title: ControlSampleForFSCAndH2BmGFPScreen_Rep2

city: San Francisco

first: Xiaowei

institute: UCSF

description: sgRNA pcr from genomic DNA

data_processing:
Basecalls performed using HiSeq Control Software
Reads were aligned to CRISPRa_v2_human.trim_1_39_forward.fa or CRISPRi_v2_human.trim_1_39_forward.fa based on sgRNA library identity
Data were filtered for reads over 50
Analysis was based on the ScreenProcessing pipeline developed in Weissman lab (https://github.com/mhorlbeck/ScreenProcessing)(Horlbeck, M. A. et al. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Elife 5, doi:10.7554/eLife.19760 (2016).).  The phenotypic score of each sgRNA was quantified as previously defined (ε) (Kampmann, M., Bassik, M. C. & Weissman, J. S. Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells. Proc Natl Acad Sci U S A 110, E2317-2326, doi:10.1073/pnas.1307002110 (2013).)  For the mIFP proof-of-principle screen, the phenotypic score of each group was the average score of two sgRNAs assigned to the group and averaged between two replicates except otherwise described.  For the nuclear size screen, FSC screen and H2B-mGFP screen, genes were scored based on the average phenotypic scores of the sgRNAs targeting them.  For the nuclear size screen, the phenotypic scores were further averaged between 4 runs for each replicate.  For the nuclear size screen, FSC screen and H2B-mGFP screen, sgRNAs were first clustered by transcription start site (TSS) and scored by the Mann-Whitney test against the 22 non-targeting sgRNA control set included in the library.  Control groups were generated by repeated random assignment of sgRNAs to groups and phenotypic scores of these control groups were scored in the same way.  A z score was calculated for each gene and genes with a z score higher than the top 0.1% of control groups were further analyzed.
Genome_build: CRISPRa_v2_human.trim_1_39_forward.fa and CRISPRi_v2_human.trim_1_39_forward.fa
Supplementary_files_format_and_content: tab-delimited text files include raw counts and calculated phenotypic scores

source_name: hTERT-RPE1 cell line

growth_protocol: All the hTERT-RPE1 cells were grown in DMEM/F-12 media supplemented with 10% FBS and Pen/Strep (complete DMEM/F-12 medium).

extract_protocol:
genomic DNA of large samples was extracted with Macherey Nagel Blood kit and samples less than 10,000 cells was extracted with the Arcturus PicoPure DNA Extraction Kit
Sequencing sample was prepared using a protocol from Jonathan Weissman’s lab (https://weissmanlab.ucsf.edu/CRISPR/IlluminaSequencingSamplePrep.pdf) except that genomic DNA of samples less than 10,000 cells was extracted with the Arcturus PicoPure DNA Extraction Kit.

treatment_protocol: For the mIFP proof-of-principle screen, mIFP positive cells (hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP mIFP-NLS) and mIFP negative cells (hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP) were stably transduced with the “mIFP sgRNA library” (CRISPRa library with 860 elements) and the “control sgRNA library” (CRISPRa library with 6100 elements) separately.  For the nuclear size screen, FSC screen and H2B-mGFP screen, cells (hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP) were stably transduced with the “nuclear size library” (CRISPRi library with 6190 elements).  To guarantee that cells receive no more than one sgRNA per cell, BFP was expressed on the same sgRNA construct and cells were analyzed by FACS the day after transduction.  The experiment only continued when 10-15% of the cells were BFP positive.  These cells were further enriched by puromycin selection (a puromycin resistance gene was expressed from the sgRNA construct) for 3 days to prepare for imaging.  For FSC and H2B-mGFP screens, cells were then subjected to FACS sorting.   Cells before FACS (unsorted sample for FSC and H2B-mGFP screens) and top 10% cells based on either FSC signal (high FSC sample) or GFP fluorescence signal (high GFP sample) were separately collected and prepared for high throughput sequencing.  For mIFP proof-of-principle screen and nuclear size screen, cells were then seeded into 96-well glass bottom imaging dishes (Matriplate, Brooks) and imaged starting from the morning of the next day (around 15 hr after plating).  A series of densities ranging from 0.5E4 cells/well to 2.5E4 cells/well with 0.5E4 cells/well interval were selected and seeded.  The imaging dish with cells around 70% confluency was selected to be screened on the imaging day.  For mIFP proof-of-principle screen, a single imaging plate was performed for each replicate while 4 imaging plates per replicate were imaged for the nuclear size screen.  When executing multiple imaging runs, 2 consecutive runs could be imaged on the same day (day run and night run).  64 (8x8, day run) or 81 (9x9, night run) fields of view were selected for each imaging well and each field of view was subjected to an individual round of imaging directly followed by photo-activation.  Around 200-250 cells were present in each given field of view and 60% to 80% surface area of each well was covered.  Either mIFP positive cells or cells passing the nuclear size filter were identified and photo-activated automatically using the Auto-PhotoConverter µManager plugin.  The total time to perform imaging and photo-activation of a single 96-well imaging dish with around 1.5 million cells was around 8 hr.  The night run generally took longer, since more fields of view were included than in the day run.  Cells were then harvested by trypsinization and pooled into a single tube for isolation by FACS.  Sorting gates were pre-defined using samples with different photo-activation times (e.g. 0s, 200ms, 2s).  Sorted samples were used to prepare sequencing samples.

value: hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP infected with nuclear size sgRNA library

value: Control


title: 4cell_embryo11_4 [Tn101]

status: Public on Jan 12 2021

type: SRA

city: Beijing

first: Zhiqiang

last: Yan

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

library_source: genomic

data_processing:
library strategy: Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
Illumina CASAVA version 1.8 were used to the basecalling.
Trim Galore (v0.4.1) were used to remove the first 11 bases of each read. Adaptor sequences and low quality bases were also trimmed with the command ‘trim_galore --clip_R1 11 --quality 20 --phred33 --stringency 3 --gzip --length 30’. The paired-end reads were trimed as single-end reads.
Bismark (v0.18.2) were used to map the clean reads to mouse genome mm9 with single-end and non-directional module (parameters: bismark --bowtie2 --non_directional ).
After alignment, PCR duplicates were removed with the picard tools.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: 4-cell blastomere

extract_protocol:
After removing zona pellucida, blastomeres were washed with PBS three times. Each cell was piked into a 200ul PCR tube, and incubated in mild lysis buffer. After short spin, lysate supernatant was transferred to a new tube, and nucleus precipitates were used for library preparation.
GpC methylase reaction was first setup with the nucleus precipitates, followed by scBS-seq library preparation protocol with slightly modification.

tag: strain

tag: develomental stage

value: 4-cell embryo


title: ControlSampleForFSCAndH2BmGFPScreen_Rep1

country: USA

description: sgRNA pcr from genomic DNA

organism: Homo sapiens

tag: cell type

tag: cell line

tag: treatment


title: 4cell_embryo11_2 [Tn99]


title: 4cell_embryo11_1 [Tn98]


title: HA772: Adolescent single cell RNA sequencing material

city: Montreal

first: Jack

last: Antel

state: Quebec

address: 3801 Rue University

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
All preprocessing steps were performed using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Genome_build: GRCh38
Supplementary_files_format_and_content: Log base 2 transformed gene expression. Subsetted the OL-lineage fraction via clustering followed by validation with marker genes. First column = gene names

molecule: total RNA

source_name: Human brain tissue

growth_protocol: cells were sent for sequencing immediately ex-vivo

extract_protocol:
Single cells were obtained following mechanical and enzymatic (trypsin) dissociation as previously described (Cui et al. 2017) and an isotonic percoll gradient was used to remove myelin. The whole dissociated cell population was collected from the gradient (which sits between the myelin layer and the red blood cell layer), washed 3 times in PBS, and re-suspended at a concentration of 10^6 cells per ml.
Made using the GemCode Single-Cell Instrument (10x Genomics) and Single Cell 3' Library & Gel Bead Kit v2 and Chip Kit (10x Genomics)

tag: tissue

value: brain

tag: age

value: 13 years old


title: FSCScreen_Rep1

description: sgRNA pcr from genomic DNA

value: top 10 percentile of cells based on FSC signal sorted by FACS


title: HFA567: Fetal single cell RNA sequencing material

value: second trimester fetal


title: 4cell_embryo10_4 [Tn97]


title: H2BmGFPScreen_Rep2

description: sgRNA pcr from genomic DNA

value: top 10 percentile of cells based on GFP fluorescence sorted by FACS


title: FSCScreen_Rep2

description: sgRNA pcr from genomic DNA


title: Late4cell_embryo1_3 [Tn220]

source_name: Late 4-cell blastomere

value: Late 4-cell embryo


title: 16cell_embryo1_3 [Tn58]

source_name: 16-cell blastomere

value: 16-cell embryo


title: 4cell_embryo10_3 [Tn96]


title: 4cell_embryo10_2 [Tn95]


title: H2BmGFPScreen_Rep1

description: sgRNA pcr from genomic DNA


title: 4cell_embryo10_1 [Tn94]


title: 4cell_embryo12_1 [Tn102]


title: 4cell_embryo9_4 [Tn93]


title: 4cell_embryo9_3 [Tn92]


title: 4cell_embryo9_2 [Tn91]


title: NuclearSizeScreen_UnanalyzedSample_Rep2_Run2

description: sgRNA pcr from genomic DNA

value: Unanalyzed cells sorted by FACS


title: NuclearSizeScreen_UnanalyzedSample_Rep2_Run3

description: sgRNA pcr from genomic DNA


title: NuclearSizeScreen_PositivelySortedSample_Rep2_Run4

description: sgRNA pcr from genomic DNA

value: cells with nuclear size larger than 1,000 μm² identified and photo-activated by automatic microscopy and sorted by FACS


title: 4cell_embryo8_3 [Tn88]


title: NuclearSizeScreen_PositivelySortedSample_Rep2_Run3

description: sgRNA pcr from genomic DNA


title: 4cell_embryo8_4 [Tn89]


title: NuclearSizeScreen_PositivelySortedSample_Rep2_Run2

description: sgRNA pcr from genomic DNA


title: 4cell_embryo9_1 [Tn90]


title: 4cell_embryo7_4 [Tn85]


title: NuclearSizeScreen_PositivelySortedSample_Rep2_Run1

description: sgRNA pcr from genomic DNA


title: 4cell_embryo7_2 [Tn83]


title: NuclearSizeScreen_UnanalyzedSample_Rep1_Run3and4

description: sgRNA pcr from genomic DNA


title: 4cell_embryo7_1 [Tn82]


title: NuclearSizeScreen_UnanalyzedSample_Rep1_Run1and2

description: sgRNA pcr from genomic DNA


title: NuclearSizeScreen_PositivelySortedSample_Rep1_Run4

description: sgRNA pcr from genomic DNA


title: 4cell_embryo8_2 [Tn87]


title: 4cell_embryo6_4 [Tn47]


title: NuclearSizeScreen_PositivelySortedSample_Rep1_Run2

description: sgRNA pcr from genomic DNA


title: 16cell_embryo3_1 [Tn138]


title: NuclearSizeScreen_PositivelySortedSample_Rep1_Run1

description: sgRNA pcr from genomic DNA


title: NuclearSizeScreen_PositivelySortedSample_Rep1_Run3

description: sgRNA pcr from genomic DNA


title: 4cell_embryo6_2 [Tn45]


title: NuclearSizeScreen_UnanalyzedSample_Rep2_Run1

description: sgRNA pcr from genomic DNA


title: NuclearSizeScreen_UnanalyzedSample_Rep2_Run4

description: sgRNA pcr from genomic DNA


title: 4cell_embryo6_3 [Tn46]


title: mIFPScreen_UnanalyzedSample_Rep1

description: sgRNA pcr from genomic DNA

value: Mixed cells of hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP infected with control sgRNA library and hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP mIFP-NLS infected with mIFP sgRNA library


title: 4cell_embryo5_2 [Tn41]


title: 4cell_embryo5_1 [Tn40]


title: 4cell_embryo4_4 [Tn39]


title: mIFPScreen_SortedmIFPNegativeSample_Rep2

description: sgRNA pcr from genomic DNA

value: mIFP negative cells identified and photo-activated by automatic microscopy and sorted by FACS


title: mIFPScreen_SortedmIFPPositiveSample_Rep1

description: sgRNA pcr from genomic DNA

value: mIFP positive cells identified and photo-activated by automatic microscopy and sorted by FACS


title: 4cell_embryo4_3 [Tn38]


title: MPAT hiPSC-CM RNA

city: Augusta

first: Hongyan

last: Xu

state: GA

department: Population Health Sciences

institute: Augusta 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 GRCh38 whole genome using STAR 2.7 with default parameters
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: GRCh38
Supplementary_files_format_and_content: counts-D75.csv

source_name: Induced pluripotent stem cell derived cardiomyocytes

growth_protocol: Cells were induced into cardiomyocytes by modulating Wnt signaling, followed by lactate purification 20 days post induction.  Cells were then cultured until 75 days post induction, after which they were harvested for RNA extraction.

