title: Non-injected SOD1 mutant rep6

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.9.3).
Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Reads were aligned against Mus musculus.GRCm38.86 genome using STAR (v. 2.5.2b).
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1).
Genome_build: Mus musculus.GRCm38.86
Supplementary_files_format_and_content: *.processed_counts.txt: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package.

source_name: motoneurons

extract_protocol:
Total RNA was extracted from a pool of 500 MN per mouse with the microRNeasy kit according to manufacturer’s instruction (Qiagen).
The SMARTer™ Ultra Low RNA kit from Clontech was used for reverse transcription and cDNA amplification according to manufacturer’s instructions, starting with 5 to 6 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina.

treatment_protocol: Mice were sacrificed at 65 days by intra-peritoneal injection of pentobarbital (Streuli Pharma, Uznach, Switzerland). The lumbar part of the spinal cord with the vertebrae was directly embedded in OCT and frozen at -80°C. Fourteen µm thick sections were cut on a cryostat and stained with a 1% cresyl violet solution to reveal MN in lumbar spinal cord sections and guide laser-capture microdissection (PALM microscope, 20X, Zeiss).

tag: genotype/variation

tag: age

value: 65 days

value: Motoneurons

tag: adeno-associated virus injection

value: No

tag: anti-human sod1 mir


title: 202253630017_R05C01

status: Public on Jan 31 2022

type: genomic

city: Ann Arbor

first: Maureen

last: Sartor

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

country: USA

institute: University of Michigan

description:
normal neonatal dried bloodspot sample
Sample passed quality control

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
Processed in R (Bioconductor - Enmix and minfi)
processed data file includes quantile normalized average beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: neontatal bloodspot 58

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen EZ1 DNA Investigator Kit according to standard instructions

tag: infant sex

value: Male

tag: tissue

value: neonatal blood spot

tag: arch id


title: NAFLD Patient 60

type: SRA

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

library_source: transcriptomic

data_processing:
FASTQ files were processed by HTG EdgeSeq parser software
Parser produces text file of counts per target miRNA
Genome_build: NA - set of 2083 targets used, plus 5 negative controls, 1 positive control and 13 housekeeping genes - total of 2102 observations per sample
Supplementary_files_format_and_content: txt files with target-level counts

molecule: total RNA

source_name: serum

extract_protocol:
Samples were lysed with a 1:1 ratio of HTG biofluids lysis buffer, according to manufacturer's instructions.
Lysates input into nuclease protection assays run on the HTG EdgeSeq processor. Sequence adapters were added to the samples in a 16-cycle PCR reaction. PCR products were purified using AMPure XP beads (Beckman Coulter, High Wycombe, UK).

value: peripheral blood

tag: disease state

value: Chronic Liver Disease (NAFLD)

tag: nas

tag: saf activity

tag: fibrosis stage

tag: disease group

value: NAFL


title: Olfr73 OSN replicate 2

city: Worcester

first: I-Hao

last: Wang

state: MA

address: 370 Sunderland Rd, Unit D24

department: PMM

institute: UMMS

data_processing:
The sequencing reads were processed using the DolphinNext RNAseq pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=732). The default settings were employed except STAR v2.6.1 and RSEM v1.3.1 were used for alignment and quantification, respectively
Differential analysis were conducted in DEseq2. The significant genes were deducted by computing Wald tests with corrected p < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrix/ TPM matrix was generated by RSEM

molecule: polyA RNA

organism: Mus musculus

source_name: Olfr73 expressing olfactory sensory neurons

extract_protocol:
RNA was extracted with an RNeasy micro kit (QIAGEN).
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s guidelines with one alteration, which was to increase the insert length to ~300 base pair

treatment_protocol: Mice were euthanized according to IACUC protocol, and then main olfactory epithelia were dissected and quickly immersed in ice-cold HBSS (Worthington). Olfactory epithelia were separated from the bone under a dissection microscope and then were minced into small pieces using forceps.  Each epithelium was then washed once with HBSS and resuspended in 2 ml of EBSS containing papain (20 U/mL, Worthington) and DNase I (2000 U/mL, Worthington). After 40 minutes of incubation with gentle agitation at 37°C, the suspension was washed with 5 ml of PBS + 0.02% BSA twice and passed through a 30 μm cell strainer (Miltenyi Biotec). The cell suspension was stained with 3 μM of DAPI and subjected to FACS to isolate the GFP/mCherry high and DAPI low population of cells

value: mature olfactory sensory neuron

tag: genotype


title: NAFLD Patient 59


title: Muscle_total.Rep_1

city: BOSTON

first: Laura

middle: Elisabeth

last: Wester

state: Massachusetts

address: 677 Huntington Ave

institute: Harvard T.H. Chan School of Public

description:
Total RNA for normalization Rep. 1
Muscle.deseq2_results.tsv

data_processing:
Raw reads were mapped with kallisto version 0.46.1 to reference genome ce11 ENSEMBL build 103 (kallisto quant)
Transcript Abundances were quantified in the same step (kallisto quant)
Differential gene expression was calculated using DESeq2 version 1.30.1 in R version 4.0.4 (model:  ~Library + Replicate )
kept genes with at least 10 reads over all samples
counts(dds, normalized = TRUE)
Genome_build: ce11, ensembl build 103
Supplementary_files_format_and_content: tab separated files with normalized counts and differential gene expression

organism: Caenorhabditis elegans

source_name: Whole tissue lysate

growth_protocol: All C. elegans strains were generated and maintained at 20 °C on nematode growth medium (NGM) agar plates, seeded with the Escherichia coli (E. coli) strain OP50-1 (CGC). After CRISPR engineering, all new alleles were outcrossed against the wildtype Bristol N2 strain.  Before  collections for RNAseq, all strains were bleached to E. coli strain OP50 and grown to day 1 of adulthood.

extract_protocol:
Polysome profiling: For the analysis of mRNA translation via polysome profiling based on Großhans and Ding (2009), synchronized gravid day 1 adults were grown on NGM plated seeded with OP50 (Ding and Großhans, 2009). Per genotype and replicate, about 12000 worms were harvested and washed twice with M9, once with M9 supplemented with 1 mM cycloheximide (Sigma) and once with lysis buffer (20 mM Tris pH 8.5, 140 mM KCl, 1.5 mM MgCl2, 0.5 % Nonidet P40, 1 mM DTT, 1 mM cycloheximide). Worms were pelleted and resuspended in 350 μL cold lysis buffer, supplemented with 1 % sodiumdeoxycholate (DOC, Sigma). Resuspended worms were lysed using a chilled Dounce homogenizer. Ribonuclease inhibitor RNasin (Promega) was added to samples used for RNA sequencing at a concentration of 0,4 U/μL. Samples were then mixed and incubated on ice for 30 min, followed by a centrifugation step (12000 g, 10 min, 4 °C) for clearance. The pellet was discarded and the RNA concentration of the supernatant was estimated by absorbance measurement at 260 nm. At least 50 µl of lysate were taken aside as corresponding total RNA at this point, diluted in an equal amount of TRI reagent (Zymo Research) and frozen at -80 °C. To prepare sucrose gradients, 15 % (w/v) and 60 % (w/v) sucrose solutions were prepared in basic lysis buffer (20 mM Tris pH 8.5, 140 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM cycloheximide). Linear sucrose gradients were produced using a Gradient Master (Biocomp). Equivalent amounts of sample (around 400 μg RNA) were loaded onto the gradient and centrifuged at 39000 g for 3 h at 4 °C, using an Optima L-100 XP Ultracentrifuge (Beckman Coulter) and the SW41Ti rotor. To analyze the sample on the gradient during fractionation, absorbance at 254 nm was measured and recorded (Econo UV monitor EM-1, Biorad), using the Gradient Profiler software (version 2.07). Gradient fractionation was performed from the top down using a Piston Gradient Fractionator (Biocomp) and a fraction collector (Model 2110, Biorad). Gradients were fractionated in 20 fractions of equal volume. In an initial experiment, the ribosomal fractions were validated by analyzing RNA from each fraction via agarose gel electrophoresis. The 18 S and 28 S rRNA signals were used as indicators for the 40 S ribosomal subunit, the 60 S ribosomal subunit and fully assembled ribosomes. For more precise analysis of ribosomal fractions, they were collected by hand according to their absorbance profile.  For RNA sequencing experiments, one single fraction comprising all polysomal fractions (corresponding to Figure 1, polysome profiling sequencing A) or one fraction comprising the 60 S ribosomes, the 80 S ribosomes and polysomes (corresponding to Figure 2 and Sup. Figure 2, polysome profiling sequencing B) was collected per sample. RNA extraction from total lysates and polysome fractions was performed using the Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer´s recommendations.
SKI TRIP experiments: SKI TRIP experiments were optimized based on previous TRAP models (McLachlan and Flavell, 2019; Sanz et al., 2009). Per SKI TRIP sample, 50 µl Protein G coated dynabeads (ThermoFisher) were washed with 1 ml PBS and incubated with 1 ml PBS and 0.1 μg monoclonal anti- FLAG antibody (Sigma F1804) per μL of dynabeads at 4 °C and constant rotation overnight. Per FLAG IP, 30000 synchronized day 1 worms were collected in M9 buffer, washed two times in M9 and one final time in M9 including 1 mM cycloheximide (Sigma). Samples were then washed with lysis buffer prepared in nuclease free water (10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) pH 7.4, 150 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 1 mM cycloheximide, EDTA free Protease Inhibitor). Worms were pelleted at 2000 g for 2 min and the supernatant was discarded. The residual worm pellet (about 500 μL) was shock frozen by dropping it into liquid nitrogen in fractions of approximately 20 μL using a P200 pipette. The resulting frozen worm pearls were carefully lysed using the TissueLyserII (Qiagen) or the CryoMill (Retsch) for twice 1 min at 30 Hz, using metal beads of 5 mm diameter. Keeping all parts and the samples RNase-free and frozen using dry ice and liquid nitrogen at all times was crucial. Lysed worm powder was thawed on ice in a final volume of 3.75 ml lysis buffer including 0.5 % v/v NP-40 (Sigma), 0.4 U/μL RNasin (Promega), 10 mM ribonucleoside vanadyl complex (RVC by NEB), 33 mM 1,2-diheptanoylsn-glycero-3-phosphocholine (DHPC by Merck) and 1 % w/v sodium deoxycholate (Sigma). It is crucial to add the mentioned lysis buffer in a volume to reach approximately 8 worms/μL, taking the starting volume of the ~500 µl worm pellet into account. In case of varying worm or pellet amounts, the volume of added lysis buffer should be adjusted in this step. Samples were incubated for 30 min on ice. After centrifugation at 12000 g for 10 min at 4 °C, the supernatant was transferred to new tubes (kept on ice at all times) and the pellet was discarded. As corresponding total RNA sample, 100 μL of supernatant was mixed with 100 μL of RLT buffer (Qiagen RNeasy Kit) including 1 % v/v ß-mercaptoethanol. This total RNA sample was then vortexed, incubated for 10 min at room temperature and stored at -80 °C. The remaining supernatant was pre-cleared with washed 10 μL protein G coated Dynabeads (washed once with low-KCl wash buffer: 10 mM HEPES pH 7.4, 150 mM KCl, 5 mM MgCl2, 1 % v/v NP-40) without coupled antibody for at least 1 h. Samples were then incubated with washed FLAG-antibody-coupled beads (washed once with low-KCl wash buffer) for at least 2 h at 4 °C and constant rotation. Beads were washed four times with high-KCl wash buffer (10 mM HEPES pH 7.4, 350 mM KCl, 5 mM MgCl2, 1 % v/v NP-40, 0.04 U/μL RNasin).  For RNA elution, the beads were incubated in 350 μL of RLT buffer (Qiagen RNeasy Kit) including 1 % v/v ß-mercaptoethanol for 10 min at room temperature. The eluate was separated from the beads and RNA purification was performed using the Qiagen RNeasy Kit following the manufacturer’s protocol, analyzed using Agilent Technologies 2200 TapeStation System and further processed in RNA sequencing experiments.
For sequencing of RNA obtained from polysome profiling and FLAG IP samples, RNA was eluted and purified as described above in three replicates per experiment. RNA sequencing was performed at the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute (Boston, USA). All RNA samples were processed with a Kapa mRNA library preparation using a starting amount of 200 ng RNA per sample. The RNA libraries were sequenced on an Illumina NoveSeq with the following parameters: at least 20 M reads, 50 bp paired-end sequencing for sample batch AL7663 and 150 bp paired end sequencing for sample batches AL8842 and AL9212.

