title: MD14396_A1


title: MD14388_A2

status: Public on Jun 22 2021

type: SRA

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

library_source: transcriptomic

data_processing:
Analysis run using Salmon 1.1.0.  Salmon index generated using GRCh38.primary_assembly.fa and the ensembl 96 release. Briefly, ensemble (cdna and ncrna) and the reference fasta were concatenated. The‘decoys.txt’ was prepared from GRCh38. Salmon index was then run on the concatenated fasta. R1 and R2 fastq files respectively concatenated for each sample, and Salmon run using auto-detect strandedness and ‘validateMappings’ active.salmon index -t entrome.fa.gz -d decoys.txt -p 6 -i ensembl_96_current
Genome_build: hg38
Supplementary_files_format_and_content: salmon output  files, transcript level. see https://salmon.readthedocs.io/en/latest/file_formats.html

molecule: total RNA

organism: Homo sapiens

source_name: rectal biopsy

extract_protocol:
After sampling normal mucosa samples were immediately placed in RNAlater and kept immersed for 24-72 hours prior to RNA extraction. RNA was then extracted from NM and PBMC samples using a TRIzol based proprietary RNA extraction kit (Ribopure kit, Applied Biosystems) according to manufacturer protocol.
Libraries were prepared from each total-RNA sample using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (#RS-122-2302) according to the provided protocol.  500ng of total-RNA was processed to deplete rRNA before being purified, fragmented and primed with random hexamers. The fragmentation time was shorten from 8 minutes to 1 minutes to allow for bigger RNA fragments. Primed RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. RNA templates were removed and a replacement strand synthesised incorporating dUTP in place of dTTP to generate ds cDNA. AMPure XP beads (Beckman Coulter, #A63881) were then used to separate the ds cDNA from the second strand reaction mix, providing blunt-ended cDNA. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to another during the subsequent adapter ligation reaction, and a corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. Multiple indexing adapters were then ligated to the ends of the ds cDNA to prepare them for hybridisation onto a flow cell, before 12 cycles of PCR were used to selectively enrich those DNA fragments that had adapter molecules on both ends and amplify the amount of DNA in the library suitable for sequencing.

treatment_protocol: Oral vitamin D (3200IU/day) supplements were administered for 12 weeks

value: pre

tag: gender

value: M

tag: age


title: MD14391_A2


title: MD13848_C

value: post


title: MD14047_B

value: F


title: MD13843_C


title: MD13843_A1


title: MD13840_C


title: MD14047_D


title: MD13840_A1


title: MD16168_A


title: MD13838_C


title: MD13838_A2


title: MD13837_C


title: MD14394_A1


title: MD14392_A1


title: MD13837_A


title: MD13834_A1


title: MD13834_C


title: MD13831_C


title: MD13836_B


title: MD13836_A1


title: MD13830_C


title: MD13830_A1


title: MD13848_A2


title: MD13103_D


title: MD13417_A


title: MD13417_C


title: MD13103_B


title: MD12585_D


title: MD12585_B


title: MD12446_D


title: MD12446_B


title: MD12164_D


title: MD12164_B


title: MD12114_B


title: MD12016_D


title: MD11535_D


title: MD12114_D


title: MD11535_B


title: 154_Aged_Low_scRNA-seq

status: Public on Jun 01 2021

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

country: USA

description: single cell

data_processing:
Sequencing results were demultiplex using the mkfastq function in Cell Ranger v3.1.0, then a filtered reference was created using the mkgt function starting from the Mus musculus GRCm38.98 ensembl built. Only protein coding, antisense, long intergenic ncRNA, and Immunoglobulin (IG) and T cell receptor (TR) categories were the kept transcript biotypes.
Reads alignment, filtering, and barcode count was performed using the custom filtered reference via the cellranger count pipeline
Genome_build: Mus musculus GRCm38.98 ensembl built
Supplementary_files_format_and_content: Provided processed data are the output of Cell Ranger pipeline. Filtered matrix of count number per feature per cell, plus cells barcodes and feature list per sample. Barcodes and feaures are tsv, while matrixes are mtx

organism: Mus musculus

source_name: Whole Brain

growth_protocol: Adult (1-2 months old, raised in-house) and aged (21-22 months old,  obtained from the National Institute on Aging, Bethesda, MD), male and female C57BL/6J mice were used in the current experiment. Animals were kept under a reverse 12 h light:dark cycle and given ad libitum access to water and a nutritionally complete purified AIN-93M diet (Envigo, Indianapolis, IN) beginning two months before imposition of the experimental diets to establish a baseline microbiota for this diet under our conditions. To this end, during weekly cage changes, used bedding (e.g., litter and feces) from mice similarly aged was collected, homogenized, and mixed with clean bedding before being redistributed to each cage.

extract_protocol:
After collection, fresh whole brains were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec, Germany), for 30 min at 37oC. After filtration (70µm), debris and red blood cells were removed according to the kit protocol, and the obtained pellet was depleted of myelin and dead cells, using the Myelin Removal Beads v2 (Miltenyi Biotec, Germany), and the Dead Cell Removal Kit (Miltenyi Biotec, Germany), sequentially. Final pellets were eluted in 100µL of PBS with 4% BSA.
Single-cell 3’ cDNA libraries were prepared at the DNA Services laboratory of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Single-cell 3’ cDNA libraries were prepared at the DNA Services laboratory of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. The four single-cell suspensions with an average viability of 75.5 ± 3.1 %, and concentration of 753 ± 121.3 cells/µL by AO/PI staining on the Nexcelom K2 (Nexcelom Bioscience, Lawrence, MA) were converted into individually barcoded cDNA libraries with the Single-Cell 3’ Chromium kit version 3 from 10X Genomics (Pleasanton, CA) following the manufacturer’s protocols. The target number of cells per library was 6000. On average 14.5 ± 2.2 µL of the cell suspensions were used for the preparation of the libraries. The 10X Chromium instrument separates thousands of single cells into Gel Bead Emulsions (GEMs) that add a barcode to the mRNA from each individual cell. Following ds-cDNA synthesis, individually-barcoded libraries compatible with the Illumina chemistry were constructed. The final libraries were quantitated on Qubit and the average size determined on the AATI Fragment Analyzer (Advanced Analytics, Ames, IA). Libraries were pooled evenly, and the final pool was diluted to 5nM concentration and further quantitated by qPCR on a Bio-Rad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA). The final library pool was sequenced on one lane of an Illumina NovaSeq 6000 S4 flowcell as paired-reads with 28 cycles for read 1, 8 cycles for the index read, and 150 cycles for read 2.

treatment_protocol: After the initial two months (now adult 3-4 months old, and aged 23-24 months old), mice were switched to a modified AIN-93M diet with 1% cellulose plus either 0 (Low Fiber), or 5% (High Fiber) inulin (Envigo, Indianapolis, IN).

tag: strain

value: Aged

tag: treatment

value: Low fiber

tag: tissue

value: Whole Brain


title: 140_Adult_High_scRNA-seq

institute: University of Illinois at Urbana-Champaign

description: single cell

value: Adult

value: High fiber


title: MRC5_72_R3

status: Public on Mar 03 2021

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

data_processing:
library quality control: FASTQC version 0.11.5
quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
gene counting: HTseq-count version 0.6.1/0.11.2
normalization and differential expression analysis: DESeq2 R package version 1.18.1
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Excel file containing normalized counts of RNA molecules

source_name: MRC5 cell line

growth_protocol: MRC5. Cells were grown in Eagle's Minimum Essential Medium (EMEM) supplemented with 10% fetal calf serum (FCS).

extract_protocol:
Total RNA was extracted at 0, 6, 24, 48, 72 and 96 hours post-HCoV-229E infection, using NucliSENS® easyMag®, according to the manufacturer’s protocol. At each time point, three biological repeats were tested. All RNA samples were treated with RQ1 RNase-free DNaseI (Promega, USA), according to the manufacturer’s protocol. RNA quality was assessed using the Agilent High Sensitivity RNA ScreenTape for TapeStation System (Agilent Technologies, Germany).
RNA samples (>8 RNA integrity number (RIN)) were prepared using the Illumina TruSeq RNA Library Preparation Kit v2 and sequenced in Illumina HiSeq 2500 Sequencer.

treatment_protocol: After a 24-hour culture to 80-90% confluency, cells were infected with 0.01 multiplicity of infection (MOI) of virus. HCoV-229E was grown in a humidified incubator with 5% CO2, at 35°C.

tag: cell line

value: lung fibroblast cell line

value: Infected with HCoV-229E virus for 72 hours


title: MD13831_A2


title: MRC5_72_R1


title: MRC5_72_R2


title: MRC5_48_R3

value: Infected with HCoV-229E virus for 48 hours


title: MRC5_48_R1


title: MRC5_24_R2

value: Infected with HCoV-229E virus for 24 hours


title: MRC5_48_R2


title: MRC5_6_R2

value: Infected with HCoV-229E virus for 6 hours


title: MRC5_0_R3

value: Untreated


title: MRC5_24_R1


title: MRC5_0_R2


title: MRC5_6_R3


title: MRC5_0_R1


title: SC-Cas9 cells-control-RNA-seq_rep2

city: Tianjin

first: Mulin Jun

last: Li

state: Tianjin

address: No.22, Qixiangtai Road, Hepin

department: Basic Medical Research Center

country: China

institute: Tianjin Medical University

data_processing:
All libraries were sequenced using an Illumina Novaseq sequencer and 150 bp paired-end format.
ATAC-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.2.6 with "-X2000 --mm --local --threads 2".
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.7.13 with "-q 5 -l 32 -k 2".
Unmapped reads, low quality mapped reads and PCR duplicates were discarded by picard.
4C-seq reads were aligned to the hg19 genome assembly using bwa version 0.7.13 with "mem -t 10".
Peaks were called using macs2 version 2.1.1 with "--pvalue 0.01 --keep-dup all --extsize -1 --shift 0".
The Transcripts Per Kilobase Million (TPM) produced from RSEM (Li and Dewey, 2011) was used to quantify gene expression level.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated by bedGraphToBigWig
Supplementary_files_format_and_content: Tab-delimited text files for 4C-seq were generated by Basic4Cseq
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: SC cells

