title: Hippocampus, input

city: NEW YORK

first: Estibaliz

last: Barrio Alonso

state: NY

address: 455 MAIN STREET, 8A, 8A

institute: Weill Cornell Medicine

data_processing:
Reads were aligned against mouse genome (mm10) using Bowtie2 (v2.4) and samtools (v1.14). Peaks were assigned using MACS v2.1.1 and bigwigs were generated with Deeptools 2.0, both with default options.
Assembly: mm10

source_name: Hippocampus

extract_protocol: ChIP assays were performed according to the protocol from the Merck Millipore Chromatin Immunoprecipitation Kit (EZ-ChIP Kit, #17–371; Merck Millipore). Magna ChIPTM G Tissue Kit (#17-20000; Merck Millipore) was used for isolating the mouse hippocampal tissue. Cells were fixed with 1% formaldehyde for 10 minutes.  Chromatin was sonicated after quenching and cell lysis.

value: Hippocampus

value: Adult

tag: antibody


title: mouse hippocampus tissue, Gq-CNO, GFP astrocytes, rep 3

status: Public on Apr 17 2023

type: SRA

city: Houston

first: Debosmita

last: Sardar

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.11).
Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). Mapped reads were used to build count matrices using Bioconductor packages GenomicAlignments (v1.26.0) and GenomicFeatures (v1.42.2).
UCSC transcripts were downloaded from Illumina iGenomes in GTF file format.
DESeq2 (v1.30.1) was used for normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPM values

molecule: polyA RNA

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen #74004)
cDNA synthesis and library construction with 8-bp single indices were done from 10 ng total RNA using Trio RNASeq System (NuGEN #0507-96).
A final library dilution of 1.3 pM was subjected to paired-end sequencing.

tag: cell type

value: hippocampus

tag: genotype

tag: treatment

value: Gq-CNO


title: mouse cortex tissue, Gq-CNO, GFP astrocytes, rep 1

source_name: cortex

value: cortex


title: Foxa3_2d

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

country: China

institute: CEMCS, CAS

library_source: genomic

data_processing:
CutAdapt v.1.16 was used to remove adaptor sequences from reads of rawdata.
Reads were mapped to the mouse reference genome (mm10) using bowtie v.1.1.1.
Peaks were called using macs v.1.3.7.1.
Quantile normalized to remove the bias across the samples by using haystack_bio v.0.5.5.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated for visulization data in igv.

molecule: genomic DNA

source_name: mouse tail fibroblast overexpressed Foxa3, Gata4 and Hnf1a

growth_protocol: To induce ihep cells, 5x10^5 mouse tail fibroblast were seeded in dishes and overexpressed Foxa3, Gata4 and Hnf1a by lentivirus. Culture medium was replaced to blocks medium after 48hour.

extract_protocol:
Sonicate the chromatin in nuclear extracts to fragments by ultrasonication (Covaris S220). Primary antibodies were used for immunoprecipitation in sonication supernatant by incubation at 4℃ overnight. Protein G Dynabeads (Life Technologies, 10004D) were used for pulling down antibody-chromatin complex followed by washing and eluting. Foxa3:5 micrograms for ChIP, from Santa Cruz, cat id sc-5361. Gata4:5 micrograms for ChIP, from Santa Cruz, cat id sc-1237. Hnf1a:5 micrograms for ChIP, from Santa Cruz, cat id sc-6547. CTCF:5 micrograms for ChIP, from Active Motif, cat id 61312. H3K27ac:5 micrograms for ChIP, from Abcam, cat id ab4729. H3K27me3:5 micrograms for ChIP, from CST, cat id 9733.
MinElute PCR purification kit (Qiagen) was used for ChIP fragments collection. NEBNext Ultra DNA Library Prep Kit was used for ChIP-seq library preparation.

treatment_protocol: Cell were collected by cell scraper and washed by PBS once.

tag: chip antibody

value: fibroblast undergoing iHep induction

tag: overexpression

value: Foxa3, Gata4 and Hnf1a

tag: time point

tag: strain


title: Foxa3_0d

source_name: mouse tail fibroblast

value: fibroblast


title: Hippocampus, TIMELESS, sample 3

tag: tissue

value: anti-TIMELESS


title: Hippocampus, TIMELESS, sample 2


title: mouse cortex tissue, Gq-Saline, GFP astrocytes, rep 2

value: Gq-Saline


title: LocusB5_SR13_A19

city: Berkeley

first: Sudha

last: Rajderkar

state: CA

address: 1 Cyclotron Rd

institute: Lawrence Berkeley National Laboratory

description: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.

data_processing:
base-calling using bcl2fastq
Contacts for Hi-C data were stored in the juicer Hi-C format (could be opened with Juicebox.js, Robinson et al, Cell Systems 6(2), 2018). For RNA-seq, reads were mapped to the mouse genome (mm10) using STAR align (V2.12).
Genome_build: mm10
Supplementary_files_format_and_content: Juicer hic format for Hi-C data and normalized read per million kilobases (RPKM) and expected_counts data for RNA-seq.

molecule: total RNA

source_name: Embryonic Face

extract_protocol:
For Hi-C, mouse liver samples were harvested upon euthanasia, flash frozen in liquid nitrogen and pulverized before 1% formaldehyde cross-linking for 15 mins. For RNA-seq, mouse embryonic tissues were harvested upon euthanasia and processed in a standardized manner using the Qiagen RNeasy Mini kit.
For Hi-C, thawed crosslinked tissued was dissociated with genteleMACs and processed downstream using standard protocols; chromtain was digested with Mbol.
Hi-C, RNA-seq

value: FVB

tag: Stage

value: Embryonic day 11.5

value: wildType


title: mouse cortex tissue, Gq-Saline, GFP astrocytes, rep 3


title: LocusB5_SR13_A23

source_name: Embryonic Heart


title: LocusB5_SR13_A18

description: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °

value: homozygous


title: H3K27me3_14d


title: Hippocampus, TIMELESS, sample 1


title: H3K27me3_6d


title: mouse cortex tissue, Gq-CNO, GFP astrocytes, rep 3


title: H3K27me3_Hep

source_name: primary hepatocyte

value: hepatocyte

value: primary hepatocyte


title: LocusB3_SR12_A16


title: ZT0-EX (biol rep6)

city: Las Vegas

first: Graham

last: McGinnis

state: NV

address: 4505 S Maryland Pkwy

department: Kinesiology and Nutrition Sciences

institute: University of Nevada Las Vegas

description:
flowcell 2
15-Graham45_S1_R1_001

data_processing:
Trimming with Trimmomatic v0.39 to remove Illumina adapters and 2-color polyG artifacts
Splice-aware alignment to reference genome with Ensembl transcriptome GRCm39 build 103 with Hisat2 version 2.2.1
Paired-end summarization with Subread featureCounts v2.0.1 to gene models from Ensembl GTF build 103 for GRCm39
Assembly: ENSEMBL GRCm39
Supplementary files format and content: Counts data from featureCunts, summarixed to Ensembl GRCm39 build 103 genes, 1 sample per file

source_name: Heart

growth_protocol: Mice were aged to 12 weeks and housed on a tight 12:12 light:dark cycle. Any animal handling done during the dark phase (ZT12-ZT24) was done under red light.

extract_protocol:
RNA was isolated using conventional Trizol techniques.
Poly-A selection and Illumina TruSeq library construction

treatment_protocol: Mice were habituated to treadmill exercise and subsequently performed 1 bout of exercise (60 min, 10 m/min, 0% grade) at either ZT0 or ZT12. Sedentary mice at both times of day served as control.

value: Heart

value: WT

tag: Sex

value: Male

tag: age

value: 12 weeks

value: Exercise

tag: time of_day


title: Foxa3_4d


title: mouse cortex tissue, Gq-Saline, GFP astrocytes, rep 1

value: cortex


title: LocusB3_SR12_A15


title: ZT0-EX (biol rep5)

description:
flowcell 2
14-Graham44_S17_R1_001


title: H3K27me3_2d

value: fibroblast undergoing iHep induction


title: 6_ATTAC_Kras

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
reads were mapped to the reference genome using 10X Genomics cellranger v3.0.2
Assembly: mm10
Supplementary files format and content: feature-barcode matrix file

source_name: Lung

extract_protocol:
Mice were perfused through the heart with ice-cold Dulbecco’s phosphate-buffered saline (DPBS; pH7.4) until lung lobes were clear. Dissociation of the lobes was performed following the manufacturer’s protocol (MACS, Miltenyi Biotec; Lung Dissociation Kit, mouse’ #130-095-927). Single cell suspension was incubated with red blood cell lysis solution (MACS, Miltenyi Biotec #130-094-183) for 10 min and resuspended with autoMACS buffer rinsing solution (MACS, Miltenyi Biotec #130-091-222).
Whole live cells were washed twice in 1x PBS + 0.04% BSA and immediately submitted to the Mayo Clinic Genome Analysis Core for Single Cell sorting. The cells were first counted and measured for viability using either the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter, Brea, CA) or a basic hemocytometer and light microscope. The barcoded Gel Beads were thawed from -80°C and the cDNA master mix was prepared according to the manufacture’s instruction for Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit (10x Genomics, Pleasanton, CA). A per sample concentration of 400,000 cells per milliliter was required for the standard targeted cell recovery of approximately 5000 cells. The cell suspension and master mix, thawed Gel Beads and partitioning oil were added to a Chromium Single Cell G chip. The filled chip was loaded into the Chromium Controller, where each sample was processed and the individual cells within the sample were partitioned into uniquely labeled GEMs (Gel Beads-In-Emulsion). The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up. The resulting cDNA contained a pool of uniquely barcoded molecules. A portion of the cleaned and measured pooled cDNA continued to library construction, where standard Illumina sequencing primers and a 10x Genomics unique i7 Sample index were added to each cDNA pool. All cDNA pools and resulting libraries were measured using Qubit High Sensitivity assays (Thermo Fisher Scientific, Waltham, MA) and Agilent Bioanalyzer High Sensitivity chips (Agilent, Santa Clara, CA). Libraries are sequenced at between 40,000 and 50,000 fragment reads per cell following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit (Illumina, San Diego, CA). The flow cells are sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 HD using HiSeq 3000/4000 sequencing kit and HCS v3.4.0.38 collection software. Base-calling is performed using Illumina’s RTA version 2.7.7.

