title: IEC_IPA-1

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Small intestine

extract_protocol:
Mice were euthanized using isoflurane (VETONE) and secondary cervical dislocation. The intestines were maintained in a moistened state, and the Peyer’s patches and the remaining mesentery/fat were excised. The small intestine from ileum to jejunum was collected and gently flushed with a syringe with ice cold 1 × Hanks' Balanced Salt Solution (HBSS) media (without Ca2+ and Mg2+) (SIGMA, Cat# H4641) to remove the feces. The intestine was cut open and dissected into 1 cm segments, which were then transferred into a 50 mL tube and gently shaken to let the tissue stretch. They were then washed twice with ice cold 1 × HBSS and the extra HBSS removed using a pipet. 20 ml pre-digestion solution (1 × HBSS with 5% FBS, 5 mM EDTA and 1 mM DTT) was added and incubated for 20 min at 37 °C with 250 rpm rotation in an incubator. The 1 × HBSS containing the epithelial cell layer was collected on ice after vortex and passed through a 100 μm cell strainer. For intraepithelial immune cells and intestinal epithelial cells scRNA-seq, single cell suspensions were sorted using a FACSAria III flow cytometer to purify live cells (gated as DAPI- cells).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Intraepithelial immune cells and intestinal epithelial cells

value: Small intestine

tag: age

value: 15 weeks


title: 25-KK1515-nup132-d

status: Public on Nov 13 2023

type: SRA

city: Marseille

first: Karel

last: Naiman

address: BD Lei Roure

country: France

institute: CRCM

library_source: genomic

data_processing:
The reads were mapped using bowtie2
Polymerase usage was determined by the tools published and described in detail in Daigaku et al., 2015 and Keszthelyi et al. 2015.
Assembly: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets) with inserted replication fork barrier RTS1, 10xrDNA barrier
Supplementary files format and content: CSV files contain read counts corresponding to incorporated rNTPs sorted into 300bp bins on each chromosome. They are in two files for forward and reverse strands separately.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: nup132Δ cdc6-L591G rtf1::NAT rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32

growth_protocol: Cells were grown at 30C in YE media to log phase. For ‘wt’ datasets two strains were used, both strains containing  rnh201-RED mutant deficient in rNTP recognition together with either polymerase δ (cdc6-L591G) or polymerase ε (cdc20-M630F) mutations. These strains incorporate more rNTPs on the strands synthetized by the mutant polymerase. These sites can be mapped by Pu-seq.

extract_protocol:
DNA was prepared using the QIAGEN 100/G Genomic-tip. The isolated DNA was then subjected to RnaseH2 treatment that digested the DNA at the positions of rNTP incorporation and the double strands were separeated by heating. The resulting ssDNA fragments were size selected on agarose gel (fragments between 300-500bp were isolated).
Polymerase usage sequence (Pu-seq) technique was performed as previously described (Daigaku et al., 2015 and Keszthelyi et al. 2015) with minor modifications: size selection was performed using Blue Pippin (Sage Science). We used rnh201-RED instead of rnh201::kan (see results).

tag: cell type

tag: genotype

value: nup132{delta} cdc6-L591G rtf1::NAT rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: 40-KK1517-nup132-d

source_name: nup132Δ cdc6-L591G NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32

value: nup132{delta} cdc6-L591G NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: 39-RED-d

source_name: cdc6-L591G Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: CD4HD05_EM

city: Toulouse

first: Leila

last: Khajavi

address: TOULOUSE

institute: INSERM

description: raw counts

library_source: transcriptomic

data_processing:
STAR; version 2.6.0c
RSEM; version 1.3.0
Assembly: Homo sapiens primary genome sequence, Gencode: GRCh38, v27
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Cryopreserved PBMCs were thawed and washed in RPMI medium supplemented with 1% L-glutamine (100x), 1% sodium pyruvate (100mM), 1% non essential amino acids (100x), 1% penicillin-streptomycine (10,000 U/ml), 1% HEPES (1M) and 5% filtered and inactivated human AB-serum. Cells were then resuspended in PBS at 10 million/mL. Cell sorting was performed using a BD FACSAria Fusion with an antibody panel against CD3 (BD Horizon), CD4 (BD BioSciences), CD8α (BD Pharmingen), CCR7 (BD Horizon) and CD45RA (BD BioSciences) as well as eBioscience Fixable Viability Dye AF488. The T-cell subset sorting scheme used CCR7 and CD45RA cell surface markers to identify the four T-cell subsets. Post sorting, the cell number and viability were analyzed with the FlowJo software.
Library preparation (SMART-seq v4, Takara Bio) and RNA-sequencing (Illumina NovaSeq) were performed by the Genomics Facility Basel in Switzerland.

tag: tissue

value: Blood

value: CD4 T-cell


title: IEC_con-2

country: USA

description: 10x Genomics

library_source: transcriptomic single cell

organism: Mus musculus

tag: strain


title: AD_control_s153_Cmpd-60-153

city: Amsterdam

first: Man

middle: Iman

last: Hu

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

country: Netherlands

institute: Amsterdam UMC Location University of Amsterdam

data_processing:
Reads were subjected to quality control FastQC trimmed using Trimmomatic v0.32 and aligned using HISAT2 v2.1.0. Counts were obtained using HTSeq (v0.11.0, default parameters) using the corresponding GTF taking into account the directions of the reads.
Supplementary files format and content: table delimited row counts

source_name: AD-control mouse treated with cmpd-60

growth_protocol: Natural aged, approx. 20 months old, male BL6 mice were acquired from Taconic and single housed under a 12:12-hour light-dark cycle in a room set to 23°C (+/- 0.2°C).

extract_protocol:
Mouse tissues were homogenized with a 5 mm steel bead using a TissueLyser II (QIAGEN) for 5 min at frequency of 30 times/second. RNA was extracted according to the instructions of the RNaesy Mini Kit (QIAGEN). Contaminating genomic DNA was removed using RNase-Free DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands) and stored at -80°C until use.
RNA libraries were prepared and sequenced with the Illumina platform by Genome Scan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s).
The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer.

treatment_protocol: All animals were fed a regular chow diet. Mice received daily i.p. injections with either Cmpd60 (n=6) or vehicle (n=7) for 14 days total.

value: brain

tag: Sex

value: male

tag: strain background

tag: treatment


title: 8-KK1906-nup132-ON-e

source_name: nup132::Hygro cdc20-M630F Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: CD4HD05_Ef

description: raw counts


title: AD_control_s152_Cmpd-60-152


title: CD4HD05_CM

description: raw counts


title: IEC_con-1

description: 10x Genomics


title: AD_control_s151_vehicle-151

source_name: AD-control mouse treated with vehicle

value: vehicle


title: IEC_IPA-2

description: 10x Genomics


title: CD4HD04_Nv

description: raw counts


title: AD_control_s150_vehicle-150


title: 6-KK1902-nup132-ON-d

source_name: nup132::Hygro cdc6-L591G Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: G118E MeCP2 rep 3

city: Houston

first: Hu

last: Chen

state: TX

address: 1250 Moursund St,

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
Adapter sequences were removed from sequencing reads using Trimmomatic version 0.36 (2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) from the Truseq3.PE.fa adapter library and kseq.
Alignment was performed with bowtie2-2.3.4.1 (--dovetail--phred33) to both mm10 (GENCODE GRCm38p6 primary assembly version 18) and the spike-in Ecoli K12 Genomes (GCF_000005845.2_ASM584v2).
Bedtools (v2.29.1) was used to convert BAM files to BED files, to remove blacklist (mm9 blacklist lifted over to mm10 and combined with mm10 blacklist downloaded with CUT&RUNTools), and to generate bedgraphs.
Each sample was normalized to internal Ecoli spike-in utilizing spike_in_calibration.sh as described previously (Meers et al., 2019).
Both spike-in normalized bedgraphs for each sample and merged bedgraphs were converted to bigwigs using UCSC bedGraphToBigWig. Spike-in normalized bigwigs from each genotype were merged using deeptools bigwigCompare and averaged for summary figures.
Assembly: mm10 (GENCODE GRCm38p6 primary assembly version 18) and  the spike-in Ecoli K12 Genomes (GCF_000005845.2_ASM584v2)
Supplementary files format and content: E.coli spike-in normalized bigwig tracks.

source_name: Cortex

growth_protocol: Mice were housed in an AAALAS-certified Level 3 facility on a 14-hour light cycle.

extract_protocol:
Nuclei extraction and CUT&RUN was performed following (Bajikar et al. 2022; Skene and Henikoff 2017)
Library preparation was modified from protocols.IO (dx.doi.org/10.17504/protocols.io.bagaibse) utilizing reagents from the NEB Next II DNA Ultra Kit (New England Biolabs #E7645S) and Unique Combinatorial Dual index kit (New England Biolabs #E6442S)

value: Cortex


title: 5-KK1901-nup132-ON-d

value: nup132::Hygro cdc6-L591G Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: G118E IgG rep 3


title: CD4HD04_CM

description: raw counts


title: 3-KK1894-rpn10-ON-e

source_name: rpn10::Hygro cdc20-M630F Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: AD_control_s149_vehicle-149


title: G118E MeCP2 rep 2


title: 4-KK1895-rpn10-ON-e

value: rpn10::Hygro cdc20-M630F Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: CD4HD04_Ef

description: raw counts


title: WT MeCP2 rep 3

value: wild-type


title: G118E IgG rep 2


title: APPSWE-1349_s148_Cmpd-60-148

source_name: AD-transgenic mouse treated with cmpd-60


title: APPSWE-1349_s147_Cmpd-60-147


title: CD4HD03_EM

description: raw counts


title: CD4HD03_Nv

description: raw counts


title: 1-KK1868-rpn10-ON-d

source_name: rpn10::Hygro cdc6-L591G Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: 2-KK1869-rpn10-ON-d

value: rpn10::Hygro cdc6-L591G Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: APPSWE-1349_s146_vehicle-146

source_name: AD-transgenic mouse treated with vehicle


title: 7-KK1905-nup132-ON-e

value: nup132::Hygro cdc20-M630F Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: APPSWE-1349_s145_vehicle-145


title: CD4HD03_Ef

description: raw counts


title: APPSWE-1349_s144_vehicle-144


title: CD4HD04_EM

description: raw counts


title: WT IgG rep 2


title: APPSWE-1349_s143_Cmpd-60-143


title: CD4HD03_CM

description: raw counts


title: G118E MeCP2 rep 1


title: WT MeCP2 rep 2


title: CD4HD02_Nv

description: raw counts


title: G118E IgG rep 1


title: APPSWE-1349_s142_vehicle-142


title: CD4HD02_Ef

description: raw counts


title: WT IgG rep 3


title: CD4HD02_EM

description: raw counts


title: WT MeCP2 rep 1


title: APPSWE-1349_s140_vehicle-140


title: CD4HD02_CM

description: raw counts


title: APPSWE1349 _s139_vehicle-139


title: CD4HD01_Nv

description: raw counts


title: WT IgG rep 1


title: 6cKO

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Brain

extract_protocol:
Total RNA was harvested by Trizol reagent. 2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

tag: developmental stage

value: GSDMDfl/fl;Nestin-Cre


title: Kidney_MMU_vehicle-049

source_name: Kidney of mouse treated with vehicle

value: Kidney


title: KPC1361_Pikfyve_KO_4

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

data_processing:
Transcripts were quantified by kallisto with human reference genome (hg38) and then summarized to obtain gene level counts and TPM.
Assembly: mm10

source_name: pancreatic tumor

extract_protocol:
RNAs were extracted from pancreatic tumors established from control (wildtype) KPC1361 or Pikfyve-null KPC1361 in C57BL/6 mice. Tumor tissues were lysed with a tissuelyser in QIAzol lysis reagent, and RNAs were extracted with the RNeasy Mini kit (Qiagen), according to the instructions from the manufacturer.
The Eukaryote Total RNA Nano kit (Agilent Technologies; catalog #: 5067-1511) was used to check the quality of RNAs on an Agilent bioanalyzer. A total of 800ng RNA was then used for library preparation with the KAPA RNA Hyper+RiboErase HMR kit (Roche Diagnostics; Catalog #: 08098140702), following the instructions from the user manual. Briefly, the ribosomal RNA was removed by enzymatic digestion, and then the RNA was fragmented to around 200-300 bp with heat in fragmentation buffer. Synthesis of cDNA was conducted with reverse transcriptase and random primer, and then the second strand was synthesized to generate double-stranded cDNA. Following the repair of the DNA ends, NEB adapter was ligated, and the DNA are amplified with the KAPA HiFi HotStart mix and NEB dual barcode. Quality of the library was checked using the bioanalyzer with the Agilent DNA 1000 Kit (Agilent Technologies; catalog #: 5067-1504), and the sequencing was performed using NovaSeq 6000.

