title: rpf_zuo1KO_h2o2(+)_rep1

value: oxidative-stress


title: rpf_zuo1KO_h2o2(+)_rep2

status: Public on Jun 01 2023

type: SRA

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
Sequencing data analysis is quite similar both for mRNA-seq and Ribo-seq data until P-site offset calculation step. Briefly, adapter contaminations and low-quality reads (quality score < Q30) were filtered out from the raw reads of mRNA-seq and Ribo-seq data using cutadapt tool.
Then, rRNA and tRNA contaminations were removed by aligning reads to the non-coding RNA (ncRNA) sequences using Bowtie2. Next, the remaining sequences, that do not align to ncRNAs, were then aligned against the transcriptome (coding RNA) of S. cerevisiae using Hisat2.
After that, perfect match alignments were extracted from alignment output. Finally, samtools was used to count the number of mapped reads for each gene from mRNA-seq data.
For further downstream analysis of Ribo-seq data, 3’- and 5’-end P-site offset values were determined using riboWaltz. These P-site offset values are required to find where ribosomes are located on each RPFs.
After P-site offset calculation, actively translating ribosomes that represent trinucleotide periodicity were identified. Then, number of mapped RPFs were counted for each codon position within a gene using samtools.
Genome_build: R64-1-1
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Wild type and mutant S. cerevisiae  single colonies were selected and inoculated into the 10 mL of growth media (defined synthetic complete medium (SC) with 2% glucose) in the presence/absence of selective markers to grow overnight at 30 °C.

extract_protocol:
Total RNA from 10 mL cells at 0.6 OD600 were isolated using hot acid phenol method and treated with RNase-free DNase I to get rid of residual genomic DNA contamination. Then, quantity and quality of the RNA was assessed using Qubit Fluorometer 2.0 and Bioanalyzer RNA 6000 Pico Kit, respectively. Only the RNA samples with 28S:18S ≥ 1 and the RNA integration number (RIN) ≥ 8 were used for mRNA-seq library construction.
After quality checking, mRNA-seq libraries were prepared using TruSeq mRNA Sample Preparation Kit according to manufacturer’s instructions. First, messenger RNAs (mRNAs) were purified from 1 μg of total RNA using oligo (dT) magnetic beads followed by fragmentation of purified mRNAs using fragmentation buffer. Second, fragmented mRNAs were subjected to first strand complementary DNA (cDNA) synthesis using random hexamer-primers, and then second strand of cDNA was synthesized using DNA polymerase I and RNase H. Third, the double-stranded cDNAs were purified using AMPure XP beads, eluted with resuspension buffer, and then subjected to 3′ end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the adenylated fragments and amplified with 14 rounds of PCR. Enriched cDNA libraries were used for cluster generation and sequencing. Paired-end sequencing (75 bp x 2) were carried out for two cDNA libraries (two biological replicates of each sample) using the Illumina HiSeq 4000 sequencing platform.  To prepare Ribo-seq libraries, 200 mL yeast cells were harvested and filtered using a 0.45 μM Whatman membrane using a vacuum filter apparatus. After filtration, cells were immediately scraped from the filter with a straight-edge metal spatula and plunged into 50 mL liquid nitrogen. Next, samples were grinded using Spex 6775 freezing grinding mill in the presence of 10 mL lysis buffer (20 mM Tris (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide, 1% Triton X-100, 25 U/mL DNase I). Then, RNA concentration of the cell lysates was determined using Qubit RNA HS Assay Kit with the Qubit Fluorometer 2.0. Next, 30 µg total RNA was diluted to 200 µL with polysome buffer (20 mM Tris (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide) and digested using 15 U RNase I for 45 min at room temperature. After that, 10 µL SUPERase*In RNase inhibitor was added to the samples to stop the digestion reaction. To pellet the ribosomes, samples were transferred to a 13 mm × 51 mm polycarbonate ultracentrifuge tube that contains 0.9 ml sucrose cushion (1 M sucrose in polysome buffer) and centrifuged at 70,000 rpm for 2 hours. Translucent ribosome pellets were resuspended in 300 µL polysome buffer followed by RNA purification using TRIzol reagent according to manufacturer’s instructions. Then, samples were run on 15% polyacrylamide TBE-Urea gel for 60 min at 200 V followed by gel-purification of ~20-40 nt ribosome protected footprint (RPF) fragments using 17-34 nt length oligos as markers. Next, RPFs were treated with T4 PNK in order to heal the 2′–3′ cyclic phosphate that results from RNase I cleavage. After end-healing reaction, preadenylated adapter oligos (35 nt length) were ligated to RPFs using T4 Rnl2(tr) K227Q ligase. Then, excess adapter oligos in the reaction were depleted by adding Yeast 5′-deadenylase and RecJ exonuclease enzymes directly to the ligase reaction and incubated at 30 0C for 45 min. After that, samples were purified using Oligo Clean & Concentrator kit followed by ribosomal RNA (rRNA) depletion using yeast Ribo-Zero Gold rRNA removal kit according to manufacturer’s instructions. Next, samples were reverse transcribed using Protoscript II. Then, reverse transcription products were separated from the unextended primer products by polyacrylamide TBE-Urea gel electrophoresis followed by gel-purification of the full-length reverse transcription products (80-120 nt length). Next, purified full length cDNAs were circularized using CircLigase II. Afther that, 10-15 rounds of PCR enrichment of the libraries were performed with the proper forward and reverse primers. Enriched libraries were used for cluster generation and sequencing. Single-end (50 bp) sequencing was carried out for two cDNA libraries (two biological replicates of each sample) using the Illumina HiSeq 4000 sequencing platform.

treatment_protocol: Then, cells were diluted to 0.05 OD600 with the appropriate growth media and grown until 0.6 OD600. Oxidative and heat-shock stress experiments were performed using this culture. Before stress experiments, 200 mL of cell culture was harvested and used as a control (un-stressed) to compare with stress-induced samples. To induce the oxidative stress, cells at 0.6 OD600 were treated with 0.25 mM H2O2 for 30 min at 30 °C. For heat-shock experiments cells at 30 °C were heat-shocked by adding an equal volume of fresh medium at 44 °C, to immediately reach a final temperature of 37 °C followed by incubation at 37 °C for 45 min.

tag: strain background

tag: genotype

tag: treatment

tag: molecule type

value: Ribosome protected footprints (RPFs)


title: normal peripheral blood sample (SAMPLE 30)

type: genomic

city: Changsha

first: Min

last: Deng

state: Hunan

address: Renmin Middle Road 139

department: Dermatology

country: China

institute: the Second Xiangya Hospital of Central South University

description: normal peripheral blood sample

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

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

data_processing: Data was extracted with the champ R package, the results were not normalized.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood 30

label_protocol: Standard Illumina Protocol

growth_protocol: no

extract_protocol: genomic DNA was extracted and purified from whole blood samples usingQiagen DNeasy Kit according to standard instructions

treatment_protocol: no

tag: gender

value: male

tag: age

tag: tissue

value: peripheral blood

tag: disease state

value: normal


title: Kidney organoid treated with 120 nM SAG, biological replicate 3

type: RNA

city: Toronto

first: Norman

middle: D

last: Rosenblum

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description: Gene expression data from human kidney organoid tissue treated with 120 nM SAG at day 25

hyb_protocol: Standard Affymetrix Human Gene ST 2.0 arrays were hybridized with purified RNA samples.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Human Gene 2.0 ST arrays were normalized and analyzed with Expression Console

label: Biotin Allonamide Triphosphate

source_name: Human kidney organoid tissue after 25 days of differentiation

label_protocol: Standard Affymetrix label protocol using biotin allonamide triphosphate

growth_protocol: Induced pluripotent stem cells were differentiated for 7 days to intermediate mesoderm cells. Intermediate mesoderm cells were aggreated and grown for a further 18 days. RNA was collected from kidney organoid tissue at day 25.

extract_protocol: RNA was extracted from day 25 treated organoids using the RNeasy mini kit (Quigen).

treatment_protocol: At the stage of cellular aggregation, kidney organoids were treated with either DMSO (control) or 120 nM of the Hedgehog agonist SAG.

value: kidney


title: human brain EC Nox4 5MOI

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Ad-LacZ 5MOI

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Human brain endothelial cells, initiated from normal brain cortical tissues, were purchased from Cell Systems Corporation. The cells were cultured using a CS-C complete medium kit (Cell Systems) at 37°C in 5% CO2 in a humidified incubator.

extract_protocol: Total RNAs from cells were collected by RNeasy mini kit with the RNase-free DNase set (QIAGEN).

treatment_protocol: Adenovirus harboring Nox4 (Ad-Nox4) or LacZ (Ad-LacZ, as a control) was generated using the AdMax system. Cells were transduced with Ad-LacZ or Ad-Nox4 at an MOI of 5–10 for 48 h.

tag: cell type

value: human brain endothelial cells

tag: treatement

value: Ad-LacZ 5MOI

source_name: Ad-NOX4 5MOI

value: Ad-NOX4 5MOI


title: rpf_wt_heat_shock(+)_rep2

source_name: wild type_heat-shock stress

value: wild type

value: heat-shock stress


title: Kidney organoid treated with 120 nM SAG, biological replicate 2


title: C-POPs-Mix 0.1_6

city: Ottawa

first: Hyojin

last: Lee

address: 75 Laurier Ave E

department: Biology

institute: University of Ottawa

library_source: genomic

data_processing:
Microbiome profiling was performed using EZbiocloud Apps (ChunLab inc., Korea).
Taxonomic assignment was performed using ChunLab’s 16S rRNA database (DB ver. PKSSU4.0)
OUT-picking was conducted using UCLUST algorithm
PICRUSt analysis was conducted with Comparative MTP Analyzer platform
Assembly: GRCz11 (GCA_000002035.4) v99

organism: Danio rerio

source_name: Intestine

growth_protocol: Zebrafish (Danio rerio, wild-type AB strain) aged 10–12 months were maintained in a flow-through system (Tecniplast, Buguggiate, Italy) with a 14-h light/10-h dark photoperiod at a temperature of 28.5°C ± 0.5°C and pH of 7.0–7.5. The zebrafish were fed thrice daily with Gemma micro 300 (Skretting, West-brook, Maine, USA).

extract_protocol:
Total genomic DNA was extracted individually using the isopropanol method.
Amplification of genomic DNA targeting the V3–V4 region of the 16S rRNA gene was conducted using the paired primers 341F (5′-CCTACGGGNGGCWGCAG-3′) and 805R (5′-GACTACHVGGGTATCTAATCC-3′).
PCR products were sequenced using the Illumina Miseq sequencing system (Illumina Inc., USA) according to the manufacturer’s instructions.

treatment_protocol: A total of 360 zebrafish (including 180 females and 180 males) were randomly assigned to three tanks. Each tank per concentration was comprised of 15 females and 15 males. Adult zebrafish were exposed to 0.02, 0.1, 0.5 μg/L C-POPs-Mix for 12 weeks in an automatic flow-through exposure system (TOX-MIXII, Hanalab, Daejeon, South Korea).

