultured at 37 °C with 5% CO2

extract_protocol:
For regular RNA seq, Kidneys were snap-frozen and RNA was extracted using Zymo Direct-zol RNA kit. For ribo-seq, polysome buffer (1 mL per one mouse kidney) consisted of 20 mM Tris pH 7.5 (140 µL of 1 M Tris 7.0 plus 60 µL of 1 M Tris 8.0 for 10 mL final buffer), 100 mM NaCl, 10 mM MgCl2, 1% Triton X-100, 0.1% sodium deoxycholate, DTT, 0.02 U/µL Turbo DNAse (ThermoFisher AM2238), 200 µg/mL cycloheximide, and Protease Inhibitor Cocktail Tablet.
for regular RNA seq, cDNA library preparation involved mRNA capture/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche). For ribo-seq, RNase I digested, size selected RNA fragments were treated with T4 PNK and adapter ligation was done using NEXTFLEX Small RNA-seq kit v3 (PerkinElmer NOVA-5132-05).

value: kidney

tag: timepoint

value: 4 h


title: RNA-GW5

description:
RNA-GW5
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.

value: 0 h


title: RIBO-GW5

description:
RIBO-GW5
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.

data_processing:
Library strategy: Ribo-seq
For ribo-seq, reads were first aligned to rRNA followed by mapping to the rest of the mm10 reference genome using STAR aligner. Hg38 was used for human cell lines.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: text file, featureCounts


title: RNA-GW4

description:
RNA-GW4
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: RIBO-GW6

description:
RIBO-GW6
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: RNA-GW1

description:
RNA-GW1
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: KP tumour cell line 2_input_control_rep1


title: RNA-GW2

description:
RNA-GW2
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.

value: 1 h


title: RNA-GW6

description:
RNA-GW6
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: RIBO-GW2

description:
RIBO-GW2
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: RIBO-GW4

description:
RIBO-GW4
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: RIBO-GW1

description:
RIBO-GW1
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: RIBO-GW3

description:
RIBO-GW3
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: HA6

description:
ILMN_1118_genecounts.txt
HA6


title: HA5

description:
ILMN_1118_genecounts.txt
HA5


title: HA-6R

description:
ILMN_1112_genecounts.txt
HA-6R


title: HA-5R

description:
ILMN_1112_genecounts.txt
HA-5R


title: HA4

description:
ILMN_1118_genecounts.txt
HA4


title: HA-4R

description:
ILMN_1112_genecounts.txt
HA-4R


title: HA-3R

description:
ILMN_1112_genecounts.txt
HA-3R


title: GQ201

description:
GQ201
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: SK Week 2-1

description: SK Week 2

data_processing:
ATAC-seq data were processed using the pipeline developed in (Koh et al., 2016) with default parameters. 75 bp PE reads were trimmed to 50 bp PE using FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) before analysing them. Reads were aligned to mm10 (mouse) or GRCh38 (human) genome using Bowtie 2 (Langmead and Salzberg, 2012). Duplicate and mitochondrial reads were removed. And peaks were called using MACS2 software. Peaks were annotated using HOMER (Heinz et al., 2010).
Genome_build: mm10/GRCh38
Supplementary_files_format_and_content: Peak file

extract_protocol:
Mice were anaesthetised using Avertin. Skin and muscular layers were cut to expose the abdominal and thoracic cavities. Descending aorta was cut to exsanguinate and euthanise the animal. Cold PBS was perfused through the cardiac right ventricle to flush the blood out of the lungs. Lungs were then removed and inflated with 4% PFA and fixed overnight at 40C in PFA for histology. For isolation of live primary cells, lungs were instead inflated with lung/tumour dissociation buffer (Miltenyi Biotec), cut into small pieces and incubated at 370C for 30 minutes (normal lung) or 45 minutes (lung with neoplastic growth). A single cell suspension was obtained by mechanically dissociating using gentleMACS (Miltenyi Biotec) dissociator and passing the samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). To isolate AEC2 cells from CC mice, Lysotracker dye was used as described in (der Velden et al., 2013). Briefly, dissociated lung cells were resuspended in DMEM/F12 containing Lysotracker (1 µL dye in 14 mL medium) and incubated at 370C for 30 minutes. Human normal lung and cancer samples were stored on ice in DMEM/F12 medium supplemented with 2% FBS until dissociation. Samples were dissociated using human tumour dissociation kit (Miltenyi Biotec) following the manufacturer’s recommendation. A single cell suspension was obtained by passing the dissociated samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). Samples were resuspended in PBS supplemented with 10% FBS and incubated with anti-EpCAM antibodies for 10 minutes at room temperature. Samples were then washed once in PBS supplemented with 10% FBS. Primary cells were isolated by FACS using SONY SH800 sorter. Sytox dyes (Blue, Green, Red and AADvanced) were used to exclude dead cells.
Harvested primary cells were immediately used to prepare ATAC-seq libraries as described in (Buenrostro et al., 2013). Briefly, isolated cells were washed in PBS and resuspended in buffer containing transposase Tn5 and incubated at 370C for 30 minutes. Tagmented DNA was PCR amplified for 10-16 cycles. Mitochondrial DNA present in the libraries was cleaved using a CRISPR-Cas9 based method described in (Wu et al., 2016). sgRNA library targeting mitochondrial DNA was purchased from Addgene (#82480). In vitro transcription was performed to produce the gRNAs using MEGAshortscript Kit (Thermo Fisher Scientific). ATAC-seq libraries were treated with 10 µg Cas9 protein and 15 µg of sgRNA in a 40 µL reaction for 2 hours at 370C. The libraries were purified using Qiaquick PCR purification kit (Qiagen) and sequenced using Illumina Hi-Seq 2500 (50 bp paired end) or Next-Seq (75 bp paired end).

tag: cell type

value: lung epithelial cell


title: HA3

description:
ILMN_1118_genecounts.txt
HA3


title: HA2

description:
ILMN_1118_genecounts.txt
HA2


title: HA-2R

description:
ILMN_1112_genecounts.txt
HA-2R


title: HA1

description:
ILMN_1118_genecounts.txt
HA1


title: HA-1R

description:
ILMN_1112_genecounts.txt
HA-1R


title: p75 floxed mice (p75fl/fl)

city: Baltimore

first: Aaron

middle: W

last: James

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

data_processing:
CellRanger v5.0.0
Seurat
Genome_build: mm10 "refdata-gex-mm10-2020-A" modifed to include EGFP and tdTomato to capture transgene expression
Supplementary_files_format_and_content: 10x multiplex barcode, feature and matrix .gz files

source_name: Total cells in the defect site from p75 floxed mice (p75fl/fl) calvarial tissue

growth_protocol: Skull defects were microdissected 7 days after injury (1.8 mm defect). The cells in the defect site were obtained by collagenase Type I/II (1 mg/mL) digestion (six sequential enzymatic digestions). Cell fractions (from sequential digestions 1-6) were collected and filtered at 40 μm and centrifuged. Cells were resuspended in resuspended in HBSS. Cell viability was assessed with Trypan blue exclusion on a Countess II (ThermoFisher Scientific) automated counter and showed a >85% viability.

