title: 99.IonXpress_009

city: New York

first: Madeline

last: Kim

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from tape-stripped skin

data_processing:
Input adapter trimming using Cutadapt version 1.9.1 with -a AAAAAAAAAAAAA -a TTTTTTTTTTTTT -a AGATCGGAAGAG -a CTCTTCCGATCT
Aligning the input reads to reference genome using STAR_2.4.2a
Quality assesment on aligned data using FastQC v0.11.5
Quality assesment on aligned data using QualiMap  v.2.2
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genomic features with <10 counts in at least 9 (n of smallest group) samples were filtered out (filterByExpr [edgeR R package])
Data was then transfomed to log2-counts per million by voom-transform
Fold changes (FCHs) vs. normals were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Assembly: GRCh37
Supplementary files format and content: expression matrix (csv file) of voom-transformed counts in log2 counts per million

source_name: Tape strip

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using Ion AmpliSeq Transcriptome Human Gene Expression Kits following the manufacturer's protocol and were pooled and sequenced on the Ion S5 XL System Sequencer with Ion 550 Chips.

tag: patient id

tag: disease

value: MAA

value: Male

tag: race

value: White

tag: age of asthma onset

tag: family history of atopy

value: rhinitis

tag: asthma treatment

value: ICS

tag: r20 (ios)

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)

value: tape-stripped skin


title: 94.IonXpress_004

status: Public on Jul 25 2024

type: SRA

state: NY

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: SAA

tag: age

tag: Sex

value: AD

value: ICS/LABA

tag: tissue


title: 95.IonXpress_005

value: asthma


title: CPOP-tile2-30-MTX-rep3

city: Copenhagen

first: Sven

last: Larsen-Ledet

state: N

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

library_source: other

data_processing:
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instrument's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads from each lane were merged and resulting R1 and R2 fastq files were trimmed to remove adapters and then merged. The merged fastq files were analysed using our in-house pipeline to count DHFR indel variants and calculate a score for each variant per condition.
Assembly: atggttggttctttgaactgtatcgttgctgtttcacaaaacatgggtatcggtaaaaatggtgacttgccatggccaccattaagaaacgaattcagatacttccaaagaatgactacaacttcttcagttgaaggtaaacaaaatttggttattatgggtaaaaagacttggttctctatcccagaaaagaatagaccattgaagggtagaattaatttggttttgtcaagagaattgaaagaaccaccacaaggtgctcatttcttgtctagatcattggatgatgcattgaagttgacagaacaaccagaattggctaataaggttgatatggtttggattgttggtggttcttcagtttacaaagaagcaatgaaccatccaggtcatttgaagttgttcgttactagaatcatgcaagatttcgaatctgatactttctttccagaaatcgatttggaaaagtacaagttgttgccagaatacccaggtgttttatcagatgttcaagaagaaaagggtattaaatacaagttcgaagtttacgaaaagaatgat
Supplementary files format and content: A csv file with a CPOP score for each mutation type (synonymous, stop codon, deletion and insertion) at each position for the four conditions (30 °C, 30 °C + MTX, 37 °C, 37 °C + MTX), including standard deviations.
Library strategy: Indel libraries in tiles

molecule: other

organism: synthetic construct

source_name: wild-type yeast strain (BY4741)

growth_protocol: Following library transformations, yeast cells were expanded in SC-LEU medium until saturation. Then, cells for the nonselect condition were harvested and stored at -20C prior to plasmid DNA extraction. In addition, yeast cells were washed and grown on solid SC-LEU-URA medium with and without 220 mM methotrexate and 1 mM sulfanilamide at 30C and 37C for two days. Following selection, the cells were harvested and stored at -20C prior to plasmid DNA extraction.

extract_protocol:
For all conditions, plasmid DNA was extracted from 9 OD units of yeast cells using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen).
Libraries comprising DHFR indel variants were prepared in each tile and cloned into pAG415 by Twist Bioscience.

treatment_protocol: For selection, yeast cells were grown on solid SC-LEU-URA medium with and without 220 mM methotrexate and 1 mM sulfanilamide at 30C and 37C for two days. Following selection, the cells were harvested and stored at -20C prior to plasmid DNA extraction.

tag: tile

value: human DHFR sequence

tag: cell type

value: wild-type yeast strain (BY4741)

tag: treatment

value: 30 °C + MTX


title: BAT_CR-day-6h_CT20B

city: Dallas

first: Joseph

last: Takahashi

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Sequencing libraries were constructed in house following Illumina single-stranded mRNA-seq protocol. RNA-sequencing of libraries was performed on the NextSeq 550 (Illumina) with 75 bp reads, according to the manufacturer’s instructions, by the UTSW McDermott Next Generation Sequencing Core. Read quality was assessed using the FASTQC quality control tool. Reads were mapped with STAR (Dobin et al., 2013) (with parameters:--runMode alignReads --genomeDir genomefolder --sjdbGTFfile gtf --readFilesIn sample_trim.gz --readFilesCommand zcat --outFileNamePrefix sample --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMmapqUnique 255 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterMismatchNmax 3 --twopassMode Basic --quantMode GeneCounts) following Cutadapt trimming (with parameters: -g AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 30) to M14 GENCODE (protein coding only) version of mouse genome from www.gencodegenes.org. Raw reads were quantified using featureCounts tool from Rsubread package. Reads per kilobase per million (RPKM) was used to normalize uniquely mapped reads according to the sequencing depth and gene length. RPKM calculation was performed using in-house scripts. Downstream bioinformatic analysis after RPKM calculations was performed in R environment.
Assembly: M14 from GENCODE
Supplementary files format and content: excel file includes raw counts for all samples
Supplementary files format and content: excel file includes RPKM values for all samples

molecule: polyA RNA

organism: Mus musculus

source_name: BAT

growth_protocol: C57BL/6J male mice (8 week-old) were individually housed in standard polycarbonate mouse cages (Fischer Scientific, Cat. Nos. 01-288-1B and 01-288-21) containing a 4.75 in diameter stainless steel running wheel inside isolation cabinets containing 12 cages each. Temperature and humidity levels were monitored, and the mice were housed under an LD12:12 cycle (green LEDs, ~100 lux at the level of the cage floor). Water was provided ad libitum throughout the study.

extract_protocol:
RNA from tissues was homogenized in 1mL of TRIzol and extracted according to manufacturer instructions. All RNA samples with RIN >7.5 were used; 260/280 ratio > 2; and 260/230 ratio > 2.
mRNA-Seq (polyA selection); mRNA-seq library preparation was done according to Illumina single-stranded mRNA-seq. Briefly, library was prepared with 25 ng of mRNA polyA-selected from 5ug total RNA, with 13 cycles of PCR amplification. Library size was confirmed by Tapestation 2200 (Agilent).

treatment_protocol: Mice were fed with a purified diet provided as round pellets of 300 mg each with 3.65 Kcal/g (Dustless Precision Pellets, Rodent, Purified, F0075, BioServ, Flemington, NJ, USA). Pellets composition is equivalent to regular chow, with 18.7% protein, 5.6% fat, 59.1% carbohydrates and 4.7% fiber (Acosta-Rodriguez et al., 2022). Food access was controlled by the automated feeder system designed in our lab with Phenome Technologies, Skokie, IL, USA (Acosta-Rodriguez et al., 2017). ClockLab Chamber Control Software v3.401 (Actimetrics Inc., Wilmette, IL, USA) was used to program feeding schedules and record food consumption. The feeders were monitored daily via remote access to detect and rectify any problems with the system (cages or feeder chute misalignments, motor errors, and sensor failures). A 10 min delay was programmed after each food pellet was taken before the next pellet was dropped to prevent hoarding behavior. Wheel-running behavior was recorded throughout the study using ClockLab Data Acquisition System v3.209 (Actimetrics Inc., Wilmette, IL, USA).  After three weeks of recording under ad libitum food access, mice were randomly assigned to one of 5 feeding conditions (n=72 per condition): 24h access ad libitum (AL); unlimited amount but temporally restricted to the first 6h during the dark (TR-night-6h), or light (TR-day-6h) phase; 6h access but calorically restricted (10 pellets distributed as 6:2:2 every 2h) pellets corresponding to 70% of baseline ad libitum levels fed at the start of the dark (CR-night-6h) or light (CR-day-6h) phase. Mice were weighed in the morning and cages were changed every 21 days, and bedding was checked for any evidence of food spillage.  Wheel-running behavior was recorded throughout the study using ClockLab Data Acquisition System v3.209 (Actimetrics Inc., Wilmette, IL, USA). All mice were monitored in real-time in these conditions  until the time points for the tissue collections (see tissue collection, n=24 per feeding). Samples were collected, snap frozen and stored at -80ºC until RNA extraction.

value: BAT

tag: strain

tag: genotype

value: WT

value: male

value: 6 months-old

tag: light condition

value: 12h light / 12h dark

tag: feeding

tag: collectiontime hours


title: BAT_CR-day-6h_CT16B


title: BAT_CR-day-6h_CT40B


title: CPOP-tile2-30-MTX-rep2


title: CPOP-tile2-37-rep3

value: 37 °C


title: anti-PD-1, replicate 1, scRNAseq

city: Hangzhou

first: Xiaonan

last: Xiang

address: No.866, Yuhangtang road Road

department: School of Medicine

country: China

institute: Zhejiang University

description: 10x Genomics

library_source: transcriptomic single cell

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: Orthotopic liver tumors (Hepa1-6)

extract_protocol:
Tumor samples were collected and placed in pre-cooled PBS to remove necrotic tissue, blood clots, and surrounding normal tissue. The samples were then cut into small pieces and added to a 6-well plate containing 2 mL of preheated tissue lysate (5 mg/mL collagenase IV and 1 mg/mL DNase, incubated at 37 °C on a shaker at 90-100rpm for 1 hour. Next, the cell suspension was filtered using a 70µm filter, and centrifuged at 300g, 4°C for 5 minutes. The supernatant was discarded, and the cell pellet was enriched by mouse CD45 MicroBeads (Miltenyi, Cat# 130-052-301) according to the manufacturer's instructions. Enriched cells were then stained with 7-AAD and APC-Cy7 anti-mouse CD45 antibody. Alive CD45+ cells were sorted using a BD FACSAria™ III cell sorter.  Sorted alive CD45+ 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, tumor-infiltrating CD45+ cells 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: Orthotopic liver tumors (Hepa1-6)

value: tumor-infiltration CD45+ cells


title: BAT_CR-day-6h_CT04B


title: 91.IonXpress_001

tag: patient id

tag: disease

value: MAA

value: Male

tag: race

value: White

tag: age of asthma onset

tag: family history of atopy

value: rhinitis

tag: asthma treatment

value: ICS

tag: r20 (ios)


title: BAT_CR-day-6h_CT08B

tag: Sex

tag: age


title: CPOP-tile2-37-MTX-rep1

tag: tile

value: 37 °C + MTX


title: BAT_CR-day-6h_CT00B

tag: tissue


title: CPOP-tile2-30-MTX-rep1

value: human DHFR sequence

tag: cell type

tag: treatment


title: 89.IonXpress_015

value: Female

value: no

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)

