title: BME without astrocyte and pericytes at day 6, sample 2

status: Public on Jan 18 2024

city: Kobe

first: Masaya

last: Hagiwara

state: Hyogo

address: 6-7-1 Minatojima-minamimachi Chuo-ku

institute: RIKEN BDR

data_processing:
To investigate the contribution of co-culturing astrocytes and pericytes with BMEC to BBB maturation, genes with significantly (false discovery rate, FDR < 0.05) higher expression levels in day 6 A/P only compared to day 6 BMEC only were first identified (2966 genes) and excluded to eliminate the effects from just having the presence of astrocytes and pericytes.
Then, genes that were consistently higher or lower in day 2, 4, and 6 BBB compared to day 2 BMEC only were extracted (114 genes) to study the synergistic effects of co-culturing BMEC with astrocytes and pericytes over the 6-day culture period.
Assembly: UCSC hg38 refGene
Supplementary files format and content: Supplementary Data 2.xlsx (logCPM, logFC, etc.)

source_name: IMR-90-4, Normal human primary astrocyte, Normal human primary pericytes

growth_protocol: IMR90-4 iPSCs (WiCell, WB65317; karyotyped as normal by supplier) between passages p35~45 were maintained on Matrigel-coated dishes in mTeSR Plus medium (STEMCELL Technologies, 100-0276)

extract_protocol:
Total RNA was extracted using Total RNA Extraction Miniprep System (Viogene, GR1001) and quantified using Eppendorf BioSpectrometer basic.
Libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Ligation Kit and IDT for Illumina RNA UD Indexes Set following manufacturer's protocol.

treatment_protocol: On Day 0 of differentiation, medium was switched to neural-endothelial differentiation medium which was DMEM/F12 Ham without L-glutamine (Sigma-Aldrich, D6421) supplemented with 20% KnockOut serum replacement (KOSR; Life Technologies, 10828010), 0.1 mM 2-mercaptoethanol (Nacalai Tesque, 21438-82), 1% MEM non-essential amino acid (NEAA; Nacalai Tesque, 06344-56), and 1% GlutaMAX supplement (Gibco, 35050061). After 6 days of neural-endothelial differentiation, the medium was switched to BMEC maturation medium, which comprises human endothelial serum-free medium (hESFM; Gibco, 11111044) with 1% human platelet poor-derived serum (HS; Sigma-Aldrich, P2918), 20 ng/mL basic FGF (bFGF; Fujifilm Wako, 060-04543), and 10 μM all-trans retinoic acid (ATRA; Nacalai Tesque, 36331-44).

tag: cell line

tag: treatment


title: BME without astrocyte and pericytes at day 6, sample 3

type: SRA

country: Japan

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: IMR-90-4, Normal human primary astrocyte, Normal human primary pericytes


title: BME without astrocyte and pericytes at day 4, sample 2


title: BME without astrocyte and pericytes at day 4, sample 1


title: Astrocyte and pericyte at day 6, sample 2

value: Astrocyte and pericyte at day 6


title: Astrocyte and pericyte at day 6, sample 3


title: BME without astrocyte and pericytes at day 6, sample 1


title: BME without astrocyte and pericytes at day 4, sample 3


title: R15274

status: Public on Jan 19 2024

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 E Cornwallis Rd

country: USA

institute: RTI  International

data_processing:
Transcripts were quantified using GENCODE v40 (GRCh38) transcriptome with Salmon (v 1.1.0).
Gene-level quantification was done with the tximport R package (v1.14.2).
Assembly: GRCh38/ GENCODE v40
Supplementary files format and content: compressed tab-deliminated text file including raw counts for each sample

source_name: Nucleus Accumbens

extract_protocol:
Total RNA was extracted from ~100 mg of tissue using the RNeasy kit (Qiagen) according to the manufacturer's protocol.
Illumina TruSeq Total RNA Stranded RiboZero Gold (Illumina Inc, San Diego, CA) was used for library prep.

tag: tissue

value: Nucleus Accumbens

tag: dsm-5 aud status

tag: Sex

value: F

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: current smoker at death

value: Control

tag: pmi

tag: rin

tag: sample plate

tag: sample well

tag: brain number


title: BME with astrocyte and pericytes at day 4, sample 1


title: BME with astrocyte and pericytes at day 2, sample 2


title: BME without astrocyte and pericytes at day 2, sample 3


title: BME with astrocyte and pericytes at day 2, sample 1


title: WTC-11, 3CHIR+tranilast, rep3, ATACseq

city: Birsbane

first: Nathan

middle: J.

last: Palpant

state: QLD

address: 306 Carmody Road

country: Australia

institute: University of Queensland

library_source: genomic

data_processing:
The quality of raw sequencing data (fastq files) was assessed using FastQC (v 0.11.8)
Bowtie2 was used for alignment
Picard tools was used to mark and remove duplicates
SAMtools was used to sort and obtain high-quality mapped reads and to remove reads from the mitochondrial chromosome
Peak calling was performed using the MACS2 callpeak command
Assembly: hg38
Supplementary files format and content: bw files and txt files

molecule: genomic DNA

extract_protocol:
The samples were processed following protocol described in Corces et al. (DOI: 10.1038/nmeth.4396).
The sequencing libraries were generated following protocol described in Corces et al. (DOI: 10.1038/nmeth.4396)

treatment_protocol: WTC-11 hiPSCs were seeded onto a 24-well plate at a density of 150k cells per well. Cells were differentiated at day 0 under 1 µM CHIR, 1 µM CHIR+50 µM Tranilast, 3 µM CHIR, and 3 µM CHIR+50 µM Tranilast in the presence of 500 µg/mL BSA and 213 µg/mL AA.

tag: cell type

value: human iPSCs

tag: genotype

value: WT

value: 3 uM CHIR+50 uM Tranilast


title: WTC-11, 3CHIR+tranilast, rep1, ATACseq


title: BME with astrocyte and pericytes at day 6, sample 2


title: BME with astrocyte and pericytes at day 4, sample 2


title: BME with astrocyte and pericytes at day 2, sample 3


title: Astrocyte and pericyte at day 6, sample 1


title: BME without astrocyte and pericytes at day 2, sample 2


title: BME with astrocyte and pericytes at day 6, sample 3


title: BME without astrocyte and pericytes at day 2, sample 1


title: WTC-11, 1CHIR+tranilast, rep2, ATACseq

value: 1 uM CHIR+50 uM Tranilast


title: BME with astrocyte and pericytes at day 6, sample 1


title: WTC-11, 3CHIR, rep3, ATACseq

value: 3 uM CHIR


title: WTC-11, 3CHIR, rep2, ATACseq


title: BME with astrocyte and pericytes at day 4, sample 3


title: WTC-11, 1CHIR+tranilast, rep1, ATACseq


title: WTC-11, 1CHIR, rep1, ATACseq

value: 1 uM CHIR


title: WTC-11, 3CHIR, rep1, ATACseq


title: WTC-11, 1CHIR+tranilast, rep3, ATACseq


title: WTC-11, 1CHIR, rep2, ATACseq


title: root, CK, rep1

city: Harbin

first: Yang

last: Shangjun

address: Mucai Street

country: China

institute: Northeast Agricultural University

organism: Glycine max

source_name: root

extract_protocol: RNA was extracted with TRIzol (thermofisher, 15596018), and the repository was constructed with illumina NovaseqTM 6000 (LC Bio Technology CO.,Ltd. Hangzhou,China).

treatment_protocol: Cd 70mg/L

value: root

value: control

value: Soybean root cell

tag: cultivar

value: Williams 82


title: root, CKOP, rep1

value: control+OP


title: root, CKOP, rep2


title: root, CK, rep3


title: WTC-11, 3CHIR+tranilast, rep2, ATACseq


title: root, CKOP, rep3


title: root, CdOP, rep1

value: Cd+OP


title: root, CdOP, rep2


title: root, CK, rep2


title: root, CdOP, rep3


title: root, Cd, rep3

value: Cd


title: root, Cd, rep2


title: root, Cd, rep1


title: GEX, sample 4, scRNAseq

city: Boston

first: Dan

last: Duda

state: MA

address: 55 Fruit St

department: Radiation Oncology

institute: Massachusetts General Hospital

description: 10X Genomics Cell Multiplexing Oligo Labeling technology

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Cells were clustered by Seurat and were annotated by the representative markers.
Assembly: mm10-2020-A
Supplementary files format and content: h5 and rds files, matrix files

organism: Mus musculus

source_name: tumor

extract_protocol:
Tissue samples from 5 mice (2 mice from GC group, 3 mice from GC+ICB group) were processed with mechanical chopping with blades, then disociated with Collagenase Type I (Worthington), Hyaluronidase (Sigma H3506), and DNase I (Sigma DN25). The cell suspension was passed through a 70-um filter, followed by 1×RBC lysis buffer treatment. A magnetically activated cell sorting (MACS) column was used to obtain CD45+ and CD45– cells from each tumor sample, and then the cells were mixed at a ratio of 1:1 and captured using the 10x Chromium controller.
Single cells were processed with the Chromium Controller Single Cell Platform using the Gel Bead, Chip and Libraray Kits (10x Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, samples were processed using kits pertaining to the Chromium Next GEM Single Cell 3' Kit v3.1 barcoding chemistry of 10x Genomics. Libraries were constructed according to the standard 10x Genomics protocol (Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols, and Single Cell 3’ Reagent Kits v3.1 (dual index) User Guide) with dual index and performed the paired-end sequencing on NextSeq 2000 (llumina, San Diego, CA). The same library was sequenced across two flowcells, with two lanes per flowcell (4 lanes in total).

