title: VK008L; input_ChIP-seq_CTCF-AID_untreated_rep1

data_processing:
ChIP-seq. Fastq files were trimmed using the fastq-mcf program, aligned to the mm9 reference genome with bowtie2 (Langmead and Salzberg, 2012). Reads with a mapq score of 30 or greater were retained, using Samtools. PCR duplicates were filtered out.  CTCF (FLAG) peaks were called using the geome wide Event finding and Motif Discovery (GEM) algorithm.
We processed each Hi-C dataset using distiller (https://github.com/mirnylab/distiller, doi:10.5281/zenodo.3350937), mapping reads to mm10 and saving processed data in the cooler format.
5C. Adapters were trimmed and aligment was performed using Bowtie2 against a pseudo-genome composed of all possible Forward-Reverse pairs of 5C oligonucleotides and matrices were analyzed using my5C (Lajoie et al. 2009 Nature Methods).
Genome_build: mm9 for ChIP-seq
Genome_build: custon 5C genome for 5C (provided as supplementary information) positions referring to mm9
Genome_build: mm10 for Hi-C
Supplementary_files_format_and_content: Hi-C .cool: valid Hi-C pairs mapped at 10kb resolution
Supplementary_files_format_and_content: ChIP-seq .bed: position of the CTCF (FLAG) peaks.
Supplementary_files_format_and_content: 5C - for all forward-reverse possible ligation pair we provide one file with raw 5C counts (not read normalized, including anchors ultimately removed from analysis), and one file with filtered symmetrical read-normalized balanced (Iterative Correction method - ICE) matrices.

source_name: mouse ES cells, line EN52.9.1


title: VK008K; Flag_ChIP-seq_CTCF-AID_untreated_rep1

status: Public on Aug 30 2020

type: SRA

city: San Francisco

first: Elphege

last: Nora

state: CA

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

country: USA

institute: University of California San Francisco

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and subclones were cultured in DMEM+Glutamax (ThermoFisher cat 10566-016) supplemented with 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1mM Sodium Pyruvate (ThermoFisher 11360-070), 1X non-essential amino-acids (ThermoFisher 11140-50) and 104U of Leukemia inhibitory factor (Millipore ESG1107). Cells were maintained at a density of 0.2-1.5x105 cells / cm² by passaging using TrypLE (12563011) every 24-48h on 0.1% gelatin-coated dishes (Millipore cat ES-006-B) at 37°C and 7% CO2. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
For ChIP-seq and Hi-C cells were  trypsinized and fixed in suspension; For 5C cells were fixed in tissue culture plates and scrapped off
ChIP libraries were prepared using standard Illumina protocols;5C (in-situ ligation with HindIII) and Hi-C (dilution ligation, Arima genomics kit) were assembled based on Illumina-compatible protocols. Detailed experimental procedures can be found in the supplementary information of the linked manuscript

treatment_protocol: For induction of the auxin-inducible degron indole-3-acetic acid (IAA, chemical analog of auxin) was added in the medium at 500µM from a 1000X stock diluted in sterile water and kept at 4°C up to 4 weeks or -20°C for long term storage. Doxycycline was added at 1ug/ml final from a 1mg/ml stock.

tag: genotype

value: CTCF-AID, Tir1

tag: treatment

value: untreated


title: VKC016; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox2days_rep2

source_name: mouse ES cells, line EN186.6


title: EN5C77; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep1

data_processing:
Library strategy: 5C
ChIP-seq. Fastq files were trimmed using the fastq-mcf program, aligned to the mm9 reference genome with bowtie2 (Langmead and Salzberg, 2012). Reads with a mapq score of 30 or greater were retained, using Samtools. PCR duplicates were filtered out.  CTCF (FLAG) peaks were called using the geome wide Event finding and Motif Discovery (GEM) algorithm.
We processed each Hi-C dataset using distiller (https://github.com/mirnylab/distiller, doi:10.5281/zenodo.3350937), mapping reads to mm10 and saving processed data in the cooler format.
5C. Adapters were trimmed and aligment was performed using Bowtie2 against a pseudo-genome composed of all possible Forward-Reverse pairs of 5C oligonucleotides and matrices were analyzed using my5C (Lajoie et al. 2009 Nature Methods).
Genome_build: mm9 for ChIP-seq
Genome_build: custon 5C genome for 5C (provided as supplementary information) positions referring to mm9
Genome_build: mm10 for Hi-C
Supplementary_files_format_and_content: Hi-C .cool: valid Hi-C pairs mapped at 10kb resolution
Supplementary_files_format_and_content: ChIP-seq .bed: position of the CTCF (FLAG) peaks.
Supplementary_files_format_and_content: 5C - for all forward-reverse possible ligation pair we provide one file with raw 5C counts (not read normalized, including anchors ultimately removed from analysis), and one file with filtered symmetrical read-normalized balanced (Iterative Correction method - ICE) matrices.

source_name: mouse ES cells, line EN133.10


title: VKC008; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep3

source_name: mouse ES cells, line EN186.4


title: VKC007; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep3


title: VKC006; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep4


title: VKC011; input_ChIP-seq_CTCF-AID_auxin2days_rep4


title: VKC012; Rad21_ChIP-seq_CTCF-AID_auxin2days_rep4


title: VKC005; input_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep4


title: VKC013; input_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep3


title: VKC003; input_ChIP-seq_CTCF-AID_auxin2days_rep3


title: VKC004; Rad21_ChIP-seq_CTCF-AID_auxin2days_rep3


title: VKC014; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep3


title: VKC036; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep2


title: VKC001; input_ChIP-seq_CTCF-AID_untreated_rep4


title: VKC009; input_ChIP-seq_CTCF-AID_untreated_rep5


title: VKC010; Rad21_ChIP-seq_CTCF-AID_untreated_rep5


title: EN5C85; 5C_CTCF-AID_TetO-CTCF(Del_615-736)_auxin+dox4days_rep1

source_name: mouse ES cells, line EN142.1


title: VKC033; input_ChIP-seq_CTCF-AID_untreated_rep3


title: VKC035; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep2


title: VKC034; Rad21_ChIP-seq_CTCF-AID_untreated_rep3


title: VKC032; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox2days_rep1


title: VKC015; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox2days_rep2


title: VKC031; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox2days_rep1


title: VKC024; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep1


title: VKC030; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep2


title: VKC029; input_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep2


title: VKC027; input_ChIP-seq_CTCF-AID_auxin2days_rep2


title: VKC028; Rad21_ChIP-seq_CTCF-AID_auxin2days_rep2


title: VKC023; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep1


title: VKC022; Rad21_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep1


title: VKC021; input_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep1


title: VKC020; Rad21_ChIP-seq_CTCF-AID_auxin2days_rep1


title: VKC002; Rad21_ChIP-seq_CTCF-AID_untreated_rep4


title: VKC019; input_ChIP-seq_CTCF-AID_auxin2days_rep1


title: ENC206; FLAG_ChIP-seq_CTCF-AID_TetO-CTCF(Del_615-736)_auxin+dox2days_rep2


title: VKC017; input_ChIP-seq_CTCF-AID_untreated_rep1


title: ENC205; FLAG_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep2


title: ENC207; FLAG_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep2


title: EN5C357; 5C_CTCF-AID, Tir1_untreated_rep3


title: EN5C353; 5C_endogenous CTCF(Delta13-33) clone 1_untreated_rep3

source_name: mouse ES cells, line EN276.4

value: endogenous CTCF(Delta13-33) clone 1


title: VKC018; Rad21_ChIP-seq_CTCF-AID_untreated_rep1


title: ENC180; FLAG_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep1


title: ENC192; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep2


title: ENC181; FLAG_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox2days_rep1


title: ENC178; FLAG_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep1


title: ENC174; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox2days_rep1


title: ENC190; input_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep2


title: ENC179; FLAG_ChIP-seq_CTCF-AID_TetO-CTCF(Del_615-736)_auxin+dox2days_rep1


title: ENC173; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox2days_rep1


title: ENC191; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_615-736)_auxin+dox2days_rep2


title: ENC172; input_ChIP-seq_CTCF-AID_TetO-CTCF(Del_615-736)_auxin+dox2days_rep1


title: ENC133; Rad21_(2017_protocol)_ChIP-seq_CTCF-AID_auxin2days_rep2


title: ENC170; input_ChIP-seq_CTCF-AID_auxin2days_rep1


title: ENC171; input_ChIP-seq_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox2days_rep1


title: ENC132; Rad21_(2017_protocol)_ChIP-seq_CTCF-AID_untreated_rep2


title: ENHIC13; Hi-C_CTCF-AID_TetO-CTCF(del_13-33-Y226A-F228A)_auxin+dox2days_rep2

source_name: mouse ES cells, line EN298.4


title: ENC169; input_ChIP-seq_CTCF-AID_untreated_rep1


title: ENC130; Rad21_(2017_protocol)_ChIP-seq_CTCF-AID_untreated_rep1


title: ENHIC12; Hi-C_CTCF-AID_TetO-CTCF(Y226A-F228A)_auxin+dox2days_rep2

source_name: mouse ES cells, line EN297.3


title: ENHIC14; Hi-C_CTCF-AID_TetO-CTCF(Del_13-33)_auxin+dox2days_rep2

source_name: mouse ES cells, line EN281.1


title: ENHIC10; Hi-C_CTCF-AID_TetO-CTCF(del_13-33-Y226A-F228A)_auxin+dox2days_rep1


title: ENHIC9; Hi-C_CTCF-AID_TetO-CTCF(Y226A-F228A)_auxin+dox2days_rep1


title: ENHIC8; Hi-C_CTCF-AID_TetO-CTCF(Del_1-265)_auxin+dox2days_rep2


title: ENHIC11; Hi-C_CTCF-AID_TetO-CTCF(Del_13-33)_auxin+dox2days_rep1


title: ENHIC6; Hi-C_CTCF-AID_auxin2days_rep2


title: ENHIC5; Hi-C_CTCF-AID_TetO-CTCF(Del_1-265)_auxin+dox2days_rep1


title: ENHIC2; Hi-C_untagged_untreated_rep2

source_name: mouse ES cells, line E14Tg2a

value: WT parental


title: ENHIC4; Hi-C_CTCF-AID_TetO-CTCF(full-length)_auxin+dox2days_rep1


title: ENHIC3; Hi-C_CTCF-AID_auxin2days_rep1


title: ENC131; Rad21_(2017_protocol)_ChIP-seq_CTCF-AID_auxin2days_rep1


title: ENHIC1; Hi-C_untagged_untreated_rep1


title: High responder to training -trained 1

city: Stockholm

first: Jorge

last: Ruas

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor_6.0 whole genome using TopHat v2.1.1 with parameters -p 15 -N 18 --read-edit-dist 18
Differential gene expression analysis was done using cufflinks with parameters --multi-read-correct --upper-quartile-norm --frag-bias-correct and subsequently cuffdiff with parameters -b -u
Normalized gene counts were obtained from bam files using featureCounts program and DESeq2 package
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab delimited text files containing raw counts

molecule: total RNA

organism: Rattus norvegicus

source_name: Gastrocnemius muscle

extract_protocol:
Gastrocnemius muscles were dissected, flash frozen 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.

