title: CTEC_P1_2

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

description: library of 96 Ly51+ TEC cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: library of 96 Ly51+ TEC cells

growth_protocol: Mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.

extract_protocol:
Thymic stromal cell isolation was done with slight modifications as described earlier (Rode et al., 2015). In contrast to the published method, minced thymi were directly subjected to digestion without discarding any fractions, and lymphoid cells (anti-CD45 beads, Miltenyi Biotec) and erythrocytes (anti-Ter119 beads, Miltenyi Biotec) were manually depleted using MACS technology.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: No Treatment was performed.

tag: genotype/variation

value: WT

value: Thymus

tag: age

value: 4 weeks

tag: gender

value: male

value: thymic epithelial cells


title: CTEC_P1_8

status: Public on Mar 30 2022

type: SRA

country: Germany

description: library of 96 Ly51+ TEC cells

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: cell type


title: CTEC_P1_1

description: library of 96 Ly51+ TEC cells


title: 1359.C2

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description:
small RNAsequencing analysis
JManyeDE_report.xlsx

data_processing:
BCL basecall files were converted to FASTQ per sample using CASAVA v1.8.2 (Illumina) with default parameters to generate demultiplexed per sample fastq raw sequencing data files.
Per sample read quality was assessed using the fastx_quality stats software (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
A filtering step was introduced to leave out miRNAs detected at very low levels -i.e. absent in a fraction of samples- which were not considered in statistical analysis.  Analysis was only done at the mature miRNA level.
Statistically significant differences in miRNA expression were determined both by EdgeR and DESeq2 (Love, 2014) with multiple testing adjustment.
Genome_build: Reads were mapped to the human genome hg19 assembly (UCSC) and assigned to different RNA collections based on ENSEMBL annotation.
Supplementary_files_format_and_content: Processed miRNA expression profiling (miRNA identifiers based on miRBase 20) data tables are provided as a supplementary file in excel workbook (.xlsx) format. It includes 6 worksheets named 'RawCounts' (table of summarized read counts for each miRNA in every sample), 'NormDESeq2'  and 'NormEdgeR'  (normalized read counts for all samples derived from the two programs used, DESeq2 and egdeR respectively), 'rLog' (rLog transformed normalized counts used as input for clustering and visualization by DESeq2), 'diffExp' and 'diffExp_sin_285-C1' (differential expression results from all samples and excluding one outlier sample); each table includes separate sets of columns for each comparison with the default output from edgeR (logFC, logCPM, PValue, FDR) and DESeq2 (baseMean, log2FoldChange, lfcSE, stat, pvalue, padj) for all comparisons. Column headers: logFC or log2FoldChange (log2 fold changes), average abundance measure (logCPM -average log counts per million from edgeR-, baseMean -average normalized counts from DESeq2-), nominal p value (PValue, pvalue), adjusted p value (FDR -false discovery rate from edgeR-, padj -adjusted pvalue by default Benjamini and Hochberg method from DESeq2-), and statistics (lfcSE -log fold change standard error-, stat -Wald-test statistic- both measures as determined by DESeq2).

organism: Homo sapiens

source_name: plasma

extract_protocol:
Blood samples were collected in EDTA tubes, then, plasma samples were obtained by a single centrifugation (1000g, 15min. at room temperature). For RNA extraction from 200ul of plasma, miRCURY RNA insolation kit-Biofluids (#300112) was used following manufacturer indications with modifications that included using glycoingen as carrier and a 1:50 dilution of spike in RNA.
Barcoded sequencing libraries were prepared using the TrueSeq SmallRNA library kit (Illumina) with slight modifications from the default recommendations (Part # 15004197 Rev. F, February 2014). Modifications included using all RNA extracted from 200 ul of plasma, in the subnanogram range, and increasing the number of cycles in the final PCR reaction (from 12 to 15).
Libraries were quality assessed with Bioanalyzer DNA 1000 assays (Agilent). Bioanalyzer concentration estimates were used to generate an equimolar library mix. The library pool was automatically size selected (135-160bp) using 3% agarose dye free cassettes with 3% DF marker F on a Pippin Prep system with software v.6.0 (Sage Science). QIAquick (Qiagen) column purifications were performed prior and after to size selection. The library pool was quantifiedby PCR with theKAPA Library Quantification Kit following manufacturer’s instructions (Roche). The library pool was run on 4 lanes of 1x50 bp sequencing was performed on HiSeq2500 platform (Illumina) using adapted protocols for TruSeq SR cluster kit v3 (Part#15023335) following cBot™ (Part#15006165) and HiSeq2500 System (Part#15035786) user guidelines. Raw data were analysed by Real Time Analysis software v. 1.17.21.3 and Sequence Analysis Viewer software v. 1.8.20 (Illumina.).

tag: disease state

value: UC

tag: corticosteroid response

value: Glucocorticoid responder

tag: collection time

value: 3rd day after starting Glucocorticoid treatment

tag: age (years)

tag: Sex

value: Female

tag: individual

tag: sample type

value: plasma


title: D283MED cell lines conditionally expressing KBTBD4 R311PR - Replicate 3

city: Oxford

first: Vincenzo

last: D'Angiolella

state: Oxfordshire

address: Old Road Campus Research Building, Old Road Campus, Off, Roosevelt Dr

country: United Kingdom

institute: University of Oxford

data_processing:
basecallling: Illumina CASAVA
mapping to reference : HISAT2 v2.0.5
transcript assembly :  StringTie v1.3.1
QC: removing reads containing adapter and poly-N sequences and reads with low quality from raw data
Raw gene-level count generation: StringTie v1.3.1
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: D283Med cells were grow in MEM supplemented with 10% FBS (tetracycline-free)

extract_protocol: After washed once in phosphate-buffered saline, cell pellet was resuspended in TRIzol Reagent (Thermo Fisher Scientific cat # 15596026) and extracted following the manufacturer's protocol.

treatment_protocol: Cells were treated with 1ug/ml of doxycycline for 4 days

tag: treatment

value: no treatment

value: D283Med - medulloblastoma cell line


title: input_ESC_dTAG_24h_Pol2

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: ChIP sequencing of mESCs

library_source: genomic

data_processing:
Raw reads of treatment and input samples were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC). Reads were aligned separately to the mouse genome (mm10) and to the fly genome (D. Melanogaster, dm6) using bwa with the 'mem' command (version 0.7.17, default parameters). A sorted BAM file was obtained and indexed using samtools with the 'sort' and 'index' commands (version 1.10). Duplicate reads were identified and removed using gatk (version 4.1.4.1) with the 'MarkDuplicates' command and default parameters. Technical replicates of treatment and input samples were merged respectively using samtools 'merge'.
Peaks were called with reads aligning to the mouse genome only using MACS2 'callpeak' (version 2.1.2; parameters --bdg --SPMR) using the input samples as control samples. For H3K9me3 only, the '--broad' option was used. Genome-wide coverage tracks for single and merged replicates normalized by library size were computed using bamCoverage (version: 3.4.3; parameters: --normalizeUsing CPM --extendReads) and in addition normalized by the spike-in factor obtained from the reads aligning to the drosophila genome.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig coverage files
Raw reads of treatment and input samples were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC). Reads were aligned to the mouse genome (mm10) using bwa with the 'mem' command (version 0.7.17, default parameters). A sorted BAM file was obtained and indexed using samtools with the 'sort' and 'index' commands (version 1.10). Duplicate reads were identified and removed using gatk (version 4.1.4.1) with the 'MarkDuplicates' command and default parameters. Technical replicates of treatment and input samples were merged respectively using samtools 'merge'.
Peaks were called with reads aligning to the mouse genome using MACS2 'callpeak' (version 2.1.2; parameters --bdg --SPMR) using the input samples as control samples. Genome-wide coverage tracks for single and merged replicates normalized by library size were computed using bamCoverage (version: 3.4.3; parameters: --normalizeUsing CPM --extendReads).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig coverage files

molecule: genomic DNA

source_name: mESC

growth_protocol: During expansions, cells were cultured on irradiated primary mouse embryonic fibroblasts (MEFs) under serum/LIF conditions: knockout DMEM containing 15 % fetal bovine serum,  50 µg/ml penicillin/streptomycin, 2 mM L-Glutamine, 100 µM non-essential amino acids, 80 µM ß-mercaptoethanol and 1000 U/ml LIF. Before starting ChIP-Seq experiments, mESCs were depleted from MEFs by incubating them on gelatin coated cell culture plates for 45 min in +37 C allowing MEFs to attach while mESCs remain in suspension. MEF depletion was performed two times after which mESCs were seeded on gelatin coated plates and maintained in serum/LIF conditions with 2000 U/ml LIF.

extract_protocol:
Cells were detached with TrypLE, washed once with PBS, and protein-protein crosslinking was performed by incubating cells in rotation with 2 mM disuccimidyl glutarate in PBS for 45 min in room temperature. Cells were washed twice with PBS and DNA-protein crosslinking was performed with 1 % formaldehyde for 10 minutes in room temperature followed by quenching with 125 mM glycine. For each sample, 30 million mESCs (and an exogenous genome spike-in of 7.5 million S2 cells) were lysed in LB1 (50 mM HEPES-KOH, 140 nM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % Igepal ca-630 and 0.25 % Triton X-100, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and collected by sentrifugation. Lysis was continued in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 5 mM Na-butarate and 1 x protease inhibitor cocktail) followed by sentrifugation, nuclei were lysed in sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM EDTA, 1 mM EDTA, 1 mM EGTA, 1 % Triton X-100, 0.1 % Na-deoxycholate, 0.1 % SDS and 1x protease inhibitors (Roche)) and sonicated for 50 cycles by using Bioruptor NextGen (high setting). Ten percent of sample material was set aside as input and stored in +4C. Voume was adjusted to 200 µl with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA and 1% SDS) and crosslinks were reversed by incubating samples in 65C for 16 hours. Samples were topped up with 200 µl TE buffer and 8 µl of RNAse A, incubated in 37 C for 2 hours followed by addition of 7 µl of 300 mM CaCl2, 2 µl Proteinase K (Ambion) and 30 minutes incubation in 37C. DNA purified from samples with phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation.
10 ng of DNA was used to prepare sequencing libraries with KAPA HyperPrep Kit (Roche) according to manufacturer's instructions.

treatment_protocol: For degradation of TRIM28, 500 nM of dTAG-13 (or 0.05 % DMSO) was mixed with mESC medium and added to the cells 24h before samples were collected.

value: dTAG


title: input_ESC_DMSO_Pol2

description: ChIP sequencing of mESCs

value: DMSO


title: input_ESC_DMSO_Med23

description: ChIP sequencing of mESCs

extract_protocol:
Cells were detached with TrypLE, washed once with PBS, and protein-protein crosslinking was performed by incubating cells in rotation with 2 mM disuccimidyl glutarate in PBS for 45 min in room temperature. Cells were washed twice with PBS and DNA-protein crosslinking was performed with 1 % formaldehyde for 10 minutes in room temperature followed by quenching with 125 mM glycine. For each sample, ten million mESCs were lysed in LB1 (50 mM HEPES-KOH, 140 nM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % Igepal ca-630 and 0.25 % Triton X-100, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and collected by sentrifugation. Lysis was continued in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 5 mM Na-butarate and 1 x protease inhibitor cocktail) followed by sentrifugation, nuclei were lysed in sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM EDTA, 1 mM EDTA, 1 mM EGTA, 1 % Triton X-100, 0.1 % Na-deoxycholate, 0.1 % SDS and 1x protease inhibitors (Roche)) and sonicated for 50 cycles by using Bioruptor NextGen (high setting). Ten percent of sample material was set aside as input and stored in +4C. Voume was adjusted to 200 µl with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA and 1% SDS) and crosslinks were reversed by incubating samples in 65C for 16 hours. Samples were topped up with 200 µl TE buffer and 8 µl of RNAse A, incubated in 37 C for 2 hours followed by addition of 7 µl of 300 mM CaCl2, 2 µl Proteinase K (Ambion) and 30 minutes incubation in 37C. DNA purified from samples with phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation.
10 ng of DNA was used to prepare sequencing libraries with KAPA HyperPrep Kit (Roche) according to manufacturer's instructions.