value: tape-stripped skin


title: CPOP-tile2-30-rep3

value: wild-type yeast strain (BY4741)

value: 30 °C


title: BAT_AL_CT40A

value: BAT

tag: strain

tag: genotype

value: WT

value: male

value: 6 months-old

tag: light condition

tag: feeding

value: Ad Libitum

tag: collectiontime hours


title: BAT_AL_CT44A

value: 12h light / 12h dark


title: 87.IonXpress_013

tag: patient id

tag: disease

value: MAA

value: Male

tag: race

tag: age of asthma onset

tag: family history of atopy

value: rhinitis and asthma

tag: asthma treatment

tag: r20 (ios)


title: 92.IonXpress_002

value: SAA

tag: age

tag: Sex

value: White

value: ICS/LABA

tag: r5 (ios)

tag: tissue


title: BAT_AL_CT32A


title: BAT_CR-day-6h_CT12B


title: 84.IonXpress_010

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)


title: BAT_AL_CT36A

tag: strain

tag: genotype

tag: light condition

tag: feeding


title: CPOP-tile2-30-rep2

tag: tile

value: human DHFR sequence

tag: cell type

tag: treatment


title: CPOP-tile2-30-rep1


title: BAT_AL_CT24A

tag: collectiontime hours


title: BAT_AL_CT28A


title: 83.IonXpress_009

tag: patient id

tag: disease

tag: race

tag: age of asthma onset

tag: family history of atopy

tag: asthma treatment

tag: r20 (ios)


title: CPOP-tile2-no-sele-rep3

value: control


title: BAT_AL_CT20A

tag: tissue

tag: Sex

tag: age


title: Pancreatic islets, non-diabetic, biological replicate 11

city: New Orleans

first: Franck

last: Mauvais-Jarvis

state: LA

address: 1430 Tulane Avenue Lab# 2301

department: Department of Medicine - Section of Endocrinology and Metabolism

institute: Tulane University

description: Single cell RNAseq Dataset containing FASTQ and Cellranger outputs

data_processing:
We utilized CellRanger v4.0.0 software using the [-mkfastq] command to de-multiplex FASTQ data. Reads were mapped and aligned to the human genome (10X genomics pre-built GRCh38-2020-A Homo sapiens reference transcriptome assembly) with STAR (95.33±0.75% of reads confidently mapped to the human genome).
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell Ranger Output

source_name: Pancreas

growth_protocol: Human islets (500 IEQ per condition) were cultured overnight in a humidified incubator containing 5% CO2 at 37°C.

extract_protocol:
Islet cells were then dispersed using TrypLE (Thermofischer), and immediately evaluated for viability (90.61±3.04%) by Cellometer Automated Cell Counter (Nexcelom Bioscience) prior to single cell RNAseq library preparation.
For 10x single cell RNAseq library preparation, 5000-6500 individual live cells per sample were targeted by using 10x Single Cell 3’ RNAseq technology provided by 10x Genomics (10X Genomics Inc). Briefly, viable single cell suspensions were partitioned into nanoliter-scale Gel Beads-In-EMulsion (GEMs). Full-length barcoded cDNAs were then generated and amplified by PCR to obtain sufficient mass for library construction. Following enzymatic fragmentation, end-repair, A-tailing, and adaptor ligation, single cell 3’ libraries comprising standard Illumina P5 and P7 paired-end constructs were generated. Library quality controls were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer (Agilent) and quantified by Qubit 2.0 fluorometer (ThermoFisher).

treatment_protocol: No treatments

value: Pancreas

tag: disease state

value: non-diabetic

value: Pancreatic Islets

value: No treatment


title: BAT_AL_CT12A

value: BAT

tag: strain

tag: genotype

value: WT

tag: light condition


title: BAT_AL_CT16A

value: male

value: 6 months-old

tag: feeding


title: 148.IonXpress_010

value: Control

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)

value: tape-stripped skin


title: CPOP-tile2-no-sele-rep2

tag: tile

tag: cell type

value: wild-type yeast strain (BY4741)

tag: treatment


title: BAT_AL_CT00A

value: 12h light / 12h dark

value: Ad Libitum

tag: collectiontime hours


title: BAT_AL_CT04A

tag: tissue


title: 147.IonXpress_009

tag: patient id

tag: disease

tag: Sex

value: Male

tag: race

value: White

tag: age of asthma onset

tag: family history of atopy

tag: asthma treatment

tag: r20 (ios)


title: BAT_AL_CT08A

tag: strain

tag: genotype

tag: age

tag: light condition

tag: feeding


title: CPOP-tile2-no-sele-rep1

tag: tile

value: human DHFR sequence

tag: cell type


title: 144.IonXpress_006

value: Female

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)


title: CPOP-tile1-37-MTX-rep3

tag: treatment

value: 37 °C + MTX


title: Liver_TR-night-6h_CT40B

source_name: Liver

tag: tissue

value: Liver

tag: Sex

tag: collectiontime hours


title: 142.IonXpress_004

tag: patient id

tag: disease

tag: race

tag: age of asthma onset

tag: family history of atopy

tag: asthma treatment

tag: r20 (ios)


title: Liver_TR-night-6h_CT32B

tag: strain

tag: genotype

tag: age

tag: light condition

tag: feeding


title: CPOP-tile1-37-MTX-rep2

tag: tile

tag: cell type


title: 141.IonXpress_003

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)

tag: tissue


title: Liver_TR-night-6h_CT36B

tag: Sex

tag: collectiontime hours


title: Liver_TR-night-6h_CT24B


title: 137.IonXpress_015

tag: patient id

tag: disease

tag: race

tag: age of asthma onset

tag: family history of atopy

tag: asthma treatment


title: CPOP-tile1-37-MTX-rep1

tag: treatment


title: Liver_TR-night-6h_CT28B

tag: strain

tag: genotype

tag: age

tag: light condition

tag: feeding


title: Liver_TR-night-6h_CT16B


title: Liver_TR-night-6h_CT20B


title: CPOP-tile1-37-rep3

tag: tile

tag: cell type

value: 37 °C


title: 135.IonXpress_014

tag: r20 (ios)

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)

tag: tissue


title: CPOP-tile1-37-rep2


title: Liver_TR-night-6h_CT08B

tag: Sex

tag: collectiontime hours


title: Liver_TR-night-6h_CT04B


title: Liver_TR-night-6h_CT12B


title: CPOP-tile1-37-rep1

tag: treatment


title: Liver_TR-night-6h_CT44B

tag: strain


title: Liver_TR-night-6h_CT00B

tag: genotype


title: 134.IonXpress_013

tag: patient id

tag: disease

tag: age

tag: race

tag: age of asthma onset

tag: family history of atopy

tag: asthma treatment


title: 133.IonXpress_012

tag: r20 (ios)

tag: r5 (ios)

tag: feno


title: Liver_TR-night-6h_CT40A

tag: light condition

tag: feeding


title: BAT_CR-day-6h_CT24B

tag: tissue

tag: Sex


title: 132.IonXpress_011

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)


title: CPOP-tile1-30-MTX-rep3

tag: tile

tag: cell type

tag: treatment

value: 30 °C + MTX


title: Liver_TR-night-6h_CT44A

tag: strain

tag: genotype

tag: age

tag: collectiontime hours


title: Liver_TR-night-6h_CT36A


title: CPOP-tile1-30-MTX-rep2


title: Liver_TR-night-6h_CT32A


title: 129.IonXpress_008

tag: patient id

tag: disease

tag: race

tag: age of asthma onset

tag: family history of atopy

tag: asthma treatment

tag: r20 (ios)


title: Liver_TR-night-6h_CT28A

tag: tissue

tag: Sex

tag: light condition

tag: feeding


title: CPOP-tile1-30-MTX-rep1

tag: tile

tag: cell type


title: Liver_TR-night-6h_CT24A

tag: strain


title: 126.IonXpress_005

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)


title: Liver_TR-night-6h_CT16A

tag: genotype

tag: age

tag: collectiontime hours


title: Liver_TR-night-6h_CT20A


title: CPOP-tile1-30-rep2

tag: treatment

value: 30 °C


title: 125.IonXpress_004

tag: patient id

tag: disease

value: SAA

tag: race

tag: age of asthma onset

tag: family history of atopy

value: rhinitis

tag: asthma treatment

value: ICS/LABA

tag: r20 (ios)


title: Liver_TR-night-6h_CT12A

tag: tissue

tag: strain

value: WT

tag: Sex

value: male

value: 6 months-old

tag: light condition

tag: feeding


title: Liver_TR-night-6h_CT08A

value: 12h light / 12h dark


title: Liver_TR-night-6h_CT04A


title: CPOP-tile1-30-rep1

tag: tile

tag: cell type

value: wild-type yeast strain (BY4741)


title: Liver_TR-day-6h_CT44B

tag: genotype

tag: age


title: 117.IonXpress_010

value: MAA

value: no

value: ICS

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)

value: tape-stripped skin


title: CPOP-tile1-no-sele-rep3

value: human DHFR sequence

tag: treatment

value: control


title: 113.IonXpress_006

tag: patient id

tag: disease

value: Male

tag: race

value: White

tag: age of asthma onset

tag: family history of atopy

value: rhinitis and asthma

tag: asthma treatment


title: CPOP-tile1-no-sele-rep2


title: 112.IonXpress_005

value: SAA

tag: Sex

value: Female

tag: r20 (ios)

tag: tissue


title: Liver_TR-day-6h_CT36B

value: Liver

tag: strain

tag: genotype

tag: light condition

tag: feeding

tag: collectiontime hours


title: Liver_TR-day-6h_CT32B

value: WT

tag: age


title: 111.IonXpress_004

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)


title: CPOP-tile1-no-sele-rep1

tag: tile

tag: cell type

tag: treatment


title: 8_WT_si_SAG

city: Chiba

first: SAISHU

last: YOSHIDA

address: 2-2-1 Miyama, Funabashi-shi

department: Department of Biomolecular Science,

country: Japan

institute: Toho University

data_processing:
Cutadapt v1.9.1 was used to trim and filter reads, and clean data were aligned to the reference genome (ENSEMBLE, GRCm38.97) using the software HISAT 2 (v2.0.1).
Assembly: ENSEMBL, GRCm38.97
Supplementary files format and content: Relative gene expression was quantified and normalized in a FPKM format

source_name: primary MEF

extract_protocol:
Total cellular RNA was extracted with using RNeasy mini kit (QIAGEN) with DNase I treatment (QIAGEN).
stranded library preparation with polyA selection

value: primary MEF

value: siDyrk2  in the presence of 100 nM SAG for 24 h


title: Liver_TR-day-6h_CT28B

tag: Sex

value: male

value: 6 months-old

value: 12h light / 12h dark


title: 6_WT_siNeg_SAG

value: siNegative (siNeg) in the presence of 100 nM SAG for 24 h


title: CPOP-tile1-30-rep3

value: wild-type yeast strain (BY4741)

value: 30 °C


title: 4_KO_SAG

value: 100 nM SAG for 24 h


title: 109.IonXpress_002

tag: patient id

tag: disease

value: MAA

tag: race

tag: age of asthma onset

tag: family history of atopy

tag: asthma treatment

value: ICS

tag: r20 (ios)