tag: group

value: High responder to training -trained

tag: tissue

value: Skeletal muscle


title: High responder to training -trained 3


title: Low responder to training -trained 1

value: Low responder to training -trained


title: Low responder to training 1

value: low response trainers


title: Low responder to training 3


title: Low responder to training -trained 2


title: Low responder to training -trained 3


title: Low responder to training 2


title: High responder to training -trained 2


title: LS-NTS IP Rep 2

city: New York

first: Jeffrey

middle: M

last: Friedman

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
RNA sequencing raw data was uploaded and analyzed using BaseSpace apps (RNA-seq Alignment (Star aligner) and RNA-seq Differential Expression (DEseq2); Illumina) using an alignment to annotated mRNAs in the mouse genome (UCSC, Mus musculus assembly mm10).
RNA reads were aligned with BaseSpace STAR aligner
Differential expression of novel and reference transcripts with DEseq2 in Baseplace RNA-seq Differential Expression
Genome_build: mm10
Supplementary_files_format_and_content: gene expression counts for each individual sample

source_name: Lateral Septum

extract_protocol:
Affinity purification of EGFP-tagged polysomes was done 3 or 4 weeks after virus injections (Nectow et al., 2017). Briefly, mice were separated into 3 biological replicate groups of 4-6 mice per group and euthanized. Brains were removed, and the lateral septum was dissected on ice and pooled. Tissue was homogenized in buffer containing 10 mM HEPES-KOH (pH 7.4), 150 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 100 μg/mL cycloheximide, RNasin (Promega) and SUPERase-In™ (Life Technologies) RNase inhibitors, and Complete-EDTA-free protease inhibitors (Roche) and then cleared by two-step centrifugation to isolate polysome-containing cytoplasmic supernatant. Polysomes were immunoprecipitated using monoclonal anti-EGFP antibodies (clones 19C8 and 19F7; see Heiman et al., 200830) bound to biotinylated-Protein L (Pierce; Thermo Fisher Scientific)-coated streptavidin-conjugated magnetic beads (Life Technologies). A small amount of tissue RNA was saved before the immunoprecipitation (Input) and both input and immunoprecipitated RNA (IP) were then purified using RNAeasy Mini kit (QIAGEN). RNA quality was checked using an RNA PicoChip on a bioanalyzer. RIN values >7 were used. Experiments were performed in triplicates for each group.
cDNA was amplified using SMARTer Ultralow Input RNA for Illumina Sequencing Kit and sequenced on an Illumina HiSeq2500 platform.

treatment_protocol: Neurotensin-Cre Mice (Jax 017525) were injected with AAV5-Introvert-NBL10 in the lateral septum

tag: strain

value: Brain

tag: antibody

value: anti-EGFP


title: High responder to training 3

value: high response trainers


title: ENHIC7; Hi-C_CTCF-AID_TetO-CTCF(full-length)_auxin+dox2days_rep2


title: High responder to training 2


title: LS-NTS Input Rep3


title: Low capacity runner 3

value: low-capacity runners


title: LS-NTS Input Rep1


title: Low capacity runner 2


title: LS-NTS IP Rep1


title: High responder to training 1


title: High capacity runner 2

value: high-capacity runners


title: High capacity runner 3


title: Stressed - Rep 2 (IP)

extract_protocol:
Mice were euthanized 1 hour post-restraint, brains were removed, and the lateral septi were dissected on ice and pooled into 3 replicates per group of 4-6 mice each. Tissue was homogenized and clarified by centrifugation. Ribosomes were immunoprecipitated by using 4 ug of polyclonal antibodies against pS6 (Invitrogen) previously conjugated to Protein A-coated magnetic beads (Thermofisher). A small amount of tissue RNA was saved before the immunoprecipitation (Input) and both input and immunoprecipitated RNA (IP) were then purified using RNAeasy Mini kit (QIAGEN). RNA quality was checked using a RNA PicoChip on a bioanalyzer. RIN values > 8 were used.
cDNA was amplified using SMARTer Ultralow Input RNA for Illumina Sequencing Kit and sequenced on an Illumina HiSeq2500 platform.

treatment_protocol: Mice were either left in their homecase (Naïve) or placed into a flexible restraint cone for one hour.

tag: antibodies


title: Low capacity runner 1


title: Naïve - Rep1 (IP)


title: Stressed - Rep1 (IP)


title: LS-NTS IP Rep 3


title: Naïve - Rep2 (IP)


title: Stressed - Rep 2 (Input)

value: input


title: Naïve - Rep2 (Input)


title: Naïve - Rep1 (Input)


title: High capacity runner 1


title: hPSC_ChIP_H3K27ac_rep2

city: Hong Kong

first: Elly

middle: Sau-Wai

last: NGAN

address: 2/F, Professorial Block  Queen Mary Hospital  102 Pokfulam Road  Hong Kong SAR, China

department: Department of Surgery, Li Ka Shing Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Basecalls performed using bcl2fastq v1.8.4
ATAC-seq and ChIP-seq data were processed using standard ENCODE pipeline, from respectively https://github.com/ENCODE-DCC/atac-seq-pipeline and https://github.com/kundajelab/chipseq_pipeline
Specifically, ATAC-seq reads were trimmed using cutadapt.
ATAC-seq data were aligned using bowtie2 with default parameters; ChIP-seq data were aligned using bwa with '-q 5 -l 32 -k 2' and filtered and deduplicated with MAPQ>30 using sambamba.
Replicates were pooled for peak calling. ATAC-seq peaks were called using MACS2 with P-value and IDR threshold 0.1. ChIP-seq peaks were called using MACS2 with P-value cutoff 0.01, and IDR threshold 0.05
ChromHMM (Ernst and Kellis 2012) (v1.20) was used to perform genome segmentation based on the ChIP-seq and ATAC-seq peaks. We defined an initial set of enhancers as the genomic segments in chromatin states that emitted both H3K4me1 and H3K27ac marks and overlapped an ATAC-seq peak. These enhancers were then size-normalized to 1kbp each, covering the +/- 500bp regions around the corresponding ATAC-seq peak summits. Target promoters were defined as the +/-500bp regions around all the TSSs of all the genes in GENCODE (v28). Identified enhancers were also liftovered to hg19.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: bed defined enhancer regions on hg38 and hg19

organism: Homo sapiens

source_name: Induced pluripotent cells (hPSC)

growth_protocol: A control hPSC line (UE02302) was established as previously described (Lau et al. 2019). hPSCs were maintained in Matrigel (Corning)-coated plate in mTeSR1 medium (Stem Cell Technologies) in a 37 °C humidified 5% CO2 incubator. The hPSCs were regularly passaged by treating with Dispase (Stem Cell Technologies).

extract_protocol:
2.5-5x105 FACS enriched hNC or hPSC were collected and fixed with 37% formaldehyde for 10 minutes at room temperature. Chromatin was sonicated by Bioruptor Plus UCD-300 (Diagenode, Belgium).
ChIP-seq libraries were prepared by MicroPlex Library Preparation kit v2 (Diagenode)

tag: cell type

value: IMR90-derived hPSC

tag: chip antibody

value: H3K27ac antibodies (Abcam, Cat. no.:ab4729)


title: 2-315 (Ctrl)

city: montpellier

first: florence

last: cammas

address: 208 rue des apothicaires

country: France

institute: ircm

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using CASAVA 1.8.2 (Illumina).
Alignment was performed with TopHat 2.1.1 (with Bowtie 2.2.9) to the mm10 version of the Mus muculus genome. The transcript annotation was retrieved from UCSC on May 23, 2014.
Counting of reads aligned to a gene was performed with HTSeq-count 0.9.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file. First column is the gene identifier (gene symbol), the following columns are the raw counts (non-normalized) for each sample.

source_name: liver

extract_protocol:
liver were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

value: ctl

tag: strain background

value: mix C57BL/6, 129sv

value: liver


title: hPSC_ChIP_input_rep2

value: normal IgG


title: hPSC_ChIP_H3K4me1_rep2

value: H3K4me1 (Abcam, Cat. no.:ab8895)


title: Stressed - Rep1 (Input)


title: hPSC_ChIP_H3K27ac_rep1


title: 2-316 (TKO)

value: triple KO for the HP1 proteins (TKO)


title: hPSC_ChIP_input_rep1


title: LS-NTS Input Rep2


title: hPSC_ChIP_H3K4me1_rep1


title: 2-248 (TKO)


title: 2-208 (Ctrl)


title: 2-207 (TKO)


title: hPSC_ATAC_rep4

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al. 2015). In brief, around 35,000 FACS- enriched hNC or hPSCs were collected and washed in cold PBS. Transposition reaction was performed according the manufacturer’s protocol for Nextra Tn5 transposase Nextra kit (Illumina, Cat. No.: FC-121-1030). Transposed DNA fragments were purified by Qiagen MiniElute PCR purification kit (Qiagen).
DNA libraries were then prepared by PCR amplification using NEBNext High-Fidelity PCR kit (New England Biolabs) in the presence of barcoded PCR primers (sequences provided in Ref. (Buenrostro et al. 2015)). After the PCR amplification, DNA libraries were purified twice by 1.8x AMPure XP beads (Bechman Coulter A63880). The quality of the purified DNA library was assessed by a Bioanalyzer High-Sensitivity DNA Analysis Kit (Agilent).