title: D283MED cell lines conditionally expressing KBTBD4 R313PRR - Replicate 2


title: D283MED cell lines conditionally expressing KBTBD4 R313PRR - Replicate 1


title: 1267.C2

value: Male


title: D283MED cell lines conditionally expressing KBTBD4 R313PRR - Replicate 3


title: CTEC_P1_3

description: library of 96 Ly51+ TEC cells


title: 0168.C2


title: Med23_ESC_dTAG_24h_rep2

description: ChIP sequencing of mESCs

extract_protocol:
Cells were detached with TrypLE, washed once with PBS, and protein-protein crosslinking was performed by incubating cells in rotation with 2 mM disuccimidyl glutarate in PBS for 45 min in room temperature. Cells were washed twice with PBS and DNA-protein crosslinking was performed with 1 % formaldehyde for 10 minutes in room temperature followed by quenching with 125 mM glycine. For each sample, ten million mESCs were lysed in LB1 (50 mM HEPES-KOH, 140 nM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % Igepal ca-630 and 0.25 % Triton X-100, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and collected by sentrifugation. Lysis was continued in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 5 mM Na-butarate and 1 x protease inhibitor cocktail) followed by sentrifugation, nuclei were lysed in sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM EDTA, 1 mM EDTA, 1 mM EGTA, 1 % Triton X-100, 0.1 % Na-deoxycholate, 0.1 % SDS and 1x protease inhibitors (Roche)) and sonicated for 50 cycles by using Bioruptor NextGen (high setting). Lysates were clarified and protein-DNA complexes were isolated with MED23 antibodies (A300-425A; Bethyl Laboratories) bound to Protein A Dynabeads (Invitrogen). Beads were washed twice with sonication buffer, once with sonication buffer containing 500 nM NaCl, once with LiCl wash buffer (20 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5 % Igepal CA-630, 0.5 % Na-deoxycholate, 1x protease inhibitors) and once with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA, 1x protease inhibitors). Samples were eluted from beads with 200 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA and 1% SDS) and crosslinks were reversed by incubating samples in 65C for 16 hours. Samples were topped up with 200 µl TE buffer and 8 µl of RNAse A, incubated in 37 C for 2 hours followed by addition of 7 µl of 300 mM CaCl2, 2 µl Proteinase K (Ambion) and 30 minutes incubation in 37C. DNA purified from samples with phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation.
10 ng of DNA was used to prepare sequencing libraries with KAPA HyperPrep Kit (Roche) according to manufacturer's instructions.


title: MTEC_P1_10

description: library of 96 UEA1+ TEC cells

source_name: library of 96 UEA1+ TEC cells


title: MTEC_P1_11

description: library of 96 UEA1+ TEC cells


title: 0074.C2


title: Med23_ESC_dTAG_24h_rep1

description: ChIP sequencing of mESCs


title: MTEC_P1_12

description: library of 96 UEA1+ TEC cells


title: D283MED cell lines conditionally expressing KBTBD4 WT - Replicate 4


title: 1229.C2


title: MTEC_P1_9

description: library of 96 UEA1+ TEC cells


title: D283MED cell lines conditionally expressing KBTBD4 WT - Replicate 3


title: Med23_ESC_DMSO_rep2

description: ChIP sequencing of mESCs


title: 1289.C2


title: 0039.C2


title: FGF7WT_P2_24

description: library of 96 FGF7 Tg TEC cells

source_name: library of 96 FGF7 Tg TEC cells

value: FVB/N background backcrossed to a C57BL/6J background


title: D283MED cell lines conditionally expressing KBTBD4 WT - Replicate 2


title: FGF7WT_P2_23

description: library of 96 FGF7 Tg TEC cells


title: 0285.C2


title: Med23_ESC_DMSO_rep1

description: ChIP sequencing of mESCs


title: Pol2_ESC_dTAG_24h_rep2

description: ChIP sequencing of mESCs

extract_protocol:
Cells were detached with TrypLE, washed once with PBS, and protein-protein crosslinking was performed by incubating cells in rotation with 2 mM disuccimidyl glutarate in PBS for 45 min in room temperature. Cells were washed twice with PBS and DNA-protein crosslinking was performed with 1 % formaldehyde for 10 minutes in room temperature followed by quenching with 125 mM glycine. For each sample, 30 million mESCs (and an exogenous genome spike-in of 7.5 million S2 cells) were lysed in LB1 (50 mM HEPES-KOH, 140 nM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % Igepal ca-630 and 0.25 % Triton X-100, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and collected by sentrifugation. Lysis was continued in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 5 mM Na-butarate and 1 x protease inhibitor cocktail) followed by sentrifugation, nuclei were lysed in sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM EDTA, 1 mM EDTA, 1 mM EGTA, 1 % Triton X-100, 0.1 % Na-deoxycholate, 0.1 % SDS and 1x protease inhibitors (Roche)) and sonicated for 35 cycles by using Bioruptor NextGen (high setting). Lysates were clarified and protein-DNA complexes were isolated with RNAPII antibodies (8WG16; Biolegend) and Spike-in antibody (61686, Active Motif) bound to Protein A Dynabeads (Invitrogen). Beads were washed twice with sonication buffer, once with sonication buffer containing 500 nM NaCl, once with LiCl wash buffer (20 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5 % Igepal CA-630, 0.5 % Na-deoxycholate, 1x protease inhibitors) and once with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA, 1x protease inhibitors). Samples were eluted from beads with 200 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA and 1% SDS) and crosslinks were reversed by incubating samples in 65C for 16 hours. Samples were topped up with 200 µl TE buffer and 8 µl of RNAse A, incubated in 37 C for 2 hours followed by addition of 7 µl of 300 mM CaCl2, 2 µl Proteinase K (Ambion) and 30 minutes incubation in 37C. DNA purified from samples with phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation.
10 ng of DNA was used to prepare sequencing libraries with KAPA HyperPrep Kit (Roche) according to manufacturer's instructions.


title: D283MED cell lines conditionally expressing KBTBD4 WT - Replicate 1


title: PANC-1_H2O2

city: Guangzhou

first: Shihua

last: Liu

state: Guangdong

address: 651 Dongfeng East Road

department: Collaborative Innovation Center for Cancer Medicine

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PANC-1 cells

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS (Corning, NY) at 37℃ in a 5% CO2 cell culture incubator.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method. Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 250~300 bp fragments, and first strand cDNA was reverse transcribed using fragmented RNA and dNTPs. RNA was degraded using RNase H, and second strand cDNA was synthesized using DNA polymerase I and dNTPs. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/ polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptor were ligated to the cDNA. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Uridine digestion was performed using Uracil-N-Glycosylase, which was followed by the cDNA amplification using PCR.

treatment_protocol: HPNE and PANC-1 cell lines were treated with hydrogen peroxide (H2O2, Sigma) 0.3 mM and 1.0 mM for 12 h, respectively.

value: pancreatic tissue

value: pancreatic cancer cell line PANC-1


title: 0773.C2


title: PANC-1_Ctrl

value: untreated


title: 1279.C1

value: Glucocorticoid non-responder

value: before glucocorticoid treatment


title: HPNE_Ctrl

source_name: hTERT-HPNE cells

value: pancreatic normal epithelial cell line hTERT-HPNE


title: 1306.C2

value: UC


title: FGF7WT_P2_22

description: library of 96 FGF7 Tg TEC cells

value: Thymus

value: 4 weeks

value: male

value: thymic epithelial cells


title: Pol2_ESC_dTAG_24h_rep1

description: ChIP sequencing of mESCs


title: 1193.C1

value: plasma


title: FGF7WT_P2_21

description: library of 96 FGF7 Tg TEC cells


title: 16D-CRPC-10d-ENZ-Rep3-ATAC

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

data_processing:
Base calling was performed using Bcl2fastq 2.17.1.14 with default parameters as per recommendation from Illumina.
Demultiplexing was also performed using Bcl2fastq 2.17.1.14 with default parameters as per recommendation from Illumina.
FastQC version 0.11.9 was used for quality control analysis of fastq files. Cutadapt v1.18 was used to trim adapter.
Raw reads were aligned to the hg38 (human) reference genome using BWA-MEM software (version 0.7.17) with default parameters. Alignments with mapping quality less than 60 were filtered out (leaving only uniquely mapped reads). Accessible DNA fragments datapoints were extracted using custom AWK script. The sam files were converted to bam files using Samtools software (version 1.1.2).
Narrow peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAMPE -g 2.9e9 --keep-dup=1 -B -q 0.05 or -q 0.000001. Bedtools intersect (v2.28.0) program suite was used to generate shared (-wa -u -f 0.5 -F 0.5 -e) and unique (-v -f 0.5 -F 0.5 -e) peak set between samples.
Deeptools (v2.30.0) program suite was used to generate bigWig files.
HOMER (v4.11) program suite was used to annotate peaks and perform motif enrichment analysis.
Genome_build: hg38

source_name: 16D Prostate cancer cell line generated from mouse xenograft of LNCaP

growth_protocol: 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum, 42D ENZ-resistant (ENZR) cells were cultured in RPMI-1640 media containing 5% fetal bovine serum supplemented with 10mM ENZ, NCI-H660 cells were cultured HITES medium following ATCC recommendation.

extract_protocol:
Cell pellet of 50,000 cells per sample was used for library preparation. Genomic DNA fragments for ATAC seq library was prepared as per protocol published in Buenrostro et al. 2013 and Chen et al. 2018 with some modifications. Briefly, cells were collected by incubating in trypsin for 5 minutes at room temperature and subsequent centrifugation at 2300 rpm for 5 minutes at 4°C. Cells were washed twice and re-suspended in PBS. 5 x 104 cell pellet was used for tagmentation by incubating in 50 µl of 1x THS-seq buffer (25µl 2x THS-buffer, 5µl 10x Digitonin, 2µl Illumina-TDE1 (Cat FC-121-1030) or ActiveMotif-Tn5 (Cat 53150)) for 20 minutes at 37°C with 800 rpm in ThermoMixer (Eppendorf). To stop the tagmentation reaction, equal volume of 2x Tagmentation Stop Buffer [10mM Tris-HCl (pH 8.0), 20mM EDTA (pH 8.0)] was added to reaction and incubated for 10 minutes on ice. For cell lysis, equal volume of 2x Lysis Buffer [100 mM Tris-HCl (pH8.0), 100 mM NaCl, 40 µg/ml Proteinase K, 0.4% SDS] was added to the tagmentation mix and incubated at 65°C for 15 minutes. The tagmented DNA library was purified in 20 µl EB using Qiaquick PCR purification kit (Qiagen).
Library fragments were amplified using NEB Next High-Fidelity 2x PCR Master Mix (New England Biolab Cat #M0541) and custom Nextera PCR primers. Libraries were amplified for a total of 11 to 12 cycles and purified using Qiaquick PCR purification kit. Libraries were quantified by Qubit 1x dsDNA HS Assay kit (Cat Q33230), quality assessed by Agilent Bioanalyzer run using Agilent High Sensitivity Assay (kit no. 5067-4626) and sequenced using 75bp or 125bp or  150bp Paired-end sequencing on a Illumina HiSeq 2500 or NOVAseq 6000 sequencer following manufacturer's protocol.