value: pancreatic tumor

tag: cell line

value: KPC

value: Pancreatic ductal adenocarcinoma

value: Pikfyve knockout


title: Kidney_MMU_vehicle-048


title: CD4HD01_EM

description: raw counts

value: Blood


title: 5WT

value: WT


title: 4WT


title: KPC1361_Pikfyve_KO_2


title: APPSWE-1349_s14_Cmpd-60-141

value: brain


title: CD4HD01_Ef

description: raw counts

value: CD4 T-cell


title: Kidney_MMU_vehicle-047

value: male


title: 2cKO


title: CD4HD01_CM

description: raw counts


title: CML Pt#1, CD34+, shZFX

type: RNA

city: Suzhou

first: Xiuyan

last: Zhang

address: 199 Ren'ai Road

institute: Soochow University

description: Gene expression of shZFX virus infected CML#1 CD34+ cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction buffer containing Agilent fragmentation agent and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, same volume of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-074348 Human LncRNA Oligo Microarrays (v6 4X180K) for 17 hours at 65°C in a rotating hybridization oven (Agilent, G2545A) with a speed of 10rpm. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3μm, Dye channel is set to Green).

data_processing: After generating the microarray scan images, the .tif images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028680_D_20199527) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CML patient #1, CD34+ cells, scramble

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent, 5190-2305) according to the manufacturer's instructions, followed by RNAeasy mini spin column purification (QIAGEN, 74106). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: The CD34+ cells, purified with EasySep CD34 positive selection kit, were cultured with SFM medium supplemented with a cocktail of cytokines, including SCF (100 ng/mL), Flt3-L (100 ng/mL), interleukin-3 (20 ng/mL), interleukin-6 (20 ng/mL) and G-CSF (20 ng/mL) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the Rneasy mini kit (QIAGEN, 74104) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 UV-VIS spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: CML CD34+ cells were infected with Scramble and shZFX virus, and after 72 hours GFP+ cells were sorted for RNA extraction.

tag: source name

value: CML CD34+ stem/progenitor cells


title: CML Pt#3, CD34+, shZFX

description: Gene expression of shZFX virus infected CML#3 CD34+ cells

source_name: CML patient #3, CD34+ cells, scramble


title: KPC1361_control_tumor_4


title: Kidney_MMU_vehicle-046


title: CML Pt#3, CD34+, scramble

description: Gene expression of scramble virus infected CML#3 CD34+ cells

source_name: CML patient #2, CD34+ cells, scramble


title: Mus musculus Liver MT10ppm [340287]

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

data_processing:
Data were processed using the Partek Flow software pipeline (2022 Partek Inc., St. Louis, MO, USA).
Read ends were trimmed by quality (Phred score <20), and read with lengths less than 25 base pairs were removed. Cleaned reads from the mouse liver study were aligned to Mus musculus (mm39)
Aligned mouse liver reads were quantified to Ensembl transcript release 106 while aligned larval fathead minnow reads were quantified to Refseq GCA_016745375.1 using Partek E/M.
Counts were filtered using a noise reduction function where it excludes any gene features with a median ≤ 8 counts across all samples. Counts were normalized to account for differences in library sizes using counts per million mapped reads (CPM). A pseudo count of 1 was added to all genes prior to log2 transformation.
Mouse transcriptomics data was also adjusted for batch effects resulting from experimental blocking and batch effects resulting from differences in who performed RNA isolations using a general linear model in Partek
Assembly: mm39
Supplementary files format and content: Raw count matrix in tab delimited format; Partek_OP-seq_mouse_raw_counts.txt
Supplementary files format and content: Normalized count matrix; Partek_OP-seq_mouse_processed_counts.txt
Library strategy: TempO-Seq

source_name: Liver

extract_protocol:
RNA was isolated and homogenized from ~20 mg of archived frozen liver tissue using RNAzol®RT (Molecular Research Center, Cincinnati, OH).RNA was purified using the RNeasy MinElute column protocol (Qiagen GmbH, Hilden, Germany) and evaluated for integrity using the Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). RNA was quantified spectrophotometrically (NanoDrop Technologies, Wilmington, DE). RNA samples were isolated and purified at Expression Analysis Genomic Services, Q2 Solutions (Durham, NC) or at U.S. EPA (Durham, NC).
Changes in gene expression were measured on purified RNA by Templated Oligo-Sequencing (TempO-Seq; BioSpyder Technologies, Carlsbad, CA) using the mouse whole transcriptome assay (30,146 probes targeting 21,448 genes) as previously described by Yeakley et al. 2017 (Yeakley, Shepard et al. 2017). Pre-designed Detector Oligo (DO) pairs were bound near each other on mouse mRNA target sequence sites allowing ligation. Unbound DOs were removed while bound and ligated DOs were amplified by PCR. During PCR sequencing adaptors and sample specific barcodes compatible with Illumina sequencers and software were also introduced. The PCR-amplified and barcoded samples were pooled into libraries for 50 base-pair sequencing on an Illumina HiSeq2500.
Templated Oligo-Sequencing (TempO-Seq) mouse whole transcriptome assay

value: Male

value: 8-weeks old

value: Liver

tag: time

value: 7 days

tag: dose (ppm)

tag: agent

value: Methidathion

tag: block

tag: rna isolator

value: EPA


title: RNF14 knockout, 30 min, rep2

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: ribosome footprints

data_processing:
Reads in the raw FASTQ files were trimmed to remove the adaptor, UMI sequence, and barcode with cutadapt. Noncoding sequence reads were removed via alignment by STAR 2.7.10a to a reference genome containing only noncoding RNA. Remaining reads were then mapped with STAR 2.7.10a the hg38 genome. Subsequent analyses were performed with custom python scripts.
Assembly: hg38
Supplementary files format and content: One CSV file containing the number of reads per gene in each of the samples in dataset 2 (in rpkm).
Library strategy: Ribo-seq

growth_protocol: HAP1 cells were grown in IMEM media at 37 C.

extract_protocol:
Cells were lysed with a buffer containing NP40 and cycloheximide to arrest translation.
Lysates were treated with RNase I. Ribosomes were then pelleted through a sucrose cushion. The pellets were resuspended and treated with proteinase K for 30 min and then mRNA footprints were extracted by phenol/chloroform. Footprint size selection (15-70 nt) was performed by gel extraction, followed by dephosphorylation, linker ligation, and reverse transcription. cDNA was circularized and amplified by PCR with barcode-containing primers.

treatment_protocol: Samples were treated with 5 uM 4SU for 18 h and irradiated with 6 kJ/m² UVA. Cells were then harvested after 0 or 30 min recovery.

value: RNF14 knockout

value: 5 uM 4SU and 6 kJ/m2 UVA


title: CML Pt#2, CD34+, shZFX

description: Gene expression of shZFX virus infected CML#2 CD34+ cells


title: Mus musculus Liver Con0ppm [340073]

value: Control

value: EA


title: KPC1361_control_tumor_3

value: pancreatic tumor

value: KPC

value: Pancreatic ductal adenocarcinoma


title: Kidney_MMU_Cmpd-60-055

source_name: Kidney of mouse treated with cmpd-60

value: Kidney

value: vehicle


title: CML Pt#1, CD34+, scramble

description: Gene expression of scramble virus infected CML#1 CD34+ cells


title: RNF14 knockout, 30 min, rep1

description: ribosome footprints


title: RNF14 knockout, 0 min, rep2

description: ribosome footprints


title: KPC1361_Pikfyve_KO_3

value: Pikfyve knockout


title: KPC1361_control_tumor_2

value: WT


title: Kidney_MMU_vehicle-045

value: male


title: Mus musculus Liver Con0ppm [340071]

value: Male

value: 8-weeks old


title: KPC1361_Pikfyve_KO_1


title: Kidney_MMU_Cmpd-60-054


title: Mus musculus Liver Con0ppm [340072]

value: Liver

value: 7 days


title: CML Pt#2, CD34+, scramble

description: Gene expression of scramble virus infected CML#2 CD34+ cells

value: CML CD34+ stem/progenitor cells


title: KPC1361_control_tumor_1


title: RNF14 knockout, 0 min, rep1

description: ribosome footprints

value: RNF14 knockout


title: EZH2_WT_3_D4

city: Cologne

first: Simon

last: Poepsel

address: Robert-Koch-Str. 21

department: Center for Molecular Medicine Cologne

country: Germany

institute: University of Cologne

data_processing:
Trimming was performed using bbduk1 (k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20)
Alingment with STAR2 v2.7.3a to mm10
Down sampling to 8 million reads with samtools3 v1.13
Reads were counted by HTSeq4 v2.0.1 (-m union -s no -t exon)
Differential expression analysis was performed using DESeq25 v1.38.3
Assembly: mm10
Supplementary files format and content: .txt file contains coun matrix per sample
Supplementary files format and content: .txt file contains up or down regulated genes rleative to WT

source_name: mESC-WT

growth_protocol: mESCs were maintained in GMEM supplemented with 20 % FBS, 2 mM Glutamine, 0.1 mM Non-essential amino acids, 1 mM Sodium pyruvate, 1x PenStrep, 50 µM 2-mercaptoethanol, 1000 U/mL LIF, 3 µM CHIR99021, and 1 µM PD0325901 on gelatinised plates at 37 °C with 5 % CO2.