value: Intestine

tag: Sex

value: Female

value: WT

tag: time

value: 84 days


title: rpf_wt_heat_shock(+)_rep1


title: C-POPs-Mix 0.1_5


title: psoriatic arthritis peripheral blood sample (SAMPLE 27)

source_name: peripheral blood 27

value: psoriatic arthritis


title: psoriasis vulgaris peripheral blood sample (SAMPLE 28)

source_name: peripheral blood 28

value: female

value: psoriasis vulgaris


title: normal peripheral blood sample (SAMPLE 29)

description: normal peripheral blood sample

source_name: peripheral blood 29


title: normal peripheral blood sample (SAMPLE 26)

description: normal peripheral blood sample

source_name: peripheral blood 26


title: C-POPs-Mix 0.1_3


title: C-POPs-Mix 0.1_4


title: psoriatic arthritis peripheral blood sample (SAMPLE 25)

source_name: peripheral blood 25


title: rpf_wt_h2o2(+)_rep2

source_name: wild type_oxidative-stress

value: oxidative-stress

value: Ribosome protected footprints (RPFs)


title: psoriatic arthritis peripheral blood sample (SAMPLE 32)

source_name: peripheral blood 32

value: male

value: peripheral blood


title: rpf_wt_h2o2(+)_rep1


title: psoriatic arthritis peripheral blood sample (SAMPLE 33)

source_name: peripheral blood 33


title: Kidney organoid treated with DMSO, biological replicate 2

description: Gene expression data from human kidney organoid tissue treated with DMSO at day 25

value: kidney


title: C-POPs-Mix 0.1_2


title: Kidney organoid treated with DMSO, biological replicate 3


title: MelanA cells poly(A) seq F

city: Seattle

first: Austin

middle: Max

last: Gabel

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Center

description:
MelanA.poly(A).F
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv

data_processing:
RNA-seq was analyzed as previously described (Dvinge et al., 2014). RNA-seq reads were mapped to an annotated transcriptome created using Ensembl 71 (Flicek et al., 2013), UCSC knownGene (Meyer et al., 2013) and Misov2.0 (Katz et al., 2010) annotations using RSEM version 1.2.4(Li & Dewey, 2011) (modified to call Bowtie (Langmead et al., 2009) with option ‘-v 2’).
RNA-seq reads were mapped to an annotated transcriptome created using Ensembl 71 (Flicek et al., 2013), UCSC knownGene (Meyer et al., 2013) and Misov2.0 (Katz et al., 2010) annotations using RSEM version 1.2.4(Li & Dewey, 2011) (modified to call Bowtie (Langmead et al., 2009) with option ‘-v 2’).
Unaligned reads were then mapped to the corresponding genome (hg19/GRCh37 assembly, mm10/GRCmc38 assembly) and a database containing all possible pairings of 5’ and 3′ splice sites per gene in our merged transcriptome annotation using TopHat version 20.8b (Trapnell et al., 2009).
For Poly(A)-seq, data was mapped similarly but in a stranded fashion. BAM files were input into the APAlyzer package in R (R. Wang & Tian, 2020) and the gene level log2(distal reads / proximal reads) was computed per sample for each respective strand.
Assembly: mm10
Supplementary files format and content: csv file for Poly(A)-seq data, output of APAlyzer (Wang & Tian, 2019) as raw data per sample quantifying reads in the proximal and distal UTR isoforms per gene. tsv style table for the RNA-seq which includes the reads per gene per condition, the log-fold changes per gene and the p value.

molecule: polyA RNA

organism: Mus musculus

source_name: Melan-A

extract_protocol:
RNA was harvested using Direct-zol RNA MiniPrep kit (Zymo Research)
Poly(A)-seq:.RNA was isolated from cell pellets with the Direct-zol RNA MiniPrep kit (Zymo Research). Protocol was adapted from Derti et al. 2012. In brief, 5 ug of RNA was heated at 65 degrees for 2 minutes and then placed on ice. Poly(A) selected mRNA was isolated using DynaBeads (ThermoFischer 61006) per the manufacturer’s instructions. 1st strand cDNA synthesis using SuperScript IV Reverse Transcriptase (ThermoFischer 18090010) and the primer RKB4087 (a modified oligo d(TVN) primer) to generate cDNA reads which begin synthesis just before the poly(A) tail. This mixture was then purified using a 2x SPRI bead clean up and then followed by 2nd strand synthesis and then a 1x SPRI bead clean up. This cDNA library was then subject to PCR (NEBNExt High Fidelity 2x Master Mix) and primers RKB4089 (universal primer) and RKB4090-RKB4101 (indexed primers). The final libraries generate a broad range of fragment sizes, as such we gel extracted libraries from a 2% agarose gel corresponding to 300-500 bp size. Following extraction and purification, library size was analyzed with a 4200 TapeStation System before sequencing. RNA-seq:Poly(A)-selected, unstranded Illumina libraries were prepared following the TruSeq protocol per the manufacturer’s instructions. Library size and distribution was analyzed with a 4200 TapeStation System before sequencing.

tag: cell line

value: Melan-A

value: immortalized melanocyte


title: normal peripheral blood sample (SAMPLE 24)

description: normal peripheral blood sample

source_name: peripheral blood 24

value: normal


title: rpf_wt_control_rep1

source_name: wild type_unstressed (control)

value: wild type

value: unstressed (control)


title: MelanA cells poly(A) seq E

description:
MelanA.poly(A).E
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: Kidney organoid treated with 120 nM SAG, biological replicate 1


title: mrna_zuo1KO_heat_shock(+)_rep2

source_name: zuo1Δ_heat-shock stress

value: heat-shock stress


title: C-POPs-Mix 0.02_10

value: Intestine

value: Female


title: MelanA cells poly(A) seq D

description:
MelanA.poly(A).D
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv

value: WT


title: Kidney organoid treated with DMSO, biological replicate 1

source_name: Human kidney organoid tissue after 25 days of differentiation


title: mrna_zuo1KO_h2o2(+)_rep2


title: MelanA cells poly(A) seq C

description:
MelanA.poly(A).C
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: rpf_wt_control_rep2


title: mrna_zuo1KO_h2o2(+)_rep1


title: psoriatic arthritis peripheral blood sample (SAMPLE 23)

source_name: peripheral blood 23

value: psoriatic arthritis


title: MelanA cells poly(A) seq B

description:
MelanA.poly(A).B
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: C-POPs-Mix 0.02_9

value: 84 days


title: C-POPs-Mix 0.1_1


title: C-POPs-Mix 0.02_8


title: normal peripheral blood sample (SAMPLE 19)

description: normal peripheral blood sample

source_name: peripheral blood 19

value: female


title: C-POPs-Mix 0.02_6


title: C-POPs-Mix 0.02_7


title: mrna_zuo1KO_control_rep2

source_name: zuo1Δ_unstressed (control)


title: B16-F10 cells poly(A) seq F

description:
B16-F10.poly(A).F
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv

value: melanoma


title: psoriatic arthritis peripheral blood sample (SAMPLE 22)

source_name: peripheral blood 22


title: B16-F10 cells poly(A) seq E

description:
B16-F10.poly(A).E
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: psoriasis vulgaris peripheral blood sample (SAMPLE 20)

source_name: peripheral blood 20

value: psoriasis vulgaris


title: mrna_zuo1KO_control_rep1


title: normal peripheral blood sample (SAMPLE 16)

description: normal peripheral blood sample

source_name: peripheral blood 16

value: male


title: C-POPs-Mix 0.02_4

source_name: Intestine


title: mrna_wt_heat_shock(+)_rep2

source_name: wild type_heat-shock stress


title: mrna_wt_heat_shock(+)_rep1


title: C-POPs-Mix 0.02_3


title: F1_nXb E12.5 07

city: Boston

first: Evan

last: Kingsley

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Trimmed reads using Cutadapt 1.13
Mapped reads using STAR 2.7.1
Estimated transcript abundance with RSEM 1.3.0
Genome_build: GCA_003704035.3

organism: Peromyscus maniculatus nubiterrae x Peromyscus maniculatus bairdii

source_name: E12.5 embryonic tail

extract_protocol:
We extracted total RNA in 50µl Direct-zol (Zymo) RNA Isolation kit (ThermoFisher Scientific).
We constructed libraries using a PrepX PolyA kit on an Apollo 324 System

tag: Stage


title: B16-F10 cells poly(A) seq C

description:
B16-F10.poly(A).C
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: normal peripheral blood sample (SAMPLE 17)

description: normal peripheral blood sample

source_name: peripheral blood 17

value: peripheral blood


title: C-POPs-Mix 0.02_5


title: MelanA cells poly(A) seq A

description:
MelanA.poly(A).A
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: mrna_wt_h2o2(+)_rep2

source_name: wild type_oxidative-stress

value: oxidative-stress


title: F1_nXb E14.5 05

source_name: E14.5 embryonic tail


title: B16-F10 cells poly(A) seq B

description:
B16-F10.poly(A).B
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: psoriatic arthritis peripheral blood sample (SAMPLE 18)

source_name: peripheral blood 18


title: psoriatic arthritis peripheral blood sample (SAMPLE 15)

source_name: peripheral blood 15


title: C-POPs-Mix 0.02_2


title: mrna_zuo1KO_heat_shock(+)_rep1


title: C-POPs-Mix 0.02_1


title: B16-F10 cells poly(A) seq A

description:
B16-F10.poly(A).A
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: F1_nXb E12.5 02


title: Control_5

value: DMSO


title: F1_nXb E14.5 15


title: mrna_wt_control_rep2

source_name: wild type_unstressed (control)


title: F1_nXb E14.5 14


title: mrna_wt_control_rep1


title: mrna_wt_h2o2(+)_rep1


title: aco2i_PA_d1_3

city: Daejeon

first: Seung-Jae

middle: V

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

description: mRNA

data_processing:
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 103) by using STAR (v.2.7.0e). Aligned pairs on genes or transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
Genome_build: WBcel235 (ce11)
Supplementary_files_format_and_content: *.genes.txt: Tab-delimited text files with read counts were generated by using RSEM (v.1.3.1).