treatment_protocol: 16D cells in RPMI-1640 media containing 5% fetal bovine serum were treated with 10mM ENZ for 3 or 10 days. First, ASCL1 was knock down using short-hairpin (sh) RNA strategy in 42D-ENZR to generate 42D-ENZR-shASCL1 cell line before being used for ATAC seq sample preparation.

value: Castration Resistant Prostate Cancer (CRPC)

value: Enzalutamide

value: Castration resistant


title: 0730.C1

value: Female


title: Pol2_ESC_DMSO_rep2

description: ChIP sequencing of mESCs

value: DMSO


title: HPNE_H2O2

value: pancreatic tissue


title: FGF7WT_P4_17

description: library of 96 FGF7 Tg TEC cells

value: FVB/N background backcrossed to a C57BL/6J background


title: FGF7WT_P4_18

description: library of 96 FGF7 Tg TEC cells


title: input_ESC_dTAG_24h_rep2

description: ChIP input sequencing of mESCs

data_processing:
Raw reads of treatment and input samples were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC). Reads were aligned separately to the mouse genome (mm10) and to the fly genome (D. Melanogaster, dm6) using bwa with the 'mem' command (version 0.7.17, default parameters). A sorted BAM file was obtained and indexed using samtools with the 'sort' and 'index' commands (version 1.10). Duplicate reads were identified and removed using gatk (version 4.1.4.1) with the 'MarkDuplicates' command and default parameters. Technical replicates of treatment and input samples were merged respectively using samtools 'merge'.
Peaks were called with reads aligning to the mouse genome only using MACS2 'callpeak' (version 2.1.2; parameters --bdg --SPMR) using the input samples as control samples. For H3K9me3 only, the '--broad' option was used. Genome-wide coverage tracks for single and merged replicates normalized by library size were computed using bamCoverage (version: 3.4.3; parameters: --normalizeUsing CPM --extendReads) and in addition normalized by the spike-in factor obtained from the reads aligning to the drosophila genome.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig coverage files

extract_protocol:
Cells were detached with TrypLE, washed once with PBS, fixed with 1 % formaldehyde for 10 minutes in room temperature followed by quenching with 125 mM glycine. For each sample, three million mESCs and 750 000 S2 cells were lysed in LB1 (50 mM HEPES-KOH, 140 nM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % Igepal ca-630 and 0.25 % Triton X-100, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and collected by sentrifugation. Lysis was continued in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 5 mM Na-butarate and 1 x protease inhibitor cocktail) followed by sentrifugation, nuclei were lysed in LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1 % Na-deoxycholate, 0.5 % N-Lauroylsarcosine, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and chromatin fragmented with Bioruptor NextGen for 35 cycles (high-setting). Lysates were clarified and protein-DNA complexes were isolated with ab4729 (Abcam) antibody for H3K27Ac and ab8898 (Abcam) antibody for H3K9me3 and Protein A Dynabeads (Invitrogen). 10 % of sample was taken as input before adding the antibody and stored in +4 C until de-crosslinking step. Beads were washed 7 times with RIPA buffer (50 mM HEPES-KOH pH7.5, 1 mM EDTA, 1 % Igepal CA-630, 0.7 % Na-deoxycholate, 500 mM LiCl, 5 mM Na-butyrate and 1 x protease inhibitor cocktail), once with TE buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA and 50 mM NaCl) and eluted from beads with Elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA and 1% SDS). Samples were decrosslinked for 16 h in +65 C with 550 mM NaCl and proteinase K, treated with RNAseA and DNA was extracted with Phenol:Chloroform:Isoamylalcohol followed by chloroform extraction and precipitation with 30 µg glycogen, 0.3 M Na-acetate and ethanol.
10 ng of DNA was used to prepare sequencing libraries with KAPA HyperPrep Kit (Roche) according to manufacturer's instructions.

tag: cell line

value: dTAG


title: 16D-CRPC-0d-ENZ-Rep3-ATAC


title: 1238.C1

value: Glucocorticoid non-responder


title: 0577.C1

value: before glucocorticoid treatment


title: Pol2_ESC_DMSO_rep1

description: ChIP sequencing of mESCs


title: 0462.C1

value: Male


title: 16D-CRPC-3d-ENZ-Rep3-ATAC


title: 16D-CRPC-10d-ENZ-Rep2-ATAC


title: input_ESC_dTAG_24h_rep3

description: ChIP input sequencing of mESCs


title: FGF7WT_P3_15

description: library of 96 FGF7 Tg TEC cells


title: FGF7WT_P3_14

description: library of 96 FGF7 Tg TEC cells


title: FGF7WT_P4_20

description: library of 96 FGF7 Tg TEC cells


title: FGF7WT_P3_16

description: library of 96 FGF7 Tg TEC cells


title: 16D-CRPC-3d-ENZ-Rep2-ATAC


title: FGF7WT_P4_19

description: library of 96 FGF7 Tg TEC cells


title: RPS2-STAMP IP PABPC RNA Rep3

city: La Jolla

first: Amy

last: Pasquinelli

state: CA

address: 9500 Gilman Drive

department: Biological Sciences

country: USA

institute: University of California, San Diego

description: 24 hour induction with doxycycline at 50ng/mL

data_processing:
All reads were aligned to the human genome hg38 primary assembly using STAR.
featureCounts version 2.0.2 was used to annotate reads, using the flag --minOverlap 20 and a custom GTF file derived from gencode v34
EPKM values were determined as in (Brannan et al., 2021). Furthermore, for each gene, EPKM values obtained in the Control-STAMP cell line were subtracted from the RPS2-STAMP EPKM values, giving a normalized EPKM value for each gene which indicates the degree of translation of that transcript. Control-STAMP PABPC IP Rep3 was not a successful immunoprecipitation and thus was excluded from analysis.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated file with normalized epkm values calculated for each gene in each condition (Input, PABPN IP or PABPC IP). Transcript per kilobase Million (TPM) values are included for each condition so that users can filter based on the overall abundance of a gene

source_name: HEK293T RPS2-APOBEC1 Cell line

growth_protocol: HEK293T cells were cultured as recommended by the manufacturer, in Dulbecco’s modified Eagle medium (DMEM, Gibco #11965092) supplemented with 10% fetal bovine serum (Gibco #10437-028) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was isolated using a standard Trizol (Life Technologies) RNA extraction. RNA was DNAse treated before libraries were prepared for sequencing.
cDNA libraries from three independent biological replicates were prepared from 200-300ng RNA using Illumina ribodepleted RNA stranded kit. Libraries were sequenced on the Illumina NovaSeq 6000, paired-end reads (100 nucleotides).

treatment_protocol: Prior to collection, the STAMP constructs were induced for 24 hours using 50ng/mL doxycycline. Formaldehyde crosslinking was performed as follows, followed by RNA Immunoprecipitation of PABPC or PABPN: Cells were washed twice on the plate with phosphate-buffered saline (PBS) and then collected into conical tubes with PBS and spun down. Cell pellets were resuspended in 0.1% formaldehyde in PBS and incubated at room temperature for 10 minutes. Glycine was added to a final concentration of 0.17 mM to quench the formaldehyde and incubated for 5 min. Cells were then spun down and washed with PBS two times before pellets were snap frozen on liquid nitrogen for storage at -80C. Cells were resuspended in RIPA buffer supplemented with rRNAseIn Plus, DTT, EDTA, and protease inhibitors. Cell pellets were sonicated and RNA Immunprecipitation was performed. After washing, reverse crosslinking was performed.

tag: stamp condition

value: Induced RPS2-APOBEC1

value: formaldehyde crosslinked

tag: immunoprecipitation

value: PABPC


title: WTTEC_P1_12

description: library of 96 WT TEC cells, Technical Replicate

tag: genotype/variation

value: WT

value: Thymus

value: 4 weeks

value: male


title: input_ESC_dTAG_24h_rep1

description: ChIP input sequencing of mESCs


title: FGF7WT_P3_13

description: library of 96 FGF7 Tg TEC cells

tag: age

value: thymic epithelial cells


title: 0285.C1

value: UC

value: Glucocorticoid responder

value: plasma


title: 1106.C1

value: Female


title: RPS2-STAMP IP PABPC RNA Rep2


title: WTTEC_P1_11

source_name: library of 96 WT TEC cells, Technical Replicate

tag: gender


title: 1213.C1


title: TT-SLAM-Seq_ESC_6h_dTAG13_rep2

description: TT-SLAM sequencing of mESCs

data_processing:
Raw reads were adapter and quality trimmed using cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --overlap 20 --minimum-length 25 --adapter "A{100}" --adapter "T{100}"). Trimmed reads were aligned with STAR (version 2.7.5a) with parameters '--outFilterMultimapNmax 50 --outReadsUnmapped Fastx' to the SILVA database (download: March 6, 2020) in order to remove rRNA content. Recovered unaligned reads were afterwards reverse-complemented using the seqtk 'seq' command (version 1.3-r106; parameters: -r).
Reverse-complemented reads were processed using SLAMDUNK with the 'all' command (version 0.4.1; parameters: -rl 100 -5 0) and the GENCODE gene annotation (VM19) as '-b' option. FPKM values per gene were calculated based on the obtained counts.
For genome-wide coverage tracks, reads harboring 'T>C' conversions representing nascent transcription were filtered from the BAM files using the alleyoop 'read-separator' command. Technical replicates were merged using samtools 'merge' (version: 1.10). Coverage tracks for single and merged replicates were obtained using bamCoverage (version 3.4.3; parameters: --normalizeUsing CPM) separately for the forward and reverse strand.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file containing FPKM values for all samples.

growth_protocol: For expanding cell culture, cells were cultured on irradiated primary mouse embryonic fibroblasts (MEFs) under serum/LIF conditions: knockout DMEM containing 15 % fetal bovine serum,  50 µg/ml penicillin/streptomycin, 2 mM L-Glutamine, 100 µM non-essential amino acids, 80 µM ß-mercaptoethanol and 1000 U/ml LIF. Before starting ChIP-Seq experiments, mESCs were depleted from MEFs by incubating them on gelatin cell culture plates for 45 min in +37 C allowing MEFs to attach while mESCs remain in suspension. MEF depletion was performed two times after which mESCs were seeded on gelatin coated plates and maintained in serum/LIF conditions with 2000 U/ml LIF.