extract_protocol:
NucleoSpin RNA Kit (MACHEREY NAGEL, cat. no. 740955) according to manufacturer’s protocol
QuantSeq 3’ mRNA Seq Library Prep Kit FWD with Unique Dual Indices for Illumina (Lexogen, cat. no 115.384)

treatment_protocol: Cells were differentiated with 0.1 µM retinoic acid in culture medium without LIF, CHIR99021, and PD0325901

value: mESC-WT

value: differentiated cell

value: RA

tag: time point

value: 4 days


title: WT, 30 min, rep2

description: ribosome footprints

value: 5 uM 4SU and 6 kJ/m2 UVA


title: Mus musculus Liver Con0ppm [340070]

tag: age

value: Control

value: EA


title: Kidney_MMU_Cmpd-60-052

value: Kidney

value: vehicle


title: Mus musculus Liver Con0ppm [340069]

value: EPA


title: EZH2_WT_3_D1

tag: cell type

value: 1 day


title: WT, 30 min, rep1

description: ribosome footprints

tag: genotype

value: WT


title: Kidney_MMU_Cmpd-60-051

tag: tissue

value: male


title: EZH2_WT_3_D0

value: murine embryonic stem cell


title: WT, 0 min, rep2

description: ribosome footprints


title: Kidney_MMU_Cmpd-60-053


title: EZH2_WT_2_D4


title: Kidney_MMU_Cmpd-60-050


title: Mus musculus Liver Con0ppm [340065]

tag: strain

value: Male

value: 8-weeks old

value: Liver

value: 7 days


title: Heart_MMU_vehicle-067

source_name: Heart of mouse treated with vehicle

value: Heart

tag: Sex


title: WT, 0 min, rep1

description: ribosome footprints


title: Mus musculus Liver PT80ppm [340063]

value: Parathion


title: RNA_RASGRP1-/-#3

city: New York

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt v3.5; then mapped to the human hg19 reference genome using STAR v2.7.9a.
Raw read counts were extracted using HTSeq-count v0.13.5.
Differential expression analysis was performed using DESeq2 v1.26.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read counts per gene for each Sample

extract_protocol:
RNA was harvested using Agilent Absolutely RNA microprep kit. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated using TruSeq RNA Sample Preparation (Illumina) following manufacturer's protocols.

value: hESC derived beta cells

value: Day 23


title: EZH2_WT_2_D1

value: mESC-WT

value: differentiated cell

value: RA


title: Heart_MMU_vehicle-066

tag: strain background

value: vehicle


title: EZH2_WT_2_D0

tag: treatment


title: Mus musculus Liver PT80ppm [340062]

value: EA


title: RNA_RASGRP1-/-#1


title: Mus musculus Liver PT80ppm [340061]


title: EZH2_WT_1_D4

value: 4 days


title: Heart_MMU_vehicle-065


title: RNA_RASGRP1-/-#2


title: EZH2_WT_1_D1

value: 1 day


title: Heart_MMU_vehicle-064

value: male


title: Mus musculus Liver PT80ppm [340060]


title: RNA_WT#3 (RASGRP1)

value: WT


title: Heart_MMU_vehicle-063


title: EZH2_WT_1_D0

value: murine embryonic stem cell


title: Heart_MMU_vehicle-062


title: RNA_WT#2 (RASGRP1)


title: Mus musculus Liver PT80ppm [340059]

value: Male

value: 8-weeks old


title: Mus musculus Liver Con0ppm [340066]

value: Liver

value: 7 days

value: Control


title: Mus musculus Liver PT80ppm [340056]

value: Parathion


title: RNA_WT#1 (RASGRP1)

value: hESC derived beta cells

value: Day 23


title: EZH2_EV_3_D4

source_name: mESC-EV

value: mESC-EV

value: differentiated cell


title: Heart_MMU_Cmpd-60-072

source_name: Heart of mouse treated with cmpd-60

value: Heart


title: RNA_DLK1-/-#3


title: Mus musculus Liver PT80ppm [340055]

value: EA


title: Heart_MMU_Cmpd-60-071


title: EZH2_EV_3_D0


title: Mus musculus Liver MT50ppm [340044]

value: Methidathion


title: EZH2_EV_3_D1

value: RA

value: 1 day


title: Heart_MMU_Cmpd-60-070

value: male


title: RNA_DLK1-/-#2


title: Heart_MMU_Cmpd-60-069


title: Mus musculus Liver MT50ppm [340043]


title: EZH2_EV_2_D1


title: EZH2_EV_2_D4

value: 4 days


title: Heart_MMU_Cmpd-60-068


title: Mus musculus Liver MT50ppm [340042]

value: Male


title: RNA_WT#2 (DLK1)

value: WT


title: Mus musculus Liver MT50ppm [340041]

value: 8-weeks old

value: Liver


title: EZH2_EV_2_D0

value: murine embryonic stem cell


title: EZH2_EV_1_D4


title: RNA_WT#3 (DLK1)


title: EZH2_EV_1_D0


title: Mus musculus Liver MT50ppm [340040]

value: 7 days


title: RNA_WT#1 (DLK1)

value: hESC derived beta cells


title: Brain_MMU_vehicle-031

source_name: Brain of mouse treated with vehicle

value: Brain

value: vehicle


title: Brain_MMU_vehicle-030


title: EZH2_EV_1_D1

value: mESC-EV

value: differentiated cell


title: ATAC_RASGRP1-/-#2

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt v3.4; then mapped to the human hg19 reference genome using Bowtie2 v2.26.2 with the parameters -X 2000 --very-sensitive -k 5.
Duplicate reads were discarded using Picard v2.26.2.
Genrich v0.6.1 was utilized to identify peaks in each replicate sample with the parameters -j -q 0.05 -a 200.0, -e to remove mitochondrial genome and regions not assembled into chromosomes, and -E to exclude ‘N’ homopolymers or high mappability regions in the genome.
The identified peaks were loaded into the R DiffBind package v3.2.1 for differential binding analysis.
Assembly: hg19
Supplementary files format and content: narrowPeak

extract_protocol:
50,000 cells are sorted in Weill Cornell Medicine Flow Cytometry Core Facility. Then cells were washed with 1000 μl of ice-cold PBS and resuspend the pellet in 25 μl of ice cold 1X ATAC Buffer [20mM Tris-HCl (pH 7.4), 20mM NaCl and 6mM MgCl2]. Incubate for 5 min on ice. Add 25 μl of ice cold ATAC-Detergent-buffer [20mM Tris-HCl (pH 7.4), 20mM NaCl and 6mM MgCl2, 0.2% Igepal CA-630, 0.2% Tween 20 and 0.02% Digitonin]. Mix throughout well. Incubate the samples on ice for another 3 min. Then samples are centrifuged and pellets are collected. Resuspend the pellet in the following transposase mixture (Per reaction): 25 μl 2X TD Buffer (Illumina 15027866), 2.5 μl TDE1 (Illumina 15027865), 16.5 ul PBS, 0.5 ul 1% Digitonin, 0.5 ul, 10% Tween-20 and 5 ul H2O. Incubate the reaction at 37°C for 30 min in thermomixer (Benchmark) set to 500 rpm. Tagmented DNA are purified with Zymo DNA clean and concentrator (Zymo research) according to manufacture instruction.
samples are submitted to Weill Cornell Medicine Epigenetics Core facility for library preparation

value: Day 23


title: Mus musculus Liver MT50ppm [340036]

value: Methidathion

value: EA


title: Brain_MMU_vehicle-029


title: Mus musculus Liver MT50ppm [340037]


title: RNA_DLK1-/-#1


title: EZH2_AMKR_3_D4

source_name: mESC-amKR

value: mESC-amKR

value: RA


title: ATAC_RASGRP1-/-#1


title: Brain_MMU_vehicle-028

value: male


title: Brain_MMU_vehicle-032


title: ATAC_WT#3 (RASGRP1)


title: Mus musculus Liver FT5ppm [340034]

value: Male

value: Fenthion


title: Brain_MMU_vehicle-027


title: Mus musculus Liver FT5ppm [340033]

value: 8-weeks old


title: EZH2_AMKR_3_D0


title: Mus musculus Liver FT5ppm [340032]

value: Liver


title: ATAC_WT#2 (RASGRP1)

value: WT


title: EZH2_AMKR_2_D4

value: 4 days


title: ATAC_RASGRP1-/-#3

value: hESC derived beta cells


title: Mus musculus Liver FT5ppm [340031]

value: 7 days


title: Brain_MMU_Cmpd-60-038

source_name: Brain of mouse treated with cmpd-60

value: Brain


title: Brain_MMU_Cmpd-60-037


title: EZH2_AMKR_2_D1

value: 1 day


title: ATAC_DLK1-/-#3


title: Brain_MMU_Cmpd-60-036


title: Mus musculus Liver FT5ppm [340030]


title: ATAC_DLK1-/-#1


title: Brain_MMU_Cmpd-60-035


title: EZH2_AMKR_3_D1

value: differentiated cell


title: EZH2_AMKR_1_D4


title: EZH2_AMKR_1_D1


title: Brain_MMU_Cmpd-60-034


title: EZH2_AMKR_1_D0

value: murine embryonic stem cell


title: ATAC_WT#2 (DLK1)

value: Day 23


title: Mus musculus Liver FT5ppm [340026]

value: EA


title: Mus musculus Liver PT40ppm [340024]

value: Parathion


title: ATAC_WT#3 (DLK1)


title: Mus musculus Liver PT40ppm [340025]


title: Brain_MMU_Cmpd-60-033


title: ATAC_WT#1 (RASGRP1)


title: Mus musculus Liver PT40ppm [340023]


title: ATAC_WT#1 (DLK1)


title: 4_A34

city: Shanghai

first: Pingping

last: Xu

address: 145 Middle Shandong Road

institute: Shanghai Institute of Digestive Diseases, Renji Hospital, Shanghai Jiao-Tong University School of Medicine

data_processing:
The raw data was checked by FastQC
Clean reads were aligned to the mouse genome using STAR 2.5
The expression of the transcripts was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: B16 tumor

extract_protocol:
Total RNA of tumor tissues was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B16 tumor

value: CHEK2-knock out

tag: condition

value: B16 CHEK2-knock out+anti-PD-1


title: BMDM, M2, B (biol rep 2)

city: Santa Barbara

first: Denise

middle: J.

last: Montell

state: CA

address: University of California Santa Barbara

department: Molecular Cellular and Developmental Biology

institute: University of California Santa Barbara

data_processing:
Subio Platform:1.24.5853
Sequence reads were trimmed and filtered for adaptor sequence/poly-G tail with the following parameters (cut mean quality: 20, unqualified percent limit: 20, length required: 30) using Fastp (0.20.1)
Trimmed reads were mapped to GRCm38 using HISAT2 (2.1.0) within Subio Platform (1.24.5853)
Read alignments were converted into assembled transcripts via StringTie (2.1.5) within Subio Platform (1.24.5853)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts and TPM values

molecule: polyA RNA

source_name: bone marrow

growth_protocol: Whole Bone Marrow (WBM) cells were plated in BMM medium (lymphocyte medium + 20% L929-conditioned medium) and differentiated for eight days to produce bone marrow-derived macrophages (BMDMs).

extract_protocol:
BMDMs were collected by detaching them using ice cold PBS+2%FBS+5mM EDTA. 1×106 cells were freshly frozen and frozen pellet was shipped to Genewiz (Azenta Life Sciences) to perform RNA-seq analysis
Illumina, RNA with PolyA selection

treatment_protocol: On day 7, fresh stimulation medium was added: for M1 activation, BMM with 100 ng/ml LPS with 50 ng/ml IFN-γ; for M2 activation, BMM with 20 ng/ml IL-4  was used.