value: tumor


title: GEX, sample 3, scRNAseq


title: CMO, sample 4, scRNAseq


title: CMO, sample 3, scRNAseq


title: GEX, sample 2, scRNAseq


title: CMO, sample 2, scRNAseq


title: GEX, sample 1, scRNAseq


title: WTC-11, 1CHIR, rep3, ATACseq


title: Cortical cells, AAV-CTRL,

city: New Haven

first: Jean

last: Bouchart

state: CT

address: 300 Georges Street

department: Neurology

country: France

institute: Yale University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.1.1 (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: Brain

extract_protocol:
To generate single nuclei transcriptome profiles for mouse brains we used a total of 10 brain samples from adult male mice (8 weeks-old). Five brains from  AAV-mVEGF-C and AAV-CTRL mice were collected,  cryopreserved, pooled, and then processed according to the procedure of nuclei isolation, as previously reported (S. Ma et al. 2022). The brain cell nuclei were isolated according to our previous protocol (10, 13, 41). To avoid anatomical experimental bias for cell nuclei isolation, frozen samples were next finely pulverized to powder in liquid nitrogen with mortar and pestle (Coorstek #60316, #60317). All buffers were ice-cold and all reagents used for consequent nuclear isolation were molecular biology grade unless stated otherwise. 20-30 mg of pulverized tissue was added into 5 ml of ice-cold “lysis buffer”: 320 mM sucrose (Sigma #S0389), 5 mM CaCl2 (Sigma #21115), 3 mM Mg(Ace)2 (Sigma #63052), 10mM Tris-HCl (pH 8; AmericanBio #AB14043), protease inhibitors without EDTA (Roche #11836170001), 0.1 mM EDTA (AmericanBio #AB00502), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186), 0.1% TX-100 (v/v) (Sigma #T8787) nuclease-free water (AmericanBio #AB02123). Reagents: DTT, RNAse Protector, protease inhibitors, TX-100 were added immediately before use. The suspension was transferred to Dounce tissue grinder (15ml volume, Wheaton #357544; autoclaved, RNAse free, ice-cold) and homogenized with loose and tight pestles, 30 cycles each, with constant pressure and without introduction of air. The homogenate was strained through 40-µm tube top cell strainer (Corning #352340) pre-wetted with 1ml “isolation buffer”: 1800 mM sucrose (Sigma #S0389), 3 mM Mg(Ace)2 (Sigma #63052), 10mM Tris-HCl (pH 8) (AmericanBio #AB14043), protease inhibitors without EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186), nuclease-free water (AmericanBio #AB02123). Additional 9 ml of “isolation buffer” was added to wash the strainer. Final 15 ml of solution was mixed by inverting the tube 10x and carefully pipetted into 2 ultracentrifuge tubes (Beckman Coulter #344059) onto the “isolation buffer” cushion (5 ml) without disrupting the phases. The tubes were centrifuged at 30000 x g, for 60 min at 4 ˚C on the ultracentrifuge (Beckman L7-65) and rotor (Beckman SW41-Ti). Upon end of ultracentrifugation, the supernatant was carefully and completely removed and 100 ul of resuspension buffer (250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186), nuclease-free water (AmericanBio #AB02123)) was added dropwise on the pellet in each tube and incubated on ice for 15 minutes. Pellets were gently dissolved by pipetting 30x with 1ml pipette tip, pooled and filtered through 35-µm tube top cell strainer (Corning #352235). Finally, nuclei were counted on hemocytometer and diluted to 1 million/ml with “sample-run buffer”: 0.1% BSA (Gemini BioProducts #700-106P), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186) in DPBS (Gibco #14190). The nuclei samples were placed on ice and taken to Yale Center for Genome Analysis core facility and processed within 15 minutes for snRNA-seq with targeted nuclei recovery of 10,000 nuclei (4 reactions/technical replicates for sum of 40,000 per biological sample), respectively, on microfluidic Chromium System (10x Genomics) by following the manufacturer’s protocol (10x Genomics, CG000183_Rev_A), with Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, (10x Genomics #PN-1000075) and Chromium Single Cell B Chip Kit (10x Genomics #PN1000074), Chromium i7 Multiplex Kit (10x Genomics #PN-120262) on Chromium Controller (10x Genomics). Due to limitations imposed by source RNA quantity, cDNA from nuclei was amplified for 14 cycles
Post cDNA amplification cleanup and construction of sample-indexed libraries and their amplification followed manufacturer’s directions (10x Genomics, CG000183_Rev_A), with the amplification step directly dependent on the quantity of input cDNA. In order to reach sequencing depth sufficient for characterization of all cells, we targeted 30,000 raw reads per nucleus. Single nucleus libraries were run using paired end sequencing with single indexing on the HiSeq 4000 platform (Illumina) by following manufacturer’s instructions (Illumina; 10x Genomics, CG000183_Rev_A). To avoid lane bias, multiple uniquely indexed libraries were multiplexed and distributed over several lanes. The lanes product were then freezed and kept for further analysis in a second run of the same lanes.
single nuclei RNA-seq

value: Brain cells

value: Brain

tag: age

value: 8 weeks old


title: Striatal cells, AAV-VEGF-C,

description: 10x Genomics


title: Striatal cells, AAV-CTRL,

description: 10x Genomics


title: Cortical cells, AAV-VEGF-C,

description: 10x Genomics


title: HEK293T, RNA-Seq, rep1

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

description: batch1: NextSeq 500, batch2: HiSeq 2000

data_processing:
Adapter and quality trimming was performed with cutadapt v2.10 with the following parameters: "-a ATCGTAGATCGGAAGAGCACACGTCTGAA --minimum-length 20 --trimmed-only" for Ribo-Seq; "--minimum-length 20" for RNA-seq; "-q 20" and "--nextseq-trim=20" were added to the command line when processing the batches sequenced with HiSeq 2000 and NextSeq 500, respectively.
Mapping to the hg38 genome assembly with GENCODE v29 genome annotation (modified to include spike-ins) was performed with STAR v2.7.6a (default parameters). Gene-level read counts were obtained by STAR.
Assembly: hg38
Supplementary files format and content: File format: tsv, tab-separated plain text files. File contents: the files include the read counts per gene (including spike-ins) estimated by STAR.

molecule: cytoplasmic RNA

source_name: cell line

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin, and 100 µg streptomycin.

extract_protocol:
Cells were chilled on ice and washed with PBS + cycloheximide (100 µg/ml), lysed with buffer containing 20 mM Tris-HCl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide (Sigma-Aldrich), 25 U/ml TURBO DNase (Ambion). The lysate was divided into two parts for Ribo-Seq and RNA-Seq library preparation. Nuclease footprinting and ribosome recovery for Ribo-Seq library preparation were performed according to (McGlincy 2017, PMID: 28579404). The adapter for Ribo-Seq had a UMI-sequence (5 random nucleotides) for deduplication. Total RNA for RNA-Seq library preparation was isolated using TRIzol LS Reagent (Thermo Fisher Scientific). The rRNA depletion was performed using a RiboMinus™ Eukaryote Kit v2 (Thermo Fisher Scientific) according to the manufacturer’s recommendations.
RNA-Seq libraries were constructed using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).
Ribo-Seq libraries were obtained according to (McGlincy 2017, PMID: 28579404) using CircLigase II (Lucigen), custom adapter with UMI-sequence (5 random nucleotides), and NEBNext Multiplex Oligos for Illumina Index Primers Set (NEB).

value: cell line

tag: cell line

value: Human Embryonic Kidney

value: wt

tag: library type

value: RNA-Seq


title: HEK293T, Ribo-Seq, rep1

description: batch1: NextSeq 500, batch2: HiSeq 2000

data_processing:
Adapter and quality trimming was performed with cutadapt v2.10 with the following parameters: "-a ATCGTAGATCGGAAGAGCACACGTCTGAA --minimum-length 20 --trimmed-only" for Ribo-Seq; "--minimum-length 20" for RNA-seq; "-q 20" and "--nextseq-trim=20" were added to the command line when processing the batches sequenced with HiSeq 2000 and NextSeq 500, respectively.
Deduplication was performed with "seqkit rmdup --by-seq", and random 5nt barcodes were then removed with "cutadapt -u -5".
Mapping to the hg38 genome assembly with GENCODE v29 genome annotation (modified to include spike-ins) was performed with STAR v2.7.6a (default parameters). Gene-level read counts were obtained by STAR.
Assembly: hg38
Supplementary files format and content: File format: tsv, tab-separated plain text files. File contents: the files include the read counts per gene (including spike-ins) estimated by STAR.

tag: tissue

value: Ribo-Seq


title: HEK293T ΔYB-1ΔYB-3 + YB-3, RNA-Seq, rep1

description: batch1: NextSeq 500, batch2: HiSeq 2000

value: YBX3 restored expression in YBX1 knockout & YBX3 knockout


title: HEK293T ΔYB-1ΔYB-3 + YB-3, Ribo-Seq, rep1

description: batch1: NextSeq 500, batch2: HiSeq 2000


title: IP_NSP9

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Paired-end sequencing reads from eCLIP experiments, were adapter- and quality trimmed by cutadapt (v1.18) in two runs according to the ENCODE eCLIP-seq processing pipeline v. 2.2 (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)). In the first run 5' and 3' adapters were clipped from both reads using the parameters: --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
In the second run 3' adapters of read 2 were clipped to control for double ligation events. Cutadapt clipping was performed with the parameters:  --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
RNA-seq reads were aligned to the concatenated genomes of hg38 (ensembl) and SARS-CoV-2 (ensembl MN908947.3) using STAR version 2.7.10a with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterType Normal --alignSoftClipAtReferenceEnds No --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04 --scoreDelOpen -1 --alignIntronMin 20 --alignIntronMax 3000 --alignMatesGapMax 3000 --alignEndsType EndToEnd
Using the python package pyBigWig, bigWig files were generated based on the SARS-Cov-2 genome and unstranded paired-end mapped reads. Score represents the information content of IP over SMI of RNA fragments at a given genomic coordinate.
Assembly: hg38 and MN908947.3
Supplementary files format and content: bigWig

source_name: SARS-CoV-2 infected A549-ACE2

growth_protocol: We maintained A549-ACE2 cells in DMEM media (Thermo Fisher Scientific) supplemented with 10% heat-inactivated FBS (Thermo Fisher Scientific), and 100 units/ml streptomycin and 100 mg/ml penicillin. Cells were grown at 37°C and 5% CO2 atmosphere.

extract_protocol:
For immunoprecipitation procedures, lysates were combined with an equal amount of nuclease free water to adjust the lysis buffer to a 1x concentration. Subsequent steps were performed as described in the eCLIP protocol, with the following modifications. Immunoprecipitates were washed two times in 1 ml CLIP lysis buffer, two times in IP wash buffer (50 mM Tris-HCl pH 7.4, 300 mM NaCl, 1 mM EDTA, 1% (v/v) NP40, 0.5% sodium deoxycholate, 0.25 mM DTT), followed by two washes in 50 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.5% (v/v) NP40. All other steps were carried out as described in the eCLIP method (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)).
eCLIP-seq (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016))

treatment_protocol: We grew 24 million cells for each eCLIP experiment and infected them with SARS-CoV-2 at MOI 5 PFU/cell. At 24 hpi, culture media was removed, cells were briefly rinsed with PBS and subjected to UV-irradiation with a total dose of 0.8 J/cm2. Cells were scraped in PBS, pelleted at 200x g for 5 min and lysed by adding 2x CLIP lysis buffer (100 mM Tris-HCl pH 7.4, 300 mM NaCl, 2 mM EDTA, 2% (v/v) IGEPAL CA-630, 1% sodium deoxycholate, 0.5 mM DTT, EDTA-free Protease Inhibitor Cocktail). Following a 30 min incubation at room temperature, fresh lysates were lysates were directly used for immunoprecipitation procedures or stored at -80°C.