extract_protocol:
Total RNA was extracted with Trizol and 24:1 chloroform-isoamylalcohol, precipitated with 2-propanol with 0.1 mM DTT (final concentration) and 1 µg glycogen. RNA was washed with 75 % EtOH with 0.1 mM DTT and eluted to H2O with 1 mM DTT. For enrichment of nascent transcripts with TT-SLAM-Seq, 50 µg of total RNA was used for each sample. RNA was fragmented with Magnesium RNA Fragmentation Module (NEB), precipitated with Na-acetate, glycogen and ethanol in presence of 0.1 mM DTT in -80C, washed with 75 % ethanol (0.1 mM DTT), and resuspended in water. RNA was biotinylated in 200 mM HEPES pH 7.5 and 10 mM EDTA with 5 µg of MTS-biotin (Biotium) by incubating in room temperature and protecting from light. Unbound biotin was removed from samples with phenol:chloroform extraction and precipitated from aqueous phase with NaCl and glycogen. Biotinylated RNA was denatured in 65C for 10 minutes and captured with µMACS streptavidin beads by incubating 15 minutes in rotation while keeping samples protected from light. µMACS columns were equilibrated with nucleic acid equilibration buffer and two times with biotinylation buffer (20 mM HEPES, 1 mM EDTA, pH 8). Beads were transferred to columns, washed three times with wash buffer (100 mM Tris-HCl pH7.5, 10 mM EDTA, 1 M NaCl and 0.1 % Tween 20) and labeled RNA was eluted with 100 mM DTT. RNA was cleaned up with RNEasy Minelute colums (Qiagen) and eluted to RNAse-free water with 1 mM DTT. RNA was alkylated with buffer containing 10 mM iodoacetamide, 50 mM NaPO4 (pH 8) and 50 % DMSO and by incubating reaction in 50 C for 15 minutes followed by quenching with 20 mM DTT. RNA was precipitated with glycogen, sodium acetate and ethanol, treated with Turbo DNAse (Invitrogen), and prepared into sequencing libraries with NEBNext Ultra II Directional RNA Library Prep Kit and NEBNext Multiplex Oligos (NEB), according to manufacturer's instructions, except using 8 minutes incubation time in fragmentation step.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: For degradation of TRIM28, 500 nM of dTAG-13 (or 0.05 % DMSO) was mixed with mESC medium and added to the cells 2, 6 or 24 h before samples were collected. For metabolic labeling of nascent transcripts, cells were pulsed with 500 µM 4-Thiouridine (Sigma) for 15 minutes.


title: input_ESC_DMSO_rep1

description: ChIP input sequencing of mESCs

value: DMSO


title: input_ESC_DMSO_rep3

description: ChIP input sequencing of mESCs


title: RPS2-STAMP IP PABPN RNA Rep3

value: PABPN


title: input_ESC_DMSO_rep2

description: ChIP input sequencing of mESCs


title: 0714.C1

value: Glucocorticoid non-responder


title: RPS2-STAMP IP PABPN RNA Rep1


title: WTTEC_P1_9

tag: strain


title: TT-SLAM-Seq_ESC_6h_dTAG13_rep3

description: TT-SLAM sequencing of mESCs

value: dTAG


title: 1229.C1

value: before glucocorticoid treatment

value: Male


title: 16D-CRPC-0d-ENZ-Rep2-ATAC

value: Castration Resistant Prostate Cancer (CRPC)

value: Castration resistant


title: WTTEC_P1_10

value: WT

tag: tissue


title: TT-SLAM-Seq_ESC_6h_dTAG13_rep1

description: TT-SLAM sequencing of mESCs


title: 0039.C1


title: RPS2-STAMP IP PABPC RNA Rep1

value: Induced RPS2-APOBEC1

value: formaldehyde crosslinked

value: PABPC


title: 1289.C1


title: WTTEC_7

description: library of 96 WT TEC cells, Biological Replicate

value: Thymus

value: 4 weeks

value: male

tag: cell type

value: thymic epithelial cells


title: RPS2-STAMP Input RNA Rep3


title: WTTEC_6

source_name: library of 96 WT TEC cells, Biological Replicate


title: 0773.C1

tag: disease state

value: UC

value: Glucocorticoid responder

value: plasma


title: WTTEC_8


title: TT-SLAM-Seq_ESC_2h_dTAG13_rep3

description: TT-SLAM sequencing of mESCs


title: TT-SLAM-Seq_ESC_24h_dTAG13_rep3

description: TT-SLAM sequencing of mESCs


title: RPS2-STAMP IP PABPN RNA Rep2

value: PABPN


title: RPS2-STAMP Input RNA Rep1


title: C12

description: library of 96 WT TEC cells

source_name: library of 96 WT TEC cells


title: 1306.C1

tag: corticosteroid response


title: TT-SLAM-Seq_ESC_24h_dTAG13_rep2

description: TT-SLAM sequencing of mESCs

value: dTAG


title: Control-STAMP IP PABPC RNA Rep2

source_name: HEK293T Control-APOBEC1 Cell line

value: Induced Control-APOBEC1


title: 1267.C1

tag: collection time

value: before glucocorticoid treatment

value: Male


title: RPS2-STAMP Input RNA Rep2


title: 0168.C1

tag: age (years)

value: Female


title: TT-SLAM-Seq_ESC_2h_dTAG13_rep1

description: TT-SLAM sequencing of mESCs


title: WTTEC_5

value: WT


title: TT-SLAM-Seq_ESC_2h_dTAG13_rep2

description: TT-SLAM sequencing of mESCs


title: VC11

value: reference

value: No IBD treatment

value: no IBD treatment

tag: Sex


title: Control-STAMP IP PABPC RNA Rep1

value: formaldehyde crosslinked

value: PABPC


title: 0074.C1

tag: individual


title: VC9

tag: sample type


title: 1359.C1


title: Control-STAMP IP PABPN RNA Rep3

tag: treatment


title: Control-STAMP IP PABPN RNA Rep2

tag: cell line


title: C9

description: library of 96 WT TEC cells

value: Thymus

value: 4 weeks

value: male


title: C11

description: library of 96 WT TEC cells

value: thymic epithelial cells


title: C10

description: library of 96 WT TEC cells


title: TT-SLAM-Seq_ESC_0h_DMSO_rep2

description: TT-SLAM sequencing of mESCs

value: DMSO


title: C8

description: library of 96 WT TEC cells


title: RNAseq_ESC_96h_dTAG13_rep3

description: RNA sequencing of mESCs

data_processing:
Raw reads were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --overlap 20 --minimum-length 25 --adapter "A{100}" --adapter "T{100}").
Reads were aligned to the mouse reference (mm10) using STAR (version 2.7.5a; parameters: --runMode alignReads --chimSegmentMin 20 --outSAMstrandField intronMotif --quantMode GeneCounts) and transcripts were assembled using stringtie (version 2.0.6; parameters: -e) with GENCODE annotation (VM19).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file containing gene abundances: <Gene ID> <Gene Name> <Reference> <Strand> <Start> <End> <Coverage> <FPKM> <TPM>

molecule: polyA RNA

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) including the DNaseI treatment, following manufacturer's protocol
1 ug of RNA was used to prepare sequencing libraries with TrueSeq Stranded mRNA capture library prep kit (Roche) according to manufacturer's instructions.

treatment_protocol: For degradation of TRIM28, 500 nM of dTAG-13 was mixed with mESC medium and added to the cells 96h before samples were collected.


title: TT-SLAM-Seq_ESC_0h_DMSO_rep1

description: TT-SLAM sequencing of mESCs


title: RNAseq_ESC_96h_dTAG13_rep2

description: RNA sequencing of mESCs


title: Control-STAMP IP PABPN RNA Rep1

tag: stamp condition

value: PABPN


title: C7

description: library of 96 WT TEC cells


title: Control-STAMP Input RNA Rep2

tag: immunoprecipitation


title: VC6

value: plasma


title: C5

description: library of 96 WT TEC cells

tag: genotype/variation


title: Control-STAMP Input RNA Rep1

value: Induced Control-APOBEC1


title: TT-SLAM-Seq_ESC_0h_DMSO_rep3

description: TT-SLAM sequencing of mESCs


title: VC2


title: RNAseq_ESC_96h_dTAG13_rep1

description: RNA sequencing of mESCs

value: dTAG


title: VC8


title: Control-STAMP Input RNA Rep3


title: VC5

value: Male


title: C4

description: library of 96 WT TEC cells

tag: age


title: TT-SLAM-Seq_ESC_24h_dTAG13_rep1

description: TT-SLAM sequencing of mESCs


title: RNAseq_ESC_6h_dTAG13_rep3

description: RNA sequencing of mESCs

treatment_protocol: For degradation of TRIM28, 500 nM of dTAG-13 was mixed with mESC medium and added to the cells 6h before samples were collected.


title: C3

description: library of 96 WT TEC cells

tag: gender


title: RNAseq_ESC_6h_dTAG13_rep1

description: RNA sequencing of mESCs


title: C2

description: library of 96 WT TEC cells

tag: strain


title: VC1


title: HEK293T- Cytoplasm fraction RNA Rep1

data_processing:
All reads were aligned to the human genome hg38 primary assembly using STAR.
featureCounts version 2.0.2 was used to annotate reads, using the flag --minOverlap 20 and a custom GTF file derived from gencode v34
Differential expression was calculated using DESeq2. Cut-offs used to determine significant differential expression were baseMean > 50 and padj <=0.01. In this comparison, a negative log2FoldChange indicates that a transcript was more nuclear, while a positive log2FoldChange indicates that a transcript was more cytoplasmic.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated files with output of DESeq2; normalized abudnance measurements for all genes when comparing the nuclear and cytoplasmic fractions. In this comparison, a negative log2FoldChange indicates that a transcript was more nuclear, while a positive log2FoldChange indicates that a transcript was more cytoplasmic

molecule: cytoplasmic RNA

source_name: HEK293T Total cell

extract_protocol:
RNA was isolated using a standard Trizol (Life Technologies) RNA extraction. RNA was DNAse treated before libraries were prepared for sequencing.
cDNA libraries from two independent biological replicates were prepared from 400ng RNA using Illumina ribodepleted RNA stranded kit. Libraries were sequenced on the Illumina NovaSeq 6000, paired-end reads (100 nucleotides).

treatment_protocol: Formaldehyde crosslinking followed by subcellular fractionation, using a protocol which was adapted from Gagnon et al., 2014, with slight modifications to buffer recipes (Gagnon et al., 2014). Section B, “Preparation of cytoplasmic, total nuclear, nucleoplasmic and chromatin fractions for biochemical assays” was followed for total nuclear and cytoplasmic fractions. Changes to buffer recipes consisted of eliminating MgCl2 and adding EDTA, which helps prevent deadenylation from occurring post-lysis. Hypotonic lysis buffer consisted of 10 mM Tris, pH 7.5, 10 mM NaCl, 1 mM EDTA, 0.3% NP-40 (vol/vol), and 10% glycerol (vol/vol). Nuclear Lysis buffer consisted of 20 mM Tris, pH 7.5, 150 mM KCl, 1 mM EDTA, 0.3% NP-40 (vol/vol), and 10% glycerol (vol/vol).

tag: genotype

value: wildtype

tag: fraction

value: Cytoplasmic


title: HEK293T- Cytoplasm fraction RNA Rep2


title: SAM1 infection of Staphylococcus aureus at 45 mins (replicate 2)

city: Cork

first: Colin

last: Buttimer

state: Cork

address: College Road

department: APC Microbiome Ireland

country: Ireland

institute: University College Cork

data_processing:
Reads where mapped to genomes of Staphylococcus phage SAM1 and that of host Staphylococcus aureus strain E1185(IV)ST12 using bowtie2 (v.2.3.4.1) by end-to-end alignment
Read alignments were then sorted by Samtools (v.1.7)
Read counts and coverage tables were then imported into R environment and then compared using DESeq2, using Wald test and parametric fit
Genome_build: MT338525.1
Supplementary_files_format_and_content: tab-delimited text file containg DESEQ calculated differential expression of genes of Staphylococcus phage SAM1 during host infection

organism: Staphylococcus phage SAM1

source_name: Staphylococcus phage SAM1

extract_protocol:
Supernatants were subject to total RNA extraction using the Direct-zol RNA miniprep kit (Zymo research, USA, as per manufacturer instructions). RNA samples were subject to rRNA depletion and before library creation
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: 45 mins


title: SAM1 infection of Staphylococcus aureus at 45 mins (replicate 3)


title: HEK293T- Nuclear fraction RNA Rep2

molecule: nuclear RNA

value: Nuclear


title: RNAseq_ESC_2h_dTAG13_rep3

description: RNA sequencing of mESCs

treatment_protocol: For degradation of TRIM28, 500 nM of dTAG-13 was mixed with mESC medium and added to the cells 2h before samples were collected.