value: bone marrow

value: macrophage


title: BMDM, M2, C (biol rep 3)


title: Mus musculus Liver PT40ppm [340022]

value: Male

value: 8-weeks old

value: Liver


title: Mus musculus Liver FT5ppm [340027]

value: Fenthion


title: EZH2_AMKR_2_D0

tag: cell line

value: mESC-amKR


title: 4_A32


title: ATAC_DLK1-/-#2

value: hESC derived beta cells


title: Rx32F-3ug-RNA-75ngul-T

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
STAR aligner for alignment
HTSeq for gene counts
Assembly: hg38
Supplementary files format and content: tab-delimited file with gene count data

source_name: Skeletal Muscle

extract_protocol: TruSeq Stranded

value: Skeletal Muscle

value: Primary Culture

value: Female

value: Testesterone


title: Mus musculus Liver PT40ppm [340021]

value: 7 days

value: EA


title: Rx32F-3ug-RNA-75ngul-E

value: Estrogen


title: BMDM, M1, C (biol rep 3)

value: IFN-gamma and LPS


title: 3_A49

value: B16 tumor

value: CHEK2-knock out

value: +PBS

value: B16 CHEK2-knock out+PBS


title: Rx32F-3ug-RNA-75ngul-C

value: Control


title: 3_44


title: Mus musculus Liver PT40ppm [340016]

value: Male

value: 8-weeks old

value: Liver

value: Parathion


title: PHO406-3ug-RNA-75ngul-T

value: Skeletal Muscle


title: 4_A36

value: B16 CHEK2-knock out+anti-PD-1


title: BMDM, M1, B (biol rep 2)

value: bone marrow

value: macrophage


title: BMDM, M1, A (biol rep 1)


title: Mus musculus Liver MT25ppm [340015]

value: 7 days

value: Methidathion


title: 3_30


title: BMDM, EK, C (biol rep 3)


title: 2_36

value: parental CHEK2-WT

value: B16 parental CHEK2-WT+PBS


title: Mus musculus Liver MT25ppm [340014]

value: EA


title: BMDM, M2, A (biol rep 1)


title: PHO406-3ug-RNA-75ngul-C

value: Primary Culture

value: Female


title: M522-3ug-RNA-75ngul-T

value: Testesterone


title: 2_35

value: B16 tumor

value: +PBS


title: Mus musculus Liver MT25ppm [340013]

value: Male

value: 8-weeks old


title: Mus musculus Liver MT25ppm [340012]

value: Liver


title: 2_21


title: M522-3ug-RNA-75ngul-E

value: Skeletal Muscle

value: Estrogen


title: 1_C97

value: B16 parental CHEK2-WT+anti-PD-1


title: Mus musculus Liver MT25ppm [340011]


title: BMDM, EK, A (biol rep 1)

value: bone marrow

value: macrophage


title: BMDM, WT, C (biol rep 3)


title: M522-3ug-RNA-75ngul-C

value: Control


title: Mus musculus Liver PT40ppm [340018]

value: 7 days

value: Parathion


title: BMDM, WT, B (biol rep 2)


title: 1_C57

value: parental CHEK2-WT


title: Mus musculus Liver MT25ppm [340008]

value: Methidathion

value: EA


title: BMDM, WT, A (biol rep 1)


title: J422-3ug-RNA-75ngul-T

value: Primary Culture

value: Testesterone


title: 1_A50

value: B16 tumor


title: BMDM, EK, B (biol rep 2)


title: Mus musculus Liver MT25ppm [340007]

value: Male


title: J422-3ug-RNA-75ngul-E


title: PHO406-3ug-RNA-75ngul-E

value: Female


title: Rasgef1b_cKO_LPS_4h_rep3

city: Jersey City

first: Thomas

middle: S

last: Postler

state: New Jersey

address: 95 Greene Street 5-018

department: Discovery Science

institute: International AIDS Vaccine Initiative

data_processing:
Base-calling with HiSeq Control Software (HCS). Raw sequence datawere converted into fastq files and de-multiplexed using Illumina bcl2fastq v2.17. One  mismatch  was  allowed  for  index  sequence identification.
Clipping and trimming of fastq files with Trimmomatic v0.39
Alignment with STAR v2.7.4a
Read counting with featureCounts function of Subread package v2.0.1
Read normalization with DESeq2 package v1.32.0 in R v4.1.2
Genome_build: Mus musculus GRCm38.100
Supplementary_files_format_and_content: Tab-delimited text file contains DESeq2-normalized counts for every gene and every sample

source_name: Bone-marrow-derived macrophages

growth_protocol: Eight- to 12-week-old mice were used to isolate bone marrow cells from the femurs and tibia bones to make cultures of BMDMs. Briefly, bone marrow cells were plated in non-treated tissue 10-cm plates and cultured in RPMI 1640 medium supplemented with 20% heat-inactivated FBS (Gibco Invitrogen, USA), 25 mM HEPES, 2 mM glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco, Invitrogen), 2-mercaptoethanol as well as 30% (v/v) L929 cell-conditioned medium. Culture medium was replaced by fresh medium every 2-3 days. Adherent macrophage monolayers were obtained within 7 to 9 days; these cells were >95% positive for F4/80 and CD11b antibodies staining as determined by flow cytometric analysis, identifying them as mature macrophages. Differentiated bone marrow-derived macrophages (BMDMs) were then harvested by gently resuspending the cells from the dishes using cold PBS and seeded onto cell cultures plates for the experiments. BMDMs were plated at 2x 10^6 cells per well in 6-well tissue culture plates. Cells were then left untreated or treated with 100ng/ml of lipopolysaccharide (LPS) from Escherichia coli O55:B5. After 4 hours incubation at 37oC in atmosphere of 5% CO2, the medium was discarded and the cells were washed in cold phosphate-buffered saline (PBS).

extract_protocol:
RNA was extracted with TRIzol.
mRNAs were enriched with Oligo(dT) beads. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: 100 ng/ml LPS for 4 h, as indicated

tag: mouse strain

tag: mouse genotype

value: 100 ng/ml LPS for 4 h


title: C66

source_name: MC38 tumor

value: MC38 tumor

value: CHEK2-knock out

value: MC38 CHEK2-knock out+anti-PD-1


title: J422-3ug-RNA-75ngul-C

value: Skeletal Muscle


title: C64


title: Rasgef1b_cKO_LPS_4h_rep2


title: Mus musculus Liver FT20ppm [340004]

value: 8-weeks old

value: Liver

tag: time

tag: dose (ppm)

value: Fenthion

value: EPA


title: C56


title: Mus musculus Liver FT20ppm [340003]

value: 7 days

tag: agent

tag: block


title: C62

value: +PBS

value: MC38 CHEK2-knock out+PBS


title: Ig29M-3ug-RNA-75ngul-E

value: Primary Culture

value: Estrogen


title: Mus musculus Liver FT20ppm [340002]

tag: rna isolator


title: Rasgef1b_cKO_untreated_rep3

value: untreated


title: Rasgef1b_cKO_LPS_4h_rep1


title: Ig29M-3ug-RNA-75ngul-T

value: Male

value: Testesterone


title: C19


title: Rasgef1b_cKO_untreated_rep2


title: HAN171-3ug-RNA-75ngul-T

value: Female


title: Rasgef1b_cKO_untreated_rep1


title: C8

value: MC38 tumor


title: Mus musculus Liver PT20ppm [340000]

tag: age

value: Parathion

value: EA


title: Mus musculus Liver FT20ppm [340005]


title: 977

value: parental CHEK2-WT

value: MC38 parental CHEK2-WT+anti-PD-1


title: Mus musculus Liver PT20ppm [339999]

value: 8-weeks old

value: Liver


title: HAN171-3ug-RNA-75ngul-E

value: Skeletal Muscle


title: HAN171-3ug-RNA-75ngul-C

value: Control


title: C25


title: WT_LPS_4h_rep2

value: wildtype

value: 100 ng/ml LPS for 4 h


title: 941


title: Mus musculus Liver PT20ppm [339997]

value: 7 days


title: WT_LPS_4h_rep1


title: H721-3ug-RNA-75ngul-E

value: Primary Culture

value: Estrogen


title: H721-3ug-RNA-75ngul-T


title: Ig29M-3ug-RNA-75ngul-C

value: Male


title: WT_untreated_rep3

value: untreated


title: C18

value: +PBS

value: MC38 parental CHEK2-WT+PBS


title: Mus musculus Liver FT20ppm [340001]

value: Fenthion


title: WT_untreated_rep2


title: H721-3ug-RNA-75ngul-C

value: Female


title: Dom24M-3ug-RNA-75ngul-T

value: Testesterone


title: C16

value: MC38 tumor

value: parental CHEK2-WT


title: Mus musculus Liver PT20ppm [339993]

value: 8-weeks old

value: Liver

value: Parathion

value: EA


title: Mus musculus Liver PT20ppm [339996]


title: C1


title: Mus musculus Liver PT20ppm [339992]


title: Dom24M-3ug-RNA-75ngul-E

value: Skeletal Muscle


title: WT_LPS_4h_rep3

value: wildtype

value: 100 ng/ml LPS for 4 h


title: 225VEH CONT

first: Raji

middle: M

last: Kumar

state: MINNESOTA

address: 200 1st street SW

department: Nephrology and Hypertension

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.6.1c
Gene counts were generated using the featureCounts facility from subread package 1.5.1 (http://subread.sourceforge.net/)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: GASTROCNEMIUS MUSCLE

growth_protocol: Muscle specific Vdr knock-out mice were generated;Briefly, male mice whose Vdr exon 3 was flanked with loxP sites (Vdrfl/fl mIce, a gift of S. Kato) were bred with female actin.iCre (Tg(ACTA1-cre/Esr1*)2Kesr) mice from Jackson Laboratories (Stock No. 025750). After weening, male mice were group-housed using a 12-hr light/dark cycle and fed a PicoLab Mouse Diet 205058 (LabDiet, St. Louis, MO) containing 3.4 IU/g vitamin D3 and 0.81% calcium ad libitum.

extract_protocol:
Flash-frozen skeletal muscle was crushed in a chilled mortar and pestle and homogenized in QIAZOL lysis reagent using a needle and syringe (Qiagen). QIAGEN miRNEASY Mini Kit was used to isolate total RNA from tissue homogenates
Illumina TruSeq Stranded mRNA library prep protocol

treatment_protocol: At age 6 months, male Vdrfl/fl.actin iCre mice were randomly assigned to receive tamoxifen (TAM) to induce expression of the Cre recombinase in skeletal muscle, or vehicle (corn oil) for 5 days. A group of Vdrfl/fl mice also received TAM to control for the potential effects of TAM in the absence of Cre recombinase. 75 microliters of TAM (100 mg/kg BW dissolved in 10% ethanol in corn oil) or vehicle (10% ethanol in corn oil) was administered intraperitoneally to Vdrfl/fl.actin iCre mice or Vdrfl/f mice for 5 days (Day 1 to Day 5). Glucose tolerance tests were performed before the administration of tamoxifen or vehicle and 10 days after the last tamoxifen or vehicle injection. Muscle strength was tested 10 days following the administration of tamoxifen or vehicle. Upon completion of in vivo studies, mice were euthanized, and peripheral skeletal muscle tissue was immediately collected and stored at -80 oC for analyses.