extract_protocol:
Total RNA was extracted using Trizol/chloroform extraction, using 273-400,000 cells per condition.  Total RNA was treated with DNAase I and recrystallized, followed by quality control analysis via Tapestation.
Library preparation was conducted by BGI.  mRNA was purified via oligo(dT) purification. First strand cDNA was synthesized using random hexamers, followed by second strand synthesis.  End repair was conducted, followed by 3’-adenylation, adapter ligation, PCR amplification, and circularization.

tag: enrichment

value: OligoDT-enriched mRNA

tag: culture time (post induction)

value: MF750 (reprogrammed male fibroblast)

value: hiPSC-CMs

tag: culture condition

value: MPAT


title: MM hiPSC-CM RNA

value: MM


title: 4cell_embryo4_2 [Tn37]

value: 4-cell embryo


title: GLUC hiPSC-CM RNA

value: GLUC


title: 4cell_embryo3_3 [Tn34]


title: 4cell_embryo4_1 [Tn36]


title: 4cell_embryo3_4 [Tn35]


title: Is1CRAC1: Nab3 CTRL_R1

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

description: strain expressing empty control

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor was clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (martin M. embnet.journal, 2011) and the resulting insert  quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
Genome_build: R64
Supplementary_files_format_and_content: Bigwig files providing coverage for all samples. All values are normalized to 10,000,000 reads.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae culture

growth_protocol: For all datasets, 2L of yeast cells expressing Nab3-HTP tag were grown at 30°C to OD600=0.6 in DO-Trp-Ura (drop out without tryptophan and uracil).

extract_protocol:
See Villa et al.  Cell Reports 32, 107942 (2020).
Library construction is described in Candelli et al., EMBO J, 2018 and in Villa et al.  Cell Reports 32, 107942 (2020)
See Villa et al.  Cell Reports 32, 107942 (2020) for details

treatment_protocol: Cells were crosslinked for 80 seconds using a W5 UV crosslinking unit (UVO3). Cells were broken and extracts were prepared as described in   Villa, T., Barucco, M., Martin-Niclos, M.-J., Jacquier, A. & Libri, D. Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Reports 32, 107942 (2020).

value: W303-derived strain

tag: genotype


title: Is2CRAC1: Nab3 CTRL_R2

description: strain expressing empty control


title: ICRAC2: Nab3 CTRL_R3

description: strain expressing empty control


title: 4cell_embryo3_2 [Tn33]


title: 4cell_embryo2_4 [Tn31]


title: mIFPScreen_UnanalyzedSample_Rep2

description: sgRNA pcr from genomic DNA


title: CUTCRAC2: Nab3 Decoy_R3

description: strain expressing circular RNA decoy


title: 4cell_embryo6_1 [Tn44]


title: CUTs2CRAC1: Nab3 Decoy_R2

description: strain expressing circular RNA decoy


title: mIFPScreen_SortedmIFPNegativeSample_Rep1

description: sgRNA pcr from genomic DNA


title: 4cell_embryo2_3 [Tn30]


title: CUTs1CRAC1: Nab3 Decoy_R1

description: strain expressing circular RNA decoy


title: 4cell_embryo1_4 [Tn27]


title: 4cell_embryo2_1 [Tn28]


title: 4cell_embryo1_3 [Tn26]


title: 4cell_embryo1_1 [Tn24]


title: MEL_LRS_induced_1_RSII

city: New Haven

first: Karla

middle: M.

last: Neugebauer

state: CT

address: 333 Cedar Street

department: Molecular Biophysics & Biochemistry

institute: Yale University

description: nascent RNA

data_processing:
For genome-wide LRS: Combined consensus sequence (CCS) reads were generated in FASTQ format, and Porechop was used to separate chimeric reads and trim external adapters with the SMRTer IIA sequences AAGCAGTGGTATCAACGCAGAGTAC and GTACTCTGCGTTGATACCACTGCTT with settings --extra_end_trim 0 --extra_middle_trim_good_side 0 --extra_middle_trim_bad_side 0 --min_split_read_size 100. Cutadapt was used to remove the unique 3′ end adapter on all reads in two rounds of filtering. First any reads with the adapter at the 3′ end were trimmer with settings -a CTGTAGGCACCATCAAT -e 0.1 -m 15 --untrimmed-output=untrimmed.fastq, and any reads which did not contain the full adapter were retained and their reverse complement was generated. Then, a second round of filtering with cutadapt using the settings -a CTGTAGGCACCATCAAT -e 0.1 -m 15 --discard-untrimmed was used to remove adapters from the reverse complement reads, and reads without the 3′ adapter were discarded. This ensures that each read contains a successfully ligated 3′ adapter which marks RNAPII position, and since sequencing occurs in both forward and reverse orientations randomly, it places all reads in the correct 5′ to 3′ orientation. Reads from the two adapter trimming steps were combined into a single file, then Prinseq-lite was used to remove PCR duplicates with settings -derep 1. Prinseq-lite was used again to trim 6 non-templated nucleotides added at the 5′ end by the strand-switching reverse transcriptase and the 5 nucleotides of the 3′ end adapter UMI with settings -trim_left 6 -trim_right 5. Reads were then mapped to the mm10 genome using minimap2 with settings -ax splice -uf -C5 --secondary=no, and the resulting SAM files were converted to BAM and BED files using samtools and bedtools. Reads overlapping the 7SK genomic region (chr9:78175302,78175633 in the mm10 genome) were filtered using samtools before all downstream analyses. Mapped reads in SAM format were filtered to remove reads that contained a polyA tail using a custom script (available at https://github.com/kirstenreimer/MEL_LRS). Briefly, mapped reads that had soft-clipped bases at the 3′ end were discarded if the soft-clipped region of the read contained 4 or more A’s and the fraction of A’s was greater than 0.9. Similarly, reads with soft-clipped bases at the 5′ end (resulting from minus strand reads) containing at least 4 T’s and having a fraction of T’s greater than 0.9 were discarded.
For HBB-targeted LRS: Porechop was used on raw FASTQ reads to remove external adapters and separate chimeric reads with the common forward sequence and the SMRTer IIA reverse sequence GACGTGTGCTCTTCCGATCT and GTACTCTGCGTTGATACCACTGCTT (as well as the reverse complement sequences) with settings --extra_end_trim 0 --extra_middle_trim_good_side 0 --extra_middle_trim_bad_side 0 --min_split_read_size 100 --middle_threshold 75. Reads were filtered and trimmed if they contained the 3′ end adapter as described above using the 3′ end adapter sequence plus the barcode sequence. Prinseq was used to demultiplex and trim reads as above, then cleaned FASTQ files were mapped to a custom annotation of the integrated HBB locus (available at https://github.com/kirstenreimer/MEL_LRS), which is based on the GLOBE vector (Miccio et al., 2008). Additional parameters were added to the above criteria for removing polyA-containing reads from targeted data mapped to the HBB locus based on empirical observation. Since the HBB locus is integrated randomly in the MEL genome, long readthrough transcripts that have coverage past the annotated HBB locus read into random genomic regions and cause long stretches of mismatched soft-clipped bases. A custom script was used to filter polyA-containing reads, but retain readthrough transcripts (available at https://github.com/kirstenreimer/MEL_LRS). Briefly, reads were discarded if: they contained a fraction of A’s or T’s greater than 0.7 in the soft-clipped region that starts past the end of the HBB locus annotation; they contained a fraction of A’s or T’s greater than 0.7 and 4 or more A’s or T’s in the soft-clipped region starting within 50 nucleotides of the annotated polyA site; they contained a stretch of soft-clipped reads greater than 20 nucleotides that starts within the annotated HBB gene.
For PRO-seq: Cutadapt was used to trim paired-end reads to 40 nt, removing adapter sequence and low quality 3′ ends, and discarding reads that were shorter than 20 nucleotides (-m20 -q 1). Additionally, in order to align reads using Bowtie, one nucleotide was removed from the 3′ end of all trimmed reads. Trimmed paired-end reads were first mapped to the dm3 reference genome using Bowtie,  and subsequent uniquely mapped reads to the dm3 genome were used to determine percent spike-in return across all samples. Paired-end reads that failed to align to the dm3 genome were mapped to the mm10 reference genome. Read alignment to the dm3 and mm10 genomes were performed with settings - k1 -v2 –best -X1000 --un. SAM files were sorted using samtools. Read pairs uniquely aligned to the mm10 genome were separated, and strand-specific single nucleotide bedGraphs of the 3′ end mapping positions, corresponding to the biotinylated RNA 3′ end, were generated. Due to the “forward/reverse” orientation of Illuminia paired-end sequencing, “+” and “-“ stranded bedGraph files were switched at the end of the pipeline (Mahat et al., 2016). bedGraph files across replicates in each cell treatment were merged by summing the read counts per nucleotide position.
Genome_build: mm10 or custom HBB locus
Supplementary_files_format_and_content: [bedGraph files]: PROseq reads mapped to the mm10 genome containing combined counts of end 1 3' mapping locations for all replicates in a given induction condition.
Supplementary_files_format_and_content: [coSE_values_per_intron.txt]: coSE values in uninduced and induced conditions for introns in the mm10 genome which have coverage of at least 10 reads (spliced + unspliced).
Supplementary_files_format_and_content: [NIC_and_SSscore_per_intron.txt] NIC values and intron length, GC content, and splice site sequences for introns in the mm10 genome which have coverage of at least 10 reads (spliced + intermediates).

source_name: MEL cells

growth_protocol: Murine Erythroleukemia cells (MEL) were maintained at 37°C and 5% CO2 in DMEM + Glutamax medium (GIBCO) containing 100 U/ml penicillin, 100 μg/ml streptomycin (GIBCO), and 10% fetal bovine serum (GIBCO).

extract_protocol:
Cells were fractionated according to the protocol published in (Pandya-Jones and Black, 2009), with modifications to centrifugation speeds in order to retain intact nuclei. All steps were performed on ice, and all buffers contained 25 uM α-amanitin, 40 U/ml SUPERase.IN, and 1x Roche cOmplete protease inhibitor mix. Briefly, 20 million cells were rinsed once with PBS/1 mM EDTA, then lysed in 250 μl cytoplasmic lysis buffer (10 mM Tris-HCl pH 7.5, 0.05% NP40, 150 mM NaCl) by gently resuspending then incubating on ice for 5 minutes. Lysate was then layered on top of a 500 μl cushion of 24% sucrose in cytoplasmic lysis buffer and spun at 2000 rpm for 10 min at 4°C. The supernatant (cytoplasm fraction) was removed, and the pellet (nuclei) were rinsed once with 500 μl PBS/1 mM EDTA. Nuclei were resuspended in 100 μl nuclear resuspension buffer (20 mM Tris-HCl pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 50% glycerol) by gentle flicking, then lysed by the addition of 100 μl nuclear lysis buffer (20 mM HEPES pH 7.5, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M Urea, 1% NP-40), vortexed for 2 x 2 seconds, then incubated on ice for 3 min. Chromatin was pelleted by spinning at 14,000 rpm for 2 min at 4°C. The supernatant (nucleoplasm fraction) was removed, and the chromatin was rinsed once with PBS/1 mM EDTA. Chromatin was immediately dissolved in 100 μl PBS and 300 μl TRIzol Reagent (ThermoFisher). RNA was purified from chromatin pellets in TRIzol Reagent (ThermoFisher) using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol, including the on-column DNase I digestion. Samples were depleted three times of polyA(+) RNA using the Dynabeads mRNA DIRECT Micro Purification Kit (ThermoFisher), each time keeping the supernatant, then depleted of ribosomal RNA using the Ribo-Zero Gold rRNA Removal Kit (Illumina).
A DNA adapter (/5rApp/NNNNNCTGTAGGCACCATCAAT/3ddC/) was ligated to 3′ ends of nascent RNA using the T4 RNA ligase kit (NEB) by mixing 50 pmol adapter with 300-600 ng nascent RNA. cDNA was generated from the adapter ligated RNA using the SMARTer PCR cDNA Synthesis Kit (Clontech), replacing the CDS Primer IIA with a custom primer complementary to the 3′ end adapter for first strand synthesis (AAGCAGTGGTATCAACGCAGAGTACATTGATGGTGCCTACAG). cDNA was amplified by 15 cycles of PCR using the Advantage 2 PCR Kit (Clontech), cleaned up using a 1x volume of AMPure beads (Agencourt), then PacBio library preparation was performed by the Yale Center for Genome Analysis using the SMRTbell Template Prep Kit 1.0 (Pacific Biosciences).

treatment_protocol: To induce erythroid differentiation, MEL cells were diluted to 50,000 cells/ml in 10 ml fresh culture medium and incubated in growth conditions for 16 hours. DMSO was then added directly to the culture medium to a final concentration of 2% and incubated in growth conditions for 5 days.

