title: cdMipPs, rep110

description:
sc3_UT.rds
S520  AAGGCTAT  N707  CTCTCTAC


title: cdMipPs, rep111

status: Public on Jun 12 2021

type: SRA

city: Leuven (3000)

first: Maurilio

last: Sampaolesi

address: herestraat, 49

department: Development and regeneration

country: Belgium

institute: KU Leuven

description:
sc3_UT.rds
S521  GAGCCTTA  N707  CTCTCTAC

library_source: transcriptomic

data_processing:
50 bp single reads were generated.In the Fastq files, tags were trimmed with cutadapt 1.5. The retained tags were aligned to the Ensembl GRC38p7 human reference genome using STAR 2.4.0. Quality control on aligned and counted reads was done with Scater 1.8.4, cells with less than 150,000 reads; less than 2,500 or over 8,500 detected genes; less than 6% mitochondrial DNA and less than 10% of spike-in ERCCs were removed. Read normalization was done with Scran 1.8.4.
Count-based differential expression analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor packages.The first ten principal components were used to reduce the dimensionality of the data. Afterwards, t-SNE were computed with a perplexity of 5 in the package Seurat v2.1.0. Clustering was performed with SC3 1.8.0 using k = 2-3. Differential expression between clusters was calculated using a likelihood ratio test corrected for multiple testing with a Benjamini-Hochberg False Discovery Rate correction with MAST. Marker genes defined as genes with areas under the receiver operating curve (AUROC) > 0.85 and with P < 0.01 using SC3 1.8.0
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing matrix with read counts normalized by the library size for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Gibco™ Episomal hiPSC Line  A18945

growth_protocol: one hour prior to differentiation, iPSCs were incubated with RevitaCell™ Supplement (100X, ThermoFisher Scientific). Afterwards, PSCs were seeded single-cell on Corning® Matrigel® Matrix-coated plates (VWR, Leuven, Belgium) at a density of 50,000 cells/cm². The following day, differentiation was induced by Essential 6TM Medium (ThermoFisher Scientific) supplemented with CHIR99021 (8µM, Axon Medchem, Groningen, Nederland) for two days.

extract_protocol:
CdMiPs were sorted single-cell by FACS in 96-well plates in RLT buffer. mRNA was isolated using the genome and transcriptome sequencing protocol CdMiPs were sorted single-cell by FACS in 96-well plates in RLT buffer. mRNA was isolated using the genome and transcriptome sequencing protocol
The libraries were prepared with the Nextera XT library prep and index kit (Illumina). 100pg of cDNA was tagmented by transposase Tn5 and amplified with dual-index primers (i7 and i5, 14 cycles). In total 279 single-cell libraries were pooled together and sequenced single 50bp on a single lane of a HiSeq4000 (Illumina).
SmartSeq2 single cell RNA-Seq

treatment_protocol: Afterwards, cells were cultured in Essential 6TM medium for another two days. Small molecules such as VPA (1mM, Sigma, Saint-Louis, MO, USA) or DAPT (20µM, Tocris, Bristol, UK) were added from day 2-4.

tag: treatment

value: unVPA

tag: cell type

value: mesodermal progenitor cells


title: cdMipPs, rep133

description:
sc3_UT.rds
S507  AAGGAGTA  N711  AAGAGGCA


title: cdMipPs, rep132

description:
sc3_UT.rds
S506  ACTGCATA  N711  AAGAGGCA


title: cdMipPs, rep109

description:
sc3_UT.rds
S518  CTATTAAG  N707  CTCTCTAC


title: cdMipPs, rep108

description:
sc3_UT.rds
S517  GCGTAAGA  N707  CTCTCTAC


title: cdMipPs, rep113

description:
sc3_UT.rds
S502  CTCTCTAT  N710  CGAGGCTG


title: cdMipPs, rep107

description:
sc3_UT.rds
S516  CCTAGAGT  N707  CTCTCTAC


title: cdMipPs, rep104

description:
sc3_UT.rds
S511  TCTCTCCG  N707  CTCTCTAC


title: cdMipPs, rep103

description:
sc3_UT.rds
S510  CGTCTAAT  N707  CTCTCTAC


title: cdMipPs, rep100

description:
sc3_UT.rds
S506  ACTGCATA  N707  CTCTCTAC


title: cdMipPs, rep101

description:
sc3_UT.rds
S507  AAGGAGTA  N707  CTCTCTAC


title: cdMipPs, rep99

description:
sc3_UT.rds
S505  GTAAGGAG  N707  CTCTCTAC


title: cdMipPs, rep102

description:
sc3_UT.rds
S508  CTAAGCCT  N707  CTCTCTAC


title: cdMipPs, rep96

description:
sc3_UT.rds
S522  TTATGCGA  N706  TAGGCATG


title: cdMipPs, rep97

description:
sc3_UT.rds
S502  CTCTCTAT  N707  CTCTCTAC


title: cdMipPs, rep95

description:
sc3_UT.rds
S521  GAGCCTTA  N706  TAGGCATG


title: cdMipPs, rep114

description:
sc3_UT.rds
S503  TATCCTCT  N710  CGAGGCTG


title: cdMipPs, rep93

description:
sc3_UT.rds
S518  CTATTAAG  N706  TAGGCATG


title: cdMipPs, rep92

description:
sc3_UT.rds
S517  GCGTAAGA  N706  TAGGCATG


title: cdMipPs, rep89

description:
sc3_UT.rds
S513  TCGACTAG  N706  TAGGCATG


title: cdMipPs, rep91

description:
sc3_UT.rds
S516  CCTAGAGT  N706  TAGGCATG


title: cdMipPs, rep94

description:
sc3_UT.rds
S520  AAGGCTAT  N706  TAGGCATG


title: cdMipPs, rep87

description:
sc3_UT.rds
S510  CGTCTAAT  N706  TAGGCATG


title: cdMipPs, rep85

description:
sc3_UT.rds
S507  AAGGAGTA  N706  TAGGCATG


title: cdMipPs, rep84

description:
sc3_UT.rds
S506  ACTGCATA  N706  TAGGCATG


title: cdMipPs, rep90

description:
sc3_UT.rds
S515  TTCTAGCT  N706  TAGGCATG


title: cdMipPs, rep86

description:
sc3_UT.rds
S508  CTAAGCCT  N706  TAGGCATG


title: cdMipPs, rep88

description:
sc3_UT.rds
S511  TCTCTCCG  N706  TAGGCATG


title: cdMipPs, rep105

description:
sc3_UT.rds
S513  TCGACTAG  N707  CTCTCTAC


title: cdMipPs, rep81

description:
sc3_UT.rds
S502  CTCTCTAT  N706  TAGGCATG


title: cdMipPs, rep82

description:
sc3_UT.rds
S503  TATCCTCT  N706  TAGGCATG


title: cdMipPs, rep79

description:
sc3_UT.rds
S521  GAGCCTTA  N705  GGACTCCT


title: cdMipPs, rep80

description:
sc3_UT.rds
S522  TTATGCGA  N705  GGACTCCT


title: cdMipPs, rep106

description:
sc3_UT.rds
S515  TTCTAGCT  N707  CTCTCTAC


title: cdMipPs, rep83

description:
sc3_UT.rds
S505  GTAAGGAG  N706  TAGGCATG


title: cdMipPs, rep78

description:
sc3_UT.rds
S520  AAGGCTAT  N705  GGACTCCT


title: cdMipPs, rep77

description:
sc3_UT.rds
S518  CTATTAAG  N705  GGACTCCT


title: cdMipPs, rep98

description:
sc3_UT.rds
S503  TATCCTCT  N707  CTCTCTAC


title: cdMipPs, rep76

description:
sc3_UT.rds
S517  GCGTAAGA  N705  GGACTCCT


title: cdMipPs, rep74

description:
sc3_UT.rds
S515  TTCTAGCT  N705  GGACTCCT


title: cdMipPs, rep75

description:
sc3_UT.rds
S516  CCTAGAGT  N705  GGACTCCT


title: cdMipPs, rep72

description:
sc3_UT.rds
S511  TCTCTCCG  N705  GGACTCCT


title: cdMipPs, rep69

description:
sc3_UT.rds
S507  AAGGAGTA  N705  GGACTCCT


title: cdMipPs, rep70

description:
sc3_UT.rds
S508  CTAAGCCT  N705  GGACTCCT


title: cdMipPs, rep73

description:
sc3_UT.rds
S513  TCGACTAG  N705  GGACTCCT


title: cdMipPs, rep71

description:
sc3_UT.rds
S510  CGTCTAAT  N705  GGACTCCT


title: cdMipPs, rep65

description:
sc3_UT.rds
S502  CTCTCTAT  N705  GGACTCCT


title: cdMipPs, rep63

description:
sc3_UT.rds
S521  GAGCCTTA  N704  TCCTGAGC


title: cdMipPs, rep68

description:
sc3_UT.rds
S506  ACTGCATA  N705  GGACTCCT


title: cdMipPs, rep67

description:
sc3_UT.rds
S505  GTAAGGAG  N705  GGACTCCT


title: cdMipPs, rep66

description:
sc3_UT.rds
S503  TATCCTCT  N705  GGACTCCT


title: P1 RNA Pol II CTD S5phos-ChIP (CTD4H8) Serum

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: contains data from three replicates with different barcodes provided as raw files

library_source: genomic

data_processing:
Demultiplexing and deduplication: Sequencing was performed using 50:8:34 cycles (Read1:Index1:Read2) Illumina bcl2fastq was used to demultiplex paired-end sequencing reads by 8nt index1 read (PCR barcode). NextSeq lanes were merged into single fastq files, creating the primary fastq files. Read1 starts with 6nt UMI and 8nt barcode in the format NNNNNNABCDEFGH. A sample sheet was used with four columns corresponding to sample name, replicate name, barcode sequence, primary fastq name. For each line in the sample sheet, reads matching the barcode sequence were extracted from the primary fastq file, allowing up to two mismatches. Duplicate reads identified by identical first 24nt of read1 were discarded. Read pairs matching parts of the adaptor sequence (SBS3 or T7 promoter) in either read1 or read2 were removed. Demultiplexed and deduplicated reads were written into sample-specific fastq file used for subsequent mapping.
Mapping: Sample-specific paired fastq files were mapped using botwie2 (v2.3.4.3) using --fast parameter to the mouse genome (mm9). Alignments were processed into sorted BAM files with samtools (v1.9). Blacklisted regions were removed from BAM file using BEDTools (v2.27.1). Reads were also mapped to a metagenome of RepBase murine repetitive sequences using botwie2.
Scaling: Input coverage tracks with 1bp resolution in BigWig format were generated from BAM files using deepTools (v3.1.0) bamCoverage and scaled to a reads-per-genome-coverage of one (1xRPGC, also referred to as ‘1x normalization’) using mm9 genome size 2654895218. ChIP coverage tracks were generated from BAM files using deepTools (v3.1.0) bamCoverage. Quantitative scaling amongst samples within each pool was based on their total mapped read counts, as well as the total mapped read counts of the respective input data. One condition in the pool served as a reference (Serum condition, no treatment), which was scaled to 1xRPGC. All other samples were scaled relative to the reference using an explicit scaling factor. The RPGC was calculate by the following formula: ( #mapped[ChIP] / #mapped[Input] ) / ( #mapped[ChIP_Reference] / #mapped[Input_Reference] ).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files are scaled according to MINUTE quantification with respect to the reference of each pool (Serum condition, 1xRPGC)

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic Stem Cell

growth_protocol: Murine embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin-coated dishes.  "Serum" condition: Knockout DMEM (Life Technologies), 2 mM Glutamax (Gibco), 0.1 mM non-essential amino acids (Gibco), 15% ESC-grade fetal bovine serum (FBS) (Gibco), 0.1 mM β-mercaptoethanol, and leukemia inhibitory factor (LIF) (Millipore), "Serum2i" condition: above medium supplemented with 2i; 1 μM MEK inhibitor PD0325901 (Sigma) and 3 μM GSK3 inhibitor CHIR99021 (Sigma). "2i" condition: serum free ESGRO Complete Basal medium (Millipore) with 0.1mM LIF and 2i as described above. For all conditions cells were passaged in 48 h intervals, using accutase (Sigma) for detachment. Cell line was tested for mycoplasma contamination.

extract_protocol:
Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
Illumnina library preparation by in vitro transcription, reverse transcription and library PCR (see manuscript).

treatment_protocol: Medium was supplemented with 10 μM GSK-J4 (Sigma) for 96 h, 50 μM Zebularin for 96 h or 10 μM EPZ-6438 (BioVision) for 7 days.

tag: background

tag: condition

value: Serum

tag: antibody

value: Santa-Cruz sc-47701 (CTD4H8)

tag: minute-pool

tag: supplementary file scaling

value: 1x genome coverage


title: cdMipPs, rep60

description:
sc3_UT.rds
S517  GCGTAAGA  N704  TCCTGAGC


title: P1 H3K27me3-ChIP (C15410195) 2i + mTORi

value: Diagenode C15410195

value: relative to P1 H3K27me3-ChIP Serum


title: P1 H3K27me3-ChIP (C15410195) Serum + mTORi

value: Serum +  200nM INK128


title: P1 RNA Pol II CTD S5phos-ChIP (CTD4H8) 2i + mTORi

value: relative to P1 Pol5p Serum


title: cdMipPs, rep58

description:
sc3_UT.rds
S515  TTCTAGCT  N704  TCCTGAGC


title: cdMipPs, rep64

description:
sc3_UT.rds
S522  TTATGCGA  N704  TCCTGAGC


title: P1 RNA Pol II CTD S5phos-ChIP (CTD4H8) 2i


title: Retina_5mos_cKO_rep1

type: RNA

city: Shanghai

first: Yu-Qing

last: Rao

address: Kongjiang Road No.1665

department: Department of ophthalmology

country: China

institute: Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine

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 (G2505C) using one color scan setting for 8x60k 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: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to acquire raw data. Genespring software (version 14.8, Agilent Technologies) was applied for the basic analysis. And the raw data was normalized based on the quantile algorithm.