tag: age, sex and genomic component

value: 6 month old  male Vdrfl/fl.actin iCre mice

tag: vdr knockout inducing drug or control vehicle treatment

value: Vehicle Treated (10% ethanol in corn oil)

tag: phenotype

value: VEHICLE CONTROL


title: WT_untreated_rep1

value: untreated


title: Mus musculus Liver PT20ppm [339998]

tag: strain

value: Male

tag: tissue

value: 7 days


title: Mus musculus Liver FT20ppm [339989]

tag: Sex

value: Fenthion


title: 218VEH CONT


title: Dom24M-3ug-RNA-75ngul-C

value: Primary Culture

tag: genotype

tag: treatment

value: Control


title: CT26 POLE-mutant+anti-PD-1, 217

source_name: CT26 POLE-mutant+anti-PD-1

value: CT26 tumor

value: POLE-mutant


title: Mus musculus Liver FT20ppm [339987]

value: 8-weeks old

value: Liver


title: CT26 POLE-mutant+anti-PD-1, 203


title: AAS243-3ug-RNA-75ngul-T

tag: cell line

value: Female

value: Testesterone


title: CT26 POLE-mutant+anti-PD-1, 156


title: 217VEH CONT


title: 213VDR KO

value: Tamoxifen treated

value: VITAMIN D RECEPTOR KNOCKOUT


title: AAS243-3ug-RNA-75ngul-E

value: Skeletal Muscle

value: Estrogen


title: AAS243-3ug-RNA-75ngul-C


title: Mus musculus Liver FT2.5ppm [339985]

value: EA


title: Mus musculus Liver FT2.5ppm [339986]


title: CT26 POLE-mutant+anti-PD-1, M59


title: 200VDR KO

value: 6 month old  male Vdrfl/fl.actin iCre mice


title: A324-3ug-RNA-75ngul-T

value: Male


title: CT26 POLE-mutant+PBS, 205

source_name: CT26 POLE-mutant+PBS

value: PBS


title: A324-3ug-RNA-75ngul-E


title: Mus musculus Liver FT2.5ppm [339982]

source_name: Liver

value: 7 days

value: Fenthion


title: A324-3ug-RNA-75ngul-C

value: Primary Culture

value: Control


title: CT26 POLE-mutant+PBS, 223

value: CT26 tumor

value: POLE-mutant


title: 198VDR KO


title: MCEMP1 overexpression, TGF beta 24 hr, biol rep 2

city: Tampa

first: Theodoros

last: Karampitsakos

address: 560 Channelside D

institute: University of South Florida

data_processing:
Data were processed by Genewiz-Azenta
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text includes raw counts for each sample
Supplementary files format and content: tab-delimited text includes RPKM counts for each sample

source_name: Peripheral blood

growth_protocol: Transduced THP1 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), penicillin-streptomycin and puromycin 0.5ug/ml, in a humified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Rneasy Plus Mini Kit, with on-column DNAse digestion step.
total mRNA with poly(A) selection

treatment_protocol: Cells were transduced with lentivirus at a MOI of 50, selected with puromycin 0.5ug/ml. Cells were treated with TGF-beta 5ng/ml for 24 hours before RNA extraction.

value: Peripheral blood

tag: cell type

value: Acute leukemia monocyte

value: MCEMP1 overexpression

value: TGF beta 24 hr


title: MCEMP1 overexpression, TGF beta 24 hr, biol rep 3


title: MCEMP1 overexpression, TGF beta 24 hr, biol rep 1


title: Mus musculus Liver FT2.5ppm [339978]

value: 8-weeks old

value: Liver


title: CT26 POLE-mutant+PBS, M3


title: CT26 POLE-mutant+PBS, M44


title: MCEMP1 overexpression, no treatment, biol rep 3

value: no treatment


title: Mus musculus Liver FT2.5ppm [339979]

value: EA


title: CT26 POLE-mutant+anti-PD-1, M82


title: HAP1 cells, UV treated, rep3

description: ribosome footprints

data_processing:
Reads in the raw FASTQ files were trimmed to remove the adaptor and UMI sequence NNNNNNCACTCGGGCACCAAGGAC using the bbduk script in the BBtools suite. Noncoding sequence reads were removed via alignment by STAR 2.7.10a to a reference genome containing only noncoding RNA. Remaining reads were then mapped with STAR 2.7.10a the hg38 genome. Subsequent analyses were performed with custom python scripts.
Assembly: hg38
Supplementary files format and content: One CSV file containing the number of reads per gene in each of the samples (in rpkm).
Library strategy: Ribo-seq

treatment_protocol: Samples were treated with 5 uM 4SU for 18 h and irradiated with 6 kJ/m² UVA. Cells were then harvested after 30 min recovery.

value: near-haploid derivative of KBM-7

value: WT

value: 6 kJ/m2 UVA


title: HAP1 cells, UV treated, rep2

description: ribosome footprints


title: HAP1 cells, UV treated, rep1

description: ribosome footprints


title: Mus musculus Liver FT10ppm [339972]

value: Male

value: 7 days


title: MCEMP1 overexpression, no treatment, biol rep 2


title: Mus musculus Liver FT10ppm [339971]

value: Fenthion


title: Mus musculus Liver FT2.5ppm [339984]


title: CT26 POLE-mutant+PBS, M97

value: PBS


title: HAP1 cells, untreated, rep3

description: ribosome footprints


title: Mus musculus Liver FT2.5ppm [339983]


title: HAP1 cells, untreated, rep2

description: ribosome footprints


title: CT26-vector+anti-PD-1, 181

value: CT26 tumor

value: control


title: CT26-vector+anti-PD-1, M60


title: Mus musculus Liver FT10ppm [339970]


title: mock, TGF beta 24 hr, biol rep 3

value: Peripheral blood

value: mock


title: mock, TGF beta 24 hr, biol rep 2

value: Acute leukemia monocyte


title: HAP1 cells, untreated, rep1

description: ribosome footprints


title: Mus musculus Liver FT10ppm [339968]


title: CT26-vector+anti-PD-1, M40


title: HAP1 cells, 4SU and UV treated, rep2

description: ribosome footprints

value: 5 uM 4SU and 6 kJ/m2 UVA


title: Mus musculus Liver MT100ppm [339967]

value: 8-weeks old

value: Methidathion


title: Mus musculus Liver MT100ppm [339966]

value: Liver

value: EPA


title: mock, TGF beta 24 hr, biol rep 1

value: TGF beta 24 hr


title: mock, no treatment, biol rep 3

value: no treatment


title: MCEMP1 overexpression, no treatment, biol rep 1

value: MCEMP1 overexpression


title: HAP1 cells, 4SU and UV treated, rep1

description: ribosome footprints

value: near-haploid derivative of KBM-7

value: WT


title: CT26-vector+anti-PD-1, 176


title: CT26-vector+PBS, 183


title: CT26-vector+PBS, 155


title: Mus musculus Liver MT100ppm [339965]

value: Male

value: 7 days

value: EA


title: HAP1 cells, 4SU treated, rep3

description: ribosome footprints

value: 5 uM 4SU


title: HAP1 cells, 4SU treated, rep2

description: ribosome footprints


title: Mus musculus Liver MT100ppm [339964]


title: mock, no treatment, biol rep 2

value: Peripheral blood


title: shMCEMP1, TGF-beta 24 hr, biol rep 3

value: TGF-beta 24 hr


title: mock, no treatment, biol rep 1

value: Acute leukemia monocyte

value: mock


title: CT26-vector+PBS, M85

value: CT26 tumor

value: control

value: PBS


title: Mus musculus Liver FT10ppm [339969]

value: 8-weeks old

value: Liver

value: Fenthion


title: CT26-vector+PBS, M71


title: Mus musculus Liver MT100ppm [339963]

value: Methidathion


title: HAP1 cells, 4SU treated, rep1

description: ribosome footprints

value: near-haploid derivative of KBM-7


title: HAP1 cells, 4SU and UV treated, rep3

description: ribosome footprints

value: WT

value: 5 uM 4SU and 6 kJ/m2 UVA


title: CT26-vector+PBS, M68


title: Mus musculus Liver MT100ppm [339960]

value: Male

value: 7 days


title: PBMC of ASD patient 35 after oral medication, d

city: Daegu

first: Jong Pil

last: Kim

address: Cheomdan-ro 61

country: South Korea

institute: Korea Brain Research Institute

description: inDrops

data_processing:
inDrops single cell RNAseq
Raw fastq files were processed using inDrop.py pipline in Python availabe at https://github.com/indrops/indrops.
Cell barcodes containing fewer than 1000 total reads were discarded, and remaining reads were aligned to a reference human transcriptome (Ensembl GRCh38 release 100) using bowtie 1.2.3 (m = 200, n = 1, l = 15, e = 1000).
Aligned reads were then processed into counts of UMI-filtered transcripts per gene, and exported as a gunzipped TSV file.
(Supplementary files)  Cells with fewer than 500 UMIFM counts and 200 genes were removed.
Assembly: GRCh38.100
Supplementary files format and content: Count tab-separated values files (*counts.tsv.gz) are the raw, unfiltered gene expression matrices for each individually processed library from the Indrops processing pipeline. Metric tab-separated values files (*.metrics.tsv.gz) contain the single cell barcode information on Reads and UMIFM used for each sample.
Supplementary files format and content: (Supplementary file) For all samples, counts comma-sepearted value files (*count.matrix.csv.gz) represent filtered gene expression matrices (Genes x Cells) for each dornor with/without L-serine treatment. Cells with fewer than 500 UMIFM counts and 200 genes were discarded, and genes expressed in fewer than 10 cells were filtered out. Cells in the object were further filtered using the following parameters: log10GenesPerUMI : log10(run$nFeature_RNA) / log10(run$nCount_RNA)  > 80.

source_name: Blood

extract_protocol:
Fresh whole blood samples were obtained from volunteers using anticoagulant-containing tubes, such as BD Vacutainer® EDTA (ethylene diamine tetraacetic acid) tubes (BD Biosciences). PBMCs were isolated using SepMate-50 (StemCell Technologies) conical tubes according to the manufacturer's instructions. Briefly, 5 ml of blood was diluted with 5 ml phosphate-buffered saline (PBS). Diluted blood samples were centrifuged at 1200× g at room temperature for 10 min, and the top layer was transferred into a new 50 ml conical tube. PBMCs isolated after centrifugation (1200 × g for 10 min) were washed twice with PBS containing 2% fetal bovine serum (FBS). Enriched mononuclear cells were then filtered through a 70-μm cell strainer, which was subsequently rinsed. The cells were finally centrifuged again at 1000 × g for 5 min at 4 °C. This was followed by the removal of the supernatant and resuspension of the cell pellet in 400 µl of DMEM containing 0.04% BSA. The cells were counted and checked for viability using Trypan Blue staining.
Single-cell encapsulation were perfomed with barcoded hydrogel beads (1CellBio) to generate single-cell cDNA libraries. The cDNA libaries were prepared for sequencing, as described in Zilionis et al., 2017, Nature Protocols (PMID = 27929523)

treatment_protocol: Two ASD patients (both male, 3 and 4 years old) were oral-medicated with L-serine (400 mg) for 12 weeks

value: Blood

value: PBMC

value: L-serine (400 mg / day)


title: shMCEMP1, TGF-beta 24 hr, biol rep 1

value: Peripheral blood

value: Acute leukemia monocyte

value: TGF-beta 24 hr


title: CT26-vector+anti-PD-1, M562

value: CT26 tumor

value: control


title: scRNA_endothelial_SuHX_Myl9Abs_rep1

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for scRNA-seq were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
CD31+ endothelial cells recovered from the lungs of SuHx and control groups were stained with mouse PE anti-CD45 (103106, BioLegend), APC mouse anti-CD326 (118214, Biolegend), FITC mouse anti-CD31 (102405, Biolegend), and eBioscience Fixable Viability Dye eFluor 780 (65-0865-14, Invitrogen) for dead cell staining.  Live endothelial cells (CD31+, CD326-, CD45-) from mice were purified by BD FacsAria III (BD Bioscience) (10,000 cells each, cell viability >98%) and then encapsulated into droplets.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 following the manufacturer’s protocol (10X Genomics).  The generated scRNA-seq libraries were sequenced using a total of 127 cycles (paired-end reads) with a NovaSeq 6000 system (Illumina, Inc.)