title: hPSC_ATAC_rep2


title: hPSC_ATAC_rep3


title: hPSC_ATAC_rep1


title: EN5C284; 5C_endogenous CTCF(Del_13-33)-AID, Tir1 clone2_untreated_rep2

source_name: mouse ES cells, line EN277.2

value: untreated


title: F508del

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

description: bronchial epithelia cell line stably expressing F508del-CFTR

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10
Genome read mapping using bowtie2 (0.12.9), parameters: -l 16 -n 1 -e 50 -m 1—strata—best y
Read counting using bedtools, version 2.17.0, parameter: -s
Genome_build: Homo sapiens Ensemble build GRCh37
Supplementary_files_format_and_content: Unique read counts per gene per kilobase and million mapped readsRPKM

source_name: bronchial epithelia cell line

growth_protocol: CFBE41o- cells stably transduced with wild-type or F508del-CFTR were grown in Earles MEM (Gibco) supplemented with 10% FBS (Gibco) and 1% glutamine (Gibco), and cultured at 37°C in humidified atmosphere with 5% CO2 on dishes coated with collagen (Corning) or human fibronectin (ThermoFisher).

extract_protocol:
Total RNA from each sample was extracted in TRIzol reagent (Sigma Aldrich). Total RNA samples were DNaseI treated (5 U DNaseI / 5µg RNA), 30 min, 37°C), spiked-in and rRNA depleted using Ribo-Zero™ Magnetic Gold kit (Human/Mouse/Rat)
RNA-size selection and generation of the cDNA libraries was performed as described (Ingolia et al, 2009; doi: 10.1126/science.1168978)

tag: passenge

value: bronchial epithelia cell line


title: 2-201 (TKO)


title: hNC_ChIP_H3K27ac_rep2

source_name: Neural crest cells (hNC)

growth_protocol: Neural crest induction was performed according to a previously described protocol (Lai et al. 2017). In brief, hPSCs were dissociated into single cell suspension by Accutase (Millipore) and plated on Matrigel-coated plate in a density of 5E4 cells cm-2 in ES cell medium containing 10 ng/mL fibroblast growth factor 2 (FGF2, Peprotech). The differentiation was started by replacing ES cell medium with KSR medium and gradually switched to N2 medium from day 4 to day 10. To differentiate hPSCs to hNC cells, the cells were treated with 100 nM LDN193189 (Stemgent) from day 0 to day 3, 10 uM SB431542 (Abcam) from day 0 to day 4, 3 uM CHIR99021 (Stemgent) from day 2 to day 10 and 1 uM retinoic acid from day 6 to day 10.

value: hPSC-derived hNC


title: hNC_ChIP_H3K4me1_rep1


title: wild-type CFTR (control)

description: bronchial epithelia cell line stably expressing wildtype-CFTR


title: hNC_ChIP_H3K4me1_rep2


title: kdm3a KO-GS 12h-rep.2

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using Tophat2 (v2.0.9).
bedtools was used to get read counts for genes (bedtools multicov -split -D)
Genome_build: mm9
Supplementary_files_format_and_content: read counts were obtained for each sample for RNAseq data

source_name: MEF

growth_protocol: MEFs were cultured in DMEM+10% FBS(Gibco)+Antibiotics at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA were harvested using Trizol and RNA were extracted using Qiagen Rneasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For glucose starvation, cells were washed with PBS, then incubated with glucose-free DMEM supplemented with 10% dialyzed FBS.

tag: passages


title: hNC_ChIP_H3K27ac_rep1


title: kdm3a KO-GS 12h-rep.1


title: hNC_ChIP_input_rep2


title: hNC_ChIP_input_rep1


title: CF923

description: Human lung explant from patient #923

source_name: Human lung explant from patient #923

extract_protocol:
Total RNA from each sample was extracted in TRIzol reagent (Sigma Aldrich). Total RNA samples were DNaseI treated (5 U DNaseI / 5µg RNA, 30 min, 37°C), spiked-in and rRNA depleted using Ribo-Zero™ Magnetic Gold kit (Human/Mouse/Rat)
RNA-size selection and generation of the cDNA libraries was performed as described (Ingolia et al, 2009; doi: 10.1126/science.1168978)

value: lung explant


title: kdm3a KO 0h-rep.2


title: kdm3a KO 0h-rep.1


title: hNC_ATAC_rep2


title: WT-Glucose Starvation(GS) 12h-rep.2


title: 2-202 (Ctrl)


title: wild-type CFTR (control); colon organoids goblet-enriched

source_name: colon organoids goblet-enriched

growth_protocol: The culture medium for subsequent organoid expansion contained advanced DMEM/F12 (Invitrogen), supplemented with Glutamax (2 mmol/L; ThermoFisher), murine epidermal growth factor (50 µg/L), the cell culture supplements B27 and N2 (all from Invitrogen), [Leu-15]-Gastrin (10 nmol/L), N-acetylcysteine (1 mmol/L), nicotinamide (10 mmol/L), HEPES (10 mmol/L), CHIR99021 (10 µmol/L; only present during the first 2 days after (re-)seeding),  SB202190(3 µmol/L; all from Sigma-Aldrich), Y-27632 (10 µmol/L; only present during the first 2 days after (re-)seeding), prostaglandin E2 (10 nmol/L), A83-01 (0.5 µmol/L; all from Tocris), and an antibiotic formulation (Primocin; Invivogen). In addition, conditioned cell culture media containing the following growth factors were added: noggin (10% v/v), R-spondin 1 (20% v/v) and Wnt3a (50% v/v).

value: organoid goblet-cell enriched 7 days after seeding

value: wild-type CFTR (control)


title: F508del; colon organoids goblet-enriched


title: F508del; colon organoids undifferentiated

source_name: colon organoids undifferentiated

value: organoid undifferentiated


title: WT-Glucose Starvation(GS) 12h-rep.1


title: LB pH 3.7

city: Pune

first: Mahesh

last: Dharne

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Biochemical Sciences

country: India

institute: CSIR National Chemical Laboratory

data_processing:
The quality filtered reads (Q score >=30) were then aligned against the O. intermedium M86 genome using Hisat2 program (version 2.0.5).
The transcripts were quantified using Kallisto tool.
differential gene expression was analyzed using DESeq tool.
Genome_build: O. intermedium M86
Supplementary_files_format_and_content: tab-delimited text files

organism: Brucella intermedia

source_name: Bacteria

growth_protocol: Overnight grown culture of Ochrobactrum intermedium M86 was transferred to fresh LB medium and incubated till it reaches OD 0.7.

extract_protocol:
Total RNA was isolated using Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 ml of cells suspension was centrifuged and cell pellet was exposed to acidic conditions (Luria Bertani medium pH 3.7 and artificial gastric fluid medium pH 3.7 and 2.9).

tag: acid shock

value: 15 min

tag: presence of urea

value: 0 mM

value: Luria Bertani medium pH 3.7


title: AGF pH 3.7 + 6 mM urea

value: 6 mM

value: artificial gastric fluid medium pH 3.7 + 6 mM urea


title: wild-type CFTR (control); colon organoids undifferentiated


title: LB pH 3.7 + 6 mM urea

value: Luria Bertani medium pH 3.7 + 6 mM urea


title: AGF pH 3.7

value: artificial gastric fluid medium pH 3.7


title: AGF pH 2.9 + 6 mM urea

value: artificial gastric fluid medium pH 2.9 + 6 mM urea


title: WT 0h-rep.1

source_name: Mouse Embryonic Fibroblast(MEF)


title: wild-type CFTR (control); Ileal organoids

source_name: Ileal organoids


title: AdE44

city: La Jolla

first: William

last: Kim

state: California

address: 9500 Gilman Dr

institute: UCSD

data_processing:
The sequencing data were processed by bcbio RNA-seq pipeline. Briefly, the raw reads were aligned to reference genome GRCh37 using STAR 2.6.1;
Duplicated reads were marked by the bammarkduplicates module from biobambam 2.0.87; salmon 0.13.1 was then used for the transcript quantification.
Genome_build: GRCh37
Supplementary_files_format_and_content: TPM

source_name: HME1-E6/cyclin E overexpression

growth_protocol: HME-1 cells were cultured in MCDB 131 medium (Gibco) supplemented with 70 μg/mL bovine pituitary extract (Hammond Cell Tech), 1% newborn calf serum (Gemini Bio-Products), 5 μg/mL holotransferrin (Sigma), 10 ng/mL human epidermal growth factor (Invitrogen), 0.5 μg/mL hydrocortisone (Sigma), 5 μg/mL insulin (Sigma), 2 mM L-glutamine (Gibco), 100 U/mL penicillin (Gibco), and 100 μg/mL streptomycin (Gibco)

extract_protocol:
RNeasy extraction kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the NebNext Ultra RNA.

treatment_protocol: HME1-E6 cells were transduced with Ad-Cyc E three times per week during two weeks at 48-hour intervals.

value: Mammary epithelium

tag: genetic

value: yes


title: AdE37


title: F508del; Ileal organoids


title: hNC_ATAC_rep1


title: CF192 (F508del/F508del)

source_name: Human lung explant from patient #192


title: Chd7Gt/Gt Rep2

city: Ann Arbor

first: Donna

middle: M.