extract_protocol:
For RNA-seq, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
For ATAC-seq, ATAC-seq assay was performed as previously described (Corces et al., 2017) with modifications. Briefly, SC cells were pretreated with DNase I (Worthington, LS002007) to digest DNA from dead cells and to remove free-floating DNA. The cells were counted with Crystal Violet (Sigma-Aldrich, C0775), and ~50,000 cells (for each sample) were resuspended in 1 ml cold ATAC-Resuspension Buffer (RSB; 3 mM MgCl2 [Sigma-Aldrich, M2670], 10 mM Tris-HCl pH 7.5 [ThermoFisher, 15567027], and 10 mM NaCl [Sigma-Aldrich, S7653] in sterile H2O). After centrifugation, the supernatant was discarded, and the cell pellets were resuspended in 50 μl cold RSB containing 0.1% Tween-20 (Sigma-Aldrich, P1379), 0.1% NP-40 (ThermoFisher, FNN0021) and 0.01% Digitonin (Sigma-Aldrich, D141). After lysis, 1 ml RSB containing 0.1% Tween-20 was added, and the tube was inverted several times to mix. After centrifugation, the supernatant was removed, and the nuclei were resuspended in 50 μl Transposition Mix (Vazyme, TD501). Then, the transposition reaction was incubated at 37°C for 25 min with shaking at 1,000 rpm. The reaction products were purified with the QIAquick PCR Purification Kit (QIAGEN, 28106). The ATAC-seq library was prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202) according to the manufacturer’s instructions. The ATAC-seq analysis sequences with adaptor and low quality were trimmed for all 150-bp pair-end ATAC-seq reads. The clean reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 (v2.2.1) (Langmead and Salzberg, 2012) in the default parameters. All the samples were separately processed, and duplicate reads were removed. The ATAC-seq peak regions of each sample were called using MACS2 (v2.1.1) (Zhang et al., 2008) in the default parameters. The results were analyzed and visualized in IGV (v2.8.6) (Thorvaldsdottir et al., 2013). For ChIP-seq, ChIP assays were performed as previously described (Li et al., 2017c) with modifications. Briefly, for each sample, ~1 × 107 SC cells were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) in 10% FBS/phosphate-buffered saline (PBS) for 10 min at room temperature and quenched with 0.125 M glycine (Sigma-Aldrich, 50046). The cells were then collected and lysed twice with ice-cold lysis buffer (20 mM Tris-HCl pH 7.5 [ThermoFisher, 15567027], 2 mM EDTA [ThermoFisher, 15575020], 1% Triton X-100 [Sigma-Aldrich, T8787], 0.1% SDS [ThermoFisher, 15525017], 0.1% Sodium Deoxycholate [Sigma-Aldrich, D6750], and 1× Protease Inhibitors [ThermoFisher, 78425]) for 10 min with slow rotations at 4 °C. The nuclear lysates were sonicated to obtain DNA fragments of 200~500 bp using a Biorupter system (Diagenode, B01060001) by high energy, with a working time of 30 s and a resting time of 30 s, 30 cycles, until the solutions turned clear. After removing insoluble debris, the lysates were separately incubated with specific antibodies against Rabbit IgG (CST, 7074), ZBTB3 (Novus Biologicals, NBP1-82079), CTCF (Abcam, ab128873), RAD21 (Abcam, ab992), H3K4me1 (CST, 5326), H3K4me3 (CST, 9751), or H3K27ac (Abcam, ab4729), and then purified by protein A-agarose beads (Millipore, 16-157). The beads were washed 4 times by TE buffer (10 mM Tris-HCl pH 8.0 [ThermoFisher, 15568025], and 1 mM EDTA), TSE I buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), TSE II buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), and Buffer III (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 0.25 M LiCl [Sigma-Aldrich, L4408], and 1% Sodium Deoxycholate) before elution (20 mM Tris-HCl pH 7.5, 5 mM EDTA, 50 mM NaCl, and 1% SDS), reverse cross-linking, and subsequent DNA extraction. ChIP-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions, and then sequenced on a HiSeq X Ten platform (Illumina). For data analysis, the sequences with adaptor and low quality were trimmed for all 150-bp pair-end reads. The clean reads were mapped against the human reference genome (GRCh37/hg19) using BWA (Li and Durbin, 2009). All the samples were separately processed, and the unique mapped reads were kept. The peaks were called by MACS2 (v2.1.1) (Zhang et al., 2008) using IgG as control. The results were analyzed and visualized in IGV (v2.8.6) (Thorvaldsdottir et al., 2013). For 4C-seq, 4C assays were conducted as previously represented (Splinter et al., 2012; van de Werken et al., 2012b) with modifications. Briefly, SC cells were counted, and ~1 × 107 cells were used for each 4C experiment. The cells were cross-linked with 1.5% formaldehyde, quenched with 0.125 M glycine, lysed with cold lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, and 1× Protease Inhibitors), digested with DpnII (NEB, R0543M) for 4 h at 37°C while shaking at 900 rpm for more than 3 times until the digestion efficiency reached over 90%, and then ligated with T4 DNA ligase (NEB, M0202M) in a 7 ml reaction system after enzyme inactivation. After reversing the cross-links by adding Protein K (ThermoFisher, AM2548) for overnight at 65°C and RNase A for 45 min at 37°C, the ligation products were purified by Phenol/Chloroform/Isoamyl Alcohol (25:24:1) (ThermoFisher, 15593-049). The purified DNA samples were digested with NlaIII (NEB, R0125L) for the rs4728142-containing region (GRCh37/hg19 chr7: 128,573,714–128,574,084) or CviQI (NEB, R0639L) for the enhancer (GRCh37/hg19 chr7: 128,573,036–128,573,717) adjacent to the downstream rs4728142-containing region, and then ligated with T4 DNA ligase for overnight in a 14 ml reaction system. The ligation samples were purified by Phenol/Chloroform/Isoamyl Alcohol (25:24:1) and further purified utilizing the QIAquick PCR Purification Kit. The purified products were amplified by VAHTS HiFi Amplification Mix (Vazyme, N616) with 8 × 200 ng DNA. 4C-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3 according to the kit’s instructions and then sequenced on a HiSeq X Ten platform. For data analysis, the quality control step was processed for the 4C-seq library using FastQC. The sequences with adaptor and low quality were discarded for further analysis. A Bioconductor package Basic4Cseq (Walter et al., 2014) was used to filter, analysis, and visualize the 4C-seq data. For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: Human peripheral blood monocyte-derived SC cells


title: MRC5_6_R1


title: SC-Cas9 cells-control-RNA-seq_rep1


title: SC-Cas9 cells-rs4728142-sKO-RNA-seq_rep1


title: MD12016_B


title: SC-Cas9 cells-rs4728142-sKO-RNA-seq_rep2


title: SC cells-H3K4me3-ChIP-seq

library_source: genomic

molecule: genomic DNA

tag: chip antibody

value: Rabbit monoclonal to H3K4me3 (Cell Signaling Technology, Cat#9751)


title: SC cells-RAD21-rep1-ChIP-seq

value: Rabbit polyclonal to RAD21 (Abcam, ab992)


title: SC cells-ZBTB3_rep1-ChIP-seq

value: Rabbit polyclonal to ZBTB3 (Novus Biologicals, Cat#NBP1-82079)


title: SC cells-H3K27ac-ChIP-seq

value: Rabbit polyclonal to H3K27ac (Abcam, ab4729)


title: SC cells-H3K4me1-ChIP-seq

value: Rabbit monoclonal to H3K4me1 (Cell Signaling Technology, Cat#5326)


title: SC cells-ATAC-seq


title: SC cells-CTCF-ChIP-seq

value: Rabbit monoclonal to CTCF (Abcam, Cat#ab128873)


title: MRC5_24_R3


title: is_133_058

status: Public on Feb 19 2021

city: Uppsala

first: Anders

middle: Roger

last: Hedin

state: Uppland

address: Dag Hammarskjölds väg 20.

department: Clinical immunology

country: Sweden

institute: Uppsala University

description:
raw_counts_all
normalized_counts_log_exo

data_processing:
The raw counts were generated at a separate facility using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion 550™ Kit, and the S5 XL (IonS5XL, Thermo Fisher®) instrument with a 550 chip. The primer pool hg19_AmpliSeq_Transcriptome_21K_v1, containing primers for 20,813 amplicons, was used.  The produced reads were aligned to hg19 AmpliSeq Transcriptome ERCC v1. All further analysis was done using the raw counts estimated after mapping.
One sample (is_133_59) failed to generate a library, and is therefore excluded from further analysis.
Normalization of the raw count data was performed using the edgeR workflow(calcNormFactors and cpm(, method="TMM", log=FALSE) after filtering out lowly expressed genes with the filterByExpr command using default settings and groups as defined by tissue type and diabetes status.
Data from all samples were normalized together, but as the exocrine data and endocrine data are part of two separate projects only the exocrine normalized counts are uploaded here. The normalized endocrine counts will be uploaded separately.
In addition, a number of the endocrine samples were also used together with endocrine data from another study in a third publication and were therefore also normalized together with those separate samples. Normalized counts for those samples will therefore also be uploaded a second time.
Genome_build: hg19 AmpliSeq Transcriptome ERCC v1.
Supplementary_files_format_and_content: comma separated value (CSV) text file with TMM- CPM- log2 normalized counts for each included sample and each transcript that passed

source_name: human pancreatic exocrine tissue

extract_protocol:
Pancreases from heart-beating organ donors were used. Biopsies were immediately snap-frozen in liquid nitrogen and subsequently stored at -80 °C. The frozen biopsies  were sectione, thawed and dehydrated. Laser Capture Microdissection (LCM) was used to extract exocrine tissue regions. The regions were captured on an Arcturus CapSure HS LCM Cap which was subsequently incubated in 20 µl of RLT Plus buffer with 1% beta-Mercaptoethanol in a heating block, lysing the tissue. RNA was extracted with the RNeasy Plus Micro kit.
Libraries were constructed using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit. RNA seq was then done using the Ion 550™ Kit, and the S5 XL (IonS5XL, Thermo Fisher®) instrument with a 550 chip. The primer pool hg19_AmpliSeq_Transcriptome_21K_v1, containing primers for 20,813 amplicons, was used.

value: Exocrine tissue adjacent to islets (within 50 um from islets)

tag: disease state

value: type 1 diabetic


title: is_133_057

source_name: human pancreatic islet tissue

value: Islet tissue


title: is_133_056

value: Exocrine tissue far from islets (a minimum of 100 um from islets)


title: is_133_055

value: Exocrine tissue at a distance between 50-100 um from islets


title: is_133_053


title: is_133_054


title: is_133_051


title: is_133_050


title: is_133_052


title: is_133_049


title: is_133_047


title: is_133_048


title: is_133_045


title: is_133_044


title: is_133_043


title: is_133_042


title: SC cells-Input-ChIP-seq

value: Anti-Rabbit IgG (Cell Signaling Technology, Cat#7074)


title: is_133_060


title: is_133_040


title: is_133_046


title: is_133_039


title: is_133_036


title: is_133_038


title: is_133_035


title: is_133_030

value: non-diabetic


title: is_133_028


title: is_133_034


title: is_133_027


title: is_133_033


title: is_133_032


title: is_133_031


title: is_133_025


title: is_133_029


title: is_133_026


title: is_133_020


title: is_133_023


title: is_133_024


title: is_133_022


title: is_133_021


title: is_133_014


title: is_133_013


title: is_133_037


title: is_133_017


title: is_133_018


title: is_133_016


title: is_133_015


title: is_133_019


title: is_133_012


title: is_133_007


title: is_133_008


title: is_133_009


title: is_133_006


title: is_133_005


title: is_133_011


title: is_133_041


title: is_133_010


title: is_133_002


title: is_133_004


title: is_133_003


title: is_133_001


title: easyCLIP SMAD4 Replicate 1 HiSeq

status: Public on Jan 11 2021

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_SMAD4_GCCATG_TCA

data_processing:
Custom processing scripts used at every stage except:
Mapping with STAR (2.5.4b) using all default parameters
After adapters and read-internal barcodes removed with custom scripts, cutadapt v. 2.9 was run to clean up any remaining adapter using the parameters -A CTATACTACCCTTCGCTTCACACACACAAG -a CTTGTGTGTGTGAAGCGAAGGGTAGTATAG
The prefix 'mi' or 'hi' in the filename after the second underscore denote whether the library was sequenced on a Miseq or a Hiseq, respectively. Libraries with the same file name except for a 'mi' or 'hi' were combined before analysis. The 'hi' libraries are 2 lanes of a Hiseq 2500 Rapid Run combined. The 'mi' libraries are 1-3 miseq runs combined.
Genome_build: Human GRCh38 Gencode release 28 and a custom chromosome made of repetitive elements
Supplementary_files_format_and_content: Text file of raw read counts mapping to the indicated elements.