value: Murine Erythroleukemia cells (MEL)

tag: erythroid induction

value: 2% DMSO 5 days

tag: purification

value: chromatin fractionation, ribosomal depletion, polyA+ depletion

value: wild type


title: MEL_LRS_uninduced_2_RSII

description: nascent RNA


title: MEL_LRS_uninduced_1_RSII

description: nascent RNA


title: num_4_subpop_4

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Adaptor removal and quality trimming done with Trimmomatic v 0.36
Read alingment and gene counts was performed with RSEM v 1.2.31 and STAR v 2.5.2a
Differential expression analysis was carried out with DESeq2 package ( version 1.20.0 ) with R version 3.5.1
Genome_build: Ensembl GRCm38 release 89
Supplementary_files_format_and_content: Tab-delimited text include normalized counts per gene and per sample (generated by DESeq2).

source_name: Spleen

extract_protocol:
Spleens were crushed and filtered with a 70µM mesh strainer. Harvested splenic B-cells were enriched by CD43 negative selection using MACS LS Columns (Miltenyi Biotec). Single-cell suspensions were stained with antibodies and sorted by flow cytometry. RNA was extracted from the sorted samples by RNAeasy Micro Kit (#74004, QIAGEN, for cMyc+ GC-B cells).
Libraries were prepared with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®

treatment_protocol: 6-15 week old male and female mice were intraperitoneally immunized with 2x10^8 SRBC. Splenocytes from these mice were sorted by flow-cytometry after 7 days.

value: cMyc+ GC-B cell subpopulation_cMyc+ lateCD23lo

value: Spleen

value: 7 days after immunization with SRBC

tag: markers

value: B220+ CD38low CD95+ cMycGFP+ CD23lo CD21/35lo cells


title: 2cell_embryo11_2 [Tn79]

source_name: 2-cell blastomere

value: 2-cell embryo


title: 2cell_embryo12_1 [Tn80]


title: 4cell_embryo3_1 [Tn32]


title: 2cell_embryo12_2 [Tn81]


title: num_4_subpop_3

value: cMyc+ GC-B cell subpopulation_cMyc+ lateCD23int

value: B220+ CD38low CD95+ cMycGFP+ CD23int CD21/35int cells


title: num_4_subpop_2

value: cMyc+ GC-B cell subpopulation_cMyc+ early

value: B220+ CD38low CD95+ cMycGFP+ CD23hi CD21/35hi cells


title: 2cell_embryo11_1 [Tn78]


title: mIFPScreen_SortedmIFPPositiveSample_Rep2

description: sgRNA pcr from genomic DNA

value: Mixed cells of hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP infected with control sgRNA library and hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP mIFP-NLS infected with mIFP sgRNA library

value: mIFP positive cells identified and photo-activated by automatic microscopy and sorted by FACS


title: num_4_subpop_1

value: cMyc+ GC-B cell subpopulation_cMyc+ prePB

value: B220+ CD38low CD95+ cMycGFP+ CD69hi cells


title: 2cell_embryo9_1 [Tn74]


title: num_3_subpop_4


title: num_3_subpop_1


title: 2cell_embryo10_1 [Tn76]


title: 2cell_embryo8_2 [Tn73]


title: num_3_subpop_2


title: 4cell_embryo2_2 [Tn29]

value: 4-cell embryo


title: num_3_subpop_3


title: 2cell_embryo7_2 [Tn71]


title: num_2_subpop_4


title: MEL_LRS_induced_2_RSII

description: nascent RNA

value: Murine Erythroleukemia cells (MEL)

value: 2% DMSO 5 days


title: 4cell_embryo1_2 [Tn25]


title: 2cell_embryo6_2 [Tn23]


title: num_2_subpop_3


title: num_2_subpop_2


title: num_2_subpop_1


title: 2cell_embryo5_1 [Tn20]


title: 2cell_embryo6_1 [Tn22]


title: 2cell_embryo5_2 [Tn21]


title: num_1_subpop_3


title: 2cell_embryo4_2 [Tn19]


title: 2cell_embryo3_1 [Tn16]


title: num_1_subpop_1


title: cMyc+ GC-B CELL_FL140316_DC2_H05

data_processing:
Expression data were filtered (genes expressed in ≥10% of read sets), normalized using the ERCC spike-in reads (R package scran), and assessed with an in-house pipeline (CellStrainer) for a variety of metrics: number of reads, percent duplication (as measured by picard-tools), ratio of spike-in to gene reads, number of features as a factor of number of reads mapped, Spearman's correlation to the mean, number of features lowly expressed (<10% percentile) as a factor of the number of features detected, number of features highly expressed (≥90% percentile) as a factor of the number of features detected, per-feature variance from the mean, proportion of reads mapping to cytoplasmic genes (GO0005737), and proportion of reads mapping to mitochonrial genes.
CellStrainer uses these technical metrics to fit a one-class support vector machine (SVM) to the dataset. 1000 models were built with a random 10% of the libraries and the entire dataset repeatedly qualified as inlier or outlier for a majority vote decision on whether captures represented valid (live) cells
Genome_build: mouse GRCm38.78
Supplementary_files_format_and_content: Raw counts. Rows represent Ensembl mouse genes and columns represent individual samples.

source_name: cMyc+ GC-B CELL

extract_protocol:
Spleens were crushed and filtered with a 70µM mesh strainer. Harvested splenic B-cells were enriched by CD43 negative selection using MACS LS Columns (Miltenyi Biotec). Single-cell suspensions were stained with antibodies and sorted by flow cytometry. The Fluidigm C1 automated microfluidic system was used to randomly capture 96 individual cells onto the 5–10 μm C1 IFCs (Fluidigm) for mRNA-seq. The SMARTer Ultra Low Input RNA kit for Sequencing (Takara Bio) was used to reverse transcribe poly(A) RNA and amplify cDNA.
Amplified cDNA at a concentration of 0.10–0.3 ng/μL was used for preparing libraries with the Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: 6-15 week old male and female mice were intraperitoneally immunized with 100 µg NP-CGG in Alum and 10 days later splenocytes were sorted by flow-cytometry.

value: Ten days after immunization with NP-CGG

value: B220+ CD19+ CD38low CD95+ cells


title: 2cell_embryo1_2 [Tn13]


title: 2cell_embryo1_1 [Tn12]


title: cMyc+ GC-B CELL_FL140316_DC2_G12

value: Spleen


title: Zygote13 [Tn69]

source_name: Zygote

value: zygote


title: cMyc+ GC-B CELL_FL140316_DC2_G06


title: Zygote11 [Tn67]


title: 2cell_embryo7_1 [Tn70]


title: Zygote12 [Tn68]


title: num_1_subpop_4

value: cMyc+ GC-B cell subpopulation_cMyc+ lateCD23lo

value: 7 days after immunization with SRBC

value: B220+ CD38low CD95+ cMycGFP+ CD23lo CD21/35lo cells


title: 2cell_embryo2_2 [Tn15]

value: 2-cell embryo


title: 4cell_embryo7_3 [Tn84]


title: cMyc+ GC-B CELL_FL140316_DC2_G02


title: cMyc+ GC-B CELL_FL140316_DC2_G03


title: cMyc+ GC-B CELL_FL140316_DC2_F02


title: Zygote9 [Tn65]


title: num_1_subpop_2

value: cMyc+ GC-B cell subpopulation_cMyc+ early


title: cMyc+ GC-B CELL_FL140316_DC2_F10


title: Zygote6 [Tn6]


title: Zygote7 [Tn7]


title: cMyc+ GC-B CELL_FL140316_DC2_D02


title: cMyc+ GC-B CELL_FL140316_DC2_B07


title: cMyc+ GC-B CELL_FL140316_DC2_E01


title: cMyc+ GC-B CELL_FL140316_DC2_C12


title: Zygote3 [Tn3]


title: Zygote5 [Tn5]


title: cMyc+ GC-B CELL_FL140316_DC2_A09


title: Zygote2 [Tn2]


title: Zygote1 [Tn1]


title: cMyc+ GC-B CELL_FL140316_DC1_H12


title: cMyc+ GC-B CELL_FL140316_DC1_H10


title: 32cell_embryoMixed_23 [Tr439]

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The raw reads were trimed using trim_galore (parameter: trim_galore --paired --quality 20 --phred33 --stringency 3 --gzip --length 36)
The clean reads were mapped to mouse genome (GENCODE NCBIM37) using STAR with default parameter.
The reads of each gene were counted by featureCounts.
TPM value were calculated by in house script.
Genome_build: GENCODE NCBIM37
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample

source_name: 32-cell blastomere

extract_protocol:
After removing zona pellucida, blastomeres were washed with PBS three times. Each cell was piked into a 200ul PCR tube, and incubated in mild lysis buffer. After short spin, lysate supernatant was transferred to a new tube.
RNA-Seq libraries were prepared using MATQ-seq protocol with slightly modification

value: 32-cell embryo


title: 32cell_embryoMixed_22 [Tr438]


title: cMyc+ GC-B CELL_FL140316_DC1_H06


title: cMyc+ GC-B CELL_FL140316_DC1_G08


title: 32cell_embryoMixed_24 [Tr440]


title: cMyc+ GC-B CELL_FL140316_DC1_H05


title: 32cell_embryoMixed_21 [Tr437]


title: cMyc+ GC-B CELL_FL140316_DC1_G06


title: 32cell_embryoMixed_19 [Tr435]


title: Zygote8 [Tn64]


title: cMyc+ GC-B CELL_FL140316_DC1_G04


title: 32cell_embryoMixed_20 [Tr436]


title: cMyc+ GC-B CELL_FL140316_DC1_F11


title: 32cell_embryoMixed_18 [Tr434]


title: 32cell_embryoMixed_17 [Tr433]


title: cMyc+ GC-B CELL_FL140316_DC1_F08


title: 32cell_embryoMixed_15 [Tr430]


title: cMyc+ GC-B CELL_FL140316_DC2_A03


title: 32cell_embryoMixed_13 [Tr428]


title: cMyc+ GC-B CELL_FL140316_DC1_F04


title: cMyc+ GC-B CELL_FL140316_DC1_F05


title: 32cell_embryoMixed_16 [Tr431]


title: cMyc+ GC-B CELL_FL140316_DC1_F01


title: cMyc+ GC-B CELL_FL140316_DC1_F03


title: 32cell_embryoMixed_12 [Tr427]


title: cMyc+ GC-B CELL_FL140316_DC1_E10


title: 32cell_embryoMixed_11 [Tr426]


title: cMyc+ GC-B CELL_FL140316_DC1_E04


title: 32cell_embryoMixed_8 [Tr422]


title: 32cell_embryoMixed_10 [Tr425]


title: 2cell_embryo9_2 [Tn75]


title: cMyc+ GC-B CELL_FL140316_DC1_C12


title: 32cell_embryoMixed_6 [Tr420]


title: 32cell_embryoMixed_7 [Tr421]


title: cMyc+ GC-B CELL_FL140316_DC1_C06


title: cMyc+ GC-B CELL_FL140316_DC1_B05


title: 32cell_embryoMixed_5 [Tr419]


title: 32cell_embryoMixed_14 [Tr429]


title: cMyc+ GC-B CELL_FL140316_DC1_A12


title: cMyc+ GC-B CELL_FL140316_DC1_A05


title: cMyc+ GC-B CELL_FL150216_DC2_H04


title: 32cell_embryoMixed_3 [Tr417]


title: 32cell_embryoMixed_2 [Tr416]


title: cMyc+ GC-B CELL_FL140316_DC1_F10


title: cMyc+ GC-B CELL_FL150216_DC2_G06


title: cMyc+ GC-B CELL_FL150216_DC2_G05


title: cMyc+ GC-B CELL_FL150216_DC2_F10


title: 32cell_embryo6_8 [Tr449]


title: 32cell_embryo6_7 [Tr448]


title: 32cell_embryoMixed_9 [Tr423]


title: 32cell_embryo6_6 [Tr447]


title: cMyc+ GC-B CELL_FL150216_DC2_G04


title: 32cell_embryo6_5 [Tr446]


title: 32cell_embryoMixed_1 [Tr415]


title: cMyc+ GC-B CELL_FL140316_DC1_D06


title: 32cell_embryo6_4 [Tr445]


title: 32cell_embryo6_3 [Tr444]


title: 32cell_embryo6_2 [Tr443]


title: cMyc+ GC-B CELL_FL150216_DC2_D10


title: cMyc+ GC-B CELL_FL150216_DC2_B10


title: cMyc+ GC-B CELL_FL150216_DC2_D11


title: cMyc+ GC-B CELL_FL150216_DC2_F09


title: 32cell_embryo6_1 [Tr442]


title: 32cell_embryoMixed_4 [Tr418]


title: 32cell_embryo5_5 [Tr414]


title: cMyc+ GC-B CELL_FL150216_DC2_B07


title: 32cell_embryo5_4 [Tr413]


title: cMyc+ GC-B CELL_FL150216_DC2_B02


title: cMyc+ GC-B CELL_FL150216_DC1_H12


title: 32cell_embryo5_3 [Tr412]


title: cMyc+ GC-B CELL_FL150216_DC1_H06


title: 32cell_embryo4_5 [Tr409]