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: Worms were grown on NGM plates as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.

extract_protocol:
RNA extraction was performed as previously described with minor modifications (Jeong et al., 2020). Total RNA in the animals was extracted using RNAiso plus (Takara, Seta, Kyoto, Japan) and was subsequently purified by using 75% ethanol.
Libraries were constructed with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, CA, USA) by Macrogen Inc. (Seoul, South Korea) following the manufacturer’s instruction.

treatment_protocol: Wild-type worms fed with control RNAi and aco-2 RNAi bacteria were allowed to develop to L4 stage larvae at 20°C and then transferred to control RNAi bacteria- or PA14-seeded big-lawn plates after washing with M9 buffer two to three times. After 12 hrs incubation at 25°C, worms were harvested by washing with M9 buffer two to three times to remove residual bacteria.

tag: strain

value: Wild type

tag: developmental stage

value: Day 1 adult

value: Whole body

tag: RNAi

value: aco-2 RNAi

tag: infection


title: Control_4

tag: genotype


title: aco2i_PA_d1_2

description: mRNA


title: Control_2

tag: treatment


title: Control_3


title: F1_nXb E14.5 13


title: psoriasis vulgaris peripheral blood sample (SAMPLE 14)

source_name: peripheral blood 14


title: psoriatic arthritis peripheral blood sample (SAMPLE 12)

source_name: peripheral blood 12


title: F1_nXb E12.5 11


title: B16-F10 cells poly(A) seq D

description:
B16-F10.poly(A).D
read_counts_fwd.csv, read_counts_rev.csv, pas_targets_diffapa.csv


title: Control_1


title: aco2i_PA_d1_1

description: mRNA


title: psoriatic arthritis peripheral blood sample (SAMPLE 21)

source_name: peripheral blood 21


title: aco2i_ctrl_d1_3

description: mRNA


title: F1_nXb E12.5 01


title: aco2i_ctrl_d1_2

description: mRNA


title: XCR1 KO LPS & rXCL1

city: Seoul

first: Yeon Duk

last: Woo

address: 103 Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

institute: Seoul National University, College of Medicine

description: 150603_KO_LPS_XCLI_(MoGene-2_0-st).rma-gene-full-Signal

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: Biotin

source_name: XCR1 KO LPS & rXCL1

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Mice at age 10 weeks old were used

extract_protocol: TRIzol according to the manufacturer's protocol

treatment_protocol: LPS (100 ng/ml) and rmXCL1 (100 ng/ml) in complete RPMI medium

value: LPS (100 ng/ml) and rmXCL1 (100 ng/ml)


title: Bone Marrow Erythroid Cells 4

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

description: We performed mRNA profiling for 579 target genes, for 14 housekeeping genes, for 8 negative and 6 positive spike-in controls

hyb_protocol: 50ng of total RNA was hybridized with NanoString Immunology V2 panel according to the manufacturer's protocols.

data_processing: We performed QC on the raw data, performed background thresholding using the (mean of negative controls + 2 SD) + mean of POS_E controls, normalized gene expression using 15 housekeeping genes.

source_name: Bone Marrow Erythroid Cells

extract_protocol: We obtained adult bone marrow mononucler cells (MNCs) using Ficoll-paque density gradient, then labeled the MNCs or in vitro grown erythroid cells with anti-CD71-biotin-magnetic bead antibody and sorted the cells using a magnetic separator.

value: 23 years

value: Adult Human Bone Marrow

value: Bone Marrow Erythroid Cells


title: psoriasis vulgaris peripheral blood sample (SAMPLE 13)

source_name: peripheral blood 13


title: aco2i_ctrl_d1_1

description: mRNA


title: Bone Marrow Erythroid Cells 3

value: 25 years


title: Bone Marrow Erythroid Cells 2

value: 26 years


title: PB-58 42hpi rep2

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

institute: University of Notre Dame

hyb_protocol: Cy3 labeled cDNA was allowed to hybridize for 17 h to a custom Agilent microarray (GPL22280)  at 65°C at 10 rpm

scan_protocol: The microarray image was taken using a 2 μM scanner and probe intensity values were obtained using Agilent Feature Extraction software.

data_processing: Probe intensities for all samples were quantile normalized. Samples were visualized using Principle Component Analysis. Combat and SVA packages in R were used to remove batch effects due to RNA processing, cDNA creation, cDNA labeling and microarray hybridization. Transcript expression levels were summarized for each gene by averaging the batch corrected processed signal intensity of all the probes across its exons.

organism: Plasmodium falciparum

label_protocol: 1µg of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I.

growth_protocol: The parasite strains NF54 and PB58 were maintained in identical standard culture conditions in human red blood cells (Indiana Regional Blood Center, Indianapolis, Indiana) suspended in complete medium (CM) containing RPMI 1640 with L-glutamine (Invitrogen Corp.), 50 mg/L hypoxanthine (Sigma-Aldrich), 25 mM HEPES (Cal Biochem), 0.5% Albumax II (Invitrogen Corp.), 10 mg/L gentamicin (Invitrogen Corp.) and 0.225% NaHCO3 (Biosource) at 5% hematocrit. Cultures were grown separately in sealed flasks at 37˚C under an atmosphere of 5% CO2, 5% O2, and 90% N2. Three replicated cultures were thawed and triple sorbitol synchronized. The time points collected were 6 (n=3), 26 (n=5),  and 38 (n=3) hours post invasion (hpi).

extract_protocol: RNA was extracted using TriZol reagent (Invitrogen, Carlsbad, CA) and the quality and quantity determined by NanoDrop (NanoDrop Technologies). 300ng of RNA was used as starting material for cDNA synthesis using the Sigma WTA2 whole transcriptome amplification kit (Sigma Aldrich, St Louis, MO).

treatment_protocol: Culture were maintained under standard culture conditions.

value: Isogenic mutant of NF54

tag: time point (hours post invasion)


title: normal peripheral blood sample (SAMPLE 10)

description: normal peripheral blood sample

source_name: peripheral blood 10

tag: gender

value: normal


title: PyMT/P11-KO tumour, biological rep2

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 5850 College Street

department: Pathology

institute: Dalhousie University

description: PyMT/P11-KO mammary tumours

hyb_protocol: Hybridized 16 hours at 45C; Washing FS450_0002

data_processing: Transcriptome Analysis Console software (ThermoFisher Scientific) was used to normalize the data and calculate fold changes in expression

label: biotin allonamide triphosphate

source_name: PyMT/P11-KO mammary tumour 12-week

label_protocol: The Centre for Applied Genomics at The Hospital for Sick Children performed Biotin Allonamide Triphosphate Labelling

growth_protocol: PyMT/P11-WT or PyMT/P11-KO mice formed spontaneous mammary tumours over 12 weeks.

extract_protocol: Tumours were collected in Trizol (Invitrogen) and RNA was purified using a PureLink RNA kit (Invitrogen Thermo Fisher Scientific) following the manufacturer’s instructions

treatment_protocol: Mammary tumours were excised and homogenized.

tag: p11 status


title: WT LPS & XCL1

description: 150609_WT_LPS_XCLI_(MoGene-2_0-st).rma-gene-full-Signal

source_name: WT LPS & XCL1

value: Female

value: WT


title: XCR1 KO LPS

description: 150603_KO_LPS_(MoGene-2_0-st).rma-gene-full-Signal

source_name: XCR1 KO LPS

value: LPS (100 ng/ml)


title: psoriatic arthritis peripheral blood sample (SAMPLE 9)

source_name: peripheral blood 9

value: male

tag: age

tag: tissue

value: peripheral blood

value: psoriatic arthritis


title: normal peripheral blood sample (SAMPLE 11)

description: normal peripheral blood sample

source_name: peripheral blood 11

tag: disease state


title: ctrl_PA_d1_2

description: mRNA

value: Wild type

value: Day 1 adult

value: control RNAi


title: WT LPS

description: 150609_WT_LPS_(MoGene-2_0-st).rma-gene-full-Signal

source_name: WT LPS


title: PB-58 46hpi rep3


title: PB-58 30hpi rep3


title: PyMT/WT tumour, biological rep3

description: PyMT/P11-WT mammary tumours

source_name: PyMT/WT mammary tumour 12-week


title: PyMT/P11-KO tumour, biological rep1

description: PyMT/P11-KO mammary tumours


title: PB-58 34hpi rep1


title: PyMT/WT tumour, biological rep2

description: PyMT/P11-WT mammary tumours


title: Bone Marrow Erythroid Cells 1

tag: cell type


title: In Vitro Grown Erythroid Cells 4

source_name: In Vitro Grown Erythroid Cells

value: In Vitro Grown Erythroid Cells


title: ctrl_PA_d1_3

description: mRNA

value: Whole body


title: PB-58 22hpi rep2


title: ctrl_PA_d1_1

description: mRNA


title: PyMT/P11-KO tumour, biological rep3

description: PyMT/P11-KO mammary tumours


title: PyMT/WT tumour, biological rep1

description: PyMT/P11-WT mammary tumours


title: psoriatic arthritis peripheral blood sample (SAMPLE 8)

source_name: peripheral blood 8

value: female


title: HUMAN KD HEPG2 Sample 11

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

country: Germany

institute: Max Planck Institute for heart and lung research

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19,mm10, dm6, sacCer1, GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HUMAN

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

value: KD


title: HUMAN KD HEPG2 Sample 10


title: ctrl_ctrl_d1_2

description: mRNA

source_name: Whole body


title: In Vitro Grown Erythroid Cells 3

value: 25 years

value: Adult Human Bone Marrow


title: HUMAN WT HEPG2 Sample 9


title: In Vitro Grown Erythroid Cells 2

value: 26 years


title: ctrl_ctrl_d1_1

description: mRNA


title: HUMAN WT 293T Sample 4


title: PB-58 18hpi rep1

value: Isogenic mutant of NF54


title: PB-58 14hpi rep3


title: Achrs144_2

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCF_000007985.2_ASM798v2_genomic genome assembly using bowtie2
The number of reads falling in the genes  were counted using coveragebed software and normalized with edgeR software
Genome_build: GCF_000007985.2_ASM798v2_genomic
Supplementary_files_format_and_content: tab-delimited text file include the differential expression results of edgeR and raw and normalized counts  for each sample.

organism: Geobacter sulfurreducens

source_name: cells bacterial

extract_protocol:
For each biological sample, total RNA were extracted using Rneasy mini kit (Qiagen), then were examinated with Agilent 2100 Bioanalizer and quantified using NanoDrop 200c (Thermo Scientific).
Illumina sequencing was performed at the UUSMD (UNAM, México). After removing residual DNA using DNaseI (Thermo Scientific) and ribosomal RNA with Terminator 5´-Phosphate-dependent exonuclease (Epicentre). The mRNA-enriched was chemical fragmented to 150~200 bp. Based on these cleaved RNA fragments, cDNA was synthesized using a random hexamer primer and reverse transcriptase. After end reparation and ligation of adaptors, the products were amplified by PCR, further purified, and used to create the final cDNA library. Libraries were sequenced on an Illumina Genome Analyzer IIx

treatment_protocol: RNA later (Ambion) was added to culture before harvesting cells

value: PCA strain

value: PCA incubated with hydrogen-nitrate for 144 hours


title: Patient vs Control

city: Tokyo

first: Maki

last: Fukami

address: 2-10-1 Okura, Setagaya

department: Molecular Endocrinology

institute: National Research Institute for Child Health and Development

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Oligo aCGH/ChIP-on-Chip Hybridization Kit ) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Data analyses were performed using Genomic Workbench (ver. 7.0, Agilent Technologies). Normalized log10 ratio (Cy5/Cy3) representing test/reference.