extract_protocol:
Calvarial defects were created after 14 d of the last TM administration. A 1.8 mm diameter, full-thickness, circular frontal bone defect was created in the non-suture associated frontal bone (right side) using a micro surgical drill and a trephine drill bit.
10X mRNA Library V3.1 Prep Kit using standard paired-end protocol.

treatment_protocol: For p75 deletion, tamoxifen (TM; Sigma-Aldrich) was dissolved in sunflower seed oil (Sigma-Aldrich) and injected intraperitoneally (TM: 150 mg/kg/d for 5 d).

tag: genotype/variation

value: p75 floxed mice (p75fl/fl)

tag: stimulation

value: Tamoxifen injection; 1.8 mm Calvarial defect


title: GQ206

description:
GQ206
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.

tag: genotype


title: ZR1969

city: Stanford

first: Christopher

last: Murray

state: California

address: 1291 Welch Rd. B261, Beckman Center

department: Genetics

institute: Stanford University

data_processing:
Feature-barcode matrices were generated with cellranger count (expected cells: 5000)
Feature-barcode matrices were then merged with cellranger aggr (without depth normalization)
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger aggr filtered output: features, cells, and count matrix. Cloupe file contains depth-normalized data, whereas the count matrix contains non-normalized counts.

source_name: sorted neoplastic cells from lung tumors

growth_protocol: Lung tumors were initiated via intratracheal delivery of Lenti-Cre in 60 µL PBS. Lung tumors were developed for 20 weeks.

extract_protocol:
Microdissected lung tumors were dissociated with collagenase IV, dispase, and trypsin at 37 °C for 30 min. After dissociation, the samples were maintained on ice, in the presence of 2 mM EDTA and 1 U/mL DNase to prevent aggregation.  For the sorting of neoplastic cells, the dissociated cells were stained with antibodies against CD45 (BioLegened, 103112), CD31 (BioLegend, 303116), F4/80 (BioLegend, 123116), and Ter119 (BioLegend, 116212) to exclude hematopoietic and endothelial cells (lineage-positive (Lin+) cells). DAPI was used to exclude dead cells. FACSAria sorters (BD Biosciences) were used for cell sorting. Cells were loaded in each channel of Chromium Chip B (10X Genomics: 1000074) with a recovery target of 8,000 cells per sample, and emulsions were generated on the Chromium Controller (10X Genomics)
Libraries were constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 kit (10X Genomics: 1000075).

treatment_protocol: Mice were subjected to treatment with either vehicle or tamoxifen (4 mg doses in 200 µL corn oil) for two weeks prior to harvesting lung tumors.

tag: Sex

value: Tamoxifen

tag: cohort

value: Restored


title: ZR1966

value: Female

value: Vehicle

value: NonRestored


title: ZR1932

value: Male


title: GQ203

description:
GQ203
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: SK Week 2-2

description: SK Week 2


title: CM0884


title: CM0879


source_name: Total cells in the defect site from p75 conditional knockout mice (p75PDGFRα) calvarial tissue

value: p75 conditional knockout mice (p75PDGFR{alpha})


title: GQ202

description:
GQ202
Sample was used for library prep optimizations where inspection of reads length distribution on fastq files was sufficient. No quantified processed data produced for this sample.


title: Skin WT 5

city: Nagoya

first: Takuya

last: Takeichi

address: 65 Tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate of School

data_processing:
Next-generation sequencing was performed using an Illumina Novaseq 6000 platform to obtain 101-bp paired-end reads. Reads were adapter-trimmed using our in-house script and aligned to the mm9 reference genome using TopHat2 (https://ccb.jhu.edu/software/tophat/).
Reads per kilobase of exon per million mapped reads (RPKM) values were calculated using GFOLD.
Genome_build: mm9
Supplementary_files_format_and_content: htseq (DESeq) output

source_name: Skin

extract_protocol:
Total RNA extracted from the brain, the liver, and the skin of P0 newborns was purified using a RNeasy Mini Kit (QIAGEN, Hiden Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Skin

tag: age

value: wild type


title: Liver WT 5

source_name: Liver

value: Liver


title: Liver KI 2

value: Jak1 KI +/-


title: Brain WT 4

source_name: Brain

value: Brain


title: CM0875


title: HSC_dmPGE2

first: Eva

last: Fast

address: 1 Portland st

institute: Pfizer

description: stimulation scRNAseq experiment

data_processing:
scRNA-Seq: For HSC_Repl1 cellranger (v2.1.0) was used for demultiplexing and count matrix generation. For stimulation scRNA-Seq experiment Cellranger (v3.0.1) command ‘mkfastq’ was used to demutliplex raw base call (BCL) files into individual samples and separate cDNA fastq files and HTO surface fastq files. The cellranger ‘count’ command was used with default options to generate count matrices from cDNA fastq files.
scRNA-Seq: For HTO surface libraries, fastq files split into different lanes but from the same read (e.g. L001_R2, L002_R2) were combined using 'cat'. Reads shorter than 26bp were filtered using 'cutadapt'. CITE-Seq 'count' (version 1.4.3) was used to generate surface count by cell matrices from the HTO surface fastq libraries using the following barcodes: MPP - GGTCGAGAGCATTCA, MPP1 - ACCCACCAGTAAGAC, MPP2 - CTTGCCGCATGTCAT, MPP3/4 - AAGCATTCTTCACG and expected cell numbers per conditions: control - 5064 cells, dmPGE2 - 6497 cells, GCSF - 5297 cells, indo - 4665 cells and pIC - 5035 cells. Final pooled HTO/cDNA dataset including all stimulated HSC and MPP conditions is available here: https://mouse-hsc.cells.ucsc.edu.
scATAC-Seq: For scATAC-seq cellranger-atac mkfastq and count (1.2.0) was used for demultiplexing, alignment and generation of the fragment file. To generate the count matrix MACS2 was run with default parameters (keeping duplicates) on the aligned reads. Resulting peak summits were extended to 300 bp and this peak file was used to extract a count matrix from the fragment file via a custom script (see https://github.com/evafast/scrnaseq_paper).
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq matrixes are defined by barcode, features (both .tsv) and count matrix (.mtx)
Supplementary_files_format_and_content: scATAC-Seq count matrixes can be generated with peak (.bed) and fragments file (.tsv). Barcode file (.tsv) indicates cell identities and .csv file provides metadata.

source_name: FACS sorted bone marrow

growth_protocol: All cells were isolated from 9-12 week old male and female mice pooled at equal ratios. For treatment with niche stimulants and for scATAC-seq mice were ordered from Jackson Laboratories (C57BL/6J, #00664). Mice were kept for at least one week in the animal facility before initiating experiments. Control HSC replicate 1 (HSC_Repl1) is derived from the following mouse strain (Jackson Laboratories #016617) which carries a GFP transgene and was bred in house.