last: Martin

state: MI

address: 1150 W. Medical Ctr. Dr., 8220C MSRB III

department: Pediatrics and Communicable Diseases

institute: University of Michigan

description: Barcode: ACAGTG

data_processing:
Groomed reads were aligned to the mouse reference genome (NCBI mm9) using Bowtie2 v.2.0.6. Unique reads were retained and normalized to the total number of mapped reads for each sample.
Expression levels of mapped reads were calculated in units of fragments per kilobase of transcript per million mapped reads (FPKM). Genes with low FPKM (<0.3) were removed from analysis. Differential expression between genotypes was calculated using DESeq v.1.22.1 and genes were considered statistically significant with a Benjamini-Hochberg p < 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: processed data file includes log2 fold change and adjusted p-values for each differentially expressed transcript

molecule: polyA RNA

source_name: otocyst

extract_protocol:
Otocyst were dissected from E10.5 embryos into cold PBS. After brief centrifugation at 1000 rpm, PBS was removed and samples stored at -80 °C. Poly-adenylated RNA was extracted from each microdissected ear sample using the Ambion kit. RNA was reverse transcribed and sequencing libraries prepared with Illumina TruSeq RNA-seq v2 kit.
Libraries were prepared according to Illumina's protocol and barcodes were assigned as follows: E10.5_Chd7_GtGt_Rep1_R1.fastq.gz;CGATGT, E10.5_Chd7_GtGt_Rep1_R2.fastq.gz;CGATGT, E10.5_Chd7_PlPl_Rep1_R1.fastq.gz;GCCAAT, E10.5_Chd7_PlPl_Rep1_R2.fastq.gz;GCCAAT, E10.5_Chd7_PlPl_Rep2_R1.fastq.gz;CAGATC, E10.5_Chd7_PlPl_Rep2_R2.fastq.gz;CAGATC, E10.5_Chd7_GtPl_Rep1_R1.fastq.gz;CTTGTA, E10.5_Chd7_GtPl_Rep1_R2.fastq.gz;CTTGTA, E10.5_Chd7_GtPl_Rep2_R1.fastq.gz;TGACCA, E10.5_Chd7_GtPl_Rep2_R2.fastq.gz;TGACCA, E10.5_Chd7_GtGt_Rep2_R1.fastq.gz;ACAGTG, E10.5_Chd7_GtGt_Rep2_R2.fastq.gz;ACAGTG.  The Barcode information for each sample has been included in the sample description field.

value: otocyst

tag: age

value: embryonic day 10.5


title: AdE27


title: AdE17


title: Chd7Gt/Gt Rep1

description: Barcode: CGATGT


title: AdE32


title: AdE13


title: AdE10


title: AdE7


title: LB pH 7.0

value: Luria Bertani medium pH 7.0


title: Chd7Gt/+ Rep2

description: Barcode: TGACCA


title: AdE1


title: Chd7Gt/+ Rep1

description: Barcode: CTTGTA


title: HME1-E6

source_name: Non-transformed human mammary epithelial cell line expressing HPV-E6.

value: no


title: WT 0h-rep.2


title: AdE45


title: AdE33


title: Chd7+/+ Rep2

description: Barcode: CAGATC


title: MLE12 10% CSE-treated 10h -2_seq

city: Cleveland

first: Anna

last: Blumental Perry

state: OH

address: 10900 Euclid Ave.

institute: Case Western Reserve University

description: Sample 2

data_processing:
files were trimmed of library adapter sequences and converted to FASTA files
BlastN analysis was then performed against the target mouse mitochondrial sequence (mtDNA 16116-16210). The single best BLAST hit for each read was used in the summary data (duplicates were removed, and any remaining hits were filtered to the single hit with the highest identity). After reverse complementing any BLAST hits on the opposite strand (to ensure the same orientation) the lengths of the sequence alignments were tabulated.
Genome_build: NC_005089 (RefSeq Mus musculus mitochondrion, complete genome)
Supplementary_files_format_and_content: Abundance of reads for the transcript of interest as well as transcripts originating from the same region. Other small RNAs are not included.

source_name: Mouse lung epithelium cells, passage 3

growth_protocol: MLE12 cells were cultured in RPMI complete media: RPMI1640 medium (Cellgro, Manassas, VA, USA) supplemented with 4% fetal bovine serum (FBS; Serum International, Laval, QC, Canada), insulin-transferrin-selenous acid (ITS) premix (BD Biosciences, San Jose, CA, USA), 10nM hydrocortisone (Sigma-Aldrich), 10nM -estradiol (Sigma-Aldrich), 10mM HEPES, 2mM glutamine (CellGro), 100 U/ml penicillin, and 100 g/ml streptomycin.

extract_protocol:
Total RNA was extracted, labelled with P-32, run on acrilamide gel, band 15-100 bp in length were extracted and used for the library construction
RNA was isolated from the two biological replicates of control and two of 10% CSE-treated MLE cells using Trizol (15596018, Ambion). The samples were treated with DNase I  (Sigma, 04716728001), re-isolated using Trizol, and RNA quality was checked using Agilent Bioanalyzer. The RNA was further treated with CIP (neb, M0290S), labeled with γ32P[ATP] using T4 PNK (neb, M0201S) and resolved on the 10% TBE-Urea polyacrylamide gels. 15-100 nt RNAs were isolated and used for the construction of libraries. 22nt 3’-DNA adaptor (/5Phos/NNNNCTGTAGGCACCATCAAT/3ddC) was ligated to the isolated RNAs using RNA-ligase T4 RNA-Ligase 2 (NEB, M0373S, RNL2 truncated KQ).  Each small RNA sample was reverse transcribed with a different, 102 nt long DNA primer(from RT-1 to RT-4). Each RT primer contained unique 3-nucleotide sample barcode (see "Reverse/- tag" and "Forward/+ tag" columns in the Characteristics field) to identify it after pooling and sequencing
Paired-end sequencing was performed on an Illumina NextSeq platform (PE 2X 75 bp)

treatment_protocol: Research-grade 1R5F cigarettes (Kentucky Tobacco and Health Research Institute, Lexington, KY, USA) were used to prepare the CSE. CSE was made fresh for each experiment by bubbling the smoke from 1 cigarette through 5 ml of serum-free medium in a 15-ml conical tube and filtering it through a 0.22um filter to remove large particles and maintain sterility. This solution was designated as 100% CSE and diluted in culture medium to yield concentrations specified for each experiment.

tag: cell line

tag: agent

value: CSE

tag: reverse/- tag

value: CGGNNN

tag: forward/+ tag

value: (Phos)NNNCCG


title: H37Ra Δwag

city: Wuhan

first: Weize

last: Xu

state: Hubei

address: shizishan street No.1

country: China

institute: Huazhong Agricultural University

data_processing:
Trim adapter use Trimmomatic (parameters: PE, -phred33, nextra-primer.fa:3:30:5 MINLEN:100 version: Trimmomatic-0.36)
Alignment reads to reference use bwa (bwa mem, Version: 0.7.15-r1140)
Call Variance with GATK and samtools(the pipelines can be fouond at https://gist.github.com/Nanguage/7707960ed56e45be2e43e72a634e21fc, GATK version:v3.7-0-gcfedb67, Picard version:2.9.2-6-gbb529af, samtools version:1.2, bcftools:1.4.1-34-g0932add)
Genome_build: EnsemblBacteria ASM1614v1 assembly for Mycobacterium tuberculosis H37Ra
Supplementary_files_format_and_content: vcf file

organism: Mycobacterium tuberculosis H37Ra

source_name: H37Ra Δwag

growth_protocol: Mycobacterium Tubeculosis H37Ra was cultured cultured in Middlebrook 7H9 broth (Becton Dickinson) supplemented with 10% OADC, 0.02% tween 80 and 0.5% glycerol or on Middlebrook 7H10 agar supplemented with 10% OADC and 0.5% glycerol containing kanamycin (25 μg/ml) when needed

extract_protocol:
The bacteril culture was centrifuged, the pellets were washed and gringded in liqued nitrogen chilled grinders. The lysates were treated with TritonX-100 and proteinase K solution The genomic DNA was extracted by phenole/chloropharm  method.
The DNA liabraries were prepared by for High-througput DNA sequencin by Nextera Iilumina DNA library Kit

value: post- culture day 14.

tag: genotype

value: Wag KO


title: Chd7+/+ Rep1

description: Barcode: GCCAAT

tag: strain

tag: tissue


title: H37Ra CK

source_name: H37Ra CK

value: Wildtype


title: MLE12 10% CSE-treated 10h -1_seq

description: Sample 1

value: AATNNN

value: (Phos)NNNATT


title: AdE25


title: CF222 (F508del/G524X)

source_name: Human lung explant from patient #222

value: lung explant


title: H37Ra ΔesxQ

source_name: H37Ra ΔesxQ

value: esxQ KO


title: CF209 (F508del/F508del)

source_name: Human lung explant from patient #209


title: MLE12 Untreated-2_seq

description: Sample 4

value: control

value: TAGNNN

value: (Phos)NNNCTA


title: MLE12 Untreated-1_seq

description: Sample 3

value: GCTNNN

value: (Phos)NNNAGC


title: P0 mouse kidney bulk ATAC-seq sample 2

status: Public on Aug 29 2020

first: Katalin

last: Susztak

state: Pennsylvania

address: 3400 Civic Center Boulevard, 12th floor

description: P02-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig

data_processing:
snATAC raw fastq files were aligned to the mm10 (GRCm38) reference genome and quantified using Cell Ranger ATAC (v. 1.1.0). We only kept valid barcodes with number of fragments ranging from 1,000 to 40,000, mitochondria ratio less than 10%, and promoter ratio more than 20%. clustering was conducted using snapATAC.
snATAC peak calling was conducted for each cell type separately using MACS2 with parameters “--nomodel --keep-dup all --shift 100 --ext 200 --qval 1e-2 -B --SPMR --call-summits”.
Bulk ATAC-seq raw fastq files were processed using the end-to-end tool ENCODE ATAC-seq pipeline
scRNA raw fastq files were aligned to the mm10 (Ensembl GRCm38.93) reference genome and quantified using CellRanger v3.1.0. Seurat R package v3.0 was used for data quality control, preprocessing and dimensional reduction analysis. After gene-cell data matrix generation of both P0 and adult datasets, matrices were merged and poor-quality cells with <200 or >3,000 expressed genes and mitochondrial gene percentages >50 were excluded
Genome_build: mm10

source_name: P0 mouse kidney

extract_protocol:
50,000 nuclei/sample were tagmented with Tn5 transposase (Illumina) in 50 ml reaction volume including Tween-20 (0.1%) (Sigma) and digitonin (0.01%) (Promega). The reaction was carried out at 37 °C for 30 min in a thermomixer at 1,000 RPM. After purification of DNA with Qiagen Minelute Reaction Cleanup kit (Qiagen), samples were subjected to library amplification (8-10 cycles).
Libraries were purified with AmpureXP beads (Beckman Coulter) and their quality was assessed by Agilent High sensitivity DNA Bioanalysis chip (Agilent).