treatment_protocol: All mice were treated with AP treatment from birth

tag: tumor stage

value: Adenoma


title: 5_Kras


title: 4_ATTAC

value: WT - Healthy lung


title: ZT0-EX (biol rep4)

description:
flowcell 2
13-Graham43_S13_R1_001


title: 3_ATTAC_Kras


title: LocusB3_SR12_A14


title: LocusB3_SR12_A13


title: H3K27me3_0d

value: fibroblast


title: ZT0-EX (biol rep3)

description:
flowcell 1
15-CES32_S5_R1_001


title: LocusB5_SR13_A17


title: 2_Kras


title: H3K27ac_Hep


title: H3K27ac_14d

value: Foxa3, Gata4 and Hnf1a


title: ZT0-EX (biol rep2)

description:
flowcell 1
14-CES26_S3_R1_001


title: LocusB3_SR12_A12

value: FVB


title: LocusB3_SR12_A11

value: Embryonic day 11.5


title: H3K27ac_6d


title: ZT0-SED (biol rep6)

description:
flowcell 2
12-Graham41_S3_R1_001

value: Sedentary Control


title: 1_ATTAC


title: ZT0-EX (biol rep1)

description:
flowcell 1
13-CES25_S16_R1_001


title: LocusB3_SR12_A10

value: homozygous


title: WildType_Rep1

source_name: Adult liver

value: Post natal day 57


title: LocusB6_SR3_A8


title: H3K27ac_4d


title: ZT0-SED (biol rep4)

description:
flowcell 2
10-Graham33_S16_R1_001


title: H3K27me3_4d


title: LocusB3_SR12_A9


title: LocusB7_D4054

value: Post natal day 55


title: ZT0-SED (biol rep5)

description:
flowcell 2
11-Graham36_S14_R1_001

value: Heart


title: H3K27ac_2d


title: H3K27ac_0d


title: LocusB6_SR3_A7


title: LocusB7_D4024

value: Post natal day 56


title: LocusB5_D2926


title: ZT0-SED (biol rep3)

description:
flowcell 1
12-CES38_S4_R1_001

value: WT

value: Male


title: ZT0-SED (biol rep2)

description:
flowcell 1
11-CES37_S17_R1_001

value: 12 weeks


title: LocusB6_SR3_A6


title: LocusB5_D2925


title: LocusB6_SR3_A5


title: ZT0-SED (biol rep1)

description:
flowcell 1
10-CES35_S10_R1_001


title: WildType_Rep2


title: LocusB6_D2851


title: LocusB7_SR9_A4


title: ZT12-EX (biol rep6)

description:
flowcell 2
6-Graham49_S12_R1_001

value: Exercise


title: Inhibitory neuron_F1r

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

country: Taiwan

institute: National Taiwan University

data_processing:
ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation. The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene ID, Associated gene name, Description, Gene Biotype, Locus, FPKM. The ASE (allele-specific expression) means the  RNA-Seq data  were processed with allele-specific expression analysis. The gene means the RNA-Seq data were processed with gene expression analysis. The isoform means the RNA-Seq data were processed with gene isoform expression analysis.  )

source_name: Cerebral cortex

extract_protocol:
Total RNA of the single cells of mouse cerebral cortex was extracted by miRNeasy Micro Kit (QIAGEN, 217084).
Library for RNA-Seq was built up using a SureSelect Strand-Specific RNA Library Prep Kit (Agilent Technologies, G9691A).

value: inhibitory neurons

tag: tracking number


title: Astrocyte_F1i

value: astrocytes


title: LocusB7_SR9_A3


title: ZT12-EX (biol rep5)

description:
flowcell 2
5-Graham10_S4_R1_001


title: Astrocyte_F1r


title: LocusB6_D2843


title: Excitatory neuron_F1r

value: excitatory neurons


title: Inhibitory neuron_F1i


title: ZT12-EX (biol rep4)

description:
flowcell 2
4-Graham18_S8_R1_001


title: Excitatory neuron_F1i


title: SUM159_pLV-KRAB+all-4-gRNAs_rep3 [All.gRNA3]

type: genomic

city: Clayton

first: Joe

last: Cursons

state: VIC

address: 19 Innovation Walk

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description: SUM159 (triple negative breast cancer) cell line transfected with a pLV-KRAB dCas9/CRISPRi system + 4 gRNAs targeting the ZEB1 promoter

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

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

data_processing: Methylation data analysis were conducted using the minfi R package to read.idat files into R (version 3.6.3), and the missMethyl R package was used for data processing and normalization. Specifically, we identified low quality probes and removed them from the data normalized by SWAN. We then extracted β and M-values (with an offset of 100 for calculating M values). Data quality control was performed using PCA and MDS plots as well as histograms of β values, probe-level differential methylation analysis was performed on M-values using limma, and probes with an adjusted p-value < 0.05 and absolute log fold change; 0.5 were considered as differentially methylated probes (DMPs). To map probes to their associated genes and gene regions, we used the IlluminaHumanMethylationEPICanno.ilm10b2.hg19 R package.

label: Cy5 and Cy3

organism: Homo sapiens

source_name: SUM159 cells, transfected with pLV-KRAB dCas9/CRISPRi system + 4 targeting gRNAs against the ZEB1 promoter

label_protocol: Standard Illumina Protocol

growth_protocol: F12 Medium supplemented with 0.6% 1M Hepes, 5 µg/mL insulin, 1 µg/mL hydrocortisone, 1% Anti-Anti and 10% heat inactivated FBS

extract_protocol: Cells were washed twice in PBS before being collected. DNA was extracted with the Monarch Genomic DNA Purification kit (New England Biolabs).  After QC, 500ng of purified DNA was processed using Illumina Methylation EPIC 850k Array.

treatment_protocol: Lentiviral particles were produced using HEK293T with co-transfection using third generation VSVG (Addgene plasmid #12259), GAG/POL (Addgene plasmid #12260) and pLV dCas9-KRAB +/-gRNA as previously described [doi:10.1039/c9sc01432b & 10.1016/j.omtn.2018.12.003]. Four days following transduction, 1.25 µg/mL puromycin was used to select SUM159 cells.

tag: cell line

tag: gender

value: Female

value: triple negative breast cancer cell line


title: iPS differentiation d15 [muc6880]

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description:
Drop-seq
MUC6880_S53_L008

data_processing:
For preprocessing of the single cell data of tissue culture, the Dropseq computational pipeline was used (version 2.3.0) as previously described (Pubmed ID: 26000488). Briefly, STAR (version 2.5.3a) was used for mapping. Reads were aligned to the hg19 reference genome (GSE63269). For barcode filtering, we retained the first 1200 cells, sorted by number of transcripts per cell. We excluded barcodes with less than 200 genes detected and more han 5000 UMIs. A high proportion (> 20%) of transcript counts derived from mitochondria-encoded genes may indicate low cell quality, and we removed these unqualified cells from the downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Raw count matrix (IPS_differentiation_raw_counts.mtx) from Drop-seq experiments with 26936 genes and 10667 cells in market matrix format and corresponding column (IPS_differentiation_genes.txt) and row (IPS_differentiation_barcodes.txt) labels. Cell-level metadata (IPS_differentiation_metadata.txt).

source_name: Tissue culture

growth_protocol: single-cell suspension protocol: Daily sampling of cells during differentiation was performed by detaching the cells from the tissue culture plate using Accutase. Cells where thereafter centrifuged for 5 min at 300 × g (4 °C), counted using a Neubauer chamber and critically assessed for single-cell separation and viability. A total of 250,000 cells were aliquoted in 2.5 ml of PBS supplemented with 0.04% of bovine serum albumin (BSA) and loaded for DropSeq at a final concentration of 100 cells/μl.

extract_protocol:
Dropseq experiments were performed according to the original Dropseq protocol (Macosko et al., 2015; Ziegenhain et al., 2017). Using a microfluidic polydimethylsiloxane device (Nanoshift) single cell (100/µl) suspensions were co-encapsulated in droplets with barcoded beads (120b/µl, purchased from ChemGenes Corporation, Wilmington, MA) at rates of 4000 µl/h. Droplet emulsions were collected for 15 min/each prior to droplet breakage by perfluorooctanol (Sigma-Aldrich). After breakage, beads were harvested and the hybridized mRNA transcripts reverse transcribed (Maxima RT, Thermo Fisher). Unused primers were removed by the addition of exonuclease I (New England Biolabs), following which beads were washed, counted, and aliquoted for pre-amplification (2000 beads/reaction, equals ~100 cells/reaction) using a total of 10 PCR cycles.
PCR details: (Smart PCR primer: AAGCAGTGGTATCAACGCAGAGT (100 µM), 2× KAPA HiFi Hotstart Readymix (KAPA Biosystems), cycle conditions: 3 min 95 °C, 4 cycles of 20 s 98 °C, 45 s 65 °C, 3 min 72 °C, followed by 8 cycles of 20 s 98 °C, 20 s 67 °C, 3 min 72 °C, then 5 min at 72 °C) (Macosko et al., 2015).
PCR products of each sample were pooled and purified twice by 0.6× clean-up beads (CleanNA), following the manufacturer’s instructions. Prior to tagmentation, complementary DNA (cDNA) samples were loaded on a DNA High Sensitivity Chip on the 2100 Bioanalyzer (Agilent) to ensure transcript integrity, purity, and amount. For each sample, 1 ng of pre-amplified cDNA from an estimated 600 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single-cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 µM Read1CustSeqB was used (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC).

value: human pluripotent stem cells (hPSCs)

tag: differentiation day

value: day 15

tag: differentiation stage

value: Early lung progenitors and hepatoblasts

tag: number of cells


title: iPS differentiation d14 [muc6879]

description:
Drop-seq
MUC6879_S52_L008

tag: cell type

value: day 14


title: LocusB7_SR9_A1

value: FVB

value: Embryonic day 11.5

tag: genotype

value: homozygous


title: LocusB2_D4932

value: Post natal day 57


title: SUM159_pLV-KRAB+all-4-gRNAs_rep2 [All.gRNA2]


title: LocusB7_SR9_A2


title: ZT12-EX (biol rep2)

description:
flowcell 1
5-CES17_S7_R1_001

value: Heart

value: WT

tag: treatment


title: ZT12-EX (biol rep1)

description:
flowcell 1
4-CES11_S13_R1_001

value: Male

value: 12 weeks


title: iPS differentiation d12 [muc6877]

description:
Drop-seq
MUC6877_S50_L008

value: day 12


title: iPS differentiation d13 [muc6878]

description:
Drop-seq
MUC6878_S51_L008

value: day 13


title: SUM159_pLV-KRAB+all-4-gRNAs_rep1 [All.gRNA1]


title: SUM159_pLV-KRAB+empty-vector_rep3 [EV3]

description: SUM159 (triple negative breast cancer) cell line transfected with a pLV-KRAB dCas9/CRISPRi system

source_name: SUM159 cells, transfected with pLV-KRAB dCas9/CRISPRi system


title: ZT12-SED (biol rep6)

description:
flowcell 2
3-Graham42_S9_R1_001

value: Sedentary Control


title: LocusB2_E1558

value: Post natal day 56


title: iPS differentiation d11 [muc6876]

description:
Drop-seq
MUC6876_S49_L008

value: day 11


title: iPS differentiation d10 [muc6875]

description:
Drop-seq
MUC6875_S48_L008

value: human pluripotent stem cells (hPSCs)

value: day 10

value: Foregut endoderm


title: SUM159_pLV-KRAB+empty-vector_rep2 [EV2]

value: Female

value: triple negative breast cancer cell line


title: ZT12-SED (biol rep5)

description:
flowcell 2
2-Graham13_S18_R1_001


title: LocusB2_E1557

value: FVB


title: LocusB8_D5376


title: SUM159_wildtype_rep2 [WT2]

description: SUM159 (triple negative breast cancer) cell line

source_name: SUM159 cells


title: LocusB2_E1556


title: ZT12-SED (biol rep3)

description:
flowcell 1
3-CES14_S11_R1_001


title: ZT12-SED (biol rep4)

description:
flowcell 2
1-Graham2_S15_R1_001


title: LocusB4_D4715

value: Post natal day 53


title: LocusB2_E1559


title: SUM159_pLV-KRAB+empty-vector_rep1 [EV1]


title: SUM159_wildtype_rep1 [WT1]