tag: infection

tag: rip antibody


title: SMI_NSP9


title: HEK293T ΔYB-1ΔYB-3, RNA-Seq, rep1

description: batch1: NextSeq 500, batch2: HiSeq 2000

value: YBX1 knockout & YBX3 knockout


title: CMO, sample 1, scRNAseq


title: HEK293T ΔYB-1ΔYB-3 + YB-1 + YB-3, Ribo-Seq, rep1

description: batch1: NextSeq 500, batch2: HiSeq 2000

value: YBX1 & YBX3 restored expression in YBX1 knockout & YBX3 knockout


title: HEK293T ΔYB-1ΔYB-3 + YB-1, RNA-Seq, rep1

description: batch1: NextSeq 500, batch2: HiSeq 2000

value: YBX1 restored expression in YBX1 knockout & YBX3 knockout


title: HEK293T ΔYB-1ΔYB-3, RNA-Seq, rep2

description: batch1: NextSeq 500, batch2: HiSeq 2000


title: HEK293T ΔYB-1ΔYB-3 + YB-1, Ribo-Seq, rep1

description: batch1: NextSeq 500, batch2: HiSeq 2000


title: HEK293T ΔYB-1ΔYB-3, Ribo-Seq, rep2

description: batch1: NextSeq 500, batch2: HiSeq 2000


title: SMI_ZAP


title: IP_ZAP

value: ZAP


title: WTC-11, tranilast, rep3, RNAseq

data_processing:
Raw sequencing read quality was assessed using FastQC software (v 0.11.9). Reads were then aligned to the human reference genome GRCh38 using HISAT2 (v 2.2.1)
“SAM” files were converted to “BAM” format, sorted, and indexed using SAMtools (v 1.13)
The "htseq-count" module in HTSeq package (v2.0.2) was utilised to quantify the gene expression level and generate a raw count matrix for each sample
Genes with read counts above 10 in at least 2 samples were retained for downstream analyses
Assembly: hg38
Supplementary files format and content: count matrix

extract_protocol:
RNA was extracted using RNeasy Mini Kit with on-column DNase digestion using the RNase-Free DNase Set
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep Kit following manufacturer's protocol

treatment_protocol: WTC-11 hiPSCs were seeded onto a 24-well plate at a density of 150k cells per well. Cells were differentiated at day 0 under 50 µM Tranilast, 1 µM CHIR, 1 µM CHIR+50 µM Tranilast, 3 µM CHIR, and 3 µM CHIR+50 µM Tranilast in the presence of 500 µg/mL BSA and 213 µg/mL AA.

value: human iPSCs

value: WT

tag: treatment

value: 50 uM Tranilast


title: WTC-11, 3CHIR+tranilast, rep2, RNAseq

value: 3 uM CHIR+50 uM Tranilast


title: WTC-11, tranilast, rep1, RNAseq


title: WTC-11, tranilast, rep2, RNAseq


title: WTC-11, 3CHIR+tranilast, rep3, RNAseq


title: WTC-11, 3CHIR+tranilast, rep1, RNAseq


title: WTC-11, 3CHIR, rep2, RNAseq

value: 3 uM CHIR


title: WTC-11, 3CHIR, rep3, RNAseq


title: HEK293T ΔYB-1ΔYB-3 + YB-1 + YB-3, RNA-Seq, rep1

description: batch1: NextSeq 500, batch2: HiSeq 2000


title: WTC-11, 1CHIR+tranilast, rep2, RNAseq

value: 1 uM CHIR+50 uM Tranilast


title: WTC-11, 1CHIR, rep3, RNAseq

value: 1 uM CHIR


title: WTC-11, 1CHIR+tranilast, rep3, RNAseq


title: WTC-11, 1CHIR+tranilast, rep1, RNAseq


title: WTC-11, 1CHIR, rep2, RNAseq


title: WTC-11, 1CHIR, rep1, RNAseq


title: si Control BioRep2 72h Ribo

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

description: Ribo-Seq

data_processing:
We mapped all RNA-seq reads against the human genome (Ensembl v90) using STAR 2.5.3a with standard parameters. We computed log2 fold changes using PsiLFC.
For Ribo-seq processing, we first mapped all reads against human rRNA sequences (U13369.1) using bowtie 1.2 with parameters “-a -m 100 -v 3 --best --strata --norc” and discarded all mapped reads.
Then, all remaining reads were mapped against the human genome and transcriptome (Ensembl v90) using bowtie with parameters “with parameters -a -m 100 -v 3 --best –strata” (genome) or “with parameters -a -m 100 -v 3 --best --strata --norc” (transcriptome).
We then used Price version 1.0 with parameters “-percond -plot” to identify and quantify translated codons.
Assembly: Ensembl v90
Supplementary files format and content: For RNA-seq libraries, all reads (or read pairs) compatible with a gene were counted, and fractional counts were used for multimapping reads.
Supplementary files format and content: For Ribo-seq libraries, the major isoform was determined per gene, and only reads uniquely mapping to the coding part of this transcript were considered.

source_name: HeLa

growth_protocol: DMEM (high glucose)+10%FCS+1%PenStrep

extract_protocol:
direct TriZOL lysis of cells for RNA-Seq, Nuclease treatment of soluble cell lysate, gradient centrifugation to pool monosome-associated RNA for Ribo-Seq
SENSE mRNA-Seq Library Prep Kit V2 for 72h RNA-Seq, TruSeq stranded mRNA library kit with oligo-dT capture for 96h RNA-Seq, Ribo-Seq libraries were prepared  as described in Ingolia et al., 2012
RNA-Seq, Ribo-Seq respectively

treatment_protocol: 50pmol siRNA  was  transfected into each well of a 6-well plate  at 40% cell confluency using Lipofectamine RNAi Max and OptiMEM as per manufacturer's protocol

value: HeLa

value: Control siRNA (siLuciferase)  72h


title: si Control BioRep1 72h Ribo

description: Ribo-Seq


title: si THOC1+2 BioRep3 96h

description: RNA-Seq

molecule: polyA RNA

value: THOC1+THOC2 siRNA  96h


title: si THOC2 BioRep3 96h

description: RNA-Seq

value: THOC2 siRNA 96h


title: si Ighmbp2 BioRep2 72h Ribo

description: Ribo-Seq

value: Ighmbp2 siRNA 72h


title: si THOC1+2 BioRep1 96h

description: RNA-Seq


title: si THOC2 BioRep1 96h

description: RNA-Seq


title: si Ighmbp2 BioRep1 72h Ribo

description: Ribo-Seq


title: si THOC1 BioRep3 96h

description: RNA-Seq

value: THOC1 siRNA 96h


title: si THOC1+2 BioRep2 96h

description: RNA-Seq


title: si THOC1 BioRep2 96h

description: RNA-Seq


title: si THOC2 BioRep2 96h

description: RNA-Seq


title: WTC-11, 3CHIR, rep1, RNAseq


title: si Control BioRep3 96h

description: RNA-Seq

value: Control siRNA (siLuciferase) 96h


title: si Control BioRep1 96h

description: RNA-Seq


title: si Ighmbp2 BioRep3 96h

description: RNA-Seq

value: Ighmbp2 siRNA 96h


title: si Ighmbp2 BioRep3  72h

description: RNA-Seq


title: si THOC1 BioRep1 96h

description: RNA-Seq


title: si Control BioRep2 96h

description: RNA-Seq


title: si Ighmbp2 BioRep2 72h

description: RNA-Seq


title: si Ighmbp2 BioRep2 96h

description: RNA-Seq


title: si Ighmbp2 BioRep1 72h

description: RNA-Seq


title: si Control BioRep3 72h

description: RNA-Seq

value: Control siRNA (siLuciferase) 72h


title: si Control Biorep2 72h

description: RNA-Seq


title: 22-12360-tRet

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral Retina

extract_protocol:
Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye. RNA was extracted using the ALLPrep DNA/RNA Mini Kit (Qiagen). All RNA had an RNA integrity number of ≥8.
Strand specific RNA library was prepared from 100 ng total RNA using the Encore Complete RNA-Seq library kit (Nugen Technologies, San Carlos, CA).

value: Peripheral Retina

tag: disease state

value: Intermediate AMD


title: 22-12360-tRPE

source_name: Periphery Choroid

value: Periphery Choroid


title: 22-12360-mRPE

source_name: Macula Choroid

value: Macula Choroid


title: si Control BioRep1 72h

description: RNA-Seq


title: si Ighmbp2 BioRep1 96h

description: RNA-Seq


title: 22-49933-tRet


title: 22-12359-tRet


title: 22-12359-mRet

source_name: Macula Retina

value: Macula Retina


title: 22-12359-tRPE


title: 22-12360-mRet


title: 22-49933-tRPE


title: 22-49933-mRPE


title: 22-48820-tRPE

value: Atrophic AMD


title: 22-49933-mRet


title: 22-47878-tRet


title: 22-47878-mRet


title: 22-48820-tRet


title: 22-48820-mRPE


title: 22-44151-mRPE


title: 22-47878-tRPE


title: 22-44151-mRet


title: 22-47878-mRPE


title: U2932_Control_shRNA_72h_TrAEL

city: Lausanne

first: Filipe

last: Martins

address: Station 19

country: Switzerland

institute: Epfl

data_processing:
library strategy: Transferase-Activated End Ligation sequencing (TrAEL-seq)
UMI processed files were aligned to the T2T-CHM13v2.0 genome using Bowtie2
Alignment files (bams) were then deduplicated using umit_tools
Reads were then summed in running windows using the bamCoverage function from deepTools
Bigwig files were computed using the bedGraphToBigWig software
Assembly: T2T-CHM13v2.0
Supplementary files format and content: BigWigs for read polarity = (R − F)/(R + F), where F and R relate to the total forward and reverse read counts respectively

growth_protocol: RPMI 1640 + 10% FCS + 1% Pen-Strep

extract_protocol: Performed as described in Kara N, Krueger F, Rugg-Gunn P, Houseley J. Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq. Paull T, editor. PLoS Biol. 2021 Mar 24;19(3):e3000886.

treatment_protocol: Lentiviral transduction

value: Diffuse large B cell lymphoma

value: Control

value: lentiviral transduction

tag: time


title: 22-44151-tRPE


title: U2932_shZNF587-417v1_72h_gH2AX_Rep2

data_processing:
library strategy: CUT&Tag
Reads were aligned to the T2T-CHM13v2.0 genome74using bowtie2
Only proper read pairs with MAPQ>10 were kept
CUT&Tag peaks were called using SEACR v1.3104on “stringent” mode
Peaks with maximum distance of 2000bp for H3K9me3 and 0bp for γH2AX were merged with bedtools 2.27.1. Peaks overlapping ENCODE blacklist were filtered out.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: BigWigs containing MAPQ>10 mapped reads

extract_protocol: Performed as described in Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun. 2019 Dec;10(1):1930.

value: ZNF587,ZNF417 knockdown

tag: chip antibody


title: U2932_shZNF587-417v1_72h_H3K9me3_Rep1


title: U2932_shZNF587-417v1_72h_gH2AX_Rep1


title: 22-12359-mRPE


title: U2932_shZNF587-417_v1_72h_TrAEL


title: U2932_Control_shRNA_72h_H3K9me3_Rep1


title: U2932_Control_shRNA_72h_gH2AX_Rep2


title: U2932_Control_shRNA_72h_H3K9me3_Rep2


title: U2932_shZNF587-417v1_72h_H3K9me3_Rep2


title: U2932_Control_shRNA_72h_gH2AX_Rep1


title: 22-48820-mRet


title: Unstim_mCherry_CD8 rep1 (RNA-seq)