extract_protocol:
Whole Bone marrow was isolated from femur, tibia, hip and vertebrae via gentle crushing using a mortar and pestle. Stem and progenitor cells were enriched via lineage depletions (Miltenyi Biotech, 130-090-858). For treatment with niche stimulants cells were FAC-sorted  into the following populations: HSCs (Lin-, c-Kit+, Sca1+, CD48-, CD150+, CD34-), MPP1s (Lin-, c-Kit+, Sca1+, CD48-, CD150+, CD34+), MPPs (Lin-, c-Kit+, Sca1+, CD48-, CD150-), MPP2s (Lin-, c-Kit+, Sca1+, CD48+, CD150+), and MPP3/4s (Lin-, c-Kit+, Sca1+, CD48+, CD150-). Sorted MPPs were each labeled with different hashtag oligonucleotide (HTO) conjugated antibodies (Biolegend, TotalSeq™-A Cell Hashing). After 30min incubation cells were washed and the four MPP samples were pooled at equal ratios into a single MPP sample per condition (control, dmPGE2, pIC, GCSF, indo) for library preparation.
scRNA-Seq: Library for HSC_Repl1 were processed according to manufacturer’s recommendations (10X Genomics V2, CG00052 Rev B). Libraries were sequenced on a Next-seq 500 using a 75 cycle kit. Libraries for stimulated HSC and MPP scRNA-Seq samples were processed according to manufacturer’s recommendations (10X Genomics V3, CG000185 Rev B) through Post Gem-RT Cleanup – Dynabeads (step 2.1). At the cDNA amplification step (Step 2.2) an HTO additive primer was added to the amplification mix and steps 2.3A and 2.3B (using 70 µL of SPRI beads) were followed exactly to separate HTOs from cDNAs. cDNA library preparation was finished according to 10x Genomics recommendations. Purified HTO fraction was amplified using SI PCR primer and TruSeq D70x_s indexes according to HTO antibody manufacturer instructions (Biolegend).
scATAC-Seq: For ATAC-seq nuclei were isolated from HSCs and MPPs (pooled MPP, MPP1, MPP2 and MPP3/4) according to manufacturer's recommendations (CG000169 Rev D - Low Cell Input Nuclei Isolation). ScATAC-Seq libraries were prepared using manufacturers recommendations (10x Chromium Single Cell ATAC , CG000168 Rev B). ScRNA-Seq libraries form niche stimulation experiment and scATAC-Seq libraries were sequenced on a NOVAseq 6000 using a 100 cycle kit.

treatment_protocol: For the niche stimulation scRNA-Seq experiment the following treatments were used: Indomethacin (Sigma, 6mg/l) was administered for 7 days in acidified drinking water to maintain stability. Mice were injected with the following drugs and euthanized after 2 hours: Poly(I:C) HMW (Invivogen), IP injection 10mg/kg. G-CSF Recombinant Human Protein (Thermo fisher), IP injection, 0.25mg/kg. DmPGE2 (Cayman), SC injection, 2mg/kg.

value: HSC


title: HSC_ct

description: stimulation scRNAseq experiment, control Replicate 2

value: control


title: HSC_indo

description: stimulation scRNAseq experiment

value: indomethacin


title: Skin WT 3


title: Brain WT 5


title: HSC_GCSF

description: stimulation scRNAseq experiment

value: G-CSF


title: MPP_scATAC

description:
tagmented DNA
scATAC

value: MPP


title: HSC_scATAC

description:
tagmented DNA
scATAC


title: Skin WT 4


title: Skin WT 2


title: Brain WT 3


title: Skin WT 1


title: Skin KI 2


title: Liver WT 3


title: Liver WT 1


title: Brain KI 2


title: Brain KI 1


title: HSC_pIC

description: stimulation scRNAseq experiment


title: P-IV rep 2

city: Seoul

first: Seul Hye

last: Ryu

address: 50-1 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description:
sorted from GM-CSF-treated mouse
118

data_processing:
Illumina bcl2fastq2-v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using HISAT2 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie 1.3.4d software in default options.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: P-IV

extract_protocol:
flow cytometric sorting
Reverse transcription of mRNA and generation of cDNA libraries were carried out with SMARTer Ultra low input RNA library kit and sequencing with Illumina NovaSeq

treatment_protocol: For GM-CSF-treated sample, three once-daily injection of GM-CSF

value: Spleen

value: post natal week 12


title: Liver WT 2


title: Brain WT 2


title: Skin KI 1


title: Brain WT 1


title: P-IV rep 1

description:
sorted from GM-CSF-treated mouse
116


title: Liver WT 4


title: Liver KI 1


title: P-III rep 2

description:
sorted from GM-CSF-treated mouse
117

source_name: P-III


title: GM-CSF DC-Xs rep 1

description:
sorted from GM-CSF-treated mouse
11

source_name: GM-CSF DC-Xs


title: GM-CSF cDC1s rep 1

description:
sorted from GM-CSF-treated mouse
12

source_name: GM-CSF cDC1s


title: control cDC2s rep 2

description:
sorted from control mouse
90

source_name: control cDC2s


title: P-III rep 1

description:
sorted from GM-CSF-treated mouse
115


title: GM-CSF cDC2s rep 2

description:
sorted from GM-CSF-treated mouse
92

source_name: GM-CSF cDC2s


title: GM-CSF DC-Xs rep 2

description:
sorted from GM-CSF-treated mouse
41


title: control cDC2s rep 1

description:
sorted from control mouse
8


title: control cDC1s rep 2

description:
sorted from control mouse
100

source_name: control cDC1s


title: P-I rep 1

description:
sorted from GM-CSF-treated mouse
119

source_name: P-I


title: pESC-PGCLC 1

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

data_processing:
Bismark software (version 0.16.3) was used to perform alignments of bisulfite-treated reads to a reference genome.
The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2.
Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner.
Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred.
Genome_build: mm10

source_name: Parthenogenetic ES cell line derived PGC-like cell

extract_protocol:
Cells were collected and isolated their genomic DNA by QIAamp DNA Micro Kit (QIAGEN)
DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). A total amount of 1.5 μg DNA spiked with moderate lambda DNA was handled by MspI, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplified using KAPA HiFi HotStart Uracil and ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina Novaseq platform and 125bp/150bp paired-end reads generated. Image analysis and base calling were performed with Illumina CASAVA pipeline, and finally 125bp/150bp paired-end reads were generated.

treatment_protocol: For the induced PGCLCs, ESCs or pESCs treated with 1%KSR, 1. ng/ml bFGF and 2ng/ml Activin A for 2 days can form EpiLCs, and further treated with 500 ng/ml BMP4, 100 ng/ml SCF, 50ng/ml EGF and 1000 IU mLif for 4 days to form PGCLCs.