title: 32cell_embryo4_4 [Tr408]


title: cMyc+ GC-B CELL_FL150216_DC1_G10


title: cMyc+ GC-B CELL_FL150216_DC1_G05


title: 32cell_embryo4_3 [Tr407]


title: cMyc+ GC-B CELL_FL150216_DC2_F07


title: cMyc+ GC-B CELL_FL150216_DC1_F03


title: 32cell_embryo4_2 [Tr406]


title: 32cell_embryo4_1 [Tr405]


title: cMyc+ GC-B CELL_FL150216_DC1_F02


title: cMyc+ GC-B CELL_FL150216_DC1_F01


title: cMyc+ GC-B CELL_FL150216_DC1_E08


title: 32cell_embryo3_4_split1 [Tr335]


title: cMyc+ GC-B CELL_FL150216_DC1_D11


title: cMyc+ GC-B CELL_FL150216_DC1_E01


title: Zygote10 [Tn66]


title: cMyc+ GC-B CELL_FL150216_DC1_C11


title: cMyc+ GC-B CELL_FL150216_DC1_D02


title: 32cell_embryo2_10_split1 [Tr325]


title: cMyc+ GC-B CELL_FL150216_DC1_C10


title: 32cell_embryo2_9_split1 [Tr323]


title: 32cell_embryo2_9_split2 [Tr324]


title: 32cell_embryo2_8_split2 [Tr322]


title: 32cell_embryo2_8_split1 [Tr321]


title: cMyc+ GC-B CELL_FL150216_DC1_C03


title: cMyc+ GC-B CELL_FL150216_DC1_C02


title: 32cell_embryo2_7_split2 [Tr320]


title: 32cell_embryo2_7_split1 [Tr319]


title: 32cell_embryo3_4_split2 [Tr336]


title: 32cell_embryo2_5_split1 [Tr315]


title: cMyc+ GC-B CELL_FL150216_DC1_B08


title: cMyc+ GC-B CELL_FL150216_DC1_B12


title: cMyc+ GC-B CELL_FL150216_DC1_A01


title: cMyc+ GC-B CELL_FL150216_DC1_B05


title: 32cell_embryo2_4_split2 [Tr314]


title: cMyc+ GC-B CELL_FL110216_DC2_H12


title: cMyc+ GC-B CELL_FL150216_DC1_C08


title: 32cell_embryo2_4_split1 [Tr313]


title: cMyc+ GC-B CELL_FL150216_DC1_A02


title: 32cell_embryo2_10_split2 [Tr326]


title: 32cell_embryo2_1_split2 [Tr308]


title: cMyc+ GC-B CELL_FL110216_DC2_H06


title: 32cell_embryo1_8_split2 [Tr306]


title: cMyc+ GC-B CELL_FL110216_DC2_H03


title: 32cell_embryo1_8_split1 [Tr305]


title: cMyc+ GC-B CELL_FL110216_DC2_G10


title: cMyc+ GC-B CELL_FL110216_DC2_G09


title: 32cell_embryo1_7_split2 [Tr304]


title: 32cell_embryo2_1_split1 [Tr307]


title: 32cell_embryo1_7_split1 [Tr303]


title: cMyc+ GC-B CELL_FL110216_DC2_G08


title: cMyc+ GC-B CELL_FL110216_DC2_G05


title: 32cell_embryo3_2_split2 [Tr332]


title: cMyc+ GC-B CELL_FL110216_DC2_G03


title: 32cell_embryo1_6_split1 [Tr301]


title: 32cell_embryo1_6_split2 [Tr302]


title: 32cell_embryo2_5_split2 [Tr316]


title: 32cell_embryo1_5_split2 [Tr300]


title: cMyc+ GC-B CELL_FL110216_DC2_E07


title: 32cell_embryo1_3_split2 [Tr296]


title: 32cell_embryo1_4_split1 [Tr297]


title: cMyc+ GC-B CELL_FL110216_DC2_D03


title: cMyc+ GC-B CELL_FL110216_DC2_D06


title: 32cell_embryo1_3_split1 [Tr295]


title: cMyc+ GC-B CELL_FL110216_DC2_G02


title: cMyc+ GC-B CELL_FL110216_DC2_D10


title: cMyc+ GC-B CELL_FL110216_DC2_C06


title: cMyc+ GC-B CELL_FL110216_DC2_D11


title: 32cell_embryo1_5_split1 [Tr299]


title: cMyc+ GC-B CELL_FL110216_DC2_C05


title: 32cell_embryo1_1_split1 [Tr291]


title: cMyc+ GC-B CELL_FL110216_DC2_C11


title: 32cell_embryo1_2_split1 [Tr293]


title: 32cell_embryo1_4_split2 [Tr298]


title: 16cell_embryo3_8_split1 [Tr289]

value: 16-cell embryo


title: 16cell_embryo3_7_split2 [Tr288]


title: cMyc+ GC-B CELL_FL110216_DC2_B06


title: cMyc+ GC-B CELL_FL110216_DC2_B02


title: cMyc+ GC-B CELL_FL110216_DC2_E12


title: 16cell_embryo3_7_split1 [Tr287]


title: cMyc+ GC-B CELL_FL110216_DC2_A12


title: cMyc+ GC-B CELL_FL110216_DC2_A09


title: 16cell_embryo3_5_split2 [Tr284]


title: cMyc+ GC-B CELL_FL110216_DC2_A02


title: 16cell_embryo3_5_split1 [Tr283]


title: cMyc+ GC-B CELL_FL110216_DC1_H12


title: 16cell_embryo3_4_split2 [Tr282]


title: cMyc+ GC-B CELL_FL110216_DC1_H08


title: 32cell_embryo1_2_split2 [Tr294]


title: 16cell_embryo3_3_split2 [Tr280]


title: cMyc+ GC-B CELL_FL110216_DC2_C12


title: cMyc+ GC-B CELL_FL110216_DC1_H07


title: 16cell_embryo3_4_split1 [Tr281]


title: cMyc+ GC-B CELL_FL110216_DC1_H05


title: 16cell_embryo3_2_split2 [Tr278]


title: 16cell_embryo3_2_split1 [Tr277]


title: cMyc+ GC-B CELL_FL110216_DC1_F08


title: cMyc+ GC-B CELL_FL110216_DC2_A11


title: 16cell_embryo2_8_split2 [Tr274]


title: cMyc+ GC-B CELL_FL110216_DC1_F10


title: cMyc+ GC-B CELL_FL110216_DC1_E08


title: cMyc+ GC-B CELL_FL110216_DC1_F05


title: cMyc+ GC-B CELL_FL110216_DC1_E09


title: cMyc+ GC-B CELL_FL110216_DC2_A05


title: 16cell_embryo3_6_split1 [Tr285]


title: 16cell_embryo3_1_split2 [Tr276]


title: 16cell_embryo2_7_split2 [Tr272]


title: cMyc+ GC-B CELL_FL110216_DC1_D10


title: cMyc+ GC-B CELL_FL110216_DC1_D05


title: 16cell_embryo3_3_split1 [Tr279]


title: 16cell_embryo2_7_split1 [Tr271]


title: cMyc+ GC-B CELL_FL110216_DC1_E01


title: cMyc+ GC-B CELL_FL110216_DC1_D04


title: 16cell_embryo2_5_split1 [Tr267]


title: 16cell_embryo2_6_split2 [Tr270]


title: cMyc+ GC-B CELL_FL110216_DC1_G05


title: 16cell_embryo3_8_split2 [Tr290]


title: 16cell_embryo2_5_split2 [Tr268]


title: cMyc+ GC-B CELL_FL110216_DC1_C06


title: 16cell_embryo2_4_split2 [Tr266]


title: cMyc+ GC-B CELL_FL110216_DC1_B09


title: 16cell_embryo2_6_split1 [Tr269]


title: cMyc+ GC-B CELL_FL110216_DC1_B05


title: 16cell_embryo3_1_split1 [Tr275]


title: 16cell_embryo2_3_split2 [Tr264]


title: 16cell_embryo2_8_split1 [Tr273]


title: cMyc+ GC-B CELL_FL110216_DC1_A10


title: 16cell_embryo2_4_split1 [Tr265]


title: 16cell_embryo2_2_split2 [Tr262]


title: 16cell_embryo2_2_split1 [Tr261]


title: 16cell_embryo2_3_split1 [Tr263]


title: cMyc+ GC-B CELL_FL110216_DC1_C04


title: 16cell_embryo2_1_split2 [Tr260]


title: 16cell_embryo2_1_split1 [Tr259]


title: Rel1-H07

city: Vladivostok

first: Valeriia

last: Gulaia

address: 10 Ajax Bay

department: School of Biomedicine

country: Russia

institute: Far Eastern Federal University

data_processing:
quality control with FastQC (version 0.11.9)
trimming Nextera sequencing adapters with Trim Galore (parameter “--nextera”)
mapping to GRCh38.p12 human reference genome using STAR-2.6.0c
exclusion of cells expressing 0 genes
normal cells exclusion on the basis of particular cell markers: all hematopoietic cell - CD45 (PTPRC); naïve CD4+ T cells – IL7R, CCR7;  memory CD4+ cells – S100A4; monocytes – CD14, LYZ, FCGR3A, MS4A7; B-cells – MS4A1 (CD20); CD8+ T cells – CD8A; NK-cells – GNLY (NKG5), NKG7; dendritic cells – FCER1A, GST3; platelet – PPBP; stromal cells – CD34; endothelial cells – PECAM1 (CD31)
analysis of copy number variations (CNVs) using CaSpER
cell cycle classification performed by Cyclone
population analysis performed by SingleCellExperiment, Seurat, and Scanpy
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: loom data file containing population analysis from Seurat

molecule: polyA RNA

source_name: SOX2+ glioma nucleus

extract_protocol:
Frozen tumor tissue of approximate size 0.2-0.5 cm3 was placed in cold tissue lysis buffer (5M NaCl, 1M MgCl2, 1M Tris buffer (pH 8.0), 10% NP40 (Sigma, USA), 1uM DTT (Invitrogen), 1x Complete protease inhibitor (Roche), 0.4 U/ul RNAseIn (Takara Bio, Japan), 0.2 U/ul SuperaseIn  (ThermoFisher Scientific) and incubated on ice for 15 min with gentle swirling every 2-3 minutes. Then the tissue was triturated, filtered through 40um cell strainer and centrifuged at 1000g for 5 min at 4°C. The sedimented nuclei were resuspended in cold staining buffer (RNAse-free PBS pH 7.4, 1% BSA, RNAseIn, 1M MgCl2, 1mM DTT) and stained with anti-Sox2 antibody (Invitrogen) or respective IgG isotype control (BD), Alexa Fluor 488 Goat anti-Rabbit IgG antibody (Invitrogen) was used as secondary. Nuclei were visualized with 7-AAD (Sigma) staining. Thereafter, Sox2 positive nuclei were sorted a FACS Aria I or III at 4°C in skirted 96-well PCR plates containing 2 ul cell lysis buffer (2U/ul RNAseIn in 0,2% (vol/vol) Triton X-100 (Sigma)). After sorting plates were immediately sealed and placed on dry ice.
The library preparation was done using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer instructions, the Illumina Nextera Adapters (sequences provided on http://ngs.biodiv.tw/NGSCore/wp-content/uploads/Documents/illumina-adapter-sequences-1000000002694-08.pdf) were synthetized and HPLC purified in Biomers (http://www.biomers.net/).
single cell RNA-seq

value: patient derived glioma tissue

tag: sample name


title: Rel1-H10


title: Rel1-H09


title: Rel1-H11


title: Rel1-H12


title: Rel1-H08


title: 16cell_embryo1_7_split2 [Tr124]


title: Rel1-H05


title: 16cell_embryo1_8_split1 [Tr125]


title: Rel1-H03


title: Rel1-H01


title: 16cell_embryo1_7_split1 [Tr123]


title: 16cell_embryo1_6_split2 [Tr122]


title: 16cell_embryo1_6_split1 [Tr121]


title: Rel1-G12


title: Rel1-G10


title: Rel1-G11


title: Rel1-G09


title: 16cell_embryo1_5_split2 [Tr120]


title: Rel1-G08


title: 16cell_embryo1_4_split2 [Tr118]


title: 16cell_embryo1_4_split1 [Tr117]


title: 16cell_embryo1_8_split2 [Tr126]


title: Rel1-G07


title: 16cell_embryo1_3_split2 [Tr116]


title: Rel1-G06


title: Rel1-G03


title: 16cell_embryo1_3_split1 [Tr115]


title: 16cell_embryo1_2_split2 [Tr114]


title: Rel1-G04


title: 8cell_embryo4_8_split1 [Tr257]

source_name: 8-cell blastomere

value: 8-cell embryo


title: 16cell_embryo1_1_split2 [Tr112]


title: Rel1-G02


title: Rel1-F12


title: 8cell_embryo4_6_split2 [Tr254]


title: 8cell_embryo4_7_split2 [Tr256]