treatment_protocol: No special treatments.

tag: strain

tag: promotor driving flag

value: All tissues


title: 203490640037_R02C01

source_name: neontatal bloodspot 53


title: Non-injected SOD1 mutant rep5

country: Switzerland

tag: cell type


title: 203516060078_R08C01

source_name: neontatal bloodspot 55

value: Female


title: 203009240151_R02C01

description:
normal neonatal dried bloodspot sample
Sample failed quality control. No processed data provided.

source_name: neontatal bloodspot 52


title: 203009240151_R05C01

source_name: neontatal bloodspot 51


title: Intestine_total.Rep_3

description:
Total RNA for normalization Rep. 3
Intestine.deseq2_results.tsv


title: Non-injected SOD1 mutant rep2


title: Intestine_total.Rep_2

description:
Total RNA for normalization Rep.2
Intestine.deseq2_results.tsv


title: AAV-miR ctrl rep6

value: Yes


title: Intestine_total.Rep_1

description:
Total RNA for normalization Rep. 1
Intestine.deseq2_results.tsv


title: Intestine_IP.Rep_3

description:
RNA from SKI TRIP experiment Rep. 3
Intestine.deseq2_results.tsv

source_name: SKI TRIP from intestine

value: Intestine

tag: fraction

value: RNA from intestine-specific ribosome IP


title: AAV-miR ctrl rep4

tag: genotype/variation


title: AAV-miR ctrl rep3

tag: age


title: 202259490093_R04C01

source_name: neontatal bloodspot 49


title: AAV-miR ctrl rep5

tag: adeno-associated virus injection


title: 203009240114_R04C01

source_name: neontatal bloodspot 50


title: 203009240114_R06C01

source_name: neontatal bloodspot 48


title: 203516060072_R08C01

source_name: neontatal bloodspot 47


title: NAFLD Patient 58


title: 203483530044_R02C01

source_name: neontatal bloodspot 46


title: NAFLD Patient 52


title: NAFLD Patient 57


title: AAV-miR SOD1 rep4

tag: anti-human sod1 mir


title: NAFLD Patient 56


title: 202298850217_R02C01

source_name: neontatal bloodspot 44

tag: infant sex


title: AAV-miR SOD1 rep3


title: 203806760138_R07C01

source_name: neontatal bloodspot 45

tag: tissue


title: AAV-miR SOD1 rep2

source_name: motoneurons


title: NAFLD Patient 55


title: AAV-miR SOD1 rep1


title: NAFLD Patient 53


title: Intestine_IP.Rep_2

description:
RNA from SKI TRIP experiment Rep. 2
Intestine.deseq2_results.tsv


title: Intestine_IP.Rep_1

description:
RNA from SKI TRIP experiment Rep. 1
Intestine.deseq2_results.tsv


title: Non-injected SOD1 mutant rep3


title: NAFLD Patient 49


title: NAFLD Patient 54


title: AAV-miR ctrl rep1


title: NAFLD Patient 48


title: B16-F10 cells, sDRIP-seq carm1-/- rep2

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

library_source: genomic

data_processing:
Library strategy: sDRIP-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with tophat2 v2.1.0 (RNA-seq) or bowtie2 v2.2.6 (sDRIP-seq).
HTseq-count v0.11.2 was then used to count the total number of reads at exon of genes (RNA-seq) or whole gene and gene binned by 1kb (sDRIP-seq).
Gencode vM1 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions with adj.pvalue of at least 0.05 and log2FC of at least +/- 1
Genome_build: mm9
Supplementary_files_format_and_content: Both sDRIP-seq and RNA-seq wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).

source_name: B16-F10 cells, sDRIP-seq carm1-/-

growth_protocol: B16-F10 cells were obtained from ATCC and grown in high-glucose Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin / streptomycin. Cells were seeded 1-2 days prior to experiments and were grown to 40-60% confluency

extract_protocol:
RNA-seq: Total RNA was extracted using Trizol and poly(A) selected using poly(T) beads.
sDRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
RNA-seq: Standard paired-end TruSeq protocol.
sDRIP-seq: Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

treatment_protocol: Extracted DNA was subjected to mock or enzymatic treatments (RNase H1, RNase III, RNase T1, or RNase T1+RNase III) prior to immunoprecipitation with the S9.6 antibody.

tag: cell line

value: skin melanoma cells


title: B16-F10 cells, sDRIP-seq carm1-/- rep1


title: 202298850217_R06C01

source_name: neontatal bloodspot 40

tag: arch id


title: 203009240114_R05C01

source_name: neontatal bloodspot 41


title: NAFLD Patient 47

source_name: serum

tag: disease state

tag: nas


title: 203009240114_R08C01

source_name: neontatal bloodspot 43


title: NAFLD Patient 51

tag: saf activity

tag: fibrosis stage


title: 203806760138_R08C01

source_name: neontatal bloodspot 39


title: NAFLD Patient 46

tag: disease group


title: B16-F10 cells, sDRIP-seq wild-type rep2

source_name: B16-F10 cells, sDRIP-seq wild-type

tag: genotype

value: wild-type


title: NAFLD Patient 50


title: NAFLD Patient 5


title: 202253630017_R07C01

source_name: neontatal bloodspot 38


title: 203009240114_R03C01

source_name: neontatal bloodspot 37


title: NAFLD Patient 45


title: BRM KO CM

city: San Francisco

first: Benoit

last: Bruneau

address: 1650 Owens Street

institute: Gladstone Institute of Cardiovascular Disease

data_processing:
CellRanger followed by Seurat (Satija et. Al., 2015)
Genome_build: mm9
Supplementary_files_format_and_content: csv

source_name: cardiac myocyte

growth_protocol: directed cardiac differetiation protocl (Kattman et., 2011)

extract_protocol:
10x genomics manufacturer protocol
10X genomics single cell RNA-Seq

value: ES cell derived cardiac progenitors

value: BRG1 3XFLAG; BRM KO

tag: passage


title: 202259490093_R05C01

source_name: neontatal bloodspot 42


title: B16-F10 cells, sDRIP-seq wild-type rep1

tag: cell type


title: dairy goat mammary gland_M4

city: Hangzhou

first: Jie

last: Cai

address: Yuhangtang Rd

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were calculated.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include Reads values for each Sample.

organism: Capra hircus

source_name: dairy goat mammary gland

extract_protocol:
Mammary gland were biopsied, moved into liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mammary gland

tag: developmental stage

value: lactation

tag: Sex

value: female

tag: treatment

value: middle dose of glucose


title: dairy goat mammary gland_M2


title: NAFLD Patient 44

value: peripheral blood


title: dairy goat mammary gland_L4

value: low dose of glucose


title: Brm KO MES

source_name: mesoderm

value: ES cell derived mesoderm


title: dairy goat mammary gland_M1


title: 202262730027_R08C01

source_name: neontatal bloodspot 35

value: Male

value: neonatal blood spot


title: WT CM

value: BRG1 3XFLAG


title: WT MES


title: NAFLD Patient 42

value: Chronic Liver Disease (NAFLD)


title: NAFLD Patient 43


title: dairy goat mammary gland_L3


title: 203009240114_R07C01

source_name: neontatal bloodspot 34


title: 203490640037_R08C01

source_name: neontatal bloodspot 33


title: NAFLD Patient 40

value: NAFL


title: dairy goat mammary gland_L2


title: NAFLD Patient 41


title: dairy goat mammary gland_L1


title: EML1-heKO

city: Mannheim

first: Philipp

last: Koch

state: Deutschland

country: Germany

institute: Hector Institute for Translational Brain Research

data_processing:
demultiplexing and feature counting with cellranger count 3.0.1
Genome_build: refdata-cellranger-GRCh38-3.0.0
Supplementary_files_format_and_content: matrix.mtx.gz: Each element of the feature-barcode matrix is the number of UMIs associated with a feature (row) and a barcode (column); features.tsv.gz: Features correspond to row indices. For each feature, its feature ID and name are stored in the first and second column of the (unzipped) features.tsv.gz file, respectively. The third column identifies the type of feature; barcodes.tsv: Barcode sequences correspond to column indices

source_name: Human iPSC-derived cerebral organoids

growth_protocol: Cerebral organoids were generated as described with slight adaptations (Iefremova et al., 2017; Krefft et al., 2018). In brief, U-bottom 96-well plates were coated with 5% Pluronic F-127 (Sigma Aldrich) in phosphate buffered saline (PBS) for 15 minutes to create low-attachment wells. iPS cell colonies were dissociated using TrypLE Express (Thermo Fisher Scientific) and 6000 cells were plated per low-attachment well in 150 µl E8 medium supplemented with 50 µM Y-27632. Medium was changed every other day. At day 5 medium was changed to neural induction medium (Table 4). Medium was changed every other day. On day 9-11, when translucent neural ectoderm was visible, organoids were embedded in a 3:2 ratio of GT to neural induction medium and further cultured in Pluronic F-127 coated 6 cm dishes in neural differentiation medium (Table 5) under continuous agitation at 70 rpm on an orbital shaker (Infors Celltron HD) with a medium change every 3 to 4 days. When indicated organoids were exposed to 100 nM Verteporfin (Sigma Aldrich) or 300 nM Fluvastatin (Sigma Aldrich) for 96 hours from day 16 onwards with daily medium changes.

extract_protocol:
Organoids at day 33±2 were microdissected to enrich for cortical areas. The dissected tissue was dissociated by incubating in papain (Sigma Aldrich) solution containing papain-buffer (1 mM L-cysteine, 0,5 mM EDTA in Earle's Balanced Salt Solution), 20 units papain and 10 µg/ml of DNase (Sigma Aldrich) for 20 minutes at 37 °C. Following incubation excessive papain solution was removed, 3 ml organoid differentiation medium was added and samples were mechanically dissociated using wide-bore 1000 µl pipette tips coated with 1 % bovine serum albumin (BSA) in PBS. The cell suspension was centrifuged at 400g for 4 minutes at 4°C. The supernatant was removed, the cell pellet was resuspended in 1 ml ice cold PBS + 0,04 % BSA and filtered through a 30 µm cell strainer. Counting and viability were assessed using Trypan blue staining (Countess automatic cell counter, Thermo Fisher Scientific).
Single cell library preparation was performed using the 10x Genomics Chromium platform according to the 10x Genomics Chromium single cell 3´ library & gel bead kit v2 chemistry user guide (10x Genomics).