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

growth_protocol: Natural growth in a specific-pathogen-free (SPF) mouse facility

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Non-treatment

tag: tissue

value: whole retina

tag: gender

value: male

tag: age

tag: genotype


title: Retina_5mos_cKO_rep2


title: Retina_C57_Old_rep1


title: Retina_5mos_Control_rep2


title: cdMipPs, rep57

description:
sc3_UT.rds
S513  TCGACTAG  N704  TCCTGAGC


title: P1 H3K4me3-ChIP 2i + mTORi

value: Millipore 04-745

value: relative to P1 H3K4me3-ChIP Serum


title: P1 RNA Pol II CTD S5phos-ChIP (CTD4H8) Serum + mTORi


title: Retina_C57_Old_rep2


title: Retina_5mos_cKO_rep3


title: Retina_5mos_Control_rep3


title: cdMipPs, rep61

description:
sc3_UT.rds
S518  CTATTAAG  N704  TCCTGAGC


title: Retina_5mos_Control_rep1


title: cdMipPs, rep62

description:
sc3_UT.rds
S520  AAGGCTAT  N704  TCCTGAGC


title: BglHalo_Xist_SLAM-seq_120min

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Estimation of nuclear RNA half-life was performed using GRAND-SLAM. Briefly, the paired-end sequencing reads were mapped to mouse genome mm10 by STAR (v2.5.2b) with the key parameters (--outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --alignEndsType EndToEnd). Given that T to C conversion is the signature of SLAM-seq, then we calculated the T to C conversion rate as 4sU incorporation and average of all the rest conversions as background due to errors from sequencing or library preparation. The T to C conversion rate and background rate were calculated accordingly for each sample. We assume the nuclear RNA decay follows exponential model, so we fit the T2C conversion rate (or T2C conversion rate -corresponding background rate) to the exponential model to estimate RNA’s half-life in nucleus. In addition, the sample (Dox-treated A11B2 cells, ChrRNA-seq) without 4sU incorporation was used to estimate the background mutation rate for all 12 potential mismatches. Half-life of Xist RNA and another nuclear lncRNA Pvt1  were plotted.
Genome_build: mm10
Supplementary_files_format_and_content: text

growth_protocol: Cells were grown in gelatine-coated 6-well plates after pre-plating to discard feeder cells, with 6 wells needed for each experimental replica. When reaching 60-70% confluency, cells were induced with 1 μg/ml doxycycline for 17.5 - 20h depending on the length of the subsequent washout times. Then, transcribed RNA was labelled with 4SU by incubation with medium containing 500 μM 4SU (Lexogen) and 1 μg/ml doxycycline for 4h. Next, 4SU was withdrawn by washout for all samples except the 0 min sample. Different samples were washed with medium containing 1 μg/ml doxycycline and 50 mM Uridine (in excess, Lexogen) for 30 min, 60 min, 90 min, 120 min and 150 min respectively. Induction, 4SU labelling and withdrawal times were staggered, such that all samples could be harvested at the same time despite the different washout times.

extract_protocol:
After cells were collected by centrifugation at 1 500 g for 5 min in PBS, nuclear extracts were obtained as follows: Cells were washed again with PBS and resuspended in 10 volumes buffer A (10 mM Hepes pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.5 mM DTT and complete protease inhibitors in RNase free water). Subsequently cells were incubated on ice for 10 min and recovered by centrifugation, followed by resuspension in 3 volumes buffer A with 0.1 % NP-40 for 10 min. Nuclei were recovered by centrifugation at and TRIzol/chloroform RNA extraction was performed using the SLAMSeq Kinetics Kit (Lexogen). Then, samples were treated with Iodoacetamide to modify the 4-thiol group of S4U-containing nucleotides via the addition of a carboxyamidomethyl group using the SLAMSeq Kinetics Kit (Lexogen). The RNA was precipitated and washed again, before being resuspended in nuclease free water. 1 ng RNA of each sample were run on the bioanalyzer to determine the exact RNA concentration and RNA integrity of all samples. Based on this, 1 μg RNA of each sample was then taken forward for library preparation using the Illumina TruSeq stranded total RNA kit (RS-122-2301). Quantification of the libraries was performed by qPCR using KAPA Library Quantification DNA standards (Kapa Biosystems, KK4903). Finally, the libraries were pooled and 2 × 81 paired-end sequencing was performed using Illumina NextSeq500 (FC-404-2002).
TruSeq RNAseq

treatment_protocol: Dox + 4sU

tag: strain background

value: 129S X Cast

value: Female

tag: xist locus

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele) and Bgl-stem-loop was inserted into Xist 3'-end

tag: agent

value: Dox + 4sU

tag: time course

value: Back to Dox_only medium 120min

tag: medium

value: ES medium

tag: sequenced molecule

value: Nuclear RNA


title: P1 H3K4me3-ChIP Serum + mTORi


title: BglHalo_Xist_SLAM-seq_60min

value: Back to Dox_only medium 60min


title: cdMipPs, rep59

description:
sc3_UT.rds
S516  CCTAGAGT  N704  TCCTGAGC

tag: treatment

value: unVPA

value: mesodermal progenitor cells


title: BglHalo_Xist_SLAM-seq_30min

value: Back to Dox_only medium 30min


title: P1 Input Serum + mTORi

value: Input

value: 1x genome coverage


title: P1 Input 2i + mTORi

value: Serum +  200nM INK128


title: cdMipPs, rep49

description:
sc3_UT.rds
S502  CTCTCTAT  N704  TCCTGAGC

tag: cell type


title: cdMipPs, rep56

description:
sc3_UT.rds
S511  TCTCTCCG  N704  TCCTGAGC


title: cdMipPs, rep46

description:
sc3_UT.rds
S520  AAGGCTAT  N703  AGGCAGAA


title: SPOCmut_G1_NoDox

description:
SPOCmut_NoDox
Ratio_chrX_Spen.txt

data_processing:
The RNA-seq data mapping pipeline was similar to our previous study (Nesterova et al., 2019). Briefly, the raw fastq files of read pairs were first mapped to an rRNA build by bowtie2 (v2.3.2) (Langmead and Salzberg, 2012) and rRNA-mapped reads discarded. The remaining unmapped reads were aligned to the ‘N-masked’ genome (from mm10 coordinates) with STAR (v2.4.2a) using parameters “--outFilterMultimapNmax 1 --outFilterMismatchNmax 4 --alignEndsType EndToEnd” for all the sequencing libraries (Dobin et al., 2013). Unique alignments were retained for further analysis. We made use of 23,005,850 SNPs between Cast and 129S genomes and employed SNPsplit to split the alignment into distinct alleles (Cast and 129S) using the parameter “--paired”. The (allelic) read numbers were counted by the program featureCounts (-t transcript -g gene_id -s 2) (Liao et al., 2014) and the alignments were sorted by Samtools (Li et al., 2009). Bigwig files were generated by Bedtools (Quinlan and Hall, 2010) and visualized by IGV (Robinson et al., 2011) or UCSC Genome Browser. For biallelic analysis, counts were normalized to 1 million mapped read pairs (as CPM) by the edgeR R package. Genes with at least 10 SNP-covering reads across all the samples were further taken to calculate the allelic ratio of where Xi and Xa indicate inactive and active allele, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: text

growth_protocol: ES cells were grown in DMEM media supplemented with 10% fetal calf serum (Seralab), 2 mM L-glutamine, 1X non-essential amino acids, 50 µM β-mercaptoethanol, 1X penicillin / streptomycin (all from Life Technologies) and 1000 U/mL LIF (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2. Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 to 1.5 µg/mL of doxycycline for 24 hours.

extract_protocol:
Chromatin RNA was extracted from one confluent 15 cm dish of mESCs. Briefly, cells were trypsinised and washed in PBS. Cells were lysed on ice in RLB (10 mM Tris pH 7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40), and nuclei were purified by centrifugation through a sucrose cushion (24% sucrose in RLB). The nuclei pellet was resuspended in NUN1 (20 mM Tris pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol), then lysed with NUN2 (20 mM Hepes pH 7.9, 300 mM, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea). Samples were incubated for 15 minutes on ice then centrifuged at 2800 g to isolate the insoluble chromatin fraction. The chromatin pellet was resuspended in TRIzol by passing multiple times through a 23 gauge needle. Finally chromatin-associated RNA was purified through standard TRIzol/chloroform extraction followed by isopropanol precipitation. Samples were then treated with Turbo DNAse, and 500ng – 1µg of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by qPCR with KAPA Library Quantification DNA standards (KAPA Biosystems). The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq500.
TruSeq RNAseq

treatment_protocol: Dox treatment

tag: genotype and agent

value: Chromatin-Associated RNA


title: SPOCmut_C2_24hDox

description:
SPOCmut_Dox_24h
Ratio_chrX_Spen.txt


title: SPOCmut_G1_24hDox

description:
SPOCmut_Dox_24h
Ratio_chrX_Spen.txt


title: trans_BglHalo_noDox1

description:
TransgenicXist_chr15_NoDox
Ratio_chr15.txt

value: Male

value: transgenic Xist (with bgl-stem-loop array inserted in the 3’ end) on chr15 expressing BglG-Halo under doxycycline inducible promoter


title: BglHalo_Xist_SLAM-seq_150min

value: 129S X Cast

value: Back to Dox_only medium 150min


title: cdMipPs, rep55

description:
sc3_UT.rds
S510  CGTCTAAT  N704  TCCTGAGC


title: cdMipPs, rep54

description:
sc3_UT.rds
S508  CTAAGCCT  N704  TCCTGAGC


title: SPOCmut_C2_NoDox

description:
SPOCmut_NoDox
Ratio_chrX_Spen.txt

value: Female

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele) and Bgl-stem-loop was inserted into Xist 3'-end