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v2.10.5)
Assembly: hg19
Supplementary files format and content: count file generated by featureCounts

source_name: PMBC

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

value: PMBC

value: T cell

value: mCherry expressing

value: Unstimulated


title: Unstim_FOXO1_CD8 rep3 (RNA-seq)

value: FOXO1 overexpressing


title: Unstim_FOXO1_CD8 rep2 (RNA-seq)


title: Unstim_mCherry_CD8 rep2 (RNA-seq)


title: Unstim_mCherry_CD8 rep3 (RNA-seq)


title: Stim_mCherry_CD8 rep3 (RNA-seq)

value: Stimulated 16 hours with MCF7 tumors


title: Stim_mCherry_CD8 rep2 (RNA-seq)


title: Unstim_FOXO1_CD8 rep1 (RNA-seq)


title: Stim_mCherry_CD8 rep1 (RNA-seq)


title: Stim_FOXO1_CD8 rep3 (RNA-seq)


title: Stim_FOXO1_CD8 rep2 (RNA-seq)


title: Unstim_mCherry_CD4 rep2 (RNA-seq)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: hg19
Supplementary files format and content: count file generated by featureCounts


title: Unstim_FOXO1_CD4 rep3 (RNA-seq)


title: Unstim_FOXO1_CD4 rep2 (RNA-seq)


title: Unstim_mCherry_CD4 rep1 (RNA-seq)


title: Stim_mCherry_CD4 rep3 (RNA-seq)


title: Unstim_FOXO1_CD4 rep1 (RNA-seq)


title: Stim_FOXO1_CD4 rep2 (RNA-seq)


title: Stim_mCherry_CD4 rep1 (RNA-seq)


title: Stim_FOXO1_CD4 rep1 (RNA-seq)


title: Unstim_mCherry_CD8 rep2 (ATAC-seq)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were trimmed for adaptor sequence using Ngmerge, then mapped to the hg38 genome with bowtie2
Peaks were called with Genrich
Assembly: GRCh38
Supplementary files format and content: Peak files called with Genrich

extract_protocol:
CD8+ CAR T cells were harvested at a concentration of 500,000 cells/ml. 50,000 cells were lysed using the ZYMO research DNA isolation kit. Tagmentation then purification was performed on DNA, and isolated chromatin was amplified.
Sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit.


title: Unstim_FOXO1_CD8 rep3 (ATAC-seq)


title: Unstim_mCherry_CD8 rep1 (ATAC-seq)


title: Unstim_FOXO1_CD8 rep2 (ATAC-seq)


title: Unstim_FOXO1_CD8 rep1 (ATAC-seq)


title: Stim_mCherry_CD8 rep3 (ATAC-seq)


title: Stim_mCherry_CD8 rep2 (ATAC-seq)


title: Stim_FOXO1_CD8 rep1 (RNA-seq)


title: Stim_FOXO1_CD8 rep1 (ATAC-seq)


title: Stim_FOXO1_CD8 rep2 (ATAC-seq)


title: Unstim_mCherry_CD4 rep3 (RNA-seq)


title: Unstim_mCherry_CD8 rep3 (ATAC-seq)


title: NPC-48h-rep5

type: RNA

city: Berlin

first: Rupert

middle: W

last: Overall

state: Berlin

address: Philippstraße 13

institute: Humboldt University of Berlin

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalized using quantile normalization with beadarray (version 2.46.0) in R/BioConductor. Probes were assigned to Entrez GeneIDs using the illuminaMousev1p1.db package (version 1.26.0). Unmapped genes were removed and replicate expression data for the same GeneID were also removed, retaining only the gene with the highest mean.

label: biotin

source_name: Neural precursor cell culture

label_protocol: Amplification and biotin labeling with the TotalPrep™ RNA Amplification Kit (Illumina)

growth_protocol: Proliferating cells were maintained on poly-D-lysine/laminin-coated plates in Neurobasal media supplemented with 2 % B27, GlutaMAX,  20 ng/ml bFGF and 20 ng/ml EGF

extract_protocol: Cells were lysed on the culture dish and total RNA was prepared using the Qiagen RNeasy micro kit

treatment_protocol: Cells were harvested at different times after withdrawal of bFGF and EGF to induce differentiation

value: Adult hippocampus

tag: timepoint

value: 2 days

tag: hours differentiating


title: NPC-6h-rep4

value: 6 hours


title: NPC-96h-rep1

value: 4 days


title: Stim_mCherry_CD4 rep2 (RNA-seq)


title: NPC-12h-rep4


title: Stim_mCherry_CD8 rep1 (ATAC-seq)


title: NPC-12h-rep6

value: 12 hours


title: Stim_FOXO1_CD8 rep3 (ATAC-seq)


title: NPC-24h-rep4

value: Proliferating


title: NPC-48h-rep1


title: NPC-96h-rep3


title: NPC-6h-rep3


title: NPC-6h-rep2

value: 1 days


title: NPC-96h-rep4

value: 1 day


title: NPC-0h-rep2


title: NPC-6h-rep1


title: NPC-24h-rep2


title: NPC-24h-rep1


title: NPC-0h-rep3


title: NPC-12h-rep3


title: NPC-48h-rep4


title: NPC-0h-rep1


title: NPC-0h-rep4


title: NPC-96h-rep2


title: NPC-12h-rep2


title: NPC-24h-rep3


title: NPC-48h-rep2


title: 22-44151-tRet

value: Peripheral Retina

value: Atrophic AMD


title: NPC-0h-rep6


title: NPC-12h-rep1


title: NPC-96h-rep6


title: NPC-6h-rep6


title: NPC-12h-rep5


title: NPC-24h-rep6


title: NPC-0h-rep5


title: NPC-96h-rep5


title: NPC-48h-rep6


title: NPC-24h-rep5


title: NPC-6h-rep5


title: 1cell_MGCD0103_rep1

city: Fukuoka

first: Ruiqi

last: Shao

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

description: Gene expression of zygote treated with MGCD0103

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K; Agilent Technologies), according to the manufacturer’s instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner.

data_processing:
The scanned images were processed using the Feature Extraction Software (version 9.5.1.1, Agilent Technologies), to calculate the relative hybridization intensity and background hybridization values using default parameters. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies. Only spots with a signal flagged as “positive and significant” were used in the analysis. The remaining spots were processed as missing values. Probes with at least one valid value in three biological replicates were considered as valid detections. Probes that were valid detections in each condition were retained. We used the robust imputation method to fill-in missing values.
The signal intensity transformed by log2 was used in the subsequent analysis. Smooth quantile normalization was utilized for data normalization while preventing global modification.

source_name: Zygote, MGCD0103, replicate 1

label_protocol: cRNA was amplified and labeled using a Low input Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated and purified from 100 embryos using a PicoPure RNA Isolation Kit (Arcturus).

tag: strain

value: B6D2F1 x ICR

tag: developmental stage

value: Zygote, MGCD0103


title: 2cell_MGCD0103_rep1

description: Gene expression of embryo treated with MGCD0103 after fertilization and developed to the 2-cell stage

source_name: 2-cell stage embryo, MGCD0103, replicate 1

value: 2-cell stage embryo, MGCD0103


title: 2cell_MGCD0103_rep3

source_name: 2-cell stage embryo, MGCD0103, replicate 3


title: 1cell_T247_rep1

description: Gene expression of zygote treated with T247

source_name: Zygote, T247, replicate 1

value: Zygote, T247


title: Blastocyst_control_rep1

description: Gene expression of blastocyst

source_name: Blastocyst, control, replicate 1

value: Blastocyst, control


title: Blastocyst_control_rep3

description: Gene expression of blastocyst

source_name: Blastocyst, control, replicate 3


title: 2cell_T247_rep3

description: Gene expression of embryo treated with T247 after fertilization and developed to the 2-cell stage

source_name: 2-cell stage embryo, T247, replicate 3

value: 2-cell stage embryo, T247


title: 1cell_MGCD0103_rep2

source_name: Zygote, MGCD0103, replicate 2


title: 1cell_T247_rep3

source_name: Zygote, T247, replicate 3


title: 1cell_MGCD0103_rep3

source_name: Zygote, MGCD0103, replicate 3


title: 2cell_MGCD0103_rep2

source_name: 2-cell stage embryo, MGCD0103, replicate 2


title: Morula_control_rep3

description: Gene expression of morula

source_name: Morula, control, replicate 3

value: Morula, control


title: 2cell_T247_rep2

source_name: 2-cell stage embryo, T247, replicate 2


title: 4cell_T247_rep1

description: Gene expression of embryo treated with T247 after fertilization and developed to the 4-cell stage

source_name: 4-cell stage embryo, T247, replicate 1

value: 4-cell stage embryo, T247


title: Blastocyst_control_rep2

description: Gene expression of blastocyst

source_name: Blastocyst, control, replicate 2


title: Morula_control_rep2

description: Gene expression of morula

source_name: Morula, control, replicate 2


title: Morula_control_rep1

description: Gene expression of morula

source_name: Morula, control, replicate 1


title: 8cell_control_rep1

description: Gene expression of 8-cell stage embryo

source_name: 8-cell stage embryo, control, replicate 1

value: 8-cell stage embryo, control


title: 8cell_control_rep3

description: Gene expression of 8-cell stage embryo

source_name: 8-cell stage embryo, control, replicate 3


title: 1cell_T247_rep2

source_name: Zygote, T247, replicate 2


title: 4cell_control_rep1

description: Gene expression of 4-cell stage embryo

source_name: 4-cell stage embryo, control, replicate 1

value: 4-cell stage embryo, control


title: 2cell_control_rep3

description: Gene expression of 2-cell stage embryo

source_name: 2-cell stage embryo, control, replicate 3

value: 2-cell stage embryo, control


title: 4cell_T247_rep3

source_name: 4-cell stage embryo, T247, replicate 3


title: 2cell_T247_rep1

source_name: 2-cell stage embryo, T247, replicate 1


title: 4cell_control_rep3

description: Gene expression of 4-cell stage embryo

source_name: 4-cell stage embryo, control, replicate 3


title: 4cell_control_rep2

description: Gene expression of 4-cell stage embryo

source_name: 4-cell stage embryo, control, replicate 2


title: 2cell_control_rep2

description: Gene expression of 2-cell stage embryo

source_name: 2-cell stage embryo, control, replicate 2


title: 2cell_control_rep1

description: Gene expression of 2-cell stage embryo

source_name: 2-cell stage embryo, control, replicate 1


title: HEK293T, YB-1 PAR-CLIP, repA

data_processing:
Adapter and quality trimming was performed with cutadapt v2.10 with the following parameters: "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -m 15 -q 20"
Read mapping to hg38 genome assembly was performed with bowtie (v.1.0.0) using "--best --chunkmbs 512 -n 1 -S -M 100". The alignments were processed by wavClusteR (v.2.34.0) with readSortedBam, getAllSub with minCov = 3, fitMixtureModel with substitution = "TC", getHighConfSub, getClusters with threshold = 1, filterClusters with refBase = "T" and minWidth = 10, and, finally, exportClusters.
Assembly: hg38
Supplementary files format and content: File format: tsv, tab-separated plain text files.
Supplementary files format and content: The tsv files provide genome coordinates of YB-1-bound regions with extra information provided by wavClusteR.