title: E12.5 PGC 1

source_name: Embryo 12.5 day primordial germ cell

value: Embryo 12.5 day primordial germ cell


title: E9.5 PGC 2

source_name: Embryo 9.5 day primordial germ cell

value: Embryo 9.5 day primordial germ cell


title: E9.5 PGC 1


title: ESC-PGCLC 1

source_name: Female ES cell line derived PGC-like cell


title: ESC-PGCLC 2

value: Female ES cell line derived PGC-like cell


title: pESC-PGCLC 2

value: Parthenogenetic ES cell line derived PGC-like cell


title: P-I rep 2

description:
sorted from GM-CSF-treated mouse
123


title: pESC 2

source_name: Parthenogenetic ES cell line

value: Parthenogenetic ES cell line


title: control cDC1s rep 1

description:
sorted from control mouse
9


title: GM-CSF cDC2s rep 1

description:
sorted from GM-CSF-treated mouse
10


title: Female ESC 1

source_name: ES cell line

value: Female ES cell line


title: Female ESC 2


title: GM-CSF cDC1s rep 2

description:
sorted from GM-CSF-treated mouse
93


title: pESC 1


title: BCc038

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

source_name: post-transplant liver biopsy

extract_protocol: RNA was isolated using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

value: liver

tag: diagnosis

value: chronic hepatitis C

tag: future fibrosis progression (2 or more f stages within 5 years)

value: Yes


title: BCc035


title: BCc037


title: BCc036


title: BCc031


title: BCc034


title: BCc030


title: BCc033


title: BCc029


title: E12.5 PGC 2


title: BCc032


title: BCc028


title: BCc027

value: No


title: BCc025


title: BCc023


title: BCc024


title: BCc022


title: BCc021


title: BCc017


title: BCc020


title: BCc019


title: BCc013


title: BCc018


title: BCc016


title: BCc011


title: BCc015


title: BCc009


title: BCc005


title: BCc012


title: BCc007


title: BCc004


title: BCc003


title: BCc008


title: BCc002


title: BCc006


title: JHUc030.2

source_name: liver biopsy

value: chronic hepatitis C + HIV


title: JHUc034.2


title: JHUc024.2


title: JHUc023.2


title: BCc026


title: JHUc021


title: JHUc016


title: JHUc020


title: BCc014


title: JHUc018


title: BCc010


title: JHUc015


title: JHUc014


title: JHUc009


title: JHUc011


title: JHUc017


title: JHUc012


title: BCc001


title: JHUc005


title: JHUc007


title: JHUc029.2


title: JHUc025


title: JHUc004


title: JHUc003


title: JHUc002


title: JHUc001


title: JHUc008


title: ev227L_DMSO

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

data_processing: Raw count data were normalized by linear normalization using R statistical language (www.r-project.org).

treatment_protocol: Precision-cut liver slice (PCLS, 300-micron-thick) sections were generated from fresh surgical tissue, and cultured with various candidate anti-fibrotic and chemoprevention agents dissolved in DMSO for 24-48h at 80% O2 and 5% CO2. PCLSs were snap-frozen in RNAlater for storage until RNA isolation.

value: Liver

tag: sample group

value: Vehicle control

tag: compound

value: DMSO

tag: concentration


title: ev223L_DMSO

scan_protocol: Refer to the NanoString nCounter Assay System Manual.


title: ev228L_DMSO

label_protocol: Refer to the NanoString nCounter Assay System Manual.


title: ev260L_DMSO


title: ev272L_DMSO


title: ev268L_DMSO


title: ev347L_DMSO


title: JHUc006


title: OKF6 S. gordonii 1:100 (B)

city: Lexington

first: kuey

middle: Chu

last: Chen

state: KENTUCKY

address: 800 Rose Street, UK Med Ctr

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

description: miRNA expression in human Oral epithelial cells induced by S. gordonii at 1:100 dilution

hyb_protocol: Each sample, 500ng of labeled RNA was loaded on a miRNA 4.0 array, hybridized for 16-18 hrs at 48 C. Arrays were washed and stained in the Affymetrix Fluidics Station 450 following manufactual protocols.

scan_protocol: Arrays were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Scanned miRNA array data were collected using Commond console and Expression console (Affymetrix) to generate chp files.

source_name: Immortalized oral keratinocyte cell line OKF6/hTERT

label_protocol: RNA labeling was prepared following the protocol of polyA tailing and biotin HSR ligation in Flashtag Biotin HSR kit (Affymetrix), using 500ng purified total cellular RNA from each sample.

growth_protocol: The immortalized human oral keratinocyte cell line (OKF6/hTERT) was grown in serum-free keratinocyte medium (Ker-SFM, Gibco, Carlsbad, CA) supplemented with 25 µg/ml bovine pituitary extract and 0.2 ng/ml huma recombinant epidermal growth factor. OKF6 cells grown in 24-well plates overnight were exposed to S. gordonii growing exponentially at different multiplicity of infections.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions using the RNeasy Mini Kit (Qiagen, Germantown, MD).

treatment_protocol: OKF6 cells (1x10^5/well) in 24-well plates were challenged with S. gordonii at different MOIs (1:10, 1:50, and 1:100) for 24 hours and then cells harvested for RNA isolation and miRNA microarray analysis. Unstimulated cells (Mock/Control) were used as a negative control. Each condition was evaluted in duplicate.

value: Immortalized human oral epithelial cell line (OKF6)

tag: oec

value: S. gordonii MOIs:S. gordonii 1:100 dilution


title: OKF6 S. gordonii 1:10 (B)

description: miRNA expression in human Oral epithelial cells induced by S. gordonii at 1:10 dilution

value: S. gordonii MOIs:S. gordonii 1:10 dilution


title: OKF6 Mock/Control (A)

description: miRNA expression in human Oral epithelial cells mock control

value: S. gordonii MOIs:Mock/Control


title: ev299L_DMSO


title: ev196L_DMSO


title: ev337L_DMSO


title: ev333L_DMSO


title: OKF6 S. gordonii 1:50 (A)

description: miRNA expression in human Oral epithelial cells induced by S. gordonii at 1:50 dilution

value: S. gordonii MOIs:S. gordonii 1:50 dilution


title: OKF6 S. gordonii 1:50 (B)


title: OKF6 S. gordonii 1:100 (A)


title: ev306L_DMSO


title: ev169L_DMSO


title: ev312L_DMSO


title: ev177L_DMSO


title: OKF6 Mock/Control (B)


title: ev197L_DMSO


title: ev297L_DMSO


title: OKF6 S. gordonii 1:10 (A)