value: tape-stripped skin


title: 120.IonXpress_014

tag: age

value: Male

value: White

value: rhinitis and asthma

value: ICS/LABA/LTRA

tag: tissue


title: CPT_MCF7_DMSO_4h_2_input

city: Rehovot

first: David

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
mRNA samples from human and mouse were aligned to the mm9/hg19 genome using STAR v.2.5.3a with default settings (‘--alignIntronMax 1000000’) (Dobin et al., 2013). For gene expression (TPM) and read counts, rsem-calculate-expression (rsem/1.3.3) was employed (Li and Dewey, 2011). m6A-GI and m6A-SI metrics were derived using the bam2ReadEnds.R script (Garcia-Campos et al., 2019) as per Dierks et al. 2021, calculating m6A IP enrichment against input coverage.
Assembly: mm9 & hg19
Supplementary files format and content: RSEM hg19 counted reads and tpm tables

growth_protocol: Mammalian cell lines were grown at 37°C and 5 % CO2 in DMEM (10% FBS, with Antibiotics Penn/Strep)

extract_protocol:
Nucleozol total RNA extraction protocol according to the manufacturers protocol.
All libraries were conducted according to the libraray preparation protocol in Dierks et al. 2021. For RNA-seq, the protocol was performed as in Dierks 2021, excluding the m6A IP step, (performed as if only is the input sample.
m6A-seq2 & RNA-seq (m6A-seq2 protocol exluding the m6A IP section)

tag: cell line

value: cell line

tag: library type


title: Liver_TR-day-6h_CT24B

value: Liver

tag: strain

tag: genotype

value: WT

tag: light condition

tag: feeding

tag: collectiontime hours


title: 108.IonXpress_001

tag: Sex

value: rhinitis

tag: r5 (ios)

tag: feno

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)


title: CPT_MCF7_DMSO_4h_2_ip

tag: cell type


title: Liver_TR-night-6h_CT00A

value: male

value: 6 months-old


title: CPT_MCF7_DMSO_4h_1_input


title: CPT_MCF7_DMSO_4h_1_ip


title: Liver_TR-day-6h_CT40B

value: 12h light / 12h dark


title: 107.IonXpress_016

tag: patient id

tag: disease

value: Female

tag: race

tag: age of asthma onset

tag: family history of atopy

value: no

tag: asthma treatment

tag: r20 (ios)


title: after-patient 3

city: hefei

first: Ying

last: Tang

address: No.218 Jixi Road, Shushan District, Hefei City, Anhui Province, China.

institute: Department of Endocrinology, the First Affiliated Hospital of Anhui Medical University

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic.
We used pre-existing predictions of alternative transcripts and de novo transcript assembly with HISAT2 and StringTie software to compile a list of loci with two or more transcript isoforms.
Differential expression analysis was done using Ballgown.
Assembly: GRCm38
Supplementary files format and content: Comma-delimited text file includes FPKM values for each Sample

source_name: granulation tissue

extract_protocol:
Total RNA was extracted using RNA extraction kit (Zymo Research).
RNA-Seq libraries were generated using Illumina TruSeq Stranded mRNA library prep kit.

tag: tissue

value: granulation tissue

tag: time point

value: after treatment

tag: patient diagnosis

value: Diabetic Foot Ulcer

tag: patient number

tag: treatment

value: NPWT


title: 104.IonXpress_014

value: MAA

tag: age

tag: Sex

value: Male

value: ICS

tag: r5 (ios)

tag: feno

value: tape-stripped skin


title: Liver_TR-day-6h_CT12B

tag: strain

tag: genotype

tag: light condition

tag: feeding

tag: collectiontime hours


title: before-patient 3

value: before treatment


title: Liver_TR-day-6h_CT16B

value: Liver


title: CPT_MCF7_CPT_4h_2_ip

tag: cell line

tag: cell type

value: cell line

tag: library type

value: RNA-seq


title: after-patient 2

tag: tissue


title: Liver_TR-day-6h_CT08B

value: WT

value: male


title: before-patient 2

tag: time point


title: 102.IonXpress_012

tag: patient id

tag: disease

value: SAA

tag: race

value: White

tag: age of asthma onset

tag: family history of atopy

value: rhinitis and asthma

tag: asthma treatment

value: ICS/LABA

tag: r20 (ios)

tag: eosinophil count

tag: serum ige (ku/l)

tag: exacerbation rate (per year)


title: CPT_MCF7_CPT_4h_2_input


title: Liver_TR-day-6h_CT04B

tag: strain

tag: genotype

tag: Sex

tag: age

value: 6 months-old

tag: light condition

value: 12h light / 12h dark

tag: feeding


title: KO3,IR 45min/24h, heart ECs rep3

city: Shanghai

first: yunhao

last: duan

address: 150 Jimo Rd, Pudong New District

institute: Shanghai East Hospital

data_processing:
basecalls performed using BGISEQ-500
Removing reads containing sequencing adapter
Clean reads were obtained and stored in FASTQ format
Sequencing reads after filtering were mapped to reference genome using the HISAT software
Gene expression was quantified by RSEM software
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: xls files include fold change and p value for each Samples

source_name: endothelial cells

extract_protocol:
RNA was isolated from heart endothelial cells using TRIzol reagent (#15596018, Invitrogen, USA)
RNA libraries were prepared for sequencing using standard BGI protocols

tag: cell type

value: endothelial cells

tag: treatment

value: cardiac ischemia-reperfusion


title: Liver_TR-day-6h_CT20B

tag: tissue

tag: collectiontime hours


title: 2_WT_SAG

value: primary MEF

value: 100 nM SAG for 24 h


title: KO2,IR 45min/24h, heart ECs rep2


title: CPT_MCF7_CPT_4h_1_ip

tag: cell line

tag: library type


title: after-patient 1

value: granulation tissue

tag: time point

value: after treatment

tag: patient diagnosis

value: Diabetic Foot Ulcer

tag: patient number

value: NPWT


title: before-patient 1

value: before treatment


title: CPT_MCF7_CPT_4h_1_input

value: cell line

value: RNA-seq


title: KO1,IR 45min/24h, heart ECs rep1


title: Liver_TR-day-6h_CT44A

value: Liver

value: WT

value: male


title: Liver_TR-day-6h_CT00B


title: ActD_HEK_DMSO_9h_2


title: WT3,IR 45min/24h, heart ECs rep3


title: Liver_TR-day-6h_CT40A


title: ActD_HEK_DMSO_9h_1


title: p63KO_Esophagus_2

first: Dimitris

last: Karagiannis

institute: Columbia University

description:
QY005
RNAseq_Eso_counts.txt

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
We mapped the reads to a reference genome (Mouse: UCSC/mm9) using Tophat (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10)
The expression levels of each gene were presented as Fragments Per Kilobase of transcript per Million (FPKM) in this study
Differential gene expression analysis was done by DEseq2
Assembly: mm9
Supplementary files format and content: single txt file containing matrix of read count for each gene and all samples

source_name: Esophagus

extract_protocol:
The epithelium was isolated from the esophagus of E12.5 Trp63 KO (Trp63-CreERT2 homozygous) mutants and littermate controls, and RNA was purified with PicoPure RNA Isolation Kit (Thermo Fisher Scientific).
used Illumina TruSeq RNA prep kit (Illumina) to establish libraries which were sequenced with Illumina HiSeq400. Samples were multiplexed in each lane, which yields targeted number of single-end/pair-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane

value: Esophagus

value: epithelium

value: homozygous Trp63-CreERT2


title: WT2,IR 45min/24h, heart ECs rep2

value: endothelial cells


title: Liver_TR-day-6h_CT36A

value: 6 months-old

value: 12h light / 12h dark


title: ActD_HEK_DMSO_6h_2


title: p63KO_Esophagus_1

description:
QY004
RNAseq_Eso_counts.txt


title: ActD_HEK_DMSO_6h_1


title: WT1,IR 45min/24h, heart ECs rep1

value: cardiac ischemia-reperfusion


title: WT_Esophagus_3

description:
QY003
RNAseq_Eso_counts.txt

value: littermate control


title: KO2,IR 45min/24h, heart tissue rep2

source_name: heart

extract_protocol:
RNA was isolated from heart tissues using TRIzol reagent (#15596018, Invitrogen, USA)
RNA libraries were prepared for sequencing using standard BGI protocols

value: heart


title: Liver_TR-day-6h_CT32A


title: WT_Esophagus_2

description:
QY002
RNAseq_Eso_counts.txt


title: ActD_HEK_DMSO_3h_2


title: Liver_TR-day-6h_CT28A


title: Liver_TR-day-6h_CT24A


title: WT2,IR 45min/24h, heart tissue rep2


title: ActD_HEK_DMSO_3h_1


title: WT_Esophagus_1

description:
QY001
RNAseq_Eso_counts.txt


title: Liver_TR-day-6h_CT16A


title: p63KO_Esophagus_3

description:
QY006
RNAseq_Eso_counts.txt


title: ActD_HEK_DMSO_0h_2


title: WT1,IR 45min/24h, heart tissue rep1


title: Adult, replicate 1, scRNAseq

city: Berlin

first: Elena

last: Cano

address: Robert-Rossle str. 10

country: Germany

institute: Max-Delbruck Center

description: 10x Genomics

data_processing:
Sequence data were mapped to the mouse reference genome (mm10 pre-build references v 2.1.0) provided by 10X Genomics using the CellRanger suite (v.2.2). The count matrices generated by CellRanger as followings were used for further analysis. Mapping quality was assessed using the CellRanger summary statistics.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
Single-cell suspension of endothelial cells were prepared as described previously (Pinto et al., 2013, PMID 23578979). C57Bl6 8 weeks old adult animals, P2 postnatal, E15 and E12 were used for single-cell suspension preparation. Adult animals were sacrificed by cervical dislocation while embryonic and postnatal animals were decapitated. Adult and postnatal hearts were chopped with a scalpel until getting 1-2mm pieces of tissue. The enzymatic digestion was adapted to every stage analyzed: for E12, 20min of Collagenase/Dispase (Sigma-Aldrich) (1mg/ml), for E15, 30min of Collagenase/Dispase (1mg/ml), and for P2 and adult hearts, 20 min of Collagenase II (500units/ml) (Worthington) plus a second digestion step with Collagenase/Dispase for 30min. All steps were performed at 37ºC, under agitation and pippeting up and down the solution within the tubes every 5min. To stop the enzymatic reaction 10ml of cold FACs buffer (HBSS/2%FBS/10mM Hepes) was added to the samples and then spinned down (400G, 5 min). For adult samples, red blood cells lysis step (Invitrogen) was performed. After enzymatic digestion, cell debris removal kit (Miltenyi) was performed and finally, all suspension filtered through a 40um strainer.  Single-cell suspensions were incubated with primary antibodies in FACs buffer for 20 min on ice. The following antibodies were used: APC-conjugated anti-CD31 (Thermo Fisher, 17-0311-80) and PE-conjugated anti-CD45 (BD Biosciences, 553081). Samples were centrifuged (400G, 5 min) and resuspended on FACs buffer and stored on ice until applied to the flow cytometer. CD31+/CD45- cells were sorted on an Aria II into 1.5ml tubes with EBM2 media. Compensation controls were set up for each single channel. After completion of sorting, 10% DMSO was added and cell suspension frozen at -80ºC. Several rounds of single-cell suspension preparation, sorting and freezing was repeated for embryonic samples in order to get a significant number of cells: 8 weeks old adult animals (n=6), P2 postnatal (n=21), E15 (n=48) and E12 (n=37).  Frozen vials of sorted CD31+/CD45- cells from E12, E15, P2 and 8wo adult hearts were thawed in a water bath at 37ºC. For E12 and E15, a dead cell removal kit (Miltenyi) was applied. For P2 and adult, re-sorting by flow cytometry and selection of live cells was performed.
3′ gene expression libraries were prepared according to the manufacturer’s instructions of the v2 Chromium Single Cell Reagent Kits (10X Genomics). Quality control of cDNA and final libraries was done using Bioanalyzer 2100 (Agilent).