source_name: HEK293T cells

growth_protocol: 293Ts grown in DMEM 10% FBS, HCT116s grown in McCoy's 5A 10% FBS

extract_protocol: easyCLIP, a flavor of CLIP-seq

treatment_protocol: UV cross-linked at 253 nm on plates.

tag: expression

value: N-terminally FLAG-HA-HIS tagged ORF expressed from a pLEX-derived vector (pSLX3).


title: easyCLIP SMAD3 Replicate 4 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp94_SMAD3_GCTGTA_CAG


title: easyCLIP SMAD4-R361H Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_SMAD4-R361H_GCCATG_AGT


title: easyCLIP SMAD4 Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_SMAD4_GCCATG_AAC


title: easyCLIP UBA2 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_UBA2_GCCTAA_AAC

value: FLAG-HA-HIS tagged ORF transiently expressed from pLEX vector 2 days without selection


title: easyCLIP SMAD3 Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp93_SMAD3_GCTGTA_AAC


title: easyCLIP RPL5-E82K Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp98_RPL5-E82K_TTAGGC_AGT

value: C-terminally FLAG-HA-HIS tagged ORF expressed from a pLEX-derived vector (pSLX4).


title: easyCLIP SMAD3 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_SMAD3_GCTGTA_TCA


title: easyCLIP RPL5-E82K Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp93_RPL5-E82K_CGATTA_TCA


title: easyCLIP RPL5-E82K Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_RPL5-E82K_CGATTA_AAC


title: easyCLIP RPL5 Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp98_RPL5_TTAGGC_TCA


title: easyCLIP RPL5 Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp93_RPL5_CGATTA_CAG


title: easyCLIP RPL5 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_RPL5_CGATTA_AGT


title: easyCLIP RARS2-R6C Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_RARS2-R6C_TGCCGA_CAG


title: easyCLIP RARS2 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_RARS2_TGCCGA_AAC


title: easyCLIP RARS2 Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_RARS2_TGCCGA_TCA


title: easyCLIP KHDRBS2-R168C Replicate 4 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp99_KHDRBS2-R168C_TAGTTG_CAG

value: FLAG-HA-HIS tagged ORF transiently expressed from pLEX vector 1-2 days without selection


title: easyCLIP KHDRBS2-R168C Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_KHDRBS2-R168C_AGCTAG_TCA


title: easyCLIP KHDRBS2-R168C Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_KHDRBS2-R168C_AGCTAG_AGT


title: easyCLIP KHDRBS2 Replicate 4 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp99_KHDRBS2_TAGTTG_AAC


title: easyCLIP KHDRBS2 Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp98_KHDRBS2_TAGTTG_AGT


title: easyCLIP KHDRBS2 Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_KHDRBS2_AGCTAG_CAG


title: easyCLIP SMAD4-R361H Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_SMAD4-R361H_GCCATG_CAG


title: easyCLIP KHDRBS2 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_KHDRBS2_AGCTAG_AAC


title: easyCLIP FUBP1-R429C Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp98_FUBP1-R429C_CGAAAC_AAC


title: easyCLIP FUBP1-R429C Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_FUBP1-R429C_GCTCAT_AGT


title: easyCLIP FUBP1-R429C Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_FUBP1-R429C_TAGTTG_CAG


title: easyCLIP FUBP1 Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_FUBP1_TAGTTG_AAC


title: easyCLIP FUBP1 Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp98_FUBP1_CGAAAC_AGT


title: easyCLIP SMAD3 Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_SMAD3_GCTGTA_AGT


title: easyCLIP UBA2 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_UBA2_GCCTAA_AAC


title: easyCLIP ETS2 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_ETS2_CGAAAC_AGT


title: easyCLIP SMAD4-R361H Replicate 2 MiSeq


title: easyCLIP FUBP1 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_FUBP1_GCTCAT_TCA


title: easyCLIP SMAD4-R361H Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_SMAD4-R361H_GCCATG_AGT


title: easyCLIP CRNKL1-S128F Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_CRNKL1-S128F_TGTTGG_AGT


title: easyCLIP RARS2-R6C Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_RARS2-R6C_TGCCGA_AGT


title: easyCLIP SMAD4 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_SMAD4_GCCATG_AAC


title: easyCLIP EPB41L5 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_EPB41L5_GTAGCC_TCA


title: easyCLIP KHDRBS2-R168C Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp98_KHDRBS2-R168C_TAGTTG_TCA


title: easyCLIP CRNKL1-S128F Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_CRNKL1-S128F_TGTTGG_TCA


title: easyCLIP SMAD4 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_SMAD4_GCCATG_TCA


title: easyCLIP SMAD3 Replicate 3 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp93_SMAD3_GCTGTA_AAC


title: easyCLIP BRCA1 Replicate 4 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp94_BRCA1_GCGGAC_TCA


title: easyCLIP CRNKL1 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_CRNKL1_TGTTGG_CAG


title: easyCLIP SMAD3 Replicate 4 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp94_SMAD3_GCTGTA_CAG


title: easyCLIP CRNKL1 Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_CRNKL1_TGTTGG_AAC


title: easyCLIP SMAD3 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_SMAD3_GCTGTA_TCA


title: easyCLIP BRCA1 Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_BRCA1_CCACTC_AAC


title: easyCLIP RPL5-E82K Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp93_RPL5-E82K_CGATTA_TCA


title: easyCLIP BRCA1 Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp93_BRCA1_CCACTC_CAG


title: easyCLIP SMAD3 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_SMAD3_GCTGTA_AGT


title: easyCLIP BRCA1 Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_BRCA1_CCACTC_AGT


title: easyCLIP RPL5-E82K Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_RPL5-E82K_CGATTA_AAC


title: easyCLIP RPL5 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp93_RPL5_CGATTA_CAG


title: easyCLIP A1CF-E34K Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp98_A1CF-E34K_CGATTA_TCA


title: easyCLIP A1CF-E34K Replicate 4 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp99_A1CF-E34K_CGATTA_CAG


title: easyCLIP RPL5 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_RPL5_CGATTA_AGT


title: easyCLIP RARS2 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_RARS2_TGCCGA_TCA


title: easyCLIP RARS2-R6C Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_RARS2-R6C_TGCCGA_AGT


title: easyCLIP RARS2-R6C Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_RARS2-R6C_TGCCGA_CAG


title: easyCLIP A1CF-E34K Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_A1CF-E34K_CTGATC_AGT


title: easyCLIP A1CF Replicate 4 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp99_A1CF_CGATTA_AAC


title: easyCLIP RARS2 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_RARS2_TGCCGA_AAC


title: easyCLIP A1CF Replicate 3 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp98_A1CF_CGATTA_AGT


title: easyCLIP A1CF Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_A1CF_CTGATC_AAC


title: easyCLIP KHDRBS2-R168C Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_KHDRBS2-R168C_AGCTAG_TCA


title: easyCLIP KHDRBS2-R168C Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_KHDRBS2-R168C_AGCTAG_AGT


title: easyCLIP KHDRBS2 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_KHDRBS2_AGCTAG_AAC


title: easyCLIP A1CF Replicate 1 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_A1CF_CTGATC_TCA


title: easyCLIP FUBP1-R429C Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_FUBP1-R429C_GCTCAT_AGT


title: easyCLIP FUBP1-R429C Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_FUBP1-R429C_TAGTTG_CAG


title: easyCLIP FUBP1 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_FUBP1_GCTCAT_TCA


title: easyCLIP CRNKL1 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_CRNKL1_TGTTGG_CAG


title: easyCLIP CRNKL1-S128F Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_CRNKL1-S128F_TGTTGG_AGT


title: easyCLIP EPB41L5 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_EPB41L5_GTAGCC_TCA


title: easyCLIP CRNKL1 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_CRNKL1_TGTTGG_AAC


title: easyCLIP BRCA1 Replicate 3 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp93_BRCA1_CCACTC_CAG


title: easyCLIP CRNKL1-S128F Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_CRNKL1-S128F_TGTTGG_TCA


title: easyCLIP BRCA1 Replicate 4 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp94_BRCA1_GCGGAC_TCA


title: easyCLIP A1CF-E34K Replicate 2 HiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_A1CF-E34K_CTGATC_CAG


title: easyCLIP BRCA1 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_BRCA1_CCACTC_AGT


title: easyCLIP BRCA1 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_BRCA1_CCACTC_AAC


title: easyCLIP BARD1 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_BARD1_CGATTA_CAG


title: easyCLIP BARD1 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_BARD1_CGATTA_TCA


title: easyCLIP A1CF-E34K Replicate 2 MiSeq


title: easyCLIP A1CF Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_A1CF_CTGATC_AAC


title: easyCLIP A1CF-E34K Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_A1CF-E34K_CTGATC_AGT


title: easyCLIP A1CF Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp91_A1CF_CTGATC_TCA


title: easyCLIP KHDRBS2 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_KHDRBS2_AGCTAG_CAG


title: easyCLIP ETS2 Replicate 1 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_ETS2_CGAAAC_AGT


title: easyCLIP FUBP1 Replicate 2 MiSeq

description:
Library from RNA UV cross-linked to the indicated protein
Exp92_FUBP1_TAGTTG_AAC


title: UI2

status: Public on Jan 01 2021

type: RNA

hyb_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

data_processing: RMA (PARTEK)

label: biotin

source_name: 3-mm punch biopsies

label_protocol: Affymetrix biotin labeling_ wt kit  (Affymetrix)

extract_protocol: Skin biopsies were snap-frozen and stored in liquid nitrogen. Before thawing, epidermal layers were separated from adipose tissues using scalpel. Total RNA from fresh frozen tissues was extracted using the Qiagen RNeasy mini kit (Cat. # 74104). Quantity and quality were evaluated using Nanodrop ND-2000 (Thermo Scientific),

tag: sample type

value: psoriasis non-lesion biopsies


title: N3

scan_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

value: healthy skin biopsies


title: UI4


title: P4

value: psoriasis lesion biopsies


title: P2


title: P3


title: N2


title: UI3


title: DN008

status: Public on Dec 31 2020

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

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 hg19 whole genome using star method.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. 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: hg19
Supplementary_files_format_and_content: FPKM