source_name: Patient (FEMALE)

label_protocol: The fragmented DNA was labelled with Cy5 (Patient 12276)  or Cy3 (Control) following manufacturer's instructions (SureTag DNA Labeling kit, Agilent Technologies).

extract_protocol: The genome DNA was extracted from blood leukocyte using Gentra Puregene Blood Kit (QIAGEN) following manufacturer's instructions. 1 µg of genome DNA were fragmented with Alu I and Rsa I at 37°C for 2 h.

tag: test

value: Patient (FEMALE)

tag: patient id

source_name: FEMALE

tag: reference

value: Control (Human Reference DNA Female)

tag: catalog


title: In Vitro Grown Erythroid Cells 1

value: male


title: Achrs144_1

tag: strain

value: PCA incubated with acetate-nitrate for 144 hours


title: HUMAN WT 293T Sample 3

value: WT

tag: cell line


title: C-POPs-Mix 0.5

data_processing:
Quality trimming was performed using FastQC v0.11.9
Quality based trimming was performed using cutadapt v2.8
Alignment was performed using STAR v2.7.1a
Gene counts were performed with RSEM v1.3.3, featureCounts v2.0.0, HTSeq-count v0.11.2, and Cufflinks v2.2.1
Normalization was performed using DESeq2 v1.26.0 and edgeR v3.2.1
Functional analysis was performed using goseq v1.38.0 and GOplot v1.0.2
Supplementary files format and content: FPKM count table is a CSV format.

source_name: Liver

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen®, USA).
RNA libraries were constructed using TruSeq RNA sample preparation kit (Illumina, USA) and quantified using KAPA library quantification kit (Kapa Biosystems, USA) according to the manufacturer's protocol
The prepared RNA libraries were sequenced using the llumina HiSeq 2500 (Illumina, USA) platform.

value: Liver

tag: Sex

value: Female

tag: time

value: 84 days


title: PB-58 2hpi rep1


title: PB-58 10hpi rep2


title: psoriasis vulgaris peripheral blood sample (SAMPLE 7)

source_name: peripheral blood 7

value: peripheral blood

value: psoriasis vulgaris


title: Achrs48_2

value: PCA incubated with acetate-nitrate for 48 hours


title: NF54 46hpi rep3

value: Parent


title: HUMAN KO 293T Sample 2

tag: genotype

value: KO


title: C-POPs-Mix 0.1

tag: treatment


title: NF54 42hpi rep2

tag: time point (hours post invasion)


title: Achrs48_1


title: HUMAN KO 293T Sample 1


title: psoriatic arthritis peripheral blood sample (SAMPLE 6)

source_name: peripheral blood 6

tag: gender

value: female

value: psoriatic arthritis


title: C-POPs-Mix 0.02


title: KRAS-day59

city: Guangzhou

first: Jun

last: Liu

state: Guangdong

address: No.2 Lujing Road

department: Dermatology Hospital

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Two methods were used: Burrows-Wheeler Aligner (BWA) followed by ANOVA (ANOVA)
TopHat followed by Cufflinks
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and differential expression statistics from Cufflinks.

source_name: lung organoids

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

value: lung, tumor stage

value: lung organoids

value: day 59

value: KRAS mutation


title: KRAS-day48

value: day 48


title: NF54 34hpi rep1


title: KRAS-day30

value: day 30


title: H2hrs48_2

value: PCA strain

value: PCA incubated with hydrogen-nitrate for 48 hours


title: NF54 30hpi rep3


title: YEAST WT POMBE Sample 18

description: YEAST.counts.matrix

organism: Schizosaccharomyces pombe

source_name: YEAST

value: WT


title: H2hrs144_2

value: PCA incubated with hydrogen-nitrate for 144 hours


title: H2hrs48_1


title: normal peripheral blood sample (SAMPLE 1)

description: normal peripheral blood sample

source_name: peripheral blood 1

value: male

value: peripheral blood

value: normal


title: WT-day59


title: psoriasis vulgaris peripheral blood sample (SAMPLE 3)

source_name: peripheral blood 3

value: psoriasis vulgaris


title: normal peripheral blood sample (SAMPLE 4)

description: normal peripheral blood sample

source_name: peripheral blood 4


title: H2hrs144_1


title: Control_0

value: Liver

value: Female

value: DMSO

value: 84 days


title: YEAST WT POMBE Sample 19

description: YEAST.counts.matrix


title: YEAST KO POMBE Sample 17

description: YEAST.counts.matrix

value: KO


title: WT-day48

value: lung, tumor stage

value: lung organoids


title: WT_1

value: PCA grown in NBAF medium and harvested at exponential phase


title: NF54 14hpi rep3

value: Parent


title: NF54 18hpi rep1


title: YEAST KO POMBE Sample 16

description: YEAST.counts.matrix


title: NF54 10hpi rep2


title: WT_0

value: PCA strain


title: WT-day30

value: day 30


title: UPN-987-P

status: Public on May 31 2023

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

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

scan_protocol: Standard Illumina iScan scanner settings for Methylation EPIC Beadchips

data_processing:
unprocessed .idat files were directly uploaded to the molecularneuropathology.org portal to obtain medulloblastoma subgroup classification and CNV predictions.
IDAT files were batch normalized and background corrected using default settings of the R package ChAMP.

source_name: brain tumor: childhood PFA ependymoma

extract_protocol: DNA was extracted from snap frozen surgical samples using Qiagen Allprep (as per kit protocol)

tag: tumor stage

value: presentation


title: UPN-965-P

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol


title: UPN-928-X

value: recurrence


title: UPN-930-R1

value: male


title: NF54 22hpi rep2


title: UPN-928-R1


title: UPN-928-P


title: UPN-897-X


title: UPN-930-P


title: UPN-871-P

value: female


title: NF54 2hpi rep1


title: UPN-911-P


title: UPN-848-P


title: UPN-871-X


title: UPN-943-P


title: UPN-859-P


title: UPN-839-R1


title: UPN-897-R1


title: UPN-821-R1


title: UPN-839-P


title: UPN-816-R1


title: UPN-928-R2


title: psoriatic arthritis peripheral blood sample (SAMPLE 2)

data_processing: Data was extracted with the champ R package, the results were not normalized.

source_name: peripheral blood 2

extract_protocol: genomic DNA was extracted and purified from whole blood samples usingQiagen DNeasy Kit according to standard instructions

tag: age

value: peripheral blood

value: psoriatic arthritis


title: UPN-812-P


title: UPN-811-R4


title: UPN-811-R2


title: UPN-811-R1


title: UPN-80-P


title: UPN-727-P


title: UPN-700-P


title: UPN-781-P


title: UPN-723-P


title: UPN-691-R1


title: UPN-770-P


title: UPN-64-P


title: UPN-483-P


title: UPN-492-P


title: UPN-507-P


title: UPN-507-R1


title: UPN-816-P


title: UPN-393-P


title: UPN-816-X


title: UPN-393-R1


title: UPN-419-P


title: UPN-392-P


title: ctrl_ctrl_d1_3

description: mRNA

value: Wild type

tag: developmental stage

value: Day 1 adult

tag: tissue

value: Whole body

tag: RNAi

value: control RNAi

tag: infection


title: UPN-319-P


title: UPN-321-R1


title: UPN-318-P


title: UPN-459-R1


title: UPN-246-P


title: UPN-1536-P


title: UPN-195-R1


title: UPN-691-R2


title: UPN-1513-P


title: UPN-1347-P


title: UPN-1091-P


title: UPN-1295-P


title: UPN-110-P


title: UPN-1101-P


title: UPN-1239-P


title: UPN-1101-R1


title: normal peripheral blood sample (SAMPLE 5)

description: normal peripheral blood sample

source_name: peripheral blood 5

tag: disease state

value: normal


title: UPN-1048-P


title: UPN-1013-R1


title: UPN-1010-P


title: UPN-758-P


title: UPN-319-R1


title: UPN-811-P

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina iScan scanner settings for Methylation 450K Beadchips

data_processing:
unprocessed .idat files were directly uploaded to the molecularneuropathology.org portal to obtain medulloblastoma subgroup classification and CNV predictions.
Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

extract_protocol: DNA was extracted from snap frozen  or FFPE surgical samples using Qiagen Allprep (as per kit protocol)

value: brain tumor:PFA ependymoma


title: UPN-723-R1

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol


title: UPN-691-P


title: UPN-897-P


title: UPN-459-P


title: UPN-321-P


title: UPN-195-P


title: TR-371-R1


title: TR-371-P


title: UPN-1320-R1


title: TR-332-R1


title: TR-332-P


title: UPN-1269-P


title: TR-305-P


title: TR-331-R1


title: TR-MRSP-R1


title: TR-331-P


title: TR-305-R1


title: TR-289-P


title: TR-289-R1


title: TR-288-R3


title: TR-288-R1


title: TR-288-P


title: UPN-821-P


title: TR-287-R1


title: UPN-821-R2


title: TR-277-R4


title: TR-287-P


title: TR-MRSP-P


title: TR-256-R1


title: TR-277-P


title: TR-277-R2


title: TR-256-R2


title: TR-244-P


title: TR-244-R1


title: TR-230-P


title: TR-234-R1


title: TR-234-P


title: TR-256-P


title: TR-230-P2


title: TR-230-R1


title: TR-211-R1


title: TR-213-R1


title: TR-288-R4


title: TR-205-R2


title: TR-213-P


title: TR-203-P


title: TR-196-R2


title: TR-203-R1


title: TR-205-R1


title: TR-196-R3


title: TR-197-P


title: TR-196-R1


title: TR-196-P


title: TR-195-R1


title: TR-234-R2


title: TR-193-R2


title: TR-186-P


title: TR-193-P


title: TR-186-R1


title: TR-190-R1


title: TR-186-R2


title: TR-211-P


title: TR-205-P


title: TR-197-R1


title: TR-176-R1


title: TR-176-P


title: TR-176-R3


title: TR-176-R2


title: TR-163-P


title: TR-162-P


title: TR-162-R1


title: TR-195-P


title: TR-138-P


title: TR-147-P


title: TR-161-P


title: TR-161-R1


title: TR-138-R1


title: TR-147-R1


title: TR-136-R3


title: TR-190-P


title: TR-136-P


title: TR-136-R1


title: TR-163-R1


title: TR-122-P


title: TR-097-P


title: TR-098-P


title: TR-121-P


title: TR-097-R2


title: TR-098-R1


title: TR-121-R1


title: TR-078-R1


title: TR-085-P


title: TR-078-R2


title: TR-095-P


title: TR-122-R1


title: TR-097-R1


title: TR-136-R2


title: TR-193-R1


title: TR-059-R5


title: TR-059-P


title: TR-085-R2


title: TR-022-R1


title: TR-022-R2


title: TR-015-P


title: KP-9-P


title: TR-003-R1


title: KP-6-R1


title: KP-9-R1


title: TR-003-P


title: KP-6-P


title: TR-078-P


title: KP-42-R1


title: KP-36-P


title: KP-44-P


title: KP-40-P


title: KP-44-R1


title: KP-3-R1


title: KP-31-R1


title: KP-31-P


title: KP-40-R1


title: KP-26-P


title: KP-26-R1


title: TR-015-R3


title: KP-2-R1


title: KP-24-P


title: KP-19-R1


title: KP-24-R1


title: KP-16-R1


title: KP-19-P


title: KP-14-R1


title: KP-13-P


title: KP-14-P


title: KP-16-P


title: KP-11-R1


title: KP-13-R1


title: KP-42-P


title: KP-11-P


title: KP-3-P


title: KP-36-R1


title: KP-2-P


title: Williams 82 noninfected RNA bio rep 3

city: Knoxville

first: Tarek

last: Hewezi

state: TN

address: 2431 Joe Johnson Drive

department: Plant Sciences

institute: University of Tennessee

data_processing:
Trimmomatic - fastq trimming and pairing
STAR - mapping the reads to a reference genome
Htseq - counting the reads mapped
DEseq2 - the differential expression analysis
Assembly: Gmax_508_v4.0
Supplementary files format and content: HTseqcounts_All contains counts for each sample that correspond to a particular soybean gene ID generated from HTseq