title: ev202L_DMSO


title: ev179L_DMSO


title: ev172L_DMSO


title: ev170L_DMSO


title: ev163L_DMSO


title: ev167L_DMSO


title: ev147L_DMSO


title: ev153L_DMSO


title: ev146L_DMSO


title: ev162L_DMSO


title: ev157L_DMSO


title: ev168L_DMSO


title: ev144L_DMSO


title: ev140L_DMSO


title: ev145L_DMSO


title: ev152L_DMSO


title: ev164L_DMSO


title: ev090L_DMSO


title: ev099L_DMSO


title: ev088L_DMSO


title: ev034L_DMSO


title: ev093L_DMSO


title: ev112L_DMSO


title: ev054L_DMSO


title: ev089L_DMSO


title: ev033L_DMSO


title: ev060L_DMSO


title: ev070L_DMSO


title: ev174L_DMSO


title: ev086L_DMSO


title: ev161L_DMSO


title: ev165L_DMSO


title: ev040L_DMSO


title: ev049L_DMSO


title: ev067L_DMSO


title: ev047L_DMSO


title: ev059L_DMSO


title: ev068L_DMSO


title: ev048L_DMSO


title: ev115L_DMSO


title: ev064L_DMSO


title: ev051L_DMSO


title: ev114L_DMSO


title: ev061L_DMSO


title: ev069L_DMSO


title: ev076L_DMSO


title: ev036L_DMSO


title: ev127L_DMSO


title: ev071L_DMSO


title: ev080L_DMSO


title: ev081L_DMSO


title: ev072L_DMSO


title: ev126L_DMSO


title: ev078L_DMSO


title: ev065L_DMSO


title: ev111L_DMSO


title: ev227L_t0

value: Baseline (before culture)


title: ev223L_t0


title: ev121L_DMSO


title: ev092L_DMSO


title: ev087L_DMSO


title: ev228L_t0


title: ev058L_DMSO


title: ev260L_t0


title: ev268L_t0


title: ev196L_t0


title: ev109L_DMSO


title: ev272L_t0


title: ev297L_t0


title: ev299L_t0


title: ev312L_t0


title: ev333L_t0


title: ev347L_t0


title: ev177L_t0


title: ev202L_t0


title: ev179L_t0


title: ev170L_t0


title: ev161L_t0


title: ev172L_t0


title: ev163L_t0


title: ev337L_t0


title: ev169L_t0


title: ev165L_t0


title: ev167L_t0


title: ev306L_t0


title: ev162L_t0


title: ev174L_t0


title: ev146L_t0


title: ev168L_t0


title: ev140L_t0


title: ev144L_t0


title: ev153L_t0


title: ev197L_t0


title: ev164L_t0


title: ev152L_t0


title: ev088L_t0


title: ev099L_t0


title: ev070L_t0


title: ev093L_t0


title: ev157L_t0


title: ev147L_t0


title: ev145L_t0


title: ev086L_t0


title: ev033L_t0


title: ev054L_t0


title: ev067L_t0


title: ev034L_t0


title: ev065L_t0


title: ev114L_t0


title: ev047L_t0


title: ev059L_t0


title: ev068L_t0


title: ev049L_t0


title: ev040L_t0


title: ev064L_t0


title: ev061L_t0


title: ev090L_t0


title: ev115L_t0


title: ev069L_t0


title: ev048L_t0


title: ev060L_t0


title: ev112L_t0


title: ev051L_t0


title: ev036L_t0


title: ev076L_t0


title: ev089L_t0


title: ev127L_t0


title: ev058L_t0


title: ev081L_t0


title: ev072L_t0


title: ev080L_t0


title: ev111L_t0


title: ev071L_t0


title: ev078L_t0


title: ev126L_t0


title: ev092L_t0


title: ev087L_t0


title: ev109L_t0


title: ev228L_Nizatidine_10microM

value: Compound treatment

value: Nizatidine


title: ev227L_Nizatidine_10microM


title: ev272L_Nizatidine_10microM


title: ev260L_Captopril_100microM

value: Captopril


title: ev272L_Captopril_100microM


title: ev268L_Nizatidine_10microM


title: ev121L_t0


title: ev268L_Captopril_100microM


title: ev337L_I-BET 151_10microM

source_name: ev337L_I-BET 151_10microM

value: I-BET 151


title: ev347L_JQ1_100microM


title: ev115L_EGCG_30microM

value: EGCG


title: ev333L_I-BET 151_10microM

source_name: ev333L_I-BET 151_10microM


title: ev333L_JQ1_100microM


title: ev146L_EGCG_30microM


title: ev060L_EGCG_30microM


title: ev068L_EGCG_30microM


title: ev051L_EGCG_30microM


title: ev112L_EGCG_30microM


title: ev260L_Nizatidine_10microM


title: ev223L_Nizatidine_10microM


title: ev049L_EGCG_30microM


title: ev090L_EGCG_30microM


title: ev114L_EGCG_30microM


title: ev112L_Metformin_5microM

value: Metformin


title: ev048L_EGCG_30microM


title: ev161L_Metformin_5microM


title: ev115L_Metformin_5microM


title: ev162L_Metformin_5microM


title: ev114L_Metformin_5microM


title: ev040L_Pioglitazone_20microM

value: Pioglitazone


title: ev047L_Pioglitazone_20microM


title: ev157L_Metformin_5microM


title: ev054L_EGCG_30microM


title: ev049L_Pioglitazone_20microM


title: ev051L_Pioglitazone_20microM


title: ev048L_Pioglitazone_20microM


title: ev112L_Pioglitazone_20microM


title: ev115L_Pioglitazone_20microM


title: ev114L_Pioglitazone_20microM


title: ev090L_Pioglitazone_20microM


title: ev306L_Cenicriviroc_100microM

value: Cenicriviroc


title: ev169L_Cenicriviroc_100microM

value: Liver


title: ev054L_Pioglitazone_20microM


title: ev297L_Cenicriviroc_100microM


title: ev196L_Cenicriviroc_100microM


title: ev177L_Cenicriviroc_100microM


title: ev299L_Cenicriviroc_100microM


title: ev197L_Cenicriviroc_100microM


title: ev312L_Cenicriviroc_100microM


title: ev146L_Metformin_5microM


title: ev172L_Cenicriviroc_100microM


title: ev163L_Bortezomib_100microM

value: Bortezomib


title: ev170L_Cenicriviroc_100microM


title: ev179L_Cenicriviroc_100microM


title: ev174L_Cenicriviroc_100microM


title: ev161L_Bortezomib_100microM


title: ev165L_Metformin_5microM


title: ev167L_Bortezomib_100microM


title: ev165L_Bortezomib_100microM


title: ev162L_Bortezomib_100microM


title: ev164L_Bortezomib_100microM


title: ev168L_Bortezomib_100microM


title: ev153L_MG132_20microM


title: ev144L_MG132_20microM


title: ev202L_Cenicriviroc_100microM


title: ev157L_MG132_20microM


title: ev140L_MG132_20microM


title: ev146L_MG132_20microM


title: ev145L_MG132_20microM


title: ev147L_MG132_20microM


title: ev058L_AM095_3microM


title: ev115L_AM095_3microM


title: ev152L_MG132_20microM


title: ev076L_AM095_3microM


title: ev112L_AM095_3microM


title: ev069L_AM095_3microM


title: rRNA-depleted total RNA-seq Piwi GKD rep 2

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

data_processing:
RNA-seq TPM and read counts: sequencing reads were adapter clipped, mapped to dm3/BDGP5.78 genome/transcriptome assembly via STAR (Dobin et al., 2017). Reads mapped to transcriptome were counted for genes of BDGP5.78 annotation and converted to TPM values using Salmon (Patro et al. 2017).
RNA-Seq profiles: sequencing reads were adapter clipped, mapped to dm3/R5 genome assembly via hisat2 (Kim et al., 2019). Coverage files were generated via ‘bedtools coverage’ (Quinlan et al., 2010) using 500nt windows.
bedgrpaph files for each replica of RNA-seq represent read counts per 500-nt bins
sf files for RNA-seq replicates represent read counts per gene (in TPM) obtained in Salmon.
Genome_build: dm3