tag: developmental stages


title: 3-week mouse kidney bulk ATAC-seq sample 1

description: P21-1-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig

source_name: 3-week mouse kidney


title: P0 mouse kidney bulk ATAC-seq sample 1

description: P01-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig


title: 3-week mouse kidney bulk ATAC-seq sample 2

description: P21-2-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig


title: MTS_CLL

type: RNA

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

description: Circulating CLL lymphocytes

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-1_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

label: Biotin

source_name: CLL

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Cell lines were maintained in IMDM medium supplemented with 20% fetal bovine serum and 2%  penicillin/streptomycin

extract_protocol: RNA was extracted using Trizol method

treatment_protocol: Non-treatment was applied

tag: cell type

value: CLL lymphocytes


title: JLRC91_cell line

description: EBV positive cell line derived from CLL xenograft transplantation

source_name: Cell line

value: EBV positive DLBCL cell lines


title: PANOV_RS

source_name: Richter syndrome

value: EBV negative DLBCL (Richter syndrome) tumors


title: MTSL_cell line


title: CTGLI2_cell line


title: MGPL_cell line


title: MLMZL_cell line


title: 2149_cell line_2


title: TSNOV_RS


title: CGSL_cell line


title: MGP_CLL

description: Circulating CLL lymphocytes


title: MLMZLI2_cell line


title: MTSLI2_cell line


title: LO1_CLL

description: Circulating CLL lymphocytes


title: JLRC89_cell line


title: JLRC92_cell line


title: CGS_CLL

description: Circulating CLL lymphocytes


title: BEL9_RS


title: MLMZ_CLL

description: Circulating CLL lymphocytes


title: LO1P_CLL

description: Circulating CLL lymphocytes


title: CCT_CLL

description: Circulating CLL lymphocytes


title: BEL8_RS


title: JLRC_CLL

description: Circulating CLL lymphocytes


title: JFZ_cell line


title: BEL5_RS


title: BEL3_RS


title: CCT_cell line


title: BEL7_RS


title: CLIP_1

city: Yushima, Bunkyo-ku, Tokyo

first: Ryota

last: Kurimoto

state: Tokyo

department: Systems BioMedicine

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Library strategy: HITS-CLIP
Libaries were sequenced using Illumina’s MiSeq (100 bp single end sequencing)
Basecalling was done using Illumina default pipeline
Raw reads (fastq file) obtained from the Illumina pipeline were trimmed and clipped using cutadapt (v.1.2.1) and were subsequently mapped to the human genome (build hg38) using bowtie2.
To eliminate reads in which the adaptor was ligated more than one time, adaptor removal was performed 3 times. Duplicate Reads were filtered by IGV tools. All data analysis was done using a combination of custom and publicly available tools including resources available from the UCSC Genome Browser and Galaxy Bioinformatics (http://main.g2.bx.psu.edu/).
All aligned reads shorter than 10nt that mapped to more than a single position on the genome were excluded from further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each transcripts.

source_name: Flag tagged HEK293FT cells

growth_protocol: HEK293FT cells were maintained in DMEM medium (Corning) supplemented with 10% FBS (Gibco) and 1% penicillin–streptomycin (Gibco) at 37 °C with 5% CO2.

extract_protocol:
Flag-tagged cells were collected and crosslinked with 254 nm UV-crosslinking at 400 mJ/cm2 and 200mJ/cm2 on ice in a Stratalinker 1800 (Stratagene). Lysates were treated with Rnase T1 and protein-RNA complexes were isolated with antibody.
Antibody-bound proteins and RNA-protein complex were isolated by magnetic stand and wash with wash buffer (1xPBS, 0.1% SDC, 0.5% deoxycholate, 0.5% NP-40) and high-salt-wash buffer (5xPBS, 0.1% SDC, 0.5% deoxycholate, 0.5% NP-40). Purified RNA fragments were treated with CIP (Takara) and ligated with 3’ linker adaptor by using T4 RNA ligase (thermofisher) at 16°C for overnight. Treated RNA fragments were labelled with 32p-γATP, followed by electrophoresis with SDS-PAGE (NuPAGE, thermofisher) and transferred to nitrocellurose membrane. RI-labelled RNAs were detected by autoradiography. Appropriate band or smear-band were picked up from membrane and treated with ProK (Roche).  RNA fragments were purified by acid phenol - chloroform extraction (thermofisher scientific). Purified TruB1-bound RNA fragments were ligated with 5′ linker RNA, followed by the reverse-transcriptase reaction using RT primers and SuperScriptIII (thermofisher scientific). cDNA libraries were amplified by means of Phusion High-Fidelity DNA Polymerase (New England Biolabs).

value: HEK293FT cells

tag: target protein

value: Flag-tagged protein

tag: clip antibody

value: Flag FLA-1 (MBL)


title: BEL4_RS


title: Scer_WT_input_3

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

data_processing:
Reads were mapped to their respective genomes using Bowtie2
Convert SAM files to big wig read coverage files
calculate the ratio of each ChIP to input signal (both antiSfp1-ChIP in WT and antiSfp1-ChIP in deltaSfp1)
Calculate the log ratio of these ratios (ChIP_WT/input_WT)/(ChIP_dSfp1/input_dSfp1).
Extract the ratios for various genomic elements (promoters, gene bodies); identify those that are significantly bound compared to the background.
Genome_build: S288C R64 for S. cerevisiae, YGOB v7 Aug 2012 for K. lactis and N. castellii, and Scannell et al. for S. paradoxus (Scannell et al., 2011)
Supplementary_files_format_and_content: Processed data files include both raw signal tracks (.unique.bw), log ratios relative to both input and to sfp1 mutants.

organism: Saccharomyces cerevisiae

source_name: Log-phase culture in BMW

growth_protocol: Log-phase culture in rich media

extract_protocol:
The ChIP protocol was performed as described by Lefrancois et al. in The Guide to Yeast Genetics (Weissman, Jonathan F., Guthrie, 2010). Polyclonal antibodies were created (Bethyl, Inc) to bind a peptide from the conserved c-terminal portion of Sfp1 (NH2-Cys-GKRYKNLNGLKYHRGHSTH-COOH), designated, αSfp1-1, while αSfp1-3 was raised to recognize was raised to bind specifically to the N. castellii Sfp1pl (using NH2-Cys-QLKKNSTASSSHQNSNNQTH-COOH). In all cases, the antibody used for ChIP was αSfp1-1, with the exception of those N. castellii IP3 samples, which used αSfp1-3.
DNA was quantified using Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). Input samples were diluted to the same concentration of ChIP samples. End Repair was carried out with the End-It DNA repair Kit (Epicenter). An AMPure Spri XP bead (Agencourt) clean-up was performed after end repair. A-base addition was carried out with 5 ul of NEB reagents Klenow Buffer (NEB Buffer #2), 10 ul of 1mM dATP (NEB) and 1 ul of Klenow exo (3’ to 5’ exo -; NEB) to each sample. An AMPure Spri XP bead clean-up was performed after A-base addition. Adaptor ligation was completed using 15 ul of 2x Quick DNA ligase buffer (NEB),1 ul of custom indexed adapters at uM, and 1 ul of Quick T4 DNA ligase (NEB) to each sample. An AMPure Spri XP bead clean-up was performed after adapter ligation. PCR was carried out using 1 ul of the PFU enzyme (Agilent), 5 ul of Pfu Buffer (Agilent), 0.5 ul of 100 uM dNTPs, and 2.5 ul of nuclease free water. An AMPure Spri XP bead clean up and samples were eluted in 15 ul of 10 mM Tris-Cl, pH 8.5. Samples were pooled in an equal molar ratio prior to sequencing.

value: wild type

tag: replicate

tag: chip antibody

value: input


title: BEL2_RS


title: Scer_WT_input_4


title: BEL6_RS


title: Scer_WT_input_2


title: Scer_WT_input_1


title: Scer_WT_IP1_5

value: αSfp1-1 custom polyclonal antibody (Bethyl)


title: Scer_WT_input_5


title: BEL1_RS


title: Scer_WT_IP1_3


title: Scer_WT_IP1_2


title: Scer_WT_IP1_4


title: Series 2_KD

description:
test
SAMPLE 4

data_processing:
For the normalization it uses the average of five housekeeping genes: RNU6B. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_RNU6B)]
processed_data.txt normalized signal (against housekeeping genes).
Fold-change.txt  reports test/control (KD/control) ratios.

label: TaqMan

label_protocol: 3μL of RNA (1000 ng) were reverse transcribed by Megaplex RT Primers, Pool A (human) (Thermo Fisher Scientific) using the TaqMan® microRNA Reverse Transcription Kit (Thermo Fisher Scientific). For qRT-PCR, RT product was mixed with TaqMan® Universal PCR Master Mix, No AmpErase UNG (Thermo Fisher Scientific) and the appropriate amount of water, and subsequently loaded into the ports of the TaqMan array cards. RealTime PCR was performed on a 7900HT Fast Real-Time PCR System with TaqMan® Array Block (Thermo Fisher Scientific), using universal cycling conditions (95 °C/10 min, then [95 °C/15 sec, 60 °C/60 sec] for 40 cycles).

extract_protocol: Total RNA was extracted by mirVana miRNA isolation kit.

treatment_protocol: siRNAs were transfected into cells using Lipofectamine RNAiMAX (Thermofisher scientific) by manufacturer’s recommended protocol.