title: Rel1-F10


title: Rel1-F11


title: 16cell_embryo1_5_split1 [Tr119]


title: Rel1-F08


title: 8cell_embryo4_8_split2 [Tr258]


title: 8cell_embryo4_6_split1 [Tr253]


title: Rel1-G05


title: 8cell_embryo4_5_split2 [Tr252]


title: 8cell_embryo4_7_split1 [Tr255]


title: Rel1-F09


title: 8cell_embryo4_5_split1 [Tr251]


title: 16cell_embryo1_2_split1 [Tr113]


title: Rel1-G01


title: Rel1-F03


title: Rel1-F04


title: 16cell_embryo1_1_split1 [Tr111]


title: 8cell_embryo4_4_split1 [Tr249]


title: 8cell_embryo4_4_split2 [Tr250]


title: 32cell_embryo1_1_split2 [Tr292]


title: 8cell_embryo4_3_split2 [Tr248]


title: Rel1-F01


title: 8cell_embryo4_3_split1 [Tr247]


title: 8cell_embryo4_2_split2 [Tr246]


title: 8cell_embryo4_2_split1 [Tr245]


title: 8cell_embryo4_1_split2 [Tr244]


title: 8cell_embryo4_1_split1 [Tr243]


title: Rel1-E08


title: Rel1-F05


title: Rel1-F07


title: Rel1-E09


title: Rel1-E10


title: 8cell_embryo3_8_split2 [Tr242]


title: Rel1-E07


title: Rel1-E06


title: 8cell_embryo3_8_split1 [Tr241]


title: 8cell_embryo3_7_split2 [Tr240]


title: Rel1-F02


title: 8cell_embryo3_7_split1 [Tr239]


title: 8cell_embryo3_6_split1 [Tr237]


title: Rel1-E04


title: Rel1-E05


title: Rel1-E02


title: Rel1-E03


title: Rel1-E01


title: 8cell_embryo3_6_split2 [Tr238]


title: 8cell_embryo3_5_split1 [Tr235]


title: Rel1-E11


title: 8cell_embryo3_4_split2 [Tr234]


title: Rel1-D12


title: Rel1-D10


title: Rel1-D09


title: 8cell_embryo3_3_split1 [Tr231]


title: 8cell_embryo3_3_split2 [Tr232]


title: Rel1-D11


title: Rel1-D08


title: 8cell_embryo3_2_split2 [Tr230]


title: Rel1-D07


title: 8cell_embryo3_2_split1 [Tr229]


title: 8cell_embryo3_4_split1 [Tr233]


title: Rel1-D06


title: Rel1-D05


title: Rel1-D04


title: 8cell_embryo3_5_split2 [Tr236]


title: 8cell_embryo2_8_split2 [Tr226]


title: 8cell_embryo3_1_split2 [Tr228]


title: 8cell_embryo3_1_split1 [Tr227]


title: Rel1-D03


title: 8cell_embryo2_7_split1 [Tr223]


title: 8cell_embryo2_8_split1 [Tr225]


title: 8cell_embryo2_7_split2 [Tr224]


title: Rel1-D02


title: 8cell_embryo2_6_split1 [Tr221]


title: Rel1-D01


title: Rel1-C11


title: Rel1-C12


title: 8cell_embryo2_5_split2 [Tr220]


title: 8cell_embryo2_6_split2 [Tr222]


title: 8cell_embryo2_5_split1 [Tr219]


title: 8cell_embryo2_4_split2 [Tr218]


title: Rel1-C08


title: 8cell_embryo2_4_split1 [Tr217]


title: Rel1-C07


title: 8cell_embryo2_3_split2 [Tr216]


title: Rel1-C06


title: Rel1-C05


title: 8cell_embryo2_2_split2 [Tr214]


title: Rel1-C04


title: Rel1-C02


title: 8cell_embryo2_1_split2 [Tr212]


title: Rel1-C01


title: 8cell_embryo2_1_split1 [Tr211]


title: Rel1-B12


title: 8cell_embryo1_8_split2 [Tr110]


title: 16cell_embryo3_6_split2 [Tr286]


title: Rel1-C09


title: Rel1-C10


title: Rel1-B11


title: Rel1-B10


title: 8cell_embryo1_7_split2 [Tr108]


title: Rel1-B09


title: 8cell_embryo1_7_split1 [Tr107]


title: Rel1-B07


title: 8cell_embryo1_6_split2 [Tr106]


title: 8cell_embryo2_3_split1 [Tr215]


title: Rel1-B06


title: Rel1-B05


title: Rel1-B08


title: 8cell_embryo1_6_split1 [Tr105]


title: 8cell_embryo2_2_split1 [Tr213]


title: 8cell_embryo1_5_split2 [Tr104]


title: Rel1-C03


title: 8cell_embryo1_4_split2 [Tr102]


title: 8cell_embryo1_5_split1 [Tr103]


title: 8cell_embryo1_4_split1 [Tr101]


title: 8cell_embryo1_3_split2 [Tr100]


title: Rel1-B04


title: Rel1-B02


title: Rel1-B03


title: 8cell_embryo1_2_split2 [Tr98]


title: 8cell_embryo1_8_split1 [Tr109]


title: 8cell_embryo1_2_split1 [Tr97]


title: 8cell_embryo1_3_split1 [Tr99]


title: Rel1-A12


title: 8cell_embryo1_1_split2 [Tr96]


title: Rel1-A11


title: Rel1-B01


title: 8cell_embryo1_1_split1 [Tr95]


title: Late4cell_embryo6_4_split2 [Tr404]

value: Late 4-cell embryo


title: Rel1-A07


title: Rel1-A06


title: Rel1-A08


title: Rel1-A05


title: Rel1-A04


title: Late4cell_embryo6_3_split2 [Tr402]


title: Late4cell_embryo6_3_split1 [Tr401]


title: Late4cell_embryo6_2_split2 [Tr400]


title: Rel1-A02


title: Late4cell_embryo6_2_split1 [Tr399]


title: G9-H12


title: Rel1-A03


title: Late4cell_embryo6_1_split1 [Tr397]


title: Late4cell_embryo6_1_split2 [Tr398]


title: G9-H11


title: Late4cell_embryo5_4_split2 [Tr396]


title: Rel1-A10


title: G9-H10


title: Late4cell_embryo5_4_split1 [Tr395]


title: G9-H09


title: Late4cell_embryo5_3_split2 [Tr394]


title: Late4cell_embryo6_4_split1 [Tr403]


title: G9-H08


title: G9-H07


title: Late4cell_embryo5_3_split1 [Tr393]


title: Late4cell_embryo5_2_split1 [Tr391]


title: Late4cell_embryo5_2_split2 [Tr392]


title: G9-H05


title: G9-H06


title: Late4cell_embryo5_1_split2 [Tr390]


title: Late4cell_embryo5_1_split1 [Tr389]


title: Rel1-A01


title: G9-H03


title: Late4cell_embryo4_4_split1 [Tr387]


title: Late4cell_embryo4_4_split2 [Tr388]


title: G9-H04


title: Late4cell_embryo4_3_split1 [Tr385]


title: G9-H01


title: G9-G11


title: Late4cell_embryo4_2_split2 [Tr384]


title: G9-H02


title: G9-G12


title: Late4cell_embryo4_3_split2 [Tr386]


title: Rel1-F06


title: G9-G10


title: Late4cell_embryo4_2_split1 [Tr383]


title: Late4cell_embryo4_1_split2 [Tr382]


title: G9-G08


title: Late4cell_embryo4_1_split1 [Tr381]


title: Rel1-E12


title: G9-G07


title: Late4cell_embryo3_4_split2 [Tr380]


title: G9-G09


title: Late4cell_embryo3_4_split1 [Tr379]


title: G9-G06


title: Late4cell_embryo3_3_split1 [Tr377]


title: G9-G05


title: Late4cell_embryo3_3_split2 [Tr378]


title: G9-G04


title: G9-G03


title: G9-G02


title: Late4cell_embryo3_2_split2 [Tr376]


title: Late4cell_embryo3_2_split1 [Tr375]


title: G9-G01


title: G9-F11


title: Late4cell_embryo3_1_split2 [Tr374]


title: Late4cell_embryo2_4_split2 [Tr372]


title: G9-F12


title: Late4cell_embryo3_1_split1 [Tr373]


title: G9-F10


title: Late4cell_embryo2_4_split1 [Tr371]


title: G9-F09


title: Late4cell_embryo2_3_split2 [Tr370]


title: Late4cell_embryo2_3_split1 [Tr369]


title: Late4cell_embryo2_2_split2 [Tr368]


title: G9-F07


title: Late4cell_embryo2_2_split1 [Tr367]


title: G9-F06


title: G9-F08


title: G9-F05


title: Late4cell_embryo2_1_split1 [Tr365]


title: G9-F03


title: Late4cell_embryo2_1_split2 [Tr366]


title: Late4cell_embryo1_4_split2 [Tr364]


title: G9-F04


title: G9-E12


title: G9-F01


title: G9-F02


title: Late4cell_embryo1_3_split2 [Tr362]


title: G9-E11


title: Late4cell_embryo1_3_split1 [Tr361]


title: G9-E10


title: G9-E08


title: G9-E09


title: Late4cell_embryo1_1_split2 [Tr358]


title: Late4cell_embryo1_1_split1 [Tr357]


title: G9-E07


title: 4cell_embryo12_4_split2 [Tr210]

value: 4-cell embryo


title: 4cell_embryo12_4_split1 [Tr209]


title: G9-E06


title: G9-E05


title: G9-E04


title: 4cell_embryo12_3_split1 [Tr207]


title: Late4cell_embryo1_4_split1 [Tr363]


title: 4cell_embryo12_2_split2 [Tr206]


title: 4cell_embryo12_2_split1 [Tr205]


title: G9-E02


title: 4cell_embryo12_1_split2 [Tr204]


title: G9-E01


title: G9-D12


title: Late4cell_embryo1_2_split2 [Tr360]


title: 4cell_embryo11_4_split2 [Tr202]


title: G9-D11


title: Late4cell_embryo1_2_split1 [Tr359]


title: G9-D09


title: 4cell_embryo11_3_split2 [Tr200]


title: 4cell_embryo11_4_split1 [Tr201]


title: G9-D08


title: 4cell_embryo12_3_split2 [Tr208]


title: 4cell_embryo11_3_split1 [Tr199]


title: 4cell_embryo11_2_split2 [Tr198]


title: G9-D05


title: G9-D04


title: G9-D07


title: G9-E03


title: 4cell_embryo11_2_split1 [Tr197]


title: 4cell_embryo11_1_split2 [Tr196]


title: 4cell_embryo10_4_split2 [Tr194]


title: 4cell_embryo11_1_split1 [Tr195]


title: G9-D01


title: 4cell_embryo10_3_split2 [Tr192]


title: G9-D02


title: G9-C12


title: G9-D10


title: G9-C11


title: 4cell_embryo10_3_split1 [Tr191]


title: 4cell_embryo12_1_split1 [Tr203]


title: G9-C10


title: 4cell_embryo10_1_split2 [Tr188]


title: 4cell_embryo10_2_split1 [Tr189]


title: 4cell_embryo10_2_split2 [Tr190]


title: G9-C09


title: G9-D06


title: G9-C08


title: G9-C07


title: 4cell_embryo10_1_split1 [Tr187]


title: 4cell_embryo9_4_split1 [Tr185]


title: 4cell_embryo9_3_split2 [Tr184]


title: 4cell_embryo9_4_split2 [Tr186]


title: G9-C04


title: G9-C03


title: 4cell_embryo10_4_split1 [Tr193]


title: 4cell_embryo9_3_split1 [Tr183]


title: G9-C05


title: 4cell_embryo9_2_split2 [Tr182]


title: G9-D03


title: 4cell_embryo8_4_split2 [Tr178]


title: G9-B12


title: 4cell_embryo9_2_split1 [Tr181]


title: G9-C01


title: 4cell_embryo9_1_split2 [Tr180]


title: G9-C02


title: 4cell_embryo9_1_split1 [Tr179]


title: G9-B10


title: G9-B11


title: G9-B09


title: G9-B08


title: 4cell_embryo8_4_split1 [Tr177]


title: G9-B07


title: G9-C06


title: G9-B06


title: 4cell_embryo8_2_split2 [Tr174]


title: 4cell_embryo8_3_split1 [Tr175]


title: G9-B05


title: 4cell_embryo7_4_split2 [Tr170]


title: 4cell_embryo8_1_split1 [Tr171]


title: 4cell_embryo7_4_split1 [Tr169]


title: G9-B03


title: G9-B02


title: G9-B01


title: 4cell_embryo7_3_split2 [Tr168]


title: 4cell_embryo8_3_split2 [Tr176]


title: G9-A12


title: G9-A11


title: 4cell_embryo7_2_split2 [Tr166]


title: G9-A10


title: 4cell_embryo7_1_split2 [Tr164]


title: 4cell_embryo7_2_split1 [Tr165]