title: C1

description: library of 96 WT TEC cells

value: WT

tag: tissue

tag: cell type


title: C6

description: library of 96 WT TEC cells


title: HEK293T- Nuclear fraction RNA Rep1

value: formaldehyde crosslinked


title: SAM1 infection of Staphylococcus aureus at 35 mins (replicate 2)

value: 35 mins


title: U-case RNA library + DMSO (control)

city: Stanford

first: Lu

last: Xiao

state: California

address: 369 N-S Axis, Stauffer I, 109

institute: Stanford University

description:
solid-phase synthesis
2x150 paired-end sequencing (PE150), but was processed as single-end data (SE150)

data_processing:
Sequencing reads were processed by previouly established  icSHAPE pipine (https://github.com/qczhang/icSHAPE).
Data was first demultiplexed, removed PCR dplicates and trimmed by using the scripts of icSHAPE pipeline.
Read quality was checked for each sample using FastQ v0.11.9
High-quality reads were then imported into bowtie2 v2.4.5 for alignment into BAM files.
BAM files were imported into the icSHAPE pipeline to calucate the RPKM and RT-stops frequency.
Assembly: Alignment was to the designed "generic" RNA library sequences built from solid-phase synthesis.
Supplementary files format and content: excel (.xlsx); containing reactivity score of each samples calculated by RT-stop frequency per nucleotide.

organism: synthetic construct

source_name: designed "generic" RNAs

extract_protocol:
RNAs were purified by washing with Rnase-free water using centrifuge filters after probing
RNAs were all folded independently before mixing to build a library; and the mixing was done immediately before probing

treatment_protocol: A-case/U-case RNA libraries were probed with 200mM NAIN3/ 25mM 1M7/ DMSO at 37℃ for 10min

tag: rna elements

value: hairpins; bulge loops; internal loops; three-way junctions; single-stranded polyU RNA; single-stranded RNA combining all dinucleotide steps

tag: loop nucleotide

value: homogeneous polyuridine (U-case)


title: U-case RNA library + 25mM 1M7


title: VCR_NC_1

city: Xi'an

first: Xiaodi

last: Zhao

address: No.127 Changle West Road

department: Xijing Hospital of Digestive Diseases

institute: Xijing Hospital of Fourth Military Medical University

data_processing:
The genome of human genome version of hg39 was used as reference.
The sequencing quality were assessed with FastQC (v0.11.5), and then low quality data were filtered using NGSQC (v2.3.3).
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters.
The gene expression analyses were performed with StringTie (v1.3.3b).
Genome_build: hg39

source_name: Human gastric cancer cell line

extract_protocol:
Total RNA was extracted with Trizol and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strains

tag: transfection

value: scrambled control siRNA


title: SAM1 infection of Staphylococcus aureus at 35 mins (replicate 1)


title: RNAseq_ESC_2h_dTAG13_rep2

description: RNA sequencing of mESCs

tag: treatment


title: RNAseq_ESC_2h_dTAG13_rep1

description: RNA sequencing of mESCs

tag: cell line


title: SAM1 infection of Staphylococcus aureus at 35 mins (replicate 3)


title: VCR_NC_3


title: RNAseq_ESC_6h_dTAG13_rep2

description: RNA sequencing of mESCs


title: SAM1 infection of Staphylococcus aureus at 15 mins (replicate 3)

value: 15 mins


title: VCR_2_3

value: CGA siRNA


title: SAM1 infection of Staphylococcus aureus at 15 mins (replicate 2)


title: RNAseq_ESC_24h_dTAG13_rep2

description: RNA sequencing of mESCs

treatment_protocol: For degradation of TRIM28, 500 nM of dTAG-13 was mixed with mESC medium and added to the cells 24h before samples were collected.


title: SAM1 infection of Staphylococcus aureus at 45 mins (replicate 1)


title: A-case RNA library + 200mM NAIN3

value: hairpins; bulge loops; internal loops; three-way junctions; single-stranded polyA RNA; single-stranded RNA combining all dinucleotide steps

value: homogeneous polyadenosine (A-case)


title: A-case RNA library + DMSO (control)


title: A-case RNA library + 25mM 1M7


title: VCR_NC_2


title: RNAseq_ESC_24h_dTAG13_rep1

description: RNA sequencing of mESCs


title: VCR_2_2


title: VCR_2_1


title: SAM1 infection of Staphylococcus aureus at 15 mins (replicate 1)


title: RNAseq_ESC_0h_DMSO_rep2

description: RNA sequencing of mESCs

treatment_protocol: 0.05 % DMSO was mixed with mESC medium and added to the cells 24h before samples were collected.

value: DMSO


title: SiHa-3 RNA-seq

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Basecalling was performed using RTA version 2.4.11
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 1.8.4) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.16).
Mapping to the hybrid genome containing hg38 and HPV16 or HPV18 was performed using STAR 2.5.2b
The following parameters were used: "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 clip3pAdapterSeq - --readFilesCommand zcat --runThreadN 32 --outSAMtype BAM Unsorted --chimSegmentMin 20"
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing output of STAR Chimeric.out.junction

source_name: SiHa cell

growth_protocol: All cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Fisher Scientific, Waltham, MA) with 10% fetal bovine serum (FBS, GE Healthcare, Logan, UT) at 37°C under a 5% CO2 atmosphere.

extract_protocol:
The total RNA was isolated using TriPure Reagent (Millipore-Sigma, Part No. 11667165001)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SiHa

value: female

tag: cancer type

value: Cervical


title: RNAseq_ESC_24h_dTAG13_rep3

description: RNA sequencing of mESCs

value: dTAG


title: U-case RNA library + 200mM NAIN3


title: gbpl3_3

city: Berkeley

first: yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description:
gbpl3_row_counts.txt
gbpl3_FPKMs.txt

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedling plants

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 50 mg samples of 7-day-old seedlings using Direct-zol RNA Miniprep kit (Genesee Scientific, Catalog #11-330).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: whole seedlings

value: gbpl3_3 mutant


title: VCR_1_3


title: SiHa-2 RNA-seq


title: gbpl3_2

description:
gbpl3_row_counts.txt
gbpl3_FPKMs.txt

value: gbpl3_2 mutant


title: VCR_1_2


title: SiHa-1 RNA-seq


title: RNAseq_ESC_0h_DMSO_rep3

description: RNA sequencing of mESCs

source_name: mESC


title: RNAseq_ESC_0h_DMSO_rep1

description: RNA sequencing of mESCs


title: H3K9me3_ESC_dTAG_24h_rep3

description: ChIP sequencing of mESCs

extract_protocol:
Cells were detached with TrypLE, washed once with PBS, fixed with 1 % formaldehyde for 10 minutes in room temperature followed by quenching with 125 mM glycine. For each sample, three million mESCs and 750 000 S2 cells were lysed in LB1 (50 mM HEPES-KOH, 140 nM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % Igepal ca-630 and 0.25 % Triton X-100, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and collected by sentrifugation. Lysis was continued in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 5 mM Na-butarate and 1 x protease inhibitor cocktail) followed by sentrifugation, nuclei were lysed in LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1 % Na-deoxycholate, 0.5 % N-Lauroylsarcosine, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and chromatin fragmented with Bioruptor NextGen for 35 cycles (high-setting). Lysates were clarified and protein-DNA complexes were isolated with ab4729 (Abcam) antibody for H3K27Ac and ab8898 (Abcam) antibody for H3K9me3 and Protein A Dynabeads (Invitrogen). Beads were washed 7 times with RIPA buffer (50 mM HEPES-KOH pH7.5, 1 mM EDTA, 1 % Igepal CA-630, 0.7 % Na-deoxycholate, 500 mM LiCl, 5 mM Na-butyrate and 1 x protease inhibitor cocktail), once with TE buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA and 50 mM NaCl) and eluted from beads with Elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA and 1% SDS). Samples were decrosslinked for 16 h in +65 C with 550 mM NaCl and proteinase K, treated with RNAseA and DNA was extracted with Phenol:Chloroform:Isoamylalcohol followed by chloroform extraction and precipitation with 30 µg glycogen, 0.3 M Na-acetate and ethanol.
10 ng of DNA was used to prepare sequencing libraries with KAPA HyperPrep Kit (Roche) according to manufacturer's instructions.


title: gbpl3_1

description:
gbpl3_row_counts.txt
gbpl3_FPKMs.txt

value: gbpl3_1 mutant


title: Col-0_3

description:
gbpl3_row_counts.txt
gbpl3_FPKMs.txt

value: wild type


title: H3K9me3_ESC_dTAG_24h_rep1

description: ChIP sequencing of mESCs


title: CD8aa splenocytes KO replicate 2

city: Bethesda

first: Jia

last: Nie

address: Building 37, Room 3016

data_processing:
Illumina RTA 1.18.61 software used for basecalling.
Samples demultiplexed using Bcl2fastq 2.17 software
Raw RNAseq fastq reads were trimmed with Trimmomatic and aligned to mouse genome using STAR
Gene-assignment and count of RNA reads were performed with Htseq
Genome_build: mm10
Supplementary_files_format_and_content: count of RNA reads were performed with Htseq; FPM normalization was performed with the FPM function of the DEseq2 package

source_name: spleen

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMARTer Ultra Low Input reagent (Takara) and Nextera XT DNA (Illumina) were used for library.   Libraries were pooled and sequenced with paired-end reads of 76bp on a Nexseq to reach 70 million read pairs per sample

tag: population

value: Cd4 Cre+ lrffl/fl


title: H3K9me3_ESC_dTAG_24h_rep2

description: ChIP sequencing of mESCs


title: CD8aa splenocytes KO replicate 3


title: H3K9me3_ESC_DMSO_rep3

description: ChIP sequencing of mESCs


title: ADR_NC_2


title: ADR_2_3


title: X. tropicalis - Histone H4 ChIP replicate 1

first: Jessen

middle: V

last: Bredeson

address: 545 Weill Hall #3200

department: Molecular and Cell Biology

institute: University of California Berkeley

data_processing:
Pair-End (PE) reads were trimmed with Trimmomatic v.0.39 (Bolger et al. 2014) filtering for universal Illumina primers and for Nextera-PE indices.
Processed PE reads were mapped with minimap2 2.17-r941 (Li 2016) against the unmasked genome reference.
Samtools v.1.9 (Li et al. 2009) was used for sorting and indexing the alignments.
Read counts (read MQ>=0) per 10-Kb bins (non-overlapping) for all samples were calculated with multiBamSummary from deeptools 3.3.0 (Ramírez et al. 2016).
Assembly: GCF_000004195.4
Supplementary files format and content: Tabulated table with absolute read counts in bins of 10kb.

organism: Xenopus tropicalis

source_name: XTN-6 cells

growth_protocol: Xenopus tropicalis XTN-6 cells were grown in 70% calcium-free L-15 (US Biologicals cat# L2101-02-50L),pH 7.2/10% Fetal Bovine Serum/Penicillin-Streptomycin (Invitrogen cat# 15140-163) at RT.