value: TruB1 KD


title: Series 3_control

description:
control
SAMPLE 5


title: Series 3_KD

description:
test
SAMPLE 6


title: Scer_Sfp1d_input_2

value: delta sfp1


title: Scer_WT_IP1_1


title: Scer_Sfp1d_IP1_2


title: Scer_Sfp1d_input_1


title: Scer_Sfp1HA_input_2


title: Scer_Sfp1d_IP1_1


title: Series 1_KD

description:
test
SAMPLE 2


title: Series 1_control

description:
control
SAMPLE 1


title: Series 2_control

description:
control
SAMPLE 3


title: Scer_Sfp1HA_input_1


title: spar WT_C_60

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_60mins), replicateC. Used to generate column Spar_t60 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

data_processing:
Reads were mapped using RSEM (Li and Dewey, 2011) (version 1.2.11) utilizing Bowtie (Langmead, 2010) (version 1)
RSEM counts for the duplicated chromosome 2 in S. cerevisiae and S. paradoxus were similarly corrected by dividing the counts for genes on chromosome 2 by the median log fold change difference between genes on chromosome 2 and other genes between the WT and SFP1D mutant strains
We then used the edgeR package for R (Robinson, McCarthy and Smyth, 2010; McCarthy, Chen and Smyth, 2012) to TMM normalize the data and calculate the log fold changes and p-values of the gene expression differences between WT and SFP1D mutant strains.
Genome_build: The assembly (including transcriptome annotation information) from Scannell, et al. (Scannell et al., 2011) was used for S. paradoxus, and the r64 release of the S288C genome from the Saccharomyces Genome Database (Cherry et al., 2012) for S. cerevisiae. For C. glabrata, N. castellii, and K. lactis the genome and assembly and annotations were obtained from YGOB (v7 Aug 2012) and the S. pombe ASM294v2 genome assembly information was obtained from ENSEMBL (Vilella et al., 2009).
Supplementary_files_format_and_content: Files named "*.Gene.logFC.txt.gz" contain the gene-level (i.e. that species' genes) log-fold change (relative to WT) expression values for each species. Files names  "*.OG.logFC.txt.gz" contain orthogroup-level logFC values for each species. orthology_melted_aliases.txt.gz contains the orthogroup mappings for each species. Note that because gene expression was measured using both microarrays and RNA-seq, this processed data includes the data from both. The gene expression microarrays that are part of this study and described in their own GEO entry (TBD). OG_to_Scer-GNs.txt.gz contains the orthogroup to S. cerevisiae systematic name mappings.  Also included are raw counts (from RSEM) in files ending in ".counts.txt.gz" and copy-number-normalized TMM-normalized CPM values in files ending in ".TMM.txt.gz".

organism: Saccharomyces paradoxus

source_name: Yeast culture (BMW) - lag phase

growth_protocol: For log phase samples, cells were collected between O.D 0.6-0.8 Lag phase samples were collected at 30 mns and 60 mins post glucose repletion.

extract_protocol:
RNA extraction Total RNA was isolated using the RNeasyMidi or Mini Kit (Qiagen) and instructions were followed for mechanical lysis.
Library construction was completed as previously described (Engreitz et al., 2013; Schwartz et al., 2013).
Rna-seq libraries were pooled and Paired-end 25 base pair reads were performed on Illumina’s Hiseq2000.

value: C

tag: growth phase


title: Scer_Sfp1HA_HA_1

value: HA


title: glab ko 9955_B

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for delta   CAGL0M09955g Candida glabrata in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Cgla_9955_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

organism: Nakaseomyces glabratus

source_name: Yeast culture (BMW) - log phase

value: delta CAGL0M09955g

value: B

value: log


title: glab ko 9955_C

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for delta   CAGL0M09955g Candida glabrata in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Cgla_9955_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: gla ko 2_C

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for delta   CAGL0D00682g Candida glabrata in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Cgla_0682_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: delta CAGL0D00682g


title: glab ko 9955_A

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for delta   CAGL0M09955g Candida glabrata in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Cgla_9955_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: A


title: spar WT_C_30

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_30mins), replicateC. Used to generate column Spar_t30 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: spar WT_B_60

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_60mins), replicateB. Used to generate column Spar_t60 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: gla ko 2 _A

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for delta   CAGL0D00682g Candida glabrata in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Cgla_0682_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: 2149_cell line

value: EBV positive DLBCL cell lines


title: cglab wt_C

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for wild type Candida glabrata in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Cgla_0682_Log and Cgla_9955_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: cglab wt_B

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for wild type Candida glabrata in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Cgla_0682_Log and Cgla_9955_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: spar WT_B_30

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_30mins), replicateB. Used to generate column Spar_t30 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: Scer_Sfp1HA_HA_2


title: cglab wt_A

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for wild type Candida glabrata in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Cgla_0682_Log and Cgla_9955_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: spar WT_A_60

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_60mins), replicateA. Used to generate column Spar_t60 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: gla ko 2_B

description:
Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for delta   CAGL0D00682g Candida glabrata in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Cgla_0682_Log in Cgla.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: spar WT_A_30

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_30mins), replicateA. Used to generate column Spar_t30 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: Si1: siTRIM8 rep1

first: Weixiang

last: He

state: State...

address: Donghu Road

department: Urology

institute: Wuhan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with normalized abundance measurements for every gene and every sample

source_name: MCF-7 cells transfected with TRIM8 siRNA

growth_protocol: The cells were cultured in a humidified environment consisting of 95% air and 5% CO2 at 37°C, and cultured in DMEM (Gibco, China) supplemented with 10% FBS (Gibco, Australia).

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF7 cells were transfected with the control or TRIM8 siRNAs. Transfection was perfomed with Lipofectamine RNAiMAX reagent (13778100, Invitrogen).

value: breast cancer


title: Si3: siTRIM8 rep3


title: spar sfp1 ko_C_60

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_60mins), replicateC. Used to generate column Spar_t60 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: NC3: siNC rep3

source_name: MCF-7 cells transfected with control siRNA


title: Si2: siTRIM8 rep2


title: NC1: siNC rep1


title: spar sfp1 ko_C_30

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_30mins), replicateC. Used to generate column Spar_t30 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: spar sfp1 ko_B_60

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_60mins), replicateB. Used to generate column Spar_t60 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: NONCOVID_25_62y_male_NonICU

city: Albany

first: Adolfo

middle: Ariel

last: Jaitovich

address: 47 New Scotland Av

department: Molecular and Cellular Physiology

institute: Albany Medical Center

description:
NC25
genes.ec.tsv
genes.tpm.tsv

data_processing:
Basecalling via the standard Illumina Pipeline, version 1.8.2.
Trimming/Filtering for adapters and low quality via custom algorithm
Expression estimates via RSEM v1.3.0 under Python 2.7.15, using bowtie2-2.3.4.1. Executed command: rsem-calculate-expression --no-qualities --bowtie2 --bowtie2-k 200 --bowtie2-sensitivity-level sensitive --seed-length 20 --keep-intermediate-files --no-bam-output --paired-end [r1.fa.gz] [r2.fa.gz] [hg38 bowtie reference]
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited expression estimates, including non-normalized Expected Counts (EC), and normalized Transcripts Per Million (TPM)

source_name: Leukocytes from whole blood

extract_protocol:
10mL of whole blood collected from patients was filtered and RNA was isolated using LeukoLOCK Total RNA Isolation System.
TruSeq Stranded mRNA Library prep. Libraries were standardized to 2nM. Paired-end 2x50bp sequencing, using standard SBS chemistry (v3) on an Illumina NovaSeq6000 sequencer.

tag: disease state

tag: age (years)

tag: Sex

value: male

tag: icu

value: no

tag: apacheii

value: unknown

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

value: leukocyte

tag: tissue of origin

value: whole blood

tag: sample type

value: primary cells


title: NONCOVID_24_32y_female_NonICU

description:
NC24
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

value: female

tag: icu

tag: cell type


title: NONCOVID_26_36y_male_ICU

description:
NC26
genes.ec.tsv
genes.tpm.tsv

value: yes

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm


title: NC2: siNC rep2

tag: cell line


title: NONCOVID_23_42y_female_NonICU

description:
NC23
genes.ec.tsv
genes.tpm.tsv

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)


title: spar sfp1 ko_B_30

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_30mins), replicateB. Used to generate column Spar_t30 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

value: delta sfp1

tag: replicate

tag: growth phase


title: spar sfp1 ko_A_60

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_60mins), replicateA. Used to generate column Spar_t60 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: NONCOVID_20_62y_female_ICU

description:
NC20
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: NONCOVID_21_71y_male_NonICU

description:
NC21
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: cell type


title: NONCOVID_22_63y_male_NonICU

description:
NC22
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)


title: NONCOVID_19_66y_female_ICU

description:
NC19
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

tag: fibrinogen

tag: sofa


title: Sp.TCM.2

first: Ananda

last: Goldrath

data_processing:
Tophat
HT-Seq Count
DESeq from BioConductor
Genome_build: UCSC mm10
Supplementary_files_format_and_content: gct

source_name: D55 CD127hiCD62Lhi Tcm P14

extract_protocol:
Total RNA was extracted in TRIZoL reagent
PrepX RNA-seq library preperation kit (Integenex)

tag: strain

tag: age

value: 6-16 Weeks

tag: tissue

value: spleen

value: CD8+ T cells


title: T8.MP.LCMV.D7.Sp2

source_name: D7 CD127hi KLRG1lo MP P14


title: Sp.TEM.2

source_name: D55 CD127hiCD62Llo Tem P14


title: T8.TN.P14.Sp2

source_name: CD62Lhi CD44lo P14


title: Sp.TCM.1


title: Sp.Conv.TEM.1

source_name: D55 CD62Llo Conventional Tem P14


title: T8.MP.LCMV.D7.Sp1


title: T8.TE.LCMV.D7.Sp2

source_name: D7 CD127lo KLRG1hi TE P14


title: Sp.TEM.1


title: spar sfp1 ko_A_30

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_30mins), replicateA. Used to generate column Spar_t30 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

tag: growth phase


title: T8.TN.P14.Sp1

tag: cell type


title: T8.TE.LCMV.D7.Sp1


title: NONCOVID_18_88y_male_ICU

description:
NC18
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: NONCOVID_17_84y_female_ICU

description:
NC17
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa


title: Sp.Conv.TEM.2

tag: strain

tag: age

tag: tissue

tag: cell type


title: NONCOVID_16_40y_female_ICU

description:
NC16
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)


title: SPAR WT_C

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Spar_KO_Log in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

value: wild type

tag: replicate

value: C

tag: growth phase

value: log


title: NONCOVID_15_83y_unknown_ICU

description:
NC15
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: Sp.ttem.1

source_name: D55 CD127loCD62Llo terminal Tem P14

tag: strain

tag: age

tag: tissue

tag: cell type


title: SPAR WT_B

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Spar_KO_Log in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

value: B


title: NONCOVID_14_75y_female_ICU

description:
NC14
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: sofa


title: IEL.Trm.2

source_name: D55 CD103hiCD62Lhi IEL Trm P14

value: Small intestine IEL


title: NONCOVID_13_65y_male_ICU

description:
NC13
genes.ec.tsv
genes.tpm.tsv

tag: Sex

value: male

tag: icu

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: SPAR WT_A

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces paradoxus in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Spar_KO_Log in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