organism: Glycine max

source_name: Root

extract_protocol:
Hot Phenol RNA extraction from soybean root tissue
mRNA library preperation (polyA enrichment) - NoaSeq PE150 (12G raw data per sample)

value: Root

value: Williams 82 soybean

value: WT

value: uninfected


title: TR-095-R1


title: Williams 82 noninfected RNA bio rep 2


title: Williams 82 noninfected RNA bio rep 1


title: Williams 82 H. glycines infected RNA bio rep 2

value: Heterodera glycines


title: Williams 82 H. glycines infected RNA bio rep 3


title: Williams 82 H. glycines infected RNA bio rep 1


title: Nik_NAC42-1-pGWB2+H2O-4

first: Jie

last: Lin

state: Ontario

address: 4700 keele street

institute: York University

data_processing:
QC checks were conducted upon receiving the raw data from the sequencing facility using FastQC software
Ribosomal RNA (rRNA) contamination, adapter sequences and/or low expressed genes were filtered out from the raw high-throughput RNA Sequencing data
clean reads were mapped/aligned to soybean (Glycine max) reference genome (Gmax_275_V2.0.fa, https://phytozome.jgi.doe.gov/pz/portal.html) using STAR RNA-seq Aligner with default parameters based on the current gene annotation
Only the paired mapped reads were considered for further analyses and the number of reads per gene was calculated using Feature Counts to count only reads which mapped concordantly
Differentially expressed genes (DEGs) were identified using DESeq2 package which is based in Negative Binomial Distribution
Multiple hypothesis correction was carried out to obtain an adjusted P value at 0.05 with Benjamini Hochberg procedure which is a powerful tool to decrease the false discovery rate (FDR). Principle component analysis, heatmap and clustering of the samples were also conducted to check the robustness of the analysis
Assembly: Gmax_275_V2.0.fa, https://phytozome.jgi.doe.gov/pz/portal.html
Supplementary files format and content: Processed data not provided

source_name: Hairy roots

extract_protocol:
Total RNA from soybean seeds was extracted using the Spectrum Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer’s protocol with some modification as described previously (Farrell et al., 2017).
The mRNA stranded library prep kit from KAPA Biosystems and 750 ng of total RNA were used to build each library following manufacturers recommended protocol with nine cycles of PCR.

value: Hairy roots

value: Overexpressed GmNAC42-1


title: Nik_NAC42-1-pGWB2+H2O-1


title: Nik_pGWB2+H2O-4

value: Overexpressed empty vetor


title: Nik_pGWB2+H2O-5


title: Nik_MYB29A2-pGWB2+H2O-1

value: Overexpressed GmMYB29A2


title: Nik_MYB29A2-pGWB2+H2O-4


title: Nik_MYB29A2-pGWB2+H2O-3


title: KD-GmBIR1 noninfected RNA bio rep 2

value: KD-GmBIR1 overexpression


title: Nik_NAC42-1-pGWB2+H2O-2


title: KD-GmBIR1 noninfected RNA bio rep 3


title: KD-GmBIR1 noninfected RNA bio rep 1


title: WT-GmBIR1 noninfected RNA bio rep 1

value: WT-GmBIR1 overexpression


title: WT-GmBIR1 noninfected RNA bio rep 3


title: KD-GmBIR1 H. glycines infected RNA bio rep 3


title: WT-GmBIR1 noninfected RNA bio rep 2


title: Nik_pGWB2+H2O-7


title: WT-GmBIR1 H. glycines infected RNA bio rep 1


title: WT-GmBIR1 H. glycines infected RNA bio rep 3


title: KD-GmBIR1 H. glycines infected RNA bio rep 2


title: KD-GmBIR1 H. glycines infected RNA bio rep 1


title: WT-GmBIR1 H. glycines infected RNA bio rep 2


title: Plac BM 2

city: Lexington

first: Jinpeng

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

library_source: transcriptomic single cell

data_processing:
Programming language - R version 4.0.0
Programming platform - Rstudio IDE version 1.4
Single cell RNA-seq data analysis using Seurat version 3.2; 1. Quality control on the gene count matrices of samples 2. Samples merging and feature selection 3. Dimension reduction and clustering 4. Cell type identification
Differential gene expression analysis using MAST version 1.16
Supplementary files format and content: cloupe

source_name: bone marrow

extract_protocol:
Both total lung (premalignant) or lung tumors and bone marrow were collected from mice.  Lungs and tumors were dissociated mechanically and bone marrow was purified on histopaque gradient.  Single cells were captured using a 10x Genomics platform.
Library chemistry was the Single Cell 3' v3 and preparation was performed by the University of Kentucky College or Arts and Sciences Imaging Center

treatment_protocol: Mice were treated with either placebo, GSK126, anti-PD1 immunotherapy, or a combination of GSK126 and anti-PD1 immunotherapy

value: bone marrow

value: placebo


title: Plac BM 1


title: Combo BM

value: anti-PD1 + GSK126


title: GSK BM


title: PD1 BM


title: GSK Lung

source_name: lung tumor

value: lung tumor


title: PD1 Lung


title: Control mouse 3, snRNAseq

city: Shanghai

first: Jialin

middle: C.

last: Zheng

address: Xincun Road 389

institute: Tongji Hospital Affiliated to Tongji University School of Medicine

description: Singleron

data_processing:
Raw reads from snRNA seq were processed with CeleScope pipeline. Briefly, low quality reads were firstly removed. Cutadapt (Martin 2011) v1.1.7 was used to trim poly-A tail and adapter sequences.
Cell barcode and UMI were then extracted. After that, we used STAR v2.6.1a to map reads to the reference genome GRCm38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with feature Counts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
After removing cells with either lower than 200 or higher than 5000 expressed genes or higher than 30,000 UMIs, 55848 cells were obtained after QC filter for the downstream analysis. The median genes ranged from 805 to 936 and the median UMIs ranged from 1205 to 1461.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: prefrontal cortex

extract_protocol:
Frozen PFC tissue (100 mg) was dounced in 1 mL of pre-cooled Nuclear Extraction Buffer (add RNase inhibitor and DTT before use, the final concentrations of the two are 0.2 U/µL, 1 mM, respectively) and left to lyse for 10 min, after which 9 ml of pre-cooled wash buffer was added and swirled. The sample was passed through a 40μm filter and spun for 5 min at 500 × g 4°C. This step was repeated two more times. After pelleting, the nuclei were gently resuspended in 5 – 10 mL of wash buffer by pipetting up and down 8 – 10 times. After 3 washes, the nuclei were resuspended in 200 µL of pre-cooled PBS (the PBS is added with RNase inhibitor and DTT before use, the final concentration of the two is 0.2 U/µL, 1 mM).
Single nucleus suspensions (1×105 cells/mL) with PBS (HyClone) were loaded into microfluidic devices using the Singleron Matrix® Single Cell Processing System (Singleron). Subsequently, the snRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Nucleus Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM and pooled for sequencing on Illumina novaseq6000 with 150 bp paired end reads.

tag: cell type

value: all cells in prefrontal cortex

value: prefrontal cortex

value: 3-4 month

value: control


title: Plac Lung


title: Control mouse 2, snRNAseq

description: Singleron


title: Combo Lung


title: Gls1CamKIIα-Cre mouse 3, snRNAseq

description: Singleron


title: Npc1-/- mouse forebrain 2

city: Ann Arbor

last: Lieberman

address: 1150 W Medical Center Drive

institute: University of Michigan

description: Nuclei were isolated from Npc1-/- mouse forebrains at P16. RNA was sequenced using the 10X Chromium platform.

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: brain

extract_protocol:
Brains were removed from P16 mice. The forebrain was discected and flash frozen. Forebrains were homogenized using a Dounce homogenizer and nuclei were isolated using a Nuclear Isolation Kit (Millipore; nuc101)
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: brain

value: primary cells

value: forebrain nuclei


title: Gls1CamKIIα-Cre mouse 2, snRNAseq

description: Singleron


title: Gls1CamKIIα-Cre mouse 1, snRNAseq

description: Singleron


title: Npc1-/- mouse forebrain 1


title: LuCaP96_GSK_scRNA

first: Changmeng

last: Cai

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: xenograft-implant

extract_protocol: Tissue fragments were incubated in 3 ml Accumax (Innovative Cell Technologies, AM105) for 10-20 min at room temperature on a rocking shaker. Red blood cells were lysed with ACK Lysing Buffer (Thermo Fisher Scientific, A1049201) on ice for 1 min, followed by quenching with PBS and then filtered again with a 40-μm cell strainer. Cell suspensions were washed three times and resuspended with PBS plus 0.04% BSA. The final cell viability of suspensions was determined by Countess Automated Cell Counter (Thermo Fisher Scientific).

value: xenograft-implant


title: LuCaP96_VEH_scRNA

description: 10x Genomics


title: Npc1-/- mouse forebrain 3


title: WT mouse forebrain 3

description: Nuclei were isolated from WT mouse forebrains at P16. RNA was sequenced using the 10X Chromium platform.

value: wt


title: WT mouse forebrain 1


title: Plac BM Premalig


title: GSK BM Premalig


title: Plac Lung Premalig

source_name: lung

value: lung


title: GSK Lung Premalig


title: WT mouse forebrain 2


title: SKM-G4S-BBz biol rep 3

status: Public on May 28 2023

city: Yokohama

first: Taku

last: Kouro

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

institute: Kanagawa Cancer Center Research Institute

description: sample 9

data_processing:
Sequence reads were mapped to GRCh38 (GENCODE v42) using STAR (2.7.10b)
TPM were calculated using RSEM (v1.3.3)
Supplementary files format and content: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values as matrix file

source_name: Blood

growth_protocol: PBMC was prepared using lymphoprep and stimulated with plate-coated anti-CD3 mAb and 100U/ml IL-2 in AIM-V medium supplemented with 10% AB serum.