title: N16961, stationary, biol rep 3

city: Madrid

first: José

middle: Antonio

last: Escudero

state: Madrid

address: Av Puerta de Hierro s/n

department: Sanidad Animal

country: Spain

institute: Universidad Complutense de Madrid

data_processing:
Raw reads were trimmed using Trim Galore v0.6.6 with a quality threshold of 20 and removing adapters and reads shorter than 50 bp.
Trimmed paired reads were mapped to the V. cholerae N16961 reference genome (Accession number: chromosome 1 CP028827.1; chromosome 2 CP028828.1) using BWA-MEM v0.7.17.
Read count data was obtained with featureCounts from the Rsubread v2.10.2 package
The expression levels, given in TPM values (transcripts per kilobase million) for all protein-coding genes, were calculated with the Geneious Prime “Calculate Expression Level” function
Assembly: chromosome 1 CP028827.1; chromosome 2 CP028828.1
Supplementary files format and content: N16961_exponential_TPM_CP028827.1.csv includes TPM values from chrosmosome 1 (CP028827.1) of the three biological replicates in exponential phase.
Supplementary files format and content: N16961_exponential_TPM_CP028828.1.csv includes TPM values from chrosmosome 2 (CP028828.1) of the three biological replicates in exponential phase.
Supplementary files format and content: N16961_stationary_TPM_CP028827.1.csv includes TPM values from chrosmosome 1 (CP028827.1) of the three biological replicates in stationary phase.
Supplementary files format and content: N16961_stationary_TPM_CP028828.1.csv includes TPM values from chrosmosome 2 (CP028828.1) of the three biological replicates in stationary phase.
Supplementary files format and content: featureCounts_exponential.csv includes raw counts of sequencing reads for the three biological replicates in exponential phase
Supplementary files format and content: featureCounts_stationary.csv includes raw counts of sequencing reads for the three biological replicates in stationary phase

organism: Vibrio cholerae

source_name: prokaryote

growth_protocol: Vibrio cholerae was cultured in liquid Luria-Bertani (LB) medium at 37°C.

extract_protocol:
Total RNA was extracted from V. cholerae N16961 cultures grown in LB at 37˚C in both exponential (OD600 0,8) and stationary (OD600 2,8) growth phases using the RNeasy® Mini Kit (QIAGEN), following the manufacturer’s protocol.
Ribodepletion RNA library and sequencing was performed at the Oxford Genomics Centre using a NovaSeq6000 sequencing system (Illumina). Samples were depleted using NEB bacteria rRNA probes before conversion to cDNA. Second strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired end sequencing over one unit of a flow cell. Data were aligned to the reference and quality checked.

value: prokaryote

tag: time

value: stationary (OD600 2.8)


title: ZT12-SED (biol rep2)

description:
flowcell 1
2-CES7_S8_R1_001

value: Heart

tag: strain

value: WT


title: N16961, stationary, biol rep 2


title: iPS differentiation d7 [muc6872]

description:
Drop-seq
MUC6872_S45_L007

value: day 7


title: iPS differentiation d5 [muc6870]

description:
Drop-seq
MUC6870_S43_L007

value: day 5

value: Definite endoderm


title: WildType_D4053

value: Post natal day 55


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 3 [snRNA-Seq]

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

description:
8E_S1
Counts matrix provided as supplementary files: snRNA_txt.zip

library_source: transcriptomic single cell

data_processing:
RNA-Seq
HiSeq Cobtrol Software (HC) version 2.2.68 was used for base calling. The raw bcl files were converted to fastq files using software program bcl2fastq2.17.1.14.  Adaptors were trimmed from the fastq files during the conversion.
Salmon version 1.3.0 was used for this analysis. A "salmon index" was built with decoys using GRCm38 and Gencode (vM25). For each FASTQ file, "salmon quant" was used to perform quantification.
Assembly: GRCm38
Supplementary files format and content: Count matrices (gene and transcript levels) provided as supplementary files
snRNA-seq
HiSeq Cobtrol Software (HC) version 2.2.68 was used for base calling. The raw bcl files were converted to fastq files and demultiplexed using software program bcl2fastq2.17.1.14 with cellranger mkfastq.
Salmon version 1.3.0 was used for this analysis. A "salmon index" was built with decoys (including intronic regions) using GRCm38 and Gencode (vM25). For each FASTQ file, "salmon alevin" was used to perform quantification.
Assembly: GRCm38
Supplementary files format and content: Count matrix provided as supplementary file

source_name: Pre-Frontal Cortex

growth_protocol: C57BL6/J mice were house in standard cages on a 12:12 h light:dark cycle with food and water ad libitum.

extract_protocol:
Nuclei were extracted from mouse prefrontal cortical tissue using the Nuclei PURE Prep kit (Millipore Sigma, Burlington MA, USA) with the following modifications. Briefly, Pre-frontal cortex (PFC) tissue samples (~0.035 mg per sample/mouse) were processed in 2mL glass dounce homogenizers (Kimble-Chase, Vineland, NJ USA). Nuclei were purified according to manufacturer’s instructions, with all volumes reduced to one quarter the recommended amount. Nuclei were separated by centrifugation at 13,000 rcf for 45 mins at 4oC (Sorvall WX-100, F65L-6 x 13.5 rotor, Thermo Fisher, Waltham, MA USA).
Single nuclear RNA-seq libraries were generated using the Chromium Single Cell 3’ Solution microfluidics platform (10X Technologies, Pleasonton, CA USA). Single-nuclei libraries were generated from the nuclei suspensions using the 10x Genomics Chromium Controller and Single Cell 3’ Reagent Kits v3 Chemistry following manufacturer’s instructions. Briefly, we targeted capture of 10,000 single nuclei through generation of gel beads in emulsion (GEMs) which allowed partitioning of an individual nuclei along with a bead containing barcoded oligonucleotides. Reverse transcription and barcoding occurred within this emulsion resulting in transcripts from an individual nucleus having a unique molecular identifier. After barcoding, the emulsion was broken, and the cDNA processed in bulk. The barcoded cDNA was first amplified to generate sufficient mass for library construction and then sample index, P5 and P7 adapters were added for Illumina sequencing. The sizes of 10X cDNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit. The concentrations were measured by StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapabiosystems, Wilmington, MA). The libraries were diluted to 2 nM with RSB (10 mM Tris-HCl, pH8.5) and denatured with 0.1 N NaOH.  Three pM libraries were loaded onto NextSeq 500 (Illumina, San Diego, CA) for sequencing using the NextSeq 500/550 High Output Kit v2.5 (150 Cycles) . The libraries were sequenced from both ends with 28+8+0+91 cycles (red length 100 bp).

treatment_protocol: Begining at light onset, sleep deprived mice were kept awake for 5 hours via gentle handling. Prefrontal cortex tissue was collected at the conclusion of sleep deprivation (SD5, E) and immediately flash frozen in liquid nitrogen. Control animals that were left in their home cage to sleep were dissected at the same time of day (HC5, C).

tag: tissue

value: Pre-Frontal Cortex

value: Brain cell

value: 8-12 weeks

value: male

value: Sleep Deprivation

tag: insert size


title: WildType_D4059

tag: Stage


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 2 [snRNA-Seq]

description:
4E_S1
Counts matrix provided as supplementary files: snRNA_txt.zip

tag: age

tag: Sex


title: iPS differentiation d3 [muc6868]

description:
Drop-seq
MUC6868_S41_L007

value: human pluripotent stem cells (hPSCs)

value: day 3


title: iPS differentiation d4 [muc6869]

description:
Drop-seq
MUC6869_S42_L007

value: day 4


title: LocusB8_D4708

value: FVB

value: Post natal day 53


title: N16961, exponential, biol rep 3

value: prokaryote

value: exponential (OD600 0.8)


title: iPS differentiation d2 [muc6867]

description:
Drop-seq
MUC6867_S40_L007

value: day 2


title: LocusB4_D4661

value: Post natal day 54


title: iPS differentiation d8 [muc6873]

description:
Drop-seq
MUC6873_S46_L008

value: day 8

value: Foregut endoderm


title: Wildtype homecage control harvested at ZT hour 5, replicate 3 [snRNA-Seq]

description:
5C_S1
Counts matrix provided as supplementary files: snRNA_txt.zip

value: WT

value: Control


title: N16961, exponential, biol rep 2


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 1 [snRNA-Seq]

description:
2E_S1
Counts matrix provided as supplementary files: snRNA_txt.zip

value: Pre-Frontal Cortex

value: Brain cell


title: iPS differentiation d6 [muc6871]

description:
Drop-seq
MUC6871_S44_L007

value: day 6

value: Definite endoderm


title: Wildtype homecage control harvested at ZT hour 5, replicate 2 [snRNA-Seq]

description:
3C_S1
Counts matrix provided as supplementary files: snRNA_txt.zip

value: 8-12 weeks

value: male


title: LocusB3_D4439


title: LocusB3_D4438


title: iPS differentiation d1 [muc6866]

description:
Drop-seq
MUC6866_S39_L007

value: human pluripotent stem cells (hPSCs)

value: day 1


title: Liver-exp-rep2

status: Public on Apr 16 2023

city: Zheng zhou

first: Yi

middle: ze

last: Zhang

state: He nan

address: The No.1, Long hu zhong huan road, Zhengzhou

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Quality control: Cutadapt (v1.15) software was used to filter the sequencing data to get high quality sequence.
Reads mappling: The filterer reds were mapping to the reference genome mm10 using HISAT2 v2.0.5
Differential expression analysis: HTSeq (0.9.1) statistics was used to compare the Read Count values on each genes as the original expression of the gene. And difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05
GO and KEGG enrichment analysis: TopGO was used to perform GO enrichment analysis on the differential genes. ClusterProfiler (3.4.4) software was used to carry out the enrichmentanalysis of the KEGG pathway of differential genes.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

growth_protocol: Total 6 six-week old C57BL/6 mice were randomly divided into control and experimental groups (3 per group) treated with CSAA (Dyets, 518754, USA) and CDAA (Dyets, 518753, USA) feed respectively. After one week acclimatization, the experimental group was to be fed with the transitional feed for one week. During this transitional stage, the CSAA and CDSS feeds were mixed at 2:1 on the first three days, 1:1 on the fourth to fifth days, 1:2 on the sixth to seventh days, and CDAA feed was completely added after this period. At the 6th week after transitional feeding, the livers of animals of each group were sampled.