source_name: liver tissue

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

value: Dysplastic nodule


title: DN001


title: DN010


title: DN002


title: DN003


title: DN005


title: DN007


title: DN006


title: DN004


title: DN009


title: avHCC035

value: Advanced HCC


title: avHCC042


title: avHCC044


title: avHCC045


title: avHCC040


title: avHCC043


title: avHCC036


title: avHCC037


title: avHCC039


title: avHCC041


title: avHCC038


title: avHCC034


title: N4


title: avHCC031


title: avHCC029


title: avHCC033


title: avHCC030


title: avHCC032


title: avHCC028


title: avHCC027


title: avHCC023


title: avHCC026


title: avHCC025


title: avHCC024


title: avHCC022


title: avHCC020


title: avHCC017


title: avHCC016


title: avHCC011


title: avHCC014


title: avHCC010


title: avHCC021


title: avHCC008


title: avHCC015


title: avHCC012


title: avHCC009


title: avHCC013


title: avHCC006


title: avHCC005


title: avHCC001


title: eHCC017

value: Early HCC


title: avHCC002


title: eHCC018


title: avHCC004


title: eHCC016


title: avHCC019


title: avHCC018


title: avHCC007


title: eHCC015


title: eHCC014


title: eHCC009


title: eHCC013


title: eHCC012


title: eHCC011


title: eHCC008


title: eHCC007


title: eHCC004


title: eHCC002


title: eHCC001


title: LC010

value: Liver Cirrhosis


title: LC009


title: LC008


title: LC007


title: LC005


title: LC003


title: CHB019

value: Chronic hepatitis


title: CHB018


title: LC001


title: LC002


title: CHB017


title: eHCC010


title: CHB016


title: CHB011


title: CHB012


title: CHB014


title: eHCC005


title: CHB010


title: CHB015


title: eHCC003


title: CHB009


title: CHB008


title: eHCC006


title: CHB005


title: LC006


title: CHB020


title: LC004


title: CHB007


title: CHB004


title: CHB002


title: CHB001


title: N013

value: Normal


title: CHB013


title: N014


title: N011


title: N015


title: N012


title: N009


title: avHCC003


title: N010


title: N007


title: N006


title: N008


title: N005


title: N004


title: N001


title: N002


title: N003


title: CHB006


title: RM03_GZ_Hi-C

status: Public on Dec 15 2020

city: Beijing

first: Yuting

last: Liu

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Science

institute: Peking University

description:
GZ_HICCPUS_10kb_loops.bedpe
GZ_InsulationScores_boundaries.bed

data_processing:
Hi-C:Paired-end reads of the Hi-C libraries were pre-processed using HiC-Pro. In brief, reads pairs were aligned to the reference genomes ( rheMac8 ) in two steps. The first step aligns reads using bowtie2 end-to-end algorithm. The second step detect the ligation sites and the 5’ fraction of the reads were aligned back to the genome. Aligned read pairs were assigned to DpnII restriction fragments. Invalid pairs like dangling end were filtered out. The genome was divided into specific size bins, and valid pairs were counted per bins. We used 500 kb, 100 kb, 40 kb bin sizes to generate raw and ICE or KR normalized matrix.
RNA-seq:The intra-species RNA-Seq Fastq reads were aligned to Mmul_8.0.1 reference genome using STAR. ENSEMBL gene annotation was used. Duplicated alignments were removed using PicardTools. The number of alignments mapped to exons was counted using the summarizeOverlap func-tion from the GenomicAlignments package. Condi-tional quantile normalization was performed using CQN package to correct read depth, exon length and GC content. Log2 normalized FPKM was used for quantification of expression levels.
ChIP-seq:The Fastq reads were aligned to reference genome (rheMac8) using bowtie2  with settings “bowtie2 –very-sensitive”. Bam files were transferred to sam files using Samtools. Duplicated alignments were removed using PicardTools. To avoid double contigs for the paired-end alignments, only one mate count. Only uniquely mapped alignments (MAPQ > 30) were kept. Averaged reads per million of mapped reads (RPM) in 10bp bins were calculated by deepTools and transferred to coverage tracks. Technical replicates data were merged. Peaks were identified using MACS2 (for CTCF ChIP-seq) with settings “macs2 call Peak –B  –p 1e-5 –nomodle –extsize 200” or HOMER (for DNase-seq) with setting "-size 147 -gsize 2.7e09 -norm 1000000 -fragLength 147 -fdr 0.01 -style factor".
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: Hi-C:  (1) .hic  files represent all the valid paris per sample and can be used for further analysis
Supplementary_files_format_and_content: (2) .bed files represent all the boundaries per sample generated by insulation score method
Supplementary_files_format_and_content: (3) .bedpe files represent all the loops per sample generated by HICCUPS
Supplementary_files_format_and_content: RNA-seq: matrix table text file represent the log2 FPKM value per sample
Supplementary_files_format_and_content: ChIP-seq:  (1) .bw files represent the reads distribution
Supplementary_files_format_and_content: (2). txt files represent deteced peaks using MACS2 or HOMER

organism: Macaca mulatta

source_name: Brain

extract_protocol:
Cells were fixed by final concentration of 1% formaldehyde (Sigma-Aldrich, F1635), mixed for 10 mins at room temperature. Fixation was quenched using 2.5 M glycine at room temperature for 5 mins and immediately centrifuged at 800g for 10 mins. Supernatant was removed and frozen in liquid nitrogen and stored at −80°C until further use.
Fixed cells, lysis and digest the chromatin. Next, fill-in Biotin and religated in by T4 DNA ligase. Extract the DNA, shearing the DNA to 200-300 bp, size selection. Biotin pulldown. End repair, add A, add adaptor reaction and PCR amplification, DNA products size selection and sequencing.

value: Brain

tag: developmental stage

tag: genotype

value: wild type


title: RM02_GZ_Hi-C


title: RM03_CP_Hi-C

description:
CP_HICCPUS_10kb_loops.bedpe
CP_InsulationScores_boundaries.bed


title: A375_KHDRBS2_R168C_2

status: Public on Dec 01 2020

data_processing:
Paired end reads were mapped to the hg38 reference genome with GRCh38 Ensembl annotations using STAR aligner1 (version 2.5.4b) followed by generation of genes by samples counts matrices with RSEM (version 1.3.0).
BAM files generated from RSEM2 were further analyzed with the featureCounts() function in Rsubread (v 1.32.4) to generate exons by samples counts matrices in R 3.5.1.
Genes by counts matrices were further analyzed with the DESeq2 package3 (v 1.24.0) in R 3.6.1 to calculate differential expression and associated p-values across samples.
Genome_build: hg38 reference genome with GRCh38 Ensembl annotations
Supplementary_files_format_and_content: RSEM samples counts matrices

molecule: polyA RNA

source_name: A375 cells

growth_protocol: 293Ts and A375s grown in DMEM 10% FBS, HCT116s grown in McCoy's 5A 10% FBS

extract_protocol:
Qiagen RNeasy Mini Plus kit (Cat # 74134) was used to extract RNA, following Qiagen's directions.
Libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: Samples were +/- shRNA knock-down of endogenous protein and +/- expression of wild-type or mutant protein. shRNA and protein expression was via lentivirus integration and either Puromycin or Blasticidin selection.

tag: shRNA

value: No shRNA

tag: protein expression

value: pLEX KHDRBS2 R168C

tag: sample batch

value: Batch 4


title: RM02_CP_Hi-C


title: CHB003


title: A375_KHDRBS2_R168C_1


title: A375_KHDRBS2_WT_2

value: pLEX KHDRBS2


title: A375_KHDRBS2_WT_1


title: 293T_FUBP1_R429C_pLEX_and_shFUBP1_2

source_name: 293T cells

value: anti-FUBP1 shRNA

value: pLEX FUBP1 R429C

value: Batch 3


title: 293T_FUBP1_R429C_pLEX_and_shFUBP1_1


title: 293T_FUBP1_pLEX_and_shFUBP1_2

value: pLEX FUBP1


title: 293T_FUBP1_pLEX_and_shFUBP1_1


title: 293T_EV_pLEX_and_shFUBP1_2

value: Empty pLEX


title: 293T_EV_pLEX_and_shFUBP1_1


title: 293T_EV_pLEX_and_control_shRNA_2

value: control shRNA


title: HCT116_L100Q_pLEX_and_shPCBP1_2

source_name: HCT116 cells

value: anti-PCBP1 shRNA

value: pLEX PCBP1 L100Q

value: Batch 1


title: 293T_EV_pLEX_and_control_shRNA_1


title: HCT116_L100Q_50ul_virus_2

value: Batch 2


title: HCT116_L100Q_pLEX_and_shPCBP1_1


title: HCT116_PCBP1_pLEX_and_shPCBP1_2

value: pLEX PCBP1


title: HCT116_uORF_PCBP1_10ul_virus_2

value: pLEX uORF PCBP1


title: HCT116_uORF_PCBP1_pLEX_and_shPCBP1_2


title: HCT116_uORF_PCBP1_1ul_virus_1


title: HCT116_uORF_PCBP1_1ul_virus_2


title: HCT116_L100Q_25ul_virus_1


title: HCT116_uORF_PCBP1_pLEX_and_shPCBP1_1


title: HCT116_PCBP1_pLEX_and_shPCBP1_1


title: HCT116_uORF_PCBP1_10ul_virus_1


title: HCT116_uORF_PCBP1_2.5ul_virus_2


title: HCT116_EV_pLEX_and_control_shRNA_2


title: HCT116_EV_pLEX_and_shPCBP1_1


title: HCT116_EV_pLEX_and_shPCBP1_2


title: HCT116_uORF_PCBP1_2.5ul_virus_1


title: 40518M143719

status: Public on Nov 24 2020

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

description: cRNA encoding B cell receptors

data_processing:
BCR reads sequenced by V(D)J assay were aligned to GRCh38 reference transcriptome using Cell Ranger VDJ (v3.0.1, 10X Genomics).
B cells were assigned with productive heavy chain and light chain sequences. Unique combinations of heavy/light chains were recognized as BCR clonetypes and cells assigned with the same clonetypes were considered as a clone.
Genome_build: GRCH38
Supplementary_files_format_and_content: csv files include assembled BCR heavy chain and light chain sequences and VDJ annotation for each B cell

source_name: Surgically removed Ovarian Cancer tumor tissue

extract_protocol:
Tissue pieces from the ovarian tumors were mechanically sissociated and single cell suspensions were prepared after debris removal. B cells were sorted using anti-human CD19 antibodies.
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA encoding the B cell receptor library were amplified using primers provided in Chromium Single Cell Human BCR Amplification Kit. After library construction, VDJ region-enriched libraries were size selecte  with SPRI beads and sequenced on an Illumina  NextiSeq 500 instrument.
10X genomics Chromium Single Cell Immune Profiling RNA-seq

tag: cancer type

value: HGSOC

value: B cells


title: 120406

description: cRNA encoding B cell receptors


title: HCT116_L100Q_50ul_virus_1

value: No shRNA


title: HCT116_L100Q_25ul_virus_2


title: Untreated_2

data_processing:
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to hg19 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level by htseq-count (version 0.6.1) using Gencodev19 transcript annotations for human
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each sample

source_name: Ovarian Cancer Cell line (OVCAR3)

growth_protocol: OVCAR3 cells in culture in 2% FBS containing RPMI media

extract_protocol:
Cells were washed, trypsinized,follwed by total RNA was extraction using RNeasy Plus micro kit. Genomic DNA was removed by DNase treatment.
RNA libraries were prepared for sequencing using Ovation® Human FFPE RNA-Seq kit

treatment_protocol: Cells were treated with or without 0.5 μg/mL of antibodies for 24 hours.