title: BglHalo_Xist_SLAM-seq_90min

value: Dox + 4sU

value: Back to Dox_only medium 90min


title: cdMipPs, rep42

description:
sc3_UT.rds
S515  TTCTAGCT  N703  AGGCAGAA


title: cdMipPs, rep53

description:
sc3_UT.rds
S507  AAGGAGTA  N704  TCCTGAGC


title: SPOCmut_C10_24hDox

description:
SPOCmut_Dox_24h
Ratio_chrX_Spen.txt

value: ES medium


title: cdMipPs, rep41

description:
sc3_UT.rds
S513  TCGACTAG  N703  AGGCAGAA


title: SPOCmut_C10_NoDox

description:
SPOCmut_NoDox
Ratio_chrX_Spen.txt


title: cdMipPs, rep51

description:
sc3_UT.rds
S505  GTAAGGAG  N704  TCCTGAGC


title: BglHalo_Xist_SLAM-seq_0min

value: Back to Dox_only medium 0min

value: Nuclear RNA


title: cdMipPs, rep50

description:
sc3_UT.rds
S503  TATCCTCT  N704  TCCTGAGC

value: unVPA

value: mesodermal progenitor cells


title: cdMipPs, rep43

description:
sc3_UT.rds
S516  CCTAGAGT  N703  AGGCAGAA


title: trans_BglHalo_24Dox1

description:
TransgenicXist_chr15_24h
Ratio_chr15.txt


title: trans_BglHalo_24Dox2


title: cdMipPs, rep48

description:
sc3_UT.rds
S522  TTATGCGA  N703  AGGCAGAA


title: trans_BglHalo_noDox2


title: SpenKO_BglHalo_noDox2

description:
SpenKO_NoDox
Ratio_chrX_Spen.txt


title: SpenKO_BglHalo_24hDox1

description:
SpenKO_Dox_24h
Ratio_chrX_Spen.txt


title: cdMipPs, rep37

description:
sc3_UT.rds
S507  AAGGAGTA  N703  AGGCAGAA


title: cdMipPs, rep47

description:
sc3_UT.rds
S521  GAGCCTTA  N703  AGGCAGAA


title: SpenKO_BglHalo_3hDox

description:
SpenKO_Dox_3h
Ratio_chrX_Spen.txt


title: cdMipPs, rep34

description:
sc3_UT.rds
S503  TATCCTCT  N703  AGGCAGAA


title: cdMipPs, rep44

description:
sc3_UT.rds
S517  GCGTAAGA  N703  AGGCAGAA


title: cdMipPs, rep45

description:
sc3_UT.rds
S518  CTATTAAG  N703  AGGCAGAA


title: cdMipPs, rep52

description:
sc3_UT.rds
S506  ACTGCATA  N704  TCCTGAGC


title: cdMipPs, rep33

description:
sc3_UT.rds
S502  CTCTCTAT  N703  AGGCAGAA


title: cdMipPs, rep40

description:
sc3_UT.rds
S511  TCTCTCCG  N703  AGGCAGAA


title: cdMipPs, rep38

description:
sc3_UT.rds
S508  CTAAGCCT  N703  AGGCAGAA


title: cdMipPs, rep36

description:
sc3_UT.rds
S506  ACTGCATA  N703  AGGCAGAA


title: cdMipPs, rep32

description:
sc3_UT.rds
S522  TTATGCGA  N702  CGTACTAG


title: cdMipPs, rep31

description:
sc3_UT.rds
S521  GAGCCTTA  N702  CGTACTAG


title: SpenKO_BglHalo_24hDox2

description:
SpenKO_Dox_24h
Ratio_chrX_Spen.txt


title: cdMipPs, rep39

description:
sc3_UT.rds
S510  CGTCTAAT  N703  AGGCAGAA


title: CIZ1KO_BglHalo_noDox1

description:
CIZKO_NoDox
Ratio_chrX_CIZ1.txt


title: cdMipPs, rep30

description:
sc3_UT.rds
S520  AAGGCTAT  N702  CGTACTAG


title: cdMipPs, rep29

description:
sc3_UT.rds
S518  CTATTAAG  N702  CGTACTAG


title: cdMipPs, rep35

description:
sc3_UT.rds
S505  GTAAGGAG  N703  AGGCAGAA


title: BglHalo_10H_24hDox2

description:
WT_Dox_24h
Ratio_chrX_CIZ1.txt


title: CZIKO_BglHalo_NPC(d30)

description:
CIZ1KO__NPC_d30
Ratio_chrX_CIZ1.txt

value: diff NPC medium


title: cdMipPs, rep28

description:
sc3_UT.rds
S517  GCGTAAGA  N702  CGTACTAG


title: SpenKO_BglHalo_noDox1

description:
SpenKO_NoDox
Ratio_chrX_Spen.txt


title: cdMipPs, rep25

description:
sc3_UT.rds
S513  TCGACTAG  N702  CGTACTAG


title: CIZ1KO_BglHalo_24hDox2

description:
CIZKO_Dox_24h
Ratio_chrX_CIZ1.txt


title: cdMipPs, rep27

description:
sc3_UT.rds
S516  CCTAGAGT  N702  CGTACTAG


title: BglHalo_10H_NPC(d30)

description:
WT__NPC_d30
Ratio_chrX_CIZ1.txt


title: BglHalo_10H_3hDox1

description:
WT_Dox_3h
Ratio_chrX_Spen.txt


title: CIZ1KO_BglHalo_24hDox1

description:
CIZKO_Dox_24h
Ratio_chrX_CIZ1.txt


title: BglHalo_10H_24hDox1

description:
WT_Dox_24h
Ratio_chrX_CIZ1.txt


title: cdMipPs, rep26

description:
sc3_UT.rds
S515  TTCTAGCT  N702  CGTACTAG


title: BglHalo_10H_3hDox2

description:
WT_Dox_3h
Ratio_chrX_Spen.txt


title: cdMipPs, rep24

description:
sc3_UT.rds
S511  TCTCTCCG  N702  CGTACTAG


title: CIZ1KO_BglHalo_noDox2

description:
CIZKO_NoDox
Ratio_chrX_CIZ1.txt


title: cdMipPs, rep23

description:
sc3_UT.rds
S510  CGTCTAAT  N702  CGTACTAG


title: BglHalo_10H_noDox2

description:
WT_NoDox
Ratio_chrX_Spen.txt


title: cdMipPs, rep22

description:
sc3_UT.rds
S508  CTAAGCCT  N702  CGTACTAG


title: N5 - miRNA Sequencing

city: shanghai

first: Tao

last: Duan

address: NO.2699, West Gao ke Road, Pudong New District

department: obstetrics

institute: shanghai first maternity and infant hospital , tongji university school of medicine

data_processing:
The overall quality of raw reads was evaluated using program FastQC, and then raw reads were trimmed to remove adapter sequences using Cutadapt script
As for microRNA sequencing, the cleaned reads were mapped to human genomes GRCh38 by bowtie.
As for RNA sequencing, the cleaned reads were mapped to human genome hg19/GRCh37 using the Hisat2 with perfect matches (0 mismatches).
miRDeep2 was used to quantify the expression level of known mature miRNAs curated in the human miRBase database.
RNA-level quantification was performed using StringTie, which is a reads summarization program to efficiently count the mapped reads for genomic features
The miRNA-seq and RNA-seq data were analyzed by Edge R package, which employs a negative binomial generalized linear model with likelihood ratio test (glmLRT) to compare read counts of each miRNA or gene between two conditions
Differentially expressed miRNAs and genes were classified using a significance of log2 fold change > 1.5 or <-1.5 and a p -value < 0.05.
The count-per-million (CPM) at log2 scale, denoted as LogCPM, was computed for visualization of miRNA/gene abundance, heatmap-clustering analysis.
Genome_build: hg19/GRCh38/GRCh37
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: placenta

extract_protocol:
Total RNA was extracted from the frozen human placentas using TRIZOL reagent following the manufacturer’s protocol. The RNA yield and purity were determined using Agilent 2100 Bio-analyzer (Agilent Technologies, Santa Clara, CA, United States) and NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, United States). All RNA samples passed quality control.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta

tag: disease

value: preterm birth


title: P1 RNA Pol II CTD S5phos-ChIP (CTD4H8) HeLa

description: processed data file not provided since only used for quality control

source_name: HeLa

tag: background

value: Epitheloid cervix carcinoma

tag: condition

value: DMEM

tag: antibody

value: Santa-Cruz sc-47701 (CTD4H8)

value: relative to P1 Pol5p Serum


title: N2 - miRNA Sequencing

tag: tissue


title: BglHalo_10H_noDox1

description:
WT_NoDox
Ratio_chrX_Spen.txt

value: 129S X Cast

tag: gender

value: Chromatin-Associated RNA


title: cdMipPs, rep21

description:
sc3_UT.rds
S507  AAGGAGTA  N702  CGTACTAG


title: N3 - miRNA Sequencing


title: cdMipPs, rep17

description:
sc3_UT.rds
S502  CTCTCTAT  N702  CGTACTAG


title: cdMipPs, rep15

description:
sc3_UT.rds
S521  GAGCCTTA  N701  TAAGGCGA


title: PE4 - miRNA Sequencing

value: early-onset preeclampsia


title: cdMipPs, rep16

description:
sc3_UT.rds
S522  TTATGCGA  N701  TAAGGCGA


title: cdMipPs, rep19

description:
sc3_UT.rds
S505  GTAAGGAG  N702  CGTACTAG


title: cdMipPs, rep18

description:
sc3_UT.rds
S503  TATCCTCT  N702  CGTACTAG


title: PE2 - miRNA Sequencing


title: N4 - miRNA Sequencing


title: cdMipPs, rep13

description:
sc3_UT.rds
S518  CTATTAAG  N701  TAAGGCGA


title: N1 - miRNA Sequencing


title: PE5 - miRNA Sequencing


title: cdMipPs, rep14

description:
sc3_UT.rds
S520  AAGGCTAT  N701  TAAGGCGA


title: PE3 - miRNA Sequencing


title: cdMipPs, rep9

description:
sc3_UT.rds
S513  TCGACTAG  N701  TAAGGCGA


title: cdMipPs, rep20

description:
sc3_UT.rds
S506  ACTGCATA  N702  CGTACTAG


title: cdMipPs, rep12

description:
sc3_UT.rds
S517  GCGTAAGA  N701  TAAGGCGA


title: cdMipPs, rep4

description:
sc3_UT.rds
S506  ACTGCATA  N701  TAAGGCGA


title: cdMipPs, rep8

description:
sc3_UT.rds
S511  TCTCTCCG  N701  TAAGGCGA


title: cdMipPs, rep5

description:
sc3_UT.rds
S507  AAGGAGTA  N701  TAAGGCGA


title: cdMipPs, rep11

description:
sc3_UT.rds
S516  CCTAGAGT  N701  TAAGGCGA


title: cdMipPs, rep3

description:
sc3_UT.rds
S505  GTAAGGAG  N701  TAAGGCGA


title: cdMipPs, rep2

description:
sc3_UT.rds
S503  TATCCTCT  N701  TAAGGCGA


title: cdMipPs, rep7

description:
sc3_UT.rds
S510  CGTCTAAT  N701  TAAGGCGA


title: cdMipPs, rep10

description:
sc3_UT.rds
S515  TTCTAGCT  N701  TAAGGCGA


title: PE1 - miRNA Sequencing


title: hiPSCs, rep18

description:
sc3_iPSC.rds
S511  TCTCTCCG  N729  TCGACGTC

value: induced pluripotent stem cells


title: cdMipPs, rep6

description:
sc3_UT.rds
S508  CTAAGCCT  N701  TAAGGCGA


title: hiPSCs, rep16

description:
sc3_iPSC.rds
S508  CTAAGCCT  N729  TCGACGTC


title: hiPSCs, rep17

description:
sc3_iPSC.rds
S510  CGTCTAAT  N729  TCGACGTC


title: cdMipPs, rep1

description:
sc3_UT.rds
S502  CTCTCTAT  N701  TAAGGCGA


title: hiPSCs, rep15

description:
sc3_iPSC.rds
S507  AAGGAGTA  N729  TCGACGTC


title: hiPSCs, rep14

description:
sc3_iPSC.rds
S506  ACTGCATA  N729  TCGACGTC


title: dark-DAG5-bri1-116

city: Vienna

first: Ho-Seok

last: Lee

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description: 6.dark-DAG5-Col0.vs.dark-DAG5-bri1-116.xlsx

data_processing:
Basecalls performed using CASAVA v1.8.2
Tophat v2.0.13 against to Arabidopsis TAIR10
cuffdiff v2.2.0 for FPKM and fold change calculation
Genome_build: TAIR10
Supplementary_files_format_and_content: spread sheet and DEGs

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: To grow seedlings, seeds were surface-sterilized and grown on plates with ½ Murashige and Skoog (MS) with 1% sucrose and 0.8% phyto agar at 22°C under long-day (16h-Light / 8h-Dark) or dark conditions.

extract_protocol: Truseq mRNA prep kit

treatment_protocol: Mock (EtOH) or DEX 1μM containg plates

tag: cell types

value: Whole seedling

value: Mock (EtoH)

tag: ecotype

tag: genotypes

value: wildtype

tag: group

value: 5-days-after sowing in the dark


title: new-DAG9-bri1-116

value: 9-days-old seedlings in the light


title: DAG9-25-DEX

value: DEX

value: day RNAi


title: DAG9-Col0


title: DAG9-3-EtOH


title: hiPSCs, rep11

description:
sc3_iPSC.rds
S502  CTCTCTAT  N729  TCGACGTC

value: unVPA


title: merged_HNHRep2-HNHABEmax

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

data_processing:
Library strategy: DNA-seq
We directly analzed the fastq files using an online tool CRISPRESSO2. We therefore do not have any additional processed data.

source_name: HEK cells

growth_protocol: DMEM grwoth medium supplemented with 10% FBS and 1% P/S

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation
targeted amplicon sequencing; two step PCR