value: Heart

tag: developmental stage

value: 8 weeks old adult

value: Endothelial cells

tag: cell fraction


title: P2, replicate 1, scRNAseq

description: 10x Genomics

tag: strain

value: Postnatal day 2


title: ActD_HEK_DMSO_0h_1

value: cell line

value: RNA-seq


title: A375 cells, CANT2-knockout 3

first: He

last: Zhang

state: Shanghai

address: Tongji University, 1239 Siping Road, Yangpu District, Shanghai

institute: School of Life Science and Technology, Tongji University

data_processing:
Reads were trimmed using SOAPnuke
Raw reads were aligned to the reference genome (GRCh38) using HISAT2
Read counts were calculated using StringTie
Differentially expressed genes were analyzed using DEseq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene-level read counts for each Sample

source_name: skin

growth_protocol: A375 cells were cultured in DMEM (GIBCO).All media were supplemented with 10% FBS (GIBCO), 1% penicillin/streptomycin (GIBCO). All cells were incubated at 37℃ and 5% CO2.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Total RNA was processed by mRNA enrichment. mRNA enrichment: mRNA with a polyA tail was enriched with magnetic beads with OligodT. The obtained RNA was fragmented with an interruption buffer, reverse transcribed with a random N6 primer, and then the cDNA second strand was synthesized to form a double-stranded DNA. The ends of the synthesized double-stranded DNA are flattened and phosphorylated at the 5' end, and a sticky end with an "A" protruding from the 3' end is joined to a bulbous joint with a protruding "T" at the 3' end. The ligated product is amplified by PCR with specific primers, and the PCR product is heat denatured to a single strand, and a bridge primer is used to loop the single-stranded DNA to obtain a single-stranded circular DNA library. The constructed library is quality checked and sequenced after passing the test.    Translated with www.DeepL.com/Translator (free version)

value: skin

value: a cell line exhibiting epithelial morphology that was isolated from the skin of a 54-year-old, female patient with malignant melanoma

tag: genotype

value: CANT2 knockout


title: Liver_TR-day-6h_CT12A

value: Liver

value: WT

tag: Sex

value: male


title: ActD_HEK_Mettl3inhib_9h_2


title: Liver_TR-day-6h_CT04A

tag: age

value: 6 months-old


title: ActD_HEK_Mettl3inhib_9h_1


title: A375 cells, CANT2-knockout 1


title: ActD_HEK_Mettl3inhib_6h_2


title: KO1,IR 45min/24h, heart tissue rep1


title: NFKB-, biol rep 3

city: Ames

first: Raquel

last: Espin Palazon

state: Iowa

address: 2213 Pammel Drive, 3003 ATRB

institute: Iowa State University

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt.
Reads were aligned to the Danio rerio genome build danRer10 using STAR.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2.
Assembly: danRer10
Supplementary files format and content: comma-delimited text files include fold change, p-values, adjusted p-values, and normalized abundance values per sample for each gene

organism: Danio rerio

growth_protocol: Zebrafish (Danio rerio) embryos and adults were mated, staged, raised, and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.

extract_protocol:
RNA was then isolated and purified with RNeasy® Micro Kit (Qiagen). DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions.
Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB #E6420S/L) for Illumina and NEB's Unique Dual Index primers for Illumina (E6440).

treatment_protocol: 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope, dechorionated with pronase (Millipore Sigma; 11459643001), anesthetized in 1% tricaine (Pentair; TRS5) and dissociated. Specifically, the trunk region of each embryo was surgically isolated (posterior to the yolk ball and anterior to the urogenital canal) using a scalpel. The collected tissue was then gently vortexed at 28C for 5-20 mins with 50 µg/ml Liberase TM (Millipore-Sigma: 5401127001) in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ (Millipore Sigma, D8662). The resulting cell suspension was filtered through 30 µm nylon mesh (Fisher Scientific; NC9084441) using a 21-gauge syringe (Fisher Scientific; BD 309624) and stained with SYTOX™ Red (Life Technologies; S34859) to exclude dead cells. Kdrl+/NFKB- and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. ~7,000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.

value: endothelial cells

value: NFKB:d2eGFP x kdrl:mCherry

value: kdrl+/NFKB- sorted


title: E12, replicate 1, scRNAseq

description: 10x Genomics

value: Embryonic day E12


title: A375 cells, CANT2-knockout 2


title: Liver_TR-day-6h_CT00A

tag: light condition

value: 12h light / 12h dark


title: A375 cells, negative control 3

value: negative control


title: ActD_HEK_Mettl3inhib_6h_1


title: A375 cells, negative control 2


title: Liver_TR-day-6h_CT20A

tag: feeding


title: Liver_CR-night-6h_CT44B


title: NFKB-, biol rep 1

tag: cell type


title: ActD_HEK_Mettl3inhib_3h_2


title: NFKB+, biol rep 3

tag: treatment

value: kdrl+/NFKB+ sorted


title: A375 cells, negative control 1

tag: tissue


title: Liver_CR-night-6h_CT40B

tag: collectiontime hours


title: Liver_CR-night-6h_CT36B


title: ActD_HEK_Mettl3inhib_0h_2

tag: cell line


title: NFKB+, biol rep 2


title: E15, replicate 1, scRNAseq

description: 10x Genomics

value: Heart

value: Embryonic day E15

value: Endothelial cells


title: Liver_CR-night-6h_CT32B


title: Liver_TR-day-6h_CT08A


title: shp53, replicate2

city: Atlanta

first: Adam

last: Marcus

state: GA

address: 1365C Clifton Rd., N.E., Room 4092

institute: Emory University

data_processing:
Fastq reads were trimmed and filtered for quality and adapter contamination with Trimmomatic v0.38
Assembly: Post-filtered reads were mapped against Ensemble Human GRCh38.p12 release 95 reference genome using the STARaligner v2.7.0e

source_name: Bronchial tissue

extract_protocol:
Total RNA was extracted from the spheroids at day 7 of 3D spheroid invasion assay using a RNeasy Kit (Qiagen, Valencia, CA, USA).
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads.  First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.The quality control of library consists of three steps: (1) Qubit 2.0: tests the library concentration preliminarily. (2) Agilent 2100: tests the insert size. (3) Q-PCR: quantifies the library effective concentration precisely.

value: Bronchial tissue


title: shp53, replicate3


title: shp53, replicate1


title: ActD_HEK_Mettl3inhib_0h_1

value: cell line

tag: library type

value: RNA-seq


title: shLKB1, replicate3


title: Liver_CR-night-6h_CT24B

value: Liver


title: Liver_CR-night-6h_CT28B

value: WT


title: shLKB1, replicate2


title: HuH-7-CRISPRoff-PCSK9-2

city: Philadelphia

first: Yifan

last: Yang

state: PA

address: 3400 Spruce Str

institute: University of Pennsylvania

data_processing:
fastqc to check the quality of the paired-end reads
STAR aligner to align the reads to Homo sapiens GRCh38 reference genome
pcard package to mark the duplicate
Rsubread package to count the number of raw reads
Limma-Voom package to normalize the data and test the differential expression

growth_protocol: HuH-7 cells were cultured in Dulbecco’s Modified Eagle Medium (containing 4 mM L-glutamine and 1 g/L glucose) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). Ribosomal RNAs were depleted by polyA selection prior to library prep.
RNA libraries for RNA-seq were prepared by Genewiz.

treatment_protocol: HuH-7 cells were seeded at 350,000 cells per well in 6-well plates, and transfections were performed 16-24 hours following seeding. In one tube, 7.5 µL Lipofectamine MessengerMax (Thermo Fisher Scientific, catalog #LMRNA008) was added to 125 µL of Opti-MEM and incubated for 10 minutes. In another tube, 1.25 µg CRISPRoff mRNA and 1.25 µg total gRNA (individual gRNA or equal mix by weight of multiple gRNAs) was suspended in a total of 125 µL of Opti-MEM. Diluted mRNA was added to each tube of diluted MessengerMAX, and the subsequent mRNA/MessengerMax/Opti-MEM mixture was incubated for 5 minutes at room temperature and then added dropwise onto the cells.

value: hepatoma

value: CRISPRoff mRNA and synthetic PCSK9 P13+P16 gRNAs transfection

tag: time

value: 27 cell doublings after transfection


title: Liver_CR-night-6h_CT20B

value: male

value: 6 months-old


title: HuH-7-CRISPRoff-PCSK9-1


title: NFKB-, biol rep 2

value: endothelial cells

value: NFKB:d2eGFP x kdrl:mCherry

value: kdrl+/NFKB- sorted


title: ActD_HEK_Mettl3inhib_3h_1


title: Liver_CR-night-6h_CT16B

value: 12h light / 12h dark


title: HuH-7-control-3

value: control

value: CRISPRoff mRNA and synthetic radom gRNA transfection


title: Liver_CR-night-6h_CT12B


title: MKN-45 cells, GRP94 knockdown, SH-3

first: Qimeng

last: Shi

address: Ruijin Second Road

institute: Shanghai Jiaotong University School of Medcine

data_processing:
The fastp software was used to process the raw reads in fastq format.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: stomach

growth_protocol: MKN-45 cells were cultured in Dulbecco’s Modified Eagle Medium (containing Ala-Gln) supplemented with 10% FBS, 1% Penicillin/Streptomycin, and kept at 37°C in an incubator with a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA purity and quantification were determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), and RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit according to the manufacturer's instructions.