title: G9-A09


title: G9-A08


title: 4cell_embryo7_1_split1 [Tr163]


title: 4cell_embryo8_2_split1 [Tr173]


title: G9-A07


title: 4cell_embryo6_3_split2 [Tr92]


title: G9-A05


title: G9-A06


title: 4cell_embryo6_3_split1 [Tr91]


title: G9-A04


title: 4cell_embryo6_4_split1 [Tr93]


title: 4cell_embryo8_1_split2 [Tr172]


title: G9-B04


title: G9-A02


title: G9-A03


title: G9-A01


title: 4cell_embryo6_2_split1 [Tr89]


title: G18-H12


title: 4cell_embryo7_3_split1 [Tr167]


title: 4cell_embryo5_3_split2 [Tr84]


title: 4cell_embryo6_1_split2 [Tr88]


title: 4cell_embryo6_1_split1 [Tr87]


title: 4cell_embryo5_3_split1 [Tr83]


title: 4cell_embryo5_2_split2 [Tr82]


title: 4cell_embryo6_4_split2 [Tr94]


title: G18-H10


title: G18-H08


title: G18-H09


title: G18-H11


title: 4cell_embryo5_2_split1 [Tr81]


title: G18-H07


title: 4cell_embryo4_4_split2 [Tr78]


title: 4cell_embryo5_1_split2 [Tr80]


title: 4cell_embryo4_4_split1 [Tr77]


title: G18-H05


title: G18-H04


title: G18-H03


title: G18-H06


title: 4cell_embryo4_3_split2 [Tr76]


title: 4cell_embryo6_2_split2 [Tr90]


title: 4cell_embryo4_3_split1 [Tr75]


title: G18-H02


title: G18-H01


title: 4cell_embryo4_2_split2 [Tr74]


title: G18-G12


title: 4cell_embryo4_2_split1 [Tr73]


title: G18-G11


title: 4cell_embryo4_1_split2 [Tr72]


title: 4cell_embryo4_1_split1 [Tr71]


title: G18-G10


title: 4cell_embryo5_1_split1 [Tr79]


title: 4cell_embryo3_4_split2 [Tr70]


title: G18-G06


title: G18-G07


title: 4cell_embryo3_3_split2 [Tr68]


title: G18-G05


title: 4cell_embryo3_3_split1 [Tr67]


title: 4cell_embryo3_4_split1 [Tr69]


title: 4cell_embryo3_1_split1 [Tr63]


title: G18-G01


title: G18-G02


title: 4cell_embryo3_1_split2 [Tr64]


title: 4cell_embryo3_2_split1 [Tr65]


title: G18-F12


title: G18-G03


title: 4cell_embryo3_2_split2 [Tr66]


title: 4cell_embryo2_4_split1 [Tr61]


title: 4cell_embryo2_3_split2 [Tr60]


title: 4cell_embryo2_4_split2 [Tr62]


title: G18-F10


title: G18-F11


title: G18-F09


title: G18-F08


title: 4cell_embryo2_3_split1 [Tr59]


title: G18-G09


title: 4cell_embryo2_2_split2 [Tr58]


title: 4cell_embryo2_2_split1 [Tr57]


title: G18-F06


title: G18-F07


title: 4cell_embryo2_1_split2 [Tr56]


title: 4cell_embryo2_1_split1 [Tr55]


title: G18-F03


title: G18-F04


title: G18-G04


title: G18-F02


title: 4cell_embryo1_4_split1 [Tr53]


title: 4cell_embryo1_2_split2 [Tr50]


title: G18-E12


title: 4cell_embryo1_3_split1 [Tr51]


title: 4cell_embryo1_3_split2 [Tr52]


title: 4cell_embryo1_2_split1 [Tr49]


title: G18-F01


title: 2cell_embryo12_2_split1 [Tr161]


title: G18-E11


title: 4cell_embryo1_1_split2 [Tr48]


title: 2cell_embryo12_2_split2 [Tr162]


title: G18-E09


title: G18-E08


title: 4cell_embryo1_1_split1 [Tr47]


title: 2cell_embryo12_1_split2 [Tr160]


title: 4cell_embryo1_4_split2 [Tr54]


title: G18-F05


title: 2cell_embryo12_1_split1 [Tr159]


title: 2cell_embryo11_2_split2 [Tr158]


title: G18-E03


title: 2cell_embryo11_2_split1 [Tr157]


title: G18-E04


title: 2cell_embryo11_1_split1 [Tr155]


title: 2cell_embryo11_1_split2 [Tr156]


title: G18-E01


title: 2cell_embryo10_2_split2 [Tr154]


title: G18-D12


title: G18-D11


title: G18-E10


title: 2cell_embryo10_2_split1 [Tr153]


title: G18-E07


title: 2cell_embryo10_1_split2 [Tr152]


title: G18-D10


title: G18-D09


title: G18-E05


title: G18-E06


title: 2cell_embryo10_1_split1 [Tr151]


title: G18-D08


title: G18-D05


title: G18-D07


title: G18-D06


title: G18-E02


title: 2cell_embryo9_2_split2 [Tr150]


title: 2cell_embryo9_2_split1 [Tr149]


title: G18-D03


title: G18-D04


title: G18-D02


title: G18-D01


title: Healthy donor pool

type: RNA

city: Botucatu

first: Juliana

middle: Ravelli Baldassarre

last: Martins

state: SP

address: Rua Mansueto Lunardi, 37

country: Brazil

institute: Faculdade de Medicina de Botucatu

description:
control
SAMPLE 29

data_processing:
Comparative Ct analysis was used for quantification of microRNAs gene expression and differences were evaluated by Student´s t test; p<0,05 was considered to indicate statistical significance; maximun allowed Ct value: 35. Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the endogenous Mammalian U6. [delta] CT = CTsample - CTreference.
fold change ≤ 0,5 and fold change ≥ 2,0

source_name: peripheral blood sample

label_protocol: The miRNA cDNA was prepared  using the TaqMan TM MicroRNA Reverse Transcription Kit, Catalog No. 4366597, combined with Megaplex TM RT Primers, Human Pools A+B Set v2.0, catalog No. 4400928. The qPCR reaction was performed using the mix TaqMan TM Universal Master Mix II, catalog No 4440040 in combination with TaqMan TM Array Human MicroRNA A+B Cards Set v2.0, catalog No. 4400238. The reactions were amplified using the  ViiA7 equipment (ThermoFisher). For all steps, the manufacturer´s  protocol was followed.

growth_protocol: Human samples were obtained from patients treated with bone marrow tranplantation and from patients treated with imatinib mesylate. Control was constituted by a pool of healthy donors.  HUMAN SAMPLES OBTAINED FROM PATIENTS TREATED WITH BONE MARROW TRANSPLANTATION AND FROM NEWLY DIAGNOSTIC PATIENTS THAT DID NOT START TREATMENT. CONTROL WAS CONSTITUTED BY A POOL OF HEALTHY DONORS

extract_protocol: Total RNA was extracted with QIAamp RNA Blood Mini Kit (QIAGEN)

treatment_protocol: A sample of 5 mL peripheral blood were collected from the patients. For RNA isolation, was used QIAamp RNA Blood Mini Kit (QIAGEN). After purification, a NanoDrop (Thermo Scientific Waltham) was used for quantification, quality and control of RNA. Quantification and sizing were analyzed using RNA 2100 Bioanalyzer (Agilent Technologies)

tag: group

value: Healthy donor pool


title: G18-C09


title: G18-C12


title: G18-C11


title: G18-C10


title: G18-C08


title: 2cell_embryo8_2_split2 [Tr146]


title: 2cell_embryo8_1_split2 [Tr144]


title: G18-C05


title: Imatinib mesylate 13

description:
tested
SAMPLE 27

value: Imatinib mesylate


title: Imatinib mesylate 14

description:
tested
SAMPLE 28


title: G18-C04


title: 2cell_embryo8_2_split1 [Tr145]


title: Ossification of the posterior longitudinal ligament (OPLL) tissue circRNA 3

city: Harbin

first: qichang

last: gao

state: Heilongjiang

address: youzheng street, Nangang district

department: orthopedics departmnet

institute: First Affiliated Hospital of Harbin Medical University

description: circRNA expression data from Homo sapiens OPLL tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from PLL surgury and promptly frozen in liquid nitrogen.

tag: gender

value: female

tag: molecule subtype

value: circRNA


title: Ossification of the posterior longitudinal ligament (OPLL) tissue circRNA 1

value: male


title: Normal posterior longitudinal ligament (PLL) tissue circRNA 3

description: circRNA expression data from Homo sapiens PLL tissue

value: Normal posterior longitudinal ligament


title: Ossification of the posterior longitudinal ligament (OPLL) tissue circRNA 2


title: G18-C06


title: G18-C03


title: 2cell_embryo9_1_split1 [Tr147]

tag: strain

tag: develomental stage


title: G18-C02


title: Imatinib mesylate 11

description:
tested
SAMPLE 25


title: Normal posterior longitudinal ligament (PLL) tissue circRNA 1


title: 2cell_embryo7_2_split2 [Tr142]


title: Normal posterior longitudinal ligament (PLL) tissue circRNA 2


title: 2cell_embryo8_1_split1 [Tr143]


title: G18-C01


title: G18-C07


title: Imatinib mesylate 10

description:
tested
SAMPLE 24


title: G18-B12


title: 2cell_embryo9_1_split2 [Tr148]


title: 2cell_embryo7_2_split1 [Tr141]


title: G18-B11


title: G18-B09


title: G18-B10


title: Imatinib mesylate 9

description:
tested
SAMPLE 23


title: 2cell_embryo7_1_split2 [Tr140]


title: G18-B08


title: G18-B07


title: Imatinib mesylate 8

description:
tested
SAMPLE 22


title: 2cell_embryo7_1_split1 [Tr139]


title: Imatinib mesylate 7

description:
tested
SAMPLE 21


title: G18-B06


title: 2cell_embryo6_2_split2 [Tr46]


title: Imatinib mesylate 6

description:
tested
SAMPLE 20


title: G18-B05


title: G18-B03


title: 2cell_embryo6_2_split1 [Tr45]


title: G18-B02


title: Imatinib mesylate 5

description:
tested
SAMPLE 19


title: G18-B01


title: Imatinib mesylate 4

description:
tested
SAMPLE 18


title: 2cell_embryo6_1_split2 [Tr44]


title: G18-A12


title: G18-A11


title: 2cell_embryo6_1_split1 [Tr43]


title: Imatinib mesylate 3

description:
tested
SAMPLE 17


title: Imatinib mesylate 2

description:
tested
SAMPLE 16


title: G18-A08


title: G18-A09


title: G18-A07


title: G18-A10


title: 2cell_embryo5_2_split1 [Tr41]


title: G18-A06


title: 2cell_embryo5_2_split2 [Tr42]


title: Imatinib mesylate 1

description:
tested
SAMPLE 15


title: G18-A04


title: 2cell_embryo5_1_split2 [Tr40]


title: G18-B04


title: G18-A05


title: Philadelphia negative 13

description:
control
SAMPLE 13

value: Philadelphia negative


title: Philadelphia negative 14

description:
control
SAMPLE 14


title: 2cell_embryo5_1_split1 [Tr39]


title: G18-A02


title: G18-A03


title: G18-A01


title: 2cell_embryo4_2_split2 [Tr38]


title: Philadelphia negative 11

description:
control
SAMPLE 11


title: Philadelphia negative 12

description:
control
SAMPLE 12


title: G20-H11

value: wt


title: 2cell_embryo4_1_split2 [Tr36]


title: G20-H12


title: 2cell_embryo4_2_split1 [Tr37]


title: G20-H10


title: Philadelphia negative 9

description:
control
SAMPLE 9


title: G20-H06


title: 2cell_embryo4_1_split1 [Tr35]


title: G20-H07


title: 2cell_embryo3_2_split2 [Tr34]


title: G20-H03


title: Philadelphia negative 8

description:
control
SAMPLE 8


title: G20-H05


title: 2cell_embryo3_2_split1 [Tr33]


title: G20-H04


title: G20-H02


title: Philadelphia negative 7

description:
control
SAMPLE 7


title: 2cell_embryo3_1_split2 [Tr32]


title: G20-H01


title: G20-G12


title: G20-G11


title: G20-H09


title: Philadelphia negative 5

description:
control
SAMPLE 5


title: G20-G09


title: G20-G08


title: Philadelphia negative 4

description:
control
SAMPLE 4


title: G20-G07


title: Philadelphia negative 10

description:
control
SAMPLE 10


title: G20-G10


title: 2cell_embryo3_1_split1 [Tr31]


title: G20-H08


title: 2cell_embryo2_2_split1 [Tr29]


title: 2cell_embryo2_2_split2 [Tr30]


title: Philadelphia negative 3

description:
control
SAMPLE 3


title: Philadelphia negative 2

description:
control
SAMPLE 2


title: G20-G05


title: Philadelphia negative 1

description:
control
SAMPLE 1


title: G20-G02


title: G20-G04


title: 2cell_embryo2_1_split2 [Tr28]