treatment_protocol: To induce PAH in the lung of mice, male C57BL/6 mice (8-9 weeks old, Oriental Yeast Co., Ltd) were exposed to hypobaric hypoxia (370 mmHg, 10% O2) for one to three weeks as previously described43.  Meanwhile, Mice were subcutaneously injected weekly with Sugen 5416 (20 mg/kg, R&D Systems).  The control groups were housed at ambient barometric pressure (760 mmHg).  The mice were subcutaneously administered with either anti-Myl9/12 mAb (20mg/kg; 114-2G9; KAN Research Institute Inc.) or Control isotype Ab (104-6G4; KAN Research Institute Inc.) 3 times a week for 3 weeks.

value: Lung

value: endothelial cell

tag: status

value: SuHX

tag: antibody

value: Myl9 Abs


title: shMCEMP1, no treatment, biol rep 2

value: no treatment


title: Mus musculus Liver MT10ppm [339957]

value: 8-weeks old

value: Liver

tag: time

tag: dose (ppm)

value: Methidathion

value: EA


title: scRNA_endothelial_SuHX_Myl9Abs_rep2

description: 10x Genomics


title: shMCEMP1, no treatment, biol rep 3


title: PBMC of ASD patient 35 before oral medication, b

description: inDrops

value: Blood


title: PBMC of ASD patient 35 after oral medication, a

description: inDrops

value: PBMC


title: scRNA_endothelial_SuHX_rep2

description: 10x Genomics

value: Control Abs


title: scRNA_endothelial_SuHX_rep1

description: 10x Genomics


title: shMCEMP1, no treatment, biol rep 1

value: Peripheral blood


title: shControl, TGF-beta 24 hr, biol rep 3

value: Acute leukemia monocyte

value: shControl


title: Mus musculus Liver MT10ppm [339954]

value: Male

value: 7 days

tag: agent

tag: block


title: PBMC of ASD patient 35 after oral medication, c

description: inDrops

value: L-serine (400 mg / day)


title: Mus musculus Liver MT10ppm [339956]

tag: age

tag: rna isolator


title: Mus musculus Liver MT10ppm [339955]


title: scRNA_endothelial_Control_rep2

description: 10x Genomics

value: Lung

value: endothelial cell

value: Control


title: PBMC of ASD patient 72 before oral medication, c

description: inDrops


title: PBMC of ASD patient 35 after oral medication, b

description: inDrops


title: shMCEMP1, TGF-beta 24 hr, biol rep 2

value: TGF-beta 24 hr


title: scRNA_endothelial_Control_rep1

description: 10x Genomics


title: shControl, TGF-beta 24 hr, biol rep 2


title: Mus musculus Liver MT10ppm [339950]

value: 8-weeks old


title: PBMC of ASD patient 72 after oral medication, c

description: inDrops


title: P16

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

description: 10x Genomics

data_processing:
Cell barcode/feature (gene) matrices were generated from fastqs using Cellranger v6.0.2.
Assembly: mm10
Supplementary files format and content: *_barcodes.tsv.gz is a tab-separated values file with cell barcodes identified by Cellranger
Supplementary files format and content: *_features.tsv.gz is a tab-separated values file with features (genes) used by Cellranger
Supplementary files format and content: *_matrix.mtx.gz is a matrix market format sparse matrix of cell barcode/feature (gene) counts

source_name: spleen

extract_protocol:
Animals were euthanized and spleen and marrow were harvested as viable single cell suspensions.  Dead cell depletion was performed using the Miltenyi dead cell removal kit (130-090-101).
Single cells were isolated, barcoded cDNA was generated and libraries were constructed using the 10X Genomics 3' Capture kit v3 according to the manufacturer's instructions.

value: WT

value: spleen

tag: sample type

value: engraftment

tag: leukemia phenotype

value: No leukemia


title: shControl, TGF-beta 24 hr, biol rep 1


title: Mus musculus Liver MT100ppm [339959]

tag: strain

value: Liver

value: Methidathion

value: EA


title: shControl, no treatment, biol rep 3

tag: tissue

value: Peripheral blood

value: Acute leukemia monocyte

value: no treatment


title: PBMC of ASD patient 72 after oral medication, b

description: inDrops

value: Blood

value: PBMC


title: P15

description: 10x Genomics

source_name: marrow

value: marrow


title: Mus musculus Liver FT10ppm [339946]

tag: Sex

value: Male

value: 7 days

value: Fenthion


title: Mus musculus Liver FT10ppm [339945]

value: 8-weeks old


title: PBMC of ASD patient 72 after oral medication, a

description: inDrops

value: L-serine (400 mg / day)


title: shControl, no treatment, biol rep 1

tag: genotype

value: shControl


title: shControl, no treatment, biol rep 2

tag: treatment


title: PBMC of ASD patient 35 before oral medication, c

description: inDrops


title: Mouse Liver

city: San Diego

first: Viankail

middle: Osiris

last: Cedillo-Castelan

email: vcastelan@lji.org, viancastelan@gmail.com, gascui@lji.org, gabrielascuigac@gmail.com

address: 4334 Rous st

department: Bioinformatics

institute: La jolla institute for immunology

description: scRNA sequencing

data_processing:
Mouse cell libraries were mapped with Cell Ranger’s count pipeline for mm10.
Multiple libraries were aggregated with the aggr pipeline
Aggregated data were then imported into the R environment where Seurat57 (2.1.0) was used to filter and find clusters.
Cells with less than 200 genes and more than 2,500 genes were discarded. Cells with more than 5% UMIs coming from mitochondrial genes were filtered out. Genes expressed in less than 3 cells were ignored.
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized counts

source_name: Mouse Liver

extract_protocol:
Splenocytes and thymocytes were harvested by mechanical disruption on 70 μm nylon mesh followed by red blood cell (RBC) lysis and washing with Hank's Balanced Salt Solution (HBSS) (Gibco) supplemented with 10% FBS. Lung tissue was digested with Stemcell spleen dissociation medium, and mechanically dissociated using GentleMacs Dissociator (Miltenyi). Cells were strained though a 70 μm filter and washed with HBSS supplemented with 10% FBS followed by RBC lysis. Liver cells were harvested by mechanical disruption on 70 μm nylon mesh followed by 34% Percoll gradient before RBC lysis and washing. For MAIT cell enrichment before sorting, negative selection of cells was carried out using biotinylated antibodies against CD11b (clone M1/70), CD11c (clone M418), F4/80 (clone BM8.1), CD19 (clone 1D3), and TER-119 (clone TER-119).  These were used together with Rapidspheres (Stemcell Technologies) and either the Big Easy (Stemcell Technologies) or Easy eight magnets (Stemcell Technologies) and protocols from Stem Cell Technologies. MAIT cells were sorted using a FACSAria III (BD Biosciences).
Single-cell libraries prepared as per the manufacturer’s instructions (10x Genomics).
Samples were processed using 10X v2 chemistry, as per the manufacturer’s recommendations.

value: MAIT cells

value: Untreated/steady state


title: P13

description: 10x Genomics

value: engraftment

value: AML


title: Mouse Lung

description: scRNA sequencing

source_name: Mouse Lung

value: Lung


title: Mus musculus Liver MT10ppm [339953]

value: Liver

value: Methidathion

value: EA


title: PBMC of ASD patient 35 before oral medication, a

description: inDrops

value: Blood


title: Mouse Spleen

description: scRNA sequencing

source_name: Mouse Spleen

value: Spleen


title: PBMC of ASD patient 72 before oral medication, b

description: inDrops

value: PBMC


title: P11

description: 10x Genomics

value: marrow

value: T cell leukemia


title: HL60Rac2E62KLCKGFP, Dox TPA, R3 (biol rep 3)

data_processing:
Subio Platform:1.24.5849
Sequence reads were trimmed and filtered for adaptor sequence/poly-G tail with the following parameters (cut mean quality: 20, unqualified percent limit: 20, length required: 30) using Fastp (0.20.1)
Trimmed reads were mapped to GRCh38 using HISAT2 (2.2.1) within Subio Platform (1.24.5849)
Read alignments were converted into assembled transcripts via StringTie (2.1.5) within Subio Platform (1.24.5849)
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts and TPM values

growth_protocol: Cells were maintained at 37 °C with 5% CO2 in humidified atmosphere in RPMI 1640 medium with 10% heat-inactivated fetal bovine serum, 1 μg/mL puromycin.

extract_protocol:
1×106 cells were freshly frozen and frozen pellet was shipped to Genewiz (Azenta Life Sciences) to perform RNA-seq analysis
Illumina, RNA with PolyA selection

treatment_protocol: 32 nM 12-O-tetradecanoylphorbol-13-acetate (TPA) was added to differentiate HL60 cells to induce a macrophage-like phenotype and 1 μg/mL doxycycline to induce expression of control (LckGFP) or Rac2E62K-LckGFP.