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus. The guide-RNA used is indicated in short as sg (single-guide) and the targeted locus is annotated as in the manuscript (https://doi.org/10.1101/2020.11.09.371237)

tag: cell line

value: HEK

tag: treatment method

value: Lipofection

tag: treatment type

value: library


title: merged_HNHRep2-HNHABEmax-Dimer


title: merged_HNHRep2-HNHABE8e-Dimer


title: hiPSCs, rep10

description:
sc3_iPSC.rds
S511  TCTCTCCG  N728  TGCAGCTA


title: merged_HNHRep2-HNHABE8e


title: hiPSCs, rep9

description:
sc3_iPSC.rds
S510  CGTCTAAT  N728  TGCAGCTA


title: merged_HNHRep2-ABEmax


title: merged_HNHRep2-Ctrl


title: merged_HNHRep2-ABE8e


title: dark-DAG5-Col0


title: hiPSCs, rep8

description:
sc3_iPSC.rds
S508  CTAAGCCT  N728  TGCAGCTA


title: merged_HNHRep1-HNHABE8e


title: merged_HNHRep1-HNHABEmax


title: merged_HNHRep1-HNHABEmax-Dimer


title: hiPSCs, rep6

description:
sc3_iPSC.rds
S506  ACTGCATA  N728  TGCAGCTA


title: dark-DAG5-3-EtOH

description: 4.dark-DAG5-3-EtOH.vs.dark-DAG5-25-DEX.xlsx


title: hiPSCs, rep7

description:
sc3_iPSC.rds
S507  AAGGAGTA  N728  TGCAGCTA


title: dark-DAG5-25-DEX


title: hiPSCs, rep13

description:
sc3_iPSC.rds
S505  GTAAGGAG  N729  TCGACGTC


title: merged_HNHRep1-Ctrl


title: merged_HNHRep1-HNHABE8e-Dimer


title: merged_HNHRep1-ABEmax


title: hiPSCs, rep4

description:
sc3_iPSC.rds
S503  TATCCTCT  N728  TGCAGCTA


title: hiPSCs, rep12

description:
sc3_iPSC.rds
S503  TATCCTCT  N729  TCGACGTC


title: RTTG_3_2_guide25


title: RTTG_3_2_guide20


title: RTTG_3_1_guide25


title: RTTG_2_1_guide25


title: hiPSCs, rep3

description:
sc3_iPSC.rds
S502  CTCTCTAT  N728  TGCAGCTA


title: RTTG_2_2_guide25


title: RTTG_2_2_guide20


title: merged_HNHRep1-ABE8e


title: hiPSCs, rep5

description:
sc3_iPSC.rds
S505  GTAAGGAG  N728  TGCAGCTA


title: hiPSCs, rep2

description:
sc3_iPSC.rds
S511  TCTCTCCG  N727  CGATCAGT


title: RTTG_1_2_guide20


title: RTTG_1_1_guide25


title: RTTG_1_1_guide20


title: EKNS_3_2_guide25


title: RTTG_2_1_guide20


title: hiPSCs, rep1

description:
sc3_iPSC.rds
S510  CGTCTAAT  N727  CGATCAGT


title: RTTG_1_2_guide25


title: EKNS_3_1_guide25


title: EKNS_2_2_guide25


title: EKNS_2_2_guide20


title: EKNS_3_2_guide20


title: X633

city: Rotterdam

first: Dora

last: Hammerl

address: Erasmus MC Cancer Institute, Doctor Molewaterplein 40, BE430 (room)

department: Mediacl Oncology

country: Netherlands

institute: Erasmus MC Cancer Institute

data_processing:
alignment with GRCh38 using the STAR algorithm (version 2.4.2a)
geTMM normalization
log2 normalization
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized count data in log 2 format

source_name: Triple-negative breast cancer

extract_protocol:
RNA was isolated from fresh frozen triple negative breast cancer (TNBC)
RNAseq data was collected using 150 bp paired-end with LncRNA library (Ribo-zero RNA) on Illumina HiSeq.

value: Triple-negative breast cancer

tag: immunophenotype

value: excluded

tag: tcr diversity (gini simpson index)


title: X523

value: ignored


title: EKNS_3_1_guide20


title: X864


title: EKNS_2_1_guide25


title: RTTG_3_1_guide20


title: X894

value: inflamed


title: X780


title: EKNS_2_1_guide20


title: EKNS_1_2_guide25


title: X9311


title: X4423


title: EKNS_1_2_guide20


title: X4441


title: X4413


title: K562-ctrl-site18-Rep3

source_name: K562 cells


title: K562-ctrl-site18-Rep2


title: X4412


title: HNH-K562-HNHx8e-dimer-site18-Rep3


title: HNH-K562-HNHx-site18-Rep2


title: HNH-K562-HNHx-site18-Rep3


title: HNH-K562-HNHx8e-dimer-site18-Rep2


title: HNH-K562-HNHx-dimer-site18-Rep3


title: HNH-K562-HNH8e-site18-Rep2


title: HNH-K562-HNHx-dimer-site18-Rep2


title: HNH-K562-ABEmax-site18-Rep3


title: HNH-K562-ABEmax-site18-Rep2


title: X4254


title: HNH-K562-ABE8e-site18-Rep3


title: HNH-K562-ABE8e-site18-Rep2


title: X4101


title: HNH-K562-HNH8e-site18-Rep3


title: X2441


title: X4066


title: X2842


title: HNH-HEK-HNHx8e-dimer-site18-Rep2


title: EKNS_1_1_guide25


title: HNH-HEK-HNHx8e-dimer-site18-Rep3


title: X243


title: X4411


title: X4273


title: HNH-HEK-HNHx-dimer-site18-Rep2


title: HNH-HEK-HNHx-site18-Rep2


title: EKNS_1_1_guide20


title: HNH-HEK-HNHx-dimer-site18-Rep3


title: X236


title: HNH-HEK-ABEmax-site18-Rep3


title: HNH-HEK-HNH8e-site18-Rep2


title: HNH-HEK-HNH8e-site18-Rep3


title: HNH-HEK-ABE8e-site18-Rep3


title: X2266


title: X2007


title: HEK-ctrl-site18-Rep2


title: HEK-ctrl-site18-Rep3


title: X1971


title: X2049


title: HNH-HEK-HNHx-site18-Rep3


title: K562-ctrl-site11-Rep2


title: HNH-K562-HNHx8e-dimer-site11-Rep3


title: X1966


title: X1858


title: HNH-K562-HNHx-dimer-site11-Rep2


title: HNH-K562-HNHx-dimer-site11-Rep3


title: X1817


title: HNH-K562-HNHx-site11-Rep2


title: X2327


title: HNH-K562-HNH8e-site11-Rep2


title: HNH-K562-ABEmax-site11-Rep3


title: HNH-K562-HNH8e-site11-Rep3


title: HNH-K562-HNHx8e-dimer-site11-Rep2


title: X1589


title: HNH-K562-ABEmax-site11-Rep2


title: HNH-HEK-ABEmax-site18-Rep2


title: HNH-HEK-ABE8e-site18-Rep2


title: K562-ctrl-site11-Rep3


title: X1537


title: HNH-K562-HNHx-site11-Rep3


title: X1491


title: HNH-K562-ABE8e-site11-Rep3


title: X1487


title: X1634


title: X1197


title: X1482


title: X1200


title: JA121


title: JA113


title: X1563


title: JA094


title: JA074


title: JA064


title: JA061


title: HNH-K562-HNHx-site8-Rep3


title: HNH-K562-HNHx-site8-Rep2


title: HNH-K562-HNHx8e-dimer-site8-Rep3


title: HNH-K562-HNHx-dimer-site8-Rep3


title: HNH-K562-HNH8e-site8-Rep3


title: K562-ctrl-site8-Rep3


title: K562-ctrl-site8-Rep2


title: HNH-HEK-HNHx-dimer-site11-Rep2


title: HNH-HEK-HNH8e-site11-Rep2


title: HNH-HEK-HNHx8e-dimer-site11-Rep3


title: HEK-ctrl-site11-Rep2


title: HNH-HEK-ABEmax-site11-Rep3


title: HNH-HEK-HNH8e-site11-Rep3


title: HNH-HEK-HNHx-site11-Rep2


title: HNH-HEK-HNHx-site11-Rep3


title: HNH-HEK-ABE8e-site11-Rep2


title: HNH-HEK-HNHx8e-dimer-site11-Rep2


title: HEK-ctrl-site11-Rep3


title: HNH-HEK-ABE8e-site11-Rep3


title: HNH-HEK-HNHx-dimer-site11-Rep3


title: HNH-HEK-ABEmax-site11-Rep2


title: HNH-K562-ABE8e-site11-Rep2


title: HNH-K562-HNHx8e-dimer-site8-Rep2


title: HNH-K562-HNHx-dimer-site8-Rep2


title: HNH-K562-ABEmax-site8-Rep2


title: JA020


title: HNH-K562-ABEmax-site8-Rep3


title: HNH-K562-ABE8e-site8-Rep3


title: HNH-K562-HNH8e-site8-Rep2


title: ZNF-3_IFNa

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

data_processing:
Sequence reads were aligned using STAR aligner with GRCh38 reference genome.
HTSeq-count was used to generate count files.
For each individual, the fold change (FC) between unstimulated and stimulated conditions were calculated. Genes with fold change higher than 1.5 fold in all the controls were used to filter the residual responsive genes to generate heatmaps.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.

source_name: EBV-B

growth_protocol: EBV-B cells from healthy controls (n=3), D427ins17 patients’ (P1, P2, P3),  and AD HIES patients’ (n=3) heterozygous for STAT3 mutations (R382W, V463del, T708N),  were starved by incubation in pure RPMI for two hours, and then stimulated by incubation for  two hours with 100 ng/mL IL-6/IL-6Rα (R&D #8954-SR), 100 ng/mL IL-21 (R&D #8879-  IL), 100 ng/mL IL-23 (R&D #1290-IL), 50 ng/mL IL-10 (R&D #217-IL), or 104 IU/mL IFNα  (IntronA MSD).

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro Kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: AD-HIES Patient

tag: treatment

value: IFNa


title: HNH-HEK-HNHx-site8-Rep2


title: HNH-HEK-HNHx8e-dimer-site8-Rep3


title: HNH-HEK-HNHx-site8-Rep3


title: ZNF-3_IL23

treatment_protocol: EBV-B cells from healthy controls (n=3), D427ins17 patients’ (P1, P2, P3),  and AD HIES patients’ (n=3) heterozygous for STAT3 mutations (R382W, V463del, T708N),  were starved by incubation in pure RPMI for two hours, and then stimulated by incubation for  two hours with 100 ng/mL IL-6/IL-6Rα (R&D #8954-SR), 100 ng/mL IL-21 (R&D #8879-  IL), 100 ng/mL IL-23 (R&D #1290-IL), 50 ng/mL IL-10 (R&D #217-IL), or 104 IU/mL IFNα  (IntronA MSD).


title: HNH-HEK-HNHx8e-dimer-site8-Rep2


title: HNH-HEK-HNHx-dimer-site8-Rep3


title: HNH-K562-ABE8e-site8-Rep2


title: ZNF-3_NS

value: NS


title: HNH-HEK-HNH8e-site8-Rep3


title: ZNF-3_supIL6


title: HNH-HEK-ABEmax-site8-Rep3


title: ZNF-3_IL21


title: HNH-HEK-ABE8e-site8-Rep3


title: HEK-ctrl-site8-Rep3


title: HEK-ctrl-site8-Rep2


title: HNH-HEK-ABE8e-site8-Rep2


title: HNH-HEK-HNHx-dimer-site8-Rep2


title: HNH-k562-site18-ctrl


title: HNH-HEK-HNH8e-site8-Rep2


title: NRCOS555

city: Pittsburgh

first: Kathryn

last: Torok

state: Pennsylvania

address: 530 45th St, Rangos 9161 Bay1

department: Peds Rheumatology

country: USA

institute: University of Pittsburgh

data_processing:
aligned using STAR
quantified using Partek E/M
DEG using DESeq2
Genome_build: hg38 - Ensembl Transcripts release 93
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: paraffin-embedded skin from 4mm bx

extract_protocol:
Qiagen AllPrep® DNA/RNA FFPE (Qiagen #80234) and the Qiagen RNeasy Mini (Qiagen #74014) extraction kits
Illumina HTS TrueSeq Access library