treatment_protocol: CRIPSR/CAS9 mediated, heterozygous knock-out of the gene EML1

value: iPSC-derived cerebral organoids

value: heterozygous knock-out of EML1

tag: age

tag: cell types

value: Radial glia, radial glia transitioning to basal radial glia, intermediate progenitors, radial glia transitioning to neurons, young neurons


title: Control

value: healthy/normal


title: 202298850217_R04C01

source_name: neontatal bloodspot 36

tag: infant sex


title: dairy goat mammary gland_M3

tag: tissue


title: NAFLD Patient 4


title: NAFLD Patient 39


title: dairy goat mammary gland_H4

value: high dose of glucose


title: 203483530045_R06C01

source_name: neontatal bloodspot 31


title: 203009240092_R02C01

source_name: neontatal bloodspot 30

value: Female


title: dairy goat mammary gland_H3

value: Mammary gland

value: lactation


title: NAFLD Patient 38

source_name: serum


title: NeuroA_IP.Rep_2

description:
RNA from SKI TRIP experiment Rep. 2
NeuroA.deseq2_results.tsv

source_name: SKI TRIP from neurons (A)

tag: strain

tag: promotor driving flag

value: Neurons

tag: fraction

value: RNA from neuron-specific ribosome IP


title: dairy goat mammary gland_H2

value: female


title: 203009240151_R01C01

source_name: neontatal bloodspot 29

tag: arch id


title: 202253630092_R02C01

source_name: neontatal bloodspot 28


title: NAFLD Patient 36

value: peripheral blood

tag: disease state

tag: nas

tag: saf activity


title: Al_cont_rep3

city: New Haven

first: Tomokazu

middle: S

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

institute: Neurology, Yale School of Medicine

description:
rep3
Sample_97

data_processing:
After sequencing, adapter sequences and poor-quality bases (quality score < 3) were trimmed with Trimmomatic. Remaining bases were trimmed if their average quality score in a 4 bp sliding window fell below 5. FastQC was used to obtain quality control metrics before and after trimming. Remaining reads were aligned to the GRCh38 human genome with STAR 2.5.244. We used Picard to remove optical duplicates and to compile alignment summary statistics and RNA-seq summary statistics. After alignment, reads were quantitated to gene level with RSEM45 using the Ensembl annotation. Normalized Fragments Per Kilobase Million (FPKM) expression values
Genome_build: hg38
Supplementary_files_format_and_content: txt

source_name: primary T cells

growth_protocol: Naïve CD4+ T cells (CD4+/CD25neg/CD127+/CD45ROneg/CD45RA+) were sorted on a FACSAria (BD Biosciences). After a second rounds of LV transduction, cells were washed and plated into 96-well round-bottom plates pre-coated anti-human CD3 (2 mg/ml) with soluble anti-human CD28 (1 mg/ml), in the presence or absence of human IFN-b (500 U/ml). Cells were cultured in RPMI 1640 medium supplemented with 5 % Human serum, 2 nM L-glutamine, 5 mM HEPES, and 100 U/ml penicillin, 100 g/ml streptomycin, 0.5 mM sodium pyruvate, 0.05 mM nonessential amino acids, and 5% human AB serum (Gemini Bio-Products).

extract_protocol:
Total RNA was extracted from sorted GFP positive cells using RNeasy Micro Kit (QIAGEN), according to the manufacturer’s instructions.
cDNAs were generated from isolated RNAs using SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech). Barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina) and sequenced with a 2x100 bp paired-end protocol on the HiSeq 4000 Sequencing System (Illumina).

treatment_protocol: FACS-sorted naïve CD4+ T cells were plated at 50,000 cells/well in round bottom 96 well plate and chilled on ice for 15 min. 25-50 ml of Vpx-VLPs were added to each well and mixed with cold cells for an additional 15 min, then spinfected with high-speed centrifugation (1200 g) for 2 hour at 4 °C. Immediately after centrifugation, cells are cultured overnight at 37 °C. Vpx-transduced cells are spinoculated again with LV particles containing shRNAs or ORF with high-speed centrifugation (1000 g) for 1.5 hours at RT. After 24 hours of incubation, the second transduction of LV particles with shRNAs or ORF were performed as well as the first time spinoculation. After a second LV transduction, cells were washed and plated into 96-well round-bottom plates pre-coated anti-human CD3 (2 mg/ml) with soluble anti-human CD28 (1 mg/ml), in the presence or absence of human IFN-b (500 U/ml). Cells are collected at day 4-6 after anti-CD3/CD28 stimulation and GFP positive cells were sorted by FACSAria.

tag: shRNA

value: Al

tag: ifn-b treatment (cont vs ifnb)

value: cont


title: BCL3_IFNb_rep2

description:
rep2
Sample_96

tag: cell type

value: IFNb


title: Scr_cont_rep3

description:
rep3
Sample_98

value: Scr


title: PRDM1_cont_rep3

description:
rep3
Sample_99


title: dairy goat mammary gland_H1

tag: developmental stage


title: NAFLD Patient 35

value: Chronic Liver Disease (NAFLD)

tag: fibrosis stage

tag: disease group

value: NAFL


title: MAF_IFNb_rep2

description:
rep2
Sample_94

value: MAF


title: 203009240151_R03C01

source_name: neontatal bloodspot 26

value: neonatal blood spot


title: 202259490093_R06C01

source_name: neontatal bloodspot 32

value: Male


title: NAFLD Patient 34


title: 202253630092_R08C01

source_name: neontatal bloodspot 25


title: BATF3_IFNb_rep2

description:
rep2
Sample_92


title: 203009240092_R06C01

source_name: neontatal bloodspot 24


title: BATF_IFNb_rep2

description:
rep2
Sample_91

value: BATF


title: NAFLD Patient 37


title: 203516060072_R05C01

source_name: neontatal bloodspot 23

value: Female


title: NAFLD Patient 32


title: NAFLD Patient 30


title: NAFLD Patient 3


title: 203009240092_R01C01

source_name: neontatal bloodspot 22


title: 203009240092_R08C01

source_name: neontatal bloodspot 20


title: 203806760152_R08C01

source_name: neontatal bloodspot 27


title: HOPX_IFNb_rep2

description:
rep2
Sample_89

value: HOPX


title: ETS2_IFNb_rep2

description:
rep2
Sample_90


title: neg_cont_rep2

description:
rep2
Sample_9

value: neg


title: NAFLD Patient 29


title: BCL3_IFNb_rep1

description:
rep1
Sample_88


title: NAFLD Patient 28


title: NAFLD Patient 31


title: SP140_IFNb_rep1

description:
rep1
Sample_87


title: NAFLD Patient 27


title: 203490640037_R03C01

source_name: neontatal bloodspot 21


title: MAF_IFNb_rep1

description:
rep1
Sample_86


title: NAFLD Patient 26


title: 202253630016_R07C01

source_name: neontatal bloodspot 17


title: 203009240092_R04C01

source_name: neontatal bloodspot 18


title: ID3_IFNb_rep1

description:
rep1
Sample_85


title: NAFLD Patient 25


title: NAFLD Patient 24


title: 202262730027_R06C01

source_name: neontatal bloodspot 19


title: 203516060071_R08C01

source_name: neontatal bloodspot 16


title: BATF3_IFNb_rep1

description:
rep1
Sample_84


title: 202259490093_R02C01

source_name: neontatal bloodspot 15


title: BATF_IFNb_rep1

description:
rep1
Sample_83


title: 203009240114_R02C01

source_name: neontatal bloodspot 14


title: ID3_IFNb_rep2

description:
rep2
Sample_93


title: NAFLD Patient 21

source_name: serum


title: 202253630092_R04C01

source_name: neontatal bloodspot 12


title: SP140_IFNb_rep2

description:
rep2
Sample_95

source_name: primary T cells


title: NAFLD Patient 20


title: Normal_bone_4

city: Oslo

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

hyb_protocol: The samples were processed following the Infinium HD automatic protocol described by Illumina.

scan_protocol: Arrays were scanned using the Illumina iScanBeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Data extraction and initial quality control of the bead summary raw data were performed using GenomeStudioV2011.1and Methylation Module V1.9 (Illumina) with the manifest file “HumanMethylation450_15017482_v.1.2.bpm”.
non-normalized.txt: Intesity of the Unmethylated (A, Red) probe and Intensity of the Methylated (B, Green) probe. Signal A and signal B are produced by two different bead types identifying the methylated and unmethylated versions of the CpG dinucleotide.

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol. 500ng DNA from all samples were bisulfite converted using the EZ DNA MethylationTM Kit (Zymo Research).

growth_protocol: Not relevant

extract_protocol: DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega)

treatment_protocol: Not relevant

value: Tissue from Capital Biosciences, MD, USA


title: BCL3_cont_rep2

description:
rep2
Sample_80


title: 202259490093_R08C01

source_name: neontatal bloodspot 11


title: Normal_bone_3

value: Tissue obtained from amputations of cancer patients at the Norwegian Radium Hospital


title: NAFLD Patient 23


title: 202253630092_R03C01

source_name: neontatal bloodspot 10


title: NAFLD Patient 2


title: NAFLD Patient 33


title: SP140_cont_rep2

description:
rep2
Sample_79


title: Normal_bone_2


title: Osteosarcoma_patient_4

value: Primary tumor

tag: Sex


title: 203483530044_R04C01

source_name: neontatal bloodspot 9


title: MAF_cont_rep2

description:
rep2
Sample_78


title: ETS2_IFNb_rep1

description:
rep1
Sample_82


title: Osteosarcoma_patient_3

value: Primary tumor, not chemotherapy


title: Osteosarcoma_patient_7

value: Primary tumor, chemotherapy treated


title: Osteosarcoma_patient_10


title: Osteosarcoma_patient_5

value: Primary, Chemotherapy treated


title: NAFLD Patient 183

value: peripheral blood


title: NAFLD Patient 182


title: 203009240114_R01C01

source_name: neontatal bloodspot 13


title: 203483530043_R03C01

source_name: neontatal bloodspot 8


title: Osteosarcoma_patient_6


title: Osteosarcoma_patient_8

value: Primary tumor, not chemotherapy treated


title: Normal_bone_1


title: Osteosarcoma_patient_1


title: 202253630092_R05C01

source_name: neontatal bloodspot 7


title: NAFLD Patient 181

value: Chronic Liver Disease (NAFLD)


title: NAFLD Patient 180


title: 202253630016_R02C01

source_name: neontatal bloodspot 5


title: 203490640037_R01C01

source_name: neontatal bloodspot 6


title: ID3_cont_rep2

description:
rep2
Sample_77

value: cont


title: HOPX_cont_rep2

description:
rep2
Sample_73


title: BATF3_cont_rep2

description:
rep2
Sample_76


title: ETS2_cont_rep2

description:
rep2
Sample_74


title: NAFLD Patient 19


title: NAFLD Patient 18

value: NAFL


title: 202253630017_R04C01

source_name: neontatal bloodspot 4

value: neonatal blood spot


title: NAFLD Patient 22


title: 203009240092_R07C01

source_name: neontatal bloodspot 3

value: Male


title: 202253630016_R04C01

source_name: neontatal bloodspot 2


title: NAFLD Patient 179


title: BCL3_cont_rep1

description:
rep1
Sample_72


title: Al_cont_rep1

description:
rep1
Sample_8

value: Al


title: NAFLD Patient 178


title: SP140_cont_rep1

description:
rep1
Sample_71


title: HOPX_IFNb_rep1

description:
rep1
Sample_81

value: IFNb


title: NAFLD Patient 177


title: MAF_cont_rep1

description:
rep1
Sample_70

value: MAF


title: Scr_cont_rep1

description:
rep1
Sample_7

value: Scr


title: NAFLD Patient 175


title: NAFLD Patient 176


title: Osteosarcoma_patient_2

value: Female


title: ID3_cont_rep1

description:
rep1
Sample_69


title: BATF_cont_rep2

description:
rep2
Sample_75

value: BATF


title: NAFLD Patient 174


title: genomic DNA from Case 23 [post-diagnostic]

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

description:
10003885163_R04C02
human whole blood DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

source_name: human whole blood from a patient with hepatocellular carcinoma (HCC) collected after conventional diagnosis

extract_protocol: genomic DNA was extracted and purified from whole blood collected from 24 patients after diagnosis with hepatocellular carcinoma (HCC) and 24 matched healthy individuals without family history of cancer (controls), using the Gentra Puregene Blood Kit (QIAGEN)

tag: case/control

value: Case - post-diagnostic hepatocellular carcinoma (HCC)

value: hepatocellular carcinoma (HCC)

tag: sample type

value: human whole blood


title: BATF3_cont_rep1

description:
rep1
Sample_68


title: NAFLD Patient 173

tag: tissue


title: genomic DNA from Case 22 [post-diagnostic]

description:
10003885163_R02C02
human whole blood DNA


title: Osteosarcoma_patient_9


title: 203806760138_R01C01

source_name: neontatal bloodspot 1

tag: infant sex


title: genomic DNA from Case 21 [post-diagnostic]

description:
10003885163_R06C01
human whole blood DNA


title: genomic DNA from Case 20 [post-diagnostic]

description:
10003885163_R04C01
human whole blood DNA


title: BATF_cont_rep1

description:
rep1
Sample_67


title: HOPX_cont_rep1

description:
rep1
Sample_65

value: HOPX


title: NAFLD Patient 170

value: peripheral blood


title: NAFLD Patient 172


title: ETS2_cont_rep1

description:
rep1
Sample_66


title: STAT3_IFNb_rep2

description:
rep2
Sample_64


title: NAFLD Patient 171


title: genomic DNA from Case 19 [post-diagnostic]

description:
10003885163_R02C01
human whole blood DNA


title: genomic DNA from Case 18 [post-diagnostic]

description:
10003885115_R06C02
human whole blood DNA


title: STAT1_IFNb_rep2

description:
rep2
Sample_63


title: NAFLD Patient 169


title: NAFLD Patient 17


title: genomic DNA from Case 13 [post-diagnostic]

description:
10003885115_R02C01
human whole blood DNA


title: 17-078-GTS

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchips using standard Illumina protocol

label: Cy3 and Cy5

source_name: Brain

extract_protocol: Fresh post-mortem brain tissue from four brain regions was mechanically and enzymatically dissociated in a glucose- potassium-sodium buffer (GKN-BSA; 8.0 g/L NaCl, 0.4 g/L KCl, 1.77 g/L Na2HPO4.2H2O, 0.69 g/L NaH2PO4.H2O, 2.0 g/L D-(1)-glucose, 0.3% bovine serum albumin (BSA, Merck, Darmstadt, Germany); pH 7.4) and supplemented with collagenase Type I (3700 units/mL; Worthington, USA) and DNase I (200 μg/mL; Roche, Switzerland) at 37 °C for 60 min while shaking. As the composition of SVZ is different from the other regions with more white matter, this tissue was digested using an alternative protocol of 0.2% of Trypsin (Invitrogen) for 30 min while shaking. A Percoll (Amersham, Merck, Germany) gradient was generated to separate the microglia from myelin and cellular debris. The middle layer enriched for microglia was washed twice and microglia were pulled down with CD11b-conjugated magnetic beads (Miltenyi Biotec, Germany). Microglia were centrifuged and the cell pellet stored for DNA methylation analyses.