tag: cell line

value: macrophages

value: Rac2E62K expression

value: TPA/PMA


title: HL60Rac2E62KLCKGFP, Dox TPA, R2 (biol rep 2)

tag: cell type


title: HL60Rac2E62KLCKGFP, Dox TPA, R1 (biol rep 1)


title: P12

description: 10x Genomics

value: spleen


title: Mouse Thymus

description: scRNA sequencing

source_name: Mouse Thymus

value: MAIT cells

value: Thymus


title: P10

description: 10x Genomics

value: engraftment

value: PreB ALL


title: PBMC of ASD patient 72 before oral medication, a

description: inDrops


title: P9

description: 10x Genomics


title: HeLa_5ug_mito_ATAC

city: Boston

first: Richard

middle: Stefan

last: Isaac

state: MA

address: 77 Avenue Louis Pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

data_processing:
Paired-end reads were aligned using bowtie2 (2.2.9) to chrM of Hg38 using the "--very-sensitive" parameter
Aligned sam file was converted to to bam format and sorted using samtools (1.3.1)
Duplicate reads were filtered using picard (2.8.0)
Reads were filtered for a quality score >30 using samtools (1.3.1)
Coverage tracks were generated using DeepTools (3.0.2) with: "--binSize 1", "--normalizeUsing CPM", "--extendReads 100"
Assembly: Hg38
Supplementary files format and content: bigWig

source_name: HeLa S3

growth_protocol: HeLa S3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Mitochondria were isolated after cell lysis by cellular fractionation. Mitochondria were resuspended in Permeabilization Buffer and repelleted.
Permeabilized mitochondria were resuspended in 50 µL transposition reaction mix with TDE1 (Illumina) and incubated for 30 min at 37C. Samples were purified using MinElute PCR Purification Kits (Qiagen)
DNA was minimally amplified and qPCR was performed to determine the number of additional cycles necessary. Additional cycles were then performed

value: HeLa S3

value: WT

tag: input mitochondria_(ug_protein)


title: HL60LCKGFP, Dox TPA, R3 (biol rep 3)

value: control


title: scATAC-Seq SKOV3 cells, trastuzumab resistant

first: Rossin

last: Erbe

address: 401 N Broadway

institute: Johns Hopkins School of Medicine

description: SKOV3 cells, trastuzumab resistant

data_processing:
Cell Ranger ATAC version 2.1
Assembly: hg38
Supplementary files format and content: MatrixMarket, bed

extract_protocol:
Nuclei were isolated for use with Chromium Single cell ATAC kit
library preparation was performed using Chromium Single Cell ATAC Reagent kit v1.1

value: Ovarian adenocarcinoma

value: trastuzumab


title: P8

description: 10x Genomics

value: primary disease

value: No leukemia


title: scATAC-Seq SKOV3 cells, trastuzumab sensitive

description: SKOV3 cells, trastuzumab sensitive

value: Medium


title: HL60LCKGFP, Dox TPA, R1 (biol rep 1)


title: scATAC-Seq FaDu cells, Ctx resistant

description: FaDu cells, Ctx resistant

source_name: FaDu

value: FaDu

value: Pharyngeal squamous cell carcinoma

value: Cetuximab


title: HC024_T

first: Russell

last: Jenkins

address: 55 Fruit Street

institute: Masschussetts General Hospital

description: Bulk RNA-seq Hürthle cell carcinoma

data_processing:
STAR used to perform alignment and generate BAM files
featureCounts R package used to perform read quantification and generate counts matrix
Assembly: hg19
Supplementary files format and content: txt file containing raw counts

source_name: Human tissue

extract_protocol: none provided

value: thyroid

tag: tissue type

value: tumor


title: P7

description: 10x Genomics

value: marrow

value: T cell leukemia


title: PBMC of ASD patient 72 before oral medication, d

description: inDrops

value: Blood

value: PBMC


title: P6

description: 10x Genomics

value: preB ALL


title: HC023_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: P14

description: 10x Genomics

value: spleen

value: engraftment

value: AML


title: Day 28 cells, TCDD group

city: East Lansing

first: D M Isha Olive

last: Khan

state: Michigan

address: 1129 Farm Lane

department: Pharmacology and Toxicology

institute: Michigan State University

description: 10X Genomics Chromium Single Cell 3’ v3 kit

data_processing:
Reads were processed by CellRanger software (v 2.1) from 10X Genomics.
Assembly: human genome GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hematopoietic cells

growth_protocol: Human cord-blood derived CD34+ HSPCs were thawed and resuspended in RPMI. Approximately 10,000 cells per well were cultured over a 28-day period in a 96-well flat-bottomed cell culture plate in media enriched with cytokines/growth factors.

extract_protocol:
Cells were harvested on day 0 and every 7 days from at least three pooled 96-wells from both the vehicle and TCDD treated experimental groups.
Library was performed according to the manufacter’s instructions (Single cell 3’ v3 protocol (version 3.2), 10X Genomics). Briefly, cell suspension was loaded with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The cDNA libraries were subjected to quality control analysis including a double-sided size selection using Solid Phase Reversible Immobilization (SPRI) beads. DNA fragments were selected with a size range between 400-1000 base pairs. cDNA libraries were then sequenced on an Illumina HiSeq platform at an average sequencing depth of 50,000 paired end reads per cell.

treatment_protocol: Cells were treated with either the control vehicle (0.02% DMSO) or 1 nM TCDD on day 0.

value: Hematopoietic cells

value: TCDD (1 nM)

tag: time

value: Day 28


title: scATAC-Seq A431 cells, Ctx resistant

description: A431 cells, Ctx resistant

value: Epidermoid carcinoma


title: P4

description: 10x Genomics

value: WT

value: primary disease

value: No leukemia


title: HC022_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: thyroid


title: HC022_N

description: Bulk RNA-seq normal thyorid

value: normal


title: P5

description: 10x Genomics

value: marrow


title: scATAC-Seq FaDu cells, Ctx sensitive

description: FaDu cells, Ctx sensitive

value: FaDu

value: Pharyngeal squamous cell carcinoma

value: Medium


title: Day 28 cells, Vehicle group

value: Vehicle


title: Day 21 cells, Vehicle group

value: Day 21


title: HC021_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: tumor


title: CITE-Seq ADT SKOV3 cells, trastuzumab resistant

description:
SKOV3 cells, trastuzumab resistant
ADT

data_processing:
fastqc v0.11.8
trimGalore v0.6.4
kallisto v0.46.1 and bustools 0.39.3
Assembly: ensembl-96
Supplementary files format and content: ADCC_CITEseq_RNA_Matrix.mtx matrix market file with RNA expression data; ADCC_CITEseq_Protein_Matrix.csv protein expression, geneNames.csv geneNames in order of RNA data; cellIdentity.csv cell identities for RNA data

extract_protocol:
RNA was harvested using 10X kit.
RNA libraries for RNA-seq were prepared using 10X Library Prep Kit following manufacturer's protocols.
CITE-seq

value: Ovarian adenocarcinoma

value: trastuzumab

tag: antibodies/tags

value: EGFR, HER-2, F3, FAS, CD49f, EpCAM, CD44, CD81, CD55


title: Day 14 cells, TCDD group

value: Hematopoietic cells

value: TCDD (1 nM)

value: Day 14


title: P3

description: 10x Genomics

value: spleen

value: primary disease

value: T cell leukemia


title: Day 21 cells, TCDD group


title: HL60LCKGFP, Dox TPA, R2 (biol rep 2)

value: macrophages

value: control

value: TPA/PMA


title: scATAC-Seq A431 cells, Ctx sensitive

description: A431 cells, Ctx sensitive

value: Epidermoid carcinoma


title: P2

description: 10x Genomics

value: AML


title: HC021_N

description: Bulk RNA-seq normal thyorid

value: thyroid

value: normal


title: HeLa_56ug_mito_ATAC

value: HeLa S3

value: WT


title: CITE-Seq ADT SKOV3 cells, trastuzumab sensitive

description:
SKOV3 cells, trastuzumab sensitive
ADT

value: Ovarian adenocarcinoma

value: Medium


title: Day 14 cells, Vehicle group

value: Hematopoietic cells

value: Vehicle


title: HC020_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: tumor


title: P1

description: 10x Genomics

value: spleen

value: PreB ALL


title: HC019_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: Day 7 cells, TCDD group

value: TCDD (1 nM)

value: Day 7


title: CITE-Seq ADT FaDu cells, Ctx sensitive

description:
FaDu cells, Ctx sensitive
ADT

value: FaDu

value: Pharyngeal squamous cell carcinoma

value: EGFR, HER-2, F3, FAS, CD49f, EpCAM, CD44, CD81, CD55


title: Day 7 cells, Vehicle group


title: HC018_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: CITE-Seq ADT A431 cells, Ctx sensitive

description:
A431 cells, Ctx sensitive
ADT

value: Epidermoid carcinoma


title: HC017_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: thyroid


title: CITE-Seq ADT A431 cells, Ctx resistant

description:
A431 cells, Ctx resistant
ADT

value: Cetuximab


title: Day 0 HSPCs

source_name: Hematopoietic stem and progenitor cells

value: Hematopoietic stem and progenitor cells

value: Untreated

value: Day 0


title: HC016_N

description: Bulk RNA-seq normal thyorid

value: normal


title: CITE-Seq mRNA SKOV3 cells, trastuzumab sensitive

description:
SKOV3 cells, trastuzumab sensitive
mRNA

value: Ovarian adenocarcinoma

value: Medium


title: HC015_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: tumor


title: CITE-Seq mRNA SKOV3 cells, trastuzumab resistant

description:
SKOV3 cells, trastuzumab resistant
mRNA

value: trastuzumab


title: pathways_LM8_3

city: RTP

first: Rick

middle: David

last: Fannin

address: 111 Tw Alexander Dr, MD D204

department: NIEHS/NIH

institute: Mr.

description: Immortalized human leiomyoma cells, female, benign tumor, age unknown.

hyb_protocol: Reporter and Capture probes were added according to the manufacturer’s directions (nanostring.com) to 50 ng of total RNA in a final volume of 15ul followed by hybridization for at least 14 hours at 65oC

scan_protocol: After sample processing according to manufacturer’s instructions on the nCounter Prep Station Model 5S, sample cartridges were scanned on an nCounter Digital Analyzer Model 5S, using 555 Fields of Vision (FOV) and the .rlf file 'NS_Cancerpath_C2535'.

data_processing: Data were adjusted utilizing the manufacturer's positive and negative control probes, as well as internal housekeeping genes. This nSolver adjusted data were then imported into Partek(v7.0), log2 transformed and quantile normalized.

source_name: human leiomyoma

growth_protocol: A human uterine leiomyoma cell line immortalized via retroviral transfection of telemorase (ht-UtLM) was generated by our laboratory. Human fibroblast and vulvar leiomyosarcoma (SKS-LMS-1) cell lines were cultured in DMEM medium supplemented with 10% FBS. All cultures were kept in a standard tissue culture incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated by extracting with Trizol ™ Reagent (ThermoFisher Cat# 15596026) and subsequently purifying with an Rneasy Mini Kit (Qiagen Cat#74104).

treatment_protocol: For 8-week Cd-exposure experiment, the ht-UtLM cultures were maintained continuously in ht-UtLM culture medium supplemented with 10 μM CdCl2 for 8 weeks. The culture medium was replaced with fresh medium with 10 μM CdCl2 every 3 days. Passage-matched control ht-UtLM cultures were run concurrently with Cd exposed cells. All cultures were kept in a standard tissue culture incubator at 37°C with 5% CO2.

value: control

value: female


title: pathways_LM8_1

value: human uterine leiomyoma cell line immortalized via retroviral transfection of telemorase (ht-UtLM)


title: CITE-Seq mRNA FaDu cells, Ctx resistant

description:
FaDu cells, Ctx resistant
mRNA

value: FaDu


title: HC015_N

description: Bulk RNA-seq normal thyorid


title: CITE-Seq ADT FaDu cells, Ctx resistant

description:
FaDu cells, Ctx resistant
ADT

value: Pharyngeal squamous cell carcinoma


title: CITE-Seq mRNA FaDu cells, Ctx sensitive

description:
FaDu cells, Ctx sensitive
mRNA


title: pathways_CRLM8_3

value: cadmium-treated


title: KD-USF1, rep3

city: Jinan

first: Wei

last: Dong

state: Shandong

address: Jing Wu Road 324#

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

description: H1299 cells were transfected with shRNAs specific against USF1, and DEGs in cell was analyzed by DNA micro-assay.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized by GeneChip Hybridization Wash and Stain Kit for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

label_protocol: Trizol method was used to extract total RNA from the samples. The extracted total RNA was examined by NanoDrop 2000 and Agilent Bioanalyzer 2100, and qualified samples were entered into the chip experiment.