extract_protocol:
On day 11, RNA was harvested using Rneasy mini kit (Qiagen). 1.1 ~ 4.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Retrovirus supernatants for each CAR was obtained using Phoenix-Ampho packaging cell line and infected to activated PBMC using retronectin (Takara) following manufacturer's instruction.
On day 8, CAR positive cells were labelled with biotin-anti-mouse IgG (Jackson Laboratory) and streptavidin-PE and sorted on FACSAriaII cell sorter, and kept culturing

value: Blood

value: T lymphocytes

value: male

value: CD3/IL-2 stimulation, retrovirus infection

value: Day 11

tag: group


title: SKM-G4S-28z biol rep 3

description: sample 8


title: SKM-G4S-28z biol rep 2

description: sample 5


title: SKM-G4S-BBz biol rep 2

description: sample 6


title: Control mouse 1, snRNAseq

description: Singleron

tag: strain


title: no CAR biol rep 2

description: sample 4

value: CD3/IL-2 stimulation

value: no CAR


title: IL-15-cultured

status: Public on May 30 2023

city: Suwon-si

first: Kyungmin

last: Lee

state: Gyeonggi-do

address: 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea

department: Department of Immunology

institute: Sungkyunkwan University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-3.0.0
Supplementary files format and content: The cell ranger output filtered matrix files including barcodes.tsv, features.tsv and matrix.mtx were included as processed data files

source_name: Spleen

extract_protocol:
Freshly harvested spleens from chronically LCMV-infected micee were dissociated mechanically using gentle force with iron strainer and 3ml syringe. Transfer the homogenized cell solution into the 50ml conical tube and spin down at 1500rpm for 5min at RT. Aspirate the supernatant, resuspend the pellet in 2ml ACK buffer, and incubate it for 5min at RT to lyse red blood cells. After the incubation, add 10ml of R2 (2%FBS in RPMI media) and pour the splenocytes into 70um cell strainer to filter the solution. After spinning down the tube at 1500rpm for 5min, cells were stained with PE PD-1, APC GP33/GP276, APC-Cy7 CD8 antibodies, and Amcyan live/dead viability dye in FACS buffer (2% FBS and 2mM EDTA in PBS). Alive PD-1+GP33+GP276+ CD8 T cells were sorted using a FACS Aria II (BD Bioscience).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: ex vivo cultured in the recombinant murine IL-15 (Peprotech) at 100 ng/ml for 3 days

value: Spleen

value: CD8 T lymphocytes

value: 6-8 weeks old


title: pre-cultured

description: 10x Genomics


title: no CAR biol rep 3

description: sample 7


title: SKM-G4S-28z biol rep 1

description: sample 2


title: SKM-G4S-BBz biol rep 1

description: sample 3


title: no CAR biol rep 1

description: sample 1


title: ChIP anti-H3.3 – siRNA anti-PML – IFN treated

status: Public on May 25 2023

city: Lyon

first: Armelle

last: Corpet

address: 8 avenue Rockefeller

department: Laboratoire Physiopathologie et Génétique du Neurone et du Muscle

country: France

institute: Institut NeuroMyoGene

data_processing:
Sequencing and Base-calling performed by BGI
Adaptor sequence trimming and low quality base filtering using Trimmomatic SE (v0.39), with parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:20
Mapping to the hg38 human genome using bwa (v0.7.17-r1188), followed by genomic coordinates sorting and indexing, with sambamba (v0.7.0)
Marking PCR duplicates, with Picard MarkDuplicates (v2.20.8)
Filtering out unmapped reads (0x4), not primary alignments (0x100), reads failing platform/vendor quality checks (0x200), PCR or optical duplicates (0x400), supplementary alignments (0x800): samtools -F 3844 (v1.9)
Broad Peak Calling using MACS2 (2.2.7.1) : macs2 callpeak --treatment ChIP.bam --control input.bam --format BAM -g hs-q 0.01 --extsize 250 --broad --broad-cutoff 0.05 --bdg –SPMR
Mapped read ends extended to 250bp, in bed format:  `bedtools bamtobed -i bam | awk '$1!~/[_\.]/' | awk 'BEGIN {OFS="\t"} { if ($6=="+") {start=$2; end=$2+250} else {start=$3-250; end=$3}; print $1,start,end,".",$5,$6 }'`
Normalized read counts (CPM) within TES of IFN dependant genes (McFarlane et al 2019, PMID: 30901352): bedtools intersect -c -sorted -g genome.chrLen.txt -a TES.bed -b SampleX.ext250.bed | awk -v norm=$total_mapped_reads 'BEGIN{OFS="\t"}{print $1,$2,$3,$4,$5,$6,$7,($7*1000000/norm)}' ; CPM from inputs subtracted from ChIP CPM.
Assembly: hg38 human genome assembly containing Decoy sequences (https://local-run-manager.s3.amazonaws.com/genomes/Homo_sapiens_NCBI_GRCh38Decoy.zip)
Supplementary files format and content: bigwig files were generated using MACS2: macs2 bdgcmp -t treat_pileup.bdg -c control_lambda.bdg -m FE → bedClip → LC_COLLATE=C sort -k1,1 -k2,2n → bedGraphToBigWig ; Scores represent fold enrichment profiles of ChIP DNA over input DNA
Supplementary files format and content: peak files in bigbed format
Supplementary files format and content: normalized ChIP read counts at TES +/- 500bp

source_name: Human primary fibroblasts

growth_protocol: Human BJ primary foreskin fibroblasts (ATCC, CRL-2522) were cultivated in DMEM medium (Sigma-Aldrich, D6429) containing 10% of fetal calf serum (FCS) (Sigma-Aldrich, F7524), 1% of penicillin/streptomycin (Sigma-Aldrich, P4458), at 37°C under 5% CO2 and humid atmosphere.

extract_protocol:
Cells were crosslinked directly in the culture dishes by adding fixing solution (11% formaldehyde, 50mM HEPES-KOH pH 7.5, 100mM NaCl, 1mM EDTA, 0,5mM EGTA) to the medium to have 1% formaldehyde final concentration and incubated with agitation for 5 minutes at RT°C. Crosslinking was quenched by adding 125mM glycine and cells were incubated with agitation for 5 minutes at RT°C. Cells were washed with ice-cold PBS, scraped and collected in 15mL tubes. They were washed twice with ice-cold PBS and pelleted at 200g for 4 minutes at 4°C. Cell pellets were snap-frozen in liquid nitrogen and stored at -80°C before immunoprecipitation. Cells were de-frozen on ice and lysed in 1X Lysis buffer (50mM HEPES-KOH pH 7.5, 140mM NaCl, 10% Glycerol, 1mM EDTA, 0,5% NP-40, 0,25% Triton X-100) supplemented with protease inhibitors (0,2mM PMSF and 1X PIC) for 10 minutes on a rotating wheel at 4°C. Intact nuclei were pelleted by centrifugation at 1700g for 5 minutes at 4°C.  Nuclei were washed with 1X Wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0,5mM EGTA) supplemented with protease inhibitors for 10 minutes on a rotating wheel at 4°C. Intact nuclei were pelleted by centrifugation at 1700g for 5 minutes at 4°C. Nuclei were washed twice in 1X Shearing buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 0,1% SDS) supplemented with protease inhibitors, pelleted by centrifugation at 1700g for 5 minutes at 4°C and resuspended in 1X Shearing buffer with inhibitors for sonication. We used the Covaris M220 Focused-ultrasonicator to shear through chromatin (7 minutes at 140W, Duty off 10%, Burst cycles 200). After shearing, samples were supplemented with 1% Triton X-100 and 150mM NaCl. Samples were centrifuged at maximal speed for 10 minutes at 4°C to get rid of nuclear debris. The desired mass of chromatin was aliquoted into low-retention 1,5mL tubes (Axygen, MCT-150-L-C) and volume was completed to 1mL with IP buffer (10mM Tris-HCl pH 8.0, 150mM NaCl, 1mM EDTA, 0,1% SDS, 1% Triton X-100) with protease inhibitors. A separate aliquot of chromatin was reserved as the input sample and store at -20°C. Dynabeads protein A magnetic beads (Invitrogen, 10001D) were used for immunoprecipitation with rabbit primary antibodies. Dynabeads were washed twice with ice-cold PBS and resuspended in PBS 0,5% BSA supplemented with primary antibodies (anti-H3.3 (Diagenode, C15210011), anti-panH3 (Abcam, ab1791), rabbit IgG (Diagenode, C15410206)). We used 2μg of antibody for 20μL of dynabeads. Dynabeads and antibodies were incubated on a rotating wheel for 6 hours at 4°C to allow antibody conjugation. Antibody-conjugated dynabeads were then washed twice with IP buffer and resuspended in the 1mL of chromatin. ChIP samples were incubated on a rotating wheel O/N at 4°C. Using a magnetic rack, the unbound lysates were aspirated and dynabeads were washed five times with ice-cold ChIP RIPA Buffer (50mM HEPES pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0,7% Na-deoxycholate) and once with ice-cold TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA). Chromatin was then eluted in 200uL of ChIP Elution buffer (Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) for 30 minutes at 65°C with shaking and the eluates were transferred to a new tube. Reserved input samples were diluted at least 3-fold in ChIP Elution buffer. To purify DNA, ChIP eluates and input samples were decrosslinked by heating O/N at 65°C. Samples were diluted with 200μL of TE buffer and treated for 2 hours with RNase A (200g/mL) (SIGMA R6513) at 37°C followed by 2 hours with recombinant Proteinase K (200g/mL) (Thermo Scientific, 10181030) at 55°C. DNA was purified by phenol-chloroform-isoamyl alcohol extraction. The extracted aqueous phase was supplemented with 200mM of NaCl and 20μg of glycogen. DNA was precipitated with EtOH for 2 hours at -20°C and pelleted at 20 000g for 20 minutes at 4°C. DNA pellets were resuspended in ddH20 and stored at -20°C before sequencing analysis.
Library construction was made by BGI sequencing services according to their internal protocol

treatment_protocol: BJ cells were treated with the indicated siRNAs for 72h and with IFNβ at 1000U/mL for the last 24h of siRNAs treatment

tag: cell line

value: BJ cells

tag: passages

tag: chip antibody

value: H3.3 Rabbit monoclonal Antibody Diagenode #C15210011

tag: sirna

value: targeting PML

value: Interferon Beta


title: Input DNA – siRNA anti-Luc – IFN treated

value: targeting Luciferase

tag: treatment


title: ChIP anti-H3.3 – siRNA anti-Luc – No treatment


title: ChIP anti-H3.3 – siRNA anti-Luc – IFN treated


title: Input DNA – siRNA anti-HIRA – IFN treated

value: targeting HIRA


title: ChIP anti-H3.3 – siRNA anti-HIRA – IFN treated


title: Input DNA – siRNA anti-PML – IFN treated


title: Input DNA – siRNA anti-Luc – No treatment


title: The transcriptome of USA17-26-L-24h-3

status: Public on May 23 2023

city: Haikou

first: Xu

last: Hu

state: Hainan

address: 58 Renmin Avenue, Meila

institute: Hainan University

data_processing:
The raw reads were filtered for adapter sequences and low−quality bases with Trimmomatic (v0.32)
Alignment to the reference genome using HISAT2 (v2.1.0).
Normalization of gene expression was performed by calculating Reads per Kilobase per Million Mapped Reads based on Mortazavi and colleagues' method
Assembly: SeaIsle2000
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Paspalum vaginatum