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
The extracted and purified mRNA was broken to 200 to 300 bp fragments by ion interruption. The first strand of cDNA was synthesized using RNA as template, and the second strand of cDNA was synthesized using the first strand as template. The size of the library was 300 to 400 bp. The size of the library was detected by Agilent 2100, and the total concentration of the library was detected by fluorescence quantification.

treatment_protocol: The liver samples were extracted after anesthetization of each mouse.

value: Liver

value: fed with CDAA for 6 weeks


title: iPS differentiation d9 [muc6874]

description:
Drop-seq
MUC6874_S47_L008

value: day 9


title: Liver-con-rep3

value: fed with CSAA for 6 weeks


title: Liver-exp-rep1


title: N16961, exponential, biol rep 1

value: prokaryote

value: exponential (OD600 0.8)


title: Wildtype homecage control harvested at ZT hour 5, replicate 1 [snRNA-Seq]

description:
1C_S1
Counts matrix provided as supplementary files: snRNA_txt.zip


title: Liver-exp-rep3


title: DMSO_Replicate1 [ATAC-Seq]

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 1500 East Medical Center Drive

department: MM Pathology Department

institute: University of Michigan

data_processing:
Paired-end .fastq files were trimmed and uniquely aligned to the GRCh38/hg38 human genome assembly using Novoalign (Novocraft) (with the parameters -r None -k -q 13 -k -t 60 -o sam –a CTGTCTCTTATACACATCT), and converted to .bam files using SAMtools (version 1.3.1). Reads mapped to mitochondrial or duplicated reads were removed by SAMtools and PICARD MarkDuplicates (version 2.9.0), respectively. Filtered .bam files from replicates were merged for downstream analysis. MACS2 (2.1.1.20160309) was used to call ATAC-seq peaks. The coverage tracks were generated using the program bam2wig (http://search.cpan.org/dist/Bio-ToolBox/) with the following parameters: –pe–rpm–span–bw.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: Standard growth culture media

extract_protocol:
Nextera Tn5 tagmentation
ATAC-seq was performed as previously described33. In brief, 50,000 cancer cells treated with AU-15330 or ZBC-260[30] were washed in cold PBS and resuspended in cytoplasmic lysis buffer (CER-I from the NE-PER kit, Invitrogen, cat. no. 78833). This single-cell suspension was incubated on ice for 5–8 min (depending on the cell line) with gentle mixing by pipetting every 2 min. The lysate was centrifuged at 1,300g for 5 min at 4 °C. Nuclei were resuspended in 50 μl of 1× TD buffer, then incubated with 2–2.5 μl Tn5 enzyme for 30 min at 37 °C (Nextera DNA Library Preparation Kit; cat. no. FC-121-1031). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; cat. no. M0541L) following the original protocol33. qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter; cat. no. A63881). ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).

treatment_protocol: DMSO or AU15330 at 1mM for 24h

value: DIPG - cancer

value: wildtype

value: DMSO


title: Liver-con-rep2


title: N16961, stationary, biol rep 1

value: WT

value: stationary (OD600 2.8)


title: ZT12-SED (biol rep1)

description:
flowcell 1
1-CES1_S6_R1_001

value: Heart

value: Male

value: 12 weeks

value: Sedentary Control

tag: time of_day


title: AU15330_Replicate2 [ATAC-Seq]

value: AU15330 1mM for 24h


title: AU15330_Replicate1

description: SI_32464: DMSO_Rep1; SI_32465: DMSO_Rep2; SI_32466: AU15330_Rep1; SI_32467: AU15330_Rep2

data_processing:
Libraries passing quality control were trimmed of sequencing adaptors and aligned to the human reference genome, GRCh38. Samples were demultiplexed into paired-end reads using Illumina’s bcl2fastq conversion software v2.20. The reference genome was indexed using bowtie2-build, and reads were aligned onto the GRCh38/hg38 human reference genome using TopHat2 with strand-specificity and allowing only for the best match for each read. The aligned file was used to calculate strand-specific read count for each gene using HTSeq-count (version 0.13.5). EdgeR (version 3.34.1) was used to compute differential gene expression using raw read-counts as input. Heatmaps were generated using the ComplexHeatmap package in R.
Assembly: hg38
Supplementary files format and content: raw counts matrix

extract_protocol:
Qiagen mRNeasy RNA extraction kit
RNA-seq libraries were prepared using 200–1,000 ng of total RNA. RiboErase to enrich for mRNA, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (2 × 100 nucleotide read length) with sequence coverage to 15–20M paired reads.


title: DMSO_Replicate1


title: Liver-con-rep1


title: DMSO_Replicate2


title: AU15330_Replicate1 [ATAC-Seq]


title: DMSO_Replicate2 [ATAC-Seq]


title: iPS differentiation d0 [muc6865]

description:
Drop-seq
MUC6865_S38_L007

value: human pluripotent stem cells (hPSCs)

value: day 0

value: Definite endoderm


title: LocusB2_D4414

value: FVB

value: Post natal day 57


title: 20141a168, SAD, ELA

city: Tuebingen

first: Susanne

last: Edelmann

address: Calwerstraße 14

institute: University of Tuebingen

data_processing:
bbduk tool from the BBTools suite (https://sourceforge.net/projects/bbmap/) for quality trimming
Trimmed sequence reads were mapped to GRCh38.104 using the STAR aligner
Read normalization was performed using DESeq2
To control for the effect of blood cell type composition variability on gene expression, blood cell type proportions were estimated using the granulator package in R using TPM (transcripts per million) normalized counts. Benchmarking in granulator was performed using reference cell type counts of a subset of the cohort. Using an adjustment approach by Jones et al. (2017) gene counts were adjusted to cell type ratios.
Assembly: vGRCh38.104
Supplementary files format and content: Comma-separated matrix (csv file) include gene counts for each sample

source_name: peripheral blood

extract_protocol:
Total RNA from whole blood stored in PAXgene Blood RNA tubes was extracted using the PaxGene Blood miRNA kit (Qiagen, Hilden, Germany)
Libraries for 3′ RNA-seq were prepared using the 3′ method by Lexogen  as used in the NGS Competence Center Tübingen (NCCT) where both library preparation and sequencing in randomized batches was performed. First strand synthesis of polyA-tailed RNA from total RNA using oligo dT primers was followed by degradation of the RNA template, second strand synthesis with random primers containing 5′ Illumina-compatible linker sequences and amplification using random primers that add barcodes and cluster generation sequences . The libraries were sequenced on the NCCT Nova sequencing platform at a depth of about 10million reads with 100bp in length.
3’ RNA-seq

tag: sad status

value: SAD

tag: ela status

value: ELA

value: male

value: peripheral blood


title: AU15330_Replicate2

tag: cell line

value: DIPG - cancer

value: wildtype


title: 20141a166, SAD, noELA

value: noELA

tag: gender

value: female


title: 20141a164, SAD, noELA


title: 20141a165, SAD, ELA


title: 20141a160, noSAD, ELA

value: noSAD


title: 20141a159, noSAD, noELA


title: 20141a150, noSAD, ELA


title: 20141a151, noSAD, noELA


title: 20141a162, noSAD, noELA


title: 20141a146, SAD, noELA


title: 20141a149, noSAD, noELA


title: 20141a163, noSAD, noELA


title: 20141a145, SAD, noELA


title: 20141a154, noSAD, noELA


title: 20141a143, SAD, noELA


title: 20141a142, noSAD, noELA


title: 20141a141, SAD, noELA


title: 20141a167, SAD, noELA


title: 20141a138, SAD, ELA


title: 20141a137, SAD, ELA


title: 20141a144, SAD, noELA


title: 20141a136, noSAD, ELA


title: 20141a135, noSAD, noELA


title: 20141a139, noSAD, noELA


title: 20141a133, SAD, ELA


title: 20141a134, SAD, noELA


title: 20141a132, SAD, ELA


title: 20141a140, SAD, ELA


title: 20141a131, noSAD, ELA


title: 20141a155, SAD, ELA


title: 20141a129, noSAD, noELA


title: 20141a126, SAD, noELA


title: 20141a128, noSAD, noELA


title: 20141a125, SAD, noELA


title: 20141a127, noSAD, noELA


title: 20141a123, noSAD, noELA


title: 20141a121, SAD, ELA


title: 20141a118, SAD, noELA


title: 20141a124, SAD, noELA


title: 20141a119, noSAD, noELA


title: 20141a120, noSAD, noELA


title: 20141a122, noSAD, noELA


title: 20141a117, noSAD, noELA


title: 20141a115, noSAD, ELA


title: 20141a113, noSAD, ELA


title: 20141a116, noSAD, ELA


title: 20141a114, noSAD, noELA


title: 20141a112, noSAD, ELA


title: 20141a109, noSAD, noELA


title: 20141a108, SAD, noELA


title: 20141a102, noSAD, ELA


title: 20141a110, noSAD, noELA


title: 20141a107, SAD, noELA


title: 20141a106, SAD, ELA


title: 20141a111, noSAD, ELA


title: 20141a104, SAD, noELA


title: 20141a103, noSAD, noELA


title: 20141a105, SAD, noELA


title: 20141a097, SAD, noELA


title: 20141a101, SAD, noELA


title: 20141a130, noSAD, ELA


title: 20141a099, SAD, noELA


title: 20141a095, noSAD, noELA


title: 20141a096, SAD, ELA


title: 20141a100, SAD, ELA


title: 20141a093, noSAD, ELA


title: 20141a091, noSAD, noELA


title: 20141a094, noSAD, noELA


title: 20141a092, SAD, ELA


title: 20141a089, SAD, noELA


title: 20141a088, SAD, ELA


title: 20141a087, SAD, ELA


title: 20141a086, noSAD, noELA


title: 20141a098, SAD, noELA


title: 20141a085, noSAD, noELA


title: ZT12-EX (biol rep3)

description:
flowcell 1
6-CES19_S2_R1_001

value: Heart

value: WT

value: Male

value: 12 weeks

value: Exercise


title: 20141a084, SAD, noELA


title: 20141a081, noSAD, noELA


title: 20141a082, noSAD, noELA


title: 20141a079, noSAD, ELA


title: 20141a083, SAD, noELA


title: 20141a077, noSAD, noELA


title: 20141a078, noSAD, noELA


title: 20141a075, SAD, noELA


title: 20141a076, SAD, noELA


title: 20141a074, noSAD, noELA


title: 20141a073, noSAD, ELA


title: 20141a071, noSAD, noELA


title: 20141a072, noSAD, ELA


title: 20141a070, noSAD, ELA


title: 20141a069, noSAD, noELA


title: 20141a090, noSAD, noELA


title: 20141a066, noSAD, ELA


title: 20141a068, noSAD, noELA


title: 20141a065, noSAD, ELA


title: 20141a063, noSAD, ELA


title: 20141a061, SAD, noELA


title: 20141a062, noSAD, noELA


title: 20141a060, SAD, ELA


title: 20141a059, noSAD, noELA


title: 20141a058, noSAD, noELA


title: 20141a080, noSAD, noELA


title: 20141a057, SAD, ELA


title: 20141a055, SAD, ELA


title: murineCC_Myd88L252P_repl5

city: New York

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
TPM were obtained using Rsubread and RefSeq gene annotation
Assembly: mm10
Supplementary files format and content: tab-delimited

source_name: Centrocyte

extract_protocol: RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

tag: sorting


title: murineCC_Myd88L252P_repl4


title: 20141a052, noSAD, noELA


title: 20141a067, noSAD, ELA


title: 20141a064, SAD, noELA


title: 20141a050, SAD, ELA


title: 20141a051, SAD, noELA


title: 20141a054, SAD, noELA


title: murineCC_Myd88L252P_repl3


title: murineCC_Myd88L252P_repl2


title: 20141a047, noSAD, ELA


title: 20141a049, SAD, noELA


title: murineCC_Myd88L252P_repl1


title: 20141a056, noSAD, noELA


title: murineCC_Control_repl5

value: Cgamma1Cre:+/-; Myd88L252P:WT


title: MDA-MB-231_TNFa_rep3

type: RNA

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

institute: Fujian Maternity and Child Health Hospital

description: Gene expression data from TNFa treated MDA-MB-231 cells

hyb_protocol: Fragmented and biotin-labeled cRNA was hybridized to affymetrix human U133 plus 2.0 array chip using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60 rpm.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000

data_processing: Raw data were normalized by RMA algorithm

label: biotin

source_name: breast cancer cell line MDA-MB-231

label_protocol: 5 ug of total RNA was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was used to synthesize biotin-labeled cRNA with the IVT kit (Affymetrix, USA). Biotin-labeled cRNA was fragmented according to affymetrix protocol.