tag: donor

tag: region

value: GTS

tag: age

value: F

tag: diagnosis

value: Control


title: 16-065-THA

value: THA

value: MDD


title: genomic DNA from Case 12 [post-diagnostic]

description:
10003885112_R06C02
human whole blood DNA

tag: disease state


title: 17-078-GFM

value: GFM


title: genomic DNA from Case 17 [post-diagnostic]

description:
10003885115_R04C02
human whole blood DNA


title: genomic DNA from Case 14 [post-diagnostic]

description:
10003885115_R04C01
human whole blood DNA


title: genomic DNA from Case 16 [post-diagnostic]

description:
10003885115_R02C02
human whole blood DNA


title: IRF9_IFNb_rep2

description:
rep2
Sample_62


title: genomic DNA from Case 9 [post-diagnostic]

description:
10003885112_R06C01
human whole blood DNA


title: genomic DNA from Case 11 [post-diagnostic]

description:
10003885112_R04C02
human whole blood DNA


title: genomic DNA from Case 24 [post-diagnostic]

description:
10003885163_R06C02
human whole blood DNA


title: 17-097-SVZ

value: SVZ


title: NAFLD Patient 168

source_name: serum

value: Chronic Liver Disease (NAFLD)

tag: nas

tag: saf activity


title: NAFLD Patient 165


title: genomic DNA from Case 8 [post-diagnostic]

description:
10003885112_R04C01
human whole blood DNA


title: IRF1_IFNb_rep2

description:
rep2
Sample_59

tag: shRNA

tag: ifn-b treatment (cont vs ifnb)

value: IFNb


title: NAFLD Patient 166


title: 17-099-GFM

value: Bipolar


title: PRDM1_cont_rep1

description:
rep1
Sample_6

tag: cell type

value: cont


title: 17-097-GFM


title: IRF4_IFNb_rep2

description:
rep2
Sample_61


title: genomic DNA from Case 10 [post-diagnostic]

description:
10003885112_R02C02
human whole blood DNA


title: 17-099-SVZ


title: NAFLD Patient 167

tag: fibrosis stage


title: IRF2_IFNb_rep2

description:
rep2
Sample_60


title: ARID5b_IFNb_rep2

description:
rep2
Sample_58


title: 17-099-GTS


title: NAFLD Patient 164

tag: disease group


title: NAFLD Patient 163


title: ARID5a_IFNb_rep2

description:
rep2
Sample_57


title: NAFLD Patient 162


title: STAT3_IFNb_rep1

description:
rep1
Sample_56


title: NAFLD Patient 160


title: STAT1_IFNb_rep1

description:
rep1
Sample_55


title: NAFLD Patient 161


title: genomic DNA from Case 3 [post-diagnostic]

description:
10003885108_R06C01
human whole blood DNA


title: IRF9_IFNb_rep1

description:
rep1
Sample_54


title: genomic DNA from Case 6 [post-diagnostic]

description:
10003885108_R06C02
human whole blood DNA


title: NAFLD Patient 16

value: NAFL


title: genomic DNA from Case 5 [post-diagnostic]

description:
10003885108_R04C02
human whole blood DNA

value: Case - post-diagnostic hepatocellular carcinoma (HCC)


title: genomic DNA from Case 7 [post-diagnostic]

description:
10003885112_R02C01
human whole blood DNA

value: hepatocellular carcinoma (HCC)


title: IRF4_IFNb_rep1

description:
rep1
Sample_53


title: genomic DNA from Case 4 [post-diagnostic]

description:
10003885108_R02C02
human whole blood DNA

value: human whole blood


title: NAFLD Patient 159


title: 18-039-SVZ

tag: Sex


title: NAFLD Patient 158


title: IRF2_IFNb_rep1

description:
rep1
Sample_52


title: IRF1_IFNb_rep1

description:
rep1
Sample_51


title: NAFLD Patient 157


title: ARID5b_IFNb_rep1

description:
rep1
Sample_50


title: NAFLD Patient 156


title: 18-064-GFM


title: genomic DNA from Case 15 [post-diagnostic]

description:
10003885115_R06C01
human whole blood DNA

tag: case/control


title: PRDM1L_cont_rep1

description:
rep1
Sample_5


title: genomic DNA from Control 24 [post-diagnostic]

description:
10003885163_R05C02
human whole blood DNA

source_name: human whole blood from healthy individual

value: Control - Healthy

value: normal

tag: sample type


title: 18-064-GTS

value: GTS


title: 18-064-THA

value: F


title: 18-039-GFM


title: 16-112-GFM


title: 18-079-SVZ

value: M


title: NAFLD Patient 154

tag: tissue

value: peripheral blood


title: genomic DNA from Case 1 [post-diagnostic]

description:
10003885108_R02C01
human whole blood DNA


title: genomic DNA from Case 2 [post-diagnostic]

description:
10003885108_R04C01
human whole blood DNA


title: 18-079-GFM


title: 17-005-THA

value: THA

value: Control


title: ARID5a_IFNb_rep1

description:
rep1
Sample_49

source_name: primary T cells


title: 18-079-GTS


title: 16-112-GTS


title: ARID5b_cont_rep2

description:
rep2
Sample_47


title: NAFLD Patient 155


title: NAFLD Patient 152


title: IRF1_cont_rep2

description:
rep2
Sample_46


title: 17-005-SVZ

value: SVZ


title: NAFLD Patient 151

value: Chronic Liver Disease (NAFLD)


title: ARID5a_cont_rep2

description:
rep2
Sample_48


title: 17-005-GTS


title: IRF2_cont_rep2

description:
rep2
Sample_45


title: genomic DNA from Control 18 [post-diagnostic]

description:
10003885115_R05C02
human whole blood DNA


title: genomic DNA from Control 23 [post-diagnostic]

description:
10003885163_R03C02
human whole blood DNA


title: NAFLD Patient 150


title: 17-094-SVZ


title: genomic DNA from Control 20 [post-diagnostic]

description:
10003885163_R03C01
human whole blood DNA


title: 17-094-THA


title: genomic DNA from Control 17 [post-diagnostic]

description:
10003885115_R03C02
human whole blood DNA


title: IRF9_cont_rep2

description:
rep2
Sample_43


title: genomic DNA from Control 21 [post-diagnostic]

description:
10003885163_R05C01
human whole blood DNA


title: STAT1_cont_rep2

description:
rep2
Sample_42


title: genomic DNA from Control 14 [post-diagnostic]

description:
10003885115_R03C01
human whole blood DNA


title: genomic DNA from Control 19 [post-diagnostic]

description:
10003885163_R01C01
human whole blood DNA


title: NAFLD Patient 148


title: NAFLD Patient 15


title: ARID5a_cont_rep1

description:
rep1
Sample_40


title: NAFLD Patient 153


title: NAFLD Patient 149


title: NAFLD Patient 147


title: TCF7L_cont_rep1

description:
rep1
Sample_4


title: 17-004-SVZ

value: MDD


title: genomic DNA from Control 13 [post-diagnostic]

description:
10003885115_R01C01
human whole blood DNA


title: genomic DNA from Control 15 [post-diagnostic]

description:
10003885115_R05C01
human whole blood DNA


title: NAFLD Patient 146


title: ARID5b_cont_rep1

description:
rep1
Sample_39


title: 17-004-GTS


title: 17-094-GFM

value: GFM

value: Bipolar


title: IRF4_cont_rep2

description:
rep2
Sample_44

value: cont


title: 16-067-THA


title: genomic DNA from Control 22 [post-diagnostic]

description:
10003885163_R01C02
human whole blood DNA


title: genomic DNA from Control 12 [post-diagnostic]

description:
10003885112_R05C02
human whole blood DNA


title: NAFLD Patient 144


title: 16-118-SVZ


title: NAFLD Patient 143


title: 16-067-GFM


title: genomic DNA from Control 11 [post-diagnostic]

description:
10003885112_R03C02
human whole blood DNA


title: 16-067-GTS


title: IRF4_cont_rep1

description:
rep1
Sample_36


title: IRF2_cont_rep1

description:
rep1
Sample_37


title: genomic DNA from Control 9 [post-diagnostic]

description:
10003885112_R05C01
human whole blood DNA


title: NAFLD Patient 145


title: NAFLD Patient 142


title: IRF9_cont_rep1

description:
rep1
Sample_35


title: genomic DNA from Control 16 [post-diagnostic]

description:
10003885115_R01C02
human whole blood DNA


title: IRF1_cont_rep1

description:
rep1
Sample_38


title: STAT3_cont_rep1

description:
rep1
Sample_33


title: 16-118-GFM


title: genomic DNA from Control 6 [post-diagnostic]

description:
10003885108_R05C02
human whole blood DNA


title: NAFLD Patient 140


title: genomic DNA from Control 10 [post-diagnostic]

description:
10003885112_R01C02
human whole blood DNA


title: Al_IFNb_rep2

description:
rep2
Sample_32

value: Al

value: IFNb


title: NAFLD Patient 14

value: NAFL


title: genomic DNA from Control 5 [post-diagnostic]

description:
10003885108_R03C02
human whole blood DNA

value: Control - Healthy

value: human whole blood


title: genomic DNA from Control 7 [post-diagnostic]

description:
10003885112_R01C01
human whole blood DNA

value: normal


title: NAFLD Patient 141


title: Scr_IFNb_rep2

description:
rep2
Sample_31

value: Scr


title: NAFLD Patient 139


title: 16-062-THA

value: F

value: Schizophrenis


title: PRDM1_IFNb_rep2

description:
rep2
Sample_30


title: NAFLD Patient 138

value: peripheral blood


title: TCF7_cont_rep1

description:
rep1
Sample_3


title: NAFLD Patient 137


title: genomic DNA from Control 8 [post-diagnostic]

description:
10003885112_R03C01
human whole blood DNA


title: PRDM1L_IFNb_rep2

description:
rep2
Sample_29


title: 16-062-GTS

value: GTS


title: 16-118-GTS

value: M


title: NAFLD Patient 136

value: Chronic Liver Disease (NAFLD)


title: TCF7L_IFNb_rep2

description:
rep2
Sample_28


title: genomic DNA from Control 4 [post-diagnostic]

description:
10003885108_R01C02
human whole blood DNA


title: genomic DNA from Control 1 [post-diagnostic]

description:
10003885108_R01C01
human whole blood DNA


title: NAFLD Patient 135


title: genomic DNA from Control 2 [post-diagnostic]