value: epithelial tissue

value: gastric cancer cells

value: GRP94 knockdown


title: KrasG12D mutant overexpression + shp53, replicate3

value: Bronchial tissue

value: Kras G12D mutant + shp53


title: KrasG12D mutant overexpression + shp53, replicate2


title: MKN-45 cells, GRP94 knockdown, SH-2


title: HuH-7-control-1


title: NFKB+, biol rep 1

value: kdrl+/NFKB+ sorted


title: KrasG12D mutant overexpression + shp53, replicate1


title: MKN-45 cells, GRP94 knockdown, SH-1


title: Liver_CR-night-6h_CT00B

value: Liver

value: WT


title: Liver_CR-night-6h_CT04B


title: KrasG12D mutant overexpression + shLKB1, replicate3

value: Kras G12D mutant + shLKB1


title: Col-0 RNAseq ZT0 rep3

city: Valencia

first: Maria A

last: Nohales

address: Ingeniero Fausto Elio s/n

country: Spain

institute: IBMCP (CSIC/UPV)

data_processing:
Raw reads were aligned to the TAIR10 genome using STAR (v2.5.5) (Dobin et al. 2013) with the method of Maximal Mappable Prefix (MMP).
Mapped reads were counted by HTSeq v0.6.1 and then FPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression was performed using the DESeq2 R package (2_1.6.3) (Anders and Huber 2010).
Genes with adjusted p-value < 0.05 and |log2(FoldChange)| > 0 were considered as differentially expressed.
Assembly: TAIR10
Supplementary files format and content: txt file includes read counts for each sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings were grown on 0.5x  MS plates under short day photoperiods (8 h light, 16 h dark) at a light intensity of 80 umol m-2 s-1 and a constant temperature of 22 °C for 7 d. Samples were collected at ZT0 by snap-freezing in liquid nitrogen.

extract_protocol:
Total RNA was isolated using the GeneJET Plant RNA Purification Kit (Thermo Scientific) and digested with DNase Max (Qiagen).
Preparation of RNA library (non-directional 250~300 bp insert cDNA library (NEB))

value: seedlings


title: MKN-45 cells, control, NC-3


title: HuH-7-CRISPRoff-PCSK9-3

value: hepatoma

value: CRISPRoff mRNA and synthetic PCSK9 P13+P16 gRNAs transfection

value: 27 cell doublings after transfection


title: shLKB1, replicate1


title: KrasG12D mutant overexpression + shLKB1, replicate2


title: Col-0 RNAseq ZT0 rep2


title: Liver_CR-night-6h_CT44A

value: male

value: 6 months-old


title: Col-0 RNAseq ZT0 rep1


title: KrasG12D mutant overexpression + shLKB1, replicate1


title: MKN-45 cells, control, NC-2


title: MKN-45 cells, control, NC-1


title: gi-2 RNAseq ZT0 rep3


title: KrasG12D mutant overexpression, replicate3

value: Kras G12D mutant


title: Liver_CR-night-6h_CT36A

value: 12h light / 12h dark


title: HuH-7-control-2

value: control

value: CRISPRoff mRNA and synthetic radom gRNA transfection


title: WT, Day 9, replicate 3

city: Birmingham

first: Yang

last: Zhou

state: AL

address: 1825 University Blvd

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

data_processing:
The paired-end reads were mapped to the human genome (hg38) using nextflow (21.08.0.edge) with default parameters.
Assembly: hg38
Supplementary files format and content: read_counts.csv includes raw count for each sample

source_name: induced pluripotent stem cell derived cardiomyocytes

growth_protocol: hiPSCs (D0) were maintained in mTeSR plus medium with 5% CO2 at 37℃. hiPSC-CMs (D9) were differentiated from hiPSC using Gi-Wi protocol, and maintained in RPMI1640 with B27 Plus supplement with 5% CO2 at 37℃.

extract_protocol:
Total RNA was harvested using Trizol reagent followed by isopropanol precipitation. 1ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina.


title: Liver_CR-night-6h_CT32A

extract_protocol:
RNA from tissues was homogenized in 1mL of TRIzol and extracted according to manufacturer instructions. All RNA samples with RIN >7.5 were used; 260/280 ratio > 2; and 260/230 ratio > 2.
mRNA-Seq (polyA selection); mRNA-seq library preparation was done according to Illumina single-stranded mRNA-seq. Briefly, library was prepared with 25 ng of mRNA polyA-selected from 5ug total RNA, with 13 cycles of PCR amplification. Library size was confirmed by Tapestation 2200 (Agilent).


title: KrasG12D mutant overexpression, replicate2


title: gi-2 RNAseq ZT0 rep2


title: Liver_CR-night-6h_CT08B


title: KrasG12D mutant overexpression, replicate1


title: WT, Day 9, replicate 2

value: induced pluripotent stem cell derived cardiomyocytes


title: Liver_CR-night-6h_CT28A


title: gi-2 RNAseq ZT0 rep1


title: WT, Day 9, replicate 1


title: GFP-control vector only, replicate3

value: Bronchial tissue

value: Vector only


title: sciatic nerve, ASC3 (sRNA)

city: Beijing

first: Xiangling

last: Li

state: Beijing

address: Fucheng Road

institute: Chinese PLA General Hospital

data_processing:
Agilent 2100 Bioanalyze.
Trimmed sequence reads were mapped to mapped to reference Genome
Novel Transcript prediction and Structure analysis
Differential expression analysis and functional analysis.
Assembly: rn7
Supplementary files format and content: genes.readcount.txt

organism: Rattus norvegicus

source_name: Rattus sciatic nerve

growth_protocol: Sprague-Dawley rats was fed in an environment with a 12:12h light/dark cycle at controlled temperature and humidity, with free access to food and water.

extract_protocol:
RNA was extracted and purified from each sample in each group using Trizol, and agarose gel electrophoresis was utilized to analyze the integrity of RNA and the presence of DNA contamination.
RNA was isolated using TRIzol reagent, and RNA integrity was evaluated using the Agilent 2100 Bioanalyze.
RNA was isolated using TRIzol reagent and  NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was  used for the construction of sequencing libraries.
RNA-seq( long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs ))

treatment_protocol: In BMSCs and ADSCs therapy groups, a pre-digested cell suspension of 2 × 106/mL of P3-generation BMSCs and ADSCs was injected into the entire 10-mm ANA segment using an insulin syringe.

value: Rattus sciatic nerve

tag: condition

value: rat sciatic nerve deficit injury model

value: Adipose-derived mesenchymal stem cells transplantation


title: sciatic nerve, ASC2 (sRNA)


title: Liver_CR-night-6h_CT20A

first: Joseph

last: Takahashi

institute: University of Texas Southwestern Medical Center

data_processing:
Sequencing libraries were constructed in house following Illumina single-stranded mRNA-seq protocol. RNA-sequencing of libraries was performed on the NextSeq 550 (Illumina) with 75 bp reads, according to the manufacturer’s instructions, by the UTSW McDermott Next Generation Sequencing Core. Read quality was assessed using the FASTQC quality control tool. Reads were mapped with STAR (Dobin et al., 2013) (with parameters:--runMode alignReads --genomeDir genomefolder --sjdbGTFfile gtf --readFilesIn sample_trim.gz --readFilesCommand zcat --outFileNamePrefix sample --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMmapqUnique 255 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterMismatchNmax 3 --twopassMode Basic --quantMode GeneCounts) following Cutadapt trimming (with parameters: -g AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 30) to M14 GENCODE (protein coding only) version of mouse genome from www.gencodegenes.org. Raw reads were quantified using featureCounts tool from Rsubread package. Reads per kilobase per million (RPKM) was used to normalize uniquely mapped reads according to the sequencing depth and gene length. RPKM calculation was performed using in-house scripts. Downstream bioinformatic analysis after RPKM calculations was performed in R environment.
Assembly: M14 from GENCODE
Supplementary files format and content: excel file includes raw counts for all samples
Supplementary files format and content: excel file includes RPKM values for all samples

value: Liver

value: WT


title: KO, Day 9, replicate 3

value: ELMSAN1 knockout


title: Liver_CR-night-6h_CT40A


title: GFP-control vector only, replicate2


title: KO, Day 9, replicate 2


title: GFP-control vector only, replicate1


title: KO, Day 9, replicate 1


title: Liver_CR-night-6h_CT12A


title: Liver_CR-night-6h_CT16A


title: sciatic nerve, ASC1 (sRNA)


title: dog 3, macular RPE/choroid, retina off before sampling

city: Madison

first: Freya

last: Mowat

state: WI

address: 1300 University Avenue

department: Ophthalmology and Visual Sciences

institute: University of Wisconsin-Madison

data_processing:
trimmed Illumina adaptor and 5’- end 12  bases with trimmomatic v0.39
QC tirimmed sequences with FastQC v0.11.8
mapped sequences with HISAT2 v2.1.0
sorted by chromosome with samtools sort v 1.9
marked up duplicated reads by MarkDuplicate version 2.20.1
count mapped sequences with featureCounts v2.0.0
Assembly: CanFam 3.1
Supplementary files format and content: tab delimited files containing raw counts

organism: Canis lupus familiaris

source_name: macular RPE/choroid

extract_protocol:
RNA was harvested using Rneasy mini kit with on column DNAse digestion (Qiagen).A minimum of 1ug of total RNA was used as template for library preparation
RNA libraries for RNA-seq were prepared using Illumina directional library kit following manufacturer guidelines.

value: macular RPE/choroid

tag: estimated age

value: 3-4 years

tag: estimated breed

value: pitbull mixed breed

tag: eye (right_or_left)

value: Left


title: Liver_CR-night-6h_CT24A

address: 5323 Harry Hines Blvd.

tag: strain

value: male

value: 6 months-old


title: Liver_CR-night-6h_CT08A

tag: genotype

value: 12h light / 12h dark


title: sciatic nerve, BM2 (sRNA)

value: Bone marrow-derived mesenchymal stem cell transplantation


title: WT, Day 0, replicate 3

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells


title: WT, Day 0, replicate 2


title: dog 2, macular RPE/choroid, retina on at sampling

tag: Sex

value: 2-3 years

value: Right


title: Liver_CR-night-6h_CT00A

tag: age


title: Liver_CR-night-6h_CT04A

tag: light condition


title: dog 2, macular RPE/choroid, retina off before sampling


title: WT, Day 0, replicate 1


title: Liver_CR-day-6h_CT44B

tag: feeding


title: KO, Day 0, replicate 3

tag: cell type


title: dog 1, macular RPE/choroid, retina off before sampling

value: female

value: 3-5 years

value: labrador/pitbull mixed breed


title: sciatic nerve, BM3 (sRNA)

value: Rattus sciatic nerve

value: rat sciatic nerve deficit injury model

tag: treatment


title: dog 3, macular RPE/choroid,retina on at sampling

tag: tissue


title: KO, Day 0, replicate 1

value: ELMSAN1 knockout


title: dog 1, macular RPE/choroid, retina on at sampling

value: macular RPE/choroid


title: dog 18-9, peripheral retina

source_name: peripheral retina

value: peripheral retina

value: boxer mixed breed


title: KO, Day 0, replicate 2


title: sciatic nerve, ASC2 (circRNA)

value: Adipose-derived mesenchymal stem cells transplantation


title: dog 18-9, peripheral RPE/choroid

source_name: peripheral RPE/choroid

value: peripheral RPE/choroid


title: Liver_CR-day-6h_CT32B

source_name: Liver

value: Liver

value: WT

value: male

value: 6 months-old

tag: collectiontime hours


title: sciatic nerve, ASC1 (circRNA)


title: sciatic nerve, ANA1 (sRNA)

value: non-treatment


title: HEK293_HepG4-seq_NSC617145

city: Chengdu

first: Zhihong

last: Xue

state: Sichuan

address: No. 20, 3rd section, South Renmin Road

institute: Sichuan University

library_source: genomic

data_processing:
Untrimmed sequencing reads were first analyzed for quality control by fastqc software(v0.11.9).
The adaptor sequence and low-quality reads were then trimmed off using fastp software(v0.22.0)
Reads were then aligned to the UCSC hg38 genome or the UCSC mm10 genome  using bowtie2. Only uniquely mapping reads (quality score > 40) were retained.
Bam files were converted to bigwig files using Deeptool.
Assembly: hg38 or mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: DMEM, 10% FBS, 1× non-essential amino acid solution, 1× GlutaMAX, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, 100 U/mL Penicillin-Streptomycin. Cells were cultured at 37℃ at 5% CO2

extract_protocol:
Live cells were conjugated to concanavalin A–coated magnetic beads. The antibody was bound to the cell and fragmented with Tn5.Genomic DNA was extracted by ethanol precipitation.
To generate libraries, purified genomic DNA was amplified with the barcoded i5 and i7 primer using VAHTS HiFi Amplification Mix. The library PCR products were cleaned up with VAHTS DNA Clean Beads and size selected at 200-500bp in length.