growth_protocol: Human NSCLC cell lines H1299 was cultured in RPMI-1640 medium containing 0.1% double antibiotics (50 U/ml penicillin and streptomycin) and 10% fetal bovine serum, and were incubated at 37°C.

extract_protocol: Cells were collected (80% cell density in 6-well plates), centrifuged at 2000 RPM for 5 min, and supernatant was removed. 1 mL Trizol was added to the cell precipitate, which was fully mixed and stood at room temperature for 5 min, then transferred to a new 1.5 mL EP tube

treatment_protocol: H1299 cells were transfected with shRNAs specific against UGT1A3 or USF1

value: lung

value: non-small cell lung carcinoma cells

value: USF1 knockdown


title: HC014_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: thyroid


title: CITE-Seq mRNA A431 cells, Ctx resistant

description:
A431 cells, Ctx resistant
mRNA

value: Epidermoid carcinoma

value: Cetuximab


title: pathways_LM8_2


title: KD-USF1, rep2


title: NC-USF1, rep3

value: control for USF1 knockdown


title: KD-USF1, rep1


title: pathways_CRLM8_2


title: NC-USF1, rep1


title: NC-USF1, rep2


title: KD-UGT1A3

description: H1299 cells were transfected with shRNAs specific against UGT1A3 and DEGs in cell was analyzed by DNA micro-assay.

value: UGT1A3 knockdown


title: CITE-Seq mRNA A431 cells, Ctx sensitive

description:
A431 cells, Ctx sensitive
mRNA

value: Medium


title: HC016_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: tumor


title: HC014_N

description: Bulk RNA-seq normal thyorid

value: normal


title: pathways_CRLM8_1


title: HC013_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: Lung

description: scRNA sequencing

data_processing:
Libraries were mapped with Cell Ranger’s count pipeline.
Multiple libraries were aggregated with the aggr pipeline.
Aggregated data was then imported into the R environment where Seurat (v3.9.9.9008) ) was used to filter cells, normalize and find clusters.
Cells with less than 200 genes and more than 20,000 UMIs were discarded. Furthermore, cells with more than 15% UMIs coming from mitochondrial genes were filtered out. Genes expressed in less than 3 cells were ignored.
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: raw and normalized counts

source_name: Human Lung

extract_protocol:
Postnatal human thymus was obtained from children with congenital heart disease undergoing cardiac surgery at Rady Children’s Hospital, San Diego, CA. Only patients who meet the inclusion criteria and sign informed consent, are included in the study. Thymus tissue was processed by mechanical dissociation into a single cell suspension, strained and viable lymphocytes were purified by Lymphoprep (StemCell) density gradient centrifugation before cryopreservation. For lung and peripheral blood samples, written, informed consent was obtained from all subjects from the Institutional Review Board of La Jolla Institute for Immunology and the Southampton and South West Hampshire Research Ethics Board. Newly diagnosed, untreated patients with non-small cell lung cancer were prospectively recruited once referred. Freshly resected tumor tissue and, where available, matched adjacent non-tumor lung tissue was obtained from patients with lung cancer following surgical resection. Tissues were macroscopically dissected and slowly frozen in 90% FBS (Thermo Fisher Scientific) and 10% DMSO (Sigma) for storage, until samples could be prepared. Cryopreserved non-tumor lung tissue was mechanically dissociated and enzymatically digested as previously described55. Briefly, lung tissue was minced with a scalpel and digested enzymatically with 0.15 WU/mL of D-Liberase (Roche) and 800 U/mL of DNase I (Sigma-Aldrich) for 15 min at 37°C. Then it was disaggregated into a single-cell suspension by passing it through a 70 µm strainer and rinsing with cold buffer (1× phosphate-buffered saline (PBS), 2 mM EDTA, 0.5% BSA). PBMCs were isolated using density gradient before cryopreservation. MAIT cells were sorted using MR1 tetramers.
Single-cell libraries prepared as per the manufacturer’s instructions (10x Genomics).
Samples were processed using 10X v3 chemistry, as per the manufacturer’s recommendations.

value: MAIT cells were isolated from human lung.

value: Untreated/steady state

tag: donor

value: Cells were pooled from 4 donors.


title: PBMC

description: scRNA sequencing

source_name: Human PBMCs

value: MAIT cells were isolated from human PBMCs.


title: HC012_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: Thymus

description: scRNA sequencing

source_name: Human Thymus

value: MAIT cells were isolated from human thymus.

value: Cells were pooled from 5 donors.


title: p35SXAL2 roots biol rep 2

city: Milpa Alta

first: Claudio

middle: Augusto

last: Castañón-Suárez

state: Ciudad de México

address: Av. Sonora Norte #9, Barrio Santa Martha

department: Instituto de Ecología

country: Mexico

institute: UNAM

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Plants were grown in 0.2X Murashige-Skoog (MS) salt plant media (MP Biomedicals, cat #2633024), 0.5 g/L MES (Sigma-Aldrich), 1% sucrose (Sigma-Aldrich), 1% Bacto Agar (Becton, Dickinson and Company) and adjusted to pH 5.6 with KOH. Seeds were disinfected in rotation with absolute ethanol for 5 minutes followed by a 13-minute treatment with a solution containing 1% SDS and 5% chlorine. Subsequently, they were rinsed four times with sterile water. The seeds were stratified at 4 °C for 2-5 days under dark conditions and sown on square Petri dishes containing MS medium.

extract_protocol:
Root RNA was extracted from three independent biological replicates, with each replicate consisting of 100 plants. The plant tissues were rapidly frozen in liquid nitrogen and stored at -80ºC. RNA extraction was performed using the Quick-RNA Miniprep kit (Zymo Research). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The plates used for primary root growth and RT-qPCR assays were placed vertically in growth chambers kept at 21-23.5°C with a long day photoperiod (16-h light/8-h dark) and a light intensity of 110 μmoles m-2s-1.

value: Root

tag: ecotype

value: 7-day-old whole roots, excluding hypocotyls and cotyledons

value: XAL2/AGL14 overexpression

value: MS 0.2X


title: p35SXAL2 roots biol rep 3


title: xal2_2 roots biol rep 3

value: XAL2/AGL14 knockdown


title: p35SXAL2 roots biol rep 1


title: Healed stage-ODMLT  group 4

city: Hefei

first: Hui

last: Wang

address: 218 Jixi Road

institute: he First Affiliated Hospital of Anhui Medical University

description: Gene expression data from ODMLT patient at healed stage

hyb_protocol: After purification the labeled RNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies)

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test.
 The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05

source_name: ODMLT patient at healed stage

label_protocol: total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

extract_protocol: Exosomes were isolated from serum samples using the exoEasy Maxi Kit (Qiagen, Hilden, Germany), in accordance with the manufacturer’s protocol.Total RNA was extracted from exosome pellet using the miRNeasy Serum Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity(RIN) was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The blood was collected into serum-separating tubes and allowed to sit for 30-60min at room temperature prior to centrifugation.

value: serum exosome

tag: develpomental stage

value: patient at acute-stage


title: Healed stage-ODMLT  group 2


title: NC-UGT1A3

value: lung

value: non-small cell lung carcinoma cells

value: control for UGT1A3 knockdown


title: Healed stage-ODMLT  group 1


title: xal2_2 roots biol rep 2


title: Healed stage-ODMLT  group 5

value: patient at healed stage


title: HC011_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: thyroid

value: tumor


title: D028.13

city: HOUSTON

first: Rui

last: Chen

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
The quality of raw sequencing data was first evaluated by FastQC (version 0.11.9)
Low quality reads and adapters were then trimmed by Trimmomatic (version 0.4.0)
Reads that passed quality control were aligned to GRCh38 using the 2-pass mode of STAR (version 2.7.7b)
Read counts were obtained by featureCount (version 1.22.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: nuclear RNA

source_name: macula retina

extract_protocol:
These samples came from 23 individuals aged 73-84 years old, who died of respiratory or heart failure, or from a myocardial infarction. The human donor eyes were obtained with the Utah Lions Eye Bank. We include samples within 6 hours post-mortem for this study. Dissections of donor’s eyes were carried out immediately according to a previously published protocol (Owen et. al., Investig. Ophtalmol. Vis. Sci., 2019). Specifically, the macula retina tissue was collected using a 6 mm disposable biopsy punch (Integra, Cat # 33–37) and flash frozen and stored at −80 °C. Donors with any history of retinal degeneration, diabetes, macular degeneration, or drusen were not used for this study; also each donor underwent an ophthalmology check to ensure the eye is in healthy condition. Matched samples with the snRNAseq were used for RNA isolation by applying TRIzol (Invitrogen) to the separated single-nuclei resuspension. cDNA were prepared from ∼1ng of total RNA by using the Smartseq v4 ultra low input RNA Kit according to the manufacturer’s directions (Takara).
Libraries were made using Nextera XT library prep (Illumina).

tag: sample condition

value: Normal

tag: ethnicity

value: Caucasian

tag: age

tag: gender

value: Male


title: xal2_2 roots biol rep 1

tag: tissue


title: D027.13


title: Acute-stage-ODMLT  group 5

description: Gene expression data from ODMLT patient at acute-stage

source_name: ODMLT patient at acute-stage


title: Col_0 roots biol rep 3

value: WT


title: HC010_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: D026.13


title: HC013_N

description: Bulk RNA-seq normal thyorid

value: normal


title: Col_0 roots biol rep 2

value: Root

value: 7-day-old whole roots, excluding hypocotyls and cotyledons


title: HC010_N

description: Bulk RNA-seq normal thyorid


title: Acute-stage-ODMLT  group 3


title: HC012_N

description: Bulk RNA-seq normal thyorid


title: D030.13

value: Female


title: D021.13


title: Col_0 roots biol rep 1

value: MS 0.2X


title: Acute-stage-ODMLT  group 4

value: serum exosome


title: Healed stage-ODMLT  group 3

value: patient at acute-stage


title: HC009_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: Acute-stage-ODMLT  group 2


title: D019.13


title: O2: Oocytes, rep5

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

data_processing:
read trimming (Trim Galore! v0.6.1)
read mapping (Hisat2 v2.1.0)
data quantification (Seqmonk)
Assembly: HetGla2/HetGla_female_1.0; Cavpor3.0; degu sequences XM_023711114.1, XM_004630806.2 and XM_023716073.1
Supplementary files format and content: txt file with raw read counts of individual genes

organism: Heterocephalus glaber

source_name: oocytes

growth_protocol: Oocytes were isolated from freshly sacrificed females by manual disruption of the ovary in M2 media and washed in PBS.

extract_protocol:
Picopure RNA extraction kit (Arcturus)
Ribosomal RNA was depleted with NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) with sample purification beads (NEB, E7405) according to the manufacturer’s instructions, including DNase treatment by TURBO DNase (Thermo Fisher Scientific, AM2238) followed by library preparation using NEBNext Ultra II Directional RNA Library Prep with sample purification beads (NEB, E7765S) according to the manufacturer’s instructions.

value: oocytes


title: D017.13


title: O1: Oocytes, rep4