description:
10003885108_R03C01
human whole blood DNA


title: TCF7_IFNb_rep2

description:
rep2
Sample_27


title: NAFLD Patient 134


title: 16-062-SVZ

value: SVZ


title: KLF5_IFNb_rep2

description:
rep2
Sample_26


title: NAFLD Patient 133


title: 17-003-THA

value: THA

value: Control


title: neg_IFNb_rep2

description:
rep2
Sample_25

value: neg


title: genomic DNA from Control 3 [post-diagnostic]

description:
10003885108_R05C01
human whole blood DNA


title: 16-062-GFM

value: GFM


title: 17-003-GTS


title: NAFLD Patient 132


title: genomic DNA from Control 21

description: human whole blood DNA

extract_protocol: genomic DNA was extracted and purified from whole blood collected from 21 patients prior to diagnosis with hepatocellular carcinoma (HCC) and 21 matched healthy individuals without family history of cancer (controls), using the Gentra Puregene Blood Kit (QIAGEN)


title: 17-124-THA


title: NAFLD Patient 131


title: genomic DNA from Case 20

description: human whole blood DNA

source_name: human whole blood from a patient with hepatocellular carcinoma (HCC) collected prior to conventional diagnosis

value: Case - pre-diagnostic hepatocellular carcinoma (HCC)

value: hepatocellular carcinoma (HCC)


title: 17-124-SVZ


title: 17-032-SVZ

value: Bipolar


title: Scr_IFNb_rep1

description:
rep1
Sample_23

value: IFNb


title: 17-003-GFM


title: Al_IFNb_rep1

description:
rep1
Sample_24

value: Al


title: genomic DNA from Case 19

description: human whole blood DNA

value: human whole blood


title: 17-032-THA


title: PRDM1_IFNb_rep1

description:
rep1
Sample_22


title: 17-029-SVZ

value: F


title: 17-003-SVZ


title: genomic DNA from Control 20

description: human whole blood DNA

value: Control - Healthy

value: normal


title: 17-032-GTS

value: GTS


title: NAFLD Patient 13

value: peripheral blood

value: NAFL


title: NAFLD Patient 129

value: Chronic Liver Disease (NAFLD)


title: TCF7L_IFNb_rep1

description:
rep1
Sample_20


title: KLF5_cont_rep1

description:
rep1
Sample_2

value: cont


title: NAFLD Patient 127


title: NAFLD Patient 130


title: PRDM1L_IFNb_rep1

description:
rep1
Sample_21


title: TCF7_IFNb_rep1

description:
rep1
Sample_19


title: NAFLD Patient 126


title: genomic DNA from Case 17

description: human whole blood DNA


title: genomic DNA from Case 18

description: human whole blood DNA


title: KLF5_IFNb_rep1

description:
rep1
Sample_18


title: 16-056-GFM

value: M

value: Control


title: 17-029-GFM

value: GFM


title: genomic DNA from Case 16

description: human whole blood DNA

value: Case - pre-diagnostic hepatocellular carcinoma (HCC)


title: 17-029-GTS


title: genomic DNA from Control 15

description: human whole blood DNA


title: genomic DNA from Control 18

description: human whole blood DNA


title: NAFLD Patient 125


title: NAFLD Patient 124


title: NAFLD Patient 128


title: genomic DNA from Control 17

description: human whole blood DNA


title: NAFLD Patient 123


title: genomic DNA from Case 21

description: human whole blood DNA

value: hepatocellular carcinoma (HCC)


title: Scr_cont_rep2

description:
rep2
Sample_15

value: Scr


title: neg_IFNb_rep1

description:
rep1
Sample_17

value: neg

value: IFNb


title: NAFLD Patient 122


title: 18-063-THA

value: THA

value: Bipolar


title: BCL3_IFNb_rep3

description:
rep3
Sample_144


title: 18-010-THA


title: Al_cont_rep2

description:
rep2
Sample_16

value: Al


title: genomic DNA from Case 15

description: human whole blood DNA

value: human whole blood


title: NAFLD Patient 121


title: genomic DNA from Case 14

description: human whole blood DNA


title: 18-010-SVZ

value: SVZ


title: SP140_IFNb_rep3

description:
rep3
Sample_143


title: 18-063-GTS

value: GTS


title: genomic DNA from Case 13

description: human whole blood DNA


title: MAF_IFNb_rep3

description:
rep3
Sample_142

value: MAF


title: ID3_IFNb_rep3

description:
rep3
Sample_141


title: genomic DNA from Case 12

description: human whole blood DNA


title: 16-110-SVZ

value: F


title: NAFLD Patient 12

value: peripheral blood

value: Chronic Liver Disease (NAFLD)

value: NAFL


title: NAFLD Patient 120


title: NAFLD Patient 119


title: genomic DNA from Control 12

description: human whole blood DNA

value: Control - Healthy

value: normal


title: BATF3_IFNb_rep3

description:
rep3
Sample_140


title: genomic DNA from Control 13

description: human whole blood DNA


title: NAFLD Patient 118


title: genomic DNA from Case 11

description: human whole blood DNA

value: Case - pre-diagnostic hepatocellular carcinoma (HCC)

value: hepatocellular carcinoma (HCC)


title: 16-110-GFM

value: GFM


title: Blood, TCA270

city: VALENCIA

first: JUAN

middle: SANDOVAL

last: DEL AMOR

state: COMUNIDAD VALENCIANA

address: FERNANDO ABRIL MARTORELL 106

country: Spain

institute: INSTITUTO INVESTIGACION SANITARIA LA FE

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: R-package minfi (version 1.22.1)

source_name: Peripheral blood

label_protocol: Standard Illumina labelling protocol

extract_protocol: total DNA from blood was isolated by standard procedures

tag: monozigotic twin pair id

value: Non-twin

tag: pathology

value: AN

tag: gender

value: female

value: Peripheral blood


title: NAFLD Patient 117


title: BATF_IFNb_rep3

description:
rep3
Sample_139

value: BATF

value: IFNb


title: NAFLD Patient 116


title: Blood, TCA374

value: control


title: ETS2_IFNb_rep3

description:
rep3
Sample_138


title: HOPX_IFNb_rep3

description:
rep3
Sample_137

value: HOPX


title: PRDM1_cont_rep2

description:
rep2
Sample_14

value: cont


title: genomic DNA from Case 10

description: human whole blood DNA

value: human whole blood


title: NAFLD Patient 115

value: peripheral blood

value: Chronic Liver Disease (NAFLD)


title: Blood, TCA373


title: NAFLD Patient 114


title: Blood, TCA372


title: BCL3_cont_rep3

description:
rep3
Sample_136


title: genomic DNA from Control 19

description: human whole blood DNA

value: Control - Healthy


title: SP140_cont_rep3

description:
rep3
Sample_135


title: NAFLD Patient 113


title: Blood, TCA166


title: NAFLD Patient 112


title: MAF_cont_rep3

description:
rep3
Sample_134

value: MAF


title: genomic DNA from Control 10

description: human whole blood DNA

value: normal


title: genomic DNA from Control 11

description: human whole blood DNA


title: genomic DNA from Case 9

description: human whole blood DNA

value: Case - pre-diagnostic hepatocellular carcinoma (HCC)

value: hepatocellular carcinoma (HCC)


title: Blood, TCA233

value: Non-twin


title: ID3_cont_rep3

description:
rep3
Sample_133


title: genomic DNA from Control 16

description: human whole blood DNA


title: Blood, TCA38


title: NAFLD Patient 111


title: NAFLD Patient 110


title: Blood, TCA259

value: AN


title: BATF3_cont_rep3

description:
rep3
Sample_132


title: genomic DNA from Control 8

description: human whole blood DNA


title: NAFLD Patient 11

value: NAFL


title: BATF_cont_rep3

description:
rep3
Sample_131


title: Blood, TCA176

value: female

value: Peripheral blood


title: NAFLD Patient 109


title: genomic DNA from Control 9

description: human whole blood DNA


title: ETS2_cont_rep3

description:
rep3
Sample_130


title: Blood, TCA32


title: 16-110-GTS

tag: donor

tag: region

value: GTS

tag: age

value: F

value: Bipolar


title: NAFLD Patient 108

tag: disease state

tag: nas


title: genomic DNA from Case 8

description: human whole blood DNA


title: NAFLD Patient 107

tag: saf activity


title: PRDM1L_cont_rep2

description:
rep2
Sample_13

tag: shRNA

tag: ifn-b treatment (cont vs ifnb)

value: cont


title: Blood, TCA125


title: genomic DNA from Case 7

description: human whole blood DNA

value: human whole blood


title: HOPX_cont_rep3

description:
rep3
Sample_129

tag: cell type

value: HOPX


title: genomic DNA from Case 6

description: human whole blood DNA


title: genomic DNA from Control 7

description: human whole blood DNA


title: STAT3_IFNb_rep3

description:
rep3
Sample_128

value: IFNb


title: Blood, TCA25


title: NAFLD Patient 106

value: peripheral blood

value: Chronic Liver Disease (NAFLD)

tag: fibrosis stage

tag: disease group


title: genomic DNA from Control 5

description: human whole blood DNA

tag: case/control

value: Control - Healthy

value: normal


title: STAT1_IFNb_rep3

description:
rep3
Sample_127


title: genomic DNA from Control 6

description: human whole blood DNA

tag: sample type


title: genomic DNA from Case 4

description: human whole blood DNA

value: Case - pre-diagnostic hepatocellular carcinoma (HCC)

value: hepatocellular carcinoma (HCC)


title: genomic DNA from Control 14

description: human whole blood DNA


title: genomic DNA from Case 5

description: human whole blood DNA


title: NAFLD Patient 103

tag: tissue


title: IRF9_IFNb_rep3

description:
rep3
Sample_126


title: IRF4_IFNb_rep3

description:
rep3
Sample_125


title: NAFLD Patient 105


title: NAFLD Patient 102


title: NAFLD Patient 104


title: Blood, TCA71

tag: monozigotic twin pair id

value: Non-twin

value: AN


title: IRF2_IFNb_rep3

description:
rep3
Sample_124


title: Blood, 201733

value: twin 6

tag: pathology

value: female


title: IRF1_IFNb_rep3

description:
rep3
Sample_123


title: genomic DNA from Control 4

description: human whole blood DNA


title: Blood, TCA5

value: control

tag: gender

value: Peripheral blood


title: NAFLD Patient 100


title: sc-RNA seq

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

data_processing:
The Cell Ranger Single-Cell Software Suite (versions 4.0.0) were used to perform sample demultiplexing, barcode processing and single-cell gene cougting (https://www.10xgenomics.com/). First raw base BCL files were demultiplexed using the Cell Ranger mkfastq pipeline into sample FASTO files.
Second, these FASTQ files were processed individu- ally using the Cell Ranger count pipeline, which made use of the star software to align FASTQ reads to the MM10 mus musculus reference genome. Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs), resulted in a gene-barcode count matrices to be used for downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: splenic Treg cells

extract_protocol: single cell libraries were prepared using 10x Single Cell 3′ Reagent Kit (V2 chemistry).

tag: strain

value: spleen

tag: genotype

value: Tfrc fl/fl Foxp3 YFP-Cre/+


title: genomic DNA from Case 3

description: human whole blood DNA

value: human whole blood


title: ARID5b_IFNb_rep3

description:
rep3
Sample_122


title: TfR1 cko Treg cells rep2 [HE2]

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by using Trim Galore v0.6.7, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.7.9a.
Sequence reads count is calculated using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

extract_protocol:
Total RNA was isolated with RNeasy plus kit (Qiagen, CA)
mRNA libraries were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit (E6420, NEB).


title: Blood, 201724

value: twin 7


title: NAFLD Patient 101

value: NAFL


title: NAFLD Patient 10

value: peripheral blood


title: CTRL3: gDNA from circulating CD04+ T cells from CTRL3

city: Naples

first: Claudio

last: Napoli

state: Italy

address: P.za Miraglia, 2

country: Italy

institute: University of Campania "L. Vanvitelli"

description: normal CD04+ T cells

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Microarrays were scanned using the Illumina iScan-Scanner according to "Standard Illumina Scanning Protocol"

data_processing: The data were normalised for red and green channel separately using quantile normalisation with R using function normalize.quantiles from Bioconductor package "preprocessCore"

source_name: normal CD04+ T cells

label_protocol: 350-500 ng genomic DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Orange, US) according to the manufacturer recommendations. Each sample was whole genome amplified and enzymatically fragmented following the instructions in the Illumina Infinium HD Assay Methylation Protocol Guide

extract_protocol: We isolated CD04+ T cells using the EasySep™ Human CD04+ T Cell Isolation Kit (Stem Cell), according to manufacturer’s instructions.