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown at 18 °C

extract_protocol:
RNA-seq: approximately 200 ovaries from 0- to 1-day old Ctrl, Piwi-GKD, HP1a-GKD, and double-GKD females were manually dissected in cold PBS. RNA (from two biological replicates) was isolated using Trizol reagent (Invitrogen).
RNA-seq: rRNA was depleted using Illumina Ribo-Zero Plus rRNA Depletion Kit. cDNA library preparation with random primers, and single-end deep sequencing was carried out on the Illumina HiSeq 2000 platform.

value: ovary

value: 0-1 day


title: ev049L_AM095_3microM


title: ev093L_AM095_3microM


title: ev087L_AM095_3microM


title: rRNA-depleted total RNA-seq HP1a + Piwi GKD rep 2


title: ev070L_AM095_3microM


title: ev088L_AM095_3microM


title: ev090L_AM095_3microM


title: rRNA-depleted total RNA-seq HP1a GKD rep 1


title: rRNA-depleted total RNA-seq Piwi GKD rep 1


title: rRNA-depleted total RNA-seq HP1a GKD rep 2


title: ev067L_AM095_3microM


title: ev099L_AM095_3microM


title: rRNA-depleted total RNA-seq Control rep 1


title: rRNA-depleted total RNA-seq Control rep 2


title: ev064L_AM095_3microM


title: ev072L_AM095_3microM


title: ev089L_AM095_3microM


title: ev068L_AM095_3microM


title: ev114L_AM095_3microM


title: ground_rep2

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

data_processing:
CASAVA version 1.8.2 was used to perform base calling. The quality of the 2 X 125 bp reads was assessed with FastQC.
Raw reads were aligned using STAR version 2.5.3 to build version hg38 of the human genome defined by GENCODE release 25.
Counts for GENCODE basic annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package.
Normalization was carried out using edgeR R package. After removal of genes encoded on mitochondrial chromosome, raw counts were normalized according to library size to obtain counts per millions (CPM). Only genes with a CPM greater than 1 in at least 2 sample were retained for subsequent analysis.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: RNAseq_expressionMatrix_CPM.txt: Expression matrix of CPM for each sample.

source_name: HMEC-1 cell line

growth_protocol: HMEC-1 cells were seeded on Cyclic Olefin Copolymer coverslips, with 2% gelatin coating to improve cell adhesion, in MCDB131 medium supplemented with 10% Fetal Bovine Serum, hydrocortisone (1 ug/ml), EGF (10 ng/ml), 1 mM sodium bicarbonate, Penicillin (1 U/ml) Streptomycin (1 ug/ml), HEPES (20 mM). Cell cultures were incubated at 37degreeC in 5% CO2, 80% humidity, before insertion into the Experimental Units (EUs). The EUs are able to fulfil under electronic control and without human intervention, a scientific protocol for cell culture and fixing. 20 samples prepared for nucleic acid extraction were fixed with RNA Protect Cell Reagent.

extract_protocol:
Total RNA was extracted with ReliaPrep RNA Cell Miniprep System (Promega, Madison WI, USA). RNA integrity was assessed with agarose gel electrophoresis and ethidium bromide staining/UV light (GenoPlex, VWR, USA), concentration and purity with NanoView Spec- trophotometer (GE Healthcare, Pittsburgh, PA, USA).
The RNA-seq libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Library Prep Kit.

treatment_protocol: Samples were brought to the Columbus module of the ISS with the Soyuz TMA-18M 44S manned mission on September 2nd, 2015, within the IRISS mission of ESA. At rendez vous, samples were immediately transferred into the KUBIC facility, an incubator with internal centrifuge for artificial gravity. Space microg samples were exposed to environmental microgravity (µg) and named Space_microg samples; Space_1g samples were set inside the centrifuge reproducing 1g. Other samples, concomitantly prepared for ground control, flew back to Pisa with civilian airlines just when the others were flying into space, and were integrated within the KISS facility in the home laboratory. Experiment activation and media exchanges occurred contemporarily in space and on ground. At the end of the space mission, the samples were fixed in space, sent back to Earth with manned Soyuz TMA-16M 42S on September 12, 2015, retrieved by ESA personnel, brought to the PI laboratory in Pisa and stored at 6°C until processed.

tag: cell line

tag: sample type

value: Ground control, home laboratory sample

tag: exposure

value: 1g on Earth


title: ground_rep3


title: ev051L_AM095_3microM

tag: tissue


title: space_1g_rep2

value: Space flight at 1g in the onboard centrifuge

value: 1g onboard


title: space_1g_rep1


title: rRNA-depleted total RNA-seq HP1a + Piwi GKD rep 1


title: space_microg_rep1

value: Space flight

value: environmental microgravity


title: ev054L_AM095_3microM

value: Compound treatment


title: ev078L_AM095_3microM


title: ev065L_AM095_3microM


title: ev080L_AM095_3microM


title: space_microg_rep2


title: RNAseq_AEC2_3

description:
AEC2
KLP-S8

data_processing:
RNA-seq data were analysed using the RNA Express package available on Basespace (Illumina). Briefly, reads were aligned to the mm10 genome using STAR and differentially expressed genes were identified using DESeq2 (Dobin et al., 2013; Love et al., 2014). Transcripts with |FC| > 1.5 and q value < 0.05 were considered to be differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-Seq Count Matrix

source_name: lung

extract_protocol:
Mice were anaesthetised using Avertin. Skin and muscular layers were cut to expose the abdominal and thoracic cavities. Descending aorta was cut to exsanguinate and euthanise the animal. Cold PBS was perfused through the cardiac right ventricle to flush the blood out of the lungs. Lungs were then removed and inflated with 4% PFA and fixed overnight at 40C in PFA for histology. For isolation of live primary cells, lungs were instead inflated with lung/tumour dissociation buffer (Miltenyi Biotec), cut into small pieces and incubated at 370C for 30 minutes (normal lung) or 45 minutes (lung with neoplastic growth). A single cell suspension was obtained by mechanically dissociating using gentleMACS (Miltenyi Biotec) dissociator and passing the samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). Primary cells were isolated by FACS using SONY SH800 sorter. Sytox dyes (Blue, Green, Red and AADvanced) were used to exclude dead cells.
Total RNA was isolated from primary cells using RNeasy Mini kit (Qiagen). Samples with RIN > 9 were used for library preparation by Duke University’s genomics core using KAPA stranded mRNA library prep kit. Libraries were sequenced using Illumia Hi-Seq 4000 (50 bp single end).