tag: sample type

value: FFPE

tag: condition 1

value: Active LS

tag: condition 2

value: Linear Face/Scalp


title: ZNF-2_IL23


title: NRCOS546

value: Generalized Morphea


title: HNH-K562-HNHx-site18-Rep1


title: HNH-K562-HNHx8e-dimer-site18-Rep1


title: ZNF-2_IFNa


title: ZNF-3_IL10


title: HNH-HEK-ABEmax-site8-Rep2


title: HNH-K562-HNH8e-site18-Rep1


title: HNH-K562-ABEmax-site18-Rep1


title: HNH-K562-ABE8e-site18-Rep1


title: NRCOS540


title: ZNF-2_supIL6


title: HNH-K562-HNHx-dimer-site18-Rep1


title: ZNF-2_NS


title: NRCOS490

value: Circumscribed Morphea Superficial


title: NRCOS507

value: Linear Trunk/Limb


title: ZNF-2_IL21


title: HNH-HEK-HNHx8e-dimer-site18-Rep1


title: HNH-HEK-HNH8e-site18-Rep1


title: NRCOS474


title: HNH-HEK-ABE8e-site18-Rep1


title: ZNF-1_IFNa


title: HNH-HEK-ABEmax-site18-Rep1


title: ZNF-2_IL10


title: ZNF-1_IL10


title: HNH-HEK-HNHx-dimer-site18-Rep1


title: HNH-k562-site11-ctrl


title: HNH-K562-HNHx-site11-Rep1


title: HNH-K562-HNHx8e-dimer-site11-Rep1


title: ZNF-1_IL21


title: NRCOS414

value: Inactive LS


title: ZNF-1_IL23


title: NRCOS388

value: Circumscribed Morphea Deep


title: HNH-K562-HNH8e-site11-Rep1

value: Lipofection


title: NRCOS348


title: HNH-K562-ABEmax-site11-Rep1


title: P9_IFNa

value: Patient 9


title: ZNF-1_supIL6


title: NRCOS320


title: ZNF-1_NS


title: NRCOS284


title: HNH-HEK-HNHx-dimer-site11-Rep1

value: HEK


title: NRCOS262


title: P9_IL10


title: HNH-HEK-ABEmax-site11-Rep1


title: NRCOS247

value: Circumscribed


title: HNH-HEK-HNH8e-site11-Rep1


title: HNH-HEK-ABE8e-site11-Rep1


title: HNH-k562-site8-ctrl


title: P9_IL23


title: P9_IL21


title: HNH-K562-HNHx-dimer-site11-Rep1


title: HNH-K562-HNHx-site8-Rep1


title: NRCOS213


title: HNH-K562-ABE8e-site11-Rep1


title: HNH-K562-HNHx-dimer-site8-Rep1


title: HNH-K562-HNH8e-site8-Rep1


title: HNH-K562-ABEmax-site8-Rep1


title: P9_supIL6


title: HNH-HEK-HNHx-site11-Rep1


title: PHC_001

value: Healthy


title: HNH-HEK-HNHx-site18-Rep1


title: P9_NS


title: HNH-HEK-HNHx8e-dimer-site8-Rep1


title: HNH-HEK-HNHx-site8-Rep1


title: HSK042


title: P8_IFNa

value: Patient 8


title: HSK039


title: HNH-K562-HNHx8e-dimer-site8-Rep1


title: HNH-HEK-HNH8e-site8-Rep1


title: HNH-HEK-HNHx-dimer-site8-Rep1


title: P8_IL10


title: HNH-HEK-ABE8e-site8-Rep1


title: HNH-HEK-ABEmax-site8-Rep1


title: HSK037


title: N5 - RNA Sequencing

value: placenta

tag: disease

value: preterm birth


title: P8_IL23


title: NRCOS466 FFPE

description:
NRCOS466
FPKM_normalized_data.csv

data_processing:
aligned using STAR
quantified using HTseq
DEG using DESeq2
Genome_build: hg38 - Ensembl Transcripts release 93
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: LS


title: HSK035

value: FFPE


title: P8_IL21


title: PE3 - RNA Sequencing

tag: tissue

value: early-onset preeclampsia


title: N4 - RNA Sequencing


title: N3 - RNA Sequencing


title: N2 - RNA Sequencing


title: N1 - RNA Sequencing


title: HNH-K562-ABE8e-site8-Rep1


title: PE5 - RNA Sequencing


title: P8_NS

value: NS


title: NRCOS440 FFPE

description:
NRCOS440
FPKM_normalized_data.csv


title: NRCOS430 FFPE

description:
NRCOS430
FPKM_normalized_data.csv


title: NRCOS428 FFPE

description:
NRCOS428
FPKM_normalized_data.csv


title: Ctrl3_IL23

value: control


title: PE4 - RNA Sequencing


title: WT PRMT5 Rep2

city: Cambridge

first: Sellers

last: Lab

state: MA

address: 415 Main St

institute: Broad Institute

description: Cell line derived from MTAP KO single cell cloning and subsequent clonal derivation of 3X HA-PRMT5-WT lines with depletion of endogenous PRMT5

data_processing:
Reads were processed using Illumina TruSeq Stranded mRNA Sample Preparation kit
Sequence data were processed and aligned to the human genome (build hg19) using the Picard (http://broadinstitute.github.io/picard/), BWA, and GATK software packages, following best-practice pipeline
The bam files were processed using rMATS turbo v4.1.1 to create tab delimited files recording events observed for each of the different alternate splicing events among the replicates and comparing them across the ADA and WT scenarios. The generated JC files for the 5 splicing events were used for further analysis.
The normalised counts(nc) for these events were averaged out for ADA and WT followed by removing events with 0 counts for either WT or ADA. The calculation of PCI was done to get a comparison of counts across the 2 sample types, where PCI = (nc(ADA) - nc(WT))/nc(WT) *100
Genome_build: hg19; The gtf files  have been downloaded from public sources for gene annotation:
Ensembl gene annotation GRCh37.87: http://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/
Gencode gene annotation v19 for ALL regions: https://www.gencodegenes.org/human/release_19.html
Supplementary_files_format_and_content: tab delimited files containing counts and PCI for each event for our dataset (WT and ADA) across the 5 different splicing events - SE (skipped exon), MXE (mutually exclusive exons), A3SS (alternative 3' splice site), A5SS (alternative 5' splice site), RI (retained intron)
Supplementary_files_format_and_content: tab delimited files containing counts and PCI for each event for previously published dataset across the 5 different splicing events - SE (skipped exon), MXE (mutually exclusive exons), A3SS (alternative 3' splice site), A5SS (alternative 5' splice site), RI (retained intron)

source_name: HCT116 CCL-247_WT PRMT5

growth_protocol: DMEM 10% FBS, 1% Pen/Strep, 37C humidified incubator

extract_protocol:
Rneasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions
Following plating, 2uL of ERCC controls (using a 1:1,000 dilution) were spiked into each sample. An aliquot of 200ng for each sample was transferred for library preparation which uses automated variant of the Illumina TruSeq Stranded mRNA Sample Preparation kit, preserving strand orientation of the RNA transcript.
Oligo dT beads are used to select mRNA from total RNA. It is followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 400bp cDNA then goes through a dual-indexed library preparation: “A” base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters. After enrichment, the libraries were quantified by Quant-iT PicoGreen (1:200 dilution). After normalizing the samples to 5ng/uL, the set was pooled and quantified using a KAPA Library Quantification Kit for Illumina Sequencing Platforms. The above process is carried out in 96well format and automated pipetting is performed by either an Agilent Bravo or Hamilton Scarlet.

tag: tissue source

value: Colorectal

tag: age

tag: genotype

value: MTAP-/-

value: WT


title: Ctrl3_IFNa

value: IFNa


title: PE2 - RNA Sequencing


title: Ctrl3_IL10


title: P8_supIL6


title: PE1 - RNA Sequencing


title: NRCOS437 FFPE

description:
NRCOS437
FPKM_normalized_data.csv


title: HNH-HEK-HNHx8e-dimer-site11-Rep1

value: Lipofection


title: WT PRMT5 Rep3


title: WT PRMT5 Rep1


title: NRCOS409 FFPE

description:
NRCOS409
FPKM_normalized_data.csv


title: ADA PRMT5 Rep1

description: Cell line derived from MTAP KO single cell cloning and subsequent clonal derivation of 3X HA-PRMT5-ADA lines with depletion of endogenous PRMT5

source_name: HCT116 CCL-247_ADA PRMT5

value: ADA treatment


title: ADA PRMT5 Rep2


title: NRCOS461 FFPE

description:
NRCOS461
FPKM_normalized_data.csv

value: Generalized


title: Ctrl3_IL21


title: whole transcriptome resequencing [FC-3]

city: Jinan

first: Zhao

middle: Ying

last: jie

address: 07 Wenhua xi road, Jinan, Shandong

department: Department of rheumatology

institute: Qilu hospital Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
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: human GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Normal control#8

extract_protocol:
Placentas were collected immediately after C-section or vaginal delivery. 6 random biopsies from the fetal side of each placenta were sampled (using a 1x1 cm grid), snap frozen in liquid nitrogen and stored at -80C for further experiment. Total RNA was isolated using theRNeasy mini kit (cat#Qiagen, Germany), after which the RNAconcentration and quality were determined by the Qubit ® 2 .0 Fluorometer (Life Technologies,USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrityoftotal RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA),and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing. Onemicrogram of RNA were used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: race

value: Chinese Han

value: Normal


title: NRCOS379 FFPE

description:
NRCOS379
FPKM_normalized_data.csv

value: Circumscribed


title: Ctrl3_NS


title: Ctrl3_supIL6


title: ADA PRMT5 Rep3


title: NRCOS375 FFPE

description:
NRCOS375
FPKM_normalized_data.csv


title: NRCOS397 FFPE

description:
NRCOS397
FPKM_normalized_data.csv


title: whole transcriptome resequencing [FC-1]

source_name: Normal control#6

value: placenta


title: Ctrl2_IFNa


title: whole transcriptome resequencing [FC-2]

source_name: Normal control#7


title: NRCOS362 FFPE

description:
NRCOS362
FPKM_normalized_data.csv


title: whole transcriptome resequencing [MC-4]

source_name: Normal control#4


title: whole transcriptome resequencing [MC-2]

source_name: Normal control#2


title: whole transcriptome resequencing [MC-3]

source_name: Normal control#3


title: whole transcriptome resequencing [MC-5]

source_name: Normal control#5


title: NRCOS328 FFPE

description:
NRCOS328
FPKM_normalized_data.csv


title: Ctrl2_IL23


title: Ctrl2_IL10


title: whole transcriptome resequencing [FSLE-3]

source_name: Lupus patient#8

value: Lupus


title: whole transcriptome resequencing [FSLE-2]

source_name: Lupus patient#7


title: NRCOS218 FFPE

description:
NRCOS218
FPKM_normalized_data.csv

value: LS


title: Ctrl2_IL21


title: NRCOS71 FFPE

description:
NRCOS71
FPKM_normalized_data.csv

value: FFPE


title: Ctrl2_NS


title: whole transcriptome resequencing [MSLE-5]

source_name: Lupus patient#5


title: whole transcriptome resequencing [MSLE-3]

source_name: Lupus patient#3


title: whole transcriptome resequencing [MSLE-2]

source_name: Lupus patient#2


title: whole transcriptome resequencing [FSLE-1]

source_name: Lupus patient#6


title: Ctrl2_supIL6

source_name: EBV-B


title: whole transcriptome resequencing [MSLE-4]

source_name: Lupus patient#4


title: HSK020 FFPE

description:
HSK020
FPKM_normalized_data.csv

source_name: paraffin-embedded skin from 4mm bx

value: Healthy


title: Ctrl1_IFNa


title: Ctrl1_IL23


title: whole transcriptome resequencing [MC-1]

source_name: Normal control#1


title: OCI-AML3 PIG-LONA Rep1

city: Toulouse

first: Marina

last: Bousquet

address: 2 av H Curien

department: CRCT

country: France

institute: INSERM

data_processing:
Base calling is performed using Illumina Real Time Analysis (3.4.4) with default parameters.
Quality of reads was assessed for each sample using FastQC (V.0.11.4)
RNA-SeQC provides key measures of data quality.
Alignment is performed by STAR (V.2.5)
The number of reads per gene are counted by HTseq-count
Genome_build: HG38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: acute myeloid leukemia cell line

growth_protocol: The OCI-AML3 (DSMZ no. ACC 582 ) were grown in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS), 2mM L-glutamine, 100 U/mL penicillin and 100 U/mL streptomycin (Invitrogen) at 37°C in humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNAs from OCI-AML3 PIG empty and PIG-LONA were purified using the Trizol (Ambion) extraction protocol according to the manufacturer's instructions. Dosage and purity of RNAs were determined by using Clariostar. Integrity and quality of RNAs for RNA-Sequencing analysis were determined by using Fragment Analyzer. Only RNA samples with a RNA Integrity Number RIN > 9 were sent for the RNA-Sequencing analysis.
Libraries are prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations.

treatment_protocol: Two millions of OCI-AML3 were resuspended into 2ml of retroviral particles supernatant (PIG-LONA or PIG EMPTY (negative control)) containing polybrene reagent, and were centrifuged at 800 RPM, 2h at 37°C. After transduction, cells were sorted for GFP+ cells with the FACSAria (Becton Dickinson). Two independent transductions have been performed for each virus.

tag: cell type

value: acute myeloid leukemia

value: Transduced with PIG-LONA


title: Ctrl1_IL10

value: control


title: HSK0009 FFPE

description:
HSK0009
FPKM_normalized_data.csv


title: HSK013 FFPE

description:
HSK013
FPKM_normalized_data.csv


title: suvh2/9_rep2 [RNA-seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
After removing adapter and filtering low-quality reads, the clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 with the default parameters.
The reads mapped on the exon were counted using featureCounts.
The differentially expressed genes and transposable elements were identified with fold change >2 and p-value<0.05 using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include normalized reads for each sample.