value: High-Grade Serous Ovarian Cancer (HGSOC) cell line

value: Adherent cell line


title: OVCAR3-TSPAN7-2


title: OVCAR3-BDNF-2


title: OVCAR3-TSPAN7-1


title: OVCAR3-TSPAN7-3


title: Untreated_3


title: IgA_Coated_3


title: IgG_Coated_2


title: OVCAR3-Untreated-3


title: OVCAR3-Untreated-2


title: OVCAR3-BDNF-1


title: IgG_Coated_3


title: HCT116_EV_pLEX_and_control_shRNA_1


title: IgA_Coated_2


title: Med.m.24h.rep2

status: Public on Oct 31 2020

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

data_processing:
Sequencing was performed using an Illumina HiSeq 4000 instrument using paired end 75 bp lanes. Base calls were generated in real-time on the HiSeq instrument, and RTA-generated BCL files were converted to FASTQ files. equence read, base quality and other QC metrics were computed and checked with RNASeQC (v2.6.4). Sequences were aligned to mouse genome using the gencode (M11) annotation and STAR (v2.5.2b) on mouse GRCm38. Transcript abundances were quantified using RSEM (v1.2.31)
Differential gene expression between conditions was determined using DESeq2 package in R environment
Genome_build: GRCm38
Supplementary_files_format_and_content: Abundance counts

source_name: Male_lung pericyte-like cell_Media only_24hr

growth_protocol: Single cell preparations from mouse lung digests were prepared as previously described. Briefly, single cell preparations were expanded in culture in 0.2% gelatin-coated T75 flasks for 3-5 days until confluence. Cultured cells then underwent negative selection using CD31, CD45, and CD326 to isolate the stromal cell fraction (unlabeled cells). Pericyte-like cells were selected from stromal cells using PDGFRβ as positive selection marker. Selected cells were cultured on gelatin-coated tissue culture flasks in cell culture media (DMEM/F12 supplemented with 10% FBS, 1% ITS, and 1% penicillin/streptomycin) until use in experiments. Cultured pericyte-like cells were seeded at a density of 25,000 cells/well in a 12-well tissue culture plate or 250,000 cells/well in a 6-well tissue culture plate. Following attachment, they were exposed to culture media with reduced serum (DMEM/F12 supplemented with 2.5% FBS, 1% ITS, and 1% penicillin/streptomycin) mixed 1:1 with sterile PBS (“media only” hereafter), a 1:1 mixture of reduced serum media and uninjured BALF, or a 1:1 mixture of reduced serum media and injured BALF. At 6 h and 24 h following exposure to treatment conditions, cell culture supernatants and cell lysates were collected for further processing and analysis.

extract_protocol:
Total RNA was collected from treated cells using RNeasy Mini Kit per manufacturer’s protocol (QIAGEN). RNA integrity was confirmed with a Bioanalyzer 2100 (Agilent, Santa Clara, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols using TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA)

tag: Sex

value: Male

value: Lung pericyte-like cells

tag: treatment exposure

value: Media only

tag: duration of exposure (hours)


title: Med.m.6h.rep3

source_name: Male_lung pericyte-like cell_Media only_6hr


title: IgG_Coated_1


title: OVCAR3-Untreated-1


title: Med.m.6h.rep2


title: Un.m.24h.rep3

source_name: Male_lung pericyte-like cell_Uninjured BALF_24hr

value: Uninjured BALF


title: Med.m.24h.rep1


title: Un.m.6h.rep1

source_name: Male_lung pericyte-like cell_Uninjured BALF_6hr


title: Med.f.24h.rep3

source_name: Female_lung pericyte-like cell_Media only_24hr

value: Female


title: Med.m.6h.rep1


title: Untreated_1


title: Med.m.24h.rep3


title: Un.m.24h.rep2


title: Med.f.6h.rep2

source_name: Female_lung pericyte-like cell_Media only_6hr


title: Med.f.6h.rep3


title: Med.f.24h.rep1


title: Med.f.24h.rep2


title: Med.f.6h.rep1


title: Un.f.6h.rep1

source_name: Female_lung pericyte-like cell_Uninjured BALF_6hr


title: Un.m.6h.rep3


title: Un.m.24h.rep1


title: Un.m.6h.rep2


title: Un.f.6h.rep3


title: Un.f.6h.rep2


title: Un.f.24h.rep2

source_name: Female_lung pericyte-like cell_Uninjured BALF_24hr


title: Inj.m.6h.rep3

source_name: Male_lung pericyte-like cell_Injured BALF_6hr

value: Injured BALF


title: Un.f.24h.rep1


title: Inj.m.6h.rep2


title: Inj.m.24h.rep3

source_name: Male_lung pericyte-like cell_Injured BALF_24hr


title: Inj.f.6h.rep1

source_name: Female_lung pericyte-like cell_Injured BALF_6hr


title: Inj.f.6h.rep2


title: Inj.m.24h.rep1


title: Inj.f.6h.rep3


title: Inj.m.24h.rep2


title: K562 Raw species mixing human (RNA-Seq)

status: Public on Oct 23 2020

city: New York

first: Sai

last: Ma

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: K562 Raw species mixing human

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts
Paired-end reads were aligned to mm10 using bowtie or STAR.
Duplicate reads were removed using picard or UMItools.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Counts Data is indexed by genes (row), cell (column)
Supplementary_files_format_and_content: Fragments data contains fragment position (1-3 column), and assigned cell barcode (4th column)

source_name: K562 Raw species mixing human

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium (11875-093, ThermoFisher) supplemented with 15% FBS (16000044, ThermoFisher) and 1% Penicillin-Streptomycin (15140122, ThermoFisher). NIH/3T3 and RAW 264.7 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, 11965092, ThermoFisher) with the addition of 10% FBS and 1% of Penicillin-Streptomycin. The cells were incubated at 37 °C in 5% CO2 and maintained at exponential phase.

extract_protocol:
Female mouse dorsal skin was collected at first telogen (P21), anagen III (P28), late anagen (P32) and 2nd telogen (P55). The hair cycle stages were confirmed using cryosectioning. To dissociate skin cells, the skin samples were incubated in 0.25% collagenase in HBSS at 37°C for 35-45 minutes on an orbital shaker, followed by incubation in 0.25% trypsin-EDTA at 37°C for 35-45 minutes on the shaker. The skin samples were gently scraped from the dermal side. The single cell suspension was centrifuged for 5 minutes at 4°C, resuspended in 0.25% FBS in PBS and stained with fluorescent dye-conjugated antibodies and DAPI. Mouse brain were dissected, snap frozen on dry ice, and stored at -80 °C. The brain single nuclei suspension was prepared following OMNI-ATAC protocol. Mouse lungs were dissociated with fine scissors and then proteolytic digestion was performed using the Lung Dissociation kit (Miltenyi Biotech). Dissociated cells were then incubated at 37 °C for 20 minutes with rotation. Red blood cells were lysed using ACK buffer.
Libraries are contructed using SHARE-seq procotol.

tag: strain


title: Inj.f.24h.rep2

source_name: Female_lung pericyte-like cell_Injured BALF_24hr


title: Inj.f.24h.rep3


title: Inj.f.24h.rep1


title: IgA_Coated_1


title: GM12878 3T3 species mixing human (RNA-Seq)

description: GM12878 3T3 species mixing

source_name: GM12878 3T3 species mixing


title: Un.f.24h.rep3


title: GM12878 rep1 (RNA-Seq)

description: GM12878 rep1


title: GM12878 rep2 (ATAC-Seq)

description: GM12878 rep2


title: K562 Raw species mixing human (ATAC-Seq)

description: K562 Raw species mixing human


title: GM12878 rep1 (ATAC-Seq)

description: GM12878 rep1


title: GM12878 rep2 (RNA-Seq)

description: GM12878 rep2


title: mouse lung (RNA-Seq)

description: mouse lung

source_name: mouse lung


title: OVCAR3-BDNF-3


title: GM12878 3T3 species mixing human (ATAC-Seq)

description: GM12878 3T3 species mixing human

source_name: GM12878 3T3 species mixing human


title: GM12878 3T3 species mixing mouse (RNA-Seq)

description: GM12878 3T3 species mixing


title: K562 Raw species mixing mouse (RNA-Seq)

description: K562 Raw species mixing mouse

source_name: K562 Raw species mixing mouse


title: Inj.m.6h.rep1


title: mouse lung (ATAC-Seq)

description: mouse lung


title: mouse brain (ATAC-Seq)

description: mouse brain

data_processing:
The data were processed with SHARE-seq-alignment pipelinev1.0(https://github.com/masai1116/SHARE-seq-alignment/). Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Counts Data is indexed by genes or peaks (row), cell (column). The barcodes in the ATAC count matrix are converted to matched RNA barcodes. The barcode translation information can be found in celltype.txt of ATAC dataset.
Supplementary_files_format_and_content: ATAC fragments data contains fragment position (1-3 column), and assigned cell barcode (4th column).
Supplementary_files_format_and_content: celltype.txt is a cell type annotation file, including the corresponding ATAC and RNA barcode information.

source_name: mouse brain


title: K562 Raw species mixing mouse (ATAC-Seq)

description: K562 Raw species mixing mouse


title: GM12878 3T3 species mixing mouse  (ATAC-Seq)

description: GM12878 3T3 species mixing mouse

source_name: GM12878 3T3 species mixing mouse


title: GM12878 rep3 (RNA-Seq)

description: GM12878 rep3


title: mouse skin late anagen (RNA-Seq)

description: mouse skin late anagen

source_name: mouse skin late anagen


title: GM12878 rep3 (ATAC-Seq)

description: GM12878 rep3


title: mouse skin late anagen (ATAC-Seq)

description: mouse skin late anagen


title: SPL_CD11b_13

status: Public on Sep 03 2020

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: Splenic immune cells were isolated by mechanical disruption of spleens in PBS with 0.4% EDTA and 0.5% FBS. The cell suspension was spun down at 1600rpm for 4 minutes and resuspended in red blood cell lysis buffer (Sigma-Aldrich) for 2.5 minutes. Cells were then washed, resuspended in Fc block for 10 minutes followed by incubation with anti-CD11c and anti-PDCA1 (dendritic cells), anti-CD19 (B cells), anti-CD3 and anti-CD4+ (CD4 T cells), anti-CD3 and CD8 (CD8 T cells) and anti-CD11b (myeloid cells) at 4C for 15 minutes, washed, and purified by flow cytometry using FACSAria II flow cytometer (BD).

data_processing:
Raw sequencing reads were demultiplexed, and FASTQ files were used to generate estimated transcript counts against the mouse transcriptome (mm10) via Salmon v0.8.2.
TPM values summed to the gene level were generated using the R Bioconductor package DEseq2.
Median TPM values were calculated within each cell type. Genes with a median TPM value less than 0.5 within each cell type were discarded.
The union of the remaining genes from each cell type were combined, and the signal-to-noise metric (difference in mean expression divided by the sum of standard deviations) was calculated for each of these remaining genes when comparing between each genotype group within each cell type.
These gene values were ranked from highest to lowest, indicating which genes were most upregulated and downregulated with the least variation.
These sorted lists of genes were used as inputs for Gene Set Enrichment Analysis (GSEA), using 1000 permutations of the gene sets. A false discovery rate P-value less than 0.05 was accepted as significant
Genome_build: mm10 (mouse splenic immune cells) and hg38 (human MDMs)
Supplementary_files_format_and_content: comma delimited RPKM & TPM tables

source_name: FACS sorted splenic CD11b cells

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit (Thermo-Fisher Catalog # 12183018A) using the "on column DNA digestion" protocol variation (PureLink DNase, Thermo-Fisher Catalog # 12185010).  RNA quality was assessed via bioanalyzer (Agilent) and quantified via NanoDrop (Thermo).  The indicated amount of total RNA ("characteristics:  total RNA input") was used for the construction of sequencing libraries.
RNA sequencing libraries were constructed with TruSeq Stranded mRNA Library Prep from Illumina (Catalog # 20020594) using the manufactuer's standard protocol.  Libraries were indexed with TruSeq RNA Single Indexes Set A (Catalog # 20020492).  Library quality was assessed via bioanalyzer (Agilent), and quantified via Qbit (Thermo).  Libraries were normalized and pooled for sequencing (splenic dendritic cells and monocyte-derived macrophages were pooled and run separately).