extract_protocol:
Approximately 40 million cells were trypsinized and collected, nuclei were isolated by dounce extraction and collected with sucrose cushion. Chromatin was digested to mononucleosomes by MNase. Nuclei were lysed and soluble nucleosomes were extracted at 4°C overnight. Extracted mononucleosomes were precleared with Protein A dynabeads (Invitrogen cat# 100-02D) for at least 4 hrs at 4°C. A sample was taken for input after preclearing. Protein A dynabeads were bound to 10μg antibody (either Rb-anti-Xl CENP-A, cross-reactive with X. tropicalis, Rb-anti-H4 Abcam cat# 7311 or Rb-anti-H3 Abcam cat# 1791) and incubated with precleared soluble mononucleosomes at 4C overnight. Dynabeads bound to antibody were collected with a magnet and washed three times with TBST (0.1% Triton X-100) before elution with 0.1% SDS in TE and proteinase K incubation at 65°C with shaking for at least 4hrs.
Isolated genomic DNA was size-selected using Ampure beads (Beckman cat# A63880) and prepared for sequencing using the NEBNext ultra ii DNA library prep kit for Illumina (NEB cat# E7654). Three replicates were sequenced on an Illumina HiSeq 4000 lane 2x150bp by the Stanford Functional Genomics Facility.

tag: chip antibody

value: Rb-anti-H4 Abcam cat# 7311

value: Whole tadpole

value: NXR Nigerian strain

tag: developmental stage

value: NF 20


title: X. tropicalis - Input replicate 1


title: Col-0_2

description:
gbpl3_row_counts.txt
gbpl3_FPKMs.txt

tag: age


title: ADR_NC_3

value: scrambled control siRNA


title: Col-0_1

description:
gbpl3_row_counts.txt
gbpl3_FPKMs.txt


title: CD8aa IEL Ctrl replicate 3

source_name: IEL

tag: strain

value: Cd4 Cre- lrffl/fl


title: H3K27Ac_ESC_dTAG_24h_rep3

description: ChIP sequencing of mESCs


title: CD8aa IEL Ctrl replicate 2

tag: genotype


title: H3K27Ac_ESC_dTAG_24h_rep1

description: ChIP sequencing of mESCs


title: X. tropicalis - CENPA replicate 3

value: Rb-anti-Xl CENP-A


title: ADR_2_2

value: CGA siRNA


title: H3K9me3_ESC_DMSO_rep2

description: ChIP sequencing of mESCs

value: DMSO


title: H3K27Ac_ESC_DMSO_rep3

description: ChIP sequencing of mESCs


title: H3K9me3_ESC_DMSO_rep1

description: ChIP sequencing of mESCs


title: VCR_1_1


title: X. tropicalis - IgG ChIP replicate 3

value: Rabbit IgG whole molecule Jackson ImmunoResearch cat#011-000-003


title: H3K27Ac_ESC_dTAG_24h_rep2

description: ChIP sequencing of mESCs

value: dTAG


title: X. tropicalis - CENPA ChIP replicate 1


title: X. tropicalis - Input replicate 3


title: H3K27Ac_ESC_DMSO_rep1

description: ChIP sequencing of mESCs


title: 3T3 PHD2 WT 2

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

institute: Heidelberg University

description:
3T3 cells (fibroblast) inmedium cultured from BMDM wt cells (macrophage)
81__10_S65_R1_001

data_processing:
Gene-level expression was quantified using Kallisto with the mouse genome (Mus Musculus GRCm38 assembly)
Genome_build: GRCm38
Supplementary_files_format_and_content: gene read counts from Kallisto gene expression quantification

source_name: In-vitro cell culture

growth_protocol: Macrophage conditioned medium was obtained by culturing differentiated BMDM for 24h in DMEM GlutaMAX (Gibco 31966) supplemented with 2% FCS, 100U/ml Penicillin-Streptomycin, and 15% L929-conditioned medium in either normal oxygen conditions or hypoxia (0.1% O2). NIH/3T3 were cultured in DMEM (Gibco, 31966047) supplemented with 10% FCS and 100u/ml Penicillin-Streptomycin.

extract_protocol:
RNA was isolated from triplicates of WT and PHD2cko BMDMs 24 hour after seeding, and from triplicate fibroblasts after 72 hours exposure to WT or PHD2cko conditioned medium.
Bioanalyzer confirmed intact RNA (RNA Integrity number 10) for sequencing of 10µg RNA, on the NextSeq 500 system  using v 2.5 chemistry, at ~15M single reads per sample

treatment_protocol: BMDM: Bone marrow was isolated, and cells were cultured for seven days in RPMI-1640 (Gibco with Glutamax, 2g/L glucose) supplemented with 10% FCS, 100U/ml Penicillin-Streptomycin, and 15% L929-conditioned medium to generate bone marrow-derived macrophages (BMDM) for 24 hours after seeding. NIH/3T3: Before experiments with macrophage conditioned medium, NIH/3T3 were starved for 24-48 hours respectively using DMEM supplemented with 0.1% FCS. Then NIH/3T3 were cultured with the growth protocol above (conditioned medium culture by BMDM WT and KO) for 72 hours.

tag: genotype of bmdm used for culture medium

value: fibroblast


title: ADR_2_1


title: ADR_1_3


title: X. tropicalis - Histone H3 ChIP replicate 3

value: Rb-anti-H3 Abcam cat# 1791


title: ADR_NC_1


title: BMDM PHD2 WT 2

description:
BMDM wt cells (macrophage)
79__8_S63_R1_001

value: macrophage

value: BMDM


title: ADR_1_2


title: BMDM PHD2 KO 3

description:
BMDM PHD2CKO cells (macrophage)
83__12_S67_R1_001


title: CD8aa splenocytes KO replicate 1


title: ADR_1_1


title: N107L: Naïve Control rep1

city: Pittsburgh

first: XINGAN

last: WANG

state: Pennsylvania (PA)

address: 200 Lothrop Street, W1206A

department: Medicine

institute: University of Pittsburgh

description: N107L (GSM4684678)

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts.
Alignments were parsed using STAR program and differential expressions were determined through DESeq2/edgeR.
GO and KEGG enrichment were implemented by the ClusterProfiler.
Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Left lung

extract_protocol:
Left lungs were immersed in RNAlater™ Storage Solution at 4ºC for 24 h and then stored at -80ºC before delivery for RNA library preparation and high throughput RNA-sequencing  (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library preparation was conducted by Novogene Inc. (Sacramento, CA) using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs Inc., Ipswich, MA). Barcoded libraries were assessed using Qubit 2.0 (ThermoFisher, Invitrogen, Grand Island, NY), Agilent 2100 Bioanalzyer (Agilent Technologies), and quantified with qPCR. Individual libraries were pooled at equal molar concentrations and sequencing was performed using the Illumina NovaSeq 6000 platform producing paired-end 150 base pair reads and Q30 >80%.

treatment_protocol: In a mouse model of orthotopic lung transplantation from C57BL/6 to Balb/C, 1) donor lungs were stored at 0C for 24 hours and transplanted for 2 hours of reperfusion; 2) donor mice were subjected to 4 hours of hypovolemic shock (mean arterial pressure, 15+/-5 mmHg) and 20 hours of recovery, followed by 24 hours of cold ischemia and 2 hours of reperfusion.

value: Lung tissue

value: Adult

value: wild type

value: Control


title: XW744L: 4h HS/24h CI/2h Reperfusion rep3


title: X. tropicalis - CENPA replicate 2

value: Whole tadpole

value: NXR Nigerian strain


title: H3K27Ac_ESC_DMSO_rep2

description: ChIP sequencing of mESCs


title: Preterm_3_Decidua

city: New Haven

first: Liza

last: Konnikova

state: CT

address: 375 Congress Ave LSOG 407

department: Pediatrics

institute: Yale University

description: Preterm Sample 3

data_processing:
Basecalls performed using CLC Genomics Workbench
CLC Genomics Workbench was used to first trim paired reads with a quality limit of 0.05, ambiguous limit of 2 with automated read through adapter trimming from the 3’-end with a maximum length of 150.
Trimmed reads were then mapped to the homo_sapiens_sequence_hg38 reference sequence
Gene expression was calculated as Transcripts per Kilobase Million (TPM)
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files include TPM values for every sample for genes of interest in study

source_name: Preterm Placenta

extract_protocol:
Placental layers were separated with forceps under a dissecting microscope. Samples were snap frozen with dry ice and shipped to MedGenome for RNA isolation using the Qiagen All-Prep Kit (#80204)
cDNA synthesis wasprepped with the Takara SMART-seq kit (#634894)and NexteraXT (FC-131-1024, Illumina) was used to fragment and add sequencing adaptors. Quality control was completed by MedGenome via Qubit Fluorometric Quantitation and TapeStation BioAnalyzer.

tag: patient number

value: Preterm Placenta

tag: site

value: Decidua


title: CD8aa IEL Ctrl replicate 1

value: Cd4 Cre- lrffl/fl


title: N109L: Naïve Control rep3

description: N109L (GSM4684680)

tag: tissue

value: control


title: Preterm_3_Fetal_Membrane

description: Preterm Sample 1

value: Fetal Membrane


title: XW734L: 4h HS/24h CI/2h Reperfusion rep2


title: 3T3 PHD2 KO 2

description:
3T3 cells (fibroblast) in medium cultured from BMDM PHD2cKO cells (macrophage)
76__5_S60_R1_001

tag: cell type


title: BMDM PHD2 WT 1

description:
BMDM wt cells (macrophage)
82__11_S66_R1_001


title: N108L: Naïve Control rep2

description: N108L (GSM4684679)


title: Preterm_3_Villi

description: Preterm Sample 2

value: Villi


title: X. tropicalis - IgG ChIP replicate 2

value: Rabbit IgG whole molecule Jackson ImmunoResearch cat#011-000-003

value: NF 20


title: Preterm_2_Fetal_Membrane

description: Preterm Sample 1


title: 3T3 PHD2 WT 3

description:
3T3 cells (fibroblast) in medium cultured from BMDM wt cells (macrophage)
78__7_S62_R1_001

value: fibroblast


title: Preterm_1_Villi

description: Preterm Sample 2


title: Preterm_2_Decidua

description: Preterm Sample 3


title: BMDM PHD2 KO 2

description:
BMDM PHD2CKO cells (macrophage)
73__3_S58_R1_001

value: macrophage


title: X. tropicalis - Input replicate 2


title: Healthy control 11 [Olink Explore 1536 panel]

type: protein

first: William

last: Damsky

address: 333 Cedar St

institute: Yale School of Medicine

hyb_protocol: according to manufacture protocol

scan_protocol: according to manufacture protocol

data_processing:
Plasma was analyzed using the Olink Explore 1536 panel. NPX, Normalized Protein eXpression, is Olink's arbitrary unit which is in Log2 scale. It is calculated from Ct values and data pre-processing (normalization) is performed to minimize both intra- and inter-assay variation. NPX data allows users to identify changes for individual protein levels across their sample set, and then use this data to establish protein signatures:
https://www.olink.com/question/what-is-npx/#:~:text=The%20NPX%20scale%20is%20inverted,%3A%202NPX%3D%20linear%20NPX

label: NOT PROVIDED

molecule: protein

source_name: Blood

label_protocol: according to manufacture protocol

extract_protocol: Blood samples were collected from participants at baseline and again after 6 months of therapy. Samples were compared to 11 healthy, roughly age matched controls. Blood was collected in EDTA-coated tubes and centrifuged; the buffy coat was removed and stored separately from the plasma, which was aliquoted and stored at -80ºC.

treatment_protocol: 9 patients with severe, long-standing sarcoidosis were enrolled and treated with tofacitinib monotherapy (5 mg twice daily) for 6 months. Concomitant methotrexate and/or low dose prednisone was allowed so long as the dose had been stable over the prior 3 months.