tag: strain

value: mixed

value: normal


title: ground_rep1


title: ev059L_AM095_3microM

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.


title: ev060L_AM095_3microM


title: ev081L_AM095_3microM


title: ev086L_AM095_3microM


title: RNAseq_AEC2_2

description:
AEC2
KLP-S6


title: ev061L_AM095_3microM


title: RNAseq_AEC2_1

description:
AEC2
KLP-S5


title: ev048L_AM095_3microM


title: RNAseq_4wTumour_3

description:
SK4wTumour
KLP-S3

value: Kras mutant


title: RNAseq_4wTumour_1

description:
SK4wTumour
KLP-S1


title: RNAseq_4wTumour_2

description:
SK4wTumour
KLP-S2


title: The scRNA-seq of cells from Ren1c-/-;Myh11-CreERT2;tdTomato;Ren1c-YFP mice

city: Charlottesville

first: Hirofumi

last: Watanabe

state: Virginia

address: 409 Lane Rd, Bldg MR4

department: Department of Pediatrics, Child Health Research Center

institute: University of Virginia School of Medicine

data_processing:
The FASTQ file from the sequencing was processed by Cell Ranger v4.0.0 (10X Genomics).
For alignment, we made a custom reference package including YFP and tdTomato with mouse genome (mm10).  “cellranger count” was used for read alignment and gene expression quantification.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered gene-barcode matrix

source_name: Reninnull cells and surrounding vascular smooth muscle cells

growth_protocol: We generated Ren1cKO;SMMHC-CreERT2;tdTomato;Ren1c-YFP mice. Two male mice were injected 0.125 g/body weight of tamoxifen at 5 weeks of age and used at 8 weeks of age.

extract_protocol:
Cells were isolated from the kidney cortex using fluorescence-activated cell sorting. The kidneys were excised and decapsulated. Then, the kidney cortices were dissected, minced with a razor blade, and transferred into a 15 mL tube with 5 mL of enzymatic solution (0.3% collagenase A [Millipore-Sigma, Burlington, MA], 0.25% trypsin [Millipore-Sigma], and 0.0021% DNase I [Millipore-Sigma]). The tubes were placed flat inside a shaking incubator (80 RPM) for 15 minutes at 37°C. The solution was pipetted up/down 10 times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected in a fresh tube on ice. The enzymatic solution was added to the 15 mL tube containing the remaining undigested cortices, and the digestion procedure was repeated a total 3 times. The supernatants were pooled and centrifuged at 800 g for 4 minutes at 4°C using a Sorvall RT7 refrigerated centrifuge (Sorvall, Newtown, CT). The cell pellet was resuspended in fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 μm nylon cell strainer (Corning Inc., Corning, NY) and washed with buffer 1. The flow-through was poured through a sterile 40 μm nylon cell strainer (Corning Inc.) and washed with buffer 1. The flow-through was centrifuged at 1,100 g for 4 min at 4°C. The cell pellet was resuspended in 1.5 mL of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Millipore-Sigma)]. The dead cells were labeled with DAPI (Millipore-Sigma). Cells were analyzed and sorted using an Influx Cell Sorter (Becton Dickinson, Franklin Lakes, NJ) at the Flow Cytometry Core Facility of the University of Virginia. The tdTomato-YFP-double positive cells, tdTomato-positive cells, and YFP-positive cells were isolated. Cells were collected in DMEM with 10% FBS and used for single-cell capture and downstream applications.
Single cells were captured with the Chromium System (10X Genomics, Pleasanton, CA) following manufacturer’s recommendation. Briefly, sorted cells were washed with PBS containing 0.04% BSA and loaded into a Chromium Next GEM Chip G with reagents of Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics). The Cell-Gel Beads in Emulsion (GEMs) were generated and incubated to generate the barcoded cDNA. cDNA was cleaned with Dynabeads and amplified with 12 cycles of PCR. cDNA was then enzymatically fragmented, end-repaired, poly-A tailed, adaptor-ligated, and amplificated by PCR. The constructed libraries were sequenced on an Illumina HiSeq 2500/4000 platform (150-bp paired-end reads).

value: Primary kidney cells

tag: cell type


title: ev078L_Erlotinib_5microM

value: Erlotinib


title: ev033L_Erlotinib_5microM


title: ev034L_Erlotinib_5microM


first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: 12h-8: 12 hr single-cell embryo replicate 8 from experiment SLX-11171

data_processing:
Raw sequence reads (fastq) were trimmed using the fastx_trimmer command from fastx-Toolkit (version 0.0.13; respectively 5 nt from 5' and 65 nt from 3' ends)
Sequencing adapter sequences were removed by Cutadapt (1.7.1)
Mapping of the trimmed reads was by Tophat (2.0.11) using the GRCm38 genome and Ensembl 54 reference transcriptome
Transcriptome was remodelled via de novo re-assembly of transcripts based on empirical  data from mapped reads and incorporation into the original reference (Cufflinks 2.2.1)
Gene-level counts based on the updated transcriptome were then performed using ht-seq-count (0.6.1p1)
Genome_build: Grcm38
Supplementary_files_format_and_content: Raw gene-level counts in tab-delimited text format

source_name: Single-cell embryo

extract_protocol:
Single-cell embryo were directly lysed using Takara Clontech Smartseq lysis buffer with RNAse inhibitor
Whole transcriptome amplification and library preparation was performed using Takara Clontech Smarter Stranded Total RNA-Seq Kit Pico Input version 1

treatment_protocol: Epididymidal sperm isolated from 8- to 12-week-old Mus musculus musculus B6xDBA2F1 or Mus musculus castaneus (Cast) males was microinjected into MII Oocyte in-vitro.  Injected Oocytes were then cultured for 2,4,6, 8 and 12 hours before harvesting for RNASeq

value: Single-cell embryo

value: C57BL/6 x CAST F1

tag: age (hour)

tag: replicate

tag: experiment

tag: barcode


description: 10h-7: 10 hr single-cell embryo replicate 7 from experiment SLX-11171