treatment_protocol: HEK293 cells were exposed to DMSO (as a control) or 25 μM ML216 or 3 μM NSC 617145 for 16 hrs.

tag: cell line

value: Human embryonic kidney cell


title: HEK293_HepG4-seq_ML216


title: Liver_CR-day-6h_CT40B

value: 12h light / 12h dark


title: Liver_CR-day-6h_CT36B


title: HEK293_HepG4-seq_DMSO

value: DMSO


title: sciatic nerve, BM3 (circRNA)

value: Bone marrow-derived mesenchymal stem cell transplantation


title: Liver_CR-day-6h_CT24B


title: sciatic nerve, ANA3 (sRNA)

value: Rattus sciatic nerve


title: sciatic nerve, ASC3 (circRNA)

value: rat sciatic nerve deficit injury model


title: sciatic nerve, BM1 (sRNA)


title: dog 18-9, macular retina

source_name: macular retina

value: macular retina

value: female

value: 2-3 years

value: Right


title: Liver_CR-day-6h_CT28B


title: Liver_CR-day-6h_CT20B


title: dog 18-9, macular RPE/choroid

value: macular RPE/choroid

value: boxer mixed breed


title: HEK293_HBD-seq_RNase_1


title: sciatic nerve, BM2 (circRNA)


title: dog 18-7, peripheral retina

value: peripheral retina

value: 3-5 years

value: pitbull mixed breed


title: sciatic nerve, ANA2 (sRNA)


title: sciatic nerve, BM1 (circRNA)


title: dog 18-7, peripheral RPE/choroid

value: peripheral RPE/choroid


title: HEK293_HepG4-seq_Non-label_Ctrl_2

value: WT


title: sciatic nerve, ANA3 (circRNA)

value: non-treatment


title: dog 18-7, macular retina


title: sciatic nerve, ANA2 (circRNA)


title: sciatic nerve, ANA1 (circRNA)


title: Liver_CR-day-6h_CT08B

value: Liver

value: male

value: 6 months-old

value: 12h light / 12h dark


title: Liver_CR-day-6h_CT04B


title: dog 18-6, macular retina

value: mastiff mixed breed

value: Left


title: dog 18-7, macular RPE/choroid

value: female


title: sciatic nerve, ASC3 (lncRNA)

value: Rattus sciatic nerve

value: rat sciatic nerve deficit injury model

value: Adipose-derived mesenchymal stem cells transplantation


title: HEK293_HepG4-seq_2

value: Human embryonic kidney cell


title: HEK293_HBD-seq_2


title: dog 18-6, macular RPE/choroid

value: macular RPE/choroid


title: Liver_CR-day-6h_CT40A


title: dog 18-6, peripheral retina

value: peripheral retina

value: 3-5 years


title: Liver_CR-day-6h_CT16B


title: dog 18-6, peripheral RPE/choroid

value: peripheral RPE/choroid


title: sciatic nerve, BM3 (lncRNA)

value: Bone marrow-derived mesenchymal stem cell transplantation


title: Liver_CR-day-6h_CT00B

value: WT


title: sciatic nerve, ASC2 (lncRNA)


title: HEK293_HepG4-seq_1


title: Liver_CR-day-6h_CT36A

value: Liver


title: HEK293_BG4-seq_with_Hemin_2


title: HEK293_BG4-seq_with_Hemin_1


title: Liver_CR-day-6h_CT44A

value: male


title: sciatic nerve, ASC1 (lncRNA)


title: HEK293_HBD-seq_1


title: Liver_CR-day-6h_CT12B

value: 6 months-old


title: HEK293_BG4-seq_without_Hemin_2


title: sciatic nerve, BM1 (lncRNA)


title: HEK293_HepG4-seq_Non-label_Ctrl_1


title: Liver_CR-day-6h_CT32A

value: 12h light / 12h dark


title: HEK293_BG4-seq_without_Hemin_1


title: dog 18-2, peripheral retina

value: 2-3 years

value: pitbull mixed breed


title: dog 18-2, peripheral RPE/choroid

value: Left


title: HEK293_NSC617145_3

data_processing:
Untrimmed sequencing reads were analyzed for quality control by fastp software(v0.22.0). The adaptor sequence and low-quality reads were trimmed off at the same time.
Ribosome RNAs were removed from trimmed reads using SortMeRNA software.
Reads without ribosome RNAs were mapped to hg38 or mm10 reference genome using STAR software(v2.7.1a) as default parameters
Raw readcounts were calculated using RSEM software（v1.2.28）.The raw readcounts were normalized by the FPKM method.
Assembly: hg38 or mm10
Supplementary files format and content: Comma-Separated Values CSV files include FPKM values for each Sample

growth_protocol: HEK293 cells were maintained in the medium (DMEM, 10% FBS, 1× NEAA, 1× GlutaMAX, 1mM sodium pyruvate, 0.1mM β-mercaptoethanol, 100U/ml penicillin, 100 mg/ml streptomycin) in humidified atmosphere with 5% CO2 at 37oC. V6.5 ESC cells were maintained in the medium (DMEM, 10% FBS, 2,000U/ml LIF, 1× NEAA, 1×GlutaMAX, 1mM sodium pyruvate, 0.1mM β-mercaptoethanol, 100U/ml penicillin, 100 mg/ml streptomycin) in humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Total RNAs were isolated using the Trizol Reagent.
Libraries were prepared from 1 µg total RNAs. We purified the mRNA using ABclonal mRNA capture Module. The libraries were generated using ABclonal Fast RNA-seq Lib Prep Kit V2, and evaluated using Qsep with S2 Cartridge.
Strand-specific RNA-seq, the RNA strand is the same direction as R2.


title: sciatic nerve, ANA3 (lncRNA)

value: Rattus sciatic nerve

value: non-treatment


title: dog 18-2, macular retina

value: macular retina


title: Liver_CR-day-6h_CT28A


title: Liver_CR-day-6h_CT24A


title: dog 18-2, macular RPE/choroid


title: sciatic nerve, ANA2 (lncRNA)

value: rat sciatic nerve deficit injury model


title: HEK293_NSC617145_2

value: Human embryonic kidney cell


title: sciatic nerve, ANA1 (lncRNA)


title: HEK293_ML216_3


title: HEK293_NSC617145_1


title: Liver_CR-day-6h_CT16A


title: sciatic nerve, BM2 (lncRNA)


title: Cre, Replicate 3, 10 ARA

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 3 for recombinase induction concentration of 10ug/ml L-arabinose

data_processing:
Illumina sequencing data is processed using Cutadapt (25) and R version 4.3.2 (26) to convert to count matrices. Targets with fewer than 100 reads were discarded. Because of symmetry of the recombination reaction, alignment of the spacer either from the top or bottom strand of DNA is arbitrary, therefore, the strand with the highest identity to the wild-type loxP or on-target sequence was considered. To facilitate a comparative analysis between distinct screens, we computed the activity ratio for each dataset by dividing the recombination rate of individual target sites by the highest recombination rate within each dataset.
Assembly: Aligned to template for edited or non edited target sites: AGATCTATGCATAAACGCACCGAGCACGCATAACTTCGTATAATGTATGCTATACGAAGTTATTTAATTAAGGGAC, AGATCTATGCATAAACGCACCGAGCACGCATAACTTCGTATAATGTATGCTATACGAAGTTATCCGTGAAGCTTGC
Supplementary files format and content: Tab-delimited files with sequences of target sites and counts of reads carrying recombined or not recombined variants
Library strategy: DNA-seq

organism: Escherichia coli

extract_protocol:
Purified plasmid DNA and PCR amplification
Illumina Multiplexing PCR Illumina Sequencing

treatment_protocol: Treatment with either 0,1,10,100 ug/mL concentration of L-Arabinose to induce recombinase expression.

value: Target library, loxP-like spacer library, LL8

value: 10 ug/mL L-Arabinose


title: Liver_CR-day-6h_CT20A

city: Dallas


title: Cre, Replicate 3, 100 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 3 for recombinase induction concentration of 100ug/ml L-arabinose

value: 100 ug/mL L-Arabinose


title: Cre, Replicate 3, 1 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 3 for recombinase induction concentration of 1ug/ml L-arabinose

value: 1 ug/mL L-Arabinose


title: HEK293_ML216_2

value: WT


title: Cre, Replicate 3, 0 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 3 for recombinase induction concentration of 0ug/ml L-arabinose

value: 0 ug/mL L-Arabinose


title: cpt1Δept1Δ-rep2

city: Hangzhou

first: Zhu

last: Yibing

state: Zhe Jiang

address: Xihu

department: Life Of Science

institute: Zhejiang University

data_processing:
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: ENSEMBL,Saccharomyces_cerevisiae.R64-1-1.89
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Saccharomyces cerevisiae

source_name: CEN.P.K prototrophic

growth_protocol: yeast were cultured in minimal synthetic meidum with 2% glucose overnight and re-cultured to log phase

extract_protocol:
RNA was harvested using Yeast RNA purification Kit (MasterPure, biosearchtech). 2 ug of total RNA was used for the construction of sequencing libraries.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: cells were spined down and washed with fresh SD and quickly frozen in liquid nitrogen for extracting RNA

value: CEN.P.K prototrophic

value: cpt1-delta ept2-delta

value: culture in minimal SD medium to log phase


title: Liver_CR-day-6h_CT08A

value: Liver

value: male

value: 6 months-old

value: 12h light / 12h dark


title: Liver_CR-day-6h_CT12A


title: cpt1Δept1Δ-rep3

value: cpt1-delta ept3-delta


title: HEK293_ML216_1


title: cpt1Δept1Δ-rep1

value: cpt1-delta ept1-delta


title: Cre, Replicate 2, 100 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 2 for recombinase induction concentration of 100ug/ml L-arabinose


title: ect1Δpct1Δ-rep3

value: ect1-delta pct3-delta


title: Cre, Replicate 2, 10 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 2 for recombinase induction concentration of 10ug/ml L-arabinose


title: HEK293_DMSO_3

value: Human embryonic kidney cell

value: DMSO


title: Liver_CR-day-6h_CT00A


title: HEK293_DMSO_2


title: Liver_AL_CT44B

value: Ad Libitum


title: Cre, Replicate 2, 1 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 2 for recombinase induction concentration of 1ug/ml L-arabinose