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with 16 h of light at 23ºC and 8 h of darkness at 21ºC.

extract_protocol:
Total RNA was extracted from 1 g of 11-day-old Arabidopsis seedlings with Trizol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (the single-ended 50-bp strategy).

treatment_protocol: The 11-day-old seedlings grown on MS plates were harvested and subjected to RNA extraction.

value: seedlings

value: 11 days


title: HSK015 FFPE

description:
HSK015
FPKM_normalized_data.csv


title: whole transcriptome resequencing [MSLE-1]

source_name: Lupus patient#1


title: suvh2/9_rep1 [RNA-seq]


title: Ctrl1_IL21


title: Ctrl1_supIL6


title: NRCOS218 RNAlater

description:
NRCOS218
FPKM_RNAlater_vs_FFPE_data.csv

source_name: RNAlater preserved skin from 4mm bx

value: RNAlater


title: OCI-AML3 PIG-EMPTY Rep1

tag: cell line

value: Transduced with PIG-EMPTY


title: NRCOS71 RNAlater

description:
NRCOS71
FPKM_RNAlater_vs_FFPE_data.csv


title: KO TAC rep3

first: Lingfang

last: Zhuang

state: Shanghai

address: 197 Rui Jin Road II

department: Department of Vascular & Cardiology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequencing data were filtered with SOAPnuke (v1.5.2) to remove reads containing sequencing adapters and those with more than 1/5 low-quality base ratio. The resulting clean reads were saved in FASTQ format.
The transcriptional reads were mapped to the mm8 whole genome  using HISAT2 (v2.0.4) and STAR (v2.3.0).
fragments per kilobase million (FPKM) value using the DESeq2 were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Heart

extract_protocol:
WT and Fabp3-null hearts were collected at 1-week post-sham or TAC surgery and immediately frozen in liquid nitrogen. Total RNA was extracted from above tissues using Trizol according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The TAC model was conducted to induce pathological cardiac hypertrophy in vivo. Briefly, 8-week-old mice were anesthetized with isoflurane, intubated, and mechanically ventilated with a low concentration of isoflurane gas (1.0%) and the aortic arch was visualized and ligated with 6-0 silk suture against a 27-gauge needle, then removed the needle and closed the chest with 5-0 silk suture.

value: TAC

tag: strain


title: HSK015 RNAlater

description:
HSK015
FPKM_RNAlater_vs_FFPE_data.csv


title: KO TAC rep2


title: rrm1_rep2 [RNA-seq]

description: gene_expression_Col-0_rrm1_pdp123_pdp123rrm1.txt


title: HSK013 RNAlater

description:
HSK013
FPKM_RNAlater_vs_FFPE_data.csv


title: rrm1_rep1 [RNA-seq]


title: OCI-AML3 PIG-LONA Rep2


title: OCI-AML3 PIG-EMPTY Rep2


title: Spleen Macrophages (scATAC-seq)

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

data_processing:
Adapter trimming was performed using 10X cellranger atac-count
Read deduplication was performed using 10X cellranger atac-count
Cell barcode processing was performed using 10X cellranger atac-count
Fragments file was imported into ArchR for downstream analysis
Genome_build: mm10
Supplementary_files_format_and_content: 10X atac-count fragments file

source_name: Mouse spleen

extract_protocol:
Cells were isolated from the indicated tissue and prepared for scATAC-seq
10X genomics droplet-based scATAC protocol
Paired end (with cell barcodes)

value: spleen

value: Macrophages

value: adult


title: WT TAC rep3

value: WT


title: Fetal Liver Monocytes (scATAC-seq)

source_name: Mouse fetal liver

value: fetal liver

value: Monocytes


title: Yolk Sac Macrophages (scATAC-seq)

source_name: Mouse yolk sac

value: yolk sac


title: pdp1/2/3_rep1 [RNA-seq]


title: WT TAC rep2


title: WT TAC rep1


title: suvh2/9_H3Ac_rep2 [ChIP-seq]

data_processing:
Basecalls performed using bcl2fastq version 2.16.
Adapter and low-quality sequences were trimmed, and the clean reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2 (v2.4.2) allowing one mismatch.
The reads that fell in the DMR regions were counted with the BEDTools package.
The H3Ac levels of hypo-DMRs were evaluated by RPKM (reads per kilobase per million mapped reads).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage.

extract_protocol:
Two gram of 11-day-old Arabidopsis seedlings was ground in liquid nitrogen to powder and then homogenized in lysis buffer. After 5 min of rotation at 4°C, 208 μl of formaldehyde was added to fix the materials for 20 min and then 469 μl of 2 M glycine was added to terminate the reaction. The homogenate were filtered through 4 layers of Miracloth (Millipore) and pelleted by centrifugation at 1,500 g for 10 min at 4°C. The pellet was washed 4 times with NRBT buffer and resuspended in 400 μl of lysis buffer. The pellet was sonicated (30 s on /30 s off cycle) for 8 min and 3 times. After sonication, the chromatin was centrifuged at 4°C for 15 min at 13,000 g. The supernatant was then dilute 5 times with dilution buffer. The chromatin was incubated with 40 μl of Protein A for 2 h at 4°C to remove non-specific binding and then immunoprecipitated overnight with antibody. An additional 40 μl of Protein A was added to conjugate the antibody for 2 h. Thereafter, the resin was washed with low salt wash buffer, high salt wash buffer, LiCl wash buffer, and TE wash buffer. The DNA-protein complex was eluted twice from the resin with 200 μl of elution buffer. 24 ul of 5 M NaCl was added to 400 μl of the elution to reverse cross-linking for more than 10 h. After digesting the protein with proteinase K, the DNA was purified and then subjected to library preparation and Illumina sequencing.
Libraries were built for ChIP-seq (Illumina HiSeq X Ten; 150-bp pair-end sequencing).

treatment_protocol: The 11-day-old seedlings grown on MS plates were harvested and subjected to ChIP analysis.

tag: chip antibody

value: anti-acetyl-histone H3 (Millipore, 06-599)


title: fve_rep2 [RNA-seq]


title: KO sham rep3

value: sham


title: KO sham rep2


title: DM3

city: Nanning

first: Ruimen

last: Zhang

address: NO.100 University Road,Xi xiang tang

institute: Guangxi 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 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Million Mapped Fragments (FPKM)were calculated using a protocol from Trapnell, C. et al, 2010.Spliced Reads per Billion Mapping (SRPBM)  calculated using a protocol from Li, et al. 2015 . 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.
Supplementary_files_format_and_content: tab-delimited text files include FPKM/TPM/SRPBM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: muscle stem cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen，Carlsbad，CA，USA). A total amount of 3 μg RNA per sample was used as an initial material for the RNA sample preparation. The library was prepared according to the method and process of lncRNA sample preparation kit (Illumina, NEB) and Small RNA Sample Preparation Kit (Illumina, RS-200-0048) at Annoroad Gene Technology Corporation (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Muscle-derived stem cells

value: Muscle

tag: development stage

value: differentiation

tag: breed

value: Guangxi


title: Ctrl1_NS

tag: disease state

value: control

value: NS


title: pdp1/2/3;rrm1_rep2 [RNA-seq]

value: seedlings

value: 11 days


title: DM2


title: Spleen Monocytes (scATAC-seq)

value: spleen


title: KO TAC rep1

tag: treatment

value: TAC


title: suvh2/9_H3Ac_rep1 [ChIP-seq]


title: fve_rep1 [RNA-seq]


title: fve_H3Ac_rep2 [ChIP-seq]


title: Control mice

city: Memphis

first: Udai

middle: P

last: Singh

state: TN

address: 881 Madison Avenue

department: Pharmacy

institute: University of Tennessee Health Science Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

label: biotin

source_name: mice

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by the submitter

tag: sample type


title: KO sham rep1


title: EAE mice

value: EAE


title: pdp1/2/3;rrm1_rep1 [RNA-seq]


title: GM3

value: proliferation


title: Col-0_rep4 [RNA-seq]

description:
Col-0 for rrm1,pdp1/2/3 and pdp1/2/3;rrm1
gene_expression_Col-0_rrm1_pdp123_pdp123rrm1.txt

value: wild type


title: Col-0_rep3 [RNA-seq]


title: GM2


title: fve_H3Ac_rep1 [ChIP-seq]


title: pdp1/2/3_rep2 [RNA-seq]


title: WT sham rep2

value: WT


title: WT sham rep3


title: Col-0_rep2 [RNA-seq]

description:
Col-0 for fve and suvh2/9
gene_expression_Col-0_fve_suvh29.txt


title: Col-0_H3Ac_rep2 [ChIP-seq]


title: DM1


title: Col-0_H3Ac_rep1 [ChIP-seq]


title: WT sham rep1


title: Col-0_rep1 [RNA-seq]


title: Group4_GEX

status: Public on Jun 11 2021

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description:
Group4.filtered_feature_bc_matrix.h5
Group4.filtered_response_annotation.txt

data_processing:
Barcoded BAM, with Chromium cellular and molecular barcodes for each read, stored as TAG fields.
The Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-hg19-1.2.0 as reference and expected-cells number of 3000 for each sample; polymorphisms removed.
For immune profiling Cell Ranger Single Cell Software Suite 3.1.0 was used for demultiplexing, barcode processing and assembly of the TCR as well as BCR sequences, using the vdj command and refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: BAM comprising h5: aggregated gene count matrix in hdf5 format, including antibody UMI counts. fasta: high-confidence contig sequences of immune receptors with the corresponding cellular barcode and contig-id; csv: results from single cell immune profiling, comprising the annotation of the immune receptor, cellular barcode and contig-id; txt: tab delimited annotation of donors, comprising the cellular barcode and response after vaccination against COVID19.

source_name: Activated T and B cells from four patients vaccinated against COVID19 after kidney transplantation with Biotech/Pfizer 7 days after boost

extract_protocol:
Cells were enriched from the peripheral blood by MACS using StraightFrom Blood CD3, CD19 and CD138 Microbeads. Cells were subsequently incubated with barcoded and fluorochorme-conjugated antibodies and sorted by FACS as live CD3+CD14-CD16-CD38+HLA-DR+, live CD3-CD14-CD16-CD38lowCD27+ and live CD3-CD14-CD16-CD38highCD27high. The barcoded antibodies used for cell-surface protein analysis were anti-human CD138 (GTATAGACCAAAGCC), CD20 (TTCTGGGTCCCTAGA), CD4 (GAGGTTAGTGATGGA), CD8 (GCGCAACTTGATGAT), CD45RO (CTCCGAATCATGTTG), CD45RA (TCAATCCTTCCGCTT), CD25 (TTTGTCCTGTACGCC), CD127 (GTGTGTTGTCCTATG) and CD154 (GCTAGATAGATGCAA). Sorted populations from three non-reponding and one reponding donor were pooled in equal proportions and applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
The purified cDNA was amplified using 12 cycles of PCR and was subsequently used for 5’ gene expression (GEX), cell-surface protein, TCR and BCR library preparation acording to 10x Genomics Chromium Next Gem Single Cell V(D)J Reagent Kits v1.1 with Feature Barcoding technology for Cell Surface Protein. The quality of the libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (Hight Sensitivity DNA Kit, Agilent).
The sequencing was performed on a NextSeq2000 device (Illumina) using P3 reagent kit (200 cycles) with the recommended sequencing conditions for 5’ GEX and cell-surface protein libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.) and P3 reagent kit (300 cycles) for TCR and BCR libraries (read1: 151nt, read2: 151nt, index1: 8nt, index2: n.a., 2% PhiX spike-in).

tag: individual

value: mixed sample (non-demultiplexed) representing four patients vaccinated against COVID19 after kidney transplantation

tag: responder status

value: mixed sample (non-demultiplexed) representing three non-responding donors and one responding donor

value: peripheral blood

value: mixed sample (non-demultiplexed) representing FACS-sorted activated T cells (CD38+ HLA-DR+), memory B cells (CD38low CD27+) and plasmabolasts (CD38high CD27high)


title: Group4_CITE

description:
Group4.filtered_feature_bc_matrix.h5
Group4.filtered_response_annotation.txt
See "Extraction protocol" for the barcodes of antibodies.