title: G20-G03


title: G20-G06


title: Philadelphia negative 6

description:
control
SAMPLE 6


title: G20-G01


title: G20-F11


title: G20-F12


title: G20-F10


title: 2cell_embryo1_2_split1 [Tr25]


title: MEL_LRS_HBB_IVS110_2

description: nascent RNA

extract_protocol:
Cells were fractionated according to the protocol published in (Pandya-Jones and Black, 2009), with modifications to centrifugation speeds in order to retain intact nuclei. All steps were performed on ice, and all buffers contained 25 uM α-amanitin, 40 U/ml SUPERase.IN, and 1x Roche cOmplete protease inhibitor mix. Briefly, 20 million cells were rinsed once with PBS/1 mM EDTA, then lysed in 250 μl cytoplasmic lysis buffer (10 mM Tris-HCl pH 7.5, 0.05% NP40, 150 mM NaCl) by gently resuspending then incubating on ice for 5 minutes. Lysate was then layered on top of a 500 μl cushion of 24% sucrose in cytoplasmic lysis buffer and spun at 2000 rpm for 10 min at 4°C. The supernatant (cytoplasm fraction) was removed, and the pellet (nuclei) were rinsed once with 500 μl PBS/1 mM EDTA. Nuclei were resuspended in 100 μl nuclear resuspension buffer (20 mM Tris-HCl pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 50% glycerol) by gentle flicking, then lysed by the addition of 100 μl nuclear lysis buffer (20 mM HEPES pH 7.5, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M Urea, 1% NP-40), vortexed for 2 x 2 seconds, then incubated on ice for 3 min. Chromatin was pelleted by spinning at 14,000 rpm for 2 min at 4°C. The supernatant (nucleoplasm fraction) was removed, and the chromatin was rinsed once with PBS/1 mM EDTA. Chromatin was immediately dissolved in 100 μl PBS and 300 μl TRIzol Reagent (ThermoFisher). RNA was purified from chromatin pellets in TRIzol Reagent (ThermoFisher) using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol, including the on-column DNase I digestion.
A DNA adapter (/5rApp/NNNNNCTGTAGGCACCATCAAT/3ddC/) was ligated to 3′ ends of nascent RNA using the T4 RNA ligase kit (NEB) by mixing 50 pmol adapter with 300-600 ng nascent RNA. Custom RT primers were used to add barcodes during reverse transcription with SSIII reverse transcriptase (ThermoFisher; Table S2). cDNA was amplified by 26 cycles of PCR using the Advantage 2 PCR Kit (Clontech), using custom gene-specific forward primers that were complementary to a unique region in the 5′UTR of the human HBB gene in combination with the kit IIA primer. PCR amplicons were cleaned up with a 2X volume of AMPure beads (Agencourt), and PacBio library preparation was performed at the Icahn School of Medicine at Mt. Sinai Genomics Core Facility using the SMRTbell Template Prep Kit 1.0 (Pacific Biosciences).

tag: cell type

value: Murine Erythroleukemia cells (MEL)

value: 2% DMSO 5 days

value: chromatin fractionation

value: HBB IVS-110 (G>A) integrated


title: G20-F08


title: G20-F06


title: MEL_LRS_HBB_IVS110_1

description: nascent RNA


title: 2cell_embryo1_1_split2 [Tr24]

value: 2-cell embryo


title: 2cell_embryo1_1_split1 [Tr23]


title: G20-F07

value: patient derived glioma tissue


title: G20-F09


title: Imatinib mesylate 12

description:
tested
SAMPLE 26


title: MEL_LRS_HBB_WT_3

description: nascent RNA

value: HBB WT integrated


title: 2cell_embryo2_1_split1 [Tr27]


title: G20-F05


title: G20-F04


title: 2cell_embryo1_2_split2 [Tr26]


title: Zygote13_split1 [Tr137]

value: Zygote


title: MEL_LRS_HBB_WT_2

description: nascent RNA


title: G20-F02


title: MEL_LRS_HBB_WT_1

description: nascent RNA


title: G20-E12


title: MEL_LRS_HBB_IVS110_3

description: nascent RNA


title: MEL_LRS_induced_2_SQ

description: nascent RNA

value: chromatin fractionation, ribosomal depletion, polyA+ depletion

value: wild type


title: Zygote12_split2 [Tr136]


title: G20-F03


title: G20-F01


title: Zygote12_split1 [Tr135]


title: G20-E11


title: MEL_LRS_induced_1_SQ

description: nascent RNA


title: Zygote13_split2 [Tr138]


title: G20-E08


title: MEL_LRS_uninduced_2_SQ

description: nascent RNA


title: MEL_LRS_uninduced_1_SQ

description: nascent RNA


title: G20-E07


title: G20-E05


title: G20-E06


title: Zygote11_split1 [Tr133]


title: G20-E09


title: G20-E04


title: Zygote11_split2 [Tr134]


title: Zygote10_split1 [Tr131]


title: Zygote10_split2 [Tr132]


title: G20-E03


title: G20-D12


title: G20-D11


title: G20-E02


title: CP2A2_3

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

data_processing:
The sequencing was performed at BGI-Shenzhen using BGISEQ-500. The sequencing data was filtered using SOAPnuke (v1.5.2) software.
The processed FASTQ files were mapped to the human transcriptome and genome using HISAT2 (v2.0.4).
The genome version was GRCh38, with annotations from Bowtie2 (v2.2.5).
Expression level of the gene was calculated by RSEM (v1.2.12) software.
The set of differentially expressed genes identified from pairwise comparisons was identified using DEseq2 (v1.4.5) package (BGI, Wuhan, China). The number of reads per kilobase per million reads (RPKM) method was used to calculate the modification levels of unique genes. Significantly differentially expressed genes were defined as ones with at least 0.3 FPKM level of expression in at least one of the conditions and a q-value less than 0.05 by Bonferroni test. KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed genes was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test.
Genome_build: NCBI: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

source_name: Astrocytes

growth_protocol: The cells were cultured in maturation medium AGMTM Astrocyte Growth Medium BulletKitTM (Lonza, CC-3186) and kept in a 37°C incubator with a humidified.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Kit (QIAGEN, 74104) following manufacturer’s instructions. Samples were sent to BGI, Wu Han, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample
Library preparation was conducted at BGI, Shenzhen, China, following the guide of the standard protocol.
Library preparation (BGISEQ-500RS High-throughput sequencing kit, PE50, V3.0, MGI Tech Co, Ltd, Shenzhen, China), hybridization and sequencing were performed according to the manufacturer's standard procedure provided by BGI (BGI-Shenzhen).

value: iPSC-derived astrocytes

value: POLG mutate (heterozygous c.1399G>A/c.2243G>C; p.A467T/W748S)


title: CP2A2_1


title: Zygote9_split1 [Tr129]


title: G20-E10


title: G20-D10


title: CP2A1_3


title: G20-D09


title: CP2A1_2


title: G20-D08


title: G20-D07


title: G20-D04


title: CP2A1_1


title: G20-D06


title: Zygote7_split2 [Tr14]


title: WS5A3_3

value: POLG mutate (homozygous for c.2243G>C; p.W748S)


title: Zygote7_split1 [Tr13]


title: G20-D05


title: G20-D03


title: G20-E01


title: CP2A2_2


title: G20-D01


title: G20-D02


title: Zygote9_split2 [Tr130]


title: WS5A3_2


title: Zygote6_split1 [Tr11]


title: WS5A3_1


title: WS5A2_3


title: Zygote8_split2 [Tr128]


title: G20-C11


title: G20-C09


title: WS5A2_2


title: G20-C08


title: G20-C10


title: G20-C07


title: Zygote5_split2 [Tr10]


title: Zygote8_split1 [Tr127]


title: Zygote5_split1 [Tr9]


title: G20-C06


title: WS5A2_1


title: WS5A1_3


title: Zygote4_split2 [Tr8]


title: G20-C05


title: G20-C03


title: G20-C04


title: G20-C02


title: WS5A1_2


title: G20-C01


title: WS5A1_1


title: G20-C12


title: Zygote3_split2 [Tr6]


title: Zygote6_split2 [Tr12]


title: Zygote3_split1 [Tr5]


title: Zygote2_split2 [Tr4]


title: G20-B09


title: G20-B11


title: G20-B08


title: G20-B10


title: Zygote2_split1 [Tr3]


title: G20-B07


title: HNA_3

value: Human astocyte cell lines


title: HNA_2


title: G20-B06


title: Zygote1_split2 [Tr2]


title: G20-B05


title: G20-B04


title: Zygote4_split1 [Tr7]


title: ESC_3

value: ESC-derived astrocytes


title: ESC_2


title: G20-B03


title: G20-B02


title: G20-B01


title: Zygote1_split1 [Tr1]


title: G20-B12


title: G20-A12


title: ESC_1


title: RBL-2H3 - NS

city: Changsha

first: Ying

last: Wang

address: Xiangya Road

institute: Xiangya Hospital

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: RN6
Supplementary_files_format_and_content: Differential gene excel

organism: Rattus norvegicus

source_name: RBL-2H3 cell line

extract_protocol:
Using Tripure reagent to isolate total RNA from RBL-2H3 cells treated with PM2.5 or IgE-DNP-HSA
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

tag: cell line

tag: treatment

value: Normal saline


title: RBL-2H3 - PM100

value: PM2.5 plus IgE+DNP-HSA


title: G20-A09

tag: tissue

value: wt


title: G20-A08


title: CTRL4_2


title: G20-A06


title: G20-A10


title: CTRL4_3


title: G20-A11


title: G20-A05


title: CTRL4_1


title: CTRL3_3


title: G20-A03


title: HNA_1


title: CRISPRi_XIST_rep1

city: Stanford

first: Howard

middle: Y

last: Chang

state: California

address: 269 Campus Drive

institute: Stanford University

data_processing:
Library strategy: targeted amplicon sequencing
reads were mapped directly to TLR7 reference Xa and Xi allele and counted at each allele for d score analysis. The co-factors with d scoreco-factor - d scoreCtrl >0.1 were labeled as essential XIST co-factors for TLR7 XCI maintenance
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with allele-specific read counts of TLR7 for every individual sgRNA perturbation

source_name: dCas9-Krab+ GM B cell line

growth_protocol: GM related cell lines were cultured in RPMI 1640 (Thermo Fisher Scientific) with 10% FBS (Thermo Fisher Scientific) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
RNA was extracted using Direct-zol-96 RNA Kit (Zymo). TLR7 RT-PCR was performed using Stratagene Brilliant II SYBR Green QRT-PCR Master Mix (50°C for 30 min, 95°C for 10 min, then 35 cycles of 95°C for 30 seconds, 60°C for 1 min, and 72°C for  30 seconds, finally 72°C for 5 min).
The second PCR with Ad1_TLR7_F and Ad2_TLR7_R primers was performed using NEBNext Master Mix (2.5uL 1st PCR product with 500 nM primers in program: 98°C for 1 min, 20 cycles of 98°C for 30 seconds, 60°C for 30 seconds, and then 72°C for 40 seconds, finally 72°C for 5 min). The third PCR with indexed primers containing barcodes was performed using  NEBNext Master Mix (2uL of 1:10 diluted 2nd PCR product with 1uM indexed primers in program: 98°C for 1 min, 10 cycles of 98°C for 30 seconds, 72°C for 30 seconds, and then 72°C for 40 seconds, finally 72°C for 5 min). Finally, all the samples were pooled and purified using Zymo DNA clean & concentrator. The library was size-selected to 250-300 bp. The gel slices were cut and the DNA was recovered by Zymo Gel DNA recovery kit (Zymo Research). The concentration of the library was quantified by KAPA Library Quantification Kit for Illumina (Roche) and sequenced on an Illumina Miseq 2X75 cycle.