value: Target library, loxP-like spacer library, LL8


title: ect1Δpct1Δ-rep2

value: ect1-delta pct2-delta


title: ect1Δpct1Δ-rep1

value: ect1-delta pct1-delta


title: Liver_AL_CT40B

value: WT


title: HEK293_DMSO_1


title: Cre, Replicate 2, 0 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 2 for recombinase induction concentration of 0ug/ml L-arabinose

value: 0 ug/mL L-Arabinose


title: WT-rep3

value: CEN.P.K prototrophic


title: Liver_AL_CT36B


title: Cre, Replicate 1, 100 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 1 for recombinase induction concentration of 100ug/ml L-arabinose

value: 100 ug/mL L-Arabinose


title: WT-rep2

value: culture in minimal SD medium to log phase


title: Cre, Replicate 1, 10 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 1 for recombinase induction concentration of 10ug/ml L-arabinose

value: 10 ug/mL L-Arabinose


title: CWR22RV1 cells, siCE3 72 h, biological replicate 2

city: Newcastle upon Tyne

first: Luke

last: Gaughan

state: Tyne and Wear

address: Paul O'Gorman Building

department: Translational and Clinical Research Institute

country: United Kingdom

institute: Newcastle University

data_processing:
Quality control using fastqC
Sequence reads were aligned to the human geneome (GRCh38) using Salmon
Differential gene expression using DESeq2
Assembly: Refgenie salmon index. GENCODE GRCh38 primary assembly and associated GTF annotation
Supplementary files format and content: Salmon output plain-text, tab-separated file quant.sf file contains raw count data
Supplementary files format and content: DESeq2 comma seperated csv file contains normalised counts

source_name: Prostate

growth_protocol: CWR22Rv1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
Phenol/chloroform extraction using TRIzol
Illumina-compatible library samples (performed by Azenta)

treatment_protocol: CWR22Rv1 cells were reverse transfected with 25 nM siRNA for 72 hours targeted to MFAP1 (siMFAP1) or AR-V7 (siCE3) compared to a non-targeted control (siScr)

value: Prostate

value: Prostate epithelial cells


title: Liver_AL_CT32B

value: Liver

value: male

value: 6 months-old

value: 12h light / 12h dark


title: CWR22RV1 cells, siCE3 72 h, biological replicate 3


title: CWR22RV1 cells, siCE3 72 h, biological replicate 1


title: WT-rep1


title: Cre, Replicate 1, 0 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 1 for recombinase induction concentration of 0ug/ml L-arabinose


title: Cre, Replicate 1, 1 ARA

description: Recombinase Cre activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 1 for recombinase induction concentration of 1ug/ml L-arabinose

value: 1 ug/mL L-Arabinose


title: Liver_AL_CT24B

value: Ad Libitum


title: dgk1Δ-rep3

extract_protocol:
RNA was harvested using Yeast RNA purification Kit (MasterPure, biosearchtech). 2 ug of total RNA was used for the construction of sequencing libraries.
The poly(A) mRNA isolation was performed  using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand  cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and  add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of  Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.


title: CWR22RV1 cells, siMFAP1 72 h, biological replicate 2

value: siMFAP1 (pool of siMFAP1-1 and siMFAP1-4)


title: CWR22RV1 cells, siMFAP1 72 h, biological replicate 3


title: Liver_AL_CT20B


title: RecS3, Replicate 3, 100 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 3 for recombinase induction concentration of 100 ug/ml L-arabinose

value: Target library, loxP-like spacer library, LL8


title: Liver_CR-day-6h_CT04A


title: Liver_AL_CT28B


title: CWR22RV1 cells, siMFAP1 72 h, biological replicate 1


title: dgk1Δ-rep2


title: dgk1Δ-rep1


title: RecS3, Replicate 3, 10 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 3 for recombinase induction concentration of 10 ug/ml L-arabinose


title: Liver_AL_CT16B


title: CWR22RV1 cells, siScr 72 h, biological replicate 3

description: siScr

value: siScr


title: pah1Δ-rep3


title: Liver_AL_CT12B

value: WT


title: pah1Δ-rep2


title: RecS3, Replicate 3, 1 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 3 for recombinase induction concentration of 1 ug/ml L-arabinose


title: pah1Δ-rep1


title: Liver_AL_CT08B


title: RecS3, Replicate 3, 0 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 3 for recombinase induction concentration of 0ug/ml L-arabinose

value: 0 ug/mL L-Arabinose


title: CWR22RV1 cells, siScr 72 h, biological replicate 1

description: siScr


title: RecS3, Replicate 2, 100 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 2 for recombinase induction concentration of 100ug/ml L-arabinose


title: TYUC1_EZH2i_D6_3

city: New York

description:
CD009
est_counts_genes_kallisto.txt

data_processing:
Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming
We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0)
Differential expression analysis was done by DESeq2
Assembly: hg38
Supplementary files format and content: txt containing of kallisto pseudoalignment estimated counts

source_name: Neuroendocrine esophageal carcinoma

growth_protocol: DMEM/F12 (Corning) plus 10% serum and 1% penicillin/streptomycin in suspension culture

extract_protocol:
total RNA was extracted in TRIzol (Invitrogen)
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry

treatment_protocol: 2uM EPZ-6438 or DMSO

value: Neuroendocrine esophageal carcinoma

value: cancer cell line


title: RecS3, Replicate 2, 10 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 2 for recombinase induction concentration of 10 ug/ml L-arabinose


title: WT-rep3

value: CEN.P.K prototrophic

value: culture in minimal SD medium to log phase


title: Liver_AL_CT00B


title: TYUC1_EZH2i_D6_2

description:
CD008
est_counts_genes_kallisto.txt


title: WT-rep2


title: Liver_AL_CT44A


title: RecS3, Replicate 2, 1 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 2 for recombinase induction concentration of 1 ug/ml L-arabinose


title: WT-rep1


title: Liver_AL_CT40A


title: RecS3, Replicate 2, 0 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 2 for recombinase induction concentration of 0ug/ml L-arabinose


title: TYUC1_EZH2i_D3_3

description:
CD006
est_counts_genes_kallisto.txt


title: CWR22RV1 cells, siScr 72 h, biological replicate 2

description: siScr

value: Prostate


title: RecS3, Replicate 1, 100 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 1 for recombinase induction concentration of 100 ug/ml L-arabinose

value: 100 ug/mL L-Arabinose


title: Liver_AL_CT32A

value: Liver


title: TYUC1_EZH2i_D3_2

description:
CD005
est_counts_genes_kallisto.txt


title: RecS3, Replicate 1, 1 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 1 for recombinase induction concentration of 1 ug/ml L-arabinose


title: Liver_AL_CT04B

value: male


title: TYUC1_EZH2i_D3_1

description:
CD004
est_counts_genes_kallisto.txt


title: TYUC1_EZH2i_D0_3

description:
CD003
est_counts_genes_kallisto.txt


title: Liver_AL_CT28A

value: 6 months-old


title: RecS3, Replicate 1, 0 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 1 for recombinase induction concentration of 0ug/ml L-arabinose


title: TYUC1_EZH2i_D0_2

description:
CD002
est_counts_genes_kallisto.txt


title: Liver_AL_CT24A

value: 12h light / 12h dark


title: TYUC1_EZH2i_D6_1

description:
CD007
est_counts_genes_kallisto.txt


title: TYUC1_EZH2i_D0_1

description:
CD001
est_counts_genes_kallisto.txt


title: Liver_AL_CT20A


title: T120 rep3

city: Gif sur Yvette

first: Delphine

last: Naquin

address: avenue de la terrasse

country: France

institute: CNRS

data_processing:
bcl2fastq2-2.18.12
Sequence reads were trimmed for adaptor sequence using Cutadapt 1.15
Trimmed sequence reads were mapped to S288C_reference_genome_R64-2-1_20150113.fasta using tophat-2.1.1
Read count were performed using FeaturesCount from subread-2.0.1 package (parameters : -p (fragments will be counted instead of reads), -s 2 (Perform reversely-stranded read counting), -t transcript, -O (Assign reads to all their overlapping ta-features), -B (Only count read pairs that have both ends aligned), -P (Check validity of paired-end distance when counting read pairs), -C (Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands), --primary (Count primary alignments only), --ignoreDup (Ignore duplicate reads in read counting))
Differential analysis using DESeq2
Assembly: S288C_reference_genome_R64-2-1_20150113
Supplementary files format and content: tab-delimited csv files include normalized count for each sample by comparison

source_name: whole yeast cell

extract_protocol:
RNA was extracted using hot acid phenol, followed by ethanol precipitation, and suspension in Milli-Q water
500 ng of total RNA were treated with Baseline-ZERO DNAse (Epicentre) prior to ribosomal RNA depletion with the Ribo-Zero Yeast magnetic Kit (Illumina). RNA libraries for RNA-seq were prepared using the Stranded Total RNA Preparation kit following manufacturer's protocols.

value: whole yeast cell

value: sulfur depletion


title: Liver_AL_CT36A

value: Ad Libitum


title: Liver_AL_CT16A


title: T120 rep2


title: Human Naïve CD4 TAK981 Pretx 24Hr Stim Rep4

type: RNA

city: Duarte

first: Alexey

middle: V.

last: Danilov

state: CA

address: 1500 E Duarte Road

institute: City of Hope National Medical Center

description: SST-RMA Expression value derived from Expression Console software; gene-level analysis

hyb_protocol: Labelled hybridization targets were mixed with hybridization solution containing hybridization controls (Applied Biosystems) according to NuGEN Technologies protocol and hybridized with the GeneChip Clariom S Human Array (Applied Biosystems)

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Image processing was performed with GeneChip Command Console v. 3.1.1 and probe set summarization and CHP file generation was performed using Transcriptome Analysis Console v. 4.0 software.  Expression values were determined from SST-RMA normalization.

label: biotin

source_name: CLL Patient 04

label_protocol: 3ng of total RNAf or each sample were amplified and biotin labelled using the Ovation RNA Amplification System V.2, and Encore Biotin Module (NuGEN Technologies) as per manufacturer recommendations

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated using standard Ficoll-Hypaque technique (Amersham). Red blood cells were lysed using ACK buffer (Thermo Fisher Scientific). Naïve CD4+ T cells were FACS sorted by use of fluorescent antibodies in 2% FBS in PBS for 30 minutes on ice and subsequently washed. Naïve CD4+ T cells were then FACS-sorted by gating viable CD4+CD45RA+CD45RO- lymphocytes

extract_protocol: Total RNA was isolated using the total RNA Kit I and Homogenizer Mini Columns (Omega Bio-Tek). cDNA was synthesized from 500 ng of RNA using the qScript cDNA Supermix (QuantaBio)

treatment_protocol: Cells were pre-incubated with 1 µM TAK-981 or DMSO (vehicle) for 1 hour and treated with 0.5 µg/mL αCD3/CD28 in the presence of the compound for 3 or 24 Hrs

tag: agent

tag: time point

value: Peripheral Blood


title: Liver_AL_CT12A


title: Human Naïve CD4 TAK981 Pretx 24Hr Stim Rep3

source_name: CLL Patient 03


title: Human Naïve CD4 TAK981 Pretx 24Hr Stim Rep1

source_name: CLL Patient 01


title: T120 rep1

tag: time


title: RecS3, Replicate 1, 10 ARA

description: Recombinase RecS3 activity screen. Activity screen with loxP-like spacer library (LL8). Replicate 1 for recombinase induction concentration of 10 ug/ml L-arabinose

value: Target library, loxP-like spacer library, LL8

value: 10 ug/mL L-Arabinose


title: Patient 13, P013, scRNAseq

city: Zurich

first: Berend

last: Snijder

address: Otto-Stern-Weg 3, HPM building

country: Switzerland

institute: ETH Zurich

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files provided per library. Aggregated count matrix for all libraries were provided as a 'count_matrix_scRNASeq_GBM_4patients.txt' and associated a cell metadata table as 'cell_metadata_scRNASeq_GBM_4patients.txt'.