source_name: Leaf

extract_protocol:
RNA was harvested using plant RNA Kit (Omega Bio-Tek, Norcross, GA, United States)
RNA libraries for RNA-seq were prepared according to manufacturer's protocols

value: Leaf

value: salt

tag: time


title: The transcriptome of USA17-26-L-24h-1


title: The transcriptome of USA17-26-L-48h-2


title: The transcriptome of USA17-26-L-5D-3


title: The transcriptome of USA17-26-R-8h-3

value: Root


title: The transcriptome of USA17-26-L-12h-3


title: The transcriptome of USA17-26-L-5D-2


title: The transcriptome of USA17-26-L-24h-2


title: The transcriptome of USA17-26-R-8h-2


title: The transcriptome of USA17-26-R-5D-3


title: The transcriptome of USA17-26-R-48h-3


title: The transcriptome of USA17-26-R-5D-1


title: The transcriptome of USA17-26-R-5D-2


title: The transcriptome of USA17-26-R-12h-1


title: The transcriptome of USA17-26-R-0-1

value: CK


title: The transcriptome of USA17-26-R-0-3


title: The transcriptome of USA17-26-L-5D-1


title: The transcriptome of USA17-26-R-0-2


title: The transcriptome of USA17-26-R-24h-2


title: The transcriptome of USA17-26-R-8h-1


title: The transcriptome of USA17-26-R-24h-1


title: The transcriptome of USA17-26-R-12h-3


title: The transcriptome of USA17-26-L-48h-3


title: The transcriptome of USA17-26-L-48h-1


title: The transcriptome of USA17-26-R-12h-2


title: The transcriptome of USA17-26-R-24h-3


title: The transcriptome of USA17-26-R-48h-1


title: The transcriptome of USA17-26-R-48h-2


title: The transcriptome of USA17-26-L-12h-2


title: The transcriptome of USA17-26-L-12h-1


title: The transcriptome of USA17-26-L-8h-2


title: The transcriptome of USA17-18-L-5D-2


title: The transcriptome of USA17-26-L-8h-1


title: The transcriptome of USA17-18-R-24h-3


title: The transcriptome of USA17-18-R-12h-3


title: The transcriptome of USA17-26-L-0-3


title: The transcriptome of USA17-26-L-0-2


title: The transcriptome of USA17-18-R-48h-3


title: The transcriptome of USA17-18-R-5D-1


title: The transcriptome of USA17-18-R-5D-2


title: The transcriptome of USA17-18-R-0-2


title: The transcriptome of USA17-18-R-24h-2


title: The transcriptome of USA17-18-R-48h-1


title: The transcriptome of USA17-18-L-48h-1


title: The transcriptome of USA17-18-R-12h-1


title: The transcriptome of USA17-18-L-5D-3


title: The transcriptome of USA17-18-R-8h-1


title: The transcriptome of USA17-18-R-24h-1


title: The transcriptome of USA17-18-L-48h-2


title: The transcriptome of USA17-18-R-0-3


title: The transcriptome of USA17-18-L-5D-1


title: The transcriptome of USA17-26-L-8h-3


title: The transcriptome of USA17-18-R-5D-3


title: The transcriptome of USA17-18-R-12h-2


title: The transcriptome of USA17-18-R-8h-3


title: The transcriptome of USA17-18-R-0-1


title: The transcriptome of USA17-18-R-8h-2


title: The transcriptome of USA17-18-R-48h-2


title: The transcriptome of USA17-18-L-48h-3


title: The transcriptome of USA17-18-L-24h-2


title: The transcriptome of USA17-18-L-24h-3


title: The transcriptome of USA17-18-L-24h-1


title: The transcriptome of USA17-18-L-0-3


title: The transcriptome of USA17-18-L-12h-2


title: The transcriptome of USA17-18-L-0-2


title: The transcriptome of USA17-18-L-12h-1


title: The transcriptome of USA17-18-L-8h-2


title: The transcriptome of USA17-18-L-8h-3


title: The transcriptome of USA17-18-L-8h-1


title: Islet, miR_203

status: Public on May 19 2023

city: Nanjing

first: Yuqian

last: Yang

state: Jiangsu

address: 101 Longmian Avenue

department: Biochemistry and Molecular Biology

institute: Nanjing Medical University

data_processing:
First of all, we use FastQC to perform basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software
The remaining reads that passed all the filtering steps was counted as clean   reads and all subsequent analyses were based on this. At last, we use FastQC to   perform basic statistics on the quality of the clean reads.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx files.

source_name: Islet

growth_protocol: WT and  TG mice were fasted for 12 hrs, then anesthetized and sacrificed by neck broken. Cut off the auricular appendage and exhaled blood, then fulfill the vessels and wash with pre-cooling PBS.

extract_protocol:
TRIZOL was used to extract total RNA.
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Islets were collected and quick-frozen by liquid nitrogen.

value: Islet

tag: Sex

value: male

tag: genotype

value: beta cell specific miR-203 transgene

value: fasted for 12 hrs


title: The transcriptome of USA17-18-L-0-1


title: Islet, WT

tag: age

value: wild type


title: OtC0382_Abx_Morphine_2

status: Public on May 18 2023

city: Winston-Salem

first: Drew

last: Kiraly

state: NC

address: 115 South Chestnut Street

department: Physiology, Pharmacology, Psychiatry

institute: Wake Forest University School of Medicine

data_processing:
Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
Supplementary files format and content: comma separated-values (.csv)
Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)

source_name: Nucleus accumbens (brain)

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).

treatment_protocol: Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.

value: Nucleus accumbens (brain)

value: Bulk

tag: microbiome status

value: Depleted Microbiome

value: Morphine (20mg/kg/day/7 days)


title: OtC0374_Abx_Saline_6

tag: tissue

value: Saline


title: OtC0378_H2O_Morphine_4

value: Normal Microbiome


title: OtC0380_H2O_Morphine_6


title: OtC0376_H2O_Morphine_2


title: OtC0379_H2O_Morphine_5


title: OtC0372_Abx_Saline_4


title: OtC0370_Abx_Saline_2


title: OtC0381_Abx_Morphine_1


title: OtC0383_Abx_Morphine_3


title: OtC0371_Abx_Saline_3


title: OtC0384_Abx_Morphine_4


title: OtC0373_Abx_Saline_5


title: The transcriptome of USA17-18-L-12h-3


title: OtC0385_Abx_Morphine_5


title: The transcriptome of USA17-26-L-0-1


title: OtC0377_H2O_Morphine_3


title: OtC0369_Abx_Saline_1


title: OtC0364_H2O_Saline_4


title: Otc0363_H2O_Saline_3


title: OtC0365_H2O_Saline_5


title: OtC0366_H2O_Saline_6


title: RD spheres passage 5

status: Public on May 17 2023

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using in-house pipeline of Brotman Baty single-cell services pipeline.
Assembly: GRCh38
Supplementary files format and content: not provided

source_name: RD

extract_protocol:
RMS spheres were fixed in 4% paraformaldehyde and frozen in liquid nitrogen prior to nuclear extraction.
The samples were subsequently submitted to the single-cell services at the Brotman Baty Institute for Precision Medicine (University of Washington) for single-cell RNA library preparation and sequencing.

value: RD

value: Rhabdomyosarcoma

value: 5Day Passage


title: OtC0367_H2O_Saline_8


title: RD spheres passage 1

value: 1Day Passage


title: RD parental

value: adherent


title: R23: Ta_mock_water_spray_6dpi_2

status: Public on May 15 2023

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomaticv0.35
Trimmed reads were mapped to Triticum aestivum IWGSC transcriptome reference using Kallisto v0.46.1 with default parameters
Read counts were summarized using tximport v1.2.0
Read abundance normalization and differential gene expression analysis were performed with the R package DESeq2
Assembly: Triticum_aestivum.IWGSC.cdna.all
Supplementary files format and content: tab-delimited txi.kallisto abundance counts for all samples

organism: Triticum aestivum

source_name: Uninfected leaves

extract_protocol:
Three cm from the tip were discarded, and 6 cm of the adjacent leaf were flash-frozen in liquid N2 and homogenized with zirconium beads (1.4 mm diameter) using the Bead-Rupture equipped with a cooling unit (Omni International, Kennesaw, GA, USA). RNA isolation was performed using GENEzol reagent (Geneaid Biotech, Taipei, Taiwan) following the manufacturer's instructions. RNAeasy Mini Kit (Qiagen GmbH, Hilden, Germany) was used to purify the RNA, and DNA contamination was removed using the on-column DNase treatment of the RNase-Free DNase Set (Qiagen GmbH, Hilden, Germany).
Ribosomal RNA was depleted by poly A enrichment, and DNA libraries were sequenced with Illumina NovaSeq 6000 at Novogene Europe

value: Control leaves

value: Day 6

value: Chinese Spring

value: Water spray


title: R24: Ta_mock_water_spray_6dpi_3


title: R14: Ta_3D7_6dpi_2

source_name: Leaves infected with Zymoseptoria tritici

value: Infected leaves

value: Chinese Spring; ST99CH_3D7

value: Zymoseptoria tritci infection


title: R15: Ta_3D7_6dpi_3


title: R18: Ta_1E4_6dpi_3

value: Chinese Spring; ST99CH_1E4


title: R22: Ta_mock_water_spray_6dpi_1


title: R16: Ta_1E4_6dpi_1


title: R20: Ta_Mix_1E4_3D7_6dpi_2

value: Chinese Spring; ST99CH_1E4; ST99CH_3D7


title: R11: Ta_mock_water_spray_3dpi_2

value: Day 3


title: R17: Ta_1E4_6dpi_2


title: R10: Ta_mock_water_spray_3dpi_1


title: R21: Ta_Mix_1E4_3D7_6dpi_3


title: R13: Ta_3D7_6dpi_1


title: R12: Ta_mock_water_spray_3dpi_3


title: Rubella virus infected cortical organoids replicate 2

city: San Francisco

first: Chang

last: Kim

address: 505 Parnassus Ave

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38

source_name: Cortical organoid

extract_protocol:
Two organoids per experimental condition were washed with Ca2+/Mg2+-free DPBS and cut into 1 mm2 pieces   and   enzymatically   digested   with   papain   digestion   kit   (Worthington,   LK003163)  with   the addition of DNase for 1 hr at 37C.
Two organoid lines with and without microglia that were treated with RV or uninfected. Cell supernatant were combined and captured across seven lanes of 10x Genomics using Chromium single cell 3' reagent kit (v2 Chemistry) following the manufacturer’s protocol.  Multi-seq library construction was performed with standard protocol.