molecule: protein


title: Group4_TCR


title: Group4_BCR


title: PHC_002

value: FFPE

tag: condition 1

value: Healthy

tag: condition 2


title: GM1

value: Muscle-derived stem cells

tag: tissue

value: Muscle

value: Guangxi


title: C82-4_RD: female whose mother was fed FASD, biological rep 1

city: Montreal

first: Rima

last: Rozen

state: Quebec

address: 1001 Decarie Blvd

department: Departments of Human Genetics and Pediatrics

country: Canada

institute: McGill University

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were analyzed with Transcriptome Analysis Console 4.2 software (TAC 4.2) (Affymetrix default analysis settings, SST-RMA algorithm, comparison FASD male vs CD male; and comparison FASD female vs CD female).

source_name: E17.5 female placenta, FASD

label_protocol: Standard Affymetrix procedures

growth_protocol: Animal experimentation was conducted under the guidelines of the Canadian Council on Animal Care and approved by the Animal Care Committee of the Research Institute of the McGill University Health Center. Mice were housed under specific pathogen-free conditions at 18–24ºC and a 12h light/dark cycle, with ad libitum access to water and food.

extract_protocol: Total RNA was extracted from frozen placentas of E17.5 embryos using the AllPrep DNA/RNA/miRNA Universal Kit kit with on-column DNase I treatment (Qiagen).

treatment_protocol: At weaning, female C57BL/6 mice were randomly fed a CD (TD.01369, Harlan Laboratories, Inc., Madison, WI, USA) or FASD (TD.08278, Harlan Laboratories, Inc., Madison, WI, USA). The diets were modified from the standard amino acid-defined AIN-93G formulation, containing 2.5 g/kg choline bitrate, 3.3 g/kg L-methionine and 1% succinylsulfathiazole (to inhibit folate synthesis by intestinal ﬂora). CD contained 2 mg/kg diet of FA, the recommended amount for rodents. 5x FASD contained 10 mg/kg diet, 5 times higher FA than CD. Four to 5 weeks after the start of diets, females were mated with C57BL/6 males. The morning of discovering a vaginal plug was designated embryonic day 0.5 (E0.5). Diets were maintained until E17.5. Placentas were collected and cut in half; one half was used for RNA extraction and gene expression analysis by microarray.

value: E17.5 placenta

tag: diet

value: FASD

tag: Sex

value: female


title: C181-3_RB: female whose mother was fed CD, biological rep 3

source_name: E17.5 female placenta, CD

value: CD


title: C112-1_RB: female whose mother was fed CD, biological rep 2


title: C170-5_RB: male whose mother was fed FASD, biological rep 4

source_name: E17.5 male placenta, FASD

value: male


title: U87, ZNF768 knockdown, Biological replicate 3

city: Québec

first: Mathieu

last: Laplante

state: Qc

address: 2725 Chemin Sainte-Foy

department: Medicine

institute: Université Laval

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Expression values were extracted using the Robust Multichip Average (RMA) method implemented in the oligo package in R.

label: Biotin

source_name: U87, ZNF768 knockdown

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: U87 cells were obtained from American Type Culture Collection (ATCC) and cultured according to standard mammalian tissue culture protocols and sterile technique. The cell lines were cultured in complete Dulbecco’s Modified Eagle Medium (DMEM) supplemented with Fetal Bovine Serum (FBS) (10%)

extract_protocol: Total mRNA was isolated from cells and tissues using the RNeasy Lipid Tissue Mini Kit

treatment_protocol: U87 cells were transduced with lentiviruses to knockdown ZNF768 and selected. 96 hours post infection, RNA was isolated and microarrays were performed.

value: Glioblastoma


title: C171-2_RC: male whose mother was fed FASD, biological rep 3


title: C111-5_RD: female whose mother was fed FASD, biological rep 3


title: U87, ZNF768 knockdown, Biological replicate 1


title: TRIM46nc rep1

first: Zihan

address: No. 38 Xuyuan Stress

institute: Peking University

data_processing:
SOAPnuke:v1.5.2
HISAT:v2.1.0
Bowtie2 :v2.2.5
Genome_build: GRCh38.p11(hg38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: TRIM46 siControl

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was isolated and used for RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF-7 cells were treated with control siRNA or siRNA of TRIM46.

value: breast cancer cells

tag: genotype/variation

value: TRIM46 siControl


title: TRIM46si rep2

source_name: TRIM46 siTRIM46

tag: cell type

value: TRIM46 siTRIM46


title: CON_2

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

data_processing:
FastQC (version 0.11.8) was used to do quanlity control checks on clean reads.
The expression of genes was quantified by Salmon (version 0.8.0) with default parameters.
DEGs (differential expressed genes) between samples were generated by DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM for each sample.

growth_protocol: LP-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from cultured cells were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by Majorbio company (Shanghai,China).

treatment_protocol: LP-1 cells were infected with overexpression CBX3 plasmid  or vector.

value: cell strain

value: myeloma

tag: cell line


title: TRIM46nc rep2


title: OE_CBX3_1


title: OE_CBX3_2


title: C180-1_RA: female whose mother was fed CD, biological rep 4


title: U87, Control, Biological replicate 3

source_name: U87, control


title: TRIM46si rep1


title: C80-3_LD: female whose mother was fed CD, biological rep 1


title: C180-1_RC: male whose mother was fed CD, biological rep 4

source_name: E17.5 male placenta, CD


title: C109-5_LB: male whose mother was fed FASD, biological rep 2


title: TAZIND 4

city: Buffalo

first: Jianmin

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

description: RawCounts.csv

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Read counts are obtained using htseq-count from HTSeq with –intersection-strict no option
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts csv file format

source_name: cells

growth_protocol: TAZDEP and TAZIND cells were cultured in DMEM/F12 media (Corning, NY) supplemented with 5% horse serum (Invitrogen, MA), 1% Pen/Strep, 20 ng/mL EGF (ProSpec, NJ), 0.5 µg/mg hydrocortisone, 100 ng/mL cholera toxin, and 10 µg/mL insulin. TAZDEP were grown in presence of 2ug/ul doxycyclin

extract_protocol:
RNA was extracted from 60% confluent monolayers of cells, as described above.
The RNA samples were subjected to transcriptome sequencing (RNA-seq) with an Illumina HiSeq 2000 sequencer.

value: TAZ-independent

value: breast cancer


title: C170-5_LD: female whose mother was fed FASD, biological rep 4


title: C109-5_RA: female whose mother was fed FASD, biological rep 2


title: C181-3_LC: male whose mother was fed CD, biological rep 3


title: TAZIND 3

description: RawCounts.csv


title: TAZIND 1

description: RawCounts.csv


title: TAZIND 2

description: RawCounts.csv


title: C109-8_RF: male whose mother was fed CD, biological rep 2


title: C87-6_LD: male whose mother was fed CD, biological rep 1


title: C81-7_LE: male whose mother was fed FASD, biological rep 1


title: U87, Control, Biological replicate 2


title: U87, ZNF768 knockdown, Biological replicate 2


title: U87, Control, Biological replicate 1


title: TAZDEP 3

description: RawCounts.csv

value: TAZ-dependent


title: TAZDEP 2

description: RawCounts.csv


title: TAZDEP 1

description: RawCounts.csv


title: LRP1 KO 03

city: Houston

first: Xinchun

last: Pi

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Data was mapped to the mouse geneome using TopHat2 and the UCSC mm10 mouse genome as reference.
Gene expression was quantified using Cufflinks 2 and the Genecode reference.
Differential gene expression was determined using parametric t-test
Genome_build: UCSC mm10
Supplementary_files_format_and_content: xlsx file contains the FPKM for the Samples after quantile normalization.

source_name: Liver microvesicular cells

extract_protocol:
A RNeasy Miniprep Kit  (Qiagen) was used to isolate the RNA following the manufacturer's guidelines.
Illumina TruSeq kit was used in library preparation following the manufacturer's guidelines

value: Liver microvesicular cells

tag: genotype

value: LRP1 KO

tag: strain

tag: age

value: Postnatal day 14


title: LRP1 KO 02


title: Wildtype 03

value: Wild type


title: Wildtype 04


title: Wildtype 02


title: Wildtype 01


title: LRP1 KO 01


title: LRP1_KO_02

source_name: Mix of heart, liver and lung microvesicular cells


title: LRP1 KO 04


title: LRP1_KO_04

value: Mix of heart, liver and lung microvesicular cells


title: TAZDEP 4

description: RawCounts.csv


title: Wildtype_04


title: Wildtype_01


title: LRP1_KO_01


title: Rec.2_5.rep2

first: Dianbo

last: Liu

state: Massachusetts

address: Building 32, MIT, cambridge .MA USA

institute: MIT

description: PCR products

data_processing:
Fastq files were first inspected for quality control (QC) using FastQC. Fastq files were then filtered and trimmed using fastx_clipper of the FASTX-Toolkit.
Trimmed fastq files were collapsed using fastx_collapser of the FASTX-Toolkit. The collapsed fasta file was used as an input for alignment in Bowtie2 with a very sensitive alignment mode and aligned against the library reference.
The resulting SAM file was filtered for mapped reads using SAMtools, and the reads were then quantified by summing the counts of each unique promoter using an in-house R script. The reads were normalized by dividing all reads in the sample by a size factor estimated by DESeq2.
Replicability was assessed using Pearson correlation values using the cor.test function R. Differentially expressed 5’UTRs were identified using DESeq2.
Synthetic sequences
Supplementary_files_format_and_content: Files contain numbers  from 1-12000,    corresponding to the 12K 5'utr sequences. (these are not genes)
Supplementary_files_format_and_content: The DESeq2 NGS data analysis results of the 5’ UTRs for the Bin 0-2.5%, relative to the total bin (0-100%).
Supplementary_files_format_and_content: The DESeq2 NGS data analysis results of the 5’ UTRs for the Bin 2.5-5%, relative to the total bin (0-100%).
Supplementary_files_format_and_content: The DESeq2 NGS data analysis results of the 5’ UTRs for the Bin 5-10%, relative to the total bin (0-100%).
Supplementary_files_format_and_content: Supplementary Data 1. The sequences and characteristics of the selected naturally occurring 5' UTRs with flanking regions.
Supplementary_files_format_and_content: Supplementary Data 2. The sequences and characteristics of the selected synthetic 5' UTRs with flanking regions.
Supplementary_files_format_and_content: Supplementary Data 3. The sequences and characteristics of the selected synthetic 5' UTRs as a testing group with flanking regions.

source_name: Human embryonic kidney 293 cells

growth_protocol: HEK 293T cells (ATCC, VA, USA) were grown in polystyrene flasks in Dulbecco’s Modified Eagle’s Medium (Life Technologies, CA, USA) supplemented with 10% fetal bovine serum (VWR, PA, USA) and 1% penicillin/streptomycin (Life Technologies, CA, USA) at 37 °C and 5% CO2.

extract_protocol:
GenElute Mammalian Genomic DNA Miniprep Kits
The genomic DNA was extracted from each bin and 800 ng were used as the template for PCR amplification with barcoded Pi7 primer.
Amplicon-Seq

treatment_protocol: FuGene HD transfection

value: Human embryonic kidney 293 cells

value: kidney; Embryo

value: DNA transfection


title: Rec.0_100.rep2

description: PCR products


title: Wildtype_02


title: Rec.5_10.rep2

description: PCR products


title: Rec.2_5.rep1

description: PCR products


title: Rec.0_100.rep1

description: PCR products


title: Rec.5_10.rep1

description: PCR products


title: Rec.0_2.rep2

description: PCR products


title: LRP1_KO_03


title: Lent.0_100.rep2

description: PCR products

value: Lentival infection


title: Lent2.2_5.rep2

description: PCR products


title: Rec.0_2.rep1

description: PCR products


title: Lent.5_10.rep1

description: PCR products


title: Lent.0_100.rep1

description: PCR products


title: Lent.2_5.rep1

description: PCR products


title: ECA-11

city: ShangHai

first: Jacky

last: Shi

address: Handan Road.220

institute: Fudan University

data_processing:
Solexa pipeline was used to perform image analysis and base calling. Sequencing quality was examined by FastQC software and trimmed reads were aligned to mature-tRNA and pre-tRNA sequence getting from the Genomic tRNA Database using NovoAlign software. The remaining reads were aligned to transcriptome sequences (mRNA/rRNA/snRNA/snoRNA/piRNA/miRNA).
Genome_build: hg19

source_name: Endocervical adenocarcinoma

extract_protocol:
According to the manufacturer's instructions, TRIzol (Invitrogen, CA, USA) was used to extract total RNA from frozen tissue. Use NanoDrop ND-1000 instrument (NanoDrop-Thermo, DE, USA) to evaluate the quantity and concentration of each RNA sample, and check the integrity by agarose gel electrophoresis.
Before preparing the total RNA sample library, perform the following treatments to remove the modification of RNA interference small RNA sequence library construction: 3-aminoacyl (charged) deacylation to 3-OH for 3-adapter connection; 3-cP (2,3-cyclic phosphoric acid) was removed to 3-OH for 3-adapter connection; 5-OH (hydroxyl group) was phosphorylated to 5-P for 5-Adapter connection; m1A and m3C are removed for effective reverse transcription. The size of the sequencing library is selected for the RNA biotype, and the sequencing gel cutter was performed with an automatic sequencer, including 3 adaptor and 5'- adaptor connection, cDNA synthesis and library PCR amplification. The quality of the library was checked using Agilent Bioanalyzer 2100 (Invitrogen, CA, USA).