value: GM B cell


title: G20-A02


title: G20-A01


title: G19-H12


title: CRISPRi_XRCC5_rep2


title: G20-A07


title: CRISPRi_WTAP_rep2


title: G20-A04


title: CRISPRi_WTAP_rep1


title: CTRL3_2


title: CRISPRi_XRCC5_rep1


title: CRISPRi_WAC_rep2


title: G19-H09


title: CRISPRi_XIST_rep2


title: CTRL2_1


title: CRISPRi_TRIM28_rep2


title: G19-H03


title: G19-H04


title: G19-H05


title: CTRL2_2


title: G19-H02


title: G19-H06


title: CTRL2_3


title: CTRL1_3


title: CTRL1_1


title: G19-G12


title: CRISPRi_TRIM28_rep1


title: G19-H08


title: CTRL1_2


title: G19-H10


title: CRISPRi_SYNCRIP_rep1


title: CTRL3_1


title: G19-H11


title: Linc NR_033736 + C. parvum_W3

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

data_processing:
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Rmats  v3.2.5 with parameters  -analysis U -t paired -a 8.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Linc NR_033736 + C. parvum

extract_protocol:
IEC 4.1 cells were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104).  Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 platform

value: intestinal epithelial

tag: knockdown

value: siRNA to lincRNA-NR_033736

tag: infection status

value: infected with C. parvum


title: G19-G09

value: patient derived glioma tissue


title: G19-H01


title: CRISPRi_SYNCRIP_rep2


title: G19-G10


title: G19-H07


title: G19-G08


title: G19-G06


title: G19-G05


title: G19-G11


title: Linc NR_033736_V3

value: not infected


title: G19-G04


title: G19-G03


title: Linc NR_033736 + C. parvum_W2


title: G19-G02


title: Linc NR_033736_V2


title: CRISPRi_WAC_rep1


title: CRISPRi_SRSF3_rep1


title: CRISPRi_SRSF3_rep2


title: G19-F11


title: Linc NR_033736 + C. parvum_W1


title: G19-G07


title: CRISPRi_SRSF2_rep2


title: CRISPRi_SRSF1_rep1


title: CRISPRi_SRSF1_rep2


title: G19-G01


title: CtrlsiRNA + C. parvum_U2

source_name: CtrlsiRNA + C. parvum

value: control siRNA


title: G19-F12


title: Linc NR_033736_V1


title: CRISPRi_SRSF2_rep1


title: CRISPRi_SRRT_rep2


title: G19-F04


title: G19-F07


title: G19-F05


title: G19-F08


title: G19-F10


title: CRISPRi_SPEN_rep1


title: CtrlsiRNA_T2

source_name: CtrlsiRNA


title: G19-F01


title: CRISPRi_SRRT_rep1


title: CtrlsiRNA + C. parvum_U1


title: CtrlsiRNA + C. parvum_U3


title: G19-E12


title: CRISPRi_SPEN_rep2


title: CtrlsiRNA_T3


title: G19-F03


title: G19-F02


title: G19-E09


title: G19-E08


title: CRISPRi_SAFB2_rep2


title: G19-E11


title: CRISPRi_SAFB2_rep1


title: G19-E10


title: CRISPRi_RNF40_rep2


title: CRISPRi_RNF40_rep1


title: G19-E07


title: CtrlsiRNA_T1


title: G19-E06


title: G19-E05


title: CRISPRi_RNF20_rep1


title: CRISPRi_RNF20_rep2


title: G19-E02


title: CRISPRi_RBMX_rep2


title: G19-D12


title: G19-E01


title: CRISPRi_RBMX_rep1


title: CRISPRi_RBM15_rep2


title: G19-D11


title: G19-D10


title: G19-D08


title: G19-D07


title: G19-E04


title: G19-D05


title: CRISPRi_RBM14_rep2


title: 214: extended stretch

city: Tokushima

first: Masaki

last: Morishima

state: Tokushima

address: 2-50-1, Kuramoto-cho

department: Tokushima University

country: Japan

institute: Clinical Research Center for Diabetes

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 65Â°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 37Â°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 analyzed with a laser confocal scanner (g2565BA, Agilent Technologies)

source_name: atrial cardiomyocytes

label_protocol: Total RNA was labeled with Cy3 with a miRNA and hybridization kit (Agilent Technologies, Santa Clara, CA, USA) followed by procedures with the Human miRNA Microarray (8x60K, ID31181, miRBase release 16.0, Agilent Technologies).

extract_protocol: Total RNA was prepared using the Trizol reagent (Life technology) following the manufacturer's recommendations. Briefly, after homogenizing the sample with TRIzol® Reagent, chloroform is added, and the homogenate is allowed to separate into a clear upper aqueous layer (containing RNA), an interphase, and a red lower organic layer (containing the DNA and proteins). RNA is precipitated from the aqueous layer with isopropanol. The precipitated RNA is washed to remove impurities, and then resuspended for use in downstream applications. And then total RNA were cleaned up by RNeasy MinElute Cleanup Kit (QIAGEN) according to manufacture’s protocol.

treatment_protocol: Human left atrial appendage were obtained from patients undergoing open-heart surgery at Kumamoto Red Cross Hospital.  Tissue samples were immediately put in RNA later, and then stored in a deep freezer at -80°C.  The use of tissue samples for all experiments was approved by all the patients in documents and by Kumamoto Red Cross Hospital Ethics Committee.

value: extended stretch

value: atrial cardiomyocytes

value: left atrial appendage

value: male


title: 216: extended stretch


title: 205: extended stretch


title: 10: extended stretch


title: 9: extended stretch


title: 6: extended stretch


title: CRISPRi_RBM15_rep1


title: 8: extended stretch


title: G19-E03


title: G19-D04


title: G19-D02


title: G19-F09


title: 4: extended stretch


title: G19-D03


title: G19-D01


title: 1: extended stretch


title: G19-C11


title: CRISPRi_RBM12_rep1


title: CRISPRi_RBM14_rep1


title: CRISPRi_RBM12_rep2


title: G19-D09


title: 2: extended stretch


title: CRISPRi_RAVER1_rep1


title: 211: normal size of left atrium

value: normal size of left atrium


title: G19-C09


title: G19-C10


title: CRISPRi_RAVER1_rep2


title: G19-C08


title: G19-C07


title: CRISPRi_RALY_rep1


title: CRISPRi_RALY_rep2


title: G19-D06


title: G19-C12


title: G19-F06


title: G19-C02


title: G19-C06


title: G19-B12


title: G19-C05


title: CRISPRi_PTBP1_rep1


title: CRISPRi_PTBP1_rep2


title: G19-C03


title: 213: normal size of left atrium


title: cells from 48 h old biofilm rep 3

city: Werribee

first: Nirmani

last: Wickramasinghe

state: VIC

address: 671, Sneydes Road

department: Public Health

country: Australia

institute: CSIRO

data_processing:
Galaxy platform was used for data analysis. Trimming of the reads were not due to high quality of data.
The reads were mapped to the P. fragi 1793 reference genome (Gene bank accession no NQKS00000000) with the Burrows-Wheeler Aligner (version 0.7.17) using the BWA-MEM algorithm. The mapped reads, which were in BAM format, were visualised using Jbrowse genome browser (version 1.16.4) to determine the efficiency of mapping. Mapped reads were used in subsequent analyses.
To estimate the number of genes overlapping with each gene in the reference genome, the SAM/BAM to count matrix of Galaxy was used.
Differential expression was examined using the Voom tool (Galaxy Version 0.28) ,
The gene expression of P. fragi in the three stages of the biofilm: (Initiation vs Maturation), (Initiation vs Dispersal), and (Maturation vs Dispersal) were compared pairwise using the DEGUST tool (http://degust.erc.monash.edu/).
Supplementary_files_format_and_content: Differential counts, xls format

organism: Pseudomonas fragi

source_name: Bacterial biofilm cells

growth_protocol: P. fragi biofilms were grown on surface sterilized beef cuts kept at 10  P. fragi biofilms were grown on surface sterilized beef cuts kept at 10  ͦC under aerobic conditions

extract_protocol:
RNA was extracted with the RNeasy minikit (Qiagen, MD, cat no-74104) using the protocol for disruption of bacteria grown on solid media,
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bacterial biofilm cells


title: CRISPRi_PCBP2_rep2


title: G19-B10


title: cells from 48 h old biofilm rep 4


title: 204: normal size of left atrium


title: G19-B11


title: cells from 48 h old biofilm rep 2


title: 38: normal size of left atrium


title: G19-C04


title: G19-C01


title: G19-B09


title: cells from 48 h old biofilm rep 1


title: CRISPRi_PABPC1_rep2


title: CRISPRi_PCBP2_rep1


title: 36: normal size of left atrium


title: CRISPRi_PABPC1_rep1


title: cells from 76 h old biofilm rep 4


title: 209: normal size of left atrium


title: P. putida JE2212 NO3 rep 3

city: Richland

first: Joshua

last: Elmore

state: WA

address: 902 Battelle Blvd

institute: PNNL

data_processing:
Reads were trimmed and filtered using Geneious v11.1.5 with an error probability limit of 0.05
Filtered reads were mapped to the reference genome using Geneious v11.1.5 default "Map to Reference: Geneious RNA" parameters
Raw read count and FPKM were calculated for each annotated gene using "Calculate Expression Levels" within Geneious v11.1.5 and exported
Genome_build: NC_002947 with additional sequences for heterologous genes
Supplementary_files_format_and_content: csv files with Raw Read Count and FPKM values for each sample

organism: Pseudomonas putida KT2440

source_name: bacterial cells

growth_protocol: Samples were prepared by pre-cultivating strains in MME medium with glucose and the nitrogen source used in the experiment (ammonium or nitrate) until cells reached stationary phase. Experimental cultures were innoculated to an OD600 of 0.01 and incubated until OD600 reached ~0.2 and harvested by centrifugation at 4 C.

extract_protocol:
RNAs were extracted using Trizol reagent and QIAGEN Rneasy kit following manufacturer's protocol.
rRNAs were depleted using RiboZero rRNA removal kit, depleted RNAs were purified using ZymoResearch RNA Clean & Concentrator-5 kit, and libraries were prepared using Illumina's ScriptSeq v2 RNA-Seq Library Preparation Kit

tag: nitrogen source

value: nitrate

tag: growth phase harvested

value: mid-log


title: 33: normal size of left atrium


title: P. putida JE2212 NO3 rep 2


title: G19-B07

tag: genotype


title: G19-B08


title: G19-B06


title: CRISPRi_NT_rep2

value: Non targeting control


title: cells from 76 h old biofilm rep 3


title: 35: normal size of left atrium


title: P. putida JE2212 NO3 rep 1


title: cells from 76 h old biofilm rep 2


title: CRISPRi_NT_rep1


title: G19-B05

value: wt


title: cells from 76 h old biofilm rep 1


title: P. putida JE2212 NH4 rep 3

value: ammonium


title: CRISPRi_NONO_rep2

value: GM B cell


title: 32: normal size of left atrium


title: G19-B04


title: P. putida JE2212 NH4 rep 2


title: cells from 115 h old biofilm rep 4


title: cells from 115 h old biofilm rep 3


title: 31: normal size of left atrium


title: G19-B03


title: P. putida JE2212 NH4 rep 1


title: 37: normal size of left atrium


title: G19-B02


title: CRISPRi_NONO_rep1


title: CRISPRi_NCL_rep1


title: P. putida JE1657 NO3 rep 4


title: cells from 115 h old biofilm rep 1


title: CRISPRi_MATR3_rep2


title: P. putida JE1657 NO3 rep 3


title: G19-B01


title: G19-A12


title: P. putida JE1657 NO3 rep 1


title: P. putida JE1657 NO3 rep 2


title: G19-A11


title: G19-A10


title: CRISPRi_MATR3_rep1


title: CRISPRi_KHSRP_rep2


title: CRISPRi_KHSRP_rep1


title: G19-A09


title: P. putida JE1657 NH4 rep 4


title: G19-A08


title: CRISPRi_KHDRBS1_rep2


title: CRISPRi_NCL_rep2


title: G19-A07


title: CRISPRi_KHDRBS1_rep1


title: Pangasianodon hypophthalmus 11dpf_rep2

city: Auburn University

first: Xu

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

description: Illumina mRNA-seq

data_processing:
Illumina CASAVA 1.9.1 software was used for basecalling. Fastqc software was used for quality check.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic v 0.36, and masked for low-complexity or low-quality sequence.
The ramaining high-quality clean reads were mapped to pangasius whole genome using STAR v2.7.0
HTSeq-count was conducted to calculate the number of aligned reads of each gene overlapping its exons.
DESeq2 was employed to calculate the log2-fold change (log2FC), a criterion with |log2FC| ≥ 1 and p-value < 0.05 was used as the threshold for evaluating the DEGs.
Genome_build: Pangasianodon hypophthalmus genome GENO_Phyp_1.0 (GenBank assembly accession GCA_009078355.1)
Supplementary_files_format_and_content: Gzipped, tab-delimiited text file inlcuding raw reads counts for every gene in every sample

organism: Pangasianodon hypophthalmus

source_name: whole fry

extract_protocol:
RNA extraction was conducted using the Qiagen RNeasy Plus Kit following the manufacture protocols.
The RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Ribosomal RNA depletion was conducted using Ribozero rRNA Removal Kit (Illumina, San Diego, CA, USA). RNA sequencing library preparation was performed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA). Enriched RNAs were fragmented for 15 minutes at 94 °C. The first strand and second strand cDNA were subsequently synthesized. The cDNA fragments were end-repaired and adenylated at 3'ends, and a universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA) and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA).

tag: age

value: 11 days post fertilization

value: whole-body


title: cells from 115 h old biofilm rep 2


title: P. putida JE1657 NH4 rep 2


title: P. putida JE1657 NH4 rep 1


title: Pangasianodon hypophthalmus 10dpf_rep2

description: Illumina mRNA-seq

value: 10 days post fertilization


title: Pangasianodon hypophthalmus 10dpf_rep1

description: Illumina mRNA-seq


title: Pangasianodon hypophthalmus 9dpf_rep2

description: Illumina mRNA-seq

value: 9 days post fertilization