value: CTRL

value: CD04+ T cells


title: ARID5a_IFNb_rep3

description:
rep3
Sample_121

value: IFNb


title: Blood, 201719

value: twin 5


title: genomic DNA from Case 2

description: human whole blood DNA

value: Case - pre-diagnostic hepatocellular carcinoma (HCC)

value: hepatocellular carcinoma (HCC)


title: TfR1 cko Treg cells rep1 [HE1]


title: genomic DNA from Control 2

description: human whole blood DNA

value: Control - Healthy

value: normal


title: WT Treg cells rep2 [WT2]

value: Tfrc +/+ Foxp3 YFP-Cre/+


title: Blood, 201726

value: twin 8

value: control

value: female


title: CTRL2: gDNA from circulating CD04+ T cells from CTRL2

description: normal CD04+ T cells


title: CTRL1: gDNA from circulating CD04+ T cells from CTRL1

description: normal CD04+ T cells


title: Stars_500_Basolateral_EA.hy296_rep3

city: Belvaux

first: Sebastien

last: Cambier

state: - select a state -

address: 41 rue du brill

department: ERIN

country: Luxembourg

institute: LIST - Luxembourg Institute of Science and Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p13 human whole genome using CLC Software (Genomics Workbench v.11)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated directly by the CLC Software (Genomics Workbench v. 11)
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cell line

extract_protocol:
Total RNA was harvested using QIAGEN® – RNA purification kit. SMARTer® Stranded Total RNA Sample Prep Kit – HI Mammalian was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard SMARTer® Stranded oligonucleotides protocol

tag: cell composition

tag: culture conditions

value: Submerged

tag: treatment

value: Au stars NP


title: TCF7L_cont_rep2

description:
rep2
Sample_12

value: cont


title: STAT3_cont_rep3

description:
rep3
Sample_120


title: Blood, 201734

value: twin 6

value: Peripheral blood


title: WT Treg cells rep1 [WT1]

value: spleen


title: Stars_500_Basolateral_EA.hy296_rep2


title: NAFLD Patient 1

extract_protocol:
Samples were lysed with a 1:1 ratio of HTG biofluids lysis buffer, according to manufacturer's instructions.
Lysates input into nuclease protection assays run on the HTG EdgeSeq processor. Sequence adapters were added to the samples in a 16-cycle PCR reaction. PCR products were purified using AMPure XP beads (Beckman Coulter, High Wycombe, UK).

value: peripheral blood

tag: disease state

value: Chronic Liver Disease (NAFLD)

tag: nas

tag: saf activity

value: NAFL


title: Stars_500_Basolateral_EA.hy296_rep1


title: Blood, 201723

value: twin 7

value: AN


title: genomic DNA from Control 3

description: human whole blood DNA

value: Control - Healthy

value: human whole blood


title: Stars_1000_Basolateral_EA.hy296_rep2


title: PAH5: gDNA from circulating CD04+ T cells from PAH5

description: PAH CD04+ T cells

source_name: PAH CD04+ T cells

value: PAH

tag: cell type

value: CD04+ T cells


title: STAT1_cont_rep3

description:
rep3
Sample_119

tag: shRNA

tag: ifn-b treatment (cont vs ifnb)


title: heart: 1484

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

data_processing:
Reads were quantified against mouse transcriptome reference from GRCm38.p6 (Ensembl release 97) using kallisto v0.46
Gene counts and TPM values were tabulated with tximport.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *.txt files are tab-delimited text containing either gene counts or gene TPMs

extract_protocol:
Total RNA from mouse heart samples (one mouse per strain) was purified using the Qiagen miRNeasy kit (Qiagen cat#217004) per the manufacturer’s instructions.
Libraries were prepared using the Nugen Universal Plus mRNA kit (Tecan Genomics Inc, Redwood City, CA)

treatment_protocol: Mice were fed a chow diet for 8 weeks, followed by a high-fat/high-sucrose diet for 8 weeks.  Tissues were collected at 16 weeks of age.

value: heart

tag: Sex

value: F


title: heart: 1527

value: M


title: Blood, 201714

value: Twin 2

value: control

value: female


title: heart: 1489


title: PAH4: gDNA from circulating CD04+ T cells from PAH4

description: PAH CD04+ T cells


title: IRF9_cont_rep3

description:
rep3
Sample_118

value: cont


title: Stars_1000_Basolateral_EA.hy296_rep3

value: Submerged

value: Au stars NP


title: PAH3: gDNA from circulating CD04+ T cells from PAH3

description: PAH CD04+ T cells


title: IRF4_cont_rep3

description:
rep3
Sample_117


title: Blood, 201718

value: twin 4

value: Peripheral blood


title: Blood, 201720

value: twin 5


title: PAH2: gDNA from circulating CD04+ T cells from PAH2

description: PAH CD04+ T cells


title: CTRL: gDNA from circulating CD04+ T cells from CTRL

description: normal CD04+ T cells

value: CTRL


title: IRF2_cont_rep3

description:
rep3
Sample_116


title: IRF1_cont_rep3

description:
rep3
Sample_115


title: Stars_1000_Basolateral_EA.hy296_rep1


title: PAH1: gDNA from circulating CD04+ T cells from PAH1

description: PAH CD04+ T cells


title: heart: 1472

value: NZB/BlNJ


title: Rods_500_Basolateral_EA.hy296_rep2

value: Au rods NP


title: genomic DNA from MCF10A cells treated with vehicle control (ethanol), biological replicate 2

description: human mammary epithelial cell line

extract_protocol: genomic DNA was extracted and purified from human mammary epithelial MCF10A cells using standard phenol:chloroform extraction protocol

tag: cell line

value: Ethanol vehicle control

value: mammary epithelial cells

value: normal


title: Rods_500_Basolateral_EA.hy296_rep3


title: genomic DNA from Case 1

description: human whole blood DNA

tag: case/control

value: Case - pre-diagnostic hepatocellular carcinoma (HCC)

tag: sample type

value: human whole blood

value: hepatocellular carcinoma (HCC)


title: ARID5a_cont_rep3

description:
rep3
Sample_113


title: genomic DNA from MCF10A cells treated with 15 µM  RSV (resveratrol) for 9 days , biological replicate 2

description: human mammary epithelial cell line

source_name: MCF10A cells treated with RSV

value: RSV tested sample


title: Rods_500_Basolateral_EA.hy296_rep1


title: heart: 1464

tag: tissue

value: heart

value: F


title: ARID5b_cont_rep3

description:
rep3
Sample_114

value: cont


title: Young panicle, KD_Rep1

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

data_processing:
3’ adapter (5’-TGGAATTCTCGGGTGCCAAGG-3’) was removed from sequenced reads using UEA small RNA workbench.
The small RNA reads of length 19nt-25nt filtered and were analyzed.
Supplementary_files_format_and_content: Text file containing 19nt-25nt long unique reads and their raw abundance after removal of adapter.

organism: Oryza sativa Indica Group

source_name: Young panicle (pre-emergence)

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees Celsius.

extract_protocol:
Total RNA from young panicle (5 to 10cm) of both wild-type and transgenic lines were extracted using Trizol (Invitrogen) reagent.
Size fractionation

treatment_protocol: WT, overexpression and knockdown lines were handled in the same manner.

value: Young panicle (pre-emergence)

tag: cultivar

value: Pusa Basmati 1 (PB1)

value: OsRDR4 KD


title: neg_IFNb_rep3

description:
rep3
Sample_112

value: neg

value: IFNb


title: Rods_1000_Basolateral_EA.hy296_rep3

value: Submerged


title: heart: 1446

tag: strain

value: I/LnJ


title: Blood, 201711

tag: monozigotic twin pair id

value: Twin 1

tag: pathology

value: control

tag: gender

value: female

value: Peripheral blood


title: genomic DNA from Control 1

description: human whole blood DNA

value: Control - Healthy

value: human whole blood

value: normal


title: heart: 1476

value: heart

value: NZB/BlNJ


title: genomic DNA from MCF10A cells treated with vehicle control (ethanol), biological replicate 1

description: human mammary epithelial cell line

tag: treatment

value: Ethanol vehicle control

value: mammary epithelial cells


title: Young panicle, OE_Rep1

value: Young panicle (pre-emergence)

value: Pusa Basmati 1 (PB1)

tag: genotype

value: OsRDR4 OE


title: KLF5_IFNb_rep3

description:
rep3
Sample_111

value: IFNb


title: Rods_1000_Basolateral_EA.hy296_rep1

tag: cell composition

tag: culture conditions

value: Submerged

value: Au rods NP


title: Young panicle, OE_Rep2


title: Rods_1000_Basolateral_EA.hy296_rep2


title: Spheres_500_Basolateral_EA.hy296_rep3

value: Au spherical NP


title: Young panicle, WT_Rep1

value: WT


title: genomic DNA from MCF10A cells treated with 15 µM  RSV (resveratrol) for 9 days , biological replicate 3

description: human mammary epithelial cell line

value: RSV tested sample

tag: cell type

tag: disease state


title: Blood, 201717

value: twin 4

value: control

value: female

value: Peripheral blood


title: heart: 1435

value: heart

value: A/J

value: F


title: Blood, 201713

value: Twin 2

value: AN


title: TCF7_IFNb_rep3

description:
rep3
Sample_110

tag: shRNA

tag: ifn-b treatment (cont vs ifnb)


title: TCF7_cont_rep2

description:
rep2
Sample_11

value: cont


title: heart: 1443

value: I/LnJ

tag: Sex

value: M


title: heart: 1433

value: MA/MyJ


title: Blood, 201725

value: twin 8


title: genomic DNA from MCF10A cells treated with 15 µM  RSV (resveratrol) for 9 days , biological replicate 1

description: human mammary epithelial cell line

tag: cell line

value: mammary epithelial cells

value: normal


title: Young panicle, WT_Rep2

value: Young panicle (pre-emergence)

value: Pusa Basmati 1 (PB1)

value: WT


title: genomic DNA from MCF10A cells treated with vehicle control (ethanol), biological replicate 3

description: human mammary epithelial cell line

value: Ethanol vehicle control


title: TCF7L_IFNb_rep3

description:
rep3
Sample_109

value: IFNb


title: Spheres_1000_Basolateral_EA.hy296_rep3

value: Submerged

value: Au spherical NP


title: heart: 1424

value: heart


title: heart: 1448


title: PRDM1L_IFNb_rep3

description:
rep3
Sample_108


title: Spheres_500_Basolateral_EA.hy296_rep1


title: Young panicle, KD_Rep2

value: OsRDR4 KD


title: heart: 1429

value: A/J


title: Blood, 201712

value: Twin 1

value: AN

value: female

value: Peripheral blood


title: Scr_IFNb_rep3

description:
rep3
Sample_106

value: Scr


title: PRDM1_IFNb_rep3

description:
rep3
Sample_107


title: Spheres_1000_Basolateral_EA.hy296_rep1


title: Al_IFNb_rep3

description:
rep3
Sample_105

value: Al


title: kcng4 cas inject-RZE039

city: Singapore

first: Hyungwon

last: Choi

address: 14 Medical Drive, MD6 #08-01

country: Singapore

institute: National University of Singapore

description: total RNA extracted from pooled embryos

data_processing: none provided by the submitter

organism: Danio rerio

source_name: Zebrafish embryos

extract_protocol:
One hundred embryos for each sample were pooled, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos were wildtype, or microinjected at 1-cell stage with either kcng4b CRISPR or kcng4b MO