growth_protocol: Breast cancer MDA-MB-231 and LM2-4175 cells were cultured with L15 medium in 10% FBS.

extract_protocol: Cellular RNA was isolated by Tri-Reagent using the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: MDA-MB-231 and LM2-4175 cells were treated with ATO 5μM for 0, 6, 12, 24 and 36 hours. MDA-MB-231 cells were treated with TGFβ or TNFα for 2 hours.

value: breast cancer

value: TNFa


title: MDA-MB-231_TNFa_rep2


title: MDA-MB-231_TGFb_rep1

description: Gene expression data from TGFb treated MDA-MB-231 cells

value: TGFb


title: MDA-MB-231_CON_rep3

description: Gene expression data from untreated MDA-MB-231 cells

value: untreated


title: 20141a046, SAD, noELA

value: SAD


title: 20141a053, SAD, ELA

value: ELA

value: male

value: peripheral blood


title: MDA-MB-231_TNFa_rep1


title: MDA-MB-231_CON_rep2


title: 20141a045, noSAD, noELA

value: noELA


title: 20141a043, noSAD, noELA


title: MDA-MB-231_TGFb_rep3


title: MDA-MB-231_TGFb_rep2


title: 20141a042, SAD, noELA

value: female


title: 20141a048, noSAD, ELA

value: noSAD


title: 20141a040, SAD, ELA


title: murineCC_Control_repl2


title: 20141a041, SAD, noELA


title: murineCC_Control_repl4


title: MDA-MB-231_CON_rep1


title: 20141a038, noSAD, noELA


title: 20141a039, SAD, noELA


title: MDA-MB-231_ATO_36h

description: Gene expression data from ATO treated MDA-MB-231 cells

value: ATO


title: MDA-MB-231_ATO_12h


title: MDA-MB-231_ATO_24h


title: 20141a037, noSAD, noELA


title: 20141a044, noSAD, noELA


title: murineCB_Myd88L252P_repl5

source_name: Centroblast


title: murineCC_Control_repl1


title: 20141a034, noSAD, ELA


title: 20141a033, noSAD, noELA


title: 20141a036, noSAD, noELA


title: murineCB_Myd88L252P_repl4


title: MDA-MB-231_ATO_0h


title: 20141a031, noSAD, noELA


title: LM2-4175_ATO_36h

description: Gene expression data from ATO treated LM2-4175 cells

source_name: lung metastasis of breast cancer LM2-4175 cell


title: murineCC_Control_repl3


title: 20141a035, noSAD, noELA


title: 20141a030, noSAD, noELA


title: murineCB_Myd88L252P_repl3


title: LM2-4175_ATO_12h


title: 20141a032, noSAD, noELA


title: 20141a027, noSAD, ELA


title: murineCB_Myd88L252P_repl1


title: 20141a029, noSAD, noELA


title: 20141a028, noSAD, noELA


title: 20141a025, noSAD, ELA


title: MDA-MB-231_ATO_6h


title: LM2-4175_ATO_6h


title: 20141a026, noSAD, ELA


title: 20141a023, noSAD, noELA


title: 20141a024, noSAD, ELA


title: murineCB_Control_repl5


title: murineCB_Myd88L252P_repl2


title: murineCB_Control_repl4


title: LM2-4175_ATO_0h

description: Gene expression data from untreated LM2-4175 cells


title: IL1403_vs_594_R2

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

hyb_protocol: Labeled probes were hybridized to custom designed microarrays in 8x15k format, made by Agilent (Design ID: 084868) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.

scan_protocol: After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).

data_processing: GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized Log2 Ratio data from biological and technical replicates were averaged.

organism: Lactococcus lactis

source_name: cells from batch culture

label_protocol: Samples of total RNA (100ng) were labeled with Low Input QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.

growth_protocol: Bacteria cells were grown in an M17 medium supplemented with cellobiose. Cells were harvested at mid-exponential growth phase at OD600 0.6-0.7.

extract_protocol: Total RNA was prepared using GeneMATRIX Universal RNA Purification Kit (EURx, Poland), according to the manufacturer protocol.

tag: carbon source

value: cellobiose

tag: growth phase

value: mid-exponential


title: 20141a022, noSAD, noELA


title: LM2-4175_ATO_24h

tag: cell type


title: 20141a019, noSAD, noELA


title: 20141a020, noSAD, noELA


title: 20141a021, noSAD, noELA


title: murineCB_Control_repl1

tag: genotype


title: 20141a016, SAD, ELA


title: 20141a017, SAD, ELA


title: 20141a018, SAD, noELA


title: 20141a015, SAD, ELA


title: IL1403_vs_594_R1


title: 20141a014, SAD, noELA


title: IL1403_vs_IL1420_R2


title: IL1403_vs_IL1530_R1


title: IL1403_vs_IL1420_R1


title: 20141a013, SAD, noELA


title: 𝚫aim29 + pmTDH3-ZPR1 rep3

city: Cambridge

first: Vladimir

last: Denic

state: MA

address: 52 Oxford St, Room 442

department: Molecular and Cellular Biology

institute: Harvard University

data_processing:
Raw reads from Illumina HiSeq were checked for read quality using FastQC (v. 0.11.5) and aligned to the reference genome S288c (v. R64-3-1) using the RNA-seq aligner STAR (v.2.7.0)
Genewise counts obtained from STAR were passed to the Bioconductor package DESeq2 (v. 1.34.0) to identify differentially expressed genes after ZPR1 depletion relative to the DMSO vehicle control (Benjamini-Hochberg FDR < 0.05).
Assembly: S288c (v. R64-3-1)
Supplementary files format and content: csv file with raw read counts per gene for all samples

organism: Saccharomyces cerevisiae W303

growth_protocol: Three isolates of VDY3334, VDY5662, and VDY5849 were grown to mid-log phase in YPD. When cells reached OD600 0.4-0.6, 1 OD600 unit was collected for RNA isolation by rapid centrifugation for 1 min at 20,000 x g.

extract_protocol:
RNA samples were extracted by the NGS facility at GENEWIZ according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aim29 deltion mutant + pmTDH3-ZPR1


title: 𝚫aim29 + pmTDH3-ZPR1 rep2


title: IL1403_vs_IL1619_R2


title: murineCB_Control_repl3


title: IL1403_vs_IL1619_R1


title: 𝚫aim29 + pmTDH3-ZPR1 rep1


title: 20141a010, SAD, ELA


title: 20141a012, SAD, noELA


title: 20141a009, SAD, noELA


title: 20141a011, SAD, noELA


title: murineCB_Control_repl2


title: 20141a007, SAD, noELA


title: IL1403_vs_IL1530_R2


title: IL1403_vs_IL2661_R1


title: 𝚫aim29 rep2

value: aim29 deletion mutant


title: 𝚫aim29 rep3


title: IL1403_vs_IL2661_R2


title: 20141a006, SAD, ELA


title: 20141a005, SAD, ELA


title: KO, MeRIP

first: Jiajun

last: Sun

state: Shanghai City

address: 197 Rui Jing Er Rd

institute: Shanghai Jiao Tong University Medical School Affiliated Ruijin Hospital

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software
Assembly: mm10
Supplementary files format and content: XLS sheet "Methylated_RNA_sites.mRNA.xlsx" illustrated the m6A methylation sites information, including m6A peak start site, peak stop site, peak ID, m6A peak score, peak length, generated by MACS software. Additional statistical enrichment information and gene annotation information was also provided

source_name: Pancreatic cell

extract_protocol:
Total RNA was subjected to immunoprecipitation with the GenSeq® m6A-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified.
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).
RNA-seq(MeRIP-seq)

value: Pancreatic cell

value: KO


title: 𝚫aim29 rep1


title: Wild-type rep3

value: wild-type


title: IL1403_vs_IL1421_R2


title: 20141a003, noSAD, noELA


title: WT, MeRIP

value: WT


title: IL1403_vs_IL1392_R2


title: IL1403_vs_IL1421_R1


title: 20141a004, SAD, noELA


title: Wild-type rep2


title: Wild-type rep1


title: 20141a002, noSAD, noELA


title: IL1403_vs_IL1392_R1


title: WT, input


title: 20141a008, noSAD, noELA


title: IL1403_vs_IL1618_R2


title: IL1403_vs_IL1618_R1


title: Fertard_flower_bud_rep3_15/01/2018

status: Public on Apr 15 2023

city: Villenave d'Ornon

first: Benedicte

last: Wenden

address: 71 avenue Edouard Bourlaux

country: France

institute: INRA

data_processing:
trimming: Trimmomatic 0.36 (Bolger et al., 2014) with following settings fa:2:10:5:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the sweet cherry ‘Regina’ reference genome v.1 (Vimont et al., 2021) using STAR (Dobin et al., 2013)
Raw read count was performed using HTSeq count (Anders et al., 2015)
Assembly: sweet cherry ‘Regina’ reference genome v.1 (Le Dantec L, Girollet N, Gouzy J, Sallet E, Carrère S, Fouché M, Quero-García J, Dirlewanger E (2020) Assembly and annotation of ‘Regina’ sweet cherry genome. V1. Portail Data INRAE. https://doi.org/10.15454/KEW474)

organism: Prunus avium

source_name: flower bud

extract_protocol:
Total RNA was extracted from 100 mg of frozen and grinded flower buds using RNeasy Plant Mini kit (Qiagen) with minor modification: 1.5% PVP-40 was added in the extraction buffer RLT
Library preparation was performed on 1 μg of high quality RNA (RNA integrity number equivalent superior or equivalent to 8.5) using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina cat. no. RS-122-2103)

value: flower bud

tag: cultivar

value: Fertard

tag: date


title: Fertard_flower_bud_rep2_12/03/2018

tag: tissue


title: Fertard_flower_bud_rep3_12/03/2018


title: Fertard_flower_bud_rep3_12/02/2018


title: Fertard_flower_bud_rep1_12/03/2018


title: Fertard_flower_bud_rep2_12/02/2018


title: Fertard_flower_bud_rep2_15/01/2018


title: Fertard_flower_bud_rep1_12/02/2018


title: Fertard_flower_bud_rep1_15/01/2018


title: KO, input

city: Shanghai


title: Fertard_flower_bud_rep2_03/01/2018


title: Fertard_flower_bud_rep1_03/01/2018


title: Fertard_flower_bud_rep1_17/12/2012


title: Fertard_flower_bud_rep3_17/12/2012


title: Fertard_flower_bud_rep3_17/10/2017


title: Fertard_flower_bud_rep1_17/10/2017


title: Fertard_flower_bud_rep2_17/12/2012


title: Fertard_flower_bud_rep2_17/10/2017


title: 20141a001, noSAD, noELA


title: Nef_m3

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: WT mice with 42-day Angiotensin-II (500ng/kg/min) and neferine (1mg/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

organism: Mus

source_name: abdominal aorta

extract_protocol:
The abdominal aorta tissues were dissected and  stored in RNA later.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

tag: strain

value: abdominal aorta

tag: treatment

value: Angiotensin-II

value: Neferine

tag: group

value: AngII+neferine


title: Nef_m2


title: AngII6

description: WT mice with 42-day Angiotensin-II (500ng/kg/min) treatment

value: double distilled water

value: AngII


title: AngII5


title: AngII4


title: Nef_m1


title: Nef_m4

description: WT mice with 42-day Angiotensin-II (500ng/kg/min) and neferine(1mg/kg/d) treatment


title: Nef_m5


title: Nef_m6


title: AngII1


title: Ctrl6

description: WT mice with 42-day Saline treatment

value: Saline

value: Control


title: Ctrl4

description: WT mice with 42-day Saline treatment


title: AngII3


title: Ctrl5

description: WT mice with 42-day Saline treatment


title: Fertard_flower_bud_rep3_03/01/2018


title: Ctrl1

description: WT mice with 42-day Saline treatment


title: 6_mac_IL27_RP3

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

data_processing:
Raw fastq files were trimmed using trimmomatic v. 0.33, and aligned using STAR v.2.5.2b using the mouse genome mm10 (GRCm38.p5) with gtf release v.M12
Gene-specific counts were derived using RSEM v.1.3.0
Downstream analysis was performed in R.  RSEM counts were normalized with quantile normalization using limma package, and analysis of differentially expressed genes using the batch information as a covariate
Assembly: mouse genome mm10 (GRCm38.p5)
Supplementary files format and content: The RawCountFile_rsemgenes.txt file provides RSEM raw counts for the gene expression.
Supplementary files format and content: The Normalized_Counts_RSEM.txt file provides quantile normalized log CPM values.