source_name: cell line

extract_protocol:
After crosslinking cells were washed twice with cold PBS, pelleted by centrifugation (500g), lysed with 3 volumes of NP40 buffer (50 mM Hepes-KOH (pH 7.5), 150 mM KCl, 2 mM EDTA, 0.5% NP40, 0.5 mM DTT and a mixture of protease inhibitors (Roche, Switzerland)) and cell debris was pelleted at 13000g for 10 min at 4°C. Further steps of PAR-CLIP were performed according to Danan et al. 2016  (PMID: 26463383). RNA-protein complexes treated with RNase T1, radiolabeled, immunoprecipitated using antibodies against YB-1 (polyclonal rat antibody against 14 a.a. C-terminal peptide of YB-1 (IMTEK, Russia)) and purified using acid-urea electrophoresis. After recovery from Nitrocellulose Membrane and protein digestion, RNA fragments were used for library preparation.
PAR-CLIP libraries were obtained  using the ARTseq™ Ribosome Profiling Kit (Epicentre).
PAR-CLIP

treatment_protocol: Cells were treated for 16 h before crosslinking with 100 μM 4-Thiouridine, then irradiated in a Bio-link BLX-365 UV irradiation system (Vilber) 0.15 J/cm2 (wavelength 365 nm).

value: cell line

tag: cell type

value: Human Embryonic Kidney

value: wt

value: PAR-CLIP


title: 8cell_control_rep2

description: Gene expression of 8-cell stage embryo

source_name: 8-cell stage embryo, control, replicate 2


title: HEK293T ΔYB-1ΔYB-3 + YB-3, RNA-Seq, rep2

description: batch1: HiSeq 2000

tag: genotype

value: YBX3 restored expression in YBX1 knockout & YBX3 knockout

value: RNA-Seq


title: HEK293T ΔYB-1ΔYB-3 + YB-3, Ribo-Seq, rep3

description: batch1, batch2: HiSeq 2000

value: Ribo-Seq


title: HEK293T ΔYB-1ΔYB-3 + YB-1 + YB-3, Ribo-Seq, rep3

description: batch1, batch2: HiSeq 2000

value: YBX1 & YBX3 restored expression in YBX1 knockout & YBX3 knockout


title: HEK293T, YB-1 PAR-CLIP, repB


title: HEK293T ΔYB-1ΔYB-3 + YB-1 + YB-3, Ribo-Seq, rep2

description: batch1, batch2: HiSeq 2000


title: HEK293T ΔYB-1ΔYB-3, RNA-Seq, rep3

description: batch1, batch2: HiSeq 2000

value: YBX1 knockout & YBX3 knockout


title: 1cell_control_rep3

description: Gene expression of zygote

source_name: Zygote, control, replicate 3

value: B6D2F1 x ICR

value: Zygote, control


title: HEK293T ΔYB-1ΔYB-3, Ribo-Seq, rep1

description: batch1, batch2: HiSeq 2000


title: 1cell_control_rep1

description: Gene expression of zygote

source_name: Zygote, control, replicate 1


title: HEK293T ΔYB-1ΔYB-3 + YB-3, Ribo-Seq, rep2

description: batch1, batch2: HiSeq 2000


title: HEK293T ΔYB-1ΔYB-3 + YB-1 + YB-3, RNA-Seq, rep2

description: batch1: HiSeq 2000


title: MII_control_rep2

description: Gene expression of metaphase II stage oocyte

source_name: MII stage oocyte, control, replicate 2

value: MII stage oocyte, control


title: HEK293T ΔYB-1ΔYB-3 + YB-1, RNA-Seq, rep2

description: batch1: HiSeq 2000

value: YBX1 restored expression in YBX1 knockout & YBX3 knockout


title: HEK293T ΔYB-1ΔYB-3, Ribo-Seq, rep3

description: batch1, batch2: HiSeq 2000


title: 23-20066-tRPE

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (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: Peripheral Choroid

value: Peripheral Choroid

value: Intermediate AMD


title: HEK293T ΔYB-1ΔYB-3 + YB-1, Ribo-Seq, rep2

description: batch1, batch2: HiSeq 2000


title: GV_control_rep3

description: Gene expression of germinal vesicle stage oocyte

source_name: GV stage oocyte, control, replicate 3

value: GV stage oocyte, control


title: 23-20066-mRet

source_name: Macula Retina

value: Macula Retina


title: 23-20066-tRet

source_name: Peripheral Retina

value: Peripheral Retina


title: GV_control_rep1

source_name: GV stage oocyte, control, replicate 1


title: MII_control_rep3

source_name: MII stage oocyte, control, replicate 3


title: HEK293T, Ribo-Seq, rep2

description: batch1, batch2: HiSeq 2000

value: cell line

value: Human Embryonic Kidney


title: 1cell_control_rep2

description: Gene expression of zygote

source_name: Zygote, control, replicate 2


title: MII_control_rep1

source_name: MII stage oocyte, control, replicate 1


title: GV_control_rep2

source_name: GV stage oocyte, control, replicate 2


title: 23-19958-tRet

value: Atrophic AMD


title: 23-19958-tRPE


title: 23-17278-tRPE


title: 23-20066-mRPE

source_name: Macula Choroid

value: Macula Choroid


title: 23-19958-mRet


title: 23-17278-mRet


title: HEK293T, RNA-Seq, rep2

description: batch1, batch2: HiSeq 2000

value: wt

value: RNA-Seq


title: 23-17278-tRet


title: 23-16220-mRet


title: 23-159870-tRPE


title: 23-16220-tRet


title: 23-159870-tRet


title: 23-14437-tRet

value: Normal


title: 23-14437-mRPE


title: 23-1099-tRPE

source_name: Periphery Choroid

extract_protocol:
Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye. RNA was extracted using the ALLPrep DNA/RNA Mini Kit (Qiagen). All RNA had an RNA integrity number of ≥8.
Strand specific RNA library was prepared from 100 ng total RNA using the Encore Complete RNA-Seq library kit (Nugen Technologies, San Carlos, CA).
RNA-Seq on the Illumina HiSeq 2000.

value: Periphery Choroid


title: 23-1099-mRet


title: 23-1099-tRet


title: 23-1099-mRPE


title: 23-1018-tRet

value: Early-Intermediate AMD


title: 23-0809-tRPE


title: 23-0809-tRet


title: 23-1018-mRet


title: 23-159870-mRet


title: 23-1018-mRPE


title: 23-0809-mRPE


title: 22-3910-tRPE


title: 23-17278-mRPE


title: VP11

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: Deseq2_normalized_gene_expression_with_annotations.txt

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: taeGut1
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Zebrafinch FAST DB v2017_1 were also provide

organism: Taeniopygia guttata

source_name: skin

growth_protocol: Male and female individuals of Taeniopygia guttata were obtained from local suppliers (Oisellerie du Temple, Animotopia) and bred in the bird facility of the Collège de France for collection of fertilized eggs. Fertilized eggs were incubated at 37°C in Brinsea ova-easy 190 incubators.

extract_protocol:
Skin was dissected out on ice, kept in RNA later and stored at -80°C until RNA extraction was performed. Total RNA was extracted using the Rneasy micro kit (Qiagen) following the manufacturer's protocol.
10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). An average of 150 pg of amplified cDNA was used for library preparation following Nextera XT DNA kit (Illumina).

value: skin

value: wild type

tag: location

value: ventral posterior


title: VP8

tag: age


title: 23-0809-mRet


title: 22-3910-mRPE


title: 22-3910-tRet


title: VA8

value: ventral anterior


title: 23-159870-mRPE

value: Intermediate AMD


title: 22-1575-tRPE


title: VA11


title: 22-1575-tRet


title: VD11

value: flank


title: VV11

value: ventral-most


title: 22-1575-mRPE


title: 22-3910-mRet

value: Macula Retina


title: VV8


title: 22-1042-tRPE


title: DP8

value: dorsal posterior


title: DS11

value: dorsal saddle


title: DP11


title: 22-1575-mRet


title: 22-1042-mRPE

value: Atrophic AMD


title: 22-1042-tRet

value: Peripheral Retina


title: DS8


title: 22-1036-tRPE


title: 22-1042-mRet


title: 22-1036-tRet


title: DA11

value: dorsal anterior


title: DA8


title: 22-1036-mRPE

value: Macula Choroid


title: 22-0754-tRet

value: Normal


title: VA3


title: 22-0754-mRPE


title: DP3


title: Spinner_3

city: La Jolla

last: Kaufman

state: California

address: 9500 Gilman Dr.

institute: University of California San Diego

data_processing:
Raw image data file from high-throughput sequencing (illumina) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base calling)
Raw sequencing reads were filted as follow: (1) Remove reads containing adaptors;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Clean reads were mapped to human genome using STAR software. In order to avoid losing a lot of effective junction reads,  we use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely. Reads were mapped to exon, intron and intergenic.
Gene expression level was estimated by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008).
Assembly: Homo_sapiens_hg38
Supplementary files format and content: tab-delimited excel files include FPKM values for all the samples

source_name: iPSC-macrophage by spinner system

growth_protocol: NK cells were harvested after they reached maturity and co-cultured X-vivo media containing RANKL (100 ng/ml)

extract_protocol:
Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: induced pluripotent stem cell

value: spinner system differentiation


title: 22-1036-mRet


title: VD3

value: skin


title: DA3

value: wild type


title: Spinner_1


title: Adherence_3

source_name: iPSC-macrophage by adherence system

value: adherence system differentiation


title: Activated TA

first: Glenda

middle: Evangelina

last: Comai

address: 25-28 rue du Dr Roux

institute: Institut Pasteur

description: 10X Genomics

data_processing:
Demultiplexing, alignement and gene quantification were performed using 10X CellRanger 3.0.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tibialis Anterior

growth_protocol: To get activated MuSCs, cells isolated by FACS were plated onto Matrigel® (Corning, 354248) coated dishes and cultured in growth media at 3% O2, 5% CO2, 37°C for the indicated time. Activated MuSCs were subsequently trypsinized and washed in DMEM/F12 2% FBS.

extract_protocol: NOT PROVIDED; REQUESTED

value: Tibialis Anterior

value: Muscle Stem Cells

value: 2-4 months


title: VV3

value: ventral-most


title: DS3


title: Adherence_2


title: Adherence_1


title: Paromomycin/Neomycin-treated heart (biol rep 2)

city: Dallas

first: Hesham A.

last: Sadek

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
76bp
Sample_PN3

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Fastq files were mapped to mouse reference genome using STAR (v2.5.3a)
Read counts were generated using featureCounts (subread) for coding genes using igenomes gft file
Differential expression analysis was performed using edgeR
Assembly: mm10
Supplementary files format and content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: Heart

extract_protocol:
The collected samples were ground to powder in liquid nitrogen, resuspended in 1 mL of TRIzol™ Reagent (Invitrogen, 15596026) per 30 mg of tissue. After chloroform extraction, the aqueous phase was mixed with an equal volume of 75% ethanol and further purified using a RNeasy® Mini Kit (QIAGEN, 74106) according to the manufacturer’s protocol.
RNA integrity was assessed using an Agilent 2100 TapeStation and only samples with RIN > 7 were used for the library prep. Stranded mRNA-Seq libraries were generated using a KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol.