value: Homozygous C9orf72 (3110043O21Rik) Knock-Out; Homozygous Tmem173 Knock-Out (Golden Ticket)

tag: age at collection

value: 3 Months

tag: age of onset

tag: days in culture

tag: total rna input

value: FACS sorted splenic CD11b cells


title: SPL_CD11b_11

value: Homozygous C9orf72 (3110043O21Rik) Knock-Out

tag: cell type


title: SPL_CD11b_15


title: SPL_CD11b_12


title: SPL_CD11b_14


title: SPL_CD11b_9


title: SPL_CD11b_10


title: SPL_CD11b_7

value: Homozygous C9orf72 Conditional Knock-Out; Hemizygous Cx3Cr1-Cre


title: SPL_CD11b_8


title: SPL_CD11b_6


title: mouse brain (RNA-Seq)

description: mouse brain


title: SPL_CD11b_5


title: SPL_CD8_15

source_name: FACS sorted splenic CD8 cells

value: FACS sorted splenic CD8 cells


title: SPL_CD8_14


title: SPL_CD11b_4

value: Wild Type


title: SPL_CD11b_2


title: SPL_CD11b_3


title: SPL_CD8_13


title: SPL_CD8_10


title: SPL_CD8_9


title: SPL_CD8_11


title: SPL_CD8_8


title: SPL_CD8_12


title: SPL_CD8_7


title: SPL_CD8_6


title: SPL_CD8_3


title: SPL_CD8_4


title: SPL_CD8_5


title: SPL_CD8_1


title: SPL_CD8_2


title: SPL_CD4_13

source_name: FACS sorted splenic CD4 cells

value: FACS sorted splenic CD4 cells


title: SPL_CD4_14


title: SPL_CD4_10


title: SPL_CD4_9


title: SPL_CD4_15


title: SPL_CD4_7


title: SPL_CD4_12


title: SPL_CD11b_1


title: SPL_CD4_11


title: SPL_CD4_8


title: SPL_CD4_6


title: SPL_B_CELLS_15

source_name: FACS sorted splenic B-cells

value: FACS sorted splenic B-cells


title: SPL_CD4_3


title: SPL_CD4_2


title: SPL_CD4_4


title: SPL_B_CELLS_12


title: SPL_CD4_5


title: SPL_B_CELLS_14


title: SPL_B_CELLS_11


title: SPL_B_CELLS_13


title: SPL_CD4_1


title: SPL_B_CELLS_9


title: SPL_B_CELLS_10


title: SPL_B_CELLS_6


title: SPL_B_CELLS_7


title: SPL_B_CELLS_5


title: SPL_DC_KO_3

data_processing:
Raw sequencing reads were demultiplexed, and FASTQ files were aligned to the mouse genome (mm10) via Tophat v2.1.1 and Bowtie v2.3.2.
BAM files were indexed with Samtools v1.6 and annotated using Partek software v7.17.0918 to generate RPKM values for each gene
Genome_build: mm10 (mouse splenic immune cells) and hg38 (human MDMs)
Supplementary_files_format_and_content: comma delimited RPKM & TPM tables

source_name: FACS sorted splenic dendritic cells

value: 10 Weeks

value: FACS sorted splenic dendritic cells


title: SPL_B_CELLS_1


title: SPL_B_CELLS_2


title: SPL_B_CELLS_3


title: SPL_B_CELLS_4


title: SPL_DC_WT_3


title: SPL_DC_WT_2


title: SPL_DC_WT_1


title: SPL_DC_WT_4


title: MDM_C9ALS_7_H151

description:
Peripheral blood mononuclear cells (PBMCs) were isolated from human blood samples collected in BD Vacutainer CPT tubes and centrifuged at 1600 RCF for 20 minutes. The plasma and PBMCs were collected and centrifugation (300 xg, 10 minutes) to isolate the PBMCs. For monocyte derived macrophages (MDMs), the CD14+ cells were isolated from the PBMCs using the magnetic CD14 beads from Miltenyi biotec according to the manufacturer’s instructions, then cultured in IMDM + 10% FBS + hMCSF (50ng/ml) for at least 7 days, and collected for RNA at the day indicated.
476-H151

data_processing:
Raw sequencing reads were demultiplexed, and FASTQ files were used to generate estimated transcript counts against the human transcriptome (hg38) via Salmon v0.8.2.
TPM values summed to the gene level were generated using the R Bioconductor package DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: comma delimited TPM tables

source_name: Monocyte-derived macrophages

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit (Thermo-Fisher Catalog # 12183018A) using the "on column DNA digestion" protocol variation (PureLink DNase, Thermo-Fisher Catalog # 12185010).  RNA quality was assessed via bioanalyzer (Agilent) and quantified via NanoDrop (Thermo).  The indicated amount of total RNA ("characteristics:  total RNA input") was used for the construction of sequencing libraries.
RNA sequencing libraries were constructed with TruSeq Stranded mRNA Library Prep from Illumina (Catalog # 20020594) using the manufactuer's standard protocol.  Libraries were indexed with TruSeq RNA Single Indexes Set A (Catalog # 20020492).  Library quality was assessed via bioanalyzer (Agilent), and quantified via Qbit (Thermo).  Libraries were normalized and pooled for sequencing.

treatment_protocol: 1µM STING antagonist H151 (Cayman chemicals) in DMSO (Sigma) was added on day 7 for 6 hours before RNA was collected

value: Positive for C9orf72 repeat expansion

value: unknown

value: 72 ng


title: MDM_C9ALS_6_H151

description:
Peripheral blood mononuclear cells (PBMCs) were isolated from human blood samples collected in BD Vacutainer CPT tubes and centrifuged at 1600 RCF for 20 minutes. The plasma and PBMCs were collected and centrifugation (300 xg, 10 minutes) to isolate the PBMCs. For monocyte derived macrophages (MDMs), the CD14+ cells were isolated from the PBMCs using the magnetic CD14 beads from Miltenyi biotec according to the manufacturer’s instructions, then cultured in IMDM + 10% FBS + hMCSF (50ng/ml) for at least 7 days, and collected for RNA at the day indicated.
450-H151

value: 49 Years


title: MDM_C9ALS_7_DMSO

description:
Peripheral blood mononuclear cells (PBMCs) were isolated from human blood samples collected in BD Vacutainer CPT tubes and centrifuged at 1600 RCF for 20 minutes. The plasma and PBMCs were collected and centrifugation (300 xg, 10 minutes) to isolate the PBMCs. For monocyte derived macrophages (MDMs), the CD14+ cells were isolated from the PBMCs using the magnetic CD14 beads from Miltenyi biotec according to the manufacturer’s instructions, then cultured in IMDM + 10% FBS + hMCSF (50ng/ml) for at least 7 days, and collected for RNA at the day indicated.
476-DMSO

treatment_protocol: The same volume as H151 of DMSO (Sigma) was added on day 7 for 6 hours before RNA was collected

value: 32 ng


title: MDM_sALS_4

description: Peripheral blood mononuclear cells (PBMCs) were isolated from human blood samples collected in BD Vacutainer CPT tubes and centrifuged at 1600 RCF for 20 minutes. The plasma and PBMCs were collected and centrifugation (300 xg, 10 minutes) to isolate the PBMCs. For monocyte derived macrophages (MDMs), the CD14+ cells were isolated from the PBMCs using the magnetic CD14 beads from Miltenyi biotec according to the manufacturer’s instructions, then cultured in IMDM + 10% FBS + hMCSF (50ng/ml) for at least 7 days, and collected for RNA at the day indicated.

data_processing:
Raw sequencing reads were demultiplexed, and FASTQ files were aligned to the human genome (hg38) via Tophat v2.1.1 and Bowtie v2.3.2.
BAM files were indexed with Samtools v1.6 and annotated using Partek software v7.17.0918 to generate RPKM values for each gene.
RPKM values were log2 transformed after adding a pseudocount of 1.
Genes with a median log2 transformed RPKM value less than 0.5 were discarded.
Signal to noise ratios of the remaining genes were calculated for each group comparison, and the sorted list of these genes was used as the input for GSEA using 1000 permutations of the gene sets. A false discovery rate P-value of less than 0.05 was accepted as significant.
Genome_build: mm10 (mouse splenic immune cells) and hg38 (human MDMs)
Supplementary_files_format_and_content: comma delimited RPKM & TPM tables

value: Negative for known ALS mutations (sporadic)

value: 56 Years

value: 54 Years

value: Monocyte-derived macrophages


title: MDM_sALS_5

value: 67 Years

value: 65 Years


title: SPL_B_CELLS_8

value: Homozygous C9orf72 Conditional Knock-Out; Hemizygous Cx3Cr1-Cre

value: 3 Months


title: MDM_C9ALS_5

value: 45 Years

value: 42 Years


title: MDM_sALS_2

value: 68 Years

value: 66 Years


title: MDM_sALS_1

value: 63 Years


title: MDM_C9ALS_4

value: Positive for C9orf72 repeat expansion

value: 62 Years

value: 61 Years


title: MDM_C9ALS_3

value: 49 Years

value: 46 Years


title: MDM_C9ALS_2

value: 60 Years


title: MDM_C9ALS_1

value: 69 Years

value: 64 Years


title: MDM_WT_4

value: Normal control

value: 53 Years

value: Monocyte-derived macrophages


title: SPL_DC_KO_1

value: Homozygous C9orf72 (3110043O21Rik) Knock-Out

value: 10 Weeks

value: FACS sorted splenic dendritic cells


title: SPL_DC_KO_2


title: MDM_WT_3

value: 42 Years


title: 20_P11D7: Patient #11 Day 7

status: Public on Jul 31 2020

data_processing:
Single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 10 million reads per sample. Basecalls were processed to FASTQs on BaseSpace (Illumina), and a base call quality trimming step was applied to remove low-confidence base calls from the ends of reads.  The FASTQs were aligned to the human reference genome (GRCh38.91), using STAR v.2.4.2a (PMID: 23104886) and gene counts were generated using htseq-count
Differential gene expression between Day 0 and Day 7 conditions was determined using paried analysis in DESeq2 package in R environment
Genome_build: GRCh38.91
Supplementary_files_format_and_content: Abundance counts

source_name: Human peripheral blood monoctye

extract_protocol:
Whole blood was collected into K-EDTA tubes from subjects before (day 0) and seven days after initiation of ivacaftor. One aliquot was used for separation of plasma from blood cells. The remaining blood was separated using gradient centrifugation over Ficoll-paque (GE) to separate peripheral blood mononuclear cells (PBMCs) from neutrophils and red blood cells. The Miltenyi Monocyte Isolation Kit (a positive selection kit that uses magnetic beads conjugated to CD14 antibody) was used to isolate monocytes.
Total RNA was isolated from human peripheral blood monocytes using Qiagen's RNeasy Plus kit per manufactures' instructions. Briefly, freshly isolate monocytes were homogenized in Qiagen RLT buffer, snap frozen, and stored at -80oC until further processing via the Qiagen kit. Purified RNA from samples was eluted in Ambion's RNA storage solution and stored frozen at -80oC until use. cDNA was first synthesized from RNA using the High-Capacity cDNA Reverse Transcription Kit (Thermofisher) and stored until use for RNA-seq.
For each sample, libraries were constructed from 100 ng of total RNA using the TruSeq Stranded mRNA kit (Illumina) with poly(A) selection.  Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