value: A

tag: growth phase


title: NONCOVID_12_82y_male_ICU

description:
NC12
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: apacheii

tag: charlson score

tag: mechanical ventilation

value: no

tag: ventilator-free days

tag: dm

value: unknown

tag: cell type


title: IEL.Trm.1

tag: strain

tag: age

tag: tissue


title: NONCOVID_08_53y_female_ICU

description:
NC8
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: icu

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

value: leukocyte

value: whole blood


title: SPAR SFP1 ko_C

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Spar_KO_Log in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

tag: growth phase


title: NONCOVID_11_58y_female_NonICU

description:
NC11
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

value: female

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: cell type

tag: tissue of origin

tag: sample type

value: primary cells


title: NONCOVID_10_67y_male_ICU

description:
NC10
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: icu

value: yes

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)


title: SP.ttem.2

tag: strain

tag: age

value: 6-16 Weeks

tag: tissue


title: KO_tunicamycin_rep2

city: Istanbul

first: seref

last: gul

address: Yalikoy Mh., Beykoz

department: Institute of Life Sciences and Biotechnology

country: Turkey

institute: Bezmialem Vakif University

data_processing:
The fluorescent images were processed into sequences, and base calling and quality value calculations were performed using the Illumina data processing pipeline (v1.5). FastQC (v0.11.5) was utilized to evaluate the initial quality of the reads.
Adaptor sequence and low-quality bases (quality score < Q30) were trimmed from the sequence reads by using Trimmomatic (v0.35).
Clean high quality data were mapped to the reference hg38 genome using the STAR  aligner (v2.5.3) with the following options --outSJfilterReads Unique --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate.
Fragments per kilobases of exons per million mapped read (FPKM) and fold changes were calculated using the Cuffdiff command from the Cufflinks suite. Quartile library normalization and pooled dispersion estimation methods were performed for the differential expression analysis. We used a minimum alignment count of 10, false discovery rate (FDR) < 0.05 and the absolute value of log2|Fold change| ≥ 0.5 as the threshold to judge significant differences in gene expression. To identify differentially expressed genes (DEGs) in WT and KO samples, the FPKM values for each gene (in KO samples) were compared to controls (WT sample) of each subject. To further evaluate the effect of drugs (treatment (TR)) e.g. cisplatin, doxorubicin and tunicamycin in BMAL1 KO cells the following formula was applied to determine DEGs: |log2[(KO_TR/KO_VC)/(WT_TR/WT_VC)]|. VC stands for vehicle control.
To determine the enriched gene sets, we used the Gene Set Enrichment Analysis (GSEA) by providing DEG values calculated from equation as preranked input to GSEA program wiith default parameters.   ClueGo extension of Cytoscape (v.3.6.0) was used to find significantly altered KEGG pathways for each DEG lists (p-value   0.05).   To construct protein-protein interaction (PPI) network for common DEGs in cisplatin and doxorubicin treated KO cells, a list of genes was submitted to STRING database to retrieve the experimentally determined PPI data.    Properties of PPI network were calculated by using Cytoscape (v. 3.6.0).
Genome_build: hg38
Supplementary_files_format_and_content: Text files for all genes having differential expression, p-val and q-val data obtained as a result of comparing WT vs KO cells for each conditions e.g. control (vc), cisplatin (CP), doxorubicin(DR), and tunicamycin (TM) were provided: WT_VC-KO_VC_gene_exp.txt; WT_CP-KO_CP_gene_exp.txt; WT_DR-KO_DR_gene_exp.txt; WT_TM-KO_TM_gene_exp.txt, respectively

source_name: invasive breast cancer cells

extract_protocol:
Total RNA from the fibroblast cell lines was extracted using the RNeasy Mini Kit (Qiagen, USA) protocol according to manufacturer’s instructions including the DNase I treatment.
After checking the quality and quantity of total RNA via 2100 BioAnalyzer, RNA-seq library preparation was performed using TruSeq mRNA Sample Preparation Kit (Illumina, USA) according to the manufacturer’s instructions. Paired-end sequencing was performed for the two cDNA libraries (two biological replicates) for each condition in Illumina HiSeq sequencing platform. All sequence data were PE 2x100 bp. Illumina data processing pipeline (v1.5) was utilized to perform the image processing, base calling, and quality calculation. High quality reads were saved in FASTQ format.

tag: cell line

tag: passage

tag: genotype

value: BMAL1 -/-

tag: treatment

value: tunicamycin


title: SPAR SFP1 ko_B

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Spar_KO_Log in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: delta sfp1

tag: replicate

tag: growth phase


title: NONCOVID_09_49y_female_NonICU

description:
NC9
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

tag: tissue of origin

tag: sample type


title: NONCOVID_06_75y_female_ICU

description:
NC6
genes.ec.tsv
genes.tpm.tsv

tag: icu

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)


title: SPAR SFP1 ko_A

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Spar_KO_Log in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

tag: growth phase


title: gGM-13

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

institute: University of Valencia

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts

source_name: BMDMs

growth_protocol: Bone marrow was isolated from the femur and tibia of C57BL/6 mice and cultured in IMDM medium supplemented with 10 ng/ml mMCSF, 10% FBS and 1% Penicilin-Streptomycin.

extract_protocol:
Cells were lysed in TRIzol (Invitrogen)
RNA-Seq analysis was performed after ribodepletion and standard library construction using Illumina HiSeq2500 V4 2x100 PE  (Genewiz, South Plainfield, NJ).

treatment_protocol: Transfection of customized GapmeRs for MAARS or negative control #1 (25nM) was performed using Lipofectamine 3000 (Invitrogen, 11668-019).

value: bone marrow-derived macrophages

tag: strain

tag: transfected with

value: MAARS gapmeRs


title: gGM-11


title: NONCOVID_05_83y_female_NonICU

description:
NC5
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: fibrinogen

tag: sofa


title: gGM-9

tag: cell type


title: NONCOVID_04_90y_male_NonICU

description:
NC4
genes.ec.tsv
genes.tpm.tsv

tag: icu

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: gGM-15

tag: strain

tag: transfected with


title: KO_tunicamycin_rep1

tag: cell line

tag: passage

tag: genotype

tag: treatment


title: gCT-5

tag: cell type

value: control gapmeRs


title: NONCOVID_03_65y_male_ICU

description:
NC3
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: fibrinogen

tag: sofa


title: COVID_101_58y_male_ICU

description:
C101
genes.ec.tsv
genes.tpm.tsv

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: KO_doxorubicin_rep1

tag: cell line

tag: passage

tag: genotype

tag: treatment

value: doxorubicin


title: gCT-2

tag: cell type

tag: strain

tag: transfected with


title: KO_doxorubicin_rep2


title: NONCOVID_02_65y_male_ICU

description:
NC2
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

value: male

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: fibrinogen

tag: sofa


title: gCT-6


title: COVID_102_84y_male_NonICU

description:
C102
genes.ec.tsv
genes.tpm.tsv

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: COVID_99_71y_male_ICU

description:
C99
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

tag: cell type


title: COVID_100_74y_female_NonICU

description:
C100
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm


title: COVID_103_83y_male_NonICU

description:
C103
genes.ec.tsv
genes.tpm.tsv

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: fibrinogen

tag: sofa


title: gCT-7

tag: strain

tag: transfected with


title: KO_cisplatin_rep1

tag: cell line

tag: passage

tag: genotype

tag: treatment

value: cisplatin


title: NONCOVID_07_50y_male_ICU

description:
NC7
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

value: no

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: associated controlled-vocabulary terms

tag: cell type

tag: tissue of origin

tag: sample type


title: COVID_98_81y_male_NonICU

description:
C98
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

value: unknown

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: fibrinogen

tag: sofa


title: COVID_97_76y_male_ICU

description:
C97
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

tag: ddimer (mg/l_feu)

value: leukocyte


title: KO_Control_rep2

tag: cell line

tag: passage

tag: genotype

tag: treatment

value: control


title: COVID_96_51y_male_NonICU

description:
C96
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: associated controlled-vocabulary terms

tag: cell type

tag: tissue of origin

value: whole blood

tag: sample type


title: KO_cisplatin_rep2


title: 2018-424/8

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

description:
8-2018-424-8_S26
8.bam

data_processing:
Adaptor removing and quality trimming was conducted using the TrimGalore 0.4.2 wrapper tool and default parameters. Library quality was investigated using fastQC imbedded in the TrimGalore wrapper (https://github.com/FelixKrueger/TrimGalore)
Mapping was counducted using HiSat2 software.
Read counts were generated using FeatureCounts
Read counst were filtered and normalized using the DESeq2 software.
Genome_build: Gene annotation files and assembly were downloaded from illumina Igenome (http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html?langsel=/no/) containing the mus musculus Ensembl release 66 (NCBIM37).
Supplementary_files_format_and_content: Normalized read counts (FPKM) from all samples

extract_protocol:
Total RNA was extracted and treated BioRobot® EZ1 and RNA Tissue Mini Kit (Qiagen, Hilden, Germany). RNA quality and integrity were validated using a NanoDrop ND-1000 UV–vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA) and Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, USA) respectively.
DNA libraries were prepared as using 90 ng total RNA input to the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturers instrucitons. For multiplexing, standard Illumina adaptors were used.
One library was made for each individual RNA sample. The libraries were sequenced using the NextSeq Illumina platform according to manufacturer instructions, generating single end 75bp read libraries with an average library size of 25 ± 6 million reads.

tag: strain

value: BALB/c

value: LD

tag: tissue

value: hippocampus


title: KO_Control_rep1

value: BMAL1 -/-


title: Cultured cortical neurons, D3 (array)

type: genomic

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

institute: China Medical University

description: SAMPLE 6

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850k Human MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Cultured cortical neuron

label_protocol: Standard Illumina Protocol

growth_protocol: Lentivirus Infected cells were cultured in Neurobasal+2%B27 for 4 days

extract_protocol: The genomic DNA of each sample was extracted from the lentivirus infected, early differentiated HNPs with ZsGreen (n=3) or DNMT3L (n=3) overexpression. The DNA was isolated and cleaned by following the manufacturer’s protocol with DNA purification kit (Qiagen, MD, USA).