tag: subject status

value: healthy control

value: Blood


title: X. tropicalis - Histone H3 ChIP replicate 2

value: Rb-anti-H3 Abcam cat# 1791


title: BMDM PHD2 WT 3

description:
BMDM wt cells (macrophage)
80__9_S64_R1_001

value: BMDM


title: Healthy control 9 [Olink Explore 1536 panel]


title: Healthy control 10 [Olink Explore 1536 panel]


title: Preterm_2_Villi

description: Preterm Sample 2


title: BMDM PHD2 KO 1

description:
BMDM PHD2CKO cells (macrophage)
77__6_S61_R1_001


title: XW749L: 24h CI/2h Reperfusion rep2

value: Lung tissue

value: Adult

value: wild type


title: 3T3 PHD2 KO 1

description:
3T3 cells (fibroblast) in medium cultured from BMDM PHD2cKO cells (macrophage)
74__4_S59_R1_001


title: Preterm_1_Decidua

description: Preterm Sample 3

value: Preterm Placenta


title: XW745L: 24h CI/2h Reperfusion rep1


title: Term_3_Villi

description: Term Sample 2

source_name: Term Placenta

value: Term Placenta


title: control_Input1

data_processing:
Illumina RTA 2.4.11 software used for basecalling.
Samples demultiplexed using Bcl2fastq 2.17 software
Sequenced reads were trimmed for adaptor sequence and low-quality sequence (phred < 32) on the Partek Flow server
Filtered reads were mapped to mm10 whole genome using bowtie v1.0.0 with defauft parameters on the Partek Flow serve
Peaks were called using MACS2 callpeak
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated with the bamCoverage function of the deeptools package

source_name: CD4+ T cells

growth_protocol: Splenic CD4+ T cells from Rosa26BirA or Rosa26BirA animals were enriched using Dynabeads Untouched Mouse CD4 cells kit (Invitrogen) and stimulated with anti-CD3 (1mg/ml), anti-CD28 (3mg/ml) and IL-12 (10ng/ml) . One day after activation, cells were transduced with pMRX-LRFbio-tag-IRES-Thy1.1 retrovirus, or with a control retrovirus expressing Thy1.1 only. Cells were cultured for two additional days with anti-CD3, anti-CD28 and IL-12 and then with IL-2 (100 ng/ml) for another day.

extract_protocol: DNA was treated with proteinase K and RNase (both at 0.2mg/ml) before purification using the QIAquick PCR purification kit (Qiagen)  Accel-NGS 2S DNA reagent (Swift)  Libraries were sequenced with paired-end reads of 76bp on a NextSeq sequencer (Illumina)

treatment_protocol: Live cells were sorted, washed in PBS and fixed in 1% formaldehyde-containing PBS for 5 min at 37 degrees. Following quenching with 0.125M glycine, cells pellets were snap-frozen on dry ice and stored at -80 degrees. Frozen fixed cells were then lysed in 1% SDS RIPA buffer (20 mM Tris-HCl pH 7.6, 2 mM EDTA, 150 mM NaCl, 0.1% sodium deoxycholate, 1% TritonX100) for 30 minutes at 4°C, spun down and sonicated in 0.1% SDS RIPA buffer using a Qsonica Q800R sonicator (30s on, 59s off, 85% amplitude) to obtain a sheared chromatin with an average size of 200bp. Sheared chromatin was pre-cleared with protein-A magnetic beads (Invitrogen 10001D) followed by immunoprecipitation with M280 Streptavidin beads (Invitrogen 11205D). After washing, immunoprecipitated chromatin was reverse-crosslinked by overnight incubation at 70°C in 50nM 50mM Tris-HCl pH 8., 10mM EDTA , 1% SDS buffer

value: BirA

tag: transduction

tag: cell population

tag: immunoprecipitation

value: Streptavidin


title: Term_3_Fetal_Membrane

description: Term Sample 1

value: Fetal Membrane


title: 4 h PAL-induced I/R injury rep3

treatment_protocol: Left pulmonary artery was ligated with a 6-0 silk slot for 4 h or 5 h before releasing ligation to restore the blood flow. Spontaneous breathing resumed shortly after closing the chest cavity. The animal was anesthetized and intubated once again at the end of warm ischemia.

tag: treatment

value: Treated


title: LRF_Input2


title: XW755L: 24h CI/2h Reperfusion rep3


title: Healthy control 6 [Olink Explore 1536 panel]


title: Healthy control 4 [Olink Explore 1536 panel]


title: Healthy control 3 [Olink Explore 1536 panel]


title: Term_3_Decidua

description: Term Sample 3

value: Decidua


title: XW721L: 4h HS/24h CI/2h Reperfusion rep1


title: 3T3 PHD2 KO 3

description:
3T3 cells (fibroblast) in medium cultured from BMDM PHD2cKO cells (macrophage)
72__2_S57_R1_001

tag: cell line


title: Term_2_Fetal_Membrane

description: Term Sample 1


title: Healthy control 8 [Olink Explore 1536 panel]


title: Healthy control 7 [Olink Explore 1536 panel]


title: Healthy control 5 [Olink Explore 1536 panel]


title: LRF_Input1


title: Naïve Control rep2

value: control


title: 4 h PAL-induced I/R injury rep2


title: 4 h PAL-induced I/R injury rep1


title: Term_2_Decidua

description: Term Sample 3


title: LRF_CHIP1


title: Healthy control 1 [Olink Explore 1536 panel]


title: Term_2_Villi

description: Term Sample 2

value: Villi


title: Naïve Control rep3


title: Term_1_Fetal_Membrane

description: Term Sample 1


title: Preterm_1_Fetal_Membrane

description: Preterm Sample 1


title: Healthy control 2 [Olink Explore 1536 panel]


title: control_CHIP1


title: Adiopcyte Derived from iMSC3, D3, with Rosiglatazone added in induction and maintainance media

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

data_processing:
The constructed libraries were subjected to high throughput mRNA sequencing using Illumina NovaSeq 6000.
Raw reads obtained in FASTQ format were processed through fastp.
Reference genome and gene model annotation files were directly downloaded from genome website browser (NCBI, UCSC, and Ensembl). Using the Spliced Transcripts Alignment to a Reference (STAR) software, the paired-end clean reads were aligned to the reference genome
FeatureCounts was used to count the reads number mapped to each gene. The FPKM (Fragment Per Kilobase per Million mapped reads) was calculated for each gene
Differential gene expression analysis was performed using DESeq2 R package, followed by GO and KEGG enrichment analysis using clusterProfiler R package

source_name: Derived adipocytes

growth_protocol: iMSC3 were grown and maitained in MEM complete media supplemented with 10% FBS, 1% Glutamine, and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNAs were extracted from all groups A, B, C and D. The harvested cells were first lysed using Qiazol lysis reagent. Then, the extraction was carried out using miRNeasy extraction kit following the manufacturer’s instructions (Qiagen, Germany). The RNA quantity and purity were determined using Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with a hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments, preferentially\preferably  of 150-200  bp in length, the library fragments were purified using AMPure XP system (Beckman Coulter, USA). Then, 3µl of USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95°C. After that, PCR was performed using Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. Finally, the PCR products were purified (AMPure XP system) and library quality was assessed using the Agilent Bioanalyzer 2100 system.

treatment_protocol: iMSC3 were differentiated into adipocytes without and with Rosiglitazone treatment: adipocytes (B) derived with no Rosiglitazone treatment; adipocytes (C) derived with Rosiglitazone present in induction media only while adipocytes (D) derived with Rosiglatazone present in both induction and maintenance media

value: Rosiglitazone treated


title: IELp LRF KO replicate 3

description: Sample 6

source_name: IELp LRF KO

value: Thymus

value: thymic IEL precursors (IELp)

tag: population

value: Cd4 Cre+ lrffl/fl


title: Sarcoidosis patient 1 treated with 5 mg tofacitinib [Olink Explore 1536 panel]

value: Sarcoidosis patient

value: tofacitinib

value: Blood


title: Term_1_Decidua

description: Term Sample 3


title: LRF_CHIP2


title: 3T3 PHD2 WT 1

description:
3T3 cells (fibroblast)  in medium cultured from BMDM wt cells (macrophage)
71__1_S56_R1_001

value: fibroblast


title: PHD2cKO_single-cell_RNA

description: pool (n=9) atherosclerotic plaques from mice with PHD2 cKO (knock-out)

data_processing:
Raw sequencing data (FastQ files) were processed (alignment and gene-level expression quantification) using the CellRanger pipeline (10x Genomics, version 3.1) with the mouse genome (mm10 assembly). Seurat R package (v.3.0.0) was used to perform a standard analysis.
Raw UMI counts are presented as processed data. No filtering criteria either on genes or cells has been applied yet on this processed data. Thus it is recommended to follow filtering settings depending on the purpose of the study when using this data, such as cell doublet detection, filter-out cell death based on mitochondrial expression, etc. Follow the section of  material and methods section and code repository to reproduce the analysis of the cited publications, or use another settings based on the purpose of your study.
Genome_build: mm10
Supplementary_files_format_and_content: gene read counts matrix from CellRanger (v3.1) read by Seurat (v.3.0.0)

source_name: Plaque-resident cells from atherosclerotic PHD2 cKO mice

growth_protocol: Plaque-resident cells from atherosclerotic mice

extract_protocol:
PHD2 WT and PHD2 cko mice (n=11 and 9, respectively) were euthanized with a pentobarbital overdose (100 mg/kg i.p.) after 20 weeks of HCD and blood was withdrawn via the vena cava, followed by PBS perfusion via the left ventricle. The aortic root was subsequently excised and fixed in 4% paraformaldehyde overnight and paraffin-embedded. Aortic arches of either genotype were pooled, sliced in pieces using a scalpel, and enzymatically digested for 15 minutes at 37°C using collagenase B (0.00284g/ml, Sigma 110088807001), pronase (0.01g/ml, Sigma 10165921001) and DNAse (0.1mg/ml, Roche 11284932001). Tissue was filtered through a 70µM strainer and subjected to red blood cell lysis (8.4g NH4CL + 0.84g NaHCO3 in 1 liter H2O, pH 7.2-7.4). All single, DAPI-negative living, cells were sorted on FACS Aria III for SCS. Cell count and viability of sorted cells was confirmed by trypan blue staining, and a total of ~12.000 DAPI- plaque cells were loaded on a chromium single cell controller using V2 reagent kit (10X Genomics) to create cDNA sequencing libraries per manufacturers protocol.
The Chromium Single-Cell 3' Library Kit was then used to generate indexed sequencing libraries

treatment_protocol: Myeloid specific PHD knockout (PHDko) mice were fed 0.25% cholesterol diet for 6-12 weeks to induce atherosclerosis

value: PHD 2cKO

value: atherosclerotic plaques

tag: cells

value: total cells


title: heart, 8W-post-TAC1

first: Xiang

last: Li

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Original data were filtered to remove reads with joints, indeterminate base information and low quality, followed by sequencing error rate check and GC content distribution check to obtain clean reads used in subsequent analysis.
Clean  reads were than mapped to mm10 genome with HISAT2 compares software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids.
Genome_build: mm10
Supplementary_files_format_and_content: Expression_Gene.txt (Tab-delimited text file includes RPKM values for each Sample)

source_name: heart

extract_protocol:
Total RNAs from the ventricular tissues of the sham group and the pressure overload groups (2, 4 and 8 weeks after TAC) were isolated using TRIzol® Reagent(Thermo Fisher Scientific, USA). Each group contains two independent samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: heart


title: heart, 8W-post-TAC2


title: IELp LRF KO replicate 2

description: Sample 5


title: Term_1_Villi

description: Term Sample 2

value: Term Placenta


title: heart, 4W-post-TAC2


title: Adiopcyte Derived from iMSC3, RD2, with Rosiglatazone added in induction and maintainance media


title: Sarcoidosis patient 10 prior to treated with tofacitinib [Olink Explore 1536 panel]