growth_protocol: DMEM cell culture media containing 1% penicillin/streptomycin and 10% fetal bovine serum in a humidified, 5% CO2 atmosphere at 37C

extract_protocol:
TRIzol reagent (Invitrogen) per manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100 ng/ml IL-27 for 24 hours

value: macrophage

value: WT C57BL/6NCr

value: 100 ng/ml IL-27 for 24 hours

tag: batch


title: Ctrl2

description: WT mice with 42-day Saline treatment


title: 4_mac_IL27_RP2


title: 5_mac_unstim_RP3

value: unstimulated


title: 1_mac_unstim_RP1


title: Pol2 Chia-Pet Ronin KO

first: Marion

middle: Dejosez

last: Zwaka

address: 1425 Madison Ave

department: Black Family Stem Cell Institute

institute: Icahn School of Medicine at Mount Sinai

description:
ESCs derived from blastocysts of CreERT2 animals crossed with Roninflox/flox animals.
Chromatin Interaction
Pol2 bound genomic DNA

data_processing:
Replicates were merged. All datasets were processed with a custom script as previously described (Hnisz et al., Cell, 2016; Dowen et al., Cell, 2014). Image analysis and base calling were performed using the Solexa pipeline (Illumina). Reads were examined for the presence of at least 10 base pairs (bp) of linker sequence, and those lacking a linker were excluded from further processing. Reads containing a linker were trimmed using cutadapt (cutadapt -m 17; –a forward = ACG CGA TAT CTT ATC TGA CT, and –a reverse = AGT CAG ATA AGA TAT CGC GT; overlap=10) (http://code.google.com/p/cutadapt/). Trimmed mate pairs were mapped independently to mm9 using Bowtie version 1.1.1 (bowtie -e70-k1-m1-v2-p4--best--strata--S) (Langmead et al., GEnom Biol, 20019). Aligned reads were paired with mates using an in-house script based on read identifiers. To remove PCR bias artifacts, reads were filtered for redundancy: Paired End Tags (PETs) with identical genomic coordinates and strand information at both ends were collapsed into a single PET. The PETs were further categorized into intrachromosomal or interchromosomal PETs. Regions of local enrichment (PET peaks) were called using MACS 1.4.2 (Zhang et al., Genome Biol, 2008) with the parameters “-p 1e-09 -no-lambda –no-model”. To identify long-range chromatin interactions, we first removed intrachromosomal PETs < 4 kb in length because these PETs may reflect self-ligation of DNA ends from a single chromatin fragment in the ChIA-PET procedure( Dowen et al., Cell, 2014). We next identified PETs that overlapped with PET peaks by at least 1 bp at both ends. These PETs were defined as putative interactions. A statistical model based upon the hypergeometric distribution was applied to identify high-confidence interactions, representing high-confidence physical contacts between the PET peaks. Specifically, the numbers of PET sequences that overlapped with PET peaks at both ends as well as the number of PETs within PET peaks at each end were counted. The PET count between two PET peaks represented the frequency of the interaction between the two genomic locations. A hypergeometric distribution was used to determine the probability of seeing at least the observed number of PETs linking the two PET peaks. A background distribution of interaction frequencies was then obtained by performing random shuffling of the links between two ends of PETs, and a cutoff threshold for calling significant interactions was set to the corresponding p-value of the most significant proportion of shuffled interactions. The p-values were corrected to control for multiple hypothesis testing by the Benjamini-Hochberg procedure to control for multiple hypothesis testing.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: CSV files: File contains all putative interactions. Column 1 represents the left end of the putative interaction, Column 2 is the right end of the putative interaction, Column 3 represents the interaction ID, Column 4 is the number of PETs supporting the putative interaction, Column 5 shows the distance between the left and right end of the putative interaction, Column 6 represents the interaction class (intra- versus interchromosomal), Column 7 lists the left end count, Column 8 the right end count, Column 9 shows the p-value of the putative interaction, Column 10 lists the FDR value of the putative interaction.
Supplementary_files_format_and_content: WIG files: Sequencing data as track format.

source_name: mouse ES cells

growth_protocol: Mouse ES cells were grown under standard mES cell culture conditions (DMEM supplemented with serum and LIF) on gelatine.

extract_protocol:
Whole cell extracts from 500.000 million cells were sonicated. The chromatin extracts containing DNA fragments with an average size of 300-700 bp were immunoprecipitated with anti-RNAPII (Pol2, Clone 8WG16, Ab817, Abcam). Immunoprecipitated DNA was end-repaired, A-tailed, and proximity ligation was performed in the presence of a bridge-linker (5'-ACGCGATATCTTATCTGACT) with T4 DNA ligase. Unligated DNA was digested with exonuclease treatment followed by RNase A, and Proteinase K treatment. DNA was then phenol:chloroform:isoamyl alcohol precipitated and subjected to library preparation.
Purified immunoprecipitated DNA was tagmented and amplified with Nextera DNA Flex Library Prep (20018704, Illumina) and Nextera DNA CD Indexes (115055289, Illumina), according to the manufacturer’s protocol. Following amplification, the PCR products were purified with AMPure beads (Beckman Coulter) and resuspended in 40 μl Buffer EB (Qiagen). The purified library was size selected (200-700 bp) with a Pippin prep machine.
Illumina Hi-Seq 2500 platform at the Genome Tech Core at the Whitehead Institute for Biomedical Research. 100x100 paired-end sequencing.

value: Embryonic stem cells

value: Tamoxifen for 4 days

tag: genotype/variation

value: CreERT2; Roninflox/flox (Ronin KO)

tag: antibody

value: anti-RNAPII (Clone 8WG16, Ab817, Abcam)


title: Pol2 Chia-Pet Control

value: Ethanol for 4 days

value: CreERT2; Roninflox/flox (Control)


title: Ronin ChIA-PET

description:
Chromatin Interaction
Ronin bound genomic DNA

source_name: mouse ES cells (R1)

extract_protocol:
Whole cell extracts from 500.000 million cells were sonicated. The chromatin extracts containing DNA fragments with an average size of 300-700 bp were immunoprecipitated with anti-Ronin (clone P56-507, Becton Dickinson, 562548). Immunoprecipitated DNA was end-repaired, A-tailed, and proximity ligation was performed in the presence of a bridge-linker (5'-ACGCGATATCTTATCTGACT) with T4 DNA ligase. Unligated DNA was digested with exonuclease treatment followed by RNase A, and Proteinase K treatment. DNA was then phenol:chloroform:isoamyl alcohol precipitated and subjected to library preparation.
Purified immunoprecipitated DNA was resuspended in Nextera DNA resuspension buffer (Illumina FC-121-1030) and then tagmented with a Nextera Tagmentation kit (Illumina, FC-121-1030). The tagmented libraries were purified with Zymo DNA purification columns (Zymo, D4003) and subsequently bound to Streptavidin beads (Life Technologies, 11205D) to enrich for ligation fragments containing the biotinylated bridge linker. Fifteen cycles of polymerase chain reaction (PCR) were performed to amplify the library using standard Nextera primers (Illumina FC-121-1030 Following amplification, the PCR products were purified with AMPure beads (Beckman Coulter) and resuspended in 40 μl Buffer EB (Qiagen). The purified library was size selected (200-500 bp) with a Pippin prep machine.
Illumina Hi-Seq 2500 platform at the Genome Tech Core at the Whitehead Institute for Biomedical Research. 100x100 paired-end sequencing.

value: WT


title: 39_4M

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 10.1.1; Qiagen, Redwood City, CA).
Genome_build: hg19

source_name: Whole blood cells

extract_protocol:
Whole blood was collected with PAXgene blood RNA tubes (Qiagen). Silica-membrane-based RNA isolation and purification in a spin-column format was performed using PAXgene Blood RNA kit (Qiagen). Extracted RNA was globin-cleared using the Ambion GLOBINclear kit (Thermo Fisher, Waltham, MA). 500 ng total RNA was rRNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Libraries were validated with Bioanalyzer (Agilent Technologies) to determine size distribution and concentration. Sequencing was performed by Tsukuba i-Laboratory LLP (Tsukuba, Japan) using NextSeq500 (Illumina) with paired-end 36-base read option. Sequencing reads were mapped on the hg19 human reference genome and quantified using CLC Genomics Workbench (CLC-GW) version 10.1.1 (Qiagen). Differentially expressed genes were identified by filtering according to p-value obtained by Empirical Analysis of DGE tool in CLC-GW.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time point

value: 4 months after starting of benralizumab treatment

value: Whole blood cells

tag: act-responder

value: yes

value: no

tag: gete-responder

tag: ae-responder

tag: disease state

value: severe eosinophilic asthma


title: 41_4M


title: 40_4M


title: 37_4M


title: 38_4M


title: 30_4M


title: 35_4M


title: 32_4M


title: 31_4M


title: 33_4M


title: 36_4M


title: AngII2

value: abdominal aorta

value: Angiotensin-II

value: double distilled water

value: AngII


title: 28_4M


title: 41_0M

value: at baseline


title: 40_0M


title: 3_mac_unstim_RP2

value: macrophage

value: WT C57BL/6NCr

value: unstimulated


title: 39_0M


title: 36_0M


title: 35_0M


title: 38_0M


title: 2_mac_IL27_RP1

value: 100 ng/ml IL-27 for 24 hours


title: 34_0M


title: 32_0M


title: 33_0M


title: 31_0M


title: 30_0M


title: 28_0M


title: 34_4M


title: 29_0M


title: 27_4M


title: 29_4M


title: 19_4M


title: 18_4M


title: 24_4M


title: 20_4M


title: 21_4M


title: 22_4M


title: 25_4M


title: 15_4M


title: 16_4M


title: 17_4M


title: 14_4M


title: 37_0M


title: 13_4M


title: 11_4M


title: 9_4M


title: 10_4M


title: 12_4M


title: 26_4M


title: DSF-X-1

city: Shijiazhuang

first: Fang

last: Liu

state: HeBei

address: 46th, South Street of Friendship

department: Biology Institute

institute: Biology Institute, Hebei Academy of Sciences

data_processing:
The data generated from Illumina (or BGI) platform were used for bioinformatics analysis. All of the  analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology. The major software and parameters are as follows
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis  step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a  string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N  (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain  clean reads that can be used for subsequent analysi
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2  software (http://daehwankimlab.github.io/hisat2/) to obtain mapp
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene
Differential expression analysis was performed using the DESeq2  (http://bioconductor.org/packages/release/bioc/html/DESeq2.html), DEGs with | log2FC | > 1 and  Padj < 0.05 were considered to be significantly different expressed genes
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
RNA was harvested using TRIzol kit (Qiagen). 1. ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Abclonal Mrna-seq Lib Prep Kit following manufacturer's protocols.