source_name: Brain tumor, enzymatically dissociated

extract_protocol:
Cryopreserved single-cell suspensions of glioblastoma patients samples were thawed in reduced serum media (DMEM containing 2% FBS) and used for single-cell RNA-Seq experiments. Viability markers SYTOX Blue and DRAQ5  were added to the cell suspension at least 15 minutes before sorting. FACS gates were set based on CD45, SYTOX Blue, and DRAQ5 intensities to isolate live CD45+ and CD45- populations.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.0 protocol, 10x Genomics).

value: Glioblastoma

value: Brain tumor, enzymatically dissociated

tag: tumor type

value: primary tumor

value: 67 years


title: Human Naïve CD4 TAK981 Pretx 3Hr Stim Rep4


title: Patient 13, P012, scRNAseq

description: 10x Genomics

value: 71 years


title: T80 rep3


title: Patient 11, P011, scRNAseq

description: 10x Genomics

value: recurrent tumor

value: 58 years


title: Liver_AL_CT08A

value: Liver

value: WT


title: Liver_AL_CT04A

value: male

value: 6 months-old


title: T80 rep2

value: whole yeast cell


title: Patient 7, P007, scRNAseq

description: 10x Genomics

value: 73 years


title: Human Naïve CD4 TAK981 Pretx 24Hr Stim Rep2

source_name: CLL Patient 02


title: Human Naïve CD4 TAK981 Pretx 3Hr Stim Rep3


title: Human Naïve CD4 TAK981 Pretx 3Hr Stim Rep2


title: T80 rep1

value: sulfur depletion


title: Control2_3

city: Lanzhou

first: TANG

middle: JIAN

last: MING

state: Gansu

address: 1604 No.1 Donggang West Road, Chengguan District

institute: The First Clinical Medical College of Lanzhou University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: Quality filtered reads were then mapped to GRCh38 using Hisat2

growth_protocol: MDA-MB-231 were grown in RPMI 1640 supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

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

treatment_protocol: treatment protocol ：25 uM Roscovitinen was used for erythroid differentiation of MDA-MB-231 cells. 25 uM Roscovitinen or DMSO was incubated with MDA-MB-231 cells for 1 hour.

value: MD Anderson-Metastatic Breast-231

value: DMSO


title: Liver_AL_CT00A

growth_protocol: C57BL/6J male mice (8 week-old) were individually housed in standard polycarbonate mouse cages (Fischer Scientific, Cat. Nos. 01-288-1B and 01-288-21) containing a 4.75 in diameter stainless steel running wheel inside isolation cabinets containing 12 cages each. Temperature and humidity levels were monitored, and the mice were housed under an LD12:12 cycle (green LEDs, ~100 lux at the level of the cage floor). Water was provided ad libitum throughout the study.

value: 12h light / 12h dark

value: Ad Libitum


title: FACS-purified MuSCs, in vitro cultured for 5days, Add 100nM Neurotensin, replicate 2

city: Bad Nauheim

first: Yundong

last: Peng

state: Hessen

address: Ludwigstrasse, 43

department: I

institute: Max Planck Institute for Heart and Lung Research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (ensembl release 101) using STAR 2.7.7a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner). The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Only genes with a minimum fold change of +- 1), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: library size normalized counts

source_name: Muscle stem cell

extract_protocol:
RNA was isolated from FACS-isolated  Ctrl (DMSO)or ET-3/NT treated MuSCs using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). Approx. 4ng of total RNA was used as input for SMART®-Seq HT Kit (Takara Bio).

value: 8 weeks old

value: Muscle stem cell

value: NT treated


title: Human Naïve CD4 TAK981 Pretx 3Hr Stim Rep1

value: Peripheral Blood


title: Control2_2


title: T40 rep2


title: Control2_1


title: Case1_3

value: Roscovitinen


title: FACS-purified MuSCs, in vitro cultured for 5days, Add 100nM Endothelin-3, replicate 2

value: ET-3 treated


title: FACS-purified MuSCs, in vitro cultured for 5days, Add 100nM Neurotensin, replicate 1


title: T40 rep1


title: FACS-purified MuSCs, in vitro cultured for 5days, Add 100nM Endothelin-3, replicate 1


title: T0 rep3

description:
T40_vs_T0_DESeq_results.csv
T80_vs_T0_DESeq_results.csv
T120_vs_T0_DESeq_results.csv

value: control


title: Human Naïve CD4 DMSO Pretx 24Hr Stim Rep3


title: Case1_2


title: Human Naïve CD4 DMSO Pretx 24Hr Stim Rep2


title: T0 rep1


title: FACS-purified MuSCs, in vitro cultured for 5days, Add DMSO, replicate 1

value: WT

value: DMSO control


title: Human Naïve CD4 DMSO Pretx 24Hr Stim Rep4


title: Human Naïve CD4 DMSO Pretx 3Hr Stim Rep4


title: FACS-purified MuSCs, in vitro cultured for 5days, Add DMSO, replicate 2


title: T0 rep2


title: Human Naïve CD4 DMSO Pretx 24Hr Stim Rep1


title: T40 rep3


title: iSN-rDRG coculture Replicate 2

status: Public on Jul 24 2024

city: Boston

first: Chelsey

last: LeBlang

state: Massachusetts

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
Fastq files were generated using bcl2fastq v2.20
Reads were aligned with STAR (v2.7.3a)
Assembly: UCSC Hg38 and UCSC Rn6
Supplementary files format and content: CSV file contains raw counts aligned to human genome
Supplementary files format and content: CSV file contains raw counts aligned to rat genome

organism:
Homo sapiens
Rattus norvegicus

source_name: iPSC NCRM5

growth_protocol: Primary e14.5 rat DRG glia were cultured for one week in base media. After one week, rDRG glia were either maintained in base media, treated with neuronal maturation media, or cocultured with terminally differentiating human induced neural crest precursors for one week. Human induced neural crest precursors were also plated alone and terminally differentiated one week.

extract_protocol:
RNA was collected using the RNeasy Plus Mini Kit from Qiagen acording to manufacturer's protocol.
Roche Kapa mRNA HyperPrep strand specific sample preparation kits  according to the manufacturer’s protocol on a Beckman Coulter Biomek i7.

value: induced human sensory neurons/ mixed primary rat dorsal root ganglion cells

value: iPSC NCRM5

value: Coculture


title: iSN-rDRG coculture Replicate 3


title: Human Naïve CD4 DMSO Pretx 3Hr Stim Rep2


title: iSN-rDRG coculture Replicate 1

source_name: iPSC Gr1.1

value: iPSC Gr1.1


title: Human Naïve CD4 DMSO Pretx 3Hr Stim Rep3


title: Human Naïve CD4 DMSO Pretx 3Hr Stim Rep1


title: Case1_1

value: MD Anderson-Metastatic Breast-231


title: Chip2_exp3_Ribotag

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Assembly: Genome_build: RDNA reference sequence from Krogh et al, NAR 2016
Supplementary files format and content: Supplementary_files_format_and_content: MS Excel files contains 5' and 3' read count, calculated RiboMeth-seq score at all positions in the rRNA sequence, and barcodes for fastq files.

extract_protocol:
Tissue samples were homogenized prior to RNA extraction, otherwise was whole cell RNA extracted using Trizol according to the manufacturer. RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description
Total RNA was extracted using TRI Reagent (Sigma-Aldrich, St. Louis, MO), according to the manufacturers instructions RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description
RiboMeth-seq


title: Chip2_exp1_Sham_MOV


title: Chip1_exp3_Ribotag


title: N2 wildtype, 219 embryo cells

city: Atlanta

first: David

last: Katz

address: 615 Michael St, WBRB Room 435

department: Cell Biology

institute: Emory University

description: 10X Genomics

data_processing:
The Cell Ranger Software Suite 3.0.2 (10X Genomics) was used for the alignment of the single-cell RNA-seq output reads and generation of feature, barcode and matrices. Seurat analysis was used for unsupervised hierarchical cluster formation.
Assembly: ce11
Supplementary files format and content: tab-separated value files and matrix files

organism: Caenorhabditis elegans

source_name: 100-200 cell embryos

extract_protocol:
Synchronized 100-200 cell N2 wildtype and spr-5; met-2 mutant embryos were obtained by starving moms at L1 stage then bleaching the moms at young adult stage, allowing for isolation of early embryos. Embryos were grown to 100-200 cell stage then prepped for scRNA sequencing using Chromium Next GEM Single Cell 3' LT Reagent Kits v3.1 (Dual Index).
Libraries were consturcted using 10X Genomics Single-Cell Capturing System

value: 100-200 cell embryos


title: OxyR mutant cultivated in LB 1

city: Montpellier

first: Anne

last: Lanois

address: 75 rue du Truel CC54

institute: INRA

data_processing:
Alignment to the Xenorhabdus nematophila F1 (XENF1.2) genome was performed with BWA v0.7.17-r1188. The resulting file were sorted and filtered (with option -q 3) with Samtools v1.9
The counting by CDS was performed using featureCounts v2.0.0, with a gff file downloaded on 07-27-2020 from the MaGe platform (https://mage.genoscope.cns.fr)
Assembly: XENF1.2
Supplementary files format and content: tab-delimited text file include raw gene counts for every gene and every sample

organism: Xenorhabdus nematophila F1

growth_protocol: logarithmic culture phase in LB broth supplemented or not with paraquat (during 30 min) at 28°C

extract_protocol:
RNEasy miniprep QIAGEN kit
MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) was used to remove ribosomal RNA
Illumina TruSeq Stranded mRNA Sample Preparation kit

treatment_protocol: RNA Protect Bacteria reagent 5 min

value: OxyR mutant

value: no treatment


title: OxyR mutant  cultivated in LB supplemented with Paraquat 3

value: Paraquat 30min


title: OxyR mutant cultivated in LB 3


title: OxyR mutant  cultivated in LB supplemented with Paraquat 1


title: OxyR mutant  cultivated in LB supplemented with Paraquat 2


title: Chip1_exp1_Sham_MOV


title: spr-5;met-2 double mutant, 686 embryo cells

description: 10X Genomics


title: OxyR mutant cultivated in LB 2


title: Wild Type cultivated in LB supplemented with Paraquat 2

value: Wild type


title: Wild Type cultivated in LB supplemented with Paraquat 1