value: Cortical organoid cells

value: Cortical organoid

value: 10 weeks old


title: Rubella virus infected cortical organoids replicate 1

description: 10x Genomics


title: R9: Ta_Mix_1E4_3D7_3dpi_3


title: R8: Ta_Mix_1E4_3D7_3dpi_2


title: OtC0368_H2O_Saline_9

value: Nucleus accumbens (brain)

value: male

value: Bulk

value: Normal Microbiome

value: Saline


title: R7: Ta_Mix_1E4_3D7_3dpi_1


title: R6: Ta_1E4_3dpi_3


title: R19: Ta_Mix_1E4_3D7_6dpi_1

value: Day 6


title: R3: Ta_3D7_3dpi_3


title: R2: Ta_3D7_3dpi_2


title: R4: Ta_1E4_3dpi_1


title: SBR-72h

city: Basel

first: Nadim

last: Aizarani

address: Maulbeerstrasse 66

institute: FMI

data_processing:
Reference and Quantification: Genome sequence and transcript annotation was obtained from Gencode Mouse release M24 (GRCm38 primary assembly and annotation gtf file from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M24), and the coordinates of transcripts and introns were extracted using R (https://r-project.org, version 3.6) and the getFeatureRanges function from the eisaR package (version 0.9 available from https://github.com/fmicompbio/eisaR/tree/bbd8787d7e4b87d158a276af0787226530867b88) with arguments featureType = c("spliced", "intron"), intronType = "separate", flankLength = 0, joinOverlappingIntrons = FALSE. A transcript-to-gene map was created using the getTx2Gene function from eisaR, which links transcripts to genes, and introns to distinct genes for simultaneous quantification (see below). Sequences were extracted from the genome using extractTranscriptSeqs from the GenomicFeatures package (version 1.38.2, )94 and indexed with Salmon (version 1.1.095) with arguments -k 23 –gencode and using the genome as a decoy. Reads were then quantified using Salmon/Alevin (version 1.1.096) with parameters -l ISR --chromiumV3 and the transcript-to-gene map created above.
Quality control and filtering: Technical quality of single cell experiments, cell barcode identification and quantification were assessed using the Bioconductor package alevinQC (version 1.4.0, https://doi.org/doi:10.18129/B9.bioc.alevinQC). Salmon/Alevin counts from all twelve timepoints were imported into R (version 4.0.2) using the tximeta package (version 1.6.397) and stored in a SingleCellExperiment container for downstream analysis. The number of detected genes per cell and the fraction of counts in genes encoded on the mitochondrion (chrM) were calculated using the addPerCellQC function from the scater package (version 1.16.298), and cells with more than 1800 detected genes and less than 10% mitochondrial counts were retained. Gms, mitochondrial, and ribosomal protein genes (genes associated with the GeneOntology term "structural constituent of ribosome", GO:0003735, based on the org.Mm.eg.db package, version 3.11.4) were removed, resulting in a final analysis set of 27027 genes and 71005 cells.
Assembly: GRCm38 primary assembly

source_name: Gastruloids

growth_protocol: ESCs were grown in GMEM supplemented with 10% embryonic stem cell qualified FBS, GlutaMAX, sodium pyruvate, EmbryoMAX MEM NEAA, beta-mercaptoethanol, 0.1 µg/ml LIF, 3 µM CHIR99021, and 1 µM PD0305901. Gastruloids were generated from 300 cells and grown in 96-well ulta-low-attachment U-bottom plates in N2B27 medium (DMEM/F-12, Neurobasal medium, N2, B-27, GlutaMAX, HEPES, and beta-mercaptoethanol) and pulsed with 3 µM CHIR99021 from 48 to 72 hours.

extract_protocol:
0h ESC, gastruloids 12, 24, 36, 48, 52, 56, 60, 72, 84,96, and 120 hours were dissociated with Accutase and per sample 12,000 alive cells were sorted by FACS. Cellular supensions were loaded on a 10x Genomics Chromium Single Cell instrument.
Single cell RNAseq libraries were prepared using the 10x Genomics Single Cell 3’ Gel Bead and Library Kit according to CG000183 Single Cell 3' Reagent Kit v3 User Guide_RevA. GEMRT was performed in a Bio-Rad PTC-200 Thermal Cycler with 0.2ml PCR Tube Strips (Eppendorf P/N 0030 124.359): 53 °C for 45 minutes, 85 °C for 5 minutes; held at 4 °C. After RT, GEMs were broken and the single strand cDNA was cleaned up with DynaBeads® MyOneTM Silane Beads (Life Technologies P/N 37002D). cDNA was amplified using a Bio-Rad PTC-200 Thermal cycler with 0.2ml PCR Tube Strips (Eppendorf P/N 0030 124.359): 98 °C for 3 min; cycled 11x: 98 °C for 15 s, 63 °C for 20 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6X SPRI). Indexed sequencing libraries were constructed using the reagents in the Chromium Single Cell 3’ library kit V3 ( 10x Genomics P/N1000078), following these steps: 1) Fragmentation, End Repair and A-Tailing; 2) Post Fragmentation, End Repair & A-Tailing Double Sided Size Selection with SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI); 3) adaptor ligation; 4) post-ligation cleanups with SPRIselect (0.8X SPRI); 5) sample index PCR using the Chromium Multiplex kit (10x Genomics P/N-120262); 6) Post Sample Index Double Sided Size Selection- with SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI). The barcode sequencing libraries were quantified using a Qubit 2.0 with a Qubit TM dsDNA HS Assay Kit (Invitrogen P/N Q32854) and the quality of the libraries were performed on a 2100 Bioanalyzer from Agilent using an Agilent High Sensitivity DNA kit (Agilent P/N 5067-4626). Sequencing libraries were loaded at 1.6pM on an Illumina Nextseq500 with 75cycle kits using the following read length: 28 cycles Read1, 8 cycles i7 Index and 56 cycles Read2.

treatment_protocol: Gastruloids were not treated.

value: Gastruloids

value: embryonic stem cells

value: SBR (Sox1/Brachyury reporter)/CGR8


title: SBR-84h_B


title: SBR-48h


title: SBR-36h


title: SBR-24h


title: NUP98::NSD1 cells, Day 12, Mock-2

status: Public on May 14 2023

city: UTRECHT

first: Olaf

last: Heidenreich

state: UTRECHT

address: Prinses Máxima Centrum voor kinderoncologie | Postbus 113| 3720 AC BILTHOVEN | Heidelberglaan 25 |  3584CS UTRECHT | Nederland

country: Netherlands

data_processing:
For RNAseq data, the fastq files were trimmed using trim_galore 0.6.5.
The data were mapped to the Homo_sapiens GRCh38 reference sequence using STAR 2.7.10a.
The read counts were retrieved with subread/1.6.5.
Assembly: GRCh38
Supplementary files format and content: Matrix table, raw counts

source_name: Bone Marrow

extract_protocol:
RNA was harvested using MACHEREY‑NAGEL kit (MN). 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Bone Marrow

value: Primary AML cells

value: NUP98::NSD1, FLT3-ITD

value: DMSO

value: Day 12


title: NUP98::NSD1 cells, Day 7, SNDX-1

institute: Prinses Máxima Centrum voor kinderoncologie

value: Day 7


title: NUP98::NSD1 cells, Day 12, SNDX-3


title: NUP98::NSD1 cells, Day 7, Mock-3


title: fat, normal saline supplementary, rep2

status: Public on May 08 2023

city: Guangzhou

first: Zehua

last: Li

address: Huangpu Avenue

institute: Jinan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: adipose

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: adipose

value: normal saline supplement


title: NUP98::NSD1 cells, Day 12, SNDX-2


title: NUP98::NSD1 cells, Day 12, SNDX-1


title: fat, normal saline supplementary, rep1


title: NUP98::NSD1 cells, Day 7, SNDX-3


title: NUP98::NSD1 cells, Day 12, Mock-3


title: fat, Glutathione supplementary, rep3

value: Glutathione supplement


title: fat, Glutathione supplementary, rep2


title: NUP98::NSD1 cells, Day 7, SNDX-2


title: fat, normal saline supplementary, rep3


title: NUP98::NSD1 cells, Day 12, Mock-1


title: NUP98::NSD1 cells, Day 7, Mock-2


title: R1: Ta_3D7_3dpi_1

value: Infected leaves

value: Day 3

value: Chinese Spring; ST99CH_3D7

value: Zymoseptoria tritci infection


title: SBR-60h


title: NUP98::NSD1 cells, Day 7, Mock-1


title: fat, Glutathione supplementary, rep1


title: SBR-84h_A


title: R5: Ta_1E4_3dpi_2

value: Chinese Spring; ST99CH_1E4


title: PAO1 ∆phrS pPhrS∆seed replicate B

status: Public on May 03 2023

city: Iowa City

first: Michael

middle: J

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

description: Sample 3B

data_processing:
fastq records trimming (cutadapt 2.10) (Samples 5 - 8)
Quality control and adapter trimming (bcl2fastq 2.20.0.445) (Samples 9-10)
short reads mapping (bowtie2 2.4.4) (Samples 5-10)
BED file conversion (bedtools 2.30.0) (Samples 5-10)
bigwig file conversion (bedGraphToBigWig 2.9) (Samples 5-10)
Read quantification (htseq-count 2.0.2) (Samples 9-10)
Assembly: P. aerugionsa PAO1, NC_002516.2
Supplementary files format and content: Supplementary_files_format_and_content: bigwig format for samples 5 - 10.

organism: Pseudomonas aeruginosa

source_name: ∆phrS strain with vector for pulsed expression of PhrS-∆seed allele (pMJG448)

growth_protocol: Bacterial strains were grown at 37˚C , shaking at 200 rpm, in LB rich medium and samples 1&2 were collected at OD ≈ 0.5, samples 3&4 were collected at OD ≈ 2.0.

extract_protocol:
Standard TRI Reagent protocol was used for RNA extraction
Libary construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al., 2015) for samples 5 - 8.

treatment_protocol: Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen in a dry ice - ethanol bath.

value: {delta}phrS pMJG448

value: Growth:OD ≈ 2.0 in LB + gentamicin (30 µg/mL)

value: 20 minutes pulse of 0.2% (w/v) arabinose


title: PAO1 ∆phrS pPhrS replicate C

description: Sample 2C

source_name: ∆phrS strain with vector for pulsed expression of PhrS-WT allele (pTK60)

value: {delta}phrS pTK60


title: PAO1 ∆phrS pPhrS replicate B

description: Sample 2B


title: PAO1 ∆phrS pPhrS replicate A

description: Sample 2A


title: PAO1 ∆phrS pEV replicate C

description: Sample 1C

source_name: ∆phrS strain with empty vector (pKH6)

value: {delta}phrS pKH6


title: PAO1 ∆phrS pEV replicate B

description: Sample 1B


title: PAO1 ∆phrS pPhrS∆seed replicate A

description: Sample 3A