value: Leaf

value: after DSF pretreatment  inoculated with Xcc


title: DSF-X-2


title: CK-X-3

value: inoculated with Xcc


title: CK-X-2


title: DSF-3

value: DSF pretreated


title: 8_4M

value: 4 months after starting of benralizumab treatment

value: Whole blood cells


title: CK-X-1


title: 7_4M

value: yes


title: 6_4M

value: severe eosinophilic asthma


title: 5_4M

value: no


title: 23_4M


title: 4_4M


title: DSF-2


title: CK-3


title: 3_4M


title: DSF-1


title: CK-2


title: CK-1


title: 1_4M


title: 2_4M


title: 18_ZO2_ko_3

city: Boston

first: Steen

last: Hansen

address: Enders Building, Room 1016

department: GI Division

institute: Boston Children's Hospital

data_processing:
Sequence reads were filtered with SOAPnuke software to remove read with adapters, unknown bases, and low-quality reads.
Genome mapping of filtered reads to reference genome GRCh38 was performed using HISAT2 and Bowtie2 software.
Raw data of RNA-seq were normalized and processed using R package DEseq2
Assembly: GRCh38
Supplementary files format and content: counts_raw.csv include raw count values for all the samples

source_name: cell line

growth_protocol: H661 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen) (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was subjected to Oligo dT selection for enrichment of mRNA followed by reverse transcription and second strand synthesis.

treatment_protocol: 1x10^6 cells were plated in a 6-well plate and cultured for 1 week to reach saturation density

value: cell line

tag: cell line

value: TJP2 knockdown

value: culture to saturation density


title: 16_ZO2_ko_1


title: 17_ZO2_ko_2


title: DSF-X-3


title: 5xFAD Inpp5dfl/flCx3cr1ERT2Cre (5xBOAT)

city: Charlottesville

first: Joshua

last: Samuels

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

description: 10x Genomics

data_processing:
Raw fastq files were further processed with the CellRanger (7.0.1, 10X Genomics) cellranger count pipeline with introns included using the mouse (mm10) genome. Raw feature matrices containing the barcodes, features, and matrix files for each sample were used for further analysis in RStudio (4.2.1).
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files containing raw gene counts.

molecule: nuclear RNA

source_name: Brain, Cortex

extract_protocol:
Mice were euthanized using CO2 asphyxiation and transcardially perfused with ~25 mL of ice cold 1xPhosphate Buffered Saline. Brains were dissected out and the cortex from the right half of the brain was microdissected and flash-frozen on dry ice and stored at -80°C. Brain cortices from three individual mice were pooled based on genotype (5xFAD Inpp5dfl/flCx3cr1ERT2Cre or 5xFAD) and submitted to GENEWIZ (Azenta Life Sciences) for nuclei extraction and sequencing.
Nuclei extraction was performed using the Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec) following the manufacturer’s guidelines with gentle MACS Dissociation and C tubes (Miltenyi Biotec). Following isolation, nuclei were counted using a Countess 3 Automated Cell Counter (Thermo Fisher). Single-nuclei 3’ RNA libraries were generated using the Chromium Single Cell 3’ kit (10X Genomics). For each sample, a target capture of ~3,000 Gel Beads-in-Emulsion per sample was loaded onto the Chromium Controller (10X Genomics) and processed following the standard manufacturer’s specifications. Sequencing libraries were evaluated for quality using the Agilent TapeStation (Agilent Technologies) and quantified using a Qubit 2.0 Fluorometer (Invitrogen). Pooled libraries were quantified using qPCR (Applied Biosystems) and sequenced using a HiSeq 4000 (Illumina). Samples were sequenced at a configuration compatible with the recommended guidelines as outlined by 10X Genomics and raw sequence data were converted into fastq files.

treatment_protocol: Upon weaning (~3 weeks of age), female 5xFAD Inpp5dfl/flCx3cr1ERT2Cre mice and 5xFAD littermate controls were fed tamoxifen diet ad libitum for two weeks and then returned to normal chow for the remainder of the experiment.

value: Brain, Cortex

value: 5xFAD Inpp5dfl/flCx3cr1ERT2Cre

tag: Sex

value: Female

tag: age

value: 5 months


title: 15_ZO1_ko_3

tag: genotype

value: TJP1 knockdown


title: 27_0M

value: at baseline


title: 5xFAD Inpp5dfl/fl (5xFAD)

description: 10x Genomics

value: 5xFAD Inpp5dfl/fl


title: 13_ZO1_ko_1


title: 26_0M


title: 14_ZO1_ko_2


title: MC3T3_NCM4

city: Rochester

first: Xuewei

address: 200 1st street

institute: Mayo Clinic

data_processing:
Base calling by CASAVA
Alignment by STAR
Gene count by FeatureCount
Genome_build: mm10
Supplementary_files_format_and_content: excel file for gene count

growth_protocol: MC3T3 osteoblasts were grown in culture medium in the presence of 10 mM beta-glycerophosphate and and 100 micro g per mL of ascorbic acid and   25% LLC1 conditioned medium or vehicle for 7 days. Cells were lysed an RNA was isolated.  LLC1 cells were grown in high glucose DMEM.  24 hours later, serum free medium was added to the cells.  Cells were grown in serum free medium for 48 hours.  The medium was harvested, filtered and used for assessing the effect on MC3T3  cells.

extract_protocol:
RNA was prepared using RNA/protein spin columns (Clontech).
mRNA-seq libraries were prepared using 200 ng of total RNA with a TruSeq RNA Sample Prep Kit v2 (Illumina) as described previously (Ryan et al J. Biol Chem. 2016 Jan 15;291(3):1514-28. doi: 10.1074/jbc.M115.684399. Epub 2015 Nov 24). RNA libraries were prepared with a TruSeq RNA Sample Prep Kit version 2 (Illumina). Reverse transcription and adaptor ligation steps were performed manually. Poly(A) mRNA was purified from total RNA using oligo(dT) magnetic beads. RNA was treated with RNase-free DNase during preparation of RNAs using the Nucleospin RNA/Protein kit (Clontech). Purified mRNA was fragmented at 95 °C for 8 min, eluted from the beads, and primed for first strand cDNA synthesis. The RNA fragments were then copied into first strand cDNA using SuperScript III reverse transcriptase and random primers (Invitrogen). Second strand cDNA synthesis was performed using DNA polymerase I and RNase H. The double-stranded cDNA was purified using a single AMPure XP bead (Agencourt) clean-up step. The cDNA ends were repaired and phosphorylated using Klenow, T4 polymerase, and T4 polynucleotide kinase followed by AMPure XP bead clean-up. The blunt-ended cDNAs were modified to include a single 3′-adenylate (A) residue using Klenow exo− (3′–5′ exo minus). Paired end DNA adaptors (Illumina) with a single “T” base overhang at the 3′-end were immediately ligated to the “A-tailed” cDNA population. Unique indexes, included in the standard TruSeq Kits (12-Set A and 12-Set B) were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells. The adaptor-modified DNA fragments were enriched by 12 cycles of PCR using primers included in the Illumina Sample Prep Kit. The concentration and size distribution of the libraries were determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA).
Libraries were sequenced at approximately 75 million reads/sample following Illumina's protocol using the Illumina cBot and HiSeq 3000/4000 PE cluster kit. The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using Hiseq 3000/4000 sequencing kits and HCS v3.3.20 data collection software. Base-calling was performed using Illumina's RTA version 2.5.2.

treatment_protocol: MC3T3 cells were treated with 25% LLC1 conditioned medium for a period of 7 days.  Control cells received vehicle alone.


title: 7_Y2F_1

value: p190A Y2F mutant expression


title: 9_Y2F_3


title: 25_0M


title: 6_p190A_3

value: wild-type p190A expression


title: 24_0M


title: MC3T3_NCM3


title: 3_control_3

value: wild type


title: 23_0M

value: Whole blood cells


title: MC3T3_NCM2


title: 2_control_2


title: 22_0M

value: yes


title: 4_p190A_1


title: 1_control_1


title: MC3T3_NCM1


title: MC3T3_LLC-CM4


title: 5_p190A_2


title: MC3T3_LLC-CM3


title: MSC-osteoblast-SCUBE2 KD1

first: Guohong

last: Hu

address: No.320, Yueyang Roda, Xuhui disteict

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

data_processing:
Read quality was calculated for all samples by using FastQC (version 0.11.2) (Andrews.2010) software with the default parameters.
PE 150 was applied to sequence the samples. Skewer (v0.2.2) (Jiang H, el at. 2014) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed.
Sequence alignment was performed with STAR (v2.4.2a) (Dobin A, et al. 2013) software.
Expression estimation of gene and transcript was performed by using RSEM (V1.2.29) (Li B, et al. 2011) with setting --estimate-rspd parameter to estimate the distribution of the starting position of the sequence (RSPD) and other parameters were set as defalut.
EdgeR (Robinson, M.D., McCarthy et al. 2010) used the overdispersed Poisson model and empirical Bayes model to estimate the dispersion of all gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Mesenchymal stem cells

growth_protocol: Osteoblasts were differentiated from MSCs in osteogenic medium (α-MEM with 10% FBS and antibiotics supplied with 100 nM Dexamethasone, 10 mM β-phosphoglycerol and 50 µM L-ascorbic acid) for 13 days. Medium was changed every 3 days.

extract_protocol:
RNAs of cells were harvested with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CMs of control or SCUBE2-deficient MCF7 were added in osteogenic medium and accounts for 25% of final volume.

tag: cell type

value: MSC-derived osteoblast

value: treated with CM of MCF7 SCUBE2 KD1

tag: differentiation stage

value: differentiated in osteogenic medium for 13 days


title: 20_0M

tag: tissue

value: no

value: severe eosinophilic asthma


title: MSC-osteoblast-CTRL

tag: strain

tag: treatment

value: treated with CM of MCF7


title: MSC-osteoblast-SCUBE2 KD2

value: treated with CM of MCF7 SCUBE2 KD2


title: MSC

value: MSC

value: untreated

value: undifferentiated


title: 8_Y2F_2

value: cell line

value: culture to saturation density


title: MC3T3_LLC-CM2


title: 21_0M

value: at baseline


title: 19_0M


title: ZH11, NP

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

description: ZH11 (CK+NP).xlsx

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Oryza MSU7.0 database using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: Oryza MSU7.0 database
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

organism: Oryza sativa

source_name: leaves

growth_protocol: Seedlings were cultivated in glass test tubes using 0.5× Murashige and Skoog (½ MS) solid medium, at 26 °C under a photoperiod of 13h/11h (light/dark).