value: AB

tag: Stage

value: 24 hpf

tag: genetic manipulation

value: kcng4b CRISPR injected


title: kcng4 MO-RZE040

description: total RNA extracted from pooled embryos

value: kcng4b MO injected


title: WT-RZE038

description: total RNA extracted from pooled embryos

value: wild-type


title: heart: 1410

tag: tissue

value: PL/J

value: F


title: heart: 1413

tag: strain

value: M


title: Control_Basolateral_EA.hy296_rep3

value: Submerged

value: no treatment


title: heart: 1404

value: heart


title: Control_Basolateral_EA.hy296_rep2


title: neg_cont_rep3

description:
rep3
Sample_104

value: neg

value: cont


title: KLF5_cont_rep3

description:
rep3
Sample_103


title: Control_Basolateral_EA.hy296_rep1


title: heart: 1394

value: SJL/J


title: Spheres_1000_Basolateral_EA.hy296_rep2

value: Au spherical NP


title: heart: 1420


title: TCF7_cont_rep3

description:
rep3
Sample_102


title: heart: 1386


title: Stars_500_Apical_A549+THP1_rep3

value: A549 with differentiated THP1

value: Air Liquid Interface

value: Au stars NP


title: Stars_500_Apical_A549+THP1_rep2


title: heart: 1379

value: CE/J


title: heart: 1364


title: heart: 1355


title: heart: 1366


title: KLF5_cont_rep2

description:
rep2
Sample_10


title: Stars_500_Apical_A549+THP1_rep1


title: Stars_1000_Apical_A549+THP1_rep2


title: neg_cont_rep1

description:
rep1
Sample_1


title: Stars_1000_Apical_A549+THP1_rep3


title: PRDM1L_cont_rep3

description:
rep3
Sample_100


title: CD8_IFNb_96h_3

data_processing:
After sequencing, adapter sequences and poor-quality bases (quality score < 3) were trimmed with Trimmomatic. Remaining bases were trimmed if their average quality score in a 4 bp sliding window fell below 5. FastQC was used to obtain quality control metrics before and after trimming. Remaining reads were aligned to the GRCh38 human genome with STAR 2.5.244. We used Picard to remove optical duplicates and to compile alignment summary statistics and RNA-seq summary statistics. After alignment, reads were quantitated to gene level with RSEM45 using the Ensembl annotation. Normalized Fragments Per Kilobase Million (FPKM) expression values
Genome_build: hg38
Supplementary_files_format_and_content: count matrix

growth_protocol: Naïve CD4+ T cells (CD4+/CD25neg/CD127+/CD45ROneg/CD45RA+) and naïve CD8+ T cells (CD8++/CD25neg/CD127+/CD45ROneg/CD45RA+) were sorted on a FACSAria (BD Biosciences). Sorted cells were plated in 96-well round-bottom plates (Corning) and cultured in RPMI 1640 medium supplemented with 5 % Human serum, 2 nM L-glutamine, 5 mM HEPES, and 100 U/ml penicillin, 100 g/ml streptomycin, 0.5 mM sodium pyruvate, 0.05 mM nonessential amino acids, and 5% human AB serum (Gemini Bio-Products).

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (QIAGEN), or ZR-96 Quick-RNA kit (Zymo Research), according to the manufacturer’s instructions.
cDNAs were generated from isolated RNAs using SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech). Barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina) and sequenced with a 2x100 bp paired-end protocol on the HiSeq 4000 Sequencing System (Illumina).

treatment_protocol: Cells were seeded (30,000-50,000/wells) into wells pre-coated with anti-human CD3 (2 ug/ml, clone UCHT1, BD Biosciences) along with soluble anti-human CD28 (1ug/ml, clone 28.2, BD Biosciences) in the presence or absence of human IFN beta (500 U/ml: Pestka Biomedical Laboratories) without adding IL-2.

value: IFNb

tag: time points


title: TCF7L_cont_rep3

description:
rep3
Sample_101


title: Stars_1000_Apical_A549+THP1_rep1


title: CD8_con_96h_3

value: con


title: heart: 1352

value: SM/J


title: heart: 1347


title: CD4_IFNb_96h_3


title: Rods_500_Apical_A549+THP1_rep3

value: Au rods NP


title: Rods_500_Apical_A549+THP1_rep2


title: heart: 1338

value: F


title: CD4_con_96h_3


title: Rods_500_Apical_A549+THP1_rep1


title: heart: 1329


title: genomic DNA from LDRC_643_1T

city: Houston

first: Oxana

middle: Yu.

last: Naumova

state: TX

address: 4849 Calhoun Rd, TIMES, Rm 373

department: Psychology

institute: University of Houston

description: normal development

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan in accodance to the standard recommended Illumina scanner setting

data_processing: Illumina GenomeStudio Methylation Module v1.8

source_name: T cells LDRC_643_1T

extract_protocol: T-cells from blood samples were isolated using monoclonal anti-biotin antibody coupled to MicroBeads according to standard instructions. Genomic DNA was extracted (1) from T-cells using the Qiagen DNeasy Kit, (2) from blood samples using the Qiagen  FlexiGene kit, and (3) from the Oragene (OGR-50) saliva samples using the DNA Genotek prepIT.L2P reagents. All the procedures have been performed according to the manufacturer's protocol

value: Male

value: T cells

value: normal


title: CD8_con_72h_3


title: Rods_1000_Apical_A549+THP1_rep3


title: heart: 1334

value: heart


title: heart: 1312

value: KK/HlJ


title: CD8_IFNb_72h_3


title: Rods_1000_Apical_A549+THP1_rep2


title: genomic DNA from LDRC_618_1T

description: normal development

source_name: T cells LDRC_618_1T

value: Female


title: heart: 1304

value: M


title: genomic DNA from LDRC_614_1T

description: normal development

source_name: T cells LDRC_614_1T


title: CD4_con_72h_3


title: Rods_1000_Apical_A549+THP1_rep1


title: CD4_IFNb_72h_3


title: genomic DNA from LDRC_591_1T

description: normal development

source_name: T cells LDRC_591_1T


title: heart: 1270

value: NZW/LacJ


title: heart: 1265

value: LP/J


title: CD4_IFNb_48h_3


title: genomic DNA from LDRC_587_1T

description: normal development

source_name: T cells LDRC_587_1T


title: genomic DNA from LDRC_594_1T

description: normal development

source_name: T cells LDRC_594_1T


title: genomic DNA from LDRC_609_1T

description: normal development

source_name: T cells LDRC_609_1T


title: genomic DNA from LDRC_610_1T

description: normal development

source_name: T cells LDRC_610_1T


title: Spheres_500_Apical_A549+THP1_rep3

value: A549 with differentiated THP1

value: Air Liquid Interface

value: Au spherical NP


title: heart: 1279


title: CD8_IFNb_16h_3

source_name: primary T cells

value: IFNb


title: genomic DNA from LDRC_290_1T

description: normal development

source_name: T cells LDRC_290_1T


title: CD8_IFNb_48h_3


title: heart: 1272


title: Spheres_500_Apical_A549+THP1_rep1


title: Spheres_1000_Apical_A549+THP1_rep3


title: Spheres_1000_Apical_A549+THP1_rep2


title: CD8_con_48h_3

value: con


title: CD4_con_48h_3


title: genomic DNA from LDRC_470_1T

description: normal development

source_name: T cells LDRC_470_1T


title: Spheres_500_Apical_A549+THP1_rep2


title: genomic DNA from LDRC_399_1T

description: normal development

source_name: T cells LDRC_399_1T


title: genomic DNA from LDRC_326_1T

description: normal development

source_name: T cells LDRC_326_1T


title: heart: 1241


title: Spheres_1000_Apical_A549+THP1_rep1

source_name: cell line


title: Control_Apical_A549+THP1_rep3

value: no treatment


title: CD8_con_16h_3


title: heart: 1243


title: genomic DNA from LDRC_326_1S

description: normal development

source_name: saliva LDRC_326_1S

value: saliva


title: genomic DNA from LDRC_570_1T

description: normal development

source_name: T cells LDRC_570_1T


title: Control_Apical_A549+THP1_rep2


title: heart: 1228

value: F


title: CD4_con_16h_3


title: Control_Apical_A549+THP1_rep1


title: heart: 1230


title: heart: 1206


title: heart: 1214


title: heart: 1202


title: CD4_IFNb_16h_3


title: CD4_IFNb_8h_3


title: heart: 1195


title: CD8_con_8h_3


title: heart: 1181


title: heart: 1178


title: CD4_con_8h_3


title: heart: 1168


title: CD8_con_4h_3


title: genomic DNA from LDRC_290_1S

description: normal development

source_name: saliva LDRC_290_1S

value: Male


title: CD4_IFNb_4h_3


title: CD8_IFNb_4h_3


title: heart: 1149


title: heart: 1159


title: CD4_con_4h_3


title: heart: 1139


title: CD8_IFNb_2h_3


title: CD8_con_2h_3


title: heart: 1133


title: heart: 1130


title: CD8_IFNb_1h_3


title: CD8_IFNb_8h_3


title: heart: 1115


title: genomic DNA from LDRC_165_1S

description: normal development

source_name: saliva LDRC_165_1S


title: genomic DNA from LDRC_265_1S

description: normal development

source_name: saliva LDRC_265_1S


title: CD8_con_1h_3


title: CD4_IFNb_2h_3


title: heart: 1112


title: CD4_IFNb_1h_3


title: heart: 1120


title: genomic DNA from LDRC_158_1S

description: normal development

source_name: saliva LDRC_158_1S


title: CD4_con_2h_3


title: genomic DNA from LDRC_160_1S

description: normal development

source_name: saliva LDRC_160_1S


title: CD4_con_1h_3


title: heart: 1099


title: CD8_naïve_0h_3


title: genomic DNA from LDRC_594_1S

description: normal development

source_name: saliva LDRC_594_1S


title: heart: 1088


title: heart: 1103


title: CD4_naive_0h_3


title: heart: 1078


title: heart: 1069


title: genomic DNA from LDRC_609_1B

description: normal development

source_name: whole blood LDRC_609_1B

value: whole blood


title: heart: 1059


title: CD8_con_96h_2


title: genomic DNA from LDRC_570_1S

description: normal development

source_name: saliva LDRC_570_1S

value: normal


title: genomic DNA from LDRC_470_1S

description: normal development

source_name: saliva LDRC_470_1S


title: genomic DNA from LDRC_587_1S

description: normal development

source_name: saliva LDRC_587_1S


title: CD8_IFNb_96h_2

source_name: primary T cells


title: heart: 1049

value: heart


title: genomic DNA from LDRC_610_1B

description: normal development

source_name: whole blood LDRC_610_1B


title: genomic DNA from LDRC_591_1B

description: normal development

source_name: whole blood LDRC_591_1B


title: CD4_con_96h_2


title: CD8_IFNb_72h_2


title: genomic DNA from LDRC_594_1B

description: normal development

source_name: whole blood LDRC_594_1B


title: genomic DNA from LDRC_399_1S

description: normal development

source_name: saliva LDRC_399_1S


title: genomic DNA from LDRC_591_1S

description: normal development

source_name: saliva LDRC_591_1S


title: genomic DNA from LDRC_470_1B

description: normal development

source_name: whole blood LDRC_470_1B


title: genomic DNA from LDRC_290_1B

description: normal development

source_name: whole blood LDRC_290_1B


title: genomic DNA from LDRC_587_1B

description: normal development

source_name: whole blood LDRC_587_1B


title: heart: 1028


title: CD8_con_72h_2


title: genomic DNA from LDRC_165_1B

description: normal development

source_name: whole blood LDRC_165_1B


title: CD4_IFNb_72h_2


title: heart: 1017


title: CD4_con_72h_2


title: CD8_IFNb_48h_2


title: genomic DNA from LDRC_570_1B

description: normal development

source_name: whole blood LDRC_570_1B


title: heart: 1013


title: heart: 1032


title: genomic DNA from LDRC_326_1B

description: normal development

source_name: whole blood LDRC_326_1B


title: heart: 1010


title: CD8_con_48h_2


title: heart: 1003


title: genomic DNA from LDRC_643_1S

description: normal development

source_name: saliva LDRC_643_1S


title: genomic DNA from LDRC_265_1B

description: normal development

source_name: whole blood LDRC_265_1B


title: genomic DNA from LDRC_399_1B

description: normal development

source_name: whole blood LDRC_399_1B


title: heart: 1007


title: CD4_IFNb_48h_2


title: CD4_IFNb_96h_2


title: CD8_IFNb_16h_2


title: genomic DNA from LDRC_158_1B

description: normal development

source_name: whole blood LDRC_158_1B


title: heart: 995


title: heart: 994


title: heart: 987


title: genomic DNA from LDRC_160_1B

description: normal development

source_name: whole blood LDRC_160_1B


title: heart: 984

value: NOD/ShiLtJ


title: CD4_IFNb_16h_2

source_name: primary T cells


title: CD4_con_16h_2


title: genomic DNA from LDRC_610_1S

description: normal development

source_name: saliva LDRC_610_1S


title: heart: 1018


title: CD8_IFNb_8h_2


title: PAO1- TREATED REPLICATE 2

city: Hyderabad

first: Sanhita

last: Roy

state: Telangana

address: Banjara Hills Road no2

department: BHERC

institute: L V Prasad Eye Institute

description:
His-tag protein purification kit with nickel affinity column chromatography was used to purify the S100A12 protein
PM2604