treatment_protocol: 3-month old CD1 mice received daily injections of PBS (Ctrl)  or Paro/Neo (150 mg/kg, twice daily, i.p.) for 14 days. For each condition, ventricles from 3 snap-frozen mouse hearts were used as biological triplicates for the RNA-Seq experiments.

value: Heart

value: Paromomycin/Neomycin


title: Activated EOM

description: 10X Genomics

source_name: Extra Ocular Muscle

value: Extra Ocular Muscle


title: 22-0754-tRPE

value: Periphery Choroid


title: VD8

value: flank


title: Quiescent TA

description: 10X Genomics


title: Spinner_2


title: Hoxb13-PN2

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806)
Trimmed fastq files were mapped to reference genome using Bowtie2
Duplicates were removed using picard-tools (v1.127)
Peaks were called using MACS2.
Peak annotation was performed using Homer
Assembly: mm10
Supplementary files format and content: tab dellimted text file which contains peak calls
Supplementary files format and content: bigWig file

extract_protocol:
For each sample, ventricles from 2 mouse hearts were used as biological duplicates for the ChIP-Seq experiments. Tissue samples were ground to powder and crosslinked with 2% formaldehyde in PBS for 30 min followed by quenching with 0.125 M glycine for 10 min at room temperature. Crosslinked samples were then washed with cold 1X PBS and further homogenized with a Dounce tissue grinder. Samples were collected by a brief spin and treated with 10 mM Tris-HCl (pH 8.0), 10mM NaCl and 0.2% NP-40 for 30 min to collect nuclei. After nuclear extraction, chromatin was sheared on a Bioruptor Pico (Diagenode) for 20 cycles (30 sec on/ 30 sec off for each cycle) at 4°C in sonication buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1 mM DTT, 1x cOmplete Protease Inhibitor Cocktail (Roche), and 200 µM PMSF, pH 8.0). 1% of the sonicated chromatin from each sample was taken out as “input” samples at this step. A sonication buffer was added to the remaining sonicated chromatin to make the final volume 1 mL. NaCl was then added to a final concentration of 300 mM for each sample. Meis1/2 (Santa Cruz, sc-10599X; 1:200) or Hoxb13 (GeneTex, GTX129245; 1:100) was added to each sample and incubated at 4°C overnight with gentle rotation. The next day, 30 µL of pre-washed Dynabeads Protein G (Invitrogen, 10004D) was added to each sample for a two-hour incubation. After that, the beads were washed twice with 1 mL RIPA 0 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, pH 8.0), twice with 1 mL RIPA 0.3 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 300 mM NaCl, pH 8.0), twice with 1 mL LiCl wash buffer (250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0), and finally twice with 1 mL TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). For each ChIP sample or input sample, 100 uL of SDS elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) was added and incubation was done at 65°C overnight on a ThermoMixer (Eppendorf) at 1000 rpm. The next day, supernatant was collected and further treated with 0.5 µg RNaseA (Sigma, 11119915001) for 30 min at 37°C, followed by 20 µg Proteinase K (NEB, P8107S) treatment at 37°C for 2h. DNA was recovered using MinElute PCR Purification Kit (QIAGEN, 28004) according to manufacturer’s protocol.
ChIP–seq libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) according to manufacturer’s protocol. Final ChIP–seq libraries were pooled and sequenced on an Illumina Nextseq 500 system using the 75-bp high output sequencing kit for single-end sequencing

treatment_protocol: Neonatal mice received daily injections of PBS (Ctrl) or Paro/Neo (150 mg/kg, twice daily, i.p.) starting from p7 for 7 days

value: Hoxb13 (GeneTex, GTX129245)


title: Quiescent EOM

description: 10X Genomics


title: 23-1018-tRPE

value: Early-Intermediate AMD


title: Input-PN1


title: Paromomycin/Neomycin-treated heart (biol rep 1)

description:
76bp
Sample_PN2


title: Input-C1

value: Vehicle


title: Input-C2


title: VP3

value: ventral posterior


title: Vehicle-treated heart (biol rep 2)

description:
76bp
Sample_CTL2


title: 22-0754-mRet

value: Macula Retina

value: Normal


title: Meis1-Paro/Neo 1

value: Meis1/2 (Santa Cruz, sc-10599X)


title: Hoxb13-C1


title: Hoxb13-C2


title: Input-PN2


title: Meis1-Ctrl 2


title: Vehicle-treated heart (biol rep 3)

description:
76bp
Sample_CTL3


title: Input-Ctrl 2


title: Meis1-Ctrl 1


title: Hoxb13-PN1


title: Input-Paro/Neo 2


title: Vehicle-treated heart (biol rep 1)

description:
76bp
Sample_CTL1


title: Meis1-Paro/Neo 2


title: Stimulated_Foxo1-ada_rep2 (RNA-seq)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: mm10
Supplementary files format and content: count file generated by featureCounts

source_name: Spleen

value: Spleen

value: T cell

value: Foxo1-ADA overexpressing

value: Plate bound anti-c-Myc antibody stimulation for 72 hours


title: Input-Paro/Neo 1


title: Stimulated_NGFR_control_rep2 (RNA-seq)

description: h-NGFR-stim

value: Control


title: Input-Ctrl 1

value: Heart


title: Stimulated_NGFR_control_rep1 (RNA-seq)

description: g-NGFR-stim


title: Unstimulated_NGFR_control_rep1 (RNA-seq)

description: a-NGFR-US

value: No stimulation


title: Stimulated_Foxo1-ada_rep1 (RNA-seq)


title: Unstimulated_Foxo1-ada_rep2 (RNA-seq)


title: Unstimulated_Foxo1-ada_rep1 (RNA-seq)


title: PCts>Pvr RNAi

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) using default setting.
The counts matrices were then analyzed in Seurat and batch correction was performed using the Harmony algorithm before creating a UMAP and performing clustering analysis.
Assembly: BDGP6.32
Supplementary files format and content: normalized count matrix
Supplementary files format and content: cell annotation

organism: Drosophila melanogaster

source_name: Malpighian tubule

growth_protocol: All flies were kept on standard cornmeal fly food supplemented with yeast and agar. Crosses were grown at 18°C to inactivate Gal4. Adult offspring flies were collected within 48 hours after emerging, kept at 18°C for another 24 hours and then incubated at 29°C for 8 days to induce transgene expression.

extract_protocol:
90 pairs of Drosophila MTs were dissociated for each sample, which were flash-frozen using liquid nitrogen and were homogenized in 1ml dounce in buffer of 250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCl, 5mM MgCl, 0.1% Triton-X, 0.5% RNasin plus (Promega, N2615), 1X protease inhibitor (Promega, G652A), 0.1 mM DTT, then filtered through 40 um cell strainer and 40 um Flowmi (BelArt, H13680-0040). Samples were centrifuged, washed, and resuspended in 1 X PBS with 0.5% BSA and 0.5% RNasin plus. The suspension was filtered again with 40 um Flowmi immediately before FACS sorting. Nuclei were stained with DRAQ7TM Dye (Invitrogen, D15106) and sorted using Sony SH800Z Cell Sorter at Systems Biology Flow Cytometry Facility at Harvard Medical School. After sorting, nuclei were collected and re-suspend at 700-800 cells/µl in 1 X PBS buffer with 0.5% BSA and 0.5% RNasin plus. snRNAseq was performed according to the 10X genomics protocol (Chromium Next GEM Single Cell 3’_v3.1_Rev_D)
Libraries were generated according to 10X genomics Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1
10x snRNA-seq

treatment_protocol: Female flies were incubated for 8 days at 29°C

value: Malpighian tubule

value: CG31272-GAL4, tub-GAL80TS > UAS-Pvr RNAi

value: Female flies were incubated for 5 days at 29 C


title: Unstimulated_NGFR_control_rep2 (RNA-seq)

description: b-NGFR-US


title: PCts>Pvr Activation

description: 10x Genomics

value: CG31272-GAL4, tub-GAL80TS > UAS-Pvr act


title: PCts>W1118

description: 10x Genomics

value: CG31272-GAL4, tub-GAL80TS > +


title: EGT>Yki

description: 10x Genomics

value: esg-GAL4, tub-GAL80TS > UAS-GFP, UAS-yki3SA


title: EGT>w1118

description: 10x Genomics

value: esg-GAL4, tub-GAL80TS > UAS-GFP


title: Paromomycin/Neomycin-treated heart (biol rep 3)

description:
76bp
Sample_PN4

value: Paromomycin/Neomycin


title: AlCl3_0ug_48H_4

city: Ottawa

first: Sabina

last: Halappanavar

state: ON

address: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

hyb_protocol: An equimolar amount of UMRR cRNA was mixed with each experimental cRNA and was hybridized to 8x60K Agilent SurePrint G3 Mouse Gene Expression v2 Microarray (Agilent Technologies, Inc., Santa Clara, USA) slides in a hybridization chamber for 17 h at 65°C rotating at 10 rpm.

scan_protocol: Microarray slides were washed according to manufacturer’s protocol and scanned on an Agilent G4900DA Microarray Scanner (Agilent Technologies, Inc., Santa Clara, USA). Data was retrieved using the Feature Extraction 11.0.1.1 software (Agilent). Data analysis is described below.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Immortalized Lung Epithelial cells (FE1)

label_protocol: In brief, 200 ng of total RNA per cell pellet sample or Universal Mouse Reference RNA (UMRR; Agilent Technologies) were used to synthesise labelled cDNAs and cRNAs using the Linear Amplification Kit (Agilent Technologies). T7 RNA polymerase-transcribed cRNA from experimental samples were labelled with Cyanine-5 and UMRR was labelled with Cyanine-3.

growth_protocol: FE1 immortalized alveolar lung epithelial cells were cultured as described in Decan et al 2015, in Dulbecco’s Modified Eagle’s Medium Nutrient Mixture F-12HAM (DMEM F12HAM) supplemented with 2 % fetal bovine serum (FBS), 1 ng/mL epidermal growth factor (EGF), 1 U/mL penicillin G, and 1 µg/mL streptomycin and maintained at 37°C, with 5 % CO2.

extract_protocol: RNA extraction, quantification, and integrity analysis were conducted as in Boyadzhiev et al., 2021. Following exposure and collection of cell pellets, TRIzol reagent was used to isolate RNA in conjunction with Direct-zol RNA Miniprep Kit (Zymo Research Corp, Irvine, USA) according to manufacturer’s protocol . Total RNA concentration and purity was determined using a NanoDropOne spectrophotometer (Thermo Fisher Scientific Inc, Waltham, USA). RNA integrity and quality analysis was conducted using an Agilent 2100 Bioanalyzer system and an Agilent 4200 Tapestation System (Agilent Technologies, Inc., Santa Clara, USA). RNA samples with an RNA Integrity Number (RIN) of ≥6 were used for subsequent microarray experiments.