title: Naïve Control rep1

value: Lung tissue

tag: age

value: Adult

value: wild type

value: Control


title: IELp LRF KO replicate 1

description: Sample 4

tag: strain


title: Adiopcyte Derived from iMSC3, C3, with Rosiglitazone added in induction media

value: Rosiglitazone treated


title: Sarcoidosis patient 3 treated with 15 mg tofacitinib [Olink Explore 1536 panel]


title: WT_single-cell_RNA

description: pool (n=11) atherosclerotic plaques from mice with PHD2 wt

source_name: Plaque-resident cells from atherosclerotic PHD2 wt mice

tag: genotype

value: PHD2 WT


title: IELp Ctrl replicate 3

description: Sample 3

source_name: IELp Ctrl

value: Thymus

value: thymic IEL precursors (IELp)

value: Cd4 Cre- lrffl/fl


title: Adiopcyte Derived from iMSC3, C1, with Rosiglitazone added in induction media


title: heart, 2W-post-TAC2


title: IELp Ctrl replicate 1

description: Sample 1


title: Sarcoidosis patient 10 after treated with tofacitinib for six months [Olink Explore 1536 panel]

value: Sarcoidosis patient

value: tofacitinib


title: Adiopcyte Derived from iMSC3, D1, with Rosiglatazone added in induction and maintainance media


title: heart, 4W-post-TAC1


title: Sarcoidosis patient 8 after treated with tofacitinib for six months [Olink Explore 1536 panel]

value: Blood


title: IELp Ctrl replicate 2

description: Sample 2


title: heart, 2W-post-TAC1


title: Sarcoidosis patient 8 prior to treated with tofacitinib [Olink Explore 1536 panel]


title: Sarcoidosis patient 7 after treated with tofacitinib for six months [Olink Explore 1536 panel]


title: heart, Sham2

value: Sham


title: Pax7-CE1

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
processed data file:
filtered_counts_190926.txt
QSC_Gli3_Ctr_vs_ASC_Gli3_Ctr_190926.txt
QSC_Gli3_Ctr_vs_QSC_Gli3_KO_190926.txt

data_processing:
RNA-seq reads were mapped to transcripts from GRCm38_GENCODE.vM19 using salmon v0.13.158.
Data were loaded into R using the tximport library and the gene/count matrix was filtered to retain only genes with five or more mapped reads in two or more samples.
Differential expression was assessed using DESeq2. Expression differences were calculated using the lfcShrink function, applying the apeglm method (v1.6.0). Lists of significantly changed genes were identified using a qvalue (Benjamini-Hochberg corrected p-value) cut-off of 0.05 and absolute fold changes greater than or equal to
Genome_build: GRCm38_GENCODE.vM19
Supplementary_files_format_and_content: Attached files are annotated DESEq2 fold change and read counts from which these were derived.

source_name: QSC Gli3 Ctr

growth_protocol: Satellite cells were sorted by gating a mononuclear cell population of α7-INTEGRIN+, CD34+, CD31neg, CD45neg, SCA1neg, CD11bneg (quiescent satellite cells) or α7-INTEGRIN+, VCAM1+, CD31neg, CD45neg, SCA1neg, CD11bneg (activated satellite cells) using a MoFlo XDP cell sorter (Beckman Coulter).

extract_protocol:
RNA was extracted using the ARCTURUS Picopure RNA extraction kit (ThermoFisher), according to the manufacturers’ instructions.
Library construction was performed with 20 ng of input total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina - polyA mRNA workflow (New England Biolabs).

tag: genotype/variation

value: quiescent satellite cell


title: Pax7-CE2


title: Gli3-3

description:
processed data file:
filtered_counts_190926.txt
QSC_Gli3_KO_vs_ASC_Gli3_KO_190926.txt
QSC_Gli3_Ctr_vs_QSC_Gli3_KO_190926.txt

source_name: QSC Gli3 KO

value: Gli3 Knockout


title: Adiopcyte Derived from iMSC3, RB3

value: Untreated


title: Sarcoidosis patient 7 prior to treated with tofacitinib [Olink Explore 1536 panel]


title: heart, Sham1

value: heart


title: Pax7-CE3


title: Sarcoidosis patient 6 prior to treated with tofacitinib [Olink Explore 1536 panel]


title: Adiopcyte Derived from iMSC3, C2, with Rosiglitazone added in induction media


title: Sarcoidosis patient 5 after treated with tofacitinib for six months [Olink Explore 1536 panel]


title: Sarcoidosis patient 5 prior to treated with tofacitinib [Olink Explore 1536 panel]


title: Immortalized Human Bone Marrow Mesenchymal Stromal Cells - hTERT (iMSC3), A3

source_name: Stromal cells

tag: transformation

value: Telomerase transformed


title: granulosa_cell_1-5

first: Xiaoping

last: Liu

address: Shougouling Road

institute: The Sixth Affliated Hospital of Sun Yat-sen University

data_processing:
RNAs were subjected to first strand and second strand cDNA synthesis following by
adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library
Prep Kit for Illumina (NEB, USA).
Genome_build: hs37d5
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample ...

source_name: granulosa cells

extract_protocol:
Granulosa cells were collected and total RNA were extracted using Trizol reagent. Fragmented  RNA (the average length was approximately 200 bp) were subjected to first strand and second strand cDNA  synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext®  Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Five samples were collected from the patients underlying COS protocol and 5 samples from mild protocol

value: mild ovarian stimulation


title: Sarcoidosis patient 6 after treated with tofacitinib for six months [Olink Explore 1536 panel]


title: granulosa_cell_1_9


title: Gli3-2


title: Adiopcyte Derived from iMSC3, B1


title: Immortalized Human Bone Marrow Mesenchymal Stromal Cells - hTERT (iMSC3), A2


title: granulosa_cell_1_4


title: Adiopcyte Derived from iMSC3, RB2


title: Immortalized Human Bone Marrow Mesenchymal Stromal Cells - hTERT (iMSC3), A1


title: granulosa_cell_1_1


title: CMT2A MFN2 T105M

city: St. Louis

first: Xiawei

last: Dang

state: MO

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

description: CMT2A CPM.txt

data_processing:
Partek Flow software was used to process data, trimmed base on quality score with default setting
RNA-seq reads were aligned to the Homo sapiens-hg19_chr22 assembly with STAR
CPM (counts per million) were calculated by using Refseq as annotation mode and normalized by adding 0.0001 to CPM
Genome_build: hg19_chr22
Supplementary_files_format_and_content: text files including cpm for each cell line

source_name: Fibroblats

growth_protocol: Human fibroblasts were maintained in DMEM supplemented with 15% (v/v) FBS (Gibco, Cat#: A4766801) and 1% (v/v) penicillin/streptomycin (Gibco, Cat#: 15140122) at 37°C in 5% CO2-95% air.

extract_protocol:
Total RNA from human fibroblasts was isolated using TRIzol Reagent (Cat: 15596-026, Ambion RNA Life technologies) and treated with DNase I (Invitrogen, Cat: 18068015).
mRNA sequencing was performed using the RiboErase protocol, with indexing and pooled sequencing on a NovaSeq S4. Sequencing depth was 30M reads per sample.

treatment_protocol: transitioned to no glucose DMEM from Thermo Fisher Scientific (Waltham, Massachusetts, USA; Catalog No: A1443001) with 4.5g/l galactose (Sigma, St. Louis, Missouri, USA; Catalog No: SLBP0699V), 1% FBS, 5 mM sodium pyruvate from Thermo Fisher Scientific (Waltham, Massachusetts, USA; Catalog No:  11360-070) and 2mM L-glutamine from Corning (Corning, NewYork, USA; Catalog No: 34717007).

value: MFN2 T105M

value: Galactose medium for 48h

value: Fibroblats


title: ASC-Pax7-CE3

description:
processed data file:
filtered_counts_190926.txt
QSC_Gli3_KO_vs_ASC_Gli3_KO_190926.txt
ASC_Gli3_Ctr_vs_ASC_Gli3_KO_190926.txt

source_name: ASC Gli3 KO

value: activated satellite cell


title: ASC-Pax7-CE2

description:
processed data file:
filtered_counts_190926.txt
QSC_Gli3_Ctr_vs_ASC_Gli3_Ctr_190926.txt
ASC_Gli3_Ctr_vs_ASC_Gli3_KO_190926.txt

source_name: ASC Gli3 Ctr

value: Control


title: CMT2A MFN2 H361Y

description: CMT2A CPM.txt

value: MFN2 H361Y


title: Normal3

description: Normal CPM.txt


title: ASC-Gli3-3


title: Sarcoidosis patient 4 prior to treated with tofacitinib [Olink Explore 1536 panel]


title: Sarcoidosis patient 3 after treated with tofacitinib for six months [Olink Explore 1536 panel]


title: Sarcoidosis patient 3 prior to treated with tofacitinib [Olink Explore 1536 panel]


title: granulosa_cell_2-4

value: controlled ovarian stimulation


title: granulosa_cell_2_3


title: Normal2

description: Normal CPM.txt


title: Sarcoidosis patient 4 after treated with tofacitinib for six months [Olink Explore 1536 panel]

value: Sarcoidosis patient


title: Sarcoidosis patient 2 after treated with tofacitinib for six months [Olink Explore 1536 panel]

value: tofacitinib


title: Sarcoidosis patient 2 prior to treated with tofacitinib [Olink Explore 1536 panel]

value: Blood


title: ASC-Gli3-2


title: CMT2A MFN2 R274W

description: CMT2A CPM.txt

value: MFN2 R274W


title: Sarcoidosis patient 1 after treated with tofacitinib for six months [Olink Explore 1536 panel]


title: granulosa_cell_2_5


title: Gli3-1

value: quiescent satellite cell


title: Normal1

description: Normal CPM.txt


title: granulosa_cell_2_2


title: ASC-Gli3-1

value: Gli3 Knockout


title: Sarcoidosis patient 1 prior to treated with tofacitinib [Olink Explore 1536 panel]


title: granulosa_cell_2_1


title: ASC-Pax7-CE1


title: donor 99.40, MSA

status: Public on Mar 29 2022

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

data_processing:
Reads alignment:  STAR
Gene level summarization:  featureCounts
Normalization:  DESeq2
Assembly: GRCh37
Supplementary files format and content: *txt, raw counts by gene and sample

source_name: post-mortem cerebellum (white matter)

extract_protocol:
Total DNAse-treated RNA was extracted using the Qiagen RNAeasy kit (Qiagen). Quality was assessed by Bioanalyzer (Agilent)
Sequencing libraries were prepared with 250 ng of total RNA using Illumina’s Truseq RNA Sample Preparation Kit v2 (Illumina, Inc.) following the manufacturer’s protocol and purifying poly-A mRNAs with poly-T oligos attached to magnetic beads. The final library was sequenced by 50 bp paired-end sequencing on a HiSeq 2500 (Illumina, Inc.)

value: post-mortem cerebellum (white matter)

tag: Sex

value: Male

tag: age at death

tag: post mortem interval (hours)

tag: disease state

value: Multiple system atrophy (MSA)

tag: diagnosis

value: MSA

tag: source

value: Brain and Body Donor Program, Sun City, Arizona


title: donor 98.34, control

tag: tissue

value: Female

value: control


title: donor 08.64, control


title: donor 97.09, control


title: donor 04.51, MSA


title: donor 11.46, MSA


title: donor 10.70, control


title: donor 08.55, control


title: donor 14.49, MSA


title: donor 12.18, MSA


title: donor 04.56, MSA


title: donor 99.02, control


title: donor 10.22, control