data_processing:
BCL to Fastq conversion by bcl2fastq 2.19.0.316
The sequence data quality was checked using FastQC v0.11.9 and MultiQC v1.9 software. The data was checked for base call quality distribution, % bases above Q20, Q30, %GC, and sequencing adapter contamination. All the samples passed QC threshold (Q20>95%).
The sequence data was processed using fastp v0.20.1 to remove adapter sequences, low quality reads, filtering reads shorther than 50 bp.
The QC passed reads were mapped onto indexed Pseudomonas aeruginosa (PAO1) reference genome using Bowtie2 v2.1.0 aligner.
Gene expression values were obtained as read counts using ensembl annotation file (Pseudomonas aeruginosa (PAO1)) and featureCounts v2.0.1 software.
Genome_build: assembly (GCF_000006765.1; ASM676v1)
Supplementary_files_format_and_content: Raw reads counts in excel format

organism: Pseudomonas aeruginosa PAO1

source_name: Bacteria

growth_protocol: 200 μl of overnight culture of PAO1 was grown for 2 hours to get an OD600 of 0.2 and then 10^6 cfu was taken.

extract_protocol:
The RNA extraction was performed using TRIzol method.
Library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina.

treatment_protocol: 10^6 cfu of PAO1 was incubated with 500 μg/ml of S100A12 for 6 hours

value: BACTERIAL PELLET

value: treated with 500 μg/ml of S100A12


title: PAO1- TREATED REPLICATE 1

description:
His-tag protein purification kit with nickel affinity column chromatography was used to purify the S100A12 protein
PM2603


title: heart: 974


title: genomic DNA from LDRC_618_1S

description: normal development

source_name: saliva LDRC_618_1S

value: Female


title: heart: 964

value: M


title: genomic DNA from LDRC_614_1S

description: normal development

source_name: saliva LDRC_614_1S


title: genomic DNA from LDRC_265_1T

description: normal development

source_name: T cells LDRC_265_1T

value: T cells


title: PAO1- UNTREATED REPLICATE 2

value: untreated


title: PAO1- UNTREATED REPLICATE 1


title: CD4_IFNb_8h_2


title: heart: 951


title: NTERT_CRISPRa_Screen1

city: Minneapolis

first: Jakub

last: Tolar

state: Minnesota

address: 2001 6th St SE

department: Pediatrics

institute: University of Minnesota - Twin Cities

description:
Sequencing of sgRNAs from pilot CRISPRa screen.
DNA sequencing of single guide RNAs.

data_processing:
Cutadapt was used to filter reads based on the presence of the 'CACCG' sequence that appears directly 5' to the sgRNA sequence; this "adapter" and any bases preceding it were removed.
Cutadapt was used to trim reads from the 3' end such that only the first 20 bases (the sgRNA sequence) remained.
Galaxy was used to convert FASTQ files into FASTA files and FASTA files into tab-delimited text files.
Galaxy was used to filter the text files such that only the column containing the sgRNA sequence was retained.
Matlab was used to map the reads to the sgRNA library and calculate mapping efficiency (% of reads that mapped to an sgRNA); no mismatches were allowed.
Matlab was used to calculate the counts-per-million (CPM) value for each sgRNA; CPM was calculated based on the number of sgRNA reads, not the total number of reads.
Matlab was used to calculate fold change (FC) and log2FC for each sgRNA relative to the input material (plasmid DNA).
Genome_build: List of sgRNA sequences in the library.
Supplementary_files_format_and_content: COL7A1_CRISPRaScreen_Data.xlsx
Supplementary_files_format_and_content: COL7A1_CRISPRaScreen_sgRNA.tabular.txt

source_name: Cell Line; Skin

growth_protocol: Cells were expanded in normal growth media, put into selection media after transduction with lenti-dCas9-VP64 (blasticidin) and the sgRNA library (puromycin), then returned to normal growth media after selection.

extract_protocol:
Cells were pelleted and genomic DNA was extracted using the Gentra Puregene Cell Kit from QIAGEN according to manufacturer's instructions.
The region of the sgRNA lentiviral construct containing the sgRNA sequence was PCR-amplified from genomic DNA using primers containing Illumina P5 and P7 adapters. Product size was confirmed via gel electrophoresis. PCR products were cleaned up using AMPure XP beads. Library concentrations were determined with a NanoDrop.

treatment_protocol: Cells were trypsinized, resuspended, and sorted with FACS based on tdTomato fluorescence; gates were established such that the top 10% of cells (by mean fluorescence intensity) were sorted separately.

value: Keratinocyte

tag: genotype/variation

tag: transduction


title: heart: 959


title: heart: 932


title: genomic DNA from LDRC_158_1T

description: normal development

source_name: T cells LDRC_158_1T

tag: gender


title: CD4_con_8h_2

tag: treatment


title: CD8_IFNb_4h_2

value: IFNb


title: heart: 931


title: genomic DNA from LDRC_160_1T

description: normal development

source_name: T cells LDRC_160_1T


title: genomic DNA from LDRC_165_1T

description: normal development

source_name: T cells LDRC_165_1T


title: CD8_con_4h_2

value: con


title: heart: 927


title: PLVX/IRX5 rep2

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

data_processing:
Library construction and sequencing were performed at Shanghai Sinomics Corporation. An Average of 49 million reads per sample were obtained.
Trim Galore was applied for automatic quality and adapter trimming (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
The processed reads were aligned to the human reference genome HG38 by HISAT2. As a result, an average alignment rate of 85% was obtained.
Sample read counts were summarized by StringTie2 with the GENCODE V32 annotation file. Differential expression analysis was determined based on read counts by using DESeq2. P-values of DESeq2 were corrected using the Benjamini-Hochberg procedure for multiple testing adjustment. The genes were ranked by the Wald statistics reported by DESeq2 followed by the pre-ranked GO term GSEA analysis.
Genome_build: hg38

source_name: bone marrow

growth_protocol: Human bone marrow-derived mesenchymal stem cells (hMSCs) were purchased from ScienCell research laboratories (CA, USA) and cultured in mesenchymal stem cell medium (MSCM; ScienCell, CA, USA). hMSCs were incubated at 37°C in a humidified atmosphere of 5% CO2 and were used at passage 3-7.

extract_protocol:
A RNeasy mini kit (Qiagen, Düsseldorf, Germany) was used to isolate total RNA from hMSCs followed by its instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The lentivirus vector (pGLV8/ mCherry/ Puro) overexpressing IRX5 were packaged and purified by GenePharma (Shanghai, China). hMSCs were infected with lentivirus in the presence of 5 μg/mL polybrene (Sigma-Aldrich, MO, USA) for 12-24h. 48 hr later, the infection efficiency was observed by fluorescent microscopy. Puromycin (2ug/ml) was used to select infected cells. For brevity, hMSCs with IRX5-overexpressing/empty lentivirus were referred as Plvx/IRX5, PLVX/CTRL, respectively.

value: human bone marrow-derived mesenchymal stem cells

value: Transferred with IRX5-overexpression plasmid

tag: genotype

value: IRX5 overexpressed


title: genomic DNA from LDRC_609_1S

description: normal development

source_name: saliva LDRC_609_1S

value: saliva


title: CD8_con_16h_2


title: CD4_IFNb_4h_2


title: PLVX/IRX5 rep1


title: heart: 920

value: F


title: CD8_IFNb_2h_2


title: PLVX/CTRL rep2

value: Transferred with empty plasmid

value: CTRL


title: CD4_con_48h_2


title: heart: 903

value: heart


title: heart: 897


title: CD4_con_4h_2


title: PLVX/CTRL rep3


title: heart: 914


title: PLVX/CTRL rep1


title: CD8_con_2h_2


title: CD4_IFNb_2h_2


title: genomic DNA from LDRC_614_1B

description: normal development

source_name: whole blood LDRC_614_1B

value: whole blood

value: normal


title: heart: 890


title: 3.2-hiPSCs

city: Edinburgh

first: Mona

last: Elhendawi

state: Midlothian

address: 7 George Square

institute: The University of Edinburgh

data_processing:
Reads were trimmed using Cutadapt
Reads were aligned to the Homo sapiens reference genome (GRCh38; from Ensembl) using STAR
The raw count data were filtered to remove very low-expressed genes (genes consisting predominantly of near-zero counts)
Reads were normalised using the weighted trimmed mean of M-values method.
Differential analysis (comparing the low-treated group to the control group, or the high-treated group to the control group) was carried out using edgeR4.
we used the 100 most-significantly increased transcripts to perform a gene ontology (GO-term)-enrichment analysis using the PANTHER over-representation test (we first selected the 400 genes with the lowest p value corrected for FDR, then from these picked the 100 most strongly up-regulated and used them for the analysis)
Genome_build: GRCh38; from Ensembl
Supplementary_files_format_and_content: Microsoft Excel Comma Separated Values file

source_name: Renal organoids

growth_protocol: An established protocol (Takasato et al., 2015) was applied to the hiPSCs to induce renal differentiation. The protocol included treating hiPSCs with CHIR (8 uM) for three days, followed by 9 days of FGF9 (200 ng/ml) and Heparin (1 ug/ml) treatment. Then the cells were cultured in the differentiation media, APEL, for further 8 days for maturation, without adding extra growth factors.

extract_protocol:
Total RNA was isolated from organoids using the Qiagen RNeasy mini kit. Organoids were dissociated and processed as per the kit protocol.
1 mg of total RNA/sample was used for sequencing library preparation using an Illumina TruSeq stranded mRNA kit. Sequencing was performed using a Novaseq S1 50 Paired-end run to produce 50-64-million read-pairs per sample.

treatment_protocol: Samples were treated with gentamicin for 24 hrs, control samples were left untreated

value: hiPSC-derived renal organoids

value: High-dose-gentamicin treatment (4mg/ml)


title: CD8_IFNb_1h_2


title: 3.3-hiPSCs


title: CD8_con_8h_2


title: heart: 885


title: 2.3-hiPSCs

value: Low-dose-gentamicin treatment (1mg/ml)


title: 3.1-hiPSCs


title: heart: 876


title: 2.2-hiPSCs


title: CD8_con_1h_2


title: CD4_IFNb_1h_2


title: heart: 916

value: M


title: 2.1-hiPSCs


title: PLVX/IRX5 rep3


title: heart: 867


title: CD4_con_1h_2


title: genomic DNA from LDRC_643_1B

description: normal development

source_name: whole blood LDRC_643_1B

value: Male


title: 0.3-hiPSCs

value: Untreated


title: CD8_naïve_0h_2


title: heart: 863


title: heart: 853


title: 0.2-hiPSCs


title: CD4_naive_0h_2


title: genomic DNA from LDRC_481_1B

description: normal development

source_name: whole blood LDRC_481_1B


title: heart: 763

value: NOD/ShiLtJ


title: CD8_IFNb_96h_1

value: IFNb


title: heart: 873


title: genomic DNA from LDRC_567_1T

description: normal development

source_name: T cells LDRC_567_1T

value: T cells


title: genomic DNA from LDRC_567_1B

description: normal development

source_name: whole blood LDRC_567_1B


title: 0.1-hiPSCs


title: heart: 758


title: CD4_IFNb_96h_1

source_name: primary T cells


title: genomic DNA from LDRC_481_1S

description: normal development

source_name: saliva LDRC_481_1S


title: genomic DNA from LDRC_618_1B

description: normal development

source_name: whole blood LDRC_618_1B

value: Female


title: CD4_con_2h_2

value: con


title: heart: 755