treatment_protocol: Cells were plated at a cell density of 130 000 cells/well in 6-well plates. Following overnight incubation, cells were exposed to 1.8 mL of 0 - 118 ug/mL metal oxide NPs, MPs, or metal chlorides. For all exposures, blank media exposed cells served as negative controls. Following 2, 24, and 48 h of exposure, cell supernatant was harvested, cells were washed with PBS, trypsinized and suspended in fresh cell culture media. An aliquot of cell suspension was used for Trypan Blue dye exclusion staining and the rest of the cells were pelleted by centrifugation (8000 rpm, 10 minutes, 4°C) and frozen at -80°C for microarray analysis. Two to four biological replicates were used for each condition.

value: MutaMouse

value: Aluminum Chloride

tag: time point

value: 48 Hour

tag: dose

value: Media Control

tag: biological replicate

source_name: Universal Mouse Reference RNA

tag: sample type

value: 11 mouse cell lines


title: AlCl3_118ug_24H_4

value: 24 Hour

value: 118 ug/mL


title: AlCl3_47ug_48H_4

value: 47 ug/mL


title: AlCl3_2.36ug_24H_4


title: AlCl3_2.36ug_48H_4


title: AlCl3_0ug_48H_2


title: AlCl3_2.36ug_2H_4

value: 2 Hour


title: AlCl3_47ug_24H_4


title: AlCl3_47ug_2H_4


title: AlCl3_0ug_24H_4


title: AlCl3_47ug_48H_2


title: AlCl3_2.36ug_2H_3


title: AlCl3_118ug_2H_3


title: AlCl3_118ug_2H_4


title: AlCl3_2.36ug_48H_2


title: AlCl3_118ug_48H_4


title: AlCl3_0ug_2H_3


title: AlCl3_118ug_48H_2


title: AlCl3_0ug_2H_4


title: AlCl3_47ug_2H_2


title: NPC-15min

data_processing: The data were log2 transformed and normalized using quantile normalization with beadarray (version 2.46.0) in R/BioConductor. Probes were assigned to Entrez GeneIDs using the illuminaMousev2.db package (version 1.26.0). Unmapped genes were removed and replicate expression data for the same GeneID were also removed, retaining only the gene with the highest mean.

source_name: Neural precursor cell culture

tag: tissue

value: Adult hippocampus

value: 15 min

tag: minutes differentiating


title: AlCl3_47ug_48H_1

tag: treatment


title: AlCl3_47ug_2H_3


title: AlCl3_0ug_48H_1


title: AlCl3_0ug_2H_2


title: 4cell_T247_rep2

source_name: 4-cell stage embryo, T247, replicate 2

value: B6D2F1 x ICR

value: 4-cell stage embryo, T247


title: NPC-360min

value: 6 h


title: NPC-150min


title: NPC-300min

value: 5 h


title: AlCl3_118ug_48H_1


title: AlCl3_2.36ug_24H_3


title: AlCl3_47ug_24H_3


title: AlCl3_2.36ug_48H_1


title: NPC-0min

value: Proliferating


title: AlCl3_118ug_2H_2


title: AlCl3_118ug_24H_3


title: NPC-120min

value: 2 h


title: AlCl3_0ug_24H_3

value: MutaMouse


title: AlCl3_2.36ug_2H_2

value: Aluminum Chloride


title: NPC-720min


title: NPC-90min


title: NPC-180min

value: 3 h


title: AlCl3_0ug_24H_1

value: Media Control


title: NPC-600min


title: NPC-420min

value: 7 h


title: NPC-480min

value: 8 h


title: AlCl3_2.36ug_48H_3

value: 48 Hour

value: 11 mouse cell lines


title: AlCl3_118ug_24H_1

value: 24 Hour

value: 118 ug/mL


title: AlCl3_47ug_24H_1

value: 47 ug/mL


title: NPC-540min

value: Adult hippocampus

value: 9 h


title: AlCl3_0ug_48H_3


title: AlCl3_47ug_48H_3


title: AlCl3_118ug_48H_3


title: NPC-60min

value: 1 h


title: M5_4

city: wuhan

first: Zeng

last: Fanfan

address: No. 13, Hanghang Road, Qiaokou District, Wuhan

institute: Huazhong University of Science and Technology

data_processing:
Data filtering: The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping：The clean data were mapped to the reference genome by HISAT (v2.1.0).
Reference gene mapping: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5). The expression level of genes was calculated by RSEM (v1.2.8).
Gene Annotation: Annotating assembled Unigene with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors.
Assembly: mm10
Supplementary files format and content: rna_expression.txt

source_name: Hacat cells

extract_protocol:
RNA was harvested by using TRIZOL (Introgen). 1.2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

tag: cell line

value: Hacat cells

value: keratinocytes

value: wild type

value: TOPK inhibitor


title: AlCl3_2.36ug_24H_1

value: MutaMouse

value: Aluminum Chloride


title: M5_3


title: PSC033_SC_5pr

city: Toronto

first: Diana

last: Nakib

address: 101 College Street

institute: University of Toronto

description: 3pr scRNA-seq, 10x Genomics

data_processing:
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes (raw feature matrix)
Supplementary files format and content: features.tsv.gz: list of gene IDs (raw feature matrix)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format (raw feature matrix)
Supplementary files format and content: possorted_genome_bam.bam: raw data

source_name: single-cell RNA-seq

extract_protocol:
Samples were prepared as outlined by the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Sample viability was assessed via Trypan Blue (Thermo Fisher) and using a haemocytometer (Thermo Fisher). Following counting, the appropriate volume for each sample was calculated for a target capture of 6000 cells. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/µl) were pelleted and re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles. A median sequencing depth of 60,000 reads/cell was targeted for each sample.

value: Human liver


title: NPC-240min

value: 4 h


title: M5_1


title: M5_2


title: PSC019_SN_3pr

description: 3pr scRNA-seq, 10x Genomics

source_name: single-nucleus RNA-seq


title: M5_O5_4

value: No treament


title: PSC019_SC_5pr

description: 3pr scRNA-seq, 10x Genomics


title: PSC024_SC_5pr

description: 3pr scRNA-seq, 10x Genomics


title: M5_O5_2


title: NPC-45min

value: 45 min


title: M5_O5_1


title: PSC018_SN_3pr

description: 3pr scRNA-seq, 10x Genomics


title: AlCl3_2.36ug_2H_1

value: 2 Hour

value: 11 mouse cell lines


title: AlCl3_0ug_24H_2

value: 24 Hour

value: Media Control


title: AlCl3_118ug_24H_2

value: 118 ug/mL


title: NPC-30min

value: Adult hippocampus

value: 30 min


title: AlCl3_47ug_24H_2

value: 47 ug/mL


title: SMI_LARP4

data_processing:
Paired-end sequencing reads from eCLIP experiments, were adapter- and quality trimmed by cutadapt (v1.18) in two runs according to the ENCODE eCLIP-seq processing pipeline v. 2.2 (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)). In the first run 5' and 3' adapters were clipped from both reads using the parameters: --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
In the second run 3' adapters of read 2 were clipped to control for double ligation events. Cutadapt clipping was performed with the parameters:  --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
RNA-seq reads were aligned to the concatenated genomes of hg38 (ensembl) and SARS-CoV-2 (ensembl MN908947.3) using STAR version 2.7.10a with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterType Normal --alignSoftClipAtReferenceEnds No --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04 --scoreDelOpen -1 --alignIntronMin 20 --alignIntronMax 3000 --alignMatesGapMax 3000 --alignEndsType EndToEnd
Using the python package pyBigWig, bigWig files were generated based on the SARS-Cov-2 genome and unstranded paired-end mapped reads. Score represents the information content of IP over SMI of RNA fragments at a given genomic coordinate.
Assembly: hg38 and MN908947.3
Supplementary files format and content: bigWig

source_name: SARS-CoV-2 infected A549-ACE2

extract_protocol:
For immunoprecipitation procedures, lysates were combined with an equal amount of nuclease free water to adjust the lysis buffer to a 1x concentration. Subsequent steps were performed as described in the eCLIP protocol, with the following modifications. Immunoprecipitates were washed two times in 1 ml CLIP lysis buffer, two times in IP wash buffer (50 mM Tris-HCl pH 7.4, 300 mM NaCl, 1 mM EDTA, 1% (v/v) NP40, 0.5% sodium deoxycholate, 0.25 mM DTT), followed by two washes in 50 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.5% (v/v) NP40. All other steps were carried out as described in the eCLIP method (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)).
eCLIP-seq (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016))

tag: infection

tag: rip antibody


title: AlCl3_47ug_2H_1


title: PSC018_SC_5pr

description: 3pr scRNA-seq, 10x Genomics


title: IP_LARP4


title: PSC016_SC_5pr

description: 3pr scRNA-seq, 10x Genomics


title: AlCl3_0ug_2H_1


title: AlCl3_2.36ug_24H_2


title: M5_O5_3

value: Hacat cells

value: keratinocytes


title: AlCl3_118ug_2H_1


title: Ts12M-1

city: Lanzhou

first: QI

last: Wang

state: Gansu

address: Yintan Road Street

department: College of Animal Science and Technology

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: muscle tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: muscle tissues

value: wild-type

value: acute hypoxia


title: Ts12M-3


title: Ts12M-2


title: Tm12M-3

value: chronic hypoxia


title: Tm12M-2


title: PSC014_SC_5pr

description: 3pr scRNA-seq, 10x Genomics

value: Human liver


title: NiCl2_80ug_24H_2

value: MutaMouse

value: Nickel Chloride

value: 80 ug/mL


title: CM-3

value: control


title: CM-2


title: PSC012_SN_3pr

description: 3pr scRNA-seq, 10x Genomics


title: CM-1


title: PSC012_SC_5pr

description: 3pr scRNA-seq, 10x Genomics


title: durva029

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Ave

department: Biochemistry

institute: Weill Cornell Medicine

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
All reads were independently aligned with STAR_2.4.0f1 for sequence alignment against the human genome build hg19, downloaded via the UCSC genome browser, and SAMTOOLS v0.1.19 for sorting and indexing reads.
HTSeq was used to quantity counts.
Cufflinks (2.0.2) was used to get the expression values (FPKMs), and Gencode v19 GTF file for annotation.
Assembly: hg19
Supplementary files format and content: Gene Expression values quantified as FPKMs

source_name: Lung Tissue, Archival FFPE

growth_protocol: Archival FFPE human lung tissue

extract_protocol:
RNA was extracted from FFPE samples with RNeasy FFPE kit from Qiagen, Part# 73504.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760, New England BioLabs, Ipswich, MA) was used for sample library preparation according to the manufacturer’s instruction.  PCR enrichment of adaptor ligated cDNA were pooled and hybridized with probes from Twist Exome Kit #2 (Twist Bioscience, San Francisco, CA). After post capture PCR amplification and purification, the quality of final libraries was checked and loaded to Illumina NovaSeq6000 for sequencing at PE2x100 cycles