extract_protocol:
the total RNA was isolated from the leaf tissue using the RNA extraction kit (Huayueyang, China).
The RNA-Seq library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) following the manufacturer’s instructions.

treatment_protocol:
The 2-weaks cultivated seedlings were transferring to low-Pi condition,leaves were harvested at 6 d after the treatment.
The 2-weaks cultivated seedlings were transferring to non-Pi condition,leaves were harvested at 1 d after the treatment.

value: leaves

value: WT (ZH11)

value: Non-Pi treatment

tag: time

value: 24 h after treatment


title: 17_0M

value: Whole blood cells

value: yes


title: MC3T3_LLC-CM1


title: NIH3T3_Insoluble_rep1

city: Newark

first: Bin

last: Tian

email: btian@wistar.org, dinghaiz@gmail.com

state: NJ

address: 205 South Orange Ave., F-Bay 7

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University, New Jersey Medical School

description:
NIH3T3_Insoluble_rep1
pA_sites_with_read_counts_NIH3T3.csv
Figure S4 , Sample 3

data_processing:
3'READS+: Sequenced reads (R1) were trimmed to remove adaptor sequence and low-quality sequence (at the 3' end of the reads) using cutadapt (version 2.6) using the following command arguments: -a NNNNTGGAATTCTCGGGTGCCAAGG -n 1 -O 10 -m 25 -f fastq -q 10
3'READS+: Random nucleotides and 5' T-stretches were removed using a custom python script.
3'READS+: The trimmed reads were mapped to the genome using STAR (version 2.7.3a) using the following command arguments: --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMmultNmax 1 --alignIntronMin 20 --alignIntronMax 1000000.
3'READS+: Reads with a mapping quality score (MAPQ) of ≥10 and ≥2 non-genomic 5'-Ts after alignment (called polyA site supporting (PASS) reads) were identified using a custom python script.
3'READS+: PASS reads with 5' ends (corresponding to the 3' end of 3'UTRs) within 24 nt from one another were clustered into pA sites using a custom python script.
RNA-seq: Sequenced reads (R1 and R2) were trimmed to remove adaptor sequence using cutadapt (version 2.6) using the following command arguments: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -n 1 -O 10 -m 25 -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -f fastq -q 20
RNA-seq:  The trimmed reads were mapped to the genome using STAR (version 2.7.3a) using the following command arguments: --alignEndsType Local --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMmultNmax 1 --alignIntronMin 20 --alignIntronMax 1000000
Genome_build: mm9
Supplementary_files_format_and_content: csv files include all cluster sites (chromosome, strand, position) with count values for each sample.
RNAseq_counts_in_cUTRs_and_aUTRs.csv: RNAseq read counts
pA_sites*csv: 3'READS+ clusters with read counts

source_name: NIH3T3 cells

growth_protocol: DMEM supplemented with 10% calf serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
TRIZol
RNAseq libraries: 250 ng of total RNA was used for library construction using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®.
3'READS+ libraries: The READS+ procedure has been previously described (Zheng et al., 2016). Briefly, polyA+ RNA in 0.1 ~ 2.5 µg of total-cell RNA was captured using 10 µl of oligo(dT)25 magnetic beads (NEB) in 100 µl of 1x Binding Buffer (10 mM Tris-Cl pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III (NEB) in 30 µl of RNase III Buffer (10 mM Tris-Cl pH 8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) for 15 min at 37 °C. After washing away unbound RNA fragments using Binding Buffer, polyA+ fragments were eluted from the beads using TE Buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated using ethanol, followed by ligation to 3 pmol of heat-denatured 5'-adapter (5'-CCUUGGCACCCGAGAAUUCCANNNN-3') in the presence of 1 mM ATP, 0.1 µl of SuperaseIn (ThermoFisher Scientific), and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 hr. Ligation products were captured using 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1 (ThermoFisher Scientific). After washing with Washing Buffer (10 mM Tris-Cl pH 7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H (Epicentre) for 30 min at 37 °C in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H Buffer, RNA fragments were eluted from the beads in Elution Buffer (1 mM NaCl, 1 mM EDTA pH7.5, and 0.05% TWEEN 20) at 50 °C, precipitated using ethanol, and then ligated to 3 pmol of heat-denatured 5'-adenylated 3'-adapter (5'-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC-3') using 0.25 µl of T4 RNA ligase 2 (truncated KQ version) for 1 hr at 22 °C in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. Ligation products were precipitated and reverse-transcribed using M-MLV reverse transcriptase, and PCR-amplified using Phusion high-fidelity DNA polymerase (NEB) and bar-coded PCR primers (Sigma-Aldrich) for 15 cycles. Both RT primer (5'-GTTCAGAGTTCTACAGTCCGACGATC-3') and PCR primers with indexes have been described previously (Hoque et al., 2013). PCR products were size-selected twice using 0.6 volume of AMPure XP beads (Beckman Coulter) relative to the PCR reaction volume to remove large DNA molecules, followed by an additional 0.4 volume of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The sizes of the libraries eluted from the AMPure beads were examined using a high-sensitivity DNA kit (Agilent) and an Agilent Bioanalyzer. Library concentrations were measured using the Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). Equal amounts of libraries were mixed and sequenced using an Illumina NextSeq 500 (1x75 bases).

tag: status

value: Proliferating

tag: cell fraction

value: Insoluble

tag: protocol


title: C2C12P_Puromycin60min_Membrane_rep1

description:
C2C12P_Puromycin60min_Membrane_rep1
pA_sites_with_read_counts_C2C12P_Puromycin.csv
Figure 3&4 , Sample 6

source_name: Proliferating C2C12 Cells

growth_protocol: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

value: 100 ug/ml Puromycin for 60 min

value: Membrane


title: NIH3T3_Membrane_rep1

description:
NIH3T3_Membrane_rep1
pA_sites_with_read_counts_NIH3T3.csv
Figure S4 , Sample 2


title: C2C12P_Puromycin30min_Membrane_rep1

description:
C2C12P_Puromycin30min_Membrane_rep1
pA_sites_with_read_counts_C2C12P_Puromycin.csv
Figure 3&4 , Sample 5

value: 100 ug/ml Puromycin for 30 min


title: NIH3T3_Cytosol_rep1

description:
NIH3T3_Cytosol_rep1
pA_sites_with_read_counts_NIH3T3.csv
Figure S4 , Sample 1

value: Cytosol


title: C2C12P_Puromycin0min_Membrane_rep1

description:
C2C12P_Puromycin0min_Membrane_rep1
pA_sites_with_read_counts_C2C12P_Puromycin.csv
Figure 3&4 , Sample 4


title: ZH11, CK

description: ZH11 (CK+NP).xlsx

value: Control


title: C2C12P_Puromycin60min_Cytosol_rep1

description:
C2C12P_Puromycin60min_Cytosol_rep1
pA_sites_with_read_counts_C2C12P_Puromycin.csv
Figure 3&4 , Sample 3


title: C2C12P_Puromycin0min_Cytosol_rep1

description:
C2C12P_Puromycin0min_Cytosol_rep1
pA_sites_with_read_counts_C2C12P_Puromycin.csv
Figure 3&4 , Sample 1


title: C2C12P_Puromycin30min_Cytosol_rep1

description:
C2C12P_Puromycin30min_Cytosol_rep1
pA_sites_with_read_counts_C2C12P_Puromycin.csv
Figure 3&4 , Sample 2


title: glk1glk2, LP

description: DJ+dgp1+glk1glk2 (CK+LP).xlsx

value: glk1glk2 double mutant

value: Low-Pi treatment

value: 6 day after treatment


title: 16_0M

tag: time point

value: at baseline

tag: act-responder

value: no

value: severe eosinophilic asthma


title: 15_0M

tag: gete-responder

tag: ae-responder


title: C2C12D_Membrane_Polysome_rep2

description:
C2C12D_Membrane_Polysome_rep2
pA_sites_with_read_counts_C2C12_polysome.csv
Figure 2 , Sample 8

source_name: Differentiating C2C12 Cells

growth_protocol: DMEM supplemented with 2% horse serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Phenol/Choloroform
RNAseq libraries: 250 ng of total RNA was used for library construction using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®.
3'READS+ libraries: The READS+ procedure has been previously described (Zheng et al., 2016). Briefly, polyA+ RNA in 0.1 ~ 2.5 µg of total-cell RNA was captured using 10 µl of oligo(dT)25 magnetic beads (NEB) in 100 µl of 1x Binding Buffer (10 mM Tris-Cl pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III (NEB) in 30 µl of RNase III Buffer (10 mM Tris-Cl pH 8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) for 15 min at 37 °C. After washing away unbound RNA fragments using Binding Buffer, polyA+ fragments were eluted from the beads using TE Buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated using ethanol, followed by ligation to 3 pmol of heat-denatured 5'-adapter (5'-CCUUGGCACCCGAGAAUUCCANNNN-3') in the presence of 1 mM ATP, 0.1 µl of SuperaseIn (ThermoFisher Scientific), and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 hr. Ligation products were captured using 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1 (ThermoFisher Scientific). After washing with Washing Buffer (10 mM Tris-Cl pH 7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H (Epicentre) for 30 min at 37 °C in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H Buffer, RNA fragments were eluted from the beads in Elution Buffer (1 mM NaCl, 1 mM EDTA pH7.5, and 0.05% TWEEN 20) at 50 °C, precipitated using ethanol, and then ligated to 3 pmol of heat-denatured 5'-adenylated 3'-adapter (5'-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC-3') using 0.25 µl of T4 RNA ligase 2 (truncated KQ version) for 1 hr at 22 °C in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. Ligation products were precipitated and reverse-transcribed using M-MLV reverse transcriptase, and PCR-amplified using Phusion high-fidelity DNA polymerase (NEB) and bar-coded PCR primers (Sigma-Aldrich) for 15 cycles. Both RT primer (5'-GTTCAGAGTTCTACAGTCCGACGATC-3') and PCR primers with indexes have been described previously (Hoque et al., 2013). PCR products were size-selected twice using 0.6 volume of AMPure XP beads (Beckman Coulter) relative to the PCR reaction volume to remove large DNA molecules, followed by an additional 0.4 volume of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The sizes of the libraries eluted from the AMPure beads were examined using a high-sensitivity DNA kit (Agilent) and an Agilent Bioanalyzer. Library concentrations were measured using the Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). Equal amounts of libraries were mixed and sequenced using an Illumina NextSeq 500 (1x75 bases).

value: Differentiating

value: Membrane Polysome


title: glk1glk2, CK

description: DJ+dgp1+glk1glk2 (CK+LP).xlsx

value: leaves


title: C2C12D_Cytosol_Polysome_rep2

description:
C2C12D_Cytosol_Polysome_rep2
pA_sites_with_read_counts_C2C12_polysome.csv
Figure 2 , Sample 7

value: Cytosol Polysome


title: 14_0M

value: Whole blood cells

value: yes

tag: disease state


title: dgp1, LP

description: DJ+dgp1+glk1glk2 (CK+LP).xlsx

value: dgp1 mutant


title: C2C12P_Cytosol_Polysome_rep2

description:
C2C12P_Cytosol_Polysome_rep2
pA_sites_with_read_counts_C2C12_polysome.csv
Figure 2 , Sample 5

value: Proliferating


title: 13_0M


title: dgp1, CK

description: DJ+dgp1+glk1glk2 (CK+LP).xlsx