title: space_microg_rep3


title: ev076L_Erlotinib_5microM

value: Liver


description: 8h-6: 8 hr single-cell embryo replicate 6 from experiment SLX-11171


description: 4h-8: 4 hr single-cell embryo replicate 8 from experiment SLX-11171


description: 2h-8: 2 hr single-cell embryo replicate 8 from experiment SLX-11171


title: ev112L_Erlotinib_5microM


title: ev054L_Erlotinib_5microM


title: 0h-6: Single MII oocyte (0) replicate 6

description: 0h-6: Single MII oocyte (0) replicate 6 from experiment SLX-11171

value: MII oocyte (0)


description: 12h-7: 12 hr single-cell embryo replicate 7 from experiment SLX-11133


description: 10h-6: 10 hr single-cell embryo replicate 6 from experiment SLX-11133


title: ev040L_Erlotinib_5microM


title: ev061L_Erlotinib_5microM


title: ev067L_Erlotinib_5microM


title: ev065L_Erlotinib_5microM


title: ev072L_Erlotinib_5microM


description: 4h-7: 4 hr single-cell embryo replicate 7 from experiment SLX-11133


description: 2h-7: 2 hr single-cell embryo replicate 7 from experiment SLX-11133


title: 0h-5: Single MII oocyte (0) replicate 5

description: 0h-5: Single MII oocyte (0) replicate 5 from experiment SLX-11133


description: 6h-8: 6 hr single-cell embryo replicate 8 from experiment SLX-11171


description: 12h-6: 12 hr single-cell embryo replicate 6 from experiment SLX-10914


title: ev087L_Erlotinib_5microM


title: ev059L_Erlotinib_5microM


title: ev080L_Erlotinib_5microM


title: ev047L_Erlotinib_5microM


description: 10h-5: 10 hr single-cell embryo replicate 5 from experiment SLX-10914


description: 8h-4: 8 hr single-cell embryo replicate 4 from experiment SLX-10914


title: ev114L_Erlotinib_5microM


title: ev064L_Erlotinib_5microM


title: ev069L_Erlotinib_5microM


title: ev048L_Erlotinib_5microM


title: 0h-4: Single MII oocyte (0) replicate 4

description: 0h-4: Single MII oocyte (0) replicate 4 from experiment SLX-10914


description: 6h-6: 6 hr single-cell embryo replicate 6 from experiment SLX-10914


description: 8h-5: 8 hr single-cell embryo replicate 5 from experiment SLX-11133


title: ev049L_Erlotinib_5microM


title: ev115L_Erlotinib_5microM


title: ev051L_Erlotinib_5microM


title: ev076L_Galunisertib_10microM

value: Galunisertib


description: 2h-6: 2 hr single-cell embryo replicate 6 from experiment SLX-10914


description: 6h-7: 6 hr single-cell embryo replicate 7 from experiment SLX-11133


title: ev036L_Erlotinib_5microM


title: ev068L_Erlotinib_5microM


description: 10h-4: 10 hr single-cell embryo replicate 4 from experiment SLX-10684


title: ev058L_Erlotinib_5microM


description: 12h-5: 12 hr single-cell embryo replicate 5 from experiment SLX-10684


description: 6h-5: 6 hr single-cell embryo replicate 5 from experiment SLX-10684


description: 2h-5: 2 hr single-cell embryo replicate 5 from experiment SLX-10684


description: 4h-5: 4 hr single-cell embryo replicate 5 from experiment SLX-10684


title: 0h-3: Single MII oocyte (0) replicate 3

description: 0h-3: Single MII oocyte (0) replicate 3 from experiment SLX-10684


title: ev127L_Galunisertib_10microM


description: 12h-4: 12 hr single-cell embryo replicate 4 from experiment SLX-11288

value: C57BL/6 x DBA2 F2


description: 4h-6: 4 hr single-cell embryo replicate 6 from experiment SLX-10914


title: ev072L_Galunisertib_10microM


description: 8h-3: 8 hr single-cell embryo replicate 3 from experiment SLX-11288


title: ev080L_Galunisertib_10microM


title: ev071L_Galunisertib_10microM


description: 6h-4: 6 hr single-cell embryo replicate 4 from experiment SLX-11288


description: 4h-4: 4 hr single-cell embryo replicate 4 from experiment SLX-11288


description: 2h-4: 2 hr single-cell embryo replicate 4 from experiment SLX-11171


title: ev111L_Galunisertib_10microM


title: ev081L_Galunisertib_10microM


title: ev078L_Galunisertib_10microM


title: ev087L_Galunisertib_10microM


title: ev126L_Galunisertib_10microM


title: ev109L_Galunisertib_10microM


description: 6h-3: 6 hr single-cell embryo replicate 3 from experiment SLX-11169


title: ev121L_Galunisertib_10microM


description: 4h-3: 4 hr single-cell embryo replicate 3 from experiment SLX-11169


title: ev092L_Galunisertib_10microM


title: MGHc_CIP006

value: liver

value: chronic hepatitis C

value: No


description: 2h-3: 2 hr single-cell embryo replicate 3 from experiment SLX-11169


title: MGHc_CIP005


description: 12h-2: 12 hr single-cell embryo replicate 2 from experiment SLX-11169


title: MGHc_CIP004

value: Yes


description: 10h-3: 10 hr single-cell embryo replicate 3 from experiment SLX-11169


description: 6h-2: 6 hr single-cell embryo replicate 2 from experiment SLX-11169


title: MGHc_CIP003


title: MGHc_CIP002


title: MGHc_CIP001


description: 4h-2: 4 hr single-cell embryo replicate 2 from experiment SLX-11169


description: 2h-2: 2 hr single-cell embryo replicate 2 from experiment SLX-11169


description: 12h-1: 12 hr single-cell embryo replicate 1 from experiment SLX-11125


description: 12h-3: 12 hr single-cell embryo replicate 3 from experiment SLX-11169


description: 10h-2: 10 hr single-cell embryo replicate 2 from experiment SLX-11125


title: MGHc_CIN013


title: MGHc_CIN012


description: 8h-2: 8 hr single-cell embryo replicate 2 from experiment SLX-11169


title: MGHc_CIN011


title: MGHc_CIN010


description: 8h-1: 8 hr single-cell embryo replicate 1 from experiment SLX-11125


title: MGHc_CIN007


title: MGHc_CIN006


description: 4h-1: 4 hr single-cell embryo replicate 1 from experiment SLX-11125


title: 0h-1: Single MII oocyte (0) replicate 1

description: 0h-1: Single MII oocyte (0) replicate 1 from experiment SLX-11125


description: 2h-1: 2 hr single-cell embryo replicate 1 from experiment SLX-11125


description: 10h-1: 10 hr single-cell embryo replicate 1 from experiment SLX-11125


title: MGHc_CIN008


description: 6h-1: 6 hr single-cell embryo replicate 1 from experiment SLX-11125


title: MGHc_CIN005


title: 0h-2: Single MII oocyte (0) replicate 2

description: 0h-2: Single MII oocyte (0) replicate 2 from experiment SLX-11169


title: MGHc_CIN003


title: MGHc_CIN001


title: MGHc_CIN002