treatment_protocol: Not applicable

value: Lung Tissue, Archival FFPE

value: Squamous


title: durva033


title: NiCl2_40ug_2H_2

value: 2 Hour

value: 40 ug/mL

value: 11 mouse cell lines


title: PSC014_SN_3pr

description: 3pr scRNA-seq, 10x Genomics


title: durva026

value: Sarcomatoid


title: durva027

value: Adenocarcinoma


title: PSC010_SN_3pr

description: 3pr scRNA-seq, 10x Genomics


title: durva028


title: durva023


title: durva017


title: durva012


title: durva018


title: Tm12M-1


title: durva030


title: PSC005_SC_5pr

description: 3pr scRNA-seq, 10x Genomics


title: PSC011_SN_3pr

description: 3pr scRNA-seq, 10x Genomics


title: durva021


title: durva009


title: PBC004_SN_3pr

description: 3pr scRNA-seq, 10x Genomics


title: durva008


title: PBC005_SC_5pr

description: 3pr scRNA-seq, 10x Genomics


title: NiCl2_0ug_24H_2

value: 24 Hour

value: Media Control


title: NiCl2_1.6ug_24H_2

value: 1.6 ug/mL


title: NiCl2_40ug_48H_2

value: 48 Hour


title: NiCl2_80ug_48H_2


title: NiCl2_0ug_48H_2


title: NiCl2_1.6ug_48H_2


title: NiCl2_40ug_2H_3


title: NiCl2_80ug_48H_1


title: NiCl2_80ug_2H_3


title: PBC001_SC_5pr

description: 3pr scRNA-seq, 10x Genomics


title: PSC005_SN_3pr

description: 3pr scRNA-seq, 10x Genomics


title: durva003


title: durva006


title: NiCl2_1.6ug_48H_1


title: PBC001_SN_3pr

description: 3pr scRNA-seq, 10x Genomics


title: durva001


title: durva061


title: durva060


title: durva055


title: durva046


title: durva056


title: C68_SC_3pr

description: 3pr scRNA-seq, 10x Genomics

data_processing:
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Assembly: Genome_build: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes (raw feature matrix)
Supplementary files format and content: features.tsv.gz: list of gene IDs (raw feature matrix)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format (raw feature matrix)

source_name: Human liver


title: durva057


title: durva045


title: C64_SC_5pr

description: 5pr scRNA-seq, 10x Genomics


title: durva042


title: NiCl2_1.6ug_2H_3


title: C69_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: C66_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: durva007


title: durva044


title: C70_SC_5pr

description: 5pr scRNA-seq, 10x Genomics


title: durva038


title: durva039


title: C64_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: durva037


title: NiCl2_40ug_48H_1


title: NiCl2_80ug_24H_3


title: NiCl2_0ug_48H_1


title: NiCl2_0ug_2H_3


title: durva053


title: NiCl2_80ug_2H_2


title: durva040

value: NOS


title: C63_SC_3pr

description: 5pr scRNA-seq, 10x Genomics

value: Human liver


title: LNCaP siHIBCH Replicate 2

city: Brisbane

first: Charles

middle: Liam

last: Bidgood

address: Translational Research Institute, 37 Kent Street, Woolloongabba

department: School of Biomedical Sciences

institute: Queensland University of Technology

data_processing:
Raw reads were trimmed using TrimGalore, Data quality control checked using FastQC.
Reads were aligned to the human genome (GRCh38 / hg38) using STAR2 aligner and quantified using RSEM4.
Differential expression (DE) between siCTR and siHIBCH samples was calculated after sample normalization using edgeR (no replicates: Fisher Exact Test; replicates: General Linear Model).
Assembly: GRCh38 / hg38
Supplementary files format and content: Tab-delimited text file containing gene annotations, FPKM, TPM and CPM values, fold change, and p values for all samples.

source_name: LNCaP

growth_protocol: LNCaP prostate cancer cells were maintained in RPMI 1640 (Without Phenol Red) supplemented with 5% foetal bovine serum (FBS)

extract_protocol:
Total cellular RNA from LNCaP cells following 96 hours of transfection was extracted using the Norgen RNA Purification PLUS kit (Norgen, #48400) according to the manufacturer's instructions. RNA quality and quantity were determined on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) and Qubit® 2.0 Fluorometer (ThermoFisher).
Library preparation and paired-end sequencing was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (strand-specific, polyA enriched, Illumina, San Diego, USA) with an input of 1 µg total RNA.

treatment_protocol: Transfection of 10 nM siHIBCH (Sigma Aldrich #SASI_Hs01_00064760) or 10 nM siCTR (Sigma Aldrich, #SIC001) small interfering siRNAs (siRNAs) was carried out using RNAiMAX transfection reagent diluted 1:25 in serum free RPMI 1640. Following 5 hours of transfection, standard serum conditions were restored by the addition of FBS (5%).

value: LNCaP

value: siHIBCH


title: LNCaP siHIBCH Replicate 1


title: LNCaP siCTR Replicate 1

value: siCTR


title: LNCaP siCTR Replicate 2


title: C61_SC_5pr

description: 5pr scRNA-seq, 10x Genomics


title: durva036


title: C59_SC_5pr

description: 5pr scRNA-seq, 10x Genomics


title: C63_SC_5pr

description: 5pr scRNA-seq, 10x Genomics


title: BPC430T

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

institute: INSERM

data_processing:
Reads were aligned using STAR and gene expression counts obtained with FeatureCount
Assembly: hg38
Supplementary files format and content: tab_delimited text file includes raw counts for each Sample

source_name: pancreatic adenocarcinoma

extract_protocol:
EUS-FNAB from primary tumors were performed prior to any treatment using 19 to 22 G FNA needles (Wilson Cook, Ireland; Boston Scientific, USA as previously described. The material for cytopathology was reclaimed by the use of a dedicated stylet and was instantly fixed in formalin. The remaining material was obtained by air blushing the FNA needle (so-called EUS-FNAB wash – EUS-FNAB-W) and immediately collected in 500 µl of RNAprotect cell reagent (Qiagen, Les Ulis, France). This procedure was previously validated in the coordinating center. EUS-FNA-W were centrifuged at 8 000 rpm Cell pellets were immediately frozen at – 80°C until nucleic acid extraction. Extraction of nucleic acids was centralized in a single platform of molecular biology at the IUCT Oncopole of Toulouse. DNA and mRNA  were extracted using AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Les Ulis, France) according the manufacturer’s protocol
150 ng of total RNA was used to generate RNA-seq sequencing libraries using Lexogen Quantseq 3’ FWD kit and sequenced by the Institut du cerveau (Paris, France) iGenseq platform on a NovaSeq 6000 apparatus aiming for a minimum of 10 million reads.

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

value: CHU Lille

tag: sizeprimary

tag: diseasestage

value: resectable

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC431T

tag: tissue

tag: age

value: M

value: CHU de Lille

value: GEMCITABINE


title: BPC428T

tag: sample id

value: CLB


title: BPC427T

tag: historicpatient id


title: lung sample, IPF patient, scRNA-seq

city: Chengdu

first: Mu

last: Yang

state: Sichuan Province

address: No. 55, Section 4, Renmin South Road

department: Centre for Translational Research in Cancer

institute: Sichuan Cancer Hospital & Institute, University of Electronic Science and Technology of China

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
The lung sample (n=1) from IPF patient was harvested and dissociated into single cells suspensions by mixed digestion buffer. Cells were collected after filtering through a 70 μm and 40 μm strainer. The viability and concentration of cells were calculated in a Counting Star system.
Library was performed according to the manufacter's instructions (single cell 5' protocol, 10x Genomics). Briefly, GEMs (Gel Bead-in-Emulsions) are generated using Single Cell 5’ Gel Beads, Master Mix, cells, and Partitioning Oil on a microfluidic chip to achieve single cell resolution. The majority of GEMs are cell-free, while a minority contain a single cell. Upon GEM formation, Gel Bead dissolution releases oligonucleotides including Illumina® R1 sequence, 10x Barcode, Unique Molecular Identifier (UMI), and Switch Oligo into the cell lysate, followed by reverse transcription to create barcoded cDNA from mRNA. Post GEM-RT, Silane magnetic beads purify barcoded cDNA, which is then amplified via PCR for library construction. cDNA amplification is performed with PCR primers against common 5’ and 3’ ends, preparing for multiple library types, including T/B cell-enriched and 5’ gene expression libraries. For target enrichment, barcoded V(D)J segments from amplified cDNA are enriched via PCR using TCR or Ig constant region-specific primers, with separate reactions for T and B cells if both are present. Enriched library construction involves Enzymatic Fragmentation and Size Selection for V(D)J segments, incorporating sequencing elements like R1, P5, P7, R2, and sample index during different stages, producing final libraries compatible with Illumina® bridge amplification. The Single Cell V(D)J Reagent Kit is used for Illumina-ready V(D)J enriched and 5’ gene expression sequencing libraries, which have standard Illumina paired-end constructs encoding barcode and primer sequences, as well as sample indices.

value: lung

tag: disease state

value: Idiopathic pulmonary fibrosis (IPF)


title: NiCl2_1.6ug_24H_3

tag: strain

value: MutaMouse

tag: treatment

value: Nickel Chloride

tag: time point

value: 24 Hour

tag: dose

value: 1.6 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: C59_SC_3pr

description: 3pr scRNA-seq, 10x Genomics

value: Human liver


title: NiCl2_0ug_2H_2

value: 2 Hour

value: Media Control


title: C58_SC_5pr

description: 5pr scRNA-seq, 10x Genomics


title: BPC426T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay

value: FOLFOX 4 AMB;LV5FU2 AMB SIMPLIFIE


title: NiCl2_0ug_24H_3


title: NiCl2_40ug_24H_3

value: 40 ug/mL


title: NiCl2_1.6ug_48H_3

value: 48 Hour


title: NiCl2_80ug_24H_1

value: 80 ug/mL


title: C61_SC_3pr

description: 3pr scRNA-seq, 10x Genomics

tag: tissue


title: C56_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: NiCl2_0ug_48H_3


title: BPC423T

tag: sample id

tag: historicpatient id

tag: age

value: M

value: CLB

tag: osevent

tag: osdelay


title: BPC422T

value: locAdvanced

tag: firsttreatment

value: FOLFIRINOX


title: C54_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: C53_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: BPC419T

value: GEMCITABINE


title: NiCl2_0ug_24H_1

tag: strain

value: MutaMouse

tag: treatment

value: Nickel Chloride

tag: time point

value: 24 Hour

tag: dose

tag: biological replicate


title: BPC421T

tag: normpatient id

tag: Sex

tag: clinicalcenter


title: BPC424T

tag: diseasestage

tag: pfsevent


title: BPC420T

tag: tissue

tag: ecog

tag: sizeprimary

value: resectable

tag: pfsdelay

tag: surgerytype

value: PC

tag: surgerymargin


title: BPC425T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: age

tag: osevent

tag: osdelay

tag: firsttreatment


title: BPC429T

tag: normpatient id

value: CHU Lille


title: C52_SC_3pr

description: 3pr scRNA-seq, 10x Genomics

value: Human liver


title: BPC418T

tag: Sex

value: FOLFIRINOX;FOLFOX 4


title: BPC416T

tag: clinicalcenter

value: meta