value: Pattern C

value: endocervical adenocarcinoma


title: Wildtype_03


title: ECA-10


title: Lent.0_2.rep2

description: PCR products


title: ECA-13

value: Gastric type


title: ECA-14


title: ECA-9


title: ECA-12


title: ECA-5

value: Pattern B


title: ECA-7


title: ECA-8


title: ECA-4


title: ECA-2

value: Pattern A


title: ECA-3


title: Lent.5_10.rep2

description: PCR products


title: ECA-1


title: Lent.0_2.rep1

description: PCR products


title: FSL-R8-7037_rep1_planktonic

city: Burlington

first: Andrea

last: Etter

state: VT

address: 109 Carrigan Drive

department: Nutrition and Food Science

institute: University of Vermont

description: Persistent food contact surface isolate from retail deli

data_processing:
Criteria for removal of bases/reads were: Phred33 score <30 or read length <50 bases
Trimmed reads were mapped to  L. monocytogenes 10403S using Bowtie2 (v. 2.2.8) (Sciences 2016)
HTSeq (v. 0.6.1) (Lemon and others 2010) determined read counts
DESeq2 (v. 2.1.2) (Love and others 2014) was used to determine significant differences between biofilm and planktonic samples for each isolate
Supplementary_files_format_and_content: HTSeq files for each sample containg gene counts after mapping to 10403S

organism: Listeria monocytogenes

source_name: Bacteria

extract_protocol:
Following incubation, coupons were washed three times with sterile PBS to remove non-adherent cells, then immediately mixed with 1:10 volume ice-cold 10% acidified phenol:chloroform (Life Technologies, Grand Island, NY) in ethanol. Biofilm cells were detached from the coupons in stop solution using a spatula and subsequent vortexing. Cells were pelleted (15,300 x g, 20 min, 4°C), coupons removed, and pellets re-suspended in 1 mL TRIzol® (Life Technologies). RNA extraction proceeded as previously described in biological triplicate (Pleitner and others 2014; Raengpradub and others 2008). Sample quality was assessed via the 2100 Bioanalyzer system (Agilent, Foster City, CA). DNA removal was evaluated  via qRT-PCR as previously described (Pleitner and others 2014)
RNA libraries were prepared using the Epicentre ScriptSeqTM complete kit (Illumina) and ScriptSeqTM Index PCR primers (Illumina)

treatment_protocol: Early stationary phase cells (8ml; OD600=0.7-0.8) were incubated statically with sterile coupons (n= 20 coupons/isolate) in a sterile petri dish with BHI (20°C for 2 hours) (Chavant and others 2002). Coupons were rinsed three times in PBS to remove non-adherent cells, placed in a new sterile petri dish containing 8 ml BHI broth, and incubated for three days; BHI was replaced daily. For planktonic controls, overnight cultures were diluted with BHI to OD600 0.7-0.8  (total volume: 8 ml) (Chavant and others 2002), and then incubated in test tubes at 20oC, 200 rpm for 24 hours.

value: Planktonic

tag: Stage

value: Early stationary phase

tag: medium

value: BHI


title: FSL-R8-5963_rep3_planktonic

description: Transient isolate from retail deli


title: FSL-R8-7802_rep2_planktonic

description: Transient non-food contact isolate from retail deli


title: FSL-R8-7802_rep1_planktonic


title: FSL-R8-7037_rep2_planktonic


title: FSL-R8-7037_rep3_planktonic


title: FSL-R8-5963_rep1_planktonic

description: Transient isolate from retail deli


title: FSL-R8-5963_rep2_planktonic

description: Transient isolate from retail deli


title: ECA-6

tag: disease state


title: FSL-R8-5446_rep1_planktonic

tag: sample type


title: FSL-R8-7802_rep3_bf

value: Biofilm

value: On stainless steel


title: FSL-R8-5446_rep2_planktonic


title: FSL-R8-7802_rep2_bf


title: FSL-R8-5446_rep3_planktonic


title: FSL-R8-5963_rep3_bf


title: FSL-R8-7037_rep3_bf


title: FSL-R8-7037_rep1_bf


title: FSL-R8-5963_rep2_bf


title: FSL-R8-7802_rep1_bf


title: FSL-R8-5446_rep3_bf

description: Persistent non-food contact surface isolate from retail deli


title: FSL-R8-7037_rep2_bf


title: Ring1flESCs_TAM_BAF155_r2

first: Christopher

middle: Michael

last: Weber

state: CA

address: B209 Beckman Center

department: Pathology

data_processing:
Genome build: mm10
Reads were aligned to mm10 genome build using Bowtie 2 version 2.3.4.1 with option --very-sensitive. Multimapping, secondary alignment, supplementary alignment, low-quality (q<20), and PCR duplicates were removed using Samtools and Picard.
Bigwig files were generated with deeptools 3.3.0 bamCoverage with the following flags: --binSize 10, --normalizeUsing RPGC, --ignoreForNormalization chrM ChrUn ChrRandom, --extendReads 200, --effectiveGenomeSize 2652783500.

growth_protocol: Before experiments cells were grown on gelatin coated dishes in KO DMEM supplemented with 7.5% ES-qualified serum and 7.5% KSR, with LIF.

extract_protocol:
Extracts were made by crosslinking cells with formaldehyde and then shearing DNA by sonication
NEBNext Ultra II

treatment_protocol: Cells were treated with 0.5mM auxin, 10 µM triptolide, 0.5mM auxin plus 10 µM triptolide for 8h, or 1µM Tamoxifen for 72h unless otherwise specified.

tag: drug

value: 1 µM Tamoxifen

tag: time treated

value: mESC

tag: chip antibody

value: BAF155 Crabtree laboratory


title: Ring1flESCs_EtOH_BAF155_input

value: EtOH

value: none (Input control)


title: FSL-R8-5446_rep1_bf


title: Ring1flESCs_EtOH_BAF155_r2


title: Ring1flESCs_TAM_BAF155_input


title: FSL-R8-5446_rep2_bf


title: Ring1flESCs_TAM_BAF155_r1


title: Ring1flESCs_EtOH_BAF155_r1


title: Suz12-trp-rep3

source_name: mESC TC1 (129) passage 15-20

value: 10 µM triptolide

value: Active Motif Cat #39057; RRID:AB_2614929


title: FSL-R8-5963_rep1_bf


title: Suz12-trpaux-rep4

value: 0.5mM auxin, 10 µM triptolide


title: Suz12-trp-rep4


title: Suz12-DMSO-rep3

value: DMSO control


title: Suz12-aux-rep2

value: 0.5mM auxin


title: Suz12-trpaux-rep2


title: Suz12-trp-rep2


title: Suz12-trpaux-rep1


title: Suz12-DMSO-rep2


title: Suz12-trpaux-rep3


title: Suz12-aux-rep1


title: Suz12-aux-rep4


title: Suz12-DMSO-rep1


title: Suz12-aux-rep3


title: Ring1b-trp-rep1

value: Cell Signalling Technologies Cat #5694; RRID:AB_10705604


title: Ring1b-trp-rep3


title: Ring1b-trpaux-rep4


title: Ring1b-trp-rep2


title: Ring1b-trpaux-rep3


title: Ring1b-trpaux-rep2


title: Ring1b-trpaux-rep1


title: Ring1b-DMSO-rep4


title: Ring1b-DMSO-rep3


title: CON_1

value: cell strain

value: myeloma


title: Suz12-DMSO-rep4


title: Ring1b-DMSO-rep1


title: Ring1b-aux-rep4


title: Ring1b-aux-rep3


title: Ring1b-aux-rep2


title: Input-DMSO-rep2


title: Input-aux-rep1


title: H3K27ac-DMSO-rep2

value: Abcam #Ab4729


title: H3K4me3-aux-rep1


title: H3K4me3-DMSO-rep1


title: Ring1b-aux-rep1


title: H3K27ac-DMSO-rep1


title: Input-aux-rep2


title: H3K4me3-DMSO-rep2


title: H3K27ac-aux-rep2


title: H3K4me3-aux-rep2


title: H3K27ac-aux-rep1


title: Suz12-trp-rep1


title: Ring1b-DMSO-rep2


title: RNA-Brg1-DMSO-rep2

data_processing:
Transcriptome: Ensembl v96 transcriptome (https://github.com/pachterlab/kallisto-transcriptome-indices/releases)
The first three bases from read 1 were trimmed with cutadapt 1.16 using -u 3 option. Transcripts were quantified using Kallisto version 0.44.0 using -l 280-s 20 (or paired-end) and --fr-stranded.
Trimmed reads were aligned to mm10 genome build with hisat2 using --rna-strandness FR (version 2.1.0), .bam files were merged with samtools merge (version 1.7), .bw files were generated using deeptools --binSize 10 --normalizeUsing RPKM (version 3.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: Kallisto abundance estimates and merged .bw files

growth_protocol: Cells were treated with DMSO, 0.5mM auxin, or dTAG13 (5x10^-11 to 5x10^-7M) for indicated time.

extract_protocol:
SMARTer Stranded Total RNA Sample Prep Kit - HI
Ribosomal RNA depleted total RNA

treatment_protocol: Cells were washed 1x with PBS and resuspended in Trisure. RNA was extracted and DNase I digested. The reaction was cleaned up with acid phenol and the RNA was precipitated.


title: RNA-Brg1-2h-aux-rep1

value: 0.5mM Auxin


title: RNA-Brg1-DMSO-rep1


title: RNA-Brg1-8h-aux-rep2


title: RNA-Brg1-8h-aux-rep1


title: RNA-Brg1-2h-aux-rep2


title: RNA-Brg1-4h-aux-rep1


title: 24_month_old_fractured 3

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

data_processing:
Bulk mRNA sequencing data was analyzed as described before (PMID: 32792541). Briefly, raw FASTQ reads from each lane were merged and then aligned to the GENCODE vM20 mouse reference transcripts (GRCm38.p6) with Salmon (PMID: 28263959) v0.12.0 using the --seqBias, --gcBias, --posBias, --useVBOpt, --rangeFactorizationBins 4, and --validateMappings flags and otherwise default parameters for paired-end mapping. Salmon results were merged into a single gene-level transcripts per million (TPM) matrix using the R package, tximport (PMID: 26925227) v1.10.1 and log2-normalized.
Genome_build: GENCODE vM20 mouse reference transcripts (GRCm38.p6)
Supplementary_files_format_and_content: Excel spreadsheet containing log2-and-TPM-normalized gene expression matrix

source_name: Day 10 fracture callus

extract_protocol:
For RNA extraction of mSSCs, 500 to 1,000 cells were FAC-sorted directly into 1 mL TRIzol LS (Invitrogen, Cat#10296028).
Bulk mRNA was processed and sequenced as described before (PMID: 32792541). Briefly, RNA was isolated with Qiagen miRNeasy kit (Cat. 1071023), cDNA was prepared using the Clontech Smarter Ultra Low Input RNA kit (Takara Bio, Cat. 634848), and libraries were generated with the Clontech Low Input Library Prep kit (Takara Bio, Cat. 634947). The barcoded samples were pooled and then sequenced on four lanes of NextSeq 500 (Illumina) to obtain 2x76 base pair paired-end reads (average no. of mapped reads per sample: ~45 million).

value: Femur

tag: cell

value: mSSC

value: 24 months

tag: treatment

tag: gating strategy


title: Input-DMSO-rep1

value: mESC


title: 24_month_old_fractured 2

tag: tissue


title: 24_month_old_fractured 1


title: 12_month_old_fractured 3

value: 12 months


title: Old_PBS-treated

data_processing:
Barcoded samples were demultiplexed, aligned to the mouse genome (vM20), and UMI-collapsed with the Cellranger toolkit with standard settings and --force-cells=10,000 (version 4.0.0, 10X Genomics Inc)
Supplementary_files_format_and_content: feature matrix output by cellranger

source_name: Femur Fracture Callus

extract_protocol:
Callus tissue with mechanically and enzymatically digested, stained with PI and Ter119, and sorted for living singlets (PI-Ter119-) via FACS.
According to 10X Genomics manufacturer instructions

treatment_protocol: Hydrogel placed on fracture site either containg PBS or anti-CSF1 (2 ug) + rBMP2 (5 ug).

value: Femur Fracture Callus

tag: number of animals in pool

tag: Sex

value: male


title: 12_month_old_fractured 1