treatment_protocol: 1st passage of human neuroprogenitors were infected with letivirus carrying ZsGreen or DNMT3L gene

value: neurons differentiated from 1st passage of neuroprogenitors from fetal frontal cortex

tag: developmental stage

value: 21 week of gestational age

tag: karyotype

value: 1st passage neuroprogenitors infected with lentivirus carrying DNMT3L-ZsGreen gene and cultured for 4 days

value: DNMT3L overexpression


title: COVID_94_24y_female_NonICU

description:
C94
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

value: female

tag: icu

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: fibrinogen

tag: sofa

value: primary cells


title: Cultured cortical neurons, Z3 (array)

description: SAMPLE 3

tag: cell type

tag: treatment

value: 1st passage neuroprogenitors infected with lentivirus carrying ZsGreen gene and cultured for 4 days

tag: genotype

value: CON


title: COVID_93_81y_female_ICU

description:
C93
genes.ec.tsv
genes.tpm.tsv

value: yes

tag: apacheii

tag: charlson score

tag: mechanical ventilation

value: no

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: COVID_92_82y_female_ICU

description:
C92
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

value: leukocyte


title: 2018-424/7

description:
7-2018-424-7_S23
7.bam

tag: strain

value: male

tag: treatment

value: Ctr

tag: tissue


title: COVID_90_86y_female_NonICU

description:
C90
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

value: unknown

tag: fibrinogen

tag: sofa

tag: cell type

value: whole blood


title: WT_tunicamycin_rep2

tag: cell line

tag: passage

tag: genotype

value: Wild type

value: tunicamycin


title: Cultured cortical neurons, Z1 (array)

description: SAMPLE 1

value: neurons differentiated from 1st passage of neuroprogenitors from fetal frontal cortex

tag: developmental stage

tag: karyotype


title: 2018-424/5

description:
5-2018-424-5_S16
5.bam

value: BALB/c

tag: Sex

value: hippocampus


title: COVID_91_29y_female_NonICU

description:
C91
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: 2018-424/6

description:
6-2018-424-6_S20
6.bam

tag: strain

tag: treatment

tag: tissue


title: COVID_87_61y_male_ICU

description:
C87
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: fibrinogen

tag: sofa

tag: cell type


title: COVID_89_90y_female_NonICU

description:
C89
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)


title: WT_doxorubicin_rep2

tag: cell line

tag: passage

tag: genotype

tag: treatment

value: doxorubicin


title: Cultured cortical neurons, D1 (array)

description: SAMPLE 4

tag: developmental stage

value: 21 week of gestational age

tag: karyotype

value: 1st passage neuroprogenitors infected with lentivirus carrying DNMT3L-ZsGreen gene and cultured for 4 days

value: DNMT3L overexpression


title: WT_doxorubicin_rep1


title: WT_tunicamycin_rep1


title: COVID_86_52y_female_NonICU

description:
C86
genes.ec.tsv
genes.tpm.tsv

value: female

tag: apacheii

tag: charlson score

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: fibrinogen

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type

value: primary cells


title: 2018-424/4

description:
4-2018-424-4_S12
4.bam

tag: strain

tag: Sex

tag: tissue


title: NONCOVID_01_54y_female_NonICU

description:
NC1
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

value: no

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: lactate (mmol/l)

tag: sofa

tag: cell type


title: COVID_84_75y_female_NonICU

description:
C84
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: fibrinogen

value: leukocyte


title: COVID_85_62y_male_ICU

description:
C85
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: Sex

value: male

value: yes

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: 2018-424/3

description:
3-2018-424-3_S8
3.bam

tag: strain

tag: treatment

value: HD

tag: tissue


title: Cultured cortical neurons, D2 (array)

description: SAMPLE 5

tag: developmental stage

tag: karyotype

tag: genotype


title: COVID_83_85y_female_NonICU

description:
C83
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: icu

tag: apacheii

value: unknown

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: lactate (mmol/l)

tag: sofa

tag: cell type

value: whole blood


title: COVID_82_67y_male_NonICU

description:
C82
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: Sex

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: fibrinogen

tag: associated controlled-vocabulary terms

tag: tissue of origin

tag: sample type


title: 2018-424/30

description:
30-2018-424-30_S19
30.bam

tag: strain

tag: treatment

tag: tissue


title: COVID_80_71y_male_ICU

description:
C80
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)


title: WT_cisplatin_rep1

tag: cell line

tag: passage

tag: genotype

value: Wild type

value: cisplatin


title: WT_cisplatin_rep2


title: 2018-424/29

description:
29-2018-424-29_S15
29.bam

value: BALB/c

tag: Sex


title: COVID_77_55y_female_ICU

description:
C77
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

tag: tissue of origin


title: WT_Control_rep2

tag: treatment

value: control


title: 2018-424/28

description:
28-2018-424-28_S11
28.bam

tag: strain

tag: tissue

value: hippocampus


title: COVID_74_55y_female_ICU

description:
C74
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: sample type


title: COVID_75_55y_male_NonICU

description:
C75
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: Sex

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen


title: WT_Control_rep1

tag: cell line

tag: passage

tag: genotype

tag: treatment


title: COVID_76_73y_female_ICU

description:
C76
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

tag: tissue of origin


title: adult mouse kidney scRNA-seq sample 1

description:
P0_adult_counts.rds
P0_adult_clusters.txt
P0_adult_umap.txt
P0_adult_pheno.txt

source_name: adult mouse kidney

extract_protocol:
Adult mouse was decapitated with surgical scissors, 2 kidneys were harvested and minced into 1 mm3 pieces and incubated with digestion solution containing Enzyme D, Enzyme R and Enzyme A from Multi Tissue Dissociation Kit (Miltenyi, 130-110-201) at 37 °C for 15 min with agitation. Reaction was deactivated by adding 10% FBS, then solution was passed through a 40 μm cell strainer. After centrifugation at 1,000 RPM for 5 min, cell pellet was incubated with 500 μL of RBC lysis buffer on ice for 3 min. We centrifuged the cells at 1,000 RPM for 5 min at 4 °C and resuspended the cells in the buffer for further steps. Cell number and viability were analyzed using Countess AutoCounter (Invitrogen, C10227). The cell concentration was 2.2 million cells/mL with 92% viability. 10,000 cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Single Cell B Chip (10X Genomics, PN-120262) and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, CG000183).
The library was generated using the Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics, PN-1000092) and Chromium i7 Multiplex Kit (10X Genomics, PN-120262) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) for qualitative analysis. Quantification analysis was performed by Illumina Library Quantification Kit (KAPA Biosystems, KK4824).

tag: developmental stages

value: adult


title: 2018-424/27

description:
27-2018-424-27_S7
27.bam

tag: strain

tag: Sex

tag: tissue


title: COVID_73_82y_male_NonICU

description:
C73
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sample type


title: COVID_72_50y_female_NonICU

description:
C72
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type


title: COVID_71_37y_male_ICU

description:
C71
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: Sex

tag: ventilator-free days

tag: dm

tag: tissue of origin


title: 2018-424/26

description:
26-2018-424-26_S3
26.bam

tag: strain

tag: treatment

value: LD

tag: tissue


title: COVID_95_49y_male_NonICU

description:
C95
genes.ec.tsv
genes.tpm.tsv

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sample type


title: P0 mouse kidney scRNA-seq sample 1

source_name: P0 mouse kidney

extract_protocol:
1-day-old mouse neonate was decapitated with surgical scissors, 2 kidneys were harvested and minced into 1 mm3 pieces and incubated with digestion solution containing Enzyme D, Enzyme R and Enzyme A from Multi Tissue Dissociation Kit (Miltenyi, 130-110-201) at 37 °C for 15 min with agitation. Reaction was deactivated by adding 10% FBS, then solution was passed through a 40 μm cell strainer. After centrifugation at 1,000 RPM for 5 min, cell pellet was incubated with 500 μL of RBC lysis buffer on ice for 3 min. We centrifuged the cells at 1,000 RPM for 5 min at 4 °C and resuspended the cells in the buffer for further steps. Cell number and viability were analyzed using Countess AutoCounter (Invitrogen, C10227). The cell concentration was 2.2 million cells/mL with 92% viability. 10,000 cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Single Cell B Chip (10X Genomics, PN-120262) and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, CG000183).
The library was generated using the Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics, PN-1000092) and Chromium i7 Multiplex Kit (10X Genomics, PN-120262) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) for qualitative analysis. Quantification analysis was performed by Illumina Library Quantification Kit (KAPA Biosystems, KK4824).

tag: developmental stages


title: 8-week mouse kidney snATAC-seq sample 2

description:
snATAC_cell_by_peak_matrix.txt
snATAC_peak_list.csv
snATAC_UMAP_coordinates.csv
snATAC_metadata.csv

source_name: 8-week mouse kidney

extract_protocol:
3-week-old and 8-week-old mice were euthanized and perfused with chilled 1x PBS via left ventricle. Kidneys (0.25 g) were harvested, minced and lysed in 5 mL lysis buffer (10 mM Tris HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NonidetTM P40 Substitute in nuclease-free water) for 15 min. 1-day-old mice were decapitated with surgical scissors, and both kidneys were harvested. Kidneys were minced and lysed in 2 mL lysis buffer for 15 min. Tissue lysis reaction was then blocked by adding 10 mL 1x PBS into each tube, and solution was passed through a 40 μm cell strainer. Cell debris and cytoplasmic contaminants were removed by Nuclei PURE Prep Nuclei Isolation Kit (Sigma, NUC-201) after centrifugation at 13,000 RPM for 45 min. Nuclei concentration was calculated with Countess AutoCounter (Invitrogen, C10227). Diluted nuclei suspension was loaded and incubated in transposition mix from Chromium Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000110) by targeting 10,000 nuclei recovery. GEMs were then captured on the Chromium Chip E (10x Genomics, PN-1000082) in the Chromium Controller according to the manufacturer’s protocol (10X Genomics, CG000168).
Libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit and Chromium i7 Multiplex Kit N (10X Genomics, PN-1000084) according to the manufacturer’s manual. Quality control for constructed library was perform by Agilent Bioanalyzer High Sensitivity DNA kit.


title: COVID_70_81y_male_NonICU

description:
C70
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type


title: 2018-424/25

description:
25-2018-424-25_S28
25.bam

tag: strain

tag: Sex

tag: treatment

value: Ctr

tag: tissue