tag: diagnosis

value: cystic fibrosis

value: peripheral blood monoctye

tag: exposure

value: Treatment (7 days of ivacaftor)

value: F


title: MDM_WT_2


title: MDM_WT_1

value: 48 Years


title: MDM_sALS_3

value: Negative for known ALS mutations (sporadic)

value: 50 Years


title: SPL_DC_KO_4


title: MDM_C9ALS_6_DMSO

description:
Peripheral blood mononuclear cells (PBMCs) were isolated from human blood samples collected in BD Vacutainer CPT tubes and centrifuged at 1600 RCF for 20 minutes. The plasma and PBMCs were collected and centrifugation (300 xg, 10 minutes) to isolate the PBMCs. For monocyte derived macrophages (MDMs), the CD14+ cells were isolated from the PBMCs using the magnetic CD14 beads from Miltenyi biotec according to the manufacturer’s instructions, then cultured in IMDM + 10% FBS + hMCSF (50ng/ml) for at least 7 days, and collected for RNA at the day indicated.
450-DMSO

value: Positive for C9orf72 repeat expansion

value: 49 Years

value: unknown


title: 19_P10D7: Patient #10 Day 7

value: M


title: 16_P7D7: Patient #7 Day 7


title: 17_P8D7: Patient #8 Day 7


title: 18_P9D7: Patient #9 Day 7


title: 12_P2D7: Patient #2 Day 7


title: 15_P5D7: Patient #5 Day 7


title: 14_P4D7: Patient #4 Day 7


title: MDM_WT_5

value: Normal control

value: 46 Years


title: 11_P1D7: Patient #1 Day 7


title: 13_P3D7: Patient #3 Day 7


title: 10_P11D0: Patient #11 Day 0

value: Baseline (no ivacaftor)


title: 9_P10D0: Patient #10 Day 0


title: 6_P7D0: Patient #7 Day 0


title: 5_P5D0: Patient #5 Day 0


title: 8_P9D0: Patient #9 Day 0


title: 2_P2D0: Patient #2 Day 0


title: 1_P1D0: Patient #1 Day 0


title: 4_P4D0: Patient #4 Day 0


title: shEsrrb_Dex Rep2 (RNA-seq)

status: Public on Jul 20 2020

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

description:
17_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes

data_processing:
Basecalls performed using CASAVA version 1.4
Clean reads are mapped to reference using HISAT/Bowtie2
Gene expression level quantified by RSEM
Differential genes screened by EBseq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the annotation of the genes and the FPKM values from RSEM for each sample

source_name: T-ALL cell line

growth_protocol: 6 hours with 100 nM dexamethasone

extract_protocol:
Purelink RNA mini kit
BGI-Seq500 Library prep method; MultiPLEX single End

tag: background strain

value: FVBN

tag: tissue

value: Thymic tumor

value: T-ALL cell line

tag: RNAi knockdown

value: shEsrrb


title: shEsrrb_Dex Rep1 (RNA-seq)

description:
16_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes

tag: genotype


title: shEsrrb_Dex Rep3 (RNA-seq)

description:
18_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: shEsrrb_DMSO Rep2 (RNA-seq)

description:
14_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: shEsrrb_DMSO Rep1 (RNA-seq)

description:
13_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: shNr3c1_Dex Rep3 (RNA-seq)

description:
12_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: shNr3c1_Dex Rep2 (RNA-seq)

description:
11_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: shNr3c1_Dex Rep1 (RNA-seq)

description:
10_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: 7_P8D0: Patient #8 Day 0

value: cystic fibrosis

value: peripheral blood monoctye


title: shNr3c1_DMSO Rep3 (RNA-seq)

description:
9_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: shNr3c1_DMSO Rep2 (RNA-seq)

description:
8_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: NS_Dex Rep1 (RNA-seq)

description:
4_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes

value: non-targeting shRNA


title: shNr3c1_DMSO Rep1 (RNA-seq)

description:
7_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: NS_Dex Rep2 (RNA-seq)

description:
5_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: NS_DMSO Rep3 (RNA-seq)

description:
3_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: 3_P3D0: Patient #3 Day 0

value: F


title: 4C-siCONT

status: Public on Jul 02 2020

city: Oslo

first: Eivind

last: Hovig

address: PO Box 4950 Nydalen

department: Tumor biology

country: Norway

institute: Oslo University Hospital

data_processing:
RNASeq data on MITF knockdown in 3c and 4c cells were analysed using STAR (v 20201) with default parameters for alignment to hg19. Resulting bam files were then fed into cuffdiff (v 2.2.1 ) using all conditions to build base for transcript analysis.
both significantly and non significanttly differentially expressed genes are given in the processed files
Genome_build: hg19
Supplementary_files_format_and_content: gene_exp.diff file containing info on the differentially expressed genes between all conditions

growth_protocol: The immortalized melanocyte cell line Hermes 3C and 4C were purchased from Wellcome Trust Functional Genomics Cell Bank. Hermes 3C and 4C were cultured and maintained in 254 medium (Gibco, Invitrogen, Oslo, Norway) supplemented with 10% fetal calf serum (FCS) (PAA, New Bedford, MA, USA), 200nM phorbol-12-myristate-13-acetate (TPA; Sigma-Aldrich), 200pM (Hermes 3C) and 2pM (Hermes 4C) cholera toxin (Sigma-Aldrich), 10ng/ml human stem cell factor (hSCF; Thermo Fisher) and 10nM endothilin (EDN1; Millipore, Oslo, Norway).

extract_protocol:
Total RNA was isolated using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, Steinheim, Germany) according to manufacturer's instructions.
Libraries were prepared according Illumina's instructions

treatment_protocol: The cells were incubated for 72h to ensure optimal target reduction at the protein level. The cells were transfected with a final concentration of 25pmol siRNA, using Lipofectamine RNAiMAX (Invitrogen) as described in the manufacturers protocol. Sequences for siRNA are Sense (5´-GCA-GUA-CCU-UUC-UAC-CAC-U-3´) anti sense (5´-AGU-GGU-AGA-AAG-GUA-CUG-C-3´).

tag: cell line

tag: sirna transfection

value: si-control


title: NS_DMSO Rep2 (RNA-seq)

description:
2_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: 4C-siMITF

value: siMITF


title: NS_DMSO Rep1 (RNA-seq)

description:
1_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: 3C-siCONT


title: 4C-HA-MITF input_1

data_processing:
reads were aligned to hg19 using Bowtie v.1.0.0 allowing a maximum of 2 mismatches and suppressing multiple reads alignments if found. Peak calling was performed using MACS (v macs14 1.4.2; PMID: 18798982) with default parameters and using option “-g 2.63e9” for effective genome size.
Peak detection (i.e., binding site detection)  was performed with MACS1.4 with default parameters using the input file as control in each peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: bed files

source_name: Hermes4c - lentiviral transduction of a HA-tagged MITF-M construct (pLX3xHAvar4mCherry)

extract_protocol:
Hermes cells were transduced by lentiparticles carrying pLX3xHAvar4mCherry. Stable cell lines expressing the 3xHA tagged MITFvar4 were subsequently sorted based on the presence of mCherry and used further. Chromatin immuno-precipitation sequencing (ChIPseq) experiments were performed twice. Cross-linking was performed with 1% formaldehyde for 8min. Cross-linking was stopped with 125mM glycine for 5min. Cells were rinsed twice in phosphate buffered saline (PBS), harvested using trypsination and sedimented. Cells were resuspended in ice-cold lysis buffer (1% SDS, 10mM EDTA, 50mM Tris–HCl, pH 8.0) containing protease and phosphatase inhibitors. Cells were sonicated at 4°C using a Covaris S2 instrument to yield chromatin fragments of 300–500 bp. Chromatin was cleared by centrifugation, concentration determined by A260, and chromatin was diluted in RIPA buffer (0.1% SDS, 0.1% Na-deoxycholate, 1% Triton X-100, 1mM EDTA, 0.5mM EGTA, 140mM NaCl, 10mM Tris–HCl, pH 8.0) to 2 A260 units. Each immunoprecipitation was performed in 250μl RIPA buffer with 1μg antibody overnight at 4°C. The antibody: anti-HA-tag (12CA5, Roche) was used. Antibody-bound chromatin was precipitated using Dynabeads protein G (Invitrogen) and washed 3 times in RIPA buffer, once in TE buffer (10mM Tris–HCl, pH 8.0, 10mM EDTA) and eluted in 1% SDS with 100mM NaHCO3. Eluted chromatin was incubated at 65°C with proteinase K (Sigma-Aldrich; 50μg/ml) over night, and DNA was purified by phenol-chloroform-isoamylalcohol extraction (25:24:1) and once with chloroform/isoamylalcohol (24:1) followed by ethanol precipitation. DNA was dissolved in H2O and used for high-throughput sequencing using an Illumina Hiseq 2500 sequencer.
Libraries were prepared according Illumina's instructions accompanying the TruSeq library preparation kit.

treatment_protocol: no treatment

tag: antibody

value: no antibody


title: 3C-siMITF


title: 4C-HA-MITF ChIP_1

value: anti-HA-tag (12CA5, Roche)


title: 4C-HA-MITF ChIP_2


title: shEsrrb_DMSO Rep3 (RNA-seq)

description:
15_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: 4C-HA-MITF input_2


title: 3C-HA-MITF input_2

source_name: Hermes3c - lentiviral transduction of a HA-tagged MITF-M construct (pLX3xHAvar4mCherry)


title: 3C-HA-MITF ChIP_2


title: 3C-HA-MITF ChIP_1


title: 3C-HA-MITF input_1


title: NS_Dex Rep3 (RNA-seq)

description:
6_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes


title: 3C

description: replicate 1

hyb_protocol: 750 ng of biotin labeled cRNA was hybridized to Illumina’s HumanHT-12 v4 Expression BeadChip

scan_protocol: After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Here the quality of each array and scan is investigated, and text files with both non-normalized and quantile normalized data exported.

data_processing: Data extraction, quantile normalization and initial quality control of the bead summary raw data were performed using GenomeStudio v2011.1 from Illumina and the Gene Expression module v1.9.0. The data were annotated using the HumanHT-12_V4_0_R2_15002873_B.bgx annotation file from Illumina.

source_name: Hermes 3c

label_protocol: Labelling was performed with Illumina® TotalPrep™-96 RNA Amplification Kit according to manufacturer's instructions

extract_protocol: Total RNA was isolated using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, Steinheim, Germany) according to the manufacturer’s manual.

value: Hermes 3c

tag: transduction

value: control


title: HL60-EV-Dox-1 [oxRRBS-seq]

status: Public on Jun 12 2020

data_processing:
Basecalling and quality scoring are performed on the NextSeq instrument with the Real-Time Analysis (RTA) v2 software
Read trimming were performed using Trim Galore v0.4.5 and NuGEN's custom script (https://github.com/nugentechnologies/NuMetRRBS)
Read alignment using Bismark v0.20.0
CpG methylation calls using Bismark methylation extractor v0.20.0
Genome_build: hs37d5
Supplementary_files_format_and_content: GZIP format; CpG methylation calls in rows with chromosome, start position, end postion, methylation percentage, count methylated, count unmethylated in columns

source_name: HL60 EV + doxycycline

growth_protocol: RPMI-1640 media with 10% FBS

extract_protocol:
DNAs were extracted using QIAamp DNA mini kit
Reduced representation oxidation BS-Seq was performed using the NuGEN Ovation RRBS methyl-seq system 1-16

treatment_protocol: Doxycyline 1ug/ml for 48 hours

value: Human AML cells

tag: genotype/variation

value: transduced with pRRL-EV-puro

tag: treatment

value: doxycycline


title: HL60-TFEB-Dox-1 [oxRRBS-seq]

source_name: HL60 TFEB + doxycycline

value: transduced with pRRL-TFEBS211A-puro


title: HL60-EV-Dox-2 [oxRRBS-seq]


title: HL60-TFEB-Dox-2 [oxRRBS-seq]


title: HL60-TFEB-Veh-2 [oxRRBS-seq]

source_name: HL60 TFEB + vehicle

value: vehicle


title: HL60-TFEB-Dox-3 [oxRRBS-seq]


title: HL60-EV-Veh-2 [oxRRBS-seq]

source_name: HL60 EV + vehicle


title: HL60-EV-Dox-3 [oxRRBS-seq]


title: HL60-TFEB-Veh-3 [oxRRBS-seq]


title: HL60-EV-Veh-3 [oxRRBS-seq]


title: HL60-EV-Veh-1 [oxRRBS-seq]


title: HL60-TFEB-Dox-2 [RRBS-seq]

extract_protocol:
DNAs were extracted using QIAamp DNA mini kit
Reduced representation BS-Seq was performed using the NuGEN Ovation RRBS methyl-seq system 1-16


title: HL60-TFEB-Dox-1 [RRBS-seq]


title: HL60-TFEB-Dox-3 [RRBS-seq]


title: HL60-EV-Dox-1 [RRBS-seq]


title: HL60-TFEB-Veh-3 [RRBS-seq]


title: HL60-TFEB-Veh-2 [RRBS-seq]


title: HL60-EV-Dox-3 [RRBS-seq]


title: HL60-EV-Veh-3 [RRBS-seq]


title: HL60-EV-Dox-2 [RRBS-seq]


title: HL60-EV-Veh-2 [RRBS-seq]


title: HL60-TFEB-Dox-3 [RNA-seq]

data_processing:
Basecalling and quality scoring are performed on the NextSeq instrument with the Real-Time Analysis (RTA) v2 software
Read trimming were performed.
Read alignment using STAR_2.5.3a
Abundance calculation using HTSeq-0.6.1
Genome_build: hs375d
Supplementary_files_format_and_content: Comma separated text file containing normalized reads count of samples in columns and gene symbols in rows

extract_protocol:
RNAs were extracted using NucleoSpin RNA II kit from Macherey-Nagel
RNA-Seq was performed using the NuGEN Ovation Human RNA-Seq FFPE kit


title: HL60-EV-Veh-1 [RRBS-seq]


title: 3C-HA-MITF

description: replicate 1

value: HA-tagged MITF-M construct (pLX3xHAvar4mCherry)


title: 4C

description: replicate 1

source_name: Hermes 4c

value: Hermes 4c


title: 4C-HA-MITF

description: replicate 1


title: HL60-TFEB-Veh-1 [oxRRBS-seq]


title: HL60-TFEB-Dox-2 [RNA-seq]


title: HL60-TFEB-Veh-1 [RRBS-seq]


title: HL60-EV-Veh-2 [RNA-seq]


title: HL60-EV-Veh-3 [RNA-seq]


title: HL60-TFEB-Veh-3 [RNA-seq]


title: HL60-EV-Dox-3 [RNA-seq]


title: HL60-EV-Dox-2 [RNA-seq]


title: HL60-TFEB-Veh-2 [RNA-seq]


title: HL60-EV-Dox-1 [RNA-seq]


title: HL60-EV-Veh-1 [RNA-seq]


title: 3198_S44

status: Public on May 25 2020

first: Alfonso

last: Urbanucci

state: Oslo

address: Trondheimsveien 8

data_processing:
Raw sequence reads were checked for the quality of sequencing experiment through FASTQC.
Trimmomatic (V0.38)  as used as a read trimming tool for Illumina data.
To quantify the transcript abundances, Kallisto (V 0.44.0) is used to build an index from the mouse reference genome (EnsDb.Mmusculus.v79) with default parameters.
To import and summarize transcript-level abundance of Kallisto, Tximport the R package was used.
Differential expression was assessed using DSeq2.
Genome_build: EnsDb.Mmusculus.v79
Supplementary_files_format_and_content: Raw (non normlaized) counts for all genes (also non coding) in all mice

source_name: PWScrm+/p+ control mice G3

extract_protocol:
Total RNA was homogenizated in Trizol Reagent (Sigma Aldrich). Libraries were prepared using TruSeq polyA mRNA kit (Illumina) according to manufacturer instructions, and sequenced by using the NovaSeq 6000 System (Illumina). Raw sequence reads were quality controlled through FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using Trimmomatic (v0.38) (http://www.ncbi.nlm.nih.gov/pubmed/24695404). To quantify the transcripts abundances we used Kallisto (v0.44.0) (Bray et al., 2016). Kallisto is also used to build an index from the mouse reference genome (EnsDb.Mmusculus.v79) with default parameters To import and summarize transcript-level abundance of Kallisto, Tximport an R package is used. Differential expression was assessed using DSeq2 (Love et al., 2014). Adjusted p-value less than 0.05 were selected as well as only genes > 2 fold change were considered in the analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were investigated at the beginning of the light period ZT0 (group 1, G1), six hours later at ZT6 (group 2, G2) and at same ZT6 but following 6-hrs of sleep deprivation (SD, group 3, G3).

value: Hypothalamus

value: PWScrm+/p+ control mice

tag: group


title: 3206_S46

source_name: PWScrm+/p− mutant mice G2

value: PWScrm+/p- mutant mice


title: 3143_S7


title: 3135_S16

source_name: PWScrm+/p+ control mice G1


title: 3200_S45

source_name: PWScrm+/p+ control mice G2


title: 3140_S5

source_name: PWScrm+/p− mutant mice G3


title: 3133_S9


title: 3119_S14


title: 3120_S8


title: 3121_S17


title: 3112_S13

source_name: PWScrm+/p− mutant mice G1


title: HL60-TFEB-Dox-1 [RNA-seq]


title: 3110_S12


title: 3111_S4


title: 3106_S10


title: 3107_S11


title: HL60-TFEB-Veh-1 [RNA-seq]


title: 3197_S43


title: 3103_S2


title: 3104_S3


title: 158I scRNAseq

status: Public on May 12 2020

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

department: PCCSM

institute: Yale School of Medicine

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq
Trimming of Read 2 for TSO and poly(A) with cutadapt
filtering, alligning, and barcode collapsing with zUMIs 2.0 (STAR 2.6.0 for alignment)
Cells filtered with > 12% of transcriptome from intron-spanning reads; < 20% mitochondrial origin; at least 1000 unique genes
ensembl gene IDs translated to HGNC only when a 1:1 translation was feasible using the R package biomaRt with the "Oct 2018" ensembl archive
Genome_build: GRCh38 Release 91
Supplementary_files_format_and_content:
RawCounts_sparse.mtx.gz: gunzipped, gene expression UMI count matrix of all intron and exon spanning transcripts are in sparse matrix format, generated with R package 'Matrix' and writeMM() function; 312,928 cells x 45,947 genes
AllCells.GeneIDs.txt: tab delimited table of corresponding gene identities for the count matrix. 2 columns: Ensembl_GeneID is the original gene ensembl IDs, HGNC_EnsemblAlt_GeneID is the mixed HGNC/ensemblIDs used for analysis in the manuscript.
AllCells.cellBarcodes.txt: tab delimited list of corresponding cell barcode identities for the count matrix
Cell_MetaData.txt: MetaData to describe all 312,928 cells; including subject and library source, disease status and cell-type identities we assigned in our study
Sample-Associated .rds files: R object files specific to each sequenced library, representing gene expression count data per cell, formatted with ensembl gene IDs. These are the primary data outputs by the processing program zUMIs 2.0. Each one is a nested list of intron spanning, exon spanning and combined intron and exon spanning UMI and read counts for the top 8,000-10,000 cell barcodes in each library ranked by total number of reads

source_name: Whole Lung Dissociate

extract_protocol:
Thawed Cells were rinsed with 10% FBS; passed through 40 uM strainer
10X Genomics 3 prime v2

treatment_protocol: Enzymatic and Mechanical Digestion; Cryopreservation in 10% DMSO

value: Whole Lung Dissociate

tag: disease

value: IPF

tag: Sex

value: M

tag: age


title: 177I scRNAseq


title: 034I scRNAseq


title: 123I scRNAseq


title: 3134_S15


title: 063I scRNAseq


title: 3142_S6


title: 3136_S18


title: 59I scRNAseq

value: F


title: 053I scRNAseq


title: 49I scRNAseq


title: 021I scRNAseq


title: 025I scRNAseq


title: 47I scRNAseq


title: 041I scRNAseq


title: 010I scRNAseq


title: 022I scRNAseq


title: 040I scRNAseq


title: 228I scRNAseq


title: 221I scRNAseq


title: 222I scRNAseq


title: 051I scRNAseq


title: 212I scRNAseq


title: 225I scRNAseq


title: 214I scRNAseq


title: 3102_S1


title: 209I scRNAseq


title: 179I scRNAseq


title: 174I scRNAseq


title: 166I scRNAseq


title: 135I scRNAseq


title: 157I scRNAseq


title: 138I scRNAseq


title: 137CO scRNAseq

value: COPD


title: 210I scRNAseq


title: 145I scRNAseq


title: 056CO scRNAseq


title: 238CO scRNAseq


title: 052CO scRNAseq


title: 8CO scRNAseq


title: 237CO scRNAseq


title: 235CO scRNAseq


title: 29I scRNAseq


title: 23CO scRNAseq


title: 207CO scRNAseq


title: 217CO scRNAseq


title: 186CO scRNAseq


title: 193CO scRNAseq


title: 192CO scRNAseq


title: 178CO scRNAseq


title: 153CO scRNAseq


title: 152CO scRNAseq


title: 084C scRNAseq

value: Control


title: 081C scRNAseq


title: 137C scRNAseq


title: 454C scRNAseq


title: 253C scRNAseq


title: 003C scRNAseq


title: 484C scRNAseq


title: 483C scRNAseq


title: 388C scRNAseq


title: 192C scRNAseq


title: 092C scRNAseq


title: 065C scRNAseq


title: 439C scRNAseq


title: 160C scRNAseq


title: 222C scRNAseq


title: 208C scRNAseq


title: 296C scRNAseq


title: 396C scRNAseq


title: 194CO scRNAseq


title: 244C scRNAseq


title: 098C scRNAseq


title: 465C scRNAseq


title: 226C scRNAseq


title: 184CO scRNAseq


title: 218C scRNAseq


title: 034C scRNAseq


title: 1372C scRNAseq


title: 002C scRNAseq


